Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015497.1 Corchorus capsularis cultivar CVL-1 contig15518, 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: 91466
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:559 original size:2 final size:2
Alignment explanation
Indices: 552--577 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
542 ATTAAATTTG
552 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
578 TAAGGAAATC
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:2899 original size:19 final size:19
Alignment explanation
Indices: 2877--2966 Score: 103
Period size: 19 Copynumber: 4.7 Consensus size: 19
2867 TTGGAGAATA
* *
2877 ACTTTAAGTTTAGGGTTTG
1 ACTTTCAGTTTGGGGTTTG
*
2896 ACTTTCATTTTGGGGTTTG
1 ACTTTCAGTTTGGGGTTTG
2915 ACTTT-ATGTTTGGGGGTTT-
1 ACTTTCA-GTTT-GGGGTTTG
* *
2934 ACTTTCATTTTGGGGATTG
1 ACTTTCAGTTTGGGGTTTG
2953 ACTTTCAGTTTGGG
1 ACTTTCAGTTTGGG
2967 CTTTCAGTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
18 7 0.12
19 45 0.75
20 8 0.13
ACGTcount: A:0.14, C:0.09, G:0.28, T:0.49
Consensus pattern (19 bp):
ACTTTCAGTTTGGGGTTTG
Found at i:2908 original size:38 final size:38
Alignment explanation
Indices: 2866--2964 Score: 92
Period size: 38 Copynumber: 2.6 Consensus size: 38
2856 TTACAATCGG
2866 TTTGGAGAATAACTTTAAGTTT-AGGGTTTGACTTTCAT
1 TTTGGAGAATAACTTTAAGTTTGAGGGTTT-ACTTTCAT
* ** * * *
2904 TTTGGGGTTTGACTTTATGTTTGGGGGTTTACTTTCAT
1 TTTGGAGAATAACTTTAAGTTTGAGGGTTTACTTTCAT
* * * *
2942 TTTGGGGATTGACTTTCAGTTTG
1 TTTGGAGAATAACTTTAAGTTTG
2965 GGCTTTCAGT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 45 0.88
39 6 0.12
ACGTcount: A:0.17, C:0.08, G:0.26, T:0.48
Consensus pattern (38 bp):
TTTGGAGAATAACTTTAAGTTTGAGGGTTTACTTTCAT
Found at i:2965 original size:38 final size:39
Alignment explanation
Indices: 2889--2966 Score: 124
Period size: 38 Copynumber: 2.0 Consensus size: 39
2879 TTTAAGTTTA
*
2889 GGGTTTGACTTTCATTTTGGGGTTTGACTTTATGTTTGG
1 GGGTTTGACTTTCATTTTGGGGATTGACTTTATGTTTGG
2928 GGGTTT-ACTTTCATTTTGGGGATTGACTTTCA-GTTTGG
1 GGGTTTGACTTTCATTTTGGGGATTGACTTT-ATGTTTGG
2966 G
1 G
2967 CTTTCAGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
38 30 0.81
39 7 0.19
ACGTcount: A:0.12, C:0.09, G:0.31, T:0.49
Consensus pattern (39 bp):
GGGTTTGACTTTCATTTTGGGGATTGACTTTATGTTTGG
Found at i:10390 original size:17 final size:17
Alignment explanation
Indices: 10368--10403 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
10358 CTGAAGAATC
*
10368 CTATGGGTACTTATATG
1 CTATGGGTAATTATATG
10385 CTATGGGTAATTATATG
1 CTATGGGTAATTATATG
10402 CT
1 CT
10404 TCTAATTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (17 bp):
CTATGGGTAATTATATG
Found at i:14010 original size:26 final size:27
Alignment explanation
Indices: 13981--14033 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
13971 CACCTCTGCT
13981 TCCTCCATAACTATATT-CCCTGTTCA
1 TCCTCCATAACTATATTCCCCTGTTCA
14007 TCCTCCATAACTATATTCCCCTGTTCA
1 TCCTCCATAACTATATTCCCCTGTTCA
14034 CATTCAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.23, C:0.36, G:0.04, T:0.38
Consensus pattern (27 bp):
TCCTCCATAACTATATTCCCCTGTTCA
Found at i:23225 original size:23 final size:23
Alignment explanation
Indices: 23195--23252 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
23185 CCAAGATCTA
*
23195 AAGATCTGGAGACTCAAACATCC
1 AAGATCTGAAGACTCAAACATCC
23218 AAGATCTGAAGACTCAAACATCC
1 AAGATCTGAAGACTCAAACATCC
*
23241 AAGATCTAAAGA
1 AAGATCTGAAGA
23253 GATCAACAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.45, C:0.22, G:0.16, T:0.17
