Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013715.1 Corchorus capsularis cultivar CVL-1 contig13736, 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: 98751
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1066 original size:30 final size:29
Alignment explanation
Indices: 999--1069 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
989 ACACCGAACC
****
999 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
1028 GCCAAATAAGCCCCTGAACTCTTAAAAAA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
1057 GGTCAAATAAGCC
1 -GTCAAATAAGCC
1070 TTGTTGCCAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Found at i:1686 original size:2 final size:2
Alignment explanation
Indices: 1675--1741 Score: 93
Period size: 2 Copynumber: 34.5 Consensus size: 2
1665 AATTTAGACT
* * *
1675 TA TA TA -A TA TA TA GA TA TA GA TA TA TA -A CA 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
1715 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 T
1742 GCAACTGCAA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3971 original size:13 final size:13
Alignment explanation
Indices: 3953--3977 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3943 AATTAGCATT
3953 GAAAAAAAGAAAA
1 GAAAAAAAGAAAA
3966 GAAAAAAAGAAA
1 GAAAAAAAGAAA
3978 CATGAAGCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAAAAAAGAAAA
Found at i:6180 original size:3 final size:3
Alignment explanation
Indices: 6172--6254 Score: 67
Period size: 3 Copynumber: 27.7 Consensus size: 3
6162 GGAAGATAGC
* * * * * *
6172 GAT GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GCT GAA GAA GAA GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * * * *
6220 GAA GAA GAA GAA GAA GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
6255 ATAAATTCAT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.45, C:0.01, G:0.34, T:0.20
Consensus pattern (3 bp):
GAT
Found at i:11793 original size:348 final size:348
Alignment explanation
Indices: 11293--11972 Score: 1049
Period size: 348 Copynumber: 2.0 Consensus size: 348
11283 CAATAACATC
* * *
11293 TTGCAGAGAGTAAGTGAAGTAATTGACCGCATTGTTATTCCAGTTGCTTTAGAATTTCAAGAGCC
1 TTGCAGAGAGTAAGCGAAGTAATTGACCGCATTGTTATTCCAGTTGATTTACAATTTCAAGAGCC
* * * * *
11358 TATAGAGAAGCTGGAGTGGCTTGCTGGGTATATAGTTGATTGTCAGACTGCCAAGGCACAGACTG
66 TATAGAGAAGCTGGACTGGCTTGCCGGGTATATAGATGATTGTCAGACTGCAAAGACACAGACTG
* * *
11423 AACAAGAGTTGAGAGAAGTAAAGGAAGAGGCTGGTAATCTGGCTGGCAAGTTAGCAGAAGCCGAA
131 AACAAGAGTTGAGAGAAGTAAAGGAAGAGGCTAGTAACCTGGCTGGCAAGTTAGCAGAAGCCCAA
*
11488 GCAACTATAAAATCAGTGGAAGATGCATTGGCTGTTGCGCAGAATGATTCAAATCAACTGGCCGA
196 GCAACTATAAAATCACTGGAAGATGCATTGGCTGTTGCGCAGAATGATTCAAATCAACTGGCCGA
11553 AGAGAAGAGGGAGATGGAATTTGGGAAGAAAAATATAGAAATAGAGTTGCAGAAAGCAATGGAAG
261 AGAGAAGAGGGAGATGGAATTTGGGAAGAAAAATATAGAAATAGAGTTGCAGAAAGCAATGGAAG
11618 AAGCTCATTTGCAAAAGAGTATA
326 AAGCTCATTTGCAAAAGAGTATA
* ** * *
11641 TTGCAGAGAGTGAGCGAAGTGGTTGATCGCATTGTTATTCCAGTTGATTTACAATTTGAAGAGCC
1 TTGCAGAGAGTAAGCGAAGTAATTGACCGCATTGTTATTCCAGTTGATTTACAATTTCAAGAGCC
* *
11706 TACT-GAGAAGCTGTACTGGCTTGCCGGGTATATTGATGATTGTCAGACTGCAAAGACACAGACT
66 TA-TAGAGAAGCTGGACTGGCTTGCCGGGTATATAGATGATTGTCAGACTGCAAAGACACAGACT
*
11770 GAGA-AAGAGTTGAGGGAAGTAAAGGAAGAGGCTAGTAACCTGGCTGGCAAGTTAGCAGAAGCCC
130 GA-ACAAGAGTTGAGAGAAGTAAAGGAAGAGGCTAGTAACCTGGCTGGCAAGTTAGCAGAAGCCC
* * * * * ** *
11834 AAGCAACTATGAAATCCCTTGAAGATGCATTGGTTGTTGCGCAGAATGATTTATCTCAACTGGCT
194 AAGCAACTATAAAATCACTGGAAGATGCATTGGCTGTTGCGCAGAATGATTCAAATCAACTGGCC
* * *
11899 GAAGAGAAGAGGGAGATTGAATTTGGGAAGAAAAATATAGAAATCGAGTTGCAGAAAGGAATGGA
