Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_pilon, whole genome shotgun sequence
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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 30 of 30
Found at i:6371208 original size:18 final size:18
Alignment explanation
Indices: 6371174--6371208 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6371164 TCTCGAAACT
**
6371174 GGAGGAAGAGGTGGAGGC
1 GGAGGAAGAGGAAGAGGC
6371192 GGAGGAAGAGGAAGAGG
1 GGAGGAAGAGGAAGAGG
6371209 AGGTGTTACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.60, T:0.03
Consensus pattern (18 bp):
GGAGGAAGAGGAAGAGGC
Found at i:6372210 original size:18 final size:17
Alignment explanation
Indices: 6372177--6372210 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6372167 GAATAATTAA
6372177 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
6372194 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
6372211 AAACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:6373208 original size:20 final size:20
Alignment explanation
Indices: 6373183--6373240 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
6373173 TTTGGTTCAC
6373183 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
6373203 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
6373223 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
6373241 GGAATAGGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.36, C:0.10, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:6375997 original size:21 final size:21
Alignment explanation
Indices: 6375973--6376043 Score: 124
Period size: 21 Copynumber: 3.4 Consensus size: 21
6375963 CCAGGGAGAG
*
6375973 TATCTATACTCAGGGTGACAA
1 TATCGATACTCAGGGTGACAA
6375994 TATCGATACTCAGGGTGACAA
1 TATCGATACTCAGGGTGACAA
*
6376015 TATCGATACTCAGGGTGACAG
1 TATCGATACTCAGGGTGACAA
6376036 TATCGATA
1 TATCGATA
6376044 TTGAGGCCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (21 bp):
TATCGATACTCAGGGTGACAA
Found at i:6380331 original size:2 final size:2
Alignment explanation
Indices: 6380326--6380354 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6380316 ACACACACAC
6380326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6380355 CACCTAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6383818 original size:19 final size:20
Alignment explanation
Indices: 6383781--6383821 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
6383771 ATATGTAGAA
6383781 AAAAAATTTATCAATAAAAT
1 AAAAAATTTATCAATAAAAT
*
6383801 AAAAAATTTATTAA-AAAAT
1 AAAAAATTTATCAATAAAAT
6383820 AA
1 AA
6383822 TACATAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAATTTATCAATAAAAT
Found at i:6385230 original size:27 final size:27
Alignment explanation
Indices: 6385199--6385255 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
6385189 AAACACAACC
6385199 AAAATATAAATAAAGAAAACGATCGAT
1 AAAATATAAATAAAGAAAACGATCGAT
6385226 AAAATATAAATAAAGAAAACGATCGAT
1 AAAATATAAATAAAGAAAACGATCGAT
6385253 AAA
1 AAA
6385256 GCTGGGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.65, C:0.07, G:0.11, T:0.18
Consensus pattern (27 bp):
AAAATATAAATAAAGAAAACGATCGAT
Found at i:6388938 original size:2 final size:2
Alignment explanation
Indices: 6388931--6388973 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
6388921 AGAATGTTGA
6388931 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
6388973 A
1 A
6388974 GAGAGAGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6390984 original size:20 final size:20
Alignment explanation
Indices: 6390953--6391026 Score: 71
Period size: 19 Copynumber: 3.7 Consensus size: 20
6390943 TAGTGTTTAT
*
6390953 AGTTTGGAAACTTT-GTAAG
1 AGTTTTGAAACTTTAGTAAG
*
6390972 AGTTTTTGAAACTTTTATTAAG
1 AG-TTTTGAAAC-TTTAGTAAG
* *
6390994 AGTTTTGAAACTTTA-CAAA
1 AGTTTTGAAACTTTAGTAAG
*
6391013 AATTTTGAAACTTT
1 AGTTTTGAAACTTT
6391027 GCACCCAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
19 17 0.36
20 12 0.26
21 12 0.26
22 6 0.13
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (20 bp):
AGTTTTGAAACTTTAGTAAG
Found at i:6392340 original size:16 final size:17
Alignment explanation
Indices: 6392301--6392342 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
6392291 ATGGAAAAGG
6392301 AGAAAGAACAAGAAGAAA
1 AGAAAGAA-AAGAAGAAA
*
6392319 A-TAAGAAAAG-AGAAA
1 AGAAAGAAAAGAAGAAA
6392334 AGAAAGAAA
1 AGAAAGAAA
6392343 CCTTGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 6 0.29
16 9 0.43
17 5 0.24
18 1 0.05
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (17 bp):
AGAAAGAAAAGAAGAAA
Found at i:6392735 original size:4 final size:4
Alignment explanation
Indices: 6392726--6392817 Score: 56
Period size: 4 Copynumber: 25.0 Consensus size: 4
6392716 AAATAATTAT
* * * *
6392726 TATA TATA TATA TATA TA-A TAT- TATT TA-A TTTA -ATT TA-A TTTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
6392769 AAT- TATA TATA TATA TATA TATA TTTA TAT- TA-A TTTA AATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
6392814 TATA
1 TATA
6392818 CCCGGCCCGA
Statistics
Matches: 65, Mismatches: 15, Indels: 16
0.68 0.16 0.17
Matches are distributed among these distances:
3 14 0.22
4 51 0.78
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
TATA
Found at i:6392737 original size:6 final size:6
Alignment explanation
Indices: 6392726--6392817 Score: 56
Period size: 6 Copynumber: 16.7 Consensus size: 6
6392716 AAATAATTAT
* * * *
6392726 TATATA TATATA TATATA -ATAT- TATTTA -ATTTA -ATTTA -ATTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
6392769 AAT-TA TATATA TATATA TATATA TTTATA T-TA-A TTTAAA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
6392814 TATA
1 TATA
6392818 CCCGGCCCGA
Statistics
Matches: 75, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
4 2 0.03
5 30 0.40
6 43 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TATATA
Found at i:6392739 original size:10 final size:10
Alignment explanation
Indices: 6392726--6392817 Score: 56
Period size: 10 Copynumber: 10.0 Consensus size: 10
6392716 AAATAATTAT
6392726 TATATATATA
1 TATATATATA
6392736 TATATATA-A
1 TATATATATA
*
6392745 TAT-TATTTA
1 TATATATATA
* *
6392754 -ATTTA-ATT
1 TATATATATA
* *
6392762 TA-ATTTAAA
1 TATATATATA
6392771 T-TATATATA
1 TATATATATA
6392780 TATATATATA
1 TATATATATA
*
6392790 TATTTATAT-
1 TATATATATA
* *
6392799 TA-ATTTAAA
1 TATATATATA
6392808 TATATATATA
1 TATATATATA
6392818 CCCGGCCCGA
Statistics
Matches: 59, Mismatches: 15, Indels: 16
0.66 0.17 0.18
Matches are distributed among these distances:
8 10 0.17
9 20 0.34
10 29 0.49
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TATATATATA
Found at i:6399722 original size:21 final size:21
Alignment explanation
Indices: 6399680--6399723 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6399670 ACCCCGGGAG
*
6399680 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
6399701 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
6399722 CT
1 CT
6399724 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:6400374 original size:31 final size:31
Alignment explanation
