Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019121.1 Corchorus olitorius cultivar O-4 contig19154, 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: 183065
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:15380 original size:1 final size:1
Alignment explanation
Indices: 15374--15413 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
15364 TTTTACTCAG
15374 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
15414 CTCGTTTCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:18366 original size:11 final size:11
Alignment explanation
Indices: 18341--18380 Score: 71
Period size: 11 Copynumber: 3.5 Consensus size: 11
18331 CCCTTTCCTA
18341 TATAAAATAAAT
1 TATAAAAT-AAT
18353 TATAAAATAAT
1 TATAAAATAAT
18364 TATAAAATAAT
1 TATAAAATAAT
18375 TATAAA
1 TATAAA
18381 TTTGTTATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 20 0.71
12 8 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TATAAAATAAT
Found at i:19600 original size:64 final size:67
Alignment explanation
Indices: 19494--19636 Score: 229
Period size: 64 Copynumber: 2.2 Consensus size: 67
19484 TAGGAATAAC
* * *
19494 ACGATTTCATATTCAAATTAGACACGATTAATTTATATTAATCAGT-A-AA-TAAGCATATTGAA
1 ACGACTTCATATTCAAATTAGACACGATTAATTTATATTAATCAATAATAATTAAGCATATCGAA
19556 TG
66 TG
19558 ACGACTTCATATTCAAATTAGACACGATTAATTTATATTAATCAATAAATAATTAAGCATATCGA
1 ACGACTTCATATTCAAATTAGACACGATTAATTTATATTAATCAAT-AATAATTAAGCATATCGA
19623 ATG
65 ATG
19626 ACGACTTCATA
1 ACGACTTCATA
19637 CATAATTGGT
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
64 44 0.61
66 1 0.01
67 2 0.03
68 25 0.35
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (67 bp):
ACGACTTCATATTCAAATTAGACACGATTAATTTATATTAATCAATAATAATTAAGCATATCGAA
TG
Found at i:21627 original size:2 final size:2
Alignment explanation
Indices: 21620--21649 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21610 CGATCCCTAC
*
21620 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21650 GACACAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22113 original size:2 final size:2
Alignment explanation
Indices: 22108--22160 Score: 79
Period size: 2 Copynumber: 25.5 Consensus size: 2
22098 TATATAGCAC
*
22108 TA TA TA TA TA TA TA GCA CTA 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 TA TA TA TA TA
22152 TA TA TA TA T
1 TA TA TA TA T
22161 TTCTACGCTA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:22119 original size:18 final size:18
Alignment explanation
Indices: 22096--22155 Score: 97
Period size: 18 Copynumber: 3.4 Consensus size: 18
22086 TACTATACTG
22096 TATATATAGCACTATATA
1 TATATATAGCACTATATA
22114 TATATATAGCACTATATA
1 TATATATAGCACTATATA
*
22132 TATATATA-TA-TATATA
1 TATATATAGCACTATATA
22148 TATATATA
1 TATATATA
22156 TATATTTCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
16 14 0.34
17 1 0.02
18 26 0.63
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (18 bp):
TATATATAGCACTATATA
Found at i:24401 original size:131 final size:127
Alignment explanation
Indices: 24149--24403 Score: 394
Period size: 131 Copynumber: 2.0 Consensus size: 127
24139 ATTTAAGAAA
*
24149 TATATTTAAATAATTCTAATATATTAAAGTTTTTTAATCAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATTAAAGTTTTTTAATCAAAATAGTAAAATGGTAAAAAT---A
24214 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 TA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
24279 G
127 G
*
24280 TATATTTAAAAAATTCTAATATA-TATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA
1 TATATTTAAAAAATTCTAATATATTA-AAGTTTTTTAATCAAAATAGTAAAATGGTAAAAATATA
* *
24343 -TA-AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAAG
65 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
24403 T
1 T
