Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016180.1 Corchorus capsularis cultivar CVL-1 contig16201, 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: 76476
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:17 original size:2 final size:2
Alignment explanation
Indices: 11--43 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 GAAAAGATAA
11 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44 ACTCATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4698 original size:24 final size:24
Alignment explanation
Indices: 4662--4707 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
4652 ATCACCACCT
*
4662 CTAACCTCATGCAGCAGCTTCAGC
1 CTAACCTCATGCAGCACCTTCAGC
*
4686 CTAACCTCTTGCAGCACCTTCA
1 CTAACCTCATGCAGCACCTTCA
4708 CCCTCACCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.39, G:0.13, T:0.24
Consensus pattern (24 bp):
CTAACCTCATGCAGCACCTTCAGC
Found at i:5690 original size:112 final size:113
Alignment explanation
Indices: 5517--5720 Score: 277
Period size: 112 Copynumber: 1.8 Consensus size: 113
5507 GAAAGCACCG
* * * * * * *
5517 CTAATTTAACGAAATTATGGAGAGATATATTTTTTTCGTATTTTTTCCCTAGAAATACAAATTTC
1 CTAATTTAACGAAATTAGGGAAAGAAATATATTATTCATATTTTTTCCCTAGAAATACAAATGTC
5582 AAAAAAAAAAAGACAAA-CATTTAGTGGAGTTTTAACCCGTAAACGCCA
66 AAAAAAAAAAAGA-AAATCATTTAGTGGAGTTTTAACCCGTAAACGCCA
* *
5630 CTAATTTAACGAAATTAGGGAAAGAAATA-ATTATTCATATTTTTTTCCTAGAAATGCAAATGTC
1 CTAATTTAACGAAATTAGGGAAAGAAATATATTATTCATATTTTTTCCCTAGAAATACAAATGTC
** *
5694 TCAAAAATAAAGAAAATCATTTAGTGG
66 AAAAAAAAAAAGAAAATCATTTAGTGG
5721 TCTTTTTTAG
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
111 3 0.04
112 49 0.63
113 26 0.33
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (113 bp):
CTAATTTAACGAAATTAGGGAAAGAAATATATTATTCATATTTTTTCCCTAGAAATACAAATGTC
AAAAAAAAAAAGAAAATCATTTAGTGGAGTTTTAACCCGTAAACGCCA
Found at i:19393 original size:1 final size:1
Alignment explanation
Indices: 19387--19418 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
19377 TGTATGTGTC
19387 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19419 GTCTTTTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:27174 original size:7 final size:7
Alignment explanation
Indices: 27162--27188 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
27152 GTCTAGCTGG
27162 TTAGGAC
1 TTAGGAC
27169 TTAGGAC
1 TTAGGAC
27176 TTAGGAC
1 TTAGGAC
27183 TTAGGA
1 TTAGGA
27189 ATACTCATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (7 bp):
TTAGGAC
Found at i:32057 original size:40 final size:40
Alignment explanation
Indices: 32002--32083 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
31992 GCGGTGATGT
* *
32002 GAGGTGAGGTGAGGCGGTGATGGCAGCGACCAACTGGAAA
1 GAGGTGAGGTAAGGCGGTGATGGCAGCGACCAACTAGAAA
* * *
32042 GAGGTGAGGTAAGGCGGTGGTGGCAGGGACCAAGTAGAAA
1 GAGGTGAGGTAAGGCGGTGATGGCAGCGACCAACTAGAAA
32082 GA
1 GA
32084 AACCTAGGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.29, C:0.12, G:0.46, T:0.12