259 GAAGAGAAGAGGGAGATGGAATTTGGGAAGAAAAATATAGAAATAGAGTTGCAGAAAGCAATGGA
11964 AGAAGCTCA
324 AGAAGCTCA
11973 ATTACAAGCA
Statistics
Matches: 299, Mismatches: 31, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
348 297 0.99
349 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.23
Consensus pattern (348 bp):
TTGCAGAGAGTAAGCGAAGTAATTGACCGCATTGTTATTCCAGTTGATTTACAATTTCAAGAGCC
TATAGAGAAGCTGGACTGGCTTGCCGGGTATATAGATGATTGTCAGACTGCAAAGACACAGACTG
AACAAGAGTTGAGAGAAGTAAAGGAAGAGGCTAGTAACCTGGCTGGCAAGTTAGCAGAAGCCCAA
GCAACTATAAAATCACTGGAAGATGCATTGGCTGTTGCGCAGAATGATTCAAATCAACTGGCCGA
AGAGAAGAGGGAGATGGAATTTGGGAAGAAAAATATAGAAATAGAGTTGCAGAAAGCAATGGAAG
AAGCTCATTTGCAAAAGAGTATA
Found at i:16812 original size:32 final size:32
Alignment explanation
Indices: 16756--16834 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 32
16746 ACTTTTGGAT
16756 ACTTATGATGCTTCA----TTTTTTTTTAATA
1 ACTTATGATGCTTCATTTTTTTTTTTTTAATA
16784 ACTTATGATGCTTCATTTTTTTTTTTTTAATA
1 ACTTATGATGCTTCATTTTTTTTTTTTTAATA
16816 ACTTATGATGCTTCATTTT
1 ACTTATGATGCTTCATTTT
16835 GATTCTTGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
28 15 0.32
32 32 0.68
ACGTcount: A:0.23, C:0.11, G:0.08, T:0.58
Consensus pattern (32 bp):
ACTTATGATGCTTCATTTTTTTTTTTTTAATA
Found at i:17074 original size:11 final size:12
Alignment explanation
Indices: 17048--17074 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17038 GCTGTATTTG
17048 AAAAATAAAACA
1 AAAAATAAAACA
17060 AAAAATAAAACA
1 AAAAATAAAACA
17072 AAA
1 AAA
17075 CAAAACAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAATAAAACA
Found at i:29452 original size:20 final size:20
Alignment explanation
Indices: 29429--29529 Score: 54
Period size: 20 Copynumber: 5.2 Consensus size: 20
29419 CATAATAACA
29429 ATCTAAATTAATTAATTTTG
1 ATCTAAATTAATTAATTTTG
****
29449 ATCTAACA--ACA-TAATAACA
1 ATCTAA-ATTA-ATTAATTTTG
*
29468 ATCTAAAATAATTAATTTTG
1 ATCTAAATTAATTAATTTTG
**
29488 ATCTAAATTGTTTAA-TTT-
1 ATCTAAATTAATTAATTTTG
29506 A--TAAATTAGATTAATTTGTG
1 ATCTAAATTA-ATTAATTT-TG
29526 ATCT
1 ATCT
29530 TCCTTTTCAT
Statistics
Matches: 57, Mismatches: 13, Indels: 20
0.63 0.14 0.22
Matches are distributed among these distances:
16 6 0.11
17 4 0.07
18 4 0.07
19 16 0.28
20 25 0.44
21 1 0.02
22 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.44
Consensus pattern (20 bp):
ATCTAAATTAATTAATTTTG
Found at i:29469 original size:39 final size:39
Alignment explanation
Indices: 29415--29493 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
29405 CTTTTATACT
*
29415 ACAACATAATAACAATCTAAATTAATTAATTTTGATCTA
1 ACAACATAATAACAATCTAAAATAATTAATTTTGATCTA
29454 ACAACATAATAACAATCTAAAATAATTAATTTTGATCTA
1 ACAACATAATAACAATCTAAAATAATTAATTTTGATCTA
29493 A
1 A
29494 ATTGTTTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.34
Consensus pattern (39 bp):
ACAACATAATAACAATCTAAAATAATTAATTTTGATCTA
Found at i:29887 original size:17 final size:19
Alignment explanation
Indices: 29859--29895 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
29849 AGTTTATGAC
29859 AGTTTTTGTTAAATG-TAT
1 AGTTTTTGTTAAATGATAT
29877 AGTTTTT-TTAAATGATAT
1 AGTTTTTGTTAAATGATAT
29895 A
1 A
29896 AATAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (19 bp):
AGTTTTTGTTAAATGATAT
Found at i:30412 original size:20 final size:21
Alignment explanation
Indices: 30379--30418 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
30369 AAATATTATA
* *
30379 TTTATTCTATAATGGGTAGTT
1 TTTATTCTAAAATGAGTAGTT
30400 TTTA-TCTAAAATGAGTAGT
1 TTTATTCTAAAATGAGTAGT
