Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021488.1 Corchorus olitorius cultivar O-4 contig21521, 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: 46720
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2150 original size:65 final size:65
Alignment explanation
Indices: 2046--2170 Score: 223
Period size: 65 Copynumber: 1.9 Consensus size: 65
2036 GTTTTTATAC
* *
2046 GTGACATATTGTTTATATCACGTATTGTATTAAATTATTTGTGATATAAAGTAATGTCACTAAAT
1 GTGACACATTGTTTATATCACGTATTGTATTAAATTATTTGTGACATAAAGTAATGTCACTAAAT
*
2111 GTGACACATTGTTTATGTCACGTATTGTATTAAATTATTTGTGACATAAAGTAATGTCAC
1 GTGACACATTGTTTATATCACGTATTGTATTAAATTATTTGTGACATAAAGTAATGTCAC
2171 CAAAATTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (65 bp):
GTGACACATTGTTTATATCACGTATTGTATTAAATTATTTGTGACATAAAGTAATGTCACTAAAT
Found at i:4951 original size:2 final size:2
Alignment explanation
Indices: 4940--4975 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
4930 AAGTTACAAT
4940 TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4976 AGTACAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5090 original size:105 final size:104
Alignment explanation
Indices: 4959--5182 Score: 380
Period size: 105 Copynumber: 2.1 Consensus size: 104
4949 TATATATATA
*
4959 TATATATATTATATATAAGTACAATTTTTCTTTTTCAATCAAATAGCTTATTATTGTTTACAGTA
1 TATATATA-TATATAAAAGTACAATTTTTCTTTTTCAATCAAATAGCTTATTATTGTTTACAGTA
*
5024 TCACTTAC-TGCAATTTTTTTTCTTAGATCCGTTTGTTTGTT
65 TCACTTACAT-CAA-TTTTTTTCTTAGATACGTTTGTTTGTT
*
5065 TATATATATATATAAAAGTAGAATTTTTCTTTTTCAATCAAATAGCTTATTATTGTTTACAGTAT
1 TATATATATATATAAAAGTACAATTTTTCTTTTTCAATCAAATAGCTTATTATTGTTTACAGTAT
5130 CACTTACATCAATTTTTTTCTTAGATACGTTTGTTTGTT
66 CACTTACATCAATTTTTTTCTTAGATACGTTTGTTTGTT
5169 TATATATATA-ATAA
1 TATATATATATATAA
5183 TCTTTCATTC
Statistics
Matches: 114, Mismatches: 3, Indels: 5
0.93 0.02 0.04
Matches are distributed among these distances:
103 4 0.04
104 36 0.32
105 65 0.57
106 9 0.08
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (104 bp):
TATATATATATATAAAAGTACAATTTTTCTTTTTCAATCAAATAGCTTATTATTGTTTACAGTAT
CACTTACATCAATTTTTTTCTTAGATACGTTTGTTTGTT
Found at i:5145 original size:54 final size:55
Alignment explanation
Indices: 4978--5146 Score: 133
Period size: 54 Copynumber: 3.2 Consensus size: 55
4968 TATATATAAG
4978 TACAATTTTTCTTTTTCAATCAAATAGCTTATTATTGTTTACAGTATCACTTAC-
1 TACAATTTTTCTTTTTCAATCAAATAGCTTATTATTGTTTACAGTATCACTTACA
* *** * * * * * *
5032 TGCAATTTTT-TTTCTT-AGATCCGTTTG-TT-TGT-TTATATATA-TAT-A-TAAAA
1 TACAATTTTTCTTT-TTCA-ATCAAATAGCTTAT-TATTGTTTACAGTATCACTTACA
*
5082 GTAGAATTTTTCTTTTTCAATCAAATAGCTTATTATTGTTTACAGTATCACTTACA
1 -TACAATTTTTCTTTTTCAATCAAATAGCTTATTATTGTTTACAGTATCACTTACA
5138 T-CAATTTTT
1 TACAATTTTT
5147 TTCTTAGATA
Statistics
Matches: 80, Mismatches: 22, Indels: 26
0.62 0.17 0.20
Matches are distributed among these distances:
49 2 0.03
50 1 0.01
51 18 0.22
52 14 0.17
53 14 0.17
54 26 0.32
55 2 0.03
56 3 0.04
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (55 bp):
TACAATTTTTCTTTTTCAATCAAATAGCTTATTATTGTTTACAGTATCACTTACA
Found at i:5671 original size:51 final size:51
Alignment explanation