Consensus pattern (40 bp):
GAGGTGAGGTAAGGCGGTGATGGCAGCGACCAACTAGAAA
Found at i:33068 original size:15 final size:15
Alignment explanation
Indices: 33050--33084 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
33040 ACTAACTCAA
*
33050 CAAACTCAACTGACT
1 CAAACTAAACTGACT
33065 CAAACTAAACTGACT
1 CAAACTAAACTGACT
33080 CAAAC
1 CAAAC
33085 ATCCAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.46, C:0.31, G:0.06, T:0.17
Consensus pattern (15 bp):
CAAACTAAACTGACT
Found at i:33464 original size:22 final size:22
Alignment explanation
Indices: 33438--33481 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
33428 GTCATTTTCT
33438 AATTCACTT-TTGGCATTTAGTA
1 AATTCACTTCTT-GCATTTAGTA
33460 AATTCACTTCTTGCATTTAGTA
1 AATTCACTTCTTGCATTTAGTA
33482 TAACATAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (22 bp):
AATTCACTTCTTGCATTTAGTA
Found at i:36067 original size:10 final size:10
Alignment explanation
Indices: 36054--36088 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
36044 AGTTATATCG
36054 AAAAATATAA
1 AAAAATATAA
*
36064 AAAAAAATAA
1 AAAAATATAA
36074 AAAAATA-AA
1 AAAAATATAA
36083 AAAAAT
1 AAAAAT
36089 TTGACCAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAATATAA
Found at i:41926 original size:24 final size:24
Alignment explanation
Indices: 41894--41951 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
41884 TTTTTTATTA
41894 TTAC-TTTGGG-CTC-TTAATTCTT
1 TTACATTTGGGCCTCTTTAATT-TT
*
41916 TTACTATTTGGGCCTCTTTTATTTT
1 TTAC-ATTTGGGCCTCTTTAATTTT
41941 TTACATTTGGG
1 TTACATTTGGG
41952 TTTGGATTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 4 0.13
24 13 0.42
25 9 0.29
26 5 0.16
ACGTcount: A:0.14, C:0.16, G:0.16, T:0.55
Consensus pattern (24 bp):
TTACATTTGGGCCTCTTTAATTTT
Found at i:42533 original size:48 final size:48
Alignment explanation
Indices: 42462--43033 Score: 607
Period size: 48 Copynumber: 12.0 Consensus size: 48
42452 AATTCAAAAG
* * *
42462 GTTTTCAATGTCTATTTCCTGTTTTGCCCTTCTCGGTCGGAAGGCGCT
1 GTTTTCAATGTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* *
42510 GTTTTCAATGCCTCTTTCCTGTTTTGCCCTTCACGGTCGGAAGGTGCT
1 GTTTTCAATGTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* * * * *
42558 GTCTTCAGTGTCTTTTTCCTGTTTCGCCCTTCCTGGTCGGAAGGTGCT
1 GTTTTCAATGTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
** * * **
42606 GTTTTCGGTGTCTATTTCCGGTTTTGCCCTTCTTGGTCGGAAGGTGCT
1 GTTTTCAATGTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
** * *
42654 GTTTTCGGTGTTTCTTTCCTATTTTGCCCTTCCCGGTCGGAAGGTGCT
1 GTTTTCAATGTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* * * **
42702 -ATTTCTAGTGTCTATTTCCTGTTTTGCGATTCCCGGTCGGAAGGTGCT
1 GTTTTC-AATGTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* * * *
42750 ATTTTTAATGTCTGTTTCCTGTTTTGCCCTTCCCGGTCTGAAGGTGCT
1 GTTTTCAATGTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
** * * * * *
42798 GTTTTCTGTGTTTCTTTTCTGTTTTGCCCTTCCCGGTCAGAAGATGTT
