Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012527.1 Corchorus capsularis cultivar CVL-1 contig12548, 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: 152398
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:12062 original size:14 final size:15
Alignment explanation
Indices: 12038--12067 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12028 ACTACTCTAC
12038 AGTATAGTACTAAGT
1 AGTATAGTACTAAGT
12053 AGTA-AGTACTAAGT
1 AGTATAGTACTAAGT
12067 A
1 A
12068 CTCATAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (15 bp):
AGTATAGTACTAAGT
Found at i:19687 original size:2 final size:2
Alignment explanation
Indices: 19680--19710 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19670 AAATTATTAC
19680 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 T
19711 CCATTATCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23778 original size:39 final size:38
Alignment explanation
Indices: 23735--23827 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 38
23725 AATTATCATA
23735 TTCAAGTCTCACT-TTCAACAAAAAAAAAAAAAAAAAAAT
1 TTCAAGTCTCACTATTC-AC-AAAAAAAAAAAAAAAAAAT
*
23774 TTCAAGTCTCACTAGTTCTCAAAAAAAAAAAAAAAAAAT
1 TTCAAGTCTCACTA-TTCACAAAAAAAAAAAAAAAAAAT
23813 TTCAAGTCTCACTAT
1 TTCAAGTCTCACTAT
23828 ATGAATTCTC
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
38 1 0.02
39 46 0.90
40 1 0.02
41 3 0.06
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25
Consensus pattern (38 bp):
TTCAAGTCTCACTATTCACAAAAAAAAAAAAAAAAAAT
Found at i:42746 original size:51 final size:51
Alignment explanation
Indices: 42691--42793 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
42681 TCATGCTTCA
* **
42691 CCCTCTTGGCAATTAGGCCTTTGGGTTATGTTTGCTTTATAAATTTGGCAT
1 CCCTCTTGACAATTAGGCCTTTGGGAAATGTTTGCTTTATAAATTTGGCAT
*
42742 CCCTCTTGACAATTAGGCCTTTGGGAAATGTTTGCTTTATATATTTGGCAT
1 CCCTCTTGACAATTAGGCCTTTGGGAAATGTTTGCTTTATAAATTTGGCAT
42793 C
1 C
42794 ATCAATTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.42
Consensus pattern (51 bp):
CCCTCTTGACAATTAGGCCTTTGGGAAATGTTTGCTTTATAAATTTGGCAT
Found at i:56080 original size:2 final size:2
Alignment explanation
Indices: 56073--56104 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
56063 AAACAAAGAG
*
56073 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56105 TTAAAAGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:56182 original size:15 final size:14
Alignment explanation
Indices: 56140--56183 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
56130 CCGTCAAGGG
56140 GAAAAAAAGGGAAA
1 GAAAAAAAGGGAAA
*
56154 GAAACAAAACGGAAA
1 GAAA-AAAAGGGAAA
56169 GAAAAAAAGAGGAAA
1 GAAAAAAAG-GGAAA
56184 ACAGGGGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.70, C:0.05, G:0.25, T:0.00
Consensus pattern (14 bp):
GAAAAAAAGGGAAA
Found at i:57584 original size:117 final size:119
Alignment explanation
Indices: 57404--57636 Score: 276
Period size: 117 Copynumber: 2.0 Consensus size: 119
57394 TATCCGAATT
* * * * *
57404 GACTAATTTAGGGTTGAATCACGTCAAAGCTCATAATCGAGTTTAATTTCTAATTTTATCAATCA
1 GACTAATGTAGGGTTGAATCACATCAAAGCTCATAATCGAGTCTAATGTATAATTTTATCAATCA
* * * *
57469 CAATACTTTAACTTCATTATTCGTTGG-TCAGAGATATCGAATTT-TACCAACC
66 CAATACTTAAACATCATGATTCGTTGGTTAAGAGATATCGAATTTATACCAACC
* ** *
57521 GACTAATGTA-GGTTGAGTCACATCAAATTTCA-AGATCGAGTCTAATGTATATATTTTTTCAAT
1 GACTAATGTAGGGTTGAATCACATCAAAGCTCATA-ATCGAGTCTAATGTATA-ATTTTATCAAT
* * *
