Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 32 of 82
Found at i:11567298 original size:21 final size:21
Alignment explanation
Indices: 11567274--11567346 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
11567264 CTTGATCAGA
*
11567274 TGTAGTGTCATCCTCGAGCAT
1 TGTAGTGTCATCCTCCAGCAT
*
11567295 TGTAATG-CATCCTCCAGCAT
1 TGTAGTGTCATCCTCCAGCAT
** *
11567315 CATAGTGTCATCCTCCATCAT
1 TGTAGTGTCATCCTCCAGCAT
* *
11567336 CGTAGTATCAT
1 TGTAGTGTCAT
11567347 TTGAAAATGG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 16 0.37
21 27 0.63
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.33
Consensus pattern (21 bp):
TGTAGTGTCATCCTCCAGCAT
Found at i:11569608 original size:17 final size:17
Alignment explanation
Indices: 11569586--11569620 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
11569576 ACTTCTATGT
*
11569586 TAGAGATTTTTTCATGG
1 TAGAGATTTTTCCATGG
11569603 TAGAGATTTTTCCATGG
1 TAGAGATTTTTCCATGG
11569620 T
1 T
11569621 TTTTGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.46
Consensus pattern (17 bp):
TAGAGATTTTTCCATGG
Found at i:11575492 original size:11 final size:11
Alignment explanation
Indices: 11575476--11575500 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11575466 ATTGTTTGCT
11575476 TTTTCTTTTTC
1 TTTTCTTTTTC
11575487 TTTTCTTTTTC
1 TTTTCTTTTTC
11575498 TTT
1 TTT
11575501 GTTCGGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:11576293 original size:12 final size:13
Alignment explanation
Indices: 11576270--11576298 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
11576260 CTTGCAAGAT
11576270 AACAATCAAATGA
1 AACAATCAAATGA
11576283 AACAA-CAAATGA
1 AACAATCAAATGA
11576295 AACA
1 AACA
11576299 CATCTTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.66, C:0.17, G:0.07, T:0.10
Consensus pattern (13 bp):
AACAATCAAATGA
Found at i:11589533 original size:30 final size:30
Alignment explanation
Indices: 11589498--11589558 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
11589488 TGCAAAGGAG
*
11589498 GAGAAAGAAGAAAAAGAGAAGCAGCAATCT
1 GAGAAAGAAGAAAAAGAGAAGCAGAAATCT
* * * *
11589528 GAGAAAGATGAGAATGAGAAGGAGAAATCT
1 GAGAAAGAAGAAAAAGAGAAGCAGAAATCT
11589558 G
1 G
11589559 CTGATGATGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.52, C:0.07, G:0.31, T:0.10
Consensus pattern (30 bp):
GAGAAAGAAGAAAAAGAGAAGCAGAAATCT
Found at i:11589607 original size:30 final size:30
Alignment explanation
Indices: 11589570--11589683 Score: 131
Period size: 30 Copynumber: 3.7 Consensus size: 30
11589560 TGATGATGCC
11589570 AAGAAGTGAAAGAGAATGGTATGGCAGAAA
1 AAGAAGTGAAAGAGAATGGTATGGCAGAAA
* * *
11589600 AAAAAGTGAAAGAGAATGGTGTCAT-CCATTAATA
1 AAGAAGTGAAAGAGAAT-G-GT-ATGGCA-GAA-A
* *
11589634 AAGAAGTGAAAAAGAATGGTATGGCAGCAA
1 AAGAAGTGAAAGAGAATGGTATGGCAGAAA
11589664 AAGAAGTGAAAGAGAATGGT
1 AAGAAGTGAAAGAGAATGGT
11589684 GTCATCCGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
30 36 0.52
31 4 0.06
32 8 0.12
33 5 0.07
34 16 0.23
ACGTcount: A:0.49, C:0.05, G:0.29, T:0.17
Consensus pattern (30 bp):
AAGAAGTGAAAGAGAATGGTATGGCAGAAA
Found at i:11589650 original size:34 final size:34
Alignment explanation
Indices: 11589603--11589706 Score: 110
Period size: 30 Copynumber: 3.1 Consensus size: 34
11589593 GCAGAAAAAA
11589603 AAGTGAAAGAGAATGGTGTCATCCATTAATAAAG
1 AAGTGAAAGAGAATGGTGTCATCCATTAATAAAG
* * **
11589637 AAGTGAAAAAGAAT-G-GT-ATGGCA-GCA-AAAG
1 AAGTGAAAGAGAATGGTGTCAT-CCATTAATAAAG
*
11589667 AAGTGAAAGAGAATGGTGTCATCCGTTAATAGAAG
1 AAGTGAAAGAGAATGGTGTCATCCATTAATA-AAG
11589702 AAGTG
1 AAGTG
11589707 CATCTCTTTG
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
30 17 0.31
31 4 0.07
32 7 0.13
33 4 0.07
34 14 0.26
35 8 0.15
ACGTcount: A:0.44, C:0.08, G:0.28, T:0.20
Consensus pattern (34 bp):
AAGTGAAAGAGAATGGTGTCATCCATTAATAAAG
Found at i:11589650 original size:64 final size:65
Alignment explanation
Indices: 11589570--11589706 Score: 231
Period size: 64 Copynumber: 2.1 Consensus size: 65
11589560 TGATGATGCC
*
11589570 AAGAAGTGAAAGAGAATGGTATGGCAGAAAAAAAAGTGAAAGAGAATGGTGTCATCCATTAATA-
1 AAGAAGTGAAAAAGAATGGTATGGCAGAAAAAAAAGTGAAAGAGAATGGTGTCATCCATTAATAG
* * *
11589634 AAGAAGTGAAAAAGAATGGTATGGCAGCAAAAGAAGTGAAAGAGAATGGTGTCATCCGTTAATAG
1 AAGAAGTGAAAAAGAATGGTATGGCAGAAAAAAAAGTGAAAGAGAATGGTGTCATCCATTAATAG
11589699 AAGAAGTG
1 AAGAAGTG
11589707 CATCTCTTTG
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
64 60 0.88
65 8 0.12
ACGTcount: A:0.47, C:0.07, G:0.28, T:0.18
Consensus pattern (65 bp):
AAGAAGTGAAAAAGAATGGTATGGCAGAAAAAAAAGTGAAAGAGAATGGTGTCATCCATTAATAG
Found at i:11593427 original size:22 final size:23
Alignment explanation
Indices: 11593397--11593443 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
11593387 ATATAGAGTT
11593397 ATTTGAGCTTAATTTTGATAGTA
1 ATTTGAGCTTAATTTTGATAGTA
* *
11593420 ATTT-AGCTTAGTTTTTATAGTA
1 ATTTGAGCTTAATTTTGATAGTA
11593442 AT
1 AT
11593444 GCATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.51
Consensus pattern (23 bp):
ATTTGAGCTTAATTTTGATAGTA
Found at i:11600352 original size:14 final size:14
Alignment explanation
Indices: 11600327--11600374 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
11600317 AGTTTCAATA
11600327 TCTCTTT-TTTTTT
1 TCTCTTTGTTTTTT
11600340 T-TCTTTGTTTTTT
1 TCTCTTTGTTTTTT
*
11600353 TCTCTTT-TCTTTT
1 TCTCTTTGTTTTTT
*
11600366 TCTTTTTGT
1 TCTCTTTGT
11600375 CACGACCTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 5 0.17
13 19 0.63
14 6 0.20
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (14 bp):
TCTCTTTGTTTTTT
Found at i:11600360 original size:7 final size:6
Alignment explanation
Indices: 11600329--11600372 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
11600319 TTTCAATATC
*
11600329 TCTTTT TTTTTT TCTTTGT T-TTTT TCTCTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTT-T TCTTTT TCT-TTT TCTTTT TCTTTT T
11600373 GTCACGACCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 2 0.06
6 23 0.70
7 8 0.24
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:11606601 original size:2 final size:2
Alignment explanation
Indices: 11606591--11606622 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
11606581 ACATATTTAC
*
11606591 AT AT GT 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
11606623 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11615480 original size:2 final size:2
Alignment explanation
Indices: 11615473--11615528 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
11615463 NNNNNNNNNN
11615473 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
*
11615515 TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA
11615529 CCCATCATCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11615594 original size:20 final size:19
Alignment explanation
Indices: 11615533--11615595 Score: 81
Period size: 20 Copynumber: 3.2 Consensus size: 19
11615523 TATATACCCA
11615533 TCATCATCATCTCACCAAC
1 TCATCATCATCTCACCAAC
* * *
11615552 CCATTATCATCATCACCAGC
1 TCATCATCATC-TCACCAAC
11615572 TCATCATCATCGTCACCAAC
1 TCATCATCATC-TCACCAAC
11615592 TCAT
1 TCAT
11615596 GCGCACTCCT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 9 0.25
20 27 0.75
ACGTcount: A:0.30, C:0.40, G:0.03, T:0.27
Consensus pattern (19 bp):
TCATCATCATCTCACCAAC
Found at i:11618096 original size:22 final size:23
Alignment explanation
Indices: 11618066--11618112 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
11618056 ATATAGAGTT
11618066 ATTTGAGCTTAATTTTGATAGTA
1 ATTTGAGCTTAATTTTGATAGTA
* *
11618089 ATTT-AGCTTAGTTTTTATAGTA
1 ATTTGAGCTTAATTTTGATAGTA
11618111 AT
1 AT
11618113 GCATGGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.51
Consensus pattern (23 bp):
ATTTGAGCTTAATTTTGATAGTA
Found at i:11626151 original size:21 final size:22
Alignment explanation
Indices: 11626125--11626172 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
11626115 CCCTAGGTGG
* *
11626125 AAAAATTCAAGGGAA-AAGTGT
1 AAAAATTCAAGGAAACAAGTGA
11626146 AAAAATTCAAGGAAACAAGTGA
1 AAAAATTCAAGGAAACAAGTGA
11626168 AAAAA
1 AAAAA
11626173 GGTAAGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.60, C:0.06, G:0.19, T:0.15
Consensus pattern (22 bp):
