Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010361.1 Corchorus capsularis cultivar CVL-1 contig10382, 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: 95492
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:222 original size:48 final size:48
Alignment explanation
Indices: 61--233 Score: 156
Period size: 48 Copynumber: 3.6 Consensus size: 48
51 CTTTAGGTCT
****
61 TTTTTCGCC-CCGAAAGTCGTGATAG-TACCCCTTTGGATTTTTCATGA
1 TTTTT-GCCTCCGAAAGTCGTGATAGTTACCCCTTTGGATTTTTGGCCA
* * * * *
108 TTTTTGGCCCCCTAAAGTCGTGATGGTTA-GCCTTTGCATTTTTTGGCCA
1 TTTTT-GCCTCCGAAAGTCGTGATAGTTACCCCTTTGGA-TTTTTGGCCA
* *
157 ATTTTGTCCTCCAAAAGTCGTGAT-GTTACCCCTTTGGATTTTTGGCCA
1 TTTTTG-CCTCCGAAAGTCGTGATAGTTACCCCTTTGGATTTTTGGCCA
* *
205 TTTTTAGCCTCCGAAAGTCATGATGGTTA
1 TTTTT-GCCTCCGAAAGTCGTGATAGTTA
234 GCATTTAAAT
Statistics
Matches: 102, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
47 8 0.08
48 55 0.54
49 39 0.38
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.39
Consensus pattern (48 bp):
TTTTTGCCTCCGAAAGTCGTGATAGTTACCCCTTTGGATTTTTGGCCA
Found at i:497 original size:48 final size:48
Alignment explanation
Indices: 305--532 Score: 197
Period size: 48 Copynumber: 4.9 Consensus size: 48
295 TTCGAAAATT
* * *
305 GTGATGGTTAGCCTTTGCACTTTAGTCCATTTTT--TACTCCCGAAAGTC
1 GTGATGGTTAGCCTTTGCATTTTAGGCAATTTTTGGT-C-CCCGAAAGTC
* * *
353 GTGATGGTTAGTCTTTGCATTTTAGGTCATTTTTTGCT-CCCGAAAGTC
1 GTGATGGTTAGCCTTTGCATTTTAGG-CAATTTTTGGTCCCCGAAAGTC
* * * * *
401 GTGAT-G---CCCTTTGGCATTTTAGCCAA-TTTTGG-CCCTCCAAAATT
1 GTGATGGTTAGCCTTT-GCATTTTAGGCAATTTTTGGTCCC-CGAAAGTC
**
445 GTGATGGTTAGCCTTTATATTTTAGGCAATTTTTGGTCCCCGAAAGTC
1 GTGATGGTTAGCCTTTGCATTTTAGGCAATTTTTGGTCCCCGAAAGTC
* * *
493 GTGATGCTTAGCCTTTGTATTTTAGGCCATTTTT-GTCCCC
1 GTGATGGTTAGCCTTTGCATTTTAGGCAATTTTTGGTCCCC
533 TTTGGATTTT
Statistics
Matches: 145, Mismatches: 23, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
43 7 0.05
44 16 0.11
45 10 0.07
47 17 0.12
48 85 0.59
49 9 0.06
51 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (48 bp):
GTGATGGTTAGCCTTTGCATTTTAGGCAATTTTTGGTCCCCGAAAGTC
Found at i:542 original size:27 final size:27
Alignment explanation
Indices: 504--557 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
494 TGATGCTTAG
*
504 CCTTTGTATTTTAGGCCATTTTTGTCC
1 CCTTTGGATTTTAGGCCATTTTTGTCC
* *
531 CCTTTGGATTTTTGGTCATTTTTGTCC
1 CCTTTGGATTTTAGGCCATTTTTGTCC
558 ACCAAAAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.09, C:0.20, G:0.17, T:0.54
Consensus pattern (27 bp):
CCTTTGGATTTTAGGCCATTTTTGTCC
Found at i:590 original size:48 final size:48
Alignment explanation
Indices: 529--650 Score: 108
Period size: 49 Copynumber: 2.5 Consensus size: 48
519 CCATTTTTGT
* *
529 CCCCTTTG-GATTTTTGGTCATTTTTGTCCACCAAAAGTCATGATGGTTA
1 CCCCTTTGACATTTTTGG-CATTTTTGGCCACCAAAAGTCATGATGG-TA
* * * * *
578 -GCCTTT-ACATTTTAGGCAATTTTTTGGCCTCTAAAAGTCGTGATGGTA
