Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 12 of 325
Found at i:2686510 original size:51 final size:52
Alignment explanation
Indices: 2686433--2686546 Score: 124
Period size: 51 Copynumber: 2.2 Consensus size: 52
2686423 ATTGGTATAA
* * * *
2686433 TAACAAATTTAATCATAAAAATTTTACACATTGTGTCAAATTGGTATTG-TT
1 TAACAAATTTAACCACAAAAATTTTACACATTGTATCAAATTGATATTGATT
* * * * *
2686484 TAACAAATTTAACCCACAAACA-TTTACATATTTTATCAATTTGATCTTGATT
1 TAACAAATTTAA-CCACAAAAATTTTACACATTGTATCAAATTGATATTGATT
2686536 TAACAAATTTA
1 TAACAAATTTA
2686547 GCTCGTAACA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
51 33 0.63
52 19 0.37
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (52 bp):
TAACAAATTTAACCACAAAAATTTTACACATTGTATCAAATTGATATTGATT
Found at i:2689481 original size:26 final size:28
Alignment explanation
Indices: 2689421--2689481 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 28
2689411 TTTTAATTCA
*
2689421 TATTATTAAAAAATATATTTAATAATAAT
1 TATTATT-AAAAATATAGTTAATAATAAT
* *
2689450 TA-TATT-AAAATATAGTTAA-ATTATT
1 TATTATTAAAAATATAGTTAATAATAAT
2689475 TATTATT
1 TATTATT
2689482 TTTATTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 6 0.21
26 16 0.57
28 4 0.14
29 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
TATTATTAAAAATATAGTTAATAATAAT
Found at i:2692326 original size:22 final size:21
Alignment explanation
Indices: 2692301--2692411 Score: 64
Period size: 19 Copynumber: 5.7 Consensus size: 21
2692291 TACAAATTAA
2692301 ATCTCCAAGATTACAGGATCAT
1 ATCTCCAAGATTACA-GATCAT
* * *
2692323 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
2692344 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
2692363 ATCT--AAGATT---GTATCAT
1 ATCTCCAAGATTACAG-ATCAT
* *
2692380 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
2692399 ATCT--AAGATTACA
1 ATCTCCAAGATTACA
2692412 TATCCTTAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
17 15 0.19
19 42 0.53
21 9 0.11
22 13 0.16
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:2692353 original size:19 final size:19
Alignment explanation
Indices: 2692318--2692415 Score: 155
Period size: 19 Copynumber: 5.2 Consensus size: 19
2692308 AGATTACAGG
2692318 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
2692339 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
2692358 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
2692375 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
*
2692394 ATCATATCTAAGATTACAT
1 ATCATATCTAAGATTGCAT
2692413 ATC
1 ATC
2692416 CTTAAAGATT
Statistics
Matches: 74, Mismatches: 1, Indels: 6
0.91 0.01 0.07
Matches are distributed among these distances:
17 17 0.23
19 48 0.65
20 1 0.01
21 8 0.11
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:2692360 original size:14 final size:15
Alignment explanation
Indices: 2692340--2692396 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
2692330 AGATTGCATA
2692340 TCATATCTAAGATTG
1 TCATATCTAAGATTG
2692355 CATATCATATCTAAGATTG
1 ----TCATATCTAAGATTG
2692374 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
2692391 -CATATC
1 TCATATC
2692397 ATATCTAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.16
17 17 0.45
19 15 0.39
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:2692382 original size:36 final size:37
Alignment explanation
Indices: 2692318--2692408 Score: 148
Period size: 36 Copynumber: 2.4 Consensus size: 37
2692308 AGATTACAGG
2692318 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT
1 ATCATATC-T-AAGATTG-ATATCATATCTAAGATTGCAT
2692358 ATCATATCTAAGATTG-TATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
2692394 ATCATATCTAAGATT
1 ATCATATCTAAGATT
2692409 ACATATCCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
36 35 0.69
38 7 0.14
39 1 0.02
40 8 0.16
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (37 bp):
ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
Found at i:2692837 original size:53 final size:53
Alignment explanation
Indices: 2692755--2692857 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
2692745 TCATGGAAAT
* * * *
2692755 ATGTGATTATGTACTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATG
1 ATGTGATTATGTACCTCCGTATAAGACCATAGCTAGGATATGACATCGGTATG
* * * *
2692808 ATGTGATTATGTGCCTCTGTATAATACCATATCTAGGATATGACATCGGT
1 ATGTGATTATGTACCTCCGTATAAGACCATAGCTAGGATATGACATCGGT
2692858 GCGATATGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (53 bp):
ATGTGATTATGTACCTCCGTATAAGACCATAGCTAGGATATGACATCGGTATG
Found at i:2697060 original size:28 final size:28
Alignment explanation
Indices: 2697020--2697079 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
2697010 GTCATTATCA
2697020 ACCCCATAAGTTATAAAACTCTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
* * *
2697048 ACCCCATAAGTTATGAGACTTTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
2697076 ACCC
1 ACCC
2697080 TATTAATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.32
Consensus pattern (28 bp):
ACCCCATAAGTTATAAAACTCTTCCTAT
Found at i:2702966 original size:28 final size:28
Alignment explanation
Indices: 2702926--2702985 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
2702916 GTCATTATCA
2702926 ACCCCATAAGTTATAAAACTCTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
* *
2702954 ACCCCATAAGTTATAAGACTTTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
2702982 ACCC
1 ACCC
2702986 TATTAATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (28 bp):
ACCCCATAAGTTATAAAACTCTTCCTAT
Found at i:2705376 original size:14 final size:15
Alignment explanation
Indices: 2705347--2705376 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2705337 TTTTTTGGTT
2705347 TCAGTTGTTCTTTTA
1 TCAGTTGTTCTTTTA
2705362 TCAGTTGTT-TTTTA
1 TCAGTTGTTCTTTTA
2705376 T
1 T
2705377 TATTTGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.63
Consensus pattern (15 bp):
TCAGTTGTTCTTTTA
Found at i:2713028 original size:48 final size:48
Alignment explanation
Indices: 2712906--2713239 Score: 362
Period size: 48 Copynumber: 6.9 Consensus size: 48
2712896 AAAAGGCTAA
* * ** * *
2712906 AATGCTGATGCCATGTCTCGGACATGGTCTTACTCTGGCTCTCATACATC
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATA-A-C
* * *
2712956 AGTGTCGATGCCATGTCCCAAACATGATCTTACACTGGCTCACATAAC
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAAC
* * **
2713004 AATGCCAATGCCATGTCCCAAACATAGTCTTACACTGGCTCACATATT
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAAC
* * * **
2713052 GAGGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTTATAAC
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAAC
* * *** **
2713100 AATGCCGATGCCATGTTCCAAGCATGGTCTTACACTGGCTTGTATATT
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAAC
* * * * *
2713148 GAGGCCGATGCCATGTCCCAAACATGTTCTTACACTAGCTCTCATAAC
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAAC
* *
2713196 AATGCTGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACA
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACA
2713240 CATAACCCTA
Statistics
Matches: 232, Mismatches: 52, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
48 194 0.84
49 1 0.00
50 37 0.16
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (48 bp):
AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAAC
Found at i:2713086 original size:96 final size:96
Alignment explanation
Indices: 2712927--2713239 Score: 446
Period size: 96 Copynumber: 3.2 Consensus size: 96
2712917 CATGTCTCGG
* * * * *
2712927 ACATGGTCTTACTCTGGCTCTCATACATCAGTGTCGATGCCATGTCCCAAACATGATCTTACACT
1 ACATGGTCTTACACTGGCTCACATA-TTGAG-GCCGATGCCATGTCCCAAACATGATCTTACACT
* * * *
2712992 GGCTCACATAACAATGCCAATGCCATGTCCCAA
64 AGCTCTCATAACAATGCCGATGCCATGTTCCAA
* *
2713025 ACATAGTCTTACACTGGCTCACATATTGAGGCCGATGCCATGTCCCAAACATGGTCTTACACTAG
1 ACATGGTCTTACACTGGCTCACATATTGAGGCCGATGCCATGTCCCAAACATGATCTTACACTAG
*
2713090 CTCTTATAACAATGCCGATGCCATGTTCCAA
66 CTCTCATAACAATGCCGATGCCATGTTCCAA
* *** *
2713121 GCATGGTCTTACACTGGCTTGTATATTGAGGCCGATGCCATGTCCCAAACATGTTCTTACACTAG
1 ACATGGTCTTACACTGGCTCACATATTGAGGCCGATGCCATGTCCCAAACATGATCTTACACTAG
*
2713186 CTCTCATAACAATGCTGATGCCATGTTCCAA
66 CTCTCATAACAATGCCGATGCCATGTTCCAA
2713217 ACATGGTCTTACACTGGCTCACA
1 ACATGGTCTTACACTGGCTCACA
2713240 CATAACCCTA
Statistics
Matches: 191, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
96 166 0.87
97 3 0.02
98 22 0.12
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (96 bp):
ACATGGTCTTACACTGGCTCACATATTGAGGCCGATGCCATGTCCCAAACATGATCTTACACTAG
CTCTCATAACAATGCCGATGCCATGTTCCAA
Found at i:2717656 original size:26 final size:26
Alignment explanation
Indices: 2717626--2717733 Score: 207
Period size: 26 Copynumber: 4.2 Consensus size: 26
2717616 TGAAATTCCC
2717626 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
2717652 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2717678 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2717704 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2717730 ATCA
1 ATCA
2717734 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2718784 original size:19 final size:19
Alignment explanation
Indices: 2718757--2718793 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2718747 TGTAATATTG
*
2718757 AATTTAATTAAATGCAATT
1 AATTAAATTAAATGCAATT
*
2718776 AATTAAATTAATTGCAAT
1 AATTAAATTAAATGCAAT
2718794 GATTTTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
