Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019023.1 Corchorus olitorius cultivar O-4 contig19056, 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: 190007
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2229 original size:11 final size:9
Alignment explanation
Indices: 2205--2229 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2195 TTAAGGCTGC
2205 CATATATTT
1 CATATATTT
2214 CATATATTT
1 CATATATTT
2223 CATATAT
1 CATATAT
2230 GCTTTCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (9 bp):
CATATATTT
Found at i:5918 original size:57 final size:57
Alignment explanation
Indices: 5830--5944 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
5820 TTTTTAAATT
5830 CAGAAATTGTTAAAAACCAAATACTTTCCAAAGATATAGATGCAGAAAACTAACCGC
1 CAGAAATTGTTAAAAACCAAATACTTTCCAAAGATATAGATGCAGAAAACTAACCGC
*
5887 CAGAAATTGTTAAAAACCAAATAGTTTCCAAAGATATAGATGCAGAAAACTAACCGC
1 CAGAAATTGTTAAAAACCAAATACTTTCCAAAGATATAGATGCAGAAAACTAACCGC
5944 C
1 C
5945 CGGCGCCCTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (57 bp):
CAGAAATTGTTAAAAACCAAATACTTTCCAAAGATATAGATGCAGAAAACTAACCGC
Found at i:9594 original size:14 final size:15
Alignment explanation
Indices: 9571--9604 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
9561 GGCCTAGCTT
*
9571 AAAGCTCTTCT-GAA
1 AAAGCGCTTCTGGAA
9585 AAAGCGCTTCTGGAA
1 AAAGCGCTTCTGGAA
9600 AAAGC
1 AAAGC
9605 TTCAATTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (15 bp):
AAAGCGCTTCTGGAA
Found at i:14740 original size:27 final size:27
Alignment explanation
Indices: 14702--14756 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
14692 CTTTAGATAC
14702 TGAGTAGAGAGATTTTGAATTGAAACG
1 TGAGTAGAGAGATTTTGAATTGAAACG
14729 TGAGTAGAGAGATTTTGAATTGAAACG
1 TGAGTAGAGAGATTTTGAATTGAAACG
14756 T
1 T
14757 AAGTTTGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.31
Consensus pattern (27 bp):
TGAGTAGAGAGATTTTGAATTGAAACG
Found at i:19676 original size:24 final size:24
Alignment explanation
Indices: 19644--19691 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
19634 GTTTATTAAC
19644 TTTTTTTTATCGAATTTGACTTTA
1 TTTTTTTTATCGAATTTGACTTTA
19668 TTTTTTTTATCGAATTTGACTTTA
1 TTTTTTTTATCGAATTTGACTTTA
19692 AAATACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.62
Consensus pattern (24 bp):
TTTTTTTTATCGAATTTGACTTTA
Found at i:20303 original size:24 final size:24
Alignment explanation
Indices: 20267--20314 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
20257 AGTTAAAAAT
20267 TTAGAAAGGTAGAAATGATTTGAG
1 TTAGAAAGGTAGAAATGATTTGAG
*
20291 TTAGAAAGTTAGAAATGATTTGAG
1 TTAGAAAGGTAGAAATGATTTGAG
20315 AGAATTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (24 bp):
TTAGAAAGGTAGAAATGATTTGAG
Found at i:20396 original size:20 final size:20
Alignment explanation
Indices: 20358--20396 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20348 AATCTTTTGA
*
20358 GGGGCGGTAACTAGTAATAG
1 GGGGCGGTAACTAGAAATAG
**
20378 GGGGCGGTATTTAGAAATA
1 GGGGCGGTAACTAGAAATA
20397 CTCATAACCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.38, T:0.23
Consensus pattern (20 bp):
GGGGCGGTAACTAGAAATAG
Found at i:26637 original size:48 final size:48
Alignment explanation
Indices: 26582--26678 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
26572 TGAGACTTAA
26582 ACTTAGAATCTCAATATTCAAATATCATATACTCCTATCAATTAAGTT
1 ACTTAGAATCTCAATATTCAAATATCATATACTCCTATCAATTAAGTT
26630 ACTTAGAATCTCAATATTCAAATATCATATACTCCTATCAATTAAGTT
1 ACTTAGAATCTCAATATTCAAATATCATATACTCCTATCAATTAAGTT
26678 A
1 A
26679 ATTAACACAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37
Consensus pattern (48 bp):
ACTTAGAATCTCAATATTCAAATATCATATACTCCTATCAATTAAGTT
