Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022524.1 Corchorus olitorius cultivar O-4 contig22557, 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: 136831
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:1201 original size:21 final size:22
Alignment explanation
Indices: 1175--1219 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
1165 ACTTGGTGTC
1175 AACTGTCATGAAAC-AAAAAAA
1 AACTGTCATGAAACGAAAAAAA
1196 AACTGTCATGAAACGAAAAAAA
1 AACTGTCATGAAACGAAAAAAA
1218 AA
1 AA
1220 AGTGGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.62, C:0.13, G:0.11, T:0.13
Consensus pattern (22 bp):
AACTGTCATGAAACGAAAAAAA
Found at i:2002 original size:2 final size:2
Alignment explanation
Indices: 1990--2029 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
1980 TTCGTGATTT
1990 TA TA TA GTA 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 TA TA TA TA T
2030 CAAATTAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2611 original size:178 final size:178
Alignment explanation
Indices: 2319--2648 Score: 450
Period size: 178 Copynumber: 1.9 Consensus size: 178
2309 CCGATTCAGG
* *
2319 TGATTTAAGTGTCTATTAAAAGATTGTTTCATCATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTCGAAAACTA
* * * *
2384 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTTGCTGTTTCGATTAACGGGAATAGA
66 AATTTAATGATTCAAGTATCAAAAATGCTTCCGAAAAATTAGCTGTTTCGATTAAAGGAAATAGA
*
2449 CGGTCCACTTAATATTATATAACTTTTGCTCCAGATGTCTAATTGAGA
131 CGGTCCACTTAATATTACATAACTTTTGCTCCAGATGTCTAATTGAGA
* * * * * *
2497 TGATTCAAGTGTTTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGGCTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTCGAAAACTA
* * * *
2562 AATTTAAT-ATTCGAGGTAT-AAAAATTGCTTTC-AAAGAATTAGTTGTTTCGGTTAAAGGAAAT
66 AATTTAATGATTC-AAGTATCAAAAA-TGCTTCCGAAA-AATTAGCTGTTTCGATTAAAGGAAAT
*
2624 AGACGGTCTACTTAATATTACATAA
128 AGACGGTCCACTTAATATTACATAA
2649 TTTGTGTTTA
Statistics
Matches: 131, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
177 11 0.08
178 120 0.92
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGATTCAAGTATCAAAAATGCTTCCGAAAAATTAGCTGTTTCGATTAAAGGAAATAGA
CGGTCCACTTAATATTACATAACTTTTGCTCCAGATGTCTAATTGAGA
Found at i:3256 original size:2 final size:2
Alignment explanation
Indices: 3249--3274 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3239 TTTGTGCATG
3249 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3275 ATGCATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3737 original size:18 final size:18
Alignment explanation
Indices: 3714--3762 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3704 CTAAAATTCA
3714 AGCTCGAGCTCGA-ACTCG
1 AGCTCGAGCTCGATAC-CG
**
3732 AGCTCGAATTCGATACCG
1 AGCTCGAGCTCGATACCG
*
3750 AGTTCGAGCTCGA
1 AGCTCGAGCTCGA
3763 CAGGTATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (18 bp):
AGCTCGAGCTCGATACCG
Found at i:4074 original size:31 final size:31
Alignment explanation
Indices: 4039--4114 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
4029 TAAATTACCA
* *
4039 ATTGATCCCATTAAAATTAAAGTTTTATCA-C
1 ATTGATCCCATTAAAATAAAAGATTTAT-AGC
*
4070 ATTGATCCTC-CTAAAATAAAAGATTTATAGC
1 ATTGATCC-CATTAAAATAAAAGATTTATAGC
4101 ATTGA-CCCATTAAA
1 ATTGATCCCATTAAA
