Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015697.1 Corchorus capsularis cultivar CVL-1 contig15718, 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: 104199
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2558 original size:26 final size:26
Alignment explanation
Indices: 2492--2558 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
2482 TGAGGGAACA
*
2492 AAGTTCATAGGATTCTTTTTTTAATT
1 AAGTTCATAGGATTTTTTTTTTAATT
2518 AAGTTCATAGGATTTTTTTTTTAATT
1 AAGTTCATAGGATTTTTTTTTTAATT
2544 AAGTTCATAGGATTT
1 AAGTTCATAGGATTT
2559 AAATTAAGGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.28, C:0.06, G:0.13, T:0.52
Consensus pattern (26 bp):
AAGTTCATAGGATTTTTTTTTTAATT
Found at i:8282 original size:22 final size:22
Alignment explanation
Indices: 8257--8483 Score: 68
Period size: 22 Copynumber: 10.3 Consensus size: 22
8247 ATGATTCCAT
8257 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCA
***
8279 TATGAAATTTT-AGTAATGAT-A
1 TATGAAATTTTGA-TAACCTTCA
* * * **
8300 CTATGGAATTTCGAGAACCTTTT
1 -TATGAAATTTTGATAACCTTCA
* ** * *
8323 TAT-AATTTTTTTTTAGCCTTCT
1 TATGAA-ATTTTGATAACCTTCA
* * *
8345 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCA
* * ** *
8367 TAAGGAATTTTGAGGATC-TCAA
1 TATGAAATTTTGATAACCTTC-A
**
8389 TATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTTCA
* * * *
8411 CTATGAGATGTTGATAACATCCA
1 -TATGAAATTTTGATAACCTTCA
* * * *
8434 TATGATATATTGATAACC-ACGT
1 TATGAAATTTTGATAACCTTC-A
* *
8456 TATGAAATTTTAAAAACCTTCA
1 TATGAAATTTTGATAACCTTCA
8478 TATGAA
1 TATGAA
8484 TTGTTAGTAA
Statistics
Matches: 141, Mismatches: 53, Indels: 22
0.65 0.25 0.10
Matches are distributed among these distances:
21 5 0.04
22 114 0.81
23 22 0.16
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:18384 original size:11 final size:11
Alignment explanation
Indices: 18368--18393 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18358 AATTGGACTT
18368 TTTTAGTTGTG
1 TTTTAGTTGTG
18379 TTTTAGTTGTG
1 TTTTAGTTGTG
18390 TTTT
1 TTTT
18394 GGTCATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.23, T:0.69
Consensus pattern (11 bp):
TTTTAGTTGTG
Found at i:22061 original size:13 final size:13
Alignment explanation
Indices: 22043--22069 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22033 TAAGCTGGAG
22043 ATTCAAGATAGCT
1 ATTCAAGATAGCT
22056 ATTCAAGATAGCT
1 ATTCAAGATAGCT
22069 A
1 A
22070 GGGGTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATTCAAGATAGCT
Found at i:23773 original size:29 final size:30
Alignment explanation
Indices: 23734--23810 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
23724 CATAAGAAAA
23734 GGGCTTATTTGGCCTTTTAA-AGAGTTCAG
1 GGGCTTATTTGGCCTTTTAATAGAGTTCAG
* **
23763 GGGTTTATTTGG-C-TGCAATTAGAGTTCAG
1 GGGCTTATTTGGCCTTTTAA-TAGAGTTCAG
23792 GGGCTTATTTGGCCGTTTT
1 GGGCTTATTTGGCC-TTTT
23811 GTGTAAGTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
27 3 0.08
28 1 0.03
29 31 0.84
30 1 0.03
32 1 0.03
ACGTcount: A:0.17, C:0.13, G:0.30, T:0.40
Consensus pattern (30 bp):
GGGCTTATTTGGCCTTTTAATAGAGTTCAG
Found at i:32895 original size:12 final size:12
Alignment explanation
Indices: 32878--32906 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
32868 CAATCATCTA
32878 ATTAAACCTACT
1 ATTAAACCTACT
32890 ATTAAACCTACT
1 ATTAAACCTACT
32902 ATTAA
1 ATTAA
32907 TTTTATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (12 bp):
ATTAAACCTACT