Found at i:30789 original size:21 final size:21
Alignment explanation
Indices: 30760--30799 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30750 CCACTAATAA
*
30760 TAATTATTATAATAATAAGTT
1 TAATAATTATAATAATAAGTT
*
30781 TAATAATTATAATATTAAG
1 TAATAATTATAATAATAAG
30800 ATGTTTAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
TAATAATTATAATAATAAGTT
Found at i:30798 original size:15 final size:16
Alignment explanation
Indices: 30754--30798 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
30744 TACATACCAC
*
30754 TAATAATAATTATT-A
1 TAATAATAAGTATTAA
30769 TAATAATAAGT-TTAA
1 TAATAATAAGTATTAA
*
30784 TAATTATAA-TATTAA
1 TAATAATAAGTATTAA
30799 GATGTTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 3 0.12
15 23 0.88
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TAATAATAAGTATTAA
Found at i:30805 original size:24 final size:24
Alignment explanation
Indices: 30757--30807 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
30747 ATACCACTAA
* *
30757 TAATAATTATTATAATAATAAGTT
1 TAATAATTATAATAATAAGAAGTT
* *
30781 TAATAATTATAATATTAAGATGTT
1 TAATAATTATAATAATAAGAAGTT
30805 TAA
1 TAA
30808 CGTAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TAATAATTATAATAATAAGAAGTT
Found at i:36232 original size:15 final size:15
Alignment explanation
Indices: 36212--36241 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36202 CATTGTATTT
*
36212 TAGCAACAGCAACAA
1 TAGCAACAACAACAA
36227 TAGCAACAACAACAA
1 TAGCAACAACAACAA
36242 GAACTCAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.27, G:0.10, T:0.07
Consensus pattern (15 bp):
TAGCAACAACAACAA
Found at i:46915 original size:1 final size:1
Alignment explanation
Indices: 46909--46935 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
46899 CTTTCATTGA
46909 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
46936 AAAGTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:52277 original size:22 final size:24
Alignment explanation
Indices: 52252--52295 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
52242 AACTTTCATT
*
52252 AATTGATG-ATAAT-TAATTAATG
1 AATTGATGCAAAATATAATTAATG
52274 AATTGATGCAAAATATAATTAA
1 AATTGATGCAAAATATAATTAA
52296 CCATGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (24 bp):
AATTGATGCAAAATATAATTAATG
Found at i:57277 original size:22 final size:24
Alignment explanation
Indices: 57252--57295 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
57242 AACTTTCATT
*
57252 AATTGATG-ATAAT-TAATTAATG
1 AATTGATGCAAAATATAATTAATG
57274 AATTGATGCAAAATATAATTAA
1 AATTGATGCAAAATATAATTAA
57296 CCATGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (24 bp):
AATTGATGCAAAATATAATTAATG
Found at i:59180 original size:6 final size:6
Alignment explanation
Indices: 59171--59220 Score: 91
Period size: 6 Copynumber: 8.3 Consensus size: 6
59161 GTAAAAAAAA
*
59171 AAACAC AAACAC AAATAC AAACAC AAACAC AAACAC AAACAC AAACAC
1 AAACAC AAACAC AAACAC AAACAC AAACAC AAACAC AAACAC AAACAC
59219 AA
1 AA
59221 TCCTAAAGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.68, C:0.30, G:0.00, T:0.02
Consensus pattern (6 bp):
AAACAC
Found at i:59587 original size:27 final size:27
Alignment explanation
Indices: 59552--59613 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
59542 CCCTTTTTTC
*
59552 AAAT-ATATTTCTAAATTA-CCATTATT-
1 AAATAATATTT-T-AATTATCCATCATTA
59578 AAATAATATTTTAATTATTCCATCATTA
1 AAATAATATTTTAATTA-TCCATCATTA
59606 AAATAATA
1 AAATAATA
59614 AAAATTTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 5 0.16
26 5 0.16
27 13 0.42
28 8 0.26
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.44
Consensus pattern (27 bp):
AAATAATATTTTAATTATCCATCATTA
