Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold17
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1562583
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.27
Warning! 255143 characters in sequence are not A, C, G, or T
File 4 of 9
Found at i:502405 original size:32 final size:33
Alignment explanation
Indices: 502364--502429 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
502354 AGTAGCTTAT
502364 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
502396 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
502429 A
1 A
502430 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:504002 original size:20 final size:20
Alignment explanation
Indices: 503975--504049 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
503965 AAAATGCCTA
*
503975 AATGTATCGATACATTGAA-
1 AATGTATCGATACAATGAAT
503994 AATTGTATCGATACAATGAAT
1 AA-TGTATCGATACAATGAAT
* *
504015 AATGTATCGATACAATAAAC
1 AATGTATCGATACAATGAAT
*
504035 AATGTATCAATACAA
1 AATGTATCGATACAA
504050 ATTGTGAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
19 2 0.04
20 46 0.92
21 2 0.04
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAAT
Found at i:516447 original size:12 final size:13
Alignment explanation
Indices: 516430--516458 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
516420 AGTCAAAAGT
516430 AAAAACACA-AAA
1 AAAAACACACAAA
516442 AAAAACACACAAA
1 AAAAACACACAAA
516455 AAAA
1 AAAA
516459 GAGTGCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACACACAAA
Found at i:517200 original size:21 final size:21
Alignment explanation
Indices: 517176--517252 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
517166 CTTTTATCCA
517176 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
517197 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
517218 AATGTATCGATAC-GTTGTACA
1 AATGTATCGATACATTTGTA-G
517239 AATGTATCGATACA
1 AATGTATCGATACA
517253 AGGTCCCAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
20 4 0.08
21 46 0.92
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:517313 original size:19 final size:19
Alignment explanation
Indices: 517289--517339 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
517279 TTTCAGTGAT
517289 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
517308 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
517327 TTGTATCGATACA
1 TTGTATCGATACA
517340 ATATATCGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:517352 original size:32 final size:32
Alignment explanation
Indices: 517311--517384 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
517301 ATAAGTGTTG
* *
517311 TATCGATACATAAGTGTTGTATCGATACAATA
1 TATCGATACACAAGTGATGTATCGATACAATA
*
517343 TATCGATACACAAGTGATGTATCGATACAATG
1 TATCGATACACAAGTGATGTATCGATACAATA
*
517375 TATCGCTACA
1 TATCGATACA
517385 AAGCTACTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (32 bp):
TATCGATACACAAGTGATGTATCGATACAATA
Found at i:517367 original size:19 final size:19
Alignment explanation
Indices: 517290--517371 Score: 86
Period size: 19 Copynumber: 4.6 Consensus size: 19
517280 TTCAGTGATT
* *
517290 TGTATCGATACATAAGTGT
1 TGTATCGATACACAAGTGA
* *
517309 TGTATCGATACATAAGTGT
1 TGTATCGATACACAAGTGA
517328 TGTATCGAT--ACAA-T-A
1 TGTATCGATACACAAGTGA
517343 --TATCGATACACAAGTGA
1 TGTATCGATACACAAGTGA
517360 TGTATCGATACA
1 TGTATCGATACA
517372 ATGTATCGCT
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
13 7 0.13
15 4 0.07
16 2 0.04
17 4 0.07
19 38 0.69
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (19 bp):
TGTATCGATACACAAGTGA
Found at i:519929 original size:27 final size:28
Alignment explanation
Indices: 519899--519974 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
519889 ATTTTTCACA
519899 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTACATC
* *
519926 ATCGGGGATACTCCAACCTCGTTACCTC
1 ATCGGGGATACTCCAACCCCGTTACATC
***
519954 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
519975 GCTTTATTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.20
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACATC
Found at i:520025 original size:51 final size:52
Alignment explanation
Indices: 519957--520178 Score: 234
Period size: 52 Copynumber: 4.3 Consensus size: 52
519947 TTACCTCCGA
* * * * *
519957 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCT-CATAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTCTCCACAATC
* * * *
520008 GGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTCTCCACAATC
* * **
520060 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTT-TCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTCTCC-ACAATC
** * * *
520112 GGGGATACTCCAACTTCGATTTTATTTCCAAAAACACCAATTT-TTCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCC-AAAACACTAATTTCTCCACAATC
*
520164 GAGGATACTCCAACC
1 GGGGATACTCCAACC
520179 TCGTTATTTC
Statistics
Matches: 143, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
51 39 0.27
52 89 0.62
53 15 0.10
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTCTCCACAATC
Found at i:520161 original size:104 final size:103
Alignment explanation
Indices: 519957--520178 Score: 286
Period size: 104 Copynumber: 2.1 Consensus size: 103
519947 TTACCTCCGA
* ***
519957 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAATTTCTCATAATCGGGGATACTCCAAC
* * *
520022 CCCGATTTTATTGCTAAAACACTAATTTTTCCACAATC
66 CCCGATTTTATTCCAAAAACACCAATTTTTCCACAATC
* * *
520060 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTT-TCCTTTAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAATTTCT-C-ATAATCGGGGATACTCCA
**
520124 ACTTCGATTTTATTTCCAAAAACACCAATTTTT-CACAATC
64 ACCCCGATTTTA-TTCCAAAAACACCAATTTTTCCACAATC
*
520164 GAGGATACTCCAACC
1 GGGGATACTCCAACC
520179 TCGTTATTTC
Statistics
Matches: 103, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
102 1 0.01
103 37 0.36
104 48 0.47
105 17 0.17
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (103 bp):
GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAATTTCTCATAATCGGGGATACTCCAAC
CCCGATTTTATTCCAAAAACACCAATTTTTCCACAATC
Found at i:520197 original size:28 final size:28
Alignment explanation
Indices: 520161--520265 Score: 111
Period size: 28 Copynumber: 3.8 Consensus size: 28
520151 ATTTTTCACA
* * **
520161 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
*
520189 ATCGGGGATGCTCCAACCCCGTTACCTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
***
520217 CGAGGGGATACTCCAACCCCGTTACCTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
***
520245 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
520266 GCTTTATTCC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 68 1.00
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACCTC
Found at i:532779 original size:14 final size:13
Alignment explanation
Indices: 532757--532826 Score: 52
Period size: 14 Copynumber: 5.2 Consensus size: 13
532747 CTTCTTTTCT
*
532757 AAAGAAAAAAAACA
1 AAAGCAAAAAAA-A
532771 AAAGCAAAAAAAA
1 AAAGCAAAAAAAA
*
532784 AACAACAAAAAAAAA
1 AA-AGC-AAAAAAAA
* *
532799 CAAAACAAAGAAAA
1 -AAAGCAAAAAAAA
*
532813 AGAG-AAAAAAAA
1 AAAGCAAAAAAAA
532825 AA
1 AA
532827 GAGAGAAGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
12 8 0.17
13 5 0.11
14 20 0.43
15 11 0.24
16 2 0.04
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAGCAAAAAAAA
Found at i:532781 original size:15 final size:14
Alignment explanation
Indices: 532761--532826 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 14
532751 TTTTCTAAAG
532761 AAAAAAAACAAAAGC
1 AAAAAAAACAAAA-C
532776 AAAAAAAA-AACAAC
1 AAAAAAAACAA-AAC
532790 AAAAAAAAACAAAAC
1 -AAAAAAAACAAAAC
*
532805 AAAGAAAAAGAGAAA-
1 AAA-AAAAACA-AAAC
532820 AAAAAAA
1 AAAAAAA
532827 GAGAGAAGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
14 10 0.22
15 30 0.67
16 5 0.11
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAAAACAAAAC
Found at i:532793 original size:10 final size:10
Alignment explanation
Indices: 532761--532803 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
532751 TTTTCTAAAG
532761 AAAAAAAACA
1 AAAAAAAACA
*
532771 AAAGCAAAA-A
1 AAA-AAAAACA
*
532781 AAAAACAACA
1 AAAAAAAACA
532791 AAAAAAAACA
1 AAAAAAAACA
532801 AAA
1 AAA
532804 CAAAGAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
9 3 0.11
10 20 0.74
11 4 0.15
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:532807 original size:29 final size:30
Alignment explanation
Indices: 532761--532826 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
532751 TTTTCTAAAG
532761 AAAAAAAACAAAAGCAAA-AAAAAAACAACA
1 AAAAAAAACAAAAGCAAAGAAAAAAACAA-A
* *
532791 AAAAAAAACAAAA-CAAAGAAAAAGAGAAA
1 AAAAAAAACAAAAGCAAAGAAAAAAACAAA
532820 AAAAAAA
1 AAAAAAA
532827 GAGAGAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (30 bp):
AAAAAAAACAAAAGCAAAGAAAAAAACAAA
Found at i:532830 original size:13 final size:13
Alignment explanation
Indices: 532759--532826 Score: 57
Period size: 13 Copynumber: 4.9 Consensus size: 13
532749 TCTTTTCTAA
*
532759 AGAAAAAAAACAAA
1 AGAAAAAAAA-AAC
532773 AGCAAAAAAAAAAC
1 AG-AAAAAAAAAAC
532787 A-ACAAAAAAAAAC
1 AGA-AAAAAAAAAC
* *
532800 AAAACAAAGAAAAAG
1 AGAA-AAA-AAAAAC
532815 AGAAAAAAAAAA
1 AGAAAAAAAAAA
532827 GAGAGAAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
12 1 0.02
13 17 0.37
14 12 0.26
15 16 0.35
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAC
Found at i:532831 original size:15 final size:15
Alignment explanation
Indices: 532758--532839 Score: 55
Period size: 15 Copynumber: 5.5 Consensus size: 15
532748 TTCTTTTCTA
532758 AAGAAAAAAAACA-A-
1 AAGAAAAAAAA-AGAG
*
532772 AAGCAAAAAAAAA-AC
1 AAG-AAAAAAAAAGAG
* * *
532787 AACAAAAAAAAACAA
1 AAGAAAAAAAAAGAG
* *
532802 AACAAAGAAAAAGAG
1 AAGAAAAAAAAAGAG
532817 AA-AAAAAAAAGAGAG
1 AAGAAAAAAAA-AGAG
532832 AAGAAAAA
1 AAGAAAAA
532840 TCTGCTTAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
14 21 0.37
15 31 0.54
16 5 0.09
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAGAG
Found at i:532838 original size:13 final size:13
Alignment explanation
Indices: 532805--532839 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
532795 AAAACAAAAC
532805 AAAGAAAAAGAGA
1 AAAGAAAAAGAGA
*
532818 AAAAAAAAAGAGA
1 AAAGAAAAAGAGA
*
532831 GAAGAAAAA
1 AAAGAAAAA
532840 TCTGCTTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAGA
Found at i:533962 original size:55 final size:55
Alignment explanation
Indices: 533822--535284 Score: 1758
Period size: 55 Copynumber: 26.0 Consensus size: 55
533812 GATGCCTGTT
* * *
533822 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGATGCTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA--C----A
* * * * *
533882 CTTTTCAAAACCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAGGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
*
533937 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAAGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* * *
533992 -CTTGTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTT
1 CCTT-TCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA--C---A
* *
534052 CCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCCCAAAGAGCAGGACA
1 CC-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
534108 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* * * *
534163 -CTTGTTAAAGCCCACACAAGTTAGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTT
1 CCTT-TCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA--C----A
* * *
534224 CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCCCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
*
534279 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAAGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* *
534334 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* *
534389 CTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAAGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACA
* *
534444 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAACAGGATGCTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGA--C----A
* *
534505 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* *
534560 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
534615 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* *
534670 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* *
534725 CTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAAGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* *
534780 CCTTTCAAAGCCTACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGA--C----A
* *
534841 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* **
534896 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATG
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* *
534951 CTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAAGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
*
535006 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCACTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* * * * *
535061 CCTCTT-AAACCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGCATGCTTTTT
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA--C----A
* * * * *
535122 CTTTTCAAAGCCCACACAAGTTAGTGACACCTTTCAGTCCTCAAAGAGTAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
*
535177 CCTCTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACG
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* * * *
535232 CCTTTCAAAGCCCACACGAGTTGGCGGCACTTTTTAGTCCTCAAAAAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
535285 TGTACTTTAT
Statistics
Matches: 1234, Mismatches: 107, Indels: 129
0.84 0.07 0.09
Matches are distributed among these distances:
54 40 0.03
55 870 0.71
56 30 0.02
57 5 0.00
59 6 0.00
60 29 0.02
61 244 0.20
62 10 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
Found at i:534110 original size:171 final size:165
Alignment explanation
Indices: 533823--535284 Score: 1938
Period size: 171 Copynumber: 8.7 Consensus size: 165
533813 ATGCCTGTTC
**
533823 CTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA--C---ACCTTTT
* * * *