30419 AGTTTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.47
Consensus pattern (21 bp):
TTTATTCTAAAATGAGTAGTT
Found at i:32403 original size:19 final size:18
Alignment explanation
Indices: 32374--32418 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
32364 GGCAAATTAA
32374 CATTTTTTTATGTATATG
1 CATTTTTTTATGTATATG
*
32392 CATTTTTATTATGTCTATG
1 CATTTTT-TTATGTATATG
32411 -ATTTTTTT
1 CATTTTTTT
32419 TGCCATATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 13 0.52
19 10 0.40
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.64
Consensus pattern (18 bp):
CATTTTTTTATGTATATG
Found at i:33366 original size:121 final size:121
Alignment explanation
Indices: 33149--33387 Score: 424
Period size: 121 Copynumber: 2.0 Consensus size: 121
33139 GTCCACCACA
* * *
33149 TCATTCATGGTCCTGGTCAATAAGATCGTGACACGTTAGATTTTTTTCTAAAATTCAAGCACAAA
1 TCATTCATGGTCCTGATCAATAAGATCGTGACACGTCAGATTTTTTCCTAAAATTCAAGCACAAA
* * *
33214 TTTAGCATCAGGTTTAGCCCCAACTTTAACCATATGTGAGATTTACAGGGTAAATC
66 GTTAGCACCAGGTTTAGCCCCAACTTAAACCATATGTGAGATTTACAGGGTAAATC
33270 TCATTCATGGTCCTGATCAATAAGATCGTGACACGTCAGATTTTTTCCTAAAATTCAAGCACAAA
1 TCATTCATGGTCCTGATCAATAAGATCGTGACACGTCAGATTTTTTCCTAAAATTCAAGCACAAA
33335 GTTAGCACCAGGTTTAGCCCCAACTTAAACCATATGTGAGATTTACAGGGTAA
66 GTTAGCACCAGGTTTAGCCCCAACTTAAACCATATGTGAGATTTACAGGGTAA
33388 GCCCCTAAAT
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 112 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (121 bp):
TCATTCATGGTCCTGATCAATAAGATCGTGACACGTCAGATTTTTTCCTAAAATTCAAGCACAAA
GTTAGCACCAGGTTTAGCCCCAACTTAAACCATATGTGAGATTTACAGGGTAAATC
Found at i:34399 original size:167 final size:164
Alignment explanation
Indices: 33908--34399 Score: 607
Period size: 167 Copynumber: 3.0 Consensus size: 164
33898 TCATTTGTCA
*
33908 ATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAA
1 ATTGAGAAATGACCAAAAAG-TTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAA
* * * * *
33973 GTAATCTGCCAAGTAGGTAAAGACG-AAAAAATTAGTTCTCTAGCTCATCATCAATCCTTGATGG
65 GTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCATTAATCCTTGGTAG
* * * *
34037 GGATCTTTTATTAATTCCACTACTCTATTCAAGTCC
130 GGATCTTTTAGTAATTCCACTAGTTTATTAAAGT-C
* * *
34073 ATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTTAATAATCAAAAGTTAGGACATTTAA
1 ATTGAGAAATGACCAAAAAG-TTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAA
* * * *
34138 GTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACT-C-CAATAGCATGTCTTGG
65 GTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCATTA--AT-CCTTGG
*
34201 TAGGGATCTTTTAGTAATTCCACTGGTTTATTAAAGTC
127 TAGGGATCTTTTAGTAATTCCACTAGTTTATTAAAGTC
* * *
34239 AGTTGAGAAATGACCAAAAAGTCTAATTATTTAATCACCTCAAGAATAAAAAGTTAGGGCATTTA
1 A-TTGAGAAATGACCAAAAAGT-TAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTA
* * * **
34304 AGTAATCGGTCAAGT-GTGAAAAGACGAAAAAAATTAGTTCTCTCGCTCCTCATTAATCCGGGGT
64 AGTAATCTGCCAAGTAG-GAAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCATTAATCCTTGGT
*
34368 AGGAATCTTTTAGTAATTTCCA-TATGTTTATT
128 AGGGATCTTTTAGTAA-TTCCACTA-GTTTATT
34400 CAAATAATAT
Statistics
Matches: 281, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
164 3 0.01
165 85 0.30
166 44 0.16
167 144 0.51
168 1 0.00
169 4 0.01
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (164 bp):
ATTGAGAAATGACCAAAAAGTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAG
TAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCATTAATCCTTGGTAGG
GATCTTTTAGTAATTCCACTAGTTTATTAAAGTC
Found at i:35072 original size:18 final size:18
Alignment explanation