Found at i:60262 original size:2 final size:2
Alignment explanation
Indices: 60255--60281 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
60245 TTTTATGTTT
60255 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
60282 TATTGGCCAA
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:62378 original size:23 final size:22
Alignment explanation
Indices: 62312--62479 Score: 141
Period size: 22 Copynumber: 7.8 Consensus size: 22
62302 CTCAAGGGAT
* *
62312 GTTATCAAAA-ATCATAGAAAG
1 GTTATCAAAATTTCATAGGAAG
*
62333 GTTA-CAGAATTTCATAGGAAG
1 GTTATCAAAATTTCATAGGAAG
* **
62354 GTTTATTAAAATTTCATAGTTAG
1 G-TTATCAAAATTTCATAGGAAG
*
62377 GTTATCAAAGTTTCATATGG-A-
1 GTTATCAAAATTTCATA-GGAAG
* *
62398 GTTATCACAATTTTATAGGAA-
1 GTTATCAAAATTTCATAGGAAG
* * * *
62419 ATTATCAAAGTTTCATAGCATG
1 GTTATCAAAATTTCATAGGAAG
*
62441 GTTATCAAAATTTAATAGGATA-
1 GTTATCAAAATTTCATAGGA-AG
62463 GTTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
62480 AAAATATTCA
Statistics
Matches: 115, Mismatches: 25, Indels: 13
0.75 0.16 0.08
Matches are distributed among these distances:
20 6 0.05
21 44 0.38
22 50 0.43
23 15 0.13
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGAAG
Found at i:62446 original size:43 final size:43
Alignment explanation
Indices: 62378--62479 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 43
62368 CATAGTTAGG
* * *
62378 TTATCAAAGTTTCATATGGAGTTATCACAATTTTATAGGA-AA
1 TTATCAAAGTTTCATATGCAGTTATCAAAATTTAATAGGATAA
*
62420 TTATCAAAGTTTCATA-GCATGGTTATCAAAATTTAATAGGATAG
1 TTATCAAAGTTTCATATGCA--GTTATCAAAATTTAATAGGATAA
*
62464 TTATCAAAATTTCATA
1 TTATCAAAGTTTCATA
62480 AAAATATTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
41 2 0.04
42 16 0.31
43 18 0.35
44 16 0.31
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (43 bp):
TTATCAAAGTTTCATATGCAGTTATCAAAATTTAATAGGATAA
Found at i:70626 original size:2 final size:2
Alignment explanation
Indices: 70619--70647 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
70609 GTAAATATTT
70619 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
70648 TTTGGTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:77672 original size:3 final size:3
Alignment explanation
Indices: 77664--77699 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
77654 TTTCAACATC
*
77664 TCT TCT TCT TCT TCT TCT TCT TCT TCA TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
77700 ACAAATTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:80396 original size:58 final size:58
Alignment explanation
Indices: 80306--80418 Score: 217
Period size: 58 Copynumber: 1.9 Consensus size: 58
80296 TATTGTTTCG
80306 GTTATGCATTTTGATGCATTTCCATGTCCTTGTCATGGGATCTTGATGTTTTCGTTCA
1 GTTATGCATTTTGATGCATTTCCATGTCCTTGTCATGGGATCTTGATGTTTTCGTTCA
*
80364 GTTATGCATTTTGATGCATTTCCATGTCCTTGTCTTGGGATCTTGATGTTTTCGT
1 GTTATGCATTTTGATGCATTTCCATGTCCTTGTCATGGGATCTTGATGTTTTCGT
80419 GTAGTATTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (58 bp):
GTTATGCATTTTGATGCATTTCCATGTCCTTGTCATGGGATCTTGATGTTTTCGTTCA
Found at i:83658 original size:10 final size:11
Alignment explanation
Indices: 83639--83663 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
83629 CGTTTCTCAC
83639 TTTTCTTTTTT
1 TTTTCTTTTTT
83650 TTTTCTTTTTT
1 TTTTCTTTTTT
83661 TTT
1 TTT
83664 GTAAAGCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:84101 original size:96 final size:98
Alignment explanation
Indices: 83937--84130 Score: 311
Period size: 96 Copynumber: 2.0 Consensus size: 98
83927 CAATAGGGTG
* * *
83937 GCACCATTTTTGCTCTGTAAGTCAACCCAGATCTTGCTTTCTTTGTTTAGTCATCTTCCCAATTT
1 GCACCATTTTTGCTCTGTAAGTCAACCCAGATCTTGCTTCCTTTATATAGTCATCTTCCCAATTT