Indices: 5595--5699 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
5585 ACTGAACCAG
5595 CTCCTGCAGCTGACTTGCAACAAAATGTGCCGATAGAACCAAACCTTGGAA
1 CTCCTGCAGCTGACTTGCAACAAAATGTGCCGATAGAACCAAACCTTGGAA
* *
5646 CTCCTGCATCTGACTTGCAACAAAATGTGCCGATAGAACCAACCCTTGGAA
1 CTCCTGCAGCTGACTTGCAACAAAATGTGCCGATAGAACCAAACCTTGGAA
5697 CTC
1 CTC
5700 AAGATGCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (51 bp):
CTCCTGCAGCTGACTTGCAACAAAATGTGCCGATAGAACCAAACCTTGGAA
Found at i:7315 original size:12 final size:12
Alignment explanation
Indices: 7298--7322 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7288 TGTAAAGAAG
7298 GTTCCACTGCTT
1 GTTCCACTGCTT
7310 GTTCCACTGCTT
1 GTTCCACTGCTT
7322 G
1 G
7323 CTATTGCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.32, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTCCACTGCTT
Found at i:8160 original size:120 final size:118
Alignment explanation
Indices: 7754--8240 Score: 456
Period size: 119 Copynumber: 4.1 Consensus size: 118
7744 TTTACCTAGT
* * * * ** * * *
7754 TTTTGTGACGATCAACAATTGTTAGTGACGTTATAATCTCATATTGCATAATGAAACTTACGTCA
1 TTTTGTGACAATCAACAATTATTAGTGACGTTATAATTTAATATTTTATGACGAAA-TTTCGTCA
** * ** **
7819 CCTATACCCGTGGCGTTCTGAC-TTTT-GTCACGA-ATAA-TGAAAAACTTCCTCATA
65 CCTATACATGTGACGTTC--ACATTTTCGTCAC-ATATAACT-AGCATTTTCCTCATA
* * * *
7873 TTTTGTGACAATCAACAATTATGAGTGACGTTAT-ATTGTAGTATTTTGTGACGTACATTGT-GT
1 TTTTGTGACAATCAACAATTATTAGTGACGTTATAATT-TAATATTTTATGACG-AAATT-TCGT
** *
7936 CACCTATACATGTGACGTT-ACAATTTTCGTCACGA-ATAA-TGGAATATTTTCCT-ATT
63 CACCTATACATGTGACGTTCAC-ATTTTCGTCAC-ATATAACT--AGCATTTTCCTCATA
* * * *
7992 TTTTGTGACAACCAACAATTGTTAGTGACGTTTTATTTTAATATTTTATGACGAAATTTACGTCA
1 TTTTGTGACAATCAACAATTATTAGTGACGTTATAATTTAATATTTTATGACGAAATTT-CGTCA
* *
8057 CCGATACATTTGACGTTCACATTTTCGTCACATATAACTACGCATTTTCCTCATA
65 CCTATACATGTGACGTTCACATTTTCGTCACATATAACTA-GCATTTTCCTCATA
*
8112 TTTTGTGACAATCAACAATTTTTAGTGACGTTATAATTTAATATTTTATGAC-AACATTTGCGTC
1 TTTTGTGACAATCAACAATTATTAGTGACGTTATAATTTAATATTTTATGACGAA-ATTT-CGTC
*
8176 ACCTATACATGTGACATTCACATTTTCGTCACATATAACTAAGCATTTTCCTCATA
64 ACCTATACATGTGACGTTCACATTTTCGTCACATATAACT-AGCATTTTCCTCATA
*
8232 TTTGGTGAC
1 TTTTGTGAC
8241 GACCCATTAT
Statistics
Matches: 309, Mismatches: 42, Indels: 33
0.80 0.11 0.09
Matches are distributed among these distances:
116 2 0.01
117 1 0.00
118 12 0.04
119 160 0.52
120 133 0.43
121 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (118 bp):
TTTTGTGACAATCAACAATTATTAGTGACGTTATAATTTAATATTTTATGACGAAATTTCGTCAC
CTATACATGTGACGTTCACATTTTCGTCACATATAACTAGCATTTTCCTCATA
Found at i:8260 original size:120 final size:120
Alignment explanation
Indices: 7864--8240 Score: 432
Period size: 120 Copynumber: 3.1 Consensus size: 120
7854 AATGAAAAAC
* ** * * *
7864 TTCCTCATATTTTGTGACAATCAACAATTATGAGTGACGTTAT-ATTGTAGTATTTTGTGACGTA
1 TTCCTCATATTTTGTGACAACCAACAA-TATTTGTGACGTTATAATT-TAATATTTTATGACGAA
* *
7928 CA-TTGTGTCACCTATACATGTGACGTT-ACAATTTTCGTCACGA-ATAA-TGGAA-TATT
64 CATTTGCGTCACCTATACATGTGACGTTCAC-ATTTTCGTCAC-ATATAACT--AAGCATT
* * *
7984 TTCCT-ATTTTTTGTGACAACCAACAAT-TGTTAGTGACGTTTTATTTTAATATTTTATGACGAA
1 TTCCTCATATTTTGTGACAACCAACAATAT-TT-GTGACGTTATAATTTAATATTTTATGACGAA
* * * *
