Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 193 of 410
Found at i:59003456 original size:45 final size:43
Alignment explanation
Indices: 59003390--59003513 Score: 149
Period size: 45 Copynumber: 2.8 Consensus size: 43
59003380 ACAAGTTACA
* *
59003390 AATCTTATCTCCCCAATGTTGCAGTTGAGCAGATTAAAGATAACG
1 AATCTTATCTCCCTAA-GTTGCAGTGGAGCAGATTAAAGAT-ACG
* * * *
59003435 AATCTTATTTCCCTAAGGTTGCAGTGGAGCAGATTGAAGCTACT
1 AATCTTATCTCCCTAA-GTTGCAGTGGAGCAGATTAAAGATACG
*
59003479 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATT
1 AATCTTATCTCCCT-AAGTTGCAGTGGAGCAGATT
59003514 GAAGCGACAA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
44 32 0.46
45 37 0.54
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (43 bp):
AATCTTATCTCCCTAAGTTGCAGTGGAGCAGATTAAAGATACG
Found at i:59003505 original size:44 final size:44
Alignment explanation
Indices: 59003390--59003549 Score: 159
Period size: 44 Copynumber: 3.6 Consensus size: 44
59003380 ACAAGTTACA
* * * * *
59003390 AATCTTATCTCCC-CAATGTTGCAGTTGAGCAGATTAAAGATAAC
1 AATCTTATCTCCCTGAAGGTTGCAGTGGAGCAGATTGAAGCT-AC
*
59003434 GAATCTTATTTCCCT-AAGGTTGCAGTGGAGCAGATTGAAGCTAC
1 -AATCTTATCTCCCTGAAGGTTGCAGTGGAGCAGATTGAAGCTAC
* *
59003478 TAATCTTATCTCCCTGAA-GTTGTAGTGGAGCAGATTGAAGCGAC
1 -AATCTTATCTCCCTGAAGGTTGCAGTGGAGCAGATTGAAGCTAC
*
59003522 AATTTCTATAC-CCCTGAA-GTTGCAGTGG
1 AATCT-TAT-CTCCCTGAAGGTTGCAGTGG
59003550 GTTAGAATAA
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
43 4 0.04
44 58 0.58
45 38 0.38
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGGTTGCAGTGGAGCAGATTGAAGCTAC
Found at i:59009391 original size:36 final size:35
Alignment explanation
Indices: 59009351--59009428 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 35
59009341 ACTCTTTGTT
*
59009351 TTGGTGTATTTAGGTTGGACTAGCTCTTCG-GAGCCA
1 TTGGTGTATTTAGGATGGACTAGCTCTT-GTGAG-CA
* * * *
59009387 TTGGTGTGTTTCGGATGGATTATCTCTTGTGAGCA
1 TTGGTGTATTTAGGATGGACTAGCTCTTGTGAGCA
59009422 TTGGTGT
1 TTGGTGT
59009429 GTCTTGGGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
35 10 0.28
36 26 0.72
ACGTcount: A:0.14, C:0.13, G:0.32, T:0.41
Consensus pattern (35 bp):
TTGGTGTATTTAGGATGGACTAGCTCTTGTGAGCA
Found at i:59010440 original size:25 final size:25
Alignment explanation
Indices: 59010406--59010462 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
59010396 CTCAAGAGTT
* *
59010406 ACACAGCCTGGCACACGGGCGTGTG
1 ACACGGCCTGGAACACGGGCGTGTG
*
59010431 ACACGGCCTGGAACATGGGCGTGTG
1 ACACGGCCTGGAACACGGGCGTGTG
59010456 ACACGGC
1 ACACGGC
59010463 TGTGTGACAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.21, C:0.30, G:0.37, T:0.12
Consensus pattern (25 bp):
ACACGGCCTGGAACACGGGCGTGTG
Found at i:59010479 original size:11 final size:12
Alignment explanation
Indices: 59010418--59010483 Score: 62
Period size: 13 Copynumber: 5.2 Consensus size: 12
59010408 ACAGCCTGGC
59010418 ACACGGGCGTGTG
1 ACAC-GGCGTGTG
*
59010431 ACACGGCCTG-G
1 ACACGGCGTGTG
*
59010442 AACATGGGCGTGTG
1 -ACA-CGGCGTGTG
59010456 ACACGGCTGTGTG
1 ACACGGC-GTGTG
59010469 ACACGGCTGTGTG
1 ACACGGC-GTGTG
59010482 AC
1 AC
59010484 CTTACTCAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
11 1 0.02
12 11 0.24
13 32 0.71
14 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.39, T:0.18
Consensus pattern (12 bp):
ACACGGCGTGTG
Found at i:59018409 original size:43 final size:42
Alignment explanation
Indices: 59018320--59018431 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 42
59018310 GATATTTACG
* * *
59018320 TGTAAGACCATATCTGGGATATGGCATCGATACAGGACTTCG
1 TGTAAGACCATAGCTAGGATATGGCATCGATACAGGACTTCA
* *
59018362 TGTAAGACCATAGCTAGGCTATTGGCATCGATAC-GAGATTTCA
1 TGTAAGACCATAGCTAGGATA-TGGCATCGATACAG-GACTTCA
* *
59018405 TGTAAGACCATATCTGGGATATGGCAT
1 TGTAAGACCATAGCTAGGATATGGCAT
59018432 TGGTATGGTA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 25 0.42
43 35 0.58
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (42 bp):
TGTAAGACCATAGCTAGGATATGGCATCGATACAGGACTTCA
Found at i:59023356 original size:14 final size:14
Alignment explanation
Indices: 59023337--59023366 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59023327 ATTTTATTCC
59023337 AAAATTTCGAAAAT
1 AAAATTTCGAAAAT
*
59023351 AAAATTTCTAAAAT
1 AAAATTTCGAAAAT
59023365 AA
1 AA
59023367 TTATTTAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (14 bp):
AAAATTTCGAAAAT
Found at i:59023466 original size:18 final size:18
Alignment explanation
Indices: 59023439--59023476 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
59023429 TTTGAAATTA
*
59023439 TTTATTAATTTAT-TATTT
1 TTTATGAATTT-TCTATTT
59023457 TTTATGAATTTTCTATTT
1 TTTATGAATTTTCTATTT
59023475 TT
1 TT
59023477 ATAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTATGAATTTTCTATTT
Found at i:59023619 original size:16 final size:16
Alignment explanation
Indices: 59023594--59023645 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
59023584 TGGTTCACTG
* *
59023594 TAATGAAATAGGGCTA
1 TAATGGAATAGAGCTA
* *
59023610 TAATTGAATAGAGCTG
1 TAATGGAATAGAGCTA
*
59023626 TAATGGAATAGAGCTG
1 TAATGGAATAGAGCTA
59023642 TAAT
1 TAAT
59023646 CAGTAATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (16 bp):
TAATGGAATAGAGCTA
Found at i:59023713 original size:44 final size:46
Alignment explanation
Indices: 59023627--59023720 Score: 149
Period size: 44 Copynumber: 2.1 Consensus size: 46
59023617 ATAGAGCTGT
59023627 AATGGAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGG
*
59023673 AATGGAATAGAGCTGTAAT-AG-AATTCTTA-TGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTC-AACTGTTTGGTTGAATGG
59023717 AATG
1 AATG
59023721 ATGTTGTAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
44 24 0.52
45 3 0.07
46 19 0.41
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGG
Found at i:59023824 original size:25 final size:26
Alignment explanation
Indices: 59023791--59023841 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
59023781 GTTGGTAGAT
*
59023791 GATTATTGTT-ATTAAATTTTAATAA
1 GATTATTGTTAAATAAATTTTAATAA
*
59023816 GATTATTGTTAAATATATTTTAATAA
1 GATTATTGTTAAATAAATTTTAATAA
59023842 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (26 bp):
GATTATTGTTAAATAAATTTTAATAA
Found at i:59024142 original size:14 final size:14
Alignment explanation
Indices: 59024106--59024146 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
59024096 ATTATTAAAT
*
59024106 TTTAAT-AAAATTA
1 TTTAATAAAAATAA
*
59024119 -TTATTAAAAATAA
1 TTTAATAAAAATAA
59024132 TTTAATAAAAATAA
1 TTTAATAAAAATAA
59024146 T
1 T
59024147 AAATAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTAATAAAAATAA
Found at i:59024235 original size:58 final size:58
Alignment explanation
Indices: 59024102--59024237 Score: 184
Period size: 58 Copynumber: 2.3 Consensus size: 58
59024092 TATTATTATT
* * *
59024102 AAATTTTAATAAAATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAATC
1 AAATTTTAATATAATTATTACTAAAAATAATTTAATAAAAATAATAAATAATTTAATA
* * * * *
59024160 ATATTTTAACATGATTATTACTAAATATAATTTAAT-AAAATAATATATAATTTAATA
1 AAATTTTAATATAATTATTACTAAAAATAATTTAATAAAAATAATAAATAATTTAATA
59024217 AAATTCTTAATATAATTATTA
1 AAATT-TTAATATAATTATTA
59024238 TTATATGAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
57 23 0.35
58 43 0.65
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.43
Consensus pattern (58 bp):
AAATTTTAATATAATTATTACTAAAAATAATTTAATAAAAATAATAAATAATTTAATA
Found at i:59024433 original size:62 final size:62
Alignment explanation
Indices: 59024357--59024482 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
59024347 AAATAATTTG
*
59024357 ATTATTCTACAATAAAAAGTAAAATATAAGAAGTAATAAATAACTTGATAATCATATTTCAC
1 ATTATTCTACAATAAAAAGTAAAATATAAGAAGTAATAAATAACTTGAGAATCATATTTCAC
59024419 ATTATTCTACAATAAAAAGTAAAATATAAGAAGTAATAAATAACTTGAGAATCATATTTCAC
1 ATTATTCTACAATAAAAAGTAAAATATAAGAAGTAATAAATAACTTGAGAATCATATTTCAC
59024481 AT
1 AT
59024483 CTAAACATAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.32
Consensus pattern (62 bp):
ATTATTCTACAATAAAAAGTAAAATATAAGAAGTAATAAATAACTTGAGAATCATATTTCAC
Found at i:59031422 original size:38 final size:38
Alignment explanation
Indices: 59031380--59031461 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
59031370 AAAGAAGTTC
59031380 TTAAAATG-ATTTTA-AAATTTTATTAATTTTTATATTT
1 TTAAAATGTATTTTATAAATTTTATTAA-TTTTATATTT
* * *
59031417 ATTAAAA-GTATTTTATATATTTTTTTAATTTTCTATTT
1 -TTAAAATGTATTTTATAAATTTTATTAATTTTATATTT
59031455 TTAAAAT
1 TTAAAAT
59031462 TTAAATTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
37 7 0.18
38 21 0.55
39 10 0.26
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (38 bp):
TTAAAATGTATTTTATAAATTTTATTAATTTTATATTT
Found at i:59032543 original size:16 final size:16
Alignment explanation
Indices: 59032512--59032541 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
59032502 TTGACATCTC
59032512 TTTTTTTAAATATTTA
1 TTTTTTTAAATATTTA
59032528 TTTTTTT-AATATTT
1 TTTTTTTAAATATTT
59032542 TACTATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:59033253 original size:28 final size:29
Alignment explanation
Indices: 59033189--59033253 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
59033179 CTTATTTTCG
* *
59033189 TAAATTTTTAAAAAAATTATCTATTTTTA
1 TAAATTTTTAAAAAAATGATATATTTTTA
*
59033218 TAATATTTTT-AAAAAATGATAT-TTTTTT
1 TAA-ATTTTTAAAAAAATGATATATTTTTA
59033246 TAGAATTT
1 TA-AATTT
59033254 AATTTGAGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 11 0.35