84002 TAAACTAAGTGCATTG-TTTTTTTTT-CTTTTT
66 TAAACTAAGTGCATTGATTTTTTTTTCCTTTTT
* *
84033 GCACCATTTTTGCTCTGTAAGTTAACCCAGATCTTGCTTCCTTTATATAGTCATCTTCCCATTTT
1 GCACCATTTTTGCTCTGTAAGTCAACCCAGATCTTGCTTCCTTTATATAGTCATCTTCCCAATTT
* *
84098 TAAATTTAGTGCATTGATTTTTTTTTCCTTTTT
66 TAAACTAAGTGCATTGATTTTTTTTTCCTTTTT
84131 TTGATCATTA
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
96 74 0.83
97 9 0.10
98 6 0.07
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.49
Consensus pattern (98 bp):
GCACCATTTTTGCTCTGTAAGTCAACCCAGATCTTGCTTCCTTTATATAGTCATCTTCCCAATTT
TAAACTAAGTGCATTGATTTTTTTTTCCTTTTT
Found at i:85844 original size:24 final size:24
Alignment explanation
Indices: 85798--85844 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
85788 CTAACGTTAA
* * *
85798 CGTTTCTATGGCTATGATTTGGGT
1 CGTTTCTAAGGCAATGATGTGGGT
*
85822 CGTTTCTAAGGCAATGGTGTGGG
1 CGTTTCTAAGGCAATGATGTGGG
85845 ACCCAGCAAT
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:0.15, C:0.13, G:0.34, T:0.38
Consensus pattern (24 bp):
CGTTTCTAAGGCAATGATGTGGGT
Found at i:87070 original size:16 final size:16
Alignment explanation
Indices: 87049--87135 Score: 75
Period size: 16 Copynumber: 5.4 Consensus size: 16
87039 AGCTCGGGCT
87049 GGTTCGGGTTTTTTCG
1 GGTTCGGGTTTTTTCG
***
87065 GGTTCGGGTTAAGTCG
1 GGTTCGGGTTTTTTCG
* * *
87081 GGTTCAGATATTTTCG
1 GGTTCGGGTTTTTTCG
* * *
87097 GGCTCGGGTTATGTCG
1 GGTTCGGGTTTTTTCG
* *
87113 AGTTCGGGTATTTTCG
1 GGTTCGGGTTTTTTCG
87129 GGTTCGG
1 GGTTCGG
87136 TCTCGGGTAG
Statistics
Matches: 50, Mismatches: 21, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.09, C:0.14, G:0.38, T:0.39
Consensus pattern (16 bp):
GGTTCGGGTTTTTTCG
Found at i:87095 original size:32 final size:32
Alignment explanation
Indices: 87059--87135 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
87049 GGTTCGGGTT
*
87059 TTTTCGGGTTCGGGTTAAGTCGGGTTCAGATA
1 TTTTCGGGTTCGGGTTAAGTCGAGTTCAGATA
* * * *
87091 TTTTCGGGCTCGGGTTATGTCGAGTTCGGGTA
1 TTTTCGGGTTCGGGTTAAGTCGAGTTCAGATA
87123 TTTTCGGGTTCGG
1 TTTTCGGGTTCGG
87136 TCTCGGGTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.10, C:0.14, G:0.36, T:0.39
Consensus pattern (32 bp):
TTTTCGGGTTCGGGTTAAGTCGAGTTCAGATA
Found at i:87618 original size:31 final size:31
Alignment explanation
Indices: 87583--87654 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
87573 TAAATTATTG
*
87583 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
87614 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
87645 CAAATTAAAA
1 CAAATTAAAA
87655 GCTAATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:90946 original size:13 final size:13
Alignment explanation
Indices: 90930--90960 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
90920 TTTTACAATA
90930 AAATACTATTATT
1 AAATACTATTATT
90943 AAATACTATTATT
1 AAATACTATTATT
90956 AAATA
1 AAATA
90961 TATATGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATACTATTATT
Found at i:94711 original size:51 final size:51
Alignment explanation
Indices: 94654--94760 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 51
94644 TCATGGTAAG
* * * *
94654 AAATTAACTCTGAAAATTAAAGTTTTAATTTTTAGGTTAAGGTTAGCTTAA
1 AAATTAACTCTGAAAATTAAAGTTTGAATTTTTAGGTTAAAGTTAACTAAA
* ** * *
94705 AAATTAATTCTTTAACTTAAAGTTTGGATTTTTAGGTTAAAGTTAACTAAA
1 AAATTAACTCTGAAAATTAAAGTTTGAATTTTTAGGTTAAAGTTAACTAAA
94756 AAATT
1 AAATT
94761 GATTCTTTGG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (51 bp):
AAATTAACTCTGAAAATTAAAGTTTGAATTTTTAGGTTAAAGTTAACTAAA
Found at i:94766 original size:51 final size:50
Alignment explanation
Indices: 94668--94876 Score: 177
Period size: 51 Copynumber: 4.3 Consensus size: 50
