Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010089.1 Corchorus capsularis cultivar CVL-1 contig10110, 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: 60868
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:335 original size:2 final size:2
Alignment explanation
Indices: 328--352 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
318 AATTTATGTT
328 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 T
353 TGCTTAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:903 original size:33 final size:33
Alignment explanation
Indices: 861--960 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
851 AAAAGACCGT
* *
861 GCCATGGCTTGGTCACGACCCGCGCGCGACCCG
1 GCCATGGCTTGGTCGCGACCCGCTCGCGACCCG
* *
894 GCCATGGCTTGGTCGTGATCCGCTCGCGACCCG
1 GCCATGGCTTGGTCGCGACCCGCTCGCGACCCG
* *
927 GCCATGGCATGGTTGCGACCCGCTCGCGACCCG
1 GCCATGGCTTGGTCGCGACCCGCTCGCGACCCG
960 G
1 G
961 TCCAGTTTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.11, C:0.39, G:0.34, T:0.16
Consensus pattern (33 bp):
GCCATGGCTTGGTCGCGACCCGCTCGCGACCCG
Found at i:1058 original size:19 final size:19
Alignment explanation
Indices: 996--1058 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
986 TTAAATCTTA
996 ATTTTAATAATTA-TTAATT
1 ATTTT-ATAATTATTTAATT
* *
1015 AATTTATTAATTAGTTTTTATT
1 ATTTTA-TAATTA--TTTAATT
1037 ATTTTATAATTATTTAATT
1 ATTTTATAATTATTTAATT
1056 ATT
1 ATT
1059 GACTAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 1 0.03
19 19 0.53
21 6 0.17
22 10 0.28
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTTATAATTATTTAATT
Found at i:1299 original size:19 final size:20
Alignment explanation
Indices: 1277--1314 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1267 TTCTTTTGGG
1277 AGGGA-CGATATCTAGTAAA
1 AGGGAGCGATATCTAGTAAA
* *
1296 AGGGAGCGGTATTTAGTAA
1 AGGGAGCGATATCTAGTAA
1315 TACCTTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.37, C:0.08, G:0.32, T:0.24
Consensus pattern (20 bp):
AGGGAGCGATATCTAGTAAA
Found at i:3422 original size:31 final size:31
Alignment explanation
Indices: 3380--3458 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
3370 CGTTTCTATT
* * *
3380 TTTAGGCTCAAATTGGTTAACTTTTCAAAGG
1 TTTAGGATCAAATTGGTCAACTTTTCAAAAG
*
3411 TTTAGGATCAAATTGAG-CAACTTTTGAAAAG
1 TTTAGGATCAAATTG-GTCAACTTTTCAAAAG
3442 TTTA-GACTCAAATTGGT
1 TTTAGGA-TCAAATTGGT
3459 GGATAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 3 0.07
31 37 0.90
32 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (31 bp):
TTTAGGATCAAATTGGTCAACTTTTCAAAAG
Found at i:4870 original size:13 final size:13
Alignment explanation
Indices: 4852--4877 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4842 ATTCACATTT
4852 CACGACCCAGATC
1 CACGACCCAGATC
4865 CACGACCCAGATC
1 CACGACCCAGATC
4878 GTACTTCGAT
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:0.31, C:0.46, G:0.15, T:0.08
Consensus pattern (13 bp):
CACGACCCAGATC
Found at i:5480 original size:21 final size:21
Alignment explanation
Indices: 5456--5500 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
5446 TTGTTAGTCG
5456 TTGTTTAAAATATTTTACAAA
1 TTGTTTAAAATATTTTACAAA
*
5477 TTGTTTAAAATATTTTCCAAA
1 TTGTTTAAAATATTTTACAAA
5498 TTG
1 TTG
5501 ATTTTTGCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (21 bp):
TTGTTTAAAATATTTTACAAA
Found at i:5719 original size:38 final size:38
Alignment explanation
Indices: 5667--5747 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 38
5657 TGGATCTGGG
