Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011333.1 Corchorus olitorius cultivar O-4 contig11366, 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: 49330
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4584 original size:14 final size:14
Alignment explanation
Indices: 4565--4601 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4555 CCGCCACAGC
*
4565 GCACAAGGTGCCAG
1 GCACAAGGCGCCAG
4579 GCACAAGGCGCCAG
1 GCACAAGGCGCCAG
4593 GCACAAGGC
1 GCACAAGGC
4602 AGCAACGCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.32, G:0.35, T:0.03
Consensus pattern (14 bp):
GCACAAGGCGCCAG
Found at i:7712 original size:19 final size:18
Alignment explanation
Indices: 7688--7723 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7678 TGAAGATTTA
7688 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
7707 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
7724 ATCATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:9545 original size:25 final size:25
Alignment explanation
Indices: 9517--9567 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
9507 TTCTCAATAC
* *
9517 TAAGTCATTTTGGGAAATCCTATGT
1 TAAGTCATTATGGGAAATCCAATGT
9542 TAAGTCATTATGGGAAATCCAATGT
1 TAAGTCATTATGGGAAATCCAATGT
9567 T
1 T
9568 GGTCCATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (25 bp):
TAAGTCATTATGGGAAATCCAATGT
Found at i:11767 original size:30 final size:30
Alignment explanation
Indices: 11731--11804 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
11721 CTTTCGATTA
11731 CTGCAATTTGAGACCCATTATGTTTAATTG
1 CTGCAATTTGAGACCCATTATGTTTAATTG
**
11761 CTGCAATTTGAGACTTATTATGTTTAATTG
1 CTGCAATTTGAGACCCATTATGTTTAATTG
* *
11791 CTACGATTTGAGAC
1 CTGCAATTTGAGAC
11805 TTGATTGTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.41
Consensus pattern (30 bp):
CTGCAATTTGAGACCCATTATGTTTAATTG
Found at i:20827 original size:27 final size:27
Alignment explanation
Indices: 20770--20842 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
20760 AGGGTCACCC
* *** *
20770 AGGGGCATTTTGGTCATTCGTATGTTC
1 AGGGGCATTTTGGTCATTTGTACACTA
*
20797 AGGGGCATTTTGGTCATTTTTACACTA
1 AGGGGCATTTTGGTCATTTGTACACTA
20824 A-GGGCATTTTGGTCATTTG
1 AGGGGCATTTTGGTCATTTG
20843 CATATTCAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 17 0.44
27 22 0.56
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.41
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGTACACTA
Found at i:20853 original size:26 final size:26
Alignment explanation
Indices: 20772--20853 Score: 92
Period size: 26 Copynumber: 3.1 Consensus size: 26
20762 GGTCACCCAG
* *
20772 GGGCATTTTGGTCATTCGTATGTTCA
1 GGGCATTTTGGTCATTTGTATATTCA
* * * *
20798 GGGGCATTTTGGTCATTTTTACACTAA
1 -GGGCATTTTGGTCATTTGTATATTCA
*
20825 GGGCATTTTGGTCATTTGCATATTCA
1 GGGCATTTTGGTCATTTGTATATTCA
20851 GGG
1 GGG
20854 GGCACGTTGG
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
26 24 0.55
27 20 0.45
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (26 bp):
GGGCATTTTGGTCATTTGTATATTCA
Found at i:28326 original size:34 final size:35
Alignment explanation