Indices: 6400303--6400382 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
6400293 ATTTAACAAA
* * **
6400303 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
6400334 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
6400365 AAGGGGGAGTAAGTTTTT
1 AAGGGGGAGTAAGTTTTT
6400383 CAAAATCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:6402465 original size:32 final size:31
Alignment explanation
Indices: 6402405--6402465 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
6402395 TTAAATCTTT
*
6402405 TAATGATTTTTCATAAATTTCTTGTTCATCA
1 TAATGATTTTTCATAAATTTATTGTTCATCA
** *
6402436 TAATGATTTTTGGTCAAATTTATTTTTCAT
1 TAATGATTTTTCAT-AAATTTATTGTTCAT
6402466 GTTTTAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (31 bp):
TAATGATTTTTCATAAATTTATTGTTCATCA
Found at i:6402938 original size:15 final size:16
Alignment explanation
Indices: 6402918--6402977 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
6402908 AGGGGGAGTT
6402918 TAAATAT-TTTTTTTA
1 TAAATATATTTTTTTA
6402933 TAAATATATTTTTTTA
1 TAAATATATTTTTTTA
* *
6402949 TAAATAGATTTTTTTC
1 TAAATATATTTTTTTA
* *
6402965 CAAATAGATTTTT
1 TAAATATATTTTT
6402978 CTAAAGGGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
15 7 0.17
16 34 0.83
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
TAAATATATTTTTTTA
Found at i:6402946 original size:16 final size:16
Alignment explanation
Indices: 6402925--6402977 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
6402915 GTTTAAATAT
*
6402925 TTTTTTTATAAATATA
1 TTTTTTTATAAATAGA
6402941 TTTTTTTATAAATAGA
1 TTTTTTTATAAATAGA
**
6402957 TTTTTTTCCAAATAGA
1 TTTTTTTATAAATAGA
6402973 TTTTT
1 TTTTT
6402978 CTAAAGGGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (16 bp):
TTTTTTTATAAATAGA
Found at i:6403960 original size:13 final size:13
Alignment explanation
Indices: 6403944--6403983 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
6403934 CCTAATAATA
6403944 AGCCCAAATCTAT
1 AGCCCAAATCTAT
6403957 AGCCCAAATCTAT
1 AGCCCAAATCTAT
*
6403970 AGCCCAAATATAT
1 AGCCCAAATCTAT
6403983 A
1 A
6403984 ACACAACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.42, C:0.28, G:0.07, T:0.23
Consensus pattern (13 bp):
AGCCCAAATCTAT
Found at i:6403994 original size:26 final size:26
Alignment explanation
Indices: 6403944--6403994 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
6403934 CCTAATAATA
* * *
6403944 AGCCCAAATCTATAGCCCAAATCTAT
1 AGCCCAAATATATAACACAAATCTAT
*
6403970 AGCCCAAATATATAACACAACTCTA
1 AGCCCAAATATATAACACAAATCTA
6403995 ATATTTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.06, T:0.22
Consensus pattern (26 bp):
AGCCCAAATATATAACACAAATCTAT
Found at i:6409157 original size:74 final size:73
Alignment explanation
Indices: 6409017--6409159 Score: 232
Period size: 74 Copynumber: 1.9 Consensus size: 73
6409007 AAACGGAGCT
* * * *
6409017 CATTGGATTACCATGTTTTTGAGTTTTTTAAATAAAAAATGATGTTTAAAAATATTTTTTAATTA
1 CATTGGATTACCATGTTTTCGAGTGTTTGAAATAAAAAATGATATTTAAAAATATTTTTTAATTA
6409082 TTAAGACC
66 TTAAGACC
*
6409090 CATTGGATTATCATGTTTTCGAGTGTTTGAAATAAAAAAATGATATTTAAAAATATTTTTTAATT
1 CATTGGATTACCATGTTTTCGAGTGTTTGAAAT-AAAAAATGATATTTAAAAATATTTTTTAATT
6409155 ATTAA
65 ATTAA
6409160 ACTTAAAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
73 29 0.45
74 35 0.55
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (73 bp):
CATTGGATTACCATGTTTTCGAGTGTTTGAAATAAAAAATGATATTTAAAAATATTTTTTAATTA
TTAAGACC
Found at i:6409545 original size:29 final size:30
Alignment explanation
Indices: 6409490--6409548 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
6409480 ACAATTTTAT
6409490 TTATTTTGACCCAAAATGAATTAAGATCAA
1 TTATTTTGACCCAAAATGAATTAAGATCAA
6409520 TTATTTTGACCC-AAATGAATTAAGATCAA
1 TTATTTTGACCCAAAATGAATTAAGATCAA
6409549 ATGTTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (30 bp):
TTATTTTGACCCAAAATGAATTAAGATCAA
Found at i:6412432 original size:22 final size:22
Alignment explanation
Indices: 6412283--6413373 Score: 1257
Period size: 22 Copynumber: 50.5 Consensus size: 22
6412273 AATAATAATT
**
6412283 TTTTAAAATAAATCAATTTATA
1 TTTTAAAATAAATCAATCCATA
6412305 -TTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
6412326 TTTT-AAATAGATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
6412347 TTTT-AAATAAAT-TTTTCATA
1 TTTTAAAATAAATCAATCCATA
* *
6412367 CTTTAAAA-AAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
6412388 TTTT-AAAT-ATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
6412408 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
6412430 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
6412452 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
6412474 TTTTAAAATAAAT-ATTTCCATA
1 TTTTAAAATAAATCA-ATCCATA
*
6412496 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* **
6412518 TTTTAAAATAAA--ATTTTTATA
1 TTTTAAAATAAATCA-ATCCATA
*
6412539 TTTTAAAATCAATC-ATCCATA
1 TTTTAAAATAAATCAATCCATA
*
6412560 TTTTAAAATAAA--ATTTCCATA
1 TTTTAAAATAAATCA-ATCCATA
6412581 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
6412603 TTTTAAAAT-AATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
*
6412624 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
**
6412646 --TT-AAATAAA-CTTTTCCATA
1 TTTTAAAATAAATC-AATCCATA
6412665 TTTT-AAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
6412686 -TTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
6412707 TTTTAAAATAAAATCAATCCATA
1 TTTTAAAAT-AAATCAATCCATA
*
6412730 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* *
6412752 TTTTAAAAT-AATCATTTCATA
1 TTTTAAAATAAATCAATCCATA
6412773 -TTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
6412794 -TTTAAAAT-AATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
6412814 TTTTAAAATAAATC-ATCTATA
1 TTTTAAAATAAATCAATCCATA
6412835 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
6412857 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
*
6412879 TTTTAAAATAAATTAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
6412901 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
6412923 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
6412945 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
***
6412967 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
* ***
6412989 TTTTAAAATATATTTTTTCCATA
1 TTTTAAAATA-AATCAATCCATA
**
6413012 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
*
6413034 TTTTAAAATAAATAAATCCATA
1 TTTTAAAATAAATCAATCCATA
6413056 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
6413078 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
6413100 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
** *
6413122 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATCCATA
6413144 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
6413166 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
6413188 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
6413210 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
6413232 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
6413254 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
