Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016547.1 Corchorus olitorius cultivar O-4 contig16580, 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: 80273
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:525 original size:21 final size:22
Alignment explanation
Indices: 501--541 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
491 GTTTATAATA
*
501 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
522 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
542 CGAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:1885 original size:18 final size:15
Alignment explanation
Indices: 1848--1876 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1838 CATTTCAGTC
1848 AACAAGGACAGCGGA
1 AACAAGGACAGCGGA
1863 AACAAGGACAGCGG
1 AACAAGGACAGCGG
1877 CCGAAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.21, G:0.34, T:0.00
Consensus pattern (15 bp):
AACAAGGACAGCGGA
Found at i:12791 original size:84 final size:84
Alignment explanation
Indices: 12633--12792 Score: 198
Period size: 84 Copynumber: 1.9 Consensus size: 84
12623 ACCTTTGCCT
* * * **
12633 TCATCTCCATTAGCCAACCTCCTCAGCTTCTGCAACGACTCCGCCAGTGTCGCTTCACCTGCATT
1 TCATCTCCATTAGCCAACCTCCTAAGCTTCTGCAACGACTCCGCCAGTGTCCCTTCACCAGCAGC
*
12698 TCCTGCAATACCTTTATTC
66 ACCTGCAATACCTTTATTC
* * *
12717 TCATCTCCATTAGCCACCCTCCTAAGCTTCTGCAACGACTCTGCTAG-GCTCCCATT-ACCAGCA
1 TCATCTCCATTAGCCAACCTCCTAAGCTTCTGCAACGACTCCGCCAGTG-TCCC-TTCACCAGCA
*
12780 GCACCTTCAATAC
64 GCACCTGCAATAC
12793 TCCTCTCCTC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
83 1 0.02
84 61 0.95
85 2 0.03
ACGTcount: A:0.21, C:0.39, G:0.12, T:0.28
Consensus pattern (84 bp):
TCATCTCCATTAGCCAACCTCCTAAGCTTCTGCAACGACTCCGCCAGTGTCCCTTCACCAGCAGC
ACCTGCAATACCTTTATTC
Found at i:15153 original size:22 final size:21
Alignment explanation
Indices: 15119--15161 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
15109 GATGTGTGTG
* *
15119 TGTGATTGTTTGGTTTCGTAGA
1 TGTGATAGATTGGTTT-GTAGA
15141 TGTGATAGATTGGTTTGTAGA
1 TGTGATAGATTGGTTTGTAGA
15162 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.47
Consensus pattern (21 bp):
TGTGATAGATTGGTTTGTAGA
Found at i:28340 original size:19 final size:19
Alignment explanation
Indices: 28316--28352 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28306 ATACAGTATC
28316 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
28335 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
28353 TGCTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:37902 original size:738 final size:738
Alignment explanation
Indices: 36387--38042 Score: 2505
Period size: 738 Copynumber: 2.2 Consensus size: 738
36377 TAAGGAAAGG
* * * ** *
36387 AAATGAGT-AATTACAAAAAAAGGTAGCAGGAAAAGGAAGGGGGGAAACTCATAAATGGACTTTT
1 AAAT-AGTAAATTACAAAAAAAGGTAGCAGGAAAAGTAAGGGAGGAAATTCATCGAGGGACTTTT
* *
36451 TAGTCATCCGAAAAGTGAGAAAAGACAAAAAAAAAAACCCAAAAGGTGGCACCACATTAATCCTC
65 TAGTCACCCGAAAAGTGAGAAAAGAC--AAAAAAAAA-CCAAAAGGAGGCACCACATTAATCCTC
** * * *
36516 AATTTGGTCTTTTAGTAATTTCCCTAGTAACTAAAAATAATATATACAAGCAGGGCGGCCTGCGC
127 AATTTGACCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATACAAGCAGGGCGGCCTGCGC
* *
36581 TTGCGCTGCAATCATGTTCTTATTAGGGATATATATTTTTTGTAGTTGTTTAAGTTGGTTAGTAA
192 TTGCGCTGCAATCATCTTCTTATTAGGGATATATATTTTTTGTAGTTGTTTAAGTCGGTTAGTAA
* *
36646 GAAGATATTGCATTGGCTGTAAGTTAATTAGTTAGAAGAAACTCATACATCGAAACAAATAATTC
257 GAAAATATTGCATTGGCTGTAAGTTAATCAGTTAGAAGAAACTCATACATCGAAACAAATAATTC
*
36711 GCATATATAAAGCAAAACACATGACCTCTCTTTCATTCAAAAAGTACATTACCTAAATTCTACTC
322 GCATATATAAAGCAAAACACATAACCTCTCTTTCATTCAAAAAGTACATTACCTAAATTCTACTC
*
36776 CATCTCTAGGTAATTCATTAAAATAAAATTAATATTCTACTCCTCCATCTCTAGATATAAATTAA
387 CATCTCTAGGTAATTCATCAAAATAAAATTAATATTCTACTCCTCCATCTCTAGATATAAATTAA
* *
36841 ATAAAAGGATCTTATCAACGTCCACCTGGAAATTTTAGGAAACATAACGGAGTTCATGTGAAACC
452 ATAAAAGGATCTTATCAACGTCCACCTGGAAATTTTAGGAAACAGAACGGAGTTCATGCGAAACC
* * *
36906 AATTCAGAGAAATGTTAGGGAAGAAGAAACTCACCCAAATAGAAATGAAGTCGAAAGGAAGACAG
517 AATTCAGAGAAATGTTAGGGAAGAAGAAACCCACCCAAATAGAAATGAAGACGAAAGGAAAACAG
* * *
36971 AACTGCAATATCAATAGTTTACTCATGAATCAACCATTATTGCAGATACATTTATAGCACCAATC
582 AACTGCAATACCAATAGTTTACCCATGAATCAACCATTATTGCAGATACATTTATAGCACCAACC
* * *
37036 CTTTGGAATTCCGGTAGATGAGTTGAACCAATAAATCCTAATATCCACACACAATTAATATGTAA
647 CTTTGGAATTCCGGCAGAGGAGTTGAACCAACAAATCCTAATATCCACACACAATTAATATGTAA
*
37101 TTAAAACACACTTAATCATAAATATAA
712 CTAAAACACACTTAATCATAAATATAA
* * *
37128 AAATAATAAATTACAAAAAAAGGTAGCAGAAAAAGTAAGGGAGGAAATTCATCGAGGGCCTTTTT
1 AAATAGTAAATTACAAAAAAAGGTAGCAGGAAAAGTAAGGGAGGAAATTCATCGAGGGACTTTTT
* *
37193 AGTCACCCGAAAAGTGAGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCACATTAATCCTCAATT
66 AGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAACCAAAAGGAGGCACCACATTAATCCTCAATT
*
37258 TGACCTTTAAGTAATTTCCATTGTCACTAAAAATAATATATACAAGCAGGGCGGCCTGCGCTTGC
131 TGACCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATACAAGCAGGGCGGCCTGCGCTTGC
* *
37323 GCTGCAGTCATCTTCTTATTAGGGTTATAT-TTTTTTGTAGTTGTTTAAGTCGGTTAGTAAGAAA
196 GCTGCAATCATCTTCTTATTAGGGATATATATTTTTTGTAGTTGTTTAAGTCGGTTAGTAAGAAA
* *
37387 ATATTGCATTGGCTGTAAGTTAATCCGTTAGGAGAAACTCATGA-ATCGAAACAAATAATTCGCA
261 ATATTGCATTGGCTGTAAGTTAATCAGTTAGAAGAAACTCAT-ACATCGAAACAAATAATTCGCA
* * * *
37451 TATATAAAGCAAAACACATAACTTCTC-TTCATTCTAAAAGTACATTACCTAAATTTTACTTCAT
325 TATATAAAGCAAAACACATAACCTCTCTTTCATTCAAAAAGTACATTACCTAAATTCTACTCCAT
37515 CTCTAGGTATAATTCATCAAAAT-AAATCTAATATTCTACTCCTCCATCTCTAGATATAAATTAA
390 CTCTAGG--TAATTCATCAAAATAAAAT-TAATATTCTACTCCTCCATCTCTAGATATAAATTAA
** * * * *
37579 ATGGAATGATTTTATCAACGTCGACCTGGAAATTTTAGTAAACAGAACGGAGTTCATGCGAAACC
452 ATAAAAGGATCTTATCAACGTCCACCTGGAAATTTTAGGAAACAGAACGGAGTTCATGCGAAACC
*
37644 TATTCAGAGAAATGTTAGGGAAGAAGAAACCCACCCAAATAGAAATGAAGACGAAAGGAAAACAG
517 AATTCAGAGAAATGTTAGGGAAGAAGAAACCCACCCAAATAGAAATGAAGACGAAAGGAAAACAG
* * * * *
37709 AATTGGACTGCCAATAGTTTACCCATGAATCAACCATTATTGCAGATGCATTTATAGCACCAACC
582 AACTGCAATACCAATAGTTTACCCATGAATCAACCATTATTGCAGATACATTTATAGCACCAACC
**
37774 CTTTGGAATTCCGGCAGAGGAGTTGAACCGGCAAATCCTAATATCCACACACAATTAATATGTAA
647 CTTTGGAATTCCGGCAGAGGAGTTGAACCAACAAATCCTAATATCCACACACAATTAATATGTAA
37839 CTAAAACA-AGCTTAATCATAAATATAA
712 CTAAAACACA-CTTAATCATAAATATAA
* * *