Indices: 35049--35091 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
35039 ATTCATAACA
35049 AATTTATAATTAATTT-AT
1 AATTTATAATT-ATTTGAT
35067 AATTTATAATTATTTGAT
1 AATTTATAATTATTTGAT
35085 AATTTAT
1 AATTTAT
35092 TTTATATAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
AATTTATAATTATTTGAT
Found at i:36336 original size:32 final size:31
Alignment explanation
Indices: 36255--36350 Score: 90
Period size: 32 Copynumber: 3.2 Consensus size: 31
36245 CTACTGAAAG
**
36255 AAAAAGCCCAAATATACCATA-TTCGCCC-A
1 AAAAAGCCCAAATATACCATACTTAACCCAA
** * *
36284 AAAAA-TTCAAGTATAACATACTTAACCCAAA
1 AAAAAGCCCAAATATACCATACTTAACCC-AA
* *
36315 AAAAAGCCCAAATATACCATACTTTACCCGA
1 AAAAAGCCCAAATATACCATACTTAACCCAA
36346 AAAAA
1 AAAAA
36351 TATAAAGATG
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
28 11 0.22
29 10 0.20
31 12 0.24
32 18 0.35
ACGTcount: A:0.51, C:0.25, G:0.05, T:0.19
Consensus pattern (31 bp):
AAAAAGCCCAAATATACCATACTTAACCCAA
Found at i:38673 original size:16 final size:16
Alignment explanation
Indices: 38653--38776 Score: 115
Period size: 16 Copynumber: 7.6 Consensus size: 16
38643 ACATTTGTGT
*
38653 TCGGGTCAATCGGGTT
1 TCGGGTCAATCGGGTC
38669 TCGGGTCAATCGGGTC
1 TCGGGTCAATCGGGTC
* *
38685 TCGGGTTATTCGGGTC
1 TCGGGTCAATCGGGTC
* *
38701 TCGGGTCATTCGGTTC
1 TCGGGTCAATCGGGTC
*
38717 TCGGGTTAATCGGGTC
1 TCGGGTCAATCGGGTC
* * *
38733 TCGGATTATTCGGGT-
1 TCGGGTCAATCGGGTC
*
38748 TCGGGTTTAGACTTCGGGTC
1 TCGGG-TCA-A--TCGGGTC
38768 TCGGGTCAA
1 TCGGGTCAA
38777 ATGGGTCAGT
Statistics
Matches: 90, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
15 4 0.04
16 72 0.80
18 1 0.01
19 8 0.09
20 5 0.06
ACGTcount: A:0.11, C:0.20, G:0.35, T:0.33
Consensus pattern (16 bp):
TCGGGTCAATCGGGTC
Found at i:38698 original size:32 final size:32
Alignment explanation
Indices: 38653--38775 Score: 140
Period size: 32 Copynumber: 3.8 Consensus size: 32
38643 ACATTTGTGT
* * *
38653 TCGGGTCAATCGGGTTTCGGGTCAATCGGGTC
1 TCGGGTTAATCGGGTCTCGGGTCATTCGGGTC
* *
38685 TCGGGTTATTCGGGTCTCGGGTCATTCGGTTC
1 TCGGGTTAATCGGGTCTCGGGTCATTCGGGTC
* *
38717 TCGGGTTAATCGGGTCTCGGATTATTCGGGT-
1 TCGGGTTAATCGGGTCTCGGGTCATTCGGGTC
38748 TCGGGTTTAGACTTCGGGTCTCGGGTCA
1 TCGGG-TTA-A--TCGGGTCTCGGGTCA
38776 AATGGGTCAG
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
31 5 0.07
32 57 0.75
33 1 0.01
35 13 0.17
ACGTcount: A:0.11, C:0.20, G:0.36, T:0.33
Consensus pattern (32 bp):
TCGGGTTAATCGGGTCTCGGGTCATTCGGGTC
Found at i:38721 original size:48 final size:47
Alignment explanation
Indices: 38651--38753 Score: 154
Period size: 48 Copynumber: 2.2 Consensus size: 47
38641 GGACATTTGT
*
38651 GTTCGGGTCAATCGGGTTTCGGGTCAATCGGGTCTCGGGTTATTCGG
1 GTTCGGGTCAATCGGGTTTCGGGTCAATCGGGTCTCGGATTATTCGG
* *
38698 GTCTCGGGTCATTC-GGTTCTCGGGTTAATCGGGTCTCGGATTATTCGG
1 GT-TCGGGTCAATCGGGTT-TCGGGTCAATCGGGTCTCGGATTATTCGG
38746 GTTCGGGT
1 GTTCGGGT
38754 TTAGACTTCG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
47 12 0.24
48 39 0.76
ACGTcount: A:0.10, C:0.19, G:0.37, T:0.34
Consensus pattern (47 bp):
GTTCGGGTCAATCGGGTTTCGGGTCAATCGGGTCTCGGATTATTCGG
Found at i:39155 original size:13 final size:13
Alignment explanation
Indices: 39123--39159 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
39113 ACAAAACAAG
39123 TTTATTCTATTTTC
1 TTTATTCTA-TTTC
*
39137 TATATTCTATTTC
1 TTTATTCTATTTC
39150 TTTATTCTAT
1 TTTATTCTAT
39160 AATTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATTCTATTTC
Found at i:39327 original size:16 final size:16
Alignment explanation
Indices: 39306--39348 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