Consensus pattern (23 bp):
AAGATCTGAAGACTCAAACATCC
Found at i:23260 original size:23 final size:23
Alignment explanation
Indices: 23208--23258 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
23198 ATCTGGAGAC
* *
23208 TCAAACATCCAAGATCTGAAGAC
1 TCAAACATCCAAGATCTAAAGAA
23231 TCAAACATCCAAGATCTAAAGAGA
1 TCAAACATCCAAGATCTAAAGA-A
23255 TCAA
1 TCAA
23259 CAGATCTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (23 bp):
TCAAACATCCAAGATCTAAAGAA
Found at i:26657 original size:11 final size:11
Alignment explanation
Indices: 26641--26698 Score: 57
Period size: 10 Copynumber: 5.4 Consensus size: 11
26631 GCCTCTCTTC
*
26641 TTTCTTTTTCT
1 TTTCTTTTTGT
26652 TTTC-TTTTGT
1 TTTCTTTTTGT
*
26662 TTTGTTTTTGTT
1 TTTCTTTTTG-T
*
26674 TTTGTTTTTGT
1 TTTCTTTTTGT
*
26685 TTT-TTTTTTT
1 TTTCTTTTTGT
26695 TTTC
1 TTTC
26699 ACTCATCTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
10 17 0.41
11 13 0.32
12 11 0.27
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (11 bp):
TTTCTTTTTGT
Found at i:26678 original size:12 final size:12
Alignment explanation
Indices: 26656--26697 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
26646 TTTTCTTTTC
26656 TTTTG-TTTTGT
1 TTTTGTTTTTGT
26667 TTTTGTTTTTGT
1 TTTTGTTTTTGT
26679 TTTTGTTTTT-T
1 TTTTGTTTTTGT
26690 TTTT-TTTT
1 TTTTGTTTT
26698 CACTCATCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.13
11 10 0.33
12 16 0.53
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (12 bp):
TTTTGTTTTTGT
Found at i:31967 original size:13 final size:13
Alignment explanation
Indices: 31949--31973 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31939 TTTCCTTCTT
31949 CAGTCCATTTTTC
1 CAGTCCATTTTTC
31962 CAGTCCATTTTT
1 CAGTCCATTTTT
31974 GTTGGGTCCG
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:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (13 bp):
CAGTCCATTTTTC
Found at i:34394 original size:409 final size:410
Alignment explanation
Indices: 33634--34443 Score: 1496
Period size: 409 Copynumber: 2.0 Consensus size: 410
33624 GCTTTTGAAT
*
33634 CCTTGATGAAAGTTGTAGACCATGAAATTACCTTTAAATAGACACCTGAATTACCTTGATCGGAC
1 CCTTGATGAAAGTTGTAGACCATGAAATTACCTTTAAATAGACACCTAAATTACCTTGATCGGAC
*
33699 AAATAGAAAAAAAAATAAAAGAATTACAGCCGAAACATTCAATCATCCAACCCATAATTGTAAAG
66 AAATAGAAAAAAAAATAAAAGAATTAAAGCCGAAACATTCAATCATCCAACCCATAATTGTAAAG
*
33764 GATTAAATAGCATAAAACATAAAAGTATGAGGATCATTTGATAAATAATCCAACAAAAAAATGAT
131 GATTAAATAGCATAAAACATAAAAGTATGAGAATCATTTGATAAATAATCCAACAAAAAAATGAT
*
33829 TTGTTTATTGAGAGTGGGACCCATCAAATAGTAACTTTATCCTAAAGTTTCCAAAATACCCTCAA
196 TTGTTTATTGAGAGTGGGACCCACCAAATAGTAACTTTATCCTAAAGTTTCCAAAATACCCTCAA
* *
33894 CAATTAACAATTATAACGAAAATACCGAGTATGAAAGTACCGAAACACCCCTGACAATTTATTCT
261 CAATTAACAATAATAACGAAAATACCGAGTATGAAAGTACCGAAACACCCATGACAATTTATTCT
* *
33959 TGGGAGAATGTGGTGCATCTTATAGCTGGACAAAAGGGTATTTCCATTTTCAACTTTAATATATG
326 TGGGAGAATGTGGTGCATCTTATAGCTGGACAAAAGGATAATTCCATTTTCAACTTTAATATATG
34024 TTATAGATATAAAAGAATTA
391 TTATAGATATAAAAGAATTA
34044 CCTTGATGAAAGTTGTAGACCATGAAATTACCTTTAAATAGACACCTAAATTACCTTGATCGGAC
1 CCTTGATGAAAGTTGTAGACCATGAAATTACCTTTAAATAGACACCTAAATTACCTTGATCGGAC
* *
34109 AAATAG-AAAAAAGATAAAAGAATTAAAGCCGAAACATTCAATCGTCCAACCCATAATTGTAAAG
66 AAATAGAAAAAAAAATAAAAGAATTAAAGCCGAAACATTCAATCATCCAACCCATAATTGTAAAG
*
34173 GATTAAATAGCATAAAATATAAAAGTATGAGAATCATTTGATAAATAATCCAACAAAAAAATGAT
131 GATTAAATAGCATAAAACATAAAAGTATGAGAATCATTTGATAAATAATCCAACAAAAAAATGAT
*
34238 TTGTTTATTGAGAGTGGGATCCACCAAATAGTAACTTTATCCTAAAGTTTCCAAAATACCCTCAA
