Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2246
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: 68714
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:1215 original size:24 final size:25
Alignment explanation
Indices: 1171--1217 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1161 TAAAGAAATG
*
1171 GAAAAAAAAAGAGAAAGAAAATGAT
1 GAAAAAAAAAGAGAAAAAAAATGAT
1196 GAAAAAAAAAGA-AAAAAAAATG
1 GAAAAAAAAAGAGAAAAAAAATG
1218 TGTCCATCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (25 bp):
GAAAAAAAAAGAGAAAAAAAATGAT
Found at i:2609 original size:40 final size:39
Alignment explanation
Indices: 2435--2617 Score: 249
Period size: 39 Copynumber: 4.7 Consensus size: 39
2425 TCTGTTGATA
* * * *
2435 ACCGGGCTAGGTCCCGAAGGCACTTGTGCGGGTTATGAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAT
* *
2474 ACCGGGCTAAGTCCCAAAGGCATTTATGCGAGTTATTAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAT
* * *
2513 ACTGGGCTAAGTCCCGAAGGTATTTATGCGAGTTATTAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAT
* * *
2552 ATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAT
2591 AACCGGGCTAAGTCCCGAAGGCATTTG
1 -ACCGGGCTAAGTCCCGAAGGCATTTG
2618 AGCTAGTGGC
Statistics
Matches: 127, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 102 0.80
40 25 0.20
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAT
Found at i:2640 original size:79 final size:78
Alignment explanation
Indices: 2435--2640 Score: 218
Period size: 78 Copynumber: 2.6 Consensus size: 78
2425 TCTGTTGATA
* * * * * *
2435 ACCGGGCTAGGTCCCGAAGGCACTTGTGCGGGTTA-TGATACCGGGCTAAGTCCCAAAGGCATTT
1 ACCGGGCTAAGTCCCGAAGGCATTTATGCGAGTGACT-ATATCGGGCTAAGTCCCAAAGGCATTT
* *
2499 ATGCGAGTTATTAT
65 ATGCGAGTCACTAT
* * * * * *
2513 ACTGGGCTAAGTCCCGAAGGTATTTATGCGAGTTATTATATCGGGCTAAGTCCCGAAGGCATTTG
1 ACCGGGCTAAGTCCCGAAGGCATTTATGCGAGTGACTATATCGGGCTAAGTCCCAAAGGCATTTA
2578 TGCGAGTCACTAT
66 TGCGAGTCACTAT
* * *
2591 AACCGGGCTAAGTCCCGAAGGCATTTGA-GCTAGTGGCTATATCTGGCTAA
1 -ACCGGGCTAAGTCCCGAAGGCATTT-ATGCGAGTGACTATATCGGGCTAA
2641 ACTCCGAAGG
Statistics
Matches: 107, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
78 65 0.61
79 41 0.38
80 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (78 bp):
ACCGGGCTAAGTCCCGAAGGCATTTATGCGAGTGACTATATCGGGCTAAGTCCCAAAGGCATTTA
TGCGAGTCACTAT
Found at i:2648 original size:118 final size:117
Alignment explanation
Indices: 2437--2652 Score: 269
Period size: 118 Copynumber: 1.8 Consensus size: 117
2427 TGTTGATAAC
* * *
2437 CGGGCTAGGTCCCGAAGGCACTTGTGCGGGTTATGATACCGGGCTAAGTCCCAAAGGCATTTATG
1 CGGGCTAAGTCCCGAAGGCACTTGTGCGAGTCATGATACCGGGCTAAGTCCCAAAGGCATTTATG
* * *
2502 CGAGTTATTATACTGGGCTAAGTCCCGAAGGTATTTATGCGAGTTATTATAT
66 CGAGTGACTATACTGGGCTAACTCCCGAAGGTATTTATGCGAGTTATTATAT
* *
2554 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACT-ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCACTTGTGCGAGTCA-TGAT-ACCGGGCTAAGTCCCAAAGGCATTT-
* *
2618 A-GCTAGTGGCTATATCT-GGCTAAACT-CCGAAGGTA
63 ATGCGAGTGACTATA-CTGGGCT-AACTCCCGAAGGTA
2653 CTCGTTTGGG
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
117 31 0.37
118 47 0.56
119 6 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (117 bp):