AATTAAATTAAATGCAATT
Found at i:2721356 original size:19 final size:19
Alignment explanation
Indices: 2721332--2721368 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2721322 AAGAAAAATC
*
2721332 ATTGCAATTAATTTAATTA
1 ATTGCAATTAATTAAATTA
*
2721351 ATTGCATTTAATTAAATT
1 ATTGCAATTAATTAAATT
2721369 CAATATTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (19 bp):
ATTGCAATTAATTAAATTA
Found at i:2722315 original size:16 final size:16
Alignment explanation
Indices: 2722291--2722342 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
2722281 TGGTTCACTA
* *
2722291 TAATGGAATAGGGTTG
1 TAATGGAATAGAGCTG
*
2722307 TAATTGAATAGAGCTG
1 TAATGGAATAGAGCTG
2722323 TAATGGAATAGAGCTG
1 TAATGGAATAGAGCTG
2722339 TAAT
1 TAAT
2722343 CAATAATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.37, C:0.04, G:0.29, T:0.31
Consensus pattern (16 bp):
TAATGGAATAGAGCTG
Found at i:2722525 original size:28 final size:29
Alignment explanation
Indices: 2722494--2722549 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
2722484 GTAGATGATT
*
2722494 ATTATTATT-GTTATTAATTTA-TAATAAG
1 ATTATTATTAGATA-TAATTTACTAATAAG
2722522 ATTATTATTAGATATAATTTACTAATAA
1 ATTATTATTAGATATAATTTACTAATAA
2722550 ATAATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (29 bp):
ATTATTATTAGATATAATTTACTAATAAG
Found at i:2722800 original size:15 final size:16
Alignment explanation
Indices: 2722776--2722814 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
2722766 CAAATAATTT
2722776 AATT-ATCTT-CTATA
1 AATTAATCTTCCTATA
2722790 AATTAATCTTCCTATA
1 AATTAATCTTCCTATA
2722806 AATTAATCT
1 AATTAATCT
2722815 CAATTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 4 0.17
15 5 0.22
16 14 0.61
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTAATCTTCCTATA
Found at i:2722841 original size:12 final size:12
Alignment explanation
Indices: 2722824--2722854 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2722814 TCAATTTTAT
2722824 AGTTTCAACAAA
1 AGTTTCAACAAA
2722836 AGTTTCAACAAA
1 AGTTTCAACAAA
2722848 AGTTTCA
1 AGTTTCA
2722855 TTTGTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (12 bp):
AGTTTCAACAAA
Found at i:2725027 original size:2 final size:2
Alignment explanation
Indices: 2725022--2725070 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2725012 AAAATGATTA
2725022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2725064 AT AT AT A
1 AT AT AT A
2725071 AACCATATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2725318 original size:21 final size:21
Alignment explanation
Indices: 2725247--2725319 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
2725237 TTAGTGTATA
* * *
2725247 ATATAAT-TTATAACCAAAAT
1 ATATAATAATATAAACAATAT
* *
2725267 ATATAATGATATAAACCATAT
1 ATATAATAATATAAACAATAT
2725288 A-ATAAGTAATATAAA-AATAT
1 ATATAA-TAATATAAACAATAT
2725308 ATATATATAATA
1 ATATA-ATAATA
2725320 AAATGTGATA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
20 16 0.37
21 26 0.60
22 1 0.02
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (21 bp):
ATATAATAATATAAACAATAT
Found at i:2725335 original size:17 final size:17
Alignment explanation
Indices: 2725310--2725351 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2725300 AAAAATATAT
2725310 ATATATAATAAAATGTG
1 ATATATAATAAAATGTG
*
2725327 ATATGTAATAAAATGT-
1 ATATATAATAAAATGTG
*
2725343 AAATATAAT
1 ATATATAAT
2725352 GAAGGATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (17 bp):
ATATATAATAAAATGTG
Found at i:2725496 original size:19 final size:19
Alignment explanation
Indices: 2725433--2725503 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
2725423 TAAAAATAAT
*
2725433 ATATATAAGATATATAAATA
1 ATATATAATATA-ATAAATA
* *
2725453 A-ATATAAT-TTATAAGTA
1 ATATATAATATAATAAATA
* *
2725470 AAAAATAATATAATAAATA
1 ATATATAATATAATAAATA
*
2725489 ATATATAAAATAATA
1 ATATATAATATAATA
2725504 TATACTATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
17 7 0.17
18 7 0.17
19 25 0.62
20 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATATAATATAATAAATA
Found at i:2725506 original size:12 final size:12
Alignment explanation
Indices: 2725425--2725507 Score: 61
Period size: 12 Copynumber: 7.1 Consensus size: 12
2725415 TAATTTTTTA
2725425 AAAATAATATAT
1 AAAATAATATAT
* *
2725437 ATAA-GATATAT
1 AAAATAATATAT
2725448 -AAATAA-ATAT
1 AAAATAATATAT
*
2725458 AATTTATAAGTA-A-
1 AA--AATAA-TATAT
2725471 AAAATAATATA-
1 AAAATAATATAT
2725482 ATAAATAATATAT
1 A-AAATAATATAT
2725495 AAAATAATATAT
1 AAAATAATATAT
2725507 A
1 A
2725508 CTATTTTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
10 8 0.14
11 14 0.25
12 25 0.45
13 7 0.12
14 1 0.02
15 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
AAAATAATATAT
Found at i:2725546 original size:17 final size:17
Alignment explanation
Indices: 2725526--2725558 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2725516 TTATAATTAA
2725526 TATTT-ATAGATATAAAG
1 TATTTAATAGAT-TAAAG
2725543 TATTTAATAGATTAAA
1 TATTTAATAGATTAAA
2725559 AAAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATTTAATAGATTAAAG
Found at i:2727309 original size:20 final size:20
Alignment explanation
Indices: 2727262--2727309 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2727252 GCCATATCAA
2727262 TATTCTTATCCTGAATTTCAG
1 TATT-TTATCCTGAATTTCAG
* *
2727283 GAGTTTATCCTGAATTTCAG
1 TATTTTATCCTGAATTTCAG
2727303 TATTTTA
1 TATTTTA
2727310 ATTTGGATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (20 bp):
TATTTTATCCTGAATTTCAG
Found at i:2728131 original size:25 final size:25
Alignment explanation
Indices: 2728103--2728154 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
2728093 AAATGGTTCA
2728103 GACATATTTGTGTCCCAAGTAATAT
1 GACATATTTGTGTCCCAAGTAATAT
*
2728128 GACATGTTTGTGTCCCAAGTAATAT
1 GACATATTTGTGTCCCAAGTAATAT
2728153 GA
1 GA
2728155 TTTATCATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (25 bp):
GACATATTTGTGTCCCAAGTAATAT
Found at i:2735472 original size:46 final size:48
Alignment explanation
Indices: 2735372--2735473 Score: 109
Period size: 46 Copynumber: 2.1 Consensus size: 48
2735362 ATAGTAAAAC
* * * *
2735372 TATGGTCTTACACATAGTCATATATCACACACTGAAGCAATAGCCTAGC
1 TATGGTCTTACACAGAGTCACATAT-ACACACTGAAGCAATAGCCCAGA
* * * *
2735421 CATGGTCTTACACAGA-TCACATAT-CACACTGATGCCATATCCCAGA
1 TATGGTCTTACACAGAGTCACATATACACACTGAAGCAATAGCCCAGA
2735467 TATGGTC
1 TATGGTC
2735474 CATATTGAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
46 23 0.52
48 7 0.16
49 14 0.32
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (48 bp):
TATGGTCTTACACAGAGTCACATATACACACTGAAGCAATAGCCCAGA
Found at i:2736493 original size:22 final size:21
Alignment explanation
Indices: 2736464--2736530 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
2736454 TGCACTAATA
2736464 AACAGAGAGCACTGAAGTGCT
1 AACAGAGAGCACTGAAGTGCT
*
2736485 ACACAGAGAGCAC-AAATGTGCT
1 A-ACAGAGAGCACTGAA-GTGCT
* *
2736507 AATCAGAGAGCATTGACGTGCT
1 AA-CAGAGAGCACTGAAGTGCT
2736529 AA
1 AA
2736531 ATATCAGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.11
22 33 0.87
23 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.16
Consensus pattern (21 bp):
AACAGAGAGCACTGAAGTGCT
Found at i:2736540 original size:25 final size:25
Alignment explanation
Indices: 2736506--2736668 Score: 256
Period size: 25 Copynumber: 6.5 Consensus size: 25
2736496 ACAAATGTGC
* *
2736506 TAATCAGAGAGCATTGACGTGCTAA
1 TAATCAGAGAGCACTGGCGTGCTAA
2736531 -ATATCAGAGAGCACTGGCGTGCTAA
1 TA-ATCAGAGAGCACTGGCGTGCTAA
2736556 TAATCAGAGAGCACTGGCGTGCTAA
1 TAATCAGAGAGCACTGGCGTGCTAA
* *
2736581 TATTCAGATAGCACTGGCGTGCTAA
1 TAATCAGAGAGCACTGGCGTGCTAA
*
2736606 TATTCAGAGAGCACTGGCGTGCTAA
1 TAATCAGAGAGCACTGGCGTGCTAA
*
2736631 TAATCAGATAGCACTGGCGTGCTAA
1 TAATCAGAGAGCACTGGCGTGCTAA
2736656 TAATCAGAGAGCA
1 TAATCAGAGAGCA
2736669 TGCTGAGGTC
Statistics
Matches: 128, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
24 1 0.01
25 126 0.98
26 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (25 bp):
TAATCAGAGAGCACTGGCGTGCTAA
Found at i:2743907 original size:53 final size:52
Alignment explanation
Indices: 2743828--2743929 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 52
2743818 TCATGGAAAT
* * *
2743828 ATGTGATTACGTGCTTCCTATAAGACCATAGCTGGGCTATGACATCGGTATG
1 ATGTGATTACATGCCTCCTATAAGACCATAGCTGGGATATGACATCGGTATG
* * *
2743880 ATGTGATTATATGCCTCCGTATAAGACCATATCTGGGATATGGCATCGGT
1 ATGTGATTACATGCCTCC-TATAAGACCATAGCTGGGATATGACATCGGT
2743930 GCAATATGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 15 0.35
53 28 0.65
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (52 bp):
ATGTGATTACATGCCTCCTATAAGACCATAGCTGGGATATGACATCGGTATG
Found at i:2747551 original size:128 final size:127
Alignment explanation
Indices: 2747324--2747713 Score: 385
Period size: 128 Copynumber: 3.1 Consensus size: 127
2747314 TACATATCAG
* * * * * *
2747324 TCACACCCAAACTTTGAACT-TAAAAAACTCTAACTCGAAAAC-CTCAAAAAACATGAAACAACT
1 TCACACTCAAACTTTGAACTATAAAAAACTCAAACCCAAAAACACTC--TAAACTTGAAACAACT
* * * *
2747387 AAAACCCAAAATTACATGATCTAAACCTGAATCAAATTGTTATATTTATATCTACATT-CGACAC
64 AAAACCCAAAATTACATGATCTAAACCCGAATCAAATTGCTATCTTTATA-CTACATTCCAACAC
* * *
2747451 TCACACTCAAACTTTGAACTATAAAAAACTGAAACCCAAAAACACTCTCAAACTTGAAATAATTA
1 TCACACTCAAACTTTGAACTATAAAAAACTCAAACCCAAAAACACTCT-AAACTTGAAACAACTA
* *
2747516 AAACCCAAAATTA-ATTGATCTAAACCCGAATCAAATT-CTACCTCTATACT---TTCCCAACAC
