Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 19 of 196
Found at i:5457631 original size:80 final size:80
Alignment explanation
Indices: 5457444--5457643 Score: 233
Period size: 80 Copynumber: 2.5 Consensus size: 80
5457434 ATAGCCCGGT
* * *
5457444 TATAGTAATTTGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCATC
1 TATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCATC
* *
5457509 GGGACTTAACCCGGA
66 GAGACTTAACCCGAA
* * * * *
5457524 TTTAGTAACTCGCACAAATGCCGTCGGGACTTAACCCGGAATTAGTATCTCGCACAAATGCCTTC
1 TATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCATC
**
5457589 -AGATCTTAGTCCGAA
66 GAGA-CTTAACCCGAA
* * *
5457604 TATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TATAGTAAC-TAGCACAAATGCCTTCGGGACTTAACCCGGA
5457644 CACCATTCAA
Statistics
Matches: 101, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
79 2 0.02
80 91 0.90
81 8 0.08
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (80 bp):
TATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCATC
GAGACTTAACCCGAA
Found at i:5473093 original size:11 final size:12
Alignment explanation
Indices: 5473077--5473109 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5473067 GTTCTTTAAA
5473077 TTTTTC-TCTTT
1 TTTTTCTTCTTT
5473088 TTTTTCTTCTTT
1 TTTTTCTTCTTT
*
5473100 TTTTTTTTCT
1 TTTTTCTTCT
5473110 ATTCTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCTTCTTT
Found at i:5476091 original size:5 final size:5
Alignment explanation
Indices: 5476063--5476128 Score: 73
Period size: 5 Copynumber: 13.4 Consensus size: 5
5476053 AAAATATCAT
* *
5476063 ATTTA TTTTA A-TTA ATTTG A-TTA ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
* *
5476111 ATTTCA AATTA CTTTA AT
1 ATTT-A ATTTA ATTTA AT
5476129 CAAATTCTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
4 7 0.14
5 39 0.78
6 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (5 bp):
ATTTA
Found at i:5477027 original size:9 final size:9
Alignment explanation
Indices: 5477003--5477039 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
5476993 TGAGTTTTCG
*
5477003 AATTCAAAT
1 AATTCGAAT
*
5477012 AACTCGAAT
1 AATTCGAAT
5477021 AATTCGAAT
1 AATTCGAAT
5477030 AATTCGAAT
1 AATTCGAAT
5477039 A
1 A
5477040 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5477964 original size:5 final size:5
Alignment explanation
Indices: 5477954--5477979 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5477944 GAACAAATAT
5477954 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
5477980 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:5478732 original size:10 final size:10
Alignment explanation
Indices: 5478696--5478750 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
5478686 TAAAATAATT
*
5478696 AAAAAGAAAC
1 AAAAAGAAAG
*
5478706 AAAGAAAAAACG
1 AAA-AAGAAA-G
*
5478718 AAAAAGAAGG
1 AAAAAGAAAG
5478728 AAAAAGAAAG
1 AAAAAGAAAG
5478738 --AAAGAAAG
1 AAAAAGAAAG
5478746 AAAAA
1 AAAAA
5478751 TAAAATGGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
8 8 0.22
10 16 0.44
11 9 0.25
12 3 0.08
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:5479386 original size:25 final size:25
Alignment explanation
Indices: 5479358--5479419 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
5479348 TGGCTCTCCG
*
5479358 GAGCTTCCCGTTATACAGCTC-ACAT
1 GAGCTTCCCGTTATACAGCTCGA-AA
* **
5479383 GAGCTTCCCTTTATATGGCTCGAAA
1 GAGCTTCCCGTTATACAGCTCGAAA
5479408 GAGCTTCCCGTT
1 GAGCTTCCCGTT
5479420 TATGTGCTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCGTTATACAGCTCGAAA
Found at i:5486216 original size:24 final size:26
Alignment explanation
Indices: 5486184--5486232 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
5486174 CTTAACCTTT
*
5486184 TTATTTTTTTT-G-TCAATTTGATTC
1 TTATTTTTTTTAGTTAAATTTGATTC
5486208 TTATTTTTTTTAGTTAAATTTGATT
1 TTATTTTTTTTAGTTAAATTTGATT
5486233 TTCAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
25 1 0.05
26 10 0.45
ACGTcount: A:0.20, C:0.04, G:0.08, T:0.67
Consensus pattern (26 bp):
TTATTTTTTTTAGTTAAATTTGATTC
Found at i:5490017 original size:18 final size:18
Alignment explanation
Indices: 5489975--5490020 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5489965 TATTTTCAAT
*
5489975 AATTTATAATTAAAACTAT
1 AATTT-TAATTAAAACTAA
* *
5489994 ATTTTTAATTAAAAGTAA
1 AATTTTAATTAAAACTAA
5490012 AATTTTAAT
1 AATTTTAAT
5490021 CAAATAAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
AATTTTAATTAAAACTAA
Found at i:5496338 original size:125 final size:125
Alignment explanation
Indices: 5495914--5496357 Score: 683
Period size: 126 Copynumber: 3.5 Consensus size: 125
5495904 GATAAAATCA
* * * *
5495914 AAGCAGGATGTTTTATCAGAAGAATTTCTGAAATCGCGCCCATGTGGACGCGCTTTTGCTATAGT
1 AAGCAGGATGCTTTATCAAAAGAATTTCTGAAATCACGCCCATGTGGACGCGCTTTTGCTACAGT
* *
5495979 AGGTCTTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTACAAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTA-TAAAAAACGCTTC
* * *
5496040 AGGCAGGATGCTTTATCAAAAAAATTTCTGATATCACGCCCATGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAAAAGAATTTCTGAAATCACGCCCATGTGGACGCGCTTTTGCTACAGT
*
5496105 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAATATAAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTAT-AAAAAACGCTTC
** **
5496166 AAGCAGGATGCTTTATCAAAAGAATTTCTGAAATCGTGCCCATGTGGACATGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAAAAGAATTTCTGAAATCACGCCCATGTGGACGCGCTTTTGCTACAGT
** *
5496231 AGGTCCTGAAAAAATAATTTCAAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
* *
5496291 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCACGCCC-TCGTGGACGCGCTTTTACTACAG
1 AAGCAGGATGCTTTATCAAAAGAATTTCTGAAATCACGCCCAT-GTGGACGCGCTTTTGCTACAG
5496355 TAG
65 TAG
5496358 CATGTTTGGG
Statistics
Matches: 289, Mismatches: 27, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
124 1 0.00
125 71 0.25
126 217 0.75
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (125 bp):
AAGCAGGATGCTTTATCAAAAGAATTTCTGAAATCACGCCCATGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
Found at i:5503462 original size:10 final size:9
Alignment explanation
Indices: 5503444--5503565 Score: 81
Period size: 9 Copynumber: 13.0 Consensus size: 9
5503434 TTTTTTAAAT
5503444 TAATTTTTA
1 TAATTTTTA
5503453 TAAGTTTTTA
1 TAA-TTTTTA
*
5503463 TAAGTTTATA
1 TAA-TTTTTA
5503473 TAAATTTTGTA
1 T-AATTTT-TA
*
5503484 AATATTTTTA
1 TA-ATTTTTA
5503494 -AATATTTTA
1 TAAT-TTTTA
*
5503503 TTATTTTTA
1 TAATTTTTA
5503512 TAATTTTTA
1 TAATTTTTA
*
5503521 TAAGTTTATA
1 TAA-TTTTTA
*
5503531 TAAATTTT-
1 TAATTTTTA
*
5503539 TAATATTT-
1 TAATTTTTA
5503547 TAATATTTTA
1 TAAT-TTTTA
5503557 -ATATTTTTA
1 TA-ATTTTTA
5503566 CGATTTCTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
8 12 0.13
9 37 0.40
10 34 0.37
11 9 0.10
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (9 bp):
TAATTTTTA
Found at i:5503496 original size:68 final size:56
Alignment explanation
Indices: 5503446--5503565 Score: 190
Period size: 58 Copynumber: 2.1 Consensus size: 56
5503436 TTTTAAATTA
5503446 ATTTTTATAAGTTTTTATAAGTTTATATAAATTTTGTAAATATTTTTAAATATTTTATT
1 ATTTTTATAA-TTTTTATAAGTTTATATAAATTTT-T-AATATTTTTAAATATTTTATT
*
5503505 ATTTTTATAATTTTTATAAGTTTATATAAATTTTTAATA-TTTT-AATATTTTAAT
1 ATTTTTATAATTTTTATAAGTTTATATAAATTTTTAATATTTTTAAATATTTTATT
5503559 ATTTTTA
1 ATTTTTA
5503566 CGATTTCTAT
Statistics
Matches: 60, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
54 17 0.28
55 4 0.07
56 4 0.07
57 1 0.02
58 24 0.40
59 10 0.17
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (56 bp):
ATTTTTATAATTTTTATAAGTTTATATAAATTTTTAATATTTTTAAATATTTTATT