5667 CAAGTCTCGAAATTATACTTAGACAAATTCTACCAGGT
1 CAAGTCTCGAAATTATACTTAGACAAATTCTACCAGGT
* * *
5705 TAAGTCTTGAAATTATACTTAGACAAATTCTACCTGGT
1 CAAGTCTCGAAATTATACTTAGACAAATTCTACCAGGT
5743 CAAGT
1 CAAGT
5748 GTTTTCCTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.32
Consensus pattern (38 bp):
CAAGTCTCGAAATTATACTTAGACAAATTCTACCAGGT
Found at i:9141 original size:2 final size:2
Alignment explanation
Indices: 9118--9168 Score: 61
Period size: 2 Copynumber: 25.5 Consensus size: 2
9108 GCATGTGAAA
*
9118 AT AT TT AT AT ACT AGT AT -T AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9160 AT AT AT AT A
1 AT AT AT AT A
9169 ATGTTTGGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.86
3 4 0.09
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11008 original size:32 final size:32
Alignment explanation
Indices: 10936--11009 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
10926 CAGGTTTAAG
10936 TCGGGTTCGGATTGAATTTGGATCAAGTCAAT
1 TCGGGTTCGGATTGAATTTGGATCAAGTCAAT
* * *
10968 TCGAGTTCGGATTGAATTT-GAGTCAGGTTAAT
1 TCGGGTTCGGATTGAATTTGGA-TCAAGTCAAT
*
11000 TTGGGTTCGG
1 TCGGGTTCGG
11010 GTTCAGTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 2 0.06
32 34 0.94
ACGTcount: A:0.22, C:0.11, G:0.31, T:0.36
Consensus pattern (32 bp):
TCGGGTTCGGATTGAATTTGGATCAAGTCAAT
Found at i:19232 original size:7 final size:7
Alignment explanation
Indices: 19220--19252 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
19210 TTATATGTGC
19220 TTCTTTT
1 TTCTTTT
19227 TTCTTTT
1 TTCTTTT
19234 TT-TTTT
1 TTCTTTT
19240 TTCTTTT
1 TTCTTTT
19247 TT-TTTT
1 TTCTTTT
19253 CTACTCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 10 0.40
7 15 0.60
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (7 bp):
TTCTTTT
Found at i:19241 original size:13 final size:13
Alignment explanation
Indices: 19223--19252 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
19213 TATGTGCTTC
19223 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
19236 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
19249 TTTT
1 TTTT
19253 CTACTCATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:21038 original size:46 final size:46
Alignment explanation
Indices: 20968--21062 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
20958 TGATTGTCAA
*
20968 ACCACATTAAACAATGTCCCCACCTAAGCATCCACCACCACTTCAC
1 ACCACATTAAACAATGTACCCACCTAAGCATCCACCACCACTTCAC
*
21014 ACCACATTAAATC-ATGTACTCACCTAAGCATCCACCACCACTTCAC
1 ACCACATTAAA-CAATGTACCCACCTAAGCATCCACCACCACTTCAC
21060 ACC
1 ACC
21063 TAAGGCTGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.42, G:0.04, T:0.19
Consensus pattern (46 bp):
ACCACATTAAACAATGTACCCACCTAAGCATCCACCACCACTTCAC
Found at i:22051 original size:21 final size:20
Alignment explanation
Indices: 21997--22053 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
21987 AAAGTATTTT
21997 ATTTTATGGTCAAACCCCAA
1 ATTTTATGGTCAAACCCCAA
*
22017 ATTTGATGGTCAAACCCCAA
1 ATTTTATGGTCAAACCCCAA
*
22037 ATTTTCATTGTCAAACC
1 ATTTT-ATGGTCAAACC
22054 ATGTTAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 23 0.70
21 10 0.30
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.32
Consensus pattern (20 bp):
ATTTTATGGTCAAACCCCAA
Found at i:23794 original size:42 final size:42
Alignment explanation
Indices: 23737--23823 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
23727 CTTGTTACAC
*
23737 TCAATCATATATCTCATTATGTTCAAACAATCAAATAAAAAA
1 TCAATCATATATCTCATTATGCTCAAACAATCAAATAAAAAA