AAAAATTCAAGGAAACAAGTGA
Found at i:11646507 original size:68 final size:67
Alignment explanation
Indices: 11646419--11646611 Score: 242
Period size: 68 Copynumber: 2.8 Consensus size: 67
11646409 CACATACATG
* * * * *
11646419 CTTACTCATCTCATAAGGTATATGGAATGCTCATCATATACATAATCTCATAGCATTCATCATGC
1 CTTAATCACCTCATATGGTATATGGAATG-TCATCATATACATAATCTTATGGCATTCATCATGC
11646484 ATA
65 ATA
* * *
11646487 CTTAATCACCTCATATGGTATTTGGAATTGACATCATATACATAATCTTATGGTATTCATCATGC
1 CTTAATCACCTCATATGGTATATGGAA-TGTCATCATATACATAATCTTATGGCATTCATCATGC
11646552 ATA
65 ATA
** * * *
11646555 CTTAATCAGTTTATATGGTATATGGAATTTACATCATAGACATAATCTTATGGCATT
1 CTTAATCACCTCATATGGTATATGGAATGT-CATCATATACATAATCTTATGGCATT
11646612 TATTATACCA
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
67 1 0.01
68 104 0.97
69 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (67 bp):
CTTAATCACCTCATATGGTATATGGAATGTCATCATATACATAATCTTATGGCATTCATCATGCA
TA
Found at i:11647397 original size:19 final size:19
Alignment explanation
Indices: 11647373--11647411 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
11647363 CTCAAATTAC
11647373 CAACTGGAC-GAGGGTTTCT
1 CAACTGG-CTGAGGGTTTCT
11647392 CAACTGGCTGAGGGTTTCT
1 CAACTGGCTGAGGGTTTCT
11647411 C
1 C
11647412 TTTAAAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.18, C:0.23, G:0.31, T:0.28
Consensus pattern (19 bp):
CAACTGGCTGAGGGTTTCT
Found at i:11647985 original size:42 final size:42
Alignment explanation
Indices: 11647897--11647989 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 42
11647887 ACCATCCCAC
11647897 CATCATCAACTCATGTGCACTCCCCACTCGTACATAGTTCGGT
1 CATCATCAACTCATGTGCACTCCCCACTCG-ACATAGTTCGGT
*
11647940 CATCATCAGCTCATGTGCACTCCCACACTC-ACATAGTT-GGAT
1 CATCATCAACTCATGTGCACTCCC-CACTCGACATAGTTCGG-T
11647982 CATCATCA
1 CATCATCA
11647990 TCACATAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
41 2 0.04
42 17 0.36
43 23 0.49
44 5 0.11
ACGTcount: A:0.26, C:0.34, G:0.13, T:0.27
Consensus pattern (42 bp):
CATCATCAACTCATGTGCACTCCCCACTCGACATAGTTCGGT
Found at i:11650140 original size:21 final size:21
Alignment explanation
Indices: 11650114--11650174 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
11650104 TTTAGGCCAT
11650114 ATGTATCAATACATTATGAAC
1 ATGTATCAATACATTATGAAC
* * *
11650135 ATGTATCGATATATCATGAAC
1 ATGTATCAATACATTATGAAC
*
11650156 ATGTATTAATACATT-TGAA
1 ATGTATCAATACATTATGAA
11650175 ATAGAATGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (21 bp):
ATGTATCAATACATTATGAAC
Found at i:11669508 original size:43 final size:43
Alignment explanation
Indices: 11669460--11669610 Score: 198
Period size: 43 Copynumber: 3.4 Consensus size: 43
11669450 TGTTGTGTGA
* * * *
11669460 TGATGATGACCTAGCTATGTGCAATGT-GGGAGTGCACATGAGT
1 TGATGATGACCCAGCTATGTGCGA-GTAGGGAGTGCGCATAAGT
*
11669503 TGATGATGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAAGC
1 TGATGATGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAAGT
11669546 TGATGATGA-CCAGGCTATGTGCGAGTAGGGAGTGCGCATAAGT
1 TGATGATGACCCA-GCTATGTGCGAGTAGGGAGTGCGCATAAGT
11669589 CAATGATGATGACCCAGCTATG
1 ---TGATGATGACCCAGCTATG
11669611 ACTATGAATG
Statistics
Matches: 96, Mismatches: 6, Indels: 9
0.86 0.05 0.08
Matches are distributed among these distances:
42 5 0.05
43 73 0.76
46 15 0.16
47 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (43 bp):
TGATGATGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAAGT
Found at i:11671437 original size:39 final size:38
Alignment explanation
Indices: 11671374--11671478 Score: 124
Period size: 38 Copynumber: 2.7 Consensus size: 38
11671364 CACTCCTGGC
* *
11671374 TCATGTACATCCCCCCACATCGTGCACATAGCCG-GCACCA
1 TCATGTACATACCCCCACATCGTGCACA-AGCAGTG--CCA
* *
11671414 TCATGTGCAT-CCCCCACATCGTGCACAATCAGTGCCA
1 TCATGTACATACCCCCACATCGTGCACAAGCAGTGCCA
*
11671451 TCGTGTACATACCCCCACATCGTGCACA
1 TCATGTACATACCCCCACATCGTGCACA
11671479 CGGGCACTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
37 11 0.19
38 20 0.34
39 18 0.31
40 9 0.16
ACGTcount: A:0.25, C:0.40, G:0.15, T:0.20
Consensus pattern (38 bp):
TCATGTACATACCCCCACATCGTGCACAAGCAGTGCCA
Found at i:11679721 original size:43 final size:43
Alignment explanation
Indices: 11679674--11679811 Score: 197
Period size: 43 Copynumber: 3.2 Consensus size: 43
11679664 TGTTATGTGA
* *
11679674 TGATGATGACCCAGCTCTGTGCGATGT-GGGAGTGCACATGAGC
1 TGATGATGACCCAGCTATGTGCGA-GTAGGGAGTGCACATAAGC
* * * *
11679717 TGATGATGACCCGGCTATGTTCGAGTATGGAGTGCGCATAAGC
1 TGATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGC
*
11679760 GGATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGC
1 TGATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGC
11679803 TGATGATGA
1 TGATGATGA
11679812 TAACCCGGCT
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
42 2 0.02
43 80 0.98
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (43 bp):
TGATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGC
Found at i:11693978 original size:19 final size:19
Alignment explanation
Indices: 11693954--11694017 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
11693944 TGCCTGTGTG
11693954 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGCA
**** **
11693973 CACGATG-GCACTGATTGTG
1 CACGATGTGGGGGGA-TGCA
11693992 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGCA
11694011 CACGATG
1 CACGATG
11694018 GCACCGGCTA
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
18 3 0.10
19 25 0.81
20 3 0.10
ACGTcount: A:0.22, C:0.19, G:0.41, T:0.19
Consensus pattern (19 bp):
CACGATGTGGGGGGATGCA
Found at i:11693993 original size:38 final size:40
Alignment explanation
Indices: 11693950--11694052 Score: 165
Period size: 38 Copynumber: 2.6 Consensus size: 40
11693940 ATAGTGCCTG
*
11693950 TGTGCACGATGTGGGGGGATGCACACGATGGCA-CTGAT-
1 TGTGCACGATGTGGGGGGATGCACACGATGGCACCGGATA
*
11693988 TGTGCACGATGTGGGGGGATGCACACGATGGCACCGGCTA
1 TGTGCACGATGTGGGGGGATGCACACGATGGCACCGGATA
*
11694028 TGTGCATGATGTGGGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
11694053 TGAGTCGGGT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 33 0.55
39 3 0.05
40 24 0.40
ACGTcount: A:0.20, C:0.18, G:0.41, T:0.20
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGCACACGATGGCACCGGATA
Found at i:11698304 original size:15 final size:16
Alignment explanation
Indices: 11698272--11698306 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11698262 CGAGCCTCAT
*
11698272 ACTCCTCTATTATCAA
1 ACTCCCCTATTATCAA
11698288 ACTCCCCTATT-TCAA
1 ACTCCCCTATTATCAA
11698303 ACTC
1 ACTC
11698307 AAGAATTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.34
Consensus pattern (16 bp):
ACTCCCCTATTATCAA
Found at i:11703640 original size:3 final size:3
Alignment explanation
Indices: 11703632--11703663 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
11703622 ATGATAAAAA
11703632 TAT TAT TAT T-T TAT TAT TAT T-T TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11703664 TCCTCGCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:11703647 original size:8 final size:9
Alignment explanation
Indices: 11703632--11703663 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
11703622 ATGATAAAAA
11703632 TATTATTAT
1 TATTATTAT
11703641 T-TTATTAT
1 TATTATTAT
11703649 TATT-TTAT
1 TATTATTAT
11703657 TATTATT
1 TATTATT
11703664 TCCTCGCGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TATTATTAT
Found at i:11703648 original size:11 final size:11
Alignment explanation
Indices: 11703632--11703664 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
11703622 ATGATAAAAA
11703632 TATTATTATTT
1 TATTATTATTT
11703643 TATTATTATTT
1 TATTATTATTT
11703654 TATTATTATTT
1 TATTATTATTT
11703665 CCTCGCGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTATTT
Found at i:11709463 original size:22 final size:21
Alignment explanation
Indices: 11709424--11709464 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11709414 CCTAGGTGGA
**
11709424 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGCAAAAAGTGTG
11709445 AAAATTCAAGCAAACAAGTG
1 AAAATTCAAGCAAA-AAGTG
11709465 AAAAAAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.51, C:0.10, G:0.22, T:0.17
