Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 37 of 64
Found at i:5772856 original size:20 final size:19
Alignment explanation
Indices: 5772808--5772856 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
5772798 AAAAAAACAT
* *
5772808 AAAAATATATTTTTAAATA
1 AAAAATAAATTTTAAAATA
5772827 AAAAATTAAATTTTAAAATA
1 AAAAA-TAAATTTTAAAATA
5772847 ATAAAATAAA
1 A-AAAATAAA
5772857 GACTTAGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 5 0.19
20 17 0.65
21 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATAAATTTTAAAATA
Found at i:5777963 original size:26 final size:26
Alignment explanation
Indices: 5777917--5777968 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5777907 TCACATAACT
5777917 ATTAACATATTAAAAACTATTTATTA
1 ATTAACATATTAAAAACTATTTATTA
* *
5777943 ATTAACTATATT-GAAATTATTTATTA
1 ATTAAC-ATATTAAAAACTATTTATTA
5777969 CTATATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTAACATATTAAAAACTATTTATTA
Found at i:5778143 original size:8 final size:8
Alignment explanation
Indices: 5778132--5778161 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
5778122 TTAATATAAT
5778132 AATATTAA
1 AATATTAA
5778140 AATATTAA
1 AATATTAA
5778148 AATATTAA
1 AATATTAA
5778156 AATATT
1 AATATT
5778162 TGTACTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
AATATTAA
Found at i:5779262 original size:22 final size:24
Alignment explanation
Indices: 5779237--5779280 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
5779227 TGAATATGAT
*
5779237 TCATTTAATTTTT-G-ATATTCAC
1 TCATATAATTTTTAGAATATTCAC
*
5779259 TCATATATTTTTTAGAATATTC
1 TCATATAATTTTTAGAATATTC
5779281 TTCTAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 1 0.06
24 6 0.33
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.55
Consensus pattern (24 bp):
TCATATAATTTTTAGAATATTCAC
Found at i:5780352 original size:21 final size:21
Alignment explanation
Indices: 5780301--5780353 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
5780291 GTGGTCCAAA
* ** *
5780301 ATCAATTGTTTGATTTTTATT
1 ATCAATTTTTTGATTAATATC
* *
5780322 ATCTACTTTTTGATTAATATC
1 ATCAATTTTTTGATTAATATC
5780343 ATCAATTTTTT
1 ATCAATTTTTT
5780354 ATTCTATTTT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.58
Consensus pattern (21 bp):
ATCAATTTTTTGATTAATATC
Found at i:5786680 original size:21 final size:21
Alignment explanation
Indices: 5786656--5786696 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5786646 TTTCAAGTAA
* *
5786656 ATTTAAAATGTATAATTATTC
1 ATTTAAAATGAATAAATATTC
*
5786677 ATTTGAAATGAATAAATATT
1 ATTTAAAATGAATAAATATT
5786697 AAAAAACTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (21 bp):
ATTTAAAATGAATAAATATTC
Found at i:5787033 original size:28 final size:28
Alignment explanation
Indices: 5786979--5787033 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
5786969 TATTAAGGAA
**
5786979 TCATAAAATATTATTGTTTCTTCAACTT
1 TCATAAAATATTATTGTTTAATCAACTT
*
5787007 TCATAAAATATTTATTTTTTAAT-AACT
1 TCATAAAATA-TTATTGTTTAATCAACT
5787034 GGTTACATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (28 bp):
TCATAAAATATTATTGTTTAATCAACTT
Found at i:5793559 original size:16 final size:16
Alignment explanation
Indices: 5793534--5793568 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5793524 TATGATAACA
*
5793534 TATCTTTAACAATTGG
1 TATCTATAACAATTGG
5793550 TATCTATAACAATTGG
1 TATCTATAACAATTGG
5793566 TAT
1 TAT
5793569 AAGCTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (16 bp):
TATCTATAACAATTGG
Found at i:5799101 original size:417 final size:421
Alignment explanation
Indices: 5798150--5799411 Score: 1147
Period size: 417 Copynumber: 3.0 Consensus size: 421
5798140 AAAAATAAAC
* * *
5798150 AATAATAAAAATGCAAACACTAAAAAACACGCT-ATTGGAATAAAAAGCAAACTTGAATTACCAA
1 AATAATAAAAATGCAAACACTAAAAAATACACTAATT-GACTAAAAA-CAAACTTGAA-TACCAA
* *
5798214 ATAAAAAATCATAGATTATGATTATAAAATTAAAAAAATTATGAAAATACAAACATAAT-AAAAA
63 ATAAAAAATCATAAATTATGATTATAAAATTAAAAAAATTATGAAAATACAAACACAATAAAAAA
* ** * * *
5798278 AAATCTCATGATTGAAAAAAATATAATAGTGACATGAAATACACTTATATAACGCTCCCATAAAA
128 AAATCTAATGATT-AAAAAAATATAATAGACACATAAAATACACTTAAATAACCCTCCCATAAAA
* * *
5798343 AATGAAAAATCATAAGTCATACGGTAAGTAAAAGTCAAAACATAAATGTCATAAAATAAATGGTT
192 AA-GAAAAATCATAAG-CATA--G-AAG-AAAAATCAAAACATAAATGTCAGAAAATAAATGATT
* * *
5798408 TTAATCAATTTTAACAAATAACAATTTTAAAGAACATGAATAGGAGAAAATCATAAATCTATATA
251 TCAATAAATTTTAACAAATAACAATTTTAAAGAACATGAATAGGAGAAAATCATAAATCCATATA
** * * *
5798473 AATGTTAGGCAACCAAAGTCTATTGAATTTTATGTAATAAAATTAAAAGATATATGTTTAAAATT
316 AATGTTAGGCAAAAAAAATCAATTGAATTTTATGTAATAAAATT-AAAGAGATATGTTTAAAATT
**
5798538 TATGTAAAAAAAACTTGGTATTTATTATAAAATATTTGAAAA
380 TATGTAAAAAAAACTTGACATTTATTATAAAATATTTGAAAA
* *
5798580 AAAAATAAAAATGTAAACACTAAAAAAAATACA-TAATTGACTAAAAAACAAACTTGAAATACCA
1 AATAATAAAAATGCAAACACT--AAAAAATACACTAATTGACT-AAAAACAAACTTG-AATACCA
* * * * **
5798644 AATAAAAAAACATAAATTATGATTATAAAATTATAAAAATTATAAAAATGCAAATGCAATAAAAA
62 AATAAAAAATCATAAATTATGATTATAAAATTAAAAAAATTATGAAAATACAAACACAATAAAAA
* * * **
5798709 AAAATCTAATGATT-AGAAAATATAATGGACACATAAAATATACTTAAATAACCCTCCCAT-CCA
127 AAAATCTAATGATTAAAAAAATATAATAGACACATAAAATACACTTAAATAACCCTCCCATAAAA
* *
5798772 AA-AAAAA-CA-AAG-A-A-AA-AAAAATCATAACATAAATGTTAGAAAATCAAA-GATTTCAAT
192 AAGAAAAATCATAAGCATAGAAGAAAAATCAAAACATAAATGTCAGAAAAT-AAATGATTTCAAT
** * * *
5798829 AAATTTTAACAAATAA-TGTTTT-TAGAACATGAATATGAGAAAATAAAAAGACATGAATCCATA
256 AAATTTTAACAAATAACAATTTTAAAGAACATGAATAGGAGAAAAT-------CATAAATCCATA
*
5798892 TAAATGTTAGGCAATAAAAAATCAATT-AGATTTTATGTAATAAAATT-AAGAGATAT-TTTAGA
314 TAAATGTTAGGCAA-AAAAAATCAATTGA-ATTTTATGTAATAAAATTAAAGAGATATGTTTAAA
* * *
5798954 ATTTATGTAAAAAAGATTTGACATTTATTGTAAAATATTTGAAATA
377 ATTTATGTAAAAAAAACTTGACATTTATTATAAAATATTTGAAA-A
* * *
5799000 AATAATAAAATTGCAAAGACTAAAAATATGCACTAATTGACTAAACAACAAACTTGAA-A-CAAA
1 AATAATAAAAATGCAAACACTAAAAA-ATACACTAATTGACTAAA-AACAAACTTGAATACCAAA
*
5799063 TAAAAAATCATAAATTATGATTATAAAATTAAAAAAATTATGAAAACACAAACACAAT--AAAAA
64 TAAAAAATCATAAATTATGATTATAAAATTAAAAAAATTATGAAAATACAAACACAATAAAAAAA
* * * * * * * *
5799126 ATTTTCATGATTGGAAAAAATATAATAAAGACATGAAATACACTTATATAACCCT--CATAAAAA
129 AATCTAATGATT-AAAAAAATATAATAGACACATAAAATACACTTAAATAACCCTCCCAT-AAAA
* * * * *
5799189 AATGAAAAATCATAAGTCATCAGAAAATAAAAAATCAAAACATAAATGTTAAAAAATAAA-AAAT
192 AA-GAAAAATCATAAG-CAT-AG--AA-GAAAAATCAAAACATAAATGTCAGAAAATAAATGATT
* * * * * * ** ** *
5799253 TCAATAAATTTT-----GT-TC-ATTTCATAG--GA-GAAAATCA-AATGTCATGAATCCATATA
251 TCAATAAATTTTAACAAATAACAATTTTAAAGAACATGAATAGGAGAAAATCATAAATCCATATA
* * * * * * * * *
5799307 AATATTAGACAACTAAAAGTCGATTGGATTTTATGTAATAAAATTAAGAGATATATATTTAGAAT
316 AATGTTAGGCAA-AAAAAATCAATTGAATTTTATGTAATAAAATTAA-AGAGATATGTTTAAAAT
* *
5799372 TTATATAAAAAAAACTTGACATTTATTGTAAAATATTTGA
379 TTATGTAAAAAAAACTTGACATTTATTATAAAATATTTGA
5799412 GTTTTATATT
Statistics
Matches: 693, Mismatches: 96, Indels: 100
0.78 0.11 0.11
Matches are distributed among these distances:
413 51 0.07
414 21 0.03
415 28 0.04
416 91 0.13
417 95 0.14
418 8 0.01
419 58 0.08
420 50 0.07
421 34 0.05
422 28 0.04
423 5 0.01
424 4 0.01
425 4 0.01
426 2 0.00
427 5 0.01
428 2 0.00
429 20 0.03
430 83 0.12
431 69 0.10
432 35 0.05
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (421 bp):
AATAATAAAAATGCAAACACTAAAAAATACACTAATTGACTAAAAACAAACTTGAATACCAAATA
AAAAATCATAAATTATGATTATAAAATTAAAAAAATTATGAAAATACAAACACAATAAAAAAAAA
TCTAATGATTAAAAAAATATAATAGACACATAAAATACACTTAAATAACCCTCCCATAAAAAAGA
AAAATCATAAGCATAGAAGAAAAATCAAAACATAAATGTCAGAAAATAAATGATTTCAATAAATT
TTAACAAATAACAATTTTAAAGAACATGAATAGGAGAAAATCATAAATCCATATAAATGTTAGGC
AAAAAAAATCAATTGAATTTTATGTAATAAAATTAAAGAGATATGTTTAAAATTTATGTAAAAAA
AACTTGACATTTATTATAAAATATTTGAAAA
Found at i:5809078 original size:2 final size:2
Alignment explanation
Indices: 5809071--5809100 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5809061 AACTTCTAGA
5809071 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
5809101 TCTCAAATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5809137 original size:89 final size:89
Alignment explanation
Indices: 5808986--5809160 Score: 332
Period size: 89 Copynumber: 2.0 Consensus size: 89
5808976 ATTTCGTGCC
* *
5808986 ATATATATATATATATATATATGTATTCTCAAATCTCATTTAATGTTGATTTTGAACTAATACAA
1 ATATATATATATATATATATATATATTCTCAAATCTCATTTAATGTTGATTTTGAACCAATACAA
5809051 AGCAAATCCAAACTTCTAGAATAT
66 AGCAAATCCAAACTTCTAGAATAT
5809075 ATATATATATATATATATATATATATTCTCAAATCTCATTTAATGTTGATTTTGAACCAATACAA
1 ATATATATATATATATATATATATATTCTCAAATCTCATTTAATGTTGATTTTGAACCAATACAA
5809140 AGCAAATCCAAACTTCTAGAA
66 AGCAAATCCAAACTTCTAGAA
5809161 ACAGACAAAC
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (89 bp):
ATATATATATATATATATATATATATTCTCAAATCTCATTTAATGTTGATTTTGAACCAATACAA
AGCAAATCCAAACTTCTAGAATAT
Found at i:5809415 original size:19 final size:18
Alignment explanation
Indices: 5809374--5809422 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
5809364 AAATCACTAA
*
5809374 ATAATAAACAAA-TAAAT
1 ATAATTAACAAATTAAAT
5809391 -TAATTAACAAATTAAAAT
1 ATAATTAACAAATT-AAAT
*
5809409 ATAATTAAAAAATT
1 ATAATTAACAAATT
5809423 CAACATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 10 0.37
17 1 0.04
18 4 0.15
19 12 0.44
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAATTAACAAATTAAAT
Found at i:5810773 original size:34 final size:35
Alignment explanation
Indices: 5810728--5810795 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
5810718 GAGTTTCTTA
* *
5810728 AAAATGAATATCCGAAAAATTTTGA-AATTTTTTT
