Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010241.1 Corchorus capsularis cultivar CVL-1 contig10262, 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: 54556
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2556 original size:13 final size:13
Alignment explanation
Indices: 2519--2544 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2509 TTATACTACT
2519 GATAATTTAATAA
1 GATAATTTAATAA
2532 GATAATTTAATAA
1 GATAATTTAATAA
2545 ATCATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
GATAATTTAATAA
Found at i:3343 original size:37 final size:37
Alignment explanation
Indices: 3262--3351 Score: 173
Period size: 36 Copynumber: 2.5 Consensus size: 37
3252 TGTAACCAAA
3262 AATCACTCTCAATTTTCTTTTTTCTTTTAATTTTAAT
1 AATCACTCTCAATTTTCTTTTTTCTTTTAATTTTAAT
3299 AAT-ACTCTCAATTTTCTTTTTTCTTTTAATTTTAAT
1 AATCACTCTCAATTTTCTTTTTTCTTTTAATTTTAAT
3335 AATCACTCTCAATTTTC
1 AATCACTCTCAATTTTC
3352 AATCAATTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
36 36 0.69
37 16 0.31
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.57
Consensus pattern (37 bp):
AATCACTCTCAATTTTCTTTTTTCTTTTAATTTTAAT
Found at i:5003 original size:195 final size:195
Alignment explanation
Indices: 4560--5804 Score: 1321
Period size: 195 Copynumber: 6.3 Consensus size: 195
4550 TTTTAACAAA
* * * *
4560 AACTTCTTAACCTGCTTATGGTGTCCAAATTTTACACTGACAGTGTATTGTATAATAATTCTATA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATACTATA
* * *
4625 AGAAAATTTATACAAT--A-CGTCAGT-AGAGTTTAGCAGACTGCACATGCGAGGTTTAACTTTA
66 AGAAAAATTATACAATACACCGTCAGTGA-AGTTTAGCAGACTGCACGTGC-A-G----AGTTTA
*** * *
4686 AGGGTTGACATGTGTATTCTTAGGGAATATGTATTAGT-AATATTAAATATTTAATTATGAAAT-
124 AGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATAAATATT---TAATTAATTATGAAATG
4749 AGGATATGTGTC
186 A-G-TATGTGTC
* * * *
4761 AACTTTTTAATCCGTTTATGGAGTCCAAAATTTACACTGATAGTGTATTGTATAATAATACTATA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATACTATA
* * * * * *
4826 AGAAAAATTATACAATTC-CTGTTAGTGAATTTTAGCAAACTGCACGTGCAGAATTTAAGGGTTG
66 AGAAAAATTATACAATACACCGTCAGTGAAGTTTAGCAGACTGCACGTGCAGAGTTTAAGGGTTG
* *
4890 ACATGTGT-CCCTTAGGAAATATGTATTAATCAAATATTTAATTAATTATGAAGTGCAGTATGTG
131 ACATGTGTCCCCTTAGGGAATATGTATTAAT-AAATATTTAATTAATTATGAAATG-AGTATGTG
4954 TC
194 TC
* * * * *
4956 AACTTCTTAATCCACTTATGTAGTCCAAAATTTATACTGACAGTGTATTGTATAATAATCCTATA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATACTATA
**
5021 AGAAAAATTATGTAATACACCGTCAGT-AGAGTTTAGCAGA---CACGTGC-GAGGTTTAAGGGT
66 AGAAAAATTATACAATACACCGTCAGTGA-AGTTTAGCAGACTGCACGTGCAGA-GTTTAAGGGT
* * * *
5081 TGACATTTGTCCCATCAGGGAATATGTATTAAAATTAAATATTTAATTAATTATGAAATCGGGTA
129 TGACATGTGTCCCCTTAGGGAATATGTATT--AA-TAAATATTTAATTAATTATGAAAT-GAGTA
5146 TGTGTC
190 TGTGTC
* * *
5152 AA-TTCTTAACCCGCTTATGGAGTCCAAACTTTACACTAACAATGTATTGTATAATAAT-CATAT
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATAC-TAT
* * * ** *
5215 AAAAAAAATTATACAATACACCATCAGTTG-AGTTTAGCAGACTGCACGCGTGGGGTTTAAGGGT
65 AAGAAAAATTATACAATACACCGTCAG-TGAAGTTTAGCAGACTGCACGTGCAGAGTTTAAGGGT
* * *
5279 TGACACGTGTCCCCTTAGGGAATATGTATTAATATTTTATATTTAATTAATTATGAAATTGGGTA
129 TGACATGTGTCCCCTTAGGGAATATGTATTAATA---AATATTTAATTAATTATGAAA-TGAGTA
*