8047 -ATTTACGTCACCGATACATTTGACGTTCACATTTTCGTCACATATAACTACGCATT
64 CATTTGCGTCACCTATACATGTGACGTTCACATTTTCGTCACATATAACTAAGCATT
* *
8103 TTCCTCATATTTTGTGACAATCAACAATTTTTAGTGACGTTATAATTTAATATTTTATGAC-AAC
1 TTCCTCATATTTTGTGACAACCAACAATATTT-GTGACGTTATAATTTAATATTTTATGACGAAC
*
8167 ATTTGCGTCACCTATACATGTGACATTCACATTTTCGTCACATATAACTAAGCATT
65 ATTTGCGTCACCTATACATGTGACGTTCACATTTTCGTCACATATAACTAAGCATT
*
8223 TTCCTCATATTTGGTGAC
1 TTCCTCATATTTTGTGAC
8241 GACCCATTAT
Statistics
Matches: 221, Mismatches: 25, Indels: 22
0.82 0.09 0.08
Matches are distributed among these distances:
117 1 0.00
118 4 0.02
119 88 0.40
120 127 0.57
121 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (120 bp):
TTCCTCATATTTTGTGACAACCAACAATATTTGTGACGTTATAATTTAATATTTTATGACGAACA
TTTGCGTCACCTATACATGTGACGTTCACATTTTCGTCACATATAACTAAGCATT
Found at i:9816 original size:19 final size:18
Alignment explanation
Indices: 9792--9827 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9782 TGAAGATTTA
9792 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
9811 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
9828 ATAATTTCAA
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:11739 original size:30 final size:32
Alignment explanation
Indices: 11693--11757 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
11683 GAAAATATTT
* *
11693 TTTTCTTTTTC-TAAAAACGCAAAAACAATAA
1 TTTTCTTTTTCAAAAAAACGCAAAAACAAAAA
*
11724 TTTT-TTTTTCAAAAAAAACGCAAACACAAAAA
1 TTTTCTTTTTC-AAAAAAACGCAAAAACAAAAA
11756 TT
1 TT
11758 AAAAACGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 6 0.21
31 4 0.14
32 19 0.66
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (32 bp):
TTTTCTTTTTCAAAAAAACGCAAAAACAAAAA
Found at i:12139 original size:15 final size:15
Alignment explanation
Indices: 12119--12147 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12109 GCAGAGGTTG
12119 AAAGAAAACAATTAA
1 AAAGAAAACAATTAA
12134 AAAGAAAACAATTA
1 AAAGAAAACAATTA
12148 TACTAGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAGAAAACAATTAA
Found at i:19236 original size:30 final size:31
Alignment explanation
Indices: 19191--19250 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
19181 ACTTCAAAAT
*
19191 TCTGTCTTGACTTAAACATTCTTC-TTTATAC
1 TCTGACTTGACTTAAA-ATTCTTCATTTATAC
*
19222 TCTGACTTGA-TTAAATTTCTTCATTTATA
1 TCTGACTTGACTTAAAATTCTTCATTTATA
19251 AACTTTGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 6 0.23
30 11 0.42
31 9 0.35
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (31 bp):
TCTGACTTGACTTAAAATTCTTCATTTATAC
Found at i:24847 original size:2 final size:2
Alignment explanation
Indices: 24840--24870 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
24830 AGAAAAGAAT
*
24840 AC AC AC AC AC AC TC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
24871 GATATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.48, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:24877 original size:2 final size:2
Alignment explanation
Indices: 24872--24907 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24862 ACACACACAG
24872 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
24908 GCGGCTATGA