24404 TTAAACAATG
Statistics
Matches: 119, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
123 55 0.46
124 2 0.02
125 2 0.02
127 2 0.02
130 2 0.02
131 56 0.47
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATTAAAGTTTTTTAATCAAAATAGTAAAATGGTAAAAATATAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
Found at i:24429 original size:123 final size:127
Alignment explanation
Indices: 24175--24411 Score: 329
Period size: 123 Copynumber: 1.9 Consensus size: 127
24165 TAATATATTA
24175 AAGTTTTTTAATCAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATT
1 AAGTTTTTTAATCAAAATAGTAAAATGGTAAAAAT---ATA-GTATAAGGATATTAGATTTAATT
* *** * *
24240 AAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTATATTTAAAAAATTCTAATATATA
62 AAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAACAAAAAATTCTAAGAAATA
24305 T
127 T
*
24306 AAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-AA-GATATTAGATTTAATTAAAT
1 AAGTTTTTTAATCAAAATAGTAAAATGGTAAAAATATAGTATAAGGATATTAGATTTAATTAAAT
* *
24367 AAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAAGTTTAAACAA
66 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAACAA
24412 TGGCATTTAA
Statistics
Matches: 99, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
123 59 0.60
124 2 0.02
125 2 0.02
127 2 0.02
131 34 0.34
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (127 bp):
AAGTTTTTTAATCAAAATAGTAAAATGGTAAAAATATAGTATAAGGATATTAGATTTAATTAAAT
AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAACAAAAAATTCTAAGAAATAT
Found at i:29201 original size:15 final size:16
Alignment explanation
Indices: 29176--29217 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
29166 CTGAATGTGA
29176 ATTTAGTTTGTG-ATTT
1 ATTT-GTTTGTGTATTT
29192 ATTTGTTTGTGTATTT
1 ATTTGTTTGTGTATTT
*
29208 GTTATGTTTG
1 ATT-TGTTTG
29218 GTAGTTGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.14, C:0.00, G:0.21, T:0.64
Consensus pattern (16 bp):
ATTTGTTTGTGTATTT
Found at i:31820 original size:2 final size:2
Alignment explanation
Indices: 31813--31849 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
31803 AGACAAAATC
31813 AT AT 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 AT AT A
31850 AACTGTAGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31960 original size:4 final size:4
Alignment explanation
Indices: 31953--31978 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
31943 TAATATATAT
31953 TTGA TTGA TTGA TTGA TTGA TTGA TT
1 TTGA TTGA TTGA TTGA TTGA TTGA TT
31979 TGAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (4 bp):
TTGA
Found at i:32030 original size:47 final size:47
Alignment explanation
Indices: 31961--32050 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
31951 ATTTGATTGA
31961 TTGATTGATTGATTGATTTGAATATTTTGA-TCAAATTAAAATACTAT
1 TTGATTGATTGATTGATTTGAATATTTT-ACTCAAATTAAAATACTAT
32008 TTGATTGATTGATTGATTTGAATATTTTACTCAAATTAAAATA
1 TTGATTGATTGATTGATTTGAATATTTTACTCAAATTAAAATA
32051 AAATCAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
46 1 0.02
47 41 0.98
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (47 bp):
TTGATTGATTGATTGATTTGAATATTTTACTCAAATTAAAATACTAT
Found at i:35212 original size:87 final size:87
Alignment explanation
Indices: 35066--35240 Score: 314
Period size: 87 Copynumber: 2.0 Consensus size: 87
35056 GTAAATCTCA
** *
35066 TCTTGTGCCTAAATTTTAGGAAGAAATCTGACTTGTCAAAATCTTATTGATCGGACCGGTCCACC
1 TCTTGTGCCTAAATCCTAGGAAGAAATCTGACTTGTCAAAATCTTATTGATCAGACCGGTCCACC
*
35131 TAATAATTTCTTGCTATCACCT
66 TAATAATTTCTCGCTATCACCT
35153 TCTTGTGCCTAAATCCTAGGAAGAAATCTGACTTGTCAAAATCTTATTGATCAGACCGGTCCACC
1 TCTTGTGCCTAAATCCTAGGAAGAAATCTGACTTGTCAAAATCTTATTGATCAGACCGGTCCACC
35218 TAATAATTTCTCGCTATCACCT