1 CCCCTTTGACATTTTTGGC-A-TTTTTGGCCACCAAAAGTCATGATGGTA
626 CCCCTTTGACA-TTTTGGCCATTTTT
1 CCCCTTTGACATTTTTGG-CATTTTT
651 TGGCATCTGC
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
47 1 0.02
48 20 0.34
49 33 0.57
50 4 0.07
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (48 bp):
CCCCTTTGACATTTTTGGCATTTTTGGCCACCAAAAGTCATGATGGTA
Found at i:622 original size:49 final size:49
Alignment explanation
Indices: 561--654 Score: 129
Period size: 49 Copynumber: 1.9 Consensus size: 49
551 TTTGTCCACC
*
561 AAAAGTCATGATGGTTA-GCCTTT-ACATTTTAGGCAATTTTTTGGCCTCT
1 AAAAGTCATGATGG-TACCCCTTTGACATTTT-GGCAATTTTTTGGCCTCT
* *
610 AAAAGTCGTGATGGTACCCCTTTGACATTTTGGCCATTTTTTGGC
1 AAAAGTCATGATGGTACCCCTTTGACATTTTGGCAATTTTTTGGC
655 ATCTGCAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
48 2 0.05
49 31 0.77
50 7 0.17
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (49 bp):
AAAAGTCATGATGGTACCCCTTTGACATTTTGGCAATTTTTTGGCCTCT
Found at i:750 original size:48 final size:48
Alignment explanation
Indices: 697--954 Score: 279
Period size: 48 Copynumber: 5.4 Consensus size: 48
687 AATCGTGAAC
* *
697 GCCTTTGCATTTTAGGCCATTTTTGGGCCTCGAAAGTCGTGATGGTTA
1 GCCTTTACATTTTAGGCCATTTTTCGGCCTCGAAAGTCGTGATGGTTA
* **
745 GCCTTTACATTTTAGGTCATTTTTCACCCTCGAAAGTCGTGATGGTTA
1 GCCTTTACATTTTAGGCCATTTTTCGGCCTCGAAAGTCGTGATGGTTA
* * * * * * *
793 CCCTTTGCATTTTAGGTCATTTTTTGCCCCCGAAAGTCGTAATGG-TA
1 GCCTTTACATTTTAGGCCATTTTTCGGCCTCGAAAGTCGTGATGGTTA
* ** * * *
840 CCTCTTTGGATTTTTGACCATTTTTTGG-CTCTGAAAGTCGTGATGGTTA
1 GC-CTTTACATTTTAGGCCATTTTTCGGCCTC-GAAAGTCGTGATGGTTA
* * *
889 GCCTTTACATTTTAGACCA-TTTTCGGCCTCCAAAAATCGTGATGGTTA
1 GCCTTTACATTTTAGGCCATTTTTCGGCCT-CGAAAGTCGTGATGGTTA
937 GCCTTTACATTTTAGGCC
1 GCCTTTACATTTTAGGCC
955 GACTGAAAAA
Statistics
Matches: 179, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
47 12 0.07
48 163 0.91
49 4 0.02
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (48 bp):
GCCTTTACATTTTAGGCCATTTTTCGGCCTCGAAAGTCGTGATGGTTA
Found at i:6603 original size:17 final size:16
Alignment explanation
Indices: 6581--6620 Score: 64
Period size: 15 Copynumber: 2.5 Consensus size: 16
6571 TCCATAATCC
6581 ATAATATTATATATATA
1 ATAATA-TATATATATA
6598 ATAATA-ATATATATA
1 ATAATATATATATATA
6613 ATAATATA
1 ATAATATA
6621 ATAGTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 15 0.68
16 1 0.05
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATATATATATATA
Found at i:6615 original size:12 final size:12
Alignment explanation
Indices: 6581--6620 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
6571 TCCATAATCC
6581 ATAATAT-TAT-
1 ATAATATATATA
6591 AT-ATATA-ATA
1 ATAATATATATA
6601 ATAATATATATA
1 ATAATATATATA
6613 ATAATATA
1 ATAATATA
6621 ATAGTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 6 0.23
10 4 0.15
11 5 0.19
12 11 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATATATATA
Found at i:6973 original size:13 final size:12
