Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 161 of 290
Found at i:51980498 original size:14 final size:15
Alignment explanation
Indices: 51980421--51980500 Score: 58
Period size: 15 Copynumber: 5.4 Consensus size: 15
51980411 GTATCCTAGG
*
51980421 TTTCTTTATCCTGGA
1 TTTCTTTATCTTGGA
*
51980436 TCTCTTTAT-TCTGGA
1 TTTCTTTATCT-TGGA
* **
51980451 TTTCTATATTCAAGG-
1 TTTCTTTA-TCTTGGA
*
51980466 TTTCTCTATCTTGGA
1 TTTCTTTATCTTGGA
*
51980481 TTTCTTTAT-TTGGT
1 TTTCTTTATCTTGGA
51980495 TTTCTT
1 TTTCTT
51980501 GTTATCTTTG
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
14 14 0.28
15 33 0.66
16 3 0.06
ACGTcount: A:0.14, C:0.16, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTCTTTATCTTGGA
Found at i:51982042 original size:27 final size:26
Alignment explanation
Indices: 51981994--51982051 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
51981984 GCGAGGCTGC
*
51981994 CAGATATTGTGACGAAGTCACCAAATA
1 CAGATATTGTGACGAAGCCACCAAA-A
* * * *
51982021 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAAAA
51982047 CAGAT
1 CAGAT
51982052 GTATATATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAAAA
Found at i:51982148 original size:67 final size:67
Alignment explanation
Indices: 51982054--51982229 Score: 289
Period size: 67 Copynumber: 2.6 Consensus size: 67
51982044 GAACAGATGT
* * *
51982054 ATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCTGCTAGATATTGTGATGAAGTCACCAAAAC
1 ATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAAAAC
*
51982119 AG
66 AA
* *
51982121 ATATATGTTGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGAAC
1 ATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAAAAC
51982186 AA
66 AA
*
51982188 ATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTTCCAGA
1 ATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGA
51982230 ACACTTCCTC
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 101 1.00
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.20
Consensus pattern (67 bp):
ATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAAAAC
AA
Found at i:51991229 original size:40 final size:40
Alignment explanation
Indices: 51991159--51991256 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 40
51991149 AAACCAAGTA
* * * * *
51991159 CCTTTGGGATTTAG-CCAGATATAGCTACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATG
51991198 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCACAAATG
*
51991238 CCTTCGGAACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
51991257 TTATCATCCG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
39 13 0.25
40 38 0.75
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATG
Found at i:51999203 original size:27 final size:27
Alignment explanation
Indices: 51999149--51999249 Score: 143
Period size: 27 Copynumber: 3.8 Consensus size: 27
51999139 AGCATGGCTG
* *
51999149 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
51999175 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
51999202 CCAGAACAAAT-ATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
*
51999229 CCAGATCAGATAATTGTGGCA
1 CCAGAACAGATAATTGTGGCA
51999250 TAGACAACAG
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
26 15 0.22
27 50 0.75
28 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:52000671 original size:24 final size:23
Alignment explanation
Indices: 52000644--52000743 Score: 146
Period size: 24 Copynumber: 4.2 Consensus size: 23
52000634 CAACTCTTGA
*
52000644 TCCTTGATCAGCTCCTAAATCTTC
1 TCCTT-ATCAGCTCCTAAATCCTC
*
52000668 TCCTTTATCAGATCCTAAATCCTC
1 TCC-TTATCAGCTCCTAAATCCTC
52000692 TCCCTTATCAGCTCCTAAATCCTC
1 T-CCTTATCAGCTCCTAAATCCTC
52000716 TCCCTTATCAGCTCCTAAATCCTC
1 T-CCTTATCAGCTCCTAAATCCTC
52000740 TCCT
1 TCCT
52000744 GACAGCCTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
23 3 0.04
24 64 0.90
25 4 0.06
ACGTcount: A:0.21, C:0.38, G:0.05, T:0.36
Consensus pattern (23 bp):
TCCTTATCAGCTCCTAAATCCTC
Found at i:52000709 original size:48 final size:49
Alignment explanation
Indices: 52000645--52000742 Score: 162
Period size: 48 Copynumber: 2.0 Consensus size: 49
52000635 AACTCTTGAT
* *
52000645 CCTTGATCAGCTCCTAAATCTTCTCCTTTATCAGATCCTAAATCCTCTC
1 CCTTGATCAGCTCCTAAATCCTCTCCCTTATCAGATCCTAAATCCTCTC
*
52000694 CCTT-ATCAGCTCCTAAATCCTCTCCCTTATCAGCTCCTAAATCCTCTC
1 CCTTGATCAGCTCCTAAATCCTCTCCCTTATCAGATCCTAAATCCTCTC
52000742 C
1 C
52000743 TGACAGCCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 42 0.91
49 4 0.09
ACGTcount: A:0.21, C:0.39, G:0.05, T:0.35
Consensus pattern (49 bp):
CCTTGATCAGCTCCTAAATCCTCTCCCTTATCAGATCCTAAATCCTCTC
Found at i:52002289 original size:65 final size:66
Alignment explanation
Indices: 52002202--52002331 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 66
52002192 GGCAACCCAC
*
52002202 TCACAAAGTGCATGGTTACCCTCTCCCACTTCCAAAGTGGTATCTTCACCGGCTGTAACAGTCCA
1 TCACAAAGTCCATGGTTACCCTCTCCCACTTCCAAAGTGGTATCTTCACCGGCTGTAACAGTCCA
52002267 T
66 T
52002268 TCACAAAG-CCATGGTTACCCTCTCCCACTTCCAAAGTGGTATCTTCACCGGCTGTAACAGTCCA
1 TCACAAAGTCCATGGTTACCCTCTCCCACTTCCAAAGTGGTATCTTCACCGGCTGTAACAGTCCA
52002332 GAAGGTAATT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
65 55 0.87
66 8 0.13
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (66 bp):
TCACAAAGTCCATGGTTACCCTCTCCCACTTCCAAAGTGGTATCTTCACCGGCTGTAACAGTCCA
T
Found at i:52006970 original size:27 final size:27
Alignment explanation
Indices: 52006908--52007018 Score: 147
Period size: 27 Copynumber: 4.2 Consensus size: 27
52006898 CAGCATGGCT
* *
52006908 ACCAGAACAGATAA-TGTGAC-GAGTC
1 ACCAGAACAGATAATTGTGGCAGAGCC
52006933 ACCAGAACAGATAATTGTGGCAGAGCC
1 ACCAGAACAGATAATTGTGGCAGAGCC
*
52006960 ACCAGAACAGAT-ATATGTGGCAAAGCC
1 ACCAGAACAGATAAT-TGTGGCAGAGCC
* *
52006987 ACCAGATCAGATAATTGTGGCATAGCC
1 ACCAGAACAGATAATTGTGGCAGAGCC
52007014 ACCAG
1 ACCAG
52007019 GACGCTTCCT
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
25 14 0.18
26 7 0.09
27 54 0.70
28 2 0.03
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (27 bp):
ACCAGAACAGATAATTGTGGCAGAGCC
Found at i:52008438 original size:24 final size:24
Alignment explanation
Indices: 52008411--52008504 Score: 143
Period size: 24 Copynumber: 3.9 Consensus size: 24
52008401 TTGCTCATTG
*
52008411 ATCAGCTTCTAAATCTTCTCCTTT
1 ATCAGCTTCTAAATCCTCTCCTTT
* *
52008435 ATCAGATTCTAAATCCTCTCCCTT
1 ATCAGCTTCTAAATCCTCTCCTTT
* *
52008459 ATCACCTCCTAAATCCTCTCCTTT
1 ATCAGCTTCTAAATCCTCTCCTTT
52008483 ATCAGCTTCTAAATCCTCTCCT
1 ATCAGCTTCTAAATCCTCTCCT
52008505 GACAGCCTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.22, C:0.35, G:0.03, T:0.39
Consensus pattern (24 bp):
ATCAGCTTCTAAATCCTCTCCTTT
Found at i:52011010 original size:65 final size:65
Alignment explanation
Indices: 52010934--52011062 Score: 240
Period size: 65 Copynumber: 2.0 Consensus size: 65
52010924 CTCTTGAAGT
* *
52010934 AACTTGAAGGGAGATCTCTAGTCTTGATGATGAATTCGGCTCTTGAGATGGATCAATCGGCTTTG
1 AACTTGAAGGGAGATCTCTAGTCTTGATGATGAATCCAGCTCTTGAGATGGATCAATCGGCTTTG
52010999 AACTTGAAGGGAGATCTCTAGTCTTGATGATGAATCCAGCTCTTGAGATGGATCAATCGGCTTT
1 AACTTGAAGGGAGATCTCTAGTCTTGATGATGAATCCAGCTCTTGAGATGGATCAATCGGCTTT
52011063 TCCCCATCTA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (65 bp):
AACTTGAAGGGAGATCTCTAGTCTTGATGATGAATCCAGCTCTTGAGATGGATCAATCGGCTTTG
Found at i:52023441 original size:46 final size:45
Alignment explanation
Indices: 52023374--52023548 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 45
52023364 TGTAACCCGC
*
52023374 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCAT
*
52023420 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* *** * *
52023466 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCG-GCATTCGCAT
*
52023513 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
52023549 ATGCTCAACC
Statistics
Matches: 108, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 66 0.61
47 31 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:52023494 original size:93 final size:93
Alignment explanation
Indices: 52023382--52023552 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
52023372 GCCCATAAGT
* *
52023382 GAACTCGGACTCAACTCAACGAGCTC-AGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGA-ACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
52023446 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
*
52023475 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
52023540 CGAGTTCGGATGC
66 CGAGCTCGGATGC
52023553 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
93 72 0.99
94 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:52026166 original size:29 final size:29
Alignment explanation
Indices: 52026127--52026205 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
52026117 CTTAATAATC
*
52026127 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
52026157 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
52026186 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
52026206 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:52026666 original size:12 final size:12
Alignment explanation
Indices: 52026649--52026674 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52026639 GGGCATACTC
52026649 ATGTATATATAT
1 ATGTATATATAT
52026661 ATGTATATATAT
1 ATGTATATATAT
52026673 AT
1 AT
52026675 ACTTCAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATGTATATATAT
Found at i:52029855 original size:50 final size:49
Alignment explanation
Indices: 52029782--52029967 Score: 205
Period size: 50 Copynumber: 3.7 Consensus size: 49
52029772 ATGAATACAT
*
52029782 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTATTAAGTCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACT-TCAAGTCAC
* * * *
52029832 ATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCAATGACTTCGA-TCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-C-AT-ACTTCAAGTCAC
* * * * *
52029883 GTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGA-TGGTGAGGTCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACT--TCAAGTCAC
*
52029933 GTGTGTAGTACTAAGTGCAGGCTACTACATGTACC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACC
52029968 GGATTGTTGG
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 2 0.02
50 68 0.60
51 34 0.30
52 4 0.04
53 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (49 bp):
GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTTCAAGTCAC
Found at i:52034907 original size:31 final size:31
Alignment explanation
Indices: 52034869--52034932 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
52034859 CCTTTTCATA
52034869 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
52034900 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
52034931 TT
1 TT
52034933 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:52035233 original size:25 final size:24
Alignment explanation
Indices: 52035140--52035246 Score: 162
Period size: 24 Copynumber: 4.4 Consensus size: 24
52035130 ATGGAGGCCT
52035140 AGCCTCTTTTAATAACTAGGGCA-A
1 AGCC-CTTTTAATAACTAGGGCATA
*
52035164 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTAGGGCATA
52035188 AGCCCTTTTAATAACTAGGGCATA
1 AGCCCTTTTAATAACTAGGGCATA
* *
52035212 AGCCCTTTATCATAACTGGGGCATA
1 AGCCCTTT-TAATAACTAGGGCATA
52035237 AGCCCTTTTA
1 AGCCCTTTTA
52035247 CACTTCCTCC