Indices: 28269--28337 Score: 113
Period size: 34 Copynumber: 1.9 Consensus size: 35
28259 GTAGGAACTC
28269 AACTGTATGAGTTTTTTTATATTTCTATCTTACCTCA
1 AACTGTATGAG--TTTTTATATTTCTATCTTACCTCA
28306 AACTGTATGAG-TTTTATATTTCTATCTTACCT
1 AACTGTATGAGTTTTTATATTTCTATCTTACCT
28338 TAATGGAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
34 21 0.66
37 11 0.34
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.51
Consensus pattern (35 bp):
AACTGTATGAGTTTTTATATTTCTATCTTACCTCA
Found at i:31730 original size:4 final size:4
Alignment explanation
Indices: 31716--31908 Score: 69
Period size: 4 Copynumber: 48.0 Consensus size: 4
31706 GACTAAAAAG
* * * *
31716 ATTT TTTT ATTT ATTT A-CT ATTT ATATT -TTT ATTT ATTA ATTT AGTT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT
* * ** ** *
31763 A-TT ATCT ATTT ATTT ACTATT ATCT ACTTT -TTT ACCT ACCT ATTT ATCT
1 ATTT ATTT ATTT ATTT A-T-TT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT
* * * ** * * *
31812 AATT ATCT ATAT ACCT ATTT ATCTT -TTT ATTT ATCT ATTAT TTTT ACTT
1 ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATT-T ATTT ATTT
*
31861 ATTT -TTCT ATTT ATTT ATTT ATTT ATCT A-TT ACTTT -TTT ATTTT ATTT
1 ATTT ATT-T ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT A-TTT ATTT
31909 TTATTTTAAT
Statistics
Matches: 139, Mismatches: 33, Indels: 34
0.67 0.16 0.17
Matches are distributed among these distances:
3 19 0.14
4 98 0.71
5 19 0.14
6 3 0.02
ACGTcount: A:0.24, C:0.10, G:0.01, T:0.65
Consensus pattern (4 bp):
ATTT
Found at i:31891 original size:12 final size:12
Alignment explanation
Indices: 31723--31886 Score: 82
Period size: 12 Copynumber: 14.6 Consensus size: 12
31713 AAGATTTTTT
31723 TATTTATTTA-C
1 TATTTATTTATC
*
31734 TATTTATATT-TT
1 TATTTAT-TTATC
* *
31746 TATTTATTAATT
1 TATTTATTTATC
*
31758 TAGTTA-TTATC
1 TATTTATTTATC
31769 TATTTATTTA-C
1 TATTTATTTATC
*
31780 TA-TTATCTA-C
1 TATTTATTTATC
*
31790 --TTT-TTTACC
1 TATTTATTTATC
**
31799 TACCTATTTATC
1 TATTTATTTATC
* * *
31811 TAATTATCTATA
1 TATTTATTTATC
**
31823 TACCTATTTATC
1 TATTTATTTATC
*
31835 TTTTTATTTATC
1 TATTTATTTATC
31847 TA-TTATTT-T-
1 TATTTATTTATC
* *
31856 TACTTATTTTTC
1 TATTTATTTATC
*
31868 TATTTATTTATT
1 TATTTATTTATC
31880 TATTTAT
1 TATTTAT
31887 CTATTACTTT
Statistics
Matches: 115, Mismatches: 26, Indels: 23
0.70 0.16 0.14
Matches are distributed among these distances:
8 3 0.03
9 5 0.04
10 14 0.12
11 27 0.23
12 66 0.57
ACGTcount: A:0.26, C:0.10, G:0.01, T:0.63
Consensus pattern (12 bp):
TATTTATTTATC
Found at i:32386 original size:5 final size:5
Alignment explanation
Indices: 32376--32421 Score: 65
Period size: 5 Copynumber: 8.8 Consensus size: 5
32366 CCTCTTAAAA
*
32376 AATAT AATAT AATAT AATAT AATAT ATTAT AATAAT AATAAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATAT AAT-AT AAT-AT AATA
32422 AACTAATAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 27 0.71
6 11 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:32889 original size:13 final size:13
Alignment explanation
Indices: 32866--32896 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