65 AAACCCAAAATTACA-TGATCTAAACCCGAATCAAATTGCTATCTTTATACTACATT-CCAACAC
* * * * * * *
2747576 TAACACTCAAACTCTCAACTATAAGAACATTCAAA-CCAGAAAACAC-CTAAATTTAAAACAACT
1 TCACACTCAAACTTTGAACTATAA-AAAACTCAAACCCA-AAAACACTCTAAACTTGAAACAACT
*
2747639 AAATCCCAAAATTACATGATCTAAACCCGAATCAAATTGCTATCTTTATACCTACA---CAACAC
64 AAAACCCAAAATTACATGATCTAAACCCGAATCAAATTGCTATCTTTATA-CTACATTCCAACAC
2747701 TCACA-TCCAAACT
1 TCACACT-CAAACT
2747714 CGAATAACTT
Statistics
Matches: 219, Mismatches: 29, Indels: 32
0.78 0.10 0.11
Matches are distributed among these distances:
123 2 0.01
124 47 0.21
125 57 0.26
126 18 0.08
127 27 0.12
128 65 0.30
129 3 0.01
ACGTcount: A:0.45, C:0.26, G:0.04, T:0.24
Consensus pattern (127 bp):
TCACACTCAAACTTTGAACTATAAAAAACTCAAACCCAAAAACACTCTAAACTTGAAACAACTAA
AACCCAAAATTACATGATCTAAACCCGAATCAAATTGCTATCTTTATACTACATTCCAACAC
Found at i:2747668 original size:124 final size:126
Alignment explanation
Indices: 2747379--2747680 Score: 339
Period size: 124 Copynumber: 2.4 Consensus size: 126
2747369 AAAAAACATG
* * * *
2747379 AAACAACTAAAACCCAAAATTACATGATCTAAACCTGAATCAAATTGTTATATTTATATCTACAT
1 AAACAACTAAAACCCAAAATTACATGATCTAAACCCGAATCAAATTGCTACATCTATATCT--AT
* * * * * *
2747444 TCGACACTCACACTCAAACTTTGAACTATAAAAAACTGAAACCCAAAAACACTCTCAAACTTG
64 TCAACACTAACACTCAAACTCTCAACTATAAAAAACTCAAACCCAAAAACACTCTCAAACTTA
* * *
2747507 AAATAATTAAAACCCAAAATTA-ATTGATCTAAACCCGAATCAAATT-CTACCTCTATA-CT-TT
1 AAACAACTAAAACCCAAAATTACA-TGATCTAAACCCGAATCAAATTGCTACATCTATATCTATT
* * *
2747568 CCCAACACTAACACTCAAACTCTCAACTATAAGAACATTCAAA-CCAGAAAACAC-CT-AAATTT
65 --CAACACTAACACTCAAACTCTCAACTATAA-AAAACTCAAACCCA-AAAACACTCTCAAACTT
2747630 A
126 A
*
2747631 AAACAACTAAATCCCAAAATTACATGATCTAAACCCGAATCAAATTGCTA
1 AAACAACTAAAACCCAAAATTACATGATCTAAACCCGAATCAAATTGCTA
2747681 TCTTTATACC
Statistics
Matches: 148, Mismatches: 19, Indels: 17
0.80 0.10 0.09
Matches are distributed among these distances:
123 2 0.01
124 46 0.31
125 35 0.24
126 16 0.11
127 8 0.05
128 41 0.28
ACGTcount: A:0.46, C:0.25, G:0.05, T:0.25
Consensus pattern (126 bp):
AAACAACTAAAACCCAAAATTACATGATCTAAACCCGAATCAAATTGCTACATCTATATCTATTC
AACACTAACACTCAAACTCTCAACTATAAAAAACTCAAACCCAAAAACACTCTCAAACTTA
Found at i:2747699 original size:125 final size:126
Alignment explanation
Indices: 2747379--2747714 Score: 387
Period size: 125 Copynumber: 2.7 Consensus size: 126
2747369 AAAAAACATG
* * * *
2747379 AAACAACTAAAACCCAAAATTACATGATCTAAACCTGAATCAAATTGTTATATTTATATCTACAT
1 AAACAACTAAAACCCAAAATTACATGATCTAAACCCGAATCAAATTGCTATCTTTATACCTACA-
* * * * *
2747444 TCGACACTCACACTCAAACTTTGAACTATAAAAAACTGAAACCCAAAAACACTCTCAAACTTG
65 -CAACACTCACACTCAAACTCTCAACTATAAAAAACTCAAACCCAAAAACACTCTCAAACTTA
* * * * * * *
2747507 AAATAATTAAAACCCAAAATTA-ATTGATCTAAACCCGAATCAAATT-CTACCTCTATACTTTCC
1 AAACAACTAAAACCCAAAATTACA-TGATCTAAACCCGAATCAAATTGCTATCTTTATACCTACA
* * * *
2747570 CAACACTAACACTCAAACTCTCAACTATAAGAACATTCAAA-CCAGAAAACAC-CT-AAATTTA
65 CAACACTCACACTCAAACTCTCAACTATAA-AAAACTCAAACCCA-AAAACACTCTCAAACTTA
*
2747631 AAACAACTAAATCCCAAAATTACATGATCTAAACCCGAATCAAATTGCTATCTTTATACCTACAC
1 AAACAACTAAAACCCAAAATTACATGATCTAAACCCGAATCAAATTGCTATCTTTATACCTACAC
2747696 AACACTCACA-TCCAAACTC
66 AACACTCACACT-CAAACTC
2747715 GAATAACTTA
Statistics
Matches: 173, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
124 47 0.27
125 61 0.35
126 14 0.08
127 10 0.06
128 41 0.24
ACGTcount: A:0.45, C:0.26, G:0.04, T:0.25
Consensus pattern (126 bp):
AAACAACTAAAACCCAAAATTACATGATCTAAACCCGAATCAAATTGCTATCTTTATACCTACAC
AACACTCACACTCAAACTCTCAACTATAAAAAACTCAAACCCAAAAACACTCTCAAACTTA
Found at i:2750690 original size:21 final size:22
Alignment explanation
Indices: 2750661--2750702 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2750651 CTTTTTATAT
2750661 ATTTCTTATTAAATTTAAATAA
1 ATTTCTTATTAAATTTAAATAA
**
2750683 ATTT-TTATTTTATTTAAATA
1 ATTTCTTATTAAATTTAAATA
2750703 TAAATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTCTTATTAAATTTAAATAA
Found at i:2756835 original size:10 final size:9
Alignment explanation
Indices: 2756804--2756924 Score: 81
Period size: 9 Copynumber: 13.4 Consensus size: 9
2756794 AATTTATATC
2756804 AAATTATAA
1 AAATTATAA
* *
2756813 GAATTAGAA
1 AAATTATAA
2756822 AAATTATCAA
1 AAATTAT-AA
2756832 AAA-TATAA
1 AAATTATAA
*
2756840 AAATTATTA
1 AAATTATAA
*
2756849 ATATTA-AA
1 AAATTATAA
2756857 AAA-TATTAA
1 AAATTA-TAA
*
2756866 AAA--ATGA
1 AAATTATAA
2756873 AAATTGATATA
1 AAATT-ATA-A
*
2756884 AATTTATAA
1 AAATTATAA
*
2756893 ATATTATAA
1 AAATTATAA
2756902 AATATTATAA
1 AA-ATTATAA
**
2756912 ACGTTATAA
1 AAATTATAA
2756921 AAAT
1 AAAT
2756925 ATTAAGAATA
Statistics
Matches: 85, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
7 7 0.08
8 9 0.11
9 46 0.54
10 18 0.21
11 5 0.06
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (9 bp):
AAATTATAA
Found at i:2756868 original size:34 final size:35
Alignment explanation
Indices: 2756814--2756906 Score: 93
Period size: 34 Copynumber: 2.6 Consensus size: 35
2756804 AAATTATAAG
*
2756814 AATTAGAAAAATTATCAAAAATATAAAAATT-AT-TA
1 AATTA-AAAAA-TATTAAAAATATAAAAATTGATATA
*
2756849 ATATTAAAAAATATTAAAAA-ATGAAAATTGATATA
1 A-ATTAAAAAATATTAAAAATATAAAAATTGATATA
* *
2756884 AATTTATAAATATTATAAAATAT
1 AATTAAAAAATATTA-AAAATAT
2756907 TATAAACGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
33 8 0.16
34 22 0.45
35 13 0.27
36 6 0.12
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (35 bp):
AATTAAAAAATATTAAAAATATAAAAATTGATATA
Found at i:2756891 original size:8 final size:9
Alignment explanation
Indices: 2756880--2756912 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
2756870 TGAAAATTGA
2756880 TATAAAT-T
1 TATAAATAT
2756888 TATAAATAT
1 TATAAATAT
2756897 TATAAAATAT
1 TAT-AAATAT
2756907 TATAAA
1 TATAAA
2756913 CGTTATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.30
9 7 0.30
10 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TATAAATAT
Found at i:2756911 original size:19 final size:20
Alignment explanation
Indices: 2756883--2756928 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2756873 AAATTGATAT
*
2756883 AAAT-TTATAAATATTAT-A
1 AAATATTATAAACATTATAA
*
2756901 AAATATTATAAACGTTATAA
1 AAATATTATAAACATTATAA
2756921 AAATATTA
1 AAATATTA
2756929 AGAATATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 11 0.46
20 9 0.38
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
AAATATTATAAACATTATAA
Found at i:2757062 original size:21 final size:21
Alignment explanation
Indices: 2757042--2757082 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2757032 TGATATAAAT
2757042 TTAT-AGAAATTATTAAAAAA
1 TTATAAGAAATTATTAAAAAA
2757062 TTATAAGAAATTATTAAAAAA
1 TTATAAGAAATTATTAAAAAA
2757083 ATCGGCAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (21 bp):
TTATAAGAAATTATTAAAAAA
Found at i:2757064 original size:11 final size:11
Alignment explanation
Indices: 2757048--2757082 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
2757038 AAATTTATAG
2757048 AAATTATTAAA
1 AAATTATTAAA
*
2757059 AAATTA-TAAG
1 AAATTATTAAA
2757069 AAATTATTAAA
1 AAATTATTAAA
2757080 AAA
1 AAA
2757083 ATCGGCAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (11 bp):
AAATTATTAAA
Found at i:2759315 original size:10 final size:11
Alignment explanation
Indices: 2759292--2759316 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2759282 AAATTTATTG
2759292 AAAAATACTAA
1 AAAAATACTAA
2759303 AAAAATACTAA
1 AAAAATACTAA
2759314 AAA
1 AAA
2759317 CAAAATTAAA
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATACTAA
Found at i:2762524 original size:17 final size:17
Alignment explanation
Indices: 2762453--2762525 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 17
2762443 TTTTCCCATA
2762453 AAAATTATTAAAA--AT
1 AAAATTATTAAAATTAT
2762468 AAAATTATTAAATATTA-
1 AAAATTATTAAA-ATTAT
*
2762485 AAAAATATTAACAATGATAT
1 AAAATTATTAA-AAT--TAT
*
2762505 AAACTTATTAAAATTAT
1 AAAATTATTAAAATTAT
2762522 AAAA
1 AAAA
2762526 ACATTATAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
15 12 0.26
16 1 0.02
17 18 0.38
18 2 0.04
19 5 0.11
20 9 0.19
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (17 bp):
AAAATTATTAAAATTAT
Found at i:2762526 original size:9 final size:9
Alignment explanation
Indices: 2762450--2762583 Score: 57
Period size: 9 Copynumber: 14.8 Consensus size: 9
2762440 ATTTTTTCCC
2762450 ATAAAAATT
1 ATAAAAATT
*
2762459 ATTAAAA--
1 ATAAAAATT
2762466 AT-AAAATT
1 ATAAAAATT
*
2762474 ATTAAATATT
1 A-TAAAAATT
2762484 A-AAAAA-T
1 ATAAAAATT
* *
2762491 ATTAACAATG
1 A-TAAAAATT
*
2762501 ATATAAACTT
1 ATA-AAAATT
*
2762511 ATTAAAATT
1 ATAAAAATT
2762520 ATAAAAACATT
1 AT-AAAA-ATT
*
2762531 ATAACAAAATC
1 AT-A-AAAATT
* *
2762542 ATAAATACT
1 ATAAAAATT
2762551 ATAAAAA-T
1 ATAAAAATT
*
2762559 GTAAAAA-T
1 ATAAAAATT
2762567 ATAATAAATT
1 ATAA-AAATT
2762577 ATAAAAA
1 ATAAAAA
2762584 CAATAAAACT
Statistics
Matches: 94, Mismatches: 18, Indels: 26
0.68 0.13 0.19
Matches are distributed among these distances:
6 4 0.04
7 4 0.04
8 16 0.17
9 35 0.37
10 21 0.22
11 11 0.12
12 3 0.03
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:2762682 original size:32 final size:33
Alignment explanation
Indices: 2762636--2762698 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
2762626 GAATTCTTAA
2762636 AAAAATAATAATAAATTGTAAAAAATTAAAATT
1 AAAAATAATAATAAATTGTAAAAAATTAAAATT
* *