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
23 17 0.22
24 37 0.49
25 22 0.29
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTAATAACTAGGGCATA
Found at i:52035240 original size:49 final size:47
Alignment explanation
Indices: 52035140--52035246 Score: 178
Period size: 49 Copynumber: 2.2 Consensus size: 47
52035130 ATGGAGGCCT
52035140 AGCCTCTTTTAATAACTAGGGCAAAGCCCTTTTAATAACTGGGGCATA
1 AGCC-CTTTTAATAACTAGGGCAAAGCCCTTTTAATAACTGGGGCATA
*
52035188 AGCCCTTTTAATAACTAGGGCATAAGCCCTTTATCATAACTGGGGCATA
1 AGCCCTTTTAATAACTAGGGCA-AAGCCCTTT-TAATAACTGGGGCATA
52035237 AGCCCTTTTA
1 AGCCCTTTTA
52035247 CACTTCCTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
47 18 0.32
48 13 0.23
49 25 0.45
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (47 bp):
AGCCCTTTTAATAACTAGGGCAAAGCCCTTTTAATAACTGGGGCATA
Found at i:52035324 original size:20 final size:20
Alignment explanation
Indices: 52035296--52035334 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
52035286 TACGAATACA
*
52035296 TCATGTGCATATCATACATG
1 TCATATGCATATCATACATG
52035316 TCATATGCATATCATACAT
1 TCATATGCATATCATACAT
52035335 ACCATGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (20 bp):
TCATATGCATATCATACATG
Found at i:52044998 original size:16 final size:16
Alignment explanation
Indices: 52044974--52045004 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52044964 TGGATTTATC
*
52044974 AAAATACTTTATCAAT
1 AAAAGACTTTATCAAT
52044990 AAAAGACTTTATCAA
1 AAAAGACTTTATCAA
52045005 ACCAAAGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (16 bp):
AAAAGACTTTATCAAT
Found at i:52046540 original size:22 final size:22
Alignment explanation
Indices: 52046505--52046547 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
52046495 TTTCGATTAC
*
52046505 AAAAACATAAAATGAACTAAAT
1 AAAAACATAAAATGAAATAAAT
52046527 AAAAAC-TAAGAATGAAATAAA
1 AAAAACATAA-AATGAAATAAA
52046548 AACCTAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.16
Consensus pattern (22 bp):
AAAAACATAAAATGAAATAAAT
Found at i:52051352 original size:46 final size:46
Alignment explanation
Indices: 52051302--52051477 Score: 162
Period size: 46 Copynumber: 3.8 Consensus size: 46
52051292 TGGTTGAGCA
52051302 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
52051348 TCCGAACTCGTTGAGTTGAGTCCGTGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* **
52051393 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * **
52051441 CCCGAGCTCGTTGAGTTGAGTCCAAGTTTGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52051478 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 59 0.58
47 27 0.26
48 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:52051862 original size:51 final size:51
Alignment explanation
Indices: 52051786--52051889 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
52051776 TTACTTGCTA
52051786 TTTTCATGTGAACTTATTAAGCATTTATTCTTACTCCCTCCTTTTCATTCC
1 TTTTCATGTGAACTTATTAAGCATTTATTCTTACTCCCTCCTTTTCATTCC
52051837 TTTTCATGTGAACTTATTAAGCATTTATTCTTACTCCCTCCTTTTCATTCC
1 TTTTCATGTGAACTTATTAAGCATTTATTCTTACTCCCTCCTTTTCATTCC
52051888 TT
1 TT
52051890 GTAGTTTTGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.19, C:0.25, G:0.06, T:0.50
Consensus pattern (51 bp):
TTTTCATGTGAACTTATTAAGCATTTATTCTTACTCCCTCCTTTTCATTCC
Found at i:52061238 original size:29 final size:29
Alignment explanation
Indices: 52061206--52061280 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
52061196 AATCATATTC
**
52061206 ATATGGCCCATTAGGCTC-AAATCACCTGT
1 ATATGGCCCATTAGGC-CGAAATCAAATGT
*
52061235 ATATGGCCCATTAGGCCGAAATCAAATTT
1 ATATGGCCCATTAGGCCGAAATCAAATGT
*
52061264 ATATGGCCCGTTAGGCC
1 ATATGGCCCATTAGGCC
52061281 CAGTCTCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 1 0.02
29 40 0.98
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCGAAATCAAATGT
Found at i:52061535 original size:24 final size:24
Alignment explanation
Indices: 52061506--52061556 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
52061496 GTAGCCAAAC
*
52061506 TTTCAGCT-TTTCGGCATTTCAACT
1 TTTCAG-TATTTCGACATTTCAACT
*
52061530 TTTCAGTATTTCGACATTTCAGCT
1 TTTCAGTATTTCGACATTTCAACT
52061554 TTT
1 TTT
52061557 GTCGATACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.18, C:0.22, G:0.12, T:0.49
Consensus pattern (24 bp):
TTTCAGTATTTCGACATTTCAACT
Found at i:52071134 original size:18 final size:19
Alignment explanation
Indices: 52071102--52071137 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
52071092 GGTAGAAATA
52071102 ATTCTTAGATTTTTATTTC
1 ATTCTTAGATTTTTATTTC
52071121 ATTCTTAG-TTTTTATTT
1 ATTCTTAGATTTTTATTT
52071138 ATTTTTATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (19 bp):
ATTCTTAGATTTTTATTTC
Found at i:52072252 original size:18 final size:19
Alignment explanation
Indices: 52072220--52072255 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
52072210 GGTAGAAATA
52072220 ATTCTTAGATTTTTATTTC
1 ATTCTTAGATTTTTATTTC
52072239 ATTCTTAG-TTTTTATTT
1 ATTCTTAGATTTTTATTT
52072256 ATTTTTATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (19 bp):
ATTCTTAGATTTTTATTTC
Found at i:52074669 original size:23 final size:23
Alignment explanation
Indices: 52074641--52074711 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
52074631 GAAATTGGTG
52074641 TGGAATGCCATATGAAAGCATGAA
1 TGGAATGCCATATGAAAGCATG-A
** **
52074665 T-GAAT-TAATATGAAATTAGTG-
1 TGGAATGCCATATGAAAGCA-TGA
52074686 TGGAATGCCATATGAAAGCATGA
1 TGGAATGCCATATGAAAGCATGA
52074709 TGG
1 TGG
52074712 TTTGAGCATG
Statistics
Matches: 35, Mismatches: 8, Indels: 9
0.67 0.15 0.17
Matches are distributed among these distances:
21 1 0.03
22 15 0.43
23 18 0.51
24 1 0.03
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.27
Consensus pattern (23 bp):
TGGAATGCCATATGAAAGCATGA
Found at i:52074681 original size:45 final size:44
Alignment explanation
Indices: 52074618--52074708 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 44
52074608 AGGTTTATAA
*
52074618 GAATGAATAATATGAAATTGGTGTGGAATGCCATATGAAAGCAT
1 GAATGAATAATATGAAATTAGTGTGGAATGCCATATGAAAGCAT
52074662 GAATGAATTAATATGAAATTAGTGTGGAATGCCATATGAAAGCAT
1 GAATGAA-TAATATGAAATTAGTGTGGAATGCCATATGAAAGCAT
52074707 GA
1 GA
52074709 TGGTTTGAGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 7 0.16
45 38 0.84
ACGTcount: A:0.42, C:0.07, G:0.24, T:0.27
Consensus pattern (44 bp):
GAATGAATAATATGAAATTAGTGTGGAATGCCATATGAAAGCAT
Found at i:52075239 original size:18 final size:18
Alignment explanation
Indices: 52075218--52075261 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
52075208 ATGTCCCAAG
*
52075218 CCACATGGTTGTGTGTCA
1 CCACACGGTTGTGTGTCA
52075236 CCACACGGTTGTGTGTCA
1 CCACACGGTTGTGTGTCA
52075254 CCACACGG
1 CCACACGG
52075262 CCTACCCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.25
Consensus pattern (18 bp):
CCACACGGTTGTGTGTCA
Found at i:52077172 original size:47 final size:48
Alignment explanation
Indices: 52077109--52078699 Score: 2266
Period size: 47 Copynumber: 33.6 Consensus size: 48
52077099 CCCTTCGGGA
*
52077109 CTTATCACAT-TCATACACT-TCCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATAT-ATACACTGTTCACATTCATCACATTGGCCATTCGGC
52077156 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52077203 CTTATCTCATATATGCA-TGTTCACATT-ATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52077249 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52077296 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
52077343 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52077392 CTTATCACATATGTACACT-TTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
*
52077439 CTTATCTCATATATGA-A-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATAT-ACACTGTTCACATTCATCACATTGGCCATTCGGC
* * *
52077486 CTTATCTCATATATGCA-TGTTCGCATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* * *
52077533 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCGTTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
52077580 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* **
52077629 CTTATCACATATGTACACT-TTCACATTCATCACATCAGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52077676 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52077723 CTTATCTCATATATCCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* * *
52077770 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCAGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
*
52077817 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTCAGC
1 CTTATCAC--ATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
*
52077866 CTTATCACATATATACACT-TTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52077913 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* * *
52077960 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCGTTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
52078007 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* **
52078056 CTTATCACATATGTACACT-TTCACATTCATCACATCAGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52078103 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52078150 CTTATCTCATATATCCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52078197 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
*
52078244 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTCAGC
1 CTTATCAC--ATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
*
52078293 CTTATCACATATATACACT-TTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52078340 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* * *
52078387 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGT
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
52078434 CTTATCACATATATATACACTG-TCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52078483 CTTATCACATATATACACT-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52078530 CTTATCACATATATACACT-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52078577 CTTATCACATATATATACACT-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
* *
52078626 CTTATCACATATATACACT-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
52078673 CTTATCACATATATACACT-TTCACATT
1 CTTATCACATATATACACTGTTCACATT
52078700 TATTCAAATA
Statistics
Matches: 1428, Mismatches: 85, Indels: 62
0.91 0.05 0.04
Matches are distributed among these distances:
46 52 0.04
47 1067 0.75
48 2 0.00
49 300 0.21
50 7 0.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.34
Consensus pattern (48 bp):
CTTATCACATATATACACTGTTCACATTCATCACATTGGCCATTCGGC
Found at i:52077474 original size:190 final size:189
Alignment explanation
Indices: 52077109--52078699 Score: 2229
Period size: 190 Copynumber: 8.4 Consensus size: 189
52077099 CCCTTCGGGA
*
52077109 CTTATCACAT-TCATACACTTCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
1 CTTATCACATAT-ATACA-TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
* *
52077173 CTTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCA-TGTTCACATT-ATCACA
64 CTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTGTTCACATTCATCACA
* *
52077236 TTGGCCATTCGGCCTTATCTCATATA-TGCA-TGTTCACATTCATCACATTGGCCATTCGGC
129 TTGGCCATTCGGCCTTATCACATATATTACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
52077296 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATAC
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATAC
*
52077361 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATGTACACT-TTCACATTCATCAC
63 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTGTTCACATTCATCAC
* * *
52077425 ATCGGCCATTCGGCCTTATCTCATATATGA-A-TGTTCACATTCATCACATTGGCCATTCGGC
128 ATTGGCCATTCGGCCTTATCACATATATTACACT-TTCACATTCATCACATTGGCCATTCGGC
* * * * *
52077486 CTTATCTCATATATGCATGTTCGCATTCATCACATTGGCCATTCGGCCTTATCACACATACACA-
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
*
52077550 TGTTCACATTCATCACATTGGCCGTTCGGCCTTATCACATATATATACACT-TTCACATTCATCA
65 T-TTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATACACTGTTCACATTCATCA
* **
52077614 CATTGGCCATTCGGCCTTATCACATAT-GTACACTTTCACATTCATCACATCAGCCATTCGGC
127 CATTGGCCATTCGGCCTTATCACATATATTACACTTTCACATTCATCACATTGGCCATTCGGC
* * * *
52077676 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATCCA-
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
* *
52077740 TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACA-TGTTCACATTCATCACA
65 T-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTGTTCACATTCATCACA
* *
52077804 TTGGCCATTCAGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCAGC
129 TTGGCCATTCGGCCTTATCACATATAT-TACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
52077866 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCTCATATATGCA-
1 CTTATCACATATATACA-TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
* *
52077930 TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACA-TGTTCACATTCATCACA
65 T-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTGTTCACATTCATCACA
*
52077994 TTGGCCGTTCGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
129 TTGGCCATTCGGCCTTATCACATATAT-TACACTTTCACATTCATCACATTGGCCATTCGGC
* ** * *
52078056 CTTATCACATATGTACACTTTCACATTCATCACATCAGCCATTCGGCCTTATCTCATATATGCA-
1 CTTATCACATATATACA-TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
* *
52078120 TGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATCCA-TGTTCACATTCATCACA
65 T-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTGTTCACATTCATCACA
* *
52078184 TTGGCCATTCGGCCTTATCACACATA-CACA-TGTTCACATTCATCACATTGGCCATTCGGC
129 TTGGCCATTCGGCCTTATCACATATATTACACT-TTCACATTCATCACATTGGCCATTCGGC
*
52078244 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCAGCCTTATCACATATATAC
1 CTTATCAC--ATATATACA-TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* * *
52078309 ACTTTCACATTCATCACATCGGCCATTCGGCCTTATCTCATATATGCA-TGTTCACATTCATCAC
63 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTGTTCACATTCATCAC
* * *
52078373 ATTGGCCATTCGGCCTTATCACACATA-CACA-TGTTCACATTCATCACATTGGCCATTCGGT
128 ATTGGCCATTCGGCCTTATCACATATATTACACT-TTCACATTCATCACATTGGCCATTCGGC
*
52078434 CTTATCACATATATATACACTGTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACA-TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* *
52078499 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT-TTCACATTCATCAC
63 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTGTTCACATTCATCAC
* * * *
52078563 ATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
128 ATTGGCCATTCGGCCTTATCACATATAT-TACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52078626 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACA-TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
52078691 TTTCACATT
65 TTTCACATT
52078700 TATTCAAATA
Statistics
Matches: 1303, Mismatches: 77, Indels: 45
0.91 0.05 0.03
Matches are distributed among these distances:
186 1 0.00
187 51 0.04
188 128 0.10
189 62 0.05
190 1020 0.78
191 4 0.00
192 36 0.03
193 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.34
Consensus pattern (189 bp):
CTTATCACATATATACATTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT
TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTGTTCACATTCATCACATT
GGCCATTCGGCCTTATCACATATATTACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:52077539 original size:22 final size:22
Alignment explanation
Indices: 52077467--52077541 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
52077457 GTTCACATTC
52077467 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
52077489 ATCTCATATATG-CATGTTC-GCATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
52077513 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
52077536 ATCACA
1 ATCACA
52077542 CATACACATG
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 15 0.38
23 8 0.20
24 8 0.20
25 9 0.22
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:52077572 original size:237 final size:237
Alignment explanation
Indices: 52077109--52078699 Score: 2433
Period size: 237 Copynumber: 6.7 Consensus size: 237
52077099 CCCTTCGGGA
* *
52077109 CTTATCACAT-T-CATACACTTCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
52077172 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATT-ATCACA
66 ACTTTCACATTCATCACATCGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACA
* *
52077236 TTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTAT
131 TTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTAT
52077301 CACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
196 CACACATACACACT-TTCACATTCATCACATTGGCCATTCGGC
*
52077343 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATGTAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
52077408 ACTTTCACATTCATCACATCGGCCATTCGGCCTTATCTCATATATGAATGTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACA
* * *
52077473 TTGGCCATTCGGCCTTATCTCATATATGCATGTTCGCATTCATCACATTGGCCATTCGGCCTTAT
131 TTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTAT
*
52077538 CACACATACACA-TGTTCACATTCATCACATTGGCCGTTCGGC
196 CACACATACACACT-TTCACATTCATCACATTGGCCATTCGGC
*
52077580 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATGTAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
52077645 ACTTTCACATTCATCACATCAGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACA
* *
52077710 TTGGCCATTCGGCCTTATCTCATATATCCATGTTCACATTCATCACATTGGCCATTCGGCCTTAT
131 TTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTAT
*
52077775 CACACATACACA-TGTTCACATTCATCACATTGGCCATTCAGC
196 CACACATACACACT-TTCACATTCATCACATTGGCCATTCGGC
*
52077817 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCAGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
52077882 ACTTTCACATTCATCACATCGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACA
* * *
52077947 TTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCGTTCGGCCTTAT
131 TTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTAT
* *
52078012 CACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
196 CAC--ACATACACACTTTCACATTCATCACATTGGCCATTCGGC
* ** * *
52078056 CTTATCAC--ATATGTACACTTTCACATTCATCACATCAGCCATTCGGCCTTATCTCATATATGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* *
52078119 A-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATCCATGTTCACATTCATCAC
66 ACT-TTCACATTCATCACATCGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCAC
* *
52078183 ATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTA
130 ATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTA
* * *
52078248 TCACATATATATACACTTTCACATTCATCACATTGGCCATTCAGC
195 TCAC--ACATACACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
52078293 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCTCATATATGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* * * **
52078356 A-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCAC
66 ACT-TTCACATTCATCACATCGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCAC
*
52078420 ATTGGCCATTCGGTCTTATCACATATATATACACTG-TCACATTCATCACATTGGCCATTCGGCC
130 ATTGGCCATTCGGCCTTATCAC--ATATATACA-TGTTCACATTCATCACATTGGCCATTCGGCC
* * * *
52078484 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
192 TTATCACACATACACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52078530 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATAT
* * *
52078593 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT-TTCACATTCATC
64 ACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCTCATATATGCA-TGTTCACATTCATC
* *
52078657 ACATCGGCCATTAGGCCTTATCACATATATACACT-TTCACATT
128 ACATTGGCCATTCGGCCTTATCACATATATACA-TGTTCACATT
52078700 TATTCAAATA
Statistics
Matches: 1286, Mismatches: 56, Indels: 27
0.94 0.04 0.02
Matches are distributed among these distances:
234 10 0.01
235 1 0.00
236 106 0.08
237 998 0.78
239 166 0.13
240 5 0.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.34
Consensus pattern (237 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACA
TTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTAT
CACACATACACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:52077823 original size:22 final size:22
Alignment explanation
Indices: 52077704--52077826 Score: 63
Period size: 22 Copynumber: 5.3 Consensus size: 22
52077694 GTTCACATTC
*
52077704 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCAGCCTT
* ** *
52077726 ATCTCATATATCCATGTTCA-CATT
1 ATCACAT-TGGCCA--TTCAGCCTT
*
52077750 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCAGCCTT
* * *
52077773 ATCACACAT-ACACATGTTCA-CATT
1 ATCACA-TTGGC-CA--TTCAGCCTT
52077797 CATCACATTGGCCATTCAGCCTT
1 -ATCACATTGGCCATTCAGCCTT
52077820 ATCACAT
1 ATCACAT
52077827 ATATATACAC
Statistics
Matches: 72, Mismatches: 17, Indels: 24
0.64 0.15 0.21
Matches are distributed among these distances:
22 27 0.38
23 13 0.18
24 13 0.18
25 19 0.26
ACGTcount: A:0.26, C:0.31, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCAGCCTT
Found at i:52078203 original size:22 final size:22
Alignment explanation
Indices: 52078131--52078253 Score: 63
Period size: 22 Copynumber: 5.3 Consensus size: 22
52078121 GTTCACATTC
52078131 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* ** * *
52078153 ATCTCATATATCCATGTTC-ACATT
1 ATCACAT-TGGCCA--TTCGGCCTT
52078177 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
52078200 ATCACACAT-ACACATGTTC-ACATT
1 ATCACA-TTGGC-CA--TTCGGCCTT
52078224 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
52078247 ATCACAT
1 ATCACAT
52078254 ATATATACAC
Statistics
Matches: 71, Mismatches: 18, Indels: 24
0.63 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 13 0.18
24 13 0.18
25 19 0.27
ACGTcount: A:0.25, C:0.31, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:52080208 original size:56 final size:56
Alignment explanation
Indices: 52080147--52080267 Score: 224
Period size: 56 Copynumber: 2.2 Consensus size: 56
52080137 TATTAGCTTA
52080147 TTGCCCATCCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATCCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
* *
52080203 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATCCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
52080259 TTGCCCATC
1 TTGCCCATC
52080268 ATCCCTTGTC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.45
Consensus pattern (56 bp):
TTGCCCATCCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:52081221 original size:18 final size:18
Alignment explanation
Indices: 52081198--52081233 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
52081188 ATTCTTCCAC
52081198 GAAGAATTCCAAAAGAAG
1 GAAGAATTCCAAAAGAAG
52081216 GAAGAATTCCAAAAGAAG
1 GAAGAATTCCAAAAGAAG
