Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011143.1 Corchorus capsularis cultivar CVL-1 contig11164, 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: 50961
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:122 original size:15 final size:16
Alignment explanation
Indices: 93--130 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
83 GTGTAAAAAA
93 GTAAAAAGTACAAAGG
1 GTAAAAAGTACAAAGG
* *
109 GTAAAAGGTA-AAAGT
1 GTAAAAAGTACAAAGG
124 GTAAAAA
1 GTAAAAA
131 AGAGGCGGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.58, C:0.03, G:0.24, T:0.16
Consensus pattern (16 bp):
GTAAAAAGTACAAAGG
Found at i:8323 original size:164 final size:164
Alignment explanation
Indices: 8052--8382 Score: 662
Period size: 164 Copynumber: 2.0 Consensus size: 164
8042 GTATATAAGA
8052 TTTTTCTGATAGACTTCTTTAGGATAGAGTTGAAGATTAGATTTCTGGCGCAACCTCTCAGGGCT
1 TTTTTCTGATAGACTTCTTTAGGATAGAGTTGAAGATTAGATTTCTGGCGCAACCTCTCAGGGCT
8117 GATGCACTCACAAGAATCTAAAATATACTATGAACTTCTGTCGTTTTATGGTATAATGTGGGCTC
66 GATGCACTCACAAGAATCTAAAATATACTATGAACTTCTGTCGTTTTATGGTATAATGTGGGCTC
8182 TTTAAAATACATAGATGTAGCCTCAATCTCTTAT
131 TTTAAAATACATAGATGTAGCCTCAATCTCTTAT
8216 TTTTTCTGATAGACTTCTTTAGGATAGAGTTGAAGATTAGATTTCTGGCGCAACCTCTCAGGGCT
1 TTTTTCTGATAGACTTCTTTAGGATAGAGTTGAAGATTAGATTTCTGGCGCAACCTCTCAGGGCT
8281 GATGCACTCACAAGAATCTAAAATATACTATGAACTTCTGTCGTTTTATGGTATAATGTGGGCTC
66 GATGCACTCACAAGAATCTAAAATATACTATGAACTTCTGTCGTTTTATGGTATAATGTGGGCTC
8346 TTTAAAATACATAGATGTAGCCTCAATCTCTTAT
131 TTTAAAATACATAGATGTAGCCTCAATCTCTTAT
8380 TTT
1 TTT
8383 GTATTTGAAC
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 167 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (164 bp):
TTTTTCTGATAGACTTCTTTAGGATAGAGTTGAAGATTAGATTTCTGGCGCAACCTCTCAGGGCT
GATGCACTCACAAGAATCTAAAATATACTATGAACTTCTGTCGTTTTATGGTATAATGTGGGCTC
TTTAAAATACATAGATGTAGCCTCAATCTCTTAT
Found at i:11561 original size:14 final size:14
Alignment explanation
Indices: 11544--11570 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11534 TATGTGCTAA
11544 AAAGTTTATAATTC
1 AAAGTTTATAATTC
11558 AAAGTTTATAATT
1 AAAGTTTATAATT
11571 GTTATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (14 bp):
AAAGTTTATAATTC
Found at i:13792 original size:21 final size:21
Alignment explanation
Indices: 13768--13819 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
13758 GCATACCCTT
*
13768 CATACCCTCCTCCACCAGGTG
1 CATACCCTCCTCCACCAGCTG
* **
13789 CATATCCTCCTCCACCTTCTG
1 CATACCCTCCTCCACCAGCTG
13810 CATACCCTCC
1 CATACCCTCC
13820 ACCTCCCCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.50, G:0.08, T:0.25
Consensus pattern (21 bp):
CATACCCTCCTCCACCAGCTG
Found at i:13832 original size:27 final size:27
Alignment explanation
Indices: 13794--13847 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
