Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold329
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: 4121247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 5938 characters in sequence are not A, C, G, or T
File 9 of 25
Found at i:1319742 original size:19 final size:19
Alignment explanation
Indices: 1319718--1319785 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1319708 AATTCAACGA
1319718 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1319737 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1319752 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1319769 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1319786 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1319756 original size:32 final size:32
Alignment explanation
Indices: 1319720--1319782 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1319710 TTCAACGATT
*
1319720 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1319752 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1319783 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1319757 original size:13 final size:13
Alignment explanation
Indices: 1319739--1319763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1319729 ACATAAGTTT
1319739 TGTATCGATACAA
1 TGTATCGATACAA
1319752 TGTATCGATACA
1 TGTATCGATACA
1319764 TAAGTATTGT
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:1319843 original size:13 final size:13
Alignment explanation
Indices: 1319825--1319850 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1319815 CATTTTTCTG
1319825 TGTATCGATACAT
1 TGTATCGATACAT
1319838 TGTATCGATACAT
1 TGTATCGATACAT
1319851 GGATCTTTGT
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:1319847 original size:33 final size:33
Alignment explanation
Indices: 1319805--1319871 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1319795 GCCAAGGAAA
***
1319805 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1319838 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1319871 T
1 T
1319872 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1322432 original size:51 final size:51
Alignment explanation
Indices: 1322371--1322541 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
1322361 TTATTTCTGA
* * *
1322371 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
1322422 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
1322475 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
1322527 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1322542 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:1322560 original size:28 final size:28
Alignment explanation
Indices: 1322524--1322605 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
1322514 ATTTTTCACA
* *
1322524 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTCC
*
1322552 ATCGGGGATACTCCAACCCCGTTACTTCC
1 ATCGGGGATACTCCAACCTCGTTA-TTCC
* * *
1322581 A-AGGGAACACTCCAACCTCGTTATT
1 ATCGGGGATACTCCAACCTCGTTATT
1322606 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
27 2 0.04
28 40 0.87
29 4 0.09
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTCC
Found at i:1335030 original size:23 final size:23
Alignment explanation
Indices: 1335000--1335052 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1334990 CCTTCTCTTC
* *
1335000 AAAAAAAAAAAAGAGCAAAAAAA
1 AAAAAAAAAAAAAAACAAAAAAA
*
1335023 AAAAAAAAAAAAAAACAAAACAA
1 AAAAAAAAAAAAAAACAAAAAAA
*
1335046 AGAAAAA
1 AAAAAAA
1335053 GAGAGAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAAAAAACAAAAAAA
Found at i:1335067 original size:1 final size:1
Alignment explanation
Indices: 1335000--1335052 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
1334990 CCTTCTCTTC
* ** * * *
1335000 AAAAAAAAAAAAGAGCAAAAAAAAAAAAAAAAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1335053 GAGAGAAAAG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:1336117 original size:55 final size:55
Alignment explanation
Indices: 1336031--1336830 Score: 1123
Period size: 55 Copynumber: 14.3 Consensus size: 55
1336021 TTCCGCCTTT
*
1336031 CAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC
1336086 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1336141 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1336196 CAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC
1336251 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* *
1336306 CAGTCCTCAACGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-
1 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
* **
1336361 CAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTC
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* **
1336416 CAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATCCTC
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1336471 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* *
1336526 CAGTCCTCAAAGAGTAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTT-
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA--TTTTC
* * * *
1336582 --GTCCCCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1 CAGTCCTCAAAGAGCAGGACACCTT-T-C----AAAGCCCACACAAGTTGGTGGCATTTTC
1336641 CAGTCCTCAAAGAGCAGGACGCCTTCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGA------CACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* *
1336702 CAGTCCTCCAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-
1 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
* * ** * *
1336757 CAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACGTGTTTGTGGCATTTTT
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* * *
1336812 TACTCCTCAATGAGCAGGA
1 CAGTCCTCAAAGAGCAGGA
1336831 TACACTTTAT
Statistics
Matches: 679, Mismatches: 38, Indels: 56
0.88 0.05 0.07
Matches are distributed among these distances:
54 32 0.05
55 538 0.79
56 13 0.02
57 4 0.01
58 2 0.00
60 23 0.03
61 60 0.09
65 1 0.00
66 1 0.00
67 5 0.01
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (55 bp):
CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
Found at i:1336384 original size:26 final size:26
Alignment explanation
Indices: 1336354--1336443 Score: 65
Period size: 26 Copynumber: 3.3 Consensus size: 26
1336344 AAGTTGGTGG
*
1336354 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
1336380 CACCTCTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
* *
1336409 CACCTTCCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
1336435 CACCTTTCA
1 CACCTTTCA
1336444 AAGCCCACAC
Statistics
Matches: 45, Mismatches: 14, Indels: 10
0.65 0.20 0.14
Matches are distributed among these distances:
25 3 0.07
26 18 0.40
27 6 0.13
28 6 0.13
29 9 0.20
30 3 0.07
ACGTcount: A:0.29, C:0.36, G:0.18, T:0.18
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:1337637 original size:41 final size:40
Alignment explanation
Indices: 1337576--1337657 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 40
1337566 AAAAAAAAAA
* * *
1337576 ATTCCAAATGTATTGATACATTTGTA-GAATGTATCGATAC
1 ATTCCAAATGTATCGATACA-TTCTACAAATGTATCGATAC
1337616 ATTCACAAATGTATCGATACATTCTACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATACATTCTACAAATGTATCGATAC
1337657 A
1 A
1337658 GGGTCCCAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 8 0.22
41 29 0.78
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (40 bp):
ATTCCAAATGTATCGATACATTCTACAAATGTATCGATAC
Found at i:1337646 original size:21 final size:21
Alignment explanation
Indices: 1337580--1337657 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
1337570 AAAAAAATTC
* *
1337580 CAAATGTATTGATACATTTGTA
1 CAAATGTATCGATACA-TTCTA
*
1337602 -GAATGTATCGATACATTC-A
1 CAAATGTATCGATACATTCTA
1337621 CAAATGTATCGATACATTCTA
1 CAAATGTATCGATACATTCTA
1337642 CAAATGTATCGATACA
1 CAAATGTATCGATACA
1337658 GGGTCCCAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
19 1 0.02
20 19 0.38
21 30 0.60
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTCTA
Found at i:1337717 original size:19 final size:19
Alignment explanation
Indices: 1337693--1337760 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1337683 AATTCAACGA
1337693 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1337712 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1337727 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1337744 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1337761 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1337731 original size:32 final size:32
Alignment explanation
Indices: 1337695--1337757 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1337685 TTCAACGATT
*
1337695 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1337727 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1337758 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1337732 original size:13 final size:13
Alignment explanation
Indices: 1337714--1337738 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1337704 ACATAAGTTT
1337714 TGTATCGATACAA
1 TGTATCGATACAA
1337727 TGTATCGATACA
1 TGTATCGATACA
1337739 TAAGTATTGT
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:1337818 original size:13 final size:13
Alignment explanation
Indices: 1337800--1337825 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1337790 CATTTTTCTG
1337800 TGTATCGATACAT
1 TGTATCGATACAT
1337813 TGTATCGATACAT
1 TGTATCGATACAT
1337826 GGATCTTTGT
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:1337822 original size:33 final size:33
Alignment explanation
Indices: 1337780--1337846 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1337770 GCCAAGGAAA
***
1337780 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1337813 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1337846 T
1 T
1337847 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1340499 original size:52 final size:48
Alignment explanation
Indices: 1340339--1340508 Score: 135
Period size: 52 Copynumber: 3.3 Consensus size: 48
1340329 TATTTCTGAG
* * * *
1340339 GGGATACTCCAACCCTGACTTTATTTTCAAAAATATCGATTTTTCATAATC
1 GGGATACTCCAACCC-GATTTTA-TTTCCAAAATACCAATTTTTCA-AATC
* * * * *
1340390 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTCTCCTTTAAATC
1 -GGGATACTCCAA-CCCGATTTTATTTCCAAAATACCAATT-T--TTCAAATC
1340443 -GGATACTCCAATTCCCGATTTTATTTCCAAAATACCAATTTTTCACAATC
1 GGGATACTCCAA--CCCGATTTTATTTCCAAAATACCAATTTTTCA-AATC
1340493 GAGGATACTCCCAACC
1 G-GGATACT-CCAACC
1340509 TCGTTATTTC
Statistics
Matches: 94, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
49 3 0.03
50 4 0.04
51 25 0.27
52 48 0.51
53 11 0.12
54 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (48 bp):
GGGATACTCCAACCCGATTTTATTTCCAAAATACCAATTTTTCAAATC
Found at i:1348240 original size:21 final size:21
Alignment explanation
Indices: 1348201--1348241 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1348191 CCTTCTCTTC
* *
1348201 AAAAAAAAAAAAGAGCAAAAA
1 AAAAAAAAAAAAAAACAAAAA
1348222 AAAAAAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAACAAAA
1348242 CAACAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.90, C:0.05, G:0.05, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAAAAACAAAAA
Found at i:1349318 original size:55 final size:54
Alignment explanation
Indices: 1349231--1349999 Score: 810
Period size: 54 Copynumber: 14.2 Consensus size: 54
1349221 TTGAGTCCCA
*
1349231 AAGAGCAGGACACCTCT-AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
1 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
1349284 AAGAGCAGGACCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
1 AAGAGCAGGA-CACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
1349339 AAAGAGCAGGACACC-TTCAAAGCCCACACAAGTTGGTGGGCATTTTCCAGTCCTC
1 -AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGT-GGCATTTTCCAGTCCTC
1349394 AA-AGCAGGACACCTCTT-AAAGGCCCACACAA-TTGGTGGTCATTTTCCAGTCCTC
1 AAGAGCAGGACACCT-TTCAAA-GCCCACACAAGTTGGTGG-CATTTTCCAGTCCTC
1349448 AAGAGCAGGACAACCTTTCAGAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
1 AAGAGCAGGAC-ACCTTTCA-AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
*
1349504 AACGAG-AGGACACCTCTT--AAGCCCA-ACAAGTTGGTGGCACCTTT-CAG-CCTC
1 AA-GAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTC
** *
1349555 AAAGAGCAAGGACACC-TTCAAAGCCCACACAAGTTGGTGGCA-CCTCCAGTCCCC
1 -AAGAGC-AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
**
1349609 AA-AGACAGGACACCTTTCAAAGCCCACACACAGTTGGTGGCATCCT-CAGTCCTC
1 AAGAG-CAGGACACCTTTCAAAGCCCACACA-AGTTGGTGGCATTTTCCAGTCCTC
1349663 AAAGAGCAGGACACC-TTCAAAGCCCACACACAGTT-GTGGCATTTTCCAGTCC-C
1 -AAGAGCAGGACACCTTTCAAAGCCCACACA-AGTTGGTGGCATTTTCCAGTCCTC