4115 GATGTTGGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 1 0.03
30 7 0.18
31 29 0.76
32 1 0.03
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (31 bp):
ATTGATCCCATTAAAATAAAAGATTTATAGC
Found at i:5960 original size:30 final size:29
Alignment explanation
Indices: 5895--5956 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
5885 TAGCTAAGGT
*
5895 AAAACTCTTCCACCAATTTTATCAAATTC
1 AAAACTCTTCCAACAATTTTATCAAATTC
* * *
5924 AAAACTCTTCGAATAATTTTATCCAATTC
1 AAAACTCTTCCAACAATTTTATCAAATTC
5953 AAAA
1 AAAA
5957 ACTCCAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAACTCTTCCAACAATTTTATCAAATTC
Found at i:19185 original size:15 final size:15
Alignment explanation
Indices: 19165--19202 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
19155 CTCCAATACT
19165 TCATCATCAAACTCA
1 TCATCATCAAACTCA
*
19180 TCATCATCAATCTCA
1 TCATCATCAAACTCA
*
19195 TGATCATC
1 TCATCATC
19203 TTGATCTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.32
Consensus pattern (15 bp):
TCATCATCAAACTCA
Found at i:31484 original size:31 final size:32
Alignment explanation
Indices: 31414--31484 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 32
31404 GGCCGTTTGT
* *
31414 TACTTTCCAAGGAGGGTGCTCTCCATGGAGAG
1 TACTTTCCAAGAAGAGTGCTCTCCATGGAGAG
* *
31446 T-CATTCCAAGAAGAGTGAT-TCCCAT-GAGAG
1 TACTTTCCAAGAAGAGTGCTCT-CCATGGAGAG
31476 TACTTTCCA
1 TACTTTCCA
31485 TGGAAAGTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
30 7 0.22
31 24 0.75
32 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.27
Consensus pattern (32 bp):
TACTTTCCAAGAAGAGTGCTCTCCATGGAGAG
Found at i:31669 original size:53 final size:53
Alignment explanation
Indices: 31554--31669 Score: 155
Period size: 53 Copynumber: 2.2 Consensus size: 53
31544 GAAAGTTGGG
* **
31554 TTACTTTCCCACATTTATTTAATTAAACCAAATCATAGAAAGTGTTTCCACCTT
1 TTACTTTCCCACA-TTATATAATTAAACCAAATCATAGAAAGTGTTTCCACCCA
*
31608 TTATTTTCCCAC-TTATCATAACTT-AACCAAATCATAGAAAGTGTTTCCACCCA
1 TTACTTTCCCACATTAT-ATAA-TTAAACCAAATCATAGAAAGTGTTTCCACCCA
31661 TTACTTTCC
1 TTACTTTCC
31670 TGGGAAAGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
52 4 0.07
53 38 0.69
54 13 0.24
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (53 bp):
TTACTTTCCCACATTATATAATTAAACCAAATCATAGAAAGTGTTTCCACCCA
Found at i:31993 original size:2 final size:2
Alignment explanation
Indices: 31982--32015 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
31972 ATTGAGTCCA
*
31982 AT AT -T AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32016 ATCACATAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:33621 original size:174 final size:174
Alignment explanation
Indices: 33331--33679 Score: 689
Period size: 174 Copynumber: 2.0 Consensus size: 174
33321 ATAATAATAC
33331 TTTTATTAATTTATATTATAAAATTGAAATAGGTCCAGAACTATCAAAAAGTCTCCATTTTTTAA
1 TTTTATTAATTTATATTATAAAATTGAAATAGGTCCAGAACTATCAAAAAGTCTCCATTTTTTAA
*
33396 AAATCAAAATGGTAAAAATAAAATATTTATAAAAATATTGAATTTAATTAAATAAAAATAGAGTT
66 AAATCAAAATGGTAAAAATAAAATATTTATAAAAATATTGAAATTAATTAAATAAAAATAGAGTT
33461 TTTAGTAGAATAACTGTAAAAGTTTATTTCTAACAAAAAAACTG
131 TTTAGTAGAATAACTGTAAAAGTTTATTTCTAACAAAAAAACTG
33505 TTTTATTAATTTATATTATAAAATTGAAATAGGTCCAGAACTATCAAAAAGTCTCCATTTTTTAA
1 TTTTATTAATTTATATTATAAAATTGAAATAGGTCCAGAACTATCAAAAAGTCTCCATTTTTTAA