66 TAATAATTTCTCGCTATCACCT
35240 T
1 T
35241 ACCATTATTA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (87 bp):
TCTTGTGCCTAAATCCTAGGAAGAAATCTGACTTGTCAAAATCTTATTGATCAGACCGGTCCACC
TAATAATTTCTCGCTATCACCT
Found at i:61392 original size:31 final size:31
Alignment explanation
Indices: 61357--61457 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 31
61347 TTAATTTGGC
61357 CAAATAAGGGCCTAACGTTATAAAAAATGCT
1 CAAATAAGGGCCTAACGTTATAAAAAATGCT
* ** **
61388 CAAATAAGGGCC---CGATTTTTTAATTTGGC-
1 CAAATAAGGGCCTAACG-TTATAAAAAAT-GCT
* *
61417 CAAATAAGGGCCTAATGTTATCAAAAATGCT
1 CAAATAAGGGCCTAACGTTATAAAAAATGCT
61448 CAAATAAGGG
1 CAAATAAGGG
61458 TCTGGCATCA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 2 0.04
29 18 0.34
30 4 0.08
31 28 0.53
32 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATAAAAAATGCT
Found at i:61410 original size:60 final size:60
Alignment explanation
Indices: 61298--61457 Score: 243
Period size: 60 Copynumber: 2.7 Consensus size: 60
61288 GCTAATTGCT
* * *
61298 CAAATAAGGACCTAATGTT-TACAAAAAT-CTCAAAGAAAGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTATA-AAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
* *
61357 CAAATAAGGGCCTAACGTTATAAAAAATGCTCAAATAAGGGCCCGATTTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTATAAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
61417 CAAATAAGGGCCTAATGTTATCAAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAATGTTATAAAAAATGCTCAAATAAGGG
61458 TCTGGCATCA
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
59 23 0.25
60 69 0.75
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAATGTTATAAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:61428 original size:29 final size:29
Alignment explanation
Indices: 61336--61428 Score: 82
Period size: 29 Copynumber: 3.1 Consensus size: 29
61326 CTCAAAGAAA
*
61336 GGCCCGATCTTTTAATTTGGCCAAATAAG
1 GGCCCGATTTTTTAATTTGGCCAAATAAG
* ** **
61365 GGCCTAACG-TTATAAAAAAT-GCTCAAATAAG
1 GGCC---CGATTTTTTAATTTGGC-CAAATAAG
61396 GGCCCGATTTTTTAATTTGGCCAAATAAG
1 GGCCCGATTTTTTAATTTGGCCAAATAAG
61425 GGCC
1 GGCC
61429 TAATGTTATC
Statistics
Matches: 47, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
28 2 0.04
29 22 0.47
30 4 0.09
31 17 0.36
32 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (29 bp):
GGCCCGATTTTTTAATTTGGCCAAATAAG
Found at i:63696 original size:18 final size:18
Alignment explanation
Indices: 63670--63715 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
63660 ACAACTGATT
63670 CCACTACTATGTGGCCTC
1 CCACTACTATGTGGCCTC
* *
63688 CCCCTACTATGTGGCTTC
1 CCACTACTATGTGGCCTC
63706 CCACTACTAT
1 CCACTACTAT
63716 CCTAGTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.17, C:0.39, G:0.13, T:0.30
Consensus pattern (18 bp):
CCACTACTATGTGGCCTC
Found at i:64729 original size:16 final size:16
Alignment explanation
Indices: 64703--64735 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
64693 TTGCTTTCAA
64703 ACTTCTTAAATGAATCT
1 ACTTCTTAAATG-ATCT
64720 ACTT-TTAAATGATCT
1 ACTTCTTAAATGATCT
64735 A
1 A
64736 AAACTAGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (16 bp):
ACTTCTTAAATGATCT
Found at i:66921 original size:23 final size:24
Alignment explanation
Indices: 66894--66949 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 24
66884 ACTGTAAAAC
*
66894 AAAAAGAAATA-ACTGAAAAT-AAT
1 AAAAAGAAA-AGACTGAAAATAAAG
66917 AAAAA-AAAAGACTGAAAATAAAG
1 AAAAAGAAAAGACTGAAAATAAAG
66940 AAAAAGAAAA
1 AAAAAGAAAA
66950 CAAATATTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 1 0.03
22 12 0.41
23 12 0.41
24 4 0.14
ACGTcount: A:0.75, C:0.04, G:0.11, T:0.11
Consensus pattern (24 bp):
AAAAAGAAAAGACTGAAAATAAAG
Found at i:78577 original size:15 final size:15