6413276 TTTTAAAATAACTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
6413298 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
6413320 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* **
6413342 TTTTAAAATTAATCAATATATA
1 TTTTAAAATAAATCAATCCATA
6413364 TTTTAAAATA
1 TTTTAAAATA
6413374 GATTTAAATG
Statistics
Matches: 929, Mismatches: 106, Indels: 68
0.84 0.10 0.06
Matches are distributed among these distances:
18 1 0.00
19 12 0.01
20 53 0.06
21 230 0.25
22 578 0.62
23 54 0.06
24 1 0.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:6415229 original size:24 final size:24
Alignment explanation
Indices: 6415202--6415248 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
6415192 TACTCTCCCG
*
6415202 AATCCCTAACCCTTCTTTCTCCAA
1 AATCCCTAACCCTCCTTTCTCCAA
*
6415226 AATCCCTAATCCTCCTTTCTCCA
1 AATCCCTAACCCTCCTTTCTCCA
6415249 TTCCCAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.43, G:0.00, T:0.34
Consensus pattern (24 bp):
AATCCCTAACCCTCCTTTCTCCAA
Found at i:6420387 original size:24 final size:24
Alignment explanation
Indices: 6420360--6420430 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
6420350 TACTCTCCCG
* *
6420360 AATCCCTAACCCTTCTTTCTCCAA
1 AATCCCTAATCCTCCTTTCTCCAA
6420384 AATCCCTAATCCTCCTTTCTCCAA
1 AATCCCTAATCCTCCTTTCTCCAA
6420408 AATCCCTAATCCTCCTTTCTCCA
1 AATCCCTAATCCTCCTTTCTCCA
6420431 TTCCCAAATG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.24, C:0.42, G:0.00, T:0.34
Consensus pattern (24 bp):
AATCCCTAATCCTCCTTTCTCCAA
Found at i:6423320 original size:15 final size:15
Alignment explanation
Indices: 6423300--6423330 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6423290 ACTTTGCCGA
6423300 GGAGATTATTTTCTT
1 GGAGATTATTTTCTT
6423315 GGAGATTATTTTCTT
1 GGAGATTATTTTCTT
6423330 G
1 G
6423331 CGATCTCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.23, T:0.52
Consensus pattern (15 bp):
GGAGATTATTTTCTT
Found at i:6423362 original size:15 final size:15
Alignment explanation
Indices: 6423342--6423371 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6423332 GATCTCTTCT
6423342 TTGGGCACTACTAAA
1 TTGGGCACTACTAAA
6423357 TTGGGCACTACTAAA
1 TTGGGCACTACTAAA
6423372 GCTACCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (15 bp):
TTGGGCACTACTAAA
Found at i:6424554 original size:202 final size:205
Alignment explanation
Indices: 6424112--6424569 Score: 690
Period size: 202 Copynumber: 2.2 Consensus size: 205
6424102 AGACTCGCCC
* * * *
6424112 AATGTATATTCTACATCTTACACAGGGCAACACCAACTTCAAGGTAGTTTTAAAGGACATGTAGG
1 AATGTCTATTCTACATCTTACACAGGGCAACACCAACTTTAAGGTAGTTTTAAAGCAAATGTAGG
**
6424177 TCCGCTTAGGCAATAGGTACAATCCAAAAAAAAAAGATGTATCGCCCTAATGCAGCCTAGCATGA
66 TCCGCTTAGGCAATAGGTACAATCC-AAAAAAAAAGATGTATCAACCTAATGCAGCCTAGCATGA
* *
6424242 CCAACTAAAATATTGGCAACAGGGAAAAGAGGAGATCGCAAGAAAATGATCACCTTGGCAAAGGT
130 ACAACTAAAATATTGGCAACAGGGAAAAGAGGAGATCGCAAGAAAATGATCACCTCGGCAAAGGT
6424307 GCCTCCTCAAA
195 GCCTCCTCAAA
* * * *
6424318 AATGTCTATTCTACATCTTACACAGGGCAACACCAACTTTACGATAGTTTTCAAGCAAATTTAGG
1 AATGTCTATTCTACATCTTACACAGGGCAACACCAACTTTAAGGTAGTTTTAAAGCAAATGTAGG
* *
6424383 TCCGCTTAGGTAATAGGTACAA-CC-CAAAAAAAGATGTATCAACCTAATGCAGCCTAGCATGAA
66 TCCGCTTAGGCAATAGGTACAATCCAAAAAAAAAGATGTATCAACCTAATGCAGCCTAGCATGAA
* *
6424446 CAACTAAAAT-TTGGCAACAGGGAAAAGAGGATATCGCAAGAAAATGATCACCTCGGCAAAGTTG
131 CAACTAAAATATTGGCAACAGGGAAAAGAGGAGATCGCAAGAAAATGATCACCTCGGCAAAGGTG
*
6424510 -CTCCTCTACA
196 CCTCCTC-AAA
* * *
6424520 AATGTCTATTCCACATCTTAAACAGGGTAACACCAACTTTAAGGTAGTTT
1 AATGTCTATTCTACATCTTACACAGGGCAACACCAACTTTAAGGTAGTTT
6424570 GACAAAAACA
Statistics
Matches: 229, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
201 6 0.03
202 98 0.43
203 45 0.20
205 2 0.01
206 78 0.34
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (205 bp):
AATGTCTATTCTACATCTTACACAGGGCAACACCAACTTTAAGGTAGTTTTAAAGCAAATGTAGG
TCCGCTTAGGCAATAGGTACAATCCAAAAAAAAAGATGTATCAACCTAATGCAGCCTAGCATGAA
CAACTAAAATATTGGCAACAGGGAAAAGAGGAGATCGCAAGAAAATGATCACCTCGGCAAAGGTG
CCTCCTCAAA
Found at i:6430682 original size:21 final size:21
Alignment explanation
Indices: 6430656--6430826 Score: 156
Period size: 21 Copynumber: 8.2 Consensus size: 21
6430646 GTTTCCAGAT
* **
6430656 TCGCAACGCGAACTTCAACTA
1 TCGCAATGCGAACTTGGACTA
6430677 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
6430698 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
6430719 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
6430739 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* *
6430760 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * *
6430780 TTGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
6430801 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
6430822 TCGCA
1 TCGCA
6430827 TTCCAAAATC
Statistics
Matches: 122, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
20 30 0.25
21 92 0.75
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:6430742 original size:62 final size:61
Alignment explanation
Indices: 6430676--6430826 Score: 166
Period size: 62 Copynumber: 2.4 Consensus size: 61
6430666 AACTTCAACT
*
6430676 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT-A-A
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGGA-AATCGCAATGCG-ATA-GTCACA
* * * * *
6430738 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGTAAATTGCAATGCGATAGTCGACT
1 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGGAAATCGCAATGCGATAGTC-ACA
6430800 ATCGCAATGCGAACTTGGACTATCGCA
1 ATCGCAATGCGAACTTGGACTATCGCA
6430827 TTCCAAAATC
Statistics
Matches: 75, Mismatches: 8, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
59 2 0.03
60 3 0.04
61 13 0.17
62 56 0.75
63 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (61 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGGAAATCGCAATGCGATAGTCACA
Found at i:6430743 original size:20 final size:20
Alignment explanation
Indices: 6430718--6430790 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
6430708 AACTTGGACT
6430718 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
6430738 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
6430759 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
6430779 ATTGCAATGCGA
1 ATCGCAATGCGA
6430791 TAGTCGACTA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 2 0.04
19 3 0.07
20 23 0.51
21 12 0.27
22 3 0.07
23 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:6430759 original size:41 final size:41
Alignment explanation
Indices: 6430673--6430812 Score: 194
Period size: 41 Copynumber: 3.4 Consensus size: 41
6430663 GCGAACTTCA
* * * *
6430673 ACTATCGCAATGCGAACT-TGGACTATCGCAATGCGA-ACTTGG
1 ACTATCGCAATGCGAA-TATGTA-AATCGCAATGCGATA-GTCG
6430715 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCG
1 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCG
*
6430756 ACTATCGCAATGCGAATATGTAAATTGCAATGCGATAGTCG
1 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCG
6430797 ACTATCGCAATGCGAA
1 ACTATCGCAATGCGAA
6430813 CTTGGACTAT
Statistics
Matches: 91, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
41 71 0.78
42 20 0.22