1 GTTTTCAATGTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* * *
42846 ATTTTCAATGTCTAC-TTCTTGTGTTGCCCTTCCCGGTCGGAAGGTG-T
1 GTTTTCAATGTCT-CTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* * * *
42893 CGTCTTT--A-GTCTCTTTCCTGTTTTGCCCTTCTCAGTCGGAAGGCGTT
1 -GT-TTTCAATGTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* * *
42940 GTTTTCAATGTCGCTTTCCTGTTTCGCCCTTCCCGGTCGAAAGGTGCT
1 GTTTTCAATGTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* * * * *
42988 ATCTTCAGTGTATCTTTCCTGTTTTGCCCTTCTCGGTCGGAAGGTG
1 GTTTTCAATGTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTG
43034 TAAGTTTTTA
Statistics
Matches: 437, Mismatches: 77, Indels: 20
0.82 0.14 0.04
Matches are distributed among these distances:
45 4 0.01
46 32 0.07
47 8 0.02
48 386 0.88
49 7 0.02
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.42
Consensus pattern (48 bp):
GTTTTCAATGTCTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
Found at i:43125 original size:48 final size:47
Alignment explanation
Indices: 43014--43136 Score: 151
Period size: 48 Copynumber: 2.6 Consensus size: 47
43004 TCCTGTTTTG
* * *
43014 CCCTTCTCGGTCGGAAGGTGTAAGTTTTTATCTTTATCCCTAAAATA
1 CCCTTCCCGGTCGGAAGGTGCAAGTTTTTATCTCTATCCCTAAAATA
** *
43061 CCCTTCCTAGTCGGAAGGTG-AAGGTTTTTCATCTCTATTCCC-AAAGTA
1 CCCTTCCCGGTCGGAAGGTGCAA-GTTTTT-ATCTCTA-TCCCTAAAATA
43109 CCCTTCCCGGTCGGAAGGTGCAAGTTTT
1 CCCTTCCCGGTCGGAAGGTGCAAGTTTT
43137 CTTCACATCT
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
46 2 0.03
47 23 0.35
48 34 0.52
49 6 0.09
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.34
Consensus pattern (47 bp):
CCCTTCCCGGTCGGAAGGTGCAAGTTTTTATCTCTATCCCTAAAATA
Found at i:43695 original size:3 final size:3
Alignment explanation
Indices: 43687--43747 Score: 88
Period size: 3 Copynumber: 20.7 Consensus size: 3
43677 TATATATACT
*
43687 ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA ATA ATA ATA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
43734 ATA GTA ATA TTA AT
1 ATA ATA ATA ATA AT
43748 TTTTGTTAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:53077 original size:438 final size:437
Alignment explanation
Indices: 52211--53215 Score: 1193
Period size: 438 Copynumber: 2.3 Consensus size: 437
52201 TTGCATTTTT
* * *
52211 TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTA-TCAAAAGGCAATTTCATGATATACAATTT
1 TTCTATTTGTCCGATTAAGGTGATTC-AGTGTCTATTC-AAAGGTAATTTCATGATCTACAACTT
* * * ** * *
52275 TCATGAAGAACTCAAAAGCCAATTTTAATGTTTTGATTCTAAAAAATGCTTCTGAAATTTTGTGG
64 TCATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTAAAAAAAATGCTTCTGAAATTTGGTGC
* * * * * * * *
52340 GTTTGATTGCCGATCAATTTGATATCGTATAATTTTTTGTCAACATGTCTGATTGAAGTTATTGA
129 GTTTGATTGCCGATCAATTTAATACCATATAATTTTTCGTCAACATGTCCGACTAAAGTTATTCA
* * *
52405 AGTGTCAGTTAAAAGGTTATTGCATGATTTACGACTTTCATGAAGGACCCGAAAGCTAAATTTGA
194 AGTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGAACCCGAAAGCTAAATTTGA
* * * * *
52470 TCTACGAGTTTCATGAAGGGTTTAAAAGGGAATTTTTATGCTTCAAGATCTTCATTAACAAACAT
259 TCTACGAGTTTCATAAAGGGTTCAAAAGAGAATTTTTATGCTTCAAGATATCCATTAACAAACAT
* * * *
52535 TTTCTTATTTGGATTATTTATCAAATGAAAACCCTCATATTTTTCTACTTTATACTACTTAGTCC
324 TTTCTTATTTGAATTAGTTATCAAAT--AAACCCTCATACTTTTCTACTTTATACTACTTAGTCA
*
52600 TTTACAAATTCTATCTTAATCTAGTTTTTTAGATTTTTTTT-A-TTCTTTG
387 TTTACAAATTCTATCTTAATCTAGTTTTTCAGATTTTTTTTAATTTCTTTG
*
52649 TTCTATTTGTCCGATTAAGTTGATTCATGTGTCTATTCAAAGGTAATTTCATGATCTACAACTTT
1 TTCTATTTGTCCGATTAAGGTGATTCA-GTGTCTATTCAAAGGTAATTTCATGATCTACAACTTT
* * *
52714 CATTAAGGACTCAAAAGCAAATTTTTATGTTTTAATTAAAAAAAAATGTTTCCT-AAATTTGGT-
65 CATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATT-AAAAAAAATGCTT-CTGAAATTTGGTG
** * * *
52777 CGTTTCGATTGTTGGTCTATTTAATACCATATAA-TTTTCGATCCACATGTCCGACTAAAGTTAT
128 CGTTT-GATTGCCGATCAATTTAATACCATATAATTTTTCG-TCAACATGTCCGACTAAAGTTAT
* * * *
52841 TCAAGTGTCGGTTAAAAGGTTACTGTATGATCTACGACTTTCATGAAGAACCCGAAAG-TTAGTT
191 TCAAGTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGAACCCGAAAGCTAAATT
* *
52905 TGATCTACGAGTTTCATAAAGGGTTCAAAAGAGAATTTTTATGTTTCAAGATATCCATTAAGAAA
256 TGATCTACGAGTTTCATAAAGGGTTCAAAAGAGAATTTTTATGCTTCAAGATATCCATTAACAAA
* * * *
52970 TATTTTCTTATTTGAATTAGTTATCAAAT-AACTCTCATACTTTTCTATTTTATGCTACTTAGTC
321 CATTTTCTTATTTGAATTAGTTATCAAATAAACCCTCATACTTTTCTACTTTATACTACTTAGTC
* **
53034 ATTTACAAATTCTATCTT-AT-TTGATTTAACGCTTCATTTTTTTTTTAAATTTTCTTTG
386 ATTTACAAATTCTATCTTAATCTAG-TTT-----TTCAGATTTTTTTT-AA-TTTCTTTG
* * * *
53092 TTCTATTTGTCCAATTAAGGTAATTCAGATGTCTATTAAAAGGTAATTTTATGATCTACAACTTT
1 TTCTATTTGTCCGATTAAGGTGATTCAG-TGTCTATTCAAAGGTAATTTCATGATCTACAACTTT
* * * * ** * *
53157 CATGAAAGACTCAAAAGCTAATTTTCATGTTTCAATTCTAAAAAATACTTTTGAAATTT
65 CATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTAAAAAAAATGCTTCTGAAATTT
53216 TGTGATTTCG
Statistics
Matches: 481, Mismatches: 68, Indels: 32
0.83 0.12 0.06
Matches are distributed among these distances:
433 2 0.00
434 5 0.01
435 48 0.10
437 1 0.00
438 185 0.38
439 123 0.26
440 2 0.00
441 2 0.00
442 16 0.03
443 97 0.20
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (437 bp):
TTCTATTTGTCCGATTAAGGTGATTCAGTGTCTATTCAAAGGTAATTTCATGATCTACAACTTTC
ATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTAAAAAAAATGCTTCTGAAATTTGGTGCGT
TTGATTGCCGATCAATTTAATACCATATAATTTTTCGTCAACATGTCCGACTAAAGTTATTCAAG
TGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGAACCCGAAAGCTAAATTTGATC
TACGAGTTTCATAAAGGGTTCAAAAGAGAATTTTTATGCTTCAAGATATCCATTAACAAACATTT
TCTTATTTGAATTAGTTATCAAATAAACCCTCATACTTTTCTACTTTATACTACTTAGTCATTTA
CAAATTCTATCTTAATCTAGTTTTTCAGATTTTTTTTAATTTCTTTG
Found at i:54541 original size:30 final size:31
Alignment explanation
Indices: 54471--54567 Score: 124
Period size: 31 Copynumber: 3.2 Consensus size: 31
54461 TTAACATTAG
* * * *
54471 GGACTAATTTGAGCCGATTTTGCAATGCTAG
1 GGACTGATTTGAGCCGATTTTGCAACGTTAT