Alignment explanation
Indices: 6951--6982 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
6941 GGTCGAATAG
6951 TTTTTTTGTTTT
1 TTTTTTTGTTTT
6963 TTTTGTTTGTTTT
1 TTTT-TTTGTTTT
6976 TTTTTTT
1 TTTTTTT
6983 TTTAACTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:6985 original size:9 final size:9
Alignment explanation
Indices: 6951--6984 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
6941 GGTCGAATAG
6951 TTTTTTTGT
1 TTTTTTTGT
6960 TTTTTTTGT
1 TTTTTTTGT
6969 TTGTTTTT-T
1 TT-TTTTTGT
6978 TTTTTTT
1 TTTTTTT
6985 TAACTAAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 5 0.21
9 14 0.58
10 5 0.21
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:7906 original size:15 final size:14
Alignment explanation
Indices: 7882--7913 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
7872 GGAATAAAAA
7882 TTAAATATTTTATT
1 TTAAATATTTTATT
7896 TTAATATATTTTATT
1 TTAA-ATATTTTATT
7911 TTA
1 TTA
7914 TTGAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTAAATATTTTATT
Found at i:7925 original size:20 final size:20
Alignment explanation
Indices: 7887--7927 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
7877 AAAAATTAAA
**
7887 TATTTTATTTTAATATATTT
1 TATTTTATTGAAATATATTT
*
7907 TATTTTATTGAAATTTATTT
1 TATTTTATTGAAATATATTT
7927 T
1 T
7928 TAAAAAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TATTTTATTGAAATATATTT
Found at i:9076 original size:15 final size:15
Alignment explanation
Indices: 9044--9073 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9034 AAATTTTTAA
9044 TAAAATAAAATATAT
1 TAAAATAAAATATAT
9059 TAAAATAAAA-ATAT
1 TAAAATAAAATATAT
9073 T
1 T
9074 TAATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATAAAATATAT
Found at i:9341 original size:15 final size:17
Alignment explanation
Indices: 9307--9338 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
9297 GAAAACCAAA
9307 CTTTGTTTCCGTTTTTT
1 CTTTGTTTCCGTTTTTT
9324 CTTT-TTTCCGTTTTT
1 CTTTGTTTCCGTTTTT
9339 CTTCCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.19, G:0.09, T:0.72
Consensus pattern (17 bp):
CTTTGTTTCCGTTTTTT
Found at i:24971 original size:2 final size:2
Alignment explanation
Indices: 24964--24995 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24954 TTATATTTCG
24964 TA TA 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 TA TA
24996 AATAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26340 original size:1 final size:1
Alignment explanation
Indices: 26334--26358 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
26324 TTCAATTAGG
26334 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
26359 CTGCTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:27213 original size:29 final size:30
Alignment explanation
Indices: 27146--27221 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 30
27136 AATAGCCCTT
27146 TTGCCCCCTGAACTTTGCAAATTTAGGCCAAA