196 TTGTTTATTGAGAGTGGGACCCACCAAATAGTAACTTTATCCTAAAGTTTCCAAAATACCCTCAA
34303 CAATTAACAATAATAACGAAAATACCGAGTATGAAAGTACCGAAACACCCATGACAATTTATTCT
261 CAATTAACAATAATAACGAAAATACCGAGTATGAAAGTACCGAAACACCCATGACAATTTATTCT
34368 TGGGAGAATGTGGTGCATCTTATAGCTGGACAAAAGGATAATTCCATTTTCAACTTTAATATATG
326 TGGGAGAATGTGGTGCATCTTATAGCTGGACAAAAGGATAATTCCATTTTCAACTTTAATATATG
*
34433 TTATATATATA
391 TTATAGATATA
34444 TATATATATA
Statistics
Matches: 387, Mismatches: 13, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
409 317 0.82
410 70 0.18
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (410 bp):
CCTTGATGAAAGTTGTAGACCATGAAATTACCTTTAAATAGACACCTAAATTACCTTGATCGGAC
AAATAGAAAAAAAAATAAAAGAATTAAAGCCGAAACATTCAATCATCCAACCCATAATTGTAAAG
GATTAAATAGCATAAAACATAAAAGTATGAGAATCATTTGATAAATAATCCAACAAAAAAATGAT
TTGTTTATTGAGAGTGGGACCCACCAAATAGTAACTTTATCCTAAAGTTTCCAAAATACCCTCAA
CAATTAACAATAATAACGAAAATACCGAGTATGAAAGTACCGAAACACCCATGACAATTTATTCT
TGGGAGAATGTGGTGCATCTTATAGCTGGACAAAAGGATAATTCCATTTTCAACTTTAATATATG
TTATAGATATAAAAGAATTA
Found at i:38253 original size:22 final size:22
Alignment explanation
Indices: 38227--38309 Score: 116
Period size: 21 Copynumber: 3.8 Consensus size: 22
38217 AATTAGAACT
*
38227 AATTTAGTAATTTAGAAATTAT
1 AATTTAGTAATTTAGAAATTAG
38249 AATTTAAGTAATTTTAGAAATTAG
1 AATTT-AGTAA-TTTAGAAATTAG
*
38273 AA-TAAGTAATTTAGAAATTAG
1 AATTTAGTAATTTAGAAATTAG
38294 AATTTAGTAA-TTAGAA
1 AATTTAGTAATTTAGAA
38310 CTAATTAGTA
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
21 20 0.36
22 16 0.29
23 6 0.11
24 13 0.24
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (22 bp):
AATTTAGTAATTTAGAAATTAG
Found at i:38307 original size:14 final size:14
Alignment explanation
Indices: 38209--38309 Score: 66
Period size: 14 Copynumber: 7.1 Consensus size: 14
38199 AGTAGTATTC
38209 AATTTAGTAATTAG
1 AATTTAGTAATTAG
* *
38223 AA-CTA--ATTTAG
1 AATTTAGTAATTAG
* *
38234 TAATTTAGAAATTAT
1 -AATTTAGTAATTAG
38249 AATTTAAGTAATTTTAG
1 AATTT-AGTAA--TTAG
* *
38266 AAATTAG-AATAAG
1 AATTTAGTAATTAG
*
38279 TAATTTAGAAATTAG
1 -AATTTAGTAATTAG
38294 AATTTAGTAATTAG
1 AATTTAGTAATTAG
38308 AA
1 AA
38310 CTAATTAGTA
Statistics
Matches: 66, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
11 5 0.08
12 2 0.03
13 7 0.11
14 28 0.42
15 15 0.23
16 2 0.03
17 7 0.11
ACGTcount: A:0.48, C:0.01, G:0.12, T:0.40
Consensus pattern (14 bp):
AATTTAGTAATTAG
Found at i:38316 original size:45 final size:42
Alignment explanation
Indices: 38209--38336 Score: 128
Period size: 45 Copynumber: 3.1 Consensus size: 42
38199 AGTAGTATTC
*
38209 AATTTAGTAATTAGAACTAATT--TAGTAATTTAGAAATTAT
1 AATTTAGTAATTAGAACTAATTAGTAGTAATTTAGAAATTAG
38249 AATTTAAGTAATTTTAG-A--AATTAGAATAAGTAATTTAGAAATTAG
1 AATTT-AGTAA--TTAGAACTAATTAG--T-AGTAATTTAGAAATTAG
*
38294 AATTTAGTAATTAGAACTAA-T--TAGTAATTTAGAAAATAG
1 AATTTAGTAATTAGAACTAATTAGTAGTAATTTAGAAATTAG
38333 AATT
1 AATT
38337 AAATTAAACT
Statistics
Matches: 75, Mismatches: 2, Indels: 23
0.75 0.02 0.23
Matches are distributed among these distances:
39 20 0.27
40 10 0.13
41 5 0.07
42 5 0.07
43 5 0.07
44 7 0.09
45 23 0.31
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.39
Consensus pattern (42 bp):
AATTTAGTAATTAGAACTAATTAGTAGTAATTTAGAAATTAG
Found at i:38325 original size:25 final size:24
Alignment explanation
Indices: 38288--38334 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
38278 GTAATTTAGA
* *
38288 AATTAGAATTTAGTAATTAGAACT
1 AATTAGAATTTAGAAAATAGAACT
38312 AATTAGTAATTTAGAAAATAGAA
1 AATTAG-AATTTAGAAAATAGAA
38335 TTAAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.34