52081234 TAAATCAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.22, T:0.11
Consensus pattern (18 bp):
GAAGAATTCCAAAAGAAG
Found at i:52086244 original size:37 final size:37
Alignment explanation
Indices: 52086183--52086261 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
52086173 TTATTACGAA
* * *
52086183 GTCTTACCCAGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
* *
52086220 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
52086257 GTCTT
1 GTCTT
52086262 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
Found at i:52086458 original size:47 final size:47
Alignment explanation
Indices: 52086382--52086557 Score: 192
Period size: 47 Copynumber: 3.7 Consensus size: 47
52086372 CTTCGGGACT
* * * * *
52086382 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCC
* * *
52086429 TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCC
* * *
52086476 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGTCT
1 TATCAC--ATATATACACTTTCACATTCATCACATCGGCCACTAGGCCC
* * *
52086525 TATCTCATATATGCA-TGTTCACATCCATCACAT
1 TATCACATATATACACT-TTCACATTCATCACAT
52086558 AGAATCCTAA
Statistics
Matches: 113, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
46 1 0.01
47 67 0.59
49 45 0.40
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCC
Found at i:52086505 original size:49 final size:49
Alignment explanation
Indices: 52086380--52086536 Score: 205
Period size: 49 Copynumber: 3.3 Consensus size: 49
52086370 CCCTTCGGGA
* * * * *
52086380 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
52086427 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52086474 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52086523 CTTATCTCATATAT
1 CTTATCACATATAT
52086537 GCATGTTCAC
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
46 1 0.01
47 43 0.45
49 51 0.54
ACGTcount: A:0.27, C:0.30, G:0.09, T:0.34
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52086546 original size:96 final size:94
Alignment explanation
Indices: 52086380--52086557 Score: 223
Period size: 96 Copynumber: 1.9 Consensus size: 94
52086370 CCCTTCGGGA
* * * *
52086380 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
*
52086445 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATCCATCACATCGGCCATTAGGC
* * * * * *
52086474 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGTCTTATCTCATATATGC
1 CTTATCACAT-T-TATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATAC
52086539 A-TGTTCACATCCATCACAT
64 ACT-TTCACATCCATCACAT
52086558 AGAATCCTAA
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
94 10 0.14
95 2 0.03
96 58 0.83
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (94 bp):
CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATCCATCACATCGGCCATTAGGC
Found at i:52091566 original size:46 final size:46
Alignment explanation
Indices: 52091516--52091691 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
52091506 TGGTTGAGCA
52091516 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
52091562 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
52091607 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
52091655 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52091692 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:52091672 original size:93 final size:93
Alignment explanation
Indices: 52091513--52091684 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
52091503 GGATGGTTGA
* *
52091513 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
52091578 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
52091606 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
52091671 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
52091685 CTTATGGGCG
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:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:52096558 original size:79 final size:82
Alignment explanation
Indices: 52096447--52096631 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
52096437 GCTACTCGTT
* * *
52096447 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
52096510 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
52096527 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
52096590 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
52096607 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52096632 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:52096631 original size:40 final size:40
Alignment explanation
Indices: 52096428--52096631 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
52096418 CGGAATTTAA
** *
52096428 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
52096468 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
52096508 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
52096547 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
52096587 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
52096627 CCGGA
1 CCGGA
52096632 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:52104517 original size:79 final size:81
Alignment explanation
Indices: 52104393--52104576 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
52104383 GCTACTCGTT
* *
52104393 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTC-GGATCTTAACCCG
* *
52104456 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
52104472 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCAC-AATGCCTTCGGATCTTAACCCG
* *
52104535 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
52104552 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52104577 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 48 0.53
80 19 0.21
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:52104576 original size:40 final size:40
Alignment explanation
Indices: 52104374--52104576 Score: 229
Period size: 39 Copynumber: 5.1 Consensus size: 40
52104364 CGGAATTTAA
** *
52104374 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
52104414 CCGGTTATAGTAACTCGCAC-AATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
52104453 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
52104492 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
52104532 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
52104572 CCGGA
1 CCGGA
52104577 CATCATTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.01
39 68 0.49
40 57 0.41
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:52106507 original size:47 final size:47
Alignment explanation
Indices: 52106441--52107010 Score: 971
Period size: 47 Copynumber: 12.1 Consensus size: 47
52106431 GAAATGATAG
52106441 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
52106488 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
52106537 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
52106584 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
52106631 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
52106678 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
52106725 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
52106772 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
52106819 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
52106866 TAAGGCCTAACGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
52106913 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * *
52106960 CGGGGCC-AACTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAA-TGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
52107007 TAAG
1 TAAG
52107011 TCCCGAAGGG
Statistics
Matches: 497, Mismatches: 23, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
46 2 0.00
47 448 0.90
49 47 0.09
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:52107185 original size:37 final size:37
Alignment explanation
Indices: 52107129--52107207 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
52107119 CCGAGCTCTA
* *
52107129 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
* *
52107166 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGTT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
52107203 AAGAC
1 AAGAC
52107208 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:52113445 original size:20 final size:20
Alignment explanation
Indices: 52113417--52113463 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
52113407 CGGCAATGTT
52113417 TAAGTTGTGAAAGACTATGG
1 TAAGTTGTGAAAGACTATGG
* *
52113437 TATGTTGTGAAAGATTATGG
1 TAAGTTGTGAAAGACTATGG
52113457 TAAGTTG
1 TAAGTTG
52113464 CAAGTTGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATGG
Found at i:52119816 original size:57 final size:58
Alignment explanation
Indices: 52119682--52119830 Score: 162
Period size: 57 Copynumber: 2.6 Consensus size: 58
52119672 ATTGACCTCA
* * * * *
52119682 TTATAGAAAGGATTTAGCCCAGA-TGGGTAATCCTGATATAATACCTCTCGAGCATATG
1 TTATATAAAGGATTTAGCCTAGACT-GGTAATCCTAATAGAATACCTCTCGAGCATACG
* * *
52119740 TTATGAT-TAGGATTTAGCCTAGACTTGTAATCCTAATCGAACT-CCTCT-GAGCATACG
1 TTAT-ATAAAGGATTTAGCCTAGACTGGTAATCCTAATAGAA-TACCTCTCGAGCATACG
*
52119797 TTATATAAAGGATTTAGCCTGGACTGGTAATCCT
1 TTATATAAAGGATTTAGCCTAGACTGGTAATCCT
52119831 GTTATACGAT
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
56 2 0.03
57 36 0.47
58 35 0.46
59 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (58 bp):
TTATATAAAGGATTTAGCCTAGACTGGTAATCCTAATAGAATACCTCTCGAGCATACG
Found at i:52120015 original size:19 final size:19
Alignment explanation
Indices: 52119977--52120015 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
52119967 CAACGGGCAT
*
52119977 AAAATCTTGACATGGCATG
1 AAAATCTTGACATGACATG
* *
52119996 AAAATCTTGATATGATATG
1 AAAATCTTGACATGACATG
52120015 A
1 A
52120016 TAATGACTTA
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:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (19 bp):
AAAATCTTGACATGACATG
Found at i:52135292 original size:29 final size:30
Alignment explanation
Indices: 52135259--52135317 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
52135249 TCCTTAACTC
52135259 AAACTTTGGAAAATT-ACAATTTTGCCCCT
1 AAACTTTGGAAAATTAACAATTTTGCCCCT
* * * *
52135288 AAACTTTTGCATATTAACACTTTTGCCCCT
1 AAACTTTGGAAAATTAACAATTTTGCCCCT
52135318 GGGCTCGGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (30 bp):
AAACTTTGGAAAATTAACAATTTTGCCCCT
Found at i:52141794 original size:12 final size:12
Alignment explanation
Indices: 52141772--52141800 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
52141762 AAATTGAAAC
52141772 AAATT-AGAACT
1 AAATTAAGAACT
52141783 AAATTAAGAACT
1 AAATTAAGAACT
52141795 AAATTA
1 AAATTA
52141801 TATTAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (12 bp):
AAATTAAGAACT
Found at i:52155291 original size:17 final size:17
Alignment explanation
Indices: 52155269--52155302 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
52155259 ACACATGCCA
52155269 ACCTCTTAGCATGTTAT
1 ACCTCTTAGCATGTTAT
52155286 ACCTCTTAGCATGTTAT
1 ACCTCTTAGCATGTTAT
52155303 TTGACAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (17 bp):
ACCTCTTAGCATGTTAT
Found at i:52155507 original size:24 final size:24
Alignment explanation
Indices: 52155480--52155550 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 24
52155470 TGAGGTTATT
*
52155480 TATATTATTATAAAATTAAATATA
1 TATATTATTAAAAAATTAAATATA
**
52155504 TATAAAATTAAAAAATTTAAAATATA