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
Found at i:28240 original size:21 final size:21
Alignment explanation
Indices: 28210--28259 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
28200 CAGTCTAAGT
28210 CTTTTT-AAATCTTCGAAACA
1 CTTTTTCAAATCTTCGAAACA
* *
28230 CTTTTTCAAATCTTCTAATCA
1 CTTTTTCAAATCTTCGAAACA
28251 CTTTGTTCA
1 CTTT-TTCA
28260 GTCTATGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 6 0.23
21 16 0.62
22 4 0.15
ACGTcount: A:0.28, C:0.22, G:0.04, T:0.46
Consensus pattern (21 bp):
CTTTTTCAAATCTTCGAAACA
Found at i:28552 original size:2 final size:2
Alignment explanation
Indices: 28545--28572 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28535 AGTGCTAAAC
28545 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
28573 ACTTAAAGCA
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):
TA
Found at i:28622 original size:15 final size:15
Alignment explanation
Indices: 28602--28630 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28592 AAAGTACCCT
28602 TATAATTAATTAAAG
1 TATAATTAATTAAAG
28617 TATAATTAATTAAA
1 TATAATTAATTAAA
28631 TACATGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TATAATTAATTAAAG
Found at i:32359 original size:11 final size:11
Alignment explanation
Indices: 32338--32391 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
32328 ATGTAAGATT
*
32338 TTAAATAATAA
1 TTAATTAATAA
*
32349 TTATTTAATAAA
1 TTAATTAAT-AA
* * *
32361 ATAATTATTAT
1 TTAATTAATAA
32372 TTAATTAATAA
1 TTAATTAATAA
32383 TTAATTAAT
1 TTAATTAAT
32392 TTCAGCCCTT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
11 25 0.76
12 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAATTAATAA
Found at i:32364 original size:19 final size:18
Alignment explanation
Indices: 32339--32389 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
32329 TGTAAGATTT
32339 TAAATAATAATTATTTAA
1 TAAATAATAATTATTTAA
*
32357 TAAAATAATTATTATTTAA
1 T-AAATAATAATTATTTAA
*
32376 TTAATAATTAATTA
1 TAAATAA-TAATTA
32390 ATTTCAGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATAATAATTATTTAA
Found at i:32655 original size:21 final size:21
Alignment explanation
Indices: 32625--32665 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
32615 TGGAATAGTT
* *
32625 ACTTAGCATAAATTGAACTCC
1 ACTTAACATAAATCGAACTCC
32646 ACTTAACATAAATCGAACTC
1 ACTTAACATAAATCGAACTC
32666 TTCCACTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (21 bp):
ACTTAACATAAATCGAACTCC
Found at i:34475 original size:33 final size:33
Alignment explanation
Indices: 34438--34649 Score: 197
Period size: 33 Copynumber: 6.6 Consensus size: 33
34428 TAATTCTACT
* * *
34438 GCGTTTTTGTCAGA-AAAGCGCCACCATATTGTG
1 GCGTTTTTGTCACACAAA-CGCCACAATATGGTG
* * * * * *
34471 GCGTTTTTGTCAAAAAAACACCAGAAAATTGTG
1 GCGTTTTTGTCACACAAACGCCACAATATGGTG
* *
34504 TCGTTTTTGTCAGACAAACGCCAC-A-A----G
1 GCGTTTTTGTCACACAAACGCCACAATATGGTG
* *
34531 GCGTTTTTGTCA-ATTAGACGCCACAATATGGTG
1 GCGTTTTTGTCACA-CAAACGCCACAATATGGTG
*
34564 GCGTTTTTGTAACACAAACGCCACAATATGGTG
1 GCGTTTTTGTCACACAAACGCCACAATATGGTG
*
34597 GCGTTTTTGTAACACAAACGCCACAATATGGTG
1 GCGTTTTTGTCACACAAACGCCACAATATGGTG
* *
34630 GCGCTTTTGTAACACAAACG
1 GCGTTTTTGTCACACAAACG
34650 TCACCATGTT