* *
54502 GGACTGATTTGAGACAATTTTGCAACGTTAT
1 GGACTGATTTGAGCCGATTTTGCAACGTTAT
*
54533 GG-CTGATTTTAGCCGATTTTGCAACGTTAT
1 GGACTGATTTGAGCCGATTTTGCAACGTTAT
54563 GGACT
1 GGACT
54568 TAATTAACCA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 27 0.48
31 29 0.52
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (31 bp):
GGACTGATTTGAGCCGATTTTGCAACGTTAT
Found at i:59659 original size:42 final size:42
Alignment explanation
Indices: 59580--59661 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
59570 GAACATTTTC
* * *
59580 TTAATCGAGCCGAGCTTGAACGACATTCGAACATTTTAAATT
1 TTAAACGAGCCGAGCTCGAACGACATTCAAACATTTTAAATT
**
59622 TTAAACGAGCCGAGCTCGAACGAACA-TCAAATTTTTTAAA
1 TTAAACGAGCCGAGCTCGAACG-ACATTCAAACATTTTAAA
59662 CGAACACGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (42 bp):
TTAAACGAGCCGAGCTCGAACGACATTCAAACATTTTAAATT
Found at i:61524 original size:1 final size:1
Alignment explanation
Indices: 61518--61547 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
61508 TTTGTGAGGA
61518 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
61548 GTAAATGACT
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:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:66040 original size:26 final size:27
Alignment explanation
Indices: 65987--66046 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
65977 TAATGCACCC
* * *
65987 AAAACATTTTAATAAAAATCATTTATA
1 AAAACAATTTAATAAAAATCAGTAATA
*
66014 AAAACAATTTATTAAAAAT-AGTAATA
1 AAAACAATTTAATAAAAATCAGTAATA
66040 AAAACAA
1 AAAACAA
66047 GTCCCTCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAACAATTTAATAAAAATCAGTAATA
Found at i:67593 original size:18 final size:19
Alignment explanation
Indices: 67572--67607 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
67562 TCCAGCTTTT
67572 TTCCATTTTTTCT-TTTCC
1 TTCCATTTTTTCTCTTTCC
*
67590 TTCCTTTTTTTCTCTTTC
1 TTCCATTTTTTCTCTTTC
67608 TTCAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (19 bp):
TTCCATTTTTTCTCTTTCC
Found at i:67610 original size:18 final size:18
Alignment explanation
Indices: 67567--67610 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
67557 ATTTTTCCAG
*
67567 CTTTTTTCCATTTTTTCT
1 CTTTCTTCCATTTTTTCT
*
67585 -TTTCCTTCCTTTTTTTCT
1 CTTT-CTTCCATTTTTTCT
67603 CTTTCTTC
1 CTTTCTTC
67611 AAATTTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.14
18 16 0.73
19 3 0.14
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.70
Consensus pattern (18 bp):
CTTTCTTCCATTTTTTCT
Found at i:69836 original size:26 final size:26
Alignment explanation
Indices: 69805--69874 Score: 104
Period size: 26 Copynumber: 2.6 Consensus size: 26
69795 GAATTGAAGA
69805 GAGAGAGAGTGAAGAGAGAGGATCAATC
1 GAGAGA-AGTG-AGAGAGAGGATCAATC
*
69833 GAGAGAAGTGAGAGAGTGGATCAATC
1 GAGAGAAGTGAGAGAGAGGATCAATC
*
69859 GAGATAAGTGAGAGAG
1 GAGAGAAGTGAGAGAG
69875 CCTCCTCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 30 0.75
27 4 0.10
