Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013277.1 Corchorus olitorius cultivar O-4 contig13310, 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: 42565
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:4427 original size:30 final size:30
Alignment explanation
Indices: 4391--4450 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4381 TGGAATTGCT
* * *
4391 AATCTAAACTAAGATTATGACTAAGATGAC
1 AATCTAAACTAAAAGTATAACTAAGATGAC
4421 AATCTAAACTAAAAGTATAACTAAGATGAC
1 AATCTAAACTAAAAGTATAACTAAGATGAC
4451 CAAAGAGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (30 bp):
AATCTAAACTAAAAGTATAACTAAGATGAC
Found at i:4567 original size:30 final size:29
Alignment explanation
Indices: 4467--4607 Score: 158
Period size: 29 Copynumber: 4.8 Consensus size: 29
4457 GAACCCAGAG
* * *
4467 TATGCAAAAATGACCAAAATGCCCCTGGA
1 TATGCAAAAATTACCATAATGCCCCTAGA
* * ** * *
4496 CATACAAAGGTGACCGA-AATGCCCCCAGA
1 TATGCAAAAATTACC-ATAATGCCCCTAGA
4525 TATGCAAAAATTACCATAATGCCCCTAGA
1 TATGCAAAAATTACCATAATGCCCCTAGA
*
4554 TATGCAGAAAATTATCATAATGCCCCTAGA
1 TATGCA-AAAATTACCATAATGCCCCTAGA
*
4584 TATGCAAAAATGACCATAATGCCC
1 TATGCAAAAATTACCATAATGCCC
4608 TTGGATTTGC
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.01
29 64 0.68
30 29 0.31
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (29 bp):
TATGCAAAAATTACCATAATGCCCCTAGA
Found at i:5572 original size:2 final size:2
Alignment explanation
Indices: 5565--5730 Score: 225
Period size: 2 Copynumber: 83.0 Consensus size: 2
5555 CTCTCAATTA
5565 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
* *
5607 CGT AT GT GT GT GT GT AGT GT GT GT GT GT CGT NT GT GT GT GT GT
1 -GT GT GT GT GT GT GT -GT GT GT GT GT GT -GT GT GT GT GT GT GT
*
5650 GT GT GT GT GT GT -T GT -T GT GT -T GT -T GN GT GT GT CGT GT -T
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT -GT GT GT
5688 AGT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 -GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
5731 CTAGGGCAGA
Statistics
Matches: 148, Mismatches: 6, Indels: 20
0.85 0.03 0.11
Matches are distributed among these distances:
1 5 0.03
2 134 0.91
3 9 0.06
ACGTcount: A:0.02, C:0.02, G:0.46, T:0.49
Consensus pattern (2 bp):
GT
Found at i:10231 original size:29 final size:29
Alignment explanation
Indices: 10146--10233 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
10136 CAAAGCTTTG
*
10146 ACACGAGTGCA-AACCTACACTCAAAACAA
1 ACACAAGTGCACAACCTACACT-AAAACAA
* * * * **
10175 TCCCAAGTGTACAACCCACACTTGAACAA
1 ACACAAGTGCACAACCTACACTAAAACAA
*
10204 ACACAAGTGCACAACCTGCACTAAAACAA
1 ACACAAGTGCACAACCTACACTAAAACAA
10233 A
1 A
10234 ATCAGAAAAA
Statistics
Matches: 44, Mismatches: 14, Indels: 2
0.73 0.23 0.03
Matches are distributed among these distances:
29 35 0.80
30 9 0.20
ACGTcount: A:0.45, C:0.32, G:0.10, T:0.12
Consensus pattern (29 bp):
ACACAAGTGCACAACCTACACTAAAACAA
Found at i:10635 original size:8 final size:7
Alignment explanation
Indices: 10605--10685 Score: 50
Period size: 6 Copynumber: 12.3 Consensus size: 7
10595 AAATTATTAA
10605 AATAAAT
1 AATAAAT
*
10612 AAAAAAT
1 AATAAAT
10619 AAT-AAT
1 AATAAAT
10625 AGATAAAT
1 A-ATAAAT
*
10633 -AGAAA-
1 AATAAAT
*
10638 AATAAGT
1 AATAAAT
**
10645 TTTAAA-
1 AATAAAT
10651 AAT-AAT
1 AATAAAT
10657 AAT-AAT
1 AATAAAT
10663 AAT-AAT
