Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 124 of 333
Found at i:40015762 original size:79 final size:79
Alignment explanation
Indices: 40015625--40015832 Score: 203
Period size: 79 Copynumber: 2.6 Consensus size: 79
40015615 CCTTCAGAAT
* * * *
40015625 TTAACCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCTGGTTATAGTAACTTGCACA
1 TTAACCGGATATAGCTACTCGTACAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACA
40015690 AATGCCTTCGGGAC
66 AATGCCTTCGGGAC
* * *
40015704 TTAACCCGGATTTAG-TAACTCGTACCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGC
1 TTAA-CCGGATATAGCT-ACTCGTACAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGC
40015766 ACAAATGCCTTC-GGATC
63 ACAAATGCCTTCGGGA-C
* * * * *
40015783 TTAGTCCGGATAT-GGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TTA-ACCGGATATAGCT-AC-TCGTACAAATGCCTTCGGGACATAGCCCGGA
40015833 CATCATTCGA
Statistics
Matches: 108, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
78 5 0.05
79 58 0.54
80 45 0.42
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (79 bp):
TTAACCGGATATAGCTACTCGTACAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACA
AATGCCTTCGGGAC
Found at i:40018656 original size:30 final size:30
Alignment explanation
Indices: 40018622--40018682 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40018612 TCCTTAACTC
40018622 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
40018652 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
40018682 A
1 A
40018683 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:40020291 original size:30 final size:30
Alignment explanation
Indices: 40020257--40020317 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40020247 TCCTTAACTC
40020257 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
40020287 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
40020317 A
1 A
40020318 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:40024547 original size:50 final size:50
Alignment explanation
Indices: 40024426--40024624 Score: 200
Period size: 50 Copynumber: 3.9 Consensus size: 50
40024416 ATTGTGAGAA
* * *** *
40024426 CACATGTGTAGTACTATGTGCAGGATACTATGTGTTTAAAATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGG--TTAGGT
** * *
40024478 CATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTGCCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGTTAGGT
* * * * *
40024528 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAGCTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAT-GGTTAGGT
* * **
40024579 CACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAGAGATGGTT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGTT
40024625 TTTATCACAA
Statistics
Matches: 121, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
50 45 0.37
51 41 0.34
52 35 0.29
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGTTAGGT
Found at i:40024632 original size:51 final size:50
Alignment explanation
Indices: 40024426--40024645 Score: 183
Period size: 51 Copynumber: 4.3 Consensus size: 50
40024416 ATTGTGAGAA
* * *
40024426 CACATGTGTAGTACTATGTGCAGGATACTATGTGTTTAA-A-ATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTG--TAACAGATGG-TTT-GAT
** * ** * *
40024478 CATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTGCCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTAACAGATGGTTTGAT
* * * * *
40024528 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAGCTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTAACAGAT-GGTTTGAT
* * * *
40024579 CACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAGAGATGGTTTTTAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTAACAGATGG-TTTGAT
* *
40024630 CACAAGTGTGGTACTA
1 CACATGTGTAGTACTA
40024646 TGCGAAGGCC
Statistics
Matches: 137, Mismatches: 27, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
50 41 0.30
51 63 0.46
52 33 0.24
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.32
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTAACAGATGGTTTGAT
Found at i:40026180 original size:13 final size:13
Alignment explanation
Indices: 40026162--40026191 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
40026152 GGTAAGGGGT
40026162 GTTGTATGATTGA
1 GTTGTATGATTGA
40026175 GTTGTATGATTGA
1 GTTGTATGATTGA
40026188 GTTG
1 GTTG
40026192 ATTTGTGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (13 bp):
GTTGTATGATTGA
Found at i:40030886 original size:83 final size:83
Alignment explanation
Indices: 40030787--40030963 Score: 336
Period size: 83 Copynumber: 2.1 Consensus size: 83
40030777 TGTGTGCCCT
**
40030787 GGCCGTGTGCGCCTAGATGAATGATGATGTCATAAACAAAATGTCTGGGTTTTTGGACATGGGCT
1 GGCCGTGTTAGCCTAGATGAATGATGATGTCATAAACAAAATGTCTGGGTTTTTGGACATGGGCT
40030852 ATGAAACGGGCGTGTCTA
66 ATGAAACGGGCGTGTCTA
40030870 GGCCGTGTTAGCCTAGATGAATGATGATGTCATAAACAAAATGTCTGGGTTTTTGGACATGGGCT
1 GGCCGTGTTAGCCTAGATGAATGATGATGTCATAAACAAAATGTCTGGGTTTTTGGACATGGGCT
40030935 ATGAAACGGGCGTGTCTA
66 ATGAAACGGGCGTGTCTA
40030953 GGCCGTGTTAG
1 GGCCGTGTTAG
40030964 GGAAACGGGA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 92 1.00
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.28
Consensus pattern (83 bp):
GGCCGTGTTAGCCTAGATGAATGATGATGTCATAAACAAAATGTCTGGGTTTTTGGACATGGGCT
ATGAAACGGGCGTGTCTA
Found at i:40033386 original size:29 final size:27
Alignment explanation
Indices: 40033368--40033437 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
40033358 ATATTAAGTC
40033368 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
40033395 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
40033423 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
40033438 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:40033431 original size:28 final size:28
Alignment explanation
Indices: 40033368--40033465 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
40033358 ATATTAAGTC
*
40033368 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
40033395 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
40033423 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
40033452 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40033466 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:40035809 original size:93 final size:93
Alignment explanation
Indices: 40035702--40035872 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
40035692 GCCCCTAAGT
* *
40035702 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCAA
40035767 CAAGTTCGGATGCCTAGTTACATTTCAC
66 CAAGTTCGGATGCCTAGTTACATTTCAC
* * **
40035795 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCAA
*
40035860 CGAGTTCGGATGC
66 CAAGTTCGGATGC
40035873 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCAA
CAAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40035869 original size:46 final size:46
Alignment explanation
Indices: 40035697--40035869 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
40035687 AACCCGCCCC
* * *
40035697 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCA
* * *
40035743 TAAGTGAACTCAGACTCAACTCAACAAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACATCCA
* * *
40035791 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCA
*
40035836 TAAGTGAACTTGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40035870 TGCTCAACCA
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 58 0.56
47 27 0.26
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCA
Found at i:40040599 original size:40 final size:40
Alignment explanation
Indices: 40040495--40040711 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
40040485 AAGCCAGGTA
* * * *
40040495 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
40040534 CCTTC-GGACATAGCCCGGATGTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40040573 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40040613 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
40040653 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
40040693 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40040712 TTATCATCCG
Statistics
Matches: 161, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
38 6 0.04
39 31 0.19
40 124 0.77
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40044580 original size:46 final size:46
Alignment explanation
Indices: 40044508--40044680 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 46
40044498 AACCCGCCCC
* * *
40044508 TAAGTGAACTCGGACTCAACTAAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* * * * * * *
40044554 TAAGTGAACTTGGACTCAACTCAACGAGTTCAGATGCCTAG-TTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-TTCGCATCCA
* * * *
40044600 TTTCA-CGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
40044647 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40044681 TGCTCAACCA
Statistics
Matches: 100, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
45 2 0.02
46 63 0.63
47 33 0.33
48 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
Found at i:40044672 original size:93 final size:93
Alignment explanation
Indices: 40044513--40044683 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
40044503 GCCCCTAAGT
* * *
40044513 GAACTCGGACTCAACTAAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTAAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40044578 CGAGTTCAGATGCCTAGTTACATTTCAC
66 CGAGTTCAGATGCCTAGTTACATTTCAC
* * *
40044606 GAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTAAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
40044671 CGAGTTCGGATGC
66 CGAGTTCAGATGC
40044684 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTAAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:40051309 original size:47 final size:47
Alignment explanation
Indices: 40051202--40051785 Score: 871
Period size: 47 Copynumber: 12.1 Consensus size: 47
40051192 GAAATGATAG
40051202 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
* *
40051251 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTCA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40051298 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40051345 TAAGGCCTAATGGACGATGTGATGAATGTGAAAGTGTATATATAGATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATAT--ATGTGA
40051396 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
40051445 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG----TATATATGTGA
*
40051496 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
40051543 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40051590 TAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTGTATATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG----TATATATGTGA
*
40051641 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40051688 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
40051735 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40051782 TAAG
1 TAAG
40051786 TCCCGAAGGG
Statistics
Matches: 497, Mismatches: 28, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
47 274 0.55
49 83 0.17
51 140 0.28
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:40051485 original size:145 final size:140
Alignment explanation
Indices: 40051202--40051785 Score: 835
Period size: 145 Copynumber: 4.0 Consensus size: 140
40051192 GAAATGATAG
40051202 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
* *
40051267 ATGTGATGAATGTGAAAGTGTATATACGTCATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
64 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
40051332 TGTATATATGAGA
129 TG-ATATATGTGA
*
40051345 TAAGGCCTAATGGACGATGTGATGAATGTGAAAGTGTATATATAGATGTGATAAGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATAT--ATGTGATAAGGCCTAATGGC
40051410 CGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
62 CGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
40051475 AAAGTGTATATATATATGTGA
125 AAAGTG-----ATATATGTGA
*
40051496 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* * *
40051561 GTGATGAATGTGAAAGCGTATATATGAGATAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
40051626 TATATATATATGTGA
131 -----ATATATGTGA
*
40051641 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* * * * * * *
40051706 GTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
40051771 TATAAATGTGA
131 -ATATATGTGA
40051782 TAAG
1 TAAG
40051786 TCCCGAAGGG
Statistics
Matches: 410, Mismatches: 23, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
141 13 0.03
143 42 0.10
145 220 0.54
147 85 0.21
149 5 0.01
151 45 0.11
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (140 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
ATATATGTGA
Found at i:40051630 original size:245 final size:241
Alignment explanation
Indices: 40051202--40051785 Score: 985
Period size: 245 Copynumber: 2.4 Consensus size: 241
40051192 GAAATGATAG
40051202 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
*
40051267 ATGTGATGAATGTGAAAGTGTATATACGTCATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 ATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
40051332 TGTATATATGAGATAAGGCCTAATGGACGATGTGATGAATGTGAAAGTGTATATATAGATGTGAT
131 CGTATATATGAGATAAGGCCTAATGGACGATGTGATGAATGTGAAAGTGTATATATAGATGTGAT
40051397 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
196 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
40051445 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATATGTGATAAGGCCTAATGGC
40051510 CGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
64 CGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
40051575 AGCGTATATATGAGATAAGGCCTAATGG-CTGATGTGATGAATGTGAAAGTGTATATATATATGT
129 AGCGTATATATGAGATAAGGCCTAATGGAC-GATGTGATGAATGTGAAAGTGTATATATAGATGT
*
40051639 GATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
193 GATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * *
40051688 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
* * * *
40051751 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
66 ATGTGATGAATGTGAAAGTGTATATACGTGATAAG
40051786 TCCCGAAGGG
Statistics
Matches: 325, Mismatches: 13, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
239 53 0.16
243 83 0.26
244 1 0.00
245 188 0.58
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (241 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
ATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
CGTATATATGAGATAAGGCCTAATGGACGATGTGATGAATGTGAAAGTGTATATATAGATGTGAT
AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:40051960 original size:37 final size:37
Alignment explanation
Indices: 40051904--40051982 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
40051894 CCGAGCTCTA
* * *
40051904 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
* *
40051941 AAGACCCGATAACTTCGTGTGGAGATTATGTCTGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40051978 AAGAC
1 AAGAC
40051983 TTCGTAATAA
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:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40056476 original size:17 final size:17
Alignment explanation
Indices: 40056454--40056490 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
40056444 AAAGAAAGAA
40056454 AAGAAAAAGGACAAACT
1 AAGAAAAAGGACAAACT
40056471 AAGAAAAAGGACAAACT
1 AAGAAAAAGGACAAACT
40056488 AAG
1 AAG
40056491 GGTTTAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.65, C:0.11, G:0.19, T:0.05
Consensus pattern (17 bp):
AAGAAAAAGGACAAACT
Found at i:40065028 original size:44 final size:44
Alignment explanation
Indices: 40064944--40065028 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
40064934 TATGTAATCT
* * *
40064944 GAACTCATTGAGTTGTGTCTGAATTCATGATATTTGTGACATCA
1 GAACTCATTAAGTTGTGTCTGAATTCATGATATGTATGACATCA
*
40064988 GAACTCATTAAGTTGTGTCT-AAGTTCGTGATATGTATGACA
1 GAACTCATTAAGTTGTGTCTGAA-TTCATGATATGTATGACA
40065029 CATGTTTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 2 0.06
44 34 0.94
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (44 bp):
GAACTCATTAAGTTGTGTCTGAATTCATGATATGTATGACATCA
Found at i:40066854 original size:32 final size:30
Alignment explanation
Indices: 40066778--40066859 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 30
40066768 GTATACAATT
* *
40066778 GTAACATAAATATTTAATTACTTTTTATTTAA
1 GTAA-ATAGATATTT-ATTACTTATTATTTAA
40066810 GTAAATAGATATTTATTACTTATTATTATTAA
1 GTAAATAGATATTTATTACTTATTA-T-TTAA
*
40066842 GTTAAA-ATATATTTATTA
1 G-TAAATAGATATTTATTA
40066860 ATTAAATAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
30 10 0.23
31 10 0.23
32 20 0.45
33 4 0.09
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (30 bp):
GTAAATAGATATTTATTACTTATTATTTAA
Found at i:40086764 original size:49 final size:49
Alignment explanation
Indices: 40086708--40086806 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
40086698 GAGAGTTAAA
*
40086708 CTCTAATTATATTTTGAATCTGTGTATACAAGACTCATAAATGATAATC
1 CTCTAATTATATTTTGAATCTGTGTATACAAGACTCACAAATGATAATC
40086757 CTCTAATTATATTTTGAATCTGTGTATACAAGACTCACAAATGATAATC
1 CTCTAATTATATTTTGAATCTGTGTATACAAGACTCACAAATGATAATC
40086806 C
1 C
40086807 AACTAATGTC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (49 bp):
CTCTAATTATATTTTGAATCTGTGTATACAAGACTCACAAATGATAATC
Found at i:40091823 original size:20 final size:22
Alignment explanation
Indices: 40091798--40091850 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
40091788 ATGTTATGTA
40091798 GGTATCAATACTGCCTCT-A-T
1 GGTATCAATACTGCCTCTAAGT
* * *
40091818 GGTATCGATACTTCCTTTAAGT
1 GGTATCAATACTGCCTCTAAGT
40091840 GGTATCAATAC
1 GGTATCAATAC
40091851 CACGTGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.56
21 1 0.04
22 11 0.41
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (22 bp):
GGTATCAATACTGCCTCTAAGT
Found at i:40095202 original size:29 final size:29
Alignment explanation
Indices: 40095170--40095251 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 29
40095160 ATGGTCGCCC
* *
40095170 CCATCCTTTTTCATGTTCGATGGTCGAAA
1 CCATCCTTTTTCATATTCGATGGTCAAAA
* *
40095199 CCAT-CTCTTTTCTTTAATCGATGGTCAAAA
1 CCATCCT-TTTTC-ATATTCGATGGTCAAAA
*
40095229 CCATCCCTTTTCATATTCGATGG
1 CCATCCTTTTTCATATTCGATGG
40095252 GCATTGATAC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
28 2 0.05
29 18 0.42
30 22 0.51
31 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (29 bp):
CCATCCTTTTTCATATTCGATGGTCAAAA
Found at i:40104505 original size:20 final size:21
Alignment explanation