28 6 0.15
ACGTcount: A:0.41, C:0.06, G:0.40, T:0.13
Consensus pattern (26 bp):
GAGAGAAGTGAGAGAGAGGATCAATC
Found at i:70031 original size:37 final size:37
Alignment explanation
Indices: 69980--70058 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 37
69970 TAACAAAATT
* *
69980 TTTTTTGTCTTATGTGTAGATTTTTTTG-TCTCCATA
1 TTTTTTGTCTTATGTGTAGATCTTTTTGTTCACCATA
70016 TGTTTTTGTCTTATGTGTAGATCTTTTTGTTCACCATA
1 T-TTTTTGTCTTATGTGTAGATCTTTTTGTTCACCATA
70054 TTTTT
1 TTTTT
70059 CCTTTTCCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
36 1 0.03
37 30 0.77
38 8 0.21
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.61
Consensus pattern (37 bp):
TTTTTTGTCTTATGTGTAGATCTTTTTGTTCACCATA
Found at i:70117 original size:24 final size:24
Alignment explanation
Indices: 70090--70164 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
70080 CTCCCCCTTT
70090 TCTTAGCTAACAAAATTTTTTTTG
1 TCTTAGCTAACAAAATTTTTTTTG
** *
70114 TCTTATG-T--GTAGATTTTTTTTG
1 TCTTA-GCTAACAAAATTTTTTTTG
70136 TCTTAGCTAACAAAATTTTTTTTG
1 TCTTAGCTAACAAAATTTTTTTTG
70160 TCTTA
1 TCTTA
70165 TGTGTAGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
21 1 0.02
22 17 0.41
24 22 0.54
25 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.55
Consensus pattern (24 bp):
TCTTAGCTAACAAAATTTTTTTTG
Found at i:70133 original size:127 final size:128
Alignment explanation
Indices: 69907--70138 Score: 457
Period size: 127 Copynumber: 1.8 Consensus size: 128
69897 TCAATCGATA
69907 AGATCTTTTTGTTCACCATATTTTTCCTTTTCCATTATGTTTTTCTCTCCCCCTTTTCTTAGCTA
1 AGATCTTTTTGTTCACCATATTTTTCCTTTTCCATTATGTTTTTCTCTCCCCCTTTTCTTAGCTA
69972 ACAAAATTTTTTTTGTCTTATGTGTAGA-TTTTTTTGTCTCCATATGTTTTTGTCTTATGTGT
66 ACAAAATTTTTTTTGTCTTATGTGTAGATTTTTTTTGTCTCCATATGTTTTTGTCTTATGTGT
70034 AGATCTTTTTGTTCACCATATTTTTCCTTTTCCATTATGTTTTTCTCTCCCCCTTTTCTTAGCTA
1 AGATCTTTTTGTTCACCATATTTTTCCTTTTCCATTATGTTTTTCTCTCCCCCTTTTCTTAGCTA
70099 ACAAAATTTTTTTTGTCTTATGTGTAGATTTTTTTTGTCT
66 ACAAAATTTTTTTTGTCTTATGTGTAGATTTTTTTTGTCT
70139 TAGCTAACAA
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
127 93 0.89
128 11 0.11
ACGTcount: A:0.16, C:0.19, G:0.09, T:0.56
Consensus pattern (128 bp):
AGATCTTTTTGTTCACCATATTTTTCCTTTTCCATTATGTTTTTCTCTCCCCCTTTTCTTAGCTA
ACAAAATTTTTTTTGTCTTATGTGTAGATTTTTTTTGTCTCCATATGTTTTTGTCTTATGTGT
Found at i:70175 original size:22 final size:22
Alignment explanation
Indices: 70104--70175 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
70094 AGCTAACAAA
70104 ATTTTTTTTGTCTTATGTGTAG
1 ATTTTTTTTGTCTTATGTGTAG
** *
70126 ATTTTTTTTGTCTTA-GCTAACAAA
1 ATTTTTTTTGTCTTATG-T--GTAG
70150 ATTTTTTTTGTCTTATGTGTAG
1 ATTTTTTTTGTCTTATGTGTAG
70172 ATTT
1 ATTT
70176 CTTCTGTTGC
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
21 1 0.03
22 21 0.52
24 17 0.43
25 1 0.03
ACGTcount: A:0.19, C:0.07, G:0.14, T:0.60
Consensus pattern (22 bp):
ATTTTTTTTGTCTTATGTGTAG
Found at i:71288 original size:28 final size:28
Alignment explanation
