Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014471.1 Corchorus capsularis cultivar CVL-1 contig14492, 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: 79005
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:13254 original size:20 final size:20
Alignment explanation
Indices: 13231--13304 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 20
13221 AATGAACCTT
*
13231 TCTTCTTTCTCACCCTCTTC
1 TCTTCTTTCTCACCCTCCTC
*
13251 TCTTCTTTCGGACTCACCCTCCCC
1 TCTTCTTT----CTCACCCTCCTC
13275 TCTTCTTTCTCACCCTCCTC
1 TCTTCTTTCTCACCCTCCTC
13295 -CTTTCTTTCT
1 TC-TTCTTTCT
13305 TTTCTTCTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 1 0.02
20 27 0.59
24 18 0.39
ACGTcount: A:0.05, C:0.46, G:0.03, T:0.46
Consensus pattern (20 bp):
TCTTCTTTCTCACCCTCCTC
Found at i:13304 original size:24 final size:23
Alignment explanation
Indices: 13227--13306 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 23
13217 CCCGAATGAA
13227 CCTTTCTTCTTTCTCACCCT-CT
1 CCTTTCTTCTTTCTCACCCTCCT
* ***
13249 TCTCTTCTTTCGGACTCACCCTCC-
1 CCT-TTC-TTCTTTCTCACCCTCCT
13273 CC--TCTTCTTTCTCACCCTCCT
1 CCTTTCTTCTTTCTCACCCTCCT
13294 CCTTTCTTTCTTT
1 CCTTTC-TTCTTT
13307 TCTTCTTTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
20 13 0.30
21 4 0.09
22 2 0.05
23 5 0.12
24 18 0.42
25 1 0.02
ACGTcount: A:0.05, C:0.45, G:0.03, T:0.47
Consensus pattern (23 bp):
CCTTTCTTCTTTCTCACCCTCCT
Found at i:14016 original size:32 final size:33
Alignment explanation
Indices: 13980--14051 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
13970 CCCAACCGGC
* *
13980 GCGGCCTGCT-ATGGCGAAGCCGCCCCAGTGGG
1 GCGGCCTACTCATAGCGAAGCCGCCCCAGTGGG
* * *
14012 GCGGCCTATTCATAGTGAAGCCGCCCTAGTGGG
1 GCGGCCTACTCATAGCGAAGCCGCCCCAGTGGG
14045 GCGGCCT
1 GCGGCCT
14052 TCCCATGGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 8 0.24
33 26 0.76
ACGTcount: A:0.14, C:0.32, G:0.38, T:0.17
Consensus pattern (33 bp):
GCGGCCTACTCATAGCGAAGCCGCCCCAGTGGG
Found at i:14070 original size:32 final size:33
Alignment explanation
Indices: 13995--14081 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 33
13985 CTGCTATGGC
* *
13995 GAAGCCGCCCCAGTGGGGCGGCCTATTCATAGT
1 GAAGCCGCCCTAGTGGGGCGGCCTATCCATAGT
*
14028 GAAGCCGCCCTAGTGGGGCGGCCT-TCCCATGGT
1 GAAGCCGCCCTAGTGGGGCGGCCTAT-CCATAGT
**
14061 -AAGCCGCCCTCTTGGGGCGGC
1 GAAGCCGCCCTAGTGGGGCGGC
14082 ACGGGTCATC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 20 0.42
33 28 0.58
ACGTcount: A:0.14, C:0.33, G:0.36, T:0.17
Consensus pattern (33 bp):
GAAGCCGCCCTAGTGGGGCGGCCTATCCATAGT
Found at i:18829 original size:78 final size:78
Alignment explanation
Indices: 18700--18852 Score: 279
Period size: 78 Copynumber: 2.0 Consensus size: 78
18690 AGCTTTTAGC
*
18700 TTCTTGTAATCTCTCTTGACATAGTGGAATTGTTTTCATCGCTCTCATCGTCTCTCCCCGAACCA
1 TTCTTGTAATCTCTCTTGACATAGTGGAATTATTTTCATCGCTCTCATCGTCTCTCCCCGAACCA
18765 CGTAAATCCTGTA
66 CGTAAATCCTGTA