29 14 0.45
30 6 0.19
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (29 bp):
TAAATTTTTAAAAAAATGATATATTTTTA
Found at i:59042725 original size:27 final size:28
Alignment explanation
Indices: 59042694--59042754 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
59042684 TAAGATGATT
59042694 ATATAAAAATTT-TC-AATATATAAAAGA
1 ATATAAAAATTTATCAAATAT-TAAAAGA
* * *
59042721 ATATATAAATTTATTAAATATTAAAATA
1 ATATAAAAATTTATCAAATATTAAAAGA
59042749 ATATAA
1 ATATAA
59042755 TATAAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 11 0.39
28 12 0.43
29 5 0.18
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (28 bp):
ATATAAAAATTTATCAAATATTAAAAGA
Found at i:59050627 original size:43 final size:42
Alignment explanation
Indices: 59050550--59050703 Score: 193
Period size: 43 Copynumber: 3.7 Consensus size: 42
59050540 TACCATACCA
* * *
59050550 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCATATCG
1 ATGCAATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* *
59050592 ATGTCAATAGCCCAGCTATGGTCTTACACGAAATCTCATATCG
1 ATG-CAATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * * * *
59050635 ACGCCATATCCCAAATAAGGTCTTACACAAAATCTCATA-CG
1 ATGCAATATCCCAGATATGGTCTTACACGAAATCTCATATCG
*
59050676 ATGCTATATCCCAGATATGGTCTTACAC
1 ATGCAATATCCCAGATATGGTCTTACAC
59050704 ATAATCTTGT
Statistics
Matches: 95, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
41 26 0.27
42 33 0.35
43 36 0.38
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (42 bp):
ATGCAATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:59053214 original size:61 final size:61
Alignment explanation
Indices: 59053139--59053328 Score: 344
Period size: 61 Copynumber: 3.1 Consensus size: 61
59053129 TAAACTTATG
*
59053139 TAATTTATATAAAAAATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATT
1 TAATTTATATAAAAAATTTATATTAAAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATT
59053200 TAATTTATATAAAAAATTTATATTAAAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATT
1 TAATTTATATAAAAAATTTATATTAAAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATT
* * *
59053261 TACTTTATATAAAAAATTTATATTAAAAAGTTTATTCCAATTTTTAATTTTGTAATGTATT
1 TAATTTATATAAAAAATTTATATTAAAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATT
59053322 TAATTTA
1 TAATTTA
59053329 AATTACAAAA
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 124 1.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (61 bp):
TAATTTATATAAAAAATTTATATTAAAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATT
Found at i:59053347 original size:48 final size:49
Alignment explanation
Indices: 59053275--59053378 Score: 149
Period size: 50 Copynumber: 2.1 Consensus size: 49
59053265 TTATATAAAA
* *
59053275 AATTTATATTAAAAAGTTTATTCCAATT-TTTAATTTTGTAATGTATTT
1 AATTTAAATTAAAAAGTTTATTCCAATTAATTAATTTTGTAATGTATTT
*
59053323 AATTTAAATTACAAAA-TTTGTTCCAATTAGATTAATTTTGTAATGTATTT
1 AATTTAAATTA-AAAAGTTTATTCCAATTA-ATTAATTTTGTAATGTATTT
59053373 AATTTA
1 AATTTA
59053379 TATAACGATA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
48 21 0.42
49 4 0.08
50 25 0.50
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.51
Consensus pattern (49 bp):
AATTTAAATTAAAAAGTTTATTCCAATTAATTAATTTTGTAATGTATTT
Found at i:59057767 original size:52 final size:52
Alignment explanation
Indices: 59057699--59057850 Score: 150
Period size: 52 Copynumber: 2.9 Consensus size: 52
59057689 AACATGTATA
59057699 CATCCATAATGAACTCGGACCAACTCAACGAGCTCGGATG-TCACATGCATCG
1 CATCCATAATGAACTCGGACCAACTCAACGAGCTCGGATGCTCACATGC-TCG
* * * * * * *
59057751 CATCCATAATGAACTCGGA--AACTCGGACCAACTCAACGA-GCTTAGATGCTTG
1 CATCCATAATGAACTCGGACCAACTC-AACGAGCTC--GGATGCTCACATGCTCG
* *
59057803 CATCCATAATTAACTCGGACCAACTCAATGAGCTCGGATGCTTCACAT
1 CATCCATAATGAACTCGGACCAACTCAACGAGCTCGGATGC-TCACAT
59057851 ATATCACGAA
Statistics
Matches: 77, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
50 5 0.06
51 8 0.10
52 42 0.55
53 17 0.22
54 5 0.06
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.22
Consensus pattern (52 bp):
CATCCATAATGAACTCGGACCAACTCAACGAGCTCGGATGCTCACATGCTCG
Found at i:59057894 original size:45 final size:45
Alignment explanation
Indices: 59057814--59057935 Score: 138
Period size: 45 Copynumber: 2.7 Consensus size: 45
59057804 ATCCATAATT
** * * *
59057814 AACTCGGACCAACTCAATGAGCTCGGA-TGCTTCACATATATCACG
1 AACTCGGACCAACTCAACAAGTTCGAATTTC-TCACATATATCACG
* * * *
59057859 AACTTGGACCACCTCAACAAGTTTGGATTTCTCACATATATCACG
1 AACTCGGACCAACTCAACAAGTTCGAATTTCTCACATATATCACG
*
59057904 AACTCGGACCAACTCAACGAGTTCGAATTTCT
1 AACTCGGACCAACTCAACAAGTTCGAATTTCT
59057936 AAATTCCTAG
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 62 0.97
46 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (45 bp):
AACTCGGACCAACTCAACAAGTTCGAATTTCTCACATATATCACG
Found at i:59058871 original size:28 final size:28
Alignment explanation
Indices: 59058831--59058888 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
59058821 TGGAAGCTTG
59058831 AACATAAACCCTACCCATGGCTTCCTCT
1 AACATAAACCCTACCCATGGCTTCCTCT
**
59058859 AACATAAACCCTACCTGTGGCTTCCTCT
1 AACATAAACCCTACCCATGGCTTCCTCT
59058887 AA
1 AA
59058889 GATTCGGCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.36, G:0.09, T:0.26
Consensus pattern (28 bp):
AACATAAACCCTACCCATGGCTTCCTCT
Found at i:59061948 original size:18 final size:18
Alignment explanation
Indices: 59061922--59061956 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59061912 TGCTCGACCC
*
59061922 CCTCTACCTCTCCCTATT
1 CCTCAACCTCTCCCTATT
*
59061940 CCTCAACCTGTCCCTAT
1 CCTCAACCTCTCCCTAT
59061957 AGCACTCTAG
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:0.14, C:0.49, G:0.03, T:0.34
Consensus pattern (18 bp):
CCTCAACCTCTCCCTATT
Found at i:59064210 original size:9 final size:9
Alignment explanation
Indices: 59064196--59064224 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
59064186 TCTGTTCACT
59064196 TTAGTTTAA
1 TTAGTTTAA
59064205 TTAG-TTAA
1 TTAGTTTAA
59064213 TTAGTTTAA
1 TTAGTTTAA
59064222 TTA
1 TTA
59064225 ACAACCCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (9 bp):
TTAGTTTAA
Found at i:59067284 original size:132 final size:132
Alignment explanation
Indices: 59067047--59067319 Score: 537
Period size: 132 Copynumber: 2.1 Consensus size: 132
59067037 CTACCACACC
59067047 GAATGAGGAAATCCCTCTTACGGTACTCAGTATTTTTCCATTCGGAACGATAGAGGTGAGTCACC
1 GAATGAGGAAATCCCTCTTACGGTACTCAGTATTTTTCCATTCGGAACGATAGAGGTGAGTCACC
59067112 CCAAGTTCGGCACTTTTAAGGTAAACAACACCTGATTAAAACCCTATTTTGATGAGATTGATAGC
66 CCAAGTTCGGCACTTTTAAGGTAAACAACACCTGATTAAAACCCTATTTTGATGAGATTGATAGC
59067177 AG
131 AG
*
59067179 GAATGAGGAAATCCCTCTTACGGTACTCAGTATTTTTCCATTCGGTACGATAGAGGTGAGTCACC
1 GAATGAGGAAATCCCTCTTACGGTACTCAGTATTTTTCCATTCGGAACGATAGAGGTGAGTCACC
59067244 CCAAGTTCGGCACTTTTAAGGTAAACAACACCTGATTAAAACCCTATTTTGATGAGATTGATAGC
66 CCAAGTTCGGCACTTTTAAGGTAAACAACACCTGATTAAAACCCTATTTTGATGAGATTGATAGC
59067309 AG
131 AG
59067311 GAATGAGGA
1 GAATGAGGA
59067320 GTATAAACTC
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 140 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (132 bp):
GAATGAGGAAATCCCTCTTACGGTACTCAGTATTTTTCCATTCGGAACGATAGAGGTGAGTCACC
CCAAGTTCGGCACTTTTAAGGTAAACAACACCTGATTAAAACCCTATTTTGATGAGATTGATAGC
AG
Found at i:59069834 original size:17 final size:17
Alignment explanation
Indices: 59069812--59069852 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
59069802 CCTCTTATCT
* **
59069812 TTTTATTTTTATTTTTA
1 TTTTATTTTCATTTCAA
59069829 TTTTATTTTCATTTCAA
1 TTTTATTTTCATTTCAA
59069846 TTTTATT
1 TTTTATT
59069853 ATTTTCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTTCATTTCAA
Found at i:59072753 original size:13 final size:13
Alignment explanation
Indices: 59072735--59072762 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
59072725 TTAGTTTAAC
59072735 TAGTTAATTAGTT
1 TAGTTAATTAGTT
59072748 TAGTTAATTAGTT
1 TAGTTAATTAGTT
59072761 TA
1 TA
59072763 ATAAACAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (13 bp):
TAGTTAATTAGTT
Found at i:59079017 original size:30 final size:30
Alignment explanation
Indices: 59078983--59079043 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
59078973 TTCCCGAGCC
59078983 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
59079013 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
59079043 T
1 T
59079044 GAGTTAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:59079372 original size:18 final size:19
Alignment explanation
Indices: 59079339--59079374 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
59079329 TTAAATTTAG
*
59079339 TAAATTAATTGAATTATGT
1 TAAATTAAATGAATTATGT
59079358 TAAATTAAATG-ATTATG
1 TAAATTAAATGAATTATG
59079375 GTGCCAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (19 bp):
TAAATTAAATGAATTATGT
Found at i:59088320 original size:39 final size:39
Alignment explanation
Indices: 59088277--59088359 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
59088267 ATCATTTAAC
59088277 ATCATAAAACTCGTGAATTCATCAATGGCATCTCATCAA
1 ATCATAAAACTCGTGAATTCATCAATGGCATCTCATCAA
* *
59088316 ATCATAAAACTCTTGAATTCATCAATGGCGTCTCATCAA
1 ATCATAAAACTCGTGAATTCATCAATGGCATCTCATCAA
59088355 ATCAT
1 ATCAT
59088360 CAACAATTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (39 bp):
ATCATAAAACTCGTGAATTCATCAATGGCATCTCATCAA
Found at i:59093965 original size:17 final size:17
Alignment explanation