37866 AAATAGTAAATTACAAAAAAGGGTAGCGGGAAAAGTAAGGGAGGAAATTCATCGAGGGTCTTTTT
1 AAATAGTAAATTACAAAAAAAGGTAGCAGGAAAAGTAAGGGAGGAAATTCATCGAGGGACTTTTT
* * * * * * *
37931 AGTCACCCGAAAATTGCGAAAAAAAAAACAAAAACAAAAACAAAAGGAGACATCACATTAATACT
66 AGTCACCCGAAAA--GTG--AGAAAAGACAAAAA-AAAACCAAAAGGAGGCACCACATTAATCCT
* *
37996 CAATTTGACATTTAAGTAATTTCCATAATCACTAAAAATAATATATA
126 CAATTTGACCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATA
38043 GTATATATAA
Statistics
Matches: 828, Mismatches: 76, Indels: 20
0.90 0.08 0.02
Matches are distributed among these distances:
736 41 0.05
737 121 0.15
738 498 0.60
739 7 0.01
740 4 0.00
741 77 0.09
742 11 0.01
743 69 0.08
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (738 bp):
AAATAGTAAATTACAAAAAAAGGTAGCAGGAAAAGTAAGGGAGGAAATTCATCGAGGGACTTTTT
AGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAACCAAAAGGAGGCACCACATTAATCCTCAATT
TGACCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATACAAGCAGGGCGGCCTGCGCTTGC
GCTGCAATCATCTTCTTATTAGGGATATATATTTTTTGTAGTTGTTTAAGTCGGTTAGTAAGAAA
ATATTGCATTGGCTGTAAGTTAATCAGTTAGAAGAAACTCATACATCGAAACAAATAATTCGCAT
ATATAAAGCAAAACACATAACCTCTCTTTCATTCAAAAAGTACATTACCTAAATTCTACTCCATC
TCTAGGTAATTCATCAAAATAAAATTAATATTCTACTCCTCCATCTCTAGATATAAATTAAATAA
AAGGATCTTATCAACGTCCACCTGGAAATTTTAGGAAACAGAACGGAGTTCATGCGAAACCAATT
CAGAGAAATGTTAGGGAAGAAGAAACCCACCCAAATAGAAATGAAGACGAAAGGAAAACAGAACT
GCAATACCAATAGTTTACCCATGAATCAACCATTATTGCAGATACATTTATAGCACCAACCCTTT
GGAATTCCGGCAGAGGAGTTGAACCAACAAATCCTAATATCCACACACAATTAATATGTAACTAA
AACACACTTAATCATAAATATAA
Found at i:38049 original size:2 final size:2
Alignment explanation
Indices: 38036--38081 Score: 51
Period size: 2 Copynumber: 23.0 Consensus size: 2
38026 ACTAAAAATA
*
38036 AT AT AT AGT AT AT AT A- AT AT AT AT AT AT AT AT GT AT -T AGT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
38078 AT AT
1 AT AT
38082 GATTTTTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 2 0.05
2 32 0.84
3 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38054 original size:16 final size:16
Alignment explanation
Indices: 38033--38081 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
38023 ATCACTAAAA
38033 ATAATATATAGTATAT
1 ATAATATATAGTATAT
38049 ATAATATATA-TATAT
1 ATAATATATAGTATAT
*
38064 AT-ATGTATTAGTATAT
1 ATAATATA-TAGTATAT
38080 AT
1 AT
38082 GATTTTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 17 0.57
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
ATAATATATAGTATAT
Found at i:38064 original size:22 final size:22
Alignment explanation
Indices: 38036--38081 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
38026 ACTAAAAATA
38036 ATATATAGTATATA-TAATATAT
1 ATATATA-TATATATTAATATAT
* *
38058 ATATATATATGTATTAGTATAT
1 ATATATATATATATTAATATAT
38080 AT
1 AT
38082 GATTTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
ATATATATATATATTAATATAT
Found at i:39336 original size:2 final size:2
Alignment explanation
Indices: 39329--39362 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39319 GGAGCTCTTA
39329 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
39363 TTAGAAAAGG