1 AATAAAT
10669 AATAAAT
1 AATAAAT
10676 AAATAAAT
1 -AATAAAT
10684 AA
1 AA
10686 AAGATAAATA
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
5 2 0.04
6 27 0.47
7 18 0.32
8 10 0.18
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (7 bp):
AATAAAT
Found at i:10716 original size:8 final size:8
Alignment explanation
Indices: 10669--10839 Score: 81
Period size: 8 Copynumber: 21.6 Consensus size: 8
10659 TAATAATAAT
*
10669 AATAAATA
1 AATAGATA
*
10677 AATAAATA
1 AATAGATA
10685 AA-AGATA
1 AATAGATA
*
10692 AATAGGTA
1 AATAGATA
* *
10700 TAGAGATA
1 AATAGATA
10708 AATAGATA
1 AATAGATA
*
10716 AATAGGTA
1 AATAGATA
* *
10724 CAGAGATA
1 AATAGATA
*
10732 AAAAGATAA
1 AATAGAT-A
10741 ATAGGTAGATA
1 A-A--TAGATA
*
10752 AA-AGAGA
1 AATAGATA
10759 AA-A-A-A
1 AATAGATA
*
10764 AAAAGATAA
1 AATAGAT-A
*
10773 TAATAAATA
1 -AATAGATA
10782 AATAGAT-
1 AATAGATA
*
10789 AATAGCTA
1 AATAGATA
10797 AACTA-ATA
1 AA-TAGATA
*
10805 AAAAGATA
1 AATAGATA
10813 AATAG-TA
1 AATAGATA
*
10820 AATAAAT-
1 AATAGATA
10827 AATAGATA
1 AATAGATA
10835 AATAG
1 AATAG
10840 CTATAAAAAA
Statistics
Matches: 124, Mismatches: 24, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
5 3 0.02
6 2 0.02
7 33 0.27
8 67 0.54
9 6 0.05
10 7 0.06
11 2 0.02
12 4 0.03
ACGTcount: A:0.64, C:0.02, G:0.13, T:0.21
Consensus pattern (8 bp):
AATAGATA
Found at i:10718 original size:24 final size:23
Alignment explanation
Indices: 10682--10747 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 23
10672 AAATAAATAA
*
10682 ATAAAAGATAAATAGGTATAGAG
1 ATAAAAGATAAATAGGTACAGAG
10705 ATAAATAGATAAATAGGTACAGAG
1 ATAAA-AGATAAATAGGTACAGAG
10729 ATAAAAAGATAAATAGGTA
1 AT-AAAAGATAAATAGGTA
10748 GATAAAAGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
23 5 0.12
24 32 0.80
25 3 0.08
ACGTcount: A:0.58, C:0.02, G:0.20, T:0.21
Consensus pattern (23 bp):
ATAAAAGATAAATAGGTACAGAG
Found at i:10788 original size:38 final size:41
Alignment explanation
Indices: 10727--10827 Score: 100
Period size: 38 Copynumber: 2.5 Consensus size: 41
10717 ATAGGTACAG
* **
10727 AGATAAAAAGATAAATAGGTAGATAAAAGAGAAA-AA-AAAA
1 AGATAAATA-ATAAATAAATAGATAAAAGAGAAACAATAAAA
* **
10767 AGAT-AATAATAAATAAATAGATAATAGCTAAACTAATAAAA
1 AGATAAATAATAAATAAATAGATAAAAGAGAAAC-AATAAAA
*
10808 AGATAAATAGTAAATAAATA
1 AGATAAATAATAAATAAATA
10828 ATAGATAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
38 19 0.38
39 3 0.06
40 6 0.12
41 8 0.16
42 14 0.28
ACGTcount: A:0.66, C:0.02, G:0.12, T:0.20
Consensus pattern (41 bp):
AGATAAATAATAAATAAATAGATAAAAGAGAAACAATAAAA
Found at i:10811 original size:23 final size:23
Alignment explanation
Indices: 10778--10842 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
10768 GATAATAATA
10778 AATAAATAGAT-AATAGCTAAACT
1 AATAAATAGATAAATAGCTAAA-T
*
10801 AATAAAAAGATAAATAG-TAAAT
1 AATAAATAGATAAATAGCTAAAT
10823 AA-ATAATAGATAAATAGCTA
1 AATA-AATAGATAAATAGCTA
10843 TAAAAAAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
21 1 0.03
22 15 0.41
23 16 0.43
24 5 0.14
ACGTcount: A:0.62, C:0.05, G:0.09, T:0.25
Consensus pattern (23 bp):
AATAAATAGATAAATAGCTAAAT
Found at i:12221 original size:54 final size:54
Alignment explanation
Indices: 12158--12894 Score: 754
Period size: 54 Copynumber: 13.7 Consensus size: 54
12148 TGGATCAAAA
* * **