Consensus pattern (21 bp):
AAAATTCAAGCAAAAAGTGTG
Found at i:11709470 original size:22 final size:21
Alignment explanation
Indices: 11709423--11709470 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
11709413 TCCTAGGTGG
** *
11709423 AAAAATTCAAGGGAAAAGTGT
1 AAAAATTCAAGCAAAAAGTGA
*
11709444 GAAAATTCAAGCAAACAAGTGA
1 AAAAATTCAAGCAAA-AAGTGA
11709466 AAAAA
1 AAAAA
11709471 AGTAAGATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.58, C:0.08, G:0.19, T:0.15
Consensus pattern (21 bp):
AAAAATTCAAGCAAAAAGTGA
Found at i:11711752 original size:5 final size:5
Alignment explanation
Indices: 11711708--11711748 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
11711698 GTGTGGACCC
* *
11711708 AAGTT AAGTG AAGTT AAGTT AAGTT AAGTT AAGTT AGGTT A
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT A
11711749 GGTTTAATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (5 bp):
AAGTT
Found at i:11721948 original size:99 final size:98
Alignment explanation
Indices: 11721761--11721958 Score: 344
Period size: 99 Copynumber: 2.0 Consensus size: 98
11721751 TGGTCATTTT
11721761 ACATCTTGGGTCTAAATTTTTACATTTTCGTGAACCCGAGTATTTTTAGACTATTATTGGACTTT
1 ACATCTTGGGTCTAAATTTTTACATTTTCGTGAACCCGAGTATTTTTAGACTATTATTGGACTTT
**
11721826 GTCTTAATGTCAAAAGAGTAAAATATTGCACAA
66 GTCCCAATGTCAAAAGAGTAAAATATTGCACAA
11721859 NACATCTTGGGTCTAAATTTTTACATTTTCGTGAACCCGAGTATTTTTAGACTATTA-TGGACTT
1 -ACATCTTGGGTCTAAATTTTTACATTTTCGTGAACCCGAGTATTTTTAGACTATTATTGGACTT
*
11721923 TGTCCCAGTGTCAAAAGAGTAAAAATATTGCACAA
65 TGTCCCAATGTCAAAAGAGT-AAAATATTGCACAA
11721958 A
1 A
11721959 GGATAGGAGG
Statistics
Matches: 95, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
98 25 0.26
99 70 0.74
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (98 bp):
ACATCTTGGGTCTAAATTTTTACATTTTCGTGAACCCGAGTATTTTTAGACTATTATTGGACTTT
GTCCCAATGTCAAAAGAGTAAAATATTGCACAA
Found at i:11729031 original size:59 final size:59
Alignment explanation
Indices: 11728968--11729080 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
11728958 GCCTTCCCCA
* * * *
11728968 TTTTCTTTTT-TTCTTCCTCTCTTTTCTTTTCTCCTTGGGTGAAACCTTTCAAGACCTAG
1 TTTTCTTTTTCAT-TTCCTCTATTTTCTTCTCTCCTTGGGTGAAACCTCTCAAGACCTAG
** *
11729027 TTTTCTTTTTCATTTCCTCTATTTTCTTCTCTTTTTGGGTGGAACCTCTCAAGA
1 TTTTCTTTTTCATTTCCTCTATTTTCTTCTCTCCTTGGGTGAAACCTCTCAAGA
11729081 ACCAAGCTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 45 0.98
60 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.11, T:0.53
Consensus pattern (59 bp):
TTTTCTTTTTCATTTCCTCTATTTTCTTCTCTCCTTGGGTGAAACCTCTCAAGACCTAG
Found at i:11731915 original size:2 final size:2
Alignment explanation
Indices: 11731910--11731958 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
11731900 ATTGTGTGAT
11731910 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
*
11731952 TC TA TA T
1 TA TA TA T
11731959 GATTTTGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11733574 original size:42 final size:42
Alignment explanation
Indices: 11733527--11733610 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
11733517 GTATATAAAC
*
11733527 TGCATAAAGCTCTCTATGGATTAAAACAAGCTTCTAGAGCTT
1 TGCATAAAGCTCTCTATGGATTAAAACAAGCTCCTAGAGCTT
* *
11733569 TGCATAAAGCTCTTTATGGATTAAAAGAAGCTCCTAGAGCTT
1 TGCATAAAGCTCTCTATGGATTAAAACAAGCTCCTAGAGCTT
11733611 GGTATGAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (42 bp):
TGCATAAAGCTCTCTATGGATTAAAACAAGCTCCTAGAGCTT
Found at i:11735340 original size:33 final size:35
Alignment explanation
Indices: 11735302--11735377 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 35
11735292 TTTCCCAAAA
11735302 AGAAAAGAGAAATC-AAAGGACA-T-TCAGTAGAAAG
1 AGAAAAGAGAAA-CAAAAGGACATTGTCAG-AGAAAG
*
11735336 -GAAAAAAAGAAACAAAAGGACATTGTCAGAGAAAG
1 AG-AAAAGAGAAACAAAAGGACATTGTCAGAGAAAG
11735371 AGAAAAG
1 AGAAAAG
11735378 CTTGACAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
33 2 0.06
34 17 0.49
35 11 0.31
36 5 0.14
ACGTcount: A:0.59, C:0.08, G:0.24, T:0.09
Consensus pattern (35 bp):
AGAAAAGAGAAACAAAAGGACATTGTCAGAGAAAG
Found at i:11740408 original size:54 final size:54
Alignment explanation
Indices: 11740346--11740457 Score: 215
Period size: 54 Copynumber: 2.1 Consensus size: 54
11740336 GAGGGAAATG
11740346 GATGGGATGTCCGACTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
1 GATGGGATGTCCGACTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
*
11740400 GATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
1 GATGGGATGTCCGACTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
11740454 GATG
1 GATG
11740458 CAATAATGAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.20, C:0.14, G:0.42, T:0.24
Consensus pattern (54 bp):
GATGGGATGTCCGACTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
Found at i:11744887 original size:35 final size:35
Alignment explanation
Indices: 11744848--11744939 Score: 130
Period size: 35 Copynumber: 2.6 Consensus size: 35
11744838 ACTCACAAGG
11744848 CAATATCATCATGTGCACTCCCTACACACACATTT
1 CAATATCATCATGTGCACTCCCTACACACACATTT
* *
11744883 CAATATCATCATGTGCAGTCCCTACACGCACATTT
1 CAATATCATCATGTGCACTCCCTACACACACATTT
* * **
11744918 CTATACCATCACATGCACTCCC
1 CAATATCATCATGTGCACTCCC
11744940 ACCCACATCA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.29, C:0.36, G:0.08, T:0.27
Consensus pattern (35 bp):
CAATATCATCATGTGCACTCCCTACACACACATTT
Found at i:11745968 original size:19 final size:19
Alignment explanation
Indices: 11745944--11745980 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
11745934 TAAGAAGAGA
11745944 AAGGAAAAGAAAA-GAAAAC
1 AAGG-AAAGAAAATGAAAAC
11745963 AAGGAAAGAAAATGAAAA
1 AAGGAAAGAAAATGAAAA
11745981 AACTTGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.73, C:0.03, G:0.22, T:0.03
Consensus pattern (19 bp):
AAGGAAAGAAAATGAAAAC
Found at i:11747639 original size:21 final size:22
Alignment explanation
Indices: 11747614--11747654 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
11747604 CCTAGGTGGA
*
11747614 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAATAAGTGTG
11747635 AAAATTCAAGGAAATAAGTG
1 AAAATTCAAGGAAATAAGTG
11747655 AAAAAATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.05, G:0.24, T:0.20
Consensus pattern (22 bp):
AAAATTCAAGGAAATAAGTGTG
Found at i:11747655 original size:20 final size:21
Alignment explanation
Indices: 11747614--11747658 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
11747604 CCTAGGTGGA
*
11747614 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
11747635 AAAATTCAA-GGAAATA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
11747655 AAAA
1 AAAA
11747659 AATGTAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.18
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:11747660 original size:22 final size:21
Alignment explanation
Indices: 11747613--11747661 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
11747603 CCCTAGGTGG
* *
11747613 AAAAATTCAAGGGAAAAGTGT
1 AAAAATTCAAGGAAAAAGTGA
*
11747634 GAAAATTCAAGGAAATAAGTGA
1 AAAAATTCAAGGAAA-AAGTGA
11747656 AAAAAT
1 AAAAAT
11747662 GTAAGATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.57, C:0.04, G:0.20, T:0.18
Consensus pattern (21 bp):
AAAAATTCAAGGAAAAAGTGA
Found at i:11749946 original size:22 final size:21
Alignment explanation
Indices: 11749907--11749947 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
11749897 TTATATTGGT
*
11749907 ATCAGAGCCTTGGTTTTAAAG
1 ATCAGAGCCTTGGGTTTAAAG
*
11749928 ATCAGAGCTTTTGGGTTTAA
1 ATCAGAGC-CTTGGGTTTAA
11749948 TGTTGTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (21 bp):
ATCAGAGCCTTGGGTTTAAAG
Found at i:11755006 original size:21 final size:21
Alignment explanation
Indices: 11754963--11755007 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11754953 TAGGTGGAAC
* *
11754963 AATTCAAGGGAAAAGTGTGAA
1 AATTCAAGGAAAAAGTGTAAA
*
11754984 AATTCAAGGAAATAAGTGAAAA
1 AATTCAAGGAAA-AAGTGTAAA
11755006 AA
1 AA
11755008 AGGTAAGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.18
Consensus pattern (21 bp):
AATTCAAGGAAAAAGTGTAAA
Found at i:11759009 original size:27 final size:27
Alignment explanation