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:41681 original size:11 final size:11
Alignment explanation
Indices: 41657--41691 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
41647 TTGACAGCGC
41657 AACAAAAATAA
1 AACAAAAATAA
* *
41668 AACGAAAATGA
1 AACAAAAATAA
41679 AACAAAAATAA
1 AACAAAAATAA
41690 AA
1 AA
41692 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.09, G:0.06, T:0.09
Consensus pattern (11 bp):
AACAAAAATAA
Found at i:45057 original size:28 final size:28
Alignment explanation
Indices: 44995--45057 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
44985 AAGTAAGAAT
* * *
44995 AAGAATAAGAATATCAAATAAAAATTTCT
1 AAGAAAAAGAATATCAAATAAAAA-TACA
45024 AA-AAAAAGAATATCAAATAAAAA-ACAA
1 AAGAAAAAGAATATCAAATAAAAATAC-A
45051 AAGAAAA
1 AAGAAAA
45058 TATAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.07
28 24 0.83
29 2 0.07
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.17
Consensus pattern (28 bp):
AAGAAAAAGAATATCAAATAAAAATACA
Found at i:78835 original size:21 final size:21
Alignment explanation
Indices: 78791--78877 Score: 119
Period size: 21 Copynumber: 4.2 Consensus size: 21
78781 TTTAACATGA
78791 TTTGACTATCAA-ATTTTGGGGG
1 TTTGACTATCAATA-TTT-GGGG
78813 TTTGACTATCAATATTTGGGG
1 TTTGACTATCAATATTTGGGG
*
78834 TTTGAC---CAAAATTTGGGG
1 TTTGACTATCAATATTTGGGG
78852 TTTGACTATCAATATTTGGGG
1 TTTGACTATCAATATTTGGGG
78873 TTTGA
1 TTTGA
78878 ACAAATTTTG
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
18 17 0.29
21 26 0.44
22 15 0.25
23 1 0.02
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.41
Consensus pattern (21 bp):
TTTGACTATCAATATTTGGGG
Found at i:78849 original size:18 final size:18
Alignment explanation
Indices: 78826--78888 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
78816 GACTATCAAT
78826 ATTTGGGGTTTGACCAAA
1 ATTTGGGGTTTGACCAAA
*
78844 ATTTGGGGTTTGACTATCAAT
1 ATTTGGGGTTTGAC---CAAA
*
78865 ATTTGGGGTTTGAACAAA
1 ATTTGGGGTTTGACCAAA
*
78883 TTTTGG
1 ATTTGG
78889 TGCTTGACCG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
18 22 0.58
21 16 0.42
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (18 bp):
ATTTGGGGTTTGACCAAA
Found at i:78896 original size:39 final size:39
Alignment explanation
Indices: 78800--78888 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
78790 ATTTGACTAT
*
78800 CAAATTTTGGGGGTTTGACTATCAATATTTGGGGTTTGAC
1 CAAATTTT-GGGGTTTGACTATCAATATTTGGGGTTTGAA
*
78840 CAAAATTTGGGGTTTGACTATCAATATTTGGGGTTTGAA
1 CAAATTTTGGGGTTTGACTATCAATATTTGGGGTTTGAA
78879 CAAATTTTGG
1 CAAATTTTGG
78889 TGCTTGACCG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 39 0.85
40 7 0.15
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (39 bp):
CAAATTTTGGGGTTTGACTATCAATATTTGGGGTTTGAA
Found at i:79049 original size:235 final size:234
Alignment explanation
Indices: 78617--79076 Score: 679
Period size: 235 Copynumber: 2.0 Consensus size: 234
78607 AAACTTTGAT
* *
78617 GTTTGACAGTCAATATTTGGGGTTTGACCAAAATTTGGGGCTTGACCATACATGTACAATGATTT
1 GTTTGACAGTCAATATTTGGGGTTTGAACAAAATTTGGGGCTTGACCATACATGTACAATAATTT
* ** *
78682 TTTTGTGGTTTGACTATTAAATTTTAGGGTTTGACCATTTATGTACAATGAAATGCTTTTTGAGG