94658 TAACTCTGAA
** * * *
94668 AATTAAAGTTTTAATTTTTAGGTTAAGGTTAGCTTAAAAATTAATTCTTT
1 AATTAAAGTTTGGATTTTTAGGTTAAAGTTAACTTAAAAATTGATTCTTT
*
94718 AACTTAAAGTTTGGATTTTTAGGTTAAAGTTAACTAAAAAATTGATTC--T
1 AA-TTAAAGTTTGGATTTTTAGGTTAAAGTTAACTTAAAAATTGATTCTTT
** * * *
94767 --TT---GGAT--CTTTTTAGGTTAAAGCTAACTTAAAAATTGTTTCTTT
1 AATTAAAGTTTGGATTTTTAGGTTAAAGTTAACTTAAAAATTGATTCTTT
* * * *
94810 AATTTGAAGTTTGGATTTTTAGGTTAAAGTTAGCCTAAAAATCGGA-TCTTT
1 AA-TTAAAGTTTGGATTTTTAGGTTAAAGTTAACTTAAAAAT-TGATTCTTT
94861 AATTCAAAGTTTGGAT
1 AATT-AAAGTTTGGAT
94877 CTTGGACCTT
Statistics
Matches: 125, Mismatches: 21, Indels: 25
0.73 0.12 0.15
Matches are distributed among these distances:
41 30 0.24
43 3 0.02
46 4 0.03
49 3 0.02
50 4 0.03
51 80 0.64
52 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (50 bp):
AATTAAAGTTTGGATTTTTAGGTTAAAGTTAACTTAAAAATTGATTCTTT
Found at i:94783 original size:92 final size:93
Alignment explanation
Indices: 94682--94850 Score: 259
Period size: 92 Copynumber: 1.8 Consensus size: 93
94672 AAAGTTTTAA
* * *
94682 TTTTTAGGTTAAGGTTAGCTTAAAAATTAATTCTTTAACTTAAAGTTTGGATTTTTAGGTTAAAG
1 TTTTTAGGTTAAAGCTAACTTAAAAATTAATTCTTTAACTTAAAGTTTGGATTTTTAGGTTAAAG
94747 TTA-ACTAAAAAATTGATTCTTTGGATC
66 TTAGACTAAAAAATTGATTCTTTGGATC
** * *
94774 TTTTTAGGTTAAAGCTAACTTAAAAATTGTTTCTTTAATTTGAAGTTTGGATTTTTAGGTTAAAG
1 TTTTTAGGTTAAAGCTAACTTAAAAATTAATTCTTTAACTTAAAGTTTGGATTTTTAGGTTAAAG
*
94839 TTAGCCTAAAAA
66 TTAGACTAAAAA
94851 TCGGATCTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
92 61 0.90
93 7 0.10
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (93 bp):
TTTTTAGGTTAAAGCTAACTTAAAAATTAATTCTTTAACTTAAAGTTTGGATTTTTAGGTTAAAG
TTAGACTAAAAAATTGATTCTTTGGATC
Found at i:101245 original size:21 final size:20
Alignment explanation
Indices: 101221--101259 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
101211 GAAGAGGCAA
101221 GTCGACAAGGAGAAGCAAATT
1 GTCGACAA-GAGAAGCAAATT
*
101242 GTCGACTAGAGAAGCAAA
1 GTCGACAAGAGAAGCAAA
101260 GTTGCGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.44, C:0.15, G:0.28, T:0.13
Consensus pattern (20 bp):
GTCGACAAGAGAAGCAAATT
Found at i:103032 original size:17 final size:18
Alignment explanation
Indices: 103010--103045 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
103000 AAGGGTAATT
*
103010 TAAAAA-AATTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
103027 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
103045 T
1 T
103046 GATAGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Found at i:103903 original size:11 final size:10
Alignment explanation
Indices: 103887--103938 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
103877 AAGTTCGTGT
103887 TTGAAGACTTA
1 TTGAAGA-TTA
*
103898 TTGAAGATAA
1 TTGAAGATTA
103908 TTTGAAGA-T-
1 -TTGAAGATTA
103917 TTGAAGATTA
1 TTGAAGATTA
103927 TTGAAGAATTA
1 TTGAAG-ATTA
103938 T
1 T
103939 CTCAAGAAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 7 0.20
9 1 0.03
10 8 0.23
11 19 0.54
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.38
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:103922 original size:19 final size:18
Alignment explanation
Indices: 103898--103933 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
103888 TGAAGACTTA
103898 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
103917 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
103934 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:108249 original size:20 final size:20
Alignment explanation
Indices: 108224--108261 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
108214 TCGGCATAAC
*
108224 TTTTATGAAGAGAGGCAAGT
1 TTTTATGAACAGAGGCAAGT