CGGGCTAAGTCCCGAAGGCACTTGTGCGAGTCATGATACCGGGCTAAGTCCCAAAGGCATTTATG
CGAGTGACTATACTGGGCTAACTCCCGAAGGTATTTATGCGAGTTATTATAT
Found at i:4037 original size:16 final size:17
Alignment explanation
Indices: 4018--4060 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
4008 ACTTTCCAAC
*
4018 TTTCAGCCTTTT-GGCT
1 TTTCAGCCTTTTCAGCT
*
4034 TTTC-GGCTTTTCAGCT
1 TTTCAGCCTTTTCAGCT
4050 TTTCAGCCTTT
1 TTTCAGCCTTT
4061 GCAGTTTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 6 0.27
16 11 0.50
17 5 0.23
ACGTcount: A:0.07, C:0.26, G:0.16, T:0.51
Consensus pattern (17 bp):
TTTCAGCCTTTTCAGCT
Found at i:10750 original size:38 final size:38
Alignment explanation
Indices: 10699--10776 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
10689 CAATAGCATC
10699 ATGCAAAGTTAACAAATCCATTCCCAGAATTATGTCAA
1 ATGCAAAGTTAACAAATCCATTCCCAGAATTATGTCAA
10737 ATGCAAAGTTAACAAATCCATTCCCAGAATTATGTCAA
1 ATGCAAAGTTAACAAATCCATTCCCAGAATTATGTCAA
10775 AT
1 AT
10777 TCATTGAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (38 bp):
ATGCAAAGTTAACAAATCCATTCCCAGAATTATGTCAA
Found at i:13671 original size:42 final size:41
Alignment explanation
Indices: 13621--13729 Score: 112
Period size: 43 Copynumber: 2.6 Consensus size: 41
13611 TCGATGCATC
*
13621 TGTCCCAGACAGGGTCTTACACGAAA-TCAGATACAAAGCCGA
1 TGTCCCAGACACGGTCTTACACGAAACTCA-AT-CAAAGCCGA
** * * * *
13663 TGTCCCAGACATAGTCTTATACGAAAATCTCAATCGAGGCCTA
1 TGTCCCAGACACGGTCTTACACG-AAA-CTCAATCAAAGCCGA
13706 TGTCCCAGACACGGTCTTACACGA
1 TGTCCCAGACACGGTCTTACACGA
13730 TGTCTCAAAC
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
42 21 0.38
43 29 0.53
44 2 0.04
45 3 0.05
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (41 bp):
TGTCCCAGACACGGTCTTACACGAAACTCAATCAAAGCCGA
Found at i:15337 original size:18 final size:18
Alignment explanation
Indices: 15316--15358 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
15306 CCTTTCCCCC
*
15316 TTCTTTCATTTGTTTATT
1 TTCTTTCATTTATTTATT
*
15334 TTCTTTCGTTTATTTATT
1 TTCTTTCATTTATTTATT
*
15352 TGCTTTC
1 TTCTTTC
15359 TTTTTATGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.07, T:0.70
Consensus pattern (18 bp):
TTCTTTCATTTATTTATT
Found at i:16041 original size:15 final size:15
Alignment explanation
Indices: 16021--16063 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
16011 TGGAAGATGG
16021 ATAAATAAATAAAAA
1 ATAAATAAATAAAAA
*
16036 ATAAATAAATAAAAT
1 ATAAATAAATAAAAA
*
16051 AGAATATAAATAA
1 ATAA-ATAAATAA
16064 GATAAAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (15 bp):
ATAAATAAATAAAAA
Found at i:16056 original size:5 final size:4
Alignment explanation
Indices: 16021--16069 Score: 50
Period size: 4 Copynumber: 12.2 Consensus size: 4
16011 TGGAAGATGG
16021 ATAA ATAA ATAA A-AA ATAA ATAA ATAAA ATAGA AT-- ATAA ATAA GATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATA-A ATAA ATAA ATAA -ATAA
16069 A
1 A
16070 GAGATAAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
2 2 0.05
3 3 0.08
4 23 0.59
5 11 0.28
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:17371 original size:21 final size:21
Alignment explanation
Indices: 17332--17371 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17322 TTTATTTCAA