32856 AAATTTATTG
32866 ATAAT-ATATAAT
1 ATAATAATATAAT
32878 ATAATAATATAAT
1 ATAATAATATAAT
32891 ATAATA
1 ATAATA
32897 TTATTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATAATATAAT
Found at i:33200 original size:31 final size:31
Alignment explanation
Indices: 33165--33237 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
33155 TAAATTATTG
*
33165 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
33196 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
33227 CAAATTAAAAA
1 CAAATTAAAAA
33238 CTGATAGACC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
30 7 0.20
31 24 0.69
32 4 0.11
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:34264 original size:2 final size:2
Alignment explanation
Indices: 34259--34289 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34249 ATATAAGTGT
34259 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 T
34290 TTAGTAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36947 original size:7 final size:7
Alignment explanation
Indices: 36937--36974 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
36927 ACTAAAAATA
36937 ATAGTAT
1 ATAGTAT
36944 ATAGTAT
1 ATAGTAT
36951 ATAGTAT
1 ATAGTAT
36958 ATAGTAT
1 ATAGTAT
36965 ATAGTAT
1 ATAGTAT
36972 ATA
1 ATA
36975 TATGTTGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (7 bp):
ATAGTAT
Found at i:42896 original size:22 final size:22
Alignment explanation
Indices: 42871--43090 Score: 117
Period size: 22 Copynumber: 10.0 Consensus size: 22
42861 ATTACACTAT
*
42871 TTTTGATGACCTCCTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
**
42893 TTTTGATAACCTTTTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
** * *
42915 TTTCAATAACGATAC-TATGAAA
1 TTTTGATAAC-CTCCTTATGAAA
* ** *
42937 TTTTGAGAACCTTTTTAT-AAT
1 TTTTGATAACCTCCTTATGAAA
** * * *
42958 TTTTTTTAATCTTCTTATGCAA
1 TTTTGATAACCTCCTTATGAAA
* * *
42980 TTTTGTTAACCTCCCTAAGAAA
1 TTTTGATAACCTCCTTATGAAA
43002 TTTTGA-AGACCTCAC-TATGAAA
1 TTTTGATA-ACCTC-CTTATGAAA
* *
43024 TTTTGATAACCAACAC-TATGAGA
1 TTTTGATAACC-TC-CTTATGAAA
* * *
43047 TATTGATAACCTCCATATGATA
1 TTTTGATAACCTCCTTATGAAA
* * *
43069 TATTGATAACCACGTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
43091 ATTTAAAAAC
Statistics
Matches: 151, Mismatches: 39, Indels: 16
0.73 0.19 0.08
Matches are distributed among these distances:
21 18 0.12
22 111 0.74
23 22 0.15
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TTTTGATAACCTCCTTATGAAA
Found at i:43044 original size:23 final size:23
Alignment explanation
Indices: 43014--43080 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
43004 TTGAAGACCT
*
43014 CACTATGAAATTTTGATAACCAA
1 CACTATGAAATATTGATAACCAA
* **
43037 CACTATGAGATATTGATAACCTC
1 CACTATGAAATATTGATAACCAA
*
43060 CA-TATGATATATTGATAACCA
1 CACTATGAAATATTGATAACCA
43081 CGTTATGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
22 17 0.45
23 21 0.55
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.31
Consensus pattern (23 bp):
CACTATGAAATATTGATAACCAA
Found at i:43187 original size:23 final size:22
Alignment explanation
Indices: 43120--43429 Score: 200