Indices: 71248--71304 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
71238 AATCTATATG
* *
71248 AAATGTAAATGAGTAAATGTGATTAATA
1 AAATGCAAATGAGTAAATGTGAATAATA
71276 AAATGCAAATGAGTAAATGTGAATAATA
1 AAATGCAAATGAGTAAATGTGAATAATA
71304 A
1 A
71305 GCTCGCCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.18, T:0.28
Consensus pattern (28 bp):
AAATGCAAATGAGTAAATGTGAATAATA
Found at i:71340 original size:6 final size:6
Alignment explanation
Indices: 71323--71371 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
71313 TTTTGTGATC
* *
71323 TTCTTAT TTCTCT TTCTCT TTCTTT TTCTTT TTCTTT TTCTTT TT-TTT
1 TTCTT-T TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
71371 T
1 T
71372 GTGTTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
5 4 0.10
6 32 0.80
7 4 0.10
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:71434 original size:26 final size:26
Alignment explanation
Indices: 71404--71485 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
71394 ACAATGCTAC
71404 GATGCAACTATTTAGTAACCAATGAA
1 GATGCAACTATTTAGTAACCAATGAA
* *
71430 GATGCAGACGCAATATA-TAA-C--T-AA
1 GATGCA-A--CTATTTAGTAACCAATGAA
*
71454 AATGCAACTATTTAGTAACCAATGAA
1 GATGCAACTATTTAGTAACCAATGAA
71480 GATGCA
1 GATGCA
71486 GACGCAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 5 0.12
22 3 0.07
23 2 0.05
24 7 0.17
25 2 0.05
26 13 0.31
27 2 0.05
28 3 0.07
29 5 0.12
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (26 bp):
GATGCAACTATTTAGTAACCAATGAA
Found at i:71465 original size:50 final size:50
Alignment explanation
Indices: 71405--71503 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
71395 CAATGCTACG
71405 ATGCAACTATTTAGTAACCAATGAAGATGCAGACGCAATATATAACTAAA
1 ATGCAACTATTTAGTAACCAATGAAGATGCAGACGCAATATATAACTAAA
*
71455 ATGCAACTATTTAGTAACCAATGAAGATGCAGACGCAATATCTAACTAA
1 ATGCAACTATTTAGTAACCAATGAAGATGCAGACGCAATATATAACTAA
71504 TTGCTAAATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.24
Consensus pattern (50 bp):
ATGCAACTATTTAGTAACCAATGAAGATGCAGACGCAATATATAACTAAA
Found at i:75916 original size:17 final size:17
Alignment explanation
Indices: 75888--75939 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
75878 AATTTTCTGA
75888 TTTTTCCATTTTTTTCAT
1 TTTTTCC-TTTTTTTCAT
*
75906 TTTTTCCTTTTCCTTC-T
1 TTTTTCCTTTT-TTTCAT
*
75923 TTTTTACTTTTTCTTCA
1 TTTTTCCTTTTT-TTCA
75940 AATCTTGACC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 18 0.64
18 10 0.36
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTCCTTTTTTTCAT
Found at i:75916 original size:24 final size:24
Alignment explanation
Indices: 75889--75935 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
75879 ATTTTCTGAT
*
75889 TTTTCCATT-TTTTTCATTTTTTCC
1 TTTTCC-TTCTTTTTCACTTTTTCC
*
75913 TTTTCCTTCTTTTTTACTTTTTC
1 TTTTCCTTCTTTTTCACTTTTTC
75936 TTCAAATCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.72
Consensus pattern (24 bp):
TTTTCCTTCTTTTTCACTTTTTCC
Done.