Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005982.1 Corchorus capsularis cultivar CVL-1 contig06000, 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: 50057
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:9011 original size:16 final size:16
Alignment explanation
Indices: 8990--9076 Score: 70
Period size: 16 Copynumber: 5.4 Consensus size: 16
8980 AAACCTTAAC
*
8990 CCGAAAAAATCCGAAT
1 CCGAAAAAAGCCGAAT
*
9006 CCG-AAAAAGCTCAAAT
1 CCGAAAAAAGC-CGAAT
** *
9022 CCGAAAAAATACGAAC
1 CCGAAAAAAGCCGAAT
* *
9038 CCG-AAAAAGCTCAAAC
1 CCGAAAAAAGC-CGAAT
*
9054 CCGAAAAAACCCGAAT
1 CCGAAAAAAGCCGAAT
9070 CCGAAAA
1 CCGAAAA
9077 TTTATGAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
15 11 0.20
16 33 0.60
17 11 0.20
ACGTcount: A:0.52, C:0.28, G:0.13, T:0.08
Consensus pattern (16 bp):
CCGAAAAAAGCCGAAT
Found at i:9026 original size:32 final size:32
Alignment explanation
Indices: 8987--9076 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
8977 TCTAAACCTT
8987 AACCCGAAAAAATCCGAATCCGAAAAAGCTCA
1 AACCCGAAAAAATCCGAATCCGAAAAAGCTCA
* * *
9019 AATCCGAAAAAATACGAACCCGAAAAAGCTCA
1 AACCCGAAAAAATCCGAATCCGAAAAAGCTCA
*
9051 AACCCGAAAAAACCCGAATCCGAAAA
1 AACCCGAAAAAATCCGAATCCGAAAA
9077 TTTATGAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.52, C:0.28, G:0.12, T:0.08
Consensus pattern (32 bp):
AACCCGAAAAAATCCGAATCCGAAAAAGCTCA
Found at i:9240 original size:31 final size:30
Alignment explanation
Indices: 9213--9317 Score: 147
Period size: 31 Copynumber: 3.4 Consensus size: 30
9203 ACCCAAACAG
9213 AACCCGAACCCGAATTAACCTGACCAAATTC
1 AACCCGAACCCGAATTAACCTGACCAAA-TC
*
9244 AACCCGAACCCGAATTAACCTGACCCAAATT
1 AACCCGAACCCGAATTAACCTGA-CCAAATC
* *
9275 AACCCGAACCCGAATTAACATGACCCGAATCC
1 AACCCGAACCCGAATTAACCTGA-CCAAAT-C
9307 AACCCGAACCC
1 AACCCGAACCC
9318 AATAACACGA
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 52 0.76
32 16 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.13
Consensus pattern (30 bp):
AACCCGAACCCGAATTAACCTGACCAAATC
Found at i:9274 original size:15 final size:15
Alignment explanation
Indices: 9220--9304 Score: 91
Period size: 15 Copynumber: 5.5 Consensus size: 15
9210 CAGAACCCGA
9220 ACCCGAATTAACCTG
1 ACCCGAATTAACCTG
* *
9235 A-CCAAATTCAACCCG
1 ACCCGAATT-AACCTG
9250 AACCCGAATTAACCTG
1 -ACCCGAATTAACCTG
* *
9266 ACCCAAATTAACCCG
1 ACCCGAATTAACCTG
*
9281 AACCCGAATTAACATG
1 -ACCCGAATTAACCTG
9297 ACCCGAAT
1 ACCCGAAT
9305 CCAACCCGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
14 6 0.11
15 27 0.47
16 18 0.32
17 6 0.11
ACGTcount: A:0.39, C:0.34, G:0.11, T:0.16
Consensus pattern (15 bp):
ACCCGAATTAACCTG
Found at i:9340 original size:31 final size:32
Alignment explanation
Indices: 9213--9341 Score: 117
Period size: 31 Copynumber: 4.1 Consensus size: 32
9203 ACCCAAACAG
* **
9213 AACCCGAACCCGAATTAAC-CTGA-CCAAATTC
1 AACCCGAACCCGAATTAACAC-GACCCGAACCC
***
9244 AACCCGAACCCGAATTAAC-CTGACCC-AAATT
1 AACCCGAACCCGAATTAACAC-GACCCGAACCC
