Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021876.1 Corchorus olitorius cultivar O-4 contig21909, 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: 61193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:117 original size:36 final size:35
Alignment explanation
Indices: 64--132 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
54 TCAATTAACC
* *
64 TTACATTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATTTTTGTAATTTTGATTATCATATTTCTTA
99 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACA-TTTTTGTAATTTTGATTATCATATTTCT
133 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 5 0.16
36 26 0.84
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.61
Consensus pattern (35 bp):
TTACATTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:1304 original size:12 final size:13
Alignment explanation
Indices: 1280--1308 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1270 CTTATATAAT
1280 ATATAGAATATAG
1 ATATAGAATATAG
1293 ATATAG-ATATAG
1 ATATAGAATATAG
1305 ATAT
1 ATAT
1309 GAAGGACCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (13 bp):
ATATAGAATATAG
Found at i:1414 original size:45 final size:45
Alignment explanation
Indices: 1350--1519 Score: 255
Period size: 45 Copynumber: 3.9 Consensus size: 45
1340 TTGGGTTTAG
1350 ATTGGTGTCCGACATGTATATGGACTGGTCGATGGGATCCAATAA
1 ATTGGTGTCCGACATGTATATGGACTGGTCGATGGGATCCAATAA
1395 ATTGGTGTCCGACATGTATATGGACTGGTCGATGGGATCCAATAA
1 ATTGGTGTCCGACATGTATATGGACTGGTCGATGGGATCCAATAA
*
1440 ATTGGTGTCCGACATGTATATGGACTGGTCGATGAGATCC----A
1 ATTGGTGTCCGACATGTATATGGACTGGTCGATGGGATCCAATAA
* * *
1481 A---GTGTCCGACATGCATATGGACTGATAGATGGGATCCAA
1 ATTGGTGTCCGACATGTATATGGACTGGTCGATGGGATCCAA
1520 ACATGCCCGA
Statistics
Matches: 118, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
38 32 0.27
41 2 0.02
45 84 0.71
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (45 bp):
ATTGGTGTCCGACATGTATATGGACTGGTCGATGGGATCCAATAA
Found at i:1499 original size:38 final size:38
Alignment explanation
Indices: 1444--1519 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
1434 CAATAAATTG
* * *
1444 GTGTCCGACATGTATATGGACTGGTCGATGAGATCCAA
1 GTGTCCGACATGCATATGGACTGATAGATGAGATCCAA
*
1482 GTGTCCGACATGCATATGGACTGATAGATGGGATCCAA
1 GTGTCCGACATGCATATGGACTGATAGATGAGATCCAA
1520 ACATGCCCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (38 bp):
GTGTCCGACATGCATATGGACTGATAGATGAGATCCAA
Found at i:1955 original size:6 final size:6
Alignment explanation
Indices: 1946--1974 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1936 TGCATTTGCA
1946 CATATT CATATT CATATT CATATT CATAT
1 CATATT CATATT CATATT CATATT CATAT
1975 ATATATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (6 bp):
CATATT
Found at i:12871 original size:2 final size:2
Alignment explanation
Indices: 12864--12897 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12854 CCTAGTGGAA
12864 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12898 TTTGACTGCA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28967 original size:13 final size:13
Alignment explanation
Indices: 28949--28973 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28939 TTCAATGTTC
28949 TAAATATTATTTA
1 TAAATATTATTTA
28962 TAAATATTATTT
1 TAAATATTATTT
28974 GGAATTCTAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:29567 original size:30 final size:30
Alignment explanation