* * * *
1349716 AAAGAGTAGGACACCTCTCAAAGCCCACACAAGTTGGT-GCACCTTT---GTCCCC
1 -AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTC
* *
1349768 AAAGAGCAGGAC-CCTTCTCCTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTC
1 -AAGAGCAGGACACCTT-T-C---AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
1349827 AAGAGCA-GACCCTTCACCTTTCAAAAG-CCACACAAGTTGGTGGCA-TTT-CAGTCCTCCC
1 AAGAGCAGGA-----CACCTTTC-AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT--C
*
1349885 AAGAGCAGGACACCTCTT--AAGCCCACACAAGTTGG-GGCACCTTT-CAGTCCTC
1 AAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTC
* * ** ** *
1349937 AAGAGTAGGACGCCTTTCAAAGCCCACACGTGTT-GTGGCATTTTTTACTCCTC
1 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
1349990 AAGAGCAGGA
1 AAGAGCAGGA
1350000 TACACTTATT
Statistics
Matches: 630, Mismatches: 25, Indels: 122
0.81 0.03 0.16
Matches are distributed among these distances:
51 18 0.03
52 68 0.11
53 145 0.23
54 150 0.24
55 99 0.16
56 80 0.13
57 19 0.03
58 33 0.05
59 11 0.02
61 1 0.00
62 2 0.00
63 4 0.01
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (54 bp):
AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
Found at i:1350792 original size:20 final size:20
Alignment explanation
Indices: 1350746--1350820 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
1350736 AAAATTCCAA
* * *
1350746 AATGTATTGATACATTTGTAG
1 AATGTATCGATACATTCG-AC
1350767 AATGTATCGATACATTC-AC
1 AATGTATCGATACATTCGAC
1350786 AAATGTATCGATACATTCTGAC
1 -AATGTATCGATACATTC-GAC
1350808 AA-GTATCGATACA
1 AATGTATCGATACA
1350821 GGGTCCCAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
19 1 0.02
20 28 0.58
21 17 0.35
22 2 0.04
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCGAC
Found at i:1350880 original size:19 final size:19
Alignment explanation
Indices: 1350856--1350922 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
1350846 AAATTCAACG
1350856 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1350875 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1350890 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1350907 ATTGTATCGATA-ATAA
1 TTTGTATCGATACATAA
1350923 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 4 0.10
19 23 0.55
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1350894 original size:32 final size:32
Alignment explanation
Indices: 1350858--1350918 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1350848 ATTCAACGTT
*
1350858 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1350890 TGTATCGATACATAAGTATTGTATCGATA
1 TGTATCGATACATAAGTATTGTATCGATA
1350919 ATAATTAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1350895 original size:13 final size:13
Alignment explanation
Indices: 1350877--1350901 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1350867 ACATAAGTTT
1350877 TGTATCGATACAA
1 TGTATCGATACAA
1350890 TGTATCGATACA
1 TGTATCGATACA
1350902 TAAGTATTGT
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:1361407 original size:22 final size:22
Alignment explanation
Indices: 1361379--1361430 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
1361369 CCTTCTCTTC
* *
1361379 AAAAAAAAAAAAGAGCAAAAAA
1 AAAAAAAAAAAAAAACAAAAAA
*
1361401 AAAAAAAAAAAAAAACAAAACA
1 AAAAAAAAAAAAAAACAAAAAA
*
1361423 AAGAAAAA
1 AAAAAAAA
1361431 GAGAGAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAAAAACAAAAAA
Found at i:1361414 original size:16 final size:16
Alignment explanation
Indices: 1361379--1361430 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
1361369 CCTTCTCTTC
*
1361379 AAAAAAAAAAAAGAGCA
1 AAAAAAAAAAAAAAG-A
1361396 AAAAAAAAAAAAAA-A
1 AAAAAAAAAAAAAAGA
* *
1361411 AAAAACAAAACAAAGA
1 AAAAAAAAAAAAAAGA
1361427 AAAA
1 AAAA
1361431 GAGAGAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.42
16 5 0.16
17 13 0.42
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGA
Found at i:1361445 original size:1 final size:1
Alignment explanation
Indices: 1361379--1361430 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
1361369 CCTTCTCTTC
* ** * * *
1361379 AAAAAAAAAAAAGAGCAAAAAAAAAAAAAAAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1361431 GAGAGAAAAG
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:1362498 original size:55 final size:55
Alignment explanation
Indices: 1362412--1363211 Score: 1123
Period size: 55 Copynumber: 14.3 Consensus size: 55
1362402 TTCCGCCTTT
*
1362412 CAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC
1362467 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1362522 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1362577 CAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC
1362632 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* *
1362687 CAGTCCTCAACGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-
1 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
* **
1362742 CAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTC
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* **
1362797 CAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATCCTC
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1362852 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* *
1362907 CAGTCCTCAAAGAGTAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTT-
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA--TTTTC
* * * *
1362963 --GTCCCCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1 CAGTCCTCAAAGAGCAGGACACCTT-T-C----AAAGCCCACACAAGTTGGTGGCATTTTC
1363022 CAGTCCTCAAAGAGCAGGACGCCTTCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGA------CACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* *
1363083 CAGTCCTCCAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-
1 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
* * ** * *
1363138 CAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACGTGTTTGTGGCATTTTT
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* * *
1363193 TACTCCTCAATGAGCAGGA
1 CAGTCCTCAAAGAGCAGGA
1363212 TACACTTTAT
Statistics
Matches: 679, Mismatches: 38, Indels: 56
0.88 0.05 0.07
Matches are distributed among these distances:
54 32 0.05
55 538 0.79
56 13 0.02
57 4 0.01
58 2 0.00
60 23 0.03
61 60 0.09
65 1 0.00
66 1 0.00
67 5 0.01
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (55 bp):
CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
Found at i:1362765 original size:26 final size:26
Alignment explanation
Indices: 1362735--1362824 Score: 65
Period size: 26 Copynumber: 3.3 Consensus size: 26
1362725 AAGTTGGTGG
*
1362735 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
1362761 CACCTCTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
* *
1362790 CACCTTCCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
1362816 CACCTTTCA
1 CACCTTTCA
1362825 AAGCCCACAC
Statistics
Matches: 45, Mismatches: 14, Indels: 10
0.65 0.20 0.14
Matches are distributed among these distances:
25 3 0.07
26 18 0.40
27 6 0.13
28 6 0.13
29 9 0.20
30 3 0.07
ACGTcount: A:0.29, C:0.36, G:0.18, T:0.18
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:1364019 original size:41 final size:40
Alignment explanation
Indices: 1363958--1364039 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 40
1363948 AAAAAAAAAA
* * *
1363958 ATTCCAAATGTATTGATACATTTGTA-GAATGTATCGATAC
1 ATTCCAAATGTATCGATACA-TTCTACAAATGTATCGATAC
1363998 ATTCACAAATGTATCGATACATTCTACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATACATTCTACAAATGTATCGATAC
1364039 A
1 A
1364040 GGGTCCCAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 8 0.22
41 29 0.78
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (40 bp):
ATTCCAAATGTATCGATACATTCTACAAATGTATCGATAC
Found at i:1364028 original size:21 final size:21
Alignment explanation
Indices: 1363962--1364039 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
1363952 AAAAAAATTC
* *
1363962 CAAATGTATTGATACATTTGTA
1 CAAATGTATCGATACA-TTCTA
*
1363984 -GAATGTATCGATACATTC-A
1 CAAATGTATCGATACATTCTA
1364003 CAAATGTATCGATACATTCTA
1 CAAATGTATCGATACATTCTA
1364024 CAAATGTATCGATACA
1 CAAATGTATCGATACA
1364040 GGGTCCCAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
19 1 0.02
20 19 0.38
21 30 0.60
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTCTA
Found at i:1364099 original size:19 final size:19
Alignment explanation
Indices: 1364075--1364142 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1364065 AATTCAACGA
1364075 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1364094 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1364109 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1364126 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1364143 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1364113 original size:32 final size:32
Alignment explanation
Indices: 1364077--1364139 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1364067 TTCAACGATT
*
1364077 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1364109 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1364140 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1364114 original size:13 final size:13
Alignment explanation
Indices: 1364096--1364120 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1364086 ACATAAGTTT
1364096 TGTATCGATACAA
1 TGTATCGATACAA
1364109 TGTATCGATACA
1 TGTATCGATACA
1364121 TAAGTATTGT
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:1364200 original size:13 final size:13
Alignment explanation
Indices: 1364182--1364207 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1364172 CATTTTTCTG
1364182 TGTATCGATACAT
1 TGTATCGATACAT
1364195 TGTATCGATACAT
1 TGTATCGATACAT
1364208 GGATCTTTGT
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:1364204 original size:33 final size:33
Alignment explanation
Indices: 1364162--1364228 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1364152 GCCAAGGAAA
***
1364162 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1364195 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1364228 T
1 T
1364229 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1366786 original size:51 final size:50
Alignment explanation
Indices: 1366727--1366897 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 50
1366717 TTATTTCTGA
* * *
1366727 GGGGATACTCCAACCCTGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCC-GATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
1366778 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAA-CCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
* * *
1366831 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAA-CCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
1366883 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1366898 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
51 33 0.34
52 21 0.22
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:1366916 original size:28 final size:28
Alignment explanation
Indices: 1366880--1366961 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
1366870 ATTTTTCACA
* *
1366880 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTCC
*
1366908 ATCGGGGATACTCCAACCCCGTTACTTCC
1 ATCGGGGATACTCCAACCTCGTTA-TTCC
* * *
1366937 A-AGGGAACACTCCAACCTCGTTATT
1 ATCGGGGATACTCCAACCTCGTTATT
1366962 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
27 2 0.04
28 40 0.87
29 4 0.09
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTCC
Found at i:1371447 original size:20 final size:20
Alignment explanation
Indices: 1371422--1371463 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1371412 ATTCTGGTTC
*
1371422 AGGATCATGGTTTTGTCTTT
1 AGGATCATAGTTTTGTCTTT
1371442 AGGATCATAGTTTTGTCTTT
1 AGGATCATAGTTTTGTCTTT
1371462 AG
1 AG
1371464 CTTTAGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.48
Consensus pattern (20 bp):
AGGATCATAGTTTTGTCTTT
Found at i:1372115 original size:19 final size:21
Alignment explanation
Indices: 1372070--1372123 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
1372060 TTTCAACAAT
1372070 TTGTATCGATACAAATAGTAA
1 TTGTATCGATACAAATAGTAA
* *
1372091 TTGTATCGATACATA-AGT-G
1 TTGTATCGATACAAATAGTAA
1372110 TTGTATCGATACAA
1 TTGTATCGATACAA
1372124 TGTATCGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (21 bp):
TTGTATCGATACAAATAGTAA
Found at i:1372129 original size:13 final size:13
Alignment explanation
Indices: 1372111--1372135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1372101 ACATAAGTGT
1372111 TGTATCGATACAA
1 TGTATCGATACAA
1372124 TGTATCGATACA
1 TGTATCGATACA
1372136 TGCAGGCAAA