Found at i:33666 original size:21 final size:21
Alignment explanation
Indices: 33642--33686 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
33632 ATACACTGGA
33642 TTGCTAAACACCGTCCCATTT
1 TTGCTAAACACCGTCCCATTT
**
33663 TTGCTATTCACCGTCCCATTT
1 TTGCTAAACACCGTCCCATTT
33684 TTG
1 TTG
33687 ACGCTTTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.31, G:0.11, T:0.40
Consensus pattern (21 bp):
TTGCTAAACACCGTCCCATTT
Found at i:33960 original size:32 final size:32
Alignment explanation
Indices: 33892--33976 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 32
33882 CCGTGGCGAA
33892 GCCGCCCTCATGGGGCGGCTTCACCATGGGCAG
1 GCCGCCC-CATGGGGCGGCTTCACCATGGGCAG
*
33925 GCCGCCCCACTGGGGCGGCTT-AGTCA-GGGCAG
1 GCCGCCCCA-TGGGGCGGCTTCA-CCATGGGCAG
*
33957 GCCGCCCCGGTGGGGCGGCT
1 GCCGCCCC-ATGGGGCGGCT
33977 GCGACTATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
32 27 0.57
33 20 0.43
ACGTcount: A:0.09, C:0.36, G:0.41, T:0.13
Consensus pattern (32 bp):
GCCGCCCCATGGGGCGGCTTCACCATGGGCAG
Found at i:34070 original size:31 final size:32
Alignment explanation
Indices: 34033--34102 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
34023 TTGGTCTAAT
*
34033 CGCCCCACCG-GGGCGGCCTGCCGTCGCGAAGC
1 CGCCCCA-CGAGGGCAGCCTGCCGTCGCGAAGC
* *
34065 C-CCCCATGAGGGCAGCCTGCCGTGGCGAAGC
1 CGCCCCACGAGGGCAGCCTGCCGTCGCGAAGC
34096 CGCCCCA
1 CGCCCCA
34103 GTGGAGAGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 1 0.03
31 26 0.79
32 6 0.18
ACGTcount: A:0.13, C:0.46, G:0.34, T:0.07
Consensus pattern (32 bp):
CGCCCCACGAGGGCAGCCTGCCGTCGCGAAGC
Found at i:35261 original size:20 final size:20
Alignment explanation
Indices: 35236--35278 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
35226 TTTGTTTCAT
35236 ATTGAATGCTGGTTAATATG
1 ATTGAATGCTGGTTAATATG
35256 ATTGAATGCTGGTTAATATG
1 ATTGAATGCTGGTTAATATG
35276 ATT
1 ATT
35279 TCCTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTGAATGCTGGTTAATATG
Found at i:45454 original size:45 final size:46
Alignment explanation
Indices: 45390--45482 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
45380 TAGATGAGGT
45390 CTAATAAATAATGTACGGTT-AAATTACTTTGGTTAACAATTCAAG
1 CTAATAAATAATGTACGGTTAAAATTACTTTGGTTAACAATTCAAG
* *
45435 CTAATAAATTATGTACGGTTAAAATTGCTTTGGTTAACAATTCAAG
1 CTAATAAATAATGTACGGTTAAAATTACTTTGGTTAACAATTCAAG
45481 CT
1 CT
45483 TTTGGGTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.42
46 26 0.58
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37
Consensus pattern (46 bp):
CTAATAAATAATGTACGGTTAAAATTACTTTGGTTAACAATTCAAG
Found at i:55469 original size:22 final size:22
Alignment explanation
Indices: 55444--55490 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
55434 CTTTTAGTTG
*
55444 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
55466 AGTAAAATGATAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
55488 AGT
1 AGT
55491 TATAAGGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:60695 original size:59 final size:59
Alignment explanation
Indices: 60623--60742 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
60613 ATGTTTGTAC
60623 ATCCAAAGATGACAAGCATATTTATTTGAGCATGATTAATTGTCTATTAAAGATTATAT
1 ATCCAAAGATGACAAGCATATTTATTTGAGCATGATTAATTGTCTATTAAAGATTATAT
60682 ATCCAAAGATGACAAGCATATTTATTTGAGCATGATTAATTGTCTATTAAAGATTATAT
1 ATCCAAAGATGACAAGCATATTTATTTGAGCATGATTAATTGTCTATTAAAGATTATAT
60741 AT
1 AT