1 AAAATGAATATCCGAAAAACTTTAAGAATTTTTTT
* *
5810762 AAAATGGATATCTGAAAAACTTTAAGAATTTTTT
1 AAAATGAATATCCGAAAAACTTTAAGAATTTTTT
5810796 AATATTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (35 bp):
AAAATGAATATCCGAAAAACTTTAAGAATTTTTTT
Found at i:5810814 original size:34 final size:34
Alignment explanation
Indices: 5810776--5810851 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
5810766 TGGATATCTG
*
5810776 AAAAACTTTAAGAATTTTTTAATATTTATTTTTA
1 AAAAACTTTAAGAATTTTTTAATATATATTTTTA
* * ** * *
5810810 AAAAATTTTGAGTTTTTTTTTATATATATTTTTG
1 AAAAACTTTAAGAATTTTTTAATATATATTTTTA
5810844 AAAAACTT
1 AAAAACTT
5810852 GATTTCACTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (34 bp):
AAAAACTTTAAGAATTTTTTAATATATATTTTTA
Found at i:5811438 original size:19 final size:20
Alignment explanation
Indices: 5811384--5811440 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
5811374 AGCACATCAG
*
5811384 ATTTA-TTTATTTTAATATT
1 ATTTATTTTATTTAAATATT
5811403 ATTTATTTTAAATTTAAATA-T
1 ATTTATTTT--ATTTAAATATT
5811424 ATTTATTTTATTTAAAT
1 ATTTATTTTATTTAAAT
5811441 TGAAATTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 13 0.38
20 3 0.09
21 10 0.29
22 8 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTATTTTATTTAAATATT
Found at i:5814543 original size:27 final size:27
Alignment explanation
Indices: 5814513--5814568 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
5814503 TTTTTACGGA
*
5814513 TCGACTAATCGACTTAAGTTTTATGAT
1 TCGACTAATCGACTTAAGTTTCATGAT
* *
5814540 TCGACTCATCGGCTTAAGTTTCATGAT
1 TCGACTAATCGACTTAAGTTTCATGAT
5814567 TC
1 TC
5814569 TCTATTGTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (27 bp):
TCGACTAATCGACTTAAGTTTCATGAT
Found at i:5817940 original size:9 final size:9
Alignment explanation
Indices: 5817926--5817968 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
5817916 TATTTTCAAG
5817926 ATAATAACA
1 ATAATAACA
*
5817935 ATAATAATA
1 ATAATAACA
*
5817944 GTAATAACA
1 ATAATAACA
* *
5817953 ACAACAACA
1 ATAATAACA
5817962 ATAATAA
1 ATAATAA
5817969 TAAAAACTTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.21
Consensus pattern (9 bp):
ATAATAACA
Found at i:5817964 original size:24 final size:25
Alignment explanation
Indices: 5817931--5817989 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
5817921 TCAAGATAAT
* * *
5817931 AACAATAATAATAGTAATAAC-AAC
1 AACAACAATAATAATAAAAACTAAC
*
5817955 AACAACAATAATAATAAAAACTTAC
1 AACAACAATAATAATAAAAACTAAC
5817980 -ACAACAATAA
1 AACAACAATAA
5817990 AATTCACGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 28 0.93
25 2 0.07
ACGTcount: A:0.64, C:0.15, G:0.02, T:0.19
Consensus pattern (25 bp):
AACAACAATAATAATAAAAACTAAC
Found at i:5823508 original size:20 final size:20
Alignment explanation
Indices: 5823471--5823515 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5823461 AGGTTGAAGG
* **
5823471 TAAAATAGTAATTTTATAAA
1 TAAAATAATAATAATATAAA
*
5823491 TAAAATAATAATAATATAAT
1 TAAAATAATAATAATATAAA
5823511 TAAAA
1 TAAAA
5823516 AGCTCGATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAATAATAATAATATAAA
Found at i:5824224 original size:20 final size:20
Alignment explanation
Indices: 5824199--5824236 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5824189 ATGATAATAT
*
5824199 AATATGAAAATGATATAAAA
1 AATATGAAAATGAAATAAAA
5824219 AATATGAAAATGAAATAA
1 AATATGAAAATGAAATAA
5824237 TTTAAAATTT
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:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (20 bp):
AATATGAAAATGAAATAAAA
Found at i:5824341 original size:34 final size:31
Alignment explanation
Indices: 5824271--5824344 Score: 87
Period size: 34 Copynumber: 2.3 Consensus size: 31
5824261 CTTCAATTTG
* *
5824271 ATAAAA-AAATTTTATATTTAACATGTTAAT
1 ATAAAATAAAATTTATATTTAACATATTAAT
*
5824301 ATAAAATAAAATTTATATTTTATATATATTAGAT
1 ATAAAATAAAATTTATA-TTTA-ACATATTA-AT
5824335 ATAAAATAAA
1 ATAAAATAAA
5824345 TAAATATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 6 0.16
31 9 0.24
32 4 0.11
33 6 0.16
34 12 0.32
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (31 bp):
ATAAAATAAAATTTATATTTAACATATTAAT
Found at i:5839088 original size:31 final size:31
Alignment explanation
Indices: 5839027--5839087 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
5839017 AGTTTTAATA
5839027 GTCTTACTATTACTCTTATTTTTATCTTTTT
1 GTCTTACTATTACTCTTATTTTTATCTTTTT
* *
5839058 GTCTTGCTATTACTCTTA-TTTTATTTTTTT
1 GTCTTACTATTACTCTTATTTTTATCTTTTT
5839088 TATTTATTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (31 bp):
GTCTTACTATTACTCTTATTTTTATCTTTTT
Found at i:5842325 original size:20 final size:19
Alignment explanation
Indices: 5842287--5842326 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5842277 TCGAATAATA
* *
5842287 TTAATTATTTTTATTAATT
1 TTAATTATTTTAATAAATT
5842306 TTAATTTATTTTAATAAATT
1 TTAA-TTATTTTAATAAATT
5842326 T
1 T
5842327 CAGTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTAATTATTTTAATAAATT
Found at i:5851833 original size:242 final size:242
Alignment explanation
Indices: 5851408--5851892 Score: 837
Period size: 242 Copynumber: 2.0 Consensus size: 242
5851398 ATCTTGCTGA
* * * *
5851408 CAATTATAGTAGAACATGAGTAAATAGTTGTCTTTTGTATCTTAATATAGAATCCATACCCTTTT
1 CAATTATAGTAGAACATGAGTAAATAGTTGTCTTGTGGACCTTAATATAGAATCCACACCCTTTT
*
5851473 CAACAGACGCTCATGTTCAGATTCATCCATATGATATTTCTCTATCATCAAATCAGTTGATTTTT
66 CAACAGACACTCATGTTCAGATTCATCCATATGATATTTCTCTATCATCAAATCAGTTGATTTTT
5851538 TTTGTGCTTTCATGACAACTAAAAACTAAGTTGTGTCAATAGCTCCCGTTGGTGGTGTGTAATTA
131 TTTGTGCTTTCATGACAACTAAAAACTAAGTTGTGTCAATAGCTCCCGTTGGTGGTGTGTAATTA
* *
5851603 GAGGCACCTGATTTTTTATGCTTAAAGGCACTTGATTCCCTATCAAT
196 GAGGCACCTGATTTTGTATGCTTAAAGGCACCTGATTCCCTATCAAT
* *
5851650 CAATTATAGTAGAACATGCA-TAAATAGTTGTCTTGTGGACCTTAATATAGAATCCGCACCTTTT
1 CAATTATAGTAGAACATG-AGTAAATAGTTGTCTTGTGGACCTTAATATAGAATCCACACCCTTT
*
5851714 TCAACAGACACTCATGTTCAGATTCATCTATATGATATTTCTCTATCATCAAATCAGTTGATTTT
65 TCAACAGACACTCATGTTCAGATTCATCCATATGATATTTCTCTATCATCAAATCAGTTGATTTT
*
5851779 TTTTGTGCTTTCATGACCACTAAAAACTAAGTTGTGTCAATAGCTCCCGTTGGTGGTGTGTAATT
130 TTTTGTGCTTTCATGACAACTAAAAACTAAGTTGTGTCAATAGCTCCCGTTGGTGGTGTGTAATT
* *
5851844 AGAGGCACCTGATTTTGTATGCTTAAGGGCACCTGATTCTCTATCAAT
195 AGAGGCACCTGATTTTGTATGCTTAAAGGCACCTGATTCCCTATCAAT
5851892 C
1 C
5851893 CAGAATAAAA
Statistics
Matches: 229, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
242 228 1.00
243 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (242 bp):
CAATTATAGTAGAACATGAGTAAATAGTTGTCTTGTGGACCTTAATATAGAATCCACACCCTTTT
CAACAGACACTCATGTTCAGATTCATCCATATGATATTTCTCTATCATCAAATCAGTTGATTTTT
TTTGTGCTTTCATGACAACTAAAAACTAAGTTGTGTCAATAGCTCCCGTTGGTGGTGTGTAATTA
GAGGCACCTGATTTTGTATGCTTAAAGGCACCTGATTCCCTATCAAT
Found at i:5852312 original size:359 final size:359
Alignment explanation
Indices: 5851650--5852623 Score: 1626
Period size: 359 Copynumber: 2.7 Consensus size: 359
5851640 CCCTATCAAT
* * **
5851650 CAATTATAGTAGAACATGCATAAATAGTTGTCTTGTGGACCTTAATATAGAATCCGCACCTTTTT
1 CAATTATAGTAGAACATGCATAAATAGTTGTCTTGTGTATCTTAATATAGAATCCATACCTTTTT
*
5851715 CAACAGACACTCATGTTCAGATTCATCTATATGATATTTCTCTATCATCAAATCAGTTGATTTTT
66 CAACAGACACTCATGTTCAGATTCATCCATATGATATTTCTCTATCATCAAATCAGTTGATTTTT
*
5851780 TTTGTGCTTTCATGACCACTAAAAACTAAGTTGTGTCAATAGCTCCCGTTGGTGGTGTGTAATTA
131 TTTGTGCTTTCATGACCACTAAAAACTAAGTTGTGCCAATAGCTCCCGTTGGTGGTGTGTAATTA
* *
5851845 GAGGCACCTGATTTTGTATGCTTAAGGGCACCTGATTCTCTATCAATCCAGAATAAAAGTTCTTA
196 GAGGCACCTGATTTTGTATGCTTAAAGGCACCTGATTCCCTATCAATCCAGAATAAAAGTTCTTA
* *
5851910 GTCAAACTATATTGCTTAAACTGTGTTTCTCCCTTATTTTCATTTTCAACAATTTTGTCAATGGA
261 GTCAAACTACATTGCTTAAACTGTATTTCTCCCTTATTTTCATTTTCAACAATTTTGTCAATGGA
5851975 AATTATAGTGAAAGGAAATAACATCAATTGCTGA
326 AATTATAGTGAAAGGAAATAACATCAATTGCTGA
*
5852009 CAGTTATAGTAGAACATGCATAAATAGTTGTC-TGTGTATCTTAATATAGAATCCATACCTTTTT
1 CAATTATAGTAGAACATGCATAAATAGTTGTCTTGTGTATCTTAATATAGAATCCATACCTTTTT
*
5852073 CAACAGACACTCATGTTCAGATTCATCCATATGATATTTTTCTATCATCAAATCAGTTGATTTTT
66 CAACAGACACTCATGTTCAGATTCATCCATATGATATTTCTCTATCATCAAATCAGTTGATTTTT
*
5852138 TTTGTGCTTTCATGACCACTAAAAACTAAGTTGTGCCCGATAGCTCCCGTTGGTGGTGTGTAATT
131 TTTGTGCTTTCATGACCACTAAAAACTAAGTTGTG-CCAATAGCTCCCGTTGGTGGTGTGTAATT
* * *
5852203 AGAGGCAACTGATTTTGTATGCTTAAAGGCACCTGCTTCCCTATTAATCCAGAATAAAAGTTCTT
195 AGAGGCACCTGATTTTGTATGCTTAAAGGCACCTGATTCCCTATCAATCCAGAATAAAAGTTCTT
5852268 AGTCAAACTACATTGCTTAAACTGTATTTCTCCCTTATTTTCATTTTCAACAATTTTGTCAATGG
260 AGTCAAACTACATTGCTTAAACTGTATTTCTCCCTTATTTTCATTTTCAACAATTTTGTCAATGG
* *
5852333 AATTTATAGTGAAAGGAAATAACATCAGTTGCTGA
325 AAATTATAGTGAAAGGAAATAACATCAATTGCTGA
5852368 CAATTATAGTAGAACATGCATAAATAGTTGTCTTGTGTATCTTAATATAGAATCCATACCTTTTT
1 CAATTATAGTAGAACATGCATAAATAGTTGTCTTGTGTATCTTAATATAGAATCCATACCTTTTT
* * *
5852433 TAACAGACACTCATGTTTAGATTCATCCATATGATATTTCTCTATAATCAAATCAGTTGATTTTT
66 CAACAGACACTCATGTTCAGATTCATCCATATGATATTTCTCTATCATCAAATCAGTTGATTTTT
* * * * * * *
5852498 CTTGTGCTTTCATGACCACTGAAAACCAATTTGTGCCAATAACTCCCATTTGTGGTGTGTAATTA
131 TTTGTGCTTTCATGACCACTAAAAACTAAGTTGTGCCAATAGCTCCCGTTGGTGGTGTGTAATTA
* * * * * *
5852563 GAGACACCTAATTTTTTATGCTTAAAGGCACCTGATTTCCTATCAATCCATAACAAAAGTT
196 GAGGCACCTGATTTTGTATGCTTAAAGGCACCTGATTCCCTATCAATCCAGAATAAAAGTT
5852624 TTTAATGAGC
Statistics
Matches: 573, Mismatches: 40, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
358 126 0.22
359 323 0.56
360 124 0.22
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (359 bp):
CAATTATAGTAGAACATGCATAAATAGTTGTCTTGTGTATCTTAATATAGAATCCATACCTTTTT