Indices: 59093943--59093975 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
59093933 AAAACATAAA
59093943 ATAAAAT-TTAAGAAAAC
1 ATAAAATCTTAA-AAAAC
59093960 ATAAAATCTTAAAAAA
1 ATAAAATCTTAAAAAA
59093976 TTAAAACATA
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:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (17 bp):
ATAAAATCTTAAAAAAC
Found at i:59094400 original size:23 final size:23
Alignment explanation
Indices: 59094374--59094419 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
59094364 TAACATTAAT
59094374 CCATTAATTTATAACAAAAATAA
1 CCATTAATTTATAACAAAAATAA
*
59094397 CCATTAATTTTTAACAAAAATAA
1 CCATTAATTTATAACAAAAATAA
59094420 TTAACCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (23 bp):
CCATTAATTTATAACAAAAATAA
Found at i:59094476 original size:21 final size:21
Alignment explanation
Indices: 59094442--59094496 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
59094432 TTTCTATTTT
*
59094442 TTTCTTCTCTTTCTCCTTCTC
1 TTTCTTCTCTTTCTCCTTCAC
59094463 TTTC-TCTCTGTTCTCCTTCAC
1 TTTCTTCTCT-TTCTCCTTCAC
*
59094484 TTT-TTTTCTTTCT
1 TTTCTTCTCTTTCT
59094497 TTTTCCCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 9 0.30
21 21 0.70
ACGTcount: A:0.02, C:0.33, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTCTTCTCTTTCTCCTTCAC
Found at i:59095242 original size:33 final size:33
Alignment explanation
Indices: 59095205--59095275 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
59095195 GAAGTCCAAG
* *
59095205 GAGCTTGCTTTTGAAGCCTCCAAGAAA-GCCGAT
1 GAGCTGGCTCTTGAAGCCTCCAA-AAAGGCCGAT
*
59095238 GAGCTGGCTCTTGAAGCTTCCAAAAAGGCCGAT
1 GAGCTGGCTCTTGAAGCCTCCAAAAAGGCCGAT
59095271 GAGCT
1 GAGCT
59095276 CAGAGTCGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 31 0.91
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (33 bp):
GAGCTGGCTCTTGAAGCCTCCAAAAAGGCCGAT
Found at i:59096705 original size:6 final size:6
Alignment explanation
Indices: 59096694--59096747 Score: 108
Period size: 6 Copynumber: 9.0 Consensus size: 6
59096684 ATTATTCAGT
59096694 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
59096742 TGATGG
1 TGATGG
59096748 GAGTTTTGGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
TGATGG
Found at i:59099091 original size:36 final size:36
Alignment explanation
Indices: 59099044--59099121 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
59099034 CCACACACTC
** *
59099044 GTGTGGGTCACATGGCCGTGTGGAATGGTTTAGCCG
1 GTGTGGGTCACATGGCCACGTGGAATGGTTCAGCCG
*
59099080 GTGTGGGTCACATGGCCACGTGGAATGGTTCAGCCT
1 GTGTGGGTCACATGGCCACGTGGAATGGTTCAGCCG
59099116 GTGTGG
1 GTGTGG
59099122 CTCCTGCAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.14, C:0.18, G:0.41, T:0.27
Consensus pattern (36 bp):
GTGTGGGTCACATGGCCACGTGGAATGGTTCAGCCG
Found at i:59102582 original size:48 final size:48
Alignment explanation
Indices: 59102527--59102647 Score: 188
Period size: 48 Copynumber: 2.5 Consensus size: 48
59102517 ATATATTTGT
*
59102527 GCCGATGCCATGTCCCAGACATGGTCTTATACTAGCAAACATATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAAACATATCAAC
* * * * *
59102575 GCTGATGCCATGTCTCAGACATGGTCTTACACTGGCACACATATCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAAACATATCAAC
59102623 GCCGATGCCATGTCCCAGACATGGT
1 GCCGATGCCATGTCCCAGACATGGT
59102648 TTTTGTGACA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAAACATATCAAC
Found at i:59104357 original size:41 final size:41
Alignment explanation
Indices: 59104300--59104449 Score: 221
Period size: 41 Copynumber: 3.7 Consensus size: 41
59104290 TCGGGGTTTA
59104300 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
59104341 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
* * * * * * * *
59104382 AA-CCGAACCTAGTTTCGAAGGGCCTTCGGGCCAATGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
59104422 AATCCGAGCTTGGTCTCGAAGGGCTTTT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTT
59104450 TGAGTCAGCG
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 32 0.34
41 62 0.66
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (41 bp):
AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
Found at i:59112569 original size:41 final size:41
Alignment explanation
Indices: 59112512--59112661 Score: 221
Period size: 41 Copynumber: 3.7 Consensus size: 41
59112502 TCGGGGTTTA
59112512 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
59112553 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
* * * * * * * *
59112594 AA-CCGAACCTAGTTTCGAAGGGCCTTCGGGCCAATGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
59112634 AATCCGAGCTTGGTCTCGAAGGGCTTTT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTT
59112662 TGAGTCAGCG
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 32 0.34
41 62 0.66
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (41 bp):
AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
Found at i:59116656 original size:38 final size:38
Alignment explanation
Indices: 59116565--59116785 Score: 192
Period size: 38 Copynumber: 5.7 Consensus size: 38
59116555 ATAGCGACAT
* *
59116565 AAAGCCTGCTAGGCATAAAGCCTGATATAATACACCAGCAC
1 AAAGCCTGCTAGGCACAAAGCCCGA-AT-AT-CACCAGCAC
* * * *
59116606 GAAGCCTACTAGGCACAGAGCCCGAATATCACCGGCAC
1 AAAGCCTGCTAGGCACAAAGCCCGAATATCACCAGCAC
** * **
59116644 AAAGCCTGCTAGGCACATTGTCTAAATATCACCAGCAC
1 AAAGCCTGCTAGGCACAAAGCCCGAATATCACCAGCAC
* * * * * *
59116682 AAAGCCTGCTAGGTACAGAGCCCAAATATTACTAGCTC
1 AAAGCCTGCTAGGCACAAAGCCCGAATATCACCAGCAC
* * * * * *
59116720 AAAACCTTCTAGGCA-ATAAGCCTGATTATCACCGGCCC
1 AAAGCCTGCTAGGCACA-AAGCCCGAATATCACCAGCAC
59116758 AAAGCCTGCTAGGCACAAAGCCCGAATA
1 AAAGCCTGCTAGGCACAAAGCCCGAATA
59116786 ATGTTACGTT
Statistics
Matches: 141, Mismatches: 37, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
37 1 0.01
38 115 0.82
39 3 0.02
40 2 0.01
41 20 0.14
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (38 bp):
AAAGCCTGCTAGGCACAAAGCCCGAATATCACCAGCAC
Found at i:59116694 original size:76 final size:76
Alignment explanation
Indices: 59116569--59116785 Score: 213
Period size: 76 Copynumber: 2.8 Consensus size: 76
59116559 CGACATAAAG
* * *
59116569 CCTGCTAGGC-ATAAAGCCTGATATAATACACCAGCACGAAGCCTACTAGGCACAGAGCCCGAAT
1 CCTGCTAGGCAAT-AAGCCT-AAAT-AT-CACCAGCACAAAGCCTGCTAGGCACAGAGCCCGAAT
* *
59116633 ATCACCGGCACAAAG
62 ATCACCAGCACAAAA
* * * * *
59116648 CCTGCTAGGCACAT-TGTCTAAATATCACCAGCACAAAGCCTGCTAGGTACAGAGCCCAAATATT
1 CCTGCTAGGCA-ATAAGCCTAAATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCGAATATC
* *
59116712 ACTAGCTCAAAA
65 ACCAGCACAAAA
* * * * * *
59116724 CCTTCTAGGCAATAAGCCTGATTATCACCGGCCCAAAGCCTGCTAGGCACAAAGCCCGAATA
1 CCTGCTAGGCAATAAGCCTAAATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCGAATA
59116786 ATGTTACGTT
Statistics
Matches: 113, Mismatches: 22, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
75 2 0.02
76 91 0.81
77 2 0.02
78 3 0.03
79 13 0.12
81 2 0.02
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.18
Consensus pattern (76 bp):
CCTGCTAGGCAATAAGCCTAAATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCGAATATCA
CCAGCACAAAA
Found at i:59118376 original size:36 final size:35
Alignment explanation
Indices: 59118332--59118406 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 35
59118322 TGTTATTATC
59118332 ATAAATTTGCTTGAAAACCAAATCTCCACCACTAT
1 ATAAATTTGCTTGAAAACCAAATCTCCACCACTAT
*
59118367 ATAAGATTTGCTTGAAAACGAAATCTCCACCACTAT
1 ATAA-ATTTGCTTGAAAACCAAATCTCCACCACTAT
59118403 ATAA
1 ATAA
59118407 TGAGATGACA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 4 0.11
36 34 0.89
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (35 bp):
ATAAATTTGCTTGAAAACCAAATCTCCACCACTAT
Found at i:59119667 original size:15 final size:15
Alignment explanation
Indices: 59119647--59119676 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59119637 TATAAGTCCG
*
59119647 ACAAATAGAATAAAA
1 ACAAATAAAATAAAA
59119662 ACAAATAAAATAAAA
1 ACAAATAAAATAAAA
59119677 GATAGTTCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (15 bp):
ACAAATAAAATAAAA
Found at i:59120237 original size:3 final size:3
Alignment explanation
Indices: 59120229--59120271 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
59120219 AAATGGAAAT
59120229 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
59120272 AACACTCGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:59123013 original size:30 final size:29
Alignment explanation
Indices: 59122957--59123013 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
59122947 ATTTGTTGTC
* *
59122957 CACACGGCCAACGACACGGGCGTGTGTGA
1 CACACGGCCAACGAAACGGCCGTGTGTGA
*
59122986 CACACGGCCATGCGAAACGGCCGTGTGT
1 CACACGGCCA-ACGAAACGGCCGTGTGT
59123014 CCCCTGTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.23, C:0.32, G:0.33, T:0.12
Consensus pattern (29 bp):
CACACGGCCAACGAAACGGCCGTGTGTGA
Found at i:59141356 original size:28 final size:29
Alignment explanation
Indices: 59141289--59141360 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
59141279 ATAGTGAATC
*
59141289 CGCACACTTAGTGCTATATATATTCAGCT
1 CGCACACTTAGTGCTATATATATTCAACT
59141318 CGCACACTTAGTGCTATATA-A-TCAAACT
1 CGCACACTTAGTGCTATATATATTC-AACT
59141346 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
59141361 GTACAATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATATTCAACT
Found at i:59141382 original size:30 final size:28
Alignment explanation
Indices: 59141288--59141389 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 28