Found at i:5503547 original size:8 final size:8
Alignment explanation
Indices: 5503536--5503563 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5503526 TTATATAAAT
5503536 TTTTAATA
1 TTTTAATA
5503544 TTTTAATA
1 TTTTAATA
5503552 TTTTAATA
1 TTTTAATA
5503560 TTTT
1 TTTT
5503564 TACGATTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTAATA
Found at i:5505209 original size:10 final size:10
Alignment explanation
Indices: 5505172--5505202 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5505162 TAGATTACCA
5505172 ATATCAATTC
1 ATATCAATTC
5505182 ATATCAATTC
1 ATATCAATTC
*
5505192 ATACCAATTC
1 ATATCAATTC
5505202 A
1 A
5505203 AGTCAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (10 bp):
ATATCAATTC
Found at i:5510399 original size:82 final size:82
Alignment explanation
Indices: 5510255--5510415 Score: 241
Period size: 82 Copynumber: 2.0 Consensus size: 82
5510245 GGGAGGTTCT
* * * *
5510255 GAATCAAAAGGGAAAACAACCAAAAAATTTCGGTGAAGTTGATGTTATAGAATACTACAGCGATG
1 GAATCAAAAGGGAAAACAACCAAAAAATTTCGGTGAAGCTGATGCTATAGAAGACTACAGCGATA
*
5510320 GTGAACTTCTAGTCTGC
66 GTAAACTTCTAGTCTGC
* * * *
5510337 GAATCAAAAGGGAAAACAACCAGAAAATTTTGGTGAAGCTGATGCTGTAGAAGACTATAGCGATA
1 GAATCAAAAGGGAAAACAACCAAAAAATTTCGGTGAAGCTGATGCTATAGAAGACTACAGCGATA
5510402 GTAAACTTCTAGTC
66 GTAAACTTCTAGTC
5510416 GCTTCTGTCA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (82 bp):
GAATCAAAAGGGAAAACAACCAAAAAATTTCGGTGAAGCTGATGCTATAGAAGACTACAGCGATA
GTAAACTTCTAGTCTGC
Found at i:5523145 original size:23 final size:23
Alignment explanation
Indices: 5523119--5523171 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
5523109 ATAAGTGCCA
5523119 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
5523142 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
5523165 CACTGAT
1 CACTGAT
5523172 CAATAACACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:5530332 original size:6 final size:6
Alignment explanation
Indices: 5530321--5530349 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5530311 TTGTTGTTAC
5530321 CAATGG CAATGG CAATGG CAATGG CAATG
1 CAATGG CAATGG CAATGG CAATGG CAATG
5530350 AATGATGACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.17
Consensus pattern (6 bp):
CAATGG
Found at i:5536356 original size:6 final size:6
Alignment explanation
Indices: 5536347--5536374 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5536337 ATGATTAGGA
5536347 TTTTGT TTTTGT TTTTGT TTTTGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTT
5536375 CTTAATGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTGT
Found at i:5537768 original size:14 final size:14
Alignment explanation
Indices: 5537749--5537777 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5537739 GCATCGGATA
5537749 ATTTATTTAGTAAT
1 ATTTATTTAGTAAT
5537763 ATTTATTTAGTAAT
1 ATTTATTTAGTAAT
5537777 A
1 A
5537778 AATATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
ATTTATTTAGTAAT
Found at i:5538036 original size:33 final size:33
Alignment explanation
Indices: 5537993--5538056 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
5537983 GTACACAAAA
5537993 TAAAAATTCATGA-ATCAAAATATACATTAAAGC
1 TAAAAATTCAT-ATATCAAAATATACATTAAAGC
* *
5538026 TAAAAGTTCATATATCAAATTATACATTAAA
1 TAAAAATTCATATATCAAAATATACATTAAA
5538057 ATAAAGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (33 bp):
TAAAAATTCATATATCAAAATATACATTAAAGC
Found at i:5550426 original size:18 final size:18
Alignment explanation
Indices: 5550405--5550439 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5550395 AAAAGAAGGA
5550405 AATTAAAGAAAATTAAAG
1 AATTAAAGAAAATTAAAG
**
5550423 AATTAAATTAAATTAAA
1 AATTAAAGAAAATTAAA
5550440 TTGTTGAAAA
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:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AATTAAAGAAAATTAAAG
Found at i:5551934 original size:142 final size:143
Alignment explanation
Indices: 5551734--5552013 Score: 420
Period size: 143 Copynumber: 2.0 Consensus size: 143
5551724 AAAACAGATT
* *
5551734 ATTTTTTAAGTTAAAATTGATTTTCAATCCAAACCCAAAAGCTATTACCTTC-GTAAAAAAAAAC
1 ATTTTTTAAATTAAAATTGATTTTCAATCCAAACCCAAAAGCTATTACCTTCGGAAAAAAAAAAC
* * *
5551798 ACTTTT-GGAGTCCAAGGATATTTTTAACTCTTATTTATAATCTAATGTATTTTATATAATATTT
66 A-TTTTCGGAGTCAAAGAATATTTTTAACTCTTATTTATAATCTAATATATTTTATATAATATTT
5551862 ATATTGGACCGGCC
130 ATATTGGACCGGCC
* * * * *
5551876 ATTTTTTAAATTAAATTTGTTTTTCAATCCAAACCCAAAAGCTATTGCGTTTGGAAAAAAAAAAC
1 ATTTTTTAAATTAAAATTGATTTTCAATCCAAACCCAAAAGCTATTACCTTCGGAAAAAAAAAAC
* * *
5551941 ATTTTCGGAGTCAAAGAATCTTTTTAACTCTTATTTATAATTTAATATATTTTATATAATATTTG
66 ATTTTCGGAGTCAAAGAATATTTTTAACTCTTATTTATAATCTAATATATTTTATATAATATTTA
5552006 TATTGGAC
131 TATTGGAC
5552014 TTAAATTTAT
Statistics
Matches: 123, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
142 50 0.41
143 73 0.59
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (143 bp):
ATTTTTTAAATTAAAATTGATTTTCAATCCAAACCCAAAAGCTATTACCTTCGGAAAAAAAAAAC
ATTTTCGGAGTCAAAGAATATTTTTAACTCTTATTTATAATCTAATATATTTTATATAATATTTA
TATTGGACCGGCC
Found at i:5565715 original size:29 final size:29
Alignment explanation
Indices: 5565663--5565720 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
5565653 AGGGAAATTT
5565663 TTTAATTTTTTGGGGCCATCACAT-TAAA
1 TTTAATTTTTTGGGGCCATCACATATAAA
*
5565691 TTTACATTTTTTGGGGGCC-TTACATATAAA
1 TTTA-ATTTTTT-GGGGCCATCACATATAAA
5565721 GAGAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.15
29 12 0.46
30 10 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.43
Consensus pattern (29 bp):
TTTAATTTTTTGGGGCCATCACATATAAA
Found at i:5575116 original size:12 final size:12
Alignment explanation
Indices: 5575099--5575123 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5575089 TGTTATTTCG
5575099 GGTCGGTTAACC
1 GGTCGGTTAACC
5575111 GGTCGGTTAACC
1 GGTCGGTTAACC
5575123 G
1 G
5575124 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:5578825 original size:57 final size:57
Alignment explanation
Indices: 5578737--5578854 Score: 227
Period size: 57 Copynumber: 2.1 Consensus size: 57
5578727 TAATCTGTTT
*
5578737 TTGTTTTGAGAGTATTTTAAAATAATAAATGGTTTCACGAGTTAGTTTGGACCCGTG
1 TTGTTTTGAGAGTATTTCAAAATAATAAATGGTTTCACGAGTTAGTTTGGACCCGTG
5578794 TTGTTTTGAGAGTATTTCAAAATAATAAATGGTTTCACGAGTTAGTTTGGACCCGTG
1 TTGTTTTGAGAGTATTTCAAAATAATAAATGGTTTCACGAGTTAGTTTGGACCCGTG
5578851 TTGT
1 TTGT
5578855 CTTAAGTTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (57 bp):
TTGTTTTGAGAGTATTTCAAAATAATAAATGGTTTCACGAGTTAGTTTGGACCCGTG
Found at i:5579676 original size:23 final size:23
Alignment explanation
Indices: 5579649--5579709 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
5579639 AAATTTCTTT
* *
5579649 AAAAATTCTTAAAAATGTTAAAA
1 AAAAATTCTTAAAAAAGCTAAAA
* *
5579672 GAAAAA-ACCTAAAAAAGCTAAAA
1 -AAAAATTCTTAAAAAAGCTAAAA
5579695 AAAAATT-TTAAAAAA
1 AAAAATTCTTAAAAAA
5579710 ATTATATTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 12 0.40
23 13 0.43
24 5 0.17
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (23 bp):
AAAAATTCTTAAAAAAGCTAAAA
Found at i:5580643 original size:92 final size:92
Alignment explanation
Indices: 5580486--5580670 Score: 325
Period size: 92 Copynumber: 2.0 Consensus size: 92
5580476 CAAGAGGACT
* * * *
5580486 TTTCCTATAAATATCTTGGAAAACTATGAACAGGGGATTGCCTTTTTAGCACCCTGAAGTCACTC
1 TTTCCTATAAATATCTTAGAAAACTATGAACAAGGGATCGCCTTTTTAGCACCCTAAAGTCACTC
5580551 TCAACATTTATCCTTTTAATCAGCCTG
66 TCAACATTTATCCTTTTAATCAGCCTG
5580578 TTTCCTATAAATATCTTAGAAAACTATGAACAAGGGATCGCCTTTTTAGCACCCTAAAGTCACTC
1 TTTCCTATAAATATCTTAGAAAACTATGAACAAGGGATCGCCTTTTTAGCACCCTAAAGTCACTC