5344 TGTGTT
190 TGTGTC
* * * *
5350 AACTTTTTAACTCGCTTATGAAGTCCAAAATTTACACTGACA--GTA-TGTATAATAATGA-TTT
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAAT-ACTAT
* * * * * *
5411 AA-AAAAATTATACAATACACCGTCAGTGGAGTTTAACAGACTGCATGCGCAGGGTTTAAGAGTT
65 AAGAAAAATTATACAATACACCGTCAGTGAAGTTTAGCAGACTGCACGTGCAGAGTTTAAGGGTT
* * * *
5475 GACATATGTCCCCTTAGGGAATATGTATTAATATTTTATATTTAATTAATTATGAAATAAGGCAT
130 GACATGTGTCCCCTTAGGGAATATGTATTAATA---AATATTTAATTAATTATGAAATGA-GTAT
*
5540 GTGGC
191 GTGTC
** *
5545 AACTTCTTAACCCGCTTATGGAGTCCAAGGTTTACACTGACAGTGTATTGTATAATAATCCTATA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATACTATA
* * *
5610 AAAAAAATTATATAATACACCGTCAGTGAATTTTAGCAGACTGCACGTGCATG-GTTTAAGGGTT
66 AGAAAAATTATACAATACACCGTCAGTGAAGTTTAGCAGACTGCACGTGCA-GAGTTTAAGGGTT
*
5674 GACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTAATTAATTATGAAATGGGAT
130 GACATGTGTCCCCTTAGGGAATATGTATT-A-A-T-AA-ATATTTAATTAATTATGAAATGAG-T
5739 ATGTGTC
189 ATGTGTC
** *
5746 AACTTCTTAACCCGCTTATAAAGTCCAAAATTTACA-TTAGCAGTGTATTGTATAATAAT
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGA-CAGTGTATTGTATAATAAT
5805 CATTATTATA
Statistics
Matches: 893, Mismatches: 106, Indels: 90
0.82 0.10 0.08
Matches are distributed among these distances:
192 2 0.00
193 25 0.03
194 20 0.02
195 335 0.38
196 87 0.10
197 29 0.03
198 94 0.11
199 117 0.13
200 5 0.01
201 152 0.17
202 2 0.00
203 24 0.03
204 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (195 bp):
AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATACTATA
AGAAAAATTATACAATACACCGTCAGTGAAGTTTAGCAGACTGCACGTGCAGAGTTTAAGGGTTG
ACATGTGTCCCCTTAGGGAATATGTATTAATAAATATTTAATTAATTATGAAATGAGTATGTGTC
Found at i:5581 original size:394 final size:393
Alignment explanation
Indices: 4560--5805 Score: 1470
Period size: 394 Copynumber: 3.2 Consensus size: 393
4550 TTTTAACAAA
** * *
4560 AACTTCTTAAC-CTGCTTATGGTGTCCAAATTTTACACTGACAGTGTATTGTATAATAATTCTAT
1 AACTTCTTAACTC-GCTTATGAAGTCCAAAATTTACACTGACAG-GTATTGTATAATAATCCTAT
* *
4624 AAGAAAATTTATACAAT--A-CGTCAGTAGAGTTTAGCAGACTGCACATGCGAGGTTTAACTTTA
64 AAGAAAAATTATACAATACACCGTCAGTAGAGTTTAGCAGACTG--CATGCGAGG-----GTTTA
* *** * * * *
4686 AGGGTTGACATGTGTATTCTTAGGGAATATGTATTAGTAATATTA-A-ATATTTAATTATGAAAT
122 AGGGTTGACATATGTCCCCTTAGGGAATATGTATTAAT-ATTTTATATTTAATTAATTATGAAAT
* * * *
4749 AGGATATGTGTCAACTTTTTAATCCGTTTATGGAGTCCAAAATTTACACTGATAGTGTATTGTAT
186 AGG-TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTAT
* * * * *
4814 AATAAT-ACTATAAGAAAAATTATACAATTC-CTGTTAGTGAATTTTAGCAAACTGCACGTGCAG
250 AATAATCA-TATAAAAAAAATTATACAATACACCGTCAGTGAATTTTAGCAGACTGCACGTGCAG
** * *
4877 AATTTAAGGGTTGACATGTGT-CCCTTAGGAAATATGTATTAATCA--AATATTTAATTAATTAT
314 GGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAAT-ATTTATATTTAATTAATTAT
* *
4939 GAAGTGCAGTATGTGTC
378 GAAATG-GGTATGTGTC
* * *
4956 AACTTCTTAA-TCCACTTATGTAGTCCAAAATTTATACTGACAGTGTATTGTATAATAATCCTAT
1 AACTTCTTAACT-CGCTTATGAAGTCCAAAATTTACACTGACAG-GTATTGTATAATAATCCTAT
** * *
5020 AAGAAAAATTATGTAATACACCGTCAGTAGAGTTTAGCAGAC-ACGTGCGA-GGTTTAAGGGTTG
64 AAGAAAAATTATACAATACACCGTCAGTAGAGTTTAGCAGACTGCATGCGAGGGTTTAAGGGTTG
* * * * ** *
5083 ACATTTGTCCCATCAGGGAATATGTATTAAAATTAAATATTTAATTAATTATGAAATCGGGTATG