Indices: 29531--29587 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
29521 CTTATTTAGG
* * *
29531 AAACGTTTTTCCCTAAATTGATCATTTCAA
1 AAACGTTCTGCCCTAAATTGAGCATTTCAA
29561 AAACGTTCTGCCCTAAATTGAGCATTT
1 AAACGTTCTGCCCTAAATTGAGCATTT
29588 ATTTTCTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (30 bp):
AAACGTTCTGCCCTAAATTGAGCATTTCAA
Found at i:42540 original size:106 final size:104
Alignment explanation
Indices: 42262--42556 Score: 384
Period size: 106 Copynumber: 2.8 Consensus size: 104
42252 AATTTTTCTA
*
42262 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAAC-TTAGTG-AATTAGTTATATATTTT
1 ACCCTTAAAAT-AAATTTT-ATTTTAATTTGGGGCTAAACTTTAGTGAAATTAGTTTTATATTTT
* *
42324 ATTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
64 ATTTCTAAAACCCTATAATAATATTATTAATTATGAAATTT
*** *
42365 ACCCTTAAAATAAAAATAAAAAATTTTAATTTGGGGCTAAA-TTTAGTGAAATTAGTTTTGTATT
1 ACCCTTAAAAT--AAAT--TTTATTTTAATTTGGGGCTAAACTTTAGTGAAATTAGTTTTATATT
*
42429 TTATTTCTAAAACCCTATAATAATAAATTATTAATTTTGAAATTT
62 TTATTTCTAAAACCCTATAATAAT--ATTATTAATTATGAAATTT
*
42474 ACCCTTAAAAT-AATTTTTTTTTAATTTGGGGCTAAACTTTTAGTGAAATTAGTTTTATATTTTA
1 ACCCTTAAAATAAATTTTATTTTAATTTGGGGCTAAAC-TTTAGTGAAATTAGTTTTATATTTTA
*
42538 TTTCTAAAACTCTATAATA
65 TTTCTAAAACCCTATAATA
42557 GAAAACCTTT
Statistics
Matches: 168, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
103 11 0.07
104 23 0.14
105 10 0.06
106 60 0.36
107 36 0.21
109 28 0.17
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (104 bp):
ACCCTTAAAATAAATTTTATTTTAATTTGGGGCTAAACTTTAGTGAAATTAGTTTTATATTTTAT
TTCTAAAACCCTATAATAATATTATTAATTATGAAATTT
Found at i:42579 original size:106 final size:104
Alignment explanation
Indices: 42262--42598 Score: 350
Period size: 106 Copynumber: 3.2 Consensus size: 104
42252 AATTTTTCTA
*
42262 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAAC-TTAGTG-AATTAGTTATATATTTT
1 ACCCTTAAAAT-AAATTTT-ATTTTAATTTGGGGCTAAACTTTAGTGAAATTAGTTTTATATTTT
* *
42324 ATTTCTAAAACCCTATAA-CAATATTATTAA-TTATGGAATTT
64 ATTTCTAAAACCCTATAATAAAAATTATTAATTTAT--AATTT
*** *
42365 ACCCTTAAAATAAAAATAAAAAATTTTAATTTGGGGCTAAA-TTTAGTGAAATTAGTTTTGTATT
1 ACCCTTAAAAT--AAAT--TTTATTTTAATTTGGGGCTAAACTTTAGTGAAATTAGTTTTATATT
42429 TTATTTCTAAAACCCTATAATAATAAATTATTAATTT-TGAAATTT
62 TTATTTCTAAAACCCTATAATAA-AAATTATTAATTTAT--AATTT
*
42474 ACCCTTAAAAT-AATTTTTTTTTAATTTGGGGCTAAACTTTTAGTGAAATTAGTTTTATATTTTA
1 ACCCTTAAAATAAATTTTATTTTAATTTGGGGCTAAAC-TTTAGTGAAATTAGTTTTATATTTTA
* *
42538 TTTCTAAAACTCTATAATAGAAAACCT-TTAATTTCATAATTT
65 TTTCTAAAACCCTATAATA-AAAA-TTATTAATTT-ATAATTT
* *
42580 TCTCTTAAAAATTAAATTT
1 ACCCTT-AAAA-TAAATTT
42599 CTTTTATTGT
Statistics
Matches: 199, Mismatches: 17, Indels: 30
0.81 0.07 0.12
Matches are distributed among these distances:
103 11 0.06
104 23 0.12
105 10 0.05
106 79 0.40
107 39 0.20
108 3 0.02
109 32 0.16
110 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (104 bp):
ACCCTTAAAATAAATTTTATTTTAATTTGGGGCTAAACTTTAGTGAAATTAGTTTTATATTTTAT
TTCTAAAACCCTATAATAAAAATTATTAATTTATAATTT
Found at i:43782 original size:430 final size:437
Alignment explanation
Indices: 42831--43904 Score: 1290
Period size: 431 Copynumber: 2.5 Consensus size: 437
42821 TTGTTGATCA
* * * * * ** * **
42831 ACATCTGGATAAAAAAATATATGAAATTAAATAGATTATCAATCGAAATCACAAAATTTCAAAAG
1 ACATGTGGACAAAAAATTATACGATATTAAATAGACCAACAATCGAAATCACAAAATTTCGGAAG
* * * * *
42896 TATTTTTTAGAATTTAAACATGAAAATTAGCTTTTGAGTCTTTCATGAAAGAGTTGTAGATAATA