Period size: 22 Copynumber: 14.4 Consensus size: 22
43110 AATCACACTC
* *
43120 TGAAATTTTGATAATC-ACACTA
1 TGAAATTTTGATAACCTTC-CTA
*
43142 TGAAATTGTGATAACC-TCGCTA
1 TGAAATTTTGATAACCTTC-CTA
43164 TGAAATTTTGATAAACCTTCCTA
1 TGAAATTTTGAT-AACCTTCCTA
* *
43187 TAAAATTTTGATAAACCTTTCTA
1 TGAAATTTTGAT-AACCTTCCTA
*
43210 TAAAATTTTGATAACC-TCCTTA
1 TGAAATTTTGATAACCTTCC-TA
*
43232 TGAAATCTTGATAA-----CTA
1 TGAAATTTTGATAACCTTCCTA
43249 T-AAATTTTGATAACC-TCCTTA
1 TGAAATTTTGATAACCTTCC-TA
** *
43270 TGATTTTTTGATAACC-TCATTA
1 TGAAATTTTGATAACCTTC-CTA
* * *
43292 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCTTCCTA
* * * *
43314 TGAAATTTTGATCTA-CATACTG
1 TGAAATTTTGAT-AACCTTCCTA
* * *
43336 TGAAATTTTTATAACCCTCTTA
1 TGAAATTTTGATAACCTTCCTA
* ***
43358 TGAAATTTTGA-AAACTAAAATA
1 TGAAATTTTGATAACCT-TCCTA
*
43380 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAACCTTCCTA
*
43402 TGAAATTTTGATATCCTT-C-A
1 TGAAATTTTGATAACCTTCCTA
43422 TGAAATTT
1 TGAAATTT
43430 GATTACTCCA
Statistics
Matches: 230, Mismatches: 43, Indels: 32
0.75 0.14 0.10
Matches are distributed among these distances:
16 11 0.05
17 3 0.01
18 1 0.00
20 10 0.04
21 9 0.04
22 148 0.64
23 46 0.20
24 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCCTA
Found at i:43521 original size:34 final size:34
Alignment explanation
Indices: 43478--43559 Score: 146
Period size: 34 Copynumber: 2.4 Consensus size: 34
43468 TGGTAATCAT
43478 ACTATGAAATTTTGATAACCTCCCCAGAAATACC
1 ACTATGAAATTTTGATAACCTCCCCAGAAATACC
* *
43512 ACTATGAAATTTTGATAACCTTCTCAGAAATACC
1 ACTATGAAATTTTGATAACCTCCCCAGAAATACC
43546 ACTATGAAATTTTG
1 ACTATGAAATTTTG
43560 GTAATCACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.32
Consensus pattern (34 bp):
ACTATGAAATTTTGATAACCTCCCCAGAAATACC
Found at i:43686 original size:66 final size:66
Alignment explanation
Indices: 43545--43697 Score: 182
Period size: 66 Copynumber: 2.3 Consensus size: 66
43535 TCAGAAATAC
* * * * * *
43545 CACTATGAAATTTTGGTAATCACATTTTGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACC
1 CACTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCGCTATAAAATTTTGATAACA
*
43610 C
66 A
* * * *
43611 CTCAATGAAATTTTGATAATCACATTAT-ATAATTTTGATAACCTCGCTTTGAAATTTTGATAAC
1 CACTATGAAATTTTGATAATCACATTATGA-AATTTTGATAACCTCGCTATAAAATTTTGATAAC
43675 AA
65 AA
*
43677 CACTTTGAAATTTTGATAATC
1 CACTATGAAATTTTGATAATC
43698 TTCCTATAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
65 1 0.01
66 71 0.99
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (66 bp):
CACTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCGCTATAAAATTTTGATAACA
A
Found at i:43949 original size:22 final size:22
Alignment explanation
Indices: 43548--43961 Score: 114
Period size: 22 Copynumber: 18.7 Consensus size: 22
43538 GAAATACCAC
* * *
43548 TATGAAATTTTGGTAATCACAT
1 TATGAAATTTTGATAACCTCAT
*
43570 TTTGAAATTTTGATAACCTC-T
1 TATGAAATTTTGATAACCTCAT
* * *
43591 CTATAAAATTTTGTTGACCCCTCA-
1 -TATGAAATTTTGAT-A-ACCTCAT
* *
43615 -ATGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAACCTCAT
*
43636 TAT-ATAATTTTGATAACCTCGCT