129 ACATATGTCCCCTTAGGGAATATGTATTAATATTTTATATTTAATTAATTATGAAAT-AGGTATG
* * *
5148 TGTCAA-TTCTTAACCCGCTTATGGAGTCCAAACTTTACACTAACAATGTATTGTATAATAATCA
193 TGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCA
* * * **
5212 TATAAAAAAAATTATACAATACACCATCAGTTG-AGTTTAGCAGACTGCACGCGTGGGGTTTAAG
258 TATAAAAAAAATTATACAATACACCGTCAG-TGAATTTTAGCAGACTGCACGTGCAGGGTTTAAG
*
5276 GGTTGACACGTGTCCCCTTAGGGAATATGTATTAATATTTTATATTTAATTAATTATGAAATTGG
322 GGTTGACATGTGTCCCCTTAGGGAATATGTATTAATA-TTTATATTTAATTAATTATGAAA-TGG
*
5341 GTATGTGTT
385 GTATGTGTC
* ** *
5350 AACTTTTTAACTCGCTTATGAAGTCCAAAATTTACACTGACA-GTA-TGTATAATAATGATTTAA
1 AACTTCTTAACTCGCTTATGAAGTCCAAAATTTACACTGACAGGTATTGTATAATAATCCTATAA
* * *
5413 -AAAAATTATACAATACACCGTCAGTGGAGTTTAACAGACTGCATGCGCAGGGTTTAAGAGTTGA
66 GAAAAATTATACAATACACCGTCAGTAGAGTTTAGCAGACTGCATGCG-AGGGTTTAAGGGTTGA
*
5477 CATATGTCCCCTTAGGGAATATGTATTAATATTTTATATTTAATTAATTATGAAATAAGGCATGT
130 CATATGTCCCCTTAGGGAATATGTATTAATATTTTATATTTAATTAATTATGAAAT-AGGTATGT
* ** *
5542 GGCAACTTCTTAACCCGCTTATGGAGTCCAAGGTTTACACTGACAGTGTATTGTATAATAATCCT
194 GTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCAT
* *
5607 ATAAAAAAAATTATATAATACACCGTCAGTGAATTTTAGCAGACTGCACGTGCATGGTTTAAGGG
259 ATAAAAAAAATTATACAATACACCGTCAGTGAATTTTAGCAGACTGCACGTGCAGGGTTTAAGGG
5672 TTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTAATTAATTATGAAATGGG
324 TTGACATGTGTCCCCTTAGGGAATATGTATTAATATT---TATATTTAATTAATTATGAAATGGG
5737 ATATGTGTC
386 -TATGTGTC
* * *
5746 AACTTCTTAACCCGCTTATAAAGTCCAAAATTTACA-TTAGCAGTGTATTGTATAATAATC
1 AACTTCTTAACTCGCTTATGAAGTCCAAAATTTACACTGA-CAG-GTATTGTATAATAATC
5806 ATTATTATAA
Statistics
Matches: 726, Mismatches: 94, Indels: 57
0.83 0.11 0.06
Matches are distributed among these distances:
389 3 0.00
390 139 0.19
391 87 0.12
392 29 0.04
393 77 0.11
394 206 0.28
395 10 0.01
396 138 0.19
397 1 0.00
398 4 0.01
399 32 0.04
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (393 bp):
AACTTCTTAACTCGCTTATGAAGTCCAAAATTTACACTGACAGGTATTGTATAATAATCCTATAA
GAAAAATTATACAATACACCGTCAGTAGAGTTTAGCAGACTGCATGCGAGGGTTTAAGGGTTGAC
ATATGTCCCCTTAGGGAATATGTATTAATATTTTATATTTAATTAATTATGAAATAGGTATGTGT
CAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCATAT
AAAAAAAATTATACAATACACCGTCAGTGAATTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTT
GACATGTGTCCCCTTAGGGAATATGTATTAATATTTATATTTAATTAATTATGAAATGGGTATGT
GTC
Found at i:11119 original size:22 final size:22
Alignment explanation
Indices: 11094--11195 Score: 100
Period size: 22 Copynumber: 4.6 Consensus size: 22
11084 TCACAGTGTG
11094 GTTACCAAAATTTCATATAGAA
1 GTTACCAAAATTTCATATAGAA
** *
11116 GTTATTAAAACTTCATAGT-GTAA
1 GTTACCAAAATTTCATA-TAG-AA
* * *
11139 GTTATCAAAATTTCATACAGAG
1 GTTACCAAAATTTCATATAGAA
*
11161 GTTACCAAAATTTCATA-AAAA
1 GTTACCAAAATTTCATATAGAA
11182 GGTTACCAAAATTT
1 -GTTACCAAAATTT
11196 TTTAGGGATG
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
21 2 0.03
22 45 0.68
23 19 0.29
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (22 bp):
GTTACCAAAATTTCATATAGAA
Found at i:11148 original size:23 final size:23
Alignment explanation
Indices: 11073--11177 Score: 85
Period size: 22 Copynumber: 4.7 Consensus size: 23
11063 ACATAGAAAG
