Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024429.1 Corchorus olitorius cultivar O-4 contig24462, 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: 47826
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:9248 original size:54 final size:54
Alignment explanation
Indices: 9183--10290 Score: 1053
Period size: 54 Copynumber: 20.6 Consensus size: 54
9173 CTGTATCAAT
* * *
9183 TGGAGATCAACTCGGATCATCGAAAACTTCTTGAAATGACCGTATTGGATCAT-
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * *
9236 TAGGAGATCAACTCTGGTCATCGAAAACTTCTTTG-AACGACCGCACTAGATCAAT-
1 T-GGAGATCAACTCTGATCATCGAAAACTTC-TTGAAATGACCGCACTGGATC-ATC
* * * ** *
9291 TGGAGATCAATTATGATCATCGAAAATTTCTTGAAATGGTCGCGCTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
** * *
9345 TAAAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACTGCACTGTATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * *
9399 TGGAGATCAACTCTGATCATTGAAAACTTCTTGGAATTACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * ** * *
9453 T-GAGGATTAACTCTAATCATTAAAAACTTCTT-AGAATGACCGCATTGTATCAAT-
1 TGGA-GATCAACTCTGATCATCGAAAACTTCTTGA-AATGACCGCACTGGATC-ATC
* * * *
9507 TGGAGATCAACTCTGATCGTTGAAAACTTCTTGGAACGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * *
9561 T-GAGGATCAACTCTGATC-TCTGAAAACTTCTTAAAATGACCGCATTGTATCAAT-
1 TGGA-GATCAACTCTGATCATC-GAAAACTTCTTGAAATGACCGCACTGGATC-ATC
* * * * **
9615 TGGAGATCAACTCTGATCGTTGAAAATTTCTT-AGAATGACCACACTAAATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGA-AATGACCGCACTGGATCATC
* * *
9669 T-GAGGATCAACTCTGATC-TCTAAAAACTTTTTGGAATGACCGCACTGGATCATC
1 TGGA-GATCAACTCTGATCATC-GAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * * *
9723 TGGGGAACAACTCTAATCATTGAAAACTTATTTGGAATGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTT-CTTGAAATGACCGCACTGGATCATC
* * *
9778 TAGG-GATCAACTCTGATC-TCTAAAACTTCTTGAAAAGACCGCACCGGATCATC
1 T-GGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * * *
9831 TGGAGATCAACTCTAATCATTGAAAATTTTTTGGAATGACCACACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* *
9885 TGG-GATCAACTTTAATCA-CTGAAAACTTCTTGAAATGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATC-GAAAACTTCTTGAAATGACCGCACTGGATCATC
* * *
9938 TGG-GATTCAACTCTGATCATTGAAAACTTCTTTGGAATGACCGCATTGGATCATC
1 TGGAGA-TCAACTCTGATCATCGAAAACTTC-TTGAAATGACCGCACTGGATCATC
* *
9993 TAGG-GATCAACTCTGATCTTCAAAAACTTCTT-AGAATGACCGCACTGGATCATC
1 T-GGAGATCAACTCTGATCATCGAAAACTTCTTGA-AATGACCGCACTGGATCATC
* * *
10047 TAGGA-ATCAACTCTGATC-TCTAAAAACTTCTTGGAATGACTGCACTGG-TCATC
1 T-GGAGATCAACTCTGATCATC-GAAAACTTCTTGAAATGACCGCACTGGATCATC
* * ** * * *
10100 AGG-GATCAACTCTAATCAAAGAAAACGTCTTGGAATGACCACACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * * *
10153 TAG-GATCAACTCTGATCA-CGGAAAACTTCTTGAAATGATCGTACTAGATTATT
1 TGGAGATCAACTCTGATCATC-GAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
10206 TGGGGATCAACTCTGATCATTGAAAAATTCTTGAAATGATCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
** *
10260 TCAAGATCAACTCTGAT-ATCTAAAAACTTCT
1 TGGAGATCAACTCTGATCATC-GAAAACTTCT
10291 ACGAAAGATA
Statistics