13784 AGGTGCATAT
* *
13794 CCTCCTCCACCTTCTGCATACCCTCCA
1 CCTCCCCCACCTTCAGCATACCCTCCA
*
13821 CCTCCCCCACCTTCAGCATATCCTCCA
1 CCTCCCCCACCTTCAGCATACCCTCCA
13848 GTTACATACC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.56, G:0.04, T:0.24
Consensus pattern (27 bp):
CCTCCCCCACCTTCAGCATACCCTCCA
Found at i:14808 original size:3 final size:3
Alignment explanation
Indices: 14800--14827 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
14790 ATATATATAT
14800 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
14828 GATCCCTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:24945 original size:175 final size:175
Alignment explanation
Indices: 24654--25007 Score: 708
Period size: 175 Copynumber: 2.0 Consensus size: 175
24644 GACACCAAAA
24654 ATGGGGGCAGAAGATTTTTATCCATAAATTACTAATACTAACATACAGAGAGTGAGTGACGTGTA
1 ATGGGGGCAGAAGATTTTTATCCATAAATTACTAATACTAACATACAGAGAGTGAGTGACGTGTA
24719 ATATTCTTTTTTTACAAGTTGATTACCATTTTTATCGATTCCCATTAGGTTCAAAATTATAATTA
66 ATATTCTTTTTTTACAAGTTGATTACCATTTTTATCGATTCCCATTAGGTTCAAAATTATAATTA
24784 TACAACTATCGTGTTCAAGATTCAAGAAATGAAAGTAGAAGATGC
131 TACAACTATCGTGTTCAAGATTCAAGAAATGAAAGTAGAAGATGC
24829 ATGGGGGCAGAAGATTTTTATCCATAAATTACTAATACTAACATACAGAGAGTGAGTGACGTGTA
1 ATGGGGGCAGAAGATTTTTATCCATAAATTACTAATACTAACATACAGAGAGTGAGTGACGTGTA
24894 ATATTCTTTTTTTACAAGTTGATTACCATTTTTATCGATTCCCATTAGGTTCAAAATTATAATTA
66 ATATTCTTTTTTTACAAGTTGATTACCATTTTTATCGATTCCCATTAGGTTCAAAATTATAATTA
24959 TACAACTATCGTGTTCAAGATTCAAGAAATGAAAGTAGAAGATGC
131 TACAACTATCGTGTTCAAGATTCAAGAAATGAAAGTAGAAGATGC
25004 ATGG
1 ATGG
25008 TACTATTATT
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 179 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (175 bp):
ATGGGGGCAGAAGATTTTTATCCATAAATTACTAATACTAACATACAGAGAGTGAGTGACGTGTA
ATATTCTTTTTTTACAAGTTGATTACCATTTTTATCGATTCCCATTAGGTTCAAAATTATAATTA
TACAACTATCGTGTTCAAGATTCAAGAAATGAAAGTAGAAGATGC
Found at i:36245 original size:54 final size:54
Alignment explanation
Indices: 36108--36285 Score: 286
Period size: 54 Copynumber: 3.2 Consensus size: 54
36098 AGTAGTTGGA
* * *
36108 GGAGATGGAGAAGGGTTCCCTGATTGTGTTGGAGGAGTGTAAGTTGGTGGGGTACTT
1 GGAGATGGAGGAGGGTTCCCTGATTGTGTCGGAGGGGTGTAAGTTGGTGGGG---TT
36165 GGAGATGGAGGAGGGTTCCCTGATTGTGTCGGAGGGGTGTAAGTTGGTGGGGTT
1 GGAGATGGAGGAGGGTTCCCTGATTGTGTCGGAGGGGTGTAAGTTGGTGGGGTT
36219 GGAGATGGAGGAGGGTTCCCTGATTGTGTCGGAGGGGTGTAAGTTGGTGGGGTT
1 GGAGATGGAGGAGGGTTCCCTGATTGTGTCGGAGGGGTGTAAGTTGGTGGGGTT
36273 GGAG-TGGGAGGAG
1 GGAGAT-GGAGGAG
36286 ATGGCGGAGT
Statistics
Matches: 117, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
53 1 0.01
54 67 0.57
57 49 0.42
ACGTcount: A:0.17, C:0.07, G:0.49, T:0.27
Consensus pattern (54 bp):
GGAGATGGAGGAGGGTTCCCTGATTGTGTCGGAGGGGTGTAAGTTGGTGGGGTT