1 TTGCCCCCTGAA-TTTGCAAATTTA-GCCAAA
* *
27178 TTG-CCCCTGAATTT-TAAATTGT-GCCACA
1 TTGCCCCCTGAATTTGCAAATT-TAGCCAAA
27206 TTGCCCCCTGAATTTG
1 TTGCCCCCTGAATTTG
27222 TAATATCAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 8 0.21
29 16 0.41
30 4 0.10
31 8 0.21
32 3 0.08
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.33
Consensus pattern (30 bp):
TTGCCCCCTGAATTTGCAAATTTAGCCAAA
Found at i:38020 original size:1 final size:1
Alignment explanation
Indices: 38014--38043 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
38004 TGCAATTTAC
38014 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38044 CCCATAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:48548 original size:31 final size:31
Alignment explanation
Indices: 48513--48580 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
48503 ACGGTGTGTG
* *
48513 ACGTGGCATGTCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
* ** *
48544 ACGTGACATGCCACATGTTTCAAAAAGTGAT
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
48575 ACGTGG
1 ACGTGG
48581 TGCCACGTGC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (31 bp):
ACGTGGCATGCCACATGTACCAAAAAGTGAC
Found at i:54628 original size:20 final size:22
Alignment explanation
Indices: 54590--54629 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
54580 AATATTTTTA
*
54590 AAAAATAAAATCCATTTTCTTT
1 AAAAATAAAATCCAATTTCTTT
54612 AAAAA-AAAAT-CAATTTCT
1 AAAAATAAAATCCAATTTCT
54630 CAAATTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 5 0.29
22 5 0.29
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAATAAAATCCAATTTCTTT
Found at i:60965 original size:63 final size:63
Alignment explanation
Indices: 60858--61005 Score: 181
Period size: 63 Copynumber: 2.3 Consensus size: 63
60848 GTGTGTTTGA
* * * * *
60858 ATGTATTTCCTGGAGAGCAGTGAACTCGAGTGCTTTTTCCGCCAATGA-TTTCTCAATGCTTGC
1 ATGTATTTCCTGCAGAGCAGTGAACTCAAGTCCTCTTTCCGCCAA-CATTTTCTCAATGCTTGC
* * **
60921 ATGTCTTTCCTGCAGAGCAGTGAACTCAAGTCCTCTTTCTGCCAACATTTTCTCTGTGCTTGC
1 ATGTATTTCCTGCAGAGCAGTGAACTCAAGTCCTCTTTCCGCCAACATTTTCTCAATGCTTGC
* *
60984 ATGTTTTTCGTGCAGAGCAGTG
1 ATGTATTTCCTGCAGAGCAGTG
61006 TGTCTTTCTG
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
62 1 0.01
63 72 0.99
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36
Consensus pattern (63 bp):
ATGTATTTCCTGCAGAGCAGTGAACTCAAGTCCTCTTTCCGCCAACATTTTCTCAATGCTTGC
Found at i:61245 original size:297 final size:297
Alignment explanation
Indices: 60711--61302 Score: 1049
Period size: 297 Copynumber: 2.0 Consensus size: 297
60701 TTTCTGTCCA
* * * *
60711 TCTTTCTGATGATTCTTGTCTCTCTTTCCCAAGCTGCAATTCCAGTTCTTTTTTCTGAGTCTGTA
1 TCTTTCTGATGATTCTTGTCTCTCTCTCCCAAGCTGCAATTCCAGTTCCTGTTTCTGAGTCCGTA
60776 AACAATCCAACTCCTGCTGCAAATTATTGACCTGCTCCACTAGTGCTGTTAACTTAGAAGAAGTT
66 AACAATCCAACTCCTGCTGCAAATTATTGACCTGCTCCACTAGTGCTGTTAACTTAGAAGAAGTT
60841 TCATTCTGTGTGTTTGAATGTATTTCCTGGAGAGCAGTGAACTCGAGTGCTTTTTCCGCCAATGA