59141278 TATAGTGAAT
* *
59141288 CCGCACACTTAGTGCTATATATATTC-AGC
1 CCGCACACTTAGTGCTATACA-A-TCAAAC
* *
59141317 TCGCACACTTAGTGCTATATAATCAAAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* * *
59141345 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATACAA--TCAAAC
*
59141375 CCGCACACTCAGTGC
1 CCGCACACTTAGTGC
59141390 CAATCTTGTC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.37
29 20 0.32
30 18 0.29
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.28
Consensus pattern (28 bp):
CCGCACACTTAGTGCTATACAATCAAAC
Found at i:59149346 original size:30 final size:28
Alignment explanation
Indices: 59149281--59149353 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
59149271 TATAGTGAAT
*
59149281 CCGCACACTTAGTGCTATATAATCAAAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* * *
59149309 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATACAA--TCAAAC
*
59149339 CCGCACACTCAGTGC
1 CCGCACACTTAGTGC
59149354 CAATCTTGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
28 19 0.51
30 18 0.49
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (28 bp):
CCGCACACTTAGTGCTATACAATCAAAC
Found at i:59152862 original size:13 final size:13
Alignment explanation
Indices: 59152844--59152871 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
59152834 CGTCAAGCAG
59152844 TCATTGTCGTCAA
1 TCATTGTCGTCAA
59152857 TCATTGTCGTCAA
1 TCATTGTCGTCAA
59152870 TC
1 TC
59152872 TGAATTCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.39
Consensus pattern (13 bp):
TCATTGTCGTCAA
Found at i:59157768 original size:30 final size:28
Alignment explanation
Indices: 59157703--59157775 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
59157693 TATAGTGAAT
*
59157703 CCGCACACTTAGTGCTATATAATCAAAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* * *
59157731 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATACAA--TCAAAC
*
59157761 CCGCACACTCAGTGC
1 CCGCACACTTAGTGC
59157776 CAATCTTGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
28 19 0.51
30 18 0.49
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (28 bp):
CCGCACACTTAGTGCTATACAATCAAAC
Found at i:59160190 original size:93 final size:93
Alignment explanation
Indices: 59160078--59160249 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
59160068 GCCCATAAGT
* *
59160078 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
59160143 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
59160171 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
59160236 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
59160250 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:59160245 original size:46 final size:46
Alignment explanation
Indices: 59160070--59160245 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
59160060 TGTAACCCGC
* * *
59160070 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
59160116 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
59160166 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
59160209 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
59160246 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:59167195 original size:2 final size:2
Alignment explanation
Indices: 59167188--59167216 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59167178 TAAAATAAAT
59167188 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 T
59167217 TAAAAGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59167694 original size:16 final size:16
Alignment explanation
Indices: 59167662--59167691 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
59167652 AGAAATTTAA
59167662 TAATTCAAATATAAAT
1 TAATTCAAATATAAAT
59167678 TAATTC-AATATAAA
1 TAATTCAAATATAAA
59167692 ATTCAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATTCAAATATAAAT
Found at i:59167826 original size:67 final size:68
Alignment explanation
Indices: 59167714--59167841 Score: 170
Period size: 67 Copynumber: 1.9 Consensus size: 68
59167704 AGTTATTAAA
*
59167714 AAATTTATTTAACAAAAGTATTTTAATAAAATCATAATTCCTATTTATAAGCATGATAAATGATA
1 AAATTTATTTAACAAAAGTATTTTAATAAAATCATAATTCCTATTTATAAACATGATAAATGATA
59167779 ATT
66 ATT
* * * ** *
59167782 AAATTTATTTAACCAAA-TATTTTAGTAAAATTA-AATCTTTTATTTATAAATATGATAAAT
1 AAATTTATTTAACAAAAGTATTTTAATAAAATCATAAT-TCCTATTTATAAACATGATAAAT
59167842 TTTATAAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
66 3 0.06
67 33 0.63
68 16 0.31
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (68 bp):
AAATTTATTTAACAAAAGTATTTTAATAAAATCATAATTCCTATTTATAAACATGATAAATGATA
ATT
Found at i:59167859 original size:18 final size:19
Alignment explanation
Indices: 59167822--59167867 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
59167812 TTAAATCTTT
*
59167822 TATTTATAAATATGATAAA
1 TATTTATAAATATGAAAAA
59167841 T-TTTATAAATAAT-AAAAA
1 TATTTATAAAT-ATGAAAAA
59167859 TATTTATAA
1 TATTTATAA
59167868 TGGTAGATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TATTTATAAATATGAAAAA
Found at i:59173926 original size:46 final size:46
Alignment explanation
Indices: 59173825--59173952 Score: 177
Period size: 46 Copynumber: 2.8 Consensus size: 46
59173815 AATTGAGATT
*
59173825 CGAACTCGTTGAGTTGCGTTCCGAGTTCACTTATGGATGCAAGCATC
1 CGAACTCGTTGAGTTGCGTTCCGAGTTCA-TTATGGATGCAAGCACC
* * *
59173872 CGAACTCGTTGAGTTGTGTTCCAAGTTCATTATGGATGTGAA-CACC
1 CGAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATG-CAAGCACC
* *
59173918 CGAGCTCGTTGAGTTGCGTTCCGAGTTTATTATGG
1 CGAACTCGTTGAGTTGCGTTCCGAGTTCATTATGG
59173953 GTGAAATTAT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
46 43 0.60
47 29 0.40
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATGCAAGCACC
Found at i:59178769 original size:30 final size:29
Alignment explanation
Indices: 59178735--59178793 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
59178725 ACATTTCGAG
*
59178735 TACACACATGGTATCGATTTCGATGCAAAA
1 TACACACATGGCATCGATTT-GATGCAAAA
* *
59178765 TACACATATGGCATCGATTTGATTCAAAA
1 TACACACATGGCATCGATTTGATGCAAAA
59178794 CCACTCCCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (29 bp):
TACACACATGGCATCGATTTGATGCAAAA
Found at i:59183126 original size:7 final size:7
Alignment explanation
Indices: 59183114--59183142 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
59183104 CTCTTTTTAT
59183114 AAATAAA
1 AAATAAA
59183121 AAATAAA
1 AAATAAA
59183128 AAATAAA
1 AAATAAA
59183135 AAATAAA
1 AAATAAA
59183142 A
1 A
59183143 TTTAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAATAAA
Found at i:59184896 original size:30 final size:30
Alignment explanation
Indices: 59184839--59184898 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
59184829 TTATTTTTAA
* *
59184839 TTAAATTTTACCCTAAACTTTTAAAAAAAG
1 TTAAATTTGACCATAAACTTTTAAAAAAAG
* * *
59184869 TTAAATTTGACCATCAATTTTTTAAAAAAG
1 TTAAATTTGACCATAAACTTTTAAAAAAAG
59184899 AGTTTGAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (30 bp):
TTAAATTTGACCATAAACTTTTAAAAAAAG
Found at i:59186665 original size:14 final size:15
Alignment explanation
Indices: 59186613--59186666 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 15
59186603 AGTTTTGACA
59186613 ATTTTATTTAAGTTT
1 ATTTTATTTAAGTTT
59186628 AATTTT-TTTAA-TTT
1 -ATTTTATTTAAGTTT
*
59186642 TTTTTATTTAAGTTT
1 ATTTTATTTAAGTTT
59186657 ATTTT-TTTAA
1 ATTTTATTTAA
59186667 TCAATTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 4 0.12
14 13 0.38
15 12 0.35
16 5 0.15
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (15 bp):
ATTTTATTTAAGTTT
Found at i:59187864 original size:2 final size:2
Alignment explanation
Indices: 59187857--59187893 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
59187847 AGACGGTATT
59187857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59187894 TCTTTTACCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59199481 original size:40 final size:40
Alignment explanation
Indices: 59199426--59199646 Score: 313
Period size: 40 Copynumber: 5.6 Consensus size: 40
59199416 TATTCGAATG
* * *
59199426 ATATCCGGGTTAAGTCCCTAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
*
59199466 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
59199506 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * *
59199546 ATAT-CGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * *
59199585 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATT
*
59199625 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
59199647 TACTTGGGTT
Statistics
Matches: 165, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
39 50 0.30
40 113 0.68
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
Found at i:59199593 original size:79 final size:79
Alignment explanation
Indices: 59199426--59199646 Score: 327
Period size: 79 Copynumber: 2.8 Consensus size: 79
59199416 TATTCGAATG
* * *
59199426 ATATCCGGGTTAAGTCCCTAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATAT-CGGGCTAAGTCCCGAAGGCA
*
59199491 TTTGTGCTATTGATT
65 TTTGTGCTATTGACT
*
59199506 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATATCGGGCTAAGTCCCGAAGGCTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATATCGGGCTAAGTCCCGAAGGCAT
59199571 TTGTGCTATTGACT
66 TTGTGCTATTGACT
* * * * *
59199585 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCCGGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTATATCGGGCTAAGTCCCGAAGG
59199647 TACTTGGGTT
Statistics
Matches: 130, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
79 87 0.67