* *
11073 GTTATC-AAATTTCACAGTGT-G
1 GTTATCAAAATTTCATAGTGTAA
*
11094 GTTACCAAAATTTCATA-TAG-AA
1 GTTATCAAAATTTCATAGT-GTAA
* *
11116 GTTATTAAAACTTCATAGTGTAA
1 GTTATCAAAATTTCATAGTGTAA
** *
11139 GTTATCAAAATTTCATACAG-AG
1 GTTATCAAAATTTCATAGTGTAA
*
11161 GTTACCAAAATTTCATA
1 GTTATCAAAATTTCATA
11178 AAAAGGTTAC
Statistics
Matches: 67, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
21 6 0.09
22 42 0.63
23 19 0.28
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.35
Consensus pattern (23 bp):
GTTATCAAAATTTCATAGTGTAA
Found at i:11176 original size:45 final size:44
Alignment explanation
Indices: 11054--11177 Score: 133
Period size: 45 Copynumber: 2.8 Consensus size: 44
11044 TGACAATCAA
* * * * *
11054 ACCAAAATTACATAGAAAGGTTATC-AAATTTCACAGTGTGGTT
1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT
* * * *
11097 ACCAAAATTTCATATAGAAGTTATTAAAACTTCATAGTGTAAGTT
1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGT-AGTT
* *
11142 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATA
1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATA
11178 AAAAGGTTAC
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
43 20 0.31
44 12 0.18
45 33 0.51
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (44 bp):
ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT
Found at i:11542 original size:22 final size:22
Alignment explanation
Indices: 11475--11542 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
11465 AATTTTATAG
* *
11475 GCAGATTATCAAAATTTCACACT
1 GCAG-TTACCAAAATTTCACAGT
* * *
11498 GAAGTTACCGAAATTTCATAGT
1 GCAGTTACCAAAATTTCACAGT
11520 GCAGTTACCAAAATTTCACAGT
1 GCAGTTACCAAAATTTCACAGT
11542 G
1 G
11543 TGGTTATCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 34 0.92
23 3 0.08
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (22 bp):
GCAGTTACCAAAATTTCACAGT
Found at i:11569 original size:22 final size:21
Alignment explanation
Indices: 11544--11603 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
11534 TTCACAGTGT
*
11544 GGTTATCAATTTTTCATAGGGA
1 GGTTATCAA-TTTTCATAAGGA
* *
11566 GGTTATCGAAATTTCATAATGA
1 GGTTATC-AATTTTCATAAGGA
*
11588 GGTTATTAAATTTTCA
1 GGTTA-TCAATTTTCA
11604 AAATGTGGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (21 bp):
GGTTATCAATTTTCATAAGGA
Found at i:11600 original size:21 final size:21
Alignment explanation
Indices: 11555--11619 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
11545 GTTATCAATT
** *
11555 TTTCATAGGGAGGTTATCGAAA
1 TTTCATAATGAGGTTAT-TAAA
11577 TTTCATAATGAGGTTATTAAA
1 TTTCATAATGAGGTTATTAAA
* *
11598 TTTTCAAAATGTGGTTA-TAAA
1 -TTTCATAATGAGGTTATTAAA
11619 T
1 T
11620 ATTTCTACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 7 0.19
22 29 0.78
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.40
Consensus pattern (21 bp):
TTTCATAATGAGGTTATTAAA
Found at i:11603 original size:66 final size:66
Alignment explanation
Indices: 11501--11624 Score: 151
Period size: 66 Copynumber: 1.9 Consensus size: 66
11491 TCACACTGAA
* * * * *
11501 GTTACCGAAATTTCATAGTGCAGTTACCAAAATTTCACAGTGTGGTTATCAATTTTTCATAGGGA
1 GTTACCGAAATTTCATAATGCAGTTACCAAAATTTCAAAATGTGGTTATAAATATTTCATAGGGA
11566 G
66 G
* ** *