*
5580643 TCAACATTTATCCTTTTAATTAGCCTG
66 TCAACATTTATCCTTTTAATCAGCCTG
5580670 T
1 T
5580671 CCTCTTGTCC
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (92 bp):
TTTCCTATAAATATCTTAGAAAACTATGAACAAGGGATCGCCTTTTTAGCACCCTAAAGTCACTC
TCAACATTTATCCTTTTAATCAGCCTG
Found at i:5582820 original size:25 final size:24
Alignment explanation
Indices: 5582769--5582825 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
5582759 ATGTGGACAA
* *
5582769 AATAAAACACGAAATTTTGGATAG
1 AATAAAACACGAAATTGTAGATAG
* *
5582793 AATAAAACCATGAAATTGTAGATTG
1 AATAAAA-CACGAAATTGTAGATAG
5582818 AATTAAAA
1 AA-TAAAA
5582826 ATAAAGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 7 0.26
25 15 0.56
26 5 0.19
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (24 bp):
AATAAAACACGAAATTGTAGATAG
Found at i:5594866 original size:24 final size:24
Alignment explanation
Indices: 5594811--5594869 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
5594801 ATACAAGGAG
* * *
5594811 ATGAAAGGTTTAAGGAATATGAAAG
1 ATGAAAGG-TTAAAGAAAATGAAAA
* *
5594836 GTTAAAGGTTAAAGAAAATGAAAA
1 ATGAAAGGTTAAAGAAAATGAAAA
5594860 ATGAAAGGTT
1 ATGAAAGGTT
5594870 GAACATCTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.24
Consensus pattern (24 bp):
ATGAAAGGTTAAAGAAAATGAAAA
Found at i:5596176 original size:28 final size:28
Alignment explanation
Indices: 5596124--5596180 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
5596114 ATAAAAATCG
*
5596124 TAAAAAAATATTTAAAATATTAAAATTA
1 TAAAAAAATATTTAAAATATGAAAATTA
5596152 TAAAAAAAT-TATTAGAAAT-TGAAAATTA
1 TAAAAAAATAT-TTA-AAATATGAAAATTA
5596180 T
1 T
5596181 TGTAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 1 0.04
28 21 0.81
29 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (28 bp):
TAAAAAAATATTTAAAATATGAAAATTA
Found at i:5597469 original size:19 final size:20
Alignment explanation
Indices: 5597447--5597488 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5597437 TATAATTTTA
*
5597447 TAATTTTTT-TTTCTATTTG
1 TAATTTTTTATATCTATTTG
*
5597466 TAATTTTTTATATCTTTTTG
1 TAATTTTTTATATCTATTTG
5597486 TAA
1 TAA
5597489 ATCTTTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (20 bp):
TAATTTTTTATATCTATTTG
Found at i:5597485 original size:20 final size:19
Alignment explanation
Indices: 5597442--5597488 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5597432 TATTTTATAA
* *
5597442 TTTTATAATTTTTTTTTCT
1 TTTTGTAATTTTTTTATCT
*
5597461 ATTTGTAATTTTTTATATCT
1 TTTTGTAATTTTTT-TATCT
5597481 TTTTGTAA
1 TTTTGTAA
5597489 ATCTTTTGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTTGTAATTTTTTTATCT
Found at i:5598061 original size:39 final size:40
Alignment explanation
Indices: 5598010--5598099 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
5598000 AAAAAAGCAA
*
5598010 AAAAGCGCGTTGACG-GGG-ATTCGCTTTACC-CGTGTCAGC
1 AAAAGCACGTTGACGTGGGCA-T-GCTTTACCACGTGTCAGC
*
5598049 AAAAGCACGTTGACGTGGGCATGCTTTGCCACGTGTCAGC
1 AAAAGCACGTTGACGTGGGCATGCTTTACCACGTGTCAGC
5598089 AAAAGCACGTT
1 AAAAGCACGTT
5598100 AAAGTGAACG
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
39 21 0.46
40 24 0.52
41 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
AAAAGCACGTTGACGTGGGCATGCTTTACCACGTGTCAGC
Found at i:5598115 original size:40 final size:39
Alignment explanation
Indices: 5598031--5598119 Score: 106
Period size: 40 Copynumber: 2.3 Consensus size: 39
5598021 GACGGGGATT
* * **
5598031 CGCTTTACCCGTGTCAGCAAAAGCACGTTGACGTGGGCA
1 CGCTTTACCCGTGTCAGCAAAAGCACGTTAAAGTGAACA
* * *
5598070 TGCTTTGCCACGTGTCAGCAAAAGCACGTTAAAGTGAACG
1 CGCTTTACC-CGTGTCAGCAAAAGCACGTTAAAGTGAACA
5598110 CGCTTTACCC
1 CGCTTTACCC
5598120 CGTATTTTCT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
39 8 0.20
40 32 0.80
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (39 bp):
CGCTTTACCCGTGTCAGCAAAAGCACGTTAAAGTGAACA
Found at i:5610426 original size:114 final size:112
Alignment explanation
Indices: 5610237--5610573 Score: 320
Period size: 114 Copynumber: 2.9 Consensus size: 112
5610227 CCTTTCTTAG
* * * * *
5610237 AAACACCGCAATATGCAAGAATTACCGGCG-TTTGGTCATAAACGCCGCAAAAACTGTTAAGAAA
1 AAACGCCGCAGTA-GCAAGAATTAGCGGCGCTTT-ATCATAAGCGCCGC-AAAACTGTTAAGAAA
* * * *
5610301 ATGATGTCGTTTTTAGTTTAGGTTTTGGGGACTTTAGTGGCGCTTACTGA-A
63 ATGATGCCGTTTTTA-TTTAGGTTTTAGAGACTTTAGTGGCGCTT-CTCAGA
*
5610352 AAACGCCGCTA-TAGTCAAGAATTAGCGGCGCTTTATTATAAGCGCCGCAAAACTGTTAAGAAAA
1 AAACGCCGC-AGTAG-CAAGAATTAGCGGCGCTTTATCATAAGCGCCGCAAAACTGTTAAGAAAA
* * ** * * * * *
5610416 TGTTACCGTTTTTCATTTATCTTTTCGAGACGTTAGTGGTGATTTTCAGA
64 TGATGCCGTTTTT-ATTTAGGTTTTAGAGACTTTAGTGGCGCTTCTCAGA
** * * * *
5610466 AAACGCCGCAGTAGCGAAGCTTTAGTGGCGCTTTATCACAAGTGCCGCAAAACTGTTAAGAAAAC
1 AAACGCCGCAGTAGC-AAGAATTAGCGGCGCTTTATCATAAGCGCCGCAAAACTGTTAAGAAAAT
* *
5610531 GATGCTGTTTTTAATTTAGGTTTTAGAGTCTTTAGTGGCGCTT
65 GATGCCGTTTTT-ATTTAGGTTTTAGAGACTTTAGTGGCGCTT
5610574 GTCTAAAAAT
Statistics
Matches: 180, Mismatches: 35, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
113 4 0.02
114 136 0.76
115 36 0.20
116 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (112 bp):
AAACGCCGCAGTAGCAAGAATTAGCGGCGCTTTATCATAAGCGCCGCAAAACTGTTAAGAAAATG
ATGCCGTTTTTATTTAGGTTTTAGAGACTTTAGTGGCGCTTCTCAGA
Found at i:5610588 original size:114 final size:112
Alignment explanation
Indices: 5610252--5610630 Score: 318
Period size: 114 Copynumber: 3.3 Consensus size: 112
5610242 CCGCAATATG
* * * *
5610252 CAAGAATTACCGGCG-TTTGGTCATAAACGCCGCAAAAACTGTTAAGAAAATGATG-TCGTTTTT
1 CAAGAATTAGCGGCGCTTT-ATCACAAGCGCCGC-AAAACTGTTAAGAAAATGATGCT-GTTTTT
* * * *
5610315 AGTTTAGGTTTTGGGGACTTTAGTGGCGCTTACTGAAAAACGCCGCTATAGT
63 AATTTAGGTTTTAGAGACTTTAGTGGCGCTTTCT-AAAAACGCCGC-ATAGT
* * * * * *
5610367 CAAGAATTAGCGGCGCTTTATTATAAGCGCCGCAAAACTGTTAAGAAAATGTTACCGTTTTTCAT
1 CAAGAATTAGCGGCGCTTTATCACAAGCGCCGCAAAACTGTTAAGAAAATGATGCTGTTTTTAAT
** * * * *
5610432 TTATCTTTTCGAGACGTTAGTGGTGATTT-TCAGAAAACGCCGCAGTAG-
66 TTAGGTTTTAGAGACTTTAGTGGCGCTTTCT-A-AAAACGCCGCA-TAGT
** * * *
5610480 CGAAGCTTTAGTGGCGCTTTATCACAAGTGCCGCAAAACTGTTAAGAAAACGATGCTGTTTTTAA
1 C-AAGAATTAGCGGCGCTTTATCACAAGCGCCGCAAAACTGTTAAGAAAATGATGCTGTTTTTAA
* * * *
5610545 TTTAGGTTTTAGAGTCTTTAGTGGCGCTTGTCTAAAAATGCCGCAAAAT
65 TTTAGGTTTTAGAGACTTTAGTGGCGCTT-TCTAAAAACGCCGCATAGT
* * * *
5610594 -ATAGGAATTAGCGGCGATTTCTGAAAAGCGCCGCAAA
1 CA-A-GAATTAGCGGCGCTTTATCACAAGCGCCGCAAA
5610631 GGAGTTAAGC
Statistics
Matches: 207, Mismatches: 47, Indels: 21
0.75 0.17 0.08
Matches are distributed among these distances:
112 1 0.00
113 6 0.03
114 169 0.82
115 27 0.13
116 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (112 bp):
CAAGAATTAGCGGCGCTTTATCACAAGCGCCGCAAAACTGTTAAGAAAATGATGCTGTTTTTAAT
TTAGGTTTTAGAGACTTTAGTGGCGCTTTCTAAAAACGCCGCATAGT
Found at i:5611199 original size:21 final size:21
Alignment explanation
Indices: 5611177--5611247 Score: 106
Period size: 21 Copynumber: 3.3 Consensus size: 21
5611167 TCAGGGTTTA
*
5611177 GGGTTTAAGGGATATGGGTTAG
1 GGGTTT-ATGGATATGGGTTAG
5611199 GGGTTTATGGATATGGGTTAG
1 GGGTTTATGGATATGGGTTAG
* *
5611220 GGGTTTATGGATATGGTTTAA
1 GGGTTTATGGATATGGGTTAG
5611241 GGGTTTA
1 GGGTTTA
5611248 GGGGTGAAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 40 0.87
22 6 0.13
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (21 bp):
GGGTTTATGGATATGGGTTAG
Found at i:5611304 original size:8 final size:7
Alignment explanation
Indices: 5611240--5611302 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
5611230 ATATGGTTTA
*
5611240 AGGGTTT
1 AGGGGTT
*
5611247 AGGGGTG
1 AGGGGTT
*
5611254 AAGGGTT
1 AGGGGTT
* *
5611261 AAGGGCT
1 AGGGGTT
5611268 -GGGGTT