Alignment explanation
Indices: 78557--78603 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
78547 CTCTACTAAT
78557 TTCTTTCTAGAATAG
1 TTCTTTCTAGAATAG
* * * *
78572 TTCTTTCAAAAAAAT
1 TTCTTTCTAGAATAG
78587 TTCTTTCTAGAATAG
1 TTCTTTCTAGAATAG
78602 TT
1 TT
78604 GATTTTTACT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.47
Consensus pattern (15 bp):
TTCTTTCTAGAATAG
Found at i:91598 original size:2 final size:2
Alignment explanation
Indices: 91593--91631 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
91583 AAAAAGACAG
91593 AT AT AT 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 AT AT AT A
91632 AGCTGGTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:94449 original size:10 final size:10
Alignment explanation
Indices: 94434--94459 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
94424 CCCATTCCAG
94434 AAAAGGGAAC
1 AAAAGGGAAC
94444 AAAAGGGAAC
1 AAAAGGGAAC
94454 AAAAGG
1 AAAAGG
94460 AAAAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.08, G:0.31, T:0.00
Consensus pattern (10 bp):
AAAAGGGAAC
Found at i:97808 original size:15 final size:15
Alignment explanation
Indices: 97788--97821 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
97778 GTTTCATTTC
97788 ATAAAAAAAATAATA
1 ATAAAAAAAATAATA
97803 ATAAAAAAAATAATA
1 ATAAAAAAAATAATA
97818 ATAA
1 ATAA
97822 GAATGTGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAAAAAAATAATA
Found at i:98201 original size:20 final size:20
Alignment explanation
Indices: 98176--98215 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
98166 TTAGGTTCAA
98176 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
98196 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
98216 GTTTGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CTCTCACGGAATGTGAGTTT
Found at i:112636 original size:123 final size:127
Alignment explanation
Indices: 112395--112647 Score: 415
Period size: 131 Copynumber: 2.0 Consensus size: 127
112385 ATTTAAGAAA
112395 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---A
* *
112460 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 TA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAA
112525 G
127 G
*
112526 TATATTTAAATAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAG
112589 TA-AA-GATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAA
66 TATAAGGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAA
112648 TTTTAAACAA
Statistics
Matches: 119, Mismatches: 3, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
123 53 0.45
124 2 0.02
125 2 0.02
127 2 0.02
131 60 0.50
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAG
Found at i:112773 original size:9 final size:9
Alignment explanation
Indices: 112759--112788 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
112749 AATTAATTAA
112759 TATATATAT
1 TATATATAT
112768 TATATATAT
1 TATATATAT
112777 TAT-TATAT
1 TATATATAT
112785 TATA
1 TATA
112789 CCTATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TATATATAT
Found at i:112785 original size:17 final size:17
Alignment explanation
Indices: 112763--112798 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
112753 AATTAATATA
*
112763 TATATTATATATATTAT
1 TATATTATACATATTAT
*
112780 TATATTATACCTATTAT
1 TATATTATACATATTAT
112797 TA
1 TA
112799 ATCTTATGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATACATATTAT
Found at i:113456 original size:41 final size:41
Alignment explanation
Indices: 113381--113458 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
113371 ATGACGTTCT
* * *
113381 TTTCTTAACTAAATTTTCTTAAAAACATTTATAAAATTCCA
1 TTTCTTAAATAAATTTTCTTAAAAACACTCATAAAATTCCA
*
113422 TTTCTTAAATGAATTTTCTTAAAAGA-ACTCATAAAAT