Found at i:38967 original size:4 final size:4
Alignment explanation
Indices: 38958--38985 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
38948 TTTCACATTC
38958 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
38986 ACTTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:40210 original size:18 final size:18
Alignment explanation
Indices: 40187--40245 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
40177 GTTGCCACCA
40187 TTGCCGCCTCCATTGCCG
1 TTGCCGCCTCCATTGCCG
*
40205 TTGCCG-TTCCCATTGCCG
1 TTGCCGCCT-CCATTGCCG
** *
40223 TTGTTGCCACCATTGCCG
1 TTGCCGCCTCCATTGCCG
40241 TTGCC
1 TTGCC
40246 ATTTCCGTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
17 1 0.03
18 31 0.97
ACGTcount: A:0.07, C:0.39, G:0.22, T:0.32
Consensus pattern (18 bp):
TTGCCGCCTCCATTGCCG
Found at i:40239 original size:30 final size:30
Alignment explanation
Indices: 40205--40309 Score: 141
Period size: 30 Copynumber: 3.7 Consensus size: 30
40195 TCCATTGCCG
40205 TTGCCGTTCCCATTGCCGTTGTTGCCACCA
1 TTGCCGTTCCCATTGCCGTTGTTGCCACCA
* *
40235 TTGCCGTTGCCATTTCCGTTGTTGCCACCA
1 TTGCCGTTCCCATTGCCGTTGTTGCCACCA
*
40265 TTGCCG------TTGCCGTTGTTGCCGCCA
1 TTGCCGTTCCCATTGCCGTTGTTGCCACCA
40289 TTGCCGTTCCCATTGCCGTTG
1 TTGCCGTTCCCATTGCCGTTG
40310 CCTTTGCCTG
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
24 22 0.34
30 43 0.66
ACGTcount: A:0.08, C:0.34, G:0.23, T:0.35
Consensus pattern (30 bp):
TTGCCGTTCCCATTGCCGTTGTTGCCACCA
Found at i:40271 original size:18 final size:18
Alignment explanation
Indices: 40214--40273 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 18
40204 GTTGCCGTTC
40214 CCATTGCCGTTGTTGCCA
1 CCATTGCCGTTGTTGCCA
40232 CCATTGCC---GTTG---
1 CCATTGCCGTTGTTGCCA
*
40244 CCATTTCCGTTGTTGCCA
1 CCATTGCCGTTGTTGCCA
40262 CCATTGCCGTTG
1 CCATTGCCGTTG
40274 CCGTTGTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
12 7 0.21
15 8 0.24
18 19 0.56
ACGTcount: A:0.10, C:0.33, G:0.22, T:0.35
Consensus pattern (18 bp):
CCATTGCCGTTGTTGCCA
Found at i:40294 original size:24 final size:24
Alignment explanation
Indices: 40217--40296 Score: 97
Period size: 24 Copynumber: 3.1 Consensus size: 24
40207 GCCGTTCCCA
40217 TTGCCGTTGTTGCCACCATTGCCG
1 TTGCCGTTGTTGCCACCATTGCCG
40241 TTGCCATTTCCGTTGTTGCCACCATTGCCG
1 TTG------CCGTTGTTGCCACCATTGCCG
*
40271 TTGCCGTTGTTGCCGCCATTGCCG
1 TTGCCGTTGTTGCCACCATTGCCG
40295 TT
1 TT
40297 CCCATTGCCG
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
24 25 0.51
30 24 0.49
ACGTcount: A:0.07, C:0.33, G:0.24, T:0.36
Consensus pattern (24 bp):
TTGCCGTTGTTGCCACCATTGCCG
Found at i:40628 original size:6 final size:6
Alignment explanation
Indices: 40617--40652 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
40607 AGTCAGCCCT
40617 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