533887 CAAAACCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAGGAGCAGGACACCTTTCAAAGCCCAC
61 CAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCAC
*
533952 ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACA
126 ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
*
533992 CTTGTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTCCTTT
1 CTT-TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA--C---ACCTTT
* *
534057 TCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCA
60 TCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCA
534122 CACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
125 CACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* **
534163 CTTGTTAAAGCCCACACAAGTTAGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTT
1 CTT-TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA--C---ACCTTT
* *
534228 TCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCA
60 TCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCA
*
534293 CACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACA
125 CACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* *
534334 CCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC-GCTTTTCAAA
1 -CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAA
*
534398 GCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAAGACACCTTTCAAAGCCCACACA
65 GCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACA
* *
534462 AGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGATGCTTTTT
129 AGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C----A
*
534505 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTCTT-AAA
1 CTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAA
* *
534569 GCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAA
65 GCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAA
534634 GTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
130 GTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* *
534670 CCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC-GCTTTTCAAA
1 -CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAA
* *
534734 GCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAAGACACCTTTCAAAGCCTACACA
65 GCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACA
*
534798 AGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTTTT
129 AGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C----A
*
534841 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTCTT-AAA
1 CTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAA
* ** *
534905 GCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTCAAAGCCCACACAA
65 GCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAA
*
534970 GTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACA
130 GTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* * * *
535006 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCACTCCTCAAAGAGCAGGACACCTCTT-AA
1 -CTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACACCTTTTCAA
* * * * * *
535069 ACCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGCATGCTTTTTCTTTTCAAAGCC
64 AGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCC
* * * *
535134 CACACAAGTTAGTGACACCTTT-CAGTCCTCAAAGAGTAGGACA
123 CACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
* * *
535177 CCTCTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCC-TTTCAAA
1 -CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAA
* * * *
535241 GCCCACACGAGTTGGCGGCACTTTTTAGTCCTCAAAAAGCAGGA
65 GCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
535285 TGTACTTTAT
Statistics
Matches: 1186, Mismatches: 71, Indels: 70
0.89 0.05 0.05
Matches are distributed among these distances:
164 15 0.01
165 332 0.28
166 8 0.01
167 2 0.00
169 6 0.01
170 37 0.03
171 762 0.64
172 24 0.02
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (165 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAAG
CCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAG
TTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
Found at i:534199 original size:281 final size:272
Alignment explanation
Indices: 533822--535284 Score: 1810
Period size: 281 Copynumber: 5.2 Consensus size: 272
533812 GATGCCTGTT
* ** *
533822 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGA--C----ACTTTT
* * * *
533887 CAAAACCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAGGAGCAGGACACCTTTCAAAGCCCA
60 -AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCA
*
533951 CACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAAGACACTTGTTAAAGCCCACACAAGTTG
123 CACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACACTT-TTAAAGCCCACACAAGTTG
* * *
534015 GTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTCCTTTTCAAAGCCCACACGAGTTGGTGG
186 GTGGCACCTTTCAGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGG
* *
534080 CACTTTTCAGTCCCCAAAGAGCAGGACA
245 CACTTTTCAGTCCTCAAAGAGCAGGACG
534108 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACTTGTTAAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACACTT-TTAAAG
* * * *
534173 CCCACACAAGTTAGTGGCACCTTT-CAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCC
64 CCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCC
* * *
534237 ACACGAGTTGGTGGCACTTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTG
122 ACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA-CTTTTAAAGCCCACACAAGTTG
* * *
534302 GTGGCA-TTTTCCAGTCCTCAAAGAGCAAGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCT
186 GTGGCACCTTT-CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACTT
534366 TTCAGTCCTCAAAGAGCAGGACG
250 TTCAGTCCTCAAAGAGCAGGACG
* * *
534389 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAAGACACCTTTCAAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC-AGTCCTCAAAGAGCAGGACA-CTTTTAAAG
* * *
534454 CCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGATGCTTTTTCTTTTCAAAGCCCA
64 CCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCA
* *
534519 CACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGG
123 CACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA-CTTTTAAAGCCCACACAAGTTGG
*
534584 TGGCACCTTTCAGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTT
187 TGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACTTT
*
534647 TCCAGTCCTCAAAGAGCAGGACA
251 T-CAGTCCTCAAAGAGCAGGACG
* *
534670 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCTTTTCAAA
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACACTTTT-AAA
* *
534734 GCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACACCTTTCAAAGCCTACACAA
63 GCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAA
*
534799 GTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTT
128 GTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGA--C----ACTTTT-AAAGCCCACACAAGTT
*
534863 GGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCT
185 GGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACTT
*
534928 TTCAGTCCTCAAAGAGCAGGATG
250 TTCAGTCCTCAAAGAGCAGGACG
* * *
534951 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACACCTTTCAAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACA-CTTTTAAAG
* *
535016 CCCACACAAGTTGGTGGCATTTTCCACTCCTCAAAGAGCAGGACACCTCTT-AAACCCCACACAA
64 CCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAA
* * * * *
535080 GTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGCATGCTTTTTCTTTTCAAAGCCCACACAAGTTA
128 GTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA--C----ACTTTT-AAAGCCCACACAAGTTG
* *
535145 GTGACACCTTTCAGTCCTCAAAGAGTAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACTTT
186 GTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACTTT
535210 TCAGTCCTCAAAGAGCAGGACG
251 TCAGTCCTCAAAGAGCAGGACG
* * * *
535232 CCTTTCAAAGCCCACACGAGTTGGCGGCACTTTTTAGTCCTCAAAAAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGA
535285 TGTACTTTAT
Statistics
Matches: 1063, Mismatches: 78, Indels: 77
0.87 0.06 0.06
Matches are distributed among these distances:
274 3 0.00
275 46 0.04
277 1 0.00
279 1 0.00
280 22 0.02
281 803 0.76
282 37 0.03
283 1 0.00
285 2 0.00
286 33 0.03
287 107 0.10
288 7 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (272 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACACTTTTAAAGCC
CACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTT
GGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACTTTTAAAGCCCACACAAGTTGGTGGCACCTT
TCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCA
AAGAGCAGGACG
Found at i:534562 original size:26 final size:26
Alignment explanation
Indices: 534532--534621 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
534522 AAGTTGGTGG
*
534532 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
534558 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
534587 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
534613 CACCTTTCA
1 CACCTTTCA
534622 AAGCCCACAC
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 17 0.36
27 8 0.17
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:535460 original size:44 final size:42
Alignment explanation
Indices: 535373--535462 Score: 101
Period size: 43 Copynumber: 2.1 Consensus size: 42
535363 ATGGGATGTA
* *
535373 CTTTTTTCCCTTTATCCTCAAGAAGCAGGACACTTTCCTTTT
1 CTTTTTTCCCTTTATCCTCAAGAAGCAAGACACTTTCCATTT
* * *
535415 CTTTTCTTCCTTTTGTCCTCAAGGAGCAAGAC-CTATTTCCATTT
1 CTTTT-TTCCCTTTATCCTCAAGAAGCAAGACAC--TTTCCATTT
535459 CTTT
1 CTTT
535463 CCCCTTCTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 6 0.15
43 22 0.55
44 12 0.30
ACGTcount: A:0.18, C:0.28, G:0.10, T:0.44
Consensus pattern (42 bp):
CTTTTTTCCCTTTATCCTCAAGAAGCAAGACACTTTCCATTT
Found at i:535999 original size:21 final size:21
Alignment explanation
Indices: 535973--536024 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
535963 CTTTTATCCA
* *
535973 AATGTATTGATACATTTGTAG
1 AATGTATCGATACATTTATAG
*
535994 AATGTATCGATACATTTATGG
1 AATGTATCGATACATTTATAG
536015 AATGTATCGA
1 AATGTATCGA
536025 AAAAAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (21 bp):
AATGTATCGATACATTTATAG
Found at i:536028 original size:75 final size:75
Alignment explanation
Indices: 535949--536099 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
535939 TTTGGAAGGA
*
535949 AAAAAAAAATCACACTTTTATCCAAATGTATTGATACATTTGTAGAATGTATCGATACATTTATG
1 AAAAAAAAATCACACTTTTATCCAAATGTATCGATACATTTGTAGAATGTATCGATACATTTATG
536014 GAATGTATCG
66 GAATGTATCG
*
536024 AAAAAAAAATCACACTTTTATCCAAATGTATCGATACATTTGTAGAATGTATCGATACATTTGTG
1 AAAAAAAAATCACACTTTTATCCAAATGTATCGATACATTTGTAGAATGTATCGATACATTTATG
536089 GAATGTATCG
66 GAATGTATCG
536099 A
1 A
536100 TACATTTGTG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (75 bp):
AAAAAAAAATCACACTTTTATCCAAATGTATCGATACATTTGTAGAATGTATCGATACATTTATG
GAATGTATCG
Found at i:536074 original size:21 final size:21
Alignment explanation
Indices: 536048--536145 Score: 144
Period size: 21 Copynumber: 4.7 Consensus size: 21
536038 CTTTTATCCA
536048 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
536069 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
*
536090 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
*
536111 AATGTATCGATACA-TTGTATA
1 AATGTATCGATACATTTGTA-G
*
536132 AATGTATCAATACA
1 AATGTATCGATACA
536146 AGGTCCCAAC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 4 0.06
21 68 0.94
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:536206 original size:19 final size:18
Alignment explanation
Indices: 536182--536245 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
536172 TTTTAGTGAT
536182 TTGTATCGATACATAAGCG
1 TTGTATCGATACATAAG-G
536201 TTGTATCGATAC--AA--
1 TTGTATCGATACATAAGG
536215 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAG-G
*
536233 TTTTATCGATACA
1 TTGTATCGATACA
536246 ATGTATCAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (18 bp):
TTGTATCGATACATAAGG
Found at i:536220 original size:13 final size:13
Alignment explanation
Indices: 536202--536258 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
536192 ACATAAGCGT
536202 TGTATCGATACAA
1 TGTATCGATACAA
536215 TGTATCGATACATAA
1 TGTATCGATAC--AA
536230 GTGTTTTATCGATACAA
1 -TG---TATCGATACAA
*
536247 TGTATCAATACA
1 TGTATCGATACA
536259 CAAGTGATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
15 2 0.05
16 4 0.11
17 2 0.05
19 9 0.24
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:536224 original size:32 final size:32
Alignment explanation
Indices: 536183--536294 Score: 145
Period size: 32 Copynumber: 3.5 Consensus size: 32
536173 TTTAGTGATT
536183 TGTATCGATACATAAGCGTTGTATCGATACAA
1 TGTATCGATACATAAGCGTTGTATCGATACAA
* *
536215 TGTATCGATACATAAGTGTTTTATCGATACAA
1 TGTATCGATACATAAGCGTTGTATCGATACAA
* * * * *
536247 TGTATCAATACACAAGTGATGTATCGATATAA
1 TGTATCGATACATAAGCGTTGTATCGATACAA
*
536279 TGTATCGCTACA-AAGC
1 TGTATCGATACATAAGC
536295 TACTGCCAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
31 3 0.04
32 67 0.96
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATAAGCGTTGTATCGATACAA
Found at i:538855 original size:27 final size:29
Alignment explanation
Indices: 538825--538899 Score: 102
Period size: 27 Copynumber: 2.7 Consensus size: 29
538815 ATTTTTCACA
538825 ATCGGGGATACTCCAACCCCGTTA-AT-C
1 ATCGGGGATACTCCAACCCCGTTACATCC
* *
538852 ATCGGGGATACTCCAACCTCGTTACCTCC
1 ATCGGGGATACTCCAACCCCGTTACATCC
*
538881 A-AGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
538900 AGCTTTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 23 0.55
28 17 0.40
29 2 0.05
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.20
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTACATCC
Found at i:538958 original size:51 final size:52
Alignment explanation
Indices: 538885--539104 Score: 169
Period size: 52 Copynumber: 4.2 Consensus size: 52
538875 ACCTCCAAGG
* * * * *
538885 GGATACTCCAACCCC-AGCTTTATTTCCAAAATATTGATTTCT-CATAATCAA
1 GGATACTCCAACCCCGA-TTTTATTTCCAAAACACTAATTTCTCCACAATCAA
* * * **
538936 GGATACTCCAACCCCGATTTTATTACTAAAACACTAATTTTTCCACAATCGG
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTCTCCACAATCAA
* * * * ** ***