Matches: 872, Mismatches: 140, Indels: 85
0.79 0.13 0.08
Matches are distributed among these distances:
52 39 0.04
53 158 0.18
54 570 0.65
55 99 0.11
56 6 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (54 bp):
TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
Found at i:10396 original size:160 final size:161
Alignment explanation
Indices: 10210--10595 Score: 392
Period size: 160 Copynumber: 2.4 Consensus size: 161
10200 ATTATTTGGG
* *
10210 GATCAACTCTG-ATCAT-TGAAAAATTCT-TGAAATGATCGCACTGGATCATCTCAAGATCAACT
1 GATCAACT-TGAATC-TCTGAAAAATTCTATGAAA-GACCGCACAGGATCATCTCAAGATCAACT
* * * * * ** *
10272 CTGATA-TCTAAAAACTTCTACGAAAGATAACATCGGGTCATCTGAAGATC-ACTTAGATTTCTG
63 -T-AAACTCGAAAAACTTCTACGAAAGACAACATAGGGTCATCTGAAGATCAACTTAAACCTCCG
* * *
10335 AAAGCTT-TATGAAAGACCGCACATGGTCATCATAAA
126 AAAACTTCTATGAAAGACCGCACAGGGCCATC-TAAA
* * * *
10371 -ATCAACTT-AGATCTCTGAAAAATTCTATGAAAGACCACACAGGGTCATCTGAAGATGAACTTA
1 GATCAACTTGA-ATCTCTGAAAAATTCTATGAAAGACCGCACAGGATCATCTCAAGATCAACTTA
* * ** *
10434 AACCTCGGAAAACTTCTATGAAAGACCGCATAGGGTTATCTGAAGATCAACTTAAACCTCCGAAA
65 AA-CTCGAAAAACTTCTACGAAAGACAACATAGGGTCATCTGAAGATCAACTTAAACCTCCGAAA
*
10499 ACTTCTATGAAAGACCGCATAGGGCCATCTAAA
129 ACTTCTATGAAAGACCGCACAGGGCCATCTAAA
* * * * *
10532 GATCAACTTGAATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTCATTTGAACATCAACTTA
1 GATCAACTTGAATCTCTGAAAAATTCTATGAAAGACCGCACAGGATCATCTCAAGATCAACTTA
10596 GATCTCTGAA
Statistics
Matches: 187, Mismatches: 28, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
158 2 0.01
159 3 0.02
160 80 0.43
161 24 0.13
162 77 0.41
163 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (161 bp):
GATCAACTTGAATCTCTGAAAAATTCTATGAAAGACCGCACAGGATCATCTCAAGATCAACTTAA
ACTCGAAAAACTTCTACGAAAGACAACATAGGGTCATCTGAAGATCAACTTAAACCTCCGAAAAC
TTCTATGAAAGACCGCACAGGGCCATCTAAA
Found at i:10417 original size:54 final size:54
Alignment explanation
Indices: 9340--10610 Score: 450
Period size: 54 Copynumber: 23.6 Consensus size: 54
9330 TCGCGCTGGA
* * * **
9340 TCATCTAAAGATCAACTCT-GATCATC-GAAAACTTCT-TGAAATGACTGCACTGTA
1 TCATCTGAAGATCAACT-TAGATC-TCTGAAAACTTCTATGAAA-GACCGCACAGGG
* ** * *
9394 TCATCTGGAGATCAACTCT-GATCAT-TGAAAACTTCT-TGGAATTACCGCACTGGA
1 TCATCTGAAGATCAACT-TAGATC-TCTGAAAACTTCTAT-GAAAGACCGCACAGGG
* * * * ** **
9448 TCATCTGAGGATTAACTCTA-ATCAT-TAAAAACTTCT-TAGAATGACCGCATTGTA
1 TCATCTGAAGATCAACT-TAGATC-TCTGAAAACTTCTAT-GAAAGACCGCACAGGG
* * * *
9502 TCAAT-TGGAGATCAACTCT-GATCGT-TGAAAACTTCT-TGGAACGACCGCACTGGA
1 TC-ATCTGAAGATCAACT-TAGATC-TCTGAAAACTTCTAT-GAAAGACCGCACAGGG
* * ** **
9556 TCATCTGAGGATCAACTCT-GATCTCTGAAAACTTCT-TAAAATGACCGCATTGTA
1 TCATCTGAAGATCAACT-TAGATCTCTGAAAACTTCTATGAAA-GACCGCACAGGG
* * * * **
9610 TCAAT-TGGAGATCAACTCT-GATCGT-TGAAAATTTCT-TAGAATGACCACACTA-AA
1 TC-ATCTGAAGATCAACT-TAGATC-TCTGAAAACTTCTAT-GAAAGACCGCAC-AGGG
* * * * * *
9664 TCATCTGAGGATCAACTCT-GATCTCTAAAAACTT-TTTGGAATGACCGCACTGGA
1 TCATCTGAAGATCAACT-TAGATCTCTGAAAACTTCTAT-GAAAGACCGCACAGGG
** * * * * * *
9718 TCATCTGGGGAACAACTCTA-ATCAT-TGAAAACTTATTTGGAATGACCGCACTGGA
1 TCATCTGAAGATCAACT-TAGATC-TCTGAAAACTTCTAT-GAAAGACCGCACAGGG