12158 TGGAGATCAACTCTGATCATCGAAAACTTCTTAAAATGACAGCACCCGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* *
12212 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAACGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * *
12266 TAGAGATCAAATCTGATCATCGAAAACTTCTTAAAATGACCGCACCGGATCATT
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * *
12320 TGGAGATCAACTCTAATCTTCGAAAACTTCTTGAAACGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * * *
12374 TAGAGATCAACTCTGATCTTCGAAAACTTCTTGGAAGGACTGCACTGGATCATT
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * *
12428 TGGAGATCAACTCTGATCATTGAAAACTTTTTGGAATGACCACACTGGATCATA
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
*
12482 TGG-GATCAACTCTGATCA-CTGAAAACTTCTTGAAATGACCGCACTAGATCATC
1 TGGAGATCAACTCTGATCATC-GAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * ** * *
12535 TGGGGATCAACTCTAATCATTGAAAGCTT-TATGAAA-GATTGCACTAGATCATT
1 TGGAGATCAACTCTGATCATCGAAAACTTCT-TGAAATGACCGCACTGGATCATC
* * * * *
12588 TGGGGATCAACTCTGATCATTGAAAACTTCTTTGGAATGACCGCACTGGGTCATG
1 TGGAGATCAACTCTGATCATCGAAAACTTC-TTGAAATGACCGCACTGGATCATC
* * ** * *
12643 TAGG-GATCAACCCTGATCTTTAAAAACTTCTTGGAATGACCGCACTGGGTCATC
1 T-GGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
** * ** * *
12697 CAG-GATCAACTCTAATCAAAGAAAACTTATTGGAATGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * ** * *
12750 TGGGGATCAACTCTGATCA-CTGAAAACTTCTTGGAATGATTGCACTAGATCATT
1 TGGAGATCAACTCTGATCATC-GAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * * *
12804 TGGGGCTCAACTCTGATCATTGAAAACTTCTTGAAATGATCGCACTTGATCATT
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
*
12858 TAGG-GATCAACTCTGATC-TCTAAAAACTTCTATGAAA
1 T-GGAGATCAACTCTGATCATC-GAAAACTTCT-TGAAA
12895 GATAAAACCG
Statistics
Matches: 583, Mismatches: 86, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
53 133 0.23
54 404 0.69
55 44 0.08
56 2 0.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (54 bp):
TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
Found at i:12922 original size:108 final size:105
Alignment explanation
Indices: 12161--13171 Score: 717
Period size: 108 Copynumber: 9.4 Consensus size: 105
12151 ATCAAAATGG
* * * **
12161 AGATCAACTCTGATCATCGAAAACTTCTTAAAATGACAGCACCCGATCATCTGGAGATCAACTCT
1 AGATCAACTCTGATCATTGAAAACTTCTTGAAATGACCGCACTGGATCATCTGG-GATCAACTCT
12226 GATCTTCGAAAACTTCTTGAAACGACCGCACTGGATCATCT-A
65 GATCTT-GAAAACTTCTTGAAA-GACCGCACTGGATCATCTGA
* * * * *
12268 GAGATCAAATCTGATCATCGAAAACTTCTTAAAATGACCGCACCGGATCATTTGGAGATCAACTC
1 -AGATCAACTCTGATCATTGAAAACTTCTTGAAATGACCGCACTGGATCATCTGG-GATCAACTC
*
12333 TAATCTTCGAAAACTTCTTGAAACGACCGCACTGGATCATCT-A
64 TGATCTT-GAAAACTTCTTGAAA-GACCGCACTGGATCATCTGA
* * * *
12376 GAGATCAACTCTGATC-TTCGAAAACTTCTTGGAAGGACTGCACTGGATCATTTGGAGATCAACT
1 -AGATCAACTCTGATCATT-GAAAACTTCTTGAAATGACCGCACTGGATCATCTGG-GATCAACT
* * * *
12440 CTGATCATTGAAAACTTTTTGGAATGACCACACTGGATCATATG-
63 CTGATC-TTGAAAACTTCTT-GAAAGACCGCACTGGATCATCTGA
* * *
12484 GGATCAACTCTGATCACTGAAAACTTCTTGAAATGACCGCACTAGATCATCTGGGGATCAACTCT
1 AGATCAACTCTGATCATTGAAAACTTCTTGAAATGACCGCACTGGATCATCT-GGGATCAACTCT
* * ** * * *
12549 AATCATTGAAAGCTT-TATGAAAGATTGCACTAGATCATTTGG
65 GATC-TTGAAAACTTCT-TGAAAGACCGCACTGGATCATCTGA
* * * * *
12591 GGATCAACTCTGATCATTGAAAACTTCTTTGGAATGACCGCACTGGGTCATGTAGGGATCAACCC
