Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011708.1 Corchorus capsularis cultivar CVL-1 contig11729, 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: 124991
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:850 original size:6 final size:6
Alignment explanation
Indices: 839--874 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
829 TCAATCTACC
839 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
875 TCTCAAAAGC
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):
AGAAAA
Found at i:32366 original size:5 final size:5
Alignment explanation
Indices: 32353--32383 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
32343 AGAATAAGAC
*
32353 TTGGG TTGGA TTGGG TTGGG TTGGG TTGGG T
1 TTGGG TTGGG TTGGG TTGGG TTGGG TTGGG T
32384 CTATTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.00, G:0.55, T:0.42
Consensus pattern (5 bp):
TTGGG
Found at i:41541 original size:22 final size:21
Alignment explanation
Indices: 41480--41541 Score: 51
Period size: 22 Copynumber: 3.0 Consensus size: 21
41470 AATAACATCT
41480 AATTTGATAACC-TCATA--A
1 AATTTGATAACCATCATATGA
* *
41498 AATTTTGATAATCA-CACCATGA
1 AA-TTTGATAACCATCA-TATGA
41520 AATTTCGATAACCATCATATGA
1 AATTT-GATAACCATCATATGA
41542 GAATAAAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
18 2 0.06
19 11 0.33
20 1 0.03
21 3 0.09
22 14 0.42
23 2 0.06
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (21 bp):
AATTTGATAACCATCATATGA
Found at i:41746 original size:22 final size:22
Alignment explanation
Indices: 41721--41820 Score: 116
Period size: 22 Copynumber: 4.6 Consensus size: 22
41711 ACATCCCTCA
* *
41721 GAAATTTTGGTAACCTCTTTAT
1 GAAATTTTGATAACCTCTATAT
41743 GAAATTTTGATAACCTCTATAT
1 GAAATTTTGATAACCTCTATAT
41765 GAAATTTTGATAA-CTAC-ACTAT
1 GAAATTTTGATAACCT-CTA-TAT
* * *
41787 GAAGTTTTGATGACTTCTATAT
1 GAAATTTTGATAACCTCTATAT
41809 GAAA-TTTGATAA
1 GAAATTTTGATAA
41821 TTTTTCTATG
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
21 10 0.15
22 55 0.82
23 2 0.03
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (22 bp):
GAAATTTTGATAACCTCTATAT
Found at i:45111 original size:22 final size:22
Alignment explanation
Indices: 45080--45144 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
45070 TTTGCAAAAC
*
45080 CATACA-ATGAAATTTCGATAA
1 CATACATATGAAATTTTGATAA
* * * *
45101 CCTCCATATGAATTTTTGATGA
1 CATACATATGAAATTTTGATAA
*
45123 CATACTTATGAAATTTTGATAA
1 CATACATATGAAATTTTGATAA
45145 TCTTATTATG
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (22 bp):
CATACATATGAAATTTTGATAA
Found at i:48977 original size:20 final size:20
Alignment explanation
Indices: 48952--48991 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
48942 ATGACCTATC
48952 GTTGCTGGTTTCGCTGATGT
1 GTTGCTGGTTTCGCTGATGT
48972 GTTGCTGGTTTCGCTGATGT
1 GTTGCTGGTTTCGCTGATGT
48992 TACTCAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.15, G:0.35, T:0.45
Consensus pattern (20 bp):
GTTGCTGGTTTCGCTGATGT
Found at i:50482 original size:69 final size:69
Alignment explanation
Indices: 50371--50509 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 69
50361 TAGACTTGAC
* * *
50371 GGGTTGGGCCGCACGGGGGAGAGATGAGGACTCACATGTAAATTGGGGGAGATTGTTGAGGATTT