Indices: 11758979--11759032 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
11758969 TCTCACCGCA
*
11758979 TATGATCGCATAACCCGTGGTGTAGCC
1 TATGATCACATAACCCGTGGTGTAGCC
11759006 TATGATCACATAACCCGTGGTGTAGCC
1 TATGATCACATAACCCGTGGTGTAGCC
11759033 ATTAGGCTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (27 bp):
TATGATCACATAACCCGTGGTGTAGCC
Found at i:11761555 original size:80 final size:80
Alignment explanation
Indices: 11761466--11761634 Score: 250
Period size: 80 Copynumber: 2.1 Consensus size: 80
11761456 CGAGAGTGTG
* * *
11761466 GATGATGATATTGCCTATGTGCA-TGATGTGGGGGAGCACATTATGGCATTAGTTGTGCATGATG
1 GATGATGATATTGCCTATGTG-AGTGATGTAGGGGAGCACATGATGGCATTAGTTGTGCACGATG
* *
11761530 TGGGGGAGCACACAAT
65 TAGGGGAGCACACAAA
* *
11761546 GATGATGATATTTCCTATGTGAGTGATTTAGGGGAGCACATGATGGCATTAGTTGTGCACGATGT
1 GATGATGATATTGCCTATGTGAGTGATGTAGGGGAGCACATGATGGCATTAGTTGTGCACGATGT
11761611 AGGGGAGCACACAAA
66 AGGGGAGCACACAAA
*
11761626 CATGATGAT
1 GATGATGAT
11761635 GCTGAAATGT
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
79 1 0.01
80 79 0.99
ACGTcount: A:0.27, C:0.12, G:0.32, T:0.28
Consensus pattern (80 bp):
GATGATGATATTGCCTATGTGAGTGATGTAGGGGAGCACATGATGGCATTAGTTGTGCACGATGT
AGGGGAGCACACAAA
Found at i:11761615 original size:36 final size:36
Alignment explanation
Indices: 11761483--11761621 Score: 118
Period size: 36 Copynumber: 3.6 Consensus size: 36
11761473 ATATTGCCTA
* *
11761483 TGTGCATGATGTGGGGGAGCACATTATGGCATTAGT
1 TGTGCATGATGTAGGGGAGCACATGATGGCATTAGT
* * **
11761519 TGTGCATGATGTGGGGGAGCACACAATGATGATGATATTTCCT
1 TGTGCATGATGTAGGGGAG--CAC-ATGATG--G-CA-TTAGT
*
11761562 ATGTG-AGTGATTTAGGGGAGCACATGATGGCATTAGT
1 -TGTGCA-TGATGTAGGGGAGCACATGATGGCATTAGT
*
11761599 TGTGCACGATGTAGGGGAGCACA
1 TGTGCATGATGTAGGGGAGCACA
11761622 CAAACATGAT
Statistics
Matches: 82, Mismatches: 11, Indels: 20
0.73 0.10 0.18
Matches are distributed among these distances:
36 38 0.46
37 4 0.05
38 4 0.05
39 6 0.07
41 7 0.09
42 4 0.05
43 4 0.05
44 15 0.18
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.28
Consensus pattern (36 bp):
TGTGCATGATGTAGGGGAGCACATGATGGCATTAGT
Found at i:11765777 original size:19 final size:19
Alignment explanation
Indices: 11765753--11765790 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11765743 CTACTAAACC
* *
11765753 CTCAAATTATACTCTAATA
1 CTCAAATCATACTCCAATA
11765772 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
11765791 AGTTAAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:11767451 original size:21 final size:20
Alignment explanation
Indices: 11767423--11767464 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 20
11767413 TCCTTAACCT
11767423 TTTCATAGCATATATAAACA
1 TTTCATAGCATATATAAACA
11767443 TTTCTATAGCATATATAAACA
1 TTTC-ATAGCATATATAAACA
11767464 T
1 T
11767465 CTCAATAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (20 bp):
TTTCATAGCATATATAAACA
Found at i:11767472 original size:21 final size:21
Alignment explanation
Indices: 11767427--11767472 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
11767417 TAACCTTTTC
* *
11767427 ATAGCATATATAAACATTTCT
1 ATAGCATATATAAACATCTCA
11767448 ATAGCATATATAAACATCTCA
1 ATAGCATATATAAACATCTCA
11767469 ATAG
1 ATAG
11767473 TGTAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.33
Consensus pattern (21 bp):
ATAGCATATATAAACATCTCA
Found at i:11767621 original size:35 final size:35
Alignment explanation
Indices: 11767542--11767621 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
11767532 CGCAGAAGGG
11767542 AATATCATCATGTGCACTCCCTACACGCACATTTC
1 AATATCATCATGTGCACTCCCTACACGCACATTTC
* ** *
11767577 AATGTCATCATGTGCACTCTGTACATGCACATTTC
1 AATATCATCATGTGCACTCCCTACACGCACATTTC
*
11767612 AATACCATCA
1 AATATCATCA
11767622 CACGTACTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (35 bp):
AATATCATCATGTGCACTCCCTACACGCACATTTC
Found at i:11775311 original size:42 final size:43
Alignment explanation
Indices: 11775226--11775311 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
11775216 CCCTCCATGC
* * * *
11775226 TCAGCTCATGTGCACTCCTTACTCGCACATGGCTGGGTCATCA
1 TCAGCTCATGTGCACTCCTCACACGCACATAGCTGGGTAATCA
11775269 TCAGCTCATGTGCACTCC-CACACGCACATAGCTGGGTAATCA
1 TCAGCTCATGTGCACTCCTCACACGCACATAGCTGGGTAATCA
11775311 T
1 T
11775312 TATCACACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 21 0.54
43 18 0.46
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.26
Consensus pattern (43 bp):
TCAGCTCATGTGCACTCCTCACACGCACATAGCTGGGTAATCA
Found at i:11778917 original size:73 final size:73
Alignment explanation
Indices: 11778738--11778910 Score: 265
Period size: 73 Copynumber: 2.4 Consensus size: 73
11778728 AGTTTTTGAA
* * * * * *
11778738 CCAACCACCCGAGAGTTTCTCGCTGCAACGATAAAGAATTTTGCTGCAGTGACAACCTGGGCTAG
1 CCAACCACCCGAGAGTTTCTCGCTGCAACGAGAAAGAATTTTACTGCAGCGAAAACCCGAGCTAG
11778803 CATTTTTC
66 CATTTTTC
*
11778811 CCAACCACCCAAGAGTTTCTCGCTGCAACGAGAAAGAATTTTACTGCAGCGAAAACCCGAGCTAG
1 CCAACCACCCGAGAGTTTCTCGCTGCAACGAGAAAGAATTTTACTGCAGCGAAAACCCGAGCTAG
*
11778876 CATTTTTT
66 CATTTTTC
*
11778884 CCAACCACCCGAGAGTTTCTCGTTGCA
1 CCAACCACCCGAGAGTTTCTCGCTGCA
11778911 GTGAGAATGC
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 90 1.00
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (73 bp):
CCAACCACCCGAGAGTTTCTCGCTGCAACGAGAAAGAATTTTACTGCAGCGAAAACCCGAGCTAG
CATTTTTC
Found at i:11779222 original size:55 final size:55
Alignment explanation
Indices: 11779124--11779332 Score: 278
Period size: 55 Copynumber: 3.8 Consensus size: 55
11779114 CACTACCGGC
* * *
11779124 TCATAAGCTCATGTGCACTCCCACACTGCACATAGCTGAAATCATCATCCACCAA
1 TCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCATCCACCGA
* * *
11779179 TCATCTGCTCATGTGCACTCCCACACTACACATAGTTGGAATCATCATCCACCGA
1 TCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCATCCACCGA
* * * * *
11779234 TCATCAGCTCATGTGCACTCCTACACCGCACATAACTGGAATCATTATCTC-CCGG
1 TCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCATC-CACCGA
*
11779289 TCATCAGCTCATGTGCACTCCCATA-TCGCACATAGCTGGAATCA
1 TCATCAGCTCATGTGCACTCCCACACT-GCACATAGCTGGAATCA
11779333 CCCGTCATCA
Statistics
Matches: 134, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
55 133 0.99
56 1 0.01
ACGTcount: A:0.28, C:0.34, G:0.13, T:0.24
Consensus pattern (55 bp):
TCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCATCCACCGA
Found at i:11786071 original size:27 final size:28
Alignment explanation
Indices: 11786023--11786082 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
11786013 CTAATAATAA
11786023 GAATACTTTTAACCCAACAAAAGTGGAT
1 GAATACTTTTAACCCAACAAAAGTGGAT
* *
11786051 GAATAC-TTTAACTC-ACTAAAAGTTGAT
1 GAATACTTTTAACCCAAC-AAAAGTGGAT
11786078 GAATA
1 GAATA
11786083 GTGAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 21 0.72
28 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (28 bp):
GAATACTTTTAACCCAACAAAAGTGGAT
Found at i:11792235 original size:15 final size:15
Alignment explanation
Indices: 11792215--11792250 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
11792205 AACACTACAA
11792215 GATGCTCAAACTTCC
1 GATGCTCAAACTTCC
*
11792230 GATGCTTAAACTTCC
1 GATGCTCAAACTTCC
*
11792245 AATGCT
1 GATGCT
11792251 ATAACACCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
GATGCTCAAACTTCC
Found at i:11793414 original size:17 final size:17
Alignment explanation
Indices: 11793392--11793425 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
11793382 GTTTCACCCC
11793392 GAGGAA-AAAAGAAAAGA
1 GAGGAAGAAAA-AAAAGA
11793409 GAGGAAGAAAAAAAAGA
1 GAGGAAGAAAAAAAAGA
11793426 AAGTGGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
GAGGAAGAAAAAAAAGA
Found at i:11795685 original size:54 final size:54
Alignment explanation
Indices: 11795598--11795750 Score: 252
Period size: 54 Copynumber: 2.8 Consensus size: 54
11795588 ATTAGTATAC
* * * *
11795598 CACCACATCTCATCCAGCTCATGTGCATCCCCCCACATTGTGCACATAGCCGGA
1 CACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAGA
*
11795652 CACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCTAGA
1 CACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAGA
*