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:1390642 original size:32 final size:33
Alignment explanation
Indices: 1390554--1390746 Score: 156
Period size: 34 Copynumber: 6.0 Consensus size: 33
1390544 AATTCTTCAA
* * *
1390554 ATCTCTCTTC-TCAAAGTCTACGACTCTGTGGC
1 ATCTCTTTTCTTCAAAGTCCACGACTCAGTGGC
*
1390586 A-CAT-TTTTCTTTTTAAAGTCCACGACTCAGTGGC
1 ATC-TCTTTTC--TTCAAAGTCCACGACTCAGTGGC
1390620 ATCTCTTTTCTTC-AAGTCCACGACTCAGTGGC
1 ATCTCTTTTCTTCAAAGTCCACGACTCAGTGGC
* *
1390652 A--TCTTGTC-TAAAAGTCCACGACTCAGTGGC
1 ATCTCTTTTCTTCAAAGTCCACGACTCAGTGGC
* * *
1390682 AATCTC--TTC-CCAAAGTCCATGACTCTGTGGC
1 -ATCTCTTTTCTTCAAAGTCCACGACTCAGTGGC
* *
1390713 ACCT-TTTTCTATTCAAAGTCCACGACTCCGTGGC
1 ATCTCTTTTC--TTCAAAGTCCACGACTCAGTGGC
1390747 CCCTTGTTCC
Statistics
Matches: 130, Mismatches: 16, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
29 1 0.01
30 28 0.22
31 29 0.22
32 22 0.17
33 4 0.03
34 40 0.31
35 6 0.05
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.33
Consensus pattern (33 bp):
ATCTCTTTTCTTCAAAGTCCACGACTCAGTGGC
Found at i:1390669 original size:30 final size:30
Alignment explanation
Indices: 1390593--1390746 Score: 141
Period size: 30 Copynumber: 5.0 Consensus size: 30
1390583 GGCACATTTT
1390593 TCTTTT-T-AAAGTCCACGACTCAGTGGCA
1 TCTTTTCTAAAAGTCCACGACTCAGTGGCA
**
1390621 TCTCTTTTCTTCAAGTCCACGACTCAGTGGCA
1 --TCTTTTCTAAAAGTCCACGACTCAGTGGCA
*
1390653 TCTTGTCTAAAAGTCCACGACTCAGTGGCAA
1 TCTTTTCTAAAAGTCCACGACTCAGTGGC-A
* ** * *
1390684 TCTCTTCCCAAAGTCCATGACTCTGTGGCA
1 TCTTTTCTAAAAGTCCACGACTCAGTGGCA
* *
1390714 CCTTTTTCTATTCAAAGTCCACGACTCCGTGGC
1 TC-TTTTCTA---AAAGTCCACGACTCAGTGGC
1390747 CCCTTGTTCC
Statistics
Matches: 101, Mismatches: 16, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
30 34 0.34
31 29 0.29
32 20 0.20
34 18 0.18
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.31
Consensus pattern (30 bp):
TCTTTTCTAAAAGTCCACGACTCAGTGGCA
Found at i:1390774 original size:33 final size:32
Alignment explanation
Indices: 1390694--1391456 Score: 772
Period size: 33 Copynumber: 23.8 Consensus size: 32
1390684 TCTCTTCCCA
** * * *
1390694 AAGTCCATGACTCTGTGGCACCTTTTTCTATTCA
1 AAGTCCACAACTCCGTGGCACCTTTTCCT-TT-T
* *
1390728 AAGTCCACGACTCCGTGGCCCCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
*
1390761 AAGTCCACAACTCCGTGGCA-C----CATTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
1390788 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
** *
1390821 AAGTCCACAACTTTGTGGCACC----CTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * * *
1390849 AAGTCTAGAACTCTGTGGCATTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA--CCTTTTCCTTTT
* *
1390883 AAGTCCACAACTCCGTGGTACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* *
1390915 AAGTCCACAACTCCGTGGCACTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* *
1390947 AAGTCCACAACTCCATGGCACTCTTTTTCCTTTA
1 AAGTCCACAACTCCGTGGCAC-C-TTTTCCTTTT
*
1390981 AAGTCCACAACTCCGTGGCACATTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * *
1391013 AAATCCACAACTTCGTGGCACTTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
*
1391046 AAGTCCACAACTTCGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* *
1391079 AAGTCCACAACTCCGTGGTACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
*
1391111 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * *
1391143 CAGTTCACAACTCCGTGGCACTCTTTTTCCTTTA
1 AAGTCCACAACTCCGTGGCAC-C-TTTTCCTTTT
* * *
1391177 AATTCCACAACTTCATGGCACCTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
1391209 AAGTCCACAACTCCGTGGCA-C----CCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * * *
1391236 AAGCCCACAACTCTGTGGCACTTTTTTTCTTTT
1 AAGTCCACAACTCCGTGGCAC-CTTTTCCTTTT
* *
1391269 AAGCCCACAACTCCGTGGCATTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA--CCTTTTCCTTTT
1391303 AAGTCCACAACTCCGTGGCA-C----CCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* **
1391330 AAGTCCACAACTCCGTGGTACCTTGTTTTTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* *
1391363 GAGTCCACAACTCCGTGGCATCTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTT-CCTTTT
*
1391396 AAGTCCACAACTCCGTGGCATCTTTCTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTT-TCCTTTT
* * *
1391429 AAGCCCACAAGTCAGTGGCACCCTTTTC
1 AAGTCCACAACTCCGTGGCA-CCTTTTC
1391457 AAAAGCCCAC
Statistics
Matches: 619, Mismatches: 75, Indels: 71
0.81 0.10 0.09
Matches are distributed among these distances:
27 74 0.12
28 24 0.04
30 1 0.00
31 1 0.00
32 176 0.28
33 208 0.34
34 130 0.21
35 5 0.01
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.36
Consensus pattern (32 bp):
AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
Found at i:1390795 original size:27 final size:27
Alignment explanation
Indices: 1390757--1390809 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1390747 CCCTTGTTCC
1390757 TTTTAAGTCCACAACTCCGTGGCACCA
1 TTTTAAGTCCACAACTCCGTGGCACCA
1390784 TTTTAAGTCCACAACTCCGTGGCACC
1 TTTTAAGTCCACAACTCCGTGGCACC
1390810 TTGTTCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.26
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCA
Found at i:1390874 original size:28 final size:28
Alignment explanation
Indices: 1390757--1391347 Score: 122
Period size: 32 Copynumber: 18.8 Consensus size: 28
1390747 CCCTTGTTCC
* *
1390757 TTTTAAGTCCACAACTCCGTGGCA-CCA
1 TTTTAAGTCCACAACTCTGTGGCACCCT
* *
1390784 TTTTAAGTCCACAACTCCGTGGCACCTTGTTCC
1 TTTTAAGTCCACAACTCTGTGGCACC-----CT
*
1390817 TTTTAAGTCCACAACTTTGTGGCACCCT
1 TTTTAAGTCCACAACTCTGTGGCACCCT
* *
1390845 TTTTAAGTCTAGAACTCTGTGGCATTCTTTTTCC-
1 TTTTAAGTCCACAACTCTGTGGCA--C-----CCT
* *
1390879 TTTTAAGTCCACAACTCCGTGGTACCTTTTCT
1 TTTTAAGTCCACAACTCTGTGGCACC----CT
* *
1390911 TTTTAAGTCCACAACTCCGTGGCACTTTTTCT
1 TTTTAAGTCCACAACTCTGTGGCAC----CCT
** *
1390943 TTTTAAGTCCACAACTCCATGGCACTCTTTT
1 TTTTAAGTCCACAACTCTGTGGCAC-C--CT
*
1390974 TCCTTTAAAGTCCACAACTCCGTGGCACATTTTCC-
1 T--TTT-AAGTCCACAACTCTGTGGCAC-----CCT
*
1391009 TTTTAAATCCACAACT-TCGTGGCACTTTGTTCC-
1 TTTTAAGTCCACAACTCT-GTGGCAC------CCT
*
1391042 TTTTAAGTCCACAACT-TCGTGGCACCTTGTTCC
1 TTTTAAGTCCACAACTCT-GTGGCACC-----CT
* *
1391075 TTTTAAGTCCACAACTCCGTGGTACCTTTTCT
1 TTTTAAGTCCACAACTCTGTGGCACC----CT
*
1391107 TTTTAAGTCCACAACTCCGTGGCACCTTTTCT
1 TTTTAAGTCCACAACTCTGTGGCACC----CT
* * * *
1391139 TTTTCAGTTCACAACTCCGTGGCACTCTTTT
1 TTTTAAGTCCACAACTCTGTGGCAC-C--CT
* * *
1391170 TCCTTTAAATTCCACAACT-TCATGGCACCTTTTCC
1 T--TTT-AAGTCCACAACTCT-GTGGCACC----CT
*
1391205 TTTTAAGTCCACAACTCCGTGGCACCC-
1 TTTTAAGTCCACAACTCTGTGGCACCCT
* **
1391232 TTTTAAGCCCACAACTCTGTGGCACTTTTTTT
1 TTTTAAGTCCACAACTCTGTGGCAC----CCT
* *
1391264 CTTTTAAGCCCACAACTCCGTGGCATTCTTTTTCC-
1 -TTTTAAGTCCACAACTCTGTGGCA--C-----CCT
*
1391299 TTTTAAGTCCACAACTCCGTGGCACCC-
1 TTTTAAGTCCACAACTCTGTGGCACCCT
*
1391326 TTTTAAGTCCACAACTCCGTGG
1 TTTTAAGTCCACAACTCTGTGG
1391348 TACCTTGTTT
Statistics
Matches: 458, Mismatches: 49, Indels: 114
0.74 0.08 0.18
Matches are distributed among these distances:
27 73 0.16
28 24 0.05
29 1 0.00
30 1 0.00
31 7 0.02
32 147 0.32
33 114 0.25
34 78 0.17
35 7 0.02
36 4 0.01
38 2 0.00
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (28 bp):
TTTTAAGTCCACAACTCTGTGGCACCCT
Found at i:1390973 original size:98 final size:98
Alignment explanation
Indices: 1390694--1391455 Score: 802
Period size: 98 Copynumber: 7.9 Consensus size: 98
1390684 TCTCTTCCCA
** * * * * * *
1390694 AAGTCCATGACTCTGTGGCACCTTTTTCTATTCAAAGTCCACGACTCCGTGGCCCCTTGTTCCTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCT-TT-TAAGTCCACAACTCCGTGG-CACTTTTTCCTT
*
1390759 TTAAGTCCACAACTCCGTGGCA--C-----CATTTT
63 TTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
**
1390788 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTTTGTGGCAC-----CCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTTAAGTCCACAACTCCGTGGCACTTTTTCC-TTT
* * * *
1390848 TAAGTCTAGAACTCTGTGGCATTCTTTTTCCTTTT
64 TAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
1390883 AAGTCCACAACTCCGTGGTACCTTTTCTTTTTAAGTCCACAACTCCGTGGCACTTTTTCTTTTTA
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACTTTTTCCTTTTA
* *
1390948 AGTCCACAACTCCATGGCACTCTTTTTCCTTTA
66 AGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
1390981 AAGTCCACAACTCCGTGGCACATTTTCCTTTTAAATCCACAACTTCGTGGCACTTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACTTT-TTCCTTTT
* *
1391046 AAGTCCACAACTTCGTGGCAC-CTTGTTCCTTTT
65 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * * *
1391079 AAGTCCACAACTCCGTGGTACCTTTTCTTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTTTTC
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACTTTTTCCTTTTA
* *
1391144 AGTTCACAACTCCGTGGCACTCTTTTTCCTTTA
66 AGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
1391177 AATTCCACAACTTCATGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCAC-----CCTTTTA
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACTTTTTCCTTTTA
* * *
1391237 AGCCCACAACTCTGTGGCACT-TTTTTTCTTTT
66 AGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
1391269 AAGCCCACAACTCCGTGGCATTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC-----CCTTT
1 AAGTCCACAACTCCGTGGCA--CCTTTTCCTTTTAAGTCCACAACTCCGTGGCACTTTTTCCTTT
* *
1391329 TAAGTCCACAACTCCGTGGTAC-CTTGTTT-TTTTT
64 TAAGTCCACAACTCCGTGGCACTCTT-TTTCCTTTT
* * *
1391363 GAGTCCACAACTCCGTGGCATCTTTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCTTT
1 AAGTCCACAACTCCGTGGCACCTTTT-CCTTTTAAGTCCACAACTCCGTGGCA-CTTTTTCCTTT
* * * *
1391428 TAAGCCCACAAGTCAGTGGCACCCTTTT
64 TAAGTCCACAACTCCGTGGCACTCTTTT
1391456 CAAAAGCCCA
Statistics
Matches: 565, Mismatches: 75, Indels: 51
0.82 0.11 0.07
Matches are distributed among these distances:
87 2 0.00
88 21 0.04
90 1 0.00
92 31 0.05
93 64 0.11
94 130 0.23
95 35 0.06
97 25 0.04
98 201 0.36
99 52 0.09
100 3 0.01
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.36
Consensus pattern (98 bp):
AAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACTTTTTCCTTTTA
AGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
Found at i:1391465 original size:30 final size:29
Alignment explanation
Indices: 1391429--1391524 Score: 115
Period size: 28 Copynumber: 3.3 Consensus size: 29
1391419 TTCTCCTTTT
*
1391429 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTTAGTGGCACCC-TTTCAA
* *
1391459 AAGCCCACAAGTTAGTGGCAACC-TCCAA
1 AAGCCCACAAGTTAGTGGCACCCTTTCAA
* *
1391487 AAGCACACAAGTTGGT-GCAACCCTTTCAA
1 AAGCCCACAAGTTAGTGGC-ACCCTTTCAA
1391516 AAGCCCACA
1 AAGCCCACA
1391525 CAAGTTGGTG
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
27 2 0.04
28 21 0.38
29 12 0.21
30 21 0.38
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (29 bp):
AAGCCCACAAGTTAGTGGCACCCTTTCAA
Found at i:1391496 original size:28 final size:29
Alignment explanation
Indices: 1391429--1391536 Score: 103
Period size: 30 Copynumber: 3.7 Consensus size: 29
1391419 TTCTCCTTTT
* * *
1391429 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
1 AAGCACACAAGTTAGTGGCAACC-TTTCAA
* *
1391459 AAGCCCACAAGTTAGTGGCAACC-TCCAA
1 AAGCACACAAGTTAGTGGCAACCTTTCAA
*
1391487 AAGCACACAAGTTGGT-GCAACCCTTTCAA
1 AAGCACACAAGTTAGTGGCAA-CCTTTCAA
*
1391516 AAGCCCACACAAGTTGGTGGC
1 AAG--CACACAAGTTAGTGGC
1391537 GTCTTCTTCT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.06
28 20 0.30
29 7 0.10
30 21 0.31
31 13 0.19
32 2 0.03
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (29 bp):
AAGCACACAAGTTAGTGGCAACCTTTCAA
Found at i:1391528 original size:31 final size:30
Alignment explanation
Indices: 1391448--1391534 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 30
1391438 AGTCAGTGGC
*
1391448 ACCCTTTTCAAAAGCC-CACAAGTTAGTGGCA
1 ACCC-TTTCAAAAGCCACACAAGTTGGT-GCA
*
1391479 A-CC-TCCAAAAG-CACACAAGTTGGTGCA
1 ACCCTTTCAAAAGCCACACAAGTTGGTGCA
1391506 ACCCTTTCAAAAGCCCACACAAGTTGGTG
1 ACCCTTTCAAAAG-CCACACAAGTTGGTG
1391535 GCGTCTTCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
27 5 0.10
28 19 0.40
29 7 0.15
30 2 0.04
31 15 0.31
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (30 bp):
ACCCTTTCAAAAGCCACACAAGTTGGTGCA
Found at i:1391692 original size:87 final size:87
Alignment explanation
Indices: 1391546--1391719 Score: 312
Period size: 87 Copynumber: 2.0 Consensus size: 87
1391536 CGTCTTCTTC
*
1391546 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTA
1391611 GCCTTGAATCAACACATTGGCA
66 GCCTTGAATCAACACATTGGCA
*
1391633 TAAGCCCAATATTACTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTA
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTA
* *
1391698 GCCTTGAATCAGCATATTGGCA
66 GCCTTGAATCAACACATTGGCA
1391720 CCTTGTCTTT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (87 bp):
TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTA
GCCTTGAATCAACACATTGGCA
Found at i:1391795 original size:49 final size:49
Alignment explanation
Indices: 1391647--1392292 Score: 414
Period size: 49 Copynumber: 13.5 Consensus size: 49
1391637 CCCAATATTA
* * * * *
1391647 CTGGCCTTGAATCAGCATATTGGCACCTT--GTCTCTAAGACCAATGTCG
1 CTGGCCTTGAATCAGCATATTGGCATCTTCAG-CTTTAAGTCCGATATCG
* * * * * *
1391695 CTAGCCTTGAATCAGCATATTGGCACCTT--GTCTTTAAGACCAATGTTG
1 CTGGCCTTGAATCAGCATATTGGCATCTTCAG-CTTTAAGTCCGATATCG
* * * *
1391743 CTGGCCTTGATTCAGTACATTGGAATCTTCAGCTTTAAGTCCGATATCG
1 CTGGCCTTGAATCAGCATATTGGCATCTTCAGCTTTAAGTCCGATATCG
* * * * * * *
1391792 CTGGCCTTGAATCAGCATATTGGTGCCTTTGTTATCTTTAAGACCAATGTCG
1 CTGGCCTTGAATCAGCATATT-G-GCATCT-TCAGCTTTAAGTCCGATATCG
*
1391844 CTGGCCTTGAATCAGCATAGTGGCATCTTCAGCTTTAAGTCCGATATCG
1 CTGGCCTTGAATCAGCATATTGGCATCTTCAGCTTTAAGTCCGATATCG
* * * * * *
1391893 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCG
1 CTGGCCTTGAATCAGCATATT-G-GCATCT-TCAGCTTTAAGTCCGATATCG
* * *
1391945 CTGGCCTTGAATCAGCACATTGG------CA----TAAGCCCAATATCG
1 CTGGCCTTGAATCAGCATATTGGCATCTTCAGCTTTAAGTCCGATATCG
* * * *
1391984 CTGGCCTTGAATCAGCATATTGGCACCTT--GTCTTTAAGACCAATGTCG
1 CTGGCCTTGAATCAGCATATTGGCATCTTCAG-CTTTAAGTCCGATATCG
* * *
1392032 CTGGCCTTAAATCAGCACATT-G-A----CA-C---AAG-CCCAGTATCG
1 CTGGCCTTGAATCAGCATATTGGCATCTTCAGCTTTAAGTCCGA-TATCG
* * * * *
1392071 CTCGCCTTGAATCAGCATATTGGCA-CATTTATCTTTAAGACCGATGTCG
1 CTGGCCTTGAATCAGCATATTGGCATC-TTCAGCTTTAAGTCCGATATCG
* * * ** * * *
1392120 TTGGCCTTGAATCAGCACATCGGCACCTCAACTATCTTTAAGCCCAATATCG
1 CTGGCCTTGAATCAGCATATTGGCA--TCTTC-AGCTTTAAGTCCGATATCG
* * * * *
1392172 CTGGCCTTGAATCAGCATATTGACA-CGTCATCTTTAAGTCCAATGTCG
1 CTGGCCTTGAATCAGCATATTGGCATCTTCAGCTTTAAGTCCGATATCG
* * * *
1392220 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
1 CTGGCCTTGAATCAGCATATTGGCATCTTCAGCTTTAAGTCCGATATCG
1392269 CTGGCCTTGAATCAGCATATTGGC
1 CTGGCCTTGAATCAGCATATTGGC
1392293 GCCTTCGTCA
Statistics
Matches: 482, Mismatches: 78, Indels: 75
0.76 0.12 0.12
Matches are distributed among these distances:
38 3 0.01
39 59 0.12
40 1 0.00
41 1 0.00
42 1 0.00
43 2 0.00
45 1 0.00
46 2 0.00
47 1 0.00
48 139 0.29
49 141 0.29
50 11 0.02
51 9 0.02
52 111 0.23
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (49 bp):
CTGGCCTTGAATCAGCATATTGGCATCTTCAGCTTTAAGTCCGATATCG
Found at i:1391849 original size:52 final size:52
Alignment explanation
Indices: 1391647--1391968 Score: 330
Period size: 52 Copynumber: 6.5 Consensus size: 52
1391637 CCCAATATTA
*
1391647 CTGGCCTTGAATCAGCATATTGGCACC-TTGTC-TC--TAAGACCAATGTCG
1 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCG
* * *
1391695 CTAGCCTTGAATCAGCATATTGGCACC-TTG---TCTTTAAGACCAATGTTG
1 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCG
* * * ** * * * * *
1391743 CTGGCCTTGATTCAGTACATT-G-GAATCT-TCAGCTTTAAGTCCGATATCG
1 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCG
* *
1391792 CTGGCCTTGAATCAGCATATTGGTGCCTTTGTTATCTTTAAGACCAATGTCG
1 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCG
* * * * * * *
1391844 CTGGCCTTGAATCAGCATAGT-G-GCATCT-TCAGCTTTAAGTCCGATATCG
1 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCG
1391893 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCG
1 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCG
*
1391945 CTGGCCTTGAATCAGCACATTGGC
1 CTGGCCTTGAATCAGCATATTGGC
1391969 ATAAGCCCAA
Statistics
Matches: 220, Mismatches: 42, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
46 2 0.01
47 2 0.01
48 59 0.27
49 67 0.30
50 6 0.03
51 8 0.04
52 76 0.35
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.32
Consensus pattern (52 bp):
CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCG
Found at i:1391872 original size:101 final size:99
Alignment explanation
Indices: 1391647--1392341 Score: 680
Period size: 101 Copynumber: 7.2 Consensus size: 99
1391637 CCCAATATTA
* * * * * *
1391647 CTGGCCTTGAATCAGCATATTGGCACCTT--GTCTCTAAGACCAATGTCGCTAGCCTTGAATCAG
1 CTGGCCTTGAATCAGCACA-TGGCATCTTCAG-CTTTAAGTCCAATATCGCTGGCCTTGAATCAG
* *
1391710 CATATTGGCACCTTG---TCTTTAAGACCAATGTTG
64 CATATTGGCGCCTTGTCATCTTTAAGACCAATGTCG
* * * *
1391743 CTGGCCTTGATTCAGTACATTGGAATCTTCAGCTTTAAGTCCGATATCGCTGGCCTTGAATCAGC
1 CTGGCCTTGAATCAGCACA-TGGCATCTTCAGCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
* *
1391808 ATATTGGTGCCTTTGTTATCTTTAAGACCAATGTCG
65 ATATTGGCGCC-TTGTCATCTTTAAGACCAATGTCG
* *
1391844 CTGGCCTTGAATCAGCATAGTGGCATCTTCAGCTTTAAGTCCGATATCGCTGGCCTTGAATCAGC
1 CTGGCCTTGAATCAGCACA-TGGCATCTTCAGCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
1391909 ATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCG
65 ATATTGGCGCC-TTGTCATCTTTAAGACCAATGTCG
*
1391945 CTGGCCTTGAATCAGCACATTGG------CA----TAAGCCCAATATCGCTGGCCTTGAATCAGC
1 CTGGCCTTGAATCAGCACA-TGGCATCTTCAGCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
*
1392000 ATATTGGCACCTTG---TCTTTAAGACCAATGTCG
65 ATATTGGCGCCTTGTCATCTTTAAGACCAATGTCG
* * * * *
1392032 CTGGCCTTAAATCAGCACATTG-A----CA-C---AAGCCCAGTATCGCTCGCCTTGAATCAGCA
1 CTGGCCTTGAATCAGCACATGGCATCTTCAGCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
* * *
1392088 TATTGGCACATT-T-ATCTTTAAGACCGATGTCG
66 TATTGGCGCCTTGTCATCTTTAAGACCAATGTCG
* ** * *
1392120 TTGGCCTTGAATCAGCACATCGGCACCTCAACTATCTTTAAGCCCAATATCGCTGGCCTTGAATC
1 CTGGCCTTGAATCAGCACAT-GGCA--TCTTC-AGCTTTAAGTCCAATATCGCTGGCCTTGAATC
* * *
1392185 AGCATATTGAC-AC--GTCATCTTTAAGTCCAATGTCG
62 AGCATATTGGCGCCTTGTCATCTTTAAGACCAATGTCG
* *
1392220 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
1 CTGGCCTTGAATCAGCACA-TGGCATCTTCAGCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
* * *
1392285 ATATTGGCGCCTTCGTCAACTTTAAAACCTAATGCCG
65 ATATTGGCGCCTT-GTCATCTTTAAGACC-AATGTCG
*
1392322 TTGGCCTTGAATCAGCACAT
1 CTGGCCTTGAATCAGCACAT
1392342 TGGCGTTCTT
Statistics
Matches: 515, Mismatches: 53, Indels: 57
0.82 0.08 0.09
Matches are distributed among these distances:
86 2 0.00
87 77 0.15
88 35 0.07
89 1 0.00
90 4 0.01
91 38 0.07
95 2 0.00
96 25 0.05
97 79 0.15
98 8 0.02
99 1 0.00
100 39 0.08
101 180 0.35
102 24 0.05
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.30
Consensus pattern (99 bp):
CTGGCCTTGAATCAGCACATGGCATCTTCAGCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
TATTGGCGCCTTGTCATCTTTAAGACCAATGTCG
Found at i:1391990 original size:39 final size:39
Alignment explanation
Indices: 1391931--1392095 Score: 150
Period size: 39 Copynumber: 4.0 Consensus size: 39
1391921 TTGTCATCTT
*
1391931 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* *
1391970 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * *
1392009 CCTTGTCTTTAAGACCAATGTCGCTGGCCTTAAATCAGCACATTGACA
1 ---------TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * * * *
1392057 CAAGCCCAGTATCGCTCGCCTTGAATCAGCATATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
1392096 CATTTATCTT
Statistics
Matches: 101, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
39 67 0.66
48 34 0.34
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (39 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1392045 original size:87 final size:87
Alignment explanation
Indices: 1391887--1392145 Score: 374
Period size: 87 Copynumber: 2.9 Consensus size: 87
1391877 TTTAAGTCCG
*
1391887 ATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCGCTGGCCT
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTG---TCTTTAAGACCAATGTCGCTGGCCT
*
1391952 TGAATCAGCACATTGGCATAAGCCCA
62 TGAATCAGCACATTGGCACAAGCCCA
*
1391978 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTAAA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAA
*
1392043 TCAGCACATTGACACAAGCCCA
66 TCAGCACATTGGCACAAGCCCA
* * * * * *
1392065 GTATCGCTCGCCTTGAATCAGCATATTGGCACATTTATCTTTAAGACCGATGTCGTTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCAC-CTTGTCTTTAAGACCAATGTCGCTGGCCTTGA
*
1392130 ATCAGCACATCGGCAC
65 ATCAGCACATTGGCAC
1392146 CTCAACTATC
Statistics
Matches: 154, Mismatches: 13, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
87 78 0.51
88 41 0.27
90 3 0.02
91 32 0.21
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (87 bp):
ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAA
TCAGCACATTGGCACAAGCCCA
Found at i:1392047 original size:188 final size:187
Alignment explanation
Indices: 1391647--1392345 Score: 665
Period size: 188 Copynumber: 3.7 Consensus size: 187
1391637 CCCAATATTA
* ** * * * *
1391647 CTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTAGCCTTGAATCAGCA
1 CTGGCCTTGAATCAGCACA-TGGCA-CTTCACTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
* * * * *
1391712 TATTGGCACC-TTG---TCTTTAAGACCAATGTTGCTGGCCTTGATTCAGTACATTGGAATCTTC
64 TATTGGCGCCTTTGTCATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGG---C-T-
* * **
1391773 AGCTTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTTATCTTTAAGACCA
124 A---TTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTG---TCTTTAAGACCA
1391838 ATGTCG
182 ATGTCG
* *
1391844 CTGGCCTTGAATCAGCATAGTGGCATCTTCAGCTTTAAGTCCGATATCGCTGGCCTTGAATCAGC
1 CTGGCCTTGAATCAGCACA-TGGCA-CTTCA-CTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
*
1391909 ATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGC-A-TA
63 ATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCTATTA
1391972 AGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
128 AGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
* * * * *
1392032 CTGGCCTTAAATCAGCACATTG-A---CAC---AAGCCCAGTATCGCTCGCCTTGAATCAGCATA
1 CTGGCCTTGAATCAGCACATGGCACTTCACTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA
* * * *
1392090 TTGGC-ACATT-T-ATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAAC
66 TTGGCGCCTTTGTCATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGG--------C
* * ** *
1392152 TATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGACACGTCATCTTTAAGTCCAATG
123 TA---TTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATG
1392217 TCG
185 TCG
1392220 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
1 CTGGCCTTGAATCAGCACA-TGGCA-CTTCA-CTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
* * * *
1392285 ATATTGGCGCCTTCGTCAACTTTAAAACCTAATGCCGTTGGCCTTGAATCAGCACATTGGC
63 ATATTGGCGCCTTTGTCATCTTTAAGACC-AATGTCGTTGGCCTTGAATCAGCACATTGGC
1392346 GTTCTTCTCA
Statistics
Matches: 423, Mismatches: 47, Indels: 67
0.79 0.09 0.12
Matches are distributed among these distances:
175 39 0.09
176 1 0.00
177 3 0.01
178 33 0.08
181 1 0.00
182 2 0.00
183 1 0.00
184 1 0.00
186 1 0.00
187 2 0.00
188 110 0.26
189 2 0.00
190 1 0.00
191 3 0.01
192 37 0.09
194 3 0.01
195 1 0.00
196 1 0.00
197 27 0.06
198 72 0.17
199 6 0.01
200 1 0.00
201 10 0.02
202 65 0.15
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (187 bp):
CTGGCCTTGAATCAGCACATGGCACTTCACTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA
TTGGCGCCTTTGTCATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCTATTAAGC
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
Found at i:1392391 original size:52 final size:52
Alignment explanation
Indices: 1392329--1392451 Score: 138
Period size: 55 Copynumber: 2.3 Consensus size: 52
1392319 CCGTTGGCCT
* * *
1392329 TGAATCAGCACATTGGCGTTCTTCTCATCTTCAAATCTAATGTCACTGACCG
1 TGAATCAGCACATTGGCCTTCTTCTCATCTTCAAACCTAATATCACTGACCG
* * * **
1392381 TGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAACCTAATATCGTTGACCG
1 TGAATCAGCACATTG---GCCTTCTTCTCATCTTCAAACCTAATATCACTGACCG
*
1392436 TGAATCAGCATATTGG
1 TGAATCAGCACATTGG
1392452 TCCCTTTATC
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
52 15 0.26
55 43 0.74
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (52 bp):
TGAATCAGCACATTGGCCTTCTTCTCATCTTCAAACCTAATATCACTGACCG
Found at i:1393159 original size:13 final size:13
Alignment explanation
Indices: 1393139--1393191 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
1393129 ATATAAGTGT
1393139 TGTATCGATACAA
1 TGTATCGATACAA
* *
1393152 TATATCGATACATT
1 TGTATCGATACA-A
1393166 TGTATCGATACAA
1 TGTATCGATACAA
*
1393179 TGTATCGCTACAA
1 TGTATCGATACAA
1393192 AGCTACTGCC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
13 23 0.68
14 11 0.32
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1393170 original size:27 final size:27
Alignment explanation
Indices: 1393138--1393190 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1393128 TATATAAGTG
1393138 TTGTATCGATACAATATATCGATACAT
1 TTGTATCGATACAATATATCGATACAT
* *
1393165 TTGTATCGATACAATGTATCGCTACA
1 TTGTATCGATACAATATATCGATACA