40653 TGGAAACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:43754 original size:226 final size:226
Alignment explanation
Indices: 43350--43766 Score: 780
Period size: 226 Copynumber: 1.8 Consensus size: 226
43340 TATTTTTTTT
43350 AGGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGCTTGTGGAGTTGAC
1 AGGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGCTTGTGGAGTTGAC
*
43415 ACATGTCCCTTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGACACATGT
66 ACATGTCCCTTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGACACATGT
43480 CACCCTTTAGGACCCGCTTGAGTAATTTTCTAAACTCCACCACCGGTGTATTGTATAATTTACCT
131 CACCCTTTAGGACCCGCTTGAGTAATTTTCTAAACTCCACCACCGGTGTATTGTATAATTTACCT
43545 TTTTTTATATAAAGATTATATAAATAAAATA
196 TTTTTTATATAAAGATTATATAAATAAAATA
43576 AGGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGCTTGTGGAGTTGAC
1 AGGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGCTTGTGGAGTTGAC
* *
43641 ACATGTCCCTTTTTTGAATTAATTAAGTTTTAAATATTTCAATTTAGTCCTTAAGGGACACATGT
66 ACATGTCCCTTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGACACATGT
* * *
43706 CACCCTTTAGGACCCGCTTGTGTAATTTTCTAAATTCCACCGCCGGTGTATTGTATAATTT
131 CACCCTTTAGGACCCGCTTGAGTAATTTTCTAAACTCCACCACCGGTGTATTGTATAATTT
43767 GCCATAAAAT
Statistics
Matches: 185, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
226 185 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (226 bp):
AGGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGCTTGTGGAGTTGAC
ACATGTCCCTTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGACACATGT
CACCCTTTAGGACCCGCTTGAGTAATTTTCTAAACTCCACCACCGGTGTATTGTATAATTTACCT
TTTTTTATATAAAGATTATATAAATAAAATA
Found at i:45649 original size:30 final size:30
Alignment explanation
Indices: 45614--45676 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
45604 TGCAGGGGTA
45614 TTGTTGCCACCATTACCGTTGCCATTGCCG
1 TTGTTGCCACCATTACCGTTGCCATTGCCG
* **
45644 TTGTTGCCACCATTCCCGTTGTTATTGCCG
1 TTGTTGCCACCATTACCGTTGCCATTGCCG
45674 TTG
1 TTG
45677 CCGTTGTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.11, C:0.30, G:0.21, T:0.38
Consensus pattern (30 bp):
TTGTTGCCACCATTACCGTTGCCATTGCCG
Found at i:45679 original size:36 final size:36
Alignment explanation
Indices: 45632--45718 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
45622 ACCATTACCG
* **
45632 TTGCCATTGCCGTTGTTGCCACCATTCCCGTTGTTA
1 TTGCCGTTGCCGTTGTTGCCACCATTCCCGTTGCCA
** *
45668 TTGCCGTTGCCGTTGTTGTTACCGTTCCCGTTGCCA
1 TTGCCGTTGCCGTTGTTGCCACCATTCCCGTTGCCA
45704 TTGCCGTTGCCGTTG
1 TTGCCGTTGCCGTTG
45719 CCGTTGTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.07, C:0.30, G:0.24, T:0.39
Consensus pattern (36 bp):
TTGCCGTTGCCGTTGTTGCCACCATTCCCGTTGCCA
Found at i:45680 original size:18 final size:18
Alignment explanation