*
17332 AATATAAATGATATAGAATAT
1 AATATAAATGAAATAGAATAT
*
17353 AATATAAATGAAATGGAAT
1 AATATAAATGAAATAGAAT
17372 TACTGATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (21 bp):
AATATAAATGAAATAGAATAT
Found at i:17412 original size:21 final size:21
Alignment explanation
Indices: 17379--17419 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17369 AATTACTGAT
* *
17379 AAAAGTTCTATATCTCTATAG
1 AAAAGTTCGATATATCTATAG
*
17400 AAAAGTTGGATATATCTATA
1 AAAAGTTCGATATATCTATA
17420 TAATCAATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (21 bp):
AAAAGTTCGATATATCTATAG
Found at i:17512 original size:14 final size:14
Alignment explanation
Indices: 17493--17521 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17483 TAGATAAATA
17493 ATAATCTATATAAC
1 ATAATCTATATAAC
17507 ATAATCTATATAAC
1 ATAATCTATATAAC
17521 A
1 A
17522 AAGTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATCTATATAAC
Found at i:19106 original size:14 final size:14
Alignment explanation
Indices: 19087--19123 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
19077 ATCAATCAGT
19087 TTTTCCCAAAAGTA
1 TTTTCCCAAAAGTA
19101 TTTTCCCAAAAGTA
1 TTTTCCCAAAAGTA
19115 TTTTCCCAA
1 TTTTCCCAA
19124 TTTTCTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.38
Consensus pattern (14 bp):
TTTTCCCAAAAGTA
Found at i:23114 original size:14 final size:13
Alignment explanation
Indices: 23088--23127 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
23078 GTTTAAAGAC
*
23088 TTTTATTTATTAT
1 TTTTATTTTTTAT
23101 TTTTATGTTTTTAT
1 TTTTAT-TTTTTAT
23115 TTTTATCTTTTTA
1 TTTTAT-TTTTTA
23128 AAACTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:23150 original size:11 final size:11
Alignment explanation
Indices: 23134--23170 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
23124 TTTAAAACTA
23134 ATTTTTATTTT
1 ATTTTTATTTT
23145 ATTTTTATTTT
1 ATTTTTATTTT
* *
23156 AATTTAATTTT
1 ATTTTTATTTT
23167 ATTT
1 ATTT
23171 CATTCTTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:23161 original size:16 final size:16
Alignment explanation
Indices: 23136--23170 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
23126 TAAAACTAAT
* *
23136 TTTTATTTTATTTTTA
1 TTTTAATTTAATTTTA
23152 TTTTAATTTAATTTTA
1 TTTTAATTTAATTTTA
23168 TTT
1 TTT
23171 CATTCTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTAATTTAATTTTA
Found at i:31489 original size:29 final size:29
Alignment explanation
Indices: 31392--31482 Score: 130
Period size: 29 Copynumber: 3.2 Consensus size: 29
31382 TACCTGTATC
* * *
31392 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
* *
31420 TGGCCCATTAGGCCCAAATCACCTGTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
31449 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
31478 TGGCC
1 TGGCC
31483 TGTTAGGTGC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 14 0.25
29 41 0.75
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTATA
Found at i:31743 original size:16 final size:16
Alignment explanation
Indices: 31716--31778 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
31706 GTAGCCAAAC
* *
31716 TTTCGACTTTTCAGCA
1 TTTCGGCTTTTCGGCA
*
31732 TTTTGGCTTTTCGGCA