Indices: 40104466--40104505 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
40104456 AAGGACTATT
*
40104466 TTGTAAAGTTTGTAAAATAAG
1 TTGTAAAGTGTGTAAAATAAG
*
40104487 TTGTAAA-TGTGTGAAATAA
1 TTGTAAAGTGTGTAAAATAA
40104506 TTGAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (21 bp):
TTGTAAAGTGTGTAAAATAAG
Found at i:40112482 original size:21 final size:20
Alignment explanation
Indices: 40112458--40112502 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40112448 AAATGCAGAC
40112458 AAAACCACTTAAAATCTTTTT
1 AAAACCACTT-AAATCTTTTT
* * *
40112479 AAAACTACTTATATTTTTTT
1 AAAACCACTTAAATCTTTTT
40112499 AAAA
1 AAAA
40112503 AAAGGTGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAACCACTTAAATCTTTTT
Found at i:40114609 original size:23 final size:20
Alignment explanation
Indices: 40114556--40114600 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
40114546 AGACTGCCTA
40114556 GGGATCGCATATCCTCCCTG
1 GGGATCGCATATCCTCCCTG
*
40114576 GGGATCGCATATCCTCCTTG
1 GGGATCGCATATCCTCCCTG
40114596 GGGAT
1 GGGAT
40114601 TAGCGCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (20 bp):
GGGATCGCATATCCTCCCTG
Found at i:40124689 original size:22 final size:22
Alignment explanation
Indices: 40124661--40124704 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40124651 TTTTGAACCA
40124661 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
40124683 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
40124705 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:40129188 original size:51 final size:49
Alignment explanation
Indices: 40129133--40129269 Score: 135
Period size: 51 Copynumber: 2.9 Consensus size: 49
40129123 CTACCACATA
* *
40129133 ACATGTAACACATCCATAATGAACTCGGACCTCTTAACGAGCTCAGATG
1 ACATGTAACGCATCCATAATGAACTCGGACCTCTCAACGAGCTCAGATG
* * * * *
40129182 TTACATG-AATTGCATCCATCATAAACTCGGACCACTCAACGAGCTCGGATG
1 --ACATGTAA-CGCATCCATAATGAACTCGGACCTCTCAACGAGCTCAGATG
40129233 -C---T--CGCATCCATAATGAACTCGGACCTCTCAACGAGCT
1 ACATGTAACGCATCCATAATGAACTCGGACCTCTCAACGAGCT
40129270 TGGATGCCAC
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
43 31 0.42
48 1 0.01
50 2 0.03
51 39 0.53
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (49 bp):
ACATGTAACGCATCCATAATGAACTCGGACCTCTCAACGAGCTCAGATG
Found at i:40129254 original size:43 final size:43
Alignment explanation
Indices: 40129193--40129276 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
40129183 TACATGAATT
*
40129193 GCATCCATCATAAACTCGGACCACTCAACGAGCTCGGATGCTC
1 GCATCCATAATAAACTCGGACCACTCAACGAGCTCGGATGCTC
* * *
40129236 GCATCCATAATGAACTCGGACCTCTCAACGAGCTTGGATGC
1 GCATCCATAATAAACTCGGACCACTCAACGAGCTCGGATGC
40129277 CACATATCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.20
Consensus pattern (43 bp):
GCATCCATAATAAACTCGGACCACTCAACGAGCTCGGATGCTC
Found at i:40131510 original size:17 final size:17
Alignment explanation
Indices: 40131490--40131531 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
40131480 TTAGATCTAA
*
40131490 TTACATTTTCCATTTTT
1 TTACATTTACCATTTTT
40131507 TTACA-TTACCATTTTT
1 TTACATTTACCATTTTT
40131523 TTATCATTT
1 TTA-CATTT
40131532 CAATTAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 13 0.59
17 7 0.32
18 2 0.09
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (17 bp):
TTACATTTACCATTTTT
Found at i:40132563 original size:4 final size:4
Alignment explanation
Indices: 40132550--40132580 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
40132540 CAAAAGACGG
40132550 GAAA -AAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
40132581 ACCCCTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:40135330 original size:36 final size:36
Alignment explanation
Indices: 40135290--40135360 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
40135280 CCCAAGGCTG
*
40135290 AGCACCACCCAAAAATCCTACCAGAGGAAAAATATA
1 AGCACCACCCAAAAATCCTACAAGAGGAAAAATATA
* * *
40135326 AGCACCACCCAGAATTCCTAGAAGAGGAAAAATAT
1 AGCACCACCCAAAAATCCTACAAGAGGAAAAATAT
40135361 GCAAGGTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.48, C:0.25, G:0.14, T:0.13
Consensus pattern (36 bp):
AGCACCACCCAAAAATCCTACAAGAGGAAAAATATA
Found at i:40139800 original size:40 final size:40
Alignment explanation
Indices: 40139707--40139962 Score: 349
Period size: 40 Copynumber: 6.5 Consensus size: 40
40139697 AAGCCAAGTA
* * *
40139707 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
40139745 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40139785 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
40139825 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
40139865 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
40139905 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
40139945 CCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
40139963 ATTATCATCC
Statistics
Matches: 199, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
38 12 0.06
39 17 0.09
40 170 0.85
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40146295 original size:18 final size:18
Alignment explanation
Indices: 40146245--40146296 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
40146235 GAAATTCTAT
40146245 ATCCTTCAAGGATTTTAA
1 ATCCTTCAAGGATTTTAA
* **
40146263 ACCCTT-TTGGAATTTTAA
1 ATCCTTCAAGG-ATTTTAA
40146281 ATCCTTCAAGGATTTT
1 ATCCTTCAAGGATTTT
40146297 CATATAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (18 bp):
ATCCTTCAAGGATTTTAA
Found at i:40149809 original size:18 final size:18
Alignment explanation
Indices: 40149786--40149822 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
40149776 AAGGGAACCA
40149786 AAAGTACTAGTAATAACT
1 AAAGTACTAGTAATAACT
40149804 AAAGTACTAGTAATAACT
1 AAAGTACTAGTAATAACT
40149822 A
1 A
40149823 TCTTTTTATT
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:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (18 bp):
AAAGTACTAGTAATAACT
Found at i:40150923 original size:21 final size:21
Alignment explanation
Indices: 40150889--40150930 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40150879 ATTTGGTCCG
* * *
40150889 TTTTGTCTCTTTTTGGCTCTT
1 TTTTGGCTCCTTTTGACTCTT
40150910 TTTTGGCTCCTTTTGACTCTT
1 TTTTGGCTCCTTTTGACTCTT
40150931 GGTGCTCTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.21, G:0.14, T:0.62
Consensus pattern (21 bp):
TTTTGGCTCCTTTTGACTCTT
Found at i:40151774 original size:48 final size:48
Alignment explanation
Indices: 40151639--40151869 Score: 249
Period size: 48 Copynumber: 4.9 Consensus size: 48
40151629 TAGGGTTATG
* * *
40151639 TATGGTCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCATCGATA
1 TATGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* * ** * *
40151687 TGTAATTTCGTGTAAGACCATAG-CTAGG-C-T---ATTGGCATCGATA
1 TATGATCCCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGATA
* * * *
40151730 TAAGATCCCATGTAAAACCATGTCTGAGACATGGCATTGGCATCGATC
1 TATGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
*
40151778 TATGATCCAATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
1 TATGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* * * *
40151826 TTTGATCCCATGTAAGACCATATCCGGGATATGGCATTGGCATC
1 TATGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
40151870 CTACTATGTT
Statistics
Matches: 149, Mismatches: 27, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
42 1 0.01
43 29 0.19
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 114 0.77
49 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (48 bp):
TATGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
Found at i:40163502 original size:19 final size:17
Alignment explanation
Indices: 40163462--40163510 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
40163452 TATATAATAG
*
40163462 AATTTTTTAAATTATTT
1 AATTTTTTAAATTATGT
*
40163479 TATTTTTATAAAATTATGT
1 AATTTTT-T-AAATTATGT
*
40163498 AATTTTTTTAATT
1 AATTTTTTAAATT
40163511 TTATAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 10 0.38
18 2 0.08
19 14 0.54
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
AATTTTTTAAATTATGT
Found at i:40164250 original size:6 final size:7
Alignment explanation
Indices: 40164233--40164266 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
40164223 TAATATATTT
*
40164233 TTTTTCG
1 TTTTTCA
40164240 TTTTTCA
1 TTTTTCA
40164247 TTTTTCA
1 TTTTTCA
40164254 TTTTTCA
1 TTTTTCA
40164261 TTTTTC
1 TTTTTC
40164267 TTTCTTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.09, C:0.15, G:0.03, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:40164258 original size:21 final size:21
Alignment explanation
Indices: 40164233--40164274 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40164223 TAATATATTT
*
40164233 TTTTTCGTTTTTCATTT-TTCA
1 TTTTTCATTTTTC-TTTCTTCA
40164254 TTTTTCATTTTTCTTTCTTCA
1 TTTTTCATTTTTCTTTCTTCA
40164275 AAATCGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTCATTTTTCTTTCTTCA
Found at i:40179736 original size:20 final size:20
Alignment explanation
Indices: 40179711--40179748 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40179701 GTTTAGTGGA
40179711 AAAAATTTTCT-AAGTTTTGT
1 AAAAATTTT-TAAAGTTTTGT
40179731 AAAAATTTTTAAAGTTTT
1 AAAAATTTTTAAAGTTTT