Consensus pattern (24 bp):
AATTAGAATTTAGAAAATAGAACT
Found at i:46648 original size:16 final size:16
Alignment explanation
Indices: 46627--46657 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
46617 AAATTTTAAC
46627 AAACCCTCTCCAAGCT
1 AAACCCTCTCCAAGCT
46643 AAACCCTCTCCAAGC
1 AAACCCTCTCCAAGC
46658 ACTAACTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.45, G:0.06, T:0.16
Consensus pattern (16 bp):
AAACCCTCTCCAAGCT
Found at i:47721 original size:3 final size:3
Alignment explanation
Indices: 47713--47748 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
47703 GGATGAGTAG
47713 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
47749 AATAGGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:54136 original size:16 final size:16
Alignment explanation
Indices: 54115--54147 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54105 ATTTATTAGT
54115 CAAGAGGCCCAAG-GCC
1 CAAGA-GCCCAAGTGCC
54131 CAAGAGCCCAAGTGCC
1 CAAGAGCCCAAGTGCC
54147 C
1 C
54148 TCATCATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.30, C:0.39, G:0.27, T:0.03
Consensus pattern (16 bp):
CAAGAGCCCAAGTGCC
Found at i:58695 original size:2 final size:2
Alignment explanation
Indices: 58690--58716 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58680 TATAAATCCT
58690 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
58717 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:58721 original size:2 final size:2
Alignment explanation
Indices: 58716--58743 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58706 ACACACACAC
58716 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
58744 TATCGTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59504 original size:7 final size:7
Alignment explanation
Indices: 59492--59527 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
59482 AACTGCAACC
59492 AATTTGG
1 AATTTGG
59499 AATTTGG
1 AATTTGG
59506 AATTTGG
1 AATTTGG
59513 AATTTGG
1 AATTTGG
59520 AATTTGG
1 AATTTGG
59527 A
1 A
59528 TGGCTCTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.42
Consensus pattern (7 bp):
AATTTGG
Found at i:65751 original size:67 final size:67
Alignment explanation
Indices: 65643--65776 Score: 250
Period size: 67 Copynumber: 2.0 Consensus size: 67
65633 AATACATTAG
65643 CTTCCCTATATACAAATTATCTCTAATTTCACTATCTATAACTACCAACATACTAAATACACAAA
1 CTTCCCTATATACAAATTATCTCTAATTTCACTATCTATAACTACCAACATACTAAATACACAAA
65708 CA
66 CA
* *
65710 CTTCCCTATTTACAAATTATCTCTAATTTCACTATCTATAACTATCAACATACTAAATACACAAA
1 CTTCCCTATATACAAATTATCTCTAATTTCACTATCTATAACTACCAACATACTAAATACACAAA
65775 CA
66 CA
65777 AATAAATTAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.33
Consensus pattern (67 bp):
CTTCCCTATATACAAATTATCTCTAATTTCACTATCTATAACTACCAACATACTAAATACACAAA
CA
Found at i:65970 original size:6 final size:6
Alignment explanation
Indices: 65959--65983 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
65949 CCCTGCTGAC
65959 TTTAGA TTTAGA TTTAGA TTTAGA T
1 TTTAGA TTTAGA TTTAGA TTTAGA T
65984 CTGAGATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TTTAGA
Found at i:67082 original size:439 final size:438
Alignment explanation
Indices: 66123--67093 Score: 1149
Period size: 439 Copynumber: 2.2 Consensus size: 438
66113 ATTGAATATC
* ** * ** * *
66123 TGGA-AAAAAATAATATGAAATTAAATAGATTGTCAATCGAAATTACAAAATTTCAAAAGTATTT
1 TGGACAAAAAATTATATGAAATTAAATAGACCGACAATCGAAACCAC-AAATTTCAGAAGCATTT
* * * ** *
66187 TTTAGAATTGAAACATGAAAGTTAGCTTTTGAGTTTTTCATGAAAGTTGTAGATCATAAAATTAC