80 43 0.33
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (79 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATATCGGGCTAAGTCCCGAAGGCAT
TTGTGCTATTGACT
Found at i:59214388 original size:40 final size:40
Alignment explanation
Indices: 59214314--59214522 Score: 307
Period size: 40 Copynumber: 5.2 Consensus size: 40
59214304 GCTACTCGTT
* * *
59214314 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TGGTAACTCGCA
59214353 CAAATGCCTTCGGGACTTAACCCGGATTTGGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTGGTAACTCGCA
*
59214393 CAAATGCCTTCGGGACTTAACCCGGATTTGGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTGGTAACTCGCA
59214433 CAAATGCCTTCGGGACTTAACCCGGATTTGGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTGGTAACTCGCA
** * *
59214473 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTGGTAACTCGCA
59214513 CAAATGCCTT
1 CAAATGCCTT
59214523 TGGATCTTAG
Statistics
Matches: 158, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 14 0.09
40 142 0.90
41 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTGGTAACTCGCA
Found at i:59214562 original size:120 final size:120
Alignment explanation
Indices: 59214314--59214578 Score: 299
Period size: 120 Copynumber: 2.2 Consensus size: 120
59214304 GCTACTCGTT
* *
59214314 CAAATGCCTTC-GGACAT-AGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGGAC-TCAACCCGGATT-TGGTAACTCGCACAAATGCCTTCGGGACTTAACCC
* * * *
59214376 GGATTTGGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGTAACTCACA
64 GGATTTAGTAACTCACACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCACA
* **
59214433 CAAATGCCTTCGGGACTTAACCCGGATTTGGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGACTCAACCCGGATTTGGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* ** * *
59214497 GATTTAGTAACTCACACAAATGCCTT-TGGATCTTAGTCCGGATATAGTCACTTAGCA
65 GATTTAGTAACTCACACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAACTCA-CA
* *
59214554 TAAA-GCCTTCGGGACTCAGCCCGGA
1 CAAATGCCTTCGGGACTCAACCCGGA
59214579 CATCATTCGA
Statistics
Matches: 124, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
119 18 0.15
120 99 0.80
121 7 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (120 bp):
CAAATGCCTTCGGGACTCAACCCGGATTTGGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATTTAGTAACTCACACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCACA
Found at i:59214578 original size:80 final size:79
Alignment explanation
Indices: 59214314--59214522 Score: 339
Period size: 80 Copynumber: 2.6 Consensus size: 79
59214304 GCTACTCGTT
* *
59214314 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGACTTAGCCCGGATT-TAGTAACTCACACAAATGCCTTCGGGACTTAACCCGG
59214378 ATTTGGTAACTCGCA
65 ATTTGGTAACTCGCA
* *
59214393 CAAATGCCTTCGGGACTTAACCCGGATTTGGTAACTCACACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTAACTCACACAAATGCCTTCGGGACTTAACCCGG
59214458 ATTTGGTAACTCGCA
65 ATTTGGTAACTCGCA
*
59214473 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCACACAAATGCCTT
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAACTCACACAAATGCCTT
59214523 TGGATCTTAG
Statistics
Matches: 120, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
79 14 0.12
80 104 0.87
81 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCACACAAATGCCTTCGGGACTTAACCCGGA
TTTGGTAACTCGCA
Found at i:59216649 original size:40 final size:39
Alignment explanation
Indices: 59216484--59216667 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
59216474 AAATTGAATG
* * *
59216484 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
59216524 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
59216564 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
59216604 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
59216643 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
59216668 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:59216692 original size:80 final size:81
Alignment explanation
Indices: 59216524--59216712 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
59216514 GCTGGAAATT
* * * *
59216524 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
59216589 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
59216605 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
59216668 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
59216684 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
59216713 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:59224771 original size:40 final size:39
Alignment explanation
Indices: 59224607--59224789 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
59224597 AAATTGAATG
* *
59224607 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
59224646 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
59224686 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
59224726 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
59224765 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
59224790 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 25, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 15 0.13
40 92 0.81
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:59224814 original size:80 final size:81
Alignment explanation
Indices: 59224646--59224834 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
59224636 GCTGGAAATT
* * * *
59224646 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
59224711 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
59224727 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
59224790 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
59224806 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
59224835 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:59226434 original size:18 final size:19
Alignment explanation
Indices: 59226408--59226445 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
59226398 GTTTTCATCA
*
59226408 TTTTCTTTCTCC-TTTCTT
1 TTTTCTTTCCCCATTTCTT
*
59226426 TTTTTTTTCCCCATTTCTT
1 TTTTCTTTCCCCATTTCTT
59226445 T
1 T
59226446 ATTACTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTCTTTCCCCATTTCTT
Found at i:59233007 original size:40 final size:39
Alignment explanation
Indices: 59232963--59233135 Score: 206
Period size: 40 Copynumber: 4.3 Consensus size: 39
59232953 GCTACTCGTT
* * * *
59232963 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTGGCA
1 CAAATGCCTTCGGGACTTAACCCGATT-TAGTAACTCGCA
*
59233003 CAAATGCCTTCGGGACTTAACCCGGATTTGGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCC-GATTTAGTAACTCGCA
*
59233043 CAAATGCCTTCGGGACTTAACCCAGATTTGGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCC-GATTTAGTAACTCGCA
**
59233083 CAAATGCCATT--GGATCTTAGTCCGAATTTAGTAACTCGCA
1 CAAATGCC-TTCGGGA-CTTAACCCG-ATTTAGTAACTCGCA
59233123 CAAATGCCTTCGG
1 CAAATGCCTTCGG
59233136 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 9, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
39 6 0.05
40 106 0.90
41 6 0.05
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAACCCGATTTAGTAACTCGCA
Found at i:59233172 original size:40 final size:40
Alignment explanation
Indices: 59232963--59233173 Score: 146
Period size: 40 Copynumber: 5.3 Consensus size: 40
59232953 GCTACTCGTT
* * ** *
59232963 CAAATGCCTTCGGGA-CATAGCCCGGTTATAGTAACTGGCA
1 CAAATGCCTTC-GGATCTTAGTCCGAATATAGTAACTAGCA
** * * * *
59233003 CAAATGCCTTCGGGA-CTTAACCCGGATTTGGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGTCCGAATATAGTAACTAGCA
* * * * *
59233043 CAAATGCCTTCGGGA-CTTA-ACCCAGATTTGGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGTCCGA-ATATAGTAACTAGCA
* *
59233083 CAAATGCCATT-GGATCTTAGTCCGAATTTAGTAACTCGCA
1 CAAATGCC-TTCGGATCTTAGTCCGAATATAGTAACTAGCA
*
59233123 CAAATGCCTTCGGATCTTAGTCCGAATATAGTCACTTAGCA
1 CAAATGCCTTCGGATCTTAGTCCGAATATAGTAAC-TAGCA
*
59233164 TAAA-GCCTTC
1 CAAATGCCTTC
59233174 AGGACTCAGC
Statistics
Matches: 149, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
39 7 0.05
40 130 0.87
41 12 0.08
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGATCTTAGTCCGAATATAGTAACTAGCA
Found at i:59238166 original size:41 final size:40
Alignment explanation
Indices: 59237969--59238168 Score: 240
Period size: 40 Copynumber: 5.0 Consensus size: 40
59237959 AGCGTGGTTA
* * * *
59237969 TAGTAATTCGCACAATTGCCTTCGAGAATTAGCCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT
* *
59238009 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGTTT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT
* * * *
59238049 TGGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGTTT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT
* *
59238089 TGGTAACTCGCACAAATGCCTTCGGGAATT-GACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAG-CCCGGATT
* * *
59238129 TAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGAT
1 TAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCGGAT
59238169 ACCATTCGAA
Statistics
Matches: 140, Mismatches: 17, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
40 112 0.80
41 27 0.19
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT
Found at i:59247494 original size:25 final size:27
Alignment explanation
Indices: 59247455--59247504 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
59247445 GGTGAAGAAG
59247455 AAAAAGAAGAGGGAAAAAAAAGAAAAT
1 AAAAAGAAGAGGGAAAAAAAAGAAAAT
*
59247482 AAAAAGAA-A-GGAAAGAAAAGAAA
1 AAAAAGAAGAGGGAAAAAAAAGAAA
59247505 TAAGGGGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.59