40179749 CGGTTTAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (20 bp):
AAAAATTTTTAAAGTTTTGT
Found at i:40185651 original size:14 final size:15
Alignment explanation
Indices: 40185620--40185652 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40185610 ATTAAATTAT
40185620 TTATTTTGCTATATA
1 TTATTTTGCTATATA
*
40185635 TTATTTTTCTA-ATA
1 TTATTTTGCTATATA
40185649 TTAT
1 TTAT
40185653 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (15 bp):
TTATTTTGCTATATA
Found at i:40187716 original size:87 final size:87
Alignment explanation
Indices: 40187570--40187807 Score: 329
Period size: 87 Copynumber: 2.7 Consensus size: 87
40187560 TTTGAATTCA
* *
40187570 GTGAAT-TCATCAAGTCCATCTCAATAGGACTACCCAAACTCTGGGATATGAACTCATTAAGAGT
1 GTGAATAT-ATCAAGTTCATCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGT
40187634 AATAAATTCAATCTCACATATTG
65 AATAAATTCAATCTCACATATTG
* *
40187657 GTGAATATATCAAGTTCATCTCAATAGGACCACCCAAACTTTGGGATATGAACTCATTAAGAGAA
1 GTGAATATATCAAGTTCATCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGTA
*
40187722 ATAAATTCAATCTCACATGTTG
66 ATAAATTCAATCTCACATATTG
* * * * * *
40187744 GTGAATATATCAA-ATCTGTTTTAATAGGACCACCCAAA-TCCTAGGATATGAATTCATTAAGAG
1 GTGAATATATCAAGTTC-ATCTCAATAGGACCACCCAAACT-CTGGGATATGAACTCATTAAGAG
40187807 T
64 T
40187808 GAGAACTCAA
Statistics
Matches: 135, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
86 3 0.02
87 131 0.97
88 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (87 bp):
GTGAATATATCAAGTTCATCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGTA
ATAAATTCAATCTCACATATTG
Found at i:40193156 original size:12 final size:11
Alignment explanation
Indices: 40193128--40193161 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
40193118 AGTCAAATTA
40193128 ATTATTTTA-T
1 ATTATTTTATT
40193138 ATTATTTTATT
1 ATTATTTTATT
40193149 ACTTATTTTATT
1 A-TTATTTTATT
40193161 A
1 A
40193162 GGAGAGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
11 2 0.09
12 11 0.50
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:40193305 original size:177 final size:176
Alignment explanation
Indices: 40193009--40193360 Score: 623
Period size: 177 Copynumber: 2.0 Consensus size: 176
40192999 CAAAATCTGG
* * *
40193009 TCTCTCTTTCTCTCTCTTTCTGATGCGTTTGAGGTTTACATCATATTTTGTGATTTCTGTGAAGA
1 TCTCTCTTTCTCTCTCTCTCTAATGCATTTGAGGTTTACATCATATTTTGTGATTTCTGTGAAGA
*
40193074 GTTGAAATACTTCATTTCATCTAGGTGAAAGGTTTTATGCTAGAAGTCAAATTAATTATTTTATA
66 GTTGAAATACTTCATTTCATCTAGGTGAAAGGTTTTATGCTAGAAGTCAAATTAATTA-TTTAGA
* *
40193139 TTATTTTATTACTTATTTTATTAGGAGAGGTATTAGGAGTTCAATTC
130 TTAATTTATTACTTATTTTATTAGGAGAAGTATTAGGAGTTCAATTC
40193186 TCTCTCTTTCTCTCTCTCTCTAATGCATTTGAGGTTTACATCATATTTTGTGATTTCTGTGAAGA
1 TCTCTCTTTCTCTCTCTCTCTAATGCATTTGAGGTTTACATCATATTTTGTGATTTCTGTGAAGA
*
40193251 GTTGAAATACTTCATTTCATCTAGGTGAAAGGTTTTATGTTAGAAGTCAAATTAATTATTTAGAT
66 GTTGAAATACTTCATTTCATCTAGGTGAAAGGTTTTATGCTAGAAGTCAAATTAATTATTTAGAT
*
40193316 TAATTTATTACTTATTTTATTAGTAGAAGTATTAGGAGTTCAATT
131 TAATTTATTACTTATTTTATTAGGAGAAGTATTAGGAGTTCAATT
40193361 GAAAGTATCT
Statistics
Matches: 167, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
176 48 0.29
177 119 0.71
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.46
Consensus pattern (176 bp):
TCTCTCTTTCTCTCTCTCTCTAATGCATTTGAGGTTTACATCATATTTTGTGATTTCTGTGAAGA
GTTGAAATACTTCATTTCATCTAGGTGAAAGGTTTTATGCTAGAAGTCAAATTAATTATTTAGAT
TAATTTATTACTTATTTTATTAGGAGAAGTATTAGGAGTTCAATTC
Found at i:40201028 original size:14 final size:15
Alignment explanation
Indices: 40201009--40201037 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40200999 GTAAATACTT
40201009 CTATTTT-GAGAAGA
1 CTATTTTGGAGAAGA
40201023 CTATTTTGGAGAAGA
1 CTATTTTGGAGAAGA
40201038 AAATACTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (15 bp):
CTATTTTGGAGAAGA
Found at i:40204668 original size:33 final size:33
Alignment explanation
Indices: 40204630--40204693 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
40204620 GACTGAGTGG
* *
40204630 GAGTGTTTGGTTGTTGGACAGGAGCTAGAATGT
1 GAGTGTTTGGTTGCTGGAAAGGAGCTAGAATGT
40204663 GAGTGTTTGGTTGCTGGAAAGGAGCTAGAAT
1 GAGTGTTTGGTTGCTGGAAAGGAGCTAGAAT
40204694 CTCAAGAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.06, G:0.39, T:0.31
Consensus pattern (33 bp):
GAGTGTTTGGTTGCTGGAAAGGAGCTAGAATGT
Found at i:40207033 original size:19 final size:19
Alignment explanation
Indices: 40207009--40207049 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
40206999 CTTCCCTTCA
40207009 AGAATGTACGAACCAGTTG
1 AGAATGTACGAACCAGTTG
40207028 AGAATGTACGAACCAGTTG
1 AGAATGTACGAACCAGTTG
40207047 AGA
1 AGA
40207050 CTACTTCACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.20
Consensus pattern (19 bp):
AGAATGTACGAACCAGTTG
Found at i:40213756 original size:23 final size:23
Alignment explanation
Indices: 40213721--40213795 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
40213711 AATTACTAAT
* * * *
40213721 TTGCACTGAAGTGTCACTTTCAA
1 TTGCACCGGAGTGCCACTGTCAA
* *
40213744 TTGCACCGGAGTGCCTCTGTCAG
1 TTGCACCGGAGTGCCACTGTCAA
40213767 TTGCACCGGAGTGCCA-TGATCAA
1 TTGCACCGGAGTGCCACTG-TCAA
40213790 TTGCAC
1 TTGCAC
40213796 AGAAATTTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 2 0.05
23 41 0.95
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (23 bp):
TTGCACCGGAGTGCCACTGTCAA
Found at i:40219257 original size:26 final size:26
Alignment explanation
Indices: 40219221--40219274 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
40219211 CTAGTTCTAG
* *
40219221 AATGATTCAAAAGTCTGCTGAGTCAA
1 AATGATTCAAAAGTCTACTAAGTCAA
40219247 AATGATTCAAAAGTCTACTAAGTCAA
1 AATGATTCAAAAGTCTACTAAGTCAA
40219273 AA
1 AA
40219275 GCTGGATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (26 bp):
AATGATTCAAAAGTCTACTAAGTCAA
Found at i:40219698 original size:27 final size:28
Alignment explanation
Indices: 40219638--40219703 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 28
40219628 TGGTTTTCTT
* *
40219638 ACACAAGTTGTGATACTTGAATTTGCTC
1 ACACAAGCTGTGATACTTGAAGTTGCTC
*
40219666 ACACAAGCTGTGATATTTG-AGTTGCTC
1 ACACAAGCTGTGATACTTGAAGTTGCTC
40219693 ACACAAGCTGT
1 ACACAAGCTGT
40219704 AGGTTAGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 18 0.51
28 17 0.49
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (28 bp):
ACACAAGCTGTGATACTTGAAGTTGCTC
Found at i:40220859 original size:10 final size:10
Alignment explanation
Indices: 40220834--40220873 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
40220824 TAATGAAGAA
*
40220834 AACACTTGTT
1 AACACTTTTT
40220844 -ACACTTTTT
1 AACACTTTTT
40220853 AACACTTTTT
1 AACACTTTTT
40220863 AACACTTTTT
1 AACACTTTTT
40220873 A
1 A
40220874 CCTTATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (10 bp):
AACACTTTTT
Found at i:40223020 original size:20 final size:21
Alignment explanation
Indices: 40222995--40223038 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
40222985 TAGTTCAACG
*
40222995 GGTAAGAAAAGG-AATGGCAT
1 GGTAAGAAAAGGAAATGGAAT
*
40223015 GGTAAGTAAAGGAAATGGAAT
1 GGTAAGAAAAGGAAATGGAAT
40223036 GGT
1 GGT
40223039 TCATGATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.43, C:0.02, G:0.36, T:0.18
Consensus pattern (21 bp):
GGTAAGAAAAGGAAATGGAAT
Found at i:40231648 original size:23 final size:23
Alignment explanation
Indices: 40231617--40231665 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
40231607 AACGTAAGTA
*
40231617 AAAATGATGCATTATTTATATAC
1 AAAACGATGCATTATTTATATAC
40231640 AAAACGATGCATTATTTATATAC
1 AAAACGATGCATTATTTATATAC
40231663 AAA
1 AAA
40231666 CTTATCTCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (23 bp):
AAAACGATGCATTATTTATATAC
Found at i:40235406 original size:40 final size:40
Alignment explanation
Indices: 40235351--40235531 Score: 240
Period size: 40 Copynumber: 4.5 Consensus size: 40
40235341 TATTCGGATG
* ** * *
40235351 ATATCCGGGCTAAGTCCCGGAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
40235391 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
40235431 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
* * ** *
40235471 ATATTCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAG-TGACT
*
40235511 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
40235532 ATACTTGGGT
Statistics
Matches: 127, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 13 0.10
40 112 0.88
41 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
Found at i:40238735 original size:43 final size:42
Alignment explanation
Indices: 40238613--40238735 Score: 122
Period size: 43 Copynumber: 2.9 Consensus size: 42
40238603 TACCGTACCA
* *** **
40238613 ATGCCATATCCCAGATATGGTCTTACATTTAATCTTGTATCG
1 ATGCCATATACCAGATATGGTCTTACACGAAATCTCATATCG
* *
40238655 ATGCCAATAGACCA-ACTATGGTCTTACACGAAGTCTCATATCG
1 ATGCC-ATATACCAGA-TATGGTCTTACACGAAATCTCATATCG
* *
40238698 ATGCCATATTCCAGATATAGTCTTACACGCAAATCTCA
1 ATGCCATATACCAGATATGGTCTTACACG-AAATCTCA
40238736 GTGACCCTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
42 25 0.38
43 40 0.62
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (42 bp):
ATGCCATATACCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:40246113 original size:43 final size:43