* *
18778 TTCTTGTAATCTCTCTTGGCATAGTGGAATTATTTTCATCGCTCTCATCGTCTCTCTCCGAACCA
1 TTCTTGTAATCTCTCTTGACATAGTGGAATTATTTTCATCGCTCTCATCGTCTCTCCCCGAACCA
18843 CGTAAATCCT
66 CGTAAATCCT
18853 ATGTTCTTAT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (78 bp):
TTCTTGTAATCTCTCTTGACATAGTGGAATTATTTTCATCGCTCTCATCGTCTCTCCCCGAACCA
CGTAAATCCTGTA
Found at i:19889 original size:30 final size:30
Alignment explanation
Indices: 19850--19959 Score: 134
Period size: 28 Copynumber: 3.7 Consensus size: 30
19840 TCTCGTTTTT
*
19850 AAAAGTTAAGGGGCCAATTTGTCCCAAAAA
1 AAAAATTAAGGGGCCAATTTGTCCCAAAAA
19880 AAAAATTAAGGGGCCAATTTGT-CC-AAAA
1 AAAAATTAAGGGGCCAATTTGTCCCAAAAA
* * *
19908 AAAAGTTAAGGGGACAATTTGTCCCAAAATG
1 AAAAATTAAGGGGCCAATTTGTCCCAAAA-A
* * *
19939 GATAATTAAGGGGCTAATTTG
1 AAAAATTAAGGGGCCAATTTG
19960 GGTATTAAGC
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
28 24 0.35
29 4 0.06
30 24 0.35
31 16 0.24
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.24
Consensus pattern (30 bp):
AAAAATTAAGGGGCCAATTTGTCCCAAAAA
Found at i:21097 original size:22 final size:21
Alignment explanation
Indices: 21054--21112 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
21044 AGAACAAGCC
21054 TAATAAAAATTTTACAT-TTTT
1 TAATAAAAA-TTTACATCTTTT
*
21075 TTATAACAAATTTACAATCTTTT
1 TAATAA-AAATTTAC-ATCTTTT
21098 TAATAGAAAATTTAC
1 TAATA-AAAATTTAC
21113 CTGTAATTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 10 0.31
22 5 0.16
23 16 0.50
24 1 0.03
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (21 bp):
TAATAAAAATTTACATCTTTT
Found at i:56457 original size:21 final size:21
Alignment explanation
Indices: 56428--56506 Score: 86
Period size: 21 Copynumber: 3.5 Consensus size: 21
56418 AGTAAAATTA
*
56428 GTTATTGTACGTGTTAGATTT
1 GTTACTGTACGTGTTAGATTT
*
56449 GTTACTGTACGTGTGAGAGTAAAATT
1 GTTACTGTACGTGTTAGA-T----TT
56475 AGTTACTGTACGTGTTAGATTT
1 -GTTACTGTACGTGTTAGATTT
56497 GTTACTGTAC
1 GTTACTGTAC
56507 AGATTAGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
21 26 0.53
22 3 0.06
26 3 0.06
27 17 0.35
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (21 bp):
GTTACTGTACGTGTTAGATTT
Found at i:56485 original size:48 final size:48
Alignment explanation
Indices: 56413--56506 Score: 179
Period size: 48 Copynumber: 2.0 Consensus size: 48
56403 GGTTGGTTCG
*
56413 GTGAGAGTAAAATTAGTTATTGTACGTGTTAGATTTGTTACTGTACGT
1 GTGAGAGTAAAATTAGTTACTGTACGTGTTAGATTTGTTACTGTACGT
56461 GTGAGAGTAAAATTAGTTACTGTACGTGTTAGATTTGTTACTGTAC
1 GTGAGAGTAAAATTAGTTACTGTACGTGTTAGATTTGTTACTGTAC
56507 AGATTAGAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.40
Consensus pattern (48 bp):
GTGAGAGTAAAATTAGTTACTGTACGTGTTAGATTTGTTACTGTACGT
Found at i:56487 original size:27 final size:27
Alignment explanation
Indices: 56413--56489 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 27
56403 GGTTGGTTCG
*
56413 GTGAGAGTAAAATTAGTTATTGTACGT