1 AGGGGTT
5611274 AGGGGTT
1 AGGGGTT
*
5611281 AGGAGTT
1 AGGGGTT
5611288 AGGGGTTT
1 AGGGG-TT
5611296 AGGGGTT
1 AGGGGTT
5611303 TATAGTTAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
6 4 0.09
7 34 0.76
8 7 0.16
ACGTcount: A:0.17, C:0.02, G:0.52, T:0.29
Consensus pattern (7 bp):
AGGGGTT
Found at i:5613229 original size:27 final size:29
Alignment explanation
Indices: 5613175--5613230 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
5613165 ATTTAATTTA
* *
5613175 TATTAAGTTGATTGTTACTTTATCAATTAT
1 TATTAAGTTGATTGTTA-GTGATCAATTAT
5613205 TATTAAGTTGATTGTT-GTGAT-AATTA
1 TATTAAGTTGATTGTTAGTGATCAATTA
5613231 AAATTGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 3 0.12
30 16 0.67
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (29 bp):
TATTAAGTTGATTGTTAGTGATCAATTAT
Found at i:5614145 original size:21 final size:22
Alignment explanation
Indices: 5614121--5614162 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5614111 AAATTTAAAA
* *
5614121 ATTTATTTTTTTTAAA-ATATG
1 ATTTATATATTTTAAATATATG
5614142 ATTTATATATTTTAAATATAT
1 ATTTATATATTTTAAATATAT
5614163 TTTAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTATATATTTTAAATATATG
Found at i:5614414 original size:40 final size:40
Alignment explanation
Indices: 5614357--5614433 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
5614347 TATATTTTTA
5614357 AAAATTGATACAATACATAACTTGCATAACCTACATACAT
1 AAAATTGATACAATACATAACTTGCATAACCTACATACAT
*
5614397 AAAATTGATACATTACATAACTTGCATAACCTACATA
1 AAAATTGATACAATACATAACTTGCATAACCTACATA
5614434 AAATTAAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.29
Consensus pattern (40 bp):
AAAATTGATACAATACATAACTTGCATAACCTACATACAT
Found at i:5614454 original size:20 final size:20
Alignment explanation
Indices: 5614431--5614469 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5614421 CATAACCTAC
5614431 ATAAAATTAAGATAACTTAT
1 ATAAAATTAAGATAACTTAT
*
5614451 ATAATATTAAGATAACTTA
1 ATAAAATTAAGATAACTTA
5614470 CATTCTACAG
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:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
ATAAAATTAAGATAACTTAT
Found at i:5614496 original size:25 final size:25
Alignment explanation
Indices: 5614475--5614540 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
5614465 ACTTACATTC
5614475 TACAGAACTTACATAACATACATAA
1 TACAGAACTTACATAACATACATAA
*
5614500 TACATAACTTACATAAC-TAACATAA
1 TACAGAACTTACATAACAT-ACATAA
* *
5614525 TACATAGCTTACATAA
1 TACAGAACTTACATAA
5614541 TACTCAACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 1 0.03
25 37 0.97
ACGTcount: A:0.50, C:0.20, G:0.03, T:0.27
Consensus pattern (25 bp):
TACAGAACTTACATAACATACATAA
Found at i:5614551 original size:16 final size:16
Alignment explanation
Indices: 5614462--5614552 Score: 71
Period size: 16 Copynumber: 5.6 Consensus size: 16
5614452 TAATATTAAG
**
5614462 ATAACTTACATTCTAC
1 ATAACTTACATAATAC
*
5614478 AGAACTTACATAACATAC
1 ATAACTTACAT-A-ATAC
5614496 ATAA--TACATAACTTAC
1 ATAACTTACATAA--TAC
*
5614512 ATAACTAACATAATAC
1 ATAACTTACATAATAC
*
5614528 ATAGCTTACATAATAC
1 ATAACTTACATAATAC
5614544 -TCAACTTAC
1 AT-AACTTAC
5614553 TTAGCTTACA
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
14 1 0.02
15 2 0.03
16 45 0.75
18 12 0.20
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (16 bp):
ATAACTTACATAATAC
Found at i:5614551 original size:66 final size:66
Alignment explanation
Indices: 5614466--5614662 Score: 227
Period size: 66 Copynumber: 3.0 Consensus size: 66
5614456 ATTAAGATAA
** * * * * *
5614466 CTTACATTCTACAGAACTTACATAACATACATAATACATAACTTACAT-AACTAACATA-ATACA
1 CTTACATAATACACAACTTACATAGCTTACATAATAAATAACTTACATAAAAT-ACA-ACATACA
5614529 TAG
64 TAG
* * *
5614532 CTTACATAATACTCAACTTACTTAGCTTACATAATAAATAACTTACATAAAATACAACTTACATA
1 CTTACATAATACACAACTTACATAGCTTACATAATAAATAACTTACATAAAATACAACATACATA
5614597 G
66 G
** * * *
5614598 CTTACATTCTACACAATTTACGTAGCTTACATAATAAATAACTTACATAAAATACAACTTACATA
1 CTTACATAATACACAACTTACATAGCTTACATAATAAATAACTTACATAAAATACAACATACATA
5614663 AAAAAATGAA
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
65 1 0.01
66 110 0.96
67 3 0.03
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (66 bp):
CTTACATAATACACAACTTACATAGCTTACATAATAAATAACTTACATAAAATACAACATACATA
G
Found at i:5614574 original size:25 final size:25
Alignment explanation
Indices: 5614500--5614580 Score: 87
Period size: 25 Copynumber: 3.2 Consensus size: 25
5614490 ACATACATAA
*
5614500 TACATAACTTACATAACTAACATAA--
1 TACATAGCTTACATAA-TAA-ATAACT
*
5614525 TACATAGCTTACATAAT-ACTCAACT
1 TACATAGCTTACATAATAAAT-AACT
*
5614550 TACTTAGCTTACATAATAAATAACT
1 TACATAGCTTACATAATAAATAACT
5614575 TACATA
1 TACATA
5614581 AAATACAACT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
22 1 0.02
23 3 0.06
24 1 0.02
25 40 0.85
26 2 0.04
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (25 bp):
TACATAGCTTACATAATAAATAACT
Found at i:5614578 original size:16 final size:16
Alignment explanation
Indices: 5614557--5614665 Score: 62
Period size: 16 Copynumber: 6.7 Consensus size: 16
5614547 ACTTACTTAG
*
5614557 CTTACATAATAA-ATAA
1 CTTACATAA-AATACAA
5614573 CTTACATAAAATACAA
1 CTTACATAAAATACAA
***
5614589 CTTACATAGCTTAC-A
1 CTTACATAAAATACAA
* * ** *
5614604 TTCTACACAATTTACGTAG
1 CT-TACATAAAATAC--AA
*
5614623 CTTACATAATAA-ATAA
1 CTTACATAA-AATACAA
5614639 CTTACATAAAATACAA
1 CTTACATAAAATACAA
5614655 CTTACATAAAA
1 CTTACATAAAA
5614666 AAATGAACAA
Statistics
Matches: 70, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
15 6 0.09
16 56 0.80
18 7 0.10
19 1 0.01
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.30
Consensus pattern (16 bp):
CTTACATAAAATACAA
Found at i:5614599 original size:41 final size:41
Alignment explanation
Indices: 5614487--5614604 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 41
5614477 CAGAACTTAC
* * * * * * *
5614487 ATAACATACATAATACATAACTTACATAACTAACATAATAC
1 ATAACTTACATAAAATACAACTTACATAGCTTACATAATAA
* * *
5614528 ATAGCTTACATAATACT-CAACTTACTTAGCTTACATAATAA
1 ATAACTTACATAA-AATACAACTTACATAGCTTACATAATAA
5614569 ATAACTTACATAAAATACAACTTACATAGCTTACAT
1 ATAACTTACATAAAATACAACTTACATAGCTTACAT
5614605 TCTACACAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
40 2 0.03
41 60 0.97
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (41 bp):
ATAACTTACATAAAATACAACTTACATAGCTTACATAATAA
Found at i:5614601 original size:25 final size:24
Alignment explanation
Indices: 5614573--5614646 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 24
5614563 TAATAAATAA
5614573 CTTACATAAAATACAACTTACATAG
1 CTTACATAAAA-ACAACTTACATAG
** * * *
5614598 CTTACATTCTACACAATTTACGTAG
1 CTTACA-TAAAAACAACTTACATAG
*
5614623 CTTACATAATAAATAACTTACATA
1 CTTACATAA-AAACAACTTACATA
5614647 AAATACAACT
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
24 1 0.03
25 33 0.92
26 2 0.06
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.32
Consensus pattern (24 bp):
CTTACATAAAAACAACTTACATAG
Found at i:5620121 original size:21 final size:20
Alignment explanation
Indices: 5620095--5620162 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 20
5620085 CTACAACTTA
*
5620095 AAGCAGAGACGGCAGCGAGGG
1 AAGCAGAG-CTGCAGCGAGGG
*
5620116 AAGCAGCAGTTGCAGCGAGGG
1 AAGCAG-AGCTGCAGCGAGGG
*
5620137 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGA-GCTGCAGCGAGGG
5620158 AAGCA
1 AAGCA
5620163 AAGCAGAGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.02
21 38 0.93
22 2 0.05
ACGTcount: A:0.34, C:0.19, G:0.43, T:0.04
Consensus pattern (20 bp):
AAGCAGAGCTGCAGCGAGGG
Found at i:5622135 original size:22 final size:23