538988 GGATACTCCAACCTCGGTTTTATTTTCAAAACACCAATTT-TCCTTTAATTGG
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTCTCC-ACAATCAA
** * * *
539040 GGATACTCCAACTTCGATTTTATTTCCAAAAACACCAATTT-TTCACAATCGA
1 GGATACTCCAACCCCGATTTTATTTCC-AAAACACTAATTTCTCCACAATCAA
539092 GGATACTCCAACC
1 GGATACTCCAACC
539105 TCGTTATTTC
Statistics
Matches: 137, Mismatches: 28, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.26
52 86 0.63
53 15 0.11
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.33
Consensus pattern (52 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTCTCCACAATCAA
Found at i:539009 original size:52 final size:51
Alignment explanation
Indices: 538936--539107 Score: 195
Period size: 52 Copynumber: 3.3 Consensus size: 51
538926 TCATAATCAA
* *
538936 GGATACTCCAACCCCGATTTTATTACTAAAACACTAATTTTTCCACAATCGG
1 GGATACTCCAACCTCGATTTTATT-CTAAAACACCAATTTTTCCACAATCGG
* * ** *
538988 GGATACTCCAACCTCGGTTTTATTTTCAAAACACCAA-TTTTCCTTTAATTGG
1 GGATACTCCAACCTCGATTTTATTCT-AAAACACCAATTTTTCC-ACAATCGG
* * *
539040 GGATACTCCAACTTCGATTTTATTTCCAAAAACACCAATTTTT-CACAATCGA
1 GGATACTCCAACCTCGATTTTA-TT-CTAAAACACCAATTTTTCCACAATCGG
539092 GGATACTCCAACCTCG
1 GGATACTCCAACCTCG
539108 TTATTTCATC
Statistics
Matches: 99, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
51 7 0.07
52 75 0.76
53 13 0.13
54 4 0.04
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (51 bp):
GGATACTCCAACCTCGATTTTATTCTAAAACACCAATTTTTCCACAATCGG
Found at i:539123 original size:28 final size:28
Alignment explanation
Indices: 539087--539163 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
539077 ATTTTTCACA
* * *
539087 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
*
539115 ATCGGGGATGCTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
*
539143 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
539164 GCTTTATTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 1 0.02
28 41 0.98
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:539208 original size:79 final size:78
Alignment explanation
Indices: 539117--539351 Score: 240
Period size: 79 Copynumber: 3.0 Consensus size: 78
539107 GTTATTTCAT
* *
539117 CGGGGATGCTCCAACCCCGTTACTTCTGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATAT
1 CGGGGATACTCCAACCCCGTTA-TTCTGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAATAT
*
539182 TGATTTCTCATAAT
65 TGATTTCTCATAAC
* * * * * * *
539196 TGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTA-TTCTGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAAT-A
* *
539260 TCGATTTCTCACAAC
64 TTGATTTCTCATAAC
* * * * *
539275 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGGACACTCCAACCCC-GTTATTATCTCCAAAATA
1 CGGGGATACTCCAACCCCGTTATTCT-GAGGGGATACTCCAACCCCGGTT-TTATTTCCAAAATA
*
539339 TTAAATTTCTCAT
64 TT-GATTTCTCAT
539352 CGGGAAATAT
Statistics
Matches: 123, Mismatches: 28, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
78 7 0.06
79 105 0.85
80 11 0.09
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTCTGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAATATT
GATTTCTCATAAC
Found at i:541112 original size:31 final size:31
Alignment explanation
Indices: 541066--542096 Score: 923
Period size: 31 Copynumber: 33.5 Consensus size: 31
541056 ATCTCTCTTC
*
541066 TCAAAGTTCACGACTCAGTGGCATCTTTTTT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* * * * *
541097 TTAAACTCCATGACTCAGTGGCATC-TCTTC
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* * *
541127 CCAAAGTCCACGACTCTGTGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* ** *
541158 TCAAAGTCCATGACTCAGTGGCATC-CCTTC
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* * * * *
541188 CCAAAGTTCATGACTCGGTGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* *
541219 TCAAAGTCCATGACTCAGTGGCAT-TTTTCCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTT-TT
* * *
541250 TCAAAGTCCACGACTCTGTGGCATCTCTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* * *
541281 TCAAAGTCCACGACTCAATGGCATCTCTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* *
541312 TCAAAGTCCACGACTCAGTGGCATC-TCTTC
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* * * * *
541342 CCAAAGTCCACAACTCCGTGCCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
541373 TCAAAGTCCACGACTCAGTGGCAT-TTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTT-T
** *
541404 TCAAAGTCCACGACTCAGTGGCATC-CCTTC
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* ** *
541434 CCAAAGTCCATAACTCAGTGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
*
541465 TCAAAGTCCATGACTCAGTGGCAT-TTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTT-T
* ** * *
541496 TCAAAGTCTACGACTTTGTGGCATCTCTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* *
541527 TCAAAGTCCACGACTCAGTGGCATC-TCTTC
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* * *
541557 CCAAAGTCCATGACTTC-GTGGCATCTTTTCT
1 TCAAAGTCCACGAC-TCAGTGGCATCTTTTTT
* *
541588 TCAAAGTCCAAGACTCTGTGGCAT-TTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTT-T
** *
541619 TCAAAGTCCACGACTCAGTGGCATC-CCTTC
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* *
541649 TCAAAGTCCATGACTCTGTGGCAT-TTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTT-T
* *
541680 TCAAAGTCCACGACTCAGTGGCATC-TCTTC
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* * *
541710 CCAAAGTCCACAACTCAGTGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* * *
541741 TCAAAGTCCATGACTCAGTGGCAATCTCTTCT
1 TCAAAGTCCACGACTCAGTGGC-ATCTTTTTT
* *
541773 TCAAAGTCCAC-ATCTCAGTGGCATC-TCTTC
1 TCAAAGTCCACGA-CTCAGTGGCATCTTTTTT
* * *
541803 CCAAAGTCCACAACTCAGTGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* * *
541834 TCAAAGTCCATGACTCAGTGGCAATCTCTTCT
1 TCAAAGTCCACGACTCAGTGGC-ATCTTTTTT
* *
541866 TCAAAGTCCAC-ATCTCAGTGGCATC-TCTTC
1 TCAAAGTCCACGA-CTCAGTGGCATCTTTTTT
* *
541896 CCAAAGTCCACGACCCAGTGGCAT-TTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTT-T
* * * *
541927 TTAAAGTCCATGACTCTGTGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* * * *
541958 TCAAAGTCCATGACTTAGTGGCATC-TCTTC
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* * *
541988 CCAAAGTCCATGACTGAGTGGCATCTTTTTT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
* * * *
542019 TCAAAGTCCATGACTCAGGGGCAATC-TCTTC
1 TCAAAGTCCACGACTCAGTGGC-ATCTTTTTT
* * * **
542050 TCAAAGTCCACAACTCAATGGCATCTCTTCC
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTT
*
542081 CCAAAGTCCACGACTC
1 TCAAAGTCCACGACTC
542097 TATGGTACCT
Statistics
Matches: 806, Mismatches: 162, Indels: 64
0.78 0.16 0.06
Matches are distributed among these distances:
30 251 0.31
31 488 0.61
32 67 0.08
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (31 bp):
TCAAAGTCCACGACTCAGTGGCATCTTTTTT
Found at i:541154 original size:61 final size:61
Alignment explanation
Indices: 541059--542096 Score: 1174
Period size: 61 Copynumber: 16.9 Consensus size: 61
541049 TCTTCAAATC
* * * *
541059 TCTCTTCTCAAAGTTCACGACTCAGTGGCATCTTTTTTTTAAACTCCATGACTCAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
* *
541120 TCTCTTCCCAAAGTCCACGACTCTGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
* * * * *
541181 TCCCTTCCCAAAGTTCATGACTCGGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
* * * * *
541242 T-TTTTCCTTCAAAGTCCACGACTCTGTGGCATCTCTTCTTCAAAGTCCACGACTCAATGGCA
1 TCTCTT-C-TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
* * ** * *
541304 TCTCTTCTTCAAAGTCCACGACTCAGTGGCATCTCTTC-CCAAAGTCCACAACTCCGTGCCA
1 TCTCTTC-TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
* * *
541365 TCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTTTCTTCAAAGTCCACGACTCAGTGGCA
1 TCTCTTC-TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
* * **
541427 TCCCTTCCCAAAGTCCATAACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
* * * ** * *
541488 TTTTTTCTTCAAAGTCTACGACTTTGTGGCATCTCTTCTTCAAAGTCCACGACTCAGTGGCA
1 TCTCTTC-TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
* * * *
541550 TCTCTTCCCAAAGTCCATGACTTC-GTGGCATCTTTTCTTCAAAGTCCAAGACTCTGTGGCA
1 TCTCTTCTCAAAGTCCACGAC-TCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
* * ** *
541611 TTTTTTCTTCAAAGTCCACGACTCAGTGGCATCCCTTC-TCAAAGTCCATGACTCTGTGGCA
1 TCTCTTC-TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
* * * * **
541672 TTTTTTCTTCAAAGTCCACGACTCAGTGGCATCTCTTC-CCAAAGTCCACAACTCAGTGGCA
1 TCTCTTC-TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
* * * *
541733 TCTTTTCTTCAAAGTCCATGACTCAGTGGCAATCTCTTCTTCAAAGTCCA-CATCTCAGTGGCA
1 TCTCTTC-TCAAAGTCCACGACTCAGTGGC-ATCTTTTCTTCAAAGTCCATGA-CTCAGTGGCA
* *
541796 TCTCTTCCCAAAGTCCACAACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCAA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGC-A
* * * *
541858 TCTCTTCTTCAAAGTCCAC-ATCTCAGTGGCATCTCTTC-CCAAAGTCCACGACCCAGTGGCA
1 TCTCTTC-TCAAAGTCCACGA-CTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
* * * * * *
541919 TTTTTTCTTTAAAGTCCATGACTCTGTGGCATCTTTTCTTCAAAGTCCATGACTTAGTGGCA
1 TCTCTTC-TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
* * * * *
541981 TCTCTTCCCAAAGTCCATGACTGAGTGGCATCTTTTTTTCAAAGTCCATGACTCAGGGGCAA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGC-A
* * * ** *
542043 TCTCTTCTCAAAGTCCACAACTCAATGGCATCTCTTCCCCAAAGTCCACGACTC
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTC
542097 TATGGTACCT
Statistics
Matches: 843, Mismatches: 116, Indels: 35
0.85 0.12 0.04
Matches are distributed among these distances:
60 2 0.00
61 482 0.57
62 305 0.36
63 54 0.06
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (61 bp):
TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCA
Found at i:541224 original size:92 final size:92
Alignment explanation
Indices: 541059--542096 Score: 1329
Period size: 92 Copynumber: 11.2 Consensus size: 92
541049 TCTTCAAATC
* * * * * *
541059 TCTCTTCTCAAAGTTCACGACTCAGTGGCATCTTTTTTTTAAACTCCATGACTCAGTGGCATCTC
1 TCTCTTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCATCTT
* *
541124 TTC-CCAAAGTCCACGACTCTGTGGCA
66 TTCTTCAAAGTCCACGACTCAGTGGCA
* * * ** * * *
541150 TCTTTTCTTCAAAGTCCATGACTCAGTGGCATCCCTTC-CCAAAGTTCATGACTCGGTGGCATCT
1 TCTCTTC-CCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCATCT
*
541214 TTTCTTCAAAGTCCATGACTCAGTGGCA
65 TTTCTTCAAAGTCCACGACTCAGTGGCA
* * * * *
541242 T-TTTTCCTTCAAAGTCCACGACTCTGTGGCATCTCTTCTTCAAAGTCCACGACTCAATGGCATC
1 TCTCTTCC--CAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCATC
*
541306 TCTTCTTCAAAGTCCACGACTCAGTGGCA
64 TTTTCTTCAAAGTCCACGACTCAGTGGCA
* * * * *
541335 TCTCTTCCCAAAGTCCACAACTCCGTGCCATCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTT
1 TCTCTTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCATCTT
541400 TTCTTCAAAGTCCACGACTCAGTGGCA
66 TTCTTCAAAGTCCACGACTCAGTGGCA
* ** *
541427 TCCCTTCCCAAAGTCCATAACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCATTTT
1 TCTCTTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCATCTT
* **
541492 TTCTTCAAAGTCTACGACTTTGTGGCA
66 TTCTTCAAAGTCCACGACTCAGTGGCA
* * *
541519 TCTCTTCTTCAAAGTCCACGACTCAGTGGCATCTCTTC-CCAAAGTCCATGACTTC-GTGGCATC
1 TCTCTTC-CCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGAC-TCAGTGGCATC
* *
541582 TTTTCTTCAAAGTCCAAGACTCTGTGGCA
64 TTTTCTTCAAAGTCCACGACTCAGTGGCA
* * * ** * *
541611 TTTTTTCTTCAAAGTCCACGACTCAGTGGCATCCCTTC-TCAAAGTCCATGACTCTGTGGCATTT
1 TCTCTTC-CCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCATCT
541675 TTTCTTCAAAGTCCACGACTCAGTGGCA
65 TTTCTTCAAAGTCCACGACTCAGTGGCA
*
541703 TCTCTTCCCAAAGTCCACAACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCAATCT
1 TCTCTTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGC-ATCT
*
541768 CTTCTTCAAAGTCCAC-ATCTCAGTGGCA
65 TTTCTTCAAAGTCCACGA-CTCAGTGGCA
*
541796 TCTCTTCCCAAAGTCCACAACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCAATCT
1 TCTCTTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGC-ATCT
*
541861 CTTCTTCAAAGTCCAC-ATCTCAGTGGCA
65 TTTCTTCAAAGTCCACGA-CTCAGTGGCA
* * * *
541889 TCTCTTCCCAAAGTCCACGACCCAGTGGCATTTTTTCTTTAAAGTCCATGACTCTGTGGCATCTT
1 TCTCTTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCATCTT
* *
541954 TTCTTCAAAGTCCATGACTTAGTGGCA
66 TTCTTCAAAGTCCACGACTCAGTGGCA
* * * *
541981 TCTCTTCCCAAAGTCCATGACTGAGTGGCATCTTTTTTTCAAAGTCCATGACTCAGGGGCAATCT
1 TCTCTTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGC-ATCT
* * *
542046 CTTC-TCAAAGTCCACAACTCAATGGCA
65 TTTCTTCAAAGTCCACGACTCAGTGGCA
542073 TCTCTTCCCCAAAGTCCACGACTC
1 TCTCTT-CCCAAAGTCCACGACTC
542097 TATGGTACCT
Statistics
Matches: 841, Mismatches: 91, Indels: 28
0.88 0.09 0.03
Matches are distributed among these distances:
91 63 0.07
92 498 0.59
93 275 0.33
94 5 0.01
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (92 bp):
TCTCTTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGCATCTT
TTCTTCAAAGTCCACGACTCAGTGGCA
Found at i:542921 original size:33 final size:34
Alignment explanation
Indices: 542857--542926 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
542847 CCGTTACAAG
* *
542857 CAATGTATCGATACAATTTCCTCATGTATCGATA
1 CAATGTATCAATACAATTACCTCATGTATCGATA
542891 CAATGTATCAATAC-ATTGACC-CATGTATCGATA
1 CAATGTATCAATACAATT-ACCTCATGTATCGATA
542924 CAA
1 CAA
542927 ATAGTGATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 18 0.55
34 15 0.45
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.31
Consensus pattern (34 bp):
CAATGTATCAATACAATTACCTCATGTATCGATA
Found at i:543000 original size:19 final size:19
Alignment explanation
Indices: 542954--543009 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
542944 ACTGCCAGTT
*
542954 TCATGTATCGATACAATTG
1 TCATGTATCGATACAATAG
542973 TCTATGTATCGATACAATAAG
1 TC-ATGTATCGATACAAT-AG
542994 -CATGTATCGATACAAT
1 TCATGTATCGATACAAT
543010 GTATCGATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 16 0.47
21 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (19 bp):
TCATGTATCGATACAATAG
Found at i:543013 original size:13 final size:13
Alignment explanation
Indices: 542995--543021 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
542985 TACAATAAGC
542995 ATGTATCGATACA
1 ATGTATCGATACA