1 AGATCAACTCTGATCATTGAAAACTTC-TTGAAATGACCGCACTGGATCATCT-GGGATCAACTC
* * * *
12656 TGATCTTTAAAAACTTCTTGGAATGACCGCACTGGGTCATC-CA
64 TGATC-TTGAAAACTTCTT-GAAAGACCGCACTGGATCATCTGA
* * ** * *
12699 GGATCAACTCTAATCAAAGAAAACTTATTGGAATGACCGCACTGGATCATCTGGGGATCAACTCT
1 AGATCAACTCTGATCATTGAAAACTTCTTGAAATGACCGCACTGGATCATCT-GGGATCAACTCT
* * ** * * *
12764 GATCACTGAAAACTTCTTGGAATGATTGCACTAGATCATTTGG
65 GATC-TTGAAAACTTCTT-GAAAGACCGCACTGGATCATCTGA
* * * * *
12807 GGCTCAACTCTGATCATTGAAAACTTCTTGAAATGATCGCACTTGATCATTTAGGGATCAACTCT
1 AGATCAACTCTGATCATTGAAAACTTCTTGAAATGACCGCACTGGATCATCT-GGGATCAACTCT
* **** *
12872 GATCTCTAAAAACTTCTATGAAAGATAAAACCGGATCATCTGA
65 GATCT-TGAAAACTTCT-TGAAAGACCGCACTGGATCATCTGA
* * * * *** *
12915 AGATCAACT-TAGAT-TTCTGAAAGCTT-TATGAAA-GACCGCACAGGGTCATCATAAAATCGAC
1 AGATCAACTCT-GATCAT-TGAAAACTTCT-TGAAATGACCGCACTGGATCATC-TGGGATCAAC
* * *
12976 T-TAGATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTTATCTGA
62 TCT-GATCT-TGAAAACTTCT-TGAAAGACCGCACTGGATCATCTGA
* * * * * * * **
13022 AGGTCAACT-TAAACCTCTGAAAACTTCTATGAAA-GACCACACAGGGTCATCTAAAGATCAACT
1 AGATCAACTCTGATCAT-TGAAAACTTCT-TGAAATGACCGCACTGGATCATCT-GGGATCAACT
* * * *
13085 -TAAATCTCTGAAAGCTTCTATGAAAGA-C-CACGTAGGGTTATCTGA
63 CT-GATCT-TGAAAACTTCT-TGAAAGACCGCAC-T-GGATCATCTGA
* * *
13130 AGATCAACT-TAAACCTCTGAAAACTTCTATGAAA-GACCGCAC
1 AGATCAACTCTGATCAT-TGAAAACTTCT-TGAAATGACCGCAC
13172 AGGGCCATGA
Statistics
Matches: 756, Mismatches: 123, Indels: 48
0.82 0.13 0.05
Matches are distributed among these distances:
106 23 0.03
107 237 0.31
108 474 0.63
109 22 0.03
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (105 bp):
AGATCAACTCTGATCATTGAAAACTTCTTGAAATGACCGCACTGGATCATCTGGGATCAACTCTG
ATCTTGAAAACTTCTTGAAAGACCGCACTGGATCATCTGA
Found at i:13014 original size:54 final size:54
Alignment explanation
Indices: 12862--13207 Score: 389
Period size: 54 Copynumber: 6.5 Consensus size: 54
12852 ATCATTTAGG
* ** * * *
12862 GATCAACTCT-GATCTCTAAAAACTTCTATGAAAGATAAAACCGGATCATCTGAA
1 GATCAACT-TAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTCATCTGAA
* * *
12916 GATCAACTTAGATTTCTGAAAGCTT-TATGAAAGACCGCACAGGGTCATCAT-AA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTCATC-TGAA
* * * *
12969 AATCGACTTAGATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTTATCTGAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTCATCTGAA
* * * *
13023 GGTCAACTTAAACCTCTGAAAACTTCTATGAAAGACCACACAGGGTCATCTAAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTCATCTGAA
* * ** *
13077 GATCAACTTAAATCTCTGAAAGCTTCTATGAAAGACCACGTAGGGTTATCTGAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTCATCTGAA
* * * *
13131 GATCAACTTAAACCTCTGAAAACTTCTATGAAAGACCGCACAGGGCCA--TGAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTCATCTGAA
13183 CG-TCAACTTAGATCTCTGAAAACTT
1 -GATCAACTTAGATCTCTGAAAACTT
13208 TAAAAGATCG
Statistics
Matches: 249, Mismatches: 38, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
52 25 0.10
53 44 0.18
54 180 0.72
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.25
Consensus pattern (54 bp):
GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTCATCTGAA
Found at i:13173 original size:108 final size:108
Alignment explanation
Indices: 12862--13207 Score: 441
Period size: 108 Copynumber: 3.2 Consensus size: 108
12852 ATCATTTAGG