1 TATGA-AATTTTGATAACCTC-AT
**
43659 T-TGAAATTTTGATAACAACACT
1 TATGAAATTTTGATAACCTCA-T
* *
43681 T-TGAAATTTTGATAATCTTC-C
1 TATGAAATTTTGATAA-CCTCAT
** *
43702 TAT-AAA-TTTGATAATTTGATCT
1 TATGAAATTTTGATAACCTCA--T
* * * *
43724 CTATGAAATTTCGATAATCACTT
1 -TATGAAATTTTGATAACCTCAT
*
43747 TATGAGA-TTTGATAACCT--T
1 TATGAAATTTTGATAACCTCAT
* * *
43766 CTATCAAATTTTGGT-A-CTCCT
1 -TATGAAATTTTGATAACCTCAT
*
43787 TATGAAATTAAGACTTTTATAACCTTCA-
1 TATGAAA-T-----TTTGATAACC-TCAT
* *
43815 TATTAAATTATT-ATAACCACAGT
1 TATGAAATT-TTGATAACCTCA-T
*
43838 T-TGAAATTTTGATAACCACACT
1 TATGAAATTTTGATAACCTCA-T
* **
43860 T-TGAAATTTTTATAACCTCCC
1 TATGAAATTTTGATAACCTCAT
* * *
43881 CATG-AATATT-AGTAACCTCCT
1 TATGAAATTTTGA-TAACCTCAT
* * *
43902 TATGAAATTTTGTTAACCACAC
1 TATGAAATTTTGATAACCTCAT
*
43924 TATGAAATTCTT-ATAACCTCGT
1 TATGAAATT-TTGATAACCTCAT
*
43946 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
43962 TCTCTTTGAT
Statistics
Matches: 288, Mismatches: 63, Indels: 82
0.67 0.15 0.19
Matches are distributed among these distances:
19 5 0.02
20 24 0.08
21 44 0.15
22 170 0.59
23 15 0.05
24 7 0.02
25 8 0.03
26 4 0.01
27 2 0.01
28 7 0.02
29 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAT
Found at i:44051 original size:24 final size:22
Alignment explanation
Indices: 43998--44194 Score: 87
Period size: 22 Copynumber: 8.9 Consensus size: 22
43988 TGTGATAATA
*
43998 CTATGAAATTTCAATAACCTTC
1 CTATGAAATTTTAATAACCTTC
* *
44020 CTAAGAAATTTTAATAGCCTGATC
1 CTATGAAATTTTAATAACCT--TC
** *
44044 CTATGAAATTTTGGTAACC-AC
1 CTATGAAATTTTAATAACCTTC
* ** * *
44065 ATTATTTAATTTTGATAAACTTC
1 -CTATGAAATTTTAATAACCTTC
* *
44088 CCATGAAATTTTGATAA-CTTC
1 CTATGAAATTTTAATAACCTTC
** * *
44109 CATATGAAATTTTGGTAATC-AC
1 C-TATGAAATTTTAATAACCTTC
* *
44131 ACTATGGAATTTTGATAACC-TC
1 -CTATGAAATTTTAATAACCTTC
** * *
44153 CTCATGAAATTACAAAAACCATC
1 CT-ATGAAATTTTAATAACCTTC
* *
44176 TTATGAAATTTTGATAACC
1 CTATGAAATTTTAATAACC
44195 ACACAGAGAC
Statistics
Matches: 131, Mismatches: 35, Indels: 18
0.71 0.19 0.10
Matches are distributed among these distances:
21 8 0.06
22 100 0.76
23 6 0.05
24 17 0.13
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTAATAACCTTC
Found at i:44097 original size:22 final size:22
Alignment explanation
Indices: 44072--44163 Score: 91
Period size: 22 Copynumber: 4.2 Consensus size: 22
44062 CACATTATTT
44072 AATTTTGATAAACTTCC-CATGA
1 AATTTTGAT-AACTTCCACATGA
*
44094 AATTTTGATAACTTCCATATGA
1 AATTTTGATAACTTCCACATGA
* *
44116 AATTTTGGTAA--TCACACTATGG
1 AATTTTGATAACTTC-CAC-ATGA
* *
44138 AATTTTGATAACCTCCTCATGA
1 AATTTTGATAACTTCCACATGA
44160 AATT
1 AATT
44164 ACAAAAACCA
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
20 2 0.03
21 9 0.16
22 43 0.74
23 2 0.03
24 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACTTCCACATGA
Found at i:44181 original size:66 final size:66
Alignment explanation
Indices: 44041--44198 Score: 169
Period size: 66 Copynumber: 2.4 Consensus size: 66
44031 TAATAGCCTG
* ** * *** *
44041 ATCC-TATGAAATTTTGGTAACCACATTATTTAATTTTGATAAACTTCCCATGAAATTTTGATAA