1 GTGAGAGTAAAATTAGTTACTGTACGT
*
56440 GTTAGA-T----TT-GTTACTGTACGT
1 GTGAGAGTAAAATTAGTTACTGTACGT
56461 GTGAGAGTAAAATTAGTTACTGTACGT
1 GTGAGAGTAAAATTAGTTACTGTACGT
56488 GT
1 GT
56490 TAGATTTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
21 16 0.39
22 3 0.07
26 3 0.07
27 19 0.46
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (27 bp):
GTGAGAGTAAAATTAGTTACTGTACGT
Found at i:59582 original size:31 final size:32
Alignment explanation
Indices: 59554--59613 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
59544 TGTTTTCCGT
59554 TTGTACCCTTATTTTT-AAAACATATTTCCAA
1 TTGTACCCTTATTTTTAAAAACATATTTCCAA
*
59585 TTGTACCCTTTTTTTTAAAAACATATTTC
1 TTGTACCCTTATTTTTAAAAACATATTTC
59614 TAAATTGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.48
Consensus pattern (32 bp):
TTGTACCCTTATTTTTAAAAACATATTTCCAA
Found at i:59919 original size:22 final size:21
Alignment explanation
Indices: 59850--59923 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 21
59840 GTTTAGTTTT
* * *
59850 CAAAATTTCATAAGAGGGTTAT
1 CAAAATTTCATAGGA-AGTTAA
* *
59872 CAAAATTTCATAGTATG-TAGA
1 CAAAATTTCATAGGAAGTTA-A
59893 TCAAAATTTCATAGGAAGATTAA
1 -CAAAATTTCATAGGAAG-TTAA
59916 CAAAATTT
1 CAAAATTT
59924 AGGTGTCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 2 0.05
21 1 0.02
22 36 0.86
23 1 0.02
24 2 0.05
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (21 bp):
CAAAATTTCATAGGAAGTTAA
Found at i:60014 original size:23 final size:23
Alignment explanation
Indices: 59986--60065 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
59976 CATAAGAAAG
59986 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
60009 TTATCAAAATTTTGT-GGGAAGAT
1 TTATCAAAATTTTATAGGG-AGGT
* *
60032 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
*
60054 TTATCACAATTT
1 TTATCAAAATTT
60066 CATAATGTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
22 14 0.29
23 32 0.67
24 2 0.04
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:60098 original size:44 final size:43
Alignment explanation
Indices: 60032--60147 Score: 112
Period size: 44 Copynumber: 2.6 Consensus size: 43
60022 GTGGGAAGAT
*
60032 TTATCAAAATTTCATA-GCGAGGTTATCACAA-TTTCATAATGTGA
1 TTATCAAAA-TTCATATG-GAGGTTATCA-AATTTTCATAACGTGA
* * *
60076 TTA-CTAACAATTCATATGGAGGTTTTTAAATTTTCATAACGTGG
1 TTATC-AA-AATTCATATGGAGGTTATCAAATTTTCATAACGTGA
*
60120 TTATCAATATATCATATGGAGGTTATCA
1 TTATCAAAAT-TCATATGGAGGTTATCA
60148 GCATCCCATA
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
43 5 0.08
44 50 0.85
45 4 0.07
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (43 bp):
TTATCAAAATTCATATGGAGGTTATCAAATTTTCATAACGTGA
Found at i:60238 original size:22 final size:21
Alignment explanation
Indices: 60213--60263 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
60203 TTAAGGTCTT
* *
60213 CAAAATTCCTTAGAGAGGTTAA
1 CAAAATTCATAAGA-AGGTTAA
60235 CAAAATATCATAAGAAGGTTAA
1 CAAAAT-TCATAAGAAGGTTAA
*