11795706 CATCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCAC
1 CACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCAC
11795751 GGCTAATGCC
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.23, C:0.44, G:0.13, T:0.20
Consensus pattern (54 bp):
CACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAGA
Found at i:11802081 original size:2 final size:2
Alignment explanation
Indices: 11802074--11802108 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11802064 ATTATAGTTG
*
11802074 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11802109 GTTGTGCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11806121 original size:35 final size:35
Alignment explanation
Indices: 11806082--11806189 Score: 126
Period size: 35 Copynumber: 3.1 Consensus size: 35
11806072 TTTACTCAGC
*
11806082 TCATGTGCACTCCTTACACGCACAAGGCAATATCA
1 TCATGTGCACTCCTTACACGCACATGGCAATATCA
* * ** *
11806117 TCATGTGTACTCCTTACACACGTATGGCCATATCA
1 TCATGTGCACTCCTTACACGCACATGGCAATATCA
* * **
11806152 TCATGTGCACTCCCTACATGCACATTTCAATATCA
1 TCATGTGCACTCCTTACACGCACATGGCAATATCA
11806187 TCA
1 TCA
11806190 CACACATTCC
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.29
Consensus pattern (35 bp):
TCATGTGCACTCCTTACACGCACATGGCAATATCA
Found at i:11812632 original size:13 final size:13
Alignment explanation
Indices: 11812614--11812638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11812604 TTTTAGAAAA
11812614 TTTATAAAATCAT
1 TTTATAAAATCAT
11812627 TTTATAAAATCA
1 TTTATAAAATCA
11812639 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:11817737 original size:22 final size:22
Alignment explanation
Indices: 11817712--11817772 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
11817702 GTGGTGTCAA
*
11817712 AGCTTTTAGTTTTAAAGATAAG
1 AGCTTTTGGTTTTAAAGATAAG
*
11817734 AGCTTTTGGTTTTAAAGATTAG
1 AGCTTTTGGTTTTAAAGATAAG
* *
11817756 GGCTTTTGGGTTTAAAG
1 AGCTTTTGGTTTTAAAG
11817773 TTATTTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.43
Consensus pattern (22 bp):
AGCTTTTGGTTTTAAAGATAAG
Found at i:11825526 original size:19 final size:19
Alignment explanation
Indices: 11825502--11825542 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
11825492 ACAATAGGAA
11825502 ATTTTTAGAATAAAATAAT
1 ATTTTTAGAATAAAATAAT
**
11825521 ATTTTTTTAATAAAATAAT
1 ATTTTTAGAATAAAATAAT
11825540 ATT
1 ATT
11825543 AAAATATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTTTTAGAATAAAATAAT
Found at i:11825915 original size:13 final size:12
Alignment explanation
Indices: 11825894--11825945 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
11825884 ATATAGTAAA
*
11825894 ATAATAATAGTAT
1 ATAAAAATA-TAT
11825907 ATAAAAATATAT
1 ATAAAAATATAT
* *
11825919 ATATATATATAT
1 ATAAAAATATAT
* *
11825931 ATATATATATAT
1 ATAAAAATATAT
11825943 ATA
1 ATA
11825946 TGTAAAGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
12 28 0.78
13 8 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
ATAAAAATATAT
Found at i:11825918 original size:2 final size:2
Alignment explanation
Indices: 11825913--11825946 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
11825903 GTATATAAAA
11825913 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
11825947 GTAAAGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11826268 original size:138 final size:137
Alignment explanation
Indices: 11826111--11826374 Score: 492
Period size: 138 Copynumber: 1.9 Consensus size: 137
11826101 AAAGAATAAA
*
11826111 ATATGTATATATGGGTGAATAAGTAAAGTGAAGAAGACAAGATGAAAGAGAGAAGTCGGTTAGTT
1 ATATATATATATGGGTGAATAAGTAAAGTGAAGAAGACAAGATGAAAGAGAGAAGTCGGTTAGTT
*
11826176 AAGAGAAGAAAAAGAAACAAGAAGAAGGCGTGAGCAAAGAGAACAAAAAGAAACAAGAGANATAT
66 AAGAGAAGAAAAAGAAACAAGAAGAAGGCGTGAACAAAGAGAACAAAAAGAAACAAGAGA-ATAT
11826241 ATATATAT
130 ATATATAT
11826249 ATATATATATATGGGTGAATAAGTAAAGTGAAGAAGACAAGATGAAAGAGAGAAGTCGGTTAGTT
1 ATATATATATATGGGTGAATAAGTAAAGTGAAGAAGACAAGATGAAAGAGAGAAGTCGGTTAGTT
*
11826314 AAGAGAAGAAAAAGAAAGAAGAAGAAGGCGTGAACAAAGAGAACAAAAAGAAACAAGAGAA
66 AAGAGAAGAAAAAGAAACAAGAAGAAGGCGTGAACAAAGAGAACAAAAAGAAACAAGAGAA
11826375 GGCCGAGTGG
Statistics
Matches: 123, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
137 1 0.01
138 122 0.99
ACGTcount: A:0.53, C:0.05, G:0.26, T:0.15
Consensus pattern (137 bp):
ATATATATATATGGGTGAATAAGTAAAGTGAAGAAGACAAGATGAAAGAGAGAAGTCGGTTAGTT
AAGAGAAGAAAAAGAAACAAGAAGAAGGCGTGAACAAAGAGAACAAAAAGAAACAAGAGAATATA
TATATAT
Found at i:11826552 original size:34 final size:34
Alignment explanation
Indices: 11826503--11826604 Score: 118
Period size: 36 Copynumber: 2.9 Consensus size: 34
11826493 AGCTTTAGCT
*
11826503 GCTGATTTTGAAGGTTGAAAAGTGCTGTTTTGCTA
1 GCTGATTTTGAAGGTTGAAAAGTGCAGTTTTGC-A
* *
11826538 -CT-AGTTTTGGAGGTTGAGAAGTGCAGATTTTTGCA
1 GCTGA-TTTTGAAGGTTGAAAAGTGCAG--TTTTGCA
*
11826573 GCTGATTTTGAAGGTTGTAAAGTGCAGTTTTG
1 GCTGATTTTGAAGGTTGAAAAGTGCAGTTTTG
11826605 GTTGTTAATC
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
33 1 0.02
34 26 0.46
35 1 0.02
36 27 0.48
37 1 0.02
ACGTcount: A:0.23, C:0.08, G:0.30, T:0.39
Consensus pattern (34 bp):
GCTGATTTTGAAGGTTGAAAAGTGCAGTTTTGCA
Found at i:11826672 original size:35 final size:34
Alignment explanation
Indices: 11826627--11826737 Score: 113
Period size: 34 Copynumber: 3.2 Consensus size: 34
11826617 TGTTGTTTTG
*
11826627 GCTGCTGATTTTTGGAGGGA-AAATAGAGCAGCTTA
1 GCTGCTGATTTTT-GA-GAACAAATAGAGCAGCTTA
* *
11826662 GCTGTTGATTTTTGAGAACAAATAGAGCAGCTTT
1 GCTGCTGATTTTTGAGAACAAATAGAGCAGCTTA
*
11826696 GCTGCTGA-TTTTGA-AGTC-AATATGAGCAGCCTTA
1 GCTGCTGATTTTTGAGA-ACAAATA-GAGCAG-CTTA
11826730 GCTGCTGA
1 GCTGCTGA
11826738 AAAATTATGG
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
32 5 0.08
33 15 0.23
34 34 0.52
35 12 0.18
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (34 bp):
GCTGCTGATTTTTGAGAACAAATAGAGCAGCTTA
Found at i:11826900 original size:5 final size:5
Alignment explanation
Indices: 11826883--11826922 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
11826873 GAGGAAGAAT
* *
11826883 AAAAG AGAAAG AAAAG AAAAG AAGAG AAAAA AAAAG AAAA
1 AAAAG A-AAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
11826923 ATATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:11826916 original size:19 final size:20
Alignment explanation
Indices: 11826885--11826922 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11826875 GGAAGAATAA
*
11826885 AAGAG-AAAGAAAAGAAAAG
1 AAGAGAAAAAAAAAGAAAAG
11826904 AAGAGAAAAAAAAAGAAAA
1 AAGAGAAAAAAAAAGAAAA
11826923 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAGAGAAAAAAAAAGAAAAG
Found at i:11834477 original size:31 final size:28
Alignment explanation
Indices: 11834431--11834496 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 28
11834421 AGTAATTTTT
11834431 AAAATCTACACTTTTGCCCCTATAAAAGTTCA
1 AAAAT-TACACTTTTGCCCC-A-AAAA-TTCA
* *
11834463 AAAATTACATTTTTGCCCCAAAAATTGA
1 AAAATTACACTTTTGCCCCAAAAATTCA
11834491 AAAATT
1 AAAATT
11834497 GCCCATAGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 9 0.28
29 4 0.12
30 1 0.03
31 13 0.41
32 5 0.16
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (28 bp):
AAAATTACACTTTTGCCCCAAAAATTCA
Found at i:11842895 original size:15 final size:16
Alignment explanation
Indices: 11842869--11842903 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
11842859 TCAAAAACTT
*
11842869 CTTTTAAAACCACAAG
1 CTTTTAAAACCAAAAG
11842885 CTTTT-AAACCAAAAG
1 CTTTTAAAACCAAAAG
11842900 CTTT
1 CTTT
11842904 GATACCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (16 bp):
CTTTTAAAACCAAAAG
Found at i:11845248 original size:21 final size:22
Alignment explanation
Indices: 11845208--11845248 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11845198 CCATTGGTCC
11845208 GTTTTAAAAATTTCATCCATTT
1 GTTTTAAAAATTTCATCCATTT
* *
11845230 GTTTTCAAATTTTCA-CCAT
1 GTTTTAAAAATTTCATCCAT
11845249 ACACTTGTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (22 bp):
GTTTTAAAAATTTCATCCATTT
Found at i:11847429 original size:5 final size:5
Alignment explanation
Indices: 11847412--11847461 Score: 82
Period size: 5 Copynumber: 9.8 Consensus size: 5
11847402 GAGGAAGAGA
*