1393191 AAGCTACTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (27 bp):
TTGTATCGATACAATATATCGATACAT
Found at i:1405663 original size:15 final size:17
Alignment explanation
Indices: 1405638--1405669 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1405628 TTAAAATTAT
1405638 AAATATTTAAT-ATAAA
1 AAATATTTAATCATAAA
1405654 AAAT-TTTAATCATAAA
1 AAATATTTAATCATAAA
1405670 TTTAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATTTAATCATAAA
Found at i:1405819 original size:15 final size:17
Alignment explanation
Indices: 1405789--1405825 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
1405779 AGGAATTGAT
1405789 TAAAAGAATCAAATAAA
1 TAAAAGAATCAAATAAA
1405806 TAAAA-AAT-AAATAAA
1 TAAAAGAATCAAATAAA
1405821 TAAAA
1 TAAAA
1405826 TCATATACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 12 0.60
16 3 0.15
17 5 0.25
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (17 bp):
TAAAAGAATCAAATAAA
Found at i:1410181 original size:20 final size:19
Alignment explanation
Indices: 1410152--1410242 Score: 51
Period size: 20 Copynumber: 4.4 Consensus size: 19
1410142 TTAAGTTGAT
*
1410152 TTAATTTAAATAATTATTTA
1 TTAATATAAA-AATTATTTA
**
1410172 TTAATATAAATTTTTATTTAAA
1 TTAATATAAA-AATTATTT--A
*
1410194 TTTAATTATAAAAATATATAAATA
1 -TTAA-TATAAAAAT-TAT--TTA
1410218 TTAATATAAAAA-TATTT-
1 TTAATATAAAAATTATTTA
1410235 TTAATATA
1 TTAATATA
1410243 TTTAATATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
17 8 0.14
18 1 0.02
20 19 0.33
22 9 0.16
23 9 0.16
24 10 0.18
26 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATATAAAAATTATTTA
Found at i:1410224 original size:12 final size:12
Alignment explanation
Indices: 1410170--1410227 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
1410160 AATAATTATT
1410170 TATTAATATAAA
1 TATTAATATAAA
* * *
1410182 TTTTTATTTAAA
1 TATTAATATAAA
1410194 T-TTAATTATAAA
1 TATTAA-TATAAA
*
1410206 -AAT-ATATAAA
1 TATTAATATAAA
1410216 TATTAATATAAA
1 TATTAATATAAA
1410228 AATATTTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
10 6 0.17
11 6 0.17
12 23 0.66
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATTAATATAAA
Found at i:1410225 original size:22 final size:22
Alignment explanation
Indices: 1410190--1410232 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1410180 AATTTTTATT
1410190 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
1410212 TAAATATTAA-TATAAAAATAT
1 TAAAT-TTAATTATAAAAATAT
1410233 TTTTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:1411957 original size:3 final size:3
Alignment explanation
Indices: 1411949--1411976 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1411939 TTTTGTTCCA
1411949 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1411977 TTCCTTTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1415142 original size:18 final size:19
Alignment explanation
Indices: 1415109--1415144 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1415099 TTTAAACTCT
1415109 TTTAAATATCAAATAAATC
1 TTTAAATATCAAATAAATC
*
1415128 TTTAAAT-TTAAATAAAT
1 TTTAAATATCAAATAAAT
1415145 AACTTAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAAATATCAAATAAATC
Found at i:1419979 original size:20 final size:20
Alignment explanation
Indices: 1419950--1420026 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
1419940 GTAAAAAAAC
*
1419950 AGAATATATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
1419970 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
1419990 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
1420010 AGAATGTATCGATACAT
1 AGAATGTATCGATACAT
1420027 CTAGGTACCT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1420709 original size:29 final size:29
Alignment explanation
Indices: 1420581--1421148 Score: 727
Period size: 28 Copynumber: 19.9 Consensus size: 29
1420571 AAAAAAAATG
*
1420581 GTGCCACTAACTTGTGTGGGCTTTGAAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAAGA
*
1420612 GTTGCCACCGACTCGTGTGGGCTTTGAAAAGA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
*
1420644 GTTGCCACT-AGCTTGTGGGCTTTGAAAGGA
1 G-TGCCACTGA-CTTGTGGGCTTTGAAAAGA
* * *
1420674 -TGCCACTAACTTGTGGACTTTAAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1420702 GTGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1420731 GTGCCATTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1420759 GTGCCACTGACTTATGGGCTTTG-AAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1420787 GTG-C-C--ACTTCTGGGCTTTG-AAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
1420811 GTGCCACTAACTTATGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1420839 GTACCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1420868 GTGCCACTGACTTGTGGGCATTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1420897 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1420925 GTGCCACTGACTTGTGGGCTTTG-AAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1420953 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1420981 GTGCCACTGACTTGTGGGCTTT-AAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1421009 GTGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1421038 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1421067 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1421096 -TGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
1421123 GTGCTATTGACTGGTGGGCTTTGAAA
1 GTGCCACTGACTTGTGGGCTTTGAAA
1421149 GGGATGAACA
Statistics
Matches: 486, Mismatches: 37, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
24 21 0.04
25 1 0.00
26 2 0.00
27 4 0.01
28 240 0.49
29 163 0.34
30 16 0.03
31 3 0.01
32 36 0.07
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:1420717 original size:57 final size:57
Alignment explanation
Indices: 1420581--1421149 Score: 667
Period size: 57 Copynumber: 10.0 Consensus size: 57
1420571 AAAAAAAATG
* * *
1420581 GTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGGAG-TGCCACTGACT--TGTGGGCTTT-AAAAGA
* *
1420644 GTTGCCACT-AGCTTGTGGGCTTTGAAAGGA-TGCCACTAACTTGTGGACTTTAAAAAGA
1 G-TGCCACTGA-CTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTT-AAAAGA
* * * * *
1420702 GTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCATTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTAAAAGA
* * *
1420759 GTGCCACTGACTTATGGGCTTTGAAA-GAGTG-C-C--ACTTCTGGGCTTTGAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTAAAAGA
* * * *
1420811 GTGCCACTAACTTATGGGCTTTGAAAGG-GTACCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTT-AAAAGA
* * * *
1420868 GTGCCACTGACTTGTGGGCATTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTAAAAGA
* *
1420925 GTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTAAAAGA
* *
1420981 GTGCCACTGACTTGTGGGCTTTAAAAGG-GTGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTT-AAAAGA
* *
1421038 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTAAAAGA
* * * *
1421094 GATGCCACTGACTTGTGGGCTTTGAAAGG-GTGCTATTGACTGGTGGGCTTTGAAAG
1 G-TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTAAAAG
1421150 GGATGAACAT
Statistics
Matches: 450, Mismatches: 41, Indels: 37
0.85 0.08 0.07
Matches are distributed among these distances:
52 44 0.10
53 2 0.00
54 1 0.00
55 1 0.00
56 118 0.26
57 172 0.38
58 76 0.17
60 9 0.02
62 16 0.04
63 3 0.01
64 8 0.02
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.28
Consensus pattern (57 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTAAAAGA
Found at i:1421052 original size:170 final size:169
Alignment explanation
Indices: 1420580--1421151 Score: 837
Period size: 170 Copynumber: 3.3 Consensus size: 169
1420570 TAAAAAAAAT
* *
1420580 GGTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAG
1 GGTGCCACTGAC-T-TGTGGGCTTTG-AAAGAG-TGCCACTGACT--TGTGGGCTTTG-AAAG-G
* * * *
1420645 TTGCCACTAGCTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGACTTTAAAAAGAGTGCCACT
58 GTGCCACTA-CTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACT
* *
1420710 AACTTGTGGGCTTTGAAAAGAGTGCCATTGACTTGTGGGCTTTGAAAG
122 GACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
1420758 GGTGCCACTGACTTATGGGCTTTGAAAGAGTG-C-C--ACTTCTGGGCTTTGAAAGAGTGCCACT
1 GGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
* *
1420819 AACTTATGGGCTTTGAAAGGGTACCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
66 -ACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
*
1420884 GGCATTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
130 GGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
1420924 GGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
1 GGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
*
1420989 GACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
66 -ACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
1421054 GGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
130 GGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
* * * * *
1421094 GATGCCACTGACTTGTGGGCTTTGAAAGGGTGCTATTGACTGGTGGGCTTTGAAAGGG
1 GGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGG
1421152 ATGAACATTC
Statistics
Matches: 363, Mismatches: 26, Indels: 18
0.89 0.06 0.04
Matches are distributed among these distances:
166 133 0.37
167 6 0.02
168 11 0.03
170 181 0.50
172 1 0.00
173 1 0.00
174 2 0.01
175 6 0.02
176 10 0.03
177 1 0.00
178 11 0.03
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.28
Consensus pattern (169 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
ACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
GCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:1422386 original size:1 final size:1
Alignment explanation
Indices: 1422382--1422424 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
1422372 TTTTTTGCTA
* * * *
1422382 TTTTTTCTTGTTTTTTTTTTTGTTTTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1422425 GGGTGTAAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (1 bp):
T
Found at i:1422401 original size:14 final size:13
Alignment explanation
Indices: 1422371--1422424 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
1422361 CCCCTTTCTG
* *
1422371 TTTTTTTGCTATT
1 TTTTTTTGTTTTT
*
1422384 TTTTCTTG-TTTT
1 TTTTTTTGTTTTT
1422396 TTTTTTTGTTTTTT
1 TTTTTTTG-TTTTT
1422410 TTTTTTTGTTTTT
1 TTTTTTTGTTTTT
1422423 TT
1 TT
1422425 GGGTGTAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
12 10 0.28
13 14 0.39
14 12 0.33
ACGTcount: A:0.02, C:0.04, G:0.07, T:0.87
Consensus pattern (13 bp):
TTTTTTTGTTTTT
Found at i:1422412 original size:12 final size:12
Alignment explanation
Indices: 1422371--1422424 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
1422361 CCCCTTTCTG
*
1422371 TTTTTTTGCTATT
1 TTTTTTTG-TTTT
*
1422384 TTTTCTTGTTTT
1 TTTTTTTGTTTT
1422396 TTTTTTTGTTTT
1 TTTTTTTGTTTT
*
1422408 TTTTTTT-TTGT
1 TTTTTTTGTTTT
1422419 TTTTTT
1 TTTTTT
1422425 GGGTGTAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.24
12 21 0.57
13 7 0.19
ACGTcount: A:0.02, C:0.04, G:0.07, T:0.87
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:1427427 original size:19 final size:19
Alignment explanation
Indices: 1427403--1427455 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
1427393 TGTCAATGAT
1427403 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1427422 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1427441 TTGTATCGATACATA
1 TTGTATCGATACATA
1427456 TGAAGCTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1427687 original size:21 final size:20
Alignment explanation
Indices: 1427676--1427735 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 20
1427666 AATCAAAAGT
1427676 AAACACAAAAAACAAAAAAAA
1 AAACACAAAAAA-AAAAAAAA
1427697 AAACACAAAAAAAAAAAACAAA
1 AAACAC-AAAAAAAAAAA-AAA
1427719 AAACACACACAAAAAAA
1 AAACACA-A-AAAAAAA
1427736 GTGTAAAGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.34
22 16 0.46
23 7 0.20
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (20 bp):
AAACACAAAAAAAAAAAAAA
Found at i:1427690 original size:7 final size:7
Alignment explanation
Indices: 1427680--1427723 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
1427670 AAAAGTAAAC
1427680 ACAAAAA
1 ACAAAAA
1427687 ACAAAAA
1 ACAAAAA
1427694 A-AAAAA
1 ACAAAAA
1427700 CACAAAAA
1 -ACAAAAA
1427708 A-AAAAA
1 ACAAAAA
1427714 ACAAAAA
1 ACAAAAA
1427721 ACA
1 ACA
1427724 CACACAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 11 0.32
7 18 0.53
8 5 0.15
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (7 bp):
ACAAAAA
Found at i:1427698 original size:13 final size:13
Alignment explanation
Indices: 1427682--1427735 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
1427672 AAGTAAACAC
1427682 AAAAAACAAAAAA
1 AAAAAACAAAAAA