* ** * * * *
12862 GATCAACTCT-GATCTCTAAAAACTTCTATGAAAGATAAAACCGGATCATCTGAAGATCAACTTA
1 GATCAACT-TAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTTATCTGAAGATCAACTTA
* ** *
12926 GATTTCTGAAAGCTT-TATGAAAGACCGCACAGGGTCATCATAAA
65 AACCTCTGAAAACTTCTATGAAAGACCGCACAGGGTCATC-TAAA
* * *
12970 -ATCGACTTAGATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTTATCTGAAGGTCAACTTAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTTATCTGAAGATCAACTTAA
*
13034 ACCTCTGAAAACTTCTATGAAAGACCACACAGGGTCATCTAAA
66 ACCTCTGAAAACTTCTATGAAAGACCGCACAGGGTCATCTAAA
* * **
13077 GATCAACTTAAATCTCTGAAAGCTTCTATGAAAGACCACGTAGGGTTATCTGAAGATCAACTTAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTTATCTGAAGATCAACTTAA
* * *
13142 ACCTCTGAAAACTTCTATGAAAGACCGCACAGGGCCAT-GAAC
66 ACCTCTGAAAACTTCTATGAAAGACCGCACAGGGTCATCTAAA
13184 G-TCAACTTAGATCTCTGAAAACTT
1 GATCAACTTAGATCTCTGAAAACTT
13208 TAAAAGATCG
Statistics
Matches: 207, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
106 22 0.11
107 69 0.33
108 116 0.56
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.25
Consensus pattern (108 bp):
GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTTATCTGAAGATCAACTTAA
ACCTCTGAAAACTTCTATGAAAGACCGCACAGGGTCATCTAAA
Found at i:14372 original size:39 final size:39
Alignment explanation
Indices: 14321--14399 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 39
14311 AATTTTTTTG
*
14321 AAAAACATTTTTCTTTTGAAAAGATTGA-ACTTTGAGGAA
1 AAAAACATTTTTCTTTTGAAAAGATT-ACACTTGGAGGAA
*
14360 AAAAACCTTTTTCTTTTGAAAAGATTACACTTGGAGGAA
1 AAAAACATTTTTCTTTTGAAAAGATTACACTTGGAGGAA
14399 A
1 A
14400 GTGAACTCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (39 bp):
AAAAACATTTTTCTTTTGAAAAGATTACACTTGGAGGAA
Found at i:14626 original size:26 final size:27
Alignment explanation
Indices: 14575--14641 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 27
14565 TCCCTTCCTC
*
14575 CATCTTTTGCATTTTCAACTTCTTTCTT
1 CATCTTTT-CTTTTTCAACTTCTTTCTT
*
14603 -TTCTTTTCTTTTTCAA-TTCTTTTCTT
1 CATCTTTTCTTTTTCAACTTC-TTTCTT
14629 CAT-TTTTCTTTTT
1 CATCTTTTCTTTTT
14642 TCTTTCCCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 3 0.09
26 24 0.71
27 7 0.21
ACGTcount: A:0.10, C:0.21, G:0.01, T:0.67
Consensus pattern (27 bp):
CATCTTTTCTTTTTCAACTTCTTTCTT
Found at i:15028 original size:14 final size:13
Alignment explanation
Indices: 14976--15030 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 13
14966 AAACCCTTGC
*
14976 GAAAACGATTTTTA
1 GAAAAC-ATTTTTT
14990 GAAAAC-TTTTTCT
1 GAAAACATTTTT-T
15003 GAAAACACTTTTTT
1 GAAAACA-TTTTTT
15017 GAAAAGCATTTTTT
1 GAAAA-CATTTTTT
15031 ACTTTTGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
12 5 0.14
13 6 0.17
14 18 0.50
15 7 0.19
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (13 bp):
GAAAACATTTTTT
Found at i:15248 original size:17 final size:17
Alignment explanation
Indices: 15226--15259 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
15216 TAATGATGAA
15226 TTTTGAGCATTTTAATC
1 TTTTGAGCATTTTAATC
15243 TTTTGAGCATTTTAATC
1 TTTTGAGCATTTTAATC
15260 CACCACTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (17 bp):
TTTTGAGCATTTTAATC
Found at i:17615 original size:21 final size:20
Alignment explanation
Indices: 17591--17636 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
17581 ACTTATTAAG