1 GGGTTGAGCCGCACGGGGGAGAGATGAGGACTCACATGTAAATCGGGGGAGATTGTTGAGAATTT
50436 ACAT
66 ACAT
* * *
50440 GGGTTGAGCCGCATGGGGGAGAGATGAGGACTCATATGTAAATCGGGGGGGATTGTTGAGAATTT
1 GGGTTGAGCCGCACGGGGGAGAGATGAGGACTCACATGTAAATCGGGGGAGATTGTTGAGAATTT
50505 ACAT
66 ACAT
50509 G
1 G
50510 TGAGGAAACA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.25, C:0.11, G:0.40, T:0.24
Consensus pattern (69 bp):
GGGTTGAGCCGCACGGGGGAGAGATGAGGACTCACATGTAAATCGGGGGAGATTGTTGAGAATTT
ACAT
Found at i:56043 original size:14 final size:14
Alignment explanation
Indices: 56024--56051 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56014 TTCCTCTGAC
56024 CCGTTTGTTTTGAT
1 CCGTTTGTTTTGAT
56038 CCGTTTGTTTTGAT
1 CCGTTTGTTTTGAT
56052 GTAATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.14, G:0.21, T:0.57
Consensus pattern (14 bp):
CCGTTTGTTTTGAT
Found at i:63188 original size:102 final size:102
Alignment explanation
Indices: 63016--63585 Score: 729
Period size: 103 Copynumber: 5.6 Consensus size: 102
63006 TCACTTTTCA
* * ***
63016 TAAAATCCTAGAAATAAATATTTTAAATTC-AGAACATAATTTTAAAATATTTTTTATTTAATTT
1 TAAAACCCTAAAAATAAATATTTTAAATTCAAG-ACATACCCTTAAAATATTTTTTATTTAATTT
*
63080 GGGGCTAAACCTAAATGATTTGGAATTAGACTAAAATTC
65 GAGGCTAAACCTAAATGATTTGGAATTA-ACTAAAATTC
*
63119 TAAAACCCTAAAAATAAATATTTTAGATTCAAG-CATACCCTTAAAATATTTTTTATTTAATTTG
1 TAAAACCCTAAAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTTATTTAATTTG
* *
63183 AGGCTAAGCCTAAATGATTTTGAATTAGACTAAAATTC
66 AGGCTAAACCTAAATGATTTGGAATTA-ACTAAAATTC
*
63221 TAAAACCCTAAAAATAAATATTTTAAATTCAAGATATACCCTTAAAATATTTTTTATTTAATTTG
1 TAAAACCCTAAAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTTATTTAATTTG
* * *
63286 -GGAATAAACCTAAATAATTTGGCATTAAACTAAAATTC
66 AGG-CTAAACCTAAATGATTTGGAATT-AACTAAAATTC
* *
63324 TAAAACCCTAAAAATAAATATTTTAAATTCAAGATATACCCTTAAAATATTTTTTATTTGATTTG
1 TAAAACCCTAAAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTTATTTAATTTG
* *
63389 GGGCTAAACCTAAATGATTTGGAATTTAACTAAAATTA
66 AGGCTAAACCTAAATGATTTGGAA-TTAACTAAAATTC
* * * * *
63427 TAAAACTGCCTAGAAATAAATATTTTAAATTCAAGATATATCCTTGAAATATTTTTTATATAATT
1 TAAAAC--CCTAAAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTTATTTAATT
* * * * * * *
63492 TGAAG-TTAACCTAAGTAATTTGGGACTCAATTAAAATTC
64 TGAGGCTAAACCTAAATGATTT-GGAATTAACTAAAATTC
** *
63531 TAAAACAATAAAAATAAATATTTTAAATTCAAGACATA--CTAAAAATATTTTTTAT
1 TAAAACCCTAAAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTTAT
63586 ATATAATTAA
Statistics
Matches: 417, Mismatches: 41, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
100 15 0.04
102 125 0.30
103 183 0.44
104 36 0.09
105 58 0.14
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.38
Consensus pattern (102 bp):
TAAAACCCTAAAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTTATTTAATTTG
AGGCTAAACCTAAATGATTTGGAATTAACTAAAATTC
Found at i:63321 original size:21 final size:21
Alignment explanation
Indices: 63279--63319 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
63269 ATTTTTTATT
*
63279 TAATTTGGGAATAAACCTAAA
1 TAATTTGGCAATAAACCTAAA
*
63300 TAATTTGGCATTAAA-CTAAA
1 TAATTTGGCAATAAACCTAAA
63320 ATTCTAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (21 bp):