1427695 AAAAACACAAAAAA
1 AAAAA-ACAAAAAA
1427709 AAAAAACAAAAAA
1 AAAAAACAAAAAA
* * *
1427722 CACACACAAAAAA
1 AAAAAACAAAAAA
1427735 A
1 A
1427736 GTGTAAAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
13 23 0.64
14 13 0.36
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAA
Found at i:1429030 original size:30 final size:29
Alignment explanation
Indices: 1428955--1429161 Score: 222
Period size: 30 Copynumber: 6.9 Consensus size: 29
1428945 TTCAAATACC
* * * *
1428955 TTCTTAAAGTCCACGACTCAGTGGTAATCTC
1 TTCTCAAAGTCCACGATTCAGTGG-CAT-TT
*
1428986 TTCTCAAAGCCCACGATTCAGTGGCATTT
1 TTCTCAAAGTCCACGATTCAGTGGCATTT
* *
1429015 TGTCTCATAGTCCACGATTCAGTGGCAATCTC
1 T-TCTCAAAGTCCACGATTCAGTGGC-AT-TT
* *
1429047 TTCTCAAAGCCCACGACTCAGTGGCATTT
1 TTCTCAAAGTCCACGATTCAGTGGCATTT
1429076 TGTCTCAAAGTCCACGATTCAGTGGCATTT
1 T-TCTCAAAGTCCACGATTCAGTGGCATTT
*
1429106 TATCTCAAAGTCCACGACTCAGTGGCATCTT
1 T-TCTCAAAGTCCACGATTCAGTGGCAT-TT
1429137 TTCT--AAGTCCACGACTT-AGTGGCAT
1 TTCTCAAAGTCCACGA-TTCAGTGGCAT
1429162 CCTTTTTCTT
Statistics
Matches: 153, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
28 18 0.12
29 5 0.03
30 81 0.53
31 47 0.31
32 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (29 bp):
TTCTCAAAGTCCACGATTCAGTGGCATTT
Found at i:1429057 original size:61 final size:60
Alignment explanation
Indices: 1428961--1429160 Score: 275
Period size: 61 Copynumber: 3.3 Consensus size: 60
1428951 TACCTTCTTA
* * *
1428961 AAGTCCACGACTCAGTGGTAATCTCTTCTCAAAGCCCACGATTCAGTGGCATTTTGTCTC
1 AAGTCCACGATTCAGTGGCAATCTCTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCTC
1429021 ATAGTCCACGATTCAGTGGCAATCTCTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCTC
1 A-AGTCCACGATTCAGTGGCAATCTCTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCTC
* *
1429082 AAAGTCCACGATTCAGTGGC-AT-TTTATCTCAAAGTCCACGACTCAGTGGCATCTTT-TCT-
1 -AAGTCCACGATTCAGTGGCAATCTCT-TCTCAAAGCCCACGACTCAGTGGCAT-TTTGTCTC
1429141 AAGTCCACGACTT-AGTGGCA
1 AAGTCCACGA-TTCAGTGGCA
1429161 TCCTTTTTCT
Statistics
Matches: 129, Mismatches: 5, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
58 16 0.12
59 4 0.03
60 31 0.24
61 77 0.60
62 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (60 bp):
AAGTCCACGATTCAGTGGCAATCTCTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCTC
Found at i:1429112 original size:91 final size:90
Alignment explanation
Indices: 1428954--1429162 Score: 280
Period size: 91 Copynumber: 2.3 Consensus size: 90
1428944 CTTCAAATAC
* * *
1428954 CTTCTTAAAGTCCACGACTCAGTGGTAATCTCTTCTCAAAGCCCACGATTCAGTGGCATTTTGTC
1 CTTCTCAAAGTCCACGACTCAGTGG-CATCTCTTCTCAAAGCCCACGATTCAGTGGCATTTTATC
* *
1429019 TCATAGTCCACGATTCAGTGGCAATCT
65 TCAAAGTCCACGACTCAGTGGC-ATCT
* * *
1429046 CTTCTCAAAGCCCACGACTCAGTGGCAT-TTTGTCTCAAAGTCCACGATTCAGTGGCATTTTATC
1 CTTCTCAAAGTCCACGACTCAGTGGCATCTCT-TCTCAAAGCCCACGATTCAGTGGCATTTTATC
1429110 TCAAAGTCCACGACTCAGTGGCATCT
65 TCAAAGTCCACGACTCAGTGGCATCT
* *
1429136 -TT-TCTAAGTCCACGACTTAGTGGCATC
1 CTTCTCAAAGTCCACGACTCAGTGGCATC
1429163 CTTTTTCTTT
Statistics
Matches: 104, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
88 21 0.20
89 2 0.02
90 6 0.06
91 52 0.50
92 23 0.22
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.31
Consensus pattern (90 bp):
CTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGCCCACGATTCAGTGGCATTTTATCT
CAAAGTCCACGACTCAGTGGCATCT
Found at i:1429192 original size:91 final size:91
Alignment explanation
Indices: 1428992--1429293 Score: 254
Period size: 91 Copynumber: 3.2 Consensus size: 91
1428982 TCTCTTCTCA
* * * * * *
1428992 AAGCCCACGATTCAGTGGCATTTTGTCTCATAGTCCACGATTCAGTGGCAATCTCTTCTCAAAGC
1 AAGCCCACAACTCAGTGGCATTTTATCTCAAAGTCCACGACTCAGTGGC-ATCT-TT-TCTAAGC
* * **
1429057 CCACGACTCAGTGGCAT--TTTGTC-TCA
63 CCACGACTTAGTGGCATCCTTTTTCTTTT
* * * *
1429083 AAGTCCACGATTCAGTGGCATTTTATCTCAAAGTCCACGACTCAGTGGCATCTTTTCTAAGTCCA
1 AAGCCCACAACTCAGTGGCATTTTATCTCAAAGTCCACGACTCAGTGGCATCTTTTCTAAGCCCA
1429148 CGACTTAGTGGCATCCTTTTTCTTTT
66 CGACTTAGTGGCATCCTTTTTCTTTT
* * * *
1429174 AAGCCCACAACTCCGTGGCACTCTTTTTTCTTCCAAGCCCACGACTCAGTGGCATCCTTTTTCTG
1 AAGCCCACAACTCAGTGGCA---TTTTATC-TCAAAGTCCACGACTCAGTGGCAT-C-TTTTC--
*
1429239 TAAGCCCACAACTCT-GTGGCA-CTCTTTTTCCTTTT
58 TAAGCCCACGACT-TAGTGGCATC-CTTTTT-CTTTT
* *
1429274 AAGTCCACAACTCTGTGGCA
1 AAGCCCACAACTCAGTGGCA
1429294 CCCTTTTAAG
Statistics
Matches: 176, Mismatches: 21, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
88 21 0.12
89 2 0.01
90 9 0.05
91 62 0.35
94 6 0.03
95 22 0.12
96 1 0.01
97 5 0.03
98 1 0.01
99 23 0.13
100 24 0.14
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (91 bp):
AAGCCCACAACTCAGTGGCATTTTATCTCAAAGTCCACGACTCAGTGGCATCTTTTCTAAGCCCA
CGACTTAGTGGCATCCTTTTTCTTTT
Found at i:1429212 original size:34 final size:34
Alignment explanation
Indices: 1429155--1429300 Score: 172
Period size: 34 Copynumber: 4.4 Consensus size: 34
1429145 CCACGACTTA
* *
1429155 GTGGCA-TCCTTTTTCTTTTAAGCCCACAACTCC
1 GTGGCACTCTTTTTTCTTTTAAGCCCACAACTCT
** * *
1429188 GTGGCACTCTTTTTTCTTCCAAGCCCACGACTCA
1 GTGGCACTCTTTTTTCTTTTAAGCCCACAACTCT
* *
1429222 GTGGCA-TCCTTTTTC-TGTAAGCCCACAACTCT
1 GTGGCACTCTTTTTTCTTTTAAGCCCACAACTCT
* *
1429254 GTGGCACTCTTTTTCCTTTTAAGTCCACAACTCT
1 GTGGCACTCTTTTTTCTTTTAAGCCCACAACTCT
*
1429288 GTGGCACCCTTTT
1 GTGGCACTCTTTT
1429301 AAGCCCACAA
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
32 19 0.20
33 21 0.22
34 55 0.58
ACGTcount: A:0.17, C:0.32, G:0.14, T:0.36
Consensus pattern (34 bp):
GTGGCACTCTTTTTTCTTTTAAGCCCACAACTCT
Found at i:1429264 original size:66 final size:67
Alignment explanation
Indices: 1429145--1429300 Score: 215
Period size: 66 Copynumber: 2.3 Consensus size: 67
1429135 TTTTCTAAGT
* * *
1429145 CCACGACTTAGTGGCATCCTTTTTCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTCTTCCAA
1 CCACGACTCAGTGGCATCCTTTTTCTTGTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCCAA
1429210 GC
66 GC
* **
1429212 CCACGACTCAGTGGCATCCTTTTTC-TGTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAA
1 CCACGACTCAGTGGCATCCTTTTTCTTGTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCCAA
*
1429276 GT
66 GC
* * *
1429278 CCACAACTCTGTGGCACCCTTTT
1 CCACGACTCAGTGGCATCCTTTT
1429301 AAGCCCACAA
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
66 55 0.70
67 24 0.30
ACGTcount: A:0.18, C:0.33, G:0.14, T:0.35
Consensus pattern (67 bp):
CCACGACTCAGTGGCATCCTTTTTCTTGTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCCAA
GC
Found at i:1429299 original size:27 final size:27
Alignment explanation
Indices: 1429268--1429320 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1429258 CACTCTTTTT
* *
1429268 CCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGCCCACAACTCAGTGGCAC
*
1429295 CCTTTTAAGCCCACAAGTCAGTGGCA
1 CCTTTTAAGCCCACAACTCAGTGGCA
1429321 TTTTTTCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCAGTGGCAC
Found at i:1429399 original size:30 final size:33
Alignment explanation
Indices: 1429329--1429399 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
1429319 CATTTTTTCC
*
1429329 AAAGCCCACACAAGTCGGTGGCAACCATTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCACTCTCT
*
1429362 AAAGCCCACACAAGTTGGTGGCAACC-CTC-CT
1 AAAGCCCACACAAGTCGGTGGCAACCACTCTCT
1429393 -AAGCCCA
1 AAAGCCCA
1429400 ATATAGCTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 7 0.19
31 2 0.06
32 2 0.06
33 25 0.69
ACGTcount: A:0.31, C:0.35, G:0.18, T:0.15
Consensus pattern (33 bp):
AAAGCCCACACAAGTCGGTGGCAACCACTCTCT
Found at i:1429916 original size:206 final size:205
Alignment explanation
Indices: 1429569--1431234 Score: 1663
Period size: 206 Copynumber: 8.2 Consensus size: 205
1429559 CATTGGCACC
* * * * *
1429569 TTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCA-CC-TT-T-AACTTTAAGTCCAATG
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTCTCATCTTTAAGTCCAATA
* * *
1429630 TAGCTGGCCTTGAATCAGCACATTGGCA---C-C-T-TTAAGTCTAATATCGTTGGCCTTGAATC
66 TAGCTGGCCTTGAATCAGCATATTGGCACCTCTCATCTTAAGTCCAATATCGCTGGCCTTGAATC
* * * *
1429689 AGCATATTGGCGCCCTCGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACAT
131 AGCATATTGGCGCCCTCATCATC-TTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGC-G
** *
1429754 CTTTTTCCTGATCT
194 C--CCTCCTCATCT
* *
1429768 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TT-T-ATC-TTAAGTCCAATA
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTCTCATCTTTAAGTCCAATA
* * *
1429828 TCGTTGGCCTTGAATCAGCATATTGGCACCCTCATCATCTTAAGTCCAATATCGCTTGCCTTGAA
66 TAGCTGGCCTTGAATCAGCATATTGGCA-CCTC-TCATCTTAAGTCCAATATCGCTGGCCTTGAA
* * * *
1429893 TCAGCATATTGGCGCCCTCGTCATCTTTAAATCCAATGTCGCTGGCCTTGAATCAGCACATTGAC
129 TCAGCATATTGGCGCCCTCATCATC-TTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGC
* * * *
1429958 ATCCTTTTTCTCACCT
193 -GCC--CTCCTCATCT
* * ** * * *
1429974 TTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGTA-CC-TT-T-AGCTTTAAGTCAAATG
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTCTCATCTTTAAGTCCAATA
* *
1430035 TAGCTGGCCTTGAATCAGCACATTGGCA---C-C-T-TTAAGTCCAATATAGCTGGCCTTGAATC
66 TAGCTGGCCTTGAATCAGCATATTGGCACCTCTCATCTTAAGTCCAATATCGCTGGCCTTGAATC
* * * * * *
1430094 AGCATATTGGCACCTTTAGC-T-TTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-G--
131 AGCATATTGGCGCCCTCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCGCC
*
1430153 -----CACCT
196 CTCCTCATCT
* * * *
1430158 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TT-T-AGCTTTAAGTCCAATG
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTCTCATCTTTAAGTCCAATA
*
1430219 TAGCTGGCCTTGAATCAGCACATTGGCA---C-C-T-TTAAGTCCAATATCGCTGGCCTTGAATC
66 TAGCTGGCCTTGAATCAGCATATTGGCACCTCTCATCTTAAGTCCAATATCGCTGGCCTTGAATC
* *
1430278 AGCATATTGGCGCCCTCATCATCTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCGCC
131 AGCATATTGGCGCCCTCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCGCC
*
1430343 CTCATCATCT
196 CTCCTCATCT
* *
1430353 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAGTCCAA
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCC--TTTCTCATCTTTAAGTCCAA
* *
1430418 TATAGCTGGCCTTGAATAAGCATATTGGCACCT-TTATCTTAAGTCCAATATCGCTGGCCTTGAA
64 TATAGCTGGCCTTGAATCAGCATATTGGCACCTCTCATCTTAAGTCCAATATCGCTGGCCTTGAA
* *
1430482 TCAACATATTGGCGCCCTCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCG
129 TCAGCATATTGGCGCCCTCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCG
*
1430547 CCCTCGTCATCT
194 CCCTCCTCATCT
* * *
1430559 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAACATCCTTTTTCTCATCTTTAAGTCCAA
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCC--TTTCTCATCTTTAAGTCCAA
* *
1430624 TATAGCTGGTCTTGAATCAGCATATTGGCACCT-TTATCTTAAGTCCAATATCGCTGGCCTTGAA
64 TATAGCTGGCCTTGAATCAGCATATTGGCACCTCTCATCTTAAGTCCAATATCGCTGGCCTTGAA
* * * *
1430688 TCAGCATATTGGCGCCCTTATCATCTTAAGTCTAATATCGCTGGCCTTGAATTAGCATATTGGCG
129 TCAGCATATTGGCGCCCTCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCG
* *
1430753 CCCTCGTCATAT
194 CCCTCCTCATCT
* *
1430765 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAGTCCAA
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCC--TTTCTCATCTTTAAGTCCAA
* * *
1430830 TATAGCTGGCCTTGAATCAGCATATTGGCATCC-CTTTATCTTAAGTCCAATGTAGCTGGCCTTG
64 TATAGCTGGCCTTGAATCAGCATATTGGCA-CCTC-TCATCTTAAGTCCAATATCGCTGGCCTTG
* * * *
1430894 AATCAGTACATTGGC-ACCTC--CATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
127 AATCAGCATATTGGCGCCCTCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGG
*
1430956 CGCCCTCGTCATCT
192 CGCCCTCCTCATCT
* * *
1430970 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCCCAA
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCC--TTTCTCATCTTTAAGTCCAA
* * * * *
1431035 TATCGTTAGCCGTGAATCAACATATTGGTATCTTTATCACTTTTCTCACCTTCATCTTTAAGTCC
64 TATAGCTGGCCTTGAATCAGCATATTGG---------CAC----CT---C-TCATC-TTAAGTCC
* * * * * *
1431100 AATATTGCTGGCCTTGAATCCGCATATTGGCGTCTTCATCATCTTTGAAGTCCAATGTCGTTGGC
111 AATATCGCTGGCCTTGAATCAGCATATTGGCGCCCTCATCATC-TT-AAGTCCAATATCGCTGGC
* *** *
1431165 CTTAAATCAGCACATTGGCATTCTTCTCATCT
174 CTTGAATCAGCACATTGGCGCCCTCCTCATCT
* * * * *
1431197 TCAAGTCTAAATGTCGCTGGCCATGAATCAGCACATTG
1 TTAAGTC-CAATATAGCTGGCCTTGAATCAGCACATTG
1431235 TCATTTTTCG
Statistics
Matches: 1303, Mismatches: 103, Indels: 93
0.87 0.07 0.06
Matches are distributed among these distances:
184 137 0.11
185 1 0.00
186 32 0.02
187 1 0.00
188 1 0.00
195 40 0.03
196 36 0.03
198 37 0.03
199 89 0.07
200 2 0.00
201 41 0.03
202 1 0.00
203 1 0.00
204 1 0.00
205 142 0.11
206 533 0.41
207 40 0.03
208 40 0.03
213 1 0.00
214 2 0.00
217 1 0.00
221 6 0.00
222 34 0.03
223 3 0.00