543008 ATGTATCGATACA
1 ATGTATCGATACA
543021 A
1 A
543022 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:543575 original size:21 final size:21
Alignment explanation
Indices: 543549--543615 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
543539 CGTTTTACTC
543549 CCCCTTAATTAAAGAATTTCT
1 CCCCTTAATTAAAGAATTTCT
*
543570 CTCCTT--TTAAA-AA-TTCT
1 CCCCTTAATTAAAGAATTTCT
*
543587 CCCCCTTAATCAAAGAATTTCT
1 -CCCCTTAATTAAAGAATTTCT
543609 CCGCCTT
1 CC-CCTT
543616 TGTCAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
17 4 0.11
18 7 0.19
19 5 0.14
20 4 0.11
21 9 0.24
22 8 0.22
ACGTcount: A:0.28, C:0.30, G:0.04, T:0.37
Consensus pattern (21 bp):
CCCCTTAATTAAAGAATTTCT
Found at i:543608 original size:22 final size:22
Alignment explanation
Indices: 543546--543615 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
543536 TTTCGTTTTA
543546 CTCCCCCTTAATTAAAGAATTT
1 CTCCCCCTTAATTAAAGAATTT
*
543568 CT-CTCCTT--TTAAA-AA-TT
1 CTCCCCCTTAATTAAAGAATTT
*
543585 CTCCCCCTTAATCAAAGAATTT
1 CTCCCCCTTAATTAAAGAATTT
*
543607 CTCCGCCTT
1 CTCCCCCTT
543616 TGTCAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
17 4 0.10
18 7 0.18
19 5 0.13
20 4 0.10
21 7 0.18
22 12 0.31
ACGTcount: A:0.27, C:0.31, G:0.04, T:0.37
Consensus pattern (22 bp):
CTCCCCCTTAATTAAAGAATTT
Found at i:552404 original size:27 final size:27
Alignment explanation
Indices: 552366--552464 Score: 119
Period size: 27 Copynumber: 3.5 Consensus size: 27
552356 AAAGTCCTCT
*
552366 GTGGCACCCTTTTAGGTCCACAACTCC
1 GTGGCACCCTTTTAAGTCCACAACTCC
*
552393 GTGGCACCCTTTTAAGTCCACAACTTC
1 GTGGCACCCTTTTAAGTCCACAACTCC
552420 GTGGCATCTTTTTCCTTTTAAGTCCACAACTCC
1 GTGGCA-C-----CCTTTTAAGTCCACAACTCC
552453 GTGGCA-CCTTTT
1 GTGGCACCCTTTT
552465 CTTTTTAAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
26 6 0.10
27 31 0.49
28 1 0.02
33 25 0.40
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.33
Consensus pattern (27 bp):
GTGGCACCCTTTTAAGTCCACAACTCC
Found at i:552523 original size:34 final size:33
Alignment explanation
Indices: 552373--552563 Score: 193
Period size: 34 Copynumber: 5.9 Consensus size: 33
552363 TCTGTGGCAC
*
552373 CCTTTTAGGTCCACAACTCCGTGGCA-C-----
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
552400 CCTTTTAAGTCCACAACTTCGTGGCATCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
552433 CCTTTTAAGTCCACAACTCCGTGGCACC-TTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
552465 CTTTTTAAGTCCA-AGACTCTGTGGCACCTTTTT
1 CCTTTTAAGTCCACA-ACTCCGTGGCACCTTTTT
* * *
552498 CCCTTTTAAGCCCACACCTCCGTGGCATCTCTTCTT
1 -CCTTTTAAGTCCACAACTCCGTGGCA-C-CTTTTT
* *
552534 CC-TATAAGTCCACAACTCCATGGCACCTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTT
552564 AAGTCCAATA
Statistics
Matches: 136, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
27 24 0.18
28 1 0.01
31 1 0.01
32 31 0.23
33 31 0.23
34 39 0.29
35 4 0.03
36 5 0.04
ACGTcount: A:0.19, C:0.34, G:0.13, T:0.35
Consensus pattern (33 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
Found at i:552533 original size:66 final size:65
Alignment explanation
Indices: 552373--552563 Score: 198
Period size: 66 Copynumber: 3.0 Consensus size: 65
552363 TCTGTGGCAC
* * *
552373 CCTTTTAGGTCCACAACTCCGTGGCA-C-C--C-TTTTAAGTCCACAACTTCGTGGCATCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCACCTCTTCTTTTTAAGTCCACAACTTCGTGGCACCTTTTT
* *
552433 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTTTTAAGTCCA-AGAC-TCTGTGGCACCTTT
1 CCTTTTAAGCCCACAACTCCGTGGCACCTCTTCTTTTTAAGTCCACA-ACTTC-GTGGCACCTTT
552496 TT
64 TT
* * * * *
552498 CCCTTTTAAGCCCACACCTCCGTGGCATCTCTTCTTCCTATAAGTCCACAACTCCATGGCACCTT
1 -CCTTTTAAGCCCACAACTCCGTGGCACCTCTTCTT--TTTAAGTCCACAACTTCGTGGCACCTT
552563 T
63 T
552564 AAGTCCAATA
Statistics
Matches: 109, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
60 25 0.23
61 1 0.01
64 4 0.04
65 25 0.23
66 31 0.28
68 21 0.19
69 2 0.02
ACGTcount: A:0.19, C:0.34, G:0.13, T:0.35
Consensus pattern (65 bp):
CCTTTTAAGCCCACAACTCCGTGGCACCTCTTCTTTTTAAGTCCACAACTTCGTGGCACCTTTTT
Found at i:552633 original size:49 final size:47
Alignment explanation
Indices: 552560--553396 Score: 527
Period size: 49 Copynumber: 17.8 Consensus size: 47
552550 TCCATGGCAC
* * *
552560 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACTTTTGT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC--TTGT
* * *
552609 CTTTAGGACCAATGTCGCTAGCCTTGAATCAGCACATTGG--C--GT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTGT
* * * * * *
552652 CTTTAAGTCCAATATTGTTGGCCTTGAATCAGTATATTGGCACCTTTAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-C-TTGT
* * *
552701 CTTTAAGACCAATGTCACTGGCCTTAAATCAGCACATTGGCAC----
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTGT
*
552744 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCGA-ATTGGCACCTTGT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGC-ACATTGGCA-CTTGT
* * *
552792 -TTCTAAGACCAATGTTGCTAGCCTTGAATCAGCACATTGGCA-----
1 CTT-TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTGT
* * *
552834 ---TAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACTTTGT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC-TTGT
* *
552879 CTTTAAGACCAATGTC-CTTGGCCTTGAATAAGCACATTGGCA-----
1 CTTTAAGACCAATATCGC-TGGCCTTGAATCAGCACATTGGCACTTGT
* * * *
552921 C---AAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTT-GT
** * * * *
552967 CTTTAAGACTGATGTCGTTGGCCTTGAATCAACACATTGGCACCTTAACCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTT----GT
* * * * * *
553019 CTTTAAGTCCTAATGTCACTGGTCTTGAATCAGCATATTGGCACCTTTAT
1 CTTTAAGACC-AATATCGCTGGCCTTGAATCAGCACATTGGCA-C-TTGT
* * *
553069 CTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATTGGCAC----
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTGT
* * *
553112 CTTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGCATCTTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTT-GT
* * * * * * *
553161 CTTTAAGTCCGATATCGTTGGCCTTGAATCAACATATTGGCGCATTTAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATT-G-GCACTTGT
* *
553210 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC-TT-GT
* * * *
553259 CTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCATCTT-T
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTGT
* * ** *
553306 AACATTCGTAAG-CCTAATGTCGTTGGCCTTGTCTCAGCACATTGGCA-TTCTT
1 --C-TT--TAAGACC-AATATCGCTGGCCTTGAATCAGCACATTGGCACTT-GT
* * * *
553358 CTTCAAGTCTAATATCGCTGGCCATGAATCAGCACATTG
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTG
553397 TCATTCTTCG
Statistics
Matches: 627, Mismatches: 101, Indels: 122
0.74 0.12 0.14
Matches are distributed among these distances:
39 67 0.11
40 1 0.00
42 1 0.00
43 107 0.17
44 3 0.00
46 2 0.00
47 36 0.06
48 71 0.11
49 241 0.38
50 20 0.03
51 5 0.01
52 43 0.07
53 28 0.04
54 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (47 bp):
CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTGT
Found at i:552725 original size:92 final size:92
Alignment explanation
Indices: 552554--553307 Score: 771
Period size: 92 Copynumber: 8.1 Consensus size: 92
552544 CACAACTCCA
* * * * *
552554 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACTTTTGTCTTTAGGACC
1 TGGCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
*
552619 AATGTCGCTAGCCTTGAATCAGCACAT
66 AATGTCGCTGGCCTTGAATCAGCACAT
* * * *
552646 TGGCGTCTTTAAGTCCAATATTGTTGGCCTTGAATCAGTATATTGGCACCTTTATCTTTAAGACC
1 TGGCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
* *
552711 AATGTCACTGGCCTTAAATCAGCACAT
66 AATGTCGCTGGCCTTGAATCAGCACAT
* *
552738 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCGA-ATTGGCACCTTGT-T-TCTAAGA
1 TGGCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC-ATATTGGCACCTT-TATCTTTAAGA
* *
552800 CCAATGTTGCTAGCCTTGAATCAGCACAT
64 CCAATGTCGCTGGCCTTGAATCAGCACAT
* * *
552829 TGGCA----TAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCA-CTTTGTCTTTAAGACC
1 TGGCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
*
552889 AATGTC-CTTGGCCTTGAATAAGCACAT
66 AATGTCGC-TGGCCTTGAATCAGCACAT
* * * *
552916 TGGCA-C---AAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACT
1 TGGCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
* * *
552977 GATGTCGTTGGCCTTGAATCAACACAT
66 AATGTCGCTGGCCTTGAATCAGCACAT
* * *
553004 TGGCACCTTAACCATCTTTAAGTCCTAATGTCACTGGTCTTGAATCAGCATATTGGCACCTTTAT
1 TGG---------CATCTTTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* *
553069 CTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACAT
56 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACAT
* * * * * *
553106 TGGCACCTTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCC
1 TGGCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
* * * * *
553171 GATATCGTTGGCCTTGAATCAACATAT
66 AATGTCGCTGGCCTTGAATCAGCACAT
* * *
553198 TGGCGCATTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCATCTT
1 T-G-GC----ATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-ATCTT
* * * * *
553262 TAAGTCCGATATCGTTGGCCTTGAATCAGCATAT
59 TAAGACCAATGTCGCTGGCCTTGAATCAGCACAT
553296 TGGCATCTTTAA
1 TGGCATCTTTAA
553308 CATTCGTAAG
Statistics
Matches: 573, Mismatches: 59, Indels: 60
0.83 0.09 0.09
Matches are distributed among these distances:
85 1 0.00
86 6 0.01
87 106 0.18
88 38 0.07
91 36 0.06
92 202 0.35
93 15 0.03
94 2 0.00
96 2 0.00
97 6 0.01
98 80 0.14
101 5 0.01
102 74 0.13
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (92 bp):
TGGCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
AATGTCGCTGGCCTTGAATCAGCACAT
Found at i:552855 original size:39 final size:39
Alignment explanation
Indices: 552795--552959 Score: 125
Period size: 39 Copynumber: 4.0 Consensus size: 39
552785 ACCTTGTTTC
* *
552795 TAAGACCAATGTTGCTAGCCTTGAATCAGCACATTGGCA
1 TAAGACCAATATTGCTGGCCTTGAATCAGCACATTGGCA
* *
552834 TAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCA
1 TAAGACCAATATTGCTGGCCTTGAATCAGCACATTGGCA
* * *
552873 CTTTGTCTTTAAGACCAAT-GTCCTTGGCCTTGAATAAGCACATTGGCA
1 ---------TAAGACCAATATTGC-TGGCCTTGAATCAGCACATTGGCA
* * ** *
552921 CAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCA
1 TAAGACCAATATTGCTGGCCTTGAATCAGCACATTGGCA
552960 CCTTCATCTT
Statistics
Matches: 99, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
39 65 0.66
40 1 0.01
47 2 0.02
48 31 0.31
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (39 bp):
TAAGACCAATATTGCTGGCCTTGAATCAGCACATTGGCA
Found at i:552886 original size:87 final size:87
Alignment explanation
Indices: 552563--553008 Score: 520
Period size: 87 Copynumber: 5.0 Consensus size: 87
552553 ATGGCACCTT
* *
552563 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACTTTTGTCTTTAGGACCAATGTCGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC-TTTGTCTTTAAGACCAATGTCGCT
* *
552628 AGCCTTGAATCAGCACATTGGCGTCTT
65 GGCCTTGAATCAGCACATT-G-G-C-A
* * * * *
552655 TAAGTCCAATATTGTTGGCCTTGAATCAGTATATTGGCACCTTTATCTTTAAGACCAATGTCACT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTTGTCTTTAAGACCAATGTCGCT
*
552720 GGCCTTAAATCAGCACATTGGCA
65 GGCCTTGAATCAGCACATTGGCA
*
552743 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCGA-ATTGGCACCTTGT-TTCTAAGACCAATG
1 ----TAAGTCCAATATCGCTGGCCTTGAATCAGC-ATATTGGCACTTTGTCTT-TAAGACCAATG
* *
552806 TTGCTAGCCTTGAATCAGCACATTGGCA
60 TCGCTGGCCTTGAATCAGCACATTGGCA
* *
552834 TAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACTTTGTCTTTAAGACCAATGTC-CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTGTCTTTAAGACCAATGTCGC-T
*
552898 GGCCTTGAATAAGCACATTGGCA
65 GGCCTTGAATCAGCACATTGGCA
* * * ** ** *
552921 CAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACTGATGTCGTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTTGTCTTTAAGACCAATGTCGCT
*
552986 GGCCTTGAATCAACACATTGGCA
65 GGCCTTGAATCAGCACATTGGCA
553009 CCTTAACCAT
Statistics
Matches: 307, Mismatches: 35, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
86 2 0.01
87 110 0.36
88 42 0.14
89 1 0.00
90 3 0.01
91 40 0.13
92 107 0.35
93 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (87 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTGTCTTTAAGACCAATGTCGCTG
GCCTTGAATCAGCACATTGGCA
Found at i:553305 original size:141 final size:136
Alignment explanation
Indices: 552701--553307 Score: 356
Period size: 141 Copynumber: 4.4 Consensus size: 136
552691 GCACCTTTAT
* * * * * *
552701 CTTTAAGACCAATGTCACTGGCCTTAAATCAGCACATTGG-CACCTTTAAGTCCAATATCGCTGG
1 CTTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGTCATCTTTAAGTCCGATATCGTTGG
* * * * *
552765 CCTTGAATCAGCGA-ATTGGCACCTTGT-T-TCTAAGACCAATGTTGCTAGCCTTGAATCAGCAC
66 CCTTGAATCAAC-ATATTGGCACATT-TATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCAC
552827 ATTGGCA-
129 ATTGGCAC
* ** * * * *
552834 ---TAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGG-CACTTTGTCTTTAAGACCAATGTC
1 CTTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGTCA-----TCTTTAAGTCCGATATC
* * * * *
552895 CTTGGCCTTGAAT-AAGCACATTGG--C----A-C---AAGCCCAATATCACTGGCCTTGAATCA
61 GTTGGCCTTGAATCAA-CATATTGGCACATTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCA
*
552949 GCATATTGGCACCTTC
125 GCACATTGGCA----C
* ** * ** *
552965 ATCTTTAAGACTGATGTCGTTGGCCTTGAATCAACACATTGGCACCTTAACCATCTTTAAGTCCT
1 --CTTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGG-----T---CATCTTTAAGTCC-
* * ** * * * * *
553030 AATGTCACTGGTCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCGATGTCGTTGGCCTTG
55 GATATCGTTGGCCTTGAATCAACATATTGGCACATTTATCTTTAAGACCAATGTCGCTGGCCTTG
553095 AATCAGCACATTGGCAC
120 AATCAGCACATTGGCAC
553112 CTTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGATATC
1 CTTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGG-----TCATCTTTAAGTCCGATATC
*
553177 GTTGGCCTTGAATCAACATATTGGCGCATTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAG
61 GTTGGCCTTGAATCAACATATTGGCACATTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAG
553242 CACATTGGCACTTTC
126 CACATTGGCA----C
* ** *
553257 ATCTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGG-CATCTTTAA
1 --CTTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGTCATCTTTAA
553308 CATTCGTAAG
Statistics
Matches: 368, Mismatches: 60, Indels: 84
0.72 0.12 0.16
Matches are distributed among these distances:
126 32 0.09
130 33 0.09
133 1 0.00
134 2 0.01
135 31 0.08
136 29 0.08
140 10 0.03
141 103 0.28
142 14 0.04
143 1 0.00
145 41 0.11
147 38 0.10
148 1 0.00
151 32 0.09
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (136 bp):
CTTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGTCATCTTTAAGTCCGATATCGTTGG
CCTTGAATCAACATATTGGCACATTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACAT
TGGCAC
Found at i:554225 original size:13 final size:13
Alignment explanation
Indices: 554207--554232 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
554197 ACATAAGTGT
554207 TGTATCGATACAA
1 TGTATCGATACAA
554220 TGTATCGATACAA
1 TGTATCGATACAA
554233 AGCTACCCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:559640 original size:13 final size:13
Alignment explanation
Indices: 559622--559647 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
559612 ACATTTTGTG
559622 ATGTATCGATACA
1 ATGTATCGATACA
559635 ATGTATCGATACA
1 ATGTATCGATACA
559648 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:559664 original size:32 final size:33
Alignment explanation
Indices: 559600--559667 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
559590 CGTTACAAGC
*
559600 CAATGTATCAATACATTTTGTGATGTATCGATA
1 CAATGTATCAATACATATTGTGATGTATCGATA
*
559633 CAATGTATCGATACATATTGTG-TGTATCGATA
1 CAATGTATCAATACATATTGTGATGTATCGATA
559665 CAA
1 CAA
559668 ATTTAGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (33 bp):
CAATGTATCAATACATATTGTGATGTATCGATA
Found at i:559729 original size:20 final size:20
Alignment explanation
Indices: 559700--559752 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
559690 CCAATGACTT
* **
559700 GTATCAATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
559720 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
559740 GTATCGATACATT
1 GTATCGATACATT
559753 GTATCGATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:559776 original size:20 final size:19
Alignment explanation
Indices: 559751--559803 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
559741 TATCGATACA
559751 TTGTATCGATACTGTACAAT
1 TTGTATCGATACTGTA-AAT
* *
559771 TTGTATCGATATATTTAAAT
1 TTGTATCGATA-CTGTAAAT
*
559791 GTGTATCGATACT
1 TTGTATCGATACT
559804 TTTCAGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 24 0.86
21 3 0.11
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (19 bp):
TTGTATCGATACTGTAAAT
Found at i:560346 original size:22 final size:22
Alignment explanation
Indices: 560318--560362 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
560308 TTTTCTTGTC
560318 TCTCCCCCTTAATCAAAA-AATT
1 TCTCCCCCTTAAT-AAAATAATT
560340 TCTCCCCCTTAATAAAATAATT
1 TCTCCCCCTTAATAAAATAATT
560362 T
1 T
560363 AACAATTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAATAATT
Found at i:560409 original size:25 final size:25
Alignment explanation
Indices: 560381--560453 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
560371 CGCACATTAA
560381 AAAATTCTTTCTCCCCCTTAATCAT
1 AAAATTCTTTCTCCCCCTTAATCAT
* * *
560406 AAAA---TTTC-GCACATT-A--A-
1 AAAATTCTTTCTCCCCCTTAATCAT
560423 AAAATTCTTTCTCCCCCTTAATCAT
1 AAAATTCTTTCTCCCCCTTAATCAT
560448 AAAATT
1 AAAATT
560454 TATTTACACA
Statistics
Matches: 34, Mismatches: 6, Indels: 16
0.61 0.11 0.29
Matches are distributed among these distances:
17 4 0.12
18 1 0.03
20 5 0.15
21 8 0.24
22 5 0.15
24 1 0.03
25 10 0.29
ACGTcount: A:0.36, C:0.26, G:0.01, T:0.37
Consensus pattern (25 bp):
AAAATTCTTTCTCCCCCTTAATCAT
Found at i:560412 original size:50 final size:48
Alignment explanation
Indices: 560338--560455 Score: 158
Period size: 42 Copynumber: 2.5 Consensus size: 48
560328 AATCAAAAAA
*
560338 TTTCTCCCCCTTAATAAAATAATTTAACAATTTCGCACATTAAAAAATTC
1 TTTCTCCCCCTTAATCAAA-AATTTAA-AATTTCGCACATTAAAAAATTC
560388 TTTCTCCCCCTTAATC----A--TAAAATTTCGCACATTAAAAAATTC
1 TTTCTCCCCCTTAATCAAAAATTTAAAATTTCGCACATTAAAAAATTC
560430 TTTCTCCCCCTTAATCATAAAATTTA
1 TTTCTCCCCCTTAATCA-AAAATTTA
560456 TTTACACAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 15
0.79 0.01 0.20
Matches are distributed among these distances:
42 38 0.63
43 3 0.05
45 1 0.02
47 1 0.02
49 2 0.03
50 15 0.25
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (48 bp):
TTTCTCCCCCTTAATCAAAAATTTAAAATTTCGCACATTAAAAAATTC
Found at i:560413 original size:42 final size:42
Alignment explanation
Indices: 560366--560454 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
560356 ATAATTTAAC
560366 AATTTCGCACATTAAAAAATTCTTTCTCCCCCTTAATCATAA
1 AATTTCGCACATTAAAAAATTCTTTCTCCCCCTTAATCATAA
560408 AATTTCGCACATTAAAAAATTCTTTCTCCCCCTTAATCATAA
1 AATTTCGCACATTAAAAAATTCTTTCTCCCCCTTAATCATAA
560450 AATTT
1 AATTT
560455 ATTTACACAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (42 bp):
AATTTCGCACATTAAAAAATTCTTTCTCCCCCTTAATCATAA
Found at i:561850 original size:20 final size:21
Alignment explanation
Indices: 561811--561863 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
561801 GCTGCTAGTG
*
561811 TGGGGGCTGCTCGGTTGCGACC
1 TGGGGG-TGCTCGGTCGCGACC
561833 TGGGGGTGC-CGGTCGCGACC
1 TGGGGGTGCTCGGTCGCGACC
561853 TGGTGGGTGCT
1 TGG-GGGTGCT
561864 GCTTAGGGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 13 0.46
21 9 0.32
22 6 0.21
ACGTcount: A:0.04, C:0.25, G:0.49, T:0.23
Consensus pattern (21 bp):
TGGGGGTGCTCGGTCGCGACC
Found at i:562155 original size:20 final size:21
Alignment explanation
Indices: 562126--562166 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
562116 TGTTTTTGTT
562126 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
562145 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
562167 AAGAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:562318 original size:13 final size:13
Alignment explanation
Indices: 562300--562333 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
562290 AAACCCCTTG
*
562300 TATCGATACACTA
1 TATCGATACAATA
*
562313 TATCGATACAATG
1 TATCGATACAATA
562326 TATCGATA
1 TATCGATA
562334 TAGAAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:565003 original size:20 final size:19
Alignment explanation
Indices: 564977--565032 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
564967 CTTTAACGAT
*
564977 ACATTGTATCGATACATGTT
1 ACATTGTATCGATACATG-C
* *
564997 TCATTGTA-CGATATATGC
1 ACATTGTATCGATACATGC
565015 ACAATTGTATCGATACAT
1 AC-ATTGTATCGATACAT
565033 AAAACTGGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 1 0.03
19 14 0.48
20 14 0.48
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:667551 original size:18 final size:20
Alignment explanation
Indices: 667513--667551 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
667503 CCCTAAAGCA
*
667513 GCACCCACCAGGTCGCGACC
1 GCACCCACCAGGTCGCAACC
667533 GCACCC-CCA-GTCGCAACC
1 GCACCCACCAGGTCGCAACC
667551 G
1 G
667552 AAGCAGCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.21, C:0.51, G:0.23, T:0.05
Consensus pattern (20 bp):
GCACCCACCAGGTCGCAACC
Found at i:669634 original size:19 final size:20
Alignment explanation
Indices: 669593--669636 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
669583 GTATCGATAC
**
669593 AATGTATCGATACATGACTA
1 AATGTATCGATACATGAAAA
*
669613 AATGTAT-GATACTTGAAAA
1 AATGTATCGATACATGAAAA
669632 AATGT
1 AATGT
669637 CTTGATACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:669734 original size:32 final size:33
Alignment explanation
Indices: 669677--669741 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
669667 GTAGCTAAAT
669677 TTGTATCGATACACACACAATATGTATCGATAC
1 TTGTATCGATACACACACAATATGTATCGATAC
*
669710 TTGTATCGATACATCACA-AA-ATGTATTGATAC
1 TTGTATCGATACA-CACACAATATGTATCGATAC
669742 ATTTGCTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 11 0.37
33 15 0.50
34 4 0.13
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACACACAATATGTATCGATAC
Found at i:681940 original size:19 final size:20
Alignment explanation
Indices: 681895--681946 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
681885 TTGCAAGCCA
*
681895 ATGTATCGATACATTTTGTG
1 ATGTATCGATACATATTGTG
681915 ATGTATCGATACATATTGTG
1 ATGTATCGATACATATTGTG
681935 -TGTATCGATACA
1 ATGTATCGATACA
681947 AATTTAGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATATTGTG
Found at i:682005 original size:20 final size:20
Alignment explanation
Indices: 681980--682032 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
681970 CCAATGACTT
**
681980 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
682000 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
682020 GTATCGATACATT
1 GTATCGATACATT
682033 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:692328 original size:19 final size:20
Alignment explanation
Indices: 692304--692354 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
692294 TTATGCTTTG
**
692304 TATCGATACATGTTC-ATTA
1 TATCGATACATGGACAATTA
*
692323 TATCGATACATGGACAATTG
1 TATCGATACATGGACAATTA
692343 TATCGATACATG
1 TATCGATACATG
692355 AAACTGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATACATGGACAATTA
Found at i:692348 original size:20 final size:19
Alignment explanation
Indices: 692301--692354 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
692291 ACATTATGCT
**
692301 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGGACA
*
692320 TTATATCGATACATGGACAA
1 TTGTATCGATACATGGAC-A
692340 TTGTATCGATACATG
1 TTGTATCGATACATG
692355 AAACTGGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGGACA
Found at i:692396 original size:62 final size:63
Alignment explanation
Indices: 692323--692477 Score: 260
Period size: 62 Copynumber: 2.5 Consensus size: 63
692313 ATGTTCATTA
* * *
692323 TATCGATACATGG-ACAATTGTATCGATACATGAAACTGGCAGTAGCTACTCTACCACTGTTT-
1 TATCGATACATGGCAC-ATTGTATTGATACATGAAACTGGCAGTAACTACCCTACCACTGTTTG
692385 TATCGATACATGGCACATTGTATTGATACATGAAACTGGCAGTAACTACCCTACCACTGTTTG
1 TATCGATACATGGCACATTGTATTGATACATGAAACTGGCAGTAACTACCCTACCACTGTTTG
692448 TATCGATACATGGCACATTGTATTGATACA
1 TATCGATACATGGCACATTGTATTGATACA
692478 ATATATCGAT
Statistics
Matches: 88, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
62 56 0.64
63 32 0.36
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (63 bp):
TATCGATACATGGCACATTGTATTGATACATGAAACTGGCAGTAACTACCCTACCACTGTTTG
Found at i:694102 original size:3 final size:3
Alignment explanation
Indices: 694087--694120 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
694077 AACCATCAAA
*
694087 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
694121 GTGACTCGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:698712 original size:10 final size:10
Alignment explanation
Indices: 698697--698730 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
698687 TTAACGTCAA
698697 TTCATCAAAT
1 TTCATCAAAT
698707 TTCATCAAAT
1 TTCATCAAAT
*
698717 CTTCTTCAAAT
1 -TTCATCAAAT
698728 TTC
1 TTC
698731 TTATTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (10 bp):
TTCATCAAAT
Found at i:698744 original size:21 final size:22
Alignment explanation
Indices: 698720--698769 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
698710 ATCAAATCTT
* *
698720 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
698741 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
698763 --TCAAAAT
1 CTTCAAAAT
698770 CATCAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:701161 original size:20 final size:20
Alignment explanation
Indices: 701115--701171 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
701105 TTGTATTGAT
* *
701115 ACAA-TGTATCCATACATGT
1 ACAATTGTATCGATACATGG
*
701134 TC-ATTGTATCGATACATGG
1 ACAATTGTATCGATACATGG
701153 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
701172 AAATTGGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.47
20 16 0.50
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:704093 original size:14 final size:14
Alignment explanation
Indices: 704060--704103 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
704050 CATATCCTTT
704060 TTCTTTTTCCTTTCTC
1 TTCTTTTT-CTTT-TC
704076 TTCTCTTTT-TTTTC
1 TTCT-TTTTCTTTTC
704090 TTCTTTTTCTTTTC
1 TTCTTTTTCTTTTC
704104 ATGCTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 4 0.15
14 11 0.42
15 3 0.12
16 4 0.15
17 4 0.15
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TTCTTTTTCTTTTC
Found at i:704218 original size:14 final size:13
Alignment explanation
Indices: 704201--704247 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
704191 TCCCTATGGG
704201 TTTTCATCCTTTT
1 TTTTCATCCTTTT
*
704214 CTTTTTATCC-TTT
1 -TTTTCATCCTTTT
*
704227 TTTTCATTCATTTT
1 TTTTCA-TCCTTTT
704241 TTTTCAT
1 TTTTCAT
704248 TATTTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 5 0.18
13 6 0.21
14 17 0.61
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCATCCTTTT
Found at i:704248 original size:14 final size:13
Alignment explanation
Indices: 704224--704255 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
704214 CTTTTTATCC
704224 TTTTTTTCATTCAT
1 TTTTTTTCATT-AT
704238 TTTTTTTCATTAT
1 TTTTTTTCATTAT
704251 TTTTT
1 TTTTT
704256 ATTGGATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTTCATTAT
Found at i:706311 original size:42 final size:41
Alignment explanation
Indices: 706257--706462 Score: 118
Period size: 43 Copynumber: 4.9 Consensus size: 41
706247 TAAGGTGACT
*
706257 GCAAACATAGGATAAAAAGGTTGATAGGGAATGAACCGCTAA
1 GCAAACAAAGGATAAAAAGGTTGATAGGGAATGAACCGC-AA
* * * *
706299 GTC-AACAAAGGATAAAAAGATTTACCTA--GAATTAAGCCAACAA
1 G-CAAACAAAGGATAAAAAGGTTGA--TAGGGAATGAA-CC-GCAA
* * **
706342 GCAAACAAAGGATAAAAAGGTTAACAGGGAATGAA-CTTATTA
1 GCAAACAAAGGATAAAAAGGTTGATAGGGAATGAACCGCA--A
* * * * *
706384 GTC-AACAAAGGATAAAAAGATTTACTCGGGACT-AAGCTGACAA
1 G-CAAACAAAGGATAAAAAGGTTGA-TAGGGAATGAA-CCG-CAA
* *
706427 GCAAACAAAGGATAAAAGGGTTGATAAGGAATGAAC
1 GCAAACAAAGGATAAAAAGGTTGATAGGGAATGAAC
706463 GTACAAGTTA
Statistics
Matches: 122, Mismatches: 25, Indels: 34
0.67 0.14 0.19
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 56 0.46
43 59 0.48