33570 AAATCAAAATGGTAAAAATAAAATATTTATAAAAATATTGAAATTAATTAAATAAAAATAGAGTT
66 AAATCAAAATGGTAAAAATAAAATATTTATAAAAATATTGAAATTAATTAAATAAAAATAGAGTT
33635 TTTAGTAGAATAACTGTAAAAGTTTATTTCTAACAAAAAAACTG
131 TTTAGTAGAATAACTGTAAAAGTTTATTTCTAACAAAAAAACTG
33679 T
1 T
33680 AAAATTTAAA
Statistics
Matches: 174, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (174 bp):
TTTTATTAATTTATATTATAAAATTGAAATAGGTCCAGAACTATCAAAAAGTCTCCATTTTTTAA
AAATCAAAATGGTAAAAATAAAATATTTATAAAAATATTGAAATTAATTAAATAAAAATAGAGTT
TTTAGTAGAATAACTGTAAAAGTTTATTTCTAACAAAAAAACTG
Found at i:33830 original size:93 final size:93
Alignment explanation
Indices: 33745--33929 Score: 298
Period size: 93 Copynumber: 2.0 Consensus size: 93
33735 ACTTTTTAAT
* *
33745 TAAATTAGTAATATCATAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCATAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
33810 AGTTTTTAGTTGACTAAAACTATAAAAG
66 AGTTTTTAGTTGACTAAAACTATAAAAG
** * * *
33838 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTCATTAAATAAAAATAT
1 TAAAATAGTAAAATCATAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
33903 AGTTTTTAGTTGATTAAAACTATAAAA
66 AGTTTTTAGTTGACTAAAACTATAAAA
33930 ATTTAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.34
Consensus pattern (93 bp):
TAAAATAGTAAAATCATAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:34207 original size:31 final size:30
Alignment explanation
Indices: 34135--34208 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
34125 ATACAGACTA
*
34135 CCACTTTGCACCCTACTTTTTTATTTTGAT
1 CCACTTTGCACCCTAATTTTTTATTTTGAT
*
34165 -CACTTTGCACCCTAATGTTTTGT-TTTTGTT
1 CCACTTTGCACCCTAAT-TTTT-TATTTTGAT
*
34195 CCACGTTGCACCCT
1 CCACTTTGCACCCT
34209 CCGTTATCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 15 0.39
30 10 0.26
31 13 0.34
ACGTcount: A:0.15, C:0.28, G:0.11, T:0.46
Consensus pattern (30 bp):
CCACTTTGCACCCTAATTTTTTATTTTGAT
Found at i:34297 original size:31 final size:31
Alignment explanation
Indices: 34259--34336 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
34249 AATGCTGATG
* * *
34259 TGGCATGCCACGTTAGGCGAAAATCGCCACA
1 TGGCATGCCACGTCAGACGAAAACCGCCACA
* *
34290 TGGCATGCCATGTCAGACGAAAACCGCCACG
1 TGGCATGCCACGTCAGACGAAAACCGCCACA
34321 TGGCATGCCACGTCAG
1 TGGCATGCCACGTCAG
34337 CATAAAAAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (31 bp):
TGGCATGCCACGTCAGACGAAAACCGCCACA
Found at i:35352 original size:2 final size:2
Alignment explanation
Indices: 35345--35369 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35335 TACTAGTTAT
35345 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 T
35370 TTGCTTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47118 original size:7 final size:7
Alignment explanation
Indices: 47106--47135 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
47096 ACAACAATTT
47106 TTTTTTA
1 TTTTTTA
47113 TTTTTTA
1 TTTTTTA
47120 TTTTTTTA
1 -TTTTTTA
47128 TTTTTTA
1 TTTTTTA
47135 T
1 T
47136 GATTAAGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:47118 original size:8 final size:8
Alignment explanation
Indices: 47105--47133 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
47095 AACAACAATT
47105 TTTTTTTA
1 TTTTTTTA
47113 -TTTTTTA
1 TTTTTTTA