131 TCATTCTGTGTGTTTGAATGTATTTCCTGGAGAGCAGTGAACTCGAGTGCTTTTTCCGCCAATGA
* *
60906 TTTCTCAATGCTTGCATGTCTTTCCTGCAGAGCAGTGAACTCAAGTCCTCTTTCTGCCAACATTT
196 CTTCTCAATGCTTGCATGTCTTTCCAGCAGAGCAGTGAACTCAAGTCCTCTTTCTGCCAACATTT
* *
60971 TCTCTGTGCTTGCATGTTTTTCGTGCAGAGCAGTGTG
261 TCTCAGCGCTTGCATGTTTTTCGTGCAGAGCAGTGTG
* * *
61008 TCTTTCTGATGATTCTTGTCTTTCTCTCTCAAGCTGCATTTCCAGTTCCTGTTTCTGAGTCCGTA
1 TCTTTCTGATGATTCTTGTCTCTCTCTCCCAAGCTGCAATTCCAGTTCCTGTTTCTGAGTCCGTA
* * * *
61073 AAGAATCCAACTCCTGCTGCAAATTATTGACCTGCTCGACTAGTGCTGTTAGCTTGGAAGAAGTT
66 AACAATCCAACTCCTGCTGCAAATTATTGACCTGCTCCACTAGTGCTGTTAACTTAGAAGAAGTT
61138 TCATTCTGTGTGTTTGAATGTATTTCCTGGAGAGCAGTGAACTCGAGTGCTTTTTCCGCCAATGA
131 TCATTCTGTGTGTTTGAATGTATTTCCTGGAGAGCAGTGAACTCGAGTGCTTTTTCCGCCAATGA
61203 CTTCTCAATGCTTGCATGTCTTTCCAGCAGAGCAGTGAACTCAAGTCCTCTTTCTGCCAACATTT
196 CTTCTCAATGCTTGCATGTCTTTCCAGCAGAGCAGTGAACTCAAGTCCTCTTTCTGCCAACATTT
61268 TCTCAGCGCTTGCATGTTTTTCGTGCAGAGCAGTG
261 TCTCAGCGCTTGCATGTTTTTCGTGCAGAGCAGTG
61303 ATTTCAAGCT
Statistics
Matches: 280, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
297 280 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (297 bp):
TCTTTCTGATGATTCTTGTCTCTCTCTCCCAAGCTGCAATTCCAGTTCCTGTTTCTGAGTCCGTA
AACAATCCAACTCCTGCTGCAAATTATTGACCTGCTCCACTAGTGCTGTTAACTTAGAAGAAGTT
TCATTCTGTGTGTTTGAATGTATTTCCTGGAGAGCAGTGAACTCGAGTGCTTTTTCCGCCAATGA
CTTCTCAATGCTTGCATGTCTTTCCAGCAGAGCAGTGAACTCAAGTCCTCTTTCTGCCAACATTT
TCTCAGCGCTTGCATGTTTTTCGTGCAGAGCAGTGTG
Found at i:61262 original size:63 final size:63
Alignment explanation
Indices: 61168--61334 Score: 167
Period size: 63 Copynumber: 2.7 Consensus size: 63
61158 TATTTCCTGG
* * * * *
61168 AGAGCAGTGAACTCGAGTGCTTTTTCCGCCAATGACTTCTCAATGCTTGCATGTCTTTCCAGC
1 AGAGCAGTGAACTCAAGTCCTCTTTCTGCCAATGACTTCTCAACGCTTGCATGTCTTTCCAGC
* * * * **
61231 AGAGCAGTGAACTCAAGTCCTCTTTCTGCCAA-CATTTTCTCAGCGCTTGCATGTTTTTCGTGC
1 AGAGCAGTGAACTCAAGTCCTCTTTCTGCCAATGA-CTTCTCAACGCTTGCATGTCTTTCCAGC
** * *
61294 AGAGCAGTGATTTCAAG-CTCTCTTTCTGCCAGTGTCTTCTC
1 AGAGCAGTGAACTCAAGTC-CTCTTTCTGCCAATGACTTCTC
61335 TAATTCAGAA
Statistics
Matches: 84, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
62 2 0.02
63 82 0.98
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (63 bp):
AGAGCAGTGAACTCAAGTCCTCTTTCTGCCAATGACTTCTCAACGCTTGCATGTCTTTCCAGC
Found at i:66825 original size:288 final size:288
Alignment explanation
Indices: 66306--66825 Score: 704
Period size: 288 Copynumber: 1.8 Consensus size: 288
66296 GCGGTGATAG
* *
66306 TCAATCAGGAGGCAGAGCTGCCTTATGGCTTCCCTCTTCTCTTCTTGAAGACTCAATAATGTCTC
1 TCAATCAGGAGGCAGAGCTGCCTTATGGCTTCCCTCTTCTCTTCTTGAAGACTCAACAATATCTC
*
66371 ATCTTTTTCTGTCTTAATCTTCTCCAATTCTCCCACTCTTTTCTCAACCTCATTCACTAGTTCAA
66 ATCTTTTTCTGTCATAATCTTCTCCAATTCTCCCACTCTTTTCTCAACCTCATTCACTAGTTCAA
* * * * *
66436 TAAGTCTAAGCTTTTCCTTTCCTTCCTCACCGAGCTTAGATTTCGAATCTGAGACCTTCTTACTT