TAATTTGGCAATAAACCTAAA
Found at i:65650 original size:57 final size:57
Alignment explanation
Indices: 65581--65708 Score: 202
Period size: 57 Copynumber: 2.2 Consensus size: 57
65571 AATAGATTCG
** *
65581 TCGACATGCTCTTTTTCTTTGTATCCAATCTTCAAAGGCTTATTATCTCCTCCACTA
1 TCGACATGCTCTTTTTCTTTGTATCCAATCAACAAAGGCTTATTATCTCCTCCACCA
*
65638 TCGACATGCTCTTTTTCTTTGTATCCAATCAAGAAAGGCTTATTATCTCCTCCACCA
1 TCGACATGCTCTTTTTCTTTGTATCCAATCAACAAAGGCTTATTATCTCCTCCACCA
* *
65695 TCTACAGGCTCTTT
1 TCGACATGCTCTTT
65709 ATATCCAATC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.22, C:0.28, G:0.10, T:0.40
Consensus pattern (57 bp):
TCGACATGCTCTTTTTCTTTGTATCCAATCAACAAAGGCTTATTATCTCCTCCACCA
Found at i:71774 original size:36 final size:36
Alignment explanation
Indices: 71727--71800 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
71717 ACGCTGATAA
71727 TATACTTTAACCAAATAATACATATAAATATAAACT
1 TATACTTTAACCAAATAATACATATAAATATAAACT
71763 TATACTTTAACCAAATAATACATATAAATATAAACT
1 TATACTTTAACCAAATAATACATATAAATATAAACT
71799 TA
1 TA
71801 CAAAGCAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (36 bp):
TATACTTTAACCAAATAATACATATAAATATAAACT
Found at i:72085 original size:20 final size:21
Alignment explanation
Indices: 72060--72098 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
72050 ATTAGATATA
72060 TGAAACC-CAAGGTTTCAATT
1 TGAAACCTCAAGGTTTCAATT
72080 TGAAACCTCAAGGTTTCAA
1 TGAAACCTCAAGGTTTCAA
72099 GCTTCTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (21 bp):
TGAAACCTCAAGGTTTCAATT
Found at i:82562 original size:2 final size:2
Alignment explanation
Indices: 82555--82588 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
82545 ATTTCACAAC
82555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82589 TGGCCGGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94581 original size:37 final size:36
Alignment explanation
Indices: 94493--94595 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 36
94483 ATCTAAGCCC
* *
94493 AAATAAGACGTTGGAGACAAAGACAAAAAGCAAAATT
1 AAATAAGACGTTGGAAACAAAAAC-AAAAGCAAAATT
*
94530 AAATATA-ACCTTGGAAACAAAAACAAAAGCCAAAATT
1 AAATA-AGACGTTGGAAACAAAAACAAAAG-CAAAATT
*
94567 AAATAGGACGTTGGAAACAAAAAACAAAA
1 AAATAAGACGTTGGAAAC-AAAAACAAAA
94596 TTGACTTTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
36 5 0.09
37 41 0.72
38 11 0.19
ACGTcount: A:0.59, C:0.13, G:0.15, T:0.14
Consensus pattern (36 bp):
AAATAAGACGTTGGAAACAAAAACAAAAGCAAAATT
Found at i:94770 original size:31 final size:32
Alignment explanation
Indices: 94708--94770 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
94698 TGGCAATTTA
*
94708 GAAATATATTTTAAAAAAAAAGGATACAATCG
1 GAAATATATTTTAAAAAAAAAGGATAAAATCG
* **
94740 GAAATATGTTTTTTAAAAAAA-GATAAAATCG
1 GAAATATATTTTAAAAAAAAAGGATAAAATCG
94771 AAAAACATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.54, C:0.05, G:0.13, T:0.29
Consensus pattern (32 bp):
GAAATATATTTTAAAAAAAAAGGATAAAATCG
Found at i:105054 original size:20 final size:20
Alignment explanation
Indices: 105029--105071 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
105019 ATCCATTTTC
*
105029 TTCCTCTGTTTCTCATCCCT
1 TTCCTCTGTTTCGCATCCCT
105049 TTCCTCTGTTTCGCATCCCT