47120 TTTTTTTA
1 TTTTTTTA
47128 TTTTTT
1 TTTTTT
47134 ATGATTAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:47125 original size:15 final size:15
Alignment explanation
Indices: 47105--47135 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
47095 AACAACAATT
47105 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
47120 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
47135 T
1 T
47136 GATTAAGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTTATTTTTTA
Found at i:48754 original size:21 final size:21
Alignment explanation
Indices: 48728--48777 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
48718 AGGGATCGAG
*
48728 CTGGGCGCTGA-GCCTTGTCGC
1 CTGGGCGCTGAGGCATT-TCGC
48749 CTGGGCGCTGAGGCATTTCGC
1 CTGGGCGCTGAGGCATTTCGC
48770 CTGGGCGC
1 CTGGGCGC
48778 CCAGCGGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.06, C:0.32, G:0.40, T:0.22
Consensus pattern (21 bp):
CTGGGCGCTGAGGCATTTCGC
Found at i:60756 original size:53 final size:53
Alignment explanation
Indices: 60673--60777 Score: 174
Period size: 53 Copynumber: 2.0 Consensus size: 53
60663 AATAGTATAC
**
60673 TATTTTGTTAGTGAAAGTTCAATCTATTTATTAAGATTCAAATATTTAGGATA
1 TATTTTGTTAGTGAAAACTCAATCTATTTATTAAGATTCAAATATTTAGGATA
* *
60726 TATTTTGTTGGTGAAAACTCAATCTTTTTATTAAGATTCAAATATTTAGGAT
1 TATTTTGTTAGTGAAAACTCAATCTATTTATTAAGATTCAAATATTTAGGAT
60778 TTGCTTGGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (53 bp):
TATTTTGTTAGTGAAAACTCAATCTATTTATTAAGATTCAAATATTTAGGATA
Found at i:61779 original size:16 final size:17
Alignment explanation
Indices: 61758--61798 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
61748 ATCTTAAATT
61758 AAATTTA-ATTAAATCC
1 AAATTTATATTAAATCC
* *
61774 AAATTTATGTTGAATCC
1 AAATTTATATTAAATCC
61791 AAATTTAT
1 AAATTTAT
61799 GTAATGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (17 bp):
AAATTTATATTAAATCC
Found at i:67682 original size:39 final size:39
Alignment explanation
Indices: 67638--67727 Score: 180
Period size: 39 Copynumber: 2.3 Consensus size: 39
67628 ATTAGCAATA
67638 GACAGGAATGATATCTCTCGTCAAAGAAAAAAAAAAGAG
1 GACAGGAATGATATCTCTCGTCAAAGAAAAAAAAAAGAG
67677 GACAGGAATGATATCTCTCGTCAAAGAAAAAAAAAAGAG
1 GACAGGAATGATATCTCTCGTCAAAGAAAAAAAAAAGAG
67716 GACAGGAATGAT
1 GACAGGAATGAT
67728 TATCATATCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (39 bp):
GACAGGAATGATATCTCTCGTCAAAGAAAAAAAAAAGAG
Found at i:69035 original size:5 final size:5
Alignment explanation
Indices: 69025--69051 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
69015 AGTAGTAATA
69025 ATAAG ATAAG ATAAG ATAAG ATAAG AT
1 ATAAG ATAAG ATAAG ATAAG ATAAG AT
69052 GGTAAGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (5 bp):
ATAAG
Found at i:75331 original size:19 final size:19
Alignment explanation
Indices: 75309--75352 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
75299 CCTTTTTTCA
*
75309 TATATTACATATATATAGG
1 TATATTACATACATATAGG
* *
75328 TATATTATATGCATATAGG
1 TATATTACATACATATAGG
75347 TATATT
1 TATATT
75353 TATGGATGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (19 bp):
TATATTACATACATATAGG
Found at i:76006 original size:17 final size:18
Alignment explanation
Indices: 75966--76012 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