60743 TTGAGTTGGC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (59 bp):
ATCCAAAGATGACAAGCATATTTATTTGAGCATGATTAATTGTCTATTAAAGATTATAT
Found at i:63137 original size:6 final size:6
Alignment explanation
Indices: 63126--63152 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
63116 ATTAATCTGC
63126 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
63153 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:67321 original size:23 final size:23
Alignment explanation
Indices: 67292--67350 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
67282 TGGGTTCGAG
*
67292 TTCGGTCTCGAATTGGGTTTGGA
1 TTCGGTCTCGAATAGGGTTTGGA
* *
67315 TTTGGTCTCGAATAGGGTTTGGG
1 TTCGGTCTCGAATAGGGTTTGGA
*
67338 TTCAGTCTCGAAT
1 TTCGGTCTCGAAT
67351 CGAGTTCGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.15, C:0.14, G:0.32, T:0.39
Consensus pattern (23 bp):
TTCGGTCTCGAATAGGGTTTGGA
Found at i:67361 original size:23 final size:23
Alignment explanation
Indices: 67319--67364 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
67309 TTTGGATTTG
* *
67319 GTCTCGAATAGGGTTTGGGTTCA
1 GTCTCGAATAGAGTTCGGGTTCA
*
67342 GTCTCGAATCGAGTTCGGGTTCA
1 GTCTCGAATAGAGTTCGGGTTCA
67365 ATTTCGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (23 bp):
GTCTCGAATAGAGTTCGGGTTCA
Found at i:75619 original size:28 final size:28
Alignment explanation
Indices: 75587--75643 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
75577 AAGGATCCTA
75587 TCCCTA-GATTGACTCATTCAAAGTTAGT
1 TCCCTATG-TTGACTCATTCAAAGTTAGT
75615 TCCCTATGTTGACTCATTCAAAGTTAGT
1 TCCCTATGTTGACTCATTCAAAGTTAGT
75643 T
1 T
75644 TGAGTTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (28 bp):
TCCCTATGTTGACTCATTCAAAGTTAGT
Found at i:82335 original size:37 final size:37
Alignment explanation
Indices: 82244--82392 Score: 221
Period size: 37 Copynumber: 4.1 Consensus size: 37
82234 AGATTAAACT
* *
82244 CTTTATTGACTCCACTTAATTACCCTGAATTAAG-CC
1 CTTTATTGACGCTACTTAATTACCCTGAATTAAGTCC
* *
82280 TTTTATTGACGCTACTTAATTACCCTAAATTAAGTCC
1 CTTTATTGACGCTACTTAATTACCCTGAATTAAGTCC
* *
82317 CTTTATTGACGCTGCTTAATTACCCCGAATTAAGT-C
1 CTTTATTGACGCTACTTAATTACCCTGAATTAAGTCC
82353 CTCTTATTGACGCTACTTAATTACCCTGAATTAAGTCC
1 CT-TTATTGACGCTACTTAATTACCCTGAATTAAGTCC
82391 CT
1 CT
82393 AACTTGACTT
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
36 33 0.33
37 64 0.64
38 3 0.03
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.38
Consensus pattern (37 bp):
CTTTATTGACGCTACTTAATTACCCTGAATTAAGTCC
Found at i:82658 original size:18 final size:18
Alignment explanation
Indices: 82637--82695 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
82627 TTCCTTGGAA
82637 TTAAGTCCTTAACTCTAC
1 TTAAGTCCTTAACTCTAC
* * *
82655 TTAATTCCATT-CCT-TAGAA
1 TTAAGTCC-TTAACTCT--AC
82674 TTAAGTCCTTAACTCTAC
1 TTAAGTCCTTAACTCTAC
82692 TTAA
1 TTAA
82696 TTCCCTTCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
17 1 0.03
18 16 0.53
19 12 0.40
20 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.41
Consensus pattern (18 bp):
TTAAGTCCTTAACTCTAC
Found at i:82729 original size:37 final size:37
Alignment explanation
Indices: 82380--82720 Score: 428
Period size: 37 Copynumber: 9.4 Consensus size: 37
82370 TAATTACCCT
* *
82380 GAATTAAGTCCCTAACT-TGACTTAATTTCCTTCCTTG
1 GAATTAAGTCCTTAACTCT-ACTTAATTCCCTTCCTTG
* *
82417 AAATTAAGTCCTTAACTATACTTAATTCCCTTCCTTG
1 GAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