26 1 0.05
27 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (27 bp):
AAAAAGAAGAGGGAAAAAAAAGAAAAT
Found at i:59252858 original size:43 final size:43
Alignment explanation
Indices: 59252795--59253040 Score: 305
Period size: 43 Copynumber: 5.7 Consensus size: 43
59252785 TGAAAAACCT
* * * * *
59252795 CCGCTATAGAACGTGACCTTTAGTGGCGCTTTTCTCATAAACG
1 CCGCTATAGAACGTGGCCTTTAGCGGCGCTTGTCCCACAAACG
* * *
59252838 TCGCTATAGAACGTGGCCTTTAGCGGTGCTTGTCCCATAAACG
1 CCGCTATAGAACGTGGCCTTTAGCGGCGCTTGTCCCACAAACG
** ** *
59252881 TTGCTATAGAACGTGGCCTTTAAAGGCGCTTGTCCCACAAACA
1 CCGCTATAGAACGTGGCCTTTAGCGGCGCTTGTCCCACAAACG
*
59252924 CCGCTATAGAACGTGGCCTTTAGCGGCACTTGTCCCACAAACG
1 CCGCTATAGAACGTGGCCTTTAGCGGCGCTTGTCCCACAAACG
* * *
59252967 CCGCTATAGAAAGTGGCCTTAAGCAGCGCTT-TCCCCACAAACG
1 CCGCTATAGAACGTGGCCTTTAGCGGCGCTTGT-CCCACAAACG
**
59253010 CTACTATAGAACGTGGCCTTTAGCGGCGCTT
1 CCGCTATAGAACGTGGCCTTTAGCGGCGCTT
59253041 TCACCAAAAA
Statistics
Matches: 175, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
42 1 0.01
43 174 0.99
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (43 bp):
CCGCTATAGAACGTGGCCTTTAGCGGCGCTTGTCCCACAAACG
Found at i:59253329 original size:68 final size:68
Alignment explanation
Indices: 59253216--59253347 Score: 219
Period size: 68 Copynumber: 1.9 Consensus size: 68
59253206 ATGTTAAAGG
59253216 TTATAATGTTAAAATATTTTTACATTAAGAAAACAAACATCTAGGATGGCAGATTCTGCGGCTGC
1 TTATAATGTTAAAATATTTTTACATTAAGAAAACAAACATCTAGGATGGCAGATTCTGCGGCTGC
59253281 TGA
66 TGA
* ** * *
59253284 TTATAATGTTAAATTATTTTTACATTAAGAAAACAAATGTTTAGGATGGCAGATTTTGCGGCTG
1 TTATAATGTTAAAATATTTTTACATTAAGAAAACAAACATCTAGGATGGCAGATTCTGCGGCTG
59253348 TTGAAACTCT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (68 bp):
TTATAATGTTAAAATATTTTTACATTAAGAAAACAAACATCTAGGATGGCAGATTCTGCGGCTGC
TGA
Found at i:59259045 original size:9 final size:9
Alignment explanation
Indices: 59259033--59259104 Score: 65
Period size: 9 Copynumber: 8.0 Consensus size: 9
59259023 GGGTGTAAAC
59259033 TATGTAAGT
1 TATGTAAGT
59259042 TATGTAAGT
1 TATGTAAGT
*
59259051 TATGCAAGT
1 TATGTAAGT
* *
59259060 TATGATATGA
1 TATG-TAAGT
* *
59259070 TATAT-ATT
1 TATGTAAGT
*
59259078 TATGTACGT
1 TATGTAAGT
*
59259087 TATGTAAAT
1 TATGTAAGT
59259096 TATGTAAGT
1 TATGTAAGT
59259105 CCATAGATAT
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
8 4 0.09
9 38 0.81
10 5 0.11
ACGTcount: A:0.35, C:0.03, G:0.18, T:0.44
Consensus pattern (9 bp):
TATGTAAGT
Found at i:59259099 original size:45 final size:46
Alignment explanation
Indices: 59259033--59259144 Score: 158
Period size: 45 Copynumber: 2.5 Consensus size: 46
59259023 GGGTGTAAAC
*
59259033 TATGTAAGTTATGTAAGTTATGCAAGT-TAT-GATATGATATATATT
1 TATGT-AGTTATGTAAGTTATGCAAGTCCATAGATATGATATATATT
* *
59259078 TATGTACGTTATGTAAATTATGTAAGTCCATAGATATGATATATATT
1 TATGTA-GTTATGTAAGTTATGCAAGTCCATAGATATGATATATATT
59259125 TATGTA-TTATGTAAGTTATG
1 TATGTAGTTATGTAAGTTATG
59259145 ATCTAATGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
44 1 0.02
45 36 0.60
46 2 0.03
47 21 0.35
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.45
Consensus pattern (46 bp):
TATGTAGTTATGTAAGTTATGCAAGTCCATAGATATGATATATATT
Found at i:59259850 original size:41 final size:41
Alignment explanation
Indices: 59259804--59259904 Score: 166
Period size: 41 Copynumber: 2.5 Consensus size: 41
59259794 CCATAGTAGA
* * *
59259804 GAAAATAATAAAATAAATGATAAATATAATAGTATAATAGC
1 GAAAATAATAAAATAAATGACAAATATAAGAGTACAATAGC
*
59259845 GAAAATAATAAAATAAATGACAAATATAAGAGTACAATAGT
1 GAAAATAATAAAATAAATGACAAATATAAGAGTACAATAGC
59259886 GAAAATAATAAAATAAATG
1 GAAAATAATAAAATAAATG
59259905 TAAGAATTAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.62, C:0.03, G:0.11, T:0.24
Consensus pattern (41 bp):
GAAAATAATAAAATAAATGACAAATATAAGAGTACAATAGC
Found at i:59262047 original size:41 final size:41
Alignment explanation
Indices: 59261998--59262099 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 41
59261988 AAAGAAACAT
* *
59261998 CACTATTGCTCAACCTTTTGCGGCATTTCGACCAAAAACGC
1 CACTATTGCTCAACCTTTTGCAGCATTTCGACAAAAAACGC
* *
59262039 CACTATTGCTCAA-CTTTTAGCAGCATTTTGATAAAAAACGC
1 CACTATTGCTCAACCTTTT-GCAGCATTTCGACAAAAAACGC
*
59262080 CACTATTGCTCAACTTTTTG
1 CACTATTGCTCAACCTTTTG
59262100 TGGCGCTTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 5 0.09
41 45 0.83
42 4 0.07
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (41 bp):
CACTATTGCTCAACCTTTTGCAGCATTTCGACAAAAAACGC
Found at i:59267846 original size:40 final size:40
Alignment explanation
Indices: 59267719--59267848 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
59267709 TTGCTGGAAA
* * *
59267719 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
59267759 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
59267799 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
59267839 TTATATCCGG
1 TTATATCCGG
59267849 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.05
40 73 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.23
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:59275808 original size:124 final size:124
Alignment explanation
Indices: 59275586--59275810 Score: 326
Period size: 124 Copynumber: 1.8 Consensus size: 124
59275576 GAATTATGTG
* * * * * * *
59275586 AAATGAAATATGGATGTGTATTGATTATTGATTTATGTGTGTATGAGTATTTGAATGATACCCGG
1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
* **
59275651 GCTAAGTCCCGAAGGCGATTATGCTAGTGATTATATTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA
*
59275710 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATATCCGG
1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
*
59275775 GCTAAGTCCCGAAGACG-TTATTGCTGGAAATTATAT
66 GCTAAGTCCCGAAGACGATTA-TGCTAGAAATTATAT
59275811 CCGGGTTAAG
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 3 0.03
124 85 0.97
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (124 bp):
AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA
Found at i:59275932 original size:40 final size:40
Alignment explanation
Indices: 59275805--59275934 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
59275795 TTGCTGGAAA
* * *
59275805 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
59275845 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
59275885 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
59275925 TTATATCCGG
1 TTATATCCGG
59275935 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.05
40 73 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.23
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:59278974 original size:31 final size:32
Alignment explanation
Indices: 59278936--59278995 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
59278926 TTTTTTGCCT
*
59278936 TTAGCGGCG-TTTC-TAAGCGCCGCTAAAAGTA
1 TTAGCGGCGCTTTCACAAGCGCCG-TAAAAGTA
59278967 TTAGCGGCGCTTTCACAAGCGCCGTAAAA
1 TTAGCGGCGCTTTCACAAGCGCCGTAAAA
59278996 AACGTCGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 9 0.35
32 9 0.35
33 8 0.31
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (32 bp):
TTAGCGGCGCTTTCACAAGCGCCGTAAAAGTA
Found at i:59279087 original size:43 final size:43
Alignment explanation
Indices: 59279035--59279347 Score: 380
Period size: 42 Copynumber: 7.5 Consensus size: 43
59279025 TCATGGCGTT
* * * *
59279035 TTTTA-AAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGTGC
1 TTTTATAAAAAACGCCGCTATAGACCAAGACTTTTAGCGGCGC
* *
59279077 TTTTTTAAAAAACGCTGCTATAGACCAAGA-TTTTAGCGGCGC
1 TTTTATAAAAAACGCCGCTATAGACCAAGACTTTTAGCGGCGC
*
59279119 TTTTAT-AAAAACGCCGCTATAGACC-TGTACTTTTAGCGGCGC
1 TTTTATAAAAAACGCCGCTATAGACCAAG-ACTTTTAGCGGCGC
* *
59279161 TTTT-TAAAAAAAGCCG--ATAGACTAAGAAC-TTTAGCGGCGC
1 TTTTATAAAAAACGCCGCTATAGACCAAG-ACTTTTAGCGGCGC
* *
59279201 TTTTATAAAAAACGCCGCTATAGACCTATACTTTTAGCGGCGC
1 TTTTATAAAAAACGCCGCTATAGACCAAGACTTTTAGCGGCGC
59279244 TTTTATAAAAAACGCCGCTATAGACCAAGAC-TTTAGCGGCGC
1 TTTTATAAAAAACGCCGCTATAGACCAAGACTTTTAGCGGCGC
*
59279286 TTTTAT-AAAAACGCCGCTATAGACC-TGTACTTTTAGCGGCG-
1 TTTTATAAAAAACGCCGCTATAGACCAAG-ACTTTTAGCGGCGC
* *
59279327 TTTTTTAAAAAAGCACCGCTA
1 TTTTATAAAAAA-CGCCGCTA
59279348 ATTTGCCCAG
Statistics
Matches: 236, Mismatches: 22, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
40 23 0.10
41 60 0.25
42 78 0.33
43 75 0.32
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (43 bp):
TTTTATAAAAAACGCCGCTATAGACCAAGACTTTTAGCGGCGC
Found at i:59279239 original size:167 final size:166
Alignment explanation
Indices: 59279035--59279338 Score: 511
Period size: 167 Copynumber: 1.8 Consensus size: 166
59279025 TCATGGCGTT
* * *
59279035 TTTTAAAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGTGCTTTTTTAAAAAACGCTGCTATAG
1 TTTTAAAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTATAG
*
59279100 ACCAAGATTTTAGCGGCGCTTTTATAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTT
66 ACCAAGACTTTAGCGGCGCTTTTATAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTT
59279165 TAAAAAAAGCCGATAGACTAAGAACTTTAGCGGCGC
131 TAAAAAAAGCCGATAGACTAAGAACTTTAGCGGCGC
* * *
59279201 TTTTATAAAAAACGCCGCTATAGACCTA-TACTTTTAGCGGCGCTTTTATAAAAAACGCCGCTAT
1 TTTTA-AAAAAACGCCGCTAAAGACC-AGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAT
*
59279265 AGACCAAGACTTTAGCGGCGCTTTTATAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGTTT
64 AGACCAAGACTTTAGCGGCGCTTTTATAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTT
59279330 TTTAAAAAA
129 TTTAAAAAA