1 TTTCTTAAATAAATTTTCTTAAAA-ACACTCATAAAAT
113459 AAAACAGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 31 0.97
42 1 0.03
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (41 bp):
TTTCTTAAATAAATTTTCTTAAAAACACTCATAAAATTCCA
Found at i:113881 original size:19 final size:20
Alignment explanation
Indices: 113857--113894 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
113847 AAACTCTATT
113857 AAAACTTAATT-TATTTATC
1 AAAACTTAATTATATTTATC
*
113876 AAAACTTATTTATATTTAT
1 AAAACTTAATTATATTTAT
113895 TTTATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAACTTAATTATATTTATC
Found at i:114454 original size:33 final size:33
Alignment explanation
Indices: 114417--114479 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
114407 TGCATGGTCC
**
114417 GGTCGCGAC-CGTATCGCGACTTGACCATGGCTT
1 GGTCGCG-CGCGTATCGCGACCGGACCATGGCTT
*
114450 GGTCGCGCGCGTGTCGCGACCGGACCATGG
1 GGTCGCGCGCGTATCGCGACCGGACCATGG
114480 TTAGGTGGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 1 0.04
33 25 0.96
ACGTcount: A:0.13, C:0.32, G:0.37, T:0.19
Consensus pattern (33 bp):
GGTCGCGCGCGTATCGCGACCGGACCATGGCTT
Found at i:115278 original size:19 final size:20
Alignment explanation
Indices: 115251--115288 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
115241 ATTCAAAACA
*
115251 AAATAAAAACTATCCATTTT
1 AAATAAAAACTACCCATTTT
115271 AAAT-AAAACTACCCATTT
1 AAATAAAAACTACCCATTT
115289 CAGGATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAAAAACTACCCATTTT
Found at i:118321 original size:37 final size:37
Alignment explanation
Indices: 118264--118339 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
118254 CTTGATCAAC
* * *
118264 ATACATGTCTTTTCATATAGACATAACTTTATGATTA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGAATA
*
118301 ATACATGTCTTTCCAAATAGACATACCTTTATGAATA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGAATA
118338 AT
1 AT
118340 TATGTCATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGAATA
Found at i:119372 original size:142 final size:142
Alignment explanation
Indices: 119116--119404 Score: 551
Period size: 142 Copynumber: 2.0 Consensus size: 142
119106 TTAGTTAACG
119116 GATCCGATAAATTCTTTGCTGAATTTATGTAGGAGATAGTAATCGTTCCATTAGAGATGTTATCT
1 GATCCGATAAATTCTTTGCTGAATTTATGTAGGAGATAGTAATCGTTCCATTAGAGATGTTATCT
*
119181 CTAACACAATCATAAGGATTTATCAATCCCAAACTTTATAAATTTATGCATATTTCTAATATGCT
66 CTAACACAATCATAAGGATTTATCAATCCCAAACTTAATAAATTTATGCATATTTCTAATATGCT
119246 TTAAACATTCAT
131 TTAAACATTCAT
* *
119258 GATCCGATAAATTCTTTGCTGAATTTATGTAGGAGATAGTAATCTTTCCATTAGAGATTTTATCT
1 GATCCGATAAATTCTTTGCTGAATTTATGTAGGAGATAGTAATCGTTCCATTAGAGATGTTATCT
119323 CTAACACAATCATAAGGATTTATCAATCCCAAACTTAATAAATTTATGCATATTTCTAATATGCT
66 CTAACACAATCATAAGGATTTATCAATCCCAAACTTAATAAATTTATGCATATTTCTAATATGCT
119388 TTAAACATTCAT
131 TTAAACATTCAT
119400 GATCC
1 GATCC
119405 AAGGAAATAG
Statistics
Matches: 144, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 144 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (142 bp):
GATCCGATAAATTCTTTGCTGAATTTATGTAGGAGATAGTAATCGTTCCATTAGAGATGTTATCT
CTAACACAATCATAAGGATTTATCAATCCCAAACTTAATAAATTTATGCATATTTCTAATATGCT
TTAAACATTCAT
Found at i:120959 original size:37 final size:37
Alignment explanation
Indices: 120915--120985 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
120905 CTTGATCAAC
* *
120915 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
120952 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
120986 ATAATTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:122379 original size:24 final size:24
Alignment explanation
Indices: 122340--122388 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
122330 AGAATGGTAT
*
122340 AAGAAAAAAGAGGGCGACGAAGAA