1 ATCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAAACCTCCCATGAAATTACAAAAA
44105 C
66 C
* *
44106 TTCCATATGAAATTTTGGTAATCACACTATGGAATTTTGAT-AACCTCCTCATGAAATTACAAAA
1 ATCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAAACCTCC-CATGAAATTACAAAA
44170 ACC
65 A-C
* *
44173 AT-CTTATGAAATTTTGATAACCACAC
1 ATCCATATGAAATTTTGGTAACCACAC
44199 AGAGACAAGA
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
65 9 0.12
66 65 0.86
67 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (66 bp):
ATCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAAACCTCCCATGAAATTACAAAAA
C
Found at i:44194 original size:22 final size:22
Alignment explanation
Indices: 43966--44195 Score: 80
Period size: 22 Copynumber: 10.5 Consensus size: 22
43956 TGATAATCTC
* * *
43966 TTTGATAACCTTTTTATAAAAT
1 TTTGATAACCATCTTATGAAAT
* *
43988 TGTGATAA-TA-C-TATGAAAT
1 TTTGATAACCATCTTATGAAAT
** * * *
44007 TTCAATAACCTTCCTAAGAAAT
1 TTTGATAACCATCTTATGAAAT
* * *
44029 TTTAATAGCCTGATCCTATGAAAT
1 TTTGATAACC--ATCTTATGAAAT
* **
44053 TTTGGTAACCA-CATTATTTAAT
1 TTTGATAACCATC-TTATGAAAT
* * **
44075 TTTGATAAACTTCCCATGAAAT
1 TTTGATAACCATCTTATGAAAT
* *
44097 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCAT-CTTATGAAAT
* *
44119 TTTGGTAATCACA-C-TATGGAAT
1 TTTGATAA-C-CATCTTATGAAAT
*
44141 TTTGATAACC-TCCTCATGAAAT
1 TTTGATAACCAT-CTTATGAAAT
*** *
44163 TACAAAAACCATCTTATGAAAT
1 TTTGATAACCATCTTATGAAAT
44185 TTTGATAACCA
1 TTTGATAACCA
44196 CACAGAGACA
Statistics
Matches: 148, Mismatches: 45, Indels: 30
0.66 0.20 0.13
Matches are distributed among these distances:
19 12 0.08
20 1 0.01
21 7 0.05
22 107 0.72
23 3 0.02
24 17 0.11
25 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TTTGATAACCATCTTATGAAAT
Found at i:44676 original size:14 final size:14
Alignment explanation
Indices: 44652--44699 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
44642 TTGAAATTTT
44652 ATAAGTAAATTTTAA
1 ATAA-TAAATTTTAA
44667 ATAATAAATTTT-A
1 ATAATAAATTTTAA
44680 ATAATATCAATTTATAA
1 ATAATA--AATTT-TAA
44697 ATA
1 ATA
44700 TATTTGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.24
14 8 0.28
15 9 0.31
16 1 0.03
17 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAATAAATTTTAA
Found at i:44702 original size:16 final size:15
Alignment explanation
Indices: 44657--44702 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
44647 ATTTTATAAG
44657 TAAATTTTAAATA-A
1 TAAATTTTAAATATA
44671 TAAATTTT-AATAATA
1 TAAATTTTAAAT-ATA
*
44686 TCAATTTATAAATATA
1 TAAATTT-TAAATATA
44702 T
1 T
44703 TTGAAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 3 0.11
14 9 0.33
15 7 0.26
16 5 0.19
17 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAATTTTAAATATA
Found at i:45045 original size:19 final size:19
Alignment explanation
Indices: 45021--45057 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
45011 TGTATCTGTA
45021 ACCGTTTCACCACCGTTTG
1 ACCGTTTCACCACCGTTTG
45040 ACCGTTTCACCACCGTTT
1 ACCGTTTCACCACCGTTT
45058 TGGGCTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.38, G:0.14, T:0.32
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Done.