* *
9275 AACCCGAACCCGAATTAACATGACCCGAATCC
1 AACCCGAACCCGAATTAACACGACCCGAACCC
9307 AACCCGAACCC-AA-TAACACGAGCCCGAACCC
1 AACCCGAACCCGAATTAACACGA-CCCGAACCC
9338 AACC
1 AACC
9342 TGACCCGCCC
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.08
31 64 0.74
32 15 0.17
ACGTcount: A:0.39, C:0.39, G:0.11, T:0.12
Consensus pattern (32 bp):
AACCCGAACCCGAATTAACACGACCCGAACCC
Found at i:9521 original size:17 final size:17
Alignment explanation
Indices: 9499--9531 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9489 GTGAGTATAA
*
9499 AATTTCATCTATATTAG
1 AATTTCATCCATATTAG
9516 AATTTCATCCATATTA
1 AATTTCATCCATATTA
9532 ATGTATAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (17 bp):
AATTTCATCCATATTAG
Found at i:10568 original size:31 final size:31
Alignment explanation
Indices: 10526--10584 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
10516 GTTAGATAAG
* *
10526 TAAGGATATAATATG-TATTTTAAAAGTTAAA
1 TAAGGACATAATA-GATATTTCAAAAGTTAAA
10557 TAAGGACATAATAGATATTTCAAAAGTT
1 TAAGGACATAATAGATATTTCAAAAGTT
10585 TCTCAAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (31 bp):
TAAGGACATAATAGATATTTCAAAAGTTAAA
Found at i:10622 original size:13 final size:13
Alignment explanation
Indices: 10604--10643 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
10594 TCGTATTTTT
10604 ATATATAGTATAG
1 ATATATAGTATAG
10617 ATATATAGTATAG
1 ATATATAGTATAG
*
10630 ATAGATAG-ATAG
1 ATATATAGTATAG
10642 AT
1 AT
10644 TTTGTAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.35
Consensus pattern (13 bp):
ATATATAGTATAG
Found at i:10633 original size:17 final size:18
Alignment explanation
Indices: 10603--10641 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
10593 CTCGTATTTT
10603 TATA-TATAGTATAGATA
1 TATAGTATAGTATAGATA
10620 TATAGTATAG-ATAGATA
1 TATAGTATAGTATAGATA
*
10637 GATAG
1 TATAG
10642 ATTTTGTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (18 bp):
TATAGTATAGTATAGATA
Found at i:12782 original size:28 final size:28
Alignment explanation
Indices: 12742--12799 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
12732 GTGATTCATG
*
12742 AAAGTCGTAGATCATGGAATAACCTTTT
1 AAAGTCGTAGATCATGAAATAACCTTTT
* * *
12770 AAAGTTGTAGATCATGAAATTATCTTTT
1 AAAGTCGTAGATCATGAAATAACCTTTT
12798 AA
1 AA
12800 TAGACACTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (28 bp):
AAAGTCGTAGATCATGAAATAACCTTTT
Found at i:13668 original size:426 final size:426
Alignment explanation
Indices: 12868--13672 Score: 1096
Period size: 426 Copynumber: 1.9 Consensus size: 426
12858 GATAGAATCA
* * * * *
12868 ACTAAGTAGTATAAAATAGAAAAATGTGAGGGTCCTTTGATAAATAATCCAAATAAGAAAATGTT
1 ACTAAGTAGTATAAAATAAAAAAATATGAGGATCATTCGATAAATAATCCAAATAAGAAAATGTT
* * *
12933 TGTTGGTGGAGATCTTGAAACATAAAAATTTATTTTCGAGTCCTTCATGAAACTCGTAAATCAAA
66 TGTTGATGGAAATCTTGAAACATAAAAATTTATTTTCGAGCCCTTCATGAAACTCGTAAATCAAA
* * *
12998 TTTAGCTTTCGCCCCCTTCATGAAAGTCGTAGATCATGCAATAACCTTTTAATCGAAACTTGAAT