1 AAGAAAAAAGAAGGCGACGAAGAA
*
122364 AAGAAAAGAGAAGGCGACGAAGAA
1 AAGAAAAAAGAAGGCGACGAAGAA
122388 A
1 A
122389 GTGGTTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.59, C:0.08, G:0.33, T:0.00
Consensus pattern (24 bp):
AAGAAAAAAGAAGGCGACGAAGAA
Found at i:124277 original size:55 final size:54
Alignment explanation
Indices: 124115--124281 Score: 271
Period size: 54 Copynumber: 3.1 Consensus size: 54
124105 GCATTAATAA
* * *
124115 CTCAATTGCTTCAATTACATAACCTTTTACATGCAATTACATCTGCATCTATAG
1 CTCAATTGCTTCAATTACAGAACCTTTTACAAGCAATTATATCTGCATCTATAG
*
124169 CTCAATTGCTTCAACTACAGAACCTTTTACAAGCAATTATATCTGCATCTATAG
1 CTCAATTGCTTCAATTACAGAACCTTTTACAAGCAATTATATCTGCATCTATAG
* *
124223 CTCAATTGCTTCAATTACAGAACCCTTTTACAAGCAACTATATCTGCATTTATAG
1 CTCAATTGCTTCAATTACAGAA-CCTTTTACAAGCAATTATATCTGCATCTATAG
124278 CTCA
1 CTCA
124282 CATGTGCACA
Statistics
Matches: 105, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
54 71 0.68
55 34 0.32
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (54 bp):
CTCAATTGCTTCAATTACAGAACCTTTTACAAGCAATTATATCTGCATCTATAG
Found at i:128856 original size:31 final size:31
Alignment explanation
Indices: 128819--128954 Score: 164
Period size: 31 Copynumber: 4.4 Consensus size: 31
128809 ACGGTGTCCG
*
128819 ACGTGGCATGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCACATGTACCAAAAAGCGAC
* **
128850 ATGTGGCATGCCATGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCACATGTACCAAAAAGCGAC
** *
128881 ACGTGGCACACCACATGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGCGAC
* * * *
128912 ATGTGTCACGCCACATGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGCGAC
*
128943 ACATGGCATGCC
1 ACGTGGCATGCC
128955 TCGTTCACAA
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 90 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (31 bp):
ACGTGGCATGCCACATGTACCAAAAAGCGAC
Found at i:128968 original size:62 final size:61
Alignment explanation
Indices: 128822--128981 Score: 171
Period size: 62 Copynumber: 2.6 Consensus size: 61
128812 GTGTCCGACG
* * ** *
128822 TGGCATGCCACGTGTACCAAAAAGCGACATGTGGCATGCCATGTGTACCAAAAAGCGACACG
1 TGGCATGCCACGTGTACCAAAAAG-GACATGTGTCACGCCACATGTACCAAAAAGCGACACA
** * *
128884 TGGCACACCACATGTACCAAAAAGTGACATGTGTCACGCCACATGTACCAAAAAGTGACACA
1 TGGCATGCCACGTGTACCAAAAAG-GACATGTGTCACGCCACATGTACCAAAAAGCGACACA
* * *
128946 TGGCATGCCTCGT-T-CACAAAAAAGACACGTGTCACG
1 TGGCATGCCACGTGTAC-CAAAAAGGACATGTGTCACG
128982 TGTTATTTTC
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
60 13 0.16
61 7 0.09
62 61 0.75
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (61 bp):
TGGCATGCCACGTGTACCAAAAAGGACATGTGTCACGCCACATGTACCAAAAAGCGACACA
Found at i:133276 original size:2 final size:2
Alignment explanation
Indices: 133269--133316 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
133259 ACATCAATAG
133269 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
133311 AT AT AT
1 AT AT AT
133317 CCTTACAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:141302 original size:31 final size:31
Alignment explanation
Indices: 141245--141303 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
141235 TTCAGCTCAT
* *
141245 CTGGATTCAGGTCATTCGGGTCTCGGGTCTG
1 CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
*
141276 CTGGATTTAGGGTCATGCAGGT-TCGGGT
1 CTGGATTCA-GGTCATGCAGGTCTCGGGT
141304 TTTGGCCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.12, C:0.19, G:0.37, T:0.32
Consensus pattern (31 bp):
CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
Found at i:142835 original size:2 final size:2
Alignment explanation
Indices: 142828--142868 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
142818 ATTTGATAAC