108244 TTTTATGAACAGAGGCAA
1 TTTTATGAACAGAGGCAA
108262 CCTAATCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.29
Consensus pattern (20 bp):
TTTTATGAACAGAGGCAAGT
Found at i:116164 original size:22 final size:22
Alignment explanation
Indices: 116111--116164 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
116101 AAAAATAACT
*
116111 AAGAAAAATAAAAAGTAAACAAA
1 AAGAAAAA-GAAAAGTAAACAAA
*
116134 AATAAAAAGAAAAGT-AACGAAA
1 AAGAAAAAGAAAAGTAAAC-AAA
*
116156 AAGATAAAG
1 AAGAAAAAG
116165 GTAAAGGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.12
22 16 0.62
23 7 0.27
ACGTcount: A:0.74, C:0.04, G:0.13, T:0.09
Consensus pattern (22 bp):
AAGAAAAAGAAAAGTAAACAAA
Found at i:118375 original size:19 final size:20
Alignment explanation
Indices: 118351--118390 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
118341 TTAGTTTTTA
*
118351 AATTTAAAT-AATCAAAAGG
1 AATTTAAATAAATAAAAAGG
*
118370 AATTTAAGTAAATAAAAAGG
1 AATTTAAATAAATAAAAAGG
118390 A
1 A
118391 TTTTTATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.60, C:0.03, G:0.12, T:0.25
Consensus pattern (20 bp):
AATTTAAATAAATAAAAAGG
Found at i:121167 original size:24 final size:24
Alignment explanation
Indices: 121124--121170 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
121114 AGTTGGAAAA
*
121124 AAAACTTACACTGGGACAAGACTG
1 AAAACTTACACTAGGACAAGACTG
121148 AAAACTTACACTAAGG-CAAGACT
1 AAAACTTACACT-AGGACAAGACT
121171 AAACCTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (24 bp):
AAAACTTACACTAGGACAAGACTG
Found at i:131429 original size:178 final size:178
Alignment explanation
Indices: 131107--131436 Score: 529
Period size: 178 Copynumber: 1.9 Consensus size: 178
131097 TAAACTCAAA
* * *
131107 TTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAATAATTAATTCTTTGGAAGCATTT
1 TTATATAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAATAAATTCTTTGGAAGCATTT
* *
131172 TTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAACAAC
66 TTGATACCTTGAACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATCATGAAACAAC
*
131237 CTTTGAAAAGACACTTGAATCATCTCAATCAGACATTTGGAGCAAAAG
131 CTTTGAAAAGACACTTAAATCATCTCAATCAGACATTTGGAGCAAAAG
*
131285 TTATATAATATTAAGTGGACCGTCTATTTCCGTTAACCGAAACAATAAATT-TTTCGGAAGCATT
1 TTATATAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAATAAATTCTTT-GGAAGCATT
*
131349 TTTGATA-CTTGAAACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATCATGGAACA
65 TTTGATACCTTG-AACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATCATGAAACA
* * *
131413 ATCTTTTAATAGACACTTAAATCA
129 ACCTTTGAAAAGACACTTAAATCA
131437 CCTTAATTGG
Statistics
Matches: 139, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
177 7 0.05
178 132 0.95
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (178 bp):
TTATATAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAATAAATTCTTTGGAAGCATTT
TTGATACCTTGAACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATCATGAAACAAC
CTTTGAAAAGACACTTAAATCATCTCAATCAGACATTTGGAGCAAAAG
Found at i:131469 original size:178 final size:177
Alignment explanation
Indices: 131104--131481 Score: 501
Period size: 178 Copynumber: 2.1 Consensus size: 177
131094 TCATAAACTC
* * *
131104 AAATTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAATAATTAATTCTTTGGAAGCA
1 AAATTATATAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAATAAATTCTTTGGAAGCA
* *
131169 TTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAAC
66 TTTTTGATACCTTGAACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATCATGAAAC
* * ***
131234 AACCTTTGAAAAGACACTTGAATCATCTCAATCAGACATTTGGAGCA
131 AACCTTTGAAAAGACACTTAAATCACCTCAATCAGACAACCGGAGCA
*