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (41 bp):
ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCG
Found at i:6431597 original size:42 final size:42
Alignment explanation
Indices: 6431550--6431686 Score: 220
Period size: 42 Copynumber: 3.3 Consensus size: 42
6431540 TGCGATTTTG
*
6431550 GACTATCGCAACAAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * * *
6431592 GACTATCACAATGAATTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
6431634 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
6431676 GACTATCGCAA
1 GACTATCGCAA
6431687 TGCGAATATG
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 86 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:6431683 original size:21 final size:20
Alignment explanation
Indices: 6431547--6431692 Score: 100
Period size: 21 Copynumber: 7.0 Consensus size: 20
6431537 CGTTGCGATT
*
6431547 TTGGACTATCGCAA-CAAAC
1 TTGGACTATCGCAAGCGAAC
*
6431566 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* * * *
6431589 TTCGACTATCACAA-TGAAT
1 TTGGACTATCGCAAGCGAAC
*
6431608 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
6431631 TTTGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
6431650 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
6431673 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAA-GCGAA
6431693 TATGTAAATC
Statistics
Matches: 97, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
19 24 0.25
21 45 0.46
23 28 0.29
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:6433386 original size:66 final size:67
Alignment explanation
Indices: 6433066--6433389 Score: 336
Period size: 66 Copynumber: 4.9 Consensus size: 67
6433056 TCATATATTT
* * * * * * *
6433066 ACTCCACCTTATGCACCACAAAAGTACA-CAAGTTTCATCGAGTGGTC-AGTATAGTATTCAATT
1 ACTCCACCTCATGCACCACAAAGGTACATGAAGTCTCATTGAGTGATCTA-TACAGTATTCAATT
6433129 ATC
65 ATC
* * * * ** * * * *
6433132 ATTTCATCTCATGCACCACAAAGGTACA-CAAGTAGCATTGAGAGATCTGTACAATATTCAATTG
1 ACTCCACCTCATGCACCACAAAGGTACATGAAGTCTCATTGAGTGATCTATACAGTATTCAATTA
6433196 TC
66 TC
* * * * *
6433198 ACTCCACCTCATGCACCACAAAGGTATAT-AAGTCTCATTAAGTGATATGTACGGTATTCAATTA
1 ACTCCACCTCATGCACCACAAAGGTACATGAAGTCTCATTGAGTGATCTATACAGTATTCAATTA
6433262 TC
66 TC
* * *
6433264 ACTCCACCTCATGCACCACAAAGGTACATG-AGTCTCATTGAGTAATTTATGCAGTATTCAATTA
1 ACTCCACCTCATGCACCACAAAGGTACATGAAGTCTCATTGAGTGATCTATACAGTATTCAATTA
6433328 TC
66 TC
* * * *
6433330 ACTCTACCTCGTGCACCACAAAGGTACATGAA-TCTTATTGAGTGATCTATATAGTATTCA
1 ACTCCACCTCATGCACCACAAAGGTACATGAAGTCTCATTGAGTGATCTATACAGTATTCA
6433390 GCAATCATTC
Statistics
Matches: 214, Mismatches: 40, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
66 213 1.00
67 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (67 bp):
ACTCCACCTCATGCACCACAAAGGTACATGAAGTCTCATTGAGTGATCTATACAGTATTCAATTA
TC
Found at i:6438101 original size:18 final size:17
Alignment explanation
Indices: 6438078--6438111 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6438068 CAGTCTGTTT
6438078 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
6438096 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
6438112 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:6439832 original size:118 final size:118
Alignment explanation
Indices: 6439624--6439853 Score: 372
Period size: 118 Copynumber: 1.9 Consensus size: 118
6439614 TTAAATGTTT
* * *
6439624 CTCAAGTTTTTGGGTATTACATGGGTGACCAAAATGCAATGGTCCTAAAAGTTCAGGAACTATTT
1 CTCAAATTTTTGGGTATTACATGGGTGACCAAAATACAATGATCCTAAAAGTTCAGGAACTATTT
6439689 ATATACTTTACCATAATAATAATAATAATAAAAAGAAGAAGAAGAAGGAGGTC
66 ATATACTTTACCATAATAATAATAATAATAAAAAGAAGAAGAAGAAGGAGGTC
* *
6439742 CTCAAATTTTTGGGTATTACATGGGTGACCGAAATACTA-GCATCCTAAAAGTTCAGGAACTATT
1 CTCAAATTTTTGGGTATTACATGGGTGACCAAAATACAATG-ATCCTAAAAGTTCAGGAACTATT
* * *
6439806 TATATACTTTACCCTAATACTAATAATAATATAAAGAAGAAGAAGAAG
65 TATATACTTTACCATAATAATAATAATAATAAAAAGAAGAAGAAGAAG
6439854 AAGAAGAAGA
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
117 1 0.01
118 102 0.99
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (118 bp):
CTCAAATTTTTGGGTATTACATGGGTGACCAAAATACAATGATCCTAAAAGTTCAGGAACTATTT
ATATACTTTACCATAATAATAATAATAATAAAAAGAAGAAGAAGAAGGAGGTC
Found at i:6439845 original size:3 final size:3
Alignment explanation
Indices: 6439839--6439866 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6439829 TAATAATATA
6439839 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
6439867 TATGATTTTT
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6441039 original size:2 final size:2
Alignment explanation
Indices: 6441032--6441058 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6441022 TTATTTAGTT
6441032 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6441059 TAATAATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6441516 original size:27 final size:28
Alignment explanation
Indices: 6441459--6441523 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 28
6441449 TTAATTCTAT
* *
6441459 TATATGGTCGGCTCTATCGCCTGATTGA
1 TATATGGTCGGCTCTATCCCCTGAATGA
6441487 TATATGGTCGGCTCTA-CCCCTGAATGA
1 TATATGGTCGGCTCTATCCCCTGAATGA
6441514 TATATGGTCG
1 TATATGGTCG
6441524 ACACTGCCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 19 0.54
28 16 0.46
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.34
Consensus pattern (28 bp):
TATATGGTCGGCTCTATCCCCTGAATGA
Found at i:6450336 original size:20 final size:21
Alignment explanation
Indices: 6450311--6450350 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
6450301 TATGTTACGA
6450311 TGCTGATGTGG-AGTTCACAG
1 TGCTGATGTGGCAGTTCACAG
6450331 TGCTGATGTGGCAGTTCACA
1 TGCTGATGTGGCAGTTCACA
6450351 ATATTGACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (21 bp):
TGCTGATGTGGCAGTTCACAG
Found at i:6451165 original size:16 final size:18
Alignment explanation
Indices: 6451134--6451167 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
6451124 AAACAAAATA
6451134 TTAAAAACTAAAATATTT
1 TTAAAAACTAAAATATTT
6451152 TTAAAAA-T-AAATATTT
1 TTAAAAACTAAAATATTT
6451168 AATCGGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAAAACTAAAATATTT
Found at i:6454047 original size:21 final size:19
Alignment explanation
Indices: 6454005--6454051 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
6453995 GAATACCTTC
*
6454005 AAACTTTTGATTGCTGAAA
1 AAACTTTTGATTGCTCAAA
*
6454024 AAACTTGTTGTATTGCTCAGA
1 AAACTT-TTG-ATTGCTCAAA
6454045 AAA-TTTT
1 AAACTTTT
6454052 TCTTTGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.33
20 5 0.21
21 11 0.46
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (19 bp):
AAACTTTTGATTGCTCAAA
Found at i:6454986 original size:17 final size:17
Alignment explanation
Indices: 6454964--6455005 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
6454954 GTTGAACAAG
6454964 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
6454981 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
6454998 TTCTTCTC
1 TTCTTCTC
6455006 CCTCATCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.19, C:0.26, G:0.05, T:0.50
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:6455230 original size:139 final size:139