60257 AAAAATT
1 CAAAATT
60264 TTATAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (21 bp):
CAAAATTCATAAGAAGGTTAA
Found at i:60618 original size:379 final size:377
Alignment explanation
Indices: 60068--60824 Score: 1284
Period size: 379 Copynumber: 2.0 Consensus size: 377
60058 CACAATTTCA
*
60068 TAATGTGATTACTAACAATTCATATGGAGGTTTTTAAATTTTCATAACGTGGTTATCAATATATC
1 TAATATGATTACTAACAATTCATATGGAGGTTTTTAAATTTTCATAACGTGGTTATCAATATATC
* * *
60133 ATATGGAGGTTATCAGCATCCCATAGTGTTGGTTATCAAAATTTTATTGGGAAGTTATCAAAATT
66 ATATAGAGGTTATCAACATCCCATAGTGTTGGTTATCAAAATTTCATTGGGAAGTTATCAAAATT
*
60198 TCATATTAAGGTCTTCAAAATTCCTTAGAGAGGTTAACAAAATATCATAAGAAGGTTAAAAAAAT
131 TCATATTAAGGTCTTCAAAATTACTTAGAGAGGTTAACAAAATATCATAAGAAGGTTAAAAAAA-
* * * *
60263 TTTATAAAAAAGTTCTCGAAATTTCATAGTATCATTATTAAAATTTCATAGGAAGGTTATCAAAA
195 ATTATAAAAAAGTTCTCGAAATTCCATAGTATCATTATTAAAATTTCATAAGAAGATTATCAAAA
* * *
60328 TTTCATAATGGGA-CTATAAAAAATAGTGTAATTATCATACTTTAATAGAGAGGTTATCATAATT
260 TTTCATAATGGGATC-ATAAAAAATAGTGTAATTAACATAATTTAACAGAGAGGTTATCATAATT
*
60392 TCATATGAATATTCCA-TTAAACACGTTGGGCCACGGGCAACGCACGTGAAAGC
324 TCATATGAATATTCCATTTAAACACGTTGGGCCACGGGCAACACACGTGAAAGC
60445 TAATATGATTACTAACAATTCATATGGAGGTTTTTAAATTTTCATAACGTGGTTATCAATATATC
1 TAATATGATTACTAACAATTCATATGGAGGTTTTTAAATTTTCATAACGTGGTTATCAATATATC
*
60510 ATATAGAGGTTATCAACATCTCATACAGTGTTGGTTATCAAAATTTCATTGGGAAGTTATCAAAA
66 ATATAGAGGTTATCAACATCCCAT--AGTGTTGGTTATCAAAATTTCATTGGGAAGTTATCAAAA
* * *
60575 TTTCATATTGAGGTCTTCAAAATTACTTAGGGAGGTTAACAAAATTTCATAAGAAGGTTAAAAAA
129 TTTCATATTAAGGTCTTCAAAATTACTTAGAGAGGTTAACAAAATATCATAAGAAGGTTAAAAAA
*
60640 AATTATAAAAAGGTTCTCGAAATTCCATAGTATCATTATTAAAATTTCATAAGAAGATTATCAAA
194 AATTATAAAAAAGTTCTCGAAATTCCATAGTATCATTATTAAAATTTCATAAGAAGATTATCAAA
*
60705 ATTTCATAATGGGATCATAAAAAATAGTGTAATTAACATAATTTAACAGATAGGTTATCATAATT
259 ATTTCATAATGGGATCATAAAAAATAGTGTAATTAACATAATTTAACAGAGAGGTTATCATAATT
*
60770 TCATATGAATATTCCATTTAAACACGTTGGGCCACGTGCAACACACGTGAAAGC
324 TCATATGAATATTCCATTTAAACACGTTGGGCCACGGGCAACACACGTGAAAGC
60824 T
1 T
60825 GAAACTAGTG
Statistics
Matches: 356, Mismatches: 20, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
377 85 0.24
378 134 0.38
379 137 0.38
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (377 bp):
TAATATGATTACTAACAATTCATATGGAGGTTTTTAAATTTTCATAACGTGGTTATCAATATATC
ATATAGAGGTTATCAACATCCCATAGTGTTGGTTATCAAAATTTCATTGGGAAGTTATCAAAATT
TCATATTAAGGTCTTCAAAATTACTTAGAGAGGTTAACAAAATATCATAAGAAGGTTAAAAAAAA
TTATAAAAAAGTTCTCGAAATTCCATAGTATCATTATTAAAATTTCATAAGAAGATTATCAAAAT
TTCATAATGGGATCATAAAAAATAGTGTAATTAACATAATTTAACAGAGAGGTTATCATAATTTC
ATATGAATATTCCATTTAAACACGTTGGGCCACGGGCAACACACGTGAAAGC
Found at i:60632 original size:22 final size:22
Alignment explanation
Indices: 60542--60713 Score: 93
Period size: 22 Copynumber: 7.9 Consensus size: 22
60532 ATACAGTGTT
**
60542 GGTTATCAAAATTTCATTGGGAA
1 GGTTATCAAAATTTCA-TAAGAA
*