225 4 0.00
226 2 0.00
227 47 0.04
228 28 0.02
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (205 bp):
TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTCTCATCTTTAAGTCCAATA
TAGCTGGCCTTGAATCAGCATATTGGCACCTCTCATCTTAAGTCCAATATCGCTGGCCTTGAATC
AGCATATTGGCGCCCTCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCGCC
CTCCTCATCT
Found at i:1430618 original size:640 final size:637
Alignment explanation
Indices: 1429399--1431006 Score: 2148
Period size: 640 Copynumber: 2.5 Consensus size: 637
1429389 TCCTAAGCCC
*
1429399 AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAGCTTTAAGTCCAATGTAGCTGGCCTTG
1 AATATAGCTGGCCTTGAATCAGCATATTGGCACC-----CTTTAAGTCCAATATAGCTGGCCTTG
* * * *
1429464 AATCAGCACATTGGCA-C---CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATA-T-GCACC
61 AATCAGCATATTGGCACCTTACTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
* * *
1429523 TTTAGCTTAAGTCCAATGTAGCT-GCCTTGAATCAGC-CATTGGCA-C----CTTAAGTCCAATA
126 --T---TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTACTTAAGTCCAATG
* * * *
1429581 TAGCTAGCCTTGAATCAGCATATTGGCACCTTTAACTTTAAGTCCAATGTAGCTGGCCTTGAATC
186 TAGCTGGCCTTGAATCAGCACATTGGCACC-----CTTTAAGTCCAATATCGCTGGCCTTGAATC
* * * *
1429646 AGCACATT-G-G----CA-CCT-TTAAGTCTAATATCGTTGGCCTTGAATCAGCATATTGGCGCC
246 AGCATATTGGCGCCCTCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCC
* *
1429703 CTCGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCTTTTTCCTGATCT
311 CTCATCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCTTTTTCCTCATCT
* *
1429768 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTAAGTCCAATATCGTT
376 TTAAGTCCAATATAGCTGGCCTTGAATAAGCATATTGGCACCTTTATCTTAAGTCCAATATCGCT
* *
1429833 GGCCTTGAATCAGCATATTGGCACCCTCATCATCTTAAGTCCAATATCGCTTGCCTTGAATCAGC
441 GGCCTTGAATCAACATATTGGCACCCTCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGC
*
1429898 ATATTGGCGCCCTCGTCATCTTTAAATCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCCT
506 ATATTGGCGCCCTCGTCATCTTTAAATCCAATGTCGCTGGCCTTGAATCAGCACATTAACATCCT
*
1429963 TTTTCTCACCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGTACCTTTAGCTTTAAG
571 TTTTCTCACCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAGC-TTAAG
1430028 TCA
635 TCA
* *
1430031 AATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTTTAAGTCCAATATAGCTGGCCTTGAATCA
1 AATATAGCTGGCCTTGAATCAGCATATTGGCACCCTTTAAGTCCAATATAGCTGGCCTTGAATCA
1430095 GCATATTGGCACCTTTAGCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
66 GCATATTGGCACC-TTA-CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
1430160 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAGCTTTAAGTCCAATGTAGCTG
129 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTA-C-TTAAGTCCAATGTAGCTG
1430225 GCCTTGAATCAGCACATTGGCA-CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
192 GCCTTGAATCAGCACATTGGCACCCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
*
1430289 GCCCTCATCATCTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCGCCCTCATCATCTT
257 GCCCTCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCCTCATCATCTT
1430354 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCCTTTTT-CTCATCTTTAAGTCCAA
322 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACAT-CTTTTTCCTCATCTTTAAGTCCAA
1430418 TATAGCTGGCCTTGAATAAGCATATTGGCACCTTTATCTTAAGTCCAATATCGCTGGCCTTGAAT
386 TATAGCTGGCCTTGAATAAGCATATTGGCACCTTTATCTTAAGTCCAATATCGCTGGCCTTGAAT
*
1430483 CAACATATTGGCGCCCTCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGC
451 CAACATATTGGCACCCTCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGC
* *
1430548 CCTCGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAACATCCTTTTTCTCATC
516 CCTCGTCATCTTTAAATCCAATGTCGCTGGCCTTGAATCAGCACATTAACATCCTTTTTCTCACC
* * * *
1430613 TTTAAGTCCAATATAGCTGGTCTTGAATCAGCATATTGGCACCTTTATCTTAAGTCC
581 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAGCTTAAGTCA
* * * *
1430670 AATATCGCTGGCCTTGAATCAGCATATTGGCGCCCTTATCATCTTAAGTCTAATATCGCTGGCCT
1 AATATAGCTGGCCTTGAATCAGCATATTGGC-ACC----C-T-TTAAGTCCAATATAGCTGGCCT
* * * *
1430735 TGAATTAGCATATTGGCGCCCTCGTCATATTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
59 TGAATCAGCATATTGGC-ACCT--T-A-CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
*
1430800 TGACATCCTTTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCCCT
119 TGGCA----------C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--CCT
*
1430865 TTATCTTAAGTCCAATGTAGCTGGCCTTGAATCAGTACATTGGCACCTCCATCTTAAGTCCAATA
170 TTA-CTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-CC-T-TTAAGTCCAATA
* *
1430930 TCGCTGGCCTTGAATCAGCATATTGGCGCCCTCGTCATCTTTAAGTCCAATGTCGCTGGCCTTGA
230 TCGCTGGCCTTGAATCAGCATATTGGCGCCCTCATCATC-TTAAGTCCAATATCGCTGGCCTTGA
*
1430995 ATCAGCACATTG
294 ATCAGCATATTG
1431007 ACATCCTTTT
Statistics
Matches: 866, Mismatches: 52, Indels: 79
0.87 0.05 0.08
Matches are distributed among these distances:
626 40 0.05
627 1 0.00
629 16 0.02
630 13 0.02
631 8 0.01
632 100 0.12
633 2 0.00
634 6 0.01
637 2 0.00
638 39 0.05
639 37 0.04
640 337 0.39
641 7 0.01
645 1 0.00
646 1 0.00
647 37 0.04
648 2 0.00
649 1 0.00
650 40 0.05
660 1 0.00
662 42 0.05
663 39 0.05
664 7 0.01
666 2 0.00
667 1 0.00
668 50 0.06
669 34 0.04
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (637 bp):
AATATAGCTGGCCTTGAATCAGCATATTGGCACCCTTTAAGTCCAATATAGCTGGCCTTGAATCA
GCATATTGGCACCTTACTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAA
GTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTACTTAAGTCCAATGTAGCTGGCCT
TGAATCAGCACATTGGCACCCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCC
TCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCCTCATCATCTTTAAG
TCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCTTTTTCCTCATCTTTAAGTCCAATATAG
CTGGCCTTGAATAAGCATATTGGCACCTTTATCTTAAGTCCAATATCGCTGGCCTTGAATCAACA
TATTGGCACCCTCATCATCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCCTCG
TCATCTTTAAATCCAATGTCGCTGGCCTTGAATCAGCACATTAACATCCTTTTTCTCACCTTTAA
GCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAGCTTAAGTCA
Found at i:1431051 original size:55 final size:52
Alignment explanation
Indices: 1430248--1431062 Score: 814
Period size: 55 Copynumber: 15.8 Consensus size: 52
1430238 ACATTGGCAC
* * *
1430248 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-GCCCTCATCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCCTTC-TCAT
* * * *
1430300 C-TTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGC-GCCCTCATCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCCTTC-TCAT
* *
1430351 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCC---TTCTCAT
* * *
1430406 CTTTAAGTCCAATATAGCTGGCCTTGAATAAGCATATTGGCA-CCTT-T-AT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCCTTCTCAT
* * * *
1430455 C-TTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGC-GCCCTCATCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCCTTC-TCAT
* * *
1430506 C-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-GCCCTCGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCCTTC-TCAT
* **
1430557 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCC---TTCTCAT
* * *
1430612 CTTTAAGTCCAATATAGCTGGTCTTGAATCAGCATATTGGCA-CCTT-T-AT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCCTTCTCAT
* ** *
1430661 C-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCCTTATCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCCTTCTCAT
* * * * *
1430712 C-TTAAGTCTAATATCGCTGGCCTTGAATTAGCATATTGGC-GCCCTCGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCCTTC-TCAT
* * *
1430763 ATTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCC---TTCTCAT
* *
1430818 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCCCTT-T-AT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAT-CCTTCTCAT
* * *
1430869 C-TTAAGTCCAATGTAGCTGGCCTTGAATCAGTACATTGGCA-CC-TC-CAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCCTTCTCAT
* * *
1430917 C-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-GCCCTCGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCCTTC-TCAT
* *
1430968 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCC---TTCTCAT
* * * * * *
1431023 CTTTAAGCCCAATATCGTTAGCCGTGAATCAACATATTGG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGG
1431063 TATCTTTATC
Statistics
Matches: 657, Mismatches: 71, Indels: 67
0.83 0.09 0.08
Matches are distributed among these distances:
47 1 0.00
48 118 0.18
49 12 0.02
50 44 0.07
51 157 0.24
52 142 0.22
53 10 0.02
54 4 0.01
55 159 0.24
56 10 0.02
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (52 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCCTTCTCAT
Found at i:1431165 original size:53 final size:52
Alignment explanation
Indices: 1431086--1431234 Score: 174
Period size: 53 Copynumber: 2.8 Consensus size: 52
1431076 TTTCTCACCT
* * * *
1431086 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCCGCATATTGGC-GTCTTC
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAGTCTTC
* * *
1431137 ATCATCTTTGAAGTCCAATGTCGTTGGCCTTAAATCAGCACATTGGCATTCTTC
1 -TCATCTTT-AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAGTCTTC
* * *
1431191 TCATCTTCAAGTCTAAATGTCGCTGGCCATGAATCAGCACATTG
1 TCATCTTTAAGTC-CAATGTCGCTGGCCTTGAATCAGCACATTG
1431235 TCATTTTTCG
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
52 13 0.16
53 64 0.78
54 5 0.06
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (52 bp):
TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAGTCTTC
Found at i:1431996 original size:19 final size:19
Alignment explanation
Indices: 1431972--1432037 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
1431962 TGTCAACGAT
1431972 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1431991 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
1432005 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1432023 TTGTATCGATACATA
1 TTGTATCGATACATA
1432038 TGAAGCTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.27
15 2 0.05
17 2 0.05
19 26 0.63
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1432009 original size:32 final size:32
Alignment explanation
Indices: 1431973--1432035 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
1431963 GTCAACGATT
1431973 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1432005 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
1432036 TATGAAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1432010 original size:13 final size:13
Alignment explanation
Indices: 1431992--1432016 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1431982 ACATAAGTGT
1431992 TGTATCGATACAA
1 TGTATCGATACAA
1432005 TGTATCGATACA
1 TGTATCGATACA
1432017 TAAGTGTTGT
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:1432139 original size:52 final size:52
Alignment explanation
Indices: 1432078--1432206 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1432068 CACTGATCTT
1432078 TGTATCGATACATGCAGGCAAATTTACCTAGATGCATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTACCTAGATGCATCGATACACTATGAAA
* * * *
1432130 TGTACCGATACATACAGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTACCTAGATGCATCGATACACTATGAAA
1432182 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1432207 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTACCTAGATGCATCGATACACTATGAAA
Found at i:1443266 original size:19 final size:19
Alignment explanation
Indices: 1443242--1443282 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1443232 AAATAATGGG
*
1443242 AATGAATAGCAAGAAAAAA
1 AATGAACAGCAAGAAAAAA
* *
1443261 AATGAACATCAATAAAAAA
1 AATGAACAGCAAGAAAAAA
1443280 AAT
1 AAT
1443283 AGCCTTTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.07, G:0.10, T:0.15
Consensus pattern (19 bp):
AATGAACAGCAAGAAAAAA
Found at i:1447560 original size:31 final size:31
Alignment explanation
Indices: 1447492--1447562 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
1447482 GATACATTGA
* *
1447492 AAAATGTATCGATACATCCGGGTAAAAAGAC
1 AAAATGTATCGATACATCCAGATAAAAAGAC
* * * * *
1447523 AGAATGTATCGATACATCTAGATGAAAGGAT
1 AAAATGTATCGATACATCCAGATAAAAAGAC
1447554 AAAATGTAT
1 AAAATGTAT
1447563 TAATATATTG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (31 bp):
AAAATGTATCGATACATCCAGATAAAAAGAC
Found at i:1451045 original size:88 final size:88
Alignment explanation
Indices: 1450732--1451052 Score: 303
Period size: 88 Copynumber: 3.6 Consensus size: 88
1450722 TTGTTGTGTC
* * *
1450732 ATTAGTCAAATATTTTCTGTCATGTCAGAAGGAATCTGATACCTTATGCATCTGTCATATCTTTT
1 ATTAGTCAAATATTTTCTATCATGTCAGAAGGAATCTAATACCTTATGCATCTGTCACATCTTTT
* * *
1450797 -ATTTTTCAAGAATTTTATTATA-C