66 CATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATG-AA-AGTTGTAGATCATA
* * * * *
42961 AAATAACTTTTTAATAGACACTTGAATTACCTTAATTGCACAAATAGAACAAAGAAAATAAAAAA
129 AAATAACCTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGAACAAAGAATA-AAAAAA
* *
43026 TGAAGTGTTAAATCGAGTAAGATAGAATTTGTAAAGAACTAAGTAGCATAAAATGTATAACATAG
193 T-AAATCTTAAAT--AGTAAGATAGAATTTGTAAAGAACTAAGTAG-AT--AA-GTATAACATAG
* * * * * *
43091 AAAAGTATGAGGGTCATTTGATAACTAATTCAAATAAGAAATTATTTCTTAATGGATATCTTGAA
251 AAAAATATGAGGGTCATTTAATAAATAATCCAAATAAGAAAATATTTCTTAATGGAGATCTTGAA
* * *
43156 ACATAAAAATTTCCTTTTGAACCCTTCATGAAACTCGTAGCTCAAATTAACTTTCGGATTCTTCA
316 ACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGATCCTTCA
* * * * *
43221 TGAAAGTCGTAGATCATACAGTAACCTTTTAACCAACACTTGAATAACTTTAATCGG
381 AGAAAGTCGTAAATCATACAATAACCTTTTAACCAACACTTCAATAACTTCAATCGG
* * * * * *
43278 ACATGTGGATAGAAAATTATATGGTATTAAATAGACCAACAATCGAAA-CGACCAAATTTAGGAA
1 ACATGTGGACAAAAAATTATACGATATTAAATAGACCAACAATCGAAATC-ACAAAATTTCGGAA
* *
43342 GCATTTTTTTA-AATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATG
65 GCA-TTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATA
* * *
43406 AAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAAAT
129 AAATAACCTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGAACAAAGAATAAAAAAAT
43471 AAATCTTAAAT-G-AAGATAGAATTTGTAAAGAACTAAGTAG-T-A-TA-AA-ATAGAAAAATAT
194 AAATCTTAAATAGTAAGATAGAATTTGTAAAGAACTAAGTAGATAAGTATAACATAGAAAAATAT
* * * *
43529 GAGGGTTATTTAATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCAT-AAA
259 GAGGGTCATTTAATAAATAATCCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAA
* * *
43593 ATCTCCCTTTTGAGCCCTTCATGAAACTTGTAGATCAAATTTAGCTTTCGGATCCTTCAAGAAAG
324 AT-TCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAA-TTAACTTTCGGATCCTTCAAGAAAG
* * **
43658 TCGTAAATGATGCAATAACCTTTTAACTGACACTTCAATAACTTCAATCGG
387 TCGTAAATCATACAATAACCTTTTAACCAACACTTCAATAACTTCAATCGG
* * ** *
43709 ATATGTGGACAAAAAATTATACGATATTAAATTGACCGGCAATCAAAATCACAAAATTTCGGAAG
1 ACATGTGGACAAAAAATTATACGATATTAAATAGACCAACAATCGAAATCACAAAATTTCGGAAG
* * * * * *
43774 CATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATCATTAA
66 CATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATAAA
* *
43839 ATCACCTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGGAA-AAA-AATACAAAAATA
131 ATAACCTTTTAATAGACACTTGAATCACCTTAATCGGACAAATA-GAACAAAGAATAAAAAAATA
43902 AAT
195 AAT
43905 GCGAACGCGT
Statistics
Matches: 545, Mismatches: 75, Indels: 31
0.84 0.12 0.05
Matches are distributed among these distances:
429 5 0.01
430 116 0.21
431 214 0.39
432 6 0.01
434 1 0.00
437 1 0.00
439 28 0.05
440 1 0.00
443 9 0.02
444 7 0.01
445 62 0.11
446 3 0.01
447 85 0.16
448 7 0.01
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (437 bp):
ACATGTGGACAAAAAATTATACGATATTAAATAGACCAACAATCGAAATCACAAAATTTCGGAAG
CATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATAAA
ATAACCTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGAACAAAGAATAAAAAAATAA
ATCTTAAATAGTAAGATAGAATTTGTAAAGAACTAAGTAGATAAGTATAACATAGAAAAATATGA
GGGTCATTTAATAAATAATCCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAAAT
TCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGATCCTTCAAGAAAGTCGT
AAATCATACAATAACCTTTTAACCAACACTTCAATAACTTCAATCGG
Found at i:44952 original size:33 final size:33
Alignment explanation
Indices: 44906--45027 Score: 129
Period size: 33 Copynumber: 3.7 Consensus size: 33