Alignment explanation
Indices: 5622101--5622144 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
5622091 GTGATGAGGT
**
5622101 TATCTTATGAATACGTT-AAATC
1 TATCTTAAAAATACGTTGAAATC
*
5622123 TATCTTAAAAATATGTTGAAAT
1 TATCTTAAAAATACGTTGAAAT
5622145 GGATTGGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (23 bp):
TATCTTAAAAATACGTTGAAATC
Found at i:5622724 original size:157 final size:156
Alignment explanation
Indices: 5622425--5622724 Score: 433
Period size: 157 Copynumber: 1.9 Consensus size: 156
5622415 GTCCAGCTGG
* * * * *
5622425 GAGCTTTTTTAGTATTTTTGTTGACAGTGCATCCTACTTGAAGCGTTTTTCAACCCCAACTATCA
1 GAGCTTTTTTAGTACTTTTGCTGACAGTACATCCTACTTGAAACATTTTTCAACCCCAACTATCA
* * *
5622490 GATTTCCCGTGAATCCCAGGATTTTTTTTTTCAAAAACATCTTCTCAAAAATATTTTTCAAAATC
66 GATTTCCCGTGAATCCCAAGA-TTATTTTTTCAAAAACATCTTCACAAAAATATTTTTCAAAATC
5622555 AACAGTACAAAAAAAACGTCTAGGTGA
130 AACAGTACAAAAAAAACGTCTAGGTGA
*
5622582 GAGCTTTTTTAGTACTTTTGCTGACAGTACATCCTACTTGAAACATTTTTCAACCCCAATTATCA
1 GAGCTTTTTTAGTACTTTTGCTGACAGTACATCCTACTTGAAACATTTTTCAACCCCAACTATCA
* * * * *
5622647 GATTTCCCAG-GAATCCCAAGA-TATTTTTTCGAAACCATCTTCACAAAATTATATTTTCAGATT
66 GATTTCCC-GTGAATCCCAAGATTATTTTTTCAAAAACATCTTCACAAAAATAT-TTTTCAAAAT
5622710 CAACAGTACAAAAAA
129 CAACAGTACAAAAAA
5622725 GTCCAATTGG
Statistics
Matches: 127, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
155 26 0.20
156 23 0.18
157 77 0.61
158 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (156 bp):
GAGCTTTTTTAGTACTTTTGCTGACAGTACATCCTACTTGAAACATTTTTCAACCCCAACTATCA
GATTTCCCGTGAATCCCAAGATTATTTTTTCAAAAACATCTTCACAAAAATATTTTTCAAAATCA
ACAGTACAAAAAAAACGTCTAGGTGA
Found at i:5622954 original size:27 final size:28
Alignment explanation
Indices: 5622898--5622959 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
5622888 TAAACCATAG
* *
5622898 ACCCTAAACCTTAATTTATTTTTTAAAA
1 ACCCTAAACCCTAATTTATTTTTCAAAA
*
5622926 ACCCTAAACCCTAATTT-TTTTTCCAAA
1 ACCCTAAACCCTAATTTATTTTTCAAAA
5622953 ACCCTAA
1 ACCCTAA
5622960 GCACTAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (28 bp):
ACCCTAAACCCTAATTTATTTTTCAAAA
Found at i:5622966 original size:27 final size:28
Alignment explanation
Indices: 5622898--5622967 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
5622888 TAAACCATAG
*
5622898 ACCCTAAAC-CTTAATTTATTTTTTAAAA
1 ACCCTAAACAC-TAATTTATTTTTCAAAA
* *
5622926 ACCCTAAACCCTAATTT-TTTTTCCAAA
1 ACCCTAAACACTAATTTATTTTTCAAAA
*
5622953 ACCCTAAGCACTAAT
1 ACCCTAAACACTAAT
5622968 ATGCAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 21 0.57
28 15 0.41
29 1 0.03
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (28 bp):
ACCCTAAACACTAATTTATTTTTCAAAA
Found at i:5624678 original size:31 final size:32
Alignment explanation
Indices: 5624641--5624720 Score: 96
Period size: 30 Copynumber: 2.6 Consensus size: 32
5624631 TTAAATTTTG
*
5624641 AAAAAAATATAAAAACTAAAATTCAAA-AAAT
1 AAAAAAATATAAAAATTAAAATTCAAACAAAT
* *
5624672 AAAAAAATA-AAAAATTTAAATTTAAACAAAT
1 AAAAAAATATAAAAATTAAAATTCAAACAAAT
*
5624703 --TAAAATATAAAAATTAAA
1 AAAAAAATATAAAAATTAAA
5624721 TTAACAGAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 6 0.14
30 23 0.55
31 13 0.31
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (32 bp):
AAAAAAATATAAAAATTAAAATTCAAACAAAT
Found at i:5624702 original size:16 final size:15
Alignment explanation
Indices: 5624644--5624720 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
5624634 AATTTTGAAA
*
5624644 AAAATAT-AAAAACT
1 AAAATATAAAAAATT
*
5624658 AAAAT-TCAAAAAATA
1 AAAATAT-AAAAAATT
*
5624673 AAAAAATAAAAAATT
1 AAAATATAAAAAATT
* *
5624688 TAAATTTAAACAAATT
1 AAAATATAAA-AAATT
5624704 AAAATAT-AAAAATT
1 AAAATATAAAAAATT
5624718 AAA
1 AAA
5624721 TTAACAGAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
13 1 0.02
14 13 0.26
15 25 0.50
16 11 0.22
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATATAAAAAATT
Found at i:5627418 original size:30 final size:31
Alignment explanation
Indices: 5627370--5627428 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
5627360 TGCTTATAAT
* *
5627370 ATAATTTTTATAACTTAAA-CTTGTATGAAA
1 ATAATTTTTATAAATTAAATCATGTATGAAA
5627400 ATAATTTTT-TAAAATTAAATCATGTATGA
1 ATAATTTTTAT-AAATTAAATCATGTATGA
5627429 GTGTCTAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 16 0.64
31 8 0.32
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (31 bp):
ATAATTTTTATAAATTAAATCATGTATGAAA
Found at i:5629618 original size:4 final size:4
Alignment explanation
Indices: 5629609--5629643 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
5629599 AAGAAAAGAA
*
5629609 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TTTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
5629644 CACATGTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TCTT
Found at i:5643213 original size:40 final size:40
Alignment explanation
Indices: 5643169--5643312 Score: 164
Period size: 40 Copynumber: 3.6 Consensus size: 40
5643159 GATGCAGAAC
5643169 AGGGGCACGTATGTGCATTCAGGGGTACCAAAGTACAAAT
1 AGGGGCACGTATGTGCATTCAGGGGTACCAAAGTACAAAT
* * * *
5643209 AGGGGTATGTATGTGCATTTAGGGATA-CAGAAGTACAAAT
1 AGGGGCACGTATGTGCATTCAGGGGTACCA-AAGTACAAAT
* * * * * *
5643249 AGGGGCACGCATTTGCATTTAGGGGTACCGAAGTATAAAC
1 AGGGGCACGTATGTGCATTCAGGGGTACCAAAGTACAAAT
* *
5643289 AGGAGCACATATGTGCATTCAGGG
1 AGGGGCACGTATGTGCATTCAGGG
5643313 ACATTTTCCT
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 2 0.02
40 82 0.96
41 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.23
Consensus pattern (40 bp):
AGGGGCACGTATGTGCATTCAGGGGTACCAAAGTACAAAT
Found at i:5652672 original size:21 final size:21
Alignment explanation
Indices: 5652646--5652699 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
5652636 ACAGCGGTGG
*
5652646 CGGTGAGATTAGTTACTGTAA
1 CGGTGAGATTAGGTACTGTAA
* *
5652667 CGGTGAGATTGGGTACTGTAG
1 CGGTGAGATTAGGTACTGTAA
5652688 CGGTGAGATTAG
1 CGGTGAGATTAG
5652700 AAACAATGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.09, G:0.37, T:0.30
Consensus pattern (21 bp):
CGGTGAGATTAGGTACTGTAA
Found at i:5659275 original size:12 final size:12
Alignment explanation
Indices: 5659258--5659282 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5659248 TTGCAGGAGA
5659258 TGTTTTCTTATT
1 TGTTTTCTTATT
5659270 TGTTTTCTTATT
1 TGTTTTCTTATT
5659282 T
1 T
5659283 TATCAGGTCT
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:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (12 bp):
TGTTTTCTTATT
Found at i:5659626 original size:11 final size:11
Alignment explanation
Indices: 5659610--5659635 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5659600 TTCTTAGCTA
5659610 AGAACAAGATG
1 AGAACAAGATG
5659621 AGAACAAGATG
1 AGAACAAGATG
5659632 AGAA
1 AGAA
5659636 GGAAAAACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.08, G:0.27, T:0.08
Consensus pattern (11 bp):
AGAACAAGATG
Found at i:5668477 original size:20 final size:20
Alignment explanation
Indices: 5668452--5668491 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5668442 CATGACGGAA
5668452 GCAGC-AACAGAAACAGAAAC
1 GCAGCAAACAGAAACA-AAAC
*
5668472 GCAGCAAACAGTAACAAAAC
1 GCAGCAAACAGAAACAAAAC
5668492 AACAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.25, G:0.17, T:0.03
Consensus pattern (20 bp):
GCAGCAAACAGAAACAAAAC
Found at i:5669515 original size:9 final size:10
Alignment explanation
Indices: 5669499--5669545 Score: 51
Period size: 9 Copynumber: 4.5 Consensus size: 10
5669489 TATATAGGAG
5669499 TATATATTTT
1 TATATATTTT
5669509 T-TATATTTT
1 TATATATTTT
5669518 TATATATTTAT
1 TATATATTT-T
*
5669529 ATACATACTTTT