1 TATATTATTAAAAAA-TT-AAATATA
* *
52155530 TAAATTAATAAAAAATATAAA
1 TATATTATTAAAAAAT-TAAA
52155551 AAAAAGTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
24 12 0.32
25 6 0.16
26 19 0.51
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TATATTATTAAAAAATTAAATATA
Found at i:52175534 original size:11 final size:11
Alignment explanation
Indices: 52175508--52175541 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
52175498 CCAAAAATGA
52175508 AAATTATTTATT
1 AAATTATTT-TT
52175520 AAATTATTTTT
1 AAATTATTTTT
52175531 AAATTATTTTT
1 AAATTATTTTT
52175542 CCCATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
AAATTATTTTT
Found at i:52183429 original size:27 final size:27
Alignment explanation
Indices: 52183399--52183554 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
52183389 TGCTATTCAC
* *
52183399 TCAACTCGCACACTTAGTGCCACGTAA
1 TCAATTCGCACACTTAGTGCCACATAA
* * * *
52183426 TCAAATCGCACCCTTAGTGCTACATAG
1 TCAATTCGCACACTTAGTGCCACATAA
* * **
52183453 TTAGATTCGCACACTTAGTGCCGCATGG
1 TCA-ATTCGCACACTTAGTGCCACATAA
*
52183481 TCAATTCGCACACTTAGTG-CATCATAT
1 TCAATTCGCACACTTAGTGCCA-CATAA
** *
52183508 TCCTTTCGCACACTTAGTGCAACATAA
1 TCAATTCGCACACTTAGTGCCACATAA
52183535 TCGAA-TCGCACACTTAGTGC
1 TC-AATTCGCACACTTAGTGC
52183555 TGTACAATTT
Statistics
Matches: 104, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
26 1 0.01
27 81 0.78
28 22 0.21
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (27 bp):
TCAATTCGCACACTTAGTGCCACATAA
Found at i:52183470 original size:55 final size:55
Alignment explanation
Indices: 52183404--52183555 Score: 182
Period size: 54 Copynumber: 2.8 Consensus size: 55
52183394 TTCACTCAAC
* * *
52183404 TCGCACACTTAGTGCCACGTAATCAAATCGCACCCTTAGTGCTA-CATAGTTAGAT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATA-TTACAT
* ** * * *
52183459 TCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCATATTCCTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTACAT
* *
52183513 TCGCACACTTAGTGCAACATAATCGAATCGCACACTTAGTGCT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCT
52183556 GTACAATTTA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 40 0.50
55 40 0.50
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (55 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTACAT
Found at i:52190546 original size:27 final size:27
Alignment explanation
Indices: 52190516--52190670 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
52190506 TGCTATTCAC
* *
52190516 TCAACTCGCACACTTAGTGCCACGTAA
1 TCAATTCGCACACTTAGTGCCACATAA
* * *
52190543 TCAAATCGCAC-CTTAGTGCTACATAG
1 TCAATTCGCACACTTAGTGCCACATAA
* * **
52190569 TTAGATTCGCACACTTAGTGCCGCATGG
1 TCA-ATTCGCACACTTAGTGCCACATAA
*
52190597 TCAATTCGCACACTTAGTG-CATCATAT
1 TCAATTCGCACACTTAGTGCCA-CATAA
** *
52190624 TCCTTTCGCACACTTAGTGCAACATAA
1 TCAATTCGCACACTTAGTGCCACATAA
52190651 TCGAA-TCGCACACTTAGTGC
1 TC-AATTCGCACACTTAGTGC
52190671 TGTACAATTT
Statistics
Matches: 104, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
26 15 0.14
27 74 0.71
28 15 0.14
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
TCAATTCGCACACTTAGTGCCACATAA
Found at i:52190579 original size:54 final size:55
Alignment explanation
Indices: 52190521--52190671 Score: 182
Period size: 54 Copynumber: 2.8 Consensus size: 55
52190511 TTCACTCAAC
* *
52190521 TCGCACACTTAGTGCCACGTAATCAAATCGCAC-CTTAGTGCTA-CATAGTTAGAT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATA-TTACAT
* ** * * *
52190575 TCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCATATTCCTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTACAT
* *
52190629 TCGCACACTTAGTGCAACATAATCGAATCGCACACTTAGTGCT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCT
52190672 GTACAATTTA
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
54 68 0.85
55 12 0.15
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (55 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTACAT
Found at i:52198935 original size:22 final size:23
Alignment explanation
Indices: 52198910--52198955 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
52198900 CAACCAAACC
52198910 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
52198932 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
52198955 A
1 A
52198956 CATCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:52201843 original size:52 final size:52
Alignment explanation
Indices: 52201782--52201885 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
52201772 GAGAGTCATC
52201782 CGCTCTGATACCCAAGACAAAACATCTCCACAATTGGAATTGATAATCGACA
1 CGCTCTGATACCCAAGACAAAACATCTCCACAATTGGAATTGATAATCGACA
52201834 CGCTCTGATACCCAAGACAAAACATCTCCACAATTGGAATTGATAATCGACA
1 CGCTCTGATACCCAAGACAAAACATCTCCACAATTGGAATTGATAATCGACA
52201886 TATTAATCTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (52 bp):
CGCTCTGATACCCAAGACAAAACATCTCCACAATTGGAATTGATAATCGACA
Found at i:52202869 original size:20 final size:20
Alignment explanation
Indices: 52202844--52202911 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
52202834 CAAAACAAAC
52202844 ACAAAATGCTAATGATTAAT
1 ACAAAATGCTAATGATTAAT
* *
52202864 ACAAAAATTACATAAATG-TT-TT
1 AC-AAAA-TGC-T-AATGATTAAT
52202886 ACAAAATGCTAATGATTAAT
1 ACAAAATGCTAATGATTAAT
52202906 ACAAAA
1 ACAAAA
52202912 ATTACATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
18 4 0.11
19 3 0.08
20 11 0.29
21 8 0.21
22 5 0.13
23 3 0.08
24 4 0.11
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.29
Consensus pattern (20 bp):
ACAAAATGCTAATGATTAAT
Found at i:52202903 original size:42 final size:42
Alignment explanation
Indices: 52202844--52202927 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
52202834 CAAAACAAAC
*
52202844 ACAAAATGCTAATGATTAATACAAAAATTACATAAATGTTTT
1 ACAAAATGCTAATGATTAATACAAAAATTACATAAATCTTTT
52202886 ACAAAATGCTAATGATTAATACAAAAATTACATAAATCTTTT
1 ACAAAATGCTAATGATTAATACAAAAATTACATAAATCTTTT
52202928 TAAATTGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (42 bp):
ACAAAATGCTAATGATTAATACAAAAATTACATAAATCTTTT
Found at i:52202912 original size:21 final size:21
Alignment explanation
Indices: 52202846--52202913 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
52202836 AAACAAACAC
52202846 AAAATGCTAATGATTAATACA
1 AAAATGCTAATGATTAATACA
* *
52202867 AAAATTACATAAATG-TT-TTAC-
1 AAAA-TGC-T-AATGATTAATACA
52202888 AAAATGCTAATGATTAATACA
1 AAAATGCTAATGATTAATACA
52202909 AAAAT
1 AAAAT
52202914 TACATAAATC
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
18 4 0.11
19 3 0.08
20 5 0.14
21 13 0.35
22 5 0.14
23 3 0.08
24 4 0.11
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (21 bp):
AAAATGCTAATGATTAATACA
Found at i:52214483 original size:14 final size:14
Alignment explanation
Indices: 52214462--52214502 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
52214452 TTGCAACTTG
52214462 CACAACTTGCACAT
1 CACAACTTGCACAT
** *
52214476 TGCAACTTGCAAAT
1 CACAACTTGCACAT
52214490 CACAACTTGCACA
1 CACAACTTGCACA
52214503 ATTAGGTAAG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.22
Consensus pattern (14 bp):
CACAACTTGCACAT
Found at i:52219045 original size:14 final size:14
Alignment explanation
Indices: 52219024--52219064 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
52219014 TTGCAACTTG
52219024 CACAACTTGCACAT
1 CACAACTTGCACAT
** *
52219038 TGCAACTTGCAAAT
1 CACAACTTGCACAT
52219052 CACAACTTGCACA
1 CACAACTTGCACA
52219065 ATTAGGTAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.22
Consensus pattern (14 bp):
CACAACTTGCACAT
Found at i:52220723 original size:27 final size:27
Alignment explanation
Indices: 52220685--52220744 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
52220675 TTATTGACGC
52220685 TTACTAAAGTTAGTAAAATCTTAATCT
1 TTACTAAAGTTAGTAAAATCTTAATCT
* *
52220712 TTACTAAGGTTAGTAAAATCTTGATCT
1 TTACTAAAGTTAGTAAAATCTTAATCT
52220739 TTACTA
1 TTACTA
52220745 TCACAGTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (27 bp):
TTACTAAAGTTAGTAAAATCTTAATCT
Found at i:52223948 original size:23 final size:23
Alignment explanation
Indices: 52223921--52223967 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
52223911 CCTCACCTTT
52223921 ACCAAAAAACACCCTAGTCGACC
1 ACCAAAAAACACCCTAGTCGACC
52223944 ACCAAAAAACACCCTAGTCGACC
1 ACCAAAAAACACCCTAGTCGACC
52223967 A
1 A
52223968 TACACCCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.38, G:0.09, T:0.09
Consensus pattern (23 bp):
ACCAAAAAACACCCTAGTCGACC
Found at i:52227347 original size:52 final size:51
Alignment explanation
Indices: 52227290--52227421 Score: 185
Period size: 50 Copynumber: 2.6 Consensus size: 51
52227280 ATGAACAAAT
* *
52227290 GAGTTACTTAATGCATGACTTAATTTAATGATGCAAACTTTAACTAACATGG
1 GAGTTACATAATGCATGACTTAATTTAATGATGCAAAC-TTAACTAACATGA
* * *
52227342 GAGTTACATAATGCATGTCATAATTT-ATGATGCAAACTTAACTTACATGA
1 GAGTTACATAATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGA
* *
52227392 GAGTTACATAATGCATGACTTTATTAAATG
1 GAGTTACATAATGCATGACTTAATTTAATG
52227422 CAGAACACAT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 33 0.47
51 14 0.20
52 23 0.33
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (51 bp):
GAGTTACATAATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGA
Found at i:52227488 original size:39 final size:39
Alignment explanation
Indices: 52227426--52227514 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
52227416 TAAATGCAGA
*
52227426 ACACATATTAATGATGTTCAAACTATGACATAATTAAAG
1 ACACATACTAATGATGTTCAAACTATGACATAATTAAAG
*
52227465 ACTCATACTAATGATGTTCAAACTATGACATAATTAAAG
1 ACACATACTAATGATGTTCAAACTATGACATAATTAAAG
*
52227504 ACACAAACTAA
1 ACACATACTAA
52227515 AATAACTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (39 bp):
ACACATACTAATGATGTTCAAACTATGACATAATTAAAG
Found at i:52229203 original size:20 final size:19
Alignment explanation
Indices: 52229159--52229207 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
52229149 TTCTTTCTCT
*
52229159 TTTCTTTTTTACTTTTTTT
1 TTTCTTTTTTACTTTTTTA
52229178 TATTCTTTTATT-CTTTTTTGA
1 T-TTCTTTT-TTACTTTTTT-A
52229199 TTTCTTTTT
1 TTTCTTTTT
52229208 CTTTTTCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.08, C:0.10, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTCTTTTTTACTTTTTTA
Found at i:52231805 original size:53 final size:51
Alignment explanation
Indices: 52231736--52231836 Score: 150
Period size: 50 Copynumber: 1.9 Consensus size: 51
52231726 ATACATCACT
*
52231736 TAATTTAATGATGCAAACTTTAACTGACATGGGAGTTTTACATAATGCATGTCA
1 TAATTTAATGATGCAAAC-TTAACTGACATGAGAG--TTACATAATGCATGTCA
*
52231790 TAATTT-ATGATGCAAACTTAACTTACATGAGAGTTACATAATGCATG
1 TAATTTAATGATGCAAACTTAACTGACATGAGAGTTACATAATGCATG
52231837 ACTTTGTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
50 14 0.31
52 14 0.31
53 11 0.24
54 6 0.13
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (51 bp):
TAATTTAATGATGCAAACTTAACTGACATGAGAGTTACATAATGCATGTCA
Found at i:52232987 original size:43 final size:42
Alignment explanation
Indices: 52232939--52233088 Score: 137
Period size: 44 Copynumber: 3.5 Consensus size: 42
52232929 ACAATACCAA
52232939 TGTCCCAGACGTGGTCTTACATGTAATCAAACATTGATGCCAC
1 TGTCCCAGACGTGGTCTTACATGTAATCAAA-ATTGATGCCAC
* * * * *
52232982 TGTCCCAGACAG-GGTCTTGCATGAAATC-AGATACGATGCCAA