65 TTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATAATAAAATTAC
* * * * *
66252 CTTTTAATAAACACCTGAATTACCTTAATTGGACAAATAGAACAAAGAAAATAAAAAAGAAATGA
130 CTTTTAATAAACACATGAATCAACTTAATCGGACAAATAGAACAAAGAAAAT-AAAAAGAAATAA
*
66317 AGCGTTAAATCGAATAAGATAGAATTTGTAAATGACTAAGTAGCATAAAATAGAAAAGTATGAGG
194 AGCGTTAAATCGAATAAGATAGAATTTGTAAATGACTAAGTAGCATAAAATAGAAAAATATGAGG
* * * * * * *
66382 GTCATTTCATAACTAATTCAAATAAGAAAATATTTCTTAATGGATATCTTGAAACATAAAAATTT
259 ATCATTTAATAAATAATCCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAAACTC
* * *
66447 CCTTTTAAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTCGTAG
324 CCTTTTAAACCCTTCATGAAACTCGCAGATCAAATTAACTTTCGGGTCCTTCATGAAAGTCGTAA
* * * *
66512 ATCATACAATAACCTCATGATCTACACTTGAATAACTTTAATCGGAAATG
389 ATCATACAATAACATCATGAACTACACTTCAATAACTTCAATCGGAAATG
* * * * *
66562 TGGATC-GAAAATTATATGATATTAAATAGACCAACAATCGAAACGACCAAATTT-AGGAAGCCT
1 TGGA-CAAAAAATTATATGAAATTAAATAGACCGACAATCGAAACCA-CAAATTTCA-GAAG-CA
* * *
66625 TTTTTTTGAATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATAATGAAAT
62 TTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATAATAAAAT
66690 TACCTTTTAATAGAA-ACATGAATCAACTTAATCGGACAAATAGAACAAA-AAAAT-AAAA-AAA
127 TACCTTTTAATA-AACACATGAATCAACTTAATCGGACAAATAGAACAAAGAAAATAAAAAGAAA
* * * *
66751 TAAATC-TTAAA-CGTTAGATTAAGATAGAATTTGTTAA-GCACTAAGTAGTATAAAGTAGAAAA
191 TAAAGCGTTAAATCG--A-A-TAAGATAGAATTTGTAAATG-ACTAAGTAGCATAAAATAGAAAA
* * *
66813 ATATGAGGATCATTTAATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCAT
251 ATATGAGGATCATTTAATAAATAATCCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACAT
* * *
66878 AAAAACTCCCTTTTGAACCCTTCATGAAACTCGCAGATCAAATTTAGCTTTCTGGTCCTTCATGA
316 AAAAACTCCCTTTTAAACCCTTCATGAAACTCGCAGATCAAA-TTAACTTTCGGGTCCTTCATGA
* * *
66943 AAGTCGTAAATCATGA-AATAACAT-TTTAACTGACACTTCAATAACTTCGATC-GAACATG
380 AAGTCGTAAATCAT-ACAATAACATCATGAACT-ACACTTCAATAACTTCAATCGGAA-ATG
* * * *
67002 TGGACAAAAAATTATACGAAATTAAATTGACCGGCAATCAAAACCACAAACTTTCAGAAGCATTT
1 TGGACAAAAAATTATATGAAATTAAATAGACCGACAATCGAAACCACAAA-TTTCAGAAGCATTT
* *
67067 TTTAGAATCAAAACATTAAAATTAGCT
65 TTTAGAATTAAAACATAAAAATTAGCT
67094 AAATAGCCCT
Statistics
Matches: 447, Mismatches: 67, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
435 2 0.00
436 5 0.01
437 8 0.02
438 6 0.01
439 176 0.39
440 147 0.33
441 101 0.23
442 2 0.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (438 bp):
TGGACAAAAAATTATATGAAATTAAATAGACCGACAATCGAAACCACAAATTTCAGAAGCATTTT
TTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATAATAAAATTACC
TTTTAATAAACACATGAATCAACTTAATCGGACAAATAGAACAAAGAAAATAAAAAGAAATAAAG
CGTTAAATCGAATAAGATAGAATTTGTAAATGACTAAGTAGCATAAAATAGAAAAATATGAGGAT
CATTTAATAAATAATCCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAAACTCCC
TTTTAAACCCTTCATGAAACTCGCAGATCAAATTAACTTTCGGGTCCTTCATGAAAGTCGTAAAT
CATACAATAACATCATGAACTACACTTCAATAACTTCAATCGGAAATG
Found at i:67179 original size:29 final size:30
Alignment explanation
Indices: 67137--67194 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
67127 TTAGGCCAAC
*
67137 TTGCCCCCTAAACTA-ATAATTGTGCCACA
1 TTGCCCCCTAAACTACAAAATTGTGCCACA
* *
67166 TTGCCCCTTTAACTATCAAAATTGTGCCA
1 TTGCCCCCTAAACTA-CAAAATTGTGCCA
67195 ATCTACCTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.54
31 11 0.46
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.31
Consensus pattern (30 bp):
TTGCCCCCTAAACTACAAAATTGTGCCACA
Found at i:67773 original size:15 final size:15
Alignment explanation
Indices: 67748--67789 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