75956 TTCCTTCAAA
75966 CTTCAAAATTT-TCAATT
1 CTTCAAAATTTCTCAATT
*
75983 CTCTCAAATTTTCTCAATT
1 CT-TCAAAATTTCTCAATT
*
76002 -TTCAAACTTTC
1 CTTCAAAATTTC
76013 AAACTTCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.42
18 9 0.35
19 6 0.23
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (18 bp):
CTTCAAAATTTCTCAATT
Found at i:76230 original size:33 final size:33
Alignment explanation
Indices: 76155--76235 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 33
76145 TGCGACCAAG
* * * * *
76155 GCTCGCGATCAAGTCGCGGCTCGGTCACACGCG
1 GCTCGCGACCAAGCCGCGGCACAGTCACACGCC
*
76188 GCTCACGACCAAGCCGCGGCACAGTCACGA-GCC
1 GCTCGCGACCAAGCCGCGGCACAGTCAC-ACGCC
*
76221 GCTCGCGACCGAGCC
1 GCTCGCGACCAAGCC
76236 ATGGCTTAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 38 0.97
34 1 0.03
ACGTcount: A:0.19, C:0.41, G:0.31, T:0.10
Consensus pattern (33 bp):
GCTCGCGACCAAGCCGCGGCACAGTCACACGCC
Found at i:76343 original size:27 final size:27
Alignment explanation
Indices: 76296--76348 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
76286 TTTTTTACTT
76296 TTTTTAAAAAATTAATAATTAGTTATTA
1 TTTTTAAAAAATTAATAATTA-TTATTA
* *
76324 TTTTT-AAAAATTAGTTATTATTATT
1 TTTTTAAAAAATTAATAATTATTATT
76349 TTATATGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 13 0.57
28 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (27 bp):
TTTTTAAAAAATTAATAATTATTATTA
Found at i:76359 original size:23 final size:20
Alignment explanation
Indices: 76307--76345 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
76297 TTTTAAAAAA
*
76307 TTAATAATTAGTTATTATTT
1 TTAAAAATTAGTTATTATTT
76327 TTAAAAATTAGTTATTATT
1 TTAAAAATTAGTTATTATT
76346 ATTTTATATG
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:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAAAAATTAGTTATTATTT
Found at i:77060 original size:12 final size:12
Alignment explanation
Indices: 77043--77068 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
77033 GAGTATAACT
77043 AACTATCAAACA
1 AACTATCAAACA
77055 AACTATCAAACA
1 AACTATCAAACA
77067 AA
1 AA
77069 TTTATGCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (12 bp):
AACTATCAAACA
Found at i:78173 original size:34 final size:34
Alignment explanation
Indices: 78128--78193 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
78118 CAAACCCCTA
*
78128 AACAAACAAAGCTAAACCCATAAATTATTTTCGC
1 AACAAACAAAGCTAAACCCATAAATAATTTTCGC
* *
78162 AACAAAGAAAGCTAAACCCGTAAATAATTTTC
1 AACAAACAAAGCTAAACCCATAAATAATTTTC
78194 AAACAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.23
Consensus pattern (34 bp):
AACAAACAAAGCTAAACCCATAAATAATTTTCGC
Found at i:78948 original size:22 final size:23
Alignment explanation
Indices: 78906--78948 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
78896 TGAAGCAAGA
78906 CAAACGCTCTCACAAAGGAGTCC
1 CAAACGCTCTCACAAAGGAGTCC
*
78929 CAAATGCTCTCAC-AAGGAGT
1 CAAACGCTCTCACAAAGGAGT
78949 TCTGATTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.16
Consensus pattern (23 bp):
CAAACGCTCTCACAAAGGAGTCC
Found at i:86624 original size:31 final size:31
Alignment explanation
Indices: 86586--86673 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 31
86576 TGAGATACTC
86586 TTTTTGGCACAAGAGATACTCTTAGTTTTTT