39296 TCAACTTTTT
*
39306 GGGTCATTCGGATTTC
1 GGGTCATACGGATTTC
*
39322 GGGTCATACGGGTTTC
1 GGGTCATACGGATTTC
*
39338 GGGTTATACGG
1 GGGTCATACGG
39349 GTCTCGGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.14, C:0.16, G:0.37, T:0.33
Consensus pattern (16 bp):
GGGTCATACGGATTTC
Found at i:39349 original size:16 final size:16
Alignment explanation
Indices: 39318--39360 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
39308 GTCATTCGGA
*
39318 TTTCGGGTCATACGGG
1 TTTCGGGTTATACGGG
39334 TTTCGGGTTATACGGG
1 TTTCGGGTTATACGGG
* *
39350 TCTCGGATTAT
1 TTTCGGGTTAT
39361 TTGGGTCACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.14, C:0.16, G:0.33, T:0.37
Consensus pattern (16 bp):
TTTCGGGTTATACGGG
Found at i:46295 original size:77 final size:77
Alignment explanation
Indices: 46168--46318 Score: 275
Period size: 77 Copynumber: 2.0 Consensus size: 77
46158 GATTATTGAG
* *
46168 CTTAATCAAGCGAGTTTGAATAACTTTGTAAAAATTGAATTCTACAAATAAAACTCAATCGAGTT
1 CTTAATCAAGCAAGTTTGAATAACTTCGTAAAAATTGAATTCTACAAATAAAACTCAATCGAGTT
46233 CGAGTCAAGTTT
66 CGAGTCAAGTTT
*
46245 CTTAATCAAGCAAGTTTGAATAACTTCGTTAAAATTGAATTCTACAAATAAAACTCAATCGAGTT
1 CTTAATCAAGCAAGTTTGAATAACTTCGTAAAAATTGAATTCTACAAATAAAACTCAATCGAGTT
46310 CGAGTCAAG
66 CGAGTCAAG
46319 CTTCGAGCAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (77 bp):
CTTAATCAAGCAAGTTTGAATAACTTCGTAAAAATTGAATTCTACAAATAAAACTCAATCGAGTT
CGAGTCAAGTTT
Found at i:50016 original size:336 final size:336
Alignment explanation
Indices: 49403--50076 Score: 1132
Period size: 336 Copynumber: 2.0 Consensus size: 336
49393 TAGAGATCGT
*
49403 GCAATTGATATAGTACCTCTTGAGCGTCCCAACTCTCTGATTGGTGACCACTTGAGTGATAATGC
1 GCAATTGATATAGTACCTCTAGAGCGTCCCAACTCTCTGATTGGTGACCACTTGAGTGATAATGC
* * * *
49468 TGAAAAAGATGGCACAGCTGATGGAAAAGAGGCATCAAAAAGGGATACATCCGAATATTCGCCTT
66 TGAAAAAGATGGAACAACTGATGGAAAAGAAGCATCAAAAAGGGATACATCAGAATATTCGCCTT
* * * *
49533 CAGTTACTGATATGGGAGCTGATGATGTAATTCGTGTTGTGCTGGATTCCTTGCAGCAAGACAAC
131 CAGTTACTGATATGGGAGCTGATGAAGTAACTCGTGATGTGCTGGAGTCCTTGCAGCAAGACAAC
* * *
49598 AATAGCCCAGCAAATGCAGAAAATCTGGATAAGGAGTCATCAAGGAAGAAAAGGAAGAAGAAAAG
196 AATAGCCCAGCAAATGCAGAAAATATGGATAAGAAGTCATCAAGGAAGAAAAGCAAGAAGAAAAG
*
49663 TTCAACCATTGTGGACCTTCCGGAATTGCAAGAAAAAGATGATGTTGATCACCAGGATCCAACCA
261 TTCAACCATTGTGGACCTTCCAGAATTGCAAGAAAAAGATGATGTTGATCACCAGGATCCAACCA
49728 TCCCGGCCGCA
326 TCCCGGCCGCA
49739 GCAATTGATATAGTACCTCTAGAGCGTCCCAACTCTCTGATTGGTGACCACTTGAGTGATAATGC
1 GCAATTGATATAGTACCTCTAGAGCGTCCCAACTCTCTGATTGGTGACCACTTGAGTGATAATGC
* *
49804 TGAAAAAGATGGAACAACTGATGGAAAAGAAGCATCAAAAAGGGATACATTAGAATATTTGCCTT
66 TGAAAAAGATGGAACAACTGATGGAAAAGAAGCATCAAAAAGGGATACATCAGAATATTCGCCTT
* *
49869 CAGTTACTGATATGGGAGCTGATGAAGTAACTGGTGATGTGCTGGAGTCCTTGCAGCAAGGCAAC
131 CAGTTACTGATATGGGAGCTGATGAAGTAACTCGTGATGTGCTGGAGTCCTTGCAGCAAGACAAC
* ** *
49934 AATGGCCTGGCAAATGCAGAAAATATGGTTAAGAAGTCATCAAGGAAGAAAAGCAAGAAGAAAAG
196 AATAGCCCAGCAAATGCAGAAAATATGGATAAGAAGTCATCAAGGAAGAAAAGCAAGAAGAAAAG
* * *
49999 TTCTACCATTGTGGACCTTCCAGAATTGCAAGGAAAAGATGATGTTGATCACCAGGATCCAATCA
261 TTCAACCATTGTGGACCTTCCAGAATTGCAAGAAAAAGATGATGTTGATCACCAGGATCCAACCA
50064 TCCCGGCCGCA
326 TCCCGGCCGCA
50075 GC
1 GC
50077 CGAATACTTC
Statistics
Matches: 314, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
336 314 1.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.22
Consensus pattern (336 bp):
GCAATTGATATAGTACCTCTAGAGCGTCCCAACTCTCTGATTGGTGACCACTTGAGTGATAATGC
TGAAAAAGATGGAACAACTGATGGAAAAGAAGCATCAAAAAGGGATACATCAGAATATTCGCCTT
CAGTTACTGATATGGGAGCTGATGAAGTAACTCGTGATGTGCTGGAGTCCTTGCAGCAAGACAAC