23779 TCAATCATATATCTCATTATGCTCAAACAATCAAATAAAAAA
1 TCAATCATATATCTCATTATGCTCAAACAATCAAATAAAAAA
23821 TCA
1 TCA
23824 CAAATATAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.30
Consensus pattern (42 bp):
TCAATCATATATCTCATTATGCTCAAACAATCAAATAAAAAA
Found at i:24826 original size:22 final size:22
Alignment explanation
Indices: 24785--24826 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
24775 GACAAACCCG
**
24785 TAACCCGAATAATCTGAGAAGT
1 TAACCCGAATAATCCAAGAAGT
*
24807 TAACCCGAATGATCCAAGAA
1 TAACCCGAATAATCCAAGAA
24827 TATTATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (22 bp):
TAACCCGAATAATCCAAGAAGT
Found at i:31604 original size:60 final size:60
Alignment explanation
Indices: 31524--31643 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
31514 TACATTGAGC
*
31524 AAACTATGCAATGAATACCTATAGAAATTACTTGTCTGCTAATGAGAAGCAAATTTTCAA
1 AAACTATGCAATGAATACCTATAGAAATTACTTGTCTGCTAATGAGAAGCAAAATTTCAA
*
31584 AAACTTTGCAATGAATACCTATAGAAATTACTTGTCTGCTAATGAGAAGCAAAATTTCAA
1 AAACTATGCAATGAATACCTATAGAAATTACTTGTCTGCTAATGAGAAGCAAAATTTCAA
31644 TTATATATAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (60 bp):
AAACTATGCAATGAATACCTATAGAAATTACTTGTCTGCTAATGAGAAGCAAAATTTCAA
Found at i:32363 original size:2 final size:2
Alignment explanation
Indices: 32356--32387 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
32346 AGGATTCTAG
*
32356 AT AT AT AT AT CT 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
32388 GAATATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33461 original size:24 final size:24
Alignment explanation
Indices: 33416--33462 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
33406 TTGAATTATT
* * * *
33416 TAAATTAATAAAGAGTTTAAAAAA
1 TAAATAAATAAAAAATTGAAAAAA
33440 TAAATAAATAAAAAATTGAAAAA
1 TAAATAAATAAAAAATTGAAAAA
33463 GTCATATGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (24 bp):
TAAATAAATAAAAAATTGAAAAAA
Found at i:34607 original size:78 final size:78
Alignment explanation
Indices: 34492--34636 Score: 281
Period size: 78 Copynumber: 1.9 Consensus size: 78
34482 ATAATAAAAA
34492 AAAAAAAAGACAAAAATAGTCAATGGAAAAAAATTGAAAAAGAAAATTAATAGTACAATATTATA
1 AAAAAAAAGACAAAAATAGTCAATGGAAAAAAATTGAAAAAGAAAATTAATAGTACAATATTATA
34557 AACCTATAGTAAT
66 AACCTATAGTAAT
*
34570 AAAAAAAAGACAAAAATAGTCAATGGAAAAAAGTTGAAAAAGAAAATTAATAGTACAATATTATA
1 AAAAAAAAGACAAAAATAGTCAATGGAAAAAAATTGAAAAAGAAAATTAATAGTACAATATTATA
34635 AA
66 AA
34637 AAATAGTACA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.63, C:0.06, G:0.11, T:0.21
Consensus pattern (78 bp):
AAAAAAAAGACAAAAATAGTCAATGGAAAAAAATTGAAAAAGAAAATTAATAGTACAATATTATA
AACCTATAGTAAT
Found at i:35887 original size:31 final size:31
Alignment explanation
Indices: 35849--35923 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
35839 AAAAGGATAT
35849 AATAGGTGTTTCAAAAATTAAATAAGAGTAC
1 AATAGGTGTTTCAAAAATTAAATAAGAGTAC
** * *
35880 AATAGGTGTAACAAAAATTAAATAAGGGTAT
1 AATAGGTGTTTCAAAAATTAAATAAGAGTAC
35911 AATAGGTGTTTCA
1 AATAGGTGTTTCA
35924 GATGTTTTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.29
Consensus pattern (31 bp):
AATAGGTGTTTCAAAAATTAAATAAGAGTAC
Found at i:47314 original size:169 final size:165
Alignment explanation
Indices: 47067--47511 Score: 577
Period size: 169 Copynumber: 2.7 Consensus size: 165
47057 ATGAGGAGCG
* * * *
47067 AGAGAACTAATTTTTTTCGTCTTTTCCCACTTGACCGATTACTTAAATGCCCTAACTTTTGATTC
1 AGAGAACT-ATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