Statistics
Matches: 153, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
26 1 0.01
27 20 0.13
28 1 0.01
29 1 0.01
31 1 0.01
32 1 0.01
33 124 0.81
34 4 0.03
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (33 bp):
GCGTTTTTGTCACACAAACGCCACAATATGGTG
Found at i:34602 original size:93 final size:93
Alignment explanation
Indices: 34438--34622 Score: 230
Period size: 93 Copynumber: 2.0 Consensus size: 93
34428 TAATTCTACT
* * * *
34438 GCGTTTTTGTCAGAAAAGCGCCACCATATTGTGGCGTTTTTGTCAAAAAAACACCAGAAAATTGT
1 GCGTTTTTGTCAGAAAAGCGCCACAATATGGTGGCGTTTTTGTCAAAAAAACACCACAAAATGGT
* * *
34503 GTCGTTTTTGTCAGACAAACGCCACAAG
66 GGCGTTTTTGTAACACAAACGCCACAAG
** * * *
34531 GCGTTTTTGTCA-ATTAGACGCCACAATATGGTGGCGTTTTTGT-AACACAAACGCCACAATATG
1 GCGTTTTTGTCAGAAAAG-CGCCACAATATGGTGGCGTTTTTGTCAA-AAAAACACCACAAAATG
34594 GTGGCGTTTTTGTAACACAAACGCCACAA
64 GTGGCGTTTTTGTAACACAAACGCCACAA
34623 TATGGTGGCG
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
92 5 0.06
93 73 0.94
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (93 bp):
GCGTTTTTGTCAGAAAAGCGCCACAATATGGTGGCGTTTTTGTCAAAAAAACACCACAAAATGGT
GGCGTTTTTGTAACACAAACGCCACAAG
Found at i:35298 original size:21 final size:21
Alignment explanation
Indices: 35273--35318 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
35263 TCTTTTCATT
*
35273 CGAGCACGCTCTGCTTCATGA
1 CGAGCACGCTATGCTTCATGA
*
35294 CGAGCACTCTATGCTTCATGA
1 CGAGCACGCTATGCTTCATGA
35315 CGAG
1 CGAG
35319 AACTCTCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.30, G:0.24, T:0.24
Consensus pattern (21 bp):
CGAGCACGCTATGCTTCATGA
Found at i:35323 original size:21 final size:21
Alignment explanation
Indices: 35284--35324 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
35274 GAGCACGCTC
*
35284 TGCTTCATGACGAGCACTCTA
1 TGCTTCATGACGAGAACTCTA
35305 TGCTTCATGACGAGAACTCT
1 TGCTTCATGACGAGAACTCT
35325 CCTCTTGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (21 bp):
TGCTTCATGACGAGAACTCTA
Found at i:38673 original size:13 final size:13
Alignment explanation
Indices: 38657--38685 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38647 ACTTTGAAGA
38657 GAAGAGAGTATAG
1 GAAGAGAGTATAG
38670 GAAGAGAGTATAG
1 GAAGAGAGTATAG
38683 GAA
1 GAA
38686 TCAAAAGAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.38, T:0.14
Consensus pattern (13 bp):
GAAGAGAGTATAG
Found at i:41699 original size:20 final size:20
Alignment explanation
Indices: 41674--41714 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
41664 CTACTATAAT
41674 ATTTTGGGAAATAAATTTTC
1 ATTTTGGGAAATAAATTTTC
41694 ATTTTGGGAAATAAATTTTC
1 ATTTTGGGAAATAAATTTTC
41714 A
1 A
41715 AATCACTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (20 bp):
ATTTTGGGAAATAAATTTTC
Found at i:43938 original size:25 final size:25
Alignment explanation
Indices: 43904--43952 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
43894 CCAAACAATC
43904 TTGAGCACTCTCGCTCGGTCTCTAA
1 TTGAGCACTCTCGCTCGGTCTCTAA
43929 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
43953 CAAACTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.14, C:0.33, G:0.20, T:0.33
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAA
Done.