Alignment explanation
Indices: 40245976--40246145 Score: 197
Period size: 43 Copynumber: 4.0 Consensus size: 43
40245966 ACATAGGATC
* *
40245976 CGATATGTG-TTATCGTGTAAAACCACGTCTGGGACGTTGGCAT
1 CGATATTTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
40246019 CGACT-TATGATTTGCGTGTAAGACCACGTCTGGGACGTTGGGAT
1 CGA-TATTTGA-TTACGTGTAAGACCACGTCTGGGACGTTGGCAT
*
40246063 CG-TATTTGATTCCGTGTAAGACC-CTGTCTGGGACAG-TGGCAT
1 CGATATTTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
*
40246105 CGATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGC
1 CGATATTTGATTACGTGTAAGACCACGTCTGGGACGTTGGC
40246146 GTTTATGAGT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
41 1 0.01
42 31 0.28
43 43 0.39
44 32 0.29
45 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (43 bp):
CGATATTTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:40251536 original size:25 final size:25
Alignment explanation
Indices: 40251508--40251589 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
40251498 TGTTGGTATG
40251508 TTTAATTTAGTTAATATGGCTTAAA
1 TTTAATTTAGTTAATATGGCTTAAA
* ** * * **
40251533 TTTAATTCA-TGTAAGGTTGATTGCA
1 TTTAATTTAGT-TAATATGGCTTAAA
40251558 TTTAATTTAGTTAATATGGCTTAAA
1 TTTAATTTAGTTAATATGGCTTAAA
40251583 TTTAATT
1 TTTAATT
40251590 CATGTTAGGT
Statistics
Matches: 41, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
24 1 0.02
25 39 0.95
26 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (25 bp):
TTTAATTTAGTTAATATGGCTTAAA
Found at i:40251582 original size:50 final size:50
Alignment explanation
Indices: 40251508--40251611 Score: 199
Period size: 50 Copynumber: 2.1 Consensus size: 50
40251498 TGTTGGTATG
40251508 TTTAATTTAGTTAATATGGCTTAAATTTAATTCATGTAAGGTTGATTGCA
1 TTTAATTTAGTTAATATGGCTTAAATTTAATTCATGTAAGGTTGATTGCA
*
40251558 TTTAATTTAGTTAATATGGCTTAAATTTAATTCATGTTAGGTTGATTGCA
1 TTTAATTTAGTTAATATGGCTTAAATTTAATTCATGTAAGGTTGATTGCA
40251608 TTTA
1 TTTA
40251612 GTCTACTTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (50 bp):
TTTAATTTAGTTAATATGGCTTAAATTTAATTCATGTAAGGTTGATTGCA
Found at i:40251610 original size:25 final size:25
Alignment explanation
Indices: 40251532--40251611 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
40251522 TATGGCTTAA
*
40251532 ATTTAATTCATGTAAGGTTGATTGC
1 ATTTAATTCATGTTAGGTTGATTGC
* * * **
40251557 ATTTAATTTA-GTTA-ATATGGCTTAA
1 ATTTAATTCATGTTAGGT-T-GATTGC
40251582 ATTTAATTCATGTTAGGTTGATTGC
1 ATTTAATTCATGTTAGGTTGATTGC
40251607 ATTTA
1 ATTTA
40251612 GTCTACTTAA
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
23 1 0.03
24 4 0.10
25 29 0.73
26 5 0.12
27 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.47
Consensus pattern (25 bp):
ATTTAATTCATGTTAGGTTGATTGC
Found at i:40258222 original size:51 final size:51
Alignment explanation
Indices: 40258141--40258284 Score: 252
Period size: 51 Copynumber: 2.8 Consensus size: 51
40258131 GTGGCCTTCA
*
40258141 CCTTCACATAGTACCTCACTTGTGTCCAAAGCTATTATATTCACAAAGTGG
1 CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAGTGG
*
40258192 CCTTCACATAGTACCACACTTGTGTACAAAGCTATTATATTCACAAAGTGG
1 CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAGTGG
* *
40258243 CCTTCACATAGTACCACATTTGTGTCCAAAGCTATTTTATTC
1 CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTC
40258285 CTAAGGTTCA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 88 1.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAGTGG
Found at i:40258345 original size:28 final size:28
Alignment explanation
Indices: 40258308--40258402 Score: 137
Period size: 28 Copynumber: 3.5 Consensus size: 28
40258298 GGGAAATTTC
40258308 TCACTTAGCACAATGCCATGGACTTATT
1 TCACTTAGCACAATGCCATGGACTTATT
*
40258336 TCACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACAATGCCATGGACTTATT
40258364 TCACTTAG----ATGCCATGGTA-TTATT
1 TCACTTAGCACAATGCCATGG-ACTTATT
40258388 TCACTTAGCACAATG
1 TCACTTAGCACAATG
40258403 TCATATCCTA
Statistics
Matches: 60, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
24 21 0.35
25 1 0.02
28 38 0.63
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (28 bp):
TCACTTAGCACAATGCCATGGACTTATT
Found at i:40259846 original size:46 final size:46
Alignment explanation
Indices: 40259793--40259964 Score: 170
Period size: 47 Copynumber: 3.7 Consensus size: 46
40259783 TACAAGTGCT
* * *
40259793 AGTGTAAGA-TATGTCTGGGACATGCATCAGTCTCGAGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATC-GACTCAAGATGTAAGCC
* * * *
40259839 AGTGTAAGA-CATATCGGGGACATGCATCGGCTACAAGATG-ATAGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGACT-CAAGATGTA-AGCC
* * * *
40259885 AGTGTAAGACCATGTCAGGGACACGGCATCGACTTAAGATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACA-TGCATCGACTCAAGATGTAAGCC
*
40259932 AGTGTAAGACCATGTCTGGTACATGGCATCGAC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGAC
40259965 ACCTTACCCA
Statistics
Matches: 104, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
45 4 0.04
46 43 0.41
47 49 0.47
48 8 0.08
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGACTCAAGATGTAAGCC
Found at i:40259956 original size:140 final size:141
Alignment explanation
Indices: 40259699--40259961 Score: 309
Period size: 140 Copynumber: 1.9 Consensus size: 141
40259689 TGTGTGAGCT
* * ** * *
40259699 AGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATGAGAGCCAGTATAATACCATGTCCGG
1 AGTGTAAGACATATCGAGGACATGCATCGGCCACAAGATGAGAGCCAGTATAAGACCATGTCAGG
* * * *
40259764 GACATGGCATCGGCATTGATACAAGTGCTAGTGTAAGATATGTCTGGGACAT-GCATCAGTCTCG
66 GACACGGCATCGACATTGATACAAGTGCCAGTGTAAGACATGTCTGGGACATGGCATCAGTCTCG
40259828 AGATGTAAGCC
131 AGATGTAAGCC
* * * * *
40259839 AGTGTAAGACATATCGGGGACATGCATCGGCTACAAGATGATAGTCAGTGTAAGACCATGTCAGG
1 AGTGTAAGACATATCGAGGACATGCATCGGCCACAAGATGAGAGCCAGTATAAGACCATGTCAGG
* * *
40259904 GACACGGCATCGAC-TT-A-AGATGTGAGCCAGTGTAAGACCATGTCTGGTACATGGCATC
66 GACACGGCATCGACATTGATACAAGT--GCCAGTGTAAGA-CATGTCTGGGACATGGCATC
40259962 GACACCTTAC
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
137 4 0.04
138 1 0.01
139 13 0.13
140 78 0.77
141 5 0.05
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (141 bp):
AGTGTAAGACATATCGAGGACATGCATCGGCCACAAGATGAGAGCCAGTATAAGACCATGTCAGG
GACACGGCATCGACATTGATACAAGTGCCAGTGTAAGACATGTCTGGGACATGGCATCAGTCTCG
AGATGTAAGCC
Found at i:40266082 original size:80 final size:80
Alignment explanation
Indices: 40265937--40266141 Score: 240
Period size: 80 Copynumber: 2.6 Consensus size: 80
40265927 AAATCACGTA
* ** * *
40265937 CCTTCGGAAT-TTAA-CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGCCCGATTAT
1 CCTTCGG-ATCTTAACCCGGATTTAG-TAACTCGCACAAATGCCTTCGAGACATAACCCGATTAT
40265999 AGTAACTCGCACAAATG
64 AGTAACTCGCACAAATG
*
40266016 CCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGAGACTTAACCCAGATT-T
1 CCTTC-GGATCTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGAGACATAACCC-GATTAT
40266079 AGTAACTCGCACAAATG
64 AGTAACTCGCACAAATG
** * * *
40266096 CCTTCGGATCTTAGTCCGGATTTAGTAACTCGTATAAGTGCCTTCG
1 CCTTCGGATCTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCG
40266142 GATCTTAGTT
Statistics
Matches: 109, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
79 14 0.13
80 91 0.83
81 4 0.04
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (80 bp):
CCTTCGGATCTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGAGACATAACCCGATTATAG
TAACTCGCACAAATG
Found at i:40266150 original size:40 final size:39
Alignment explanation
Indices: 40265970--40266148 Score: 225
Period size: 40 Copynumber: 4.5 Consensus size: 39
40265960 GCTACTCGTT
* *
40265970 CAAATGCCTTCGGGACATAGCCC-GATTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAACCCGGATT-TAGTAACTCGCA
40266010 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCA
*
40266050 CAAATGCCTTCGAGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCG-GACTTAACCCGGATTTAGTAACTCGCA
** *
40266090 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGA-CTTAACCCGGATTTAGTAACTCGCA
* *
40266130 TAAGTGCCTTCGGATCTTA
1 CAAATGCCTTCGGA-CTTA
40266149 GTTCGGATAT
Statistics
Matches: 127, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
39 3 0.02
40 120 0.94
41 4 0.03
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:40274044 original size:40 final size:40
Alignment explanation
Indices: 40273962--40274185 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
40273952 GCTACTCGTT
*
40273962 CAAATGCCTTCGGGACATAGCCC-G-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
40274001 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
40274041 CAAATGCCTTCGGGACTTAACCCGGA-TTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
40274080 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
40274120 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
40274161 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40274186 CATCATTCAA
Statistics
Matches: 168, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
38 3 0.02
39 54 0.32
40 99 0.59
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:40274072 original size:79 final size:80
Alignment explanation
Indices: 40273962--40274185 Score: 296
Period size: 79 Copynumber: 2.8 Consensus size: 80
40273952 GCTACTCGTT