AATAGCCCAGCAAATGCAGAAAATATGGATAAGAAGTCATCAAGGAAGAAAAGCAAGAAGAAAAG
TTCAACCATTGTGGACCTTCCAGAATTGCAAGAAAAAGATGATGTTGATCACCAGGATCCAACCA
TCCCGGCCGCA
Found at i:54204 original size:18 final size:20
Alignment explanation
Indices: 54183--54226 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
54173 ATAGTATATA
*
54183 ATATA-ATAAAT-ATATACT
1 ATATACATAAATAATAGACT
*
54201 ATATACTTAAATAATAGACT
1 ATATACATAAATAATAGACT
54221 ATATAC
1 ATATAC
54227 CTCAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 5 0.23
20 12 0.55
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.36
Consensus pattern (20 bp):
ATATACATAAATAATAGACT
Found at i:54223 original size:20 final size:19
Alignment explanation
Indices: 54189--54226 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
54179 TATAATATAA
*
54189 TAAATATATACTATATACT
1 TAAATATAGACTATATACT
54208 TAAATAATAGACTATATAC
1 TAAAT-ATAGACTATATAC
54227 CTCAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (19 bp):
TAAATATAGACTATATACT
Found at i:56138 original size:2 final size:2
Alignment explanation
Indices: 56131--56156 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56121 AATATAAGAA
56131 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
56157 TAAACTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62036 original size:25 final size:25
Alignment explanation
Indices: 62001--62049 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
61991 TTCAGGAGGA
*
62001 AAATGTTTATTAAGTCGTTACACAG
1 AAATGTGTATTAAGTCGTTACACAG
62026 AAATGTGTATTAAGTCGTTACACA
1 AAATGTGTATTAAGTCGTTACACA
62050 ATTGTAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (25 bp):
AAATGTGTATTAAGTCGTTACACAG
Found at i:62621 original size:22 final size:22
Alignment explanation
Indices: 62533--62621 Score: 76
Period size: 22 Copynumber: 4.1 Consensus size: 22
62523 TTTCATGTCC
*
62533 TAAGGAGAATACCAAAATTTCA
1 TAAGGAGATTACCAAAATTTCA
* * *
62555 TAAGAAAATTATCAAAATTTC-
1 TAAGGAGATTACCAAAATTTCA
* *
62576 TTAGTGACG-TTACC-AAATTACA
1 TAAG-GA-GATTACCAAAATTTCA
*
62598 TAAGGAGTTTACCAAAATTTCA
1 TAAGGAGATTACCAAAATTTCA
62620 TA
1 TA
62622 GTGTGGTTTT
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
20 1 0.02
21 16 0.31
22 34 0.67
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.30
Consensus pattern (22 bp):
TAAGGAGATTACCAAAATTTCA
Found at i:62679 original size:56 final size:58
Alignment explanation
Indices: 62590--62705 Score: 148
Period size: 56 Copynumber: 2.0 Consensus size: 58
62580 TGACGTTACC
* * * *
62590 AAATTACATAAGGAGTTTACCAAAATTTCATAGTGT-GGTTTTCAAAATTTTATAAGA
1 AAATTACATAAGGAGGTAACCAAAATTTCATAGTGTGGGTTATCAAAATTTCATAAGA
*
62647 AAATTA-ATAGGGAGGTAACCAAAA-TTCTATAGTGTGGGGTTATCAAAATTTCATAAGA
1 AAATTACATAAGGAGGTAACCAAAATTTC-ATAGTGT-GGGTTATCAAAATTTCATAAGA
62705 A
1 A
62706 GGTTACTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
55 3 0.06
56 22 0.43
57 6 0.12
58 20 0.39
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (58 bp):
AAATTACATAAGGAGGTAACCAAAATTTCATAGTGTGGGTTATCAAAATTTCATAAGA
Found at i:62790 original size:22 final size:22
Alignment explanation
Indices: 62685--62802 Score: 150
Period size: 22 Copynumber: 5.4 Consensus size: 22
62675 ATAGTGTGGG
*
62685 GTTATCAAAATTTCATA-AGAA
1 GTTACCAAAATTTCATAGAGAA
* * *
62706 GGTTACTAAAATTCCATAGAGAG
1 -GTTACCAAAATTTCATAGAGAA
62729 GTTACCAAAATTTCATAG-GAAA
1 GTTACCAAAATTTCATAGAG-AA
62751 GTTACCAAAATTTCATAGAGAA
1 GTTACCAAAATTTCATAGAGAA
* *
62773 GTTACCAAAATTTCATAGTGTA
1 GTTACCAAAATTTCATAGAGAA
62795 GTTACCAA
1 GTTACCAA