11847412 AAAAG AGAAAG AAAAG AAAAG AAAAG AAAAG AAGAG AAAAG AAAAG AAAA
1 AAAAG A-AAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
11847462 ATATATATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 37 0.88
6 5 0.12
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:11859860 original size:35 final size:35
Alignment explanation
Indices: 11859814--11859921 Score: 162
Period size: 35 Copynumber: 3.1 Consensus size: 35
11859804 CTTACTCAGC
*
11859814 TCATGTGCACTCCCTACATGCACAAGGCAATATCA
1 TCATGTGCACTCCCTACATGCACATGGCAATATCA
* * *
11859849 TCATGTGCACTCCTTACACGCGCATGGCAATATCA
1 TCATGTGCACTCCCTACATGCACATGGCAATATCA
**
11859884 TCATGTGCACTCCCTACATGCACATTTCAATATCA
1 TCATGTGCACTCCCTACATGCACATGGCAATATCA
11859919 TCA
1 TCA
11859922 CACACATTCC
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (35 bp):
TCATGTGCACTCCCTACATGCACATGGCAATATCA
Found at i:11864190 original size:13 final size:13
Alignment explanation
Indices: 11864172--11864196 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11864162 TTCCAGAAAA
11864172 TTTATAAAATCAT
1 TTTATAAAATCAT
11864185 TTTATAAAATCA
1 TTTATAAAATCA
11864197 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:11865447 original size:20 final size:21
Alignment explanation
Indices: 11865422--11865468 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
11865412 CTTCTAAACC
11865422 TCAAATGT-TACTCCAATAAG
1 TCAAATGTATACTCCAATAAG
* *
11865442 TCAAAT-TATATTCTAATAAG
1 TCAAATGTATACTCCAATAAG
11865462 TCAAATG
1 TCAAATG
11865469 GGGCCAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (21 bp):
TCAAATGTATACTCCAATAAG
Found at i:11869699 original size:40 final size:39
Alignment explanation
Indices: 11869639--11869745 Score: 126
Period size: 38 Copynumber: 2.7 Consensus size: 39
11869629 CTCACCCAGC
* * *
11869639 TCATGTGCATCCCCCGACATCGTGCACATAGTCGGGGTCA
1 TCATGTGCATCCCCCCACATCGTGCACATA-TCAGGGCCA
* *
11869679 TCATGTGCATCCCCCCACATCGTGCACA-ATTAGTGCCA
1 TCATGTGCATCCCCCCACATCGTGCACATATCAGGGCCA
** *
11869717 TTGTGTGCATCCCTCCACATCGTGCACAT
1 TCATGTGCATCCCCCCACATCGTGCACAT
11869746 GGGCACTTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
38 30 0.52
39 1 0.02
40 27 0.47
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.25
Consensus pattern (39 bp):
TCATGTGCATCCCCCCACATCGTGCACATATCAGGGCCA
Found at i:11884943 original size:2 final size:2
Alignment explanation
Indices: 11884936--11884982 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
11884926 TTATAGCCGN
11884936 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
11884978 TA TA T
1 TA TA T
11884983 GTTGTGCATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11885195 original size:41 final size:39
Alignment explanation
Indices: 11885113--11885196 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
11885103 ACGTGATGCA
* * *
11885113 GGGGGATGTACACGATGGCACTGATTGTGCATGATGTGG
1 GGGGGATGCACACGATGGCACCGATTGTGCACGATGTGG
* *
11885152 GGGGGATGCACACGATGGCGCCGTCTATGTGCACGATGTGG
1 GGGGGATGCACACGATGGCACCG-AT-TGTGCACGATGTGG
11885193 GGGG
1 GGGG
11885197 ATGTACATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 20 0.53
40 1 0.03
41 17 0.45
ACGTcount: A:0.18, C:0.17, G:0.44, T:0.21
Consensus pattern (39 bp):
GGGGGATGCACACGATGGCACCGATTGTGCACGATGTGG
Found at i:11895435 original size:2 final size:2
Alignment explanation
Indices: 11895428--11895458 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11895418 TATTATGTTA
11895428 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11895459 CATACATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11895631 original size:38 final size:37
Alignment explanation
Indices: 11895500--11895632 Score: 108
Period size: 36 Copynumber: 3.5 Consensus size: 37
11895490 ACCCAGCTCA
* * * *
11895500 TGTGCATCCCCCCACATTGTGCACATAGTCGAAGTCATCG
1 TGTGCATCCCCCCACA-T-CGCACACAGT-TAAGACATCG
* *** * *
11895540 CGTGCATCCCCCCACATCATGCACAGGTACAGACATCA
1 TGTGCATCCCCCCACATCGCACACAGTTA-AGACATCG
*
11895578 TGTGC-T-CCCCCACATCGCACACAGTTAATGCCATCG
1 TGTGCATCCCCCCACATCGCACACAGTTAA-GACATCG
11895614 TGTGCATCCCCCCACATCG
1 TGTGCATCCCCCCACATCG
11895633 TGCACACGGG
Statistics
Matches: 72, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
35 1 0.01
36 27 0.38
37 3 0.04
38 25 0.35
39 1 0.01
40 15 0.21
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (37 bp):
TGTGCATCCCCCCACATCGCACACAGTTAAGACATCG
Found at i:11897555 original size:15 final size:16
Alignment explanation
Indices: 11897535--11897565 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
11897525 ACCACAAAAT
11897535 AAAATAAAAT-CAAGA
1 AAAATAAAATCCAAGA
11897550 AAAATAAAATCCAAGA
1 AAAATAAAATCCAAGA
11897566 TTTGCAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (16 bp):
AAAATAAAATCCAAGA
Found at i:11905608 original size:27 final size:27
Alignment explanation
Indices: 11905572--11905656 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
11905562 TTTCGAGTAT
* * * *
11905572 AAGGGTAAAATAATCATTTTGCCACCC
1 AAGGGCAAAATTATAATTTTACCACCC
*
11905599 AATGGCAAAATTATAATTTTACCACCC
1 AAGGGCAAAATTATAATTTTACCACCC
11905626 AAGGGCAAAATTATAATTTTACATCACCC
1 AAGGGCAAAATTATAATTTTAC--CACCC
11905655 AA
1 AA
11905657 CACTTGTCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
27 43 0.86
29 7 0.14
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (27 bp):
AAGGGCAAAATTATAATTTTACCACCC
Found at i:11922194 original size:16 final size:16
Alignment explanation
Indices: 11922175--11922221 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
11922165 TGCTTTGAAA
11922175 ATTTTTTTTTTATTTT
1 ATTTTTTTTTTATTTT
*
11922191 ATTTTTTTTATATTTT
1 ATTTTTTTTTTATTTT
* *
11922207 -TTTTCTTTTTCTTTT
1 ATTTTTTTTTTATTTT
11922222 CTTCTTTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (16 bp):
ATTTTTTTTTTATTTT
Found at i:11922195 original size:14 final size:14
Alignment explanation
Indices: 11922176--11922210 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
11922166 GCTTTGAAAA
11922176 TTTTTTTTTTAT-T
1 TTTTTTTTTTATAT
11922189 TTATTTTTTTTATAT
1 TT-TTTTTTTTATAT
11922204 TTTTTTT
1 TTTTTTT
11922211 CTTTTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 15 0.75
15 3 0.15
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTTATAT
Found at i:11922801 original size:20 final size:20
Alignment explanation
Indices: 11922776--11922813 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11922766 GGGGGAGCAG
11922776 TTATATCTT-GCATGTTTTAT
1 TTATAT-TTCGCATGTTTTAT
11922796 TTATATTTCGCATGTTTT
1 TTATATTTCGCATGTTTT
11922814 GTTGTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.61
Consensus pattern (20 bp):
TTATATTTCGCATGTTTTAT
Found at i:11924134 original size:27 final size:30
Alignment explanation
Indices: 11924089--11924152 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 30
11924079 CAATTTTTAA
* *
11924089 TTATAATTTACTTA-TTTTTAGTT-GTT-T
1 TTATAATTAACTTACTTTTAAGTTAGTTAT
*
11924116 TTATAATTAAGTTACTTTTAAGTTAGTTAT
1 TTATAATTAACTTACTTTTAAGTTAGTTAT
11924146 TT-TAATT
1 TTATAATT
11924153 TTATGTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 12 0.39
28 8 0.26
29 8 0.26
30 3 0.10
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.61
Consensus pattern (30 bp):
TTATAATTAACTTACTTTTAAGTTAGTTAT
Found at i:11924160 original size:20 final size:20
Alignment explanation
Indices: 11924131--11924173 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
11924121 ATTAAGTTAC
11924131 TTTTAAGTTAGTT-ATTTTAA
1 TTTTAAGTTA-TTCATTTTAA
* *
11924151 TTTTATGTTATTCGTTTTAA
1 TTTTAAGTTATTCATTTTAA
11924171 TTT
1 TTT
11924174 GGTTATGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.65
Consensus pattern (20 bp):
TTTTAAGTTATTCATTTTAA
Found at i:11925268 original size:20 final size:21
Alignment explanation
Indices: 11925243--11925282 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11925233 TTTTCTAAAG
11925243 TTATTATT-ATTTTAATTTTT
1 TTATTATTGATTTTAATTTTT
*
11925263 TTATTATTGGTTTTAATTTT
1 TTATTATTGATTTTAATTTT
11925283 AGTTAATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (21 bp):
TTATTATTGATTTTAATTTTT
Found at i:11936751 original size:15 final size:15
Alignment explanation