60565 -GTTATCAAAATTTCATATTG-A
1 GGTTATCAAAATTTCATA-AGAA
* * * *
60586 GGTCT-TCAAAATTACTTAGGGA
1 GGT-TATCAAAATTTCATAAGAA
*
60608 GGTTAACAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
** * *
60630 GGTTAAAAAAAATT-ATAAAAA
1 GGTTATCAAAATTTCATAAGAA
* * * *
60651 GGTTCTCGAAATTCCAT-AGTAT
1 GGTTATCAAAATTTCATAAG-AA
** *
60673 CATTATTAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
*
60695 GATTATCAAAATTTCATAA
1 GGTTATCAAAATTTCATAA
60714 TGGGATCATA
Statistics
Matches: 111, Mismatches: 30, Indels: 17
0.70 0.19 0.11
Matches are distributed among these distances:
21 19 0.17
22 89 0.80
23 3 0.03
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGAA
Found at i:60727 original size:22 final size:22
Alignment explanation
Indices: 60680--60727 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
60670 TATCATTATT
* *
60680 AAAATTTCATAAGAAGATTATC
1 AAAATTTCATAAGAAGATCATA
*
60702 AAAATTTCATAATG-GGATCATA
1 AAAATTTCATAA-GAAGATCATA
60724 AAAA
1 AAAA
60728 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.29
Consensus pattern (22 bp):
AAAATTTCATAAGAAGATCATA
Found at i:62510 original size:6 final size:6
Alignment explanation
Indices: 62499--62534 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
62489 CATCACTGGT
*
62499 GCAGAA GCAGAA GCAGAA GCAGAA GCAGAA GAAGAA
1 GCAGAA GCAGAA GCAGAA GCAGAA GCAGAA GCAGAA
62535 CCACCGCCGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.53, C:0.14, G:0.33, T:0.00
Consensus pattern (6 bp):
GCAGAA
Found at i:64805 original size:27 final size:31
Alignment explanation
Indices: 64739--64805 Score: 72
Period size: 32 Copynumber: 2.3 Consensus size: 31
64729 CCACACAGTC
*
64739 TCTTTTATGGTTTTTCTTCTTTCTTCTCCTTT
1 TCTTTTTTGGTTTTTCTTCTTTCTTCT-CTTT
64771 T-TGTTTTTGGTTTTT-TTC-TT-TTCT-TTT
1 TCT-TTTTTGGTTTTTCTTCTTTCTTCTCTTT
64798 TCTTTTTT
1 TCTTTTTT
64806 CACTCAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
27 9 0.28
28 1 0.03
29 4 0.12
30 2 0.06
31 4 0.12
32 12 0.38
ACGTcount: A:0.01, C:0.15, G:0.07, T:0.76
Consensus pattern (31 bp):
TCTTTTTTGGTTTTTCTTCTTTCTTCTCTTT
Found at i:67157 original size:24 final size:23
Alignment explanation
Indices: 67125--67174 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
67115 GGAAAAAAGA
*
67125 AATTACTAATTAA-CCATTAAAAT
1 AATTACTAA-AAACCCATTAAAAT
67148 AATTACCTAAAAACCCATTAAAAT
1 AATTA-CTAAAAACCCATTAAAAT
67172 AAT
1 AAT
67175 GATAACTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (23 bp):
AATTACTAAAAACCCATTAAAAT
Found at i:67569 original size:18 final size:19
Alignment explanation
Indices: 67548--67589 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
67538 TTGGATATAT
67548 TAAAACTTTT-TTCTAATA
1 TAAAACTTTTATTCTAATA
*
67566 TAAAA-TTTTATTCTACTA
1 TAAAACTTTTATTCTAATA
67584 -AAAACT
1 TAAAACT
67590 CTATTTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAACTTTTATTCTAATA
Found at i:67616 original size:110 final size:110