131281 AAAGTTATATAATATTAAGTGGACCGTCTATTTCCGTTAACCGAAACAATAAATT-TTTCGGAAG
1 AAA-TTATATAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAATAAATTCTTT-GGAAG
*
131345 CATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATCATGG
64 CATTTTTGATACCTTG-AACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATCATGA
* * * * ** *
131409 AACAATCTTTTAATAGACACTTAAATCACCTTAATTGGATAACCGAAGAG-A
128 AACAACCTTTGAAAAGACACTTAAATCACCTCAATCAGACAACCG--GAGCA
* *
131460 AAATTATATAATGTTAAATAGA
1 AAATTATATAATATTAAGTAGA
131482 TCGTTTAACC
Statistics
Matches: 174, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
177 10 0.06
178 157 0.90
179 4 0.02
180 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (177 bp):
AAATTATATAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAATAAATTCTTTGGAAGCA
TTTTTGATACCTTGAACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATCATGAAAC
AACCTTTGAAAAGACACTTAAATCACCTCAATCAGACAACCGGAGCA
Found at i:133750 original size:22 final size:22
Alignment explanation
Indices: 133725--133773 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
133715 CAAATTTGAG
133725 AATTAGATGGCTTAATTGTCTC
1 AATTAGATGGCTTAATTGTCTC
133747 AATTAGATGGCTTAATTGTCTC
1 AATTAGATGGCTTAATTGTCTC
133769 AATTA
1 AATTA
133774 AAAATTGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (22 bp):
AATTAGATGGCTTAATTGTCTC
Found at i:143239 original size:5 final size:5
Alignment explanation
Indices: 143229--143253 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
143219 CCATATAAAC
143229 CACTT CACTT CACTT CACTT CACTT
1 CACTT CACTT CACTT CACTT CACTT
143254 TTCACATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (5 bp):
CACTT
Found at i:147958 original size:58 final size:58
Alignment explanation
Indices: 147866--147979 Score: 192
Period size: 58 Copynumber: 2.0 Consensus size: 58
147856 ATCTTATTCT
* *
147866 TATTCTAAGAAAATAATATTAGACGACTACCCATTGACCATTAATGGCTTTCAATATA
1 TATTCTAAGAAAATAATATCAGACAACTACCCATTGACCATTAATGGCTTTCAATATA
* *
147924 TATTCTAAGAAAATAATATCAGACAACTATCCATTGGCCATTAATGGCTTTCAATA
1 TATTCTAAGAAAATAATATCAGACAACTACCCATTGACCATTAATGGCTTTCAATA
147980 ATACTAGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (58 bp):
TATTCTAAGAAAATAATATCAGACAACTACCCATTGACCATTAATGGCTTTCAATATA
Found at i:148551 original size:32 final size:34
Alignment explanation
Indices: 148497--148564 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 34
148487 TATTACTAAG
* **
148497 ACTCTCATCTCCTTTTGAAAAAA-AAAAA-AAAA
1 ACTCTCATCTCCTATACAAAAAACAAAAACAAAA
*
148529 ACTCTCATCTCCTATACCAAAAACAAAAACAAAA
1 ACTCTCATCTCCTATACAAAAAACAAAAACAAAA
148563 AC
1 AC
148565 AAAAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 19 0.63
33 5 0.17
34 6 0.20
ACGTcount: A:0.53, C:0.25, G:0.01, T:0.21
Consensus pattern (34 bp):
ACTCTCATCTCCTATACAAAAAACAAAAACAAAA
Found at i:148557 original size:6 final size:6
Alignment explanation
Indices: 148546--148575 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
148536 TCTCCTATAC
148546 CAAAAA CAAAAA CAAAAA CAAAAA -AAAAA C
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA C
148576 TCTCATCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:164105 original size:2 final size:2
Alignment explanation
Indices: 164098--164152 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
164088 CCAGGTTCTT
164098 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
164140 TG TG TG TT TG TG T
1 TG TG TG TG TG TG T
164153 TTGGATATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:167453 original size:43 final size:43
Alignment explanation
Indices: 167392--167477 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
167382 GATTATTTTA
167392 TTTATTTATTTATGTTTACATGAATTCATGCTTAAAATTTGAT