131 TTTAGCTTTCGCCCCCTTCATGAAAGTCGTAGATCATGCAATAAACTTTTAACCGAAACCTGAAT
* * * * * * * *
13063 AATTTTAATCGGACATGTAGATTAAAAATTATTTGGTATTAAATAGACTGATAATCGAAACCACA
196 AAGTTTAACCGGACACGTAGATTAAAAATTATATGATATTAAATAGACCGACAATCAAAACCACA
* * * * *
13128 AAATTTTAAAAGTATTTTTTAGAATTGAAACATAAAAATTGACTTTTGACTTCTTCATGAAATTT
261 AAATTTCAAAAGCATTTTTTAGAATTGAAACATAAAAATTGACTTTTGACTCCTTCACGAAAGTT
* * *
13193 GTAGATCATGAAATTATCTTTTAGTAGACATCTAAATCACCAAAATCGGACAAATAAAAAAATAA
326 GTAGATCATGAAATTACCTTCTAATAGACATCTAAATCACCAAAATCGGACAAATAAAAAAATAA
13258 AGCTGAAACGTTAAATTAAGATAGAATTATTAAAGG
391 AGCTGAAACGTTAAATTAAGATAGAATTATTAAAGG
* * *
13294 ACTAAGTAGTATGAAGTAAAAAAATATGATGATCATTCGATAAATAATCCAAATAAGAAAATGTT
1 ACTAAGTAGTATAAAATAAAAAAATATGAGGATCATTCGATAAATAATCCAAATAAGAAAATGTT
* * * *
13359 TGTTGATGGAAATCTTGAAACATGAAAATTCTGTTTT-GAGCCCTTTATGAAACTCGTATATCAA
66 TGTTGATGGAAATCTTGAAACATAAAAATT-TATTTTCGAGCCCTTCATGAAACTCGTAAATCAA
*** **
13423 ATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAGATCATGCAATAAACTTTTAACCGGCACCTGAA
130 ATTTAGCTTTCGCCCCCTTCATGAAAGTCGTAGATCATGCAATAAACTTTTAACCGAAACCTGAA
*
13488 TAAGTTTAACCGGACAC--ACGAATTGAAAATTATATGATATTAAATAGACCGACAATCAAAACC
195 TAAGTTTAACCGGACACGTA-G-ATTAAAAATTATATGATATTAAATAGACCGACAATCAAAACC
* * * * * *
13551 ACTAAATTTCAGAAGCATTTTTTTGAATTGAAACATTAAAATTGGCTTTTGAGTCCTTCACGAAA
258 ACAAAATTTCAAAAGCATTTTTTAGAATTGAAACATAAAAATTGACTTTTGACTCCTTCACGAAA
* * **
13616 GTTGTAGATCATGAGATTACCTTCTAATAGACA-CATGAATCACCTTAATCGGACAAA
323 GTTGTAGATCATGAAATTACCTTCTAATAGACATC-TAAATCACCAAAATCGGACAAA
13673 CAGAACAAAA
Statistics
Matches: 325, Mismatches: 50, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
424 1 0.00
425 2 0.01
426 317 0.98
427 5 0.02
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (426 bp):
ACTAAGTAGTATAAAATAAAAAAATATGAGGATCATTCGATAAATAATCCAAATAAGAAAATGTT
TGTTGATGGAAATCTTGAAACATAAAAATTTATTTTCGAGCCCTTCATGAAACTCGTAAATCAAA
TTTAGCTTTCGCCCCCTTCATGAAAGTCGTAGATCATGCAATAAACTTTTAACCGAAACCTGAAT
AAGTTTAACCGGACACGTAGATTAAAAATTATATGATATTAAATAGACCGACAATCAAAACCACA
AAATTTCAAAAGCATTTTTTAGAATTGAAACATAAAAATTGACTTTTGACTCCTTCACGAAAGTT
GTAGATCATGAAATTACCTTCTAATAGACATCTAAATCACCAAAATCGGACAAATAAAAAAATAA
AGCTGAAACGTTAAATTAAGATAGAATTATTAAAGG
Found at i:13998 original size:2 final size:2
Alignment explanation
Indices: 13987--14029 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
13977 TATGGTTCTT
13987 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
14028 TA
1 TA
14030 CTAGTCATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14997 original size:149 final size:149
Alignment explanation
Indices: 14824--15121 Score: 535
Period size: 149 Copynumber: 2.0 Consensus size: 149
14814 CACAATAACA
* * *
14824 TTTTCAATTAAAATGGTAAAAATAAAATAATTATAAAAATTTTGAATTTAATTAAATGAAAATAG
1 TTTTAAATTAAAATGGCAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
*
14889 ATTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAAT
66 AGTTTTTA-TAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAAT
14954 AGT-AATGGTAAAAATAAAC
130 AGTAAATGGTAAAAATAAAC
14973 TTTTAAATTAAAATGGCAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
1 TTTTAAATTAAAATGGCAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
15038 AGTTTTTATAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAATA
66 AGTTTTTATAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAATA
15103 GTAAAATGGTAAAAATAAA
131 GT-AAATGGTAAAAATAAA
15122 GTAATTATAA
Statistics
Matches: 143, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
148 59 0.41
149 69 0.48
150 15 0.10
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (149 bp):
TTTTAAATTAAAATGGCAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
AGTTTTTATAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAATA
GTAAATGGTAAAAATAAAC
Found at i:15318 original size:2 final size:2
Alignment explanation
Indices: 15271--15305 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
15261 CTTGTACTTT
15271 TA TA TA TA -A 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
15306 CATAAACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16690 original size:38 final size:38
Alignment explanation
Indices: 16634--16707 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
16624 AGTAATCCTA
*
16634 CAAGTCCAATCTCAATTCTCATTAATGGCATCAAGTAT
1 CAAGTCCAACCTCAATTCTCATTAATGGCATCAAGTAT
*
16672 CAAGTCCAACCTCGATTCTCATTAATGGCATCAAGT
1 CAAGTCCAACCTCAATTCTCATTAATGGCATCAAGT
16708 CCAACCTCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (38 bp):
CAAGTCCAACCTCAATTCTCATTAATGGCATCAAGTAT
Found at i:18940 original size:24 final size:23
Alignment explanation
Indices: 18913--18961 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
18903 ACTAGCAAAT
18913 TTTTTTAATTTTACTTTATATTTC
1 TTTTTTAATTTTACTTTAT-TTTC
** *
18937 TTTTTTTCTTTTTCTTTATTTTC
1 TTTTTTAATTTTACTTTATTTTC
18960 TT
1 TT
18962 CTTCTTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTTAATTTTACTTTATTTTC
Found at i:18960 original size:15 final size:14
Alignment explanation
Indices: 18933--18968 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
18923 TTACTTTATA
18933 TTTCTTTTTTTCTT
1 TTTCTTTTTTTCTT
18947 TTTCTTTATTTTCTT
1 TTTCTTT-TTTTCTT
*
18962 CTTCTTT
1 TTTCTTT
18969 CTCTCCTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTCTTTTTTTCTT
Found at i:27927 original size:31 final size:31
Alignment explanation
Indices: 27861--27931 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
27851 TGTTGGCTTC
* * * **
27861 AATTGAACCAATCTTATGAGTATACGGACTG
1 AATTGATCAAATCTTATGAGTACACGGACCA
27892 AATTGATCAAATCTTATGAGTACA-GAGACCA
1 AATTGATCAAATCTTATGAGTACACG-GACCA
27923 AATTGATCA
1 AATTGATCA
27932 TTTTTTTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (31 bp):
AATTGATCAAATCTTATGAGTACACGGACCA
Found at i:31642 original size:36 final size:36
Alignment explanation
Indices: 31596--31783 Score: 272