57584 CATAATACTTAAACATGATGATTCGTTGGTTAAGAGATATCGAGTTTATACCA
64 CACAATACTTAAACATCATGATTCGTTGGTTAAGAGATATCGAATTTATACCA
57637 CTCGTTTTAT
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
115 1 0.01
116 32 0.33
117 43 0.45
118 15 0.16
119 5 0.05
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (119 bp):
GACTAATGTAGGGTTGAATCACATCAAAGCTCATAATCGAGTCTAATGTATAATTTTATCAATCA
CAATACTTAAACATCATGATTCGTTGGTTAAGAGATATCGAATTTATACCAACC
Found at i:64116 original size:25 final size:25
Alignment explanation
Indices: 64088--64140 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
64078 TTCTGGTTGC
64088 ATAACCAAGAAACTTAGAATATCAT
1 ATAACCAAGAAACTTAGAATATCAT
*
64113 ATAACCAGGAAACTTAGAATATCAT
1 ATAACCAAGAAACTTAGAATATCAT
64138 ATA
1 ATA
64141 TATTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.51, C:0.15, G:0.09, T:0.25
Consensus pattern (25 bp):
ATAACCAAGAAACTTAGAATATCAT
Found at i:71747 original size:33 final size:33
Alignment explanation
Indices: 71701--71995 Score: 500
Period size: 33 Copynumber: 8.9 Consensus size: 33
71691 TGATGAGAAG
* * **
71701 AGAAGTAATTTGAAGTCTCAGGTTTATGATAAA
1 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
71734 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
1 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
71767 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
1 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
71800 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
1 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
* *
71833 AGAAGTGACTTAAAATCTGGGGTTTATGATAAA
1 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
*
71866 AGAAGTAACTTGAAATCTGGGGTTTATGATGAA
1 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
*
71899 AGAAGTAACTTGAAATCTGGGATTTATGATAAA
1 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
71932 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
1 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
* *
71965 AGAAGTAACTTAAAATCTGAGGTTTATGATA
1 AGAAGTAACTTGAAATCTGGGGTTTATGATA
71996 TGAGTCTGCA
Statistics
Matches: 248, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 248 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (33 bp):
AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
Found at i:74390 original size:33 final size:33
Alignment explanation
Indices: 74344--74473 Score: 197
Period size: 33 Copynumber: 3.9 Consensus size: 33
74334 TGATGAGAAG
* * *
74344 AGAAGTAATTTGAAGTCTCAGGTTTATGATAAA
1 AGAAGTAACTTGAAATCTGAGGTTTATGATAAA
*
74377 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
1 AGAAGTAACTTGAAATCTGAGGTTTATGATAAA
*
74410 AGAAGTAACTTGAAATCTGGGGTTTATGATAAA
1 AGAAGTAACTTGAAATCTGAGGTTTATGATAAA
* *
74443 AGAATTAACTTAAAATCTGAGGTTTATGATA
1 AGAAGTAACTTGAAATCTGAGGTTTATGATA
74474 TGAACCTGCA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (33 bp):
AGAAGTAACTTGAAATCTGAGGTTTATGATAAA
Found at i:80849 original size:31 final size:30
Alignment explanation
Indices: 80749--80851 Score: 102
Period size: 31 Copynumber: 3.4 Consensus size: 30
80739 ATGTTCAAAT
* * *
80749 AATTAAGGGCCTAATGCTTGTGAAATTGTTC
1 AATTAAGGGCCTATTG-TTGTAAAATTGCTC
* * * *
80780 AATTTAGGGCCTATTCTTTTAAAA-AGCTC
1 AATTAAGGGCCTATTGTTGTAAAATTGCTC
80809 AGATT-AGGGCCTATTGTTGTAAAATTGGCTC
1 A-ATTAAGGGCCTATTGTTGTAAAATT-GCTC
80840 AATTAAGGGCCT
1 AATTAAGGGCCT
80852 CCTATCAAGC
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
29 21 0.36