1 -TATATA-TTTT
5669541 TATAT
1 TATAT
5669546 TTTATGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 9 0.29
10 8 0.26
11 5 0.16
12 6 0.19
13 3 0.10
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (10 bp):
TATATATTTT
Found at i:5670253 original size:109 final size:109
Alignment explanation
Indices: 5670056--5670263 Score: 355
Period size: 109 Copynumber: 1.9 Consensus size: 109
5670046 AAATGTTTCC
5670056 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* *
5670121 CTCGTTCGACCAAATAGCTAAATATCCTTTTGAAAACTTTTCAA
66 CTCGTTCAACCAAATAGCTAAATATCCTATTGAAAACTTTTCAA
*
5670165 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* *
5670230 CTCGTTTAACCAAATTG-TCAAATATCCTATTGAA
66 CTCGTTCAACCAAATAGCT-AAATATCCTATTGAA
5670264 TTTAAACTCA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 1 0.01
109 92 0.99
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (109 bp):
AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
CTCGTTCAACCAAATAGCTAAATATCCTATTGAAAACTTTTCAA
Found at i:5674460 original size:21 final size:19
Alignment explanation
Indices: 5674435--5674480 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
5674425 AAAGACAAGA
5674435 TATGAAAGATAATAATTTAAC
1 TATGAAA-AT-ATAATTTAAC
*
5674456 TATG-AAATTTAATTTAAC
1 TATGAAAATATAATTTAAC
5674474 TATGAAA
1 TATGAAA
5674481 TTTTATTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 13 0.57
19 4 0.17
20 2 0.09
21 4 0.17
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (19 bp):
TATGAAAATATAATTTAAC
Found at i:5674470 original size:18 final size:18
Alignment explanation
Indices: 5674447--5674483 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5674437 TGAAAGATAA
5674447 TAATTTAACTATGAAATT
1 TAATTTAACTATGAAATT
5674465 TAATTTAACTATGAAATT
1 TAATTTAACTATGAAATT
5674483 T
1 T
5674484 TATTAACCAA
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:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
TAATTTAACTATGAAATT
Found at i:5679574 original size:26 final size:26
Alignment explanation
Indices: 5679506--5679562 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
5679496 CCTCAATTTT
*
5679506 TTTTAAAAATAAATTAAATTATTAATC
1 TTTTAAAAA-GAATTAAATTATTAATC
5679533 TTTTAAAAAGAATTAAATTATT-AT-
1 TTTTAAAAAGAATTAAATTATTAATC
5679557 TTTTAA
1 TTTTAA
5679563 CGAAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 6 0.21
25 2 0.07
26 12 0.41
27 9 0.31
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
TTTTAAAAAGAATTAAATTATTAATC
Found at i:5682389 original size:51 final size:51
Alignment explanation
Indices: 5682325--5682664 Score: 343
Period size: 51 Copynumber: 6.7 Consensus size: 51
5682315 TATCGATGAA
* * * *
5682325 CACGTGTGTAGTACTGTGTGAAGGCTACTGCGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
* ** * * * * * *
5682376 CACATGTGTAGTACTAACTGAAGGCTACTATGTATACCAAGAAGTTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
* **
5682427 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGA-TGAA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATTGGT
* * *
5682478 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TATTGGT
* * *
5682529 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAA-ATTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA-TTGGT
* * * *
5682579 CACGCGTGTAGTACTATGTGAAGGCTACTACATGAACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA-TTGGT
*
5682629 CACGTGTGTAGTACTATGTGAAGACTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
5682665 TCGAATGATA
Statistics
Matches: 239, Mismatches: 43, Indels: 15
0.80 0.14 0.05
Matches are distributed among these distances:
50 85 0.36
51 153 0.64
52 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
Found at i:5682501 original size:102 final size:100
Alignment explanation
Indices: 5682325--5682664 Score: 411
Period size: 102 Copynumber: 3.4 Consensus size: 100
5682315 TATCGATGAA
* * * *
5682325 CACGTGTGTAGTACTGTGTGAAGGCTACTGCGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGATCACATGTGTAGTAC
*
5682390 TAACTGAAGGCTACTATGTATACC-AAGAAGTTTTGGT
65 TAAGTGAAGGCTACTATGTATACCGAA-AAG-TTTGGT
* *
5682427 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGATGAACACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGATCACATGTGTAGTAC
*
5682492 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
65 TAAGTGAAGGCTACTATGTATACCGAAAAG-TTTGGT
* * * **
5682529 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAAATTTGATCACGCGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAT-AAATATGATCACATGTGTAGTAC
* * *
5682593 TATGTGAAGGCTACTACATG-A-ACCGTAAAA-CTTGAT
65 TAAGTGAAGGCTACT--ATGTATACCG-AAAAGTTTGGT
*
5682629 CACGTGTGTAGTACTATGTGAAGACTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
5682665 TCGAATGATA
Statistics
Matches: 211, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
100 37 0.18
101 34 0.16
102 135 0.64
103 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (100 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATGATCACATGTGTAGTACT
AAGTGAAGGCTACTATGTATACCGAAAAGTTTGGT
Found at i:5686524 original size:16 final size:16
Alignment explanation
Indices: 5686483--5686530 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
5686473 ATTCAATTTC
5686483 ATAATCTCAATTCA-A
1 ATAATCTCAATTCACA
5686498 ATAATCATCAATTCACA
1 ATAATC-TCAATTCACA
** *
5686515 ATCTTCTCAAATCACA
1 ATAATCTCAATTCACA
5686531 TAAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.21
16 17 0.61
17 5 0.18
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAATCTCAATTCACA
Found at i:5704748 original size:27 final size:27
Alignment explanation
Indices: 5704710--5704763 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5704700 ATTTCTAAAA
5704710 AGCCCTTATGTTATTATTGAAGGGATT
1 AGCCCTTATGTTATTATTGAAGGGATT
5704737 AGCCCTTATGTTATTATTGAAGGGATT
1 AGCCCTTATGTTATTATTGAAGGGATT
5704764 TATGTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (27 bp):
AGCCCTTATGTTATTATTGAAGGGATT
Found at i:5705424 original size:30 final size:30
Alignment explanation
Indices: 5705383--5705444 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
5705373 CCGAATTAGG
* * *
5705383 TATGAGTATAAACTGTATAAGTAAGCATGT
1 TATGAGGATAAACTCTATAAATAAGCATGT
*
5705413 TATGAGGATAAACTCTATAAATAGGCATGT
1 TATGAGGATAAACTCTATAAATAAGCATGT
5705443 TA
1 TA
5705445 AGTCTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.32
Consensus pattern (30 bp):
TATGAGGATAAACTCTATAAATAAGCATGT
Found at i:5706142 original size:16 final size:16
Alignment explanation
Indices: 5706123--5706154 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5706113 TATTTGGTTT
*
5706123 ATTTTTAGTTTAATTA
1 ATTTTTAGGTTAATTA
5706139 ATTTTTAGGTTAATTA
1 ATTTTTAGGTTAATTA
5706155 GGTTAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
ATTTTTAGGTTAATTA
Found at i:5706601 original size:22 final size:22
Alignment explanation
Indices: 5706576--5706620 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
5706566 TGATTCAGTG
5706576 TATGACTCGAAGTGGAATTCTT
1 TATGACTCGAAGTGGAATTCTT
*
5706598 TATGACTCGGAGTGGAATTCTT
1 TATGACTCGAAGTGGAATTCTT
5706620 T
1 T
5706621 CTATCGAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.38
Consensus pattern (22 bp):
TATGACTCGAAGTGGAATTCTT
Found at i:5710276 original size:25 final size:25
Alignment explanation
Indices: 5710242--5710294 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
5710232 ACACTCCATA
5710242 CTATGTTTCTGATGCATTGGACGTG
1 CTATGTTTCTGATGCATTGGACGTG
5710267 CTATGTTTCTGATGCATTGGACGTG
1 CTATGTTTCTGATGCATTGGACGTG
5710292 CTA
1 CTA
5710295 GATATTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (25 bp):