Period size: 36 Copynumber: 5.2 Consensus size: 36
31586 CTCTTTTTAG
*
31596 ATTAAATTCTTTATTGACTTC-ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGAC-TCGACTTAATTACCCTGA
31632 ATTAAGTTCTTTATTGACTCGACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCGACTTAATTACCCTGA
* *
31668 ATTAAGTTCTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCGACTTAATTACCCTGA
*
31704 ATTAAG-TCTCTAACTTGACTCGACTTAATTACCCTGA
1 ATTAAGTTCT-TTA-TTGACTCGACTTAATTACCCTGA
* * *
31741 ATTAAGTTCTCTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCGACTTAATTACCCTGA
31777 ATTAAGT
1 ATTAAGT
31784 CTCTAACTTG
Statistics
Matches: 138, Mismatches: 10, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
35 5 0.04
36 102 0.74
37 28 0.20
38 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.40
Consensus pattern (36 bp):
ATTAAGTTCTTTATTGACTCGACTTAATTACCCTGA
Found at i:31756 original size:73 final size:73
Alignment explanation
Indices: 31617--31796 Score: 319
Period size: 73 Copynumber: 2.5 Consensus size: 73
31607 TATTGACTTC
* *
31617 ACTTAATTACCCTGAATTAAGT-TCTTTA-TTGACTCGACTTAATTACCCTGAATTAAGTTCTTT
1 ACTTAATTACCCTGAATTAAGTCTC-TAACTTGACTCGACTTAATTACCCTGAATTAAGTTCTCT
31680 ATTGACGCT
65 ATTGACGCT
31689 ACTTAATTACCCTGAATTAAGTCTCTAACTTGACTCGACTTAATTACCCTGAATTAAGTTCTCTA
1 ACTTAATTACCCTGAATTAAGTCTCTAACTTGACTCGACTTAATTACCCTGAATTAAGTTCTCTA
31754 TTGACGCT
66 TTGACGCT
31762 ACTTAATTACCCTGAATTAAGTCTCTAACTTGACT
1 ACTTAATTACCCTGAATTAAGTCTCTAACTTGACT
31797 TGATTCCCTT
Statistics
Matches: 104, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
72 24 0.23
73 80 0.77
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.39
Consensus pattern (73 bp):
ACTTAATTACCCTGAATTAAGTCTCTAACTTGACTCGACTTAATTACCCTGAATTAAGTTCTCTA
TTGACGCT
Found at i:31878 original size:37 final size:37
Alignment explanation
Indices: 31826--31912 Score: 140
Period size: 37 Copynumber: 2.4 Consensus size: 37
31816 CAAGTCCCTA
*
31826 ACTTAATTCCCTTCCTTGGAATTAAGTT-TTAAACTCT
1 ACTTAATCCCCTTCCTTGGAATTAAGTTCTT-AACTCT
*
31863 ATTTAATCCCCTTCCTTGGAATTAAGTTCTTAACTCT
1 ACTTAATCCCCTTCCTTGGAATTAAGTTCTTAACTCT
31900 ACTTAATCCCCTT
1 ACTTAATCCCCTT
31913 GGGTTAAGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 44 0.96
38 2 0.04
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.43
Consensus pattern (37 bp):
ACTTAATCCCCTTCCTTGGAATTAAGTTCTTAACTCT
Found at i:32038 original size:41 final size:40
Alignment explanation
Indices: 31987--32207 Score: 269
Period size: 41 Copynumber: 5.7 Consensus size: 40
31977 AATTACCCAG
31987 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTGCTTGA
1 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT-CTTGA
* * *
32028 AATTAAGTCTGTGCTTTTCTTTACTTAATTACC--C-TG-
1 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCTTGA
* *
32064 AATCAAGTCTGTGCTTGTCCTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT-CTTGA
* * *
32105 AATTAAGTCTGTGCTTTTCTTTACTTAATTGCC--CTT--