131 TAAGTCTAAGCTTTTCCTCTCCTTCCTCACCGAGCTTACATTTCCAATCCGAAACCTTCTTACTT
* *** **
66501 GACAATTTCTCGTTTTGTTTATCCAATTTGGCTACTACTGAACCCACATTACCGTTCAGCTGTTT
196 AACAACGCCTCGTTTTGTTTATCCAATTCAGCTACTACTGAACCCACATTACCGTTCAGCTGTTT
66566 TATATCGCCTTCCGGTGCTGTCTTGCAA
261 TATATCGCCTTCCGGTGCTGTCTTGCAA
* * * *
66594 TCAATCAGGAGGCGGAGCTGTCTTATGGCTTCCCTCTTCTCTTCTTGAAGACTCGACAATATGTC
1 TCAATCAGGAGGCAGAGCTGCCTTATGGCTTCCCTCTTCTCTTCTTGAAGACTCAACAATATCTC
* * * * * * * *
66659 ATCTTTTTGTTTCATAATCTTGTCCAGTTTTCCCATTCTTTTCTCAACTTCATTCACT-GCTTTA
66 ATCTTTTTCTGTCATAATCTTCTCCAATTCTCCCACTCTTTTCTCAACCTCATTCACTAG-TTCA
** * * *
66723 ATCTGTCTCAGCTTTTCCTCTCCTTCCTCACTGAGCTTACA-TTCCAACTCCGAAATCTTCTCT-
130 ATAAGTCTAAGCTTTTCCTCTCCTTCCTCACCGAGCTTACATTTCCAA-TCCGAAACCTTCT-TA
*
66786 TTTAACAACGCCTCGTTTTGTTTATCCAATTCAGCTACTA
193 CTTAACAACGCCTCGTTTTGTTTATCCAATTCAGCTACTA
66826 GGAAACCCAT
Statistics
Matches: 197, Mismatches: 32, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
287 6 0.03
288 190 0.96
289 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.12, T:0.40
Consensus pattern (288 bp):
TCAATCAGGAGGCAGAGCTGCCTTATGGCTTCCCTCTTCTCTTCTTGAAGACTCAACAATATCTC
ATCTTTTTCTGTCATAATCTTCTCCAATTCTCCCACTCTTTTCTCAACCTCATTCACTAGTTCAA
TAAGTCTAAGCTTTTCCTCTCCTTCCTCACCGAGCTTACATTTCCAATCCGAAACCTTCTTACTT
AACAACGCCTCGTTTTGTTTATCCAATTCAGCTACTACTGAACCCACATTACCGTTCAGCTGTTT
TATATCGCCTTCCGGTGCTGTCTTGCAA
Found at i:73236 original size:9 final size:9
Alignment explanation
Indices: 73222--73247 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
73212 CTAGGCTGAT
73222 GTCACCAAG
1 GTCACCAAG
73231 GTCACCAAG
1 GTCACCAAG
73240 GTCACCAA
1 GTCACCAA
73248 AACTACTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.35, G:0.19, T:0.12
Consensus pattern (9 bp):
GTCACCAAG
Found at i:77480 original size:19 final size:17
Alignment explanation
Indices: 77456--77490 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
77446 ATAGATCAAA
77456 TTTGTATTCTTATATTTTG
1 TTTGTATT-TT-TATTTTG
77475 TTTGTATTTTTATTTT
1 TTTGTATTTTTATTTT
77491 TAATATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTGTATTTTTATTTTG
Found at i:91381 original size:21 final size:21
Alignment explanation
Indices: 91355--91410 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
91345 TGTTGGAATT
*
91355 TCTGAACACACTGACCTCATA
1 TCTGAACAAACTGACCTCATA
* *
91376 TCTGAACAAACTGACTTGATA
1 TCTGAACAAACTGACCTCATA
91397 TCTGAACAAACTGA
1 TCTGAACAAACTGA
91411 TTTCACATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (21 bp):
TCTGAACAAACTGACCTCATA
Found at i:94502 original size:13 final size:13
Alignment explanation
Indices: 94484--94513 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
94474 CCTACTACAA
*
94484 GAAAAGGCAATTT
1 GAAAAGGCAAATT
94497 GAAAAGGCAAATT
1 GAAAAGGCAAATT
94510 GAAA
1 GAAA
94514 GAGAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.23, T:0.17
Consensus pattern (13 bp):
GAAAAGGCAAATT
Done.