* * *
40273962 CAAATGCCTTCGGGACATAGCCC-GTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
40274026 ATTTAGTAACTCGCA
66 ATTTAGTAACTCGCA
* *
40274041 CAAATGCCTTCGGGACTTAACCCGGAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCG
*
40274104 GATTTAGTAACTCGTA
65 GATTTAGTAACTCGCA
* * * *
40274120 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
40274183 GGA
64 GGA
40274186 CATCATTCAA
Statistics
Matches: 127, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
78 6 0.05
79 87 0.69
80 23 0.18
81 11 0.09
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
ATTTAGTAACTCGCA
Found at i:40294218 original size:22 final size:21
Alignment explanation
Indices: 40294193--40294233 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40294183 TTAACTCGAT
*
40294193 TTTTTTGTCACTTTTTTTTTGA
1 TTTTTT-TAACTTTTTTTTTGA
*
40294215 TTTTTTTAATTTTTTTTTT
1 TTTTTTTAACTTTTTTTTT
40294234 CGAATTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.80
Consensus pattern (21 bp):
TTTTTTTAACTTTTTTTTTGA
Found at i:40294719 original size:22 final size:22
Alignment explanation
Indices: 40294689--40294732 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40294679 TTTGGTATTT
40294689 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
40294711 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
40294733 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:40303654 original size:15 final size:16
Alignment explanation
Indices: 40303623--40303679 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
40303613 AAGAGAAAAC
40303623 AAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAGAA
*
40303639 AAAGAAAA-AGAAGAA
1 AAAGAAAAGAAAAGAA
*
40303654 AAAGAAAATG-AAATAA
1 AAAGAAAA-GAAAAGAA
*
40303670 CAAGAAAAGA
1 AAAGAAAAGA
40303680 GAGGCAAGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 15 0.44
16 19 0.56
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:40303678 original size:21 final size:20
Alignment explanation
Indices: 40303629--40303679 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
40303619 AAACAAAGAA
*
40303629 AAGAAAAGAAAAAGAAAAAG
1 AAGAAAAGAAAAAGAAAAAC
*
40303649 AAGAAAAAGAAAATGAAATAAC
1 AAG-AAAAGAAAAAGAAA-AAC
40303671 AAGAAAAGA
1 AAGAAAAGA
40303680 GAGGCAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 19 0.70
22 5 0.19
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (20 bp):
AAGAAAAGAAAAAGAAAAAC
Found at i:40303765 original size:12 final size:12
Alignment explanation
Indices: 40303748--40303772 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40303738 TTTGGAAAGC
40303748 AAAAAGAAAATG
1 AAAAAGAAAATG
40303760 AAAAAGAAAATG
1 AAAAAGAAAATG
40303772 A
1 A
40303773 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:40303782 original size:30 final size:31
Alignment explanation
Indices: 40303748--40303829 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
40303738 TTTGGAAAGC
*
40303748 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
40303778 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
40303808 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
40303830 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:40305015 original size:14 final size:14
Alignment explanation
Indices: 40304968--40305015 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
40304958 GTACGAATGG
*
40304968 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
40304982 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
40304996 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
40305010 ATTGGT
1 AATGGT
40305016 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:40307781 original size:30 final size:31
Alignment explanation
Indices: 40307747--40307843 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
40307737 AGCTTACTCC
40307747 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAACTCACGAGCTAAACCT
* * * * *
40307777 TAGCTCAAC-TTCAACTTAGGAGTTTAATCT
1 TAGCTCAACTTTCAACTCACGAGCTAAACCT
* * *
40307807 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAACTCACGAGCTAAACCT
40307837 TAGCTCA
1 TAGCTCA
40307844 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 48 0.92
31 4 0.08
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAACTCACGAGCTAAACCT
Found at i:40312639 original size:17 final size:18
Alignment explanation
Indices: 40312596--40312640 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
40312586 TCCCTATCTT
40312596 GACTTGTGTCGTAGGCAC
1 GACTTGTGTCGTAGGCAC
*
40312614 GACTAGTGTCGT-GGC-C
1 GACTTGTGTCGTAGGCAC
40312630 GGACTTGTGTC
1 -GACTTGTGTC
40312641 AGGTACGGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 12 0.50
18 11 0.46
ACGTcount: A:0.13, C:0.22, G:0.36, T:0.29
Consensus pattern (18 bp):
GACTTGTGTCGTAGGCAC
Found at i:40315789 original size:49 final size:49
Alignment explanation
Indices: 40315716--40315961 Score: 303
Period size: 49 Copynumber: 5.0 Consensus size: 49
40315706 GTAGCCGAAG
*
40315716 CTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 CTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAA
* * * *
40315765 TTATCCGGTACACGTAGTAGCCTGCTCATAGTACTACACACGTGACCTAA
1 CTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC-AA
* * * * *
40315815 CCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAA
1 CTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA
* * * * *
40315865 GTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 -CTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAA
* * *
40315915 CAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 CTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC
40315962 TCACAATAGC
Statistics
Matches: 166, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
49 82 0.49
50 46 0.28
51 38 0.23
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (49 bp):
CTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAA
Found at i:40315950 original size:100 final size:99
Alignment explanation
Indices: 40315722--40315961 Score: 347
Period size: 100 Copynumber: 2.4 Consensus size: 99
40315712 GAAGCTATCC
* * * *
40315722 GGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
1 GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAGCC
* * *
40315787 TGCTCATAGTACTACACACGTGACCTAACCATCT
66 TGCACATAGTACTACACACGCGACCTAACAATCT
* * *
40315821 GATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAG
1 GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCAGGTACACATAGTAG
* *
40315886 CCTGCACTTAGTACTACACATGCGACC-AACAATCT
64 CCTGCACATAGTACTACACACGCGACCTAACAATCT
40315921 GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
40315962 TCACAATAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
99 37 0.30
100 48 0.38
101 40 0.32
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (99 bp):
GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAGCC
TGCACATAGTACTACACACGCGACCTAACAATCT
Found at i:40317874 original size:20 final size:20
Alignment explanation
Indices: 40317849--40317888 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40317839 AATCGAATTC
40317849 AACCTTAAGGGATGATTGGT
1 AACCTTAAGGGATGATTGGT
40317869 AACCTTAAGGGATGATTGGT
1 AACCTTAAGGGATGATTGGT
40317889 CTATCCCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (20 bp):
AACCTTAAGGGATGATTGGT
Found at i:40318303 original size:6 final size:6
Alignment explanation
Indices: 40318294--40318332 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
40318284 CTAAATTAAT
*
40318294 AAAATA AAAATA AAAATA AAAATA AATAATA AAACTA AA
1 AAAATA AAAATA AAAATA AAAATA AA-AATA AAAATA AA
40318333 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:40318315 original size:13 final size:13
Alignment explanation
Indices: 40318294--40318342 Score: 55
Period size: 12 Copynumber: 3.7 Consensus size: 13
40318284 CTAAATTAAT
40318294 AAAATAAAAAT-A
1 AAAATAAAAATAA
40318306 AAAATAAAAATAA
1 AAAATAAAAATAA
* *
40318319 ATAATAAAACTAAA
1 AAAATAAAAAT-AA
40318333 TAAAATAAAA
1 -AAAATAAAA
40318343 TAATATCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 11 0.35
13 10 0.32
14 2 0.06
15 8 0.26
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:40318347 original size:13 final size:13
Alignment explanation
Indices: 40318285--40318347 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 13
40318275 AGGCTAAAGC
*
40318285 TAAATTAATAAAA
1 TAAAATAATAAAA
40318298 T-AAA-AATAAAAA
1 TAAAATAAT-AAAA
*
40318310 TAAAAATAA-ATAA
1 T-AAAATAATAAAA
40318323 TAAAACTAAATAAAA
1 TAAAA-T-AATAAAA
40318338 TAAAATAATA
1 TAAAATAATA
40318348 TCTTCTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
11 3 0.08
12 11 0.28
13 10 0.25
14 6 0.15
15 10 0.25
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATAATAAAA
Found at i:40319454 original size:24 final size:25
Alignment explanation
Indices: 40319412--40319458 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
40319402 ACAATATTTT
40319412 TCTTTTTCTTCTTTCTCTTTTCTTG
1 TCTTTTTCTTCTTTCTCTTTTCTTG
40319437 TCTTTTTC-TCATTT-TCTTTTCT
1 TCTTTTTCTTC-TTTCTCTTTTCT
40319459 CATTTTTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.72
Consensus pattern (25 bp):
TCTTTTTCTTCTTTCTCTTTTCTTG