1 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCTTGA
*
32141 AATTAAGTCTGTGCTTGTCCTTACCTAATTTCCTTTCTTGA
1 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCC-TTCTTGA
*
32182 AATTAAGTTTGTGCTTGTCTTTACCT
1 AATTAAGTCTGTGCTTGTCTTTACCT
32208 TCTTTTACTT
Statistics
Matches: 151, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
36 57 0.38
37 2 0.01
38 4 0.03
39 4 0.03
40 2 0.01
41 82 0.54
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.47
Consensus pattern (40 bp):
AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCTTGA
Found at i:32055 original size:77 final size:77
Alignment explanation
Indices: 31970--32205 Score: 391
Period size: 77 Copynumber: 3.1 Consensus size: 77
31960 CTTTGATGAA
* * *
31970 TTTACTTAATTACCCAGAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTGCTTGAAATTAAG
1 TTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCCTTACCTAATTTCCTTCCTTGAAATTAAG
32035 TCTGTGCTTTTC
66 TCTGTGCTTTTC
*
32047 TTTACTTAATTACCCTGAATCAAGTCTGTGCTTGTCCTTACCTAATTTCCTTCCTTGAAATTAAG
1 TTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCCTTACCTAATTTCCTTCCTTGAAATTAAG
32112 TCTGTGCTTTTC
66 TCTGTGCTTTTC
* * *
32124 TTTACTTAATTGCCCTTAATTAAGTCTGTGCTTGTCCTTACCTAATTTCCTTTCTTGAAATTAAG
1 TTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCCTTACCTAATTTCCTTCCTTGAAATTAAG
* *
32189 TTTGTGCTTGTC
66 TCTGTGCTTTTC
32201 TTTAC
1 TTTAC
32206 CTTCTTTTAC
Statistics
Matches: 149, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 149 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (77 bp):
TTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCCTTACCTAATTTCCTTCCTTGAAATTAAG
TCTGTGCTTTTC
Found at i:32312 original size:45 final size:45
Alignment explanation
Indices: 32209--32685 Score: 648
Period size: 45 Copynumber: 10.6 Consensus size: 45
32199 TCTTTACCTT
*
32209 CTTTTACTTAATTACCCTGAATTAAG-TCTTT-A---ACTGTGTTTT
1 CTTTT-CTTAATTACCCTGAATTAAGAT-TTTGACTGACTGTGTTTA
* *
32251 CTTTTTCTTAATTACCCTGAAATAAGACTTTGACTGACTGTGTTTA
1 C-TTTTCTTAATTACCCTGAATTAAGATTTTGACTGACTGTGTTTA
* *
32297 CTTTTCTTAATTACCCT-AATTTAAGATTTTGACTGACTAG-GGTTG
1 CTTTTCTTAATTACCCTGAA-TTAAGATTTTGACTGACT-GTGTTTA
*
32342 CTTTTCTTAATTACCCTGAATTAAGACTTT-ATCTGACTGTGTTTA
1 CTTTTCTTAATTACCCTGAATTAAGATTTTGA-CTGACTGTGTTTA
**
32387 CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGGTTGTGTTTA
1 CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGACTGTGTTTA
*
32432 CTTTTCTTAATTACCCCGAATTAAGATTTTGACTGACTGTGTTTA
1 CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGACTGTGTTTA
* * * * *
32477 CCTTTCTTAATTACCCTGAACTAAGATTTTGACTGACTCTGGTTG
1 CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGACTGTGTTTA
* *
32522 CTTTTCTTAATTATCCTGAATTAAGACTTCT-ACTGACTGTGTTTA
1 CTTTTCTTAATTACCCTGAATTAAGA-TTTTGACTGACTGTGTTTA
*
32567 CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGGCTGTGTTTA
1 CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGACTGTGTTTA
* * *
32612 GTTTTCTTAATTACCTTGAATTAAGATTTTGACTGACTATGTTTA