* * *
9773 TCATCT-AGGGATCAACTCT-GATCTCT-AAAACTTCT-TGAAAAGACCGCACCGGA
1 TCATCTGA-AGATCAACT-TAGATCTCTGAAAACTTCTATG-AAAGACCGCACAGGG
* * * * * * *
9826 TCATCTGGAGATCAACTCTA-ATCAT-TGAAAA-TTTTTTGGAATGACCACACTGGA
1 TCATCTGAAGATCAACT-TAGATC-TCTGAAAACTTCTAT-GAAAGACCGCACAGGG
* * * *
9880 TCATCTG-GGATCAACTTTA-ATCACTGAAAACTTCT-TGAAATGACCGCACTGGA
1 TCATCTGAAGATCAAC-TTAGATCTCTGAAAACTTCTATGAAA-GACCGCACAGGG
* * * ** *
9933 TCATCTG-GGATTCAACTCT-GATCAT-TGAAAACTTCTTTGGAATGACCGCATTGGA
1 TCATCTGAAGA-TCAACT-TAGATC-TCTGAAAACTTCTAT-GAAAGACCGCACAGGG
* * * * *
9988 TCATCT-AGGGATCAACTCT-GATCT-TCAAAAACTTCT-TAGAATGACCGCACTGGA
1 TCATCTGA-AGATCAACT-TAGATCTCT-GAAAACTTCTAT-GAAAGACCGCACAGGG
* * * * *
10042 TCATCT-AGGAATCAACTCT-GATCTCTAAAAACTTCT-TGGAATGACTGCAC-TGG
1 TCATCTGAAG-ATCAACT-TAGATCTCTGAAAACTTCTAT-GAAAGACCGCACAGGG
* * *** * * * * *
10095 TCATCAG-GGATCAACTCTA-ATCAAAGAAAACGTCT-TGGAATGACCACACTGGA
1 TCATCTGAAGATCAACT-TAGATCTCTGAAAACTTCTAT-GAAAGACCGCACAGGG
* * * * * *
10148 TCATCT-AGGATCAACTCT-GATCACGGAAAACTTCT-TGAAATGATCGTACTA-GA
1 TCATCTGAAGATCAACT-TAGATCTCTGAAAACTTCTATGAAA-GACCGCAC-AGGG
* * ** * * * *
10201 TTATTTGGGGATCAACTCT-GATCAT-TGAAAAATTCT-TGAAATGATCGCACTGGA
1 TCATCTGAAGATCAACT-TAGATC-TCTGAAAACTTCTATGAAA-GACCGCACAGGG
* * * * ***
10255 TCATCTCAAGATCAACTCT-GATATCTAAAAACTTCTACGAAAGATAACATC-GGG
1 TCATCTGAAGATCAACT-TAGATCTCTGAAAACTTCTATGAAAGACCGCA-CAGGG
* * *
10309 TCATCTGAAGATC-ACTTAGATTTCTGAAAGCTT-TATGAAAGACCGCACATGG
1 TCATCTGAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * *
10361 TCATCAT-AAAATCAACTTAGATCTCTGAAAAATTCTATGAAAGACCACACAGGG
1 TCATC-TGAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * * * *
10415 TCATCTGAAGATGAACTTAAACCTCGGAAAACTTCTATGAAAGACCGCATAGGG
1 TCATCTGAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * * * *
10469 TTATCTGAAGATCAACTTAAACCTCCGAAAACTTCTATGAAAGACCGCATAGGG
1 TCATCTGAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* *
10523 CCATCTAAAGATCAACTT-GAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
1 TCATCTGAAGATCAACTTAG-ATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* *
10577 TCATTTGAACATCAACTTAGATCTCTGAAAACTT
1 TCATCTGAAGATCAACTTAGATCTCTGAAAACTT
10611 TAAAAGATCG
Statistics
Matches: 1001, Mismatches: 151, Indels: 130
0.78 0.12 0.10
Matches are distributed among these distances:
51 1 0.00
52 62 0.06
53 174 0.17
54 660 0.66
55 98 0.10
56 6 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (54 bp):
TCATCTGAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
Found at i:13606 original size:36 final size:36
Alignment explanation
Indices: 13565--13653 Score: 153
Period size: 36 Copynumber: 2.5 Consensus size: 36
13555 TGACAATGAT
*
13565 AATGCATGGTGGATGCATATATACTAA-TGAATGACA
1 AATGCATGATGGATGCATATATAC-AAGTGAATGACA
13601 AATGCATGATGGATGCATATATACAAGTGAATGACA
1 AATGCATGATGGATGCATATATACAAGTGAATGACA
13637 AATGCATGATGGATGCA
1 AATGCATGATGGATGCA
13654 ATGTGTGAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
35 2 0.04
36 49 0.96
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (36 bp):
AATGCATGATGGATGCATATATACAAGTGAATGACA