1 TTCCTCTGTTTCGCATCCCT
105069 TTC
1 TTC
105072 TTCTCTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.05, C:0.40, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCCTCTGTTTCGCATCCCT
Found at i:109841 original size:20 final size:20
Alignment explanation
Indices: 109816--109854 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
109806 ATTTTCTTCT
*
109816 TCTGTTTCTCATCCCTTTCC
1 TCTGTTTCGCATCCCTTTCC
109836 TCTGTTTCGCATCCCTTTC
1 TCTGTTTCGCATCCCTTTC
109855 TTCTCTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.38, G:0.08, T:0.49
Consensus pattern (20 bp):
TCTGTTTCGCATCCCTTTCC
Found at i:113114 original size:13 final size:13
Alignment explanation
Indices: 113096--113120 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
113086 CATGTTGTCC
113096 TCTCCCCTATTTT
1 TCTCCCCTATTTT
113109 TCTCCCCTATTT
1 TCTCCCCTATTT
113121 GGTTTGAGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.40, G:0.00, T:0.52
Consensus pattern (13 bp):
TCTCCCCTATTTT
Found at i:115987 original size:32 final size:32
Alignment explanation
Indices: 115946--116012 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
115936 AACATTGAAT
115946 TTGAATCTATTTGGAGGTTTAAGACAGTGATG
1 TTGAATCTATTTGGAGGTTTAAGACAGTGATG
115978 TTGAATCTATTTGGAGGTTTAAGACAGTGATG
1 TTGAATCTATTTGGAGGTTTAAGACAGTGATG
116010 TTG
1 TTG
116013 CAGCTTTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.27, C:0.06, G:0.28, T:0.39
Consensus pattern (32 bp):
TTGAATCTATTTGGAGGTTTAAGACAGTGATG
Found at i:120758 original size:59 final size:59
Alignment explanation
Indices: 120666--120782 Score: 162
Period size: 59 Copynumber: 2.0 Consensus size: 59
120656 CCAACTCCTA
* * **
120666 TCTTTTTGGAACATTGTTTCTAATACAAATTAGACCATGATTGAAATCAATTGTCACCG
1 TCTTTTTGAAACATTGTTTCTAATACAAATTAGACCATAAAAGAAATCAATTGTCACCG
* * **
120725 TCTTTTTGAAACTTTGTTTCTAATATATGTTAGACCATAAAAGAAATCAATTGTCACC
1 TCTTTTTGAAACATTGTTTCTAATACAAATTAGACCATAAAAGAAATCAATTGTCACC
120783 ACTTTTCATT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (59 bp):
TCTTTTTGAAACATTGTTTCTAATACAAATTAGACCATAAAAGAAATCAATTGTCACCG
Found at i:123545 original size:31 final size:31
Alignment explanation
Indices: 123510--123578 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
123500 AAAAAACTGT
* *
123510 AAAAGTTAAATAAGGATATAATAGGCATTTC
1 AAAAGTTAAATAAGGATACAATAAGCATTTC
* **
123541 AAAAGTTAAATAAGGGTACAATAAGTGTTTC
1 AAAAGTTAAATAAGGATACAATAAGCATTTC
123572 AAAAGTT
1 AAAAGTT
123579 TTACAAAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (31 bp):
AAAAGTTAAATAAGGATACAATAAGCATTTC
Found at i:124418 original size:32 final size:32
Alignment explanation
Indices: 124360--124443 Score: 107
Period size: 32 Copynumber: 2.6 Consensus size: 32
124350 TTGAGTATGG
*
124360 TCGGGTTAAATTTGGGGTCAGGTTGATTTAGG-T
1 TCGGGTTAAATTT-GGGTCAGATTGA-TTAGGAT
*
124393 TCGGGTTAAATTTGGGTCAGATTGATTCGGAT
1 TCGGGTTAAATTTGGGTCAGATTGATTAGGAT
* *
124425 TCGGGTCAATTTTGGGTCA
1 TCGGGTTAAATTTGGGTCA
124444 AGTTAATTCG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
31 4 0.09
32 29 0.63
33 13 0.28
ACGTcount: A:0.19, C:0.10, G:0.33, T:0.38
Consensus pattern (32 bp):
TCGGGTTAAATTTGGGTCAGATTGATTAGGAT