11567 GTTATCGAAATTTCATAATG-AGGTTATTAAATTTTCAAAATGTGGTTATAAATATTTC
1 GTTACCGAAATTTCATAATGCA-GTTACCAAAATTTCAAAATGTGGTTATAAATATTTC
11625 TACATTGGAG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
65 1 0.02
66 47 0.98
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (66 bp):
GTTACCGAAATTTCATAATGCAGTTACCAAAATTTCAAAATGTGGTTATAAATATTTCATAGGGA
G
Found at i:11608 original size:22 final size:22
Alignment explanation
Indices: 11564--11624 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
11554 TTTTCATAGG
* *
11564 GAGGTTATCGAAA-TTTCATAAT
1 GAGGTTAT-TAAATTTTCAAAAT
11586 GAGGTTATTAAATTTTCAAAAT
1 GAGGTTATTAAATTTTCAAAAT
*
11608 GTGGTTA-TAAATATTTC
1 GAGGTTATTAAAT-TTTC
11625 TACATTGGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.24
22 26 0.76
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (22 bp):
GAGGTTATTAAATTTTCAAAAT
Found at i:15179 original size:10 final size:9
Alignment explanation
Indices: 15166--15199 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
15156 TTTTTTTTGA
15166 AAAAAACAGG
1 AAAAAA-AGG
15176 AAAAAAAGG
1 AAAAAAAGG
*
15185 GAAAAAAGG
1 AAAAAAAGG
15194 AAAAAA
1 AAAAAA
15200 TGCATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:16031 original size:21 final size:21
Alignment explanation
Indices: 15994--16033 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15984 TCACTTCTGA
*
15994 TTTTGAATGATCGCATTTTTG
1 TTTTGAATGATCACATTTTTG
16015 TTTTGAA-GAATCACATTTT
1 TTTTGAATG-ATCACATTTT
16034 AATACCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (21 bp):
TTTTGAATGATCACATTTTTG
Found at i:17000 original size:31 final size:31
Alignment explanation
Indices: 16869--17028 Score: 144
Period size: 31 Copynumber: 5.1 Consensus size: 31
16859 ACGTTGCATT
* *
16869 CCACGTGTACCAAAAAGTGACATGTGGCACG
1 CCACATGTACCAAAAAGTGACACGTGGCACG
* *
16900 CCACACTTAGTACC-AAAAGTGACACATGTCACG
1 CCACA--T-GTACCAAAAAGTGACACGTGGCACG
* * * *
16933 ACATATGTACCAAAAAGTGACATGTGACACG
1 CCACATGTACCAAAAAGTGACACGTGGCACG
*
16964 CCACATGTACCAAAAAGTGACACGTGGCATG
1 CCACATGTACCAAAAAGTGACACGTGGCACG
* * ** * *
16995 TCACATATTTC-AAAAGTGGCACGTGGCATG
1 CCACATGTACCAAAAAGTGACACGTGGCACG
17025 CCAC
1 CCAC
17029 GTGCACAAAA
Statistics
Matches: 105, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
30 26 0.25
31 54 0.51
33 20 0.19
34 5 0.05
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (31 bp):
CCACATGTACCAAAAAGTGACACGTGGCACG
Found at i:17002 original size:64 final size:63
Alignment explanation
Indices: 16874--16992 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 63
16864 GCATTCCACG
* *
16874 TGTACCAAAAAGTGACATGTGGCACGCCACACTTAGTACCAAAAGTGACACATGTCACGACATA
1 TGTACCAAAAAGTGACATGTGACACGCCACAC-TAGTACCAAAAGTGACACATGGCACGACATA
*
16938 TGTACCAAAAAGTGACATGTGACACGCCACA-T-GTACCAAAAAGTGACACGTGGCA
1 TGTACCAAAAAGTGACATGTGACACGCCACACTAGTACC-AAAAGTGACACATGGCA
16993 TGTCACATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
61 5 0.10
62 16 0.31
64 30 0.59
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (63 bp):
TGTACCAAAAAGTGACATGTGACACGCCACACTAGTACCAAAAGTGACACATGGCACGACATA
Found at i:21920 original size:20 final size:20
Alignment explanation
Indices: 21879--21921 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