Indices: 11936703--11936754 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
11936693 CTAAGAAAGT
*
11936703 AAAATAAGT-AAATA
1 AAAATAAATAAAATA
*
11936717 AATAATATATAACAAT-
1 AA-AATAAATAA-AATA
11936733 AAAATAAATAAAATA
1 AAAATAAATAAAATA
11936748 AAAATAA
1 AAAATAA
11936755 TTTTCACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.16
15 20 0.65
16 3 0.10
17 3 0.10
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (15 bp):
AAAATAAATAAAATA
Found at i:11938418 original size:36 final size:37
Alignment explanation
Indices: 11938378--11938502 Score: 136
Period size: 36 Copynumber: 3.5 Consensus size: 37
11938368 TGGTGGTGTA
*
11938378 CGGTGTGCGAGTGCACATGATGATA-TATGCCATGTG
1 CGGTGTGGGAGTGCACATGATGATACTATGCCATGTG
*
11938414 CGGTGTGGGAGTG--CAT-ATGATACT-TGCCATGTA
1 CGGTGTGGGAGTGCACATGATGATACTATGCCATGTG
* * *
11938447 CGGTGTGGGCGTGCACATGAGGATACTA-GCTATGTG
1 CGGTGTGGGAGTGCACATGATGATACTATGCCATGTG
** *
11938483 CAATGTGGAAGTGCACATGA
1 CGGTGTGGGAGTGCACATGA
11938503 GCTGAGATGA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
33 26 0.35
34 4 0.05
35 3 0.04
36 41 0.55
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.26
Consensus pattern (37 bp):
CGGTGTGGGAGTGCACATGATGATACTATGCCATGTG
Found at i:11938442 original size:33 final size:33
Alignment explanation
Indices: 11938374--11938466 Score: 107
Period size: 33 Copynumber: 2.7 Consensus size: 33
11938364 GTGATGGTGG
*
11938374 TGTACGGTGTGCGAGTGCACATGATGATATATGCCA
1 TGTACGGTGTGGGAGTG--CAT-ATGATATATGCCA
*
11938410 TGTGCGGTGTGGGAGTGCATATGATACT-TGCCA
1 TGTACGGTGTGGGAGTGCATATGATA-TATGCCA
* *
11938443 TGTACGGTGTGGGCGTGCACATGA
1 TGTACGGTGTGGGAGTGCATATGA
11938467 GGATACTAGC
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 32 0.63
34 4 0.08
36 15 0.29
ACGTcount: A:0.20, C:0.16, G:0.35, T:0.28
Consensus pattern (33 bp):
TGTACGGTGTGGGAGTGCATATGATATATGCCA
Found at i:11938463 original size:69 final size:69
Alignment explanation
Indices: 11938374--11938502 Score: 170
Period size: 69 Copynumber: 1.9 Consensus size: 69
11938364 GTGATGGTGG
* ** * *
11938374 TGTACGGTGTGCGAGTGCACATGATGATA-TATGCCATGTGCGGTGTGGGAGTGCATATGATACT
1 TGTACGGTGTGCGAGTGCACATGAGGATACTA-GCCATGTGCAATGTGGAAGTGCACATGATACT
11938438 TGCCA
65 TGCCA
* * *
11938443 TGTACGGTGTGGGCGTGCACATGAGGATACTAGCTATGTGCAATGTGGAAGTGCACATGA
1 TGTACGGTGTGCGAGTGCACATGAGGATACTAGCCATGTGCAATGTGGAAGTGCACATGA
11938503 GCTGAGATGA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
69 49 0.96
70 2 0.04
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.27
Consensus pattern (69 bp):
TGTACGGTGTGCGAGTGCACATGAGGATACTAGCCATGTGCAATGTGGAAGTGCACATGATACTT
GCCA
Found at i:11943066 original size:101 final size:101
Alignment explanation
Indices: 11942900--11943087 Score: 286
Period size: 101 Copynumber: 1.9 Consensus size: 101
11942890 ATATAACCAC
* * * * *
11942900 CGGCTCATCAACTCATGTGCACTCCCACACTGCATATAGTTGGAATCATCATGTGCATTCTCACA
1 CGGCTCATCAACTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATGTGCACTCCCACA
11942965 CCGCACATGACAAATATCATGTTCGCATAAAATCAT
66 CCGCACATGACAAATATCATGTTCGCATAAAATCAT
* * *
11943001 CGGCTCATCAGCTCATGTGTACTCCGACACCGCACATAGCTGGAATCATCATGTGCACTCCCACA
1 CGGCTCATCAACTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATGTGCACTCCCACA
* *
11943066 CTGCACATGGCAAATATCATGT
66 CCGCACATGACAAATATCATGT
11943088 ACACTTCCAC
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 77 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (101 bp):
CGGCTCATCAACTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATGTGCACTCCCACA
CCGCACATGACAAATATCATGTTCGCATAAAATCAT
Found at i:11945055 original size:25 final size:25
Alignment explanation
Indices: 11945010--11945057 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
11945000 TGATATATAC
*
11945010 GTGGCAAGGCCACCGGATGATATGT
1 GTGGCAAGGCCACCGAATGATATGT
*
11945035 GTGGCTAGGCCACC-AATTGATAT
1 GTGGCAAGGCCACCGAA-TGATAT
11945058 ACATGGTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (25 bp):
GTGGCAAGGCCACCGAATGATATGT
Found at i:11946464 original size:34 final size:35
Alignment explanation
Indices: 11946388--11946457 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
11946378 ATAAAATTTA
* * *
11946388 AATTTAAATAATCAAAAATAAATATCTCAAATATC
1 AATTTAAATAATCAAAAACAAATATCTCAAACAAC
11946423 AATTTAAATAA-CTAAAAACAAATAT-TCAAACAAC
1 AATTTAAATAATC-AAAAACAAATATCTCAAACAAC
11946457 A
1 A
11946458 TCTTAAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 9 0.29
35 22 0.71
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (35 bp):
AATTTAAATAATCAAAAACAAATATCTCAAACAAC
Found at i:11947670 original size:59 final size:59
Alignment explanation
Indices: 11947585--11947700 Score: 160
Period size: 59 Copynumber: 2.0 Consensus size: 59
11947575 AAGATTTTTT
* *
11947585 ATAATATCTTTTTATCCAAATTCATTTTATCCCAGTTTGACATTGATTAATTTTTCAGG
1 ATAATATCTTTTTATCCAAATCCATTTTATCCCAGTTTGACATTGAATAATTTTTCAGG
* * * * **
11947644 ATAATATCTTTTTGTCCAAATCCATTTTATTCTAGTTTTATGTTGAATAATTTTTCA
1 ATAATATCTTTTTATCCAAATCCATTTTATCCCAGTTTGACATTGAATAATTTTTCA
11947701 ATACATCTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.50
Consensus pattern (59 bp):
ATAATATCTTTTTATCCAAATCCATTTTATCCCAGTTTGACATTGAATAATTTTTCAGG
Found at i:11950569 original size:141 final size:142
Alignment explanation
Indices: 11950314--11950595 Score: 530
Period size: 141 Copynumber: 2.0 Consensus size: 142
11950304 AAATTACATG
*
11950314 ATATCTTTAAAAAATGTTGTTATTACATGCCATGTTCAAAAAATATTATTATAGTTGAAAAAAAG
1 ATATCTTTAAAAAATGTTGTTATTACATACCATGTTCAAAAAATATTATTATAGTTGAAAAAAAG
*
11950379 TTGTTAGATGTTTTAACTCCTAGAGTTTATGTTGTAGTAAAATACAAAGGAGAAAGTTACACGCC
66 TTGTTAGATGTTTTAACTCCTAAAGTTTATGTTGTAGTAAAATACAAAGGAGAAAGTTACACGCC
11950444 ATGTTTAATAAC
131 ATGTTTAATAAC
11950456 ATATCTTTAAAAAATGTTGTTATTACATACCATGTTCAAAAAATATTATTATAGTTG-AAAAAAG
1 ATATCTTTAAAAAATGTTGTTATTACATACCATGTTCAAAAAATATTATTATAGTTGAAAAAAAG
*
11950520 TTGTTAGATGTTTTAATTCCTAAAGTTTATGTTGTAGTAAAATACAAAGGAGAAAGTTACACGCC
66 TTGTTAGATGTTTTAACTCCTAAAGTTTATGTTGTAGTAAAATACAAAGGAGAAAGTTACACGCC
11950585 ATGTTTAATAA
131 ATGTTTAATAA
11950596 ATGTTGTTGT
Statistics
Matches: 137, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
141 81 0.59
142 56 0.41
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (142 bp):
ATATCTTTAAAAAATGTTGTTATTACATACCATGTTCAAAAAATATTATTATAGTTGAAAAAAAG
TTGTTAGATGTTTTAACTCCTAAAGTTTATGTTGTAGTAAAATACAAAGGAGAAAGTTACACGCC
ATGTTTAATAAC
Found at i:11955928 original size:21 final size:21
Alignment explanation
Indices: 11955904--11955958 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
11955894 TTCTAAAAGC
*
11955904 AAAAATATATAAATTAAAGTA
1 AAAAATATGTAAATTAAAGTA
*
11955925 AAAAATATGTAAATTAAATTA
1 AAAAATATGTAAATTAAAGTA
11955946 AAAAATATGTAAA
1 AAAAATATGTAAA
11955959 GATTAGAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAAATATGTAAATTAAAGTA
Found at i:11956148 original size:35 final size:35
Alignment explanation
Indices: 11956102--11956174 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
11956092 AGCAAATGAG
11956102 AAAGGAAGATTTCAAAAGTAGATATTATACATTGA
1 AAAGGAAGATTTCAAAAGTAGATATTATACATTGA
*
11956137 AAAGGAAGATTTTAAAAGTAGATATTATACATTGA
1 AAAGGAAGATTTCAAAAGTAGATATTATACATTGA
11956172 AAA
1 AAA
11956175 AAAATATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.29
Consensus pattern (35 bp):
AAAGGAAGATTTCAAAAGTAGATATTATACATTGA
Found at i:11956447 original size:17 final size:17
Alignment explanation
Indices: 11956425--11956468 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
11956415 TTTTATTAAT
*
11956425 TATTTTTTATTTTTATA
1 TATTTTTAATTTTTATA
*
11956442 TATTTTTAATTTTTATG
1 TATTTTTAATTTTTATA
11956459 TATTTTTAAT
1 TATTTTTAAT
11956469 ATAATTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
TATTTTTAATTTTTATA
Found at i:11957440 original size:26 final size:26
Alignment explanation
Indices: 11957386--11957444 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
11957376 TAACTGCTAA
* *
11957386 AAATGGATAGAAACAGATTTTGTTCG
1 AAATAGATAGAAACAGATTTTATTCG
*
11957412 AAATAGATAGAAATAGATTTTATAT-G
1 AAATAGATAGAAACAGATTTTAT-TCG
11957438 AAATAGA
1 AAATAGA