Found at i:14767 original size:62 final size:62
Alignment explanation
Indices: 14670--14803 Score: 268
Period size: 62 Copynumber: 2.2 Consensus size: 62
14660 ATTCCCCAGT
14670 GGAGTCGCCAAGCTGTCGTAACGTGCGGGTCCGCGAACCCTATCGCTCCGACTTAAACAACA
1 GGAGTCGCCAAGCTGTCGTAACGTGCGGGTCCGCGAACCCTATCGCTCCGACTTAAACAACA
14732 GGAGTCGCCAAGCTGTCGTAACGTGCGGGTCCGCGAACCCTATCGCTCCGACTTAAACAACA
1 GGAGTCGCCAAGCTGTCGTAACGTGCGGGTCCGCGAACCCTATCGCTCCGACTTAAACAACA
14794 GGAGTCGCCA
1 GGAGTCGCCA
14804 CTAACCAATT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.17
Consensus pattern (62 bp):
GGAGTCGCCAAGCTGTCGTAACGTGCGGGTCCGCGAACCCTATCGCTCCGACTTAAACAACA
Found at i:15455 original size:21 final size:21
Alignment explanation
Indices: 15431--15472 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15421 TAACTAATCC
15431 TAAATAAAAACTAATTAAAAT
1 TAAATAAAAACTAATTAAAAT
* **
15452 TAAATTAACTCTAATTAAAAT
1 TAAATAAAAACTAATTAAAAT
15473 AGAAATATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATAAAAACTAATTAAAAT
Found at i:27089 original size:7 final size:7
Alignment explanation
Indices: 27077--27138 Score: 67
Period size: 7 Copynumber: 9.1 Consensus size: 7
27067 GGAAAGGTTA
27077 GGGTTTT
1 GGGTTTT
27084 GGGTTTT
1 GGGTTTT
* *
27091 AGG--TA
1 GGGTTTT
27096 GGG-TTT
1 GGGTTTT
27102 GGCGTTTT
1 GG-GTTTT
27110 GGGTTTT
1 GGGTTTT
*
27117 GGATTTT
1 GGGTTTT
27124 GGGTTTT
1 GGGTTTT
27131 GGGTTTT
1 GGGTTTT
27138 G
1 G
27139 CCATTTTGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
5 3 0.07
6 3 0.07
7 35 0.76
8 5 0.11
ACGTcount: A:0.05, C:0.02, G:0.42, T:0.52
Consensus pattern (7 bp):
GGGTTTT
Found at i:27130 original size:21 final size:22
Alignment explanation
Indices: 27099--27152 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
27089 TTAGGTAGGG
*
27099 TTTGGCGTTTTGGGTTTTG-GAT
1 TTTGG-GTTTTGGGTTTTGCCAT
27121 TTTGGGTTTTGGGTTTTGCCAT
1 TTTGGGTTTTGGGTTTTGCCAT
*
27143 TTTGGATTTT
1 TTTGGGTTTT
27153 AACGGAGGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.06, C:0.06, G:0.31, T:0.57
Consensus pattern (22 bp):
TTTGGGTTTTGGGTTTTGCCAT
Found at i:29243 original size:69 final size:69
Alignment explanation
Indices: 28828--29243 Score: 579
Period size: 69 Copynumber: 6.0 Consensus size: 69
28818 GGACTCTGAT
* * *
28828 TCACCAATAGCA-TAAGGATTGTTTCTATCTTCTACTAGTTCTACTGTATCAAACTCATCATCCT
1 TCACCAATAGCATTAA-GATTATTTCTATCTTCTCCTAGTTCTACCGTATCAAACTCATCATCCT
28892 GGTCA
65 GGTCA
* * *
28897 T-AGCCAATAGCATTAAGATTGA-TTGTATCTTCTCCTTGTTC-AACGATATCAAACTCATCATC
1 TCA-CCAATAGCATTAAGATT-ATTTCTATCTTCTCCTAGTTCTACCG-TATCAAACTCATCATC
28959 CTGGTCA
63 CTGGTCA
* * * *
28966 TCGCCAATAGCATTAAGATTATTTCTATCTTCTCCTTGTTCGACGGTATCAAACTCATCATCCTG
1 TCACCAATAGCATTAAGATTATTTCTATCTTCTCCTAGTTCTACCGTATCAAACTCATCATCCTG
29031 GTCA
66 GTCA
* * * *
29035 TCGCCAATAGCATAAAGATTATTTCTATCTGCTCCTAGTTCTACTGTATCAAACTCATCATCCTG
1 TCACCAATAGCATTAAGATTATTTCTATCTTCTCCTAGTTCTACCGTATCAAACTCATCATCCTG
29100 GTCA
66 GTCA
* * **
29104 TCACCAATACCATAAAGATTATTTCTATCTTCTCCTAGTTCTATGGTATCAAACTCATCATCCTG
1 TCACCAATAGCATTAAGATTATTTCTATCTTCTCCTAGTTCTACCGTATCAAACTCATCATCCTG