* * *
47132 TTGAGGTGATTAAATAACTAAACTTTGTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAAT
65 TTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGGAAT
* * * **
47197 TACTAAAAGATCCCTA-CAAAGACTTGCTTTTGGAGTT
130 TAATAAAAGATCCCCATCAAAGA-TTGATGAT-GAGTT
*
47234 AGAGAACTTATTTTTTTTTTGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGAT
1 AGAGAAC-TA--TTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGAT
* * * *
47299 TCTTCAGGGGATTAAATAAGTAATCTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGA
63 TCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGGA
*
47364 ATTAATAAAAGATCCCCATCAAGGATTGATGATGAGTT
128 ATTAATAAAAGATCCCCATCAAAGATTGATGATGAGTT
* * * * * * *
47402 AGAGAACTAATCTTTTCGTCTTTACTTACTTGGTAGATTATTTAAATGTCCTAACTTTTGATCCT
1 AGAGAACTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCT
* * *
47467 TGAGAGGATTAAACAACTAAACTTTTTGGTCATTTCTTAATTGAC
66 TGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGAC
47512 AAATGACTCA
Statistics
Matches: 241, Mismatches: 33, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
165 86 0.36
167 10 0.04
168 13 0.05
169 127 0.53
170 5 0.02
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (165 bp):
AGAGAACTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCT
TGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGGAATT
AATAAAAGATCCCCATCAAAGATTGATGATGAGTT
Found at i:48094 original size:6 final size:6
Alignment explanation
Indices: 48083--48178 Score: 88
Period size: 6 Copynumber: 15.2 Consensus size: 6
48073 GGCAATTGGG
*
48083 CGGGTT CGGGTT CGGGATTTTT CGGGTT CGGGTATTT CGGGTT CGGGCT
1 CGGGTT CGGGTT CGGG----TT CGGGTT CGGG---TT CGGGTT CGGGTT
* *
48132 C-GGAT CGGGTT CGGGTT CGGGTT CGGGTC CGGG-T CGGGTT CGGGTT
1 CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT
48178 C
1 C
48179 ACTTTCGATA
Statistics
Matches: 76, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
5 8 0.11
6 56 0.74
9 6 0.08
10 6 0.08
ACGTcount: A:0.03, C:0.19, G:0.46, T:0.32
Consensus pattern (6 bp):
CGGGTT
Found at i:48122 original size:15 final size:16
Alignment explanation
Indices: 48087--48129 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 16
48077 ATTGGGCGGG
*
48087 TTCGGGTTCGGGATTT
1 TTCGGGTTCGGGATAT
48103 TTCGGGTTCGGG-TAT
1 TTCGGGTTCGGGATAT
48118 TTCGGGTTCGGG
1 TTCGGGTTCGGG
48130 CTCGGATCGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.05, C:0.14, G:0.42, T:0.40
Consensus pattern (16 bp):
TTCGGGTTCGGGATAT
Found at i:48141 original size:17 final size:17
Alignment explanation
Indices: 48118--48178 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
48108 GTTCGGGTAT
48118 TTCGGGTTCGGGCTC-GG
1 TTCGGGTTCGGG-TCGGG
*
48135 ATCGGGTTCGGGTTCGGG
1 TTCGGGTTCGGG-TCGGG
*
48153 TTCGGGTCCGGGTCGGG
1 TTCGGGTTCGGGTCGGG
48170 TTCGGGTTC
1 TTCGGGTTC
48179 ACTTTCGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
17 26 0.68
18 12 0.32
ACGTcount: A:0.02, C:0.21, G:0.48, T:0.30
Consensus pattern (17 bp):
TTCGGGTTCGGGTCGGG
Found at i:48158 original size:29 final size:29
Alignment explanation
Indices: 48104--48178 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 29
48094 TCGGGATTTT
48104 TCGGGTTCGGGTATTTCGGGTTCGGG-CTCGGA
1 TCGGGTTCGGG---TTCGGGTTCGGGTC-CGGA
*
48136 TCGGGTTCGGGTTCGGGTTCGGGTCCGGG
1 TCGGGTTCGGGTTCGGGTTCGGGTCCGGA
48165 TCGGGTTCGGGTTC
1 TCGGGTTCGGGTTC
48179 ACTTTCGATA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 29 0.71
30 1 0.02
32 11 0.27