* *
82454 GAATCAAGT-C----CTCTACTTAATTTCCTTCCTTG
1 GAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
* ** ** *
82486 AAATTAAGTTATTTGCTCTACTCAATTCCCTTCCTTG
1 GAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
* *
82523 GAATCAAGTCCTTTACTCTACTTAATTCCCTTCCTTG
1 GAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
*
82560 AAATTAAG-CACTTAACTCTACTTAATTCCCTTCCTTG
1 GAATTAAGTC-CTTAACTCTACTTAATTCCCTTCCTTG
*
82597 AAATTAAG-CACTTAACTCTACTTAATTCCCTTCCTTG
1 GAATTAAGTC-CTTAACTCTACTTAATTCCCTTCCTTG
* *
82634 GAATTAAGTCCTTAACTCTACTTAATTCCATTCCTTA
1 GAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
82671 GAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
1 GAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
*
82708 GAACTAAGTCCTT
1 GAATTAAGTCCTT
82721 TGTTCTACTC
Statistics
Matches: 269, Mismatches: 27, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
32 27 0.10
36 2 0.01
37 238 0.88
38 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.40
Consensus pattern (37 bp):
GAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
Found at i:82990 original size:18 final size:18
Alignment explanation
Indices: 82954--82992 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
82944 TTGACTGTTT
* *
82954 TTACTTAATTGCCCTGAA
1 TTACTTAATTACCCAGAA
*
82972 TTACTTAATTACTCAGAA
1 TTACTTAATTACCCAGAA
82990 TTA
1 TTA
82993 AGTCCTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (18 bp):
TTACTTAATTACCCAGAA
Found at i:83015 original size:55 final size:55
Alignment explanation
Indices: 82917--83029 Score: 154
Period size: 55 Copynumber: 2.1 Consensus size: 55
82907 TTGACTGTGT
* * * ** *
82917 TTACTTAATTACCCAGGATTAGGTCCTTTGACTGTTTTTACTTAATTGCCCTGAA
1 TTACTTAATTACCCAGAATTAAGTCCTTTAACTACTTTCACTTAATTGCCCTGAA
* *
82972 TTACTTAATTACTCAGAATTAAGTCCTTTAACTACTTTCACTTAATTTCCCTGAA
1 TTACTTAATTACCCAGAATTAAGTCCTTTAACTACTTTCACTTAATTGCCCTGAA
83027 TTA
1 TTA
83030 AGTTCTCTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.42
Consensus pattern (55 bp):
TTACTTAATTACCCAGAATTAAGTCCTTTAACTACTTTCACTTAATTGCCCTGAA
Found at i:83028 original size:37 final size:37
Alignment explanation
Indices: 82972--83154 Score: 161
Period size: 37 Copynumber: 4.9 Consensus size: 37
82962 TTGCCCTGAA
* * *
82972 TTACTTAATTACTCAGAATTAAGTCCTTTAACTACTT
1 TTACTTAATTACCCTGAATTAAGTCCTTTGACTACTT
* * * * ** *
83009 TCACTTAATTTCCCTGAATTAAGTTCTCTGACCGCGT
1 TTACTTAATTACCCTGAATTAAGTCCTTTGACTACTT
* * *
83046 TTACTTAATTACCCAGAATTAAGTCATTTGACTGCTT
1 TTACTTAATTACCCTGAATTAAGTCCTTTGACTACTT
* * * * *
83083 CTTACTTAATTGCCCTGAATTATGTTCTCTGACT-GTGT
1 -TTACTTAATTACCCTGAATTAAGTCCTTTGACTACT-T
* *
83121 TTACTTAATTACCCTGAATTAAGTCATTTAACTA
1 TTACTTAATTACCCTGAATTAAGTCCTTTGACTA
83155 TGTTTTCCTT
Statistics
Matches: 112, Mismatches: 31, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
37 84 0.75
38 28 0.25
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (37 bp):
TTACTTAATTACCCTGAATTAAGTCCTTTGACTACTT
Found at i:83076 original size:129 final size:129
Alignment explanation
Indices: 82860--83104 Score: 375
Period size: 129 Copynumber: 1.9 Consensus size: 129
82850 CATGCCTTGA
* * * * *
82860 AATTAGTCCTTTAACTGCTTTTACCTAATTTCCCTGAATTAAGCTCTTTGACTGTGTTTACTTAA
1 AATTAGTCCTTTAACTACTTTCACCTAATTTCCCTGAATTAAGCTCTCTGACCGCGTTTACTTAA
* * * *
82925 TTACCCAGGATTAGGTCCTTTGACTG-TTTTTACTTAATTGCCCTGAATTACTTAATTACTCAG