44896 CATGGAACGG
** *
44906 CGCCTCACTGTATGGCGAGGCACCTCTCGGGGA
1 CGCCTCACCATATGGCGAGGCACCTCCCGGGGA
* *
44939 CGCCTCACCGTATGGCGAGGCGCCTCCCGGGGA
1 CGCCTCACCATATGGCGAGGCACCTCCCGGGGA
* * * *
44972 CGCCTCCCCATATGGTGAGGCGCC-CCCTAGGGA
1 CGCCTCACCATATGGCGAGGCACCTCCC-GGGGA
**
45005 CGCCTTGCCATATGGCGAGGCAC
1 CGCCTCACCATATGGCGAGGCAC
45028 GATCCCGTCG
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
32 3 0.04
33 74 0.96
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.16
Consensus pattern (33 bp):
CGCCTCACCATATGGCGAGGCACCTCCCGGGGA
Found at i:45933 original size:2 final size:2
Alignment explanation
Indices: 45926--45961 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
45916 TGGCTAGCAT
45926 TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45962 AAAGTAATCC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:47419 original size:42 final size:42
Alignment explanation
Indices: 47359--47471 Score: 174
Period size: 42 Copynumber: 2.7 Consensus size: 42
47349 GTGGGGAAGG
47359 CATTCCCCATCCCCGTCCCCGACCCCGACGAGG-AATGAAATT
1 CATTCCCCATCCCCGTCCCCGACCCCGACG-GGCAATGAAATT
* *
47401 CATTCCCCATCCCTGTCCCCGACCTCGACGGGCAATGAAATT
1 CATTCCCCATCCCCGTCCCCGACCCCGACGGGCAATGAAATT
*
47443 CATTCCCCACCCCCGTCCCCGTACCCCGA
1 CATTCCCCATCCCCGTCCCCG-ACCCCGA
47472 ATACTTCCCC
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 2 0.03
42 56 0.88
43 6 0.09
ACGTcount: A:0.20, C:0.47, G:0.15, T:0.18
Consensus pattern (42 bp):
CATTCCCCATCCCCGTCCCCGACCCCGACGGGCAATGAAATT
Found at i:53809 original size:42 final size:43
Alignment explanation
Indices: 53758--53851 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 43
53748 AGTGCATTAC
*
53758 CTAA-ATTCTAGTCCT-TCTCTAGG-TAATTCATCAAAATAAAA
1 CTAATATTCTACTCCTCTCTCT-GGATAATTCATCAAAATAAAA
*
53799 CTAATATTCTACTCCTCCATCTCTGGATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCT-C-TCTCTGGATAATTCATCAAAATAAAA
53844 CTAATATT
1 CTAATATT
53852 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
41 4 0.09
42 10 0.22
44 2 0.04
45 30 0.65
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACTCCTCTCTCTGGATAATTCATCAAAATAAAA
Found at i:55081 original size:15 final size:16
Alignment explanation
Indices: 55042--55083 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
55032 GGAAATTTTC
55042 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
*
55058 TCGGCTCA-TCTGGG-T
1 TCGGGTCATTC-GGGTT
55073 TCGGGTCATTC
1 TCGGGTCATTC
55084 AGGTCTTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.07, C:0.24, G:0.33, T:0.36
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:55130 original size:28 final size:28
Alignment explanation
Indices: 55099--55154 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
55089 TTAGGTCTGC
* *
55099 TTGGTCTCGGGTCAGGCGGGTTCGTGTT
1 TTGGCCTCGGGTCACGCGGGTTCGTGTT
* *
55127 TTGGCCTCGGGTCACTCGGGTTCTTGTT
1 TTGGCCTCGGGTCACGCGGGTTCGTGTT
55155 CATTTGGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.04, C:0.21, G:0.38, T:0.38
Consensus pattern (28 bp):
TTGGCCTCGGGTCACGCGGGTTCGTGTT
Found at i:55453 original size:17 final size:17
Alignment explanation
Indices: 55431--55463 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
55421 TCATTACATC
55431 AATTAA-AATAATAAATT
1 AATTAATAAT-ATAAATT
55448 AATTAATAATATAAAT
1 AATTAATAATATAAAT
55464 ATCCATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTAATAATATAAATT
Found at i:55969 original size:42 final size:43