1 CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGACTGTGTTTA
32657 CTTTTCTTAATTACCCTGAATTAAGATTT
1 CTTTTCTTAATTACCCTGAATTAAGATTT
32686 CGAATGCCTT
Statistics
Matches: 383, Mismatches: 38, Indels: 25
0.86 0.09 0.06
Matches are distributed among these distances:
42 23 0.06
43 5 0.01
44 7 0.02
45 331 0.86
46 17 0.04
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (45 bp):
CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGACTGTGTTTA
Found at i:32744 original size:37 final size:36
Alignment explanation
Indices: 32657--32980 Score: 420
Period size: 37 Copynumber: 8.9 Consensus size: 36
32647 ACTATGTTTA
* *
32657 CTTTT-CTTAATTACCCTGAATTAAGATT-TCGAA-TG
1 CTTTTACTTAATTGCCCTGAATTAAG-TTCT-TAACTG
* * *
32692 CCTTTACTTAATTACCCTGAATTAAGTCCTCTAACTG
1 CTTTTACTTAATTGCCCTGAATTAAGTTCT-TAACTG
* * *
32729 CTTTTACTTAATTACCCTGAATTAAGTACCTTAACCG
1 CTTTTACTTAATTGCCCTGAATTAAGT-TCTTAACTG
* *
32766 CTTTTACTTAATTTCCCTGAATTAAGTTCTTTACCTG
1 CTTTTACTTAATTGCCCTGAATTAAGTTC-TTAACTG
* *
32803 CTTTTACTTAATTGTCCTGAAGTAAGTTCTTAACTG
1 CTTTTACTTAATTGCCCTGAATTAAGTTCTTAACTG
32839 CTCTTTACTTAATTGCCCTGAATTAAGTTCTTAACTG
1 CT-TTTACTTAATTGCCCTGAATTAAGTTCTTAACTG
32876 CTCTTTACTTAATTGCCCTGAATTAAGTTCTTAACCTG
1 CT-TTTACTTAATTGCCCTGAATTAAGTTCTTAA-CTG
*
32914 CTTTTACTTAATTGTCCTGAATTAAGTTCTTAACTG
1 CTTTTACTTAATTGCCCTGAATTAAGTTCTTAACTG
**
32950 CTTTTACTTAATTTTCCTGAATTAAGTTCTT
1 CTTTTACTTAATTGCCCTGAATTAAGTTCTT
32981 TAATCGCTTT
Statistics
Matches: 265, Mismatches: 17, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
35 5 0.02
36 66 0.25
37 186 0.70
38 8 0.03
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (36 bp):
CTTTTACTTAATTGCCCTGAATTAAGTTCTTAACTG
Found at i:36589 original size:44 final size:44
Alignment explanation
Indices: 36197--36595 Score: 545
Period size: 44 Copynumber: 9.1 Consensus size: 44
36187 AGCGACTAAA
* * *
36197 AACTGAAAAGTTGTTAGAATGCCCCCTACTTGGAGCAACTAAAT
1 AACTGAAAAGTTGTTGGAATGCCCCCTCCTTGGAGCAACTGAAT
* * * *
36241 AACTTAAAAGTTGCTGGAATGCCCCCTTCTTGGAGCAACTGAAA
1 AACTGAAAAGTTGTTGGAATGCCCCCTCCTTGGAGCAACTGAAT
*
36285 AACTGTAAAGTTGTTGGAATGCCCCCTCCTTGGAGCAACTGAAT
1 AACTGAAAAGTTGTTGGAATGCCCCCTCCTTGGAGCAACTGAAT
*
36329 AACTGAAAAGTTGTTGGAATGCCCCTTCCTTGGAGCAACTGAA-
1 AACTGAAAAGTTGTTGGAATGCCCCCTCCTTGGAGCAACTGAAT
* * * *
36372 AAGATGTAAAGTTGTTGAAATGCCCCCTCCTTGGAGCAACCGAAT
1 AA-CTGAAAAGTTGTTGGAATGCCCCCTCCTTGGAGCAACTGAAT
* * * *
36417 AAATGAAATGTTGTAGGAATGCCCCTTCCTTGGAGCAACTGAA-
1 AACTGAAAAGTTGTTGGAATGCCCCCTCCTTGGAGCAACTGAAT
* * * *
36460 AAGCTGTAAAGTTGTTGAAATGCCTCCTCCTTGGAGCAAC-CAAGT
1 AA-CTGAAAAGTTGTTGGAATGCCCCCTCCTTGGAGCAACTGAA-T
36505 AACTGAAAAGTTGTTGGAATGCCCCCTCCTTGGAGCAACTGAAT
1 AACTGAAAAGTTGTTGGAATGCCCCCTCCTTGGAGCAACTGAAT
*
36549 AACTGAAAAGTTGTTGGAATTCCCCCTCCTTGGAGCAACTGAA-
1 AACTGAAAAGTTGTTGGAATGCCCCCTCCTTGGAGCAACTGAAT
36592 AACT
1 AACT
36596 ACTGAAAGAT
Statistics
Matches: 312, Mismatches: 37, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