21869 TTCTCACAAG
*
21879 TTTCTAGCCGTTGAAGCTCT
1 TTTCTAGCCGTTGAAGCACT
21899 TTTCTAGCCGTT-ATAGCACT
1 TTTCTAGCCGTTGA-AGCACT
21919 TTT
1 TTT
21922 TCCACTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTGAAGCACT
Found at i:22759 original size:21 final size:21
Alignment explanation
Indices: 22733--22773 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
22723 ACAAATAAAC
*
22733 TCACATTCCGTGAGAGTTGAT
1 TCACATCCCGTGAGAGTTGAT
22754 TCACATCCCGTGAGAGTTGA
1 TCACATCCCGTGAGAGTTGA
22774 ACCTAAGACC
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:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
TCACATCCCGTGAGAGTTGAT
Found at i:29087 original size:642 final size:644
Alignment explanation
Indices: 28276--29442 Score: 1467
Period size: 642 Copynumber: 1.8 Consensus size: 644
28266 TAATATATGA
* * * *
28276 TTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAGATATTTCCTTCAATTTTTGGCAAAAATACT
1 TTTCGGCTAAAATTCTGCAAAAATTGACCCAAAAGATATTTCCTCCAATCTTTAGCAAAAATACT
* *
28341 CATAAAAAATATATAATTATACATTAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTTT
66 CATAAAAAATATATAATTATACATCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATCGTTTT
* * *
28406 TCCTATTTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
131 TCATATTTTTTTCGAACTAATTTCTAATTAAATCGAAACAAGAATCAGATGCTCGTAAAAACAAA
* * *
28471 TCCTTAAATCCAATGTGGCTGAGATT-TGGTTAGATGAATATAGATATTTCAAGGAGTCTTGACG
196 TCCTTAAATCCAATGTGGCTAAGATTGT-ATTAGATGAATATAGATATTTCAAGGAGTCTCGACG
* * * ** **
28535 TCAAAAATCATGCAAAACTGACCCGGAGCCTCGTAACGCGTTTTTAGGGGAAAAA-AAGCGATGG
260 CCAAAAATCATGCAAAACTGACCCGGACCCTCGAAACGCCATTTTA-GCCAAAAACAA-CGAT-G
* * *
28599 T-AC-ACGATTTCGGCT-AATATTTTGCGAAAAT-TGATCTAAAATATTTTTTCTCAATTTTTAG
322 TAACTACGATTTCGGCTCAA-ATTTTACGAAAATATGACCCAAAATATTTTTTCTCAATTTTTAG
* * * * * *
28660 CCACAATACTCATTAAAAATATATAATTCAACACTAAAAAGATTGAAGGACTTTTTACGCTTCCA
386 ACAAAATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAGGACTTTTCACGCTTCCA
* ** * * *
28725 ATATCGTTTTTCCTATTTTTT-TGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTG
451 ATATC-ATTTTAATATTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCG
*
28789 TTAAAACATTGGTTGGGATTTGGTTAGATGAATATAGATATTTCAATGAGTCTCGGTGCAAAAAA
515 TAAAAACATTGGTTGGGATTTGGTTAGATGAATATAGATATTTCAATGAGTCTCGGTGCAAAAAA
28854 TCATGCAAAACTAAACTGGGCTTCGAAACATGTTTTTAGCCAAAAATCGTGATATTATTACACGT
580 TCATGCAAAACTAAACTGGGCTTCGAAACATGTTTTTAGCCAAAAATCGTGATATTATTACACGT
* * * *
28919 TTTCGGCTAAAATTCTGCAAAATTTGACCTGAAAA-ATATTTCC-CCAATCTTTAGCCACAATAC
1 TTTCGGCTAAAATTCTGCAAAAATTGACC-CAAAAGATATTTCCTCCAATCTTTAGCAAAAATAC
* ** * * *
28982 TCAT-AAAAATATATCATTCA-AGGTCGAAAAGATTGAAGGGCTTTTTATGCTT-TAAATATCGT
65 TCATAAAAAATATATAATT-ATACATCAAAAAGATTGAAGGGCTTTTAACGCTTCT-AATATCGT
* ** *
29044 TTTTCATGTTTTTTTTTTAACTAATTTCTAGTTAAATCGAAACAAGAATCAGATGCTCGTAAAAA
128 TTTTCAT-ATTTTTTTCGAACTAATTTCTAATTAAATCGAAACAAGAATCAGATGCTCGTAAAAA
* * * *
29109 CAAATCCTTAAATGCAATGTGGCTAAGATTGTATTATATGAGTATAGATATTTTAAGGAGTCTCG
192 CAAATCCTTAAATCCAATGTGGCTAAGATTGTATTAGATGAATATAGATATTTCAAGGAGTCTCG
* * ** * * *
29174 GCGCCAAAAATCATGTAAAACTGAGTCGGACCCTCGAAACGCCATTTTAGCCAAAAACCATGATT
257 ACGCCAAAAATCATGCAAAACTGACCCGGACCCTCGAAACGCCATTTTAGCCAAAAACAACGATG