66 TTACCCAGAATTAAGTCATTTGACTGCTTCTTACTTAATTGCCCTGAATTACTTAATTACTCAG
* *
82988 AATTAAGTCCTTTAACTACTTTCACTTAATTTCCCTGAATTAAGTTCTCTGACCGCGTTTACTTA
1 AATT-AGTCCTTTAACTACTTTCACCTAATTTCCCTGAATTAAGCTCTCTGACCGCGTTTACTTA
83053 ATTACCCAGAATTAAGTCATTTGACTGCTTCTTACTTAATTGCCCTGAATTA
65 ATTACCCAGAATTAAGTCATTTGACTGCTTCTTACTTAATTGCCCTGAATTA
83105 TGTTCTCTGA
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
128 4 0.04
129 77 0.74
130 23 0.22
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (129 bp):
AATTAGTCCTTTAACTACTTTCACCTAATTTCCCTGAATTAAGCTCTCTGACCGCGTTTACTTAA
TTACCCAGAATTAAGTCATTTGACTGCTTCTTACTTAATTGCCCTGAATTACTTAATTACTCAG
Found at i:83111 original size:75 final size:74
Alignment explanation
Indices: 82972--83154 Score: 267
Period size: 75 Copynumber: 2.5 Consensus size: 74
82962 TTGCCCTGAA
* * *
82972 TTACTTAATTACTCAGAATTAAGTCCTTTAACTACTTTCACTTAATTTCCCTGAATTAAGTTCTC
1 TTACTTAATTACCCAGAATTAAGTCATTTAACTACTTTCACTTAATTGCCCTGAATTAAGTTCTC
83037 TGACCGCGT
66 TGACCGCGT
* * * *
83046 TTACTTAATTACCCAGAATTAAGTCATTTGACTGCTTCTTACTTAATTGCCCTGAATTATGTTCT
1 TTACTTAATTACCCAGAATTAAGTCATTTAACTACTT-TCACTTAATTGCCCTGAATTAAGTTCT
* *
83111 CTGACTGTGT
65 CTGACCGCGT
*
83121 TTACTTAATTACCCTGAATTAAGTCATTTAACTA
1 TTACTTAATTACCCAGAATTAAGTCATTTAACTA
83155 TGTTTTCCTT
Statistics
Matches: 96, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
74 33 0.34
75 63 0.66
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (74 bp):
TTACTTAATTACCCAGAATTAAGTCATTTAACTACTTTCACTTAATTGCCCTGAATTAAGTTCTC
TGACCGCGT
Found at i:83207 original size:41 final size:41
Alignment explanation
Indices: 83124--83298 Score: 242
Period size: 41 Copynumber: 4.2 Consensus size: 41
83114 ACTGTGTTTA
* * ** **
83124 CTTAATTACCCTGAATTAAGTCATTTAACTATGTTTTCCTTT
1 CTTAATCACCCTGGATTAAAAC-TTTAACTATGTTTGACTTT
83166 CTTAATCACCCTGGATTAAAACTTTAACTATGTTTGACTTT
1 CTTAATCACCCTGGATTAAAACTTTAACTATGTTTGACTTT
*
83207 CTTAATCGCCCTGGATTAAAACTTTAACTATGTTTGACTTT
1 CTTAATCACCCTGGATTAAAACTTTAACTATGTTTGACTTT
** * *
83248 CTTAATTGCCCTGGATTAAAGCTTTAATTATGTTTGACTTT
1 CTTAATCACCCTGGATTAAAACTTTAACTATGTTTGACTTT
83289 CTTAATCACC
1 CTTAATCACC
83299 ATGTGTTTAT
Statistics
Matches: 121, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 103 0.85
42 18 0.15
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.43
Consensus pattern (41 bp):
CTTAATCACCCTGGATTAAAACTTTAACTATGTTTGACTTT
Found at i:83539 original size:55 final size:55
Alignment explanation
Indices: 83493--83723 Score: 270
Period size: 55 Copynumber: 4.2 Consensus size: 55
83483 ATATTTCGTT
*
83493 ACACCATCAGGACCAATTAATTGGTCCAGATGATCTGAATGATAAATTGAAGGCA
1 ACACCATCAGGACCAATTAATTGGTCCAGATGATCTGAATGATAAATTGAACGCA
*
83548 ACACCATCAGGACCAATTAATTGGTCCAGATGATCTGAATGATAAATTGAAGGCA
1 ACACCATCAGGACCAATTAATTGGTCCAGATGATCTGAATGATAAATTGAACGCA
* * ** * * * * *
83603 ACACCATCAGGATCAATTTATCAGTCCCGATGATTTG-A-G-TAATTTTTAATTGACA
1 ACACCATCAGGACCAATTAATTGGTCCAGATGATCTGAATGATAA-ATTGAA-CG-CA
* ** * *
83658 ACACCAGCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAGTTGAAAGCA
1 ACACCATCAGGACCAATTAATTGGTCCAGATGATCTGAATGATAAATTGAACGCA
83713 ACACCATCAGG
1 ACACCATCAGG
83724 TTTAAGCTAT
Statistics
Matches: 150, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
52 3 0.02
53 5 0.03
54 2 0.01
55 130 0.87
56 2 0.01
57 5 0.03
58 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (55 bp):
ACACCATCAGGACCAATTAATTGGTCCAGATGATCTGAATGATAAATTGAACGCA