142828 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
142869 TCTCATATGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:144962 original size:15 final size:16
Alignment explanation
Indices: 144934--144963 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
144924 TATAAAAACT
144934 TTAATTTTTCTTAGAC
1 TTAATTTTTCTTAGAC
144950 TTAATTTTT-TTAGA
1 TTAATTTTTCTTAGA
144964 AAATTGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (16 bp):
TTAATTTTTCTTAGAC
Found at i:145303 original size:67 final size:63
Alignment explanation
Indices: 145225--145353 Score: 170
Period size: 67 Copynumber: 2.0 Consensus size: 63
145215 TTTTAGTTTA
*
145225 TATATAAAATATAATATTTGAAAATTTTAAACTAAG-ATATATATTGCTTCTAATTTCAATTTCT
1 TATATAAAATATAATATTTGAAAA---T-AACTAAGAATATATATTGCTTCTAA-TTAAATTTCT
145289 TAT
61 TAT
* *
145292 TATATAAAATATAATATTTTAAAATAATTAAGATATATATATTGCTTCTAATTAAATTTCTT
1 TATATAAAATATAATATTTGAAAATAACTAAGA-ATATATATTGCTTCTAATTAAATTTCTT
145354 TTTTTGCCAA
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
63 6 0.11
64 11 0.19
65 17 0.30
67 23 0.40
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (63 bp):
TATATAAAATATAATATTTGAAAATAACTAAGAATATATATTGCTTCTAATTAAATTTCTTAT
Found at i:147810 original size:27 final size:29
Alignment explanation
Indices: 147757--147811 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
147747 CTAAATTGAC
* *
147757 ATTATTAAAATATATTTTAATTATGCCATT
1 ATTATTAAAATATA-TTAAAATATGCCATT
147787 ATTATTAAAATATA-TAAAAT-TGCCA
1 ATTATTAAAATATATTAAAATATGCCA
147812 ATATGTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 4 0.17
30 14 0.61
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (29 bp):
ATTATTAAAATATATTAAAATATGCCATT
Found at i:148672 original size:22 final size:22
Alignment explanation
Indices: 148647--148849 Score: 121
Period size: 22 Copynumber: 9.2 Consensus size: 22
148637 AATGATATAT
*
148647 AATTTCATAGAGAGATTATCGA
1 AATTTCATAGAGAGATTATCAA
* *
148669 AATTTCATACTA-TGA-TATCAAA
1 AATTTCATA-GAGAGATTATC-AA
*
148691 AATTT-ATAGGGAGATTAAT-AA
1 AATTTCATAGAGAGATT-ATCAA
*
148712 AATTTCATAGAGAGGTTATCAA
1 AATTTCATAGAGAGATTATCAA
* * *
148734 AATTTCATAGAAAAGTTTATTAA
1 AATTTCATAG-AGAGATTATCAA
* ** * *
148757 AATTTCATGGTTAGGTTATCAG
1 AATTTCATAGAGAGATTATCAA
* * * *
148779 TATTTCATTGAGAGTTTATCAC
1 AATTTCATAGAGAGATTATCAA
* * *
148801 AGTTTCATAG-GATAATCATCAA
1 AATTTCATAGAGA-GATTATCAA
*
148823 AATTTCATAGTGTAG-TTATCAA
1 AATTTCATAGAG-AGATTATCAA
148845 AATTT
1 AATTT
148850 GGTGGTTATC
Statistics
Matches: 137, Mismatches: 33, Indels: 22
0.71 0.17 0.11
Matches are distributed among these distances:
21 20 0.15
22 94 0.69
23 22 0.16
24 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.37
Consensus pattern (22 bp):
AATTTCATAGAGAGATTATCAA
Found at i:148758 original size:23 final size:22
Alignment explanation
Indices: 148709--148764 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
148699 GGGAGATTAA
*
148709 TAAAATTTCATAGAGAGGTTAT
1 TAAAATTTCATAGAAAGGTTAT
* *
148731 CAAAATTTCATAGAAAAGTTTAT
1 TAAAATTTCATAG-AAAGGTTAT
148754 TAAAATTTCAT
1 TAAAATTTCAT
148765 GGTTAGGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (22 bp):
TAAAATTTCATAGAAAGGTTAT
Found at i:148936 original size:2 final size:2
Alignment explanation
Indices: 148929--148955 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
148919 CTAAAACTAG
148929 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
148956 TAAAAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:149365 original size:54 final size:54
Alignment explanation
Indices: 149278--149380 Score: 188
Period size: 54 Copynumber: 1.9 Consensus size: 54
149268 ATCCCCTTAA
* *
149278 TTTTCAAAATCAAGCCAAATTATCCCTTACCGTCAACGCCGTTAGTCACGTGCC