66 TTTTGTGGTTTGACTATTAAACTTTAGGGTTTGACCATGCATGTACAATGAAATGCTTTTTGAGA
* * * * * * * *
78747 TAAAATTGAGGAGGGTGATTTGATTGTGGTAAGATTTAACATGATTTGACTATCAAATTTTGGGG
131 CAAAATTGAGGACGGTGATTCGATTGCGGTAAGATTTAACATGATTTAACTAGCAAACTTCGGGG
* *
78812 GTTTGACTATCAATATTTGGGGTTTGACCAAAATTTGGG
196 GTTTGACTATCAAAATTTGGGGTTTAACCAAAATTTGGG
* * *
78851 GTTTGACTA-TCAATATTTGGGGTTTGAACAAATTTTGGTGCTTGACCGTACATGTACAATAATA
1 GTTTGAC-AGTCAATATTTGGGGTTTGAACAAAATTTGGGGCTTGACCATACATGTACAATAAT-
* * *
78915 TTTTTTGTGGTTTGACTATTAAACTTTGGGGTTTGACTATGCATGTACATTGAAATGCTTTTTGA
64 TTTTTTGTGGTTTGACTATTAAACTTTAGGGTTTGACCATGCATGTACAATGAAATGCTTTTTGA
* *
78980 GACAAAATTGAGGACGGTGATTCGATTGCGGTAAGATTTAACGTGATTTAAGTAGCAAACTTCGG
129 GACAAAATTGAGGACGGTGATTCGATTGCGGTAAGATTTAACATGATTTAACTAGCAAACTTCGG
79045 GGGTTTGACTATCAAAATTTGGGGTTTAACCA
194 GGGTTTGACTATCAAAATTTGGGGTTTAACCA
79077 TGCATGTATA
Statistics
Matches: 200, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
234 56 0.28
235 144 0.72
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (234 bp):
GTTTGACAGTCAATATTTGGGGTTTGAACAAAATTTGGGGCTTGACCATACATGTACAATAATTT
TTTTGTGGTTTGACTATTAAACTTTAGGGTTTGACCATGCATGTACAATGAAATGCTTTTTGAGA
CAAAATTGAGGACGGTGATTCGATTGCGGTAAGATTTAACATGATTTAACTAGCAAACTTCGGGG
GTTTGACTATCAAAATTTGGGGTTTAACCAAAATTTGGG
Found at i:79201 original size:71 final size:70
Alignment explanation
Indices: 79044--79272 Score: 296
Period size: 71 Copynumber: 3.2 Consensus size: 70
79034 GCAAACTTCG
* *** * * *
79044 GGGGTTTGACTATCAAAATTTGGGGTTTAACCATGCATGTATAATGATGTTTTTTTTTATTATTA
1 GGGGTTTGACCATCATCTTTTGGGGTTTGACCATGCATGTACAATGA---TTTTTTTT-TTACTA
79109 TTAAACTTT
62 TTAAACTTT
* *
79118 GGGGTTTGACCATCATCTTTTGGGGTTTGACCATGCATGTACACTGATTTTTTGTTTGACTATTA
1 GGGGTTTGACCATCATCTTTTGGGGTTTGACCATGCATGTACAATGATTTTTT-TTTTACTATTA
79183 AACTTT
65 AACTTT
* *
79189 GGGGTTTGACCATCATCTTTTGAGGTTTGACCATGCATGTACAATGGTGTTTTTTTTTACTATTA
1 GGGGTTTGACCATCATCTTTTGGGGTTTGACCATGCATGTACAATGAT-TTTTTTTTTACTATTA
*
79254 AACTTA
65 AACTTT
79260 GGGGTTTGACCAT
1 GGGGTTTGACCAT
79273 GCATGTACAA
Statistics
Matches: 139, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
71 92 0.66
72 7 0.05
74 40 0.29
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.44
Consensus pattern (70 bp):
GGGGTTTGACCATCATCTTTTGGGGTTTGACCATGCATGTACAATGATTTTTTTTTTACTATTAA
ACTTT
Found at i:79330 original size:54 final size:50
Alignment explanation
Indices: 79213--79353 Score: 131
Period size: 50 Copynumber: 2.7 Consensus size: 50
79203 ATCTTTTGAG
* * *
79213 GTTTGACCATGCATGTACAATGGTGTTTTTTTTTACTATTAAACTTAGGG
1 GTTTGACCATGCATGTACAATGATGTTTTTTTTTACTATCAAACTTAGGA
* * *
79263 GTTTGACCATGCATGTACAATGATTTTTTTGTGGTTTCACTATCAAACTTTGTA
1 GTTTGACCATGCATGTACAATGATGTTTTT-T--TTT-ACTATCAAACTTAGGA
* * *
79317 GTTTG-CCAGTGCATATACAGTGTAATGATTTTTTTTA
1 GTTTGACCA-TGCATGTACAATG--ATGTTTTTTTTTA
79354 TTTGACTATC
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
50 28 0.38
51 1 0.01
52 1 0.01
53 9 0.12
54 28 0.38
55 1 0.01
56 6 0.08
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (50 bp):
GTTTGACCATGCATGTACAATGATGTTTTTTTTTACTATCAAACTTAGGA
Done.