Indices: 45659--45718 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
45649 GCCACCATTC
45659 CCGTTGTTATTGCCGTTG
1 CCGTTGTTATTGCCGTTG
* * *
45677 CCGTTGTTGTTACCGTTC
1 CCGTTGTTATTGCCGTTG
**
45695 CCGTTGCCATTGCCGTTG
1 CCGTTGTTATTGCCGTTG
45713 CCGTTG
1 CCGTTG
45719 CCGTTGTTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.05, C:0.28, G:0.27, T:0.40
Consensus pattern (18 bp):
CCGTTGTTATTGCCGTTG
Found at i:45710 original size:12 final size:12
Alignment explanation
Indices: 45653--45724 Score: 54
Period size: 12 Copynumber: 6.0 Consensus size: 12
45643 GTTGTTGCCA
*
45653 CCATTCCCGTTG
1 CCATTGCCGTTG
**
45665 TTATTGCCGTTG
1 CCATTGCCGTTG
* ** *
45677 CCGTTGTTGTTA
1 CCATTGCCGTTG
* *
45689 CCGTTCCCGTTG
1 CCATTGCCGTTG
45701 CCATTGCCGTTG
1 CCATTGCCGTTG
*
45713 CCGTTGCCGTTG
1 CCATTGCCGTTG
45725 TTATTATTGC
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.06, C:0.31, G:0.25, T:0.39
Consensus pattern (12 bp):
CCATTGCCGTTG
Found at i:45740 original size:6 final size:6
Alignment explanation
Indices: 45668--45724 Score: 69
Period size: 6 Copynumber: 9.5 Consensus size: 6
45658 CCCGTTGTTA
** * * *
45668 TTGCCG TTGCCG TTGTTG TTACCG TTCCCG TTGCCA TTGCCG TTGCCG
1 TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG
45716 TTGCCG TTG
1 TTGCCG TTG
45725 TTATTATTGC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.04, C:0.30, G:0.28, T:0.39
Consensus pattern (6 bp):
TTGCCG
Found at i:47297 original size:73 final size:73
Alignment explanation
Indices: 47178--47324 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
47168 AGGCACAAAT
47178 AACATACTATACAATAATATTTCTTAAATTTAAATACTTATAATTATATCATGTAAAACTTAACT
1 AACATACTATACAATAATATTTCTTAAATTTAAATACTTATAATTATATCATGTAAAACTTAACT
47243 CGAGGCTA
66 CGAGGCTA
47251 AACATACTATACAATAATATTTCTTAAATTTAAATACTTATAATTATATCATGTAAAACTTAACT
1 AACATACTATACAATAATATTTCTTAAATTTAAATACTTATAATTATATCATGTAAAACTTAACT
47316 CGAGGCTA
66 CGAGGCTA
47324 A
1 A
47325 TATTCTTGTG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (73 bp):
AACATACTATACAATAATATTTCTTAAATTTAAATACTTATAATTATATCATGTAAAACTTAACT
CGAGGCTA
Found at i:48878 original size:21 final size:21
Alignment explanation
Indices: 48853--48894 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
48843 GAGGTGGCGA
* *
48853 TGGAGGAGTGTAAGTAGTTGG
1 TGGAGGAGTATAAATAGTTGG
48874 TGGAGGAGTATAAATAGTTGG
1 TGGAGGAGTATAAATAGTTGG
48895 AGTAGATGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.43, T:0.29
Consensus pattern (21 bp):
TGGAGGAGTATAAATAGTTGG
Found at i:48919 original size:42 final size:42
Alignment explanation
Indices: 48872--48951 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
48862 GTAAGTAGTT
**
48872 GGTGGAGGAGTATAAATAGTTGGAGTAGATGGTGGAGGTGGC
1 GGTGGAGGAGTATAAATAGTTGGAACAGATGGTGGAGGTGGC