CTATGTTTCTGATGCATTGGACGTG
Found at i:5714150 original size:16 final size:16
Alignment explanation
Indices: 5714129--5714160 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5714119 TAATTGGTTG
*
5714129 ATTTTTAGTTTAATTA
1 ATTTTTAGATTAATTA
5714145 ATTTTTAGATTAATTA
1 ATTTTTAGATTAATTA
5714161 GATTAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTTTTAGATTAATTA
Found at i:5715027 original size:13 final size:12
Alignment explanation
Indices: 5714989--5715031 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
5714979 TACGTTCCTC
5714989 TTTTTTTTCTT-
1 TTTTTTTTCTTA
5715000 TTCTTTTTTCATTA
1 TT-TTTTTTC-TTA
5715014 TATTTTTTTCTTA
1 T-TTTTTTTCTTA
5715027 TTTTT
1 TTTTT
5715032 ATCTTCTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 2 0.07
12 11 0.39
13 6 0.21
14 8 0.29
15 1 0.04
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTTCTTA
Found at i:5717280 original size:15 final size:15
Alignment explanation
Indices: 5717260--5717288 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5717250 ATTTCACACC
5717260 TCTTCTGTTGCAATG
1 TCTTCTGTTGCAATG
5717275 TCTTCTGTTGCAAT
1 TCTTCTGTTGCAAT
5717289 CAAAAACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (15 bp):
TCTTCTGTTGCAATG
Found at i:5726539 original size:44 final size:44
Alignment explanation
Indices: 5726451--5726565 Score: 153
Period size: 44 Copynumber: 2.6 Consensus size: 44
5726441 ACTAGTATGG
** *
5726451 GAAGACAAGATCTGCTTATTTTTGATCTACTTCATGCCAGTACAT
1 GAAGACAAGATCTGCTT-TTTCCGATCTACTTCATGCCAATACAT
*
5726496 GAAGACAAGATCTG-TTTTCTCCGATCTACTTCACT-TCAATACAT
1 GAAGACAAGATCTGCTTTT-TCCGATCTACTTCA-TGCCAATACAT
5726540 GAAGACAAGATCTGCTTTTTCCGATC
1 GAAGACAAGATCTGCTTTTTCCGATC
5726566 GATTCCACTG
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
43 2 0.03
44 42 0.67
45 19 0.30
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (44 bp):
GAAGACAAGATCTGCTTTTTCCGATCTACTTCATGCCAATACAT
Found at i:5729051 original size:49 final size:49
Alignment explanation
Indices: 5728938--5729175 Score: 266
Period size: 49 Copynumber: 4.8 Consensus size: 49
5728928 ACCGAAAAAA
* * *
5728938 ATGAATGCAACAAAAACAAACAATGAAGCATAATTAGAAACACCACTTTATTT
1 ATGAATGCAAC-AAAACAATCAATGAAACATAAATA-AAACA--ACTTTATTT
* * *
5728991 ATGAATACAACAAAACAATGAATGAAGCATAAATAAAACAACTTTATTT
1 ATGAATGCAACAAAACAATCAATGAAACATAAATAAAACAACTTTATTT
* *
5729040 ATGAATGCAACAAAACAATCAATGAAATATAAATAAAACAATTTTATTT
1 ATGAATGCAACAAAACAATCAATGAAACATAAATAAAACAACTTTATTT
* * * *
5729089 ATGAATGCAAC-AATCAATGAA-GCATAA-GTAAAGAAAACACAACTTTATTT
1 ATGAATGCAACAAAACAATCAATG-A-AACATAAA-TAAA-ACAACTTTATTT
*
5729139 ATGAATGCAACAAAACATTCAATGAAACATAAATAAA
1 ATGAATGCAACAAAACAATCAATGAAACATAAATAAA
5729176 TAAATAAAAA
Statistics
Matches: 159, Mismatches: 19, Indels: 17
0.82 0.10 0.09
Matches are distributed among these distances:
47 1 0.01
48 13 0.08
49 69 0.43
50 27 0.17
51 17 0.11
52 22 0.14
53 10 0.06
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (49 bp):
ATGAATGCAACAAAACAATCAATGAAACATAAATAAAACAACTTTATTT
Found at i:5729146 original size:99 final size:99
Alignment explanation
Indices: 5728938--5729175 Score: 293
Period size: 99 Copynumber: 2.4 Consensus size: 99
5728928 ACCGAAAAAA
* * *
5728938 ATGAATGCAACAAAAACAAACAATGAAGCATAATTAGAAACACCACTTTATTTATGAATACAACA
1 ATGAATGCAAC-AAAACAATCAATGAAACATAAATA-AAACA-CACTTTATTTATGAATACAACA
* *
5729003 AAACAATGAATGAAGCATAAATAAAACAACTTTATTT
63 AAACAATGAATGAAGAATAAAAAAAACAACTTTATTT
* * * *
5729040 ATGAATGCAACAAAACAATCAATGAAATATAAATAAAACA-ATTTTATTTATGAATGCAAC-AAT
1 ATGAATGCAACAAAACAATCAATGAAACATAAATAAAACACACTTTATTTATGAATACAACAAAA
* *
5729103 CAATGAA-GCATAAGTAAAGAAAACACAACTTTATTT
66 CAATGAATGAAGAA-TAAA-AAAA-ACAACTTTATTT
*
5729139 ATGAATGCAACAAAACATTCAATGAAACATAAATAAA
1 ATGAATGCAACAAAACAATCAATGAAACATAAATAAA
5729176 TAAATAAAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
96 3 0.03
97 13 0.11
98 21 0.17
99 47 0.39
100 5 0.04
101 20 0.17
102 11 0.09
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (99 bp):
ATGAATGCAACAAAACAATCAATGAAACATAAATAAAACACACTTTATTTATGAATACAACAAAA
CAATGAATGAAGAATAAAAAAAACAACTTTATTT
Found at i:5729188 original size:55 final size:50
Alignment explanation
Indices: 5729068--5729203 Score: 148
Period size: 55 Copynumber: 2.6 Consensus size: 50
5729058 TCAATGAAAT
* * *
5729068 ATAAATAAAACAATTTTATTTATGAATGCAACAATCAATGAAGCATAAGTAA
1 ATAAAT-AAA-AACTTTATTTATGAATGCAACAATCAATGAAACATAAATAA
* *
5729120 AGAAA-ACACAACTTTATTTATGAATGCAACAAAACATTCAATGAAACATAAATAA
1 ATAAATA-AAAACTTTATTTATGAATGCAAC---A-A-TCAATGAAACATAAATAA
5729175 ATAAATAAAAACTTTATTTATGAATGCAA
1 ATAAATAAAAACTTTATTTATGAATGCAA
5729204 ATTTGCTTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
50 21 0.30
51 1 0.01
52 4 0.06
53 1 0.01
54 1 0.01
55 41 0.59
56 1 0.01
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.28
Consensus pattern (50 bp):
ATAAATAAAAACTTTATTTATGAATGCAACAATCAATGAAACATAAATAA
Found at i:5730816 original size:31 final size:33
Alignment explanation
Indices: 5730745--5730818 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
5730735 CAGTTTTTTT
* *
5730745 TTTTACTACTTTCTTGCTTTTTTTTTTATCGTT
1 TTTTGCTACTTTCTTGCTTTTTTTTTTATCGTA
*
5730778 TTGTTGCTATTTTCTTG-TTTTTTTTTTCA-C-TA
1 TT-TTGCTACTTTCTTGCTTTTTTTTTT-ATCGTA
5730810 TTTTGCTAC
1 TTTTGCTAC
5730819 CATTTCACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
31 6 0.17
32 3 0.09
33 13 0.37
34 13 0.37
ACGTcount: A:0.09, C:0.15, G:0.08, T:0.68
Consensus pattern (33 bp):
TTTTGCTACTTTCTTGCTTTTTTTTTTATCGTA
Found at i:5759103 original size:2 final size:2
Alignment explanation
Indices: 5759096--5759130 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5759086 TAAGCTAAGT
5759096 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5759131 TCTCGAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5764664 original size:72 final size:72
Alignment explanation
Indices: 5764547--5764694 Score: 296
Period size: 72 Copynumber: 2.1 Consensus size: 72
5764537 AGGCTGATAA
5764547 AAGTCTCACCTTGAGTTCGGGAGATGCCGGATGCCACTCCGGTGGACCAAACTCAGTAAGAAGTC
1 AAGTCTCACCTTGAGTTCGGGAGATGCCGGATGCCACTCCGGTGGACCAAACTCAGTAAGAAGTC
5764612 CCATAGC
66 CCATAGC
5764619 AAGTCTCACCTTGAGTTCGGGAGATGCCGGATGCCACTCCGGTGGACCAAACTCAGTAAGAAGTC
1 AAGTCTCACCTTGAGTTCGGGAGATGCCGGATGCCACTCCGGTGGACCAAACTCAGTAAGAAGTC
5764684 CCATAGC
66 CCATAGC
5764691 AAGT
1 AAGT
5764695 GGAGATGCAC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.20
Consensus pattern (72 bp):
AAGTCTCACCTTGAGTTCGGGAGATGCCGGATGCCACTCCGGTGGACCAAACTCAGTAAGAAGTC
CCATAGC
Found at i:5766304 original size:27 final size:28
Alignment explanation
Indices: 5766274--5766334 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
5766264 ATATACTTTT
*
5766274 ATATATTTTAA-ATAAATTTTA-ATAGAA
1 ATATATTTTAATATAAATATTACATA-AA
*
5766301 ATATA-CTTAATATAAATATTACATAAA
1 ATATATTTTAATATAAATATTACATAAA
5766328 ATATATT
1 ATATATT
5766335 AAAGTATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 21 0.75
28 3 0.11
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (28 bp):
ATATATTTTAATATAAATATTACATAAA
Found at i:5766345 original size:28 final size:27
Alignment explanation
Indices: 5766281--5766346 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
5766271 TTTATATATT
*
5766281 TTAA-ATAAATTTTAATAGAAATATAC
1 TTAATATAAATATTAATAGAAATATAC
5766307 TTAATATAAATATTACATA-AAATATA-
1 TTAATATAAATATTA-ATAGAAATATAC
5766333 TTAAAGTATAAATA
1 TT-AA-TATAAATA
5766347 AGGGTTAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
26 6 0.17
27 18 0.51
28 11 0.31