Found at i:40319454 original size:33 final size:33
Alignment explanation
Indices: 40319408--40319494 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 33
40319398 TTTCACAATA
**
40319408 TTTTTCT--TTTTCTTCTTTCTC-TTTTCTTGTC
1 TTTTTCTCATTTTCTTCTTTCTCTTTTTC-CCTC
40319439 TTTTTCTCATTTTC-T-TTTCTCATTTTTCCCTC
1 TTTTTCTCATTTTCTTCTTTCTC-TTTTTCCCTC
40319471 TTTTTCTCA-TTT-TTCTTT-TCTTTT
1 TTTTTCTCATTTTCTTCTTTCTCTTTT
40319495 GTATTTTCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
30 4 0.08
31 19 0.40
32 15 0.31
33 10 0.21
ACGTcount: A:0.03, C:0.23, G:0.01, T:0.72
Consensus pattern (33 bp):
TTTTTCTCATTTTCTTCTTTCTCTTTTTCCCTC
Found at i:40319458 original size:13 final size:13
Alignment explanation
Indices: 40319440--40319464 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40319430 TTTCTTGTCT
40319440 TTTTCTCATTTTC
1 TTTTCTCATTTTC
40319453 TTTTCTCATTTT
1 TTTTCTCATTTT
40319465 TCCCTCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTCTCATTTTC
Found at i:40319494 original size:19 final size:18
Alignment explanation
Indices: 40319409--40319494 Score: 59
Period size: 19 Copynumber: 4.5 Consensus size: 18
40319399 TTCACAATAT
*
40319409 TTTTCTTTTTCTTCTTTCTC
1 TTTTC-TTTTC-TCTTTTTC
*
40319429 TTTTCTTGTCT-TTTTCTC
1 TTTTCTTTTCTCTTTT-TC
40319447 ATTTTCTTTTCTCATTTTTC
1 -TTTTCTTTTCTC-TTTTTC
**
40319467 -CCTCTTTTTCTCATTTTTC
1 TTTTC-TTTTCTC-TTTTTC
40319486 TTTTCTTTT
1 TTTTCTTTT
40319495 GTATTTTCAT
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
17 3 0.06
18 5 0.09
19 32 0.60
20 9 0.17
21 4 0.08
ACGTcount: A:0.03, C:0.23, G:0.01, T:0.72
Consensus pattern (18 bp):
TTTTCTTTTCTCTTTTTC
Found at i:40328158 original size:13 final size:12
Alignment explanation
Indices: 40328140--40328195 Score: 96
Period size: 12 Copynumber: 4.7 Consensus size: 12
40328130 TCGGTATTGT
40328140 AAAAAAAATTCA
1 AAAAAAAATTCA
40328152 AAAAAAAATTCAA
1 AAAAAAAATTC-A
40328165 AAAAAAAATTC-
1 AAAAAAAATTCA
40328176 AAAAAAAATTCA
1 AAAAAAAATTCA
40328188 AAAAAAAA
1 AAAAAAAA
40328196 GTTTGTATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.26
12 19 0.45
13 12 0.29
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:40328282 original size:27 final size:26
Alignment explanation
Indices: 40328241--40328307 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
40328231 GTATTGAAGA
* *
40328241 AAAAAAAGAAGAAAAAAATTCGGAATT
1 AAAAAAA-AAGAAAAAAAATCGAAATT
40328268 AAAAAAAAAGAAAAAAAATCGAAATT
1 AAAAAAAAAGAAAAAAAATCGAAATT
*
40328294 AAAAACAAA-AAAAA
1 AAAAAAAAAGAAAAA
40328308 GAGTGATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 5 0.14
26 25 0.68
27 7 0.19
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.10
Consensus pattern (26 bp):
AAAAAAAAAGAAAAAAAATCGAAATT
Found at i:40329229 original size:17 final size:15
Alignment explanation
Indices: 40329209--40329247 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
40329199 GCGAGCGAGA
40329209 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
40329226 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
40329241 AAGATGA
1 AA-ATGA
40329248 GTGGGACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:40333495 original size:18 final size:18
Alignment explanation
Indices: 40333472--40333562 Score: 58
Period size: 18 Copynumber: 4.9 Consensus size: 18
40333462 AACAAGTGAG
40333472 GAAAAAGAAAAAGAAAAT
1 GAAAAAGAAAAAGAAAAT
* *
40333490 GAAAAAGAGCAAAAAGAGATT
1 G-AAAA-AG-AAAAAGAAAAT
* ** *
40333511 GAGAGTGAAAAAGAAATT
1 GAAAAAGAAAAAGAAAAT
*
40333529 GAAGAAAG-AAGAGAAAAT
1 GAA-AAAGAAAAAGAAAAT
**
40333547 GAATTAGAAAAAGAAA
1 GAAAAAGAAAAAGAAA
40333563 CAAAAGAAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
17 2 0.04
18 31 0.57
19 7 0.13
20 4 0.07
21 10 0.19
ACGTcount: A:0.66, C:0.01, G:0.23, T:0.10
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAAAT
Found at i:40335012 original size:30 final size:30
Alignment explanation
Indices: 40334977--40335038 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
40334967 TTTACCCATT
40334977 TTACCTACTACCATTGTTTGAAGCCATTTA
1 TTACCTACTACCATTGTTTGAAGCCATTTA
40335007 TTACCTACTACCATTGTTTGAAGCCATTTA
1 TTACCTACTACCATTGTTTGAAGCCATTTA
40335037 TT
1 TT
40335039 CTATTTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.42
Consensus pattern (30 bp):
TTACCTACTACCATTGTTTGAAGCCATTTA
Found at i:40337669 original size:158 final size:158
Alignment explanation
Indices: 40337381--40337696 Score: 569
Period size: 158 Copynumber: 2.0 Consensus size: 158
40337371 CTTCCTTTTG
*
40337381 TGATACGAGCACGCCCCGCGAACTTCATCGAACAAGCCTGTCAAGCTGAGCATTGACATGTTGGC
1 TGATACGAGCACGCCCCGCGAACTTCATCGAACAAGCCTGTCAAGCCGAGCATTGACATGTTGGC
*
40337446 AAGCTAATCCAAGCTCGTTTCCAGCTCCACGAGCTCCATCCAGCTCAAATCTAGCTTATTCGAGC
66 AAGCTAATCCAAGCTCGTTTCCAGCTCCACGAGCTCCATCCAGCTCAAATCCAGCTTATTCGAGC
*
40337511 TCAATCCATCTTGCCTGAGCTAAACCGA
131 TCAATCCAACTTGCCTGAGCTAAACCGA
*
40337539 TGATACGAGCACGCCCTGCGAACTTCATCGAACAAGCCTGTCAAGCCGAGCATTGACATGTTGGC
1 TGATACGAGCACGCCCCGCGAACTTCATCGAACAAGCCTGTCAAGCCGAGCATTGACATGTTGGC
* * *
40337604 AAGCTAATCCAAGCTCTTTTCCAGCTCCACGAGCTTCGTCCAGCTCAAATCCAGCTTATTCGAGC
66 AAGCTAATCCAAGCTCGTTTCCAGCTCCACGAGCTCCATCCAGCTCAAATCCAGCTTATTCGAGC
40337669 TCAATCCAACTTGCCTGAGCTAAACCGA
131 TCAATCCAACTTGCCTGAGCTAAACCGA
40337697 GCTCACTCCT
Statistics
Matches: 151, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
158 151 1.00
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.23
Consensus pattern (158 bp):
TGATACGAGCACGCCCCGCGAACTTCATCGAACAAGCCTGTCAAGCCGAGCATTGACATGTTGGC
AAGCTAATCCAAGCTCGTTTCCAGCTCCACGAGCTCCATCCAGCTCAAATCCAGCTTATTCGAGC
TCAATCCAACTTGCCTGAGCTAAACCGA
Found at i:40337740 original size:30 final size:30
Alignment explanation
Indices: 40337706--40337803 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
40337696 AGCTCACTCC
40337706 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * *
40337736 TAGCTCAGCTTCAGCTTAGGAGTTTAATCC-
1 TAGCTCATATTCAGCTCACGAG-CTAAACCT
* * *
40337766 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
40337796 TAGCTCAT
1 TAGCTCAT
40337804 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
29 4 0.08
30 40 0.82
31 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:40340714 original size:13 final size:14
Alignment explanation
Indices: 40340696--40340732 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
40340686 TATACAAGTC
40340696 AAAAAAAAA-TTCA
1 AAAAAAAAATTTCA
40340709 AAAAAAAAATTTCA
1 AAAAAAAAATTTCA
40340723 AAAAGAAAAA
1 AAAA-AAAAA
40340733 AAATCTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.41
14 8 0.36
15 5 0.23
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (14 bp):
AAAAAAAAATTTCA
Found at i:40340715 original size:14 final size:14
Alignment explanation
Indices: 40340696--40340733 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
40340686 TATACAAGTC
40340696 AAAAAAAAATTCAA
1 AAAAAAAAATTCAA
*
40340710 AAAAAAAATTTCAA
1 AAAAAAAAATTCAA
40340724 AAAGAAAAAA
1 AAA-AAAAAA
40340734 AATCTGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAAAAAAATTCAA
Found at i:40340743 original size:18 final size:18
Alignment explanation
Indices: 40340710--40340744 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40340700 AAAAATTCAA
*
40340710 AAAAAAAATTTCAAAAAG
1 AAAAAAAATCTCAAAAAG
*
40340728 AAAAAAAATCTGAAAAA
1 AAAAAAAATCTCAAAAA
40340745 AAAGTGTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.14
Consensus pattern (18 bp):
AAAAAAAATCTCAAAAAG
Found at i:40343077 original size:9 final size:10
Alignment explanation
Indices: 40343070--40343126 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
40343060 AAGAGAAAAC
40343070 AAAGAAAAGA
1 AAAGAAAAGA
40343080 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
40343092 AAAGAAGA-A
1 AAAGAAAAGA
40343101 AAAGAAAATGA
1 AAAGAAAA-GA
40343112 AATA-AAAAGA
1 AA-AGAAAAGA
40343122 AAAGA
1 AAAGA
40343127 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:40343093 original size:21 final size:20
Alignment explanation
Indices: 40343059--40343126 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
40343049 ACATTCTTGT
40343059 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
40343080 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
40343101 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
40343122 AAAGA
1 AAAGA
40343127 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:40343094 original size:6 final size:5
Alignment explanation
Indices: 40343070--40343126 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
40343060 AAGAGAAAAC
*
40343070 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
40343117 AAAGA AAAGA
1 AAAGA AAAGA
40343127 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:40343101 original size:15 final size:14
Alignment explanation
Indices: 40343070--40343126 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
40343060 AAGAGAAAAC
40343070 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
40343086 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
40343101 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
40343117 AAAGAAAAGA
1 AAAGAAAAGA
40343127 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:40343204 original size:11 final size:12