17591 AAAATTAATAAAATAAATAAA
1 AAAATTAAT-AAATAAATAAA
* *
17612 AAAAGTAATAAATAAATAGA
1 AAAATTAATAAATAAATAAA
17632 AAAAT
1 AAAAT
17637 AAGTTTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAATTAATAAATAAATAAA
Found at i:17624 original size:20 final size:22
Alignment explanation
Indices: 17591--17635 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
17581 ACTTATTAAG
*
17591 AAAATTAATAAAATAAATA-AA
1 AAAAGTAATAAAATAAATAGAA
17612 AAAAGTAAT-AAATAAATAGAA
1 AAAAGTAATAAAATAAATAGAA
17633 AAA
1 AAA
17636 TAAGTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (22 bp):
AAAAGTAATAAAATAAATAGAA
Found at i:17655 original size:3 final size:3
Alignment explanation
Indices: 17647--17687 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
17637 AAGTTTTAAC
17647 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17688 ATAAATAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17692 original size:4 final size:4
Alignment explanation
Indices: 17683--17721 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
17673 TAATAATAAT
* *
17683 AATA AATA AATA AATA AATA AACA AATA AA-A GATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
17722 GGTATAGAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 2 0.07
4 28 0.93
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:17742 original size:8 final size:8
Alignment explanation
Indices: 17680--17862 Score: 91
Period size: 8 Copynumber: 23.6 Consensus size: 8
17670 TAATAATAAT
17680 AATA-ATA
1 AATAGATA
*
17687 AATAAATA
1 AATAGATA
*
17695 AATAAATA
1 AATAGATA
* *
17703 AACAAATA
1 AATAGATA
17711 AA-AGATA
1 AATAGATA
*
17718 AATAGGTA
1 AATAGATA
* *
17726 TAGAGATA
1 AATAGATA
17734 AATAGATA
1 AATAGATA
*
17742 AATAGGTA
1 AATAGATA
* *
17750 CAGAGATA
1 AATAGATA
17758 AATAGATA
1 AATAGATA
17766 AATAGGTAGGTA
1 AATA-G-A--TA
*
17778 AA-AGAGA
1 AATAGATA
*
17785 AA-A-AAA
1 AATAGATA
17791 AATA-AT-
1 AATAGATA
*
17797 AATAAATA
1 AATAGATA
17805 AATAGAT-
1 AATAGATA
*
17812 AATAGCTA
1 AATAGATA
17820 AACTA-ATA
1 AA-TAGATA
*
17828 AAAAGATA
1 AATAGATA
17836 AATAG-TA
1 AATAGATA
*
17843 AATAAAT-
1 AATAGATA
*
17850 AATTGATA
1 AATAGATA
17858 AATAG
1 AATAG
17863 CTATAAAATA
Statistics
Matches: 136, Mismatches: 26, Indels: 27
0.72 0.14 0.14
Matches are distributed among these distances:
6 8 0.06
7 36 0.26
8 81 0.60
9 4 0.03
10 2 0.01
11 1 0.01
12 4 0.03
ACGTcount: A:0.63, C:0.02, G:0.13, T:0.22
Consensus pattern (8 bp):
AATAGATA
Found at i:17745 original size:24 final size:24
Alignment explanation
Indices: 17708--17773 Score: 116
Period size: 24 Copynumber: 2.8 Consensus size: 24
17698 AAATAAACAA
*
17708 ATAAA-AGATAAATAGGTATAGAG
1 ATAAATAGATAAATAGGTACAGAG
17731 ATAAATAGATAAATAGGTACAGAG
1 ATAAATAGATAAATAGGTACAGAG
17755 ATAAATAGATAAATAGGTA
1 ATAAATAGATAAATAGGTA
17774 GGTAAAAGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 5 0.12
24 36 0.88
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.23
Consensus pattern (24 bp):
ATAAATAGATAAATAGGTACAGAG
Found at i:17815 original size:15 final size:14
Alignment explanation
Indices: 17790--17851 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
17780 AGAGAAAAAA
17790 AAATAATAATAAAT
1 AAATAATAATAAAT
**
17804 AAATAGATAATAGCT
1 AAATA-ATAATAAAT
*
17819 AAACTAATAAAAAGAT
1 AAA-TAATAATAA-AT
*
17835 AAATAGTAAATAAAT