67738 AAAAAACCCG
67748 AACCCGAAAAAGCTC-A
1 AACCCGAAAAA--TCAA
67764 AACCCGAAAAATCAA
1 AACCCGAAAAATCAA
67779 AACCCGAAAAA
1 AACCCGAAAAA
67790 ACCCGAACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.08
15 12 0.48
16 11 0.44
ACGTcount: A:0.57, C:0.29, G:0.10, T:0.05
Consensus pattern (15 bp):
AACCCGAAAAATCAA
Found at i:67814 original size:16 final size:16
Alignment explanation
Indices: 67726--67802 Score: 84
Period size: 16 Copynumber: 4.9 Consensus size: 16
67716 AACCCGTCCG
*
67726 AACCCGAACCCAAAAA
1 AACCCGAACCCGAAAA
67742 AACCCGAACCCGAAAA
1 AACCCGAACCCGAAAA
* * *
67758 AGCTCAAACCCG-AAA
1 AACCCGAACCCGAAAA
* **
67773 AATCAAAACCCGAAAA
1 AACCCGAACCCGAAAA
67789 AACCCGAACCCGAA
1 AACCCGAACCCGAA
67803 CCTGAAAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
15 11 0.22
16 38 0.78
ACGTcount: A:0.52, C:0.35, G:0.10, T:0.03
Consensus pattern (16 bp):
AACCCGAACCCGAAAA
Found at i:68039 original size:32 final size:32
Alignment explanation
Indices: 68003--68108 Score: 122
Period size: 32 Copynumber: 3.3 Consensus size: 32
67993 CAATCCGAGG
* *
68003 CCAAACCCGAATTAACCTGACCCAAAATTGAC
1 CCAAACCCGAATCAACCTGACCCAAAATTAAC
* *
68035 CCAAACCCGAATCAACATGACCCAAATTTAAC
1 CCAAACCCGAATCAACCTGACCCAAAATTAAC
* * * *
68067 CCGAACCTGAATCAACCCGACCCAAATTTAAC
1 CCAAACCCGAATCAACCTGACCCAAAATTAAC
* *
68099 TCGAACCCGA
1 CCAAACCCGA
68109 CTTAAGCCCG
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.40, C:0.36, G:0.09, T:0.15
Consensus pattern (32 bp):
CCAAACCCGAATCAACCTGACCCAAAATTAAC
Found at i:68234 original size:13 final size:14
Alignment explanation
Indices: 68216--68252 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
68206 TTAGATCTCA
68216 TGTTTTTTTT-TTC
1 TGTTTTTTTTCTTC
68229 TGTTTTTTCTTCTTC
1 TGTTTTTT-TTCTTC
68244 T-TTTTTTTT
1 TGTTTTTTTT
68253 GACAAGACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (14 bp):
TGTTTTTTTTCTTC
Found at i:68557 original size:20 final size:20
Alignment explanation
Indices: 68528--68573 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
68518 GGGATGAACA
*
68528 TTCTTAGTGTTCAT-CATTTG
1 TTCTTGGTGTTCATGC-TTTG
68548 TTCTTGGTGTTCATGCTTTG
1 TTCTTGGTGTTCATGCTTTG
68568 TTCTTG
1 TTCTTG
68574 AAAAAGGGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.09, C:0.15, G:0.20, T:0.57
Consensus pattern (20 bp):
TTCTTGGTGTTCATGCTTTG
Found at i:70546 original size:17 final size:18
Alignment explanation
Indices: 70514--70547 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
70504 AATTTTCTTT
*
70514 TAATATATTAATTAAATG
1 TAATATATTAAATAAATG
70532 TAATA-ATTAAATAAAT
1 TAATATATTAAATAAAT
70548 TATTTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TAATATATTAAATAAATG
Found at i:70656 original size:2 final size:2
Alignment explanation
Indices: 70649--70689 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
70639 GTGCAAAACA
*
70649 AT AT AT AT AT AT AT AT AT AA 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 AT AT AT AT AT AT A
70690 CTAGTAATCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:71020 original size:2 final size:2
Alignment explanation
Indices: 71013--71039 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
71003 GGACAAAAAT
71013 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
71040 TATATAACAT
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:71181 original size:136 final size:136
Alignment explanation
Indices: 71031--71281 Score: 484
Period size: 136 Copynumber: 1.8 Consensus size: 136
71021 ACACACACAC