* * * *
29239 TAACTTATACGATTTTGGTTCAAATTTTACTAAAATATGACCCAAAATTTTTTTTCTCAATTTTT
322 TAAC---TACGATTTCGGCTCAAATTTTACGAAAATATGACCCAAAATATTTTTTCTCAATTTTT
* * * * * * * *
29304 GGATAAAATACTCATAAAAAATATGTAATTTAACGCCAAAAAAATTGGAGGGCTTTTCACGCTTT
384 AGACAAAATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAGGACTTTTCACGCTTC
* *
29369 TAATATCATTTTAATATTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTTAGATGCTC
449 CAATATCATTTTAATATTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTC
29434 GTAAAAACA
514 GTAAAAACA
29443 AATTCTTAAA
Statistics
Matches: 436, Mismatches: 74, Indels: 25
0.81 0.14 0.05
Matches are distributed among these distances:
640 2 0.00
641 63 0.14
642 168 0.39
643 36 0.08
644 4 0.01
645 33 0.08
646 130 0.30
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (644 bp):
TTTCGGCTAAAATTCTGCAAAAATTGACCCAAAAGATATTTCCTCCAATCTTTAGCAAAAATACT
CATAAAAAATATATAATTATACATCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATCGTTTT
TCATATTTTTTTCGAACTAATTTCTAATTAAATCGAAACAAGAATCAGATGCTCGTAAAAACAAA
TCCTTAAATCCAATGTGGCTAAGATTGTATTAGATGAATATAGATATTTCAAGGAGTCTCGACGC
CAAAAATCATGCAAAACTGACCCGGACCCTCGAAACGCCATTTTAGCCAAAAACAACGATGTAAC
TACGATTTCGGCTCAAATTTTACGAAAATATGACCCAAAATATTTTTTCTCAATTTTTAGACAAA
ATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAGGACTTTTCACGCTTCCAATATC
ATTTTAATATTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAA
CATTGGTTGGGATTTGGTTAGATGAATATAGATATTTCAATGAGTCTCGGTGCAAAAAATCATGC
AAAACTAAACTGGGCTTCGAAACATGTTTTTAGCCAAAAATCGTGATATTATTACACGT
Found at i:39264 original size:22 final size:23
Alignment explanation
Indices: 39213--39264 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
39203 TTTTTTGGCA
39213 GAAAAAAAAACTAAATCAACTTT
1 GAAAAAAAAACTAAATCAACTTT
* * * *
39236 TATAAAAAAACTTAAT-TACTTT
1 GAAAAAAAAACTAAATCAACTTT
39258 GAAAAAA
1 GAAAAAA
39265 TTACTAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.60, C:0.10, G:0.04, T:0.27
Consensus pattern (23 bp):
GAAAAAAAAACTAAATCAACTTT
Found at i:39892 original size:20 final size:21
Alignment explanation
Indices: 39867--39906 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
39857 TGTCCTGATG
39867 ACACGA-TTAACACG-TTTAAC
1 ACACGAGTT-ACACGCTTTAAC
39887 ACACGAGTTACACGCTTTAA
1 ACACGAGTTACACGCTTTAA
39907 TTAACGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (21 bp):
ACACGAGTTACACGCTTTAAC
Found at i:40064 original size:14 final size:14
Alignment explanation
Indices: 40045--40072 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40035 CAATTATCTT
40045 TAATTATATATATA
1 TAATTATATATATA
40059 TAATTATATATATA
1 TAATTATATATATA
40073 ATTTAGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTATATATATA
Found at i:40068 original size:12 final size:12
Alignment explanation
Indices: 40051--40075 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40041 TCTTTAATTA
40051 TATATATATAAT
1 TATATATATAAT
40063 TATATATATAAT
1 TATATATATAAT
40075 T
1 T
40076 TAGTTAATTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATATATAAT
Found at i:42595 original size:57 final size:58
Alignment explanation
Indices: 42490--42600 Score: 179
Period size: 57 Copynumber: 1.9 Consensus size: 58
42480 CCAGTGGGAT