Alignment explanation
Indices: 6454671--6455311 Score: 741
Period size: 139 Copynumber: 4.6 Consensus size: 139
6454661 GGAAACAAGT
* * * *
6454671 TAAGGTTGAACAAGTTCTTCTCATTATGAATTTTTTCTCCCTCATCGGATGAGTTATTCTCATTA
1 TAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCTCATTA
* * * * **
6454736 TGAACTCTCCACTGGAAATGTTGGTCCCTCGAGTAAGGTGTTGCTGATTCAATTCCATATGCGAT
66 TGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTATTGCTGATTCAACTCCATATATGAT
6454801 GAATCGAGC
131 GAATCGAGC
* * ** *
6454810 TAAGTTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTTTTTTGGATGAGTTCTTCTCATT
1 TAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CCTTCATCGGATGAGTTCTTCTCATT
* * *
6454875 ATGAACACTCCACTGGAAATATTGATCACTCGAGTGAGGTATTGCTGATTCAACTCCATATATGA
65 ATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTATTGCTGATTCAACTCCATATATGA
*
6454940 TGAATTGAGC
130 TGAATCGAGC
* * * *
6454950 TAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCATT-AT--GA--ACTTCTTCTCCCTC
1 TAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCT-CATT
* ** * * * * * * * *
6455010 ATCGGATGAGT-TCTTCT---CAT-TATGAACTCTCCACT--GGAAATGTTGATTCAACTCCATA
65 AT--GA--ACTCTCCACTGGAAATGT-TGATCCCTCGAGTGAGGTATTGCTGATTCAACTCCATA
6455068 TATGATGAATCGAGC
125 TATGATGAATCGAGC
6455083 TAAGGTTGAACAAGTAT-TTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCTCATT
1 TAAGGTTGAACAAGT-TCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCTCATT
* * * * *
6455147 ATTAACTCTCCACTAGAAATGTTGATCCCTCGAGTGAGGTGTTGTTGATTCAACTCCATATGTGA
65 ATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTATTGCTGATTCAACTCCATATATGA
6455212 TGAATCGAGC
130 TGAATCGAGC
* * *
6455222 TAAGGTTGAACAATTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTA
1 TAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCTCATTA
6455287 TGAACTCTCCACTGGAAATGTTGAT
66 TGAACTCTCCACTGGAAATGTTGAT
6455312 TGGTTTATCT
Statistics
Matches: 420, Mismatches: 61, Indels: 42
0.80 0.12 0.08
Matches are distributed among these distances:
133 75 0.18
134 16 0.04
135 16 0.04
136 4 0.01
137 17 0.04
138 15 0.04
139 155 0.37
140 122 0.29
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (139 bp):
TAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCTCATTA
TGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTATTGCTGATTCAACTCCATATATGAT
GAATCGAGC
Found at i:6455849 original size:36 final size:36
Alignment explanation
Indices: 6455735--6455858 Score: 115
Period size: 36 Copynumber: 3.4 Consensus size: 36
6455725 AGGGAAACTT
* *
6455735 TCTCAAGCGAGATGAAATTTGTTTTAAG-AAAACAA
1 TCTCAAGCGAGATGAAACTTGTTTTAAGAAAAATAA
* * * * *
6455770 TCCCAAGTGAGATAAAATTTCTTGTTTTGAGTAAAAATTA
1 TCTCAAGCGAGATGAAA---CTTGTTTTAAG-AAAAATAA
*
6455810 TCTCAAGCGAGATGAAGCTTGTTTTAAGAAAAATAA
1 TCTCAAGCGAGATGAAACTTGTTTTAAGAAAAATAA
* *
6455846 TCTCGAGTGAGAT
1 TCTCAAGCGAGAT
6455859 AAAATTTTGT
Statistics
Matches: 69, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
35 14 0.20
36 18 0.26
37 10 0.14
38 9 0.13
40 18 0.26
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (36 bp):
TCTCAAGCGAGATGAAACTTGTTTTAAGAAAAATAA
Found at i:6455908 original size:73 final size:73
Alignment explanation
Indices: 6455729--6455972 Score: 328
Period size: 73 Copynumber: 3.3 Consensus size: 73
6455719 ATTTCAAGGG
* * * * *
6455729 AAACTTTCTCAAGCGAGATGAAATTTGTTTTAAG-AAAACAATCCCAAGTGAGATAAAATTTCTT
1 AAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAA-TT-TT
6455793 GTTTTGAGTAA
64 GTTTTGAGT-A
* * * * *
6455804 AAATTATCTCAAGCGAGATGAAGCTTGTTTTAAGAAAAATAATCTCGAGTGAGATAAAATTTTGT
1 AAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTTGT
* * *
6455869 TTCGAATG
66 TTTGAGTA
*
6455877 AAACTGTCTCAAGTGAGACGAAGTTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTTGT
1 AAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTTGT
6455942 TTTGAGTA
66 TTTGAGTA
6455950 AAACTGTCTCAAGCGAGACGAAG
1 AAACTGTCTCAAGCGAGACGAAG
6455973 ATCTCTCAAG
Statistics
Matches: 148, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
73 86 0.58
74 9 0.06
75 32 0.22
76 21 0.14
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.31
Consensus pattern (73 bp):
AAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTTGT
TTTGAGTA
Found at i:6455953 original size:37 final size:37
Alignment explanation
Indices: 6455735--6455967 Score: 163
Period size: 37 Copynumber: 6.3 Consensus size: 37
6455725 AGGGAAACTT
* *
6455735 TCTCAAGCGAGATGAAA-TTTGTTTTAAG-AAAACAA
1 TCTCAAGTGAGATAAAATTTTGTTTTAAGTAAAACAA
* *
6455770 TCCCAAGTGAGATAAAATTTCTTGTTTTGAGTAAAA-ATTA
1 TCTCAAGTGAGATAAAA-TT-TTGTTTTAAGTAAAACA--A
* * ** * *
6455810 TCTCAAGCGAGAT-GAAGCTTGTTTTAAGAAAAATAA
1 TCTCAAGTGAGATAAAATTTTGTTTTAAGTAAAACAA
* * * **
6455846 TCTCGAGTGAGATAAAATTTTGTTTCGAA-TGAAACTG
1 TCTCAAGTGAGATAAAATTTTGTTT-TAAGTAAAACAA
** * *
6455883 TCTCAAGTGAGA-CGAAGTTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAAATTTTGTTTTAAGTAAAACAA
* * **
6455919 TCTCGAGTGAGATAAAATTTTGTTTTGAGTAAAACTG
1 TCTCAAGTGAGATAAAATTTTGTTTTAAGTAAAACAA
*
6455956 TCTCAAGCGAGA
1 TCTCAAGTGAGA
6455968 CGAAGATCTC
Statistics
Matches: 146, Mismatches: 41, Indels: 20
0.71 0.20 0.10
Matches are distributed among these distances:
35 16 0.11
36 36 0.25
37 63 0.43
38 13 0.09
39 6 0.04
40 12 0.08
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (37 bp):
TCTCAAGTGAGATAAAATTTTGTTTTAAGTAAAACAA
Found at i:6456354 original size:55 final size:55
Alignment explanation
Indices: 6456290--6456568 Score: 396
Period size: 55 Copynumber: 5.1 Consensus size: 55
6456280 AAAATTTAGG
* * * * **
6456290 CTTAATTTCTTTGAAAGTTCTTTTAAAAATCACCAAGAAACTTCTGAAAATCAGA
1 CTTAATTTCTTTAAAAGCTCATTTGAAAATCGTCAAGAAACTTCTGAAAATCAGA
* * *
6456345 CTTAGTTTCTTTAAAAACTAATTTGAAAATCGTCAAGAAACTTCTGAAAATCAGA
1 CTTAATTTCTTTAAAAGCTCATTTGAAAATCGTCAAGAAACTTCTGAAAATCAGA
*
6456400 CTTAATTTCTTTAAAAGCTCATTTGAAAATCGTCAAGAAACTTCTGAAAATCATA
1 CTTAATTTCTTTAAAAGCTCATTTGAAAATCGTCAAGAAACTTCTGAAAATCAGA
* * * * * *
6456455 CTTAATTTCTTTGAAAGTTCATTTAAAAATCATTAAGAAACTTCTGAAAATTAGA
1 CTTAATTTCTTTAAAAGCTCATTTGAAAATCGTCAAGAAACTTCTGAAAATCAGA
* *
6456510 ATTAATTTCTTTAAAAGCTCATTTGAAAATTGTCAAGAAACTTCTGAAAATCAGA
1 CTTAATTTCTTTAAAAGCTCATTTGAAAATCGTCAAGAAACTTCTGAAAATCAGA
6456565 CTTA
1 CTTA
6456569 GTTAAAAAAA
Statistics
Matches: 195, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 195 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (55 bp):
CTTAATTTCTTTAAAAGCTCATTTGAAAATCGTCAAGAAACTTCTGAAAATCAGA
Found at i:6456748 original size:4 final size:4
Alignment explanation
Indices: 6456739--6457364 Score: 1234
Period size: 4 Copynumber: 156.5 Consensus size: 4
6456729 CTGTAAGAAT
6456739 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6456787 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6456835 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6456883 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6456931 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6456979 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6457027 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6457075 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6457123 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6457171 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6457219 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6457267 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