59279339 GCACCGCTAA
Statistics
Matches: 128, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
166 5 0.04
167 122 0.95
168 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (166 bp):
TTTTAAAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTATAG
ACCAAGACTTTAGCGGCGCTTTTATAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTT
TAAAAAAAGCCGATAGACTAAGAACTTTAGCGGCGC
Found at i:59279317 original size:84 final size:84
Alignment explanation
Indices: 59279035--59279347 Score: 454
Period size: 84 Copynumber: 3.7 Consensus size: 84
59279025 TCATGGCGTT
* * * * * * *
59279035 TTTTAAAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGTGCTTTTTTAAAAAACGCTGCTATAG
1 TTTTATAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTTTAAAAAACGCCGCTATAG
*
59279100 ACCAAGATTTTAGCGGCGC
66 ACCAAGACTTTAGCGGCGC
*
59279119 TTTTATAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGC-TTTTTAAAAAAAGCCG--ATAG
1 TTTTATAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTTTAAAAAACGCCGCTATAG
*
59279181 ACTAAGAACTTTAGCGGCGC
66 ACCAAG-ACTTTAGCGGCGC
* *
59279201 TTTTATAAAAAACGCCGCTATAGACCTATACTTTTAGCGGCGCTTTTATAAAAAACGCCGCTATA
1 TTTTAT-AAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTTTAAAAAACGCCGCTATA
59279266 GACCAAGACTTTAGCGGCGC
65 GACCAAGACTTTAGCGGCGC
*
59279286 TTTTATAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCG-TTTTTTAAAAAAGCACCGCTA
1 TTTTATAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTTTAAAAAA-CGCCGCTA
59279348 ATTTGCCCAG
Statistics
Matches: 206, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
81 9 0.04
82 18 0.09
83 60 0.29
84 91 0.44
85 19 0.09
86 9 0.04
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (84 bp):
TTTTATAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTTTAAAAAACGCCGCTATAG
ACCAAGACTTTAGCGGCGC
Found at i:59279671 original size:21 final size:21
Alignment explanation
Indices: 59279645--59279692 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
59279635 TCCTGTTCTG
*
59279645 CTCCGCCTCCCTTGCTGCTAC
1 CTCCGCCTCCCTCGCTGCTAC
*
59279666 CTCCGCCTCCCTCGCTGCTGC
1 CTCCGCCTCCCTCGCTGCTAC
59279687 CTCCGC
1 CTCCGC
59279693 TCTAAGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.02, C:0.56, G:0.17, T:0.25
Consensus pattern (21 bp):
CTCCGCCTCCCTCGCTGCTAC
Found at i:59280278 original size:18 final size:18
Alignment explanation
Indices: 59280246--59280283 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
59280236 TACAATATAG
59280246 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
59280265 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
59280282 TA
1 TA
59280284 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:59285571 original size:21 final size:21
Alignment explanation
Indices: 59285547--59285586 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
59285537 AAATTAATTC
*
59285547 ATACTTAAGTTGAATCAAATA
1 ATACTTAAGTTGAACCAAATA
59285568 ATACTTAAGTTGAACCAAA
1 ATACTTAAGTTGAACCAAA
59285587 ATATAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (21 bp):
ATACTTAAGTTGAACCAAATA
Found at i:59287588 original size:19 final size:20
Alignment explanation
Indices: 59287564--59287603 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
59287554 GACTTCAGTC
59287564 TGCAGAACAAAG-AATCATA
1 TGCAGAACAAAGCAATCATA
*
59287583 TGCAGACCAAAGCAATCATA
1 TGCAGAACAAAGCAATCATA
59287603 T
1 T
59287604 TCTACCTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.17
Consensus pattern (20 bp):
TGCAGAACAAAGCAATCATA
Found at i:59288209 original size:2 final size:2
Alignment explanation
Indices: 59288204--59288230 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59288194 AAAAACATTC
59288204 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
59288231 GCACTGCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59289563 original size:18 final size:19
Alignment explanation
Indices: 59289526--59289564 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
59289516 AAATCATATT
59289526 TATTATTTTCATATAAAAA
1 TATTATTTTCATATAAAAA
*
59289545 TATTATTTTGATA-AAAAA
1 TATTATTTTCATATAAAAA
59289563 TA
1 TA
59289565 AAAAAGATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTATTTTCATATAAAAA
Found at i:59290091 original size:2 final size:2
Alignment explanation
Indices: 59290084--59290111 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59290074 AGAATGTATT
59290084 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59290112 ATAAAAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59290611 original size:41 final size:41
Alignment explanation
Indices: 59290566--59290693 Score: 186
Period size: 41 Copynumber: 3.1 Consensus size: 41
59290556 TTATATAACT
* * * *
59290566 TTTAGTGGCGTTTTAGCAAAAGTGCAGTTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCAGCTAATGCTCTGGTC
* *
59290607 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCAGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCAGCTAATGCTCTGGTC
59290648 TTTAGCGGCGTTTTACCAAAAGCGCCA-CTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCG-CAGCTAATGCTCTGGTC
59290689 TTTAG
1 TTTAG
59290694 TAAAACGCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 77 0.99
42 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTACCAAAAGCGCAGCTAATGCTCTGGTC
Found at i:59290712 original size:29 final size:30
Alignment explanation
Indices: 59290665--59290722 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
59290655 GCGTTTTACC
59290665 AAAAGCGCCACTAATGCTCTGGTCTTTAGT
1 AAAAGCGCCACTAATGCTCTGGTCTTTAGT
* *
59290695 AAAA-CGCCGCTAGTGCTCTGGTCTTTAG
1 AAAAGCGCCACTAATGCTCTGGTCTTTAG
59290723 CGGCGTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAAGCGCCACTAATGCTCTGGTCTTTAGT
Found at i:59290792 original size:70 final size:70
Alignment explanation
Indices: 59290612--59290802 Score: 212
Period size: 70 Copynumber: 2.7 Consensus size: 70
59290602 TGGTCTTTAG
* *
59290612 CGGCGTTTTACCA-AAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTACCAAAAGCGCCAC
1 CGGCGTTTTA-CAGAAAACGCCGCTAATGCTC-TGTCTTTAGCGGCGTTTTACCAAAAGCGCCAC
59290676 TAATGCT
64 TAATGCT
* * * *
59290683 CTG-GTCTTT--AGTAAAACGCCGCTAGTGCTCTGGTCTTTAGCGGCGTTTTACCAACAGCGCCG
1 CGGCGT-TTTACAG-AAAACGCCGCTAATGCTCT-GTCTTTAGCGGCGTTTTACCAAAAGCGCCA
59290745 CTAATGCT
63 CTAATGCT
* * *
59290753 -GGCGTTTTAACAGAAAATGCCGCTAATGCTCTGTTTTTAGTGGCGTTTTA
1 CGGCGTTTT-ACAGAAAACGCCGCTAATGCTCTGTCTTTAGCGGCGTTTTA
59290803 ACAGAAATCA
Statistics
Matches: 101, Mismatches: 11, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
68 1 0.01
69 4 0.04
70 72 0.71
71 22 0.22
72 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (70 bp):
CGGCGTTTTACAGAAAACGCCGCTAATGCTCTGTCTTTAGCGGCGTTTTACCAAAAGCGCCACTA
ATGCT
Found at i:59298668 original size:9 final size:10
Alignment explanation
Indices: 59298651--59298757 Score: 54
Period size: 9 Copynumber: 11.4 Consensus size: 10
59298641 ACTTATTAAA
*
59298651 ATTAAAAAAT
1 ATTATAAAAT
59298661 A-TATAAAA-
1 ATTATAAAAT
59298669 ACTTAT-AAAT
1 A-TTATAAAAT
59298679 ATTAT-AAA-
1 ATTATAAAAT
59298687 ATTATAAAA-
1 ATTATAAAAT
*
59298696 ATTATAAAAA
1 ATTATAAAAT
*
59298706 ATTATGAAAT
1 ATTATAAAAT
*
59298716 -TAATAAAACTT
1 ATTATAAAA--T
*
59298727 ATT-TGAAAT
1 ATTATAAAAT
59298736 ATT-TAAAAT
1 ATTATAAAAT
* *
59298745 -TAAAAAAAT
1 ATTATAAAAT
59298754 ATTA
1 ATTA
59298758 GAATTCTTAA
Statistics
Matches: 76, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
8 7 0.09
9 48 0.63
10 15 0.20
11 5 0.07
12 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
ATTATAAAAT
Found at i:59298670 original size:28 final size:27
Alignment explanation
Indices: 59298639--59298729 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 27
59298629 ATATTGATAT
59298639 AAACTTATTAAAATTAAAAAATATATAA
1 AAACTTATTAAAATTAAAAAAT-TATAA
*
59298667 AAACTTA-TAAATATTATAAAATTATAA
1 AAACTTATTAAA-ATTAAAAAATTATAA
* **
59298694 AAA-TTATAAAAAATTATGAAATTA-ATA
1 AAACTTAT-TAAAATTAAAAAATTATA-A
59298721 AAACTTATT
1 AAACTTATT
59298730 TGAAATATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
26 4 0.07
27 27 0.50
28 23 0.43
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (27 bp):
AAACTTATTAAAATTAAAAAATTATAA
Found at i:59298676 original size:36 final size:34
Alignment explanation
Indices: 59298636--59298728 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 34
59298626 TTAATATTGA
*
59298636 TATAAACTTATTAAAATTA-AAAAATATATAAAAACT
1 TATAAA-TTA-TAAAATTATAAAAAT-TATAAAAAAT
59298672 TATAAATATTATAAAATTATAAAAATTATAAAAAAT
1 TAT-AA-ATTATAAAATTATAAAAATTATAAAAAAT
59298708 TATGAAATTAATAAAACTTAT
1 TAT-AAATT-ATAAAA-TTAT
59298729 TTGAAATATT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
35 3 0.06
36 31 0.62
37 15 0.30
38 1 0.02
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (34 bp):
TATAAATTATAAAATTATAAAAATTATAAAAAAT
Found at i:59298693 original size:17 final size:17
Alignment explanation
Indices: 59298636--59298728 Score: 80
Period size: 18 Copynumber: 5.2 Consensus size: 17
59298626 TTAATATTGA
* *
59298636 TATAAACTTATTAAAAT
1 TATAAAATTATAAAAAT
*
59298653 TAAAAAATATATAAAAACT
1 TATAAAAT-TATAAAAA-T
59298672 TATAAATATTAT-AAAAT
1 TATAAA-ATTATAAAAAT
59298689 TATAAAAATTATAAAAAAT
1 TAT-AAAATTAT-AAAAAT
* *
59298708 TATGAAATTAATAAAACT
1 TATAAAATT-ATAAAAAT
59298726 TAT
1 TAT
59298729 TTGAAATATT
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
17 15 0.24
18 27 0.43
19 19 0.30
20 2 0.03
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (17 bp):