62803 TTTTTTTTTA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
21 1 0.01
22 79 0.94
23 4 0.05
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (22 bp):
GTTACCAAAATTTCATAGAGAA
Found at i:62790 original size:44 final size:44
Alignment explanation
Indices: 62685--62928 Score: 194
Period size: 44 Copynumber: 5.8 Consensus size: 44
62675 ATAGTGTGGG
* * * * *
62685 GTTATCAAAATTTCATAAGAAGGTTACTAAAATTCCATAGAGAG
1 GTTACCAAAATTTCATAGGAAGGTTACCAAAATTTCATAGAGAA
*
62729 GTTACCAAAATTTCATAGGAAAGTTACCAAAATTTCATAGAGAA
1 GTTACCAAAATTTCATAGGAAGGTTACCAAAATTTCATAGAGAA
* * ** **
62773 GTTACCAAAATTTCATAGTGTA-GTTACC-AATTTTTTTTTAGAA
1 GTTACCAAAATTTCATAG-GAAGGTTACCAAAATTTCATAGAGAA
* *
62816 ---A--AAAA---CATAGGAAGGTTACCAAAATTTAATAGCGAA
1 GTTACCAAAATTTCATAGGAAGGTTACCAAAATTTCATAGAGAA
* * *
62852 -TTACTAAAATTTCATAAGAAGGTTACCAAGA-TTCATAGAG-A
1 GTTACCAAAATTTCATAGGAAGGTTACCAAAATTTCATAGAGAA
* *
62893 GTTTACCAAAATTTCATACG-AGGGT-CCAAAATTTCA
1 G-TTACCAAAATTTCATAGGAAGGTTACCAAAATTTCA
62929 CGAGGAGATT
Statistics
Matches: 160, Mismatches: 27, Indels: 28
0.74 0.13 0.13
Matches are distributed among these distances:
34 2 0.01
35 11 0.07
36 9 0.06
38 5 0.03
40 5 0.03
41 6 0.04
42 15 0.09
43 43 0.27
44 62 0.39
45 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (44 bp):
GTTACCAAAATTTCATAGGAAGGTTACCAAAATTTCATAGAGAA
Found at i:62886 original size:21 final size:23
Alignment explanation
Indices: 62828--62928 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 23
62818 AAACATAGGA
* *
62828 AGGTTACCAAAATTTAAT-AGCG
1 AGGTTACCAAAATTTCATAAGAG
* *
62850 A-ATTACTAAAATTTCATAAGA-
1 AGGTTACCAAAATTTCATAAGAG
*
62871 AGGTTACCAAGA-TTCAT-AGAG
1 AGGTTACCAAAATTTCATAAGAG
* *
62892 AGTTTACCAAAATTTCATACGAG
1 AGGTTACCAAAATTTCATAAGAG
62915 -GG-T-CCAAAATTTCA
1 AGGTTACCAAAATTTCA
62929 CGAGGAGATT
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
20 14 0.22
21 30 0.48
22 16 0.25
23 3 0.05
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (23 bp):
AGGTTACCAAAATTTCATAAGAG
Found at i:62904 original size:43 final size:43
Alignment explanation
Indices: 62821--62926 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 43
62811 TAGAAAAAAA
* * *
62821 CATAGGAAGGTTACCAAAATTTAATAGCGAATTACTAAAATTT
1 CATAAGAAGGTTACCAAAATTTAATAGAGAATTACCAAAATTT
* * *
62864 CATAAGAAGGTTACCAAGA-TTCATAGAGAGTTTACCAAAATTT
1 CATAAGAAGGTTACCAAAATTTAATAGAGA-ATTACCAAAATTT
* *
62907 CATACG-AGGGT-CCAAAATTT
1 CATAAGAAGGTTACCAAAATTT
62927 CACGAGGAGA
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
41 5 0.10
42 14 0.27
43 33 0.63
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (43 bp):
CATAAGAAGGTTACCAAAATTTAATAGAGAATTACCAAAATTT
Found at i:63298 original size:22 final size:22
Alignment explanation
Indices: 63270--63356 Score: 79
Period size: 22 Copynumber: 4.0 Consensus size: 22
63260 ACATGGAATT
63270 CAAAATTTCATAGGGAGATTAC
1 CAAAATTTCATAGGGAGATTAC
* * *
63292 CAAAATTTCATAAGTAGATTAT
1 CAAAATTTCATAGGGAGATTAC
* * *
63314 TAGAA-TTCAATAGGAAAGA-TAC
1 CAAAATTTC-ATAGG-GAGATTAC
*
63336 CAAAATTTCATAGAGAGATTA
1 CAAAATTTCATAGGGAGATTA
63357 TCTATCACAG
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
21 6 0.12
22 37 0.76
23 6 0.12
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (22 bp):
CAAAATTTCATAGGGAGATTAC
Found at i:64288 original size:17 final size:17
Alignment explanation
Indices: 64266--64301 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
64256 TATAATAAAC
64266 AAAACATTTAGAAAATT
1 AAAACATTTAGAAAATT
64283 AAAACATTTAGAAAATT
1 AAAACATTTAGAAAATT
64300 AA
1 AA