30 12 0.21
31 25 0.43
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (30 bp):
AATTAAGGGCCTATTGTTGTAAAATTGCTC
Found at i:95506 original size:49 final size:49
Alignment explanation
Indices: 95434--95534 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
95424 TGTTTTTTTC
95434 ATTCACAATACTCAAATATCCCAGAACTAGAACTTTCTACTTGAGATAT
1 ATTCACAATACTCAAATATCCCAGAACTAGAACTTTCTACTTGAGATAT
95483 ATTCACAATACTCAAATATCCCAGAACTAGAACTTTCTACTTGAGATAT
1 ATTCACAATACTCAAATATCCCAGAACTAGAACTTTCTACTTGAGATAT
95532 ATT
1 ATT
95535 GAGACTTCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.32
Consensus pattern (49 bp):
ATTCACAATACTCAAATATCCCAGAACTAGAACTTTCTACTTGAGATAT
Found at i:102439 original size:32 final size:31
Alignment explanation
Indices: 102403--102474 Score: 112
Period size: 29 Copynumber: 2.4 Consensus size: 31
102393 ATATATAAAT
102403 AACTATCTATATATGGCATATAATGTCAAAAA
1 AACTAT-TATATATGGCATATAATGTCAAAAA
*
102435 AACTA-TA-ATATGGCATATAATTTCAAAAA
1 AACTATTATATATGGCATATAATGTCAAAAA
102464 AACTATTATAT
1 AACTATTATAT
102475 TTTGATTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 26 0.70
30 4 0.11
31 2 0.05
32 5 0.14
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (31 bp):
AACTATTATATATGGCATATAATGTCAAAAA
Found at i:111539 original size:32 final size:32
Alignment explanation
Indices: 111459--111575 Score: 171
Period size: 32 Copynumber: 3.6 Consensus size: 32
111449 AGCCACGCGG
* * *
111459 AGCCTCCCCACTAGGACGACTCTGCCACGGCGG
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGC-T
**
111492 AGCCTTCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
111524 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
*
111556 AGCCGCCCCACTAGGGCGGC
1 AGCCGCCCCACTAGGACGGC
111576 AAGGCTTTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
32 49 0.63
33 29 0.37
ACGTcount: A:0.16, C:0.43, G:0.28, T:0.13
Consensus pattern (32 bp):
AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
Found at i:111682 original size:33 final size:32
Alignment explanation
Indices: 111632--111749 Score: 114
Period size: 33 Copynumber: 3.6 Consensus size: 32
111622 TAGTACCGGT
* *
111632 GCCGCCCCAAGGGGGCGGTCTATCCATGGTAGG
1 GCCGCCCC-AGGGGGCGGCCTAGCCATGGTAGG
* *
111665 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGT
1 GCCGCCCCAGGG-GGCGGCCTAGCCATGGTAGG
* *
111698 GCCGCCCCAGGAGGGCGGCTTGGCCATGGCTCA--
1 GCCGCCCCAGG-GGGCGGCCTAGCCATGG-T-AGG
111731 GCCGCCCCAGGGGGACGGC
1 GCCGCCCCAGGGGG-CGGC
111750 ACCGGTGGGG
Statistics
Matches: 75, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.09
33 65 0.87
34 2 0.03
35 1 0.01
ACGTcount: A:0.13, C:0.35, G:0.42, T:0.11
Consensus pattern (32 bp):
GCCGCCCCAGGGGGCGGCCTAGCCATGGTAGG
Found at i:129697 original size:49 final size:49
Alignment explanation
Indices: 129625--129722 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
129615 AAATATATTG
* *
129625 GCTAATTTGTCTCACTCAGCGTCCCAGGATGTTAGTATATGTGATGATC
1 GCTAATTTGGCTCACTCAGCGTCCCAGGATGTTAGTATATGCGATGATC
* *
129674 GCTAATTTGGCTCGCTCTGCGTCCCAGGATGTTAGTATATGCGATGATC
1 GCTAATTTGGCTCACTCAGCGTCCCAGGATGTTAGTATATGCGATGATC
129723 CTCCTAATCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.34
Consensus pattern (49 bp):
GCTAATTTGGCTCACTCAGCGTCCCAGGATGTTAGTATATGCGATGATC
Found at i:129751 original size:20 final size:20
Alignment explanation
Indices: 129726--129767 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
129716 GATGATCCTC