Found at i:85036 original size:71 final size:71
Alignment explanation
Indices: 84914--85395 Score: 820
Period size: 71 Copynumber: 6.8 Consensus size: 71
84904 TTCTTTGCTG
* ***
84914 CCTTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTATTCTTCTTAATTTTGCAAC
1 CCTTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAAC
84979 TTAGGA
66 TTAGGA
* * *
84985 CGTTGACTATACTTCCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAAC
1 CCTTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAAC
85050 TTAGGA
66 TTAGGA
*
85056 CCTTGAATGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAAC
1 CCTTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAAC
*
85121 TTAAGA
66 TTAGGA
* *
85127 CCTTGAATGTACTTTCTTTTCTTAATTACCCTGAATTAAAACTTTACTCTTCTTAATTGCCCAAC
1 CCTTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAAC
85192 TTAGGA
66 TTAGGA
* *
85198 CCTTGACTGTACTTTCCTTTCTTAATTACCCTGAATTAAGACTTTATTCTTCTTAATTGCCCAAC
1 CCTTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAAC
85263 TTAGGA
66 TTAGGA
* *
85269 CCTTGACTATACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTATTCTTCTTAATTGCCCAAC
1 CCTTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAAC
85334 TTAGGA
66 TTAGGA
*
85340 CCTTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTTTTCTTAA
1 CCTTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAA
85396 CTTTCCTTAA
Statistics
Matches: 388, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 388 1.00
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.44
Consensus pattern (71 bp):
CCTTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAAC
TTAGGA
Found at i:93756 original size:107 final size:105
Alignment explanation
Indices: 93584--93841 Score: 385
Period size: 107 Copynumber: 2.5 Consensus size: 105
93574 AGTTTAGCCT
* *
93584 TAATTTCACTAAGTTTAGCCCTAAATTAAAATTTTATTTTTATTTTAAGGATAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGATAAATTCCAAAATT
93649 AATAAATTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
66 AAT-AA-TATTATTATAGGGTTTTAGAAATAAAATACAAAAC
* * *
93691 TAATTTCATTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGATAAATTCCAAAATT
* * *
93756 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 AATAATATTATTATAGGGTTTTAGAAATAAAATACAAAAC
** *
93796 TAA-TTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAA
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAA
93842 AGGTTAGAAA
Statistics
Matches: 139, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
103 26 0.19
104 13 0.09
105 35 0.25
106 2 0.01
107 63 0.45
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGATAAATTCCAAAATT
AATAATATTATTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:95167 original size:23 final size:23
Alignment explanation
Indices: 95137--95183 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
95127 GGCGTAGCTT
95137 GGATTTCTGCAATTTTTGACCCC
1 GGATTTCTGCAATTTTTGACCCC
95160 GGATTTCTGCAATTTTTGACCCC
1 GGATTTCTGCAATTTTTGACCCC
95183 G
1 G
95184 AAAGAAGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (23 bp):
GGATTTCTGCAATTTTTGACCCC
Found at i:102857 original size:2 final size:2
Alignment explanation
Indices: 102850--102882 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
102840 AAGTAACCAT
102850 TA TA 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 T
102883 CTTTATACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.