TATAAAATTATAAAAAT
Found at i:59298774 original size:19 final size:19
Alignment explanation
Indices: 59298747--59298795 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
59298737 TTTAAAATTA
59298747 AAAAAATATTAGAATTCTT
1 AAAAAATATTAGAATTCTT
*
59298766 AAAACATATTAGAATTCTT
1 AAAAAATATTAGAATTCTT
59298785 AAAAAATATTA
1 AAAAAATATTA
59298796 AAATATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (19 bp):
AAAAAATATTAGAATTCTT
Found at i:59299270 original size:10 final size:9
Alignment explanation
Indices: 59299250--59299312 Score: 56
Period size: 9 Copynumber: 6.9 Consensus size: 9
59299240 TTTTATGATT
59299250 TTTTTATAA
1 TTTTTATAA
59299259 TTTTTATAAA
1 TTTTTAT-AA
* *
59299269 TTTATACGAA
1 TTTTTA-TAA
*
59299279 TTTTAAT-A
1 TTTTTATAA
*
59299287 TTTTTATCA
1 TTTTTATAA
*
59299296 TTTTTATGA
1 TTTTTATAA
59299305 TTTTTATA
1 TTTTTATA
59299313 TAACTGTAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
8 7 0.16
9 23 0.53
10 13 0.30
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:59299377 original size:18 final size:19
Alignment explanation
Indices: 59299348--59299408 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
59299338 AATAAATATT
59299348 TTTTTATAATTTATTAGAA
1 TTTTTATAATTTATTAGAA
* *
59299367 TTTTTAT-ATTTTTTATAA
1 TTTTTATAATTTATTAGAA
*
59299385 TTTTTTTAAGTTTATATA-AA
1 TTTTTATAA-TTTAT-TAGAA
59299405 TTTT
1 TTTT
59299409 CATATTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 15 0.43
19 8 0.23
20 10 0.29
21 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTTATAATTTATTAGAA
Found at i:59299380 original size:10 final size:9
Alignment explanation
Indices: 59299347--59299450 Score: 56
Period size: 9 Copynumber: 11.6 Consensus size: 9
59299337 AAATAAATAT
59299347 TTTTTTATAA
1 TTTTTTAT-A
* *
59299357 TTTATTAGA
1 TTTTTTATA
*
59299366 ATTTTTATA
1 TTTTTTATA
59299375 TTTTTTATAA
1 TTTTTTAT-A
59299385 TTTTTT-TAA
1 TTTTTTAT-A
* *
59299394 GTTTATATAA
1 TTTTTTAT-A
* *
59299404 ATTTTCATA
1 TTTTTTATA
59299413 TTTTTTA-A
1 TTTTTTATA
*
59299421 -TATTTA-A
1 TTTTTTATA
59299428 TTATTTTATA
1 TT-TTTTATA
59299438 TTTTTT-TA
1 TTTTTTATA
59299446 TTTTT
1 TTTTT
59299451 AAAATTTGGT
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
7 6 0.08
8 9 0.12
9 35 0.47
10 24 0.32
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTTTATA
Found at i:59299399 original size:38 final size:39
Alignment explanation
Indices: 59299345--59299419 Score: 109
Period size: 38 Copynumber: 1.9 Consensus size: 39
59299335 AAAAATAAAT
*
59299345 ATTTTTTTATAATTTAT-TAGAATTTTTATATTTTTTATA
1 ATTTTTTTATAATTTATATA-AATTTTCATATTTTTTATA
*
59299384 ATTTTTTTA-AGTTTATATAAATTTTCATATTTTTTA
1 ATTTTTTTATAATTTATATAAATTTTCATATTTTTTA
59299420 ATATTTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 22 0.67
39 11 0.33
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (39 bp):
ATTTTTTTATAATTTATATAAATTTTCATATTTTTTATA
Found at i:59299438 original size:25 final size:26
Alignment explanation
Indices: 59299404--59299452 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
59299394 GTTTATATAA
59299404 ATTTTCATATTTTTTAATATTTAATT
1 ATTTTCATATTTTTTAATATTTAATT
* *
59299430 ATTTT-ATATTTTTTTATTTTTAA
1 ATTTTCATATTTTTTAATATTTAA
59299453 AATTTGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (26 bp):
ATTTTCATATTTTTTAATATTTAATT
Found at i:59302800 original size:65 final size:65
Alignment explanation
Indices: 59302729--59302856 Score: 247
Period size: 65 Copynumber: 2.0 Consensus size: 65
59302719 AATCAATAAC
59302729 GTATAAAGCAATAATGTACATGTATGTACATAAAAGCATAGCATATAGCATGAGTAATAAAAAAT
1 GTATAAAGCAATAATGTACATGTATGTACATAAAAGCATAGCATATAGCATGAGTAATAAAAAAT
*
59302794 GTATAAAGCAATAATGTACATGTATGTACATAAAAGCATAGCATATAGCATGGGTAATAAAAA
1 GTATAAAGCAATAATGTACATGTATGTACATAAAAGCATAGCATATAGCATGAGTAATAAAAA
59302857 TCTATAATGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.26
Consensus pattern (65 bp):
GTATAAAGCAATAATGTACATGTATGTACATAAAAGCATAGCATATAGCATGAGTAATAAAAAAT
Found at i:59303350 original size:14 final size:14
Alignment explanation
Indices: 59303331--59303358 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
59303321 CAAATATACA
59303331 AATGACACGTAAAG
1 AATGACACGTAAAG
59303345 AATGACACGTAAAG
1 AATGACACGTAAAG
59303359 TTTAAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
AATGACACGTAAAG
Found at i:59304454 original size:19 final size:19
Alignment explanation
Indices: 59304421--59304459 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
59304411 TTGCTTCCTT
* *
59304421 TCGTTTTTTTTTTTGCTTG
1 TCGTTTTTCTCTTTGCTTG
*
59304440 TCGTTTTTCTCTTTGTTTG
1 TCGTTTTTCTCTTTGCTTG
59304459 T
1 T
59304460 TTCTCTGCTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.15, T:0.72
Consensus pattern (19 bp):
TCGTTTTTCTCTTTGCTTG
Found at i:59315506 original size:21 final size:21
Alignment explanation
Indices: 59315482--59315522 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
59315472 TTGCCTAGGA
*
59315482 TATGAATTAAATTAAATTGAG
1 TATGAAATAAATTAAATTGAG
**
59315503 TATGAAATGGATTAAATTGA
1 TATGAAATAAATTAAATTGA
59315523 CATTAAATTC
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:0.00, G:0.17, T:0.37
Consensus pattern (21 bp):
TATGAAATAAATTAAATTGAG
Found at i:59318745 original size:38 final size:39
Alignment explanation
Indices: 59318639--59318828 Score: 172
Period size: 40 Copynumber: 4.8 Consensus size: 39
59318629 TGAATGATGT
* * * * *
59318639 CCGGGCTAAGTCCCGTAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTACTA-AA
* * *
59318679 CCGGACTAAGAT-CCGAAGGCGTTCGTGCGAGTTAATAAA
1 CCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
59318718 TCCGGGCTAAG-CCC-AAGGCATTTGTGCGAGTTACTAAA
1 -CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
*
59318756 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTA-AA
** * *
59318797 CCGGGCTTTGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGT
59318829 CGTTATATCC
Statistics
Matches: 124, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
38 30 0.24
39 6 0.05
40 79 0.64
41 9 0.07
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:59325338 original size:40 final size:39
Alignment explanation
Indices: 59325255--59325446 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
59325245 TTGAATGATG
* * * * *
59325255 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGC-GAGTTAATAAA
* *
59325295 TCCGGACTAAGATCCGAAGGCGTTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCGAAGGCATTCGTGCGAGTTAATAAA
* * *
59325335 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGTTAATAAA
* * *
59325374 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGCGAGTTAATA-AA
** * *
59325415 -CCGGGCTTTGTCCCGAAGGCATTTGAGCGAGT
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGCGAGT
59325447 CGTTATATCC
Statistics
Matches: 128, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 33 0.26
40 86 0.67
41 9 0.07
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGTTAATAAA
Found at i:59325400 original size:79 final size:81
Alignment explanation
Indices: 59325255--59325446 Score: 232
Period size: 79 Copynumber: 2.4 Consensus size: 81
59325245 TTGAATGATG
* * * *
59325255 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCGTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
59325319 CGTGCGAGTTAATA-AA
65 CGTGCGAGTTAATATAA
* **
59325335 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
*
59325398 CGTGCGAGTTACTATAA
65 CGTGCGAGTTAATATAA
** *
59325415 -CCGGGCTTTGTCCCGAAGGCATTTGAGCGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
59325447 CGTTATATCC
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.58
80 40 0.41
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTTAATATAA
Found at i:59325461 original size:79 final size:77
Alignment explanation
Indices: 59325255--59325472 Score: 206
Period size: 79 Copynumber: 2.7 Consensus size: 77
59325245 TTGAATGATG
* * * * *
59325255 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCGTT
1 TCCGGGCTAAG-CCCGAAGGCATTTGAGC-GAGTCACTATATCCGG-TTAAG-TCCGAAGGCATT
59325319 CGTGCGAGTTAATAAA
62 CGTGCGAGTTAATAAA
* * * *
59325335 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAACCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGCTAAGCCCGAAGGCATTTGAGCGAGTCACTATATCC-GGTTAAGT-CCGAAGGCATTCG
*
59325400 TGCGAGTTACTATAA
64 TGCGAGTTAATA-AA
** ** *
59325415 -CCGGGCTTTGTCCCGAAGGCATTTGAGCGAGTCGTTATATCCGGTTAAATTCCGAAGG
1 TCCGGGCTAAG-CCCGAAGGCATTTGAGCGAGTCACTATATCCGGTT-AAGTCCGAAGG
59325473 TACGTGATTC
Statistics
Matches: 116, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
78 1 0.01
79 65 0.56
80 50 0.43
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (77 bp):
TCCGGGCTAAGCCCGAAGGCATTTGAGCGAGTCACTATATCCGGTTAAGTCCGAAGGCATTCGTG
CGAGTTAATAAA
Found at i:59330640 original size:40 final size:40
Alignment explanation
Indices: 59330448--59330633 Score: 236
Period size: 40 Copynumber: 4.7 Consensus size: 40
59330438 TCGAATGATG
* * *
59330448 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
59330488 TCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
59330528 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
59330568 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
59330609 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
59330634 AACGAGTAGC
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.01
40 122 0.92
41 9 0.07
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Done.