CAACAGACACTCATGTTCAGATTCATCCATATGATATTTCTCTATCATCAAATCAGTTGATTTTT
TTTGTGCTTTCATGACCACTAAAAACTAAGTTGTGCCAATAGCTCCCGTTGGTGGTGTGTAATTA
GAGGCACCTGATTTTGTATGCTTAAAGGCACCTGATTCCCTATCAATCCAGAATAAAAGTTCTTA
GTCAAACTACATTGCTTAAACTGTATTTCTCCCTTATTTTCATTTTCAACAATTTTGTCAATGGA
AATTATAGTGAAAGGAAATAACATCAATTGCTGA
Found at i:5864774 original size:23 final size:23
Alignment explanation
Indices: 5864731--5864774 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5864721 CTCCAGGAGA
*
5864731 TTTGGTCATAGCCCAGCAGAGTC
1 TTTGGTCATAGCCCAGAAGAGTC
*
5864754 TTTGGTTATAGTCCC-GAAGAG
1 TTTGGTCATAG-CCCAGAAGAG
5864775 CGGTTGGCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (23 bp):
TTTGGTCATAGCCCAGAAGAGTC
Found at i:5873191 original size:25 final size:26
Alignment explanation
Indices: 5873162--5873220 Score: 97
Period size: 25 Copynumber: 2.4 Consensus size: 26
5873152 AAATTATATT
5873162 TAATTTAT-TGTTTGAATGAATCATA
1 TAATTTATATGTTTGAATGAATCATA
5873187 TAA-TTATATGTTTGAATGAATCATA
1 TAATTTATATGTTTGAATGAATCATA
5873212 TAA-TTATAT
1 TAATTTATAT
5873221 CTCATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 4 0.12
25 29 0.88
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.47
Consensus pattern (26 bp):
TAATTTATATGTTTGAATGAATCATA
Found at i:5873705 original size:22 final size:22
Alignment explanation
Indices: 5873679--5873728 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
5873669 AAGTTTTATA
*
5873679 TATAAAATTTT-AA-TAAAATT
1 TATATAATTTTGAATTAAAATT
5873699 TATATAATTTTGAATTAAAATT
1 TATATAATTTTGAATTAAAATT
5873721 TAT-TAATT
1 TATATAATT
5873729 ATATTATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 7 0.26
22 10 0.37
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TATATAATTTTGAATTAAAATT
Found at i:5874033 original size:18 final size:17
Alignment explanation
Indices: 5873991--5874033 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
5873981 TATTTATATA
*
5873991 TAATAAAAATTTTAAAT
1 TAATAAAAATTTAAAAT
*
5874008 TATTTAAAAATTATAAAAT
1 TA-ATAAAAATT-TAAAAT
5874027 TAATAAA
1 TAATAAA
5874034 TAAGTAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.10
18 12 0.57
19 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATAAAAATTTAAAAT
Found at i:5874854 original size:18 final size:18
Alignment explanation
Indices: 5874821--5874858 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
5874811 TGTGTAAGGA
*
5874821 TTATGATAATATAATTTAT
1 TTATGATAATA-AAATTAT
5874840 TTATGA-AATAAAATTAT
1 TTATGATAATAAAATTAT
5874857 TT
1 TT
5874859 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 4 0.22
19 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TTATGATAATAAAATTAT
Found at i:5876735 original size:22 final size:23
Alignment explanation
Indices: 5876691--5876734 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
5876681 ATTTTGAAAT
*
5876691 CTTATTTGAAAAGATTTTTTTTA
1 CTTATTTGAAAACATTTTTTTTA
5876714 CTTATTTGAAAACATTTTTTT
1 CTTATTTGAAAACATTTTTTT
5876735 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (23 bp):
CTTATTTGAAAACATTTTTTTTA
Found at i:5876880 original size:17 final size:17
Alignment explanation
Indices: 5876860--5876892 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5876850 AATGAGTTGA
5876860 AAAATA-AAAATAAAAAT
1 AAAATAGAAAA-AAAAAT
5876877 AAAATAGAAAAAAAAA
1 AAAATAGAAAAAAAAA
5876893 ACCTTGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (17 bp):
AAAATAGAAAAAAAAAT
Found at i:5876892 original size:29 final size:29
Alignment explanation
Indices: 5876836--5876891 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
5876826 ACTATAATAA
***
5876836 AAAAATAAAAATAAAATGAGTTGAAAAAT
1 AAAAATAAAAATAAAATGAGAAAAAAAAT
5876865 AAAAATAAAAATAAAAT-AGAAAAAAAA
1 AAAAATAAAAATAAAATGAGAAAAAAAA
5876892 AACCTTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (29 bp):
AAAAATAAAAATAAAATGAGAAAAAAAAT
Found at i:5876893 original size:6 final size:6
Alignment explanation
Indices: 5876817--5876892 Score: 50
Period size: 6 Copynumber: 11.8 Consensus size: 6
5876807 AAAATTTCTC
*
5876817 AAAAAT AAAACTAT AATAA- AAAAAT AAAAAT AAAATGAGTT GAAAAAT
1 AAAAAT AAAA--AT AAAAAT AAAAAT AAAAAT AAAA--A--T -AAAAAT
5876865 AAAAAT AAAAAT -AAAAT AGAAAA- AAAAA
1 AAAAAT AAAAAT AAAAAT A-AAAAT AAAAA
5876893 ACCTTGCAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 21
0.72 0.02 0.26
Matches are distributed among these distances:
5 13 0.22
6 28 0.48
7 5 0.09
8 6 0.10
9 1 0.02
10 1 0.02
11 4 0.07
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:5877205 original size:20 final size:20
Alignment explanation
Indices: 5877182--5877245 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
5877172 ATTCATTGGT
5877182 AAATTTAAATTTTCATCAAA
1 AAATTTAAATTTTCATCAAA
* * *
5877202 AAATTCATATTTTCCA-GAAA
1 AAATTTAAATTTT-CATCAAA
*
5877222 AAATTTAGATTTT--TCAAA
1 AAATTTAAATTTTCATCAAA
5877240 AAATTT
1 AAATTT
5877246 TCAATTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 9 0.25
20 25 0.69
21 2 0.06
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (20 bp):
AAATTTAAATTTTCATCAAA
Found at i:5878825 original size:34 final size:35
Alignment explanation
Indices: 5878756--5878977 Score: 129
Period size: 34 Copynumber: 6.5 Consensus size: 35
5878746 TAGAGATTCT
**
5878756 AGATTCGTAAAGATTTCAAGTTT--GTAAGGACTTTC
1 AGATTCGTAAAGATTTCAAGTTTCACAAAGG--TTTC
*
5878791 AGATTCAT-AAGATTTCAAGTTTCACAAAGGTTTC
1 AGATTCGTAAAGATTTCAAGTTTCACAAAGGTTTC
* * * *****
5878825 AGATTCGTAAAGATTT-TAGATTCA-TAAGAAAAAA
1 AGATTCGTAAAGATTTCAAGTTTCACAAAG-GTTTC
* * * *
5878859 AGATT-TTCAAGATTTCAAGTTTCGCAAAGGTTCC
1 AGATTCGTAAAGATTTCAAGTTTCACAAAGGTTTC
* * * * * *
5878893 AGATTTGTAAAGATTT-TAGATTCATAAAGACTTTT
1 AGATTCGTAAAGATTTCAAGTTTCACAAAG-GTTTC
* *
5878928 AGATTCAT-AAGA-TTCTAAGTTTCACAAAGGTTTT
1 AGATTCGTAAAGATTTC-AAGTTTCACAAAGGTTTC
5878962 AGATTCGTAAAGATTT
1 AGATTCGTAAAGATTT
5878978 TAGATTAATA
Statistics
Matches: 136, Mismatches: 39, Indels: 23
0.69 0.20 0.12
Matches are distributed among these distances:
33 13 0.10
34 70 0.51
35 47 0.35
36 6 0.04
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (35 bp):
AGATTCGTAAAGATTTCAAGTTTCACAAAGGTTTC
Found at i:5878845 original size:17 final size:17
Alignment explanation
Indices: 5878756--5878983 Score: 79
Period size: 17 Copynumber: 13.3 Consensus size: 17
5878746 TAGAGATTCT
5878756 AGATTCGTAAAGATTTC
1 AGATTCGTAAAGATTTC
* *
5878773 A-AGTTTGTAAGGACTTTC
1 AGA-TTCGTAAAGA-TTTC
*
5878791 AGATTCAT-AAGATTTC
1 AGATTCGTAAAGATTTC
* ** *
5878807 AAGTTTCACAAAGGTTTC
1 -AGATTCGTAAAGATTTC
*
5878825 AGATTCGTAAAGATTTT
1 AGATTCGTAAAGATTTC
* ****
5878842 AGATTCAT-AAGAAAAAA
1 AGATTCGTAAAG-ATTTC
* *
5878859 AGATT-TTCAAGATTTC
1 AGATTCGTAAAGATTTC
* * * *
5878875 AAGTTTCGCAAAGGTTCC
1 -AGATTCGTAAAGATTTC
* *
5878893 AGATTTGTAAAGATTTT
1 AGATTCGTAAAGATTTC
* *
5878910 AGATTCATAAAGACTTTT
1 AGATTCGTAAAGA-TTTC
* *
5878928 AGATTCAT-AAGATTCTA
1 AGATTCGTAAAGATT-TC
* ** * *
5878945 AGTTTCACAAAGGTTTT
1 AGATTCGTAAAGATTTC
*
5878962 AGATTCGTAAAGATTTT
1 AGATTCGTAAAGATTTC
5878979 AGATT
1 AGATT
5878984 AATAAAAACT
Statistics
Matches: 153, Mismatches: 46, Indels: 24
0.69 0.21 0.11
Matches are distributed among these distances:
16 12 0.08
17 102 0.67
18 38 0.25
19 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (17 bp):
AGATTCGTAAAGATTTC
Found at i:5878877 original size:68 final size:68
Alignment explanation
Indices: 5878791--5878988 Score: 256
Period size: 68 Copynumber: 2.9 Consensus size: 68
5878781 AAGGACTTTC
5878791 AGATTCATAAGATTTCAAGTTTCACAAAGGTTTCAGATTCGTAAAGATTTTAGATTCATAAGAAA
1 AGATTCATAAGATTTCAAGTTTCACAAAGGTTTCAGATTCGTAAAGATTTTAGATTCATAAGAAA
5878856 AAA
66 AAA
* * * *
5878859 AGATT-TTCAAGATTTCAAGTTTCGCAAAGGTTCCAGATTTGTAAAGATTTTAGATTCATAAAGA
1 AGATTCAT-AAGATTTCAAGTTTCACAAAGGTTTCAGATTCGTAAAGATTTTAGATTCAT-AAGA
*****
5878923 CTTTT
64 AAAAA
* *
5878928 AGATTCATAAGA-TTCTAAGTTTCACAAAGGTTTTAGATTCGTAAAGATTTTAGATTAATAA
1 AGATTCATAAGATTTC-AAGTTTCACAAAGGTTTCAGATTCGTAAAGATTTTAGATTCATAA
5878989 AAACTTTTAT
Statistics
Matches: 111, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
67 1 0.01
68 58 0.52
69 51 0.46
70 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (68 bp):
AGATTCATAAGATTTCAAGTTTCACAAAGGTTTCAGATTCGTAAAGATTTTAGATTCATAAGAAA
AAA
Found at i:5878932 original size:35 final size:35
Alignment explanation
Indices: 5878893--5879005 Score: 122
Period size: 35 Copynumber: 3.3 Consensus size: 35
5878883 CAAAGGTTCC
*
5878893 AGATTTGTAAAGATTTTAGATTCATAAAGACTTTT
1 AGATTCGTAAAGATTTTAGATTCATAAAGACTTTT
* * * * *
5878928 AGATTCAT-AAGATTCTAAGTTTCACAAAG-GTTTT
1 AGATTCGTAAAGATT-TTAGATTCATAAAGACTTTT
* *
5878962 AGATTCGTAAAGATTTTAGATTAATAAAAACTTTT
1 AGATTCGTAAAGATTTTAGATTCATAAAGACTTTT
*
5878997 ATATTCGTA
1 AGATTCGTA
5879006 GGAAAGAAAG
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
34 26 0.43
35 35 0.57
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (35 bp):
AGATTCGTAAAGATTTTAGATTCATAAAGACTTTT
Found at i:5878978 original size:69 final size:69
Alignment explanation
Indices: 5878756--5879002 Score: 277
Period size: 69 Copynumber: 3.6 Consensus size: 69
5878746 TAGAGATTCT
* ** * *
5878756 AGATTCGTAAAGATTTCA-AGTTTGTAAGGACTTTCAGATTCATAAGATTTCAAGTTTCACAAAG
1 AGATTCGTAAAGATTTTAGA-TTCATAAAGACTTTTAGATTCATAAGATTTCAAGTTTCACAAAG
5878820 GTTTC
65 GTTTC
***** * *
5878825 AGATTCGTAAAGATTTTAGATTCAT-AAGAAAAAAAGATT-TTCAAGATTTCAAGTTTCGCAAAG
1 AGATTCGTAAAGATTTTAGATTCATAAAGACTTTTAGATTCAT-AAGATTTCAAGTTTCACAAAG
*
5878888 GTTCC
65 GTTTC
*
5878893 AGATTTGTAAAGATTTTAGATTCATAAAGACTTTTAGATTCATAAGA-TTCTAAGTTTCACAAAG