44 3 0.02
45 1 0.01
ACGTcount: A:0.48, C:0.13, G:0.22, T:0.17
Consensus pattern (41 bp):
GCAAACAAAGGATAAAAAGGTTGATAGGGAATGAACCGCAA
Found at i:706479 original size:85 final size:85
Alignment explanation
Indices: 706191--706487 Score: 316
Period size: 85 Copynumber: 3.5 Consensus size: 85
706181 AAGAATAAAC
* * * * * *
706191 GGTTGATCGAGAATGAAC-TGACAAGTTAATAAAGGATAAAAAGATTTACTTGGGACTAAGGTGA
1 GGTTGATAGGGAATGAACGT-ACAAGTCAACAAAGGATAAAAAGATTTACTCGGGACTAAGCTGA
* *
706255 C-TGCAAACATAGGATAAAAA
65 CAAGCAAACAAAGGATAAAAA
* * * *
706275 GGTTGATAGGGAATGAACCG--CTAAGTCAACAAAGGATAAAAAGATTTAC-CTAGAATTAAGCC
1 GGTTGATAGGGAATGAA-CGTAC-AAGTCAACAAAGGATAAAAAGATTTACTC-GGGACTAAGCT
*
706337 AACAAGCAAACAAAGGATAAAAA
63 GACAAGCAAACAAAGGATAAAAA
* * * **
706360 GGTTAACAGGGAATGAACTTATTAGTCAACAAAGGATAAAAAGATTTACTCGGGACTAAGCTGAC
1 GGTTGATAGGGAATGAACGTACAAGTCAACAAAGGATAAAAAGATTTACTCGGGACTAAGCTGAC
*
706425 AAGCAAACAAAGGATAAAAG
66 AAGCAAACAAAGGATAAAAA
* * * *
706445 GGTTGATAAGGAATGAACGTACAAGTTAAGAAAGGTTAAAAAG
1 GGTTGATAGGGAATGAACGTACAAGTCAACAAAGGATAAAAAG
706488 TGATAGCTGA
Statistics
Matches: 172, Mismatches: 33, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
83 1 0.01
84 49 0.28
85 121 0.70
86 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (85 bp):
GGTTGATAGGGAATGAACGTACAAGTCAACAAAGGATAAAAAGATTTACTCGGGACTAAGCTGAC
AAGCAAACAAAGGATAAAAA
Found at i:707668 original size:35 final size:35
Alignment explanation
Indices: 706632--707686 Score: 688
Period size: 35 Copynumber: 30.2 Consensus size: 35
706622 CCTAACGCCA
* * *
706632 ATACAGTCAAATAAGGATACAAAGAGTTTGACCAG
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* * * *
706667 ATAAAGTTAAATGATGATAAAAAGAGTCTGACCAG
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* * * *
706702 ATAAAGTCAAATAATGAT-GAAAAGAGTTTGATCAA
1 ATACAGTCAAATGATGATAG-AAAGAGTTTGACCAG
* * *
706737 ATACAG-CTAAACGATGAT-GAAAGAGCTTGACTAG
1 ATACAGTC-AAATGATGATAGAAAGAGTTTGACCAG
* * * *
706771 ATACTGCCAAACGATGAT-GAAAAGAGTTTGATCAG
1 ATACAGTCAAATGATGATAG-AAAGAGTTTGACCAG
* ** *
706806 ATATAG-CTAAACAATGATA-AAAGAGTTTGACCGG
1 ATACAGTC-AAATGATGATAGAAAGAGTTTGACCAG
* * * * * *
706840 ATACCGCCAAACGAGGATAAAAAGAGTTTGACCAA
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* * * * * **
706875 ATAAAGTTAAATGATGATGGAAAAAGTTTAATTAG
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* * *
706910 ATACA-ACTAAACGATGATAGAAAGAGTTCGACCAG
1 ATACAGTC-AAATGATGATAGAAAGAGTTTGACCAG
* ** * *
706945 ATACAGCCAAACAATGATGGAAAGAGTTTGACCAA
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* * *
706980 ATACAGTCAAACGATGATAGAAAGAGTTTGGCCTG
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* * * * *
707015 ATATAGTTAAAT-AGTGGT-GAGAATAGTTTGACTAG
1 ATACAGTCAAATGA-TGATAGA-AAGAGTTTGACCAG
* * ** * * *
707050 ATGCAATCAAACAATGATGGAAAGCGTTTAACCAG
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* * * * *
707085 ATAAAGTTAAATAATGATGGAAAGAGTTTAACCAG
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* * * *
707120 ATACAATCAAACGATGATGGAAAGAGTTTAACCAG
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* ** * * *
707155 ATATAACCAAATGATGGT-GAGAAGACTTTGACTAG
1 ATACAGTCAAATGATGATAGA-AAGAGTTTGACCAG
* * * *
707190 ATACAGCCAGACGATGGT-GAGAAGAGTTTGACCAG
1 ATACAGTCAAATGATGATAGA-AAGAGTTTGACCAG
** * *
707225 ATGTAGTCAAATGATGATGGAAAGAGTTTGACCAA
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* * * *
707260 ATACAATTAAATGATAATGGAAAGAGTTTGACCAG
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* *
707295 ATACAGTTAAATGATGATAGAAAGAGTTTGACTAG
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* *
707330 ATACAG-CTAAATGATGATAGAAAGAGTTTAACTAG
1 ATACAGTC-AAATGATGATAGAAAGAGTTTGACCAG
* *
707365 ATATAGTCAAATGATGATGGAAAGAGTTTGACCAG
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* * * * *
707400 ATAAAGCCAAATGATGAT-GAAAAAAGTTTCATCAG
1 ATACAGTCAAATGATGATAG-AAAGAGTTTGACCAG
* * * *
707435 ATATAGCCAAATGATAATAGAAAGAGTTTAACCAG
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* * ** * **
707470 ATATAGTTAAACAATGGTGAGAAA-AGTTTGAATAG
1 ATACAGTCAAATGATGAT-AGAAAGAGTTTGACCAG
* * * **
707505 ATACATTCAAATGATGGT-GAAAAGAGTTTAATTAG
1 ATACAGTCAAATGATGATAG-AAAGAGTTTGACCAG
* * *
707540 ATACAGTTAAATGATGGTA-ACAAGGGTTTGACCAG
1 ATACAGTCAAATGATGATAGA-AAGAGTTTGACCAG
* *
707575 ATGCAGTCAAACGAT-AGT-GAGAAGAGTTTGACCAG
1 ATACAGTCAAATGATGA-TAGA-AAGAGTTTGACCAG
*** *
707610 AGGTAGTCAAATGATGATGGAAAGAGTTTGACCAG
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
* ** * * * *
707645 ATATAGTCAAACAATGGTAGAAAGAGTTAGACTAA
1 ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
707680 ATACAGT
1 ATACAGT
707687 TAAACGAGAG
Statistics
Matches: 807, Mismatches: 184, Indels: 58
0.77 0.18 0.06
Matches are distributed among these distances:
33 1 0.00
34 65 0.08
35 725 0.90
36 16 0.02
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (35 bp):
ATACAGTCAAATGATGATAGAAAGAGTTTGACCAG
Found at i:708160 original size:91 final size:90
Alignment explanation
Indices: 707933--708367 Score: 493
Period size: 91 Copynumber: 4.8 Consensus size: 90
707923 GTCAAGATAT
* *** * *
707933 CCTTGCCCGAAGGAAATCAAGCTCCATGATGCATCAATACCATCTAGTGGCTG--GGAAAGAGGG
1 CCTTGCCCTAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTGAATG-AAG-GGG
*
707996 ATATGATTAGGGAATGTGTGGGTTGCA
64 ATATGATTAGGGAATGTGTGGGCTGCA
* * * * * *
708023 CCTTGCCCCAAGGAAATTAGGCTTTGTGATACATCATTACCATCTAGTTGTTGAATGAAGGGGAT
1 CCTTGCCCTAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTGAATGAAGGGGAT
708088 ATGATTAGGGAATGTGTGGGCTGCA
66 ATGATTAGGGAATGTGTGGGCTGCA
* * *
708113 CCCTTGCCCTAAGGAAATCAAGCTTTGCGATGCATTAATACCATCTAGTGTTTGAATGAAGGGGA
1 -CCTTGCCCTAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTGAATGAAGGGGA
* *
708178 TATGATTGGGGAATGTATGGGCTGCA
65 TATGATTAGGGAATGTGTGGGCTGCA
* * * * * *
708204 CCCTTACCTTAAAGAAATCAAGCTTTGTGATGCATTAATACCAT-TGAGTGGCTGAATGAAGGAG
1 -CCTTGCCCTAAGGAAATCAAGCTTTGTGATGCATCAATACCATCT-AGTGGTTGAATGAAGGGG
* *
708268 ATATGATT-GGGAATGTGTGGGTTACA
64 ATATGATTAGGGAATGTGTGGGCTGCA
* * *** *
708294 CCTTG-CCTCAAGGAAATCAGGCTTTGTGATGCATCATTACCATCTAGTGGTTGTGCGAAGAGGA
1 CCTTGCCCT-AAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTGAATGAAGGGGA
708358 TATGATTAGG
65 TATGATTAGG
708368 AATTTATGGT
Statistics
Matches: 293, Mismatches: 45, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
88 2 0.01
89 54 0.18
90 91 0.31
91 145 0.49
92 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (90 bp):
CCTTGCCCTAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTGAATGAAGGGGAT
ATGATTAGGGAATGTGTGGGCTGCA
Found at i:708192 original size:181 final size:180
Alignment explanation
Indices: 707933--708376 Score: 490
Period size: 181 Copynumber: 2.5 Consensus size: 180
707923 GTCAAGATAT
* ***
707933 CCTTGCCCGAAGGAAATCAAGCTCCATGATGCATCAATACCATCTAGTGGCTGGGAAAGAGGGAT
1 CCTTGCCCTAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGCTGGGAAAGAGGGAT
* * * * * * *
707998 ATGATTAGGGAATGTGTGGGTTGCA-CCTTGCCCCAAGGAAATTAGGCTTTGTGATACATCATTA
66 ATGATTAGGGAATGTATGGGCTGCACCCTTACCCCAAAGAAATCAAGCTTTGTGATACATCAATA
* * * *
708062 CCATCT-AGTTGTTGAATGAAGGGGATATGATTAGGGAATGTGTGGGCTGCA
131 CCAT-TGAGTGGCTGAATGAAGGAGATATGATT-GGGAATGTGTGGGCTACA
* * ** *
708113 CCCTTGCCCTAAGGAAATCAAGCTTTGCGATGCATTAATACCATCTAGT-G-TTTGAATGAAGGG
1 -CCTTGCCCTAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGCTGGGAAAG-A-GG
* ** * *
708176 GATATGATTGGGGAATGTATGGGCTGCACCCTTACCTTAAAGAAATCAAGCTTTGTGATGCATTA
63 GATATGATTAGGGAATGTATGGGCTGCACCCTTACCCCAAAGAAATCAAGCTTTGTGATACATCA
*
708241 ATACCATTGAGTGGCTGAATGAAGGAGATATGATTGGGAATGTGTGGGTTACA
128 ATACCATTGAGTGGCTGAATGAAGGAGATATGATTGGGAATGTGTGGGCTACA
* * *
708294 CCTTG-CCTCAAGGAAATCAGGCTTTGTGATGCATCATTACCATCTAGTGGTTGTGCG-AAGA-G
1 CCTTGCCCT-AAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGCTG-G-GAAAGAGG
*
708356 GATATGATTA-GGAATTTATGG
63 GATATGATTAGGGAATGTATGG
708377 TTTCCACGAT
Statistics
Matches: 219, Mismatches: 35, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
179 18 0.08
180 52 0.24
181 87 0.40
182 59 0.27
183 2 0.01
184 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (180 bp):
CCTTGCCCTAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGCTGGGAAAGAGGGAT
ATGATTAGGGAATGTATGGGCTGCACCCTTACCCCAAAGAAATCAAGCTTTGTGATACATCAATA
CCATTGAGTGGCTGAATGAAGGAGATATGATTGGGAATGTGTGGGCTACA
Found at i:717343 original size:22 final size:22
Alignment explanation
Indices: 717281--717343 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
717271 GACAATGGGG
* *
717281 GAGAAATTCTTTGATTAAGGGG
1 GAGAAATTCTTTAATTAAGGGA
717303 GAG-AATT-TTTAA--AA-GGA
1 GAGAAATTCTTTAATTAAGGGA
717320 GAGAAATTCTTTAATTAAGGGA
1 GAGAAATTCTTTAATTAAGGGA
717342 GA
1 GA
717344 ATAAAACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
17 5 0.15
18 6 0.18
19 5 0.15
20 4 0.12
21 6 0.18
22 8 0.24
ACGTcount: A:0.40, C:0.03, G:0.27, T:0.30
Consensus pattern (22 bp):
GAGAAATTCTTTAATTAAGGGA
Found at i:717933 original size:20 final size:21
Alignment explanation
Indices: 717908--717947 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
717898 ATACATGCTC
717908 ATTGTATCGATACAT-AAACA
1 ATTGTATCGATACATGAAACA
717928 ATTGTATCGATACATGAAAC
1 ATTGTATCGATACATGAAAC
717948 TGGCAGTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (21 bp):
ATTGTATCGATACATGAAACA
Found at i:718011 original size:13 final size:13
Alignment explanation
Indices: 717993--718018 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
717983 CATGGGACAA
717993 TGTATCGATACAT
1 TGTATCGATACAT
718006 TGTATCGATACAT
1 TGTATCGATACAT
718019 GAGGAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:718037 original size:34 final size:33
Alignment explanation
Indices: 717972--718041 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
717962 TTATCACTGT
717972 TTGTATAGATACATGGGACAATGTATCGATACA
1 TTGTATAGATACATGGGACAATGTATCGATACA
* *
718005 TTGTATCGATACATGAGGA-AATTGTATTGATACA
1 TTGTATAGATACATG-GGACAA-TGTATCGATACA
718039 TTG
1 TTG
718042 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 16 0.48
34 17 0.52
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (33 bp):
TTGTATAGATACATGGGACAATGTATCGATACA
Found at i:721926 original size:154 final size:154
Alignment explanation
Indices: 721733--722045 Score: 626
Period size: 154 Copynumber: 2.0 Consensus size: 154
721723 AAATGGTTTC
721733 CAGATTGGGTTTGAAAAAAATTAAATGTTTCGTGTCAAGCACTGGAGAGATACCGACACAGAATA
1 CAGATTGGGTTTGAAAAAAATTAAATGTTTCGTGTCAAGCACTGGAGAGATACCGACACAGAATA
721798 TCATTTTGTGATCTTTAAAAATAGTTTTTAAAGCATGAATGCATAAGGTCCCTACGAAAGGAAAC
66 TCATTTTGTGATCTTTAAAAATAGTTTTTAAAGCATGAATGCATAAGGTCCCTACGAAAGGAAAC
721863 ATGTTTGTAAATCAAAGAAAATAA
131 ATGTTTGTAAATCAAAGAAAATAA
721887 CAGATTGGGTTTGAAAAAAATTAAATGTTTCGTGTCAAGCACTGGAGAGATACCGACACAGAATA
1 CAGATTGGGTTTGAAAAAAATTAAATGTTTCGTGTCAAGCACTGGAGAGATACCGACACAGAATA
721952 TCATTTTGTGATCTTTAAAAATAGTTTTTAAAGCATGAATGCATAAGGTCCCTACGAAAGGAAAC
66 TCATTTTGTGATCTTTAAAAATAGTTTTTAAAGCATGAATGCATAAGGTCCCTACGAAAGGAAAC
722017 ATGTTTGTAAATCAAAGAAAATAA
131 ATGTTTGTAAATCAAAGAAAATAA
722041 CAGAT
1 CAGAT
722046 AAATTTACAC
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 159 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.28
Consensus pattern (154 bp):
CAGATTGGGTTTGAAAAAAATTAAATGTTTCGTGTCAAGCACTGGAGAGATACCGACACAGAATA
TCATTTTGTGATCTTTAAAAATAGTTTTTAAAGCATGAATGCATAAGGTCCCTACGAAAGGAAAC
ATGTTTGTAAATCAAAGAAAATAA
Found at i:722367 original size:51 final size:51
Alignment explanation
Indices: 722288--722388 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
722278 GTACATTTCC
* * * *
722288 CGATGGTGGAAAATCAATGCTTTGGAAATAAAACCAGGGTTAGAGTATCCT
1 CGATGGTGAAAAATCAATGCTTTAGAAATAAAACCAAGGTTAGAGCATCCT
* * * **
722339 CGATTGTGAAAAATCGATGTTTTAGAAATAAAGTCAAGGTTAGAGCATCC
1 CGATGGTGAAAAATCAATGCTTTAGAAATAAAACCAAGGTTAGAGCATCC
722389 CTTTAGAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.27
Consensus pattern (51 bp):
CGATGGTGAAAAATCAATGCTTTAGAAATAAAACCAAGGTTAGAGCATCCT
Found at i:722543 original size:79 final size:79
Alignment explanation
Indices: 722324--722980 Score: 668
Period size: 79 Copynumber: 8.4 Consensus size: 79
722314 AATAAAACCA
* * * * * * * *
722324 GGGTTAGAGTATCCTCGATTGTGAAAAATCGATGTTTTAGAAAT-AAAGTCAAGGTTAGAGCATC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACT-AGGGTTGGAGTATC
* *
722388 CCTTTAGAAATAACG
65 CCCTCAGAAATAACG
* * *
722403 GGGTTAGAGTATCCCC-ATTGTG-AAAATTGGTGTTTT-GAAATAAAAACCAGGGTTGGAGTATC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAAT-AAAACTAGGGTTGGAGTATC
* **
722465 CCCTTAGAAATAATA
65 CCCTCAGAAATAACG
* * *
722480 GGGTTGGAGTATCCCCGATGGTGAAAAATTGATGTTTTGGAAATAAAATTAGGGTTGGAGTATCT
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACTAGGGTTGGAGTATCC
722545 CCTCA-AAGATAACG
66 CCTCAGAA-ATAACG
* * * *
722559 GGTTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTGAAAATAAAACTGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACTAGGGTTGGAGTATCC
*
722623 CCTCAAAAATAACG
66 CCTCAGAAATAACG
* * * * * *
722637 GGGTTGAAGTATCCCCGATTATGGAAAATAGATGTTTTGGAAATAAAA-TCGAGGTTGGAGTATG
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACTAG-GGTTGGAGTATC
*
722701 CCCTCAGAAATAATG
65 CCCTCAGAAATAACG
* *
722716 GGATTGGAGTATCCCCGATTGTGAAAAATTAATG-TTTGGAAATAAAACTAGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACTAGGGTTGGAGTATCC
* *
722780 TCTCAGAAATAACA
66 CCTCAGAAATAACG
* * * * * * * * *
722794 AGGTTGGAGTATCCCCAATTATGAAAAATTGGTGTTCTGAAAATAAAACCAGGATTGCAGTATCC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACTAGGGTTGGAGTATCC
* * * *
722859 TCTCAAAAACAATG
66 CCTCAGAAATAACG
* * * * * ** *
722873 GGGTTGAAGTATTCTCGATGGTGAAAAATCGATGTTTTAAAAATAAAA-TCGAGGTTGGAGTATC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACTAG-GGTTGGAGTATC
722937 CCCTC-GAAAGTAACG
65 CCCTCAGAAA-TAACG
* *
722952 GGGTTGGAGTATCCCCGATGGTAAAAAAT
1 GGGTTGGAGTATCCCCGATTGTGAAAAAT
722981 CAGTATTTTA
Statistics
Matches: 478, Mismatches: 87, Indels: 26
0.81 0.15 0.04
Matches are distributed among these distances:
76 5 0.01
77 50 0.10
78 151 0.32
79 267 0.56