1 AAATAAT-AATAAAT
17850 AA
1 AA
17852 TTGATAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
14 5 0.14
15 22 0.59
16 10 0.27
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.24
Consensus pattern (14 bp):
AAATAATAATAAAT
Found at i:17827 original size:23 final size:23
Alignment explanation
Indices: 17801--17873 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
17791 AATAATAATA
17801 AATAAATAGAT-AATAGCTAAACT
1 AATAAATAGATAAATAGCTAAA-T
*
17824 AATAAAAAGATAAATAG-TAAAT
1 AATAAATAGATAAATAGCTAAAT
*
17846 AA-ATAATTGATAAATAGCTATAA-
1 AATA-AATAGATAAATAGCTA-AAT
17869 AATAA
1 AATAA
17874 TCTATTTGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
21 1 0.02
22 14 0.33
23 19 0.45
24 8 0.19
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.26
Consensus pattern (23 bp):
AATAAATAGATAAATAGCTAAAT
Found at i:20593 original size:1 final size:1
Alignment explanation
Indices: 20584--20614 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
20574 AACCAAATCG
*
20584 AAAACAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20615 GTAACAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21236 original size:6 final size:6
Alignment explanation
Indices: 21214--21263 Score: 68
Period size: 6 Copynumber: 8.3 Consensus size: 6
21204 AGGGCTTAGG
21214 AAGGAA GAA-GAA GAAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AA-GAA
1 AAGGAA -AAGGAA -AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA
21262 AA
1 AA
21264 TAGATGGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.12
6 32 0.76
7 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAGGAA
Found at i:25541 original size:3 final size:3
Alignment explanation
Indices: 25535--25590 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
25525 AGAAAAAAAA
* *
25535 AAC AAC AAC AAC AAC AAC GAC AAC AAC AA- AAC AAAC AA- AA- AAA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC -AAC AAC AAC AAC
25578 AAC AAC AA- AAC AA
1 AAC AAC AAC AAC AA
25591 AAGAGAGTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
2 8 0.17
3 35 0.76
4 3 0.07
ACGTcount: A:0.73, C:0.25, G:0.02, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:25581 original size:14 final size:14
Alignment explanation
Indices: 25527--25592 Score: 64
Period size: 15 Copynumber: 4.6 Consensus size: 14
25517 AAAAAGAAAG
*
25527 AAAAAAAAAACAAC
1 AAAACAAAAACAAC
* *
25541 AACAACAACAACGAC
1 AA-AACAAAAACAAC
25556 AACAAC-AAAACAAAC
1 AA-AACAAAAAC-AAC
25571 AAAA-AAAAACAAC
1 AAAACAAAAACAAC
25584 AAAACAAAA
1 AAAACAAAA
25593 GAGAGTGGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
13 7 0.16
14 17 0.40
15 19 0.44
ACGTcount: A:0.77, C:0.21, G:0.02, T:0.00
Consensus pattern (14 bp):
AAAACAAAAACAAC
Found at i:28561 original size:30 final size:27
Alignment explanation
Indices: 28488--28549 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
28478 AAATAGATTT
* * *
28488 TCAGAATTGATTCGGAAGACGATCTCA
1 TCAGAAATGGTTCAGAAGACGATCTCA
*
28515 TCGGAAATGGTTCAGAAGACGATCTCA
1 TCAGAAATGGTTCAGAAGACGATCTCA
28542 TCAGAAAT
1 TCAGAAAT
28550 AGATTTTCAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (27 bp):
TCAGAAATGGTTCAGAAGACGATCTCA
Found at i:28585 original size:68 final size:68
Alignment explanation
Indices: 28476--28617 Score: 239
Period size: 68 Copynumber: 2.1 Consensus size: 68