1 AGATTCGTAAAGATTTTAGATTCATAAAGACTTTTAGATTCATAAGATTTC-AAGTTTCACAAAG
*
5878957 GTTTT
65 GTTTC
* * *
5878962 AGATTCGTAAAGATTTTAGATTAATAAAAACTTTTATATTC
1 AGATTCGTAAAGATTTTAGATTCATAAAGACTTTTAGATTC
5879003 GTAGGAAAGA
Statistics
Matches: 147, Mismatches: 26, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
67 1 0.01
68 59 0.40
69 85 0.58
70 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (69 bp):
AGATTCGTAAAGATTTTAGATTCATAAAGACTTTTAGATTCATAAGATTTCAAGTTTCACAAAGG
TTTC
Found at i:5878989 original size:17 final size:17
Alignment explanation
Indices: 5878900--5878989 Score: 101
Period size: 17 Copynumber: 5.2 Consensus size: 17
5878890 TCCAGATTTG
5878900 TAAAGATTTTAGATTCA
1 TAAAGATTTTAGATTCA
5878917 TAAAGACTTTTAGATTCA
1 TAAAGA-TTTTAGATTCA
* *
5878935 T-AAGATTCTAAGTTTCA
1 TAAAGATT-TTAGATTCA
* * *
5878952 CAAAGGTTTTAGATTCG
1 TAAAGATTTTAGATTCA
*
5878969 TAAAGATTTTAGATTAA
1 TAAAGATTTTAGATTCA
5878986 TAAA
1 TAAA
5878990 AACTTTTATA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
16 2 0.03
17 40 0.68
18 17 0.29
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (17 bp):
TAAAGATTTTAGATTCA
Found at i:5879021 original size:69 final size:69
Alignment explanation
Indices: 5878883--5879024 Score: 167
Period size: 69 Copynumber: 2.1 Consensus size: 69
5878873 TCAAGTTTCG
* * * ** * *
5878883 CAAAGGTTCCAGATTTGTAAAGATTTTAGATTCATAAAGACTTTTAGATTCATAAGATTCTAAGT
1 CAAAGGTTCCAGATTCGTAAAGATTTTAGATTAATAAAAACTTTTAGATTCATAAGAAACAAAGA
5878948 TTCA
66 TTCA
** * * * *
5878952 CAAAGGTTTTAGATTCGTAAAGATTTTAGATTAATAAAAACTTTTATATTCGTAGGAAAGAAAGA
1 CAAAGGTTCCAGATTCGTAAAGATTTTAGATTAATAAAAACTTTTAGATTCATAAGAAACAAAGA
5879017 TTCA
66 TTCA
5879021 CAAA
1 CAAA
5879025 AATGAAACAT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (69 bp):
CAAAGGTTCCAGATTCGTAAAGATTTTAGATTAATAAAAACTTTTAGATTCATAAGAAACAAAGA
TTCA
Found at i:5880051 original size:34 final size:35
Alignment explanation
Indices: 5880013--5880079 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
5880003 TTTTGCAAAT
* * *
5880013 TTTTTGCCTTTTTTGTTTT-GTTTTTTTTTCTCAC
1 TTTTTGCATTTTTTGTTTTCGTTTCTCTTTCTCAC
**
5880047 TTTTTTTATTTTTTGTTTTCGTTTCTCTTTCTC
1 TTTTTGCATTTTTTGTTTTCGTTTCTCTTTCTC
5880080 TTTATTCATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 16 0.59
35 11 0.41
ACGTcount: A:0.03, C:0.15, G:0.07, T:0.75
Consensus pattern (35 bp):
TTTTTGCATTTTTTGTTTTCGTTTCTCTTTCTCAC
Found at i:5880051 original size:35 final size:35
Alignment explanation
Indices: 5880012--5880079 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
5880002 TTTTTGCAAA
* * *
5880012 TTTTTTGCCTTTTTTGTTTT-GTTTTTTTTTCTCAC
1 TTTTTT-CATTTTTTGTTTTCGTTTCTCTTTCTCAC
*
5880047 TTTTTTTATTTTTTGTTTTCGTTTCTCTTTCTC
1 TTTTTTCATTTTTTGTTTTCGTTTCTCTTTCTC
5880080 TTTATTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 11 0.39
35 17 0.61
ACGTcount: A:0.03, C:0.15, G:0.07, T:0.75
Consensus pattern (35 bp):
TTTTTTCATTTTTTGTTTTCGTTTCTCTTTCTCAC
Found at i:5884086 original size:18 final size:18
Alignment explanation
Indices: 5884058--5884098 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
5884048 TTTGTAGGGA
5884058 TTTTTATTTGAAAAAGATT
1 TTTTTATTTG-AAAAGATT
*
5884077 TTTTTA-TTGAAAGGATT
1 TTTTTATTTGAAAAGATT
5884094 TTTTT
1 TTTTT
5884099 TGTTTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
18 3 0.14
19 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (18 bp):
TTTTTATTTGAAAAGATT
Found at i:5884198 original size:25 final size:25
Alignment explanation
Indices: 5884143--5884201 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
5884133 ATTTTTTTTG
5884143 TTTTTTTTTATTATTTTGAAAAAGA
1 TTTTTTTTTATTATTTTGAAAAAGA
*
5884168 TGTTTTTTTACTTA-TTTG-AAAAG-
1 TTTTTTTTTA-TTATTTTGAAAAAGA
5884191 TTTTTTTTTAT
1 TTTTTTTTTAT
5884202 AAATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 1 0.03
23 9 0.29
24 5 0.16
25 13 0.42
26 3 0.10
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.64
Consensus pattern (25 bp):
TTTTTTTTTATTATTTTGAAAAAGA
Found at i:5884350 original size:19 final size:18
Alignment explanation
Indices: 5884328--5884375 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
5884318 TTAAAAAATT
*
5884328 AAAATAGAAATAAAATTAGA
1 AAAAAAGAAATAAAA-T-GA
*
5884348 AAACAA-AAATAAAATGA
1 AAAAAAGAAATAAAATGA
5884365 AAAAAAGAAAT
1 AAAAAAGAAAT
5884376 CTTGTGATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 7 0.29
18 5 0.21
19 8 0.33
20 4 0.17
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (18 bp):
AAAAAAGAAATAAAATGA
Found at i:5884703 original size:19 final size:19
Alignment explanation
Indices: 5884667--5884704 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5884657 AAATATTCAT
*
5884667 AAAAAAATTCATATTTTTC
1 AAAAAAATTCATAATTTTC
5884686 AAAAAAATTC-TAGATTTTC
1 AAAAAAATTCATA-ATTTTC
5884705 CCCAAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAAAAATTCATAATTTTC
Found at i:5887288 original size:12 final size:14
Alignment explanation
Indices: 5887254--5887296 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
5887244 TATTAAATTT
5887254 AATAA-ATTATATTA
1 AATAATATT-TATTA
5887268 AATAATATTT-TTA
1 AATAATATTTATTA
5887281 AA-AATATTTATTA
1 AATAATATTTATTA
5887294 AAT
1 AAT
5887297 GAATCAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.27
13 10 0.38
14 6 0.23
15 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAATATTTATTA
Found at i:5892816 original size:18 final size:20
Alignment explanation
Indices: 5892793--5892830 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
5892783 AGAAGATAAC
*
5892793 AAAAAATAAA-AG-GGAAAA
1 AAAAAACAAAGAGAGGAAAA
5892811 AAAAAACAAAGAGAGGAAAA
1 AAAAAACAAAGAGAGGAAAA
5892831 GCTGGAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAAAACAAAGAGAGGAAAA
Found at i:5894996 original size:41 final size:40
Alignment explanation
Indices: 5894938--5895023 Score: 97
Period size: 43 Copynumber: 2.1 Consensus size: 40
5894928 ATAAAAAATT
* *
5894938 TATATATTTATTAACATA-ATACAATA-A-ATATATATTTA
1 TATATATTTATTAACATACAAAC-ATACATACATATATTTA
5894976 TATATATTTATTAAATACATACAAACATACATACATATATTTA
1 TATATATTTATT--A-ACATACAAACATACATACATATATTTA
5895019 TATAT
1 TATAT
5895024 CTTGAATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
38 12 0.30
40 1 0.03
41 8 0.20
42 4 0.10
43 15 0.38
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (40 bp):
TATATATTTATTAACATACAAACATACATACATATATTTA
Found at i:5895207 original size:33 final size:33
Alignment explanation
Indices: 5895169--5895239 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
5895159 TTCTTATTGA
*
5895169 ATATAGATAAAATTATCTCTAATATATTTATTT
1 ATATAGATAAAATTATCTCTAATATATTTATAT
*
5895202 ATATAGGTAAAATTATCTCTAATATATTTATAT
1 ATATAGATAAAATTATCTCTAATATATTTATAT
5895235 ATATA
1 ATATA
5895240 TATATATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (33 bp):
ATATAGATAAAATTATCTCTAATATATTTATAT
Found at i:5895377 original size:31 final size:32
Alignment explanation
Indices: 5895319--5895379 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
5895309 ATTGAATCAA
**
5895319 TTTTTTTTTTTAAACTCATGGTTAGATTGAGT
1 TTTTTTTTTTTAAACTCATAATTAGATTGAGT
5895351 TTTTTTTTTTTAAA-TCA-AATTCAGATTGA
1 TTTTTTTTTTTAAACTCATAATT-AGATTGA
5895380 AGTCGAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 2 0.08
31 10 0.38
32 14 0.54
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (32 bp):
TTTTTTTTTTTAAACTCATAATTAGATTGAGT
Found at i:5897160 original size:18 final size:17
Alignment explanation
Indices: 5897137--5897171 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5897127 GAACGTCTCT
5897137 GATGATAAAATAGAATAA
1 GATGATAAAATA-AATAA
*
5897155 GATGATAATATAAATAA
1 GATGATAAAATAAATAA
5897172 AATTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (17 bp):
GATGATAAAATAAATAA
Found at i:5897999 original size:19 final size:19
Alignment explanation
Indices: 5897954--5898000 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
5897944 ATATAAATAA
5897954 ACACAAATAATACAGATAT
1 ACACAAATAATACAGATAT
* * *
5897973 ATATAAATAGATAC-GATTT
1 ACACAAATA-ATACAGATAT
5897992 ACACAAATA
1 ACACAAATA
5898001 TGTACAAGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (19 bp):
ACACAAATAATACAGATAT
Found at i:5898119 original size:26 final size:26
Alignment explanation
Indices: 5898061--5898119 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
5898051 AACTTAATAA
*
5898061 ATTTGACATATTAATAATATAAAAAAT
1 ATTT-ACATATTAATAAAATAAAAAAT
**
5898088 GCTTACATATTAA-AAGAATAAAAAAT
1 ATTTACATATTAATAA-AATAAAAAAT
5898114 ATTTAC
1 ATTTAC
5898120 TACCCATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 2 0.08
26 22 0.85
27 2 0.08
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (26 bp):
ATTTACATATTAATAAAATAAAAAAT
Found at i:5898267 original size:12 final size:12
Alignment explanation
Indices: 5898250--5898295 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
5898240 TATATAGGAC
5898250 TAATATTATTAT
1 TAATATTATTAT
*
5898262 TAATATTAATAT
1 TAATATTATTAT
*
5898274 TAATATT-GTAT
1 TAATATTATTAT
*
5898285 TTATATTATTA
1 TAATATTATTA
5898296 ATATAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (12 bp):
TAATATTATTAT
Found at i:5898291 original size:6 final size:6
Alignment explanation
Indices: 5898250--5898280 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5898240 TATATAGGAC
*
5898250 TAATAT TATTAT TAATAT TAATAT TAATAT T
1 TAATAT TAATAT TAATAT TAATAT TAATAT T
5898281 GTATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TAATAT