Alignment explanation
Indices: 40343174--40343204 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
40343164 TTGAGAGAAC
40343174 TTGAAAAAGCCT
1 TTGAAAAAGCCT
40343186 TTGAAAAAGCCT
1 TTGAAAAAGCCT
40343198 TTGAAAA
1 TTGAAAA
40343205 TAAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:40343270 original size:30 final size:31
Alignment explanation
Indices: 40343207--40343277 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
40343197 TTTGAAAATA
* *
40343207 AAAAAGAAA-ATGAGATTGAAAAAGAGAACG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
*
40343237 -AAAAGAAATTTGAGAGTGAAAAAGA-AGATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGA-ACG
40343267 AAAAAGAAATT
1 AAAAAGAAATT
40343278 GAAACAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 9 0.26
30 16 0.46
31 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.14
Consensus pattern (31 bp):
AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
Found at i:40346683 original size:27 final size:25
Alignment explanation
Indices: 40346644--40346693 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
40346634 GAAAAAGAAA
40346644 AAAAAGGATGAAAGA-AAGCAAAAGG
1 AAAAAGGATGAAAGAGAA-CAAAAGG
40346669 AAAAAGAGATCGAAAGAGAACAAAA
1 AAAAAG-GAT-GAAAGAGAACAAAA
40346694 AGAGATTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 11 0.50
28 2 0.09
ACGTcount: A:0.66, C:0.06, G:0.24, T:0.04
Consensus pattern (25 bp):
AAAAAGGATGAAAGAGAACAAAAGG
Found at i:40346721 original size:12 final size:12
Alignment explanation
Indices: 40346704--40346728 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40346694 AGAGATTGAG
40346704 AGTGAAAAAGAA
1 AGTGAAAAAGAA
40346716 AGTGAAAAAGAA
1 AGTGAAAAAGAA
40346728 A
1 A
40346729 AAGAGAGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (12 bp):
AGTGAAAAAGAA
Found at i:40351387 original size:20 final size:20
Alignment explanation
Indices: 40351364--40351429 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
40351354 AGCTCCCATC
*
40351364 AGCTCACTTGAGCTCAATTT
1 AGCTCACTTGAGTTCAATTT
*
40351384 AGCTCACTTGAGTTCAATTC
1 AGCTCACTTGAGTTCAATTT
**
40351404 AGCTCGTTTGAGTTCGAATTT
1 AGCTCACTTGAGTTC-AATTT
40351425 AGCTC
1 AGCTC
40351430 GTTTCAGCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 31 0.77
21 9 0.22
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (20 bp):
AGCTCACTTGAGTTCAATTT
Found at i:40352082 original size:14 final size:14
Alignment explanation
Indices: 40352065--40352104 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
40352055 CGAATGGAAT
*
40352065 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
40352079 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
40352093 GATATGAACAAA
1 GGTAGGAACAAA
40352105 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:40353654 original size:30 final size:30
Alignment explanation
Indices: 40353620--40353716 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
40353610 AGCTCACTCC
40353620 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
40353650 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * *
40353680 CAGCTCAACTTTAGCTCATGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
40353710 TAGCTCA
1 TAGCTCA
40353717 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:40357242 original size:21 final size:20
Alignment explanation
Indices: 40357210--40357267 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 20
40357200 CGAGAAAACA
40357210 AAAAAAAGAAAAGAAAAAGC
1 AAAAAAAGAAAAGAAAAAGC
* *
40357230 AAAAGAAGAAAAAGAAAAAACGA
1 AAAAAAAG-AAAAG-AAAAA-GC
40357253 AATAAAAAGAAAAGA
1 AA-AAAAAGAAAAGA
40357268 GAGGCAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 7 0.23
21 5 0.16
22 6 0.19
23 8 0.26
24 5 0.16
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAAAAGAAAAGAAAAAGC
Found at i:40357248 original size:34 final size:32
Alignment explanation
Indices: 40357202--40357267 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 32
40357192 TCTTGTAACG
40357202 AGAAAACAAAAAAAAGAAAAGAAAAAGCAAAAGA
1 AGAAAACAAAAAAAAG-AAAGAAAAAG-AAAAGA
* *
40357236 AGAAAA-AGAAAAAACGAAATAAAAAGAAAAGA
1 AGAAAACA-AAAAAAAGAAAGAAAAAGAAAAGA
40357268 GAGGCAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 6 0.21
33 10 0.34
34 13 0.45
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.02
Consensus pattern (32 bp):
AGAAAACAAAAAAAAGAAAGAAAAAGAAAAGA
Found at i:40357367 original size:18 final size:18
Alignment explanation
Indices: 40357327--40357370 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
40357317 GAAAAAGCCT
40357327 TTGAAAAACAAAAAGAAA
1 TTGAAAAACAAAAAGAAA
* * * *
40357345 ATGAAAAATAAAATGAGA
1 TTGAAAAACAAAAAGAAA
40357363 TTGAAAAA
1 TTGAAAAA
40357371 GAGAATGAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.68, C:0.02, G:0.14, T:0.16
Consensus pattern (18 bp):
TTGAAAAACAAAAAGAAA
Found at i:40360534 original size:12 final size:12
Alignment explanation
Indices: 40360500--40360533 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
40360490 TTCATTTTCT
40360500 CTTCTTTCTTCAA
1 CTTCTTT-TTCAA
40360513 CTTCTTTTTCAA
1 CTTCTTTTTCAA
40360525 CTTTCTTTT
1 C-TTCTTTT
40360534 CCGTTTCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (12 bp):
CTTCTTTTTCAA
Found at i:40366092 original size:18 final size:18
Alignment explanation
Indices: 40366071--40366105 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40366061 TTTTTCTTTT
40366071 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
40366089 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
40366106 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:40367017 original size:13 final size:13
Alignment explanation
Indices: 40367001--40367064 Score: 65
Period size: 13 Copynumber: 4.6 Consensus size: 13
40366991 TTTTGCTCGG
*
40367001 TTTTTTTTTTCAC
1 TTTTTTTTTTCAA
*
40367014 TTTTTTTTTTGAA
1 TTTTTTTTTTCAA
40367027 TTTTTTTTTCAATCAA
1 TTTTTTTTT---TCAA
*
40367043 ATTTTTTTTTCGAA
1 TTTTTTTTTTC-AA
40367057 TTTTTTTT
1 TTTTTTTT
40367065 GATTTTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
13 22 0.52
14 9 0.21
16 11 0.26
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:40369855 original size:20 final size:20
Alignment explanation
Indices: 40369832--40369897 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
40369822 AGCTCCCATC
*
40369832 AGCTCACTTGAGCTCAATTT
1 AGCTCACTTGAGTTCAATTT
*
40369852 AGCTCACTTGAGTTCAATTC
1 AGCTCACTTGAGTTCAATTT
**
40369872 AGCTCGTTTGAGTTCGAATTT
1 AGCTCACTTGAGTTC-AATTT
40369893 AGCTC
1 AGCTC
40369898 GTTTCAGCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 31 0.77
21 9 0.22
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (20 bp):
AGCTCACTTGAGTTCAATTT
Found at i:40369912 original size:10 final size:10
Alignment explanation
Indices: 40369830--40369920 Score: 51
Period size: 10 Copynumber: 9.0 Consensus size: 10
40369820 TCAGCTCCCA
*
40369830 TCAGCTCACT
1 TCAGCTCATT
*
40369840 TGAGCTCAATT
1 TCAGCTC-ATT
*
40369851 T-AGCTCACT
1 TCAGCTCATT
* * *
40369860 TGAGTTCAAT
1 TCAGCTCATT
*
40369870 TCAGCTCGTT
1 TCAGCTCATT
* *
40369880 TGAGTTCGAATT
1 TCAGCTC--ATT
*
40369892 T-AGCTCGTT
1 TCAGCTCATT
40369901 TCAGCTCATT
1 TCAGCTCATT
40369911 TCAGCTCATT
1 TCAGCTCATT
40369921 CCTTCTTCAT
Statistics
Matches: 61, Mismatches: 15, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
9 6 0.10
10 45 0.74
11 7 0.11
12 3 0.05
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.38
Consensus pattern (10 bp):
TCAGCTCATT
Found at i:40374968 original size:21 final size:21
Alignment explanation
Indices: 40374942--40375004 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
40374932 TTGGTATTTG
40374942 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
40374963 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40374984 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
40375005 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:40379024 original size:26 final size:25
Alignment explanation
Indices: 40378995--40379083 Score: 87
Period size: 26 Copynumber: 3.6 Consensus size: 25
40378985 AAATCGTAGC
40378995 TTCGAAAAAAAAAATTAAAAAAAAGT
1 TTCGAAAAAAAAAATTAAAAAAAA-T
*
40379021 TTCGAAAAAAAAAA--AGAAAAAA-
1 TTCGAAAAAAAAAATTAAAAAAAAT
* **
40379043 TCCGAAAAAAAAGAAGGAAAAAAAAT
1 TTCGAAAAAAAA-AATTAAAAAAAAT
*
40379069 TGC-AAAAAAAAAATT
1 TTCGAAAAAAAAAATT
40379084 GCATACGGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
22 11 0.21
23 2 0.04
24 9 0.17
25 15 0.28
26 16 0.30
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (25 bp):
TTCGAAAAAAAAAATTAAAAAAAAT
Found at i:40379040 original size:22 final size:23
Alignment explanation
Indices: 40379001--40379065 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 23
40378991 TAGCTTCGAA
* *
40379001 AAAAAAAATTAAA-AAAAAGTTTCG
1 AAAAAAAA-TAAAGAAAAA-ATCCG
40379025 AAAAAAAA-AAAGAAAAAATCCG
1 AAAAAAAATAAAGAAAAAATCCG
* *
40379047 AAAAAAAAGAAGGAAAAAA
1 AAAAAAAATAAAGAAAAAA
40379066 AATTGCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 14 0.39
23 14 0.39
24 8 0.22
ACGTcount: A:0.75, C:0.05, G:0.11, T:0.09
Consensus pattern (23 bp):
AAAAAAAATAAAGAAAAAATCCG
Done.