64302 CTATTGACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (17 bp):
AAAACATTTAGAAAATT
Found at i:66667 original size:2 final size:2
Alignment explanation
Indices: 66660--66688 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
66650 ACAGTTTATT
66660 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
66689 TTATTACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:71423 original size:20 final size:20
Alignment explanation
Indices: 71398--71436 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
71388 CTGTTTGGCA
*
71398 TTGTTGCCATTTTTGTTTTC
1 TTGTTGCCATTTTTATTTTC
71418 TTGTTGCCATTTTTATTTT
1 TTGTTGCCATTTTTATTTT
71437 TTGAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.13, G:0.13, T:0.67
Consensus pattern (20 bp):
TTGTTGCCATTTTTATTTTC
Found at i:72717 original size:11 final size:11
Alignment explanation
Indices: 72697--72741 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
72687 AACAGCGCAG
72697 CAAAAACAAAA
1 CAAAAACAAAA
*
72708 CAAAAGCAAAA
1 CAAAAACAAAA
72719 CAAAAACAAAA
1 CAAAAACAAAA
72730 -AACAAA-AAAA
1 CAA-AAACAAAA
72740 CA
1 CA
72742 GAAGTGATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 6 0.20
11 24 0.80
ACGTcount: A:0.80, C:0.18, G:0.02, T:0.00
Consensus pattern (11 bp):
CAAAAACAAAA
Found at i:72730 original size:6 final size:6
Alignment explanation
Indices: 72697--72737 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
72687 AACAGCGCAG
*
72697 CAAAAA C-AAAA CAAAAG C-AAAA CAAAAA CAAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA C-AAAAA CAAAAA
72738 AACAGAAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 9 0.30
6 15 0.50
7 6 0.20
ACGTcount: A:0.80, C:0.17, G:0.02, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:80934 original size:37 final size:37
Alignment explanation
Indices: 80884--80954 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
80874 CTCGAATCTA
80884 CTTAAGCTGGAACAAGTCTATGTACACAATGTCTTTG
1 CTTAAGCTGGAACAAGTCTATGTACACAATGTCTTTG
* **
80921 CTTAAGCTGGAACAAGTCTGTGTATGCAATGTCT
1 CTTAAGCTGGAACAAGTCTATGTACACAATGTCT
80955 CGAACCTGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (37 bp):
CTTAAGCTGGAACAAGTCTATGTACACAATGTCTTTG
Found at i:83048 original size:56 final size:58
Alignment explanation
Indices: 82962--83078 Score: 166
Period size: 56 Copynumber: 2.0 Consensus size: 58
82952 TATCTTCTAT
* *
82962 ACTAACAAATAAATGATTAATCGAAGTGAT-A-AGCGATCCTTATCTGAATAAGGGTA
1 ACTAACAAATAAATAATTAATCGAAGTGATAACAGCGATCCTTATCTGAACAAGGGTA
* *
83018 ACTAATAAATAATTAATTAATCGAAGTGATAAGCTAGCGATCCTTATCTGAACAAGGGTA
1 ACTAACAAATAAATAATTAATCGAAGTGATAA-C-AGCGATCCTTATCTGAACAAGGGTA
83078 A
1 A
83079 GAAGACAAGG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
56 27 0.51
57 1 0.02
60 25 0.47
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (58 bp):
ACTAACAAATAAATAATTAATCGAAGTGATAACAGCGATCCTTATCTGAACAAGGGTA
Found at i:87423 original size:15 final size:15
Alignment explanation
Indices: 87403--87432 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
87393 ACTCACTTAA
87403 TAACATATTCGGTTG
1 TAACATATTCGGTTG
87418 TAACATATTCGGTTG
1 TAACATATTCGGTTG
87433 CATGTAACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
TAACATATTCGGTTG
Found at i:92422 original size:7 final size:7
Alignment explanation
Indices: 92410--92444 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
92400 TCTTTAGTAG
92410 TTGGTAC
1 TTGGTAC
92417 TTGGTAC
1 TTGGTAC
92424 TTGGTAC
1 TTGGTAC
92431 TTGGTAC
1 TTGGTAC
92438 TTGGTAC
1 TTGGTAC
92445 CAAAATATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (7 bp):
TTGGTAC
Done.