71031 ACACACACATATATAACATGAATTTAGAATCCTTCTTAATACTTGTAATATTACATCTGAGTTTT
1 ACACACACATATATAACATGAATTTAGAATCCTTCTTAATACTTGTAATATTACATCTGAGTTTT
*
71096 GAATGTGATATAAAAACTATGTACTCACTAATTTGAAGAGTACATAACAAAATTGATTCCGGACA
66 GAATGTGATATAAAAACTATGTACTCACTAATTTGAAGAGTACAAAACAAAATTGATTCCGGACA
71161 AAATAT
131 AAATAT
*
71167 ACACACATATATATAACATGAATTTAGAATCCTTCTTAATACTTGTAATATTACATCTGAGTTTT
1 ACACACACATATATAACATGAATTTAGAATCCTTCTTAATACTTGTAATATTACATCTGAGTTTT
71232 GAATGTGATATAAAAACTATGTACTCACTAATTTGAAGAGTACAAAACAA
66 GAATGTGATATAAAAACTATGTACTCACTAATTTGAAGAGTACAAAACAA
71282 CCCAATTATG
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 113 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (136 bp):
ACACACACATATATAACATGAATTTAGAATCCTTCTTAATACTTGTAATATTACATCTGAGTTTT
GAATGTGATATAAAAACTATGTACTCACTAATTTGAAGAGTACAAAACAAAATTGATTCCGGACA
AAATAT
Found at i:76036 original size:26 final size:26
Alignment explanation
Indices: 76010--76060 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
76000 TTGTTTCTTA
* *
76010 TAATTACTTTTTTTTTTATAATTTTAT
1 TAATTAATTTTATTTTT-TAATTTTAT
*
76037 TACTTAATTTTATTTTTTAATTTT
1 TAATTAATTTTATTTTTTAATTTT
76061 TTTTAAAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (26 bp):
TAATTAATTTTATTTTTTAATTTTAT
Found at i:79927 original size:31 final size:31
Alignment explanation
Indices: 79858--79959 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 31
79848 TCCTTTTGTG
* * **
79858 CACGTGGCATGCCACGTGCCATTTTTTGAAA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* *
79889 TATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * * *
79920 CACGTGGCGTGACATGTGTCACTTTTTGGTG
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
79951 CATGTGGCA
1 CACGTGGCA
79960 CAACTTTTTG
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:79967 original size:53 final size:53
Alignment explanation
Indices: 79909--80011 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
79899 GCCACGTGTC
** * * *
79909 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTGCATGTGGCACA
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTCTTGGTCCACGTGGCACA
* *
79962 ACTTTTTGGTACATGTGGCGTGTCACATGTCACTTCTTGGTCCACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTCTTGGTCCACGTGGC
80012 GTGCCACGTC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.16, C:0.21, G:0.27, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTCTTGGTCCACGTGGCACA
Found at i:81427 original size:28 final size:29
Alignment explanation
Indices: 81376--81445 Score: 106
Period size: 28 Copynumber: 2.4 Consensus size: 29
81366 CATGATTAAT
81376 AAAGTGTCTTTTTTCTCTATTGCAAAAAAA
1 AAAGTGTCTTTTTTCTC-ATTGCAAAAAAA
81406 AAAGTGTCTTTTTTCTC-TTGCAAAAAAA
1 AAAGTGTCTTTTTTCTCATTGCAAAAAAA
**
81434 AAAAAGTCTTTT
1 AAAGTGTCTTTT
81446 CTCATATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 21 0.55
30 17 0.45
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (29 bp):
AAAGTGTCTTTTTTCTCATTGCAAAAAAA
Found at i:82731 original size:23 final size:23
Alignment explanation
Indices: 82687--82731 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
82677 AATTAAATCC
**
82687 TAAAAAAATTAAAGTATATAAAA
1 TAAAAAAATTAAAAAATATAAAA
82710 TAAAAAAATTTAAAAAAT-TAAA
1 TAAAAAAA-TTAAAAAATATAAA
82732 GTATATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
TAAAAAAATTAAAAAATATAAAA
Found at i:82740 original size:18 final size:18
Alignment explanation
Indices: 82689--82746 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
82679 TTAAATCCTA
82689 AAAAAATTAAAGTATA-T
1 AAAAAATTAAAGTATATT
*
82706 AAAATAA--AAA-AAT-TT