2762669 AAAATTAAT-ATAAATTTTAAAAAATTAAAA
1 AAAAATAATAATAAATTGTAAAAAATTAAAA
2762699 AATCATAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (33 bp):
AAAAATAATAATAAATTGTAAAAAATTAAAATT
Found at i:2763228 original size:20 final size:20
Alignment explanation
Indices: 2763198--2763248 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
2763188 GATATCTTAT
* *
2763198 ATTTTTAATATTTTTATAAT
1 ATTTATAATATTTTTATAAC
*
2763218 GTTTATAATA-TTTTATAAC
1 ATTTATAATATTTTTATAAC
2763237 ATTTATAA-ATTT
1 ATTTATAATATTT
2763249 ATATCAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 1 0.04
19 17 0.65
20 8 0.31
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTTATAATATTTTTATAAC
Found at i:2763313 original size:10 final size:9
Alignment explanation
Indices: 2763194--2763351 Score: 67
Period size: 9 Copynumber: 17.1 Consensus size: 9
2763184 ATTAGATATC
2763194 TTAT-ATTT
1 TTATAATTT
2763202 TTA-ATATTT
1 TTATA-ATTT
*
2763211 TTATAATGT
1 TTATAATTT
2763220 TTATAATATT
1 TTATAAT-TT
**
2763230 TTATAACAT
1 TTATAATTT
2763239 TTATAAATTT
1 TTAT-AATTT
*
2763249 ATATCAATTT
1 TTAT-AATTT
*
2763259 TCAT--TTT
1 TTATAATTT
2763266 TT-TAATATT
1 TTATAAT-TT
* *
2763275 TTTTAATAT
1 TTATAATTT
*
2763284 TAATAATTT
1 TTATAATTT
2763293 TTAT-ATGTT
1 TTATAAT-TT
2763302 TTGATAATTTT
1 TT-ATAA-TTT
* * *
2763313 TTCTAGTTC
1 TTATAATTT
2763322 TTATAATTT
1 TTATAATTT
*
2763331 GATATAAATTT
1 -TTAT-AATTT
*
2763342 TTATGATTT
1 TTATAATTT
2763351 T
1 T
2763352 AATATATTTA
Statistics
Matches: 110, Mismatches: 25, Indels: 29
0.67 0.15 0.18
Matches are distributed among these distances:
6 1 0.01
7 4 0.04
8 6 0.05
9 53 0.48
10 35 0.32
11 10 0.09
12 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (9 bp):
TTATAATTT
Found at i:2764296 original size:17 final size:15
Alignment explanation
Indices: 2764254--2764305 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
2764244 CAAGGTTAAC
* *
2764254 AACTAACTAACAGCT
1 AACTGACTAACTGCT
2764269 AACTGACTAACTGCT
1 AACTGACTAACTGCT
2764284 AACTGATACTAACTGCT
1 AACTG--ACTAACTGCT
2764301 AACTG
1 AACTG
2764306 CAGTAACTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
15 18 0.55
17 15 0.45
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (15 bp):
AACTGACTAACTGCT
Found at i:2780595 original size:51 final size:51
Alignment explanation
Indices: 2780471--2780604 Score: 139
Period size: 51 Copynumber: 2.6 Consensus size: 51
2780461 ATTGGTATAA
* * * *
2780471 TAACAAATTTAGTCCTCA-AAA-TTTTACACATTGTGTCAAATTGGTATTGTT
1 TAACAAATTTAG--CTCATAAACATTTACATATTCTATCAAATTGGTATTGTT
* * * *
2780522 TAACAAATTTAACCCATAAACATTTACATATTCTATCAATTTGGTCTTGATT
1 TAACAAATTTAGCTCATAAACATTTACATATTCTATCAAATTGGTATTG-TT
*
2780574 TAACAAATTTAGCTCGT-AACATTTACATATT
1 TAACAAATTTAGCTCATAAACATTTACATATT
2780605 TTGTCTAACA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
49 3 0.04
50 3 0.04
51 47 0.68
52 16 0.23
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (51 bp):
TAACAAATTTAGCTCATAAACATTTACATATTCTATCAAATTGGTATTGTT
Found at i:2781573 original size:31 final size:32
Alignment explanation
Indices: 2781521--2781586 Score: 125
Period size: 31 Copynumber: 2.1 Consensus size: 32
2781511 TATGATTGCA
2781521 TCAACTTTAATTCTTTTTTTTTTAAGTCATTC
1 TCAACTTTAATTCTTTTTTTTTTAAGTCATTC
2781553 TCAACTTTAATTC-TTTTTTTTTAAGTCATTC
1 TCAACTTTAATTCTTTTTTTTTTAAGTCATTC
2781584 TCA
1 TCA
2781587 TTCTATCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.62
32 13 0.38
ACGTcount: A:0.23, C:0.17, G:0.03, T:0.58
Consensus pattern (32 bp):
TCAACTTTAATTCTTTTTTTTTTAAGTCATTC
Found at i:2781598 original size:29 final size:31
Alignment explanation
Indices: 2781521--2781603 Score: 111
Period size: 31 Copynumber: 2.7 Consensus size: 31
2781511 TATGATTGCA
2781521 TCAACTTTAATTCTTTTTTTTTTAAGTCATTC
1 TCAACTTTAA-TCTTTTTTTTTTAAGTCATTC
2781553 TCAACTTTAAT-TCTTTTTTTTTAAGTCATTC
1 TCAACTTTAATCT-TTTTTTTTTAAGTCATTC
2781584 TC-A-TTCT-ATCTTTTTTTTTT
1 TCAACTT-TAATCTTTTTTTTTT
2781604 TGGGTATCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
29 13 0.27
30 4 0.08
31 21 0.44
32 10 0.21
ACGTcount: A:0.19, C:0.16, G:0.02, T:0.63
Consensus pattern (31 bp):
TCAACTTTAATCTTTTTTTTTTAAGTCATTC
Found at i:2782262 original size:24 final size:25
Alignment explanation
Indices: 2782183--2782284 Score: 69
Period size: 24 Copynumber: 4.4 Consensus size: 25
2782173 TTTAGGTTCT
*
2782183 TATATTATTTA-TTTCAAACTA-TTA
1 TATATTATTTACTTT-GAACTATTTA
* *
2782207 TATCTTATTTATTTTGAA--A--T-
1 TATATTATTTACTTTGAACTATTTA
*
2782227 TAT-TTATATACTTTGAACT-TTTA
1 TATATTATTTACTTTGAACTATTTA
* *
2782250 TATATTATTTACTTTGGATTATTTA
1 TATATTATTTACTTTGAACTATTTA
2782275 TATATATATT
1 TATAT-TATT
2782285 ATTTAAACGG
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
19 12 0.19
20 3 0.05
21 1 0.02
22 2 0.03
23 3 0.05
24 25 0.40
25 12 0.19
26 4 0.06
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (25 bp):
TATATTATTTACTTTGAACTATTTA
Found at i:2782623 original size:25 final size:24
Alignment explanation
Indices: 2782573--2782623 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
2782563 TCACATATTA
* **
2782573 TTTATTTTAGATATTCTATTTTTT
1 TTTATTTTAGATATACTATTCATT
*
2782597 TTTATTGTTATATATACTATTCATT
1 TTTATT-TTAGATATACTATTCATT
2782622 TT
1 TT
2782624 AAGTTGCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTATTTTAGATATACTATTCATT
Found at i:2789687 original size:45 final size:45
Alignment explanation
Indices: 2789623--2790424 Score: 241
Period size: 45 Copynumber: 18.1 Consensus size: 45
2789613 CAGATCTTGT
* * * *
2789623 AGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTCCCTGAAGTTGC
1 AGTGGAGCAGATTAAAGATCGTAGATCTTGTCTCCCTGAAGTTGC
* * * * * *
2789668 AGTGGAGCAGATTGAAGATTGCAGATCTTGCCTACCTGAAGTTGT
1 AGTGGAGCAGATTAAAGATCGTAGATCTTGTCTCCCTGAAGTTGC
* ** * *
2789713 AGTGGAGCAGATCAAAGA-CGGCGAATCTTGTCTTCCTAAAGTTGC
1 AGTGGAGCAGATTAAAGATCGTAG-ATCTTGTCTCCCTGAAGTTGC
* * * * * * * * * * ** *
2789758 AATGAAGTAGATTTAAG-CCGCCACCATCCTATCTCTCT-AAGCAGT
1 AGTGGAGCAGATTAAAGATCG-TA-GATCTTGTCTCCCTGAAGTTGC
** ** * * * *
2789803 AGTGGAATAGGCTAAATATTGTAGGTCTTGTCTCCTTGAAGTTGC
1 AGTGGAGCAGATTAAAGATCGTAGATCTTGTCTCCCTGAAGTTGC
** * ** *
2789848 AGTGGAGTGGATCAAAGA-CGGCGAATCTTGTCTTCCTGAAGTTGC
1 AGTGGAGCAGATTAAAGATCGTAG-ATCTTGTCTCCCTGAAGTTGC
* * * * * ** *
2789893 AGTGAAGCAGATTTAAGCCA-C-T--ATCCTATCTCTCT-AAGCAGT
1 AGTGGAGCAGATTAAAG--ATCGTAGATCTTGTCTCCCTGAAGTTGC
* ** * *
2789935 AGTGGAGTAGGCTAAAGATTGTAGGTCTTGTCTCCCTGAAGTTGC
1 AGTGGAGCAGATTAAAGATCGTAGATCTTGTCTCCCTGAAGTTGC
* * * * *
2789980 AGTGGAGCGGATCAAAGATGGT-GAATCTTGTTTTCCTGAAGTTGC
1 AGTGGAGCAGATTAAAGATCGTAG-ATCTTGTCTCCCTGAAGTTGC
* * * * * * *
2790025 AGTGAAGCAGATTTAAG--C-CACCATCCTATCTCCCT-AAGTTGT
1 AGTGGAGCAGATTAAAGATCGTA-GATCTTGTCTCCCTGAAGTTGC
* * ** * *
2790067 AGTAGAGTAGGCTAAAGATTGTAGATCTTGCCTCCCTGAAGTTGC
1 AGTGGAGCAGATTAAAGATCGTAGATCTTGTCTCCCTGAAGTTGC
** ** *
2790112 AGTGGAGCAGATCGAAGA-CGGCGAATCTTGTCTTCCTGAAGTTGC
1 AGTGGAGCAGATTAAAGATCGTAG-ATCTTGTCTCCCTGAAGTTGC
* * * * * * * *
2790157 AGTGAAGCAAATTTAAG--C-CACCATCCTATCTCCCT-AAGTTGT
1 AGTGGAGCAGATTAAAGATCGTA-GATCTTGTCTCCCTGAAGTTGC
* * * *
2790199 AGTGGAGTAGACTAAAGATTGTAGATCTTGTCTCCCTAAAGTTGC
1 AGTGGAGCAGATTAAAGATCGTAGATCTTGTCTCCCTGAAGTTGC
** ** * * **
2790244 AGCAGAGCAGATCGAAG-GCG-ACGAATCTTATCTTTCTGAAGTTGC
1 AGTGGAGCAGATTAAAGATCGTA-G-ATCTTGTCTCCCTGAAGTTGC
* * * ** * * * *
2790289 AGTGAAGCAGATTTAAG-CCG-CCATCCTATCTCTCT-AAGTTGT
1 AGTGGAGCAGATTAAAGATCGTAGATCTTGTCTCCCTGAAGTTGC
* * ** *
2790331 AGTAGAGTAGGCTAAAGATTGTAGATCTTGTCTCCCTGAAGTTGC
1 AGTGGAGCAGATTAAAGATCGTAGATCTTGTCTCCCTGAAGTTGC
* * ** ** *
2790376 AATGGAGCGGATCGAAGA-CGGCGAATCTTGTCTTCCTGAAGTTGC
1 AGTGGAGCAGATTAAAGATCGTAG-ATCTTGTCTCCCTGAAGTTGC
2790421 AGTG
1 AGTG
2790425 AAATAGATTT
Statistics
Matches: 520, Mismatches: 204, Indels: 66
0.66 0.26 0.08
Matches are distributed among these distances:
40 1 0.00
42 69 0.13
43 41 0.08
44 60 0.12
45 337 0.65
46 10 0.02
47 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (45 bp):
AGTGGAGCAGATTAAAGATCGTAGATCTTGTCTCCCTGAAGTTGC
Found at i:2790521 original size:132 final size:132
Alignment explanation
Indices: 2789682--2790523 Score: 1162
Period size: 132 Copynumber: 6.4 Consensus size: 132
2789672 GAGCAGATTG
* * * * *
2789682 AAGATTGCAGATCTTGCCTACCTGAAGTTGTAGTGGAGCAGATCAAAGACGGCGAATCTTGTCTT
1 AAGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTT
* * * * *
2789747 CCTAAAGTTGCAATGAAGTAGATTTAAGCCGCCACCATCCTATCTCTCTAAGCAGTAGTGGAATA
66 CCTGAAGTTGCAGTGAAGCAGATTTAA---GCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTA
2789812 GGCTA
128 GGCTA
* * * ** *
2789817 AATATTGTAGGTCTTGTCTCCTTGAAGTTGCAGTGGAGTGGATCAAAGACGGCGAATCTTGTCTT
1 AAGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTT
* *
2789882 CCTGAAGTTGCAGTGAAGCAGATTTAAGCCACTATCCTATCTCTCTAAGCAGTAGTGGAGTAGGC
66 CCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGC
2789947 TA
131 TA
* * * * * *
2789949 AAGATTGTAGGTCTTGTCTCCCTGAAGTTGCAGTGGAGCGGATCAAAGATGGTGAATCTTGTTTT
1 AAGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTT
** *
2790014 CCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTATCTCCCTAAGTTGTAGTAGAGTAGGC
66 CCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGC
2790079 TA
131 TA
*
2790081 AAGATTGTAGATCTTGCCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTT
1 AAGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTT
* ** *
2790146 CCTGAAGTTGCAGTGAAGCAAATTTAAGCCACCATCCTATCTCCCTAAGTTGTAGTGGAGTAGAC
66 CCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGC
2790211 TA
131 TA
* ** * * *
2790213 AAGATTGTAGATCTTGTCTCCCTAAAGTTGCAGCAGAGCAGATCGAAGGCGACGAATCTTATCTT
1 AAGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTT
* * * ** *
2790278 TCTGAAGTTGCAGTGAAGCAGATTTAAGCCGCCATCCTATCTCTCTAAGTTGTAGTAGAGTAGGC
66 CCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGC
2790343 TA
131 TA
* *
2790345 AAGATTGTAGATCTTGTCTCCCTGAAGTTGCAATGGAGCGGATCGAAGACGGCGAATCTTGTCTT
1 AAGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTT
** * *
2790410 CCTGAAGTTGCAGTGAAATAGATTTAAGCCACTATCTTATCTCCCTAAGCAGTAGTGGAGTAGGC
66 CCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGC
*
2790475 TG
131 TA
* * * *
2790477 AAGATTGCAGATCTTGTCTCCCTGAAGTTGTAGCGGAACAGATCGAA
1 AAGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATCGAA
2790524 AACGTTGCAG
Statistics
Matches: 634, Mismatches: 73, Indels: 3
0.89 0.10 0.00
Matches are distributed among these distances:
132 554 0.87
135 80 0.13
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (132 bp):
AAGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTT
CCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGC
TA
Found at i:2792274 original size:24 final size:25
Alignment explanation
Indices: 2792242--2792298 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
2792232 TTGAAGTTAT
2792242 TTATATACTTTGAACT-TTTATATA
1 TTATATACTTTGAACTATTTATATA
* * *
2792266 TTATTTACTTTGGATTATTTATATA
1 TTATATACTTTGAACTATTTATATA
2792291 TATATATA
1 T-TATATA
2792299 TATATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 13 0.48
25 9 0.33
26 5 0.19
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (25 bp):
TTATATACTTTGAACTATTTATATA
Found at i:2792292 original size:2 final size:2
Alignment explanation
Indices: 2792285--2792319 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2792275 TTGGATTATT
2792285 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2792320 TTAAACGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2795670 original size:26 final size:26
Alignment explanation
Indices: 2795613--2795746 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
2795603 TGATACAAAT
2795613 TGATAATAGGTTAGGTAAATG-TTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
2795638 TGATAATAGGGTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
2795664 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
2795690 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
2795716 TGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
2795741 TGATAA
1 TGATAA
2795747 GAATTTCATG
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
25 44 0.43
26 59 0.57
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:2795673 original size:51 final size:51
Alignment explanation
Indices: 2795613--2795746 Score: 227
Period size: 51 Copynumber: 2.6 Consensus size: 51
2795603 TGATACAAAT
2795613 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGG-TAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAAT-GGGTTAGGTAAATGTTTCA
2795664 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTT-CATGATAATGGGTTAGGTAAATGTTTCA
2795716 TGATAAT-GGTTAGGTAAATGTTTCATGATAA
1 TGATAATAGGTTAGGTAAATG-TTCATGATAA
2795747 GAATTTCATG
Statistics
Matches: 80, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
51 47 0.59
52 33 0.41
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (51 bp):
TGATAATAGGTTAGGTAAATGTTCATGATAATGGGTTAGGTAAATGTTTCA
Found at i:2796931 original size:8 final size:8
Alignment explanation
Indices: 2796918--2796953 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
2796908 CTAGATCGGC
2796918 AAAAGCCG
1 AAAAGCCG
2796926 AAAAGCCG
1 AAAAGCCG
*
2796934 AAATGCCG
1 AAAAGCCG
*
2796942 AAATGCCG
1 AAAAGCCG
2796950 AAAA
1 AAAA
2796954 TCGGTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.50, C:0.22, G:0.22, T:0.06
Consensus pattern (8 bp):
AAAAGCCG
Found at i:2801158 original size:46 final size:46
Alignment explanation
Indices: 2801091--2801352 Score: 389
Period size: 46 Copynumber: 5.7 Consensus size: 46
2801081 GGAAACCTGA
2801091 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
2801137 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*
2801183 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* * *
2801229 GTGTAAGACCATAGTTGAAAGATACCATGGCAACGTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*** * * *
2801275 GAACAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
** * * *
2801321 CAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
2801353 TCATGTCAAA
Statistics
Matches: 199, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 199 1.00
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.22
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
Found at i:2802564 original size:12 final size:12
Alignment explanation
Indices: 2802547--2802589 Score: 86
Period size: 12 Copynumber: 3.6 Consensus size: 12
2802537 ACTCGGGGAA
2802547 GAGGCCGTGGTC
1 GAGGCCGTGGTC
2802559 GAGGCCGTGGTC
1 GAGGCCGTGGTC
2802571 GAGGCCGTGGTC
1 GAGGCCGTGGTC
2802583 GAGGCCG
1 GAGGCCG
2802590 AGGTAGTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.09, C:0.26, G:0.51, T:0.14
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:2807458 original size:26 final size:26
Alignment explanation
Indices: 2807401--2807534 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
2807391 TGATACAAAT
2807401 TGATAATAGGTTAGGTAAATG-TTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
2807426 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
2807452 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
2807478 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
2807504 TGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
2807529 TGATAA
1 TGATAA
2807535 GAATTTCATG
Statistics
Matches: 105, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
25 45 0.43
26 60 0.57
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:2807461 original size:51 final size:51
Alignment explanation
Indices: 2807401--2807534 Score: 234
Period size: 51 Copynumber: 2.6 Consensus size: 51
2807391 TGATACAAAT
2807401 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTTCA
*
2807452 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTT-CATGATAATAGGTTAGGTAAATGTTTCA
2807504 TGATAAT-GGTTAGGTAAATGTTTCATGATAA
1 TGATAATAGGTTAGGTAAATG-TTCATGATAA
2807535 GAATTTCATG
Statistics
Matches: 80, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
51 44 0.55
52 36 0.45
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.37
Consensus pattern (51 bp):
TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTTCA
Found at i:2810499 original size:59 final size:56
Alignment explanation
Indices: 2810425--2810550 Score: 155
Period size: 59 Copynumber: 2.2 Consensus size: 56
2810415 AAAATTGAAT
* *
2810425 AGTTGGGTGACCATTTTGTAACTTTTTATAGTTGAATGACCTAAAAAAAATCTACTAAG
1 AGTTGGGTGACCATTTTGTAACATTTTAT-GTTGAATGA-CAAAAAAAAATC-ACTAAG
* **
2810484 AGTTGGGTGATCATTTTGTAACATTTTATGTTGGGTGACAAAAAAAAATCACT-AG
1 AGTTGGGTGACCATTTTGTAACATTTTATGTTGAATGACAAAAAAAAATCACTAAG
*
2810539 TAGTTGAGTGAC
1 -AGTTGGGTGAC
2810551 TACTAATGTA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
55 2 0.03
56 12 0.20
57 11 0.19
58 7 0.12
59 27 0.46
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (56 bp):
AGTTGGGTGACCATTTTGTAACATTTTATGTTGAATGACAAAAAAAAATCACTAAG
Found at i:2811552 original size:15 final size:14
Alignment explanation
Indices: 2811525--2811554 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2811515 TAACATTTTT
2811525 TAATATTTATATTA
1 TAATATTTATATTA
2811539 TAATATTATATATTA
1 TAATATT-TATATTA
2811554 T
1 T
2811555 TATAGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATATTTATATTA
Found at i:2812053 original size:12 final size:12
Alignment explanation
Indices: 2812033--2812101 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
2812023 TTTTATTTTA
*
2812033 ATTCTTTTATTT
1 ATTCATTTATTT
2812045 ATTCATTTATTT
1 ATTCATTTATTT
* * *
2812057 ATTTACTTGTTT
1 ATTCATTTATTT
* *
2812069 ATTTATTCA-TT
1 ATTCATTTATTT
*
2812080 ATTCCTTTTATTTT
1 ATT-CATTTA-TTT
2812094 ATTCATTT
1 ATTCATTT
2812102 GCTTGTTCAT
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
11 5 0.12
12 29 0.67
13 4 0.09
14 5 0.12
ACGTcount: A:0.20, C:0.10, G:0.01, T:0.68
Consensus pattern (12 bp):
ATTCATTTATTT
Found at i:2813777 original size:51 final size:50
Alignment explanation
Indices: 2813651--2813786 Score: 132
Period size: 51 Copynumber: 2.7 Consensus size: 50
2813641 ATTAGTATAA
* * * * *
2813651 TAACAAATTTAG-TCATCAAAATTTTACACATTGTGTCAAATTGGTATTGTT
1 TAACAAATTTAGCTCAT-AACA-TTTACATATTCTATCAAATTCGTATTGTT
* * * *
2813702 TAACAAATTTAACCCGCA-AACATTTACATATTCTATCAATTTCGTCTTGATT
1 TAACAAATTT-A-GCTCATAACATTTACATATTCTATCAAATTCGTATTG-TT
2813754 TAACAAATTTAGCTCATAACATTTACATATTCT
1 TAACAAATTTAGCTCATAACATTTACATATTCT
2813787 GTCTAACAAC
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
50 3 0.04
51 48 0.70
52 16 0.23
54 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (50 bp):
TAACAAATTTAGCTCATAACATTTACATATTCTATCAAATTCGTATTGTT
Found at i:2814920 original size:124 final size:124
Alignment explanation
Indices: 2814696--2815032 Score: 399