Alignment explanation
Indices: 55918--56011 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
55908 AGTGCATTAC
* * *
55918 CTAA-ATTCTA-CTCCGTCTCTAGGTAATTTATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
55959 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
56004 CTAATATT
1 CTAATATT
56012 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:57512 original size:2 final size:2
Alignment explanation
Indices: 57507--57535 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57497 CCATTCACAC
57507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57536 ATGAATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58551 original size:16 final size:15
Alignment explanation
Indices: 58532--58584 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
58522 ATACCCGAAT
58532 CCGAAAAAGTTCAAAC
1 CCGAAAAA-TTCAAAC
*
58548 CCGAAAAAATCAGAAC
1 CCGAAAAATTCA-AAC
*
58564 CCGAAAAATTTGAAAC
1 CCGAAAAA-TTCAAAC
58580 CCGAA
1 CCGAA
58585 TTCGAATCTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 3 0.09
16 27 0.84
17 2 0.06
ACGTcount: A:0.51, C:0.25, G:0.13, T:0.11
Consensus pattern (15 bp):
CCGAAAAATTCAAAC
Found at i:58822 original size:32 final size:32
Alignment explanation
Indices: 58772--58883 Score: 143
Period size: 32 Copynumber: 3.5 Consensus size: 32
58762 AATGATTTGG
* *
58772 CCAAAATCCAACCCGAACCCGAATTAACCTGTC
1 CCAAAAT-TAACCCGAACCCGAATTAACCTGAC
* * * *
58805 CCAAAATTGATCCGAACCCGAATCAATCTGAC
1 CCAAAATTAACCCGAACCCGAATTAACCTGAC
*
58837 CCAAATTTAACCCGAACCCGAATTAACCTGAC
1 CCAAAATTAACCCGAACCCGAATTAACCTGAC
*
58869 CCAAATTTAACCCGA
1 CCAAAATTAACCCGA
58884 CCTGACTCAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
32 61 0.90
33 7 0.10
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.18
Consensus pattern (32 bp):
CCAAAATTAACCCGAACCCGAATTAACCTGAC
Found at i:58864 original size:16 final size:16
Alignment explanation
Indices: 58781--58883 Score: 59
Period size: 16 Copynumber: 6.4 Consensus size: 16
58771 GCCAAAATCC
*
58781 AACCCGAACCCGAATT
1 AACCCGAACCCAAATT
* *
58797 AACCTG-TCCCAAAATT
1 AACCCGAACCC-AAATT
* * * *
58813 GATCCGAACCCGAATC
1 AACCCGAACCCAAATT
* *
58829 AATCTG-ACCCAAATTT
1 AACCCGAACCCAAA-TT
*
58845 AACCCGAACCCGAATT
1 AACCCGAACCCAAATT
*
58861 AACCTG-ACCCAAATTT
1 AACCCGAACCCAAA-TT
58877 AACCCGA
1 AACCCGA
58884 CCTGACTCAA
Statistics
Matches: 62, Mismatches: 19, Indels: 11
0.67 0.21 0.12
Matches are distributed among these distances:
15 15 0.24
16 38 0.61
17 9 0.15
ACGTcount: A:0.37, C:0.34, G:0.11, T:0.18
Consensus pattern (16 bp):
AACCCGAACCCAAATT
Found at i:58885 original size:16 final size:16
Alignment explanation
Indices: 58834--58885 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
58824 GAATCAATCT
58834 GACCCAAATTTAACCC
1 GACCCAAATTTAACCC
* *
58850 GAACCCGAA-TTAACCT
1 G-ACCCAAATTTAACCC
58866 GACCCAAATTTAACCC
1 GACCCAAATTTAACCC
58882 GACC
1 GACC
58886 TGACTCAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 6 0.20
16 18 0.60
17 6 0.20
ACGTcount: A:0.37, C:0.37, G:0.10, T:0.17
Consensus pattern (16 bp):
GACCCAAATTTAACCC
Found at i:60891 original size:6 final size:7
Alignment explanation
Indices: 60875--60900 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
60865 GCCCCTGAAC
60875 TTTTTAT
1 TTTTTAT
60882 TTTTTAT
1 TTTTTAT
60889 TTTTTAT
1 TTTTTAT
60896 TTTTT
1 TTTTT
60901 TTATAAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Done.