* *
42490 CCTCAAGAAGGAAAAAGAGTACACCCACCCCTGAAAAAGCATTCGTGTAGGCATCAGA
1 CCTCAAGAAGAAAAAAGAGTACACCCAACCCTGAAAAAGCATTCGTGTAGGCATCAGA
* *
42548 CCTCAAGAAGAAAAAAGAGTACA-CCAACCCTGAAAAAGGATTTGTGTAGGCAT
1 CCTCAAGAAGAAAAAAGAGTACACCCAACCCTGAAAAAGCATTCGTGTAGGCAT
42601 TAGGCCATGT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 27 0.55
58 22 0.45
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (58 bp):
CCTCAAGAAGAAAAAAGAGTACACCCAACCCTGAAAAAGCATTCGTGTAGGCATCAGA
Found at i:52001 original size:201 final size:201
Alignment explanation
Indices: 51656--52060 Score: 792
Period size: 201 Copynumber: 2.0 Consensus size: 201
51646 TTGGTAAGAC
*
51656 TCGAACCCCGAACCTTTCAGGCAGAAGTTTGCTTTCCTCTTGGGACTACAATTCGTCGCTGCAGC
1 TCGAACCCCAAACCTTTCAGGCAGAAGTTTGCTTTCCTCTTGGGACTACAATTCGTCGCTGCAGC
51721 CGTGGGAGAGATGAGACTACCAAAACAGACATCAAATCCAAAATTGTAGTCCGGAACATCCAAAA
66 CGTGGGAGAGATGAGACTACCAAAACAGACATCAAATCCAAAATTGTAGTCCGGAACATCCAAAA
51786 TCTCGATATTGTCCTCAATCCTCTCCCCCTTGAGATTATACCAAACTAACTTACACTTGTAGTAC
131 TCTCGATATTGTCCTCAATCCTCTCCCCCTTGAGATTATACCAAACTAACTTACACTTGTAGTAC
51851 CCATGG
196 CCATGG
51857 TCGAACCCCAAACCTTTCAGGCAGAAGTTTGCTTTCCTCTTGGGACTACAATTCGTCGCTGCAGC
1 TCGAACCCCAAACCTTTCAGGCAGAAGTTTGCTTTCCTCTTGGGACTACAATTCGTCGCTGCAGC
*
51922 CGTGGGAGAGATGAGACTACCAAAACAGACATCAAATCCAAAATTGTAGTCTGGAACATCCAAAA
66 CGTGGGAGAGATGAGACTACCAAAACAGACATCAAATCCAAAATTGTAGTCCGGAACATCCAAAA
51987 TCTCGATATTGTCCTCAATCCTCTCCCCCTTGAGATTATACCAAACTAACTTACACTTGTAGTAC
131 TCTCGATATTGTCCTCAATCCTCTCCCCCTTGAGATTATACCAAACTAACTTACACTTGTAGTAC
52052 CCATGG
196 CCATGG
52058 TCG
1 TCG
52061 TAATTATCAA
Statistics
Matches: 202, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
201 202 1.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (201 bp):
TCGAACCCCAAACCTTTCAGGCAGAAGTTTGCTTTCCTCTTGGGACTACAATTCGTCGCTGCAGC
CGTGGGAGAGATGAGACTACCAAAACAGACATCAAATCCAAAATTGTAGTCCGGAACATCCAAAA
TCTCGATATTGTCCTCAATCCTCTCCCCCTTGAGATTATACCAAACTAACTTACACTTGTAGTAC
CCATGG
Found at i:53065 original size:34 final size:33
Alignment explanation
Indices: 53020--53084 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
53010 TTATTATTAC
53020 ATATGGCGGCGT-TTAAGAAAAAATAAACGCCACT
1 ATATGGCGGCGTATT-AG-AAAAATAAACGCCACT
* *
53054 ATATGGTGGCGTATTAGTAAAATAAACGCCA
1 ATATGGCGGCGTATTAGAAAAATAAACGCCA
53085 TAATTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 13 0.46
34 13 0.46
35 2 0.07
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (33 bp):
ATATGGCGGCGTATTAGAAAAATAAACGCCACT
Found at i:53278 original size:32 final size:32
Alignment explanation
Indices: 53231--53354 Score: 178
Period size: 32 Copynumber: 3.9 Consensus size: 32
53221 GGAGCGTTTA
* *
53231 GTGGCGTTTTGTTCTTGAAACGCCACTATATG
1 GTGGCGTTTTATTCTTAAAACGCCACTATATG
* *
53263 GAGGCGTTTTATTCTTAAAATGCCACTATATG
1 GTGGCGTTTTATTCTTAAAACGCCACTATATG
* * *
53295 GTGGCGTTTTGTTCTTAAAACGCCACCATATA
1 GTGGCGTTTTATTCTTAAAACGCCACTATATG
53327 GTGGCG-TTTATTCTTAAAACGCCACTAT
1 GTGGCGTTTTATTCTTAAAACGCCACTAT
53355 TTTTGTTATA
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
31 20 0.25
32 61 0.75
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.36
Consensus pattern (32 bp):
GTGGCGTTTTATTCTTAAAACGCCACTATATG
Done.