*
29169 ATCA
66 GTCA
* *
29173 TCACCAATAGCATTAAGATTGTTTCTATCTTCTCCTAGTCCTACCGTATCAAACTCATCATCCTG
1 TCACCAATAGCATTAAGATTATTTCTATCTTCTCCTAGTTCTACCGTATCAAACTCATCATCCTG
29238 GTCA
66 GTCA
29242 TC
1 TC
29244 GAATTCATCA
Statistics
Matches: 312, Mismatches: 28, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
68 4 0.01
69 303 0.97
70 5 0.02
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.36
Consensus pattern (69 bp):
TCACCAATAGCATTAAGATTATTTCTATCTTCTCCTAGTTCTACCGTATCAAACTCATCATCCTG
GTCA
Found at i:31054 original size:36 final size:37
Alignment explanation
Indices: 31007--31078 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 37
30997 GCCCAACACT
31007 AGACTAGTAGCCTTCTCTATCGCCAAAAA-AAAAAAG
1 AGACTAGTAGCCTTCTCTATCGCCAAAAAGAAAAAAG
31043 AGACTAGTAGCCTTCTCTATCGCCAAAAAGAAAAAA
1 AGACTAGTAGCCTTCTCTATCGCCAAAAAGAAAAAA
31079 AAAAGAGACT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 29 0.83
37 6 0.17
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.19
Consensus pattern (37 bp):
AGACTAGTAGCCTTCTCTATCGCCAAAAAGAAAAAAG
Found at i:32774 original size:2 final size:2
Alignment explanation
Indices: 32767--32793 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32757 TCTTAATTAG
32767 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 A
32794 AAGAAACTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35857 original size:2 final size:2
Alignment explanation
Indices: 35850--35877 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35840 CATGATAATG
35850 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
35878 TTGTAACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37810 original size:39 final size:39
Alignment explanation
Indices: 37750--37826 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
37740 CTTGACCCTT
*
37750 CTAATAATTAAGGAAATAAATTAAATCCAGATTTAGCCC
1 CTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCC
* *
37789 CTAATAATTAA-GATAAGAAATTAAATTCAGGTTTAGCC
1 CTAATAATTAAGGA-AAGAAATTAAATCCAGATTTAGCC
37827 TCTAGTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.06
39 32 0.94
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (39 bp):
CTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCC
Found at i:41297 original size:25 final size:25
Alignment explanation
Indices: 41269--41338 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
41259 CACTGCTAGG
*
41269 AGCTCGCTGCCAGGATGCTCGTTGA
1 AGCTCGCTGCCAGGAAGCTCGTTGA
* *
41294 AGCTCGCTGCTAGGAAGCTTGTTGA
1 AGCTCGCTGCCAGGAAGCTCGTTGA
* *
41319 AACTCGCTG-CTGGAAGCTCG
1 AGCTCGCTGCCAGGAAGCTCG
41339 CTGGCGTTCG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 8 0.21
25 30 0.79
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.24
Consensus pattern (25 bp):
AGCTCGCTGCCAGGAAGCTCGTTGA
Found at i:47188 original size:2 final size:2
Alignment explanation
Indices: 47181--47216 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
47171 CAATCTACTA
47181 AT 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 AT
47217 TGTGATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.