1 TTTATTTATTTATGTTTACATGAATTCATGCTTAAAATTTGAT
167435 TTTATTTATTTATGTTTACATGAATTCATGCTTAAAATTTGAT
1 TTTATTTATTTATGTTTACATGAATTCATGCTTAAAATTTGAT
167478 AGCAAGCTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.53
Consensus pattern (43 bp):
TTTATTTATTTATGTTTACATGAATTCATGCTTAAAATTTGAT
Found at i:167566 original size:14 final size:14
Alignment explanation
Indices: 167547--167574 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
167537 TGTTTGATAA
167547 ATCAGTGAAAATTT
1 ATCAGTGAAAATTT
167561 ATCAGTGAAAATTT
1 ATCAGTGAAAATTT
167575 TCAAAATTTC
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:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
ATCAGTGAAAATTT
Found at i:168061 original size:39 final size:39
Alignment explanation
Indices: 168003--168077 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
167993 ATTTTTCATA
*
168003 TTTCTTTTTCTTTGATTTAAGATTTAACAAACTAATTTT
1 TTTCTTTTTATTTGATTTAAGATTTAACAAACTAATTTT
*
168042 TTTCTTTTTATTTGTTTTAAGATTTAACAAACTAAT
1 TTTCTTTTTATTTGATTTAAGATTTAACAAACTAAT
168078 ATCTTCCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.29, C:0.09, G:0.05, T:0.56
Consensus pattern (39 bp):
TTTCTTTTTATTTGATTTAAGATTTAACAAACTAATTTT
Found at i:169369 original size:18 final size:17
Alignment explanation
Indices: 169346--169384 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
169336 AATTTTCTTA
169346 TTATATA-TATCTTTATCT
1 TTATATATTAT-TTTAT-T
169364 TTATATATTATTTTATT
1 TTATATATTATTTTATT
169381 TTAT
1 TTAT
169385 TTTATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 12 0.60
19 3 0.15
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATATTATTTTATT
Found at i:172220 original size:22 final size:22
Alignment explanation
Indices: 172195--172238 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
172185 TTATTCTCCA
172195 GCTTAATTATCTCAACGTAGTC
1 GCTTAATTATCTCAACGTAGTC
172217 GCTTAATTATCTCAACGTAGTC
1 GCTTAATTATCTCAACGTAGTC
172239 TTGTTAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (22 bp):
GCTTAATTATCTCAACGTAGTC
Found at i:173402 original size:38 final size:38
Alignment explanation
Indices: 173351--173429 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
173341 AGTCTGGCGC
*
173351 CATATTCATTGTTGCACACAACATCTTATCACCAGAGA
1 CATATTCATTGTTGCACACAACAACTTATCACCAGAGA
*
173389 CATATTCATTGTTGCACACAACAACTTATTACCAGAGA
1 CATATTCATTGTTGCACACAACAACTTATCACCAGAGA
173427 CAT
1 CAT
173430 GAAAGGTCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.29
Consensus pattern (38 bp):
CATATTCATTGTTGCACACAACAACTTATCACCAGAGA
Found at i:182087 original size:45 final size:45
Alignment explanation
Indices: 182023--182137 Score: 194
Period size: 45 Copynumber: 2.6 Consensus size: 45
182013 AAGCAGCTGG
* *
182023 AACAAAACTAGGACTTGTGTGTTCATTATTGAGTCCCCAATCTGA
1 AACAAAGCTAGGACCTGTGTGTTCATTATTGAGTCCCCAATCTGA
*
182068 AACAAAGCTAGGACCTGTGTGTTCATTATTGAGTCCCCAATCTGG
1 AACAAAGCTAGGACCTGTGTGTTCATTATTGAGTCCCCAATCTGA
*
182113 AACAAAGCAAGGACCTGTGTGTTCA
1 AACAAAGCTAGGACCTGTGTGTTCA
182138 CAATCCCTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (45 bp):
AACAAAGCTAGGACCTGTGTGTTCATTATTGAGTCCCCAATCTGA
Found at i:184967 original size:45 final size:45
Alignment explanation
Indices: 184903--185028 Score: 234
Period size: 45 Copynumber: 2.8 Consensus size: 45
184893 AGCAACAATT
*
184903 AATATTAGGTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
*
184948 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
184993 AATATTAGCTTTATTTTGATGAATTACCTAGAGATG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATG
185029 AAGTAGAATT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
Done.