1 TTTTTGGCACAAGAGATACTCTTAGTTTTTT
86617 TTTTTGGCACAAGAGATACTCTTAGTTTTTT
1 TTTTTGGCACAAGAGATACTCTTAGTTTTTT
**
86648 TTGGT-G-A-ATAGAGATACTCTTAGTTT
1 TTTTTGGCACA-AGAGATACTCTTAGTTT
86674 ATGACATATA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.02
29 18 0.33
30 1 0.02
31 34 0.63
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (31 bp):
TTTTTGGCACAAGAGATACTCTTAGTTTTTT
Found at i:88153 original size:14 final size:15
Alignment explanation
Indices: 88120--88153 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
88110 TACTACTTTT
88120 ATATGCAGTAAGCAA
1 ATATGCAGTAAGCAA
88135 ATATGCAGTAAGC-A
1 ATATGCAGTAAGCAA
88149 ATATG
1 ATATG
88154 TATTCAGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (15 bp):
ATATGCAGTAAGCAA
Found at i:95701 original size:24 final size:24
Alignment explanation
Indices: 95674--95721 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
95664 ACTACAAAAT
* *
95674 AAAAACTAAATTAATGAACAAACAA
1 AAAAAC-AAATAAATAAACAAACAA
95699 AAAAACAAATAAATAAACAAACA
1 AAAAACAAATAAATAAACAAACA
95722 TGAGGGGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.73, C:0.12, G:0.02, T:0.12
Consensus pattern (24 bp):
AAAAACAAATAAATAAACAAACAA
Found at i:97090 original size:9 final size:9
Alignment explanation
Indices: 97076--97104 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
97066 ATTGTGATTG
97076 ATAATTATA
1 ATAATTATA
97085 ATAATTATA
1 ATAATTATA
97094 ATAATTATA
1 ATAATTATA
97103 AT
1 AT
97105 GATATGTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATAATTATA
Found at i:109295 original size:20 final size:20
Alignment explanation
Indices: 109263--109310 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
109253 TAGAACCACA
**
109263 AATCAACAACTGGGTTTATG
1 AATCAACAACTGGCCTTATG
* *
109283 AATTAACAGCTGGCCTTATG
1 AATCAACAACTGGCCTTATG
109303 AATCAACA
1 AATCAACA
109311 CCTGCCTCTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (20 bp):
AATCAACAACTGGCCTTATG
Found at i:110647 original size:147 final size:147
Alignment explanation
Indices: 110425--110716 Score: 575
Period size: 147 Copynumber: 2.0 Consensus size: 147
110415 AATGTGGTGT
110425 CTCCTTTTGGCTTTTTTTGGTCTTTTCTCACTTTTCGGGTGACTAAAAATGTCCTCGATGAATTT
1 CTCCTTTTGGCTTTTTTTGGTCTTTTCTCACTTTTCGGGTGACTAAAAATGTCCTCGATGAATTT
*
110490 CCTCCCTTACTTTTCCTGTTGCCCTTTTTTGTAATTTACTATTTTTATATTTATGGTTAAGTGTG
66 CCTCCCTTACTTTTCCTGTTGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTG
110555 TTTTAAATACATATTGC
131 TTTTAAATACATATTGC
110572 CTCCTTTTGGCTTTTTTTGGTCTTTTCTCACTTTTCGGGTGACTAAAAATGTCCTCGATGAATTT
1 CTCCTTTTGGCTTTTTTTGGTCTTTTCTCACTTTTCGGGTGACTAAAAATGTCCTCGATGAATTT
110637 CCTCCCTTACTTTTCCTGTTGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTG
66 CCTCCCTTACTTTTCCTGTTGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTG
110702 TTTTAAATACATATT
131 TTTTAAATACATATT
110717 AATTGTGTGT
Statistics
Matches: 144, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 144 1.00
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (147 bp):
CTCCTTTTGGCTTTTTTTGGTCTTTTCTCACTTTTCGGGTGACTAAAAATGTCCTCGATGAATTT
CCTCCCTTACTTTTCCTGTTGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTG
TTTTAAATACATATTGC
Found at i:112200 original size:122 final size:123