80 5 0.01
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACTAGGGTTGGAGTATCC
CCTCAGAAATAACG
Found at i:722642 original size:157 final size:157
Alignment explanation
Indices: 722322--722980 Score: 695
Period size: 157 Copynumber: 4.2 Consensus size: 157
722312 GAAATAAAAC
* * * * * * * *
722322 CAGGGTTAGAGTATCCTCGATTGTGAAAAATCGATGTTTTAGAAATAAAGTCAAGGTTAGAGCAT
1 CAGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCAGGGTTGGAGTAT
* * *
722387 CCCTTTAGAAATAACGGGGTTAGAGTATCCCC-ATTGTG-AAAATTGGTGTTTTG-AAATAAAAA
66 CCC-TCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAAT-AAAA
* * *
722449 CCAGGGTTGGAGTATCCCCTTAGAAATAA
129 CTAGGGTTGGAGTATCCCCTCAAAAATAA
* * *
722478 TAGGGTTGGAGTATCCCCGATGGTGAAAAATTGATGTTTTGGAAATAAAATTAGGGTTGGAGTAT
1 CAGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCAGGGTTGGAGTAT
* *
722543 CTCCTCA-AAGATAACGGGTTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTGAAAATAAAA
66 C-CCTCAGAA-ATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAA
*
722606 CTGGGGTTGGAGTATCCCCTCAAAAATAA
129 CTAGGGTTGGAGTATCCCCTCAAAAATAA
* * * * *
722635 CGGGGTTGAAGTATCCCCGATTATGGAAAATAGATGTTTTGGAAATAAAATC-GAGGTTGGAGTA
1 CAGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCAG-GGTTGGAGTA
* * * *
722699 TGCCCTCAGAAATAATGGGATTGGAGTATCCCCGATTGTGAAAAATTAATG-TTTGGAAATAAAA
65 T-CCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAA
* *
722763 CTAGGGTTGGAGTATCCTCTCAGAAATAA
129 CTAGGGTTGGAGTATCCCCTCAAAAATAA
* * * * * * * * *
722792 CAAGGTTGGAGTATCCCCAATTATGAAAAATTGGTGTTCTGAAAATAAAACCAGGATTGCAGTAT
1 CAGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCAGGGTTGGAGTAT
* * * * * * * * *
722857 CCTCTCAAAAACAATGGGGTTGAAGTATTCTCGATGGTGAAAAATCGATGTTTTAAAAATAAAA-
66 CC-CTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAAC
* * *
722921 TCGAGGTTGGAGTATCCCCTCGAAAGTAA
130 TAG-GGTTGGAGTATCCCCTCAAAAATAA
* * *
722950 CGGGGTTGGAGTATCCCCGATGGTAAAAAAT
1 CAGGGTTGGAGTATCCCCGATTGTGAAAAAT
722981 CAGTATTTTA
Statistics
Matches: 423, Mismatches: 68, Indels: 22
0.82 0.13 0.04
Matches are distributed among these distances:
155 2 0.00
156 80 0.19
157 266 0.63
158 75 0.18
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (157 bp):
CAGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCAGGGTTGGAGTAT
CCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACT
AGGGTTGGAGTATCCCCTCAAAAATAA
Found at i:722742 original size:236 final size:234
Alignment explanation
Indices: 722395--722980 Score: 756
Period size: 236 Copynumber: 2.5 Consensus size: 234
722385 ATCCCTTTAG
* * * *
722395 AAATAACGGGGTT-AGAGTATCCCC-ATTGT-GAAAATTGGTGTTTTGAAATAAAAACCAGGGTT
1 AAATAACGGGGTTGA-AGTATCCCCGATTGTGGAAAATAGATGTTTTGAAATAAAATCGA-GGTT
* *
722457 GGAGTATCCCCTTAGAAATAATAGGGTTGGAGTATCCCCGATGGTGAAAAATTGATGTTTTGGAA
64 GGAGTATCCCCTCAGAAATAAT-GGGTTGGAGTATCCCCGATGGTGAAAAATTAATG-TTTGGAA
* * * *
722522 ATAAAATTAGGGTTGGAGTAT-CTCCTCA-AAGATAAC-GGGTTTGGAGTATCCCCGATTGTGAA
127 ATAAAACTAGGGTTGGAGTATCCT-CTCAGAA-ATAACAAGG-TTGGAGTATCCCCAATTATGAA
** * *
722584 AAATTGGTGTT-TGAAAATAAAACTGGGGTTGGAGTATCCCCTCAA
189 AAATTGGTGTTCTGAAAATAAAACCAGGATTGCAGTATCCCCTCAA
*
722629 AAATAACGGGGTTGAAGTATCCCCGATTATGGAAAATAGATGTTTTGGAAATAAAATCGAGGTTG
1 AAATAACGGGGTTGAAGTATCCCCGATTGTGGAAAATAGATGTTTT-GAAATAAAATCGAGGTTG
* *
722694 GAGTATGCCCTCAGAAATAATGGGATTGGAGTATCCCCGATTGTGAAAAATTAATGTTTGGAAAT
65 GAGTATCCCCTCAGAAATAATGGG-TTGGAGTATCCCCGATGGTGAAAAATTAATGTTTGGAAAT
722759 AAAACTAGGGTTGGAGTATCCTCTCAGAAATAACAAGGTTGGAGTATCCCCAATTATGAAAAATT
129 AAAACTAGGGTTGGAGTATCCTCTCAGAAATAACAAGGTTGGAGTATCCCCAATTATGAAAAATT
*
722824 GGTGTTCTGAAAATAAAACCAGGATTGCAGTATCCTCTCAA
194 GGTGTTCTGAAAATAAAACCAGGATTGCAGTATCCCCTCAA
* * * * * * * *
722865 AAACAATGGGGTTGAAGTATTCTCGATGGTGAAAAATCGATGTTTTAAAAATAAAATCGAGGTTG
1 AAATAACGGGGTTGAAGTATCCCCGATTGTGGAAAATAGATGTTTT-GAAATAAAATCGAGGTTG
* *
722930 GAGTATCCCCTC-GAAAGTAACGGGGTTGGAGTATCCCCGATGGTAAAAAAT
65 GAGTATCCCCTCAGAAA-TAA-TGGGTTGGAGTATCCCCGATGGTGAAAAAT
722981 CAGTATTTTA
Statistics
Matches: 309, Mismatches: 32, Indels: 20
0.86 0.09 0.06
Matches are distributed among these distances:
234 22 0.07
235 79 0.26
236 194 0.63
237 14 0.05
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (234 bp):
AAATAACGGGGTTGAAGTATCCCCGATTGTGGAAAATAGATGTTTTGAAATAAAATCGAGGTTGG
AGTATCCCCTCAGAAATAATGGGTTGGAGTATCCCCGATGGTGAAAAATTAATGTTTGGAAATAA
AACTAGGGTTGGAGTATCCTCTCAGAAATAACAAGGTTGGAGTATCCCCAATTATGAAAAATTGG
TGTTCTGAAAATAAAACCAGGATTGCAGTATCCCCTCAA
Found at i:724678 original size:55 final size:55
Alignment explanation
Indices: 724594--724704 Score: 177
Period size: 55 Copynumber: 2.0 Consensus size: 55
724584 GCAAGGAACT
724594 TCTAAGATGACATCAATGGCCAAAACAGAAACCAAAAGGATTAAGGCAGAGAGGA
1 TCTAAGATGACATCAATGGCCAAAACAGAAACCAAAAGGATTAAGGCAGAGAGGA
* * * * *
724649 TCTAAGATGATATCAATGGCGAAAACAGAATCTAAAAGGATTAAGGTAGAGAGGA
1 TCTAAGATGACATCAATGGCCAAAACAGAAACCAAAAGGATTAAGGCAGAGAGGA
724704 T
1 T
724705 ATACCAAAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.46, C:0.13, G:0.24, T:0.17
Consensus pattern (55 bp):
TCTAAGATGACATCAATGGCCAAAACAGAAACCAAAAGGATTAAGGCAGAGAGGA
Found at i:729486 original size:41 final size:41
Alignment explanation
Indices: 729436--729600 Score: 115
Period size: 41 Copynumber: 4.1 Consensus size: 41
729426 CAACAATTAA
* * *
729436 GAATAGTTGAAT-GGGATAAAACTGGCATGCCAACTAAGAGT
1 GAATAGTTG-ATCGGGACAAAACTGACAAGCCAACTAAGAGT
* *
729477 GAATGGTTGATCGGGACAAAACTGACAAGTCAACTAAGAGT
1 GAATAGTTGATCGGGACAAAACTGACAAGCCAACTAAGAGT
* * * * * * *
729518 -AA-AGGCTGATCGAGATAAAACTGACTAGTCAACAAAGAAT
1 GAATA-GTTGATCGGGACAAAACTGACAAGCCAACTAAGAGT
* * * * *
729558 AAAGT-GTTGATTGGGACGAAACTAACAAGTCAACTAAG-GT
1 GAA-TAGTTGATCGGGACAAAACTGACAAGCCAACTAAGAGT
729598 GAA
1 GAA
729601 GGTTGACCAA
Statistics
Matches: 97, Mismatches: 22, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
40 37 0.38
41 60 0.62
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20
Consensus pattern (41 bp):
GAATAGTTGATCGGGACAAAACTGACAAGCCAACTAAGAGT
Found at i:729539 original size:40 final size:40
Alignment explanation
Indices: 729466--729630 Score: 161
Period size: 40 Copynumber: 4.1 Consensus size: 40
729456 ACTGGCATGC
* *
729466 CAACTAAGAGTGAATGGTTGATCGGGACAAAACTGACAAGT
1 CAACTAAGAGT-AAAGGTTGATCGAGACAAAACTGACAAGT
* * *
729507 CAACTAAGAGTAAAGGCTGATCGAGATAAAACTGACTAGT
1 CAACTAAGAGTAAAGGTTGATCGAGACAAAACTGACAAGT
* * * * * *
729547 CAACAAAGAATAAAGTGTTGATTGGGACGAAACTAACAAGT
1 CAACTAAGAGTAAAG-GTTGATCGAGACAAAACTGACAAGT
* * * **
729588 CAACTAAG-GTGAAGGTTGACCAAGACAAAGTTGACAAGT
1 CAACTAAGAGTAAAGGTTGATCGAGACAAAACTGACAAGT
729627 CAAC
1 CAAC
729631 AATGAGAGGT
Statistics
Matches: 98, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
39 21 0.21
40 41 0.42
41 36 0.37
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.19
Consensus pattern (40 bp):
CAACTAAGAGTAAAGGTTGATCGAGACAAAACTGACAAGT
Found at i:730334 original size:66 final size:67
Alignment explanation
Indices: 730211--730607 Score: 412
Period size: 67 Copynumber: 6.0 Consensus size: 67
730201 AATAAGCCAA
* * *
730211 AGTAGAAGATCATGATAGGGAATATGTGATTCCCATCAATA-TTCGAAACAAATTGATAAC-AGA
1 AGTAGAAGATCATGATAGGGAATATGTGGTTCCCATCAATAGCT-GAAACAAACTGATAACAAG-
*
730274 CTAG
64 CTGG
* * *
730278 AGTAGAAGATCATGATAGGG-ATATGTGATTCCCATCAACAGCTGAAACAAACTGATAACAAACT
1 AGTAGAAGATCATGATAGGGAATATGTGGTTCCCATCAATAGCTGAAACAAACTGATAACAAGCT
730342 GG
66 GG
* * * * * * * *
730344 AATAGAAAATCATGATAGGG-ATATGTGGTTCTCATCAACAGTTGAAATAAA-TTACTAACAAGT
1 AGTAGAAGATCATGATAGGGAATATGTGGTTCCCATCAATAGCTGAAACAAACTGA-TAACAAGC
*
730407 TAG
65 TGG
** *
730410 AGTAGAAGATCATGATAGGGAATATGTGGTTCCCATCAATAG-TGGAAACAAACTGATAATGAGT
1 AGTAGAAGATCATGATAGGGAATATGTGGTTCCCATCAATAGCT-GAAACAAACTGATAACAAGC
730474 TGG
65 TGG
* * * * * * *
730477 AGTAGAAGATCATGATGGGGAATAAGTGTTTCCTATCAATAGCTAAAACAAATTGATAATAAGCT
1 AGTAGAAGATCATGATAGGGAATATGTGGTTCCCATCAATAGCTGAAACAAACTGATAACAAGCT
730542 GG
66 GG
* * * * * *
730544 AATAGAAGATCAAGATGGGGAATATGTGGTTCCTATCAATAGAC-GAAACAAACTAACAACAAGC
1 AGTAGAAGATCATGATAGGGAATATGTGGTTCCCATCAATAG-CTGAAACAAACTGATAACAAGC
730608 CAAGGAAAAT
Statistics
Matches: 281, Mismatches: 41, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
65 2 0.01
66 109 0.39
67 166 0.59
68 4 0.01
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.24
Consensus pattern (67 bp):
AGTAGAAGATCATGATAGGGAATATGTGGTTCCCATCAATAGCTGAAACAAACTGATAACAAGCT
GG
Found at i:733015 original size:13 final size:14
Alignment explanation
Indices: 732999--733031 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
732989 GATTATACCA
732999 AAAAATT-AATTAG
1 AAAAATTAAATTAG
*
733012 AAAAATTAAATTAT
1 AAAAATTAAATTAG
733026 AAAAAT
1 AAAAAT
733032 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
AAAAATTAAATTAG
Found at i:734700 original size:81 final size:81
Alignment explanation
Indices: 734547--734716 Score: 180
Period size: 81 Copynumber: 2.1 Consensus size: 81
734537 ACTAAGGGTA
* * *
734547 AAGGTTGATCAAGAAAAAATTGACAAGTCAATAAAGAATGAAGTAATAACAAGGACAAAATCTAT
1 AAGGTTGATCAAGAAAAAATTGACAAGTCAACAAAGAATGAAGTAATAACAAGGACAAAACCAAT
* * *
734612 AAGTCAACTGAGAGAG
66 AAATCAACTAAAAGAG
* * * * ** * **
734628 AAGGTTGATTAGGATAAAATTGACAAGTCAGCAAAGAATGAAGTGTTGACTAA-GATGAAACCAA
1 AAGGTTGATCAAGAAAAAATTGACAAGTCAACAAAGAATGAAGTAATAAC-AAGGACAAAACCAA
*
734692 TAAATCAACTAAAAGTG
65 TAAATCAACTAAAAGAG
734709 AAGGTTGA
1 AAGGTTGA
734717 CCACGACAAA
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
81 70 0.97
82 2 0.03
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (81 bp):
AAGGTTGATCAAGAAAAAATTGACAAGTCAACAAAGAATGAAGTAATAACAAGGACAAAACCAAT
AAATCAACTAAAAGAG
Found at i:740155 original size:32 final size:32
Alignment explanation
Indices: 740112--740227 Score: 99
Period size: 32 Copynumber: 3.4 Consensus size: 32
740102 AAAATTCATC
*
740112 ATGTATTGATACAATGTATCGATATAATATGA
1 ATGTATCGATACAATGTATCGATATAATATGA
*** * *
740144 ATGTATCGATACAAACAAT-GGTAGGGTAGCTACTGA
1 ATGTATCGATACAATGTATCGATA---TA-ATA-TGA
*
740180 TCATGTATTGATACAATGTATCGATATAATATGA
1 --ATGTATCGATACAATGTATCGATATAATATGA
740214 ATGTATCGATACAA
1 ATGTATCGATACAA
740228 ACAATGGTAG
Statistics
Matches: 63, Mismatches: 13, Indels: 16
0.68 0.14 0.17
Matches are distributed among these distances:
31 3 0.05
32 28 0.44
34 5 0.08
35 4 0.06
36 5 0.08
38 15 0.24
39 3 0.05
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (32 bp):
ATGTATCGATACAATGTATCGATATAATATGA
Found at i:740191 original size:70 final size:70
Alignment explanation
Indices: 740109--740248 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
740099 GATAAAATTC
740109 ATCATGTATTGATACAATGTATCGATATAATATGAATGTATCGATACAAACAATGGTAGGGTAGC
1 ATCATGTATTGATACAATGTATCGATATAATATGAATGTATCGATACAAACAATGGTAGGGTAGC
740174 TACTG
66 TACTG
740179 ATCATGTATTGATACAATGTATCGATATAATATGAATGTATCGATACAAACAATGGTAGGGTAGC
1 ATCATGTATTGATACAATGTATCGATATAATATGAATGTATCGATACAAACAATGGTAGGGTAGC
740244 TACTG
66 TACTG
740249 CCAGTTTCAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (70 bp):
ATCATGTATTGATACAATGTATCGATATAATATGAATGTATCGATACAAACAATGGTAGGGTAGC
TACTG
Found at i:740343 original size:28 final size:28
Alignment explanation
Indices: 740303--740744 Score: 663
Period size: 28 Copynumber: 15.7 Consensus size: 28
740293 CATAATGGAT
740303 CTGACTTGTGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
* *
740331 CTGACTTGTGGGCTTTGAAGGGATACCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
*
740359 CTGAGTTGTGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
* * *
740387 CTAACTTGTGGGCTTTGAAAAGGGTGTCA
1 CTGACTTGTGGGCTTTG-AAAGGATGCCA
740416 CTGACTTGTGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
* *
740444 CTAACTTATGGGCTTTGAAAATGG-TGCCA
1 CTGACTTGTGGGCTTTG-AAA-GGATGCCA
740473 CTGACTTGTGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
* *
740501 CTAACTTGTGGGCTTTGAAAAGGGTGCCA
1 CTGACTTGTGGGCTTTG-AAAGGATGCCA
740530 CTGACTTGTGGGCTTTGAAA-GATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
* *
740557 CTGACTTGTGGACTTTGAAAAGGGTGCCA
1 CTGACTTGTGGGCTTTG-AAAGGATGCCA
*
740586 CTGACTTATGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
* *
740614 CTAACTTTTGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
* *
740642 CTAACTTATGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
740670 CTGACTTGTGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
740698 CTGACTTGTGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
*
740726 CTGACTTATGGGCTTTGAA
1 CTGACTTGTGGGCTTTGAA
740745 GAAATGAACG
Statistics
Matches: 376, Mismatches: 31, Indels: 14
0.89 0.07 0.03
Matches are distributed among these distances:
27 24 0.06
28 255 0.68
29 95 0.25
30 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
CTGACTTGTGGGCTTTGAAAGGATGCCA
Found at i:762205 original size:79 final size:78
Alignment explanation
Indices: 761982--762312 Score: 351
Period size: 79 Copynumber: 4.2 Consensus size: 78
761972 GATAATAGCG
* * ** *
761982 GGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATCAATGATT
1 GGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTT
*
762047 TAGAAATAAAATC
66 TAGAAATAAAACC
* ** * * *
762060 GGGATTGGAGTATCCCTTCGGAAA-AAGGGGGTTGGAGTATCCCCGACTATGAAAAATTGATATT
1 GGG-TTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTT
762124 TTAGAAATAAAACC
65 TTAGAAATAAAACC
** * *
762138 AGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTAGAGTATCCCCGATTATGAGAAATTGATGTT
1 -GGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTT
762203 TTAGAAATAAAACC
65 TTAGAAATAAAACC
* * * * ** * * *
762217 GAGGTTGGGGTATCCCTTCAAAAATATCGAGGTTGGAGTATCCTTGATTGTG-AAAAGTCAGTGT
1 G-GGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGA-TGT
*
762281 TTTAGAAATAAAATC
64 TTTAGAAATAAAACC
* *
762296 GGACTTGAAGTATCCCC
1 GG-GTTGGAGTATCCCC
762313 GATTATGGAA
Statistics
Matches: 211, Mismatches: 36, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
78 74 0.35
79 137 0.65
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (78 bp):
GGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTT
TAGAAATAAAACC