1 TGTCCCAGAC-GTGGTCTTACATGTAATCAAAAT-TGATGCCAC
* * *
52233024 TGTCCCAGGCATGGTCTTACACGTAAAAT-AAAATTCGATGCCAAC
1 TGTCCCAGACGTGGTCTTACATGT--AATCAAAATT-GATGCC-AC
52233069 -GTCCCAGACGTGGTCTTACA
1 TGTCCCAGACGTGGTCTTACA
52233089 CGAAATCACA
Statistics
Matches: 84, Mismatches: 15, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
41 2 0.02
42 26 0.31
43 24 0.29
44 31 0.37
45 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (42 bp):
TGTCCCAGACGTGGTCTTACATGTAATCAAAATTGATGCCAC
Found at i:52233085 original size:86 final size:85
Alignment explanation
Indices: 52232935--52233096 Score: 206
Period size: 86 Copynumber: 1.9 Consensus size: 85
52232925 ATATACAATA
* *
52232935 CCAATGTCCCAGACGTGGTCTTACATGTAATCAAACATTGATGCCACTGTCCCAGACAGGGTCTT
1 CCAATGTCCCAGACATGGTCTTACACGTAATCAAACATTGATGCCACTGTCCCAGACAGGGTCTT
* *
52233000 GCATGAAATCAGATACGATG
66 ACACGAAATCAGATACGATG
*
52233020 CCAATGTCCCAGGCATGGTCTTACACGTAAAAT-AAA-ATTCGATGCCAAC-GTCCCAGAC-GTG
1 CCAATGTCCCAGACATGGTCTTACACGT--AATCAAACATT-GATGCC-ACTGTCCCAGACAG-G
52233081 GTCTTACACGAAATCA
61 GTCTTACACGAAATCA
52233097 CATAACGAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
85 29 0.43
86 33 0.49
87 5 0.07
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (85 bp):
CCAATGTCCCAGACATGGTCTTACACGTAATCAAACATTGATGCCACTGTCCCAGACAGGGTCTT
ACACGAAATCAGATACGATG
Found at i:52234444 original size:15 final size:17
Alignment explanation
Indices: 52234405--52234444 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
52234395 ATATACTTTG
52234405 AAACTATAGAATTGTGA
1 AAACTATAGAATTGTGA
52234422 AAACTATAG-ATTGT-A
1 AAACTATAGAATTGTGA
*
52234437 ACACTATA
1 AAACTATA
52234445 AGAGACTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 5 0.23
17 9 0.41
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (17 bp):
AAACTATAGAATTGTGA
Found at i:52236088 original size:38 final size:38
Alignment explanation
Indices: 52236037--52236109 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
52236027 CCCTACTAAG
52236037 TACATGTTAAGCATATCT-ACTGCTAGTGTTGAATTGAA
1 TACATGTTAAGCATAT-TGACTGCTAGTGTTGAATTGAA
* *
52236075 TACATGTTAAGCATGTTGACTTCTAGTGTTGAATT
1 TACATGTTAAGCATATTGACTGCTAGTGTTGAATT
52236110 CTTCTATTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 1 0.03
38 31 0.97
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (38 bp):
TACATGTTAAGCATATTGACTGCTAGTGTTGAATTGAA
Found at i:52237716 original size:20 final size:21
Alignment explanation
Indices: 52237693--52237751 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
52237683 TCTCTCTCTC
*
52237693 TTTTTGGTATTCTCTT-ATAT
1 TTTTTTGTATTCTCTTCATAT
* *
52237713 TTTTTTGTA-ACTCTTCATTT
1 TTTTTTGTATTCTCTTCATAT
52237733 TTTTTTGTATTC-CTTCATA
1 TTTTTTGTATTCTCTTCATA
52237752 ACTTTGTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 5 0.16
20 26 0.81
21 1 0.03
ACGTcount: A:0.15, C:0.14, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTTTTGTATTCTCTTCATAT
Found at i:52237759 original size:18 final size:19
Alignment explanation
Indices: 52237736--52237771 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52237726 TTCATTTTTT
*
52237736 TTTGTA-TTCCTTCATAAC
1 TTTGTATTTCCCTCATAAC
52237754 TTTGTATTTCCCTCATAA
1 TTTGTATTTCCCTCATAA
52237772 TTTTTTTTTG
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:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (19 bp):
TTTGTATTTCCCTCATAAC
Found at i:52237790 original size:44 final size:41
Alignment explanation
Indices: 52237729--52237822 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 41
52237719 GTAACTCTTC
52237729 ATTTTTTTTTGTATTCCTTCATAA-CTTT-GTATTTCCCTCATA
1 ATTTTTTTTTGTATTCC-TCA-AAGCTTTGGTATTT-CCTCATA
*
52237771 ATTTTTTTTTGGTACTTCCTCAAAGTTTTTGGTATTTCCTCATA
1 ATTTTTTTTT-GTA-TTCCTCAAAG-CTTTGGTATTTCCTCATA
52237815 ATTTTTTT
1 ATTTTTTT
52237823 ATTCATCCTC
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
42 12 0.26
43 6 0.13
44 22 0.48
45 6 0.13
ACGTcount: A:0.18, C:0.16, G:0.07, T:0.59
Consensus pattern (41 bp):
ATTTTTTTTTGTATTCCTCAAAGCTTTGGTATTTCCTCATA
Found at i:52237819 original size:20 final size:20
Alignment explanation
Indices: 52237776--52237991 Score: 139
Period size: 19 Copynumber: 11.1 Consensus size: 20
52237766 TCATAATTTT
*
52237776 TTTTTGGTACTTCCTCA-AA
1 TTTTTGGTATTTCCTCATAA
52237795 GTTTTTGGTATTTCCTCATAA
1 -TTTTTGGTATTTCCTCATAA
* *
52237816 TTTTT-TTATTCATCCTCATAT
1 TTTTTGGTATT--TCCTCATAA
* ** *
52237837 TTTTTGGTATTTCATTGT-C
1 TTTTTGGTATTTCCTCATAA
** *
52237856 TTTTTGACATTTCCTC-TGA
1 TTTTTGGTATTTCCTCATAA
*
52237875 TTTTTGGTATTTTCTCATAA
1 TTTTTGGTATTTCCTCATAA
**
52237895 -TTTTAATATTTCCTCAT-A
1 TTTTTGGTATTTCCTCATAA
*
52237913 TTTTT--TATTTCCTC-TGAT
1 TTTTTGGTATTTCCTCAT-AA
52237931 TTTTTGGTATTTCCTCAT-A
1 TTTTTGGTATTTCCTCATAA
** * *
52237950 TTTTTTATACCTT-CTCATAT
1 TTTTTGGTA-TTTCCTCATAA
*
52237970 TTTTTGGTACTTCCTCATAA
1 TTTTTGGTATTTCCTCATAA
52237990 TT
1 TT
52237992 CTTGATATTG
Statistics
Matches: 152, Mismatches: 29, Indels: 30
0.72 0.14 0.14
Matches are distributed among these distances:
16 1 0.01
17 9 0.06
18 7 0.05
19 62 0.41
20 53 0.35
21 16 0.11
22 4 0.03
ACGTcount: A:0.18, C:0.17, G:0.08, T:0.57
Consensus pattern (20 bp):
TTTTTGGTATTTCCTCATAA
Found at i:52237832 original size:41 final size:43
Alignment explanation
Indices: 52237757--52237849 Score: 118
Period size: 41 Copynumber: 2.2 Consensus size: 43
52237747 TCATAACTTT
* *
52237757 GTATTTCCCTCATAATTTTTTTTTGGTACTTCCTCAAAGTTTTTG
1 GTATTT-CCTCATAATTTTTTTAT-GTACATCCTCAAAGTTTTTG
* *
52237802 GTATTTCCTCATAATTTTTTTAT-T-CATCCTCATATTTTTTG
1 GTATTTCCTCATAATTTTTTTATGTACATCCTCAAAGTTTTTG
52237843 GTATTTC
1 GTATTTC
52237850 ATTGTCTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 21 0.48
42 1 0.02
44 16 0.36
45 6 0.14
ACGTcount: A:0.18, C:0.17, G:0.09, T:0.56
Consensus pattern (43 bp):
GTATTTCCTCATAATTTTTTTATGTACATCCTCAAAGTTTTTG
Found at i:52237947 original size:37 final size:37
Alignment explanation
Indices: 52237901--52237988 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 37
52237891 ATAATTTTAA
52237901 TATTTCCTCATATTTTTTAT-TTCCTC-TGATTTTTTGG
1 TATTTCCTCATATTTTTTATCTT-CTCAT-ATTTTTTGG
52237938 TATTTCCTCATATTTTTTATACCTTCTCATATTTTTTGG
1 TATTTCCTCATATTTTTTAT--CTTCTCATATTTTTTGG
*
52237977 TACTTCCTCATA
1 TATTTCCTCATA
52237989 ATTCTTGATA
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
37 20 0.43
39 23 0.50
40 3 0.07
ACGTcount: A:0.17, C:0.19, G:0.06, T:0.58
Consensus pattern (37 bp):
TATTTCCTCATATTTTTTATCTTCTCATATTTTTTGG
Found at i:52237948 original size:56 final size:55
Alignment explanation
Indices: 52237864--52237974 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 55
52237854 TCTTTTTGAC
* *
52237864 ATTTCCTCTGATTTTTGGTATTTTCTCATAATTTTAATA-TTTCCTCATATTTTTT
1 ATTTCCTCTGATTTTTGGTATTTCCTCATAATTTTAATACCTT-CTCATATTTTTT
* *
52237919 ATTTCCTCTGATTTTTTGGTATTTCCTCATATTTTTTATACCTTCTCATATTTTTT
1 ATTTCCTCTGA-TTTTTGGTATTTCCTCATAATTTTAATACCTTCTCATATTTTTT
52237975 GGTACTTCCT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
55 11 0.22
56 37 0.74
57 2 0.04
ACGTcount: A:0.18, C:0.16, G:0.05, T:0.60
Consensus pattern (55 bp):
ATTTCCTCTGATTTTTGGTATTTCCTCATAATTTTAATACCTTCTCATATTTTTT
Found at i:52238204 original size:16 final size:16
Alignment explanation
Indices: 52238183--52238239 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
52238173 TAAAAAATAG
52238183 GAAAAATTAAATAAAT
1 GAAAAATTAAATAAAT
*
52238199 GAAAAA-AATAATAAAAT
1 GAAAAATTA-AAT-AAAT
52238216 AGGAAAAATTAAATAAAT
1 --GAAAAATTAAATAAAT
52238234 GAAAAA
1 GAAAAA
52238240 ATACTAAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
15 1 0.03
16 15 0.44
17 4 0.12
18 4 0.12
19 9 0.26
20 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (16 bp):
GAAAAATTAAATAAAT
Found at i:52238204 original size:17 final size:17
Alignment explanation
Indices: 52238184--52238241 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
52238174 AAAAAATAGG
52238184 AAAAATTAAATAAATGA
1 AAAAATTAAATAAATGA
* *
52238201 AAAAAAT-AATAAAATAGG
1 AAAAATTAAAT-AAAT-GA
52238219 AAAAATTAAATAAATGA
1 AAAAATTAAATAAATGA
52238236 AAAAAT
1 AAAAAT
52238242 ACTAAGATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 3 0.09
17 17 0.50
18 11 0.32
19 3 0.09
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (17 bp):
AAAAATTAAATAAATGA
Found at i:52238393 original size:21 final size:20
Alignment explanation
Indices: 52238305--52238401 Score: 76
Period size: 20 Copynumber: 4.8 Consensus size: 20
52238295 TGGCATCCTT
* *
52238305 TCATAATTTTT-GTACTTCC
1 TCATATTTTTTGGTATTTCC
*
52238324 AT-ATATTTTTTAGTA-TTCAC
1 -TCATATTTTTTGGTATTTC-C
* *
52238344 TCATAATTTTTGGTATTTCT
1 TCATATTTTTTGGTATTTCC
*
52238364 TCGGGT-TTTTTTGGTATTTCC
1 TC--ATATTTTTTGGTATTTCC
52238385 TCATATTTTTTGGTATT
1 TCATATTTTTTGGTATT
52238402 CCCTTGTAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
19 13 0.21
20 30 0.48
21 18 0.29
22 1 0.02
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.58
Consensus pattern (20 bp):
TCATATTTTTTGGTATTTCC
Found at i:52238414 original size:20 final size:20
Alignment explanation
Indices: 52238305--52238415 Score: 66
Period size: 20 Copynumber: 5.5 Consensus size: 20
52238295 TGGCATCCTT
*
52238305 TCATAATTTTT-GTACTTCCA
1 TCATAATTTTTGGTA-TTCCC
* * *
52238325 T-ATATTTTTTAGTATTCAC
1 TCATAATTTTTGGTATTCCC
* *
52238344 TCATAATTTTTGGTATTTCT
1 TCATAATTTTTGGTATTCCC
* * *
52238364 TCGGGT-TTTTTTGGTATTTCC
1 TC--ATAATTTTTGGTATTCCC
*
52238385 TCATATTTTTTGGTATTCCC
1 TCATAATTTTTGGTATTCCC
**
52238405 TTGTAATTTTT
1 TCATAATTTTT
52238416 TGTTATTTTC
Statistics
Matches: 70, Mismatches: 16, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
19 13 0.19
20 41 0.59
21 15 0.21
22 1 0.01
ACGTcount: A:0.18, C:0.14, G:0.11, T:0.58
Consensus pattern (20 bp):
TCATAATTTTTGGTATTCCC
Found at i:52238482 original size:21 final size:20
Alignment explanation
Indices: 52238305--52238482 Score: 63
Period size: 20 Copynumber: 8.9 Consensus size: 20
52238295 TGGCATCCTT
52238305 TCATAA-TTTTTGTACTTCCA
1 TCATAATTTTTTGTA-TTCCA
52238325 T-AT-ATTTTTTAGTATT-CA
1 TCATAATTTTTT-GTATTCCA
* * *
52238343 CTCATAATTTTTGGTATTTCT
1 -TCATAATTTTTTGTATTCCA
****
52238364 TCGGGTTTTTTTGGTATTTCC-
1 TCATAATTTTTT-GTA-TTCCA
*
52238385 TCAT-ATTTTTTGGTATTCCC
1 TCATAATTTTTT-GTATTCCA
** *
52238405 TTGTAATTTTTTGTTATTTTCA
1 TCATAATTTTTTG-TA-TTCCA
* * *
52238427 T-AGAATATTTAGTACTTCC-
1 TCATAATTTTTTGTA-TTCCA
52238446 TCAT--TTTTTT-TATTCCA
1 TCATAATTTTTTGTATTCCA
52238463 TCATAATTTTTTGTACTTCC
1 TCATAATTTTTTGTA-TTCC
52238483 TCGTATGTTT
Statistics
Matches: 116, Mismatches: 24, Indels: 35
0.66 0.14 0.20
Matches are distributed among these distances:
16 4 0.03
17 6 0.05
18 7 0.06
19 21 0.18
20 39 0.34
21 32 0.28
22 7 0.06
ACGTcount: A:0.20, C:0.15, G:0.09, T:0.57
Consensus pattern (20 bp):
TCATAATTTTTTGTATTCCA
Found at i:52242193 original size:43 final size:43
Alignment explanation
Indices: 52242138--52242260 Score: 147
Period size: 43 Copynumber: 2.9 Consensus size: 43
52242128 CGTTTATTGA
* * * *
52242138 AAAAAAACGCCGCTAAAAGTGATGCCTTTCAGCGGCGTTTGTT
1 AAAAAAGCGCCGCTAAAAGTGATGGCTTTTAGCGGCGTTTGTG
* * *
52242181 AAAAAAGCGCCGCCAAAAGTGATGGCTTTTAGTGGCATTTGTG
1 AAAAAAGCGCCGCTAAAAGTGATGGCTTTTAGCGGCGTTTGTG