Found at i:5898482 original size:18 final size:18
Alignment explanation
Indices: 5898456--5898490 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5898446 AAATATAAAA
*
5898456 AAATGTATTAAACATGTT
1 AAATATATTAAACATGTT
*
5898474 AAATATATTAAATATGT
1 AAATATATTAAACATGT
5898491 ACTTGTATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.40
Consensus pattern (18 bp):
AAATATATTAAACATGTT
Found at i:5899544 original size:23 final size:25
Alignment explanation
Indices: 5899500--5899547 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5899490 TATCTTTATT
* *
5899500 AATATAATACATATATATAAATATA
1 AATAAAATAAATATATATAAATATA
5899525 AATAAAATAAATA-ATA-AAATATA
1 AATAAAATAAATATATATAAATATA
5899548 TTCTTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 3 0.14
25 11 0.52
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
AATAAAATAAATATATATAAATATA
Found at i:5906051 original size:12 final size:12
Alignment explanation
Indices: 5906022--5906064 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5906012 GATTTAGTGA
* *
5906022 TGTTGTTGTTGA
1 TGTTATTGTTGT
* *
5906034 TCTTATTTTTGT
1 TGTTATTGTTGT
5906046 TGTTATTGTTGT
1 TGTTATTGTTGT
5906058 TGTTATT
1 TGTTATT
5906065 ATTACAGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.09, C:0.02, G:0.21, T:0.67
Consensus pattern (12 bp):
TGTTATTGTTGT
Found at i:5914280 original size:61 final size:60
Alignment explanation
Indices: 5914202--5914514 Score: 261
Period size: 62 Copynumber: 5.1 Consensus size: 60
5914192 CCTTAAAGCA
* *
5914202 TTTAAAAGTTTTTATTTTAAAAAAAAATTGATACTTTCAACTTTT-CTCCAAAAATAGTTTTT
1 TTTAAAA-TTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCT-CAAAAATAG-TTTT
** * * * **
5914264 TTTTTAATTTTTATTTTCGAGAAAAATTGGTACTTTTAACTTTTCCTCAAAAAT-GCCTT
1 TTTAAAATTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATAGTTTT
* * * *
5914323 TTCAAAATTTTAATTTTCAAGAAAAATTGAAACTTTCAACTTTTCCTCAAAAATAATTTT
1 TTTAAAATTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATAGTTTT
** * * * * * ** * *
5914383 TTTGAAGTTTTTTTTTTTGGAAAAAAAATTGATATTTTCAATTTTTTTTCAAAAAAAATATATT
1 TTT-AAAATTTTTATTTT-CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATAGT-T-TT
* * * * * **
5914447 TTTAAAAATTTTATTTTTAAGAAAAATTGGTACTTTCAACTTTTTCTTAAAAATTTTTTT
1 TTTAAAATTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATAGTTTT
5914507 TTGTAAAA
1 TT-TAAAA
5914515 AATATTCTTT
Statistics
Matches: 197, Mismatches: 47, Indels: 15
0.76 0.18 0.06
Matches are distributed among these distances:
59 48 0.24
60 9 0.05
61 55 0.28
62 69 0.35
63 11 0.06
64 5 0.03
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (60 bp):
TTTAAAATTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATAGTTTT
Found at i:5916116 original size:16 final size:17
Alignment explanation
Indices: 5916087--5916129 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
5916077 TAGACCATAA
*
5916087 AAATAAAAATTAAAATG
1 AAATAAAAATAAAAATG
5916104 AAATAAAAATAAAAATG
1 AAATAAAAATAAAAATG
5916121 -AATAAAAAT
1 AAATAAAAAT
5916130 CCCTACAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
AAATAAAAATAAAAATG
Found at i:5916415 original size:44 final size:46
Alignment explanation
Indices: 5916317--5916416 Score: 134
Period size: 44 Copynumber: 2.2 Consensus size: 46
5916307 AAAGTTACTC
*
5916317 TAAATAGAGG-TTCAATGACTTTGAGAAAAATAAATAAAGCTCATT
1 TAAATAGAGGCTTCAATGACTTTGAGAAAAATAAACAAAGCTCATT
* * *
5916362 TAATTAGAGGCTT-AATGATTTTG-GAAAAATAAACAAAGCTCTTT
1 TAAATAGAGGCTTCAATGACTTTGAGAAAAATAAACAAAGCTCATT
*
5916406 TAAACAGAGGC
1 TAAATAGAGGC
5916417 ACCGCAACTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 28 0.58
45 18 0.38
46 2 0.04
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (46 bp):
TAAATAGAGGCTTCAATGACTTTGAGAAAAATAAACAAAGCTCATT
Found at i:5916860 original size:114 final size:114
Alignment explanation
Indices: 5916725--5916956 Score: 392
Period size: 114 Copynumber: 2.0 Consensus size: 114
5916715 GTTCATATTT
5916725 AAGAAATCTTAGAGTTTCACATCTAAGTTCAAAGGTACTCACTAAAAAATTTAGAGATTCACATC
1 AAGAAATCTTAGAGTTTCACATCTAAGTTCAAAGGTACTCACTAAAAAATTTAGAGATTCACATC
*
5916790 CAAAAGTTGAGTTCAAAGATTTTCATTTGAATTTTAGAGATTCACATCC
66 CAAAAGTTGAGTACAAAGATTTTCATTTGAATTTTAGAGATTCACATCC
* **
5916839 AAGAAATCTTAGAGTTTCACATCTAAGTTCAAAGGTTCTCACTAAAAAATTTAGAGATTCGTATC
1 AAGAAATCTTAGAGTTTCACATCTAAGTTCAAAGGTACTCACTAAAAAATTTAGAGATTCACATC
* ** *
5916904 CAAAAGTTGAGTACAAAGCTTTTTGTTTGAATTTTGGAGATTCACATCC
66 CAAAAGTTGAGTACAAAGATTTTCATTTGAATTTTAGAGATTCACATCC
5916953 AAGA
1 AAGA
5916957 GTTTAAAACT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 110 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (114 bp):
AAGAAATCTTAGAGTTTCACATCTAAGTTCAAAGGTACTCACTAAAAAATTTAGAGATTCACATC
CAAAAGTTGAGTACAAAGATTTTCATTTGAATTTTAGAGATTCACATCC
Found at i:5917063 original size:20 final size:21
Alignment explanation
Indices: 5917016--5917071 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
5917006 ATTTCACATC
5917016 TCAAAGATTCTCATTTAAAAT
1 TCAAAGATTCTCATTTAAAAT
* *
5917037 TTAAAGATTCTCATTT-GAAT
1 TCAAAGATTCTCATTTAAAAT
* *
5917057 TCGAAGATTCACATT
1 TCAAAGATTCTCATT
5917072 CGACAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
TCAAAGATTCTCATTTAAAAT
Found at i:5917144 original size:20 final size:20
Alignment explanation
Indices: 5917105--5917149 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5917095 TTAAAGATTT
*
5917105 TCATTTGAATTCGAAGATTC
1 TCATTTGAATTCGAAAATTC
* *
5917125 TCATTTGATTTTGAAAATTC
1 TCATTTGAATTCGAAAATTC
*
5917145 ACATT
1 TCATT
5917150 CAATAAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (20 bp):
TCATTTGAATTCGAAAATTC
Found at i:5917145 original size:78 final size:78
Alignment explanation
Indices: 5916976--5917191 Score: 254
Period size: 78 Copynumber: 2.7 Consensus size: 78
5916966 TTTTCATTAG
* ** * * * *
5916976 TTCGAAGATTCACACCCAACAAACTTTAGGATTTCACATCTCAAAGATTCTCATTTAAAATTTAA
1 TTCGAAAATTCACATTCAACAAATTTTAGG-TTTCACACCTCAAAGATTCTCATTT-GAATTCAA
5917041 AGATTCTCATTTGAA
64 AGATTCTCATTTGAA
* * * * *
5917056 TTCGAAGATTCACATTCGACAAATTTT-GAGTTTCACACCTTAAAGATTTTCATTTGAATTCGAA
1 TTCGAAAATTCACATTCAACAAATTTTAG-GTTTCACACCTCAAAGATTCTCATTTGAATTCAAA
*
5917120 GATTCTCATTTGAT
65 GATTCTCATTTGAA
* * *
5917134 TTTGAAAATTCACATTCAATAAATTTTAGGTTTCAGACCTCAAAGATTCTCATTTGAA
1 TTCGAAAATTCACATTCAACAAATTTTAGGTTTCACACCTCAAAGATTCTCATTTGAA
5917192 AACGTCTTAA
Statistics
Matches: 116, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
78 68 0.59
79 24 0.21
80 24 0.21
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (78 bp):
TTCGAAAATTCACATTCAACAAATTTTAGGTTTCACACCTCAAAGATTCTCATTTGAATTCAAAG
ATTCTCATTTGAA
Found at i:5917326 original size:137 final size:138
Alignment explanation
Indices: 5917172--5917528 Score: 520
Period size: 137 Copynumber: 2.6 Consensus size: 138
5917162 GGTTTCAGAC
* * *
5917172 CTCAAAGATTCTCATTTGAAAACGTCTTAAATATTTTAATTTAAGACTTAAAGATTCTCATTTGA
1 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTTTAATTTAAGACTCAAAGATTCTCATTTGA
* ** *
5917237 AAATGTCTTAAAGATTCTCATTTAAGATTC-AAGATACTCATTTGGAAATGTTTTAAAGATTCTC
66 AAATGTCTTAAAGATTCTCATTTAAGATTCAAAGATACTCATTTGAAAACATCTTAAAGATTCTC
5917301 ATTTGAA-A
131 ATTT-AAGA
* * *
5917309 TTCAAAGATTCTCATTTGAAAATATCTTAAAGATTTTCATTTAAGACTCAAAGATTCTCATTTGA
1 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTTTAATTTAAGACTCAAAGATTCTCATTTGA
* * *
5917374 AAATGTTTTAAAGATTTTCATTTAAGATTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTC
66 AAATGTCTTAAAGATTCTCATTTAAGATTCAAAGATACTCATTTGAAAACATCTTAAAGATTCTC
5917439 ATTTAAGA
131 ATTTAAGA
* *
5917447 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTTCTTATTTAAAACTCAAAGATTCTCATTTG
1 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTT-TAATTTAAGACTCAAAGATTCTCATTTG
** *
5917512 AGGATTTCTTAAAGATT
65 AAAATGTCTTAAAGATT
5917529 TTTTATTTAA
Statistics
Matches: 196, Mismatches: 21, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
137 89 0.45
138 68 0.35
139 39 0.20
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (138 bp):
CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTTTAATTTAAGACTCAAAGATTCTCATTTGA
AAATGTCTTAAAGATTCTCATTTAAGATTCAAAGATACTCATTTGAAAACATCTTAAAGATTCTC
ATTTAAGA
Found at i:5917508 original size:47 final size:46
Alignment explanation
Indices: 5917172--5917584 Score: 517
Period size: 46 Copynumber: 9.0 Consensus size: 46
5917162 GGTTTCAGAC
* * *
5917172 CTCAAAGATTCTCATTTGAAAACGTCTTAAATATTTTAATTTAAGA
1 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTTAAGA
* *
5917218 CTTAAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGA
1 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTTAAGA
* * * * *
5917264 TTC-AAGATACTCATTTGGAAATGTTTTAAAGATTCTCATTTGAA-A
1 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTT-AAGA
* *
5917309 TTCAAAGATTCTCATTTGAAAATATCTTAAAGATTTTCATTTAAGA
1 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTTAAGA
*
5917355 CTCAAAGATTCTCATTTGAAAATGTTTTAAAGATTTTCATTTAAGA
1 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTTAAGA
* ** *
5917401 TTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAGA
1 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTTAAGA
* *
5917447 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTTCTTATTTAAAA
1 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTT-TCATTTAAGA
** * *
5917494 CTCAAAGATTCTCATTTGAGGATTTCTTAAAGATTTTTTATTTAA-A
1 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGA-TTTTCATTTAAGA
* * ** *
5917540 TCTCAAATATTCTCATGTGAGGATTTCTTAAAGATTTTCATTTAA