129726 CTAATCAGATGCTACCGTTG
1 CTAATCAGATGCTACCGTTG
* *
129746 CTAATCAGTTGCTACTGTTG
1 CTAATCAGATGCTACCGTTG
129766 CT
1 CT
129768 TGCAGAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (20 bp):
CTAATCAGATGCTACCGTTG
Found at i:139720 original size:21 final size:22
Alignment explanation
Indices: 139669--139719 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
139659 GTCTGTGTCT
139669 AGTCAAAATACTAGGATTTTTA
1 AGTCAAAATACTAGGATTTTTA
139691 AGTCAAAATACTAGGATTTTTA
1 AGTCAAAATACTAGGATTTTTA
*
139713 CGTCAAA
1 AGTCAAA
139720 TTGACCAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (22 bp):
AGTCAAAATACTAGGATTTTTA
Found at i:143414 original size:33 final size:33
Alignment explanation
Indices: 143371--143449 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
143361 TGGTGGAGAT
*
143371 GGAGGTGGAGGGGGTGATTATGGCGGGGGAGGA
1 GGAGGTGGAGGGGGAGATTATGGCGGGGGAGGA
* * * *
143404 GGAGGAGGAGGTGGAGATTGTGGTGGGGGAGGA
1 GGAGGTGGAGGGGGAGATTATGGCGGGGGAGGA
143437 GGAGGTGGAGGGG
1 GGAGGTGGAGGGG
143450 ATTGTGGTGG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.19, C:0.01, G:0.66, T:0.14
Consensus pattern (33 bp):
GGAGGTGGAGGGGGAGATTATGGCGGGGGAGGA
Found at i:143434 original size:27 final size:28
Alignment explanation
Indices: 143404--143461 Score: 91
Period size: 27 Copynumber: 2.0 Consensus size: 28
143394 CGGGGGAGGA
143404 GGAGGAGGAGGTGGA-GATTGTGGTGGG
1 GGAGGAGGAGGTGGAGGATTGTGGTGGG
143431 GGAGGAGGAGGTGGAGGGGATTGTGGTGGG
1 GGAGGAGGAGGTGGA--GGATTGTGGTGGG
143461 G
1 G
143462 CTGGCGGCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 15 0.54
30 13 0.46
ACGTcount: A:0.17, C:0.00, G:0.66, T:0.17
Consensus pattern (28 bp):
GGAGGAGGAGGTGGAGGATTGTGGTGGG
Found at i:143435 original size:30 final size:30
Alignment explanation
Indices: 143401--143461 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
143391 TGGCGGGGGA
*
143401 GGAGGAGGAGGAGGTGGAGATTGTGGTGGG
1 GGAGGAGGAGGAGGAGGAGATTGTGGTGGG
* *
143431 GGAGGAGGAGGTGGAGGGGATTGTGGTGGG
1 GGAGGAGGAGGAGGAGGAGATTGTGGTGGG
143461 G
1 G
143462 CTGGCGGCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.66, T:0.16
Consensus pattern (30 bp):
GGAGGAGGAGGAGGAGGAGATTGTGGTGGG
Found at i:145230 original size:9 final size:9
Alignment explanation
Indices: 145229--145265 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
145219 GTGATGATGG
145229 TGGTGGTGA
1 TGGTGGTGA
* *
145238 TGGCGCTGA
1 TGGTGGTGA
145247 TGGTGGTGA
1 TGGTGGTGA
145256 TGGTGGTGA
1 TGGTGGTGA
145265 T
1 T
145266 ACTGGCAGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.11, C:0.05, G:0.51, T:0.32
Consensus pattern (9 bp):
TGGTGGTGA
Found at i:145235 original size:24 final size:24
Alignment explanation
Indices: 145205--145261 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
145195 GTGGGGGTAA
*
145205 TGATGGTGGCGGCGGTGATGATGG
1 TGATGGTGGCGGCGCTGATGATGG
* ** *
145229 TGGTGGTGATGGCGCTGATGGTGG
1 TGATGGTGGCGGCGCTGATGATGG
145253 TGATGGTGG
1 TGATGGTGG
145262 TGATACTGGC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.11, C:0.07, G:0.54, T:0.28
Consensus pattern (24 bp):
TGATGGTGGCGGCGCTGATGATGG
Found at i:145387 original size:30 final size:30
Alignment explanation
Indices: 145363--145420 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
145353 GGTGGTGGTG
145363 GTTGGTGGGGAGGAGGTGATGGTGGAGGCA
1 GTTGGTGGGGAGGAGGTGATGGTGGAGGCA
*
145393 GTTGGTGGGGAGGAGGTGGTGGTGGAGG
1 GTTGGTGGGGAGGAGGTGATGGTGGAGG