6457315 TATG TATG TATG TATG TATG TATG TATG TATG TATT TATG TATT TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6457363 TA
1 TA
6457365 CTTAAATGAA
Statistics
Matches: 618, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 618 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:6457976 original size:11 final size:11
Alignment explanation
Indices: 6457954--6457986 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
6457944 CTTTCATTTT
6457954 TACTGTGTTTCA
1 TACTG-GTTTCA
6457966 TACTGGTTTCA
1 TACTGGTTTCA
6457977 TACTGGTTTC
1 TACTGGTTTC
6457987 TTTGGTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.48
Consensus pattern (11 bp):
TACTGGTTTCA
Found at i:6458672 original size:13 final size:13
Alignment explanation
Indices: 6458635--6458671 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
6458625 ATCTGTCTAT
6458635 TTTCTTCTTTTTC
1 TTTCTTCTTTTTC
*
6458648 CTTCTTCTTTTTC
1 TTTCTTCTTTTTC
6458661 TTTCTT-TTTTT
1 TTTCTTCTTTTT
6458672 TATTTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTCTTCTTTTTC
Found at i:6460108 original size:13 final size:14
Alignment explanation
Indices: 6460074--6460114 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
6460064 TACGATGTAT
*
6460074 AGATGCTAATGCAA
1 AGATGCAAATGCAA
6460088 AGATGCAAATGCAA
1 AGATGCAAATGCAA
6460102 A-ATGCAAATGCAA
1 AGATGCAAATGCAA
6460115 CAAAGGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.49, C:0.15, G:0.20, T:0.17
Consensus pattern (14 bp):
AGATGCAAATGCAA
Found at i:6460970 original size:21 final size:21
Alignment explanation
Indices: 6460934--6460975 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6460924 AAGCAAAATT
*
6460934 GTGCATCGATGTACTGTTACA
1 GTGCATCGATGTACTGCTACA
6460955 GTGCATCGAT-TCACTGCTACA
1 GTGCATCGATGT-ACTGCTACA
6460976 TTACTGCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (21 bp):
GTGCATCGATGTACTGCTACA
Found at i:6461605 original size:23 final size:23
Alignment explanation
Indices: 6461539--6461624 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
6461529 TAGTATAAAT
6461539 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
6461562 TTTTTC-CCGAAG-GACCGCGTAGAA
1 --TTGCACCGAAGTG-CCACGTAGAA
*
6461586 ATGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
6461609 TTGCACTGTAGTGCCA
1 TTGCACCGAAGTGCCA
6461625 TATAATATGT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
22 2 0.04
23 29 0.58
24 16 0.32
25 3 0.06
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:6461914 original size:31 final size:31
Alignment explanation
Indices: 6461865--6461944 Score: 117
Period size: 31 Copynumber: 2.5 Consensus size: 31
6461855 TTATATCGCG
6461865 TAGACATATCA-TTTCCATACCTTTATCACA
1 TAGACATATCATTTTCCATACCTTTATCACA
*
6461895 TAGACATATCATTTTCCATACTTTTATCACA
1 TAGACATATCATTTTCCATACCTTTATCACA
*
6461926 TAGCTCATATCACTTTTCC
1 TAG-ACATATCA-TTTTCC
6461945 TGCATATTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
30 11 0.24
31 21 0.47
32 7 0.16
33 6 0.13
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (31 bp):
TAGACATATCATTTTCCATACCTTTATCACA
Found at i:6462014 original size:25 final size:24
Alignment explanation
Indices: 6461970--6462018 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
6461960 CATAATGCAT
6461970 ATAATATGAATTAATGTCATGTATC
1 ATAATATGAATTAA-GTCATGTATC
6461995 ATAATATGAAATGTAA-TCATGTAT
1 ATAATATG-AAT-TAAGTCATGTAT
6462019 TAAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 16 0.73
26 3 0.14
27 3 0.14
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (24 bp):
ATAATATGAATTAAGTCATGTATC
Found at i:6464387 original size:2 final size:2
Alignment explanation
Indices: 6464375--6464409 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6464365 ATTTTTACTT
*
6464375 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6464410 TCTAAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6464598 original size:24 final size:24
Alignment explanation
Indices: 6464570--6464621 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
6464560 AAACACTTTA
6464570 ATGATACAAATAAACAATATACAT
1 ATGATACAAATAAACAATATACAT
6464594 ATGATACAAATAAACAATATACAT
1 ATGATACAAATAAACAATATACAT
6464618 ATGA
1 ATGA
6464622 ATCACTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.25
Consensus pattern (24 bp):
ATGATACAAATAAACAATATACAT
Found at i:6465826 original size:2 final size:2
Alignment explanation
Indices: 6465819--6465845 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6465809 TGCACCTTTC
6465819 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6465846 ATCCACACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6466213 original size:30 final size:30
Alignment explanation
Indices: 6466158--6466246 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
6466148 CCCGAAGGAC
6466158 CTATCCAGAGGTCACAAAG-ACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
*
6466187 CTATCCAGAGGTCATAAAGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
* * * * *
6466217 CTGTCTATAGGTCCCAAAGAACCTAGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
6466247 ACTGTCCATA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
29 18 0.35
30 34 0.65
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGTAA
Found at i:6466343 original size:32 final size:31
Alignment explanation
Indices: 6466234--6466341 Score: 121
Period size: 31 Copynumber: 3.5 Consensus size: 31
6466224 TAGGTCCCAA
* *
6466234 AGAACCTAGGTAAACTGTCCATATATTCCTT
1 AGAACATAGGTAAACTGTCCATATATTCCGT
* * *
6466265 ATAACATAGGTATACTGTCCATAT-GTCTCG-
1 AGAACATAGGTAAACTGTCCATATATTC-CGT
*
6466295 AAAGACATAGGTAAAACTGTCCATATATTCCGT
1 AGA-ACATAGGT-AAACTGTCCATATATTCCGT
6466328 AGAACATAGGTAAA
1 AGAACATAGGTAAA
6466342 ACCTCGACTC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
30 4 0.06
31 33 0.52
32 22 0.35
33 4 0.06
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (31 bp):
AGAACATAGGTAAACTGTCCATATATTCCGT
Found at i:6468180 original size:63 final size:62
Alignment explanation
Indices: 6468028--6468181 Score: 157
Period size: 63 Copynumber: 2.5 Consensus size: 62
6468018 ATCCCTAGAC
* * * * * **
6468028 GGGTGCATCGATGCACT-ATCTATACATCGGTGTATAAATCTCATTCGATGTTTGTATTTTAG
1 GGGTGCATCGATGCACTCA-CTATGCATCGATGCACAAATCGCATTCGATGTTTCCATTTTAG
* * * *
6468090 GGGATGCATCGATCCACTCATTATGCATCGATGCACCAATCGCATTCGATGTTTCCATTTTAAT
1 GGG-TGCATCGATGCACTCACTATGCATCGATGCACAAATCGCATTCGATGTTTCCATTTT-AG
* *
6468154 GGGTGCATCGATGCACTCCCTGTGCATC
1 GGGTGCATCGATGCACTCACTATGCATC
6468182 CATACACACT
Statistics
Matches: 74, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
62 3 0.04
63 66 0.89
64 5 0.07
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (62 bp):
GGGTGCATCGATGCACTCACTATGCATCGATGCACAAATCGCATTCGATGTTTCCATTTTAG