Found at i:124453 original size:32 final size:32
Alignment explanation
Indices: 124360--124461 Score: 91
Period size: 32 Copynumber: 3.2 Consensus size: 32
124350 TTGAGTATGG
* * * *
124360 TCGGGTTAAATTTGGGGTCAGGTTGATTTAGG-T
1 TCGGGTCAAATTT-GGGTCAGATT-AATTCGGAT
* *
124393 TCGGGTTAAATTTGGGTCAGATTGATTCGGAT
1 TCGGGTCAAATTTGGGTCAGATTAATTCGGAT
* *
124425 TCGGGTCAATTTTGGGTCA-AGTTAATTCGGGT
1 TCGGGTCAAATTTGGGTCAGA-TTAATTCGGAT
124457 TCGGG
1 TCGGG
124462 CTGGGTTTTG
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
31 5 0.08
32 41 0.69
33 13 0.22
ACGTcount: A:0.19, C:0.10, G:0.34, T:0.37
Consensus pattern (32 bp):
TCGGGTCAAATTTGGGTCAGATTAATTCGGAT
Found at i:124896 original size:32 final size:33
Alignment explanation
Indices: 124784--124894 Score: 134
Period size: 33 Copynumber: 3.4 Consensus size: 33
124774 GACCCGTGCT
124784 TGGGGCGGCTTCACCATTGGGCAGGCCGCCCCAC
1 TGGGGCGGCTTCACCA-TGGGCAGGCCGCCCCAC
* * *** *
124818 TAGGGCGGCTTCACTATGAATAGGCTGCCCCAC
1 TGGGGCGGCTTCACCATGGGCAGGCCGCCCCAC
* *
124851 TGGGGCGGCTTCGCCA-GGGCAGGCCGCCCCAG
1 TGGGGCGGCTTCACCATGGGCAGGCCGCCCCAC
124883 TGGGGCGGCTTC
1 TGGGGCGGCTTC
124895 GCTACGGCAG
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
32 23 0.37
33 26 0.41
34 14 0.22
ACGTcount: A:0.13, C:0.34, G:0.37, T:0.16
Consensus pattern (33 bp):
TGGGGCGGCTTCACCATGGGCAGGCCGCCCCAC
Found at i:124904 original size:32 final size:32
Alignment explanation
Indices: 124803--124909 Score: 124
Period size: 32 Copynumber: 3.3 Consensus size: 32
124793 TTCACCATTG
* * *
124803 GGCAGGCCGCCCCACTAGGGCGGCTTCACTAT
1 GGCAGGCCGCCCCACTGGGGCGGCTTCGCTAC
** * * *
124835 GAATAGGCTGCCCCACTGGGGCGGCTTCGCCAG
1 G-GCAGGCCGCCCCACTGGGGCGGCTTCGCTAC
*
124868 GGCAGGCCGCCCCAGTGGGGCGGCTTCGCTAC
1 GGCAGGCCGCCCCACTGGGGCGGCTTCGCTAC
124900 GGCAGGCCGC
1 GGCAGGCCGC
124910 GTCGGTGGGG
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
32 36 0.59
33 25 0.41
ACGTcount: A:0.13, C:0.36, G:0.37, T:0.13
Consensus pattern (32 bp):
GGCAGGCCGCCCCACTGGGGCGGCTTCGCTAC
Found at i:124918 original size:32 final size:32
Alignment explanation
Indices: 124784--124924 Score: 111
Period size: 32 Copynumber: 4.3 Consensus size: 32
124774 GACCCGTGCT
* * *
124784 TGGGGCGGCTTCACCATTGGGCAGGCCGCCCCAC
1 TGGGGCGGCTTCGCCA--CGGCAGGCCGCCCCAG
* * * * ** * *
124818 TAGGGCGGCTTCACTATGAATAGGCTGCCCCAC
1 TGGGGCGGCTTCGCCACG-GCAGGCCGCCCCAG
*
124851 TGGGGCGGCTTCGCCAGGGCAGGCCGCCCCAG
1 TGGGGCGGCTTCGCCACGGCAGGCCGCCCCAG
* ** *
124883 TGGGGCGGCTTCGCTACGGCAGGCCGCGTCGG
1 TGGGGCGGCTTCGCCACGGCAGGCCGCCCCAG
124915 TGGGGCGGCT
1 TGGGGCGGCT
124925 CGGCTATTTT
Statistics
Matches: 87, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
32 48 0.55
33 25 0.29
34 14 0.16
ACGTcount: A:0.11, C:0.33, G:0.40, T:0.16
Consensus pattern (32 bp):
TGGGGCGGCTTCGCCACGGCAGGCCGCCCCAG
Found at i:124959 original size:22 final size:22
Alignment explanation
Indices: 124929--124973 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
124919 GCGGCTCGGC
*
124929 TATTTTTTTTA-AAAAAAATAAT
1 TATTATTTTTAGAAAAAAA-AAT
124951 TATTATTTTTAGAAAAAAAAAT
1 TATTATTTTTAGAAAAAAAAAT
124973 T
1 T
124974 TGGTCTAGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTATTTTTAGAAAAAAAAAT
Done.