1 TTTCGGCTTTTCGGCA
*
31748 TTTCGGCATTTCGGCA
1 TTTCGGCTTTTCGGCA
*
31764 TTTCGGCATTTCGGC
1 TTTCGGCTTTTCGGC
31779 TTTTGCCGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (16 bp):
TTTCGGCTTTTCGGCA
Found at i:31743 original size:24 final size:24
Alignment explanation
Indices: 31716--31775 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
31706 GTAGCCAAAC
* * *
31716 TTTCGACTTTTCAGCATTTTGGCT
1 TTTCGACATTTCAGCATTTCGGCA
* *
31740 TTTCGGCATTTCGGCATTTCGGCA
1 TTTCGACATTTCAGCATTTCGGCA
*
31764 TTTCGGCATTTC
1 TTTCGACATTTC
31776 GGCTTTTGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (24 bp):
TTTCGACATTTCAGCATTTCGGCA
Found at i:31753 original size:8 final size:8
Alignment explanation
Indices: 31724--31778 Score: 83
Period size: 8 Copynumber: 6.9 Consensus size: 8
31714 ACTTTCGACT
*
31724 TTTCAGCA
1 TTTCGGCA
* *
31732 TTTTGGCT
1 TTTCGGCA
31740 TTTCGGCA
1 TTTCGGCA
31748 TTTCGGCA
1 TTTCGGCA
31756 TTTCGGCA
1 TTTCGGCA
31764 TTTCGGCA
1 TTTCGGCA
31772 TTTCGGC
1 TTTCGGC
31779 TTTTGCCGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 42 1.00
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.42
Consensus pattern (8 bp):
TTTCGGCA
Found at i:33348 original size:46 final size:47
Alignment explanation
Indices: 33244--33363 Score: 161
Period size: 46 Copynumber: 2.6 Consensus size: 47
33234 TGTTTTCGAC
** * *
33244 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCA-ATATATCTAAT
* *
33292 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
33338 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
33364 CTGTCATGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 34 0.53
48 30 0.47
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:40714 original size:46 final size:47
Alignment explanation
Indices: 40608--40723 Score: 144
Period size: 50 Copynumber: 2.4 Consensus size: 47
40598 TGTCTTCGAC
** * *
40608 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
40658 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
40704 ATGGACTTACATGGCTCATT
1 ATGGACTTACATGGCTCATT
40724 TCTGGTCCTG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
46 29 0.49
50 30 0.51
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:43115 original size:16 final size:16
Alignment explanation
Indices: 43094--43127 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
43084 ACATATAAAC
43094 TGTAATCTGTATTGGA
1 TGTAATCTGTATTGGA
43110 TGTAATCTGTATTGGA
1 TGTAATCTGTATTGGA
43126 TG
1 TG
43128 GCCTTGAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (16 bp):
TGTAATCTGTATTGGA
Found at i:43316 original size:43 final size:43
Alignment explanation
Indices: 43233--43381 Score: 117
Period size: 43 Copynumber: 3.5 Consensus size: 43
43223 CTGAGTTATT
* * * * * *
43233 GTGTAAGACCGTGTCTAGGACACATGCCTCGAT-TGAGATTTAC
1 GTGTAAGACCATGTCTGGGACAAAGGCATCGATAT-TGATTTAC
* * *
43276 GTATAAGACCATGTCTGTGA-AATCGGCATCG-TATCTGATTT-C
1 GTGTAAGACCATGTCTGGGACAA-AGGCATCGATAT-TGATTTAC
* * *
43318 GCGTAAGACCCTGTCTGGGACAAAGGCATCGATATTGAATTAC
1 GTGTAAGACCATGTCTGGGACAAAGGCATCGATATTGATTTAC
* *
43361 ATGTAAGACCATGTCCGGGAC
1 GTGTAAGACCATGTCTGGGAC
43382 GTTGGCATTG
Statistics
Matches: 81, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