1 -CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTTAA
5917585 AACTTAAAAT
Statistics
Matches: 326, Mismatches: 35, Indels: 12
0.87 0.09 0.03
Matches are distributed among these distances:
45 41 0.13
46 205 0.63
47 77 0.24
48 3 0.01
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (46 bp):
CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTTAAGA
Found at i:5918684 original size:16 final size:15
Alignment explanation
Indices: 5918660--5918721 Score: 79
Period size: 15 Copynumber: 3.9 Consensus size: 15
5918650 CATCTTGCTT
5918660 TTTTCCTTTTTTTTC
1 TTTTCCTTTTTTTTC
5918675 TTTTCTCTTTTTTTTTC
1 TTTTC-C-TTTTTTTTC
5918692 TCTTTCCTTTTTTTTC
1 T-TTTCCTTTTTTTTC
**
5918708 TCATCCTTTTTTTT
1 TTTTCCTTTTTTTT
5918722 TTTCATCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
15 16 0.38
16 11 0.26
17 11 0.26
18 4 0.10
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCCTTTTTTTTC
Found at i:5918690 original size:19 final size:17
Alignment explanation
Indices: 5918661--5918722 Score: 78
Period size: 16 Copynumber: 3.8 Consensus size: 17
5918651 ATCTTGCTTT
5918661 TTTCC-TTTTTTTTCT-
1 TTTCCTTTTTTTTTCTC
5918676 TTTCTCTTTTTTTTTCTC
1 TTTC-CTTTTTTTTTCTC
5918694 TTTCC-TTTTTTTTCTC
1 TTTCCTTTTTTTTTCTC
*
5918710 -ATCCTTTTTTTTT
1 TTTCCTTTTTTTTT
5918723 TTCATCATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
15 7 0.17
16 20 0.48
17 11 0.26
18 4 0.10
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTCCTTTTTTTTTCTC
Found at i:5918698 original size:33 final size:32
Alignment explanation
Indices: 5918661--5918722 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
5918651 ATCTTGCTTT
**
5918661 TTTCCTTTTTTTTCTTTTCTCTTTTTTTTTCTC
1 TTTCCTTTTTTTTCTCATC-CTTTTTTTTTCTC
5918694 TTTCCTTTTTTTTCTCATCCTTTTTTTTT
1 TTTCCTTTTTTTTCTCATCCTTTTTTTTT
5918723 TTCATCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 10 0.37
33 17 0.63
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (32 bp):
TTTCCTTTTTTTTCTCATCCTTTTTTTTTCTC
Found at i:5918722 original size:16 final size:16
Alignment explanation
Indices: 5918666--5918734 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
5918656 GCTTTTTTCC
**
5918666 TTTTTTTTCTTTTCTCT
1 TTTTTTTTCTCATC-CT
*
5918683 TTTTTTTTCTCTTTCC-
1 TTTTTTTTCTC-ATCCT
5918699 TTTTTTTTCTCATCCT
1 TTTTTTTTCTCATCCT
* *
5918715 TTTTTTTTTTCATCAT
1 TTTTTTTTCTCATCCT
5918731 TTTT
1 TTTT
5918735 CACCCGTTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
15 3 0.07
16 29 0.63
17 11 0.24
18 3 0.07
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTTCTCATCCT
Found at i:5922821 original size:120 final size:118
Alignment explanation
Indices: 5922558--5922829 Score: 311
Period size: 120 Copynumber: 2.3 Consensus size: 118
5922548 CATACTTTTA
* * * * * * * *
5922558 TTCAAGGAAAATTGATACTTTTAACTTTTCCT--TAAA-GCATTTGAAAGTTTTTATTTTCAAGA
1 TTCAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAATACCTTTCAAAATTTTAATTTTCAACA
* * ****
5922620 AAAATTGATGCTTTCAATTTTTCTCCAAAAATACTTTTTTTTTTAAATTTATT
66 AAAATTGATACTTTCAATTTTTCTCAAAAAATACTTTTTTAAAAAAATTTATT
*
5922673 TTCGAGAAAAATTGATACTTTTAACTTTTCCTCAAAAATACCTTTCAAAATTTTAATTTTCAACA
1 TTCAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAATACCTTTCAAAATTTTAATTTTCAACA
5922738 AAAATTGATACTTTCAACTTTTTCTCAAAAAAATA-TTTTTTAAAAAAATTTTATT
66 AAAATTGATACTTTCAA-TTTTTCTC-AAAAAATACTTTTTTAAAAAAA-TTTATT
* * *
5922793 TTTAAGAAAAATTGGTACTTTCT-ACTTTTCCTTAAAA
1 TTCAAGAAAAATTGATACTTT-TAACTTTTCCTCAAAA
5922830 GTTTTTTTTT
Statistics
Matches: 131, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
115 30 0.23
117 3 0.02
118 36 0.27
119 17 0.13
120 44 0.34
121 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (118 bp):
TTCAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAATACCTTTCAAAATTTTAATTTTCAACA
AAAATTGATACTTTCAATTTTTCTCAAAAAATACTTTTTTAAAAAAATTTATT
Found at i:5922840 original size:62 final size:63
Alignment explanation
Indices: 5922605--5922829 Score: 182
Period size: 60 Copynumber: 3.7 Consensus size: 63
5922595 CATTTGAAAG
* * * * * ****
5922605 TTTTTATTTTCAAGAAAAATTGATGCTTTCAA-TTTTTCTC-CAAAAATACTTTTTTTTTTAAA
1 TTTTAATTTTCAACAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATA-TTTTTTAAAAAAA
* * * ** *
5922667 -TTT-ATTTTCGAGAAAAATTGATACTTTTAACTTTTCCTC--AAAAATA-CCTTT--CAAAA
1 TTTTAATTTTCAACAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATATTTTTTAAAAAAA
*
5922723 TTTTAATTTTCAACAAAAATTGATACTTTCAACTTTTTCTCAAAAAAATATTTTTTAAAAAAA
1 TTTTAATTTTCAACAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATATTTTTTAAAAAAA
* * * * *
5922786 TTTT-ATTTTTAAGAAAAATTGGTACTTTCTACTTTTCCTTAAAA
1 TTTTAATTTTCAACAAAAATTGATACTTTCAACTTTTCCTCAAAA
5922830 GTTTTTTTTT
Statistics
Matches: 134, Mismatches: 21, Indels: 16
0.78 0.12 0.09
Matches are distributed among these distances:
56 3 0.02
57 3 0.02
58 35 0.26
60 38 0.28
61 13 0.10
62 34 0.25
63 8 0.06
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.46
Consensus pattern (63 bp):
TTTTAATTTTCAACAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATATTTTTTAAAAAAA
Found at i:5924447 original size:21 final size:23
Alignment explanation
Indices: 5924423--5924464 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
5924413 ATAAAAATAA
5924423 AAATAAAAAT-AA-AAAAATCTG
1 AAATAAAAATGAATAAAAATCTG
5924444 AAATAAAAATGAATAAAAATC
1 AAATAAAAATGAATAAAAATC
5924465 CCTACAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 2 0.11
23 7 0.37
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (23 bp):
AAATAAAAATGAATAAAAATCTG
Found at i:5924453 original size:6 final size:6
Alignment explanation
Indices: 5924413--5924437 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5924403 TAGATAGACC
5924413 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
5924438 AATCTGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:5938822 original size:21 final size:21
Alignment explanation
Indices: 5938781--5938824 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5938771 ATTTTTTGTT
* *
5938781 ATTATTTTGAATATATTTTTA
1 ATTATTTTGAATACATATTTA
5938802 ATTATTTT-AATACATAATTTA
1 ATTATTTTGAATACAT-ATTTA
5938823 AT
1 AT
5938825 AAAAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTATTTTGAATACATATTTA
Found at i:5939268 original size:25 final size:25
Alignment explanation
Indices: 5939234--5939285 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
5939224 TAATGAGAGA
*
5939234 TTAATAATTTAATA-AGTAGTTAATT
1 TTAAAAATTTAATACA-TAGTTAATT
5939259 TTAAAAATTTAATACATAGTTAATT
1 TTAAAAATTTAATACATAGTTAATT
5939284 TT
1 TT
5939286 TACATTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (25 bp):
TTAAAAATTTAATACATAGTTAATT
Found at i:5939518 original size:129 final size:132
Alignment explanation
Indices: 5939278--5939520 Score: 309
Period size: 129 Copynumber: 1.9 Consensus size: 132
5939268 TAATACATAG
*
5939278 TTAATTTTTACATTATATTAAAAATTAAAATATGTAATTTAATAAGAGTATTATAGTAATTTTTA
1 TTAATTTTTACATTATATTAAAAATTAAAATATGTAATTTAATAAGAGTATTATAGTAAATTTTA
* * * * * *
5939343 CATAAAATATCATATTTCAAATTTATATGAAGCGATAGTAATAGTATTTAAGTAATTTCATATTT
66 AACAAAATATCATATATCAAATTCATATGAAGCAATAGTAAGAGTATTTAAGTAATTTCATATTT
5939408 GA
131 GA
* *
5939410 TTAATTTTATA-A-TATATT-AAAATT-TAATGTGTAATTTAATAAG-GTTATTATAGTAAATTT
1 TTAATTTT-TACATTATATTAAAAATTAAAATATGTAATTTAATAAGAG-TATTATAGTAAATTT
* * *
5939470 TAAACAAAATATCATATATCAAGTTCCTATTAAGCAATTA-TAAGAGTATTT
64 TAAACAAAATATCATATATCAAATTCATATGAAGCAA-TAGTAAGAGTATTT
5939521 TTATAATTTT
Statistics
Matches: 96, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
128 1 0.01
129 70 0.73
130 8 0.08
131 6 0.06
132 9 0.09
133 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (132 bp):
TTAATTTTTACATTATATTAAAAATTAAAATATGTAATTTAATAAGAGTATTATAGTAAATTTTA
AACAAAATATCATATATCAAATTCATATGAAGCAATAGTAAGAGTATTTAAGTAATTTCATATTT
GA
Found at i:5939535 original size:23 final size:24
Alignment explanation
Indices: 5939509--5939559 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
5939499 TTAAGCAATT
5939509 ATAAGAG-TATTTTTA-TAATTTTG
1 ATAAGAGATA-TTTTAGTAATTTTG
5939532 ATAAGAGATATTTTAGTAATTTTG
1 ATAAGAGATATTTTAGTAATTTTG
5939556 ATAA
1 ATAA
5939560 ATTATGCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (24 bp):
ATAAGAGATATTTTAGTAATTTTG
Found at i:5939551 original size:24 final size:23
Alignment explanation
Indices: 5939509--5939559 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
5939499 TTAAGCAATT
5939509 ATAAGAGTATTTTTATAATTTTG
1 ATAAGAGTATTTTTATAATTTTG
5939532 ATAAGAG-ATATTTTAGTAATTTTG
1 ATAAGAGTAT-TTTTA-TAATTTTG
5939556 ATAA
1 ATAA
5939560 ATTATGCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 2 0.08
23 12 0.46
24 12 0.46
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (23 bp):
ATAAGAGTATTTTTATAATTTTG
Found at i:5946771 original size:3 final size:3
Alignment explanation
Indices: 5946763--5946798 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5946753 TTTTGAAATA
5946763 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5946799 GATGATGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5946812 original size:15 final size:15
Alignment explanation
Indices: 5946794--5946822 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5946784 AATAATAATA
5946794 ATAATGATGATGATG
1 ATAATGATGATGATG
5946809 ATAATGATGATGAT
1 ATAATGATGATGAT
5946823 TTAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.34
Consensus pattern (15 bp):
ATAATGATGATGATG
Found at i:5947777 original size:177 final size:176
Alignment explanation
Indices: 5947474--5947825 Score: 449