Alignment explanation
Indices: 111982--112225 Score: 418
Period size: 122 Copynumber: 2.0 Consensus size: 123
111972 TGCGTAAAAA
* *
111982 ATCTCTTGAGACTTTCACGATGAATATGATGCGGGGCATGTCAGTCAGTATGCAGAAATTGACAA
1 ATCTCTTGAGACTTTCACGATGAATATGATGCGGGGCATGCCAGTCAATATGCAGAAATTGACAA
112047 AGATTTGCAAAAACAATAAATTGATTTGATTGAGATAAAATAAAGATCAGACGATGTG
66 AGATTTGCAAAAACAATAAATTGATTTGATTGAGATAAAATAAAGATCAGACGATGTG
* * * *
112105 ATCTCTTGAGACTTTCGCGATGAATATGGTGCGGGGCGTGCCAGTCAAT-TGCAGAAATTGATAA
1 ATCTCTTGAGACTTTCACGATGAATATGATGCGGGGCATGCCAGTCAATATGCAGAAATTGACAA
*
112169 AGATTTGCAAAAACAATAAATTGATTTGATTGAGATAAAATAAAGATTAGACGATGT
66 AGATTTGCAAAAACAATAAATTGATTTGATTGAGATAAAATAAAGATCAGACGATGT
112226 AATTACAAGA
Statistics
Matches: 114, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
122 70 0.61
123 44 0.39
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (123 bp):
ATCTCTTGAGACTTTCACGATGAATATGATGCGGGGCATGCCAGTCAATATGCAGAAATTGACAA
AGATTTGCAAAAACAATAAATTGATTTGATTGAGATAAAATAAAGATCAGACGATGTG
Found at i:114836 original size:15 final size:15
Alignment explanation
Indices: 114816--114846 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
114806 ATAATACATT
114816 AACTATCAAATAGAA
1 AACTATCAAATAGAA
114831 AACTATCAAATAGAA
1 AACTATCAAATAGAA
114846 A
1 A
114847 CAGGTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AACTATCAAATAGAA
Found at i:114898 original size:14 final size:14
Alignment explanation
Indices: 114876--114908 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
114866 TTTTAAATTG
114876 AAATAGTAAAAATA
1 AAATAGTAAAAATA
*
114890 AAATGGTAAAAATA
1 AAATAGTAAAAATA
114904 AAATA
1 AAATA
114909 ATTATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (14 bp):
AAATAGTAAAAATA
Found at i:130179 original size:92 final size:93
Alignment explanation
Indices: 129973--130209 Score: 352
Period size: 92 Copynumber: 2.5 Consensus size: 93
129963 AATCAAAACT
* *
129973 GAATTATGTGGGCTAGACCTTTTAGCCCGCCATGACATGGTCCAAAACAGGGCAATGGATACATA
1 GAATTATGTGGGCTAGACGTTTTAGCCCGCCATGACATGGTCCAAAACAGGACAATGGATACA-A
*
130038 TGGATTCGTGCTTAATATTGACTCCATGG
65 TGGATTCGTGCTTAATATTGACTCCACGG
*
130067 GAATTATGTGGGCTAGACGTTTTAGCCCGCCATGACATGGTCCGAAACAGGACAATGGATAC-AT
1 GAATTATGTGGGCTAGACGTTTTAGCCCGCCATGACATGGTCCAAAACAGGACAATGGATACAAT
* *
130131 GGATTTGTGCTTAATATTGGCTCCAC-G
66 GGATTCGTGCTTAATATTGACTCCACGG
* * * *
130158 GAGATTATGCGGGCTAGACGTTATAGCCCGCCACGACATGATCCAAAACAGG
1 GA-ATTATGTGGGCTAGACGTTTTAGCCCGCCATGACATGGTCCAAAACAGG
130210 GCAGTGGCTC
Statistics
Matches: 131, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
91 3 0.02
92 69 0.53
94 59 0.45
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (93 bp):
GAATTATGTGGGCTAGACGTTTTAGCCCGCCATGACATGGTCCAAAACAGGACAATGGATACAAT
GGATTCGTGCTTAATATTGACTCCACGG
Found at i:130649 original size:28 final size:28
Alignment explanation
Indices: 130609--130664 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
130599 ATAAGAGTCA
*
130609 TGGGCTGATCTAGTGGGTTTTTTTTTTT
1 TGGGCTGATCTAGTGGGGTTTTTTTTTT
130637 TGGGCTGATCTAGTGGGGTTTTTTTTTT
1 TGGGCTGATCTAGTGGGGTTTTTTTTTT
130665 AATGGAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.07, C:0.07, G:0.30, T:0.55
Consensus pattern (28 bp):
TGGGCTGATCTAGTGGGGTTTTTTTTTT
Done.