Period size: 124 Copynumber: 2.7 Consensus size: 124
2814686 TAAGTTATTC
*
2814696 GAGTTTG-GATGTGAGTGTTGTGTAGGTATAAAGATAGCAATTTGATTCGGGTTTAGATCATGTA
1 GAGTTTGAG-TGTGAGTGTTGTGTAGGTATAAAGATA-AAATTTGATTCGGGTTTAGATCATGTA
* * *
2814760 ATTTTGGGATTTAGTTGTTTTAAATTTGGGTGTTTTCTG-GTTTGAATGTTTTTATAGTTGA
64 ATTTTGGGTTTTAGTTGTTTTAAATTTGAGTATTTTC-GAGTTTGAATGTTTTTATAGTTGA
* * * * *
2814821 GAGTTTGAGTGTTAGTGTTGGGTAAGTATAAAGGTAAAATTTGATTCGGGTTTAGATCATTTAAT
1 GAGTTTGAGTGTGAGTGTTGTGTAGGTATAAAGATAAAATTTGATTCGGGTTTAGATCATGTAAT
* * * * * * *
2814886 CTTGGGTTTTAATTGTTTTAAGTTTGAGTATTTTCGAGTTTGAGTTTTTTTGTAGTTTA
66 TTTGGGTTTTAGTTGTTTTAAATTTGAGTATTTTCGAGTTTGAATGTTTTTATAGTTGA
* * * * * **
2814945 AAGTTTAAGTCTGAATGTTCTGTGTAGGTATAAAGATAACAACTTGATTCAAGTTTAGATCATGT
1 GAGTTTGAGTGTGAGTG-T-TGTGTAGGTATAAAGATAA-AATTTGATTCGGGTTTAGATCATGT
2815010 AATTTTGGGTTTTAGTTGTTTTA
63 AATTTTGGGTTTTAGTTGTTTTA
2815033 TGATTTTGGA
Statistics
Matches: 177, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
123 1 0.01
124 86 0.49
125 31 0.18
126 17 0.10
127 42 0.24
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (124 bp):
GAGTTTGAGTGTGAGTGTTGTGTAGGTATAAAGATAAAATTTGATTCGGGTTTAGATCATGTAAT
TTTGGGTTTTAGTTGTTTTAAATTTGAGTATTTTCGAGTTTGAATGTTTTTATAGTTGA
Found at i:2819003 original size:51 final size:53
Alignment explanation
Indices: 2818947--2819059 Score: 135
Period size: 51 Copynumber: 2.2 Consensus size: 53
2818937 TGGTGTAATG
* * *
2818947 ACAAATTTAGTCCTC-AAAAT-TTTACACATTGTGTCAAATTGGTATTG-TTTA
1 ACAAATTTAGACC-CAAAAATATTTACACATTCTATCAAATTGGTATTGATTTA
* * *
2818998 ACAAATTTA-ACCCAAAAATATTTACATATTCTATCAATTTGGTCTTGATTTA
1 ACAAATTTAGACCCAAAAATATTTACACATTCTATCAAATTGGTATTGATTTA
2819050 ACAAATTTAG
1 ACAAATTTAG
2819060 CTCATAACAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
49 1 0.02
50 7 0.13
51 31 0.60
52 13 0.25
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (53 bp):
ACAAATTTAGACCCAAAAATATTTACACATTCTATCAAATTGGTATTGATTTA
Found at i:2819072 original size:51 final size:51
Alignment explanation
Indices: 2818980--2819078 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
2818970 ACACATTGTG
*
2818980 TCAAATTGGTATTGTTTAACAAATTTAACCCAAAAATATTTACATATTCTA
1 TCAAATTGGTATTGTTTAACAAATTTAACCCAAAAACATTTACATATTCTA
* * * * *
2819031 TCAATTTGGTCTTGATTTAACAAATTTAGCTC-ATAACATTTACATATT
1 TCAAATTGGTATTG-TTTAACAAATTTAACCCAAAAACATTTACATATT
2819079 TTGTCTAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 26 0.63
52 15 0.37
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.41
Consensus pattern (51 bp):
TCAAATTGGTATTGTTTAACAAATTTAACCCAAAAACATTTACATATTCTA
Found at i:2820670 original size:27 final size:26
Alignment explanation
Indices: 2820611--2820670 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
2820601 GGGTATTTTT
*
2820611 TTAT-TTTGAGTTTTAAGTTTAGGATT
1 TTATATTTGAGTTTTAAGTTTA-GATG
*
2820637 TTCTATTTGAGTTTTAAGTTCTA-ATCG
1 TTATATTTGAGTTTTAAGTT-TAGAT-G
2820664 TTATATT
1 TTATATT
2820671 CAATAATACC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 5 0.18
27 21 0.75
28 2 0.07
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.57
Consensus pattern (26 bp):
TTATATTTGAGTTTTAAGTTTAGATG
Found at i:2824794 original size:42 final size:42
Alignment explanation
Indices: 2824735--2824856 Score: 199
Period size: 42 Copynumber: 2.8 Consensus size: 42
2824725 CATTGTTTTT
2824735 GCCTCAACAATGACTTCTTCTTTCTTTGGGGCCTCCTTTGGA
1 GCCTCAACAATGACTTCTTCTTTCTTTGGGGCCTCCTTTGGA
2824777 GCCTCAACAATGACTTCTTCTTTCTTTGGGGCCTCCTTTGGA
1 GCCTCAACAATGACTTCTTCTTTCTTTGGGGCCTCCTTTGGA
* *
2824819 GCCTCAACAATGGCTTCTTCCACTTTCTTTGGCGCCTC
1 GCCTCAACAATGACTTCTT---CTTTCTTTGGGGCCTC
2824857 GACAATGGCG
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
42 60 0.80
45 15 0.20
ACGTcount: A:0.14, C:0.31, G:0.18, T:0.37
Consensus pattern (42 bp):
GCCTCAACAATGACTTCTTCTTTCTTTGGGGCCTCCTTTGGA
Found at i:2825698 original size:108 final size:108
Alignment explanation
Indices: 2825551--2825762 Score: 291
Period size: 108 Copynumber: 2.0 Consensus size: 108
2825541 AACCAATATT
* * * * * *
2825551 TAATCCGGTTTATGTTTTTATATTTTAAAGATTTGATTTGTAGATATCCTTTAATCGTAAATGTT
1 TAATCCAGTTTATGTTTTCATATCTTAAAGATTTGATTTGTAGATACCCGTTAATCGTAAACGTT
2825616 GATGTACTTGATCTATA-CTGTAAGATTTGGGGAGGCTCACATC
66 GATGTACTTGATCTATATCT-TAAGATTTGGGGAGGCTCACATC
* * **
2825659 TAATCCAGTTTATGTTTTCATATCTTAGAGATTTGATTTGTCGATACCCGTTAATCGTAGCCGTT
1 TAATCCAGTTTATGTTTTCATATCTTAAAGATTTGATTTGTAGATACCCGTTAATCGTAAACGTT
* * *
2825724 GCTGTACTTGATCTGTATCTTTAGATTTGGGGAGGCTCA
66 GATGTACTTGATCTATATCTTAAGATTTGGGGAGGCTCA
2825763 ACTATAAATA
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
108 88 0.98
109 2 0.02
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (108 bp):
TAATCCAGTTTATGTTTTCATATCTTAAAGATTTGATTTGTAGATACCCGTTAATCGTAAACGTT
GATGTACTTGATCTATATCTTAAGATTTGGGGAGGCTCACATC
Found at i:2829502 original size:9 final size:9
Alignment explanation
Indices: 2829490--2829514 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2829480 ACATACAGGT
2829490 AACACAGAA
1 AACACAGAA
2829499 AACACAGAA
1 AACACAGAA
2829508 AACACAG
1 AACACAG
2829515 CTCACAACAG
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:0.64, C:0.24, G:0.12, T:0.00
Consensus pattern (9 bp):
AACACAGAA
Found at i:2830593 original size:21 final size:22
Alignment explanation
Indices: 2830568--2830609 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2830558 ACCACCTTCT
2830568 TCATCAAAAG-TATTCCAATTA
1 TCATCAAAAGATATTCCAATTA
* *
2830589 TCATCACAAGATTTTCCAATT
1 TCATCAAAAGATATTCCAATT
2830610 TCTTTCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (22 bp):
TCATCAAAAGATATTCCAATTA
Found at i:2835223 original size:15 final size:15
Alignment explanation
Indices: 2835203--2835232 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2835193 CCCCTCTAAA
2835203 GGCTTGGATTCACCC
1 GGCTTGGATTCACCC
2835218 GGCTTGGATTCACCC
1 GGCTTGGATTCACCC
2835233 TTTGTTTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.33, G:0.27, T:0.27
Consensus pattern (15 bp):
GGCTTGGATTCACCC
Found at i:2842240 original size:37 final size:39
Alignment explanation
Indices: 2842189--2842261 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 39
2842179 AATTAAGATG
* **
2842189 ATTATATATAAAATTTTAA-AATATAAA-AAATATTATT
1 ATTAAATATAAAATTGAAATAATATAAATAAATATTATT
*
2842226 ATTAAATATTAAATTGAAATAATATAAATAAATATT
1 ATTAAATATAAAATTGAAATAATATAAATAAATATT
2842262 TTAAAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 15 0.50
38 8 0.27
39 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (39 bp):
ATTAAATATAAAATTGAAATAATATAAATAAATATTATT
Found at i:2848643 original size:34 final size:34
Alignment explanation
Indices: 2848597--2848663 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
2848587 CGAATTGAAT
* *
2848597 CAGATTCGGTAACTAAAAGTTCTTAAAAGAAAAA
1 CAGATTCAGTAACTAAAAGTTCTTAAAACAAAAA
2848631 CAGATTCAGTAACTAAAAGTTCTTAAAACAAAA
1 CAGATTCAGTAACTAAAAGTTCTTAAAACAAAA
2848664 GAGAGAGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.51, C:0.13, G:0.12, T:0.24
Consensus pattern (34 bp):
CAGATTCAGTAACTAAAAGTTCTTAAAACAAAAA
Found at i:2860692 original size:15 final size:14
Alignment explanation
Indices: 2860663--2860691 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2860653 AGAATATTAA
2860663 ATTAAAAAATATAT
1 ATTAAAAAATATAT
2860677 ATTAAAAAATA-AT
1 ATTAAAAAATATAT
2860690 AT
1 AT
2860692 AAATGAGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTAAAAAATATAT
Found at i:2862148 original size:18 final size:18
Alignment explanation
Indices: 2862125--2862159 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2862115 GTCTAACCCG
2862125 TATTTTAAATAAATCTAA
1 TATTTTAAATAAATCTAA
**
2862143 TATTTTATTTAAATCTA
1 TATTTTAAATAAATCTA
2862160 TTTTTTGAAT
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:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTTAAATAAATCTAA
Found at i:2865522 original size:44 final size:45
Alignment explanation
Indices: 2865427--2865541 Score: 151
Period size: 44 Copynumber: 2.6 Consensus size: 45
2865417 ACAGGACAGA
* *
2865427 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
2865473 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* **
2865517 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
2865542 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:2870980 original size:53 final size:53
Alignment explanation
Indices: 2870899--2871044 Score: 179
Period size: 53 Copynumber: 2.7 Consensus size: 53
2870889 CTTACACGGT
* * *
2870899 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTTTTATACGGAA-TCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATAC-GAAGTCACATTA
2870954 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGAAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGAAGTCACATTA
** * *
2871007 TCACATTGCACCGATTCCAAAGCCCAGCTATGGTCTTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTA
2871045 AATGGGCACA
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
52 4 0.05
53 71 0.87
54 1 0.01
55 6 0.07
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGAAGTCACATTA
Found at i:2875337 original size:44 final size:44
Alignment explanation
Indices: 2875284--2875387 Score: 131
Period size: 44 Copynumber: 2.3 Consensus size: 44
2875274 TCTTTGACAT
*
2875284 GACTTACATGAACT-ATTCCTGTCTCCAATGCCATA-TATAATATG