*
48914 GGTGGAGGAGTATAAATAGTTGGAACGGATGGTGGAGG
1 GGTGGAGGAGTATAAATAGTTGGAACAGATGGTGGAGG
48952 AGTATAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.28, C:0.03, G:0.47, T:0.23
Consensus pattern (42 bp):
GGTGGAGGAGTATAAATAGTTGGAACAGATGGTGGAGGTGGC
Found at i:48934 original size:63 final size:65
Alignment explanation
Indices: 48826--48981 Score: 199
Period size: 63 Copynumber: 2.3 Consensus size: 65
48816 TAGTTGGTGG
* *
48826 AGTTGGAGTGGATGGTGGAGGTGGCGATGGAGGAGTGTAAGTAG-T-TGGTGGAGGAGTATAAAT
1 AGTTGGAGTGGATGGTGGAGGTGGCGATGGAGGAGTATAAATAGTTGTGGTGGAGGAGTATAAAT
* *
48889 AGTTGGAGTAGATGGTGGAGGTGGCGGTGGAGGAGTATAAATAGTTGGAACGGATGGTGGAGGAG
1 AGTTGGAGTGGATGGTGGAGGTGGCGATGGAGGAGTATAAATAGTT------G-TGGTGGAGGAG
48954 TATAAAT
59 TATAAAT
48961 AGTTGGAGTGGATGGTGGAGG
1 AGTTGGAGTGGATGGTGGAGG
48982 AGTATAAATA
Statistics
Matches: 79, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
63 40 0.51
64 1 0.01
72 38 0.48
ACGTcount: A:0.26, C:0.02, G:0.47, T:0.24
Consensus pattern (65 bp):
AGTTGGAGTGGATGGTGGAGGTGGCGATGGAGGAGTATAAATAGTTGTGGTGGAGGAGTATAAAT
Found at i:48949 original size:30 final size:30
Alignment explanation
Indices: 48914--49011 Score: 169
Period size: 30 Copynumber: 3.3 Consensus size: 30
48904 TGGAGGTGGC
*
48914 GGTGGAGGAGTATAAATAGTTGGAACGGAT
1 GGTGGAGGAGTATAAATAGTTGGAATGGAT
*
48944 GGTGGAGGAGTATAAATAGTTGGAGTGGAT
1 GGTGGAGGAGTATAAATAGTTGGAATGGAT
*
48974 GGTGGAGGAGTATAAATAATTGGAATGGAT
1 GGTGGAGGAGTATAAATAGTTGGAATGGAT
49004 GGTGGAGG
1 GGTGGAGG
49012 TGTCGACGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.32, C:0.01, G:0.43, T:0.24
Consensus pattern (30 bp):
GGTGGAGGAGTATAAATAGTTGGAATGGAT
Found at i:49069 original size:24 final size:24
Alignment explanation
Indices: 49037--49128 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 24
49027 GTAATTATGA
49037 CCACCATTACCGTTGCCATTGTTG
1 CCACCATTACCGTTGCCATTGTTG
49061 CCACCATTACCGTTGCCATTGTT-
1 CCACCATTACCGTTGCCATTGTTG
* * * * *
49084 --ACCGTTTCCATTTCCGTTGTTG
1 CCACCATTACCGTTGCCATTGTTG
* *
49106 CCACCATTGCCGTTGCCGTTGTT
1 CCACCATTACCGTTGCCATTGTT
49129 ATTATTGCCG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
21 16 0.29
24 40 0.71
ACGTcount: A:0.13, C:0.33, G:0.17, T:0.37
Consensus pattern (24 bp):
CCACCATTACCGTTGCCATTGTTG
Found at i:50243 original size:28 final size:30
Alignment explanation
Indices: 50180--50236 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
50170 TAAAAGTACA
*
50180 AAATTGGTCCCTCAAGTGGAGCGAAAATAGT
1 AAATTGGTCCCTCAAGTGGA-CAAAAATAGT
50211 AAATTGGTCCCTCAAGT-GA-AAAAATA
1 AAATTGGTCCCTCAAGTGGACAAAAATA
50237 TGCAATTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
30 2 0.08
31 17 0.68
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (30 bp):
AAATTGGTCCCTCAAGTGGACAAAAATAGT
Done.