42 31 0.38
43 50 0.62
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.27
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACAAAGGCATCGATATTGATTTAC
Found at i:45059 original size:66 final size:67
Alignment explanation
Indices: 44930--45059 Score: 174
Period size: 66 Copynumber: 1.9 Consensus size: 67
44920 GGGATGTATC
*
44930 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
44995 AGGACA
62 AGGACA
* *
45001 CCATGTAGACAAGAGAGCTAC-GAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACGGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
45060 TTCACCATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
66 24 0.44
67 9 0.16
68 1 0.02
71 21 0.38
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (67 bp):
CCATGTAGACAAGAGAGCTACGGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGGA
CA
Found at i:51691 original size:369 final size:370
Alignment explanation
Indices: 51004--51744 Score: 1430
Period size: 369 Copynumber: 2.0 Consensus size: 370
50994 CTTAGTGAAA
51004 GTATTGTGGCACAGACATGGGATAGAAGAAGCTACGTGGGAACTCGAGGAAGCTATGAGGAAACA
1 GTATTGTGGCACAGACATGGGATAGAAGAAGCTACGTGGGAACTCGAGGAAGCTATGAGGAAACA
51069 GTACCTGAACCTCTTTACCGGTAAGATTTTTGGGGACGAAAATCTCTAAAGGGGGGAGAATTGTG
66 GTACCTGAACCTCTTTACCGGTAAGATTTTTGGGGACGAAAATCTCTAAAGGGGGGAGAATTGTG
*
51134 ACAACCCGAATTAGGGCCTAATCGAAATAGTGGTTTCGTGACCACAAATCTGAGATAGAAATAAT
131 ACAACCCGAATTAGGGCCTAATCGAAATAGTGGTTTCGTGACCACAAATCTGAGATACAAATAAT
51199 CATTTTATAATTATTTTGGGGTTTATGATATGATTTCATGATTTCATGAAAATTTCGTGATGAAA
196 CATTTTATAATTATTTTGGGGTTTATGATATGATTTCATGATTTCATGAAAATTTCGTGATGAAA
51264 TTCTGTGCATTTCGCGCTTAAGTTGAGAATAGGGACTAAATCGAATAAATTATAAAACTCATGTT
261 TTCTGTGCATTTCGCGCTTAAGTTGAGAATAGGGACTAAATCGAATAAATTATAAAACTCATGTT
51329 TTAGAAGTTTTTAGTATGAAATTGCTTTGGGATATTAATTAGGAG
326 TTAGAAGTTTTTAGTATGAAATTGCTTTGGGATATTAATTAGGAG
*
51374 GTATTGTGGCACAGACATGGGATAGAAGAAGCTACGTGGGAACTTGAGGAAGCTATGAGGAAACA
1 GTATTGTGGCACAGACATGGGATAGAAGAAGCTACGTGGGAACTCGAGGAAGCTATGAGGAAACA
51439 GTACCTGAACCTCTTTACCGGTAAGATTTTTGGGGACGAAAATCTCTAAA-GGGGGAGAATTGTG
66 GTACCTGAACCTCTTTACCGGTAAGATTTTTGGGGACGAAAATCTCTAAAGGGGGGAGAATTGTG
* *
51503 ACAACCCGAATTAGGGCCTAATCGGAATAGTGGTTTTGTGACCACAAATCTGAGATACAAATAAT
131 ACAACCCGAATTAGGGCCTAATCGAAATAGTGGTTTCGTGACCACAAATCTGAGATACAAATAAT
51568 CATTTTATAATTATTTTGGGGTTTATGATATGATTTCATGATTTCATGAAAATTTCGTGATGAAA
196 CATTTTATAATTATTTTGGGGTTTATGATATGATTTCATGATTTCATGAAAATTTCGTGATGAAA
*
51633 TTCTGTGCATTTCGCGCTTAAGTTGAGAATAGGGACTAAATCGAATAAATTGTAAAACTCATGTT
261 TTCTGTGCATTTCGCGCTTAAGTTGAGAATAGGGACTAAATCGAATAAATTATAAAACTCATGTT
51698 TTAGAAGTTTTTAGTATGAAATTGCTTTGGGATATTAATTAGGAG
326 TTAGAAGTTTTTAGTATGAAATTGCTTTGGGATATTAATTAGGAG
51743 GT
1 GT
51745 CTTAAATAGC
Statistics
Matches: 366, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
369 252 0.69
370 114 0.31
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (370 bp):
GTATTGTGGCACAGACATGGGATAGAAGAAGCTACGTGGGAACTCGAGGAAGCTATGAGGAAACA
GTACCTGAACCTCTTTACCGGTAAGATTTTTGGGGACGAAAATCTCTAAAGGGGGGAGAATTGTG
ACAACCCGAATTAGGGCCTAATCGAAATAGTGGTTTCGTGACCACAAATCTGAGATACAAATAAT
CATTTTATAATTATTTTGGGGTTTATGATATGATTTCATGATTTCATGAAAATTTCGTGATGAAA