11957445 CACAATTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (26 bp):
AAATAGATAGAAACAGATTTTATTCG
Found at i:11976315 original size:20 final size:20
Alignment explanation
Indices: 11976290--11976335 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
11976280 CTTCTAATCC
11976290 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
11976310 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
11976330 TCAAAT
1 TCAAAT
11976336 GGGGTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:11977005 original size:19 final size:18
Alignment explanation
Indices: 11976967--11977005 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
11976957 GTACTCTATT
* *
11976967 TTTCAAAATCATTATTAA
1 TTTCAAAATAATTATAAA
11976985 TTTCAAAATAATTTATAAA
1 TTTCAAAATAA-TTATAAA
11977004 TT
1 TT
11977006 AATTTCATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTCAAAATAATTATAAA
Found at i:11977796 original size:21 final size:20
Alignment explanation
Indices: 11977761--11977801 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
11977751 TTCGGCTAGC
11977761 CATGAATTCACCAT-GAAAA
1 CATGAATTCACCATGGAAAA
11977780 CATGAAATTCAACCATGGAAAA
1 CATG-AATTC-ACCATGGAAAA
11977802 TAAGGAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 5 0.26
22 5 0.26
ACGTcount: A:0.49, C:0.20, G:0.12, T:0.20
Consensus pattern (20 bp):
CATGAATTCACCATGGAAAA
Found at i:11979014 original size:66 final size:66
Alignment explanation
Indices: 11978901--11979024 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
11978891 TTTAATAATT
* * *
11978901 TCATAATTCATCCACATGTTTAGCCCATAGTGTACATGACATACTCAACATATACATGTCACAAT
1 TCATAATTCATCCACATGCTTAGCCCATAATGTACATGACATACTCAACACATACATGTCACAAT
11978966 C
66 C
** *
11978967 TCATAATTCATTCC-CATGCTTAGCCCATAATGT-CAATGATGTTCTCAACACATACATG
1 TCATAATTCA-TCCACATGCTTAGCCCATAATGTAC-ATGACATACTCAACACATACATG
11979025 GCATGGCATA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
65 1 0.02
66 46 0.92
67 3 0.06
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (66 bp):
TCATAATTCATCCACATGCTTAGCCCATAATGTACATGACATACTCAACACATACATGTCACAAT
C
Found at i:11982401 original size:13 final size:14
Alignment explanation
Indices: 11982373--11982415 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
11982363 AATTCCACCC
11982373 GAGAGAAAGAAAAA
1 GAGAGAAAGAAAAA
*
11982387 GAGAGAAA-TAAAA
1 GAGAGAAAGAAAAA
*
11982400 GAGAGAAAGAGAAA
1 GAGAGAAAGAAAAA
11982414 GA
1 GA
11982416 AAAAAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (14 bp):
GAGAGAAAGAAAAA
Found at i:11982407 original size:23 final size:23
Alignment explanation
Indices: 11982380--11982424 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11982370 CCCGAGAGAA
* *
11982380 AGAAAAAGAGAGAAATAAAAGAG
1 AGAAAAAGAAAGAAAAAAAAGAG
*
11982403 AGAAAGAGAAAGAAAAAAAAGA
1 AGAAAAAGAAAGAAAAAAAAGA
11982425 AAGGAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (23 bp):
AGAAAAAGAAAGAAAAAAAAGAG
Found at i:11982410 original size:19 final size:19
Alignment explanation
Indices: 11982376--11982434 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
11982366 TCCACCCGAG
11982376 AGAAAGAAAAAG--AGAGAA
1 AGAAA-AAAAAGAAAGAGAA
* * *
11982394 ATAAAAGAGAGAAAGAGAA
1 AGAAAAAAAAGAAAGAGAA
11982413 AGAAAAAAAAGAAAGGAGAA
1 AGAAAAAAAAGAAA-GAGAA
11982433 AG
1 AG
11982435 GGGAAGGAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 17 0.53
20 7 0.22
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (19 bp):
AGAAAAAAAAGAAAGAGAA
Found at i:11982427 original size:27 final size:27
Alignment explanation
Indices: 11982373--11982434 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
11982363 AATTCCACCC
* *
11982373 GAGAGAAAGAAAAAGAGAGAAATAAAA
1 GAGAGAAAGAAAAAGAGAAAAAAAAAA
*
11982400 GAGAGAAAGAGAAAGA-AAAAAAAGAAA
1 GAGAGAAAGAAAAAGAGAAAAAAA-AAA
11982427 G-GAGAAAG
1 GAGAGAAAG
11982435 GGGAAGGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.39
27 19 0.61
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (27 bp):
GAGAGAAAGAAAAAGAGAAAAAAAAAA
Found at i:11999436 original size:28 final size:28
Alignment explanation
Indices: 11999390--11999445 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
11999380 CGAAGCATAA
*
11999390 GGGCAAAATCGTAATTTTTCCACCCCAG
1 GGGCAAAATCGTAAATTTTCCACCCCAG
* *
11999418 GGGC-AAATCGATAAATTTTTCTCCCCAG
1 GGGCAAAATCG-TAAATTTTCCACCCCAG
11999446 CACTTGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (28 bp):
GGGCAAAATCGTAAATTTTCCACCCCAG
Found at i:12000866 original size:19 final size:19
Alignment explanation
Indices: 12000842--12000905 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
12000832 ACTGATCGTG
*
12000842 CATGATGTGGGGGGATGCA
1 CATGATGTGGGGGGATGTA
* ** *
12000861 CATGATGGTGTCGGCTATGTG
1 CATGAT-GTG-GGGGGATGTA
12000882 CATGATGTGGGGGGATGTA
1 CATGATGTGGGGGGATGTA
12000901 CATGA
1 CATGA
12000906 GCCGGGAGTG
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
19 17 0.50
20 6 0.18
21 11 0.32
ACGTcount: A:0.20, C:0.11, G:0.42, T:0.27
Consensus pattern (19 bp):
CATGATGTGGGGGGATGTA
Found at i:12010802 original size:25 final size:25
Alignment explanation
Indices: 12010774--12010833 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
12010764 GTGGTCGTAA
**
12010774 CCACGTATATCAACTTATGACCTAG
1 CCACGTATATCAACCCATGACCTAG
* * *
12010799 CCACGTATATCATCCCATGGCCTTG
1 CCACGTATATCAACCCATGACCTAG
12010824 CCACGTATAT
1 CCACGTATAT
12010834 ATATCATAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.27, C:0.32, G:0.13, T:0.28
Consensus pattern (25 bp):
CCACGTATATCAACCCATGACCTAG
Found at i:12011235 original size:13 final size:13
Alignment explanation
Indices: 12011217--12011241 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12011207 TCTAAATCCC
12011217 TTTACATATATAG
1 TTTACATATATAG
12011230 TTTACATATATA
1 TTTACATATATA
12011242 AATACAAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
TTTACATATATAG
Found at i:12013496 original size:42 final size:42
Alignment explanation
Indices: 12013430--12013554 Score: 153
Period size: 42 Copynumber: 3.0 Consensus size: 42
12013420 TGTTGATGTG
* * * *
12013430 GACCTGGCTATGTGCGAGTAGGAGTGCACATAAGCTGTTGTT
1 GACCAGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
* *
12013472 GACCCA-GCTATATGCAAGTGGGAGTGCACATAAGCCGTTGCT
1 GA-CCAGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
** *
12013514 GACCAGGCTATGTGCGAGTGGGAGTGTGCATAAACCGTTGC
1 GACCAGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
12013555 ATATGAAATG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 3 0.04
42 65 0.93
43 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (42 bp):
GACCAGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
Found at i:12019085 original size:15 final size:15
Alignment explanation
Indices: 12019065--12019094 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12019055 GGTTTTGGGG
12019065 AAAGTTGCACAGTTT
1 AAAGTTGCACAGTTT
12019080 AAAGTTGCACAGTTT
1 AAAGTTGCACAGTTT
12019095 GAGGGTGGAA
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:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
AAAGTTGCACAGTTT
Found at i:12021184 original size:42 final size:40
Alignment explanation
Indices: 12021125--12021249 Score: 151
Period size: 42 Copynumber: 3.0 Consensus size: 40
12021115 TGTTTATATA
*
12021125 GACCCGGCTAGGTGCGAGTAGGAGTGCACATAAGTCGTTGCT
1 GACCC-GCTATGTGCGAGT-GGAGTGCACATAAGTCGTTGCT
* *
12021167 GACCCAGCTATGTGCGAGTGAAAGTGCACATAAGTTGTTGCT
1 GACCC-GCTATGTGCGAGTG-GAGTGCACATAAGTCGTTGCT
* *
12021209 GACCCGACTATGTGCGAGTGGGAGTGCGCATAAGCCGTTGC
1 GACCCG-CTATGTGCGAGT-GGAGTGCACATAAGTCGTTGC
12021250 ATATGAAATT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
41 2 0.03
42 69 0.96
43 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.22
Consensus pattern (40 bp):
GACCCGCTATGTGCGAGTGGAGTGCACATAAGTCGTTGCT
Found at i:12021293 original size:2 final size:2
Alignment explanation
Indices: 12021286--12021329 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
12021276 GTACATGATG
*
12021286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12021328 AT
1 AT
12021330 GGTATATGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.