1 GACTTACATG-ACTCAATCCTGTCTCCAA-GCCATATTATAATATG
* *
2875328 GACTTACATGGCTCAATCCTGTCTCCAAGCCATATTTCTAATATG
1 GACTTACATGACTCAATCCTGTCTCCAAGCCATA-TTATAATATG
*
2875373 GACTTACATGGCTCA
1 GACTTACATGACTCA
2875388 TTTTGTTCTG
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
43 8 0.15
44 23 0.43
45 23 0.43
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (44 bp):
GACTTACATGACTCAATCCTGTCTCCAAGCCATATTATAATATG
Found at i:2875381 original size:45 final size:44
Alignment explanation
Indices: 2875300--2875387 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 44
2875290 CATGAACTAT
2875300 TCCTGTCTCCAATGCCATATATAATATGGACTTACATGGCTCAA
1 TCCTGTCTCCAATGCCATATATAATATGGACTTACATGGCTCAA
*
2875344 TCCTGTCTCCAA-GCCATATTTCTAATATGGACTTACATGGCTCA
1 TCCTGTCTCCAATGCCATA--TATAATATGGACTTACATGGCTCA
2875388 TTTTGTTCTG
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
43 6 0.15
44 12 0.29
45 23 0.56
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (44 bp):
TCCTGTCTCCAATGCCATATATAATATGGACTTACATGGCTCAA
Found at i:2878826 original size:45 final size:43
Alignment explanation
Indices: 2878777--2878862 Score: 136
Period size: 45 Copynumber: 2.0 Consensus size: 43
2878767 AGAACAGAAA
*
2878777 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGAT
1 TGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAGACAGAT
*
2878822 TGAGCCATGTAAGTCCATATTATATATGGCATTGGAGACAG
1 TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAG
2878863 GAATAATTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 18 0.46
45 21 0.54
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (43 bp):
TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGAT
Found at i:2884996 original size:20 final size:20
Alignment explanation
Indices: 2884971--2885009 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2884961 AATATGAATC
2884971 TTAAGTTTTACTTAAATCCA
1 TTAAGTTTTACTTAAATCCA
2884991 TTAAGTTTTACTTAAATCC
1 TTAAGTTTTACTTAAATCC
2885010 GATAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (20 bp):
TTAAGTTTTACTTAAATCCA
Found at i:2885094 original size:15 final size:16
Alignment explanation
Indices: 2885076--2885116 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2885066 TGTATTTAAT
2885076 TTTATATAATTTTC-A
1 TTTATATAATTTTCAA
2885091 TTTAT-TGAATTTTCAAA
1 TTTATAT-AATTTTC-AA
2885108 TTTATATAA
1 TTTATATAA
2885117 CTTAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.05
15 12 0.55
17 8 0.36
18 1 0.05
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTATATAATTTTCAA
Found at i:2888632 original size:31 final size:29
Alignment explanation
Indices: 2888566--2888637 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
2888556 ATTTTTTGTT
* * *
2888566 AATTTTTTTAAAATTTTAATTAGCTCCTA
1 AATTTTTTGAAAATTTGAATTAGCTCCAA
2888595 AATTTTTTGAAAATTTGAATTAGACCTCCAA
1 AATTTTTTGAAAATTTGAATTAG--CTCCAA
*
2888626 AATTTTTGGAAA
1 AATTTTTTGAAA
2888638 TTCTCATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 21 0.57
31 16 0.43
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (29 bp):
AATTTTTTGAAAATTTGAATTAGCTCCAA
Found at i:2888639 original size:30 final size:31
Alignment explanation
Indices: 2888569--2888708 Score: 103
Period size: 31 Copynumber: 4.6 Consensus size: 31
2888559 TTTTGTTAAT
* *
2888569 TTTTTTAAAATTTTAATT--AG-CTCCTAAAT
1 TTTTTAAAAATTTTAATTAGAGCCTCC-AAAA
* *
2888598 TTTTTGAAAATTTGAATTAGA-CCTCCAAAA
1 TTTTTAAAAATTTTAATTAGAGCCTCCAAAA
** * * *
2888628 TTTTTGGAAATTCTCATTA-AGCTTTCCAAAA
1 TTTTTAAAAATTTTAATTAGAGC-CTCCAAAA
* * *
2888659 -TTTTAGAAGATTTTAATTAGATCCTCCATAA
1 TTTTTA-AAAATTTTAATTAGAGCCTCCAAAA
2888690 TTTTTAAAAATTTTAATTA
1 TTTTTAAAAATTTTAATTA
2888709 CGTCTTCCAA
Statistics
Matches: 86, Mismatches: 17, Indels: 14
0.74 0.15 0.12
Matches are distributed among these distances:
29 17 0.20
30 23 0.27
31 39 0.45
32 7 0.08
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (31 bp):
TTTTTAAAAATTTTAATTAGAGCCTCCAAAA
Found at i:2888717 original size:62 final size:59
Alignment explanation
Indices: 2888569--2888720 Score: 153
Period size: 62 Copynumber: 2.5 Consensus size: 59
2888559 TTTTGTTAAT
* * *
2888569 TTTTTTAAAATTTTAATTAGC-TCCTAAATTTTTTGAAAATTTGAATTAGACCTCCAAAA
1 TTTTTAAAAATTTTAATTAGCTTCC-AAAATTTTAGAAAATTTGAATTAGACCTCCAAAA
** * * * * *
2888628 TTTTTGGAAATTCTCATTAAGCTTTCCAAAATTTTAGAAGATTTTAATTAGATCCTCCATAA
1 TTTTTAAAAATTTTAATT-AGC-TTCCAAAATTTTAGAAAATTTGAATTAGA-CCTCCAAAA
2888690 TTTTTAAAAATTTTAATTACGTCTTCCAAAA
1 TTTTTAAAAATTTTAATTA-G-CTTCCAAAA
2888721 AAAATTTAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
59 14 0.19
60 3 0.04
61 22 0.30
62 34 0.46
63 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.43
Consensus pattern (59 bp):
TTTTTAAAAATTTTAATTAGCTTCCAAAATTTTAGAAAATTTGAATTAGACCTCCAAAA
Found at i:2890867 original size:25 final size:25
Alignment explanation
Indices: 2890835--2890890 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
2890825 GAAACCCTTT
2890835 AAACACGGTCAAATAACAAAAACAC
1 AAACACGGTCAAATAACAAAAACAC
*
2890860 AAACACGGTCAAATAACACAAACAC
1 AAACACGGTCAAATAACAAAAACAC
2890885 -AACACG
1 AAACACG
2890891 AGATACACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 6 0.20
25 24 0.80
ACGTcount: A:0.57, C:0.27, G:0.09, T:0.07
Consensus pattern (25 bp):
AAACACGGTCAAATAACAAAAACAC
Found at i:2906317 original size:15 final size:15
Alignment explanation
Indices: 2906297--2906331 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2906287 TTTTTTTATA
*
2906297 TTATTTTTACCATTT
1 TTATTTTTAACATTT
*
2906312 TTATTTTTAATATTT
1 TTATTTTTAACATTT
2906327 TTATT
1 TTATT
2906332 ATTATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTTTTAACATTT
Found at i:2906335 original size:3 final size:3
Alignment explanation
Indices: 2906312--2906390 Score: 54
Period size: 3 Copynumber: 26.7 Consensus size: 3
2906302 TTTACCATTT
* * * * *
2906312 TTA TTT TTA ATA TTT TTA TTA TTA -TA TTTA CTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* * * *
2906357 TTA TTA TTA GTA -TA TTT TTA CTA TTA TTA GTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2906391 TTTTACAATT
Statistics
Matches: 56, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
2 4 0.07
3 50 0.89
4 2 0.04
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2906383 original size:20 final size:19
Alignment explanation
Indices: 2906358--2906401 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
2906348 TCATTATTAT
2906358 TATTATTAGTATATTTTTAC
1 TATTATTAGTAT-TTTTTAC
2906378 TATTATTAGTATTTTTTAC
1 TATTATTAGTATTTTTTAC
*
2906397 AATTA
1 TATTA
2906402 ATACTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTATTAGTATTTTTTAC
Found at i:2906384 original size:12 final size:12
Alignment explanation
Indices: 2906289--2906384 Score: 63
Period size: 12 Copynumber: 8.2 Consensus size: 12
2906279 CATTTTTGTT
2906289 TTTTTA-TATTA
1 TTTTTACTATTA
*
2906300 TTTTTACCATT-
1 TTTTTACTATTA
** *
2906311 TTTATTTTTAATA
1 TTT-TTACTATTA
*
2906324 TTTTTATTATTA
1 TTTTTACTATTA
*
2906336 TATTTACTATTA
1 TTTTTACTATTA
** *
2906348 TCATTATTATTA
1 TTTTTACTATTA
* *
2906360 TTATTAGTA-TA
1 TTTTTACTATTA
2906371 TTTTTACTATTA
1 TTTTTACTATTA
2906383 TT
1 TT
2906385 AGTATTTTTT
Statistics
Matches: 65, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
11 18 0.28
12 44 0.68
13 3 0.05
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (12 bp):
TTTTTACTATTA
Found at i:2906523 original size:25 final size:25
Alignment explanation
Indices: 2906478--2906533 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
2906468 TATTATGTAT
* *
2906478 ACATA-TTTAAATACTATATTATAC
1 ACATATTTTAAATACCACATTATAC
* *
2906502 ACATATTTTTAATACCACATTATAT
1 ACATATTTTAAATACCACATTATAC
2906527 ACATATT
1 ACATATT
2906534 ATTATTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (25 bp):
ACATATTTTAAATACCACATTATAC
Found at i:2906631 original size:14 final size:14
Alignment explanation
Indices: 2906601--2906658 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
2906591 ATTATATGTG
*
2906601 TATATATATACTTT
1 TATATATATACTAT
*
2906615 TATATATATAGTAT
1 TATATATATACTAT
2906629 TAT-TAT-TA-TAT
1 TATATATATACTAT
*
2906640 TATTATATTTACTAT
1 TA-TATATATACTAT
2906655 TATA
1 TATA
2906659 CTTATTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 5 0.13
12 3 0.08
13 6 0.16
14 19 0.50
15 5 0.13
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (14 bp):
TATATATATACTAT
Found at i:2906685 original size:22 final size:20
Alignment explanation
Indices: 2906632--2906692 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
2906622 ATAGTATTAT
2906632 TATTATA-TTATTATATTTAC
1 TATTATACTTATTAT-TTTAC
2906652 TATTATACTTATTATTTTCAC
1 TATTATACTTATTATTTT-AC
*
2906673 TATTGTTACTTATTATTTTA
1 TATT-ATACTTATTATTTTA
2906693 TTTTAACATT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 10 0.27
21 14 0.38
22 13 0.35
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTATACTTATTATTTTAC
Found at i:2906755 original size:19 final size:19
Alignment explanation
Indices: 2906731--2906769 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2906721 TACATATGTC
2906731 TTTTTGTAA-ATATTATTAT
1 TTTTTGTAATATA-TATTAT
*
2906750 TTTTTGTTATATATATTAT
1 TTTTTGTAATATATATTAT
2906769 T
1 T
2906770 GTTATCACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTGTAATATATATTAT
Found at i:2906773 original size:15 final size:15
Alignment explanation