** * *
52242224 GGAAAAGTGCCGCTAAAAGTCATGGCTTTTAGCGGCG
1 AAAAAAGCGCCGCTAAAAGTGATGGCTTTTAGCGGCG
52242261 CTTTTCCCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (43 bp):
AAAAAAGCGCCGCTAAAAGTGATGGCTTTTAGCGGCGTTTGTG
Found at i:52246425 original size:12 final size:12
Alignment explanation
Indices: 52246410--52246435 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52246400 ATCATCCTCT
52246410 TCATCAGATTCA
1 TCATCAGATTCA
52246422 TCATCAGATTCA
1 TCATCAGATTCA
52246434 TC
1 TC
52246436 CCTCGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCAGATTCA
Found at i:52248168 original size:9 final size:9
Alignment explanation
Indices: 52248151--52248438 Score: 77
Period size: 9 Copynumber: 31.7 Consensus size: 9
52248141 TAAGTATAAT
*
52248151 TAAGCTATG
1 TAAGTTATG
52248160 TAAGTTATG
1 TAAGTTATG
* * *
52248169 ATATGATATA
1 -TAAGTTATG
*
52248179 T-ATTTATG
1 TAAGTTATG
52248187 T-A-TTATG
1 TAAGTTATG
52248194 TAAGTTATG
1 TAAGTTATG
* *
52248203 TAAATTGTG
1 TAAGTTATG
52248212 TAAGTTATCCG
1 TAAGTTAT--G
52248223 -AA-TTATG
1 TAAGTTATG
*
52248230 TAAATTATG
1 TAAGTTATG
* *
52248239 TACGATATGATA
1 TAAG-T-T-ATG
*
52248251 TATATTTATG
1 TA-AGTTATG
52248261 TATTA-TATATG
1 TA--AGT-TATG
52248272 TAAGTTATG
1 TAAGTTATG
*
52248281 TAAATTATG
1 TAAGTTATG
52248290 TAAGTTATCCG
1 TAAGTTAT--G
52248301 -AA-TTATG
1 TAAGTTATG
*
52248308 TAAATTATG
1 TAAGTTATG
*
52248317 TACGATATAATG
1 TAAG-T-T-ATG
*
52248329 TATACTTATG
1 TA-AGTTATG
*
52248339 T--GTTACG
1 TAAGTTATG
52248346 TAAGTTATG
1 TAAGTTATG
*
52248355 TAAATTATG
1 TAAGTTATG
* *
52248364 TAAGTTGTT
1 TAAGTTATG
**
52248373 TATCTTATG
1 TAAGTTATG
*
52248382 TAATTTATG
1 TAAGTTATG
52248391 TAA--TA--
1 TAAGTTATG
*
52248396 TAAGATATATA
1 TAAG-T-TATG
*
52248407 TATATTTATG
1 TA-AGTTATG
52248417 T-A-TTATG
1 TAAGTTATG
52248424 TAAGTTATG
1 TAAGTTATG
52248433 TAAGTT
1 TAAGTT
52248439 GTTGATGGGA
Statistics
Matches: 207, Mismatches: 39, Indels: 66
0.66 0.12 0.21
Matches are distributed among these distances:
5 3 0.01
7 21 0.10
8 12 0.06
9 116 0.56
10 26 0.13
11 17 0.08
12 12 0.06
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:52248215 original size:18 final size:18
Alignment explanation
Indices: 52248188--52248393 Score: 110
Period size: 18 Copynumber: 11.0 Consensus size: 18
52248178 ATATTTATGT
52248188 ATTATGTAAGTTATGTAA
1 ATTATGTAAGTTATGTAA
* ***
52248206 ATTGTGTAAGTTATCCGA
1 ATTATGTAAGTTATGTAA
*
52248224 ATTATGTAAATTATGTACGA
1 ATTATGTAAGTTATGTA--A
* * * *
52248244 TATGATATATATTTATGTATT
1 -ATTATGTA-AGTTATGTA-A
52248265 ATATATGTAAGTTATGTAA
1 AT-TATGTAAGTTATGTAA
***
52248284 ATTATGTAAGTTATCCGA
1 ATTATGTAAGTTATGTAA
*
52248302 ATTATGTAAATTATGTACGA
1 ATTATGTAAGTTATGTA--A
* *
52248322 TATAATGTATACTTATGT--
1 -ATTATGTA-AGTTATGTAA
* *
52248340 GTTACGTAAGTTATGTAA
1 ATTATGTAAGTTATGTAA
* * *
52248358 ATTATGTAAGTTGTTTAT
1 ATTATGTAAGTTATGTAA
* *
52248376 CTTATGTAATTTATGTAA
1 ATTATGTAAGTTATGTAA
52248394 TATAAGATAT
Statistics
Matches: 136, Mismatches: 41, Indels: 22
0.68 0.21 0.11
Matches are distributed among these distances:
16 7 0.05
17 5 0.04
18 78 0.57
19 2 0.01
20 12 0.09
21 17 0.12
22 15 0.11
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (18 bp):
ATTATGTAAGTTATGTAA
Found at i:52248219 original size:27 final size:26
Alignment explanation
Indices: 52248198--52248318 Score: 92
Period size: 27 Copynumber: 4.6 Consensus size: 26
52248188 ATTATGTAAG
*
52248198 TTATGTAAATTGTGTAAGTTATCCGAA
1 TTATGTAAATTATGTAAGTTAT-CGAA
* *
52248225 TTATGTAAATTATGTACGATAT-G-A
1 TTATGTAAATTATGTAAGTTATCGAA
* *
52248249 -TATAT-ATTTATGTATTA-TATAT-GTAA
1 TTATGTAAATTATGTA--AGT-TATCG-AA
52248275 GTTATGTAAATTATGTAAGTTATCCGAA
1 -TTATGTAAATTATGTAAGTTAT-CGAA
52248303 TTATGTAAATTATGTA
1 TTATGTAAATTATGTA
52248319 CGATATAATG
Statistics
Matches: 74, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
22 8 0.11
23 4 0.05
24 5 0.07
25 1 0.01
26 1 0.01
27 39 0.53
28 7 0.09
29 9 0.12
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (26 bp):
TTATGTAAATTATGTAAGTTATCGAA
Found at i:52248293 original size:78 final size:74
Alignment explanation
Indices: 52248168--52248435 Score: 324
Period size: 78 Copynumber: 3.5 Consensus size: 74
52248158 TGTAAGTTAT
*
52248168 GATATGATATATATTTATGTATTATGTAAGTTATGTAAATTGTGTAAGTTATCCGAATTATGTAA
1 GATATGATATATATTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTATCCGAATTATGTAA
52248233 ATTATGTAC
66 ATTATGTAC
52248242 GATATGATATATATTTATGTATTATATATGTAAGTTATGTAAATTATGTAAGTTATCCGAATTAT
1 GATATGATATATATTTATG---TAT-TATGTAAGTTATGTAAATTATGTAAGTTATCCGAATTAT
52248307 GTAAATTATGTAC
62 GTAAATTATGTAC
* * * * * * ** *
52248320 GATATAATGTATACTTATGTGTTACGTAAGTTATGTAAATTATGTAAGTTGT-TTATCTTATGTA
1 GATATGATATATATTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTATCCGA-ATTATGTA
* *
52248384 ATTTATGTAATATAA
65 A---AT-T-ATGTAC
52248399 GATAT-ATATATATTTATGTATTATGTAAGTTATGTAA
1 GATATGATATATATTTATGTATTATGTAAGTTATGTAA
52248436 GTTGTTGATG
Statistics
Matches: 168, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
73 1 0.01
74 55 0.33
75 2 0.01
77 5 0.03
78 96 0.57
79 9 0.05
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (74 bp):
GATATGATATATATTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTATCCGAATTATGTAA
ATTATGTAC
Found at i:52248687 original size:106 final size:105
Alignment explanation
Indices: 52248541--52249079 Score: 790
Period size: 106 Copynumber: 5.2 Consensus size: 105
52248531 AAAATAAAAT
52248541 ATTTAAAAATAAAAT-AAAGTAGAC--AATATTTTTAGTGATTAAATTAAAATCAAGTAAAATAT
1 ATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTAGTGATTAAATTAAAATCAAGTAAAATAT
* *
52248603 TTAAAATAAAACTTTAAATAAAAATTAATTTAATTAGGTA
66 TTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTA
52248643 ATTTAAAAAATAAAATAAAAGTAGACAAAATATTTTTAGTGATTAAATTAAAATCAAGTAAAATA
1 ATTT-AAAAATAAAATAAAAGTAGACAAAATATTTTTAGTGATTAAATTAAAATCAAGTAAAATA
* * *
52248708 TTTAAAATAAAACTTTAAAGACATTTTAATTTAGTTAGGTA
65 TTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTA
* *
52248749 ATTTAAAAAATAAAATAAAAGTAGAAAAAATATTTTTTGTGATTAAATTAAAATCTAA-TAAAAT
1 ATTT-AAAAATAAAATAAAAGTAGACAAAATATTTTTAGTGATTAAATTAAAATC-AAGTAAAAT
52248813 ATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTA
64 ATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTA
* *
52248855 ATTTAAAAATTAAAA-AAAAGTAGAAAAAATATTTTTAGTGAGTAAATTAAAATCAAGTAAAATA
1 ATTTAAAAA-TAAAATAAAAGTAGACAAAATATTTTTAGTGATTAAATTAAAATCAAGTAAAATA
* *
52248919 TTTAAAATAAAACTTTAAAGACAATTAAATTTAATTAGGTA
65 TTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTA
* ** * *
52248960 ATTT--AAA-AAAATAAAAATAGACAAAATATTTTCCGTGATTAAATTAAAATCAAATTAAATA-
1 ATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTAGTGATTAAATTAAAATCAAGTAAAATAT
* * * *
52249021 TTCAAATAAAACTTTAAATACATTTTAATTTAATTCGATA
66 TTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTA
*
52249061 ATTTCAAAATAAAATAAAA
1 ATTTAAAAATAAAATAAAA
52249080 ATTTTAAAAT
Statistics
Matches: 399, Mismatches: 27, Indels: 20
0.89 0.06 0.04
Matches are distributed among these distances:
101 42 0.11
102 46 0.12
103 17 0.04
104 20 0.05
105 92 0.23
106 180 0.45
107 2 0.01
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (105 bp):
ATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTAGTGATTAAATTAAAATCAAGTAAAATAT
TTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTA
Found at i:52248961 original size:211 final size:208
Alignment explanation
Indices: 52248541--52249080 Score: 786
Period size: 211 Copynumber: 2.6 Consensus size: 208
52248531 AAAATAAAAT
*
52248541 ATTTAAAAATAAAAT-AAAGTAG-ACAATATTTTTAGTGATTAAATTAAAATCAAGTAAAATATT
1 ATTTAAAAATAAAATAAAAGTAGAAAAATATTTTTAGTGATTAAATTAAAATCAA-TAAAATATT
* * * *
52248604 TAAAATAAAACTTTAAATAAAAATTAATTTAATTAGGTAATTTAAAAAATAAAATAAAAGTAGAC
65 TAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATTAAAA-AAAAGTAGAA
* *
52248669 AAAATATTTTTAGTGATTAAATTAAAATCAAGTAAAATATTTAAAATAAAACTTTAAAGACATTT
129 AAAATATTTTTAGTGAGTAAATTAAAATCAAGTAAAATATTTAAAATAAAACTTTAAAGACAATT
* *
52248734 TAATTTAGTTAGGTA
194 AAATTTAATTAGGTA
*
52248749 ATTTAAAAAATAAAATAAAAGTAGAAAAAATATTTTTTGTGATTAAATTAAAATCTAATAAAATA
1 ATTT-AAAAATAAAATAAAAGTAG-AAAAATATTTTTAGTGATTAAATTAAAATC-AATAAAATA
52248814 TTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATTAAAAAAAAGTAGA
63 TTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATTAAAAAAAAGTAGA
52248879 AAAAATATTTTTAGTGAGTAAATTAAAATCAAGTAAAATATTTAAAATAAAACTTTAAAGACAAT
128 AAAAATATTTTTAGTGAGTAAATTAAAATCAAGTAAAATATTTAAAATAAAACTTTAAAGACAAT
52248944 TAAATTTAATTAGGTA
193 TAAATTTAATTAGGTA
* ** *
52248960 ATTT--AAA-AAAATAAAAATAGACAAAATATTTTCCGTGATTAAATTAAAATCAAATTAAATA-
1 ATTTAAAAATAAAATAAAAGTAGA-AAAATATTTTTAGTGATTAAATTAAAATC-AATAAAATAT
* * * * * *
52249021 TTCAAATAAAACTTTAAATACATTTTAATTTAATTCGATAATTTCAAAATAAAATAAAAA
64 TTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATTAAA-AAAAA
52249081 TTTTAAAATA
Statistics
Matches: 304, Mismatches: 21, Indels: 15
0.89 0.06 0.04
Matches are distributed among these distances:
206 49 0.16
207 52 0.17
208 7 0.02
209 11 0.04
210 7 0.02
211 89 0.29
212 87 0.29
213 2 0.01
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (208 bp):
ATTTAAAAATAAAATAAAAGTAGAAAAATATTTTTAGTGATTAAATTAAAATCAATAAAATATTT
AAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATTAAAAAAAAGTAGAAAA
AATATTTTTAGTGAGTAAATTAAAATCAAGTAAAATATTTAAAATAAAACTTTAAAGACAATTAA
ATTTAATTAGGTA
Found at i:52249479 original size:60 final size:61
Alignment explanation
Indices: 52249406--52249533 Score: 231
Period size: 62 Copynumber: 2.1 Consensus size: 61
52249396 CTTGTTCATT
*
52249406 AATAAACTATATC-TATATATATTACCTTGTTCATAACTAATTTGTACAAAAGAACATGGA
1 AATAAACTATATCATATATATATTACCTTGTTCATAACTAATTTCTACAAAAGAACATGGA
52249466 AATAAACTATATCTATATATATATTACCTTGTTCATAACTAATTTCTACAAAAGAACATGGA
1 AATAAACTATATC-ATATATATATTACCTTGTTCATAACTAATTTCTACAAAAGAACATGGA
52249528 AATAAA
1 AATAAA
52249534 ATTAGGCCCA
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
60 13 0.20
62 52 0.80
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.34
Consensus pattern (61 bp):
AATAAACTATATCATATATATATTACCTTGTTCATAACTAATTTCTACAAAAGAACATGGA
Found at i:52251033 original size:39 final size:39
Alignment explanation
Indices: 52250979--52251058 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
52250969 ACATTGACAG
* *
52250979 GAGCAGATCTCAAATAGTCATGCAGAATAACAAATTTAA
1 GAGCAGATCTCAAATAATCATGCAAAATAACAAATTTAA
52251018 GAGCAGATCTCAAATAATCATGCAAAATAACAAATTTAA
1 GAGCAGATCTCAAATAATCATGCAAAATAACAAATTTAA
52251057 GA
1 GA
52251059 TAGTCATATC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (39 bp):
GAGCAGATCTCAAATAATCATGCAAAATAACAAATTTAA
Found at i:52253035 original size:37 final size:37
Alignment explanation
Indices: 52252988--52253068 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
52252978 TTGATATATA
*
52252988 TTATTTTAAAATAATAATTTATATATATTTATCTTAT
1 TTATATTAAAATAATAATTTATATATATTTATCTTAT
52253025 TTATATTAAAATAATAATTTATATATATTTATCTTAT
1 TTATATTAAAATAATAATTTATATATATTTATCTTAT
52253062 TTATATT
1 TTATATT
52253069 TATCTTCTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (37 bp):
TTATATTAAAATAATAATTTATATATATTTATCTTAT
Found at i:52253066 original size:15 final size:15
Alignment explanation