145421 AGGTTTTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.14, C:0.02, G:0.64, T:0.21
Consensus pattern (30 bp):
GTTGGTGGGGAGGAGGTGATGGTGGAGGCA
Found at i:145404 original size:15 final size:15
Alignment explanation
Indices: 145365--145492 Score: 93
Period size: 15 Copynumber: 8.6 Consensus size: 15
145355 TGGTGGTGGT
145365 TGGTGG-GGAGGAGG
1 TGGTGGTGGAGGAGG
* *
145379 TGATGGTGGAGGCAGT
1 TGGTGGTGGAGG-AGG
145395 TGGTGG-GGAGGAGG
1 TGGTGGTGGAGGAGG
145409 TGGTGGTGGAGGAGG
1 TGGTGGTGGAGGAGG
** * *
145424 TTTTGATGGTGGAGG
1 TGGTGGTGGAGGAGG
** *
145439 TGGTGGTTTCA-GTGG
1 TGGTGG-TGGAGGAGG
*
145454 TGGTGGAGG-GGATGG
1 TGGTGGTGGAGGA-GG
*
145469 TGGTGGGGGAGGAGG
1 TGGTGGTGGAGGAGG
*
145484 AGGTGGTGG
1 TGGTGGTGG
145493 CGGGGCGGGG
Statistics
Matches: 85, Mismatches: 22, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
14 14 0.16
15 60 0.71
16 11 0.13
ACGTcount: A:0.13, C:0.02, G:0.62, T:0.23
Consensus pattern (15 bp):
TGGTGGTGGAGGAGG
Found at i:145435 original size:21 final size:21
Alignment explanation
Indices: 145408--145462 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
145398 TGGGGAGGAG
*
145408 GTGGTGGTGGAGGAGGTTT-T
1 GTGGTGGTGGAGGAGGTTTCA
* * *
145428 GATGGTGGAGGTGGTGGTTTCA
1 G-TGGTGGTGGAGGAGGTTTCA
145450 GTGGTGGTGGAGG
1 GTGGTGGTGGAGG
145463 GGATGGTGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.11, C:0.02, G:0.56, T:0.31
Consensus pattern (21 bp):
GTGGTGGTGGAGGAGGTTTCA
Found at i:145471 original size:18 final size:18
Alignment explanation
Indices: 145450--145492 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
145440 GGTGGTTTCA
*
145450 GTGGTGGTGGAGG-GGATG
1 GTGGTGGGGGAGGAGGA-G
145468 GTGGTGGGGGAGGAGGAG
1 GTGGTGGGGGAGGAGGAG
145486 GTGGTGG
1 GTGGTGG
145493 CGGGGCGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.12, C:0.00, G:0.70, T:0.19
Consensus pattern (18 bp):
GTGGTGGGGGAGGAGGAG
Found at i:145497 original size:21 final size:21
Alignment explanation
Indices: 145458--145497 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
145448 CAGTGGTGGT
*
145458 GGAGGGGATGGTGGTGGGGGA
1 GGAGGGGATGGTGGCGGGGGA
145479 GGAGGAGG-TGGTGGCGGGG
1 GGAGG-GGATGGTGGCGGGG
145498 CGGGGACGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.12, C:0.03, G:0.72, T:0.12
Consensus pattern (21 bp):
GGAGGGGATGGTGGCGGGGGA
Found at i:150023 original size:60 final size:60
Alignment explanation
Indices: 149930--150051 Score: 199
Period size: 60 Copynumber: 2.0 Consensus size: 60
149920 ATGATCAGAG
* *
149930 TCAGTTGCCGGAGGAAATCTACACAGAATTCCTAGAGAAATTACCCGTTAAGTCTCTTAT
1 TCAGTTGCCGGAGGAAATCTACACAGAAATCCTAAAGAAATTACCCGTTAAGTCTCTTAT
* * *
149990 TCAGTTGCCGGAGGAAATCTACATAGAAATCCTAAAGAGATTACCGGTTAAGTCTCTTAT
1 TCAGTTGCCGGAGGAAATCTACACAGAAATCCTAAAGAAATTACCCGTTAAGTCTCTTAT
150050 TC
1 TC
150052 TATATAGGGA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (60 bp):
TCAGTTGCCGGAGGAAATCTACACAGAAATCCTAAAGAAATTACCCGTTAAGTCTCTTAT
Found at i:151592 original size:3 final size:3
Alignment explanation
Indices: 151584--151640 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
151574 GGGGTAATGC
* * * * * *
151584 TGG TGG TGG CGG TGG TGA TGG TGG AGG AGG AGG TGG TGG TGG TGA TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
151632 TGG TGG TGG
1 TGG TGG TGG
151641 GGAAGATGGA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.09, C:0.02, G:0.63, T:0.26
Consensus pattern (3 bp):
TGG
Done.