Indices: 2906753--2906820 Score: 61
Period size: 15 Copynumber: 4.6 Consensus size: 15
2906743 TTATTATTTT
2906753 TTGTTATATATATTA
1 TTGTTATATATATTA
*
2906768 TTGTTATCA-CTATTA
1 TTGTTAT-ATATATTA
*
2906783 TTTTTATAT-TATTA
1 TTGTTATATATATTA
*
2906797 TTATTATATTATATT-
1 TTGTTATA-TATATTA
*
2906812 TAGTTATAT
1 TTGTTATAT
2906821 TTTTTAAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
14 14 0.32
15 25 0.57
16 5 0.11
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (15 bp):
TTGTTATATATATTA
Found at i:2906869 original size:22 final size:22
Alignment explanation
Indices: 2906839--2906895 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
2906829 TGTCTCGTTT
*
2906839 TTTACTATTA-TATGCATATATA
1 TTTATTATTATTAT-CATATATA
*
2906861 TTTATTATTATTATTATATATA
1 TTTATTATTATTATCATATATA
*
2906883 -TTATTAATATTAT
1 TTTATTATTATTAT
2906896 TAGTACTCGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.39
22 16 0.52
23 3 0.10
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTATTATTATTATCATATATA
Found at i:2906884 original size:18 final size:18
Alignment explanation
Indices: 2906857--2906895 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2906847 TATATGCATA
* *
2906857 TATATTTATTATTATTAT
1 TATATATATTATTAATAT
2906875 TATATATATTATTAATAT
1 TATATATATTATTAATAT
2906893 TAT
1 TAT
2906896 TAGTACTCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATATATTATTAATAT
Found at i:2907036 original size:13 final size:12
Alignment explanation
Indices: 2907020--2907109 Score: 56
Period size: 13 Copynumber: 7.1 Consensus size: 12
2907010 ATATATATCG
2907020 TATATGTTTTATA
1 TATAT-TTTTATA
* *
2907033 TATATCATGTATA
1 TATAT-TTTTATA
*
2907046 TATATTTTTTAAA
1 TATA-TTTTTATA
*
2907059 TATTATTAGTTATA
1 TA-TATT-TTTATA
2907073 TATATTTTTATA
1 TATATTTTTATA
** *
2907085 CTAT-TTCATGTA
1 -TATATTTTTATA
2907097 TATATTTTTATA
1 TATATTTTTATA
2907109 T
1 T
2907110 TATCCTTATT
Statistics
Matches: 57, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
11 3 0.05
12 16 0.28
13 29 0.51
14 9 0.16
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.59
Consensus pattern (12 bp):
TATATTTTTATA
Found at i:2907155 original size:13 final size:13
Alignment explanation
Indices: 2907137--2907199 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 13
2907127 TTAATATTAA
*
2907137 TATATGTTTATAT
1 TATATGTATATAT
2907150 TATATGTATATA-
1 TATATGTATATAT
*
2907162 TCT-T-TA-ATAT
1 TATATGTATATAT
2907172 ATATATGTATATAT
1 -TATATGTATATAT
2907186 T-TATGTA-ATAT
1 TATATGTATATAT
2907197 TAT
1 TAT
2907200 TAATAGGTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
9 3 0.07
10 2 0.05
11 8 0.20
12 10 0.24
13 14 0.34
14 4 0.10
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (13 bp):
TATATGTATATAT
Found at i:2907183 original size:34 final size:32
Alignment explanation
Indices: 2907131--2907204 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 32
2907121 TTATTATTAA
*
2907131 TATTAATATATGTTTATAT-TATATGTATATAT
1 TATTAATATATATTTATATATATATGTA-ATAT
*
2907163 CT-TTAATATATATATGTATATATTTATGTAATAT
1 -TATTAATATATAT-T-TATATATATATGTAATAT
2907197 TATTAATA
1 TATTAATA
2907205 GGTGTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
32 10 0.29
33 3 0.09
34 15 0.43
35 7 0.20
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.54
Consensus pattern (32 bp):
TATTAATATATATTTATATATATATGTAATAT
Found at i:2907196 original size:21 final size:23
Alignment explanation
Indices: 2907136--2907185 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
2907126 ATTAATATTA
*
2907136 ATATATGTTT-ATAT-TATATGT
1 ATATATCTTTAATATATATATGT
2907157 ATATATCTTTAATATATATATGT
1 ATATATCTTTAATATATATATGT
2907180 ATATAT
1 ATATAT
2907186 TTATGTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 9 0.35
22 4 0.15
23 13 0.50
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (23 bp):
ATATATCTTTAATATATATATGT
Found at i:2907278 original size:24 final size:24
Alignment explanation
Indices: 2907235--2907297 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
2907225 TTCTAATATG
2907235 TATATATTATGTA-A-ATATTTTAA
1 TATATATTATGTATACAT-TTTTAA
*
2907258 TACTATATTATGTATACATTTTTTA
1 TA-TATATTATGTATACATTTTTAA
*
2907283 TATATATTACGTATA
1 TATATATTATGTATA
2907298 TATATCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 2 0.06
24 23 0.66
25 8 0.23
26 2 0.06
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (24 bp):
TATATATTATGTATACATTTTTAA
Found at i:2907414 original size:25 final size:27
Alignment explanation
Indices: 2907365--2907436 Score: 87
Period size: 25 Copynumber: 2.8 Consensus size: 27
2907355 TTATATTTTT
2907365 TTATGTATATATTTTTTAATAACTATA
1 TTATGTATATATTTTTTAATAACTATA
* *
2907392 TTATGTATGTA-TTTTTAA-CACTATA
1 TTATGTATATATTTTTTAATAACTATA
* *
2907417 TTATGCACATA-TTTTTAATA
1 TTATGTATATATTTTTTAATA
2907437 TAGTATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
25 21 0.55
26 7 0.18
27 10 0.26
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.53
Consensus pattern (27 bp):
TTATGTATATATTTTTTAATAACTATA
Found at i:2907463 original size:17 final size:20
Alignment explanation
Indices: 2907425--2907467 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2907415 TATTATGCAC
2907425 ATAT-TTTTAATATAGTATT
1 ATATGTTTTAATATAGTATT
2907444 ATATGTTTT-ATATA-TA-T
1 ATATGTTTTAATATAGTATT
2907461 ATATGTT
1 ATATGTT
2907468 CACTACTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.35
18 2 0.09
19 9 0.39
20 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (20 bp):
ATATGTTTTAATATAGTATT
Found at i:2909027 original size:26 final size:26
Alignment explanation
Indices: 2908990--2909047 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
2908980 TGATACAAAT
2908990 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
2909016 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2909042 TGATAA
1 TGATAA
2909048 ATGTTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:2909050 original size:14 final size:14
Alignment explanation
Indices: 2909031--2909061 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2909021 ATGGGTTAGG
2909031 TAAATGTTTCATGA
1 TAAATGTTTCATGA
2909045 TAAATGTTTCATGA
1 TAAATGTTTCATGA
2909059 TAA
1 TAA
2909062 GAATTTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (14 bp):
TAAATGTTTCATGA
Found at i:2914768 original size:26 final size:26
Alignment explanation
Indices: 2914731--2914788 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
2914721 TGATACAAAT
2914731 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
2914757 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2914783 TGATAA
1 TGATAA
2914789 ATGTTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:2914791 original size:14 final size:14
Alignment explanation
Indices: 2914772--2914802 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2914762 ATGGGTTAGG
2914772 TAAATGTTTCATGA
1 TAAATGTTTCATGA
2914786 TAAATGTTTCATGA
1 TAAATGTTTCATGA
2914800 TAA
1 TAA
2914803 GAATTTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (14 bp):
TAAATGTTTCATGA
Found at i:2919013 original size:18 final size:19
Alignment explanation
Indices: 2918987--2919022 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2918977 TAGACTAAAT
*
2918987 TTAACTCCCT-AATTTCAC
1 TTAAATCCCTAAATTTCAC
2919005 TTAAATCCCTAAATTTCA
1 TTAAATCCCTAAATTTCA
2919023 AAATTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATCCCTAAATTTCAC
Found at i:2920672 original size:16 final size:17
Alignment explanation
Indices: 2920641--2920676 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2920631 TTTTACCAGT
*
2920641 TTGAAAAAATTGTACCA
1 TTGAAAAAAATGTACCA
2920658 TTGAAAAAAAT-TACCA
1 TTGAAAAAAATGTACCA
2920674 TTG
1 TTG
2920677 CTGGACACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (17 bp):
TTGAAAAAAATGTACCA
Found at i:2921017 original size:10 final size:10
Alignment explanation
Indices: 2921002--2921026 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2920992 AAATAAGTAT
2921002 ATAAAAATAC
1 ATAAAAATAC
2921012 ATAAAAATAC
1 ATAAAAATAC
2921022 ATAAA
1 ATAAA
2921027 TATTTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (10 bp):
ATAAAAATAC
Found at i:2923894 original size:15 final size:14
Alignment explanation
Indices: 2923873--2923914 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2923863 AAACTTATAT
*
2923873 ATAAAATATTTAAAA
1 ATAAAAT-TTGAAAA
*
2923888 GTAAAATTTGAAAA
1 ATAAAATTTGAAAA
2923902 ATAAAATTT-AAAA
1 ATAAAATTTGAAAA
2923915 TTTCTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 4 0.17
14 14 0.58
15 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (14 bp):
ATAAAATTTGAAAA
Found at i:2923914 original size:13 final size:13
Alignment explanation
Indices: 2923880--2923914 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
2923870 TATATAAAAT
*
2923880 ATTTAAAAGTAAA
1 ATTTAAAAATAAA
2923893 ATTTGAAAAATAAA
1 ATTT-AAAAATAAA
2923907 ATTTAAAA
1 ATTTAAAA
2923915 TTTCTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (13 bp):
ATTTAAAAATAAA
Found at i:2924946 original size:4 final size:4
Alignment explanation
Indices: 2924937--2924972 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
2924927 TTTAACCGAA
*
2924937 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAC AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
2924973 TTGTTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Done.