Period size: 177 Copynumber: 2.0 Consensus size: 176
5947464 AATGGTTAAA
* * *****
5947474 TTTGTGTAGTCGAGAAAGATGAATAGATTAAAGGAAGAAGTTTTAGAGTTTCCCTTTTTTTTGAA
1 TTTGTGTAGTCGAGAAAGATGAATAGATTAAAGGAAGAAGTTTTAAAGTTTCACTTTTAAAAAAA
*
5947539 ATTGAGAAAGAATCTGAACCATCTTTTGGTTTTAAGAGATGCCAAAAATCATTTAAAAATTTGGT
66 ATTGAGAAAGAATCTGAACCATCTTTTAGTTTTAAGAGATGCCAAAAATCATTTAAAAATTTGGT
* * *
5947604 AAAGAAATATAGCCAAGGGATATGATTGTTTGAATTTGATGAACAT
131 AAAGAAAGATAGCCAAGGGACATGATTGTTTGAATTGGATGAACAT
* * **
5947650 TTTGTGTAGTCTAGGAAGATGAATAGATTAGGGGAAGAAGTTTTAAAGTTT-ACTTTTAAAAAAA
1 TTTGTGTAGTCGAGAAAGATGAATAGATTAAAGGAAGAAGTTTTAAAGTTTCACTTTT--AAAAA
* * *
5947714 AAATCT-AGAAAGAATTTGAACCATCTTTTAGTTTTGAG-GAATGCCAAAAATCATTTCAAAATT
64 AAAT-TGAGAAAGAATCTGAACCATCTTTTAGTTTTAAGAG-ATGCCAAAAATCATTTAAAAATT
* * * *
5947777 TGGTGAAGAAGGATAGCTAAGGGACGTGATTGTTTGAATTGGATGAACA
127 TGGTAAAGAAAGATAGCCAAGGGACATGATTGTTTGAATTGGATGAACA
5947826 ACCTCTCCCT
Statistics
Matches: 150, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
175 5 0.03
176 47 0.31
177 97 0.65
178 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.33
Consensus pattern (176 bp):
TTTGTGTAGTCGAGAAAGATGAATAGATTAAAGGAAGAAGTTTTAAAGTTTCACTTTTAAAAAAA
ATTGAGAAAGAATCTGAACCATCTTTTAGTTTTAAGAGATGCCAAAAATCATTTAAAAATTTGGT
AAAGAAAGATAGCCAAGGGACATGATTGTTTGAATTGGATGAACAT
Found at i:5954432 original size:4 final size:4
Alignment explanation
Indices: 5954423--5954465 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
5954413 CATAATTTTC
* * *
5954423 TATT TATT TATT TATT TGTT TGTT TGTT TATTT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TATT TA-TT TATT TATT TA
5954466 ACTATTCATG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 32 0.89
5 4 0.11
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:5954991 original size:53 final size:54
Alignment explanation
Indices: 5954922--5955030 Score: 141
Period size: 53 Copynumber: 2.0 Consensus size: 54
5954912 TGAATAATAA
* * *
5954922 AAGGATATTTCTAAATTTA-ACCCAAATGGTGAAAATTTTAGAAATGAAGTTTGT
1 AAGGATATTTCTAAA-TTAGACCCAAATGGTGAAAAATTTAGAAATAAAATTTGT
* * *
5954976 AAGG-TATTTTTAAATTAGGCCTAAATGGTGAAAAATTTAGAAATAAAATTTGT
1 AAGGATATTTCTAAATTAGACCCAAATGGTGAAAAATTTAGAAATAAAATTTGT
5955029 AA
1 AA
5955031 AATAAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 3 0.06
53 41 0.85
54 4 0.08
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.35
Consensus pattern (54 bp):
AAGGATATTTCTAAATTAGACCCAAATGGTGAAAAATTTAGAAATAAAATTTGT
Found at i:5956000 original size:5 final size:5
Alignment explanation
Indices: 5955990--5956027 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
5955980 ATAGATATAG
5955990 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATA
5956028 ACAATATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:5956297 original size:60 final size:59
Alignment explanation
Indices: 5956219--5956358 Score: 149
Period size: 61 Copynumber: 2.3 Consensus size: 59
5956209 ACTATTATAC
* * *
5956219 CTTATCTTAATTATTGAAATGCTCCTCTTACTATAATT-AGCCAAAGTTACTATAA-TCATCT
1 CTTATCATAATTA-TGAAATGCTCCTC-TACCATAATTGA-CCAAAGTTACAATAAGTC-TCT
* * *
5956280 CTTATCATAATTATGAAAATGTTCTTCTACCATAATTGACTAAAGTTACAATAATGTCTCT
1 CTTATCATAATTATG-AAATGCTCCTCTACCATAATTGACCAAAGTTACAATAA-GTCTCT
*
5956341 CCTATCATAATTATGAAA
1 CTTATCATAATTATGAAA
5956359 ATTTTCTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
60 27 0.40
61 39 0.57
62 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (59 bp):
CTTATCATAATTATGAAATGCTCCTCTACCATAATTGACCAAAGTTACAATAAGTCTCT
Found at i:5956359 original size:61 final size:60
Alignment explanation
Indices: 5956261--5956378 Score: 166
Period size: 61 Copynumber: 1.9 Consensus size: 60
5956251 ATAATTAGCC
* *
5956261 AAAGTTACTATAATCATCTCTTATCATAATTATGAAAATGTTCTTCTACCATAATTGACT
1 AAAGTTACAATAATCATCTCCTATCATAATTATGAAAATGTTCTTCTACCATAATTGACT
* * *
5956321 AAAGTTACAATAATGTC-TCTCCTATCATAATTATGAAAATTTTCTTTTACCATGATTG
1 AAAGTTACAATAA--TCATCTCCTATCATAATTATGAAAATGTTCTTCTACCATAATTG
5956379 GACAAAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
60 12 0.24
61 37 0.73
62 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.41
Consensus pattern (60 bp):
AAAGTTACAATAATCATCTCCTATCATAATTATGAAAATGTTCTTCTACCATAATTGACT
Found at i:5956411 original size:61 final size:61
Alignment explanation
Indices: 5956285--5956414 Score: 138
Period size: 61 Copynumber: 2.1 Consensus size: 61
5956275 CATCTCTTAT
* ** * *
5956285 CATAATTATGAAAATGTTCTTCTACCATAATTGACTAAAGTTACAATAATGTCTCTCCTAT
1 CATAATTATGAAAATGTTCTTCTACCATAATTGACTAAAATTACAATAATAACTCTCATAC
* * * **
5956346 CATAATTATGAAAATTTTCTTTTACCATGATTGGAC-AAAATTATTATAATAAC-CATCATAC
1 CATAATTATGAAAATGTTCTTCTACCATAATT-GACTAAAATTACAATAATAACTC-TCATAC
5956407 CATAATTA
1 CATAATTA
5956415 CGAGAATACC
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
60 1 0.02
61 53 0.93
62 3 0.05
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (61 bp):
CATAATTATGAAAATGTTCTTCTACCATAATTGACTAAAATTACAATAATAACTCTCATAC
Found at i:5956616 original size:16 final size:16
Alignment explanation
Indices: 5956595--5956642 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
5956585 ACTTCTATTA
5956595 AATTACATATTAAATT
1 AATTACATATTAAATT
5956611 AATTACATA--AAACTT
1 AATTACATATTAAA-TT
* *
5956626 AACTGCATATTAAATT
1 AATTACATATTAAATT
5956642 A
1 A
5956643 TTATAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 3 0.11
15 9 0.33
16 12 0.44
17 3 0.11
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (16 bp):
AATTACATATTAAATT
Found at i:5957052 original size:17 final size:18
Alignment explanation
Indices: 5957009--5957064 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 18
5956999 ATGCCTCTAC
*
5957009 TACATATTAAATTTAAAA
1 TACATATTAAAATTAAAA
*
5957027 TA-ATA-TAAAATT-AAT
1 TACATATTAAAATTAAAA
5957042 TACATATTAAATTATTAAAA
1 TACATATTAAA--ATTAAAA
5957062 TAC
1 TAC
5957065 TCTTGCCGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 4 0.13
16 9 0.30
17 7 0.23
18 2 0.07
19 3 0.10
20 5 0.17
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
TACATATTAAAATTAAAA
Found at i:5957939 original size:21 final size:20
Alignment explanation
Indices: 5957913--5957972 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
5957903 TATGATTTTT
*
5957913 TATTAAAATAATTATAAATA
1 TATTAAAATAATTATAAAAA
5957933 TATTTAAAATAA-TATAAAAA
1 TA-TTAAAATAATTATAAAAA
*
5957953 TATT-AAATAATAATAAAAA
1 TATTAAAATAATTATAAAAA
5957972 T
1 T
5957973 TTTGATAGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
18 6 0.17
19 10 0.28
20 11 0.31
21 9 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TATTAAAATAATTATAAAAA
Found at i:5958020 original size:2 final size:2
Alignment explanation
Indices: 5958013--5958071 Score: 64
Period size: 2 Copynumber: 29.5 Consensus size: 2
5958003 ATTTGTAGTG
* * * * * *
5958013 TA TA TA TA TA TG TA TA TG TA TA TG TA TA TA TA TA CA TA TT TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5958055 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
5958072 GCAAATGACA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5958034 original size:18 final size:18
Alignment explanation
Indices: 5958013--5958072 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
5958003 ATTTGTAGTG
* * *
5958013 TATATATATATGTATATG
1 TATATGTATATATATATA
*
5958031 TATATGTATATATATACA
1 TATATGTATATATATATA
*
5958049 TATTTGTATATATATATA
1 TATATGTATATATATATA
5958067 TATATG
1 TATATG
5958073 CAAATGACAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (18 bp):
TATATGTATATATATATA
Found at i:5958951 original size:16 final size:17
Alignment explanation
Indices: 5958932--5958963 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5958922 TTTTTAATAA
5958932 TAAATAAAT-ATAAAAT
1 TAAATAAATAATAAAAT
5958948 TAAATAAATAATAAAA
1 TAAATAAATAATAAAA
5958964 AGTATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAATAAATAATAAAAT
Found at i:5959484 original size:20 final size:20
Alignment explanation
Indices: 5959459--5959526 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 20
5959449 TTATCTAATG
5959459 AAAATAAA-TAAAAAATTAAA
1 AAAATAAATTAAAAAA-TAAA
5959479 AAAATAAATTAAATGAAA-ATAA
1 AAAATAAATTAAA--AAATA-AA
*
5959501 AAAATAAAATTAGAAAATAAA
1 AAAAT-AAATTAAAAAATAAA
5959522 AAAAT
1 AAAAT
5959527 GTAGGAAGTG
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
20 8 0.20
21 15 0.37
22 8 0.20
23 10 0.24
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (20 bp):
AAAATAAATTAAAAAATAAA
Found at i:5959494 original size:35 final size:35
Alignment explanation
Indices: 5959455--5959521 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
5959445 AAATTTATCT
*
5959455 AATGAAAATAAATAA-AAAATTAAAAAAATAAATTA
1 AATGAAAATAAAAAATAAAATT-AAAAAATAAATTA
*
5959490 AATGAAAATAAAAAATAAAATTAGAAAATAAA
1 AATGAAAATAAAAAATAAAATTAAAAAATAAA
5959522 AAAATGTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 23 0.79
36 6 0.21
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (35 bp):
AATGAAAATAAAAAATAAAATTAAAAAATAAATTA
Found at i:5960566 original size:7 final size:7
Alignment explanation
Indices: 5960556--5960580 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5960546 AATAATTAAT
5960556 AAATTTA
1 AAATTTA
5960563 AAATTTA
1 AAATTTA
5960570 AAATTTA
1 AAATTTA
5960577 AAAT
1 AAAT
5960581 CTATATGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:5961013 original size:20 final size:20
Alignment explanation
Indices: 5960978--5961027 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5960968 CAATGTTAAC
*