Found at i:6470157 original size:23 final size:23
Alignment explanation
Indices: 6470115--6470176 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
6470105 TGAGGCATGT
**
6470115 TCTCTGTCTTTATGACACATCTA
1 TCTCTGTCTTTATGGTACATCTA
* *
6470138 TCTCTGTCTTTATGGTACATTTT
1 TCTCTGTCTTTATGGTACATCTA
*
6470161 TCTATGTCTTT-TGGTA
1 TCTCTGTCTTTATGGTA
6470177 GCTTATGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 5 0.15
23 29 0.85
ACGTcount: A:0.16, C:0.19, G:0.13, T:0.52
Consensus pattern (23 bp):
TCTCTGTCTTTATGGTACATCTA
Found at i:6475881 original size:22 final size:22
Alignment explanation
Indices: 6475853--6475921 Score: 117
Period size: 20 Copynumber: 3.3 Consensus size: 22
6475843 TCGGGTCGGG
6475853 TCTCGGCTGGAGACTCTCTTGT
1 TCTCGGCTGGAGACTCTCTTGT
6475875 TCTCGGCTGGAGA--CTCTTGT
1 TCTCGGCTGGAGACTCTCTTGT
6475895 TCTCGG-TGGAGACTCTCTTGT
1 TCTCGGCTGGAGACTCTCTTGT
6475916 TCTCGG
1 TCTCGG
6475922 GTCGGGTCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.13
20 13 0.29
21 13 0.29
22 13 0.29
ACGTcount: A:0.09, C:0.26, G:0.29, T:0.36
Consensus pattern (22 bp):
TCTCGGCTGGAGACTCTCTTGT
Found at i:6476182 original size:16 final size:17
Alignment explanation
Indices: 6476140--6476185 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
6476130 TTCTGTTTAA
6476140 ATTTAATTATAAATATT
1 ATTTAATTATAAATATT
*
6476157 -TATAATATTATAAA-ATT
1 AT-TTA-ATTATAAATATT
6476174 ATTTAATTATAA
1 ATTTAATTATAA
6476186 TTTAAATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
16 8 0.33
17 7 0.29
18 9 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTATAAATATT
Found at i:6486293 original size:18 final size:18
Alignment explanation
Indices: 6486248--6486294 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
6486238 TGTGGAATTG
6486248 GATTCCAATT-CTTGACA
1 GATTCCAATTCCTTGACA
* * *
6486265 AATTTCAATTCCTTTACA
1 GATTCCAATTCCTTGACA
6486283 GATTCCAATTCC
1 GATTCCAATTCC
6486295 CTCAAAACAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (18 bp):
GATTCCAATTCCTTGACA
Found at i:6503519 original size:2 final size:2
Alignment explanation
Indices: 6503508--6503549 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
6503498 CCTCAACTTG
6503508 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6503549 T
1 T
6503550 CACATAAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6503726 original size:20 final size:20
Alignment explanation
Indices: 6503684--6503729 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
6503674 CTTGACTTTG
**
6503684 CTCGAATTTTATAAACTTGA
1 CTCGAATTTTATAAACTAAA
*
6503704 CTCGAGTTTTATAAACTAAA
1 CTCGAATTTTATAAACTAAA
6503724 CTCGAA
1 CTCGAA
6503730 AAATTAAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (20 bp):
CTCGAATTTTATAAACTAAA
Found at i:6525950 original size:3 final size:3
Alignment explanation
Indices: 6525942--6525973 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6525932 ATAGTAATAT
6525942 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6525974 TATTTTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6525981 original size:9 final size:10
Alignment explanation
Indices: 6525939--6525981 Score: 54
Period size: 9 Copynumber: 4.3 Consensus size: 10
6525929 TATATAGTAA
6525939 TATTTATTAT
1 TATTTATTAT
6525949 TA-TTATTAT
1 TATTTATTAT
6525958 TATTATTATTAT
1 TA-T-TTATTAT
6525970 TATTTATT-T
1 TATTTATTAT
6525979 TAT
1 TAT
6525982 GTATCGGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 13 0.43
10 7 0.23
11 1 0.03
12 9 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTATTAT
Found at i:6537732 original size:8 final size:8
Alignment explanation
Indices: 6537719--6537759 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
6537709 CTCATTTTCA
6537719 GAGAATTT
1 GAGAATTT
6537727 GAGAATTT
1 GAGAATTT
*
6537735 -AGAGTTT
1 GAGAATTT
*
6537742 GGGAATTT
1 GAGAATTT
6537750 GAGAATTT
1 GAGAATTT
6537758 GA
1 GA
6537760 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:6538070 original size:128 final size:128
Alignment explanation
Indices: 6537840--6538199 Score: 668
Period size: 128 Copynumber: 2.8 Consensus size: 128
6537830 ACTATTCACA
*
6537840 TGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
6537905 TTATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGAGGACT
6537968 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
6538033 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGAGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGAGGACT
*
6538096 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCTTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
6538161 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCA
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCA
6538200 TTGCCCTACT
Statistics
Matches: 227, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
128 226 1.00
129 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGAGGACT
Found at i:6538954 original size:16 final size:16
Alignment explanation
Indices: 6538935--6538974 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
6538925 ATTAGCACAC
*
6538935 AAAAATTAATAATTCT
1 AAAAATTAATAATTAT
*
6538951 AAAAAATAATAATTAT
1 AAAAATTAATAATTAT
*
6538967 AAATATTA
1 AAAAATTA
6538975 TTTTAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAATTAATAATTAT
Found at i:6539009 original size:18 final size:17
Alignment explanation
Indices: 6538965--6539011 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
6538955 AATAATAATT
6538965 ATAAATATT-AT-TTTA
1 ATAAATATTAATATTTA
* *
6538980 ATAAAAAATAATATTTA
1 ATAAATATTAATATTTA
6538997 CATAAATATTAATAT
1 -ATAAATATTAATAT
6539012 AAAATATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 7 0.28
16 2 0.08
17 4 0.16
18 12 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAAATATTAATATTTA
Found at i:6539014 original size:30 final size:30
Alignment explanation
Indices: 6538950--6539023 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
6538940 TTAATAATTC
*
6538950 TAAAAAATAATAATTATAAATATTATTTTAA
1 TAAAAAATAATAATTATAAATATTA-TATAA
*
6538981 TAAAAAATAATATTTACATAAATATTA-AT-A
1 TAAAAAATAATAATT--ATAAATATTATATAA
*
6539011 TAAAATATAATAA
1 TAAAAAATAATAA
6539024 CTATTTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 12 0.32
31 15 0.41
33 10 0.27
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (30 bp):
TAAAAAATAATAATTATAAATATTATATAA
Found at i:6539023 original size:33 final size:32
Alignment explanation
Indices: 6538982--6539052 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
6538972 TTATTTTAAT
* * *
6538982 AAAA-AATAA-TATTTACATAAATATTAATATA
1 AAAATAATAACTATTTA-AAAAATACTAACATA
6539013 AAATATAATAACTATTTAAAAAATACTAACATA
1 AAA-ATAATAACTATTTAAAAAATACTAACATA
6539046 AAAATAA
1 AAAATAA
6539053 ATTTCTTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 3 0.09
32 5 0.15
33 20 0.59
34 6 0.18
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (32 bp):
AAAATAATAACTATTTAAAAAATACTAACATA
Found at i:6544376 original size:18 final size:17
Alignment explanation
Indices: 6544353--6544386 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6544343 TGATAACAAA