Alignment explanation
Indices: 67347--67643 Score: 436
Period size: 110 Copynumber: 2.7 Consensus size: 110
67337 ACTATTATAG
* * * *
67347 TTTTATTCTACTAGAAACTTTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-T---TCTAATATCTTTATAATTACTT
*
67412 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
62 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATAAAA
67461 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-TCTAATATCTTTATAATTACTTTATT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
*
67525 TTTACCAAAAAATTTGGATATATTAAAACTTTTTTCTAATATAAAA
66 TTTACCAAAAAATTTGGATATACTAAAA-TTTTTTCTAATATAAAA
* **
67571 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTC-AATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTT-TATAA-TTACTTTA
67635 TTTTTACCA
64 TTTTTACCA
67644 TTTTAATTTA
Statistics
Matches: 170, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
109 53 0.31
110 61 0.36
111 7 0.04
112 15 0.09
114 34 0.20
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (110 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
TTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATAAAA
Found at i:75672 original size:31 final size:31
Alignment explanation
Indices: 75634--75698 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
75624 AACTGAACTA
* *
75634 ACTCAAACATCCAAGATCTGAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTAGAG
75665 ACTCAAACATCCAAGATCTAAAGATCTAGAG
1 ACTCAAACATCCAAGATCTAAAGATCTAGAG
75696 ACT
1 ACT
75699 GATAACCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAGATCTAGAG
Found at i:76796 original size:23 final size:23
Alignment explanation
Indices: 76770--76869 Score: 71
Period size: 23 Copynumber: 4.2 Consensus size: 23
76760 AATTCATTAC
76770 ACATAATTTTCCATATTAAGCAT
1 ACATAATTTTCCATATTAAGCAT
** *
76793 ACATAATTGACAACCTTATTTCAAGCAT
1 ACATAATT---TTCCATA-TT-AAGCAT
*
76821 ATATAATTTTCCATATTAAGC--
1 ACATAATTTTCCATATTAAGCAT
* *
76842 ACATAA-TTCCCATATCAAGCAT
1 ACATAATTTTCCATATTAAGCAT
76864 AGCATA
1 A-CATA
76870 TCAATCCAAC
Statistics
Matches: 59, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
20 12 0.20
21 5 0.08
22 1 0.02
23 16 0.27
24 2 0.03
25 4 0.07
26 4 0.07
27 2 0.03
28 13 0.22
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (23 bp):
ACATAATTTTCCATATTAAGCAT
Found at i:77206 original size:59 final size:59
Alignment explanation
Indices: 77134--77252 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
77124 TGAGCACAAG
77134 TAACACATTCCAAAGGATTTAGTTCTTCAATCTCTCCTTAAGTTTTGATTGATCAACAC
1 TAACACATTCCAAAGGATTTAGTTCTTCAATCTCTCCTTAAGTTTTGATTGATCAACAC
77193 TAACACATTCCAAAGGATTTAGTTCTTCAATCTCTCCTTAAGTTTTGATTGATCAACAC
1 TAACACATTCCAAAGGATTTAGTTCTTCAATCTCTCCTTAAGTTTTGATTGATCAACAC
77252 T
1 T
77253 CCTCTATCTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (59 bp):
TAACACATTCCAAAGGATTTAGTTCTTCAATCTCTCCTTAAGTTTTGATTGATCAACAC
Done.