ACGTcount: A:0.03, C:0.20, G:0.47, T:0.31
Consensus pattern (29 bp):
TCGGGTTCGGGTTCGGGTTCGGGTCCGGA
Found at i:48176 original size:23 final size:23
Alignment explanation
Indices: 48118--48178 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
48108 GTTCGGGTAT
*
48118 TTCGGGTTCGGGCTCGGATCGGG
1 TTCGGGTTCGGGTTCGGATCGGG
*
48141 TTCGGGTTCGGGTTCGGGTCCGGG
1 TTCGGGTTCGGGTTCGGAT-CGGG
48165 -TCGGGTTCGGGTTC
1 TTCGGGTTCGGGTTC
48179 ACTTTCGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 31 0.89
24 4 0.11
ACGTcount: A:0.02, C:0.21, G:0.48, T:0.30
Consensus pattern (23 bp):
TTCGGGTTCGGGTTCGGATCGGG
Found at i:48952 original size:16 final size:17
Alignment explanation
Indices: 48916--48958 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
48906 TATTTTGATC
* *
48916 TCGGGCTCGGGTCGGGT
1 TCGGGTTCGGGTCGAGT
48933 TCGGGTTCGGG-CGAGT
1 TCGGGTTCGGGTCGAGT
48949 TCGGGTTCGG
1 TCGGGTTCGG
48959 ATTGTCTCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.02, C:0.21, G:0.51, T:0.26
Consensus pattern (17 bp):
TCGGGTTCGGGTCGAGT
Found at i:48956 original size:6 final size:6
Alignment explanation
Indices: 48916--49007 Score: 59
Period size: 6 Copynumber: 14.8 Consensus size: 6
48906 TATTTTGATC
* *
48916 TCGGGC TCGGG- TCGGGT TCGGGT TCGGG- -CGAGT TCGGGT TCGGATTGT
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGG---GT
48964 CTCGGGT TCGGGTATTT TCGGGT TCGGGT TCGGG- -CGGGT TCGGG
1 -TCGGGT TCGGG----T TCGGGT TCGGGT TCGGGT TCGGGT TCGGG
49008 ACGTTGACTT
Statistics
Matches: 71, Mismatches: 2, Indels: 26
0.72 0.02 0.26
Matches are distributed among these distances:
4 7 0.10
5 5 0.07
6 45 0.63
7 2 0.03
9 2 0.03
10 10 0.14
ACGTcount: A:0.03, C:0.18, G:0.48, T:0.30
Consensus pattern (6 bp):
TCGGGT
Found at i:48984 original size:16 final size:17
Alignment explanation
Indices: 48947--48992 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
48937 GTTCGGGCGA
48947 GTTCGGGTTC-GG-ATT
1 GTTCGGGTTCGGGTATT
48962 GTCTCGGGTTCGGGTATT
1 GT-TCGGGTTCGGGTATT
48980 -TTCGGGTTCGGGT
1 GTTCGGGTTCGGGT
48993 TCGGGCGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.07
16 20 0.71
17 3 0.11
18 3 0.11
ACGTcount: A:0.04, C:0.15, G:0.41, T:0.39
Consensus pattern (17 bp):
GTTCGGGTTCGGGTATT
Found at i:51957 original size:2 final size:2
Alignment explanation
Indices: 51950--51994 Score: 56
Period size: 2 Copynumber: 22.0 Consensus size: 2
51940 GTACCTAATC
*
51950 TA TA TA TA CTA T- TA TA TA TA TA TA TA TA TA TC TA TA TA CTA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
51993 TA
1 TA
51995 AGTCTAAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 1 0.03
2 33 0.87
3 4 0.11
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:60384 original size:2 final size:2
Alignment explanation
Indices: 60377--60410 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
60367 ACATACGTTC
*
60377 AT AT AT AT AT AT AT AT AT AT CT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60411 AAAGTACGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60467 original size:31 final size:31
Alignment explanation
Indices: 60429--60497 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
60419 AGTTTTGAGA
**
60429 AACTTTTGAAACGTCTATTATACCCTTATTT
1 AACTTTTGAAACACCTATTATACCCTTATTT
* *
60460 AACTTTTGAAATACCTATTATATCCTTATTT
1 AACTTTTGAAACACCTATTATACCCTTATTT
60491 AACTTTT
1 AACTTTT
60498 ACAGTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.48
Consensus pattern (31 bp):
AACTTTTGAAACACCTATTATACCCTTATTT
Done.