TTCTGTGCATTTCGCGCTTAAGTTGAGAATAGGGACTAAATCGAATAAATTATAAAACTCATGTT
TTAGAAGTTTTTAGTATGAAATTGCTTTGGGATATTAATTAGGAG
Found at i:52915 original size:66 final size:67
Alignment explanation
Indices: 52786--52915 Score: 165
Period size: 66 Copynumber: 1.9 Consensus size: 67
52776 GGGATGTATC
* *
52786 CCATGTGGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
52851 AGGACA
62 AGGACA
* *
52857 CCATGTAGACAAGAGAGCTAC-GAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACGGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
52916 TTCACCATGT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
66 24 0.44
67 9 0.17
68 1 0.02
71 20 0.37
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (67 bp):
CCATGTAGACAAGAGAGCTACGGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGGA
CA
Found at i:56576 original size:41 final size:43
Alignment explanation
Indices: 56531--56662 Score: 139
Period size: 43 Copynumber: 3.1 Consensus size: 43
56521 CAGCAGGAAG
* *
56531 CTGCTAGACTTTAAG-TCTGA-ACTCA-TTCACCGGCATT-TCGC
1 CTGCTAGACTTGAAGCTC-GATA-TCATTTCACCGGCATTATAGC
*
56572 CTGCTAGGCTTGAAGCTCGATATCATTTCACCGGCATTATAGC
1 CTGCTAGACTTGAAGCTCGATATCATTTCACCGGCATTATAGC
* * * *
56615 CTGCTAGGCTCGAAGC-CTGATATTATCTCACCGGCATTATAGC
1 CTGCTAGACTTGAAGCTC-GATATCATTTCACCGGCATTATAGC
56658 CTGCT
1 CTGCT
56663 TGGCCCGAAG
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
41 18 0.22
42 16 0.20
43 46 0.57
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (43 bp):
CTGCTAGACTTGAAGCTCGATATCATTTCACCGGCATTATAGC
Found at i:56624 original size:43 final size:43
Alignment explanation
Indices: 56556--56679 Score: 162
Period size: 43 Copynumber: 2.9 Consensus size: 43
56546 TCTGAACTCA
* *
56556 TTCACCGGCATT-TCGCCTGCTAGGCTTGAAG-CTCGATATCAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCT-GATATCAT
*
56598 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCTGATATTAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCTGATATCAT
* * * *
56641 CTCACCGGCATTATAGCCTGCTTGGCCCGAAGCCCGATA
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCTGATA
56680 ATATTATTCA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
42 12 0.16
43 59 0.81
44 2 0.03
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (43 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCTGATATCAT
Found at i:62505 original size:40 final size:40
Alignment explanation
Indices: 62253--62498 Score: 388
Period size: 40 Copynumber: 6.2 Consensus size: 40
62243 AACCCAAGTA
* * *
62253 CCTTCGGGATTTAG-TCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* * *
62292 CCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAGATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
62332 CCTTCGGGACTTAGCCTGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
62372 CCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
62412 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
62452 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
62492 CCTTCGG
1 CCTTCGG
62499 ATCTTAGTCC
Statistics
Matches: 190, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
39 13 0.07
40 177 0.93
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Done.