Indices: 52253043--52253074 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
52253033 AAATAATAAT
52253043 TTATATATATTTATC
1 TTATATATATTTATC
*
52253058 TTATTTATATTTATC
1 TTATATATATTTATC
52253073 TT
1 TT
52253075 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATATATATTTATC
Found at i:52255231 original size:18 final size:17
Alignment explanation
Indices: 52255199--52255232 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
52255189 ATGATTATTT
52255199 TAAAAAAATTAAATAAA
1 TAAAAAAATTAAATAAA
*
52255216 TAAAACAAATTTAATAA
1 TAAAA-AAATTAAATAA
52255233 GACCAACCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAAAATTAAATAAA
Found at i:52255498 original size:19 final size:19
Alignment explanation
Indices: 52255476--52255515 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
52255466 AGGGCAAGCC
52255476 AAAAATACAAGAGAATACA
1 AAAAATACAAGAGAATACA
** *
52255495 AAAAATTTAAGAGATTACA
1 AAAAATACAAGAGAATACA
52255514 AA
1 AA
52255516 TAATTATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.07, G:0.10, T:0.17
Consensus pattern (19 bp):
AAAAATACAAGAGAATACA
Found at i:52255624 original size:20 final size:20
Alignment explanation
Indices: 52255484--52255626 Score: 114
Period size: 20 Copynumber: 7.2 Consensus size: 20
52255474 CCAAAAATAC
52255484 AAGAGAATACAAAAAATT-T
1 AAGAGAATACAAAAAATTAT
* *
52255503 AAGAGATTACAAATAATTAT
1 AAGAGAATACAAAAAATTAT
*
52255523 GAA-ATAATACAAAAAATTAT
1 -AAGAGAATACAAAAAATTAT
* * *
52255543 GAGAGGATACCAAAAATTAT
1 AAGAGAATACAAAAAATTAT
**
52255563 --GATGAAGTACTAAAAAAACAT
1 AAGA-GAA-TAC-AAAAAATTAT
* * *
52255584 GAGAGAGTACCAAAAATTAT
1 AAGAGAATACAAAAAATTAT
*
52255604 AAGAGAATATAAAAAATTAT
1 AAGAGAATACAAAAAATTAT
52255624 AAG
1 AAG
52255627 GTGAGTACCA
Statistics
Matches: 95, Mismatches: 21, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
18 2 0.02
19 19 0.20
20 58 0.61
21 12 0.13
22 2 0.02
23 2 0.02
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.22
Consensus pattern (20 bp):
AAGAGAATACAAAAAATTAT
Found at i:52255633 original size:41 final size:40
Alignment explanation
Indices: 52255474--52255641 Score: 134
Period size: 41 Copynumber: 4.2 Consensus size: 40
52255464 TGAGGGCAAG
* *
52255474 CCAAAAA-TACAAGAGAATACAAAAAATT-TAAGAGATTA
1 CCAAAAATTATAAGAGAATACAAAAAATTATAAGAGAGTA
* *
52255512 -CAAATAATTATGAA-ATAATACAAAAAATTATGAGAG-GATA
1 CCAAA-AATTAT-AAGAGAATACAAAAAATTATAAGAGAG-TA
** *
52255552 CCAAAAATTAT--GATGAAGTACTAAAAAAACATGAGAGAGTA
1 CCAAAAATTATAAGA-GAA-TAC-AAAAAATTATAAGAGAGTA
* *
52255593 CCAAAAATTATAAGAGAATATAAAAAATTATAAGGTGAGTA
1 CCAAAAATTATAAGAGAATACAAAAAATTATAA-GAGAGTA
52255634 CCAGAAAA
1 CCA-AAAA
52255642 ACATGAGGGA
Statistics
Matches: 103, Mismatches: 12, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
37 4 0.04
38 3 0.03
39 18 0.17
40 27 0.26
41 41 0.40
42 8 0.08
43 2 0.02
ACGTcount: A:0.57, C:0.08, G:0.14, T:0.21
Consensus pattern (40 bp):
CCAAAAATTATAAGAGAATACAAAAAATTATAAGAGAGTA
Found at i:52259413 original size:15 final size:17
Alignment explanation
Indices: 52259395--52259426 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
52259385 TAGCATGTTT
52259395 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
52259410 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
52259427 CAAGTGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:52263341 original size:27 final size:27
Alignment explanation
Indices: 52263311--52263488 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
52263301 ATATTGAGCC
* * *
52263311 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
52263338 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
52263365 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
52263393 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
52263420 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
52263447 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
52263474 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52263489 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:52263404 original size:55 final size:55
Alignment explanation
Indices: 52263311--52263488 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
52263301 ATATTGAGCC
* * *
52263311 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
52263365 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
52263420 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
52263474 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52263489 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:52263450 original size:82 final size:81
Alignment explanation
Indices: 52263332--52263487 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
52263322 TGCTATACAA
* * *
52263332 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
52263397 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
52263414 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
52263478 CACTTAGTGC
65 CACTTAGTGC
52263488 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:52271406 original size:27 final size:25
Alignment explanation
Indices: 52271376--52271551 Score: 100
Period size: 27 Copynumber: 6.6 Consensus size: 25
52271366 ATATTGAGCC
* *
52271376 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTAT--AATCAAAT
**
52271403 CGCACACTTAGTGCCGTAATCAAAT
1 CGCACACTTAGTGCTATAATCAAAT
* * *
52271428 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCT--ATAATCA-AAT
* ** *
52271456 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTG-C-TATAATCAAAT
* **
52271483 CGCACACTTAGTGCATCATATTCATTT
1 CGCACACTTAGTGC-T-ATAATCAAAT
* * *
52271510 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGC--TATAATCAAAT
52271537 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52271552 GTACAATTTA
Statistics
Matches: 118, Mismatches: 24, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
25 21 0.18
26 1 0.01
27 74 0.63
28 21 0.18
29 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (25 bp):
CGCACACTTAGTGCTATAATCAAAT
Found at i:52271540 original size:54 final size:52
Alignment explanation
Indices: 52271400--52271551 Score: 157
Period size: 54 Copynumber: 2.8 Consensus size: 52
52271390 TATACAATCA
* *
52271400 ACTCGCACACTTAGTGCCGTAATCAAATCGCACACTTAGTGCTACATAGTTAG
1 ACTCGCACACTTAGTGCCATAGTC-AATCGCACACTTAGTGCTACATAGTTAG
*
52271453 ACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCATA-TTCA-
1 ACTCGCACACTTAGTG-C-CATAGTCAA-TCGCACACTTAGTGCTA-CATAGTT-AG
**
52271507 TTTCGCACACTTAGTGCAACATAGTCGAATCGCACACTTAGTGCT
1 ACTCGCACACTTAGTGC--CATAGTC-AATCGCACACTTAGTGCT
52271552 GTACAATTTA
Statistics
Matches: 84, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
53 17 0.20
54 41 0.49
55 26 0.31
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (52 bp):
ACTCGCACACTTAGTGCCATAGTCAATCGCACACTTAGTGCTACATAGTTAG
Found at i:52279741 original size:40 final size:40
Alignment explanation
Indices: 52279664--52279914 Score: 237
Period size: 40 Copynumber: 6.3 Consensus size: 40
52279654 AAATCACGTA
* * **
52279664 CCTTCGGAATTTAA-CCGGATATAGCT-ACTCGTTCAAATG
1 CCTTCGGGACTTAACCCGGATATAG-TAACTCGCACAAATG
* *
52279703 CCTTCGGGACATAGCCCGG-TCATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCCGGAT-ATAGTAACTCGCACAAATG
* * *
52279743 CCTTCGGGACTTAACCCGGATTTGGTAACTCGCACCAATG
1 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
* *
52279783 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATG
1 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
* * *
52279823 CCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGGACAAATG
1 CCTTCGGGACTTAACCCGGATA-TAGTAACTCGCACAAATG
** * * *
52279862 CCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-G
1 CCTTCGGGA-CTTAACCCGGATATAGTAAC-TCGCACAAATG
52279902 CCTTCGGGACTTA
1 CCTTCGGGACTTA
52279915 GCCCAGACAT
Statistics
Matches: 179, Mismatches: 23, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
38 2 0.01
39 42 0.23
40 123 0.69
41 12 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
Found at i:52279881 original size:119 final size:120
Alignment explanation
Indices: 52279699--52279914 Score: 287
Period size: 119 Copynumber: 1.8 Consensus size: 120
52279689 TACTCGTTCA
*
52279699 AATGCCTTCGGGACATAGCCCGGTCATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGTAATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* * *
52279764 TTGGTAAC-TCGCACCAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATGGTAACTTAGCA-CAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * * **
52279819 AATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCGGACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGTAA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
*
52279881 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
64 ATATGGTAACTTAGCACAAAGCCTTCGGGACTTA
52279915 GCCCAGACAT
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.05
119 63 0.76
120 16 0.19
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGTAATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATGGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:52279905 original size:79 final size:79
Alignment explanation
Indices: 52279697--52279918 Score: 234
Period size: 79 Copynumber: 2.8 Consensus size: 79
52279687 GCTACTCGTT
* * * *
52279697 CAAATGCCTTCGGGACATAGCCCGG-TCATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAACCCGGAT-ATAGTAACTAGCACAAA-GCCTTCGGGACTTAGCCCG
* *
52279761 GATTTGGTAACTCGCA
64 GAATTAGTAACTCGCA
* * * *
52279777 CCAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA-CAAAGCCTTCGGGACTTAGCCCGG
* *
52279841 AATTAGTATCTCGGA
65 AATTAGTAACTCGCA
** * *
52279856 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCC
52279919 AGACATCATT
Statistics
Matches: 119, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
78 3 0.03
79 57 0.48
80 55 0.46
81 4 0.03
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:52285953 original size:33 final size:33
Alignment explanation
Indices: 52285916--52285986 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
52285906 ATTTATGATT
52285916 TTTATTGATATGTCTTGAATTAAAACATAGGCA
1 TTTATTGATATGTCTTGAATTAAAACATAGGCA
**
52285949 TTTATTGATATGTCTTGAATTAATGCATAGGCA
1 TTTATTGATATGTCTTGAATTAAAACATAGGCA
52285982 TTTAT
1 TTTAT
52285987 GCATTGATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.44
Consensus pattern (33 bp):
TTTATTGATATGTCTTGAATTAAAACATAGGCA
Found at i:52288982 original size:18 final size:18
Alignment explanation
Indices: 52288959--52288995 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
52288949 TCTTGGCCGA
52288959 ATATTTTACATTTATTTT
1 ATATTTTACATTTATTTT
52288977 ATATTTTACATTTATTTT
1 ATATTTTACATTTATTTT
52288995 A
1 A
52288996 CACAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATTTTACATTTATTTT
Found at i:52298521 original size:24 final size:24
Alignment explanation
Indices: 52298493--52298548 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
52298483 TCCTAAAATC
*
52298493 CCTCCATAATCCTCTCCTTGATTT
1 CCTCCACAATCCTCTCCTTGATTT
* * * *
52298517 TCTCCCCCATCCTTTCCTTGATTT
1 CCTCCACAATCCTCTCCTTGATTT
52298541 CCTCCACA
1 CCTCCACA
52298549 TAAAACTCCC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.43, G:0.04, T:0.39
Consensus pattern (24 bp):
CCTCCACAATCCTCTCCTTGATTT
Done.