28466 ATAGTTATTT
* * *
28476 AGAAATAGATTTTCAGAATTGATTCGGAAGACGATCTCATCGGAAATGGTTCAGAAGACGATCTC
1 AGAAATAGATTTTCAGAAATGATTCGGAAAACGATCTCATCGGAAATAGTTCAGAAGACGATCTC
28541 ATC
66 ATC
* *
28544 AGAAATAGATTTTCAGAAATGGTTCGGAAAACGATCTCATCGGAAATAGTTCGGAAGACGATCTC
1 AGAAATAGATTTTCAGAAATGATTCGGAAAACGATCTCATCGGAAATAGTTCAGAAGACGATCTC
28609 ATC
66 ATC
28612 AGAAAT
1 AGAAAT
28618 GGTTCGGAAG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.25
Consensus pattern (68 bp):
AGAAATAGATTTTCAGAAATGATTCGGAAAACGATCTCATCGGAAATAGTTCAGAAGACGATCTC
ATC
Found at i:28595 original size:27 final size:27
Alignment explanation
Indices: 28556--28768 Score: 338
Period size: 27 Copynumber: 7.9 Consensus size: 27
28546 AAATAGATTT
*
28556 TCAGAAATGGTTCGGAAAACGATCTCA
1 TCAGAAATGGTTCGGAAGACGATCTCA
* *
28583 TCGGAAATAGTTCGGAAGACGATCTCA
1 TCAGAAATGGTTCGGAAGACGATCTCA
*
28610 TCAGAAATGGTTCGGAAGACAATCTCA
1 TCAGAAATGGTTCGGAAGACGATCTCA
*
28637 TCAGAAATGGTTCGGAAGATGATCTCA
1 TCAGAAATGGTTCGGAAGACGATCTCA
28664 TCAGAAATGGTTCGGAAGACGATCTCA
1 TCAGAAATGGTTCGGAAGACGATCTCA
*
28691 TCAGAAATGGTTTGGAAGACGATCTCA
1 TCAGAAATGGTTCGGAAGACGATCTCA
28718 TCAGAAATGGTTCGGAAGACGATCTCA
1 TCAGAAATGGTTCGGAAGACGATCTCA
* *
28745 TCA-AAATTGGTTTGGGAGACGATC
1 TCAGAAA-TGGTTCGGAAGACGATC
28769 CTTTTAAGAT
Statistics
Matches: 172, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
26 3 0.02
27 169 0.98
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (27 bp):
TCAGAAATGGTTCGGAAGACGATCTCA
Found at i:28787 original size:81 final size:81
Alignment explanation
Indices: 28556--28792 Score: 273
Period size: 81 Copynumber: 2.9 Consensus size: 81
28546 AAATAGATTT
* * * * **
28556 TCAGAAATGGTTCGGAAAACGATCTCATCGGAAATAGTTCGGAAGACGATCTCATCAGAAAT-GG
1 TCAGAAATGGTTCGGAAGACGATCTCATCAGAAATGGTTCGGAAGACGATCTCATAAGAAATAAA
28620 TTCGGAAGACAATCTCA
66 TT-GGAAGACAATCTCA
* * ***
28637 TCAGAAATGGTTCGGAAGATGATCTCATCAGAAATGGTTCGGAAGACGATCTCATCAGAAATGGT
1 TCAGAAATGGTTCGGAAGACGATCTCATCAGAAATGGTTCGGAAGACGATCTCATAAGAAATAAA
*
28702 TTGGAAGACGATCTCA
66 TTGGAAGACAATCTCA
* * ** *
28718 TCAGAAATGGTTCGGAAGACGATCTCATCA-AAATTGGTTTGGGAGACGATCCTTTTAAG-ATTA
1 TCAGAAATGGTTCGGAAGACGATCTCATCAGAAA-TGGTTCGGAAGACGAT-CTCATAAGAAATA
28781 AATTGGAAGACA
64 AATTGGAAGACA
28793 GTTCGAAGGA
Statistics
Matches: 136, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
80 3 0.02
81 125 0.92
82 8 0.06
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (81 bp):
TCAGAAATGGTTCGGAAGACGATCTCATCAGAAATGGTTCGGAAGACGATCTCATAAGAAATAAA
TTGGAAGACAATCTCA
Found at i:39257 original size:31 final size:31
Alignment explanation
Indices: 39214--39280 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
39204 TATATTTATT
39214 TATTTTTGTTTGGCACACAATAAGAATAAGA
1 TATTTTTGTTTGGCACACAATAAGAATAAGA
*
39245 TATTTTCT-TTTGGCACAGAATAAGAATAAGA
1 TATTTT-TGTTTGGCACACAATAAGAATAAGA
39276 TATTT
1 TATTT
39281 AACTATGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (31 bp):
TATTTTTGTTTGGCACACAATAAGAATAAGA
Found at i:40087 original size:2 final size:2
Alignment explanation
Indices: 40075--40116 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
40065 AATGAGAGCT
40075 TA TA T- TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
40116 T
1 T
40117 TAGGTCTCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.