6544353 AAAATTTATAGCATAAAT
1 AAAATTT-TAGCATAAAT
*
6544371 AAAATTTTAGGATAAA
1 AAAATTTTAGCATAAA
6544387 CACCATTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (17 bp):
AAAATTTTAGCATAAAT
Found at i:6552950 original size:19 final size:19
Alignment explanation
Indices: 6552926--6552962 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6552916 CGTCGTTTTG
6552926 ATTTCTGAAATTTAAACTA
1 ATTTCTGAAATTTAAACTA
*
6552945 ATTTCTTAAATTTAAACT
1 ATTTCTGAAATTTAAACT
6552963 TGTGTAACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTTCTGAAATTTAAACTA
Found at i:6553150 original size:39 final size:39
Alignment explanation
Indices: 6553096--6553175 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
6553086 CTATGAATTT
6553096 TGGATTGTTTTGAGGCCAAGTTCATTTGTTTAATTCAGC
1 TGGATTGTTTTGAGGCCAAGTTCATTTGTTTAATTCAGC
6553135 TGGATTGTTTTGAGGCCAAGTTCATTTGTTTAATTCAGC
1 TGGATTGTTTTGAGGCCAAGTTCATTTGTTTAATTCAGC
6553174 TG
1 TG
6553176 TTACGACAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.44
Consensus pattern (39 bp):
TGGATTGTTTTGAGGCCAAGTTCATTTGTTTAATTCAGC
Found at i:6555847 original size:19 final size:18
Alignment explanation
Indices: 6555812--6555875 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
6555802 TTTATTGAAA
*
6555812 AACCGATAAACCGAACCG
1 AACCGAAAAACCGAACCG
6555830 AACCGAAAAACTCGAACCG
1 AACCGAAAAAC-CGAACCG
6555849 TTAA---AAAAACCGAACCG
1 --AACCGAAAAACCGAACCG
6555866 AACCGAAAAA
1 AACCGAAAAA
6555876 ATCGATTTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.05
17 7 0.18
18 21 0.54
19 7 0.18
21 2 0.05
ACGTcount: A:0.52, C:0.28, G:0.14, T:0.06
Consensus pattern (18 bp):
AACCGAAAAACCGAACCG
Found at i:6555876 original size:19 final size:19
Alignment explanation
Indices: 6555819--6555876 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
6555809 AAAAACCGAT
6555819 AAACCGAACCGAACCG-AA
1 AAACCGAACCGAACCGAAA
*
6555837 AAACTCGAACCGTTA---AAA
1 AAAC-CGAACCG-AACCGAAA
6555855 AAACCGAACCGAACCGAAA
1 AAACCGAACCGAACCGAAA
6555874 AAA
1 AAA
6555877 TCGATTTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
16 1 0.03
17 7 0.22
18 10 0.31
19 13 0.41
20 1 0.03
ACGTcount: A:0.53, C:0.28, G:0.14, T:0.05
Consensus pattern (19 bp):
AAACCGAACCGAACCGAAA
Found at i:6559174 original size:21 final size:21
Alignment explanation
Indices: 6559148--6559350 Score: 159
Period size: 21 Copynumber: 9.5 Consensus size: 21
6559138 GTTTCCAGAT
*
6559148 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
6559169 TCGCAATGCAAACTTCG---A
1 TCGCAATGCGAACTTCGACTA
*
6559187 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
6559208 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
* *
6559228 TCGCAATGCGATA-GTCTACTA
1 TCGCAATGCGA-ACTTCGACTA
*
6559249 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* * *
6559270 TCGTAATGCAAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
6559291 TCGCATTGCGAAATGCGAACTTCGACTA
1 T--C---GC--AATGCGAACTTCGACTA
*
6559319 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
6559340 TCGCATTGCGA
1 TCGCAATGCGA
6559351 TTTACATATT
Statistics
Matches: 147, Mismatches: 19, Indels: 32
0.74 0.10 0.16
Matches are distributed among these distances:
18 16 0.11
20 17 0.12
21 93 0.63
23 3 0.02
26 2 0.01
28 16 0.11
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:6559232 original size:20 final size:22
Alignment explanation
Indices: 6559207--6559260 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 22
6559197 AACTTGGACT
*
6559207 ATCGCAATGCGAATA-TGTA-A
1 ATCGCAATGCGAATAGTCTACA
*
6559227 ATCGCAATGCG-ATAGTCTACT
1 ATCGCAATGCGAATAGTCTACA
6559248 ATCGCAATGCGAA
1 ATCGCAATGCGAA
6559261 CTTGGACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.10
20 14 0.48
21 11 0.38
22 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (22 bp):
ATCGCAATGCGAATAGTCTACA
Found at i:6559329 original size:28 final size:28
Alignment explanation
Indices: 6559274--6559330 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
6559264 GGACTATCGT
* **
6559274 AATGCAAACTTGGACTATCGCATTGCGA
1 AATGCAAACTTCGACTATCGCAACGCGA
*
6559302 AATGCGAACTTCGACTATCGCAACGCGA
1 AATGCAAACTTCGACTATCGCAACGCGA
6559330 A
1 A
6559331 CTTCGACTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (28 bp):
AATGCAAACTTCGACTATCGCAACGCGA
Found at i:6559333 original size:49 final size:49
Alignment explanation
Indices: 6559253--6559350 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
6559243 CTACTATCGC
* * * *
6559253 AATGCGAACTTGGACTATCGTAATGCAAACTTGGACTATCGCATTGCGA
1 AATGCGAACTTCGACTATCGCAACGCAAACTTCGACTATCGCATTGCGA
*
6559302 AATGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCATTGCGA
1 AATGCGAACTTCGACTATCGCAACGCAAACTTCGACTATCGCATTGCGA
6559351 TTTACATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (49 bp):
AATGCGAACTTCGACTATCGCAACGCAAACTTCGACTATCGCATTGCGA
Found at i:6559384 original size:21 final size:21
Alignment explanation
Indices: 6559340--6559427 Score: 83
Period size: 21 Copynumber: 4.2 Consensus size: 21
6559330 ACTTCGACTA
* * *
6559340 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCAAAT
6559360 TCGCATTGCGATAGTCCAAAT
1 TCGCATTGCGATAGTCCAAAT
* *
6559381 TCGCGTTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAAT
*
6559404 TCG--TTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAT
6559423 TCGCA
1 TCGCA
6559428 ACGACTGGTG
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
19 11 0.20
20 12 0.21
21 21 0.38
23 12 0.21
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:6559390 original size:41 final size:40
Alignment explanation
Indices: 6559339--6559427 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 40
6559329 AACTTCGACT
*
6559339 ATCGCATTGCGATTTA-CATATTCGCATTGCGATAGTCCAAA
1 ATCGCATTGCGATTTATCAAATTCG--TTGCGATAGTCCAAA
* *
6559380 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAA
1 ATCGCATTGCGATTTA-T-CAAATTCGTTGCGATAGTCCAAA
6559422 ATCGCA
1 ATCGCA
6559428 ACGACTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
41 14 0.35
42 19 0.47
44 7 0.17
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (40 bp):
ATCGCATTGCGATTTATCAAATTCGTTGCGATAGTCCAAA
Found at i:6559734 original size:21 final size:21
Alignment explanation
Indices: 6559560--6559733 Score: 207
Period size: 21 Copynumber: 8.4 Consensus size: 21
6559550 TTTAAAGATA
*
6559560 GCATTGCGATAGTCCAAGTTC
1 GCATTGCGATAGTCGAAGTTC
6559581 GCATTGCGATAGTCGAAGTTC
1 GCATTGCGATAGTCGAAGTTC
* *
6559602 GCGTTGCGATAGTCCAAGTTC
1 GCATTGCGATAGTCGAAGTTC
*
6559623 GCATTGCGATAGTCG-ACTATC
1 GCATTGCGATAGTCGAAGT-TC
*
6559644 GCATTGCGACT--TAC-TA-TTC
1 GCATTGCGA-TAGT-CGAAGTTC
*
6559663 GCATTGCGATAGTCCAAG-TC
1 GCATTGCGATAGTCGAAGTTC
6559683 GCATTGCGATAGTCGAAGTTC
1 GCATTGCGATAGTCGAAGTTC
*
6559704 GCATTGCGAAAGTCGAAGTTC
1 GCATTGCGATAGTCGAAGTTC
*
6559725 GCGTTGCGA
1 GCATTGCGA
6559734 ATCTGGAAAC
Statistics
Matches: 134, Mismatches: 10, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
18 1 0.01
19 12 0.09
20 25 0.19
21 95 0.71
22 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.28
Consensus pattern (21 bp):
GCATTGCGATAGTCGAAGTTC
Done.