5960978 AAATGCAATT-TTTTTAATT
1 AAATGTAATTATTTTTAATT
5960997 AAATGTAATTATTTTTAATT
1 AAATGTAATTATTTTTAATT
*
5961017 -CATGTAATTAT
1 AAATGTAATTAT
5961028 CGTTAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (20 bp):
AAATGTAATTATTTTTAATT
Found at i:5962039 original size:31 final size:31
Alignment explanation
Indices: 5961962--5962050 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 31
5961952 AAATAATCCT
* * *
5961962 TATACTCATACGAAATTTGAAA-TTAATTTA
1 TATACTCGTATGAAATTTGAAATTTAATTCA
* * * *
5961992 TATACTTGCATAAAATTTAAAATTTAATTCA
1 TATACTCGTATGAAATTTGAAATTTAATTCA
*
5962023 TGTACTCGTATGAAATTTGAAATTTAAT
1 TATACTCGTATGAAATTTGAAATTTAAT
5962051 CACTTTAATT
Statistics
Matches: 46, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 16 0.35
31 30 0.65
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (31 bp):
TATACTCGTATGAAATTTGAAATTTAATTCA
Found at i:5962979 original size:15 final size:14
Alignment explanation
Indices: 5962946--5962992 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
5962936 ATTTTGATAT
*
5962946 ATTAAT-TTAAATT
1 ATTAATATTAAATG
5962959 ATTAATATTATAATG
1 ATTAATATTA-AATG
5962974 ATTAATA-TAAATG
1 ATTAATATTAAATG
5962987 A-TAATA
1 ATTAATA
5962993 ATAATATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 5 0.16
13 11 0.35
14 5 0.16
15 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (14 bp):
ATTAATATTAAATG
Found at i:5963011 original size:23 final size:24
Alignment explanation
Indices: 5962968--5963039 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 24
5962958 TATTAATATT
* *
5962968 ATAATGATTAATATAAATGATAATA
1 ATAATAATTAAT-TAGATGATAATA
*
5962993 ATAAT-ATT-ATTAGTATGATACTA
1 ATAATAATTAATTAG-ATGATAATA
5963016 ATAATAATTAATTAGAT-ATAATA
1 ATAATAATTAATTAGATGATAATA
5963039 A
1 A
5963040 AACTAATACA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
22 2 0.05
23 21 0.51
24 8 0.20
25 10 0.24
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (24 bp):
ATAATAATTAATTAGATGATAATA
Found at i:5963102 original size:9 final size:9
Alignment explanation
Indices: 5963060--5963116 Score: 60
Period size: 9 Copynumber: 6.1 Consensus size: 9
5963050 TTAAAAGAAC
*
5963060 TAAAATTTT
1 TAAAAATTT
*
5963069 TAAAAGTTT
1 TAAAAATTT
5963078 TAAAAATTT
1 TAAAAATTT
5963087 TAAAAAATTT
1 T-AAAAATTT
*
5963097 TAAAAAATT
1 TAAAAATTT
*
5963106 CAAAATATTT
1 TAAAA-ATTT
5963116 T
1 T
5963117 TTATAATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
9 28 0.70
10 12 0.30
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (9 bp):
TAAAAATTT
Found at i:5963110 original size:19 final size:19
Alignment explanation
Indices: 5963070--5963116 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
5963060 TAAAATTTTT
* * *
5963070 AAAAGTTTTAAAAATTTTA
1 AAAAATTTTAAAAAATTCA
5963089 AAAAATTTTAAAAAATTCA
1 AAAAATTTTAAAAAATTCA
*
5963108 AAATATTTT
1 AAAAATTTT
5963117 TTATAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAAATTTTAAAAAATTCA
Found at i:5963191 original size:31 final size:31
Alignment explanation
Indices: 5963132--5963193 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
5963122 ATAAAGGGAT
** * *
5963132 TAAATTTCAAATTTTGTGTGAGTCTAAAGAC
1 TAAATTTCAAATTTTGTGCAAATATAAAGAC
5963163 TAAATTTCAAATTTTGTGCAAATATAAAGAC
1 TAAATTTCAAATTTTGTGCAAATATAAAGAC
5963194 CATTTACTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (31 bp):
TAAATTTCAAATTTTGTGCAAATATAAAGAC
Found at i:5970240 original size:15 final size:16
Alignment explanation
Indices: 5970222--5970258 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
5970212 TTCTCTATAT
5970222 TTATTTTTTAA-AAAA
1 TTATTTTTTAAGAAAA
5970237 TTA-TTTTTAAGTAAAA
1 TTATTTTTTAAG-AAAA
5970253 TTATTT
1 TTATTT
5970259 AATTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.37
15 3 0.16
16 7 0.37
17 2 0.11
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TTATTTTTTAAGAAAA
Found at i:5970245 original size:14 final size:15
Alignment explanation
Indices: 5970226--5970258 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5970216 CTATATTTAT
5970226 TTTTTAA-AAAATTA
1 TTTTTAAGAAAATTA
5970240 TTTTTAAGTAAAATTA
1 TTTTTAAG-AAAATTA
5970256 TTT
1 TTT
5970259 AATTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
16 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTTTAAGAAAATTA
Found at i:5970372 original size:34 final size:35
Alignment explanation
Indices: 5970301--5970383 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 35
5970291 TTATATTAGG
* * *
5970301 TAAATT-TTATAATTTATTGGTTATGTATATTCAA
1 TAAATTATTATAATTTATTGGATATGAAAATTCAA
**
5970335 TAAATTATTA-AATTTATTGGATATGAAAATTTGA
1 TAAATTATTATAATTTATTGGATATGAAAATTCAA
5970369 TAAATTA-TAT-ATTTA
1 TAAATTATTATAATTTA
5970384 AAATTTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
33 7 0.17
34 32 0.76
35 3 0.07
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.49
Consensus pattern (35 bp):
TAAATTATTATAATTTATTGGATATGAAAATTCAA
Found at i:5970673 original size:1 final size:1
Alignment explanation
Indices: 5970667--5970693 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
5970657 TGATTTTGAC
5970667 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
5970694 CAGGTGTGTT
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5973587 original size:9 final size:10
Alignment explanation
Indices: 5973561--5973586 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5973551 ATCAAGGTTG
5973561 AAAAAAATAT
1 AAAAAAATAT
5973571 AAAAAAATAT
1 AAAAAAATAT
5973581 AAAAAA
1 AAAAAA
5973587 TCGATTTGAA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATAT
Found at i:5974199 original size:24 final size:26
Alignment explanation
Indices: 5974163--5974212 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
5974153 TTATATCACC
* *
5974163 TTATTTGATAATAA-TTTAAA-AATT
1 TTATATGACAATAATTTTAAATAATT
5974187 TTATATGACAATAATTTTAAATAATT
1 TTATATGACAATAATTTTAAATAATT
5974213 GAGGTGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 12 0.55
25 6 0.27
26 4 0.18
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (26 bp):
TTATATGACAATAATTTTAAATAATT
Found at i:5976562 original size:23 final size:23
Alignment explanation
Indices: 5976519--5976562 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5976509 TTTACTGTAA
*
5976519 GCCCATAAAAAGCAATTCTCTAG
1 GCCCATAAAAAGCAATGCTCTAG
* *
5976542 GCCCATAAATAGTAATGCTCT
1 GCCCATAAAAAGCAATGCTCT
5976563 TAATTTATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (23 bp):
GCCCATAAAAAGCAATGCTCTAG
Found at i:5978370 original size:28 final size:28
Alignment explanation
Indices: 5978315--5978370 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
5978305 TTTTAAAAAA
*
5978315 TTAAA-TTACTTTTTAAAAAACTATTTT
1 TTAAATTTAATTTTTAAAAAACTATTTT
5978342 TTAAATTTAATTTTTATCAAAAA-TATTTT
1 TTAAATTTAATTTTTA--AAAAACTATTTT
5978371 AAAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 5 0.20
28 9 0.36
29 6 0.24
30 5 0.20
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (28 bp):
TTAAATTTAATTTTTAAAAAACTATTTT
Found at i:5978857 original size:28 final size:27
Alignment explanation
Indices: 5978826--5978896 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
5978816 AGAAAAGAGG
*
5978826 GAAAAGGGTAAAAGAA-AAAATAAAGAAA
1 GAAAAGGG-AAAAGAACAAAAAAAAG-AA
5978854 GAAAATGGGAGAAA-AACAAAAAAAAGAA
1 GAAAA-GGGA-AAAGAACAAAAAAAAGAA
*
5978882 GAAAAAGGAAAAGAA
1 GAAAAGGGAAAAGAA
5978897 GACGAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 3 0.08
27 5 0.14
28 15 0.41
29 14 0.38
ACGTcount: A:0.72, C:0.01, G:0.23, T:0.04
Consensus pattern (27 bp):
GAAAAGGGAAAAGAACAAAAAAAAGAA
Found at i:5979777 original size:7 final size:7
Alignment explanation
Indices: 5979765--5979898 Score: 56
Period size: 7 Copynumber: 20.0 Consensus size: 7
5979755 TTAATACAAC
5979765 TATTAAA
1 TATTAAA
5979772 TATTAAA
1 TATTAAA
5979779 TATTAAA
1 TATTAAA
*
5979786 TATT-AT
1 TATTAAA
*
5979792 TA-AAAA
1 TATTAAA
5979798 TATTAAA
1 TATTAAA
*
5979805 TTATT-TA
1 -TATTAAA
5979812 T-TTAAA
1 TATTAAA
* *
5979818 AATTAAT
1 TATTAAA
* *
5979825 TAATAAT
1 TATTAAA
5979832 TA-TAAA
1 TATTAAA
5979838 TAATT-AA
1 T-ATTAAA
*
5979845 TATTTCAA
1 TA-TTAAA
*
5979853 TAAT-AA
1 TATTAAA
5979859 TAATT-AA
1 T-ATTAAA
5979866 TATTAAAA
1 TATT-AAA
5979874 TATT--A
1 TATTAAA
5979879 TATT-AA
1 TATTAAA
5979885 TATTAAA
1 TATTAAA
*
5979892 CATTAAA
1 TATTAAA
5979899 ATAAAACTAT
Statistics
Matches: 99, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
5 7 0.07
6 24 0.24
7 53 0.54
8 15 0.15
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (7 bp):
TATTAAA
Found at i:5979843 original size:17 final size:17
Alignment explanation
Indices: 5979821--5979864 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
5979811 ATTTAAAAAT
5979821 TAATTAATAATTATAAA
1 TAATTAATAATTATAAA
*
5979838 TAATTAAT-ATT-TCAA
1 TAATTAATAATTATAAA
5979853 TAA-TAATAATTA
1 TAATTAATAATTA
5979865 ATATTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 4 0.17
15 9 0.38
16 3 0.12
17 8 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATTAATAATTATAAA
Found at i:5979875 original size:21 final size:20
Alignment explanation
Indices: 5979836--5979891 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
5979826 AATAATTATA
**
5979836 AATAATTAATATTTCAATAAT
1 AATAATTAATATTAAAAT-AT
5979857 AATAATTAATATTAAAATAT
1 AATAATTAATATTAAAATAT
*
5979877 TAT-ATTAATATTAAA
1 AATAATTAATATTAAA
5979892 CATTAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 12 0.38
20 4 0.12
21 16 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
AATAATTAATATTAAAATAT
Done.