1 TTTTAAAAATCAAGCCAAATTACCCCTTACCGTCAACGCCGTTAGTCACGTGCC
149332 TTTTAAAAATCAAGCCAAATTACCCCTTACCGTCAACGCCGTTAGTCAC
1 TTTTAAAAATCAAGCCAAATTACCCCTTACCGTCAACGCCGTTAGTCAC
149381 ATGACGGCAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.30, C:0.31, G:0.12, T:0.27
Consensus pattern (54 bp):
TTTTAAAAATCAAGCCAAATTACCCCTTACCGTCAACGCCGTTAGTCACGTGCC
Found at i:150094 original size:37 final size:37
Alignment explanation
Indices: 150044--150118 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
150034 TTATTTTAGT
*
150044 AAAAGTTTTAGACTAATATTTGTCATTTGACATTATC
1 AAAAGTTTTAGACTAATATTGGTCATTTGACATTATC
150081 AAAAGTTTTAGACTAATATTGGTCATTTGACATTATC
1 AAAAGTTTTAGACTAATATTGGTCATTTGACATTATC
150118 A
1 A
150119 CAATTTTTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (37 bp):
AAAAGTTTTAGACTAATATTGGTCATTTGACATTATC
Found at i:162909 original size:108 final size:108
Alignment explanation
Indices: 162715--162964 Score: 473
Period size: 108 Copynumber: 2.3 Consensus size: 108
162705 GAACTTGTCC
162715 TAAACCAAGCCTTCTTGTGGTAGATCTCGAATTTTAAACCTAGTTCATTATTAGATTGTACCCGA
1 TAAACCAAGCCTTCTTGTGGTAGATCTCGAATTTTAAACCTAGTTCATTATTAGATTGTACCCGA
*
162780 TTTTAAGGTATTGTATGCTCTAGAACTTGTCCTCTCGCTTTTT
66 TTTTAAGGTATTGTATACTCTAGAACTTGTCCTCTCGCTTTTT
*
162823 TAAACCAAGCCTTCTTGTGGTATATCTCGAATTTTAAACCTAGTTCATTATTAGATTGTACCCGA
1 TAAACCAAGCCTTCTTGTGGTAGATCTCGAATTTTAAACCTAGTTCATTATTAGATTGTACCCGA
162888 TTTTAAGGTATTGTATACTCTAGAACTTGTCCTCTCGCTTTTT
66 TTTTAAGGTATTGTATACTCTAGAACTTGTCCTCTCGCTTTTT
*
162931 TAAACCAAGCCTTCTTATGGTAGATCTCGAATTT
1 TAAACCAAGCCTTCTTGTGGTAGATCTCGAATTT
162965 GAAAGATTAT
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 138 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (108 bp):
TAAACCAAGCCTTCTTGTGGTAGATCTCGAATTTTAAACCTAGTTCATTATTAGATTGTACCCGA
TTTTAAGGTATTGTATACTCTAGAACTTGTCCTCTCGCTTTTT
Found at i:166146 original size:14 final size:14
Alignment explanation
Indices: 166127--166154 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
166117 CTATCTTAAG
166127 ATTTTAAGATTTAC
1 ATTTTAAGATTTAC
166141 ATTTTAAGATTTAC
1 ATTTTAAGATTTAC
166155 GGTACTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
ATTTTAAGATTTAC
Found at i:172830 original size:59 final size:59
Alignment explanation
Indices: 172740--172861 Score: 235
Period size: 59 Copynumber: 2.1 Consensus size: 59
172730 TTAGGCTAAT
*
172740 TTTTTCCAAATAAAAGTATATTAAATAAGGGTAATTATTTGATACACTGGTGGTGTAAA
1 TTTTTCCAAATAAAAGTATATTAAATAAGGGTAATTATTTGATACACTGGTGGGGTAAA
172799 TTTTTCCAAATAAAAGTATATTAAATAAGGGTAATTATTTGATACACTGGTGGGGTAAA
1 TTTTTCCAAATAAAAGTATATTAAATAAGGGTAATTATTTGATACACTGGTGGGGTAAA
172858 TTTT
1 TTTT
172862 GGACTCCACA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.39
Consensus pattern (59 bp):
TTTTTCCAAATAAAAGTATATTAAATAAGGGTAATTATTTGATACACTGGTGGGGTAAA
Found at i:180854 original size:7 final size:7
Alignment explanation
Indices: 180844--180881 Score: 53
Period size: 6 Copynumber: 5.6 Consensus size: 7
180834 CACTTTTTTT
180844 TTTTTGG
1 TTTTTGG
180851 TTTTTGG
1 TTTTTGG
180858 ATTTTTGG
1 -TTTTTGG
180866 -TTTTGG
1 TTTTTGG
180872 -TTTTGG
1 TTTTTGG
180878 TTTT
1 TTTT
180882 AGAAATACCG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 12 0.41
7 10 0.34
8 7 0.24
ACGTcount: A:0.03, C:0.00, G:0.26, T:0.71
Consensus pattern (7 bp):
TTTTTGG
Found at i:181000 original size:12 final size:12
Alignment explanation
Indices: 180982--181015 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
180972 AATGGGAATT
180982 GTTAAAAAAAAA
1 GTTAAAAAAAAA
*
180994 TTTAAAAAAAAA
1 GTTAAAAAAAAA
*
181006 GATAAAAAAA
1 GTTAAAAAAA
181016 TGCTAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (12 bp):
GTTAAAAAAAAA
Done.