1 AAAA-AATTAAAGTATATT
82721 AAAAAATTAAAGTATATT
1 AAAAAATTAAAGTATATT
82739 AAAAAATT
1 AAAAAATT
82747 TGTTTTGAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
14 2 0.06
15 7 0.21
16 6 0.18
17 6 0.18
18 12 0.36
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAAAATTAAAGTATATT
Found at i:82742 original size:17 final size:17
Alignment explanation
Indices: 82690--82743 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
82680 TAAATCCTAA
82690 AAAAATTAAAGTATA-T
1 AAAAATTAAAGTATATT
* **
82706 -AAAATAAAAAAAT-TT
1 AAAAATTAAAGTATATT
82721 AAAAAATTAAAGTATATT
1 -AAAAATTAAAGTATATT
82739 AAAAA
1 AAAAA
82744 ATTTGTTTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 7
0.68 0.15 0.17
Matches are distributed among these distances:
15 11 0.39
17 15 0.54
18 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (17 bp):
AAAAATTAAAGTATATT
Found at i:83464 original size:39 final size:39
Alignment explanation
Indices: 83407--83482 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
83397 CAAGAGTGAA
*
83407 AGAGTTTATTTACCAAAAATGTCAAAAGCCACTGATCGG
1 AGAGTTTATGTACCAAAAATGTCAAAAGCCACTGATCGG
* *
83446 AGAGTTTATGTACTAAAAATGTCAAAAGCCCCTGATC
1 AGAGTTTATGTACCAAAAATGTCAAAAGCCACTGATC
83483 AGAAAGAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (39 bp):
AGAGTTTATGTACCAAAAATGTCAAAAGCCACTGATCGG
Found at i:86599 original size:200 final size:199
Alignment explanation
Indices: 86221--86619 Score: 672
Period size: 200 Copynumber: 2.0 Consensus size: 199
86211 TAATTGCACG
* * *
86221 TTAGGGAAATAAATATTTTAATCATAATAATACATTAAACTATCAAATAGAATATGTCAATCACA
1 TTAGGGAAATAAAAATTTCAATCATAATAATACATTAAACTATCAAATAGAACATGTCAATCACA
*
86286 ATAACCTTTTCAATTAAAATGGTAAAAATAAAACAATTATATAATATTGAATTTAATTAAATGAA
66 ATAACCTTTTAAATTAAAATGGTAAAAATAAAACAATTATATAATATTGAATTTAATTAAATGAA
* *
86351 AATAGAGTTTTTAGTAAAATAAAACTGTGTAATAAAAATTTTAATATATCCAATTTTTATTGAAA
131 AATAGAGTTTTTAGTAAAATAAAACTGTATAATAAAAATTTAAATATATCCAATTTTTATTGAAA
86416 AATA
196 AATA
*
86420 TTAGGGAAATAATAAATTTCAATCATAATAATACATTAAACTATCAAATAGAACATGTCAATGAC
1 TTAGGGAAATAA-AAATTTCAATCATAATAATACATTAAACTATCAAATAGAACATGTCAATCAC
* *
86485 AATAATCTTTTAAATTAAAATGGTAAAAATAAAATAATTATATAATATTGAATTTAATTAAATGA
65 AATAACCTTTTAAATTAAAATGGTAAAAATAAAACAATTATATAATATTGAATTTAATTAAATGA
* * * *
86550 AAATATAGTTTTTAGTAGAATAAAACTGTATATTAGAAATTTAAATATATCCAATTTTTATTGAA
130 AAATAGAGTTTTTAGTAAAATAAAACTGTATAATAAAAATTTAAATATATCCAATTTTTATTGAA
86615 AAATA
195 AAATA
86620 GTAAAATGGT
Statistics
Matches: 186, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
199 12 0.06
200 174 0.94
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.36
Consensus pattern (199 bp):
TTAGGGAAATAAAAATTTCAATCATAATAATACATTAAACTATCAAATAGAACATGTCAATCACA
ATAACCTTTTAAATTAAAATGGTAAAAATAAAACAATTATATAATATTGAATTTAATTAAATGAA
AATAGAGTTTTTAGTAAAATAAAACTGTATAATAAAAATTTAAATATATCCAATTTTTATTGAAA
AATA
Found at i:87181 original size:12 final size:13
Alignment explanation
Indices: 87164--87198 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
87154 ACTTTAAGAA
87164 ATATAAAAAGATT
1 ATATAAAAAGATT
*
87177 A-ATAAAAAAATT
1 ATATAAAAAGATT
87189 ATATAAAAAG
1 ATATAAAAAG
87199 TAAATTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (13 bp):
ATATAAAAAGATT
Found at i:87912 original size:3 final size:3
Alignment explanation
Indices: 87904--87938 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
87894 TTTGATTACA
87904 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
87939 AAAAGAGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.