43 10 0.03
44 296 0.95
45 6 0.02
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (44 bp):
AACTGAAAAGTTGTTGGAATGCCCCCTCCTTGGAGCAACTGAAT
Found at i:36786 original size:60 final size:59
Alignment explanation
Indices: 36706--36862 Score: 190
Period size: 59 Copynumber: 2.6 Consensus size: 59
36696 AGCTGAAACT
** *
36706 TGAAAGAGACCAATCCGTGGTCGACACTTGAAGTAGGCCAGTCCGTGGCCAACTGATATC
1 TGAAAGAGACC-ATCCGTGGTCGACACTTGAAGTAGGCCAGTCCACGGCCAACTGATACC
* * * * * *
36766 TGAAAGAGACCGATCTGTGGTTGACA-ATGAAGTACGCCAGTCTACGGCCAATTGATACC
1 TGAAAGAGACC-ATCCGTGGTCGACACTTGAAGTAGGCCAGTCCACGGCCAACTGATACC
*
36825 TGAAAGAGACCAGTCCGTGGTCGATACTTGAAGTAGGC
1 TGAAAGAGACCA-TCCGTGGTCGACACTTGAAGTAGGC
36863 TAATATGTAG
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
58 1 0.01
59 47 0.59
60 32 0.40
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.21
Consensus pattern (59 bp):
TGAAAGAGACCATCCGTGGTCGACACTTGAAGTAGGCCAGTCCACGGCCAACTGATACC
Found at i:36894 original size:60 final size:61
Alignment explanation
Indices: 36691--36972 Score: 202
Period size: 60 Copynumber: 4.7 Consensus size: 61
36681 GGCTAGTCCA
* * * * * * **
36691 TAGCCAGCTGAAACTTGAAAGAGACCAATCCGTGGTCGACACTTGA-AGTAGGCCAGTCCG
1 TAGCCAACTGATACTTGAAAGAGACCAATCCGTGGTCGATACTTGAGAGTAGACTAATATG
* * * * * * * * * *
36751 TGGCCAACTGATA-TCTGAAAGAGACCGATCTGTGGTTGACA-ATGA-AGTACG-CCAGTCTA
1 TAGCCAACTGATACT-TGAAAGAGACCAATCCGTGGTCGATACTTGAGAGTA-GACTAATATG
** * * * *
36810 CGGCCAATTGATACCTGAAAGAGACCAGTCCGTGGTCGATACTTGA-AGTAGGCTAATATG
1 TAGCCAACTGATACTTGAAAGAGACCAATCCGTGGTCGATACTTGAGAGTAGACTAATATG
* * * * * *
36870 TAGCGAACTCG-TACTTGAAAGAGACCATTCCGTGGTCAATA-TTTAGAGTAGACTAGTCTG
1 TAGCCAACT-GATACTTGAAAGAGACCAATCCGTGGTCGATACTTGAGAGTAGACTAATATG
*
36930 TAGCCAACTGATGCTTGAAAGAGACCAATCCGTGGTCGATACT
1 TAGCCAACTGATACTTGAAAGAGACCAATCCGTGGTCGATACT
36973 AAAGCAAGCC
Statistics
Matches: 176, Mismatches: 37, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
59 51 0.29
60 123 0.70
61 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.23
Consensus pattern (61 bp):
TAGCCAACTGATACTTGAAAGAGACCAATCCGTGGTCGATACTTGAGAGTAGACTAATATG
Found at i:44662 original size:17 final size:17
Alignment explanation
Indices: 44640--44672 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
44630 AACTCCTAAA
44640 ATGCAG-TTTCTACTTAG
1 ATGCAGATTT-TACTTAG
44657 ATGCAGATTTTACTTA
1 ATGCAGATTTTACTTA
44673 TGCAATGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (17 bp):
ATGCAGATTTTACTTAG
Found at i:44923 original size:22 final size:22
Alignment explanation
Indices: 44889--44942 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
44879 TATGATTCAT
* *
44889 TAATA-TAAGACTAAATAATGA
1 TAATAGTAAAACTAAATAAGGA
*
44910 TAATGGTAAAACTAAATAAGGA
1 TAATAGTAAAACTAAATAAGGA
44932 TAATAGTAAAA
1 TAATAGTAAAA
44943 AGTAATGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (22 bp):
TAATAGTAAAACTAAATAAGGA
Done.