66 GAGTTTT-AAGAAATTTATTA-AGT
* * * * * * * * *
1450820 ATTAGTCAAATATTTTTTGTCGTATAAGAATGAGTCTTATTCACC--ATGCATCTATCACATCTT
1 ATTAGTCAAATATTTTCTATCATGTCAGAAGGAATC-TAAT-ACCTTATGCATCTGTCACATCTT
* ** * * *
1450883 TCG-GATTCCAAAAAAATTATCAAGT
64 TTGAG-TTTTAAGAAATTTATTAAGT
* *
1450908 ATTAGTCAAATATTTTCTATCATGTTAGAAGGAATCTAATA-CTCCATGCATCTGTCACATCTTT
1 ATTAGTCAAATATTTTCTATCATGTCAGAAGGAATCTAATACCT-TATGCATCTGTCACATCTTT
*
1450972 TGAGTTTTAAGAAATTTATTAGGT
65 TGAGTTTTAAGAAATTTATTAAGT
* **
1450996 ATTAGTCAAATATTTTCTATCGTGTCAGAAAAAATCTAATACCTTATGCATCTGTCA
1 ATTAGTCAAATATTTTCTATCATGTCAGAAGGAATCTAATACCTTATGCATCTGTCA
1451053 TATTTTCCAA
Statistics
Matches: 183, Mismatches: 40, Indels: 20
0.75 0.16 0.08
Matches are distributed among these distances:
85 1 0.01
86 1 0.01
87 4 0.02
88 167 0.91
89 7 0.04
90 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (88 bp):
ATTAGTCAAATATTTTCTATCATGTCAGAAGGAATCTAATACCTTATGCATCTGTCACATCTTTT
GAGTTTTAAGAAATTTATTAAGT
Found at i:1451047 original size:176 final size:176
Alignment explanation
Indices: 1450732--1451048 Score: 408
Period size: 176 Copynumber: 1.8 Consensus size: 176
1450722 TTGTTGTGTC
* * * *
1450732 ATTAGTCAAATATTTTCTGTCATGTCAGAAGGAATCTGATACCTTATGCATCTGTCATATCTTTT
1 ATTAGTCAAATATTTTCTATCATGTCAGAAGGAATCTAATACCTCATGCATCTGTCACATCTTTT
* * * * * ** * *
1450797 ATTTTTCAAGAATTTTATTATACATTAGTCAAATATTTTTTGTCGTATAAGAATGAGTCTTATTC
66 AGTTTTCAAGAAATTTATTAGACATTAGTCAAATATTTTCTATCGTATAAGAAAAAATCTTAATC
1450862 ACCATGCATCTATCACATCTTTCGGATTCCAAAAAAATTATCAAGT
131 ACCATGCATCTATCACATCTTTCGGATTCCAAAAAAATTATCAAGT
*
1450908 ATTAGTCAAATATTTTCTATCATGTTAGAAGGAATCTAATA-CTCCATGCATCTGTCACATCTTT
1 ATTAGTCAAATATTTTCTATCATGTCAGAAGGAATCTAATACCT-CATGCATCTGTCACATCTTT
** * *
1450972 TGAGTTTT-AAGAAATTTATTAGGTATTAGTCAAATATTTTCTATCGTGTCAGAAAAAATC-TAA
65 T-AGTTTTCAAGAAATTTATTAGACATTAGTCAAATATTTTCTATCGTATAAGAAAAAATCTTAA
1451035 T-ACCTTATGCATCT
129 TCACC--ATGCATCT
1451049 GTCATATTTT
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
174 3 0.03
175 5 0.04
176 106 0.89
177 5 0.04
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (176 bp):
ATTAGTCAAATATTTTCTATCATGTCAGAAGGAATCTAATACCTCATGCATCTGTCACATCTTTT
AGTTTTCAAGAAATTTATTAGACATTAGTCAAATATTTTCTATCGTATAAGAAAAAATCTTAATC
ACCATGCATCTATCACATCTTTCGGATTCCAAAAAAATTATCAAGT
Found at i:1451458 original size:15 final size:15
Alignment explanation
Indices: 1451414--1451459 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1451404 CATCGCCGGT
*
1451414 GCTTCTTCCTAAATG
1 GCTTCTTCCTAAGTG
* * *
1451429 GCTTATTCTTGAGTG
1 GCTTCTTCCTAAGTG
1451444 GCTTCTTCCTAAGTG
1 GCTTCTTCCTAAGTG
1451459 G
1 G
1451460 TTTCATCTGT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (15 bp):
GCTTCTTCCTAAGTG
Found at i:1455709 original size:29 final size:30
Alignment explanation
Indices: 1455637--1455709 Score: 69
Period size: 30 Copynumber: 2.4 Consensus size: 30
1455627 ATTTATATAT
* *
1455637 TATGTAAACTTTATCATATAAAGAATAAATA
1 TATGTAAAC-TTATAATATAAACAATAAATA
* * *
1455668 TATCTAATA-TTATAATGTAAACATTAAA-A
1 TATGTAA-ACTTATAATATAAACAATAAATA
1455697 TATGTAAACTTAT
1 TATGTAAACTTAT
1455710 TTATATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
28 1 0.03
29 11 0.32
30 15 0.44
31 6 0.18
32 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.38
Consensus pattern (30 bp):
TATGTAAACTTATAATATAAACAATAAATA
Found at i:1455924 original size:11 final size:11
Alignment explanation
Indices: 1455910--1455935 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1455900 AAACATTAAA
1455910 TATATAAATAC
1 TATATAAATAC
1455921 TATATAAATAC
1 TATATAAATAC
1455932 TATA
1 TATA
1455936 CTTAAACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (11 bp):
TATATAAATAC
Found at i:1457216 original size:216 final size:215
Alignment explanation
Indices: 1456939--1457346 Score: 635
Period size: 213 Copynumber: 1.9 Consensus size: 215
1456929 AATTATATAT
1456939 ATATATATAATTTGTTAAAAATTAATAATAATAATATATTTACACATGCTAAATGAAAAAAAAAA
1 ATATATATAATTTGTTAAAAATT-ATAATAATAATATATTTACACATGCTAAATGAAAAAAAAAA
* *
1457004 TTGTTCACTTAATTAGTTGTCTAGTCTTTTATATAATTATATTTATATTAAAAATTATAAAAATA
65 TTGTTCACTTAATTAGTTGTCTAGTATTTTATATAATTATATATATATTAAAAATTATAAAAATA
* * * * *
1457069 TTTTTATAAGATGAAGGATCCATC-ACACTTGTAG-AAAACTAATTATATACAATTCATCTTTGT
130 CTTTTATAAGAGGAAGAATCC-TCTACACCTGT-GTAAAACTAATTATATACAATTCATATTTGT
1457132 TAATAAAAAATTAAAAATTACTA
193 TAATAAAAAATTAAAAATTACTA
1457155 ATATATATAATTTGTTAAAAA-T-TAATAATAATATATTTACACATGCTAAATGAAAAAAAAAAT
1 ATATATATAATTTGTTAAAAATTATAATAATAATATATTTACACATGCTAAATGAAAAAAAAAAT
* *
1457218 TGTTCACTTAATTATTTGTCTAGTATTTTATATAATTATGTATATATTAAAAATTATAAAAATAC
66 TGTTCACTTAATTAGTTGTCTAGTATTTTATATAATTATATATATATTAAAAATTATAAAAATAC
* * **
1457283 TTTTATAGGAGGAAGAATCCTCTTACTCCTGTGTAAAACTAATTATATATGATTCATATTTGTT
131 TTTTATAAGAGGAAGAATCCTC-TACACCTGTGTAAAACTAATTATATACAATTCATATTTGTT
1457347 TAATTTAATT
Statistics
Matches: 176, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
212 2 0.01
213 119 0.68
214 33 0.19
215 1 0.01
216 21 0.12
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (215 bp):
ATATATATAATTTGTTAAAAATTATAATAATAATATATTTACACATGCTAAATGAAAAAAAAAAT
TGTTCACTTAATTAGTTGTCTAGTATTTTATATAATTATATATATATTAAAAATTATAAAAATAC
TTTTATAAGAGGAAGAATCCTCTACACCTGTGTAAAACTAATTATATACAATTCATATTTGTTAA
TAAAAAATTAAAAATTACTA
Found at i:1457476 original size:29 final size:29
Alignment explanation
Indices: 1457438--1457500 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
1457428 ATTCAATATA
* *
1457438 AAAAACTTTCAACCAATAAATATATATTG
1 AAAACCTTTCAACCAATAAACATATATTG
1457467 AAAACCTTTCAACCAATAAACATATATTG
1 AAAACCTTTCAACCAATAAACATATATTG
1457496 AAAAC
1 AAAAC
1457501 ACTAATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.27
Consensus pattern (29 bp):
AAAACCTTTCAACCAATAAACATATATTG
Found at i:1467617 original size:33 final size:33
Alignment explanation
Indices: 1467580--1467645 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1467570 TGGCAAAAGA
*
1467580 ACAGGAACCACTTTCA-TTAGTGATGGAGAACTG
1 ACAGGAACCACTTTCACTT-GTGATGGAAAACTG
*
1467613 ACAGGAACCACTTTCACTTGTGGTGGAAAACTG
1 ACAGGAACCACTTTCACTTGTGATGGAAAACTG
1467646 GTTTCAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (33 bp):
ACAGGAACCACTTTCACTTGTGATGGAAAACTG
Found at i:1472570 original size:33 final size:33
Alignment explanation
Indices: 1472533--1472598 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1472523 TGACAGAAGA
*
1472533 ACAGGAACCACTTTCA-TTAGTGGTGGAAGACTG
1 ACAGGAACCACTTTCACTT-GTGGTGGAAAACTG
1472566 ACAGGAACCACTTTCACTTGTGGTGGAAAACTG
1 ACAGGAACCACTTTCACTTGTGGTGGAAAACTG
1472599 GTTTCAAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (33 bp):
ACAGGAACCACTTTCACTTGTGGTGGAAAACTG
Found at i:1473916 original size:9 final size:9
Alignment explanation
Indices: 1473902--1473926 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1473892 GTCATAAAAG
1473902 AAACTGAAT
1 AAACTGAAT
1473911 AAACTGAAT
1 AAACTGAAT
1473920 AAACTGA
1 AAACTGA
1473927 TCCAACCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (9 bp):
AAACTGAAT
Found at i:1475620 original size:2 final size:2
Alignment explanation
Indices: 1475613--1475638 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1475603 TAATTAATCG
1475613 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1475639 TATTTTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1478053 original size:11 final size:14
Alignment explanation
Indices: 1478022--1478050 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1478012 ATTTTGAAAT
1478022 TTGTTTATAGTATA
1 TTGTTTATAGTATA
1478036 TTGTTTATA-TATA
1 TTGTTTATAGTATA
1478049 TT
1 TT
1478051 TTAACATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (14 bp):
TTGTTTATAGTATA
Found at i:1479394 original size:33 final size:33
Alignment explanation
Indices: 1479357--1479423 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1479347 TTCAACGATC
1479357 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1479390 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1479423 T
1 T
1479424 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1479395 original size:13 final size:13
Alignment explanation
Indices: 1479377--1479401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1479367 CATAAAATGT
1479377 TGTATCGATACAA
1 TGTATCGATACAA
1479390 TGTATCGATACA
1 TGTATCGATACA
1479402 TATTTTTTTG
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:1479485 original size:13 final size:13
Alignment explanation
Indices: 1479467--1479491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1479457 ATTACTCACA
1479467 TGTATCGATACAT
1 TGTATCGATACAT
1479480 TGTATCGATACA
1 TGTATCGATACA
1479492 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1482869 original size:43 final size:43
Alignment explanation
Indices: 1482808--1482896 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
1482798 ATGTGCTTCC
1482808 GAAAATTTGGATTGATAAAAATTACAAGTATGAGACTTGTGTG
1 GAAAATTTGGATTGATAAAAATTACAAGTATGAGACTTGTGTG
1482851 GAAAATTTGGATTGATAAAAATTACAAGTATGAGACTTGTGTG
1 GAAAATTTGGATTGATAAAAATTACAAGTATGAGACTTGTGTG
1482894 GAA
1 GAA
1482897 TCCAAATTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.31
Consensus pattern (43 bp):
GAAAATTTGGATTGATAAAAATTACAAGTATGAGACTTGTGTG
Found at i:1485828 original size:13 final size:13
Alignment explanation
Indices: 1485810--1485834 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1485800 AAATTGCACA
1485810 GTATCGATACATT
1 GTATCGATACATT
1485823 GTATCGATACAT
1 GTATCGATACAT
1485835 GACTAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1485847 original size:20 final size:20
Alignment explanation
Indices: 1485822--1485872 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1485812 ATCGATACAT
**
1485822 TGTATCGATACATGACTAAA
1 TGTATCGATACATGAAAAAA
*
1485842 TGTATCGATAC-TTAAAAAA
1 TGTATCGATACATGAAAAAA
1485861 TGTATCGATACA
1 TGTATCGATACA
1485873 AGTCATTGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:1492066 original size:26 final size:26
Alignment explanation
Indices: 1492030--1492093 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
1492020 CATGTTCCGG
1492030 TGTATCGATACATCTGGAAAATTCAA
1 TGTATCGATACATCTGGAAAATTCAA
1492056 TGTATCGATACATCTGGAAAATTCAA
1 TGTATCGATACATCTGGAAAATTCAA
1492082 TGTATCGATACA
1 TGTATCGATACA
1492094 GCATTCTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (26 bp):
TGTATCGATACATCTGGAAAATTCAA
Found at i:1494622 original size:19 final size:20
Alignment explanation
Indices: 1494578--1494628 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1494568 ATCGATAAAT
*
1494578 TGTATCGATACATGACAAAA
1 TGTATCGATACATGAAAAAA
* *
1494598 TATATCGATAC-TTAAAAAA
1 TGTATCGATACATGAAAAAA
1494617 TGTATCGATACA
1 TGTATCGATACA
1494629 AGTCATTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:1501232 original size:23 final size:22
Alignment explanation
Indices: 1501196--1501239 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
1501186 AATCGACGGC
1501196 TCAAAAGAAATG-AAAGAAAAA
1 TCAAAAGAAATGAAAAGAAAAA
1501217 TCAAAAGTAAAATGAAAAGAAAA
1 TCAAAAG--AAATGAAAAGAAAA
1501240 TCATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
23 5 0.25
24 8 0.40
ACGTcount: A:0.70, C:0.05, G:0.14, T:0.11
Consensus pattern (22 bp):
TCAAAAGAAATGAAAAGAAAAA
Found at i:1502561 original size:20 final size:20
Alignment explanation
Indices: 1502523--1502561 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1502513 TGAAGAAAGG
* *
1502523 AATCAAAGGAAAATTAAGTA
1 AATCAAAGCAAAATGAAGTA
*
1502543 AATCAAAGCAAAGTGAAGT
1 AATCAAAGCAAAATGAAGT
1502562 CTAAAAGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.08, G:0.18, T:0.18
Consensus pattern (20 bp):
AATCAAAGCAAAATGAAGTA
Found at i:1504511 original size:29 final size:29
Alignment explanation
Indices: 1504478--1504601 Score: 100
Period size: 29 Copynumber: 4.4 Consensus size: 29
1504468 AAGCAATGTA
1504478 ATGAAATGAACATTACGTGAAATGCATGC
1 ATGAAATGAACATTACGTGAAATGCATGC
**
1504507 ATGAAATGAACTCATGGCGTGAAA--CATG-
1 ATGAAATGAA--CATTACGTGAAATGCATGC
* * * *
1504535 A--AAA-AAAGCA-TGCATGAAATGTAATGC
1 ATGAAATGAA-CATTACGTGAAATG-CATGC
*
1504562 ATGAAATGTACATTACGTGAAATGCATGC
1 ATGAAATGAACATTACGTGAAATGCATGC
1504591 ATGAAATGAAC
1 ATGAAATGAAC
1504602 TCATGAGTGA
Statistics
Matches: 72, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
23 7 0.10
24 2 0.03
25 2 0.03
26 6 0.08
27 1 0.01
28 1 0.01
29 33 0.46
30 10 0.14
31 10 0.14
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.23
Consensus pattern (29 bp):
ATGAAATGAACATTACGTGAAATGCATGC
Done.