Found at i:762391 original size:51 final size:50
Alignment explanation
Indices: 762278--762414 Score: 141
Period size: 51 Copynumber: 2.7 Consensus size: 50
762268 GAAAAGTCAG
* * * * *
762278 TGTTTTAGAAATAAAATCGGACTTGAAGTATCCCCGATTATGGAAAATGGG
1 TGTTTTAGAAATAAAATCGGA-TTGGAGTATCCCCAATTAAGAAAAATGGA
* *
762329 TGCTTTAGAAATAAAATCGGAGTTGGAGTA-CCCCTAATTAAGAAAAATTGA
1 TGTTTTAGAAATAAAATCGGA-TTGGAGTATCCCC-AATTAAGAAAAATGGA
* * *
762380 TGTTTTGGAAATGAAACCAGGATTGGAGTATCCCC
1 TGTTTTAGAAATAAAATC-GGATTGGAGTATCCCC
762415 GAGATGAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
50 4 0.06
51 60 0.85
52 7 0.10
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (50 bp):
TGTTTTAGAAATAAAATCGGATTGGAGTATCCCCAATTAAGAAAAATGGA
Found at i:764736 original size:20 final size:19
Alignment explanation
Indices: 764711--764866 Score: 113
Period size: 20 Copynumber: 7.8 Consensus size: 19
764701 AAAATGCCTG
*
764711 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
764731 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
764751 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
*
764771 AATGTATCGATACATCTGGTAA
1 AATGTATCGATACA-AT-G-AA
* * *
764793 ACCCA-GAAT-G-TATCGAT-AC
1 A---ATGTATCGATA-CAATGAA
*
764812 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
764832 AATGTATCGATACAATGAA
1 AATGTATCGATACAATGAA
764851 CAATGTATCGATACAA
1 -AATGTATCGATACAA
764867 ATTGTGAAAA
Statistics
Matches: 110, Mismatches: 12, Indels: 28
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.01
17 3 0.03
18 4 0.04
19 6 0.05
20 81 0.74
21 2 0.02
22 7 0.06
23 2 0.02
24 3 0.03
25 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:764847 original size:13 final size:13
Alignment explanation
Indices: 764799--764828 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
764789 GTAAACCCAG
764799 AATGTATCGATAC
1 AATGTATCGATAC
764812 AATGTATCGATAC
1 AATGTATCGATAC
764825 AATG
1 AATG
764829 AGCAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:774766 original size:24 final size:23
Alignment explanation
Indices: 774725--774800 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 23
774715 TGAAAAAGTC
*
774725 AAAAGCAAAAGCATAAAAAAACAA
1 AAAAGCAAAA-AATAAAAAAACAA
774749 AAAAGCAAAAAATGAAAAAAA-AA
1 AAAAGCAAAAAAT-AAAAAAACAA
* *
774772 CAAATAACAAAAAAT-AAAAGACAA
1 -AAA-AGCAAAAAATAAAAAAACAA
774796 AAAAG
1 AAAAG
774801 TGCAAAAGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
22 1 0.02
23 12 0.27
24 22 0.50
25 9 0.20
ACGTcount: A:0.78, C:0.09, G:0.08, T:0.05
Consensus pattern (23 bp):
AAAAGCAAAAAATAAAAAAACAA
Found at i:776173 original size:30 final size:30
Alignment explanation
Indices: 776119--776181 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
776109 GTAATGTAAC
*
776119 CTTCTCAAATTCCACGACTCAGTGGCATCT
1 CTTCTCAAAGTCCACGACTCAGTGGCATCT
* * *
776149 CTTCTCCAAGTCCATGACTTAGTGGCATCT
1 CTTCTCAAAGTCCACGACTCAGTGGCATCT
776179 CTT
1 CTT
776182 TTCTTTTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.21, C:0.32, G:0.14, T:0.33
Consensus pattern (30 bp):
CTTCTCAAAGTCCACGACTCAGTGGCATCT
Found at i:776491 original size:160 final size:155
Alignment explanation
Indices: 776267--776631 Score: 516
Period size: 160 Copynumber: 2.3 Consensus size: 155
776257 ATACAAGTCA
* * *
776267 GTGGCAACCCTTATAAAGCCCACACAAGTCGATGGCAACCCCTTCTCAAAGCCCACATAAGTCGG
1 GTGGCAACCCTTCTAAAGCCCACACAAGTCG-TGGCAA-CCCTTCTCAAAGACCACACAAGTCGG
776332 TAGCAACCCTTCTAAAGCACACATAAGTCAGTGGCAACCCTTTTTTAAAGCCCAAACAAATTAGT
64 TAGCAACCCTTCTAAAGCACACATAAGTCAGTGGCAACCCTTTTTTAAAGCCCAAACAAATTAGT
776397 GGCAACCCTTCTCT-AAGCCCACACAAGTTG
129 GGC-A--CTT-TCTAAAGCCCACACAAGTTG
*
776427 GTGGCAACTCCTTCTAAAGCCCATACAAGTCAGTGGCAACCCTTCTCAAAGACCACACAAGTCGG
1 GTGGCAAC-CCTTCTAAAGCCCACACAAGTC-GTGGCAACCCTTCTCAAAGACCACACAAGTCGG
* * * **
776492 TGGTAACCCTTCTAAAGCACACATAAGTCGGTGGCAACCCTTTTTTAAAGCCCACGCAAATTAGT
64 TAGCAACCCTTCTAAAGCACACATAAGTCAGTGGCAACCCTTTTTTAAAGCCCAAACAAATTAGT
776557 GGCACTTTCTAAAGCCCACACAAGTTG
129 GGCACTTTCTAAAGCCCACACAAGTTG
* *
776584 GTGGCAAAACCTTCTCTAAAGCCCACACAAGTCGGTGGTAACCCTTCT
1 GTGGC--AACCCT-TCTAAAGCCCACACAAGTC-GTGGCAACCCTTCT
776632 AAGCCCAATG
Statistics
Matches: 186, Mismatches: 13, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
156 3 0.02
157 24 0.13
158 2 0.01
159 35 0.19
160 95 0.51
161 26 0.14
162 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (155 bp):
GTGGCAACCCTTCTAAAGCCCACACAAGTCGTGGCAACCCTTCTCAAAGACCACACAAGTCGGTA
GCAACCCTTCTAAAGCACACATAAGTCAGTGGCAACCCTTTTTTAAAGCCCAAACAAATTAGTGG
CACTTTCTAAAGCCCACACAAGTTG
Found at i:776502 original size:96 final size:94
Alignment explanation
Indices: 776245--776638 Score: 418
Period size: 96 Copynumber: 4.1 Consensus size: 94
776235 CATCCTTTTT
* * * * *
776245 CTTCTAAAACCTATACAAGTCAGTGGCAACCCTTATAAAGCCCACACAAGTCGATGGCAACCCCT
1 CTTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGGCAA-CCCT
* *
776310 TCTCAAAGCCCACATAAGTCGGTAGCAACC
65 TCTCAAAGCCCACACAAGTCGGTGGCAACC
* * * * * **
776340 CTTCTAAAGCACACATAAGTCAGTGGCAACCCTTTTTTAAAGCCCAAACAAATTAGTGGCAACCC
1 CTTCTAAAGCCCACACAAGTCAGTGGCAACCC--TTCTAAAGCCCACACAAGTCGGTGGCAACCC
* *
776405 TTCTCTAAGCCCACACAAGTTGGTGGCAACTC
64 TTCTCAAAGCCCACACAAGTCGGTGGCAAC-C
* * *
776437 CTTCTAAAGCCCATACAAGTCAGTGGCAACCCTTCTCAAAGACCACACAAGTCGGTGGTAACCCT
1 CTTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCT-AAAGCCCACACAAGTCGGTGGCAACCCT
* *
776502 TCT-AAAGCACACATAAGTCGGTGGCAACC
65 TCTCAAAGCCCACACAAGTCGGTGGCAACC
* * * * * * *
776531 CTTTTTTAAAGCCCACGCAAATTAGTGGC-A-CTTTCTAAAGCCCACACAAGTTGGTGGCAAAAC
1 C--TTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGGC-AACC
*
776594 CTTCTCTAAAGCCCACACAAGTCGGTGGTAACC
63 CTTCTC-AAAGCCCACACAAGTCGGTGGCAACC
776627 CTTCT-AAGCCCA
1 CTTCTAAAGCCCA
776639 ATGTCGTTGG
Statistics
Matches: 247, Mismatches: 43, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
93 26 0.11
94 18 0.07
95 52 0.21
96 99 0.40
97 52 0.21
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (94 bp):
CTTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
CTCAAAGCCCACACAAGTCGGTGGCAACC
Found at i:776648 original size:64 final size:64
Alignment explanation
Indices: 776261--776638 Score: 342
Period size: 64 Copynumber: 6.0 Consensus size: 64
776251 AAACCTATAC
* * * *
776261 AAGTCAGTGGCAACCC-T-TATAAAGCCCACACAAGTCGATGGCAACCCCTTCTCAAAGCCCACA
1 AAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGTAA-CCCTTCT-AAAGCCCACA
776324 T
64 T
* * * * * * *
776325 AAGTCGGTAGCAACCC-T-TCTAAAGCACACATAAGTCAGTGGCAACCCTTTTTTAAAGCCCAAA
1 AAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGTAACCC--TTCTAAAGCCCACA
*
776388 C
64 T
* ** * * * *
776389 AAATTAGTGGCAACCCTTCTCT-AAGCCCACACAAGTTGGTGGCAACTCCTTCTAAAGCCCATAC
1 AAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGTAAC-CCTTCTAAAGCCCACAT
* * *
776453 AAGTCAGTGGCAACCCTTCTC-AAAGACCACACAAGTCGGTGGTAACCCTTCTAAAGCACACAT
1 AAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGTAACCCTTCTAAAGCCCACAT
* * * * ** * * *
776516 AAGTCGGTGGCAACCCTTTTTTAAAGCCCACGCAAATTAGTGG-CA-CTTTCTAAAGCCCACAC
1 AAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGTAACCCTTCTAAAGCCCACAT
* *
776578 AAGTTGGTGGCAAAACCTTCTCTAAAGCCCACACAAGTCGGTGGTAACCCTTCT-AAGCCCA
1 AAGTCGGTGGC-AACCCTTCTCTAAAGCCCACACAAGTCGGTGGTAACCCTTCTAAAGCCCA
776639 ATGTCGTTGG
Statistics
Matches: 254, Mismatches: 50, Indels: 20
0.78 0.15 0.06
Matches are distributed among these distances:
62 24 0.09
63 61 0.24
64 135 0.53
65 29 0.11
66 5 0.02
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.21
Consensus pattern (64 bp):
AAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGTAACCCTTCTAAAGCCCACAT
Found at i:776864 original size:52 final size:52
Alignment explanation
Indices: 776793--776917 Score: 162
Period size: 52 Copynumber: 2.4 Consensus size: 52
776783 TTTCCTATCC
* *
776793 TTATCATCTTTAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCACCT
1 TTATCATATTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
* * * * * *
776845 TT-TTATTTCTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCT
1 TTATCATAT-TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
776897 TTATCATATTTAAGTCCAATG
1 TTATCATATTTAAGTCCAATG
776918 GTATTGAATC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
51 4 0.07
52 53 0.87
53 4 0.07
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (52 bp):
TTATCATATTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
Found at i:777124 original size:113 final size:107
Alignment explanation
Indices: 776854--777114 Score: 292
Period size: 113 Copynumber: 2.4 Consensus size: 107
776844 TTTTTATTTC
* * * * * * *
776854 TTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTATCATATTTAAGTCCAATGG
1 TTAAGTCAAATGTCGTTGACCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGTCAAATGC
* *
776919 TATTGAATCAGAATATCGACACCTTTATCATTTTTCTCATCT
66 TATTGAATCAGAATATCGACACCTTTATCATTCTTCACATCT
* *** * *
776961 TCT-AGTCTAATGTTACTAACCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCTAATA
1 T-TAAGTCAAATGTCGTTGACCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGTC-AA-A
*
777025 TCGCTAGCCTTGAATCAGCATATCGACA-CTTCTATCATTCTTCACATCT
63 T-GCTA---TTGAATCAGAATATCGACACCTT-TATCATTCTTCACATCT
777074 TTAAGTCAAATGTCGTTGACCTTGAATCAGCATATTGGCAC
1 TTAAGTCAAATGTCGTTGACCTTGAATCAGCATATTGGCAC
777115 TGTTTTCATC
Statistics
Matches: 125, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
107 47 0.38
108 2 0.02
109 2 0.02
110 3 0.02
112 4 0.03
113 67 0.54
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (107 bp):
TTAAGTCAAATGTCGTTGACCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGTCAAATGC
TATTGAATCAGAATATCGACACCTTTATCATTCTTCACATCT
Found at i:777134 original size:61 final size:62
Alignment explanation
Indices: 777007--777141 Score: 154
Period size: 61 Copynumber: 2.2 Consensus size: 62
776997 GGCACCTTTG
*
777007 TCATCTTTAAGTCTAATATCGCTAGCCTTGAATCAGCATATCGACACTTCTATCATTCTTCA
1 TCATCTTTAAGTCAAATATCGCTAGCCTTGAATCAGCATATCGACACTTCTATCATTCTTCA
* * * * *
777069 -CATCTTTAAGTCAAATGTCG-TTGACCTTGAATCAGCATATTGGCACTGT-TTTCA-TCATT-A
1 TCATCTTTAAGTCAAATATCGCTAG-CCTTGAATCAGCATATCGACACT-TCTATCATTC-TTCA
777129 TCATCTTTAAGTC
1 TCATCTTTAAGTC
777142 TAGTATTGTA
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
60 5 0.08
61 57 0.90
62 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.39
Consensus pattern (62 bp):
TCATCTTTAAGTCAAATATCGCTAGCCTTGAATCAGCATATCGACACTTCTATCATTCTTCA
Found at i:777920 original size:13 final size:13
Alignment explanation
Indices: 777902--777926 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
777892 TATCACTATT
777902 TGTATCGATACAA
1 TGTATCGATACAA
777915 TGTATCGATACA
1 TGTATCGATACA
777927 TGAAGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:778732 original size:21 final size:22
Alignment explanation
Indices: 778708--778762 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
778698 TTCTATGATT
*
778708 TGTATCGATACAATTAATG-AA
1 TGTATCGATACAATGAATGAAA
* **
778729 TGTATCAATAC-ATGCTTGAAA
1 TGTATCGATACAATGAATGAAA
778750 TGTATCGATACAA
1 TGTATCGATACAA
778763 AACCACCCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.15
21 22 0.81
22 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (22 bp):
TGTATCGATACAATGAATGAAA
Found at i:778819 original size:20 final size:20
Alignment explanation
Indices: 778783--778821 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
778773 CATACTACCA
**
778783 AGTAAATGTATTGATACATC
1 AGTAAATGTATCAATACATC
778803 AGTAAATGTATCAATACAT
1 AGTAAATGTATCAATACAT
778822 ACTTACAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (20 bp):
AGTAAATGTATCAATACATC
Found at i:798051 original size:11 final size:11
Alignment explanation
Indices: 798037--798066 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
798027 CCTGTTACAA
798037 GCTTGTTTGGT
1 GCTTGTTTGGT
798048 GCTTGTTTGGT
1 GCTTGTTTGGT
798059 GCTTGTTT
1 GCTTGTTT
798067 TCATGCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.10, G:0.33, T:0.57
Consensus pattern (11 bp):
GCTTGTTTGGT
Found at i:798286 original size:22 final size:22
Alignment explanation
Indices: 798261--798404 Score: 139
Period size: 22 Copynumber: 7.0 Consensus size: 22
798251 CAAAGAAATA
*
798261 ATGTATCGATACATCACTATTC
1 ATGTATCGATACATCACTGTTC
798283 ATGTATCGATACATCACTGTTC
1 ATGTATCGATACATCACTGTTC
* * * *
798305 AT-CA-CTATTCATCATTGTTC
1 ATGTATCGATACATCACTGTTC
798325 ATGTATCGATACATCACTGTTC
1 ATGTATCGATACATCACTGTTC
* * *
798347 AT-CA-CTATTCATCA-----C
1 ATGTATCGATACATCACTGTTC
798362 -TGT-TCGATACATCACTGTTC
1 ATGTATCGATACATCACTGTTC
798382 ATGTATCGATACATCACTGTTC
1 ATGTATCGATACATCACTGTTC
798404 A
1 A
798405 CACTATTTAA
Statistics
Matches: 96, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
14 1 0.01
15 9 0.09
20 24 0.25
21 6 0.06
22 56 0.58
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (22 bp):
ATGTATCGATACATCACTGTTC
Found at i:798309 original size:10 final size:10
Alignment explanation
Indices: 798294--798366 Score: 67
Period size: 10 Copynumber: 7.1 Consensus size: 10
798284 TGTATCGATA
798294 CATCACTGTT
1 CATCACTGTT
*
798304 CATCACTATT
1 CATCACTGTT
*
798314 CATCATTGTT
1 CATCACTGTT
* *
798324 CATGTA-TCGATA
1 CAT-CACT-G-TT
798336 CATCACTGTT
1 CATCACTGTT
*
798346 CATCACTATT
1 CATCACTGTT
798356 CATCACTGTT
1 CATCACTGTT
798366 C
1 C
798367 GATACATCAC
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
10 41 0.82
11 4 0.08
12 5 0.10
ACGTcount: A:0.25, C:0.27, G:0.08, T:0.40
Consensus pattern (10 bp):
CATCACTGTT
Found at i:798323 original size:20 final size:20
Alignment explanation
Indices: 798294--798366 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
798284 TGTATCGATA
798294 CATCACTGTTCATCACTATT
1 CATCACTGTTCATCACTATT
* * * *
798314 CATCATTGTTCATGTATCGATA
1 CATCACTGTTCAT-CA-CTATT
798336 CATCACTGTTCATCACTATT
1 CATCACTGTTCATCACTATT
798356 CATCACTGTTC
1 CATCACTGTTC
798367 GATACATCAC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 26 0.60
21 2 0.05
22 15 0.35
ACGTcount: A:0.25, C:0.27, G:0.08, T:0.40
Consensus pattern (20 bp):
CATCACTGTTCATCACTATT
Done.