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (27 bp):
TTAATATAAATATTAATAGAAATATAC
Found at i:5767415 original size:27 final size:25
Alignment explanation
Indices: 5767349--5767415 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 25
5767339 GATATTATAA
* *
5767349 AGGAAGAAGAAAGAAAAAAACAGAGAG
1 AGGAA-AA-AAAGAAAAAAAAAGAAAG
* *
5767376 AGGAAAAATAGAAAAAAAAATAAAG
1 AGGAAAAAAAGAAAAAAAAAGAAAG
5767401 AGAGAAATAAAAGAA
1 AG-GAAA-AAAAGAA
5767416 TTAATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 16 0.48
26 6 0.18
27 11 0.33
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.04
Consensus pattern (25 bp):
AGGAAAAAAAGAAAAAAAAAGAAAG
Found at i:5770736 original size:16 final size:16
Alignment explanation
Indices: 5770715--5770783 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
5770705 TTTGGTTCGC
5770715 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5770731 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5770747 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
5770764 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5770780 TGTA
1 TGTA
5770784 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:5770761 original size:33 final size:32
Alignment explanation
Indices: 5770715--5770783 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
5770705 TTTGGTTCGC
5770715 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
5770747 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
5770780 TGTA
1 TGTA
5770784 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:5770848 original size:44 final size:45
Alignment explanation
Indices: 5770764--5770854 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
5770754 GGATTAGAGG
* * *
5770764 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
5770809 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
5770853 TG
1 TG
5770855 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:5771106 original size:157 final size:157
Alignment explanation
Indices: 5770906--5771222 Score: 555
Period size: 157 Copynumber: 2.0 Consensus size: 157
5770896 TAGAATACCC
*
5770906 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * *
5770971 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAATA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAA-A
5771036 ATATATAATTTAATAAAATTCTT-ATAA
130 ATATATAATTTAATAAAATTCTTAATAA
* *
5771063 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
5771128 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
5771193 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
5771220 TTA
1 TTA
5771223 ATATTCTTAT
Statistics
Matches: 152, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
156 24 0.16
157 128 0.84
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:5771193 original size:16 final size:16
Alignment explanation
Indices: 5771156--5771197 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5771146 TTAATCATAT
*
5771156 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
5771172 TT-AAATATATTATAA
1 TTAAAATATATTATAA
5771187 TTAAAATATAT
1 TTAAAATATAT
5771198 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:5771204 original size:14 final size:15
Alignment explanation
Indices: 5771165--5771206 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5771155 TTTAAACATA
*
5771165 ATTATTATTAAATAT
1 ATTATAATTAAATAT
5771180 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5771194 A-TATAATTTAATA
1 ATTATAATTAAATA
5771207 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:5771293 original size:120 final size:121
Alignment explanation
Indices: 5771159--5771451 Score: 502
Period size: 120 Copynumber: 2.4 Consensus size: 121
5771149 ATCATATTTA
5771159 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
5771224 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA-GT-
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AAATGTG
5771279 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
5771344 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTG
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATGTG
* * *
5771400 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
5771452 TAAAATAATT
Statistics
Matches: 165, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
119 3 0.02
120 160 0.97
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATGTG
Found at i:5771324 original size:14 final size:15
Alignment explanation
Indices: 5771285--5771326 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5771275 AAGTAACATA
*
5771285 ATTATTATTAAATAT
1 ATTATAATTAAATAT
5771300 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5771314 A-TATAATTTAATA
1 ATTATAATTAAATA
5771327 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:5774996 original size:6 final size:6
Alignment explanation
Indices: 5774987--5775015 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5774977 TTGATGTTGG
5774987 GAGGGA GAGGGA GAGGGA GAGGGA GAGGG
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGG
5775016 TGGGGAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:5785491 original size:15 final size:15
Alignment explanation
Indices: 5785471--5785499 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5785461 GTATTGTTGT
5785471 TTGATAACACGGTGA
1 TTGATAACACGGTGA
5785486 TTGATAACACGGTG
1 TTGATAACACGGTG
5785500 TGTGGGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGATAACACGGTGA
Found at i:5787783 original size:20 final size:21
Alignment explanation
Indices: 5787755--5787799 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
5787745 AAAAAATCAT
5787755 TTTTAATTATTT-TCT-TTTA
1 TTTTAATTATTTCTCTCTTTA
5787774 TTTTACATTATTTCTCTCTTTA
1 TTTTA-ATTATTTCTCTCTTTA
5787796 TTTT
1 TTTT
5787800 TCTATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.22
20 7 0.30
21 3 0.13
22 8 0.35
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTAATTATTTCTCTCTTTA
Found at i:5788393 original size:13 final size:13
Alignment explanation
Indices: 5788375--5788400 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5788365 AAAATATATT
5788375 TATTTAATTAAAA
1 TATTTAATTAAAA
5788388 TATTTAATTAAAA
1 TATTTAATTAAAA
5788401 ACTTAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTTAATTAAAA
Found at i:5790037 original size:69 final size:69
Alignment explanation
Indices: 5789926--5790060 Score: 198
Period size: 69 Copynumber: 2.0 Consensus size: 69
5789916 TTGGTTTTGC
* * * * *
5789926 CTTGTGAATTTAGATTTTTCTCAATTCTGGGTTGTTGCCCTTTTAGCTTTGCGTTCTCTCATATG
1 CTTGTGAAATTAGATTTTTCTCAATTCTGGGTTGTTACCCTTTTAGCTGTGAGGTCTCTCATATG
5789991 ATTT
66 ATTT
* * *
5789995 CTTGTGAAATTAGATTTTTCTCAGTTTTGGGTTGTTACCCTTTTTGCTGTGAGGTCTCTCATATG
1 CTTGTGAAATTAGATTTTTCTCAATTCTGGGTTGTTACCCTTTTAGCTGTGAGGTCTCTCATATG
5790060 A
66 A
5790061 CTTTTTGAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (69 bp):
CTTGTGAAATTAGATTTTTCTCAATTCTGGGTTGTTACCCTTTTAGCTGTGAGGTCTCTCATATG
ATTT
Found at i:5792062 original size:29 final size:25
Alignment explanation
Indices: 5792006--5792075 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 25
5791996 TTTGAATGGT
* *
5792006 ATTTATATATATTTTATTTTTTAGA
1 ATTTATATATATTTTATTTTCTAAA
5792031 ATTTATATATATTTCCTATATATTCTAAA
1 ATTTATATATATTT--TAT-T-TTCTAAA
* *
5792060 ATTTATACATTTTTTA
1 ATTTATATATATTTTA
5792076 AAAAATGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
25 14 0.38
27 5 0.14
28 1 0.03
29 17 0.46
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (25 bp):
ATTTATATATATTTTATTTTCTAAA
Found at i:5793010 original size:123 final size:123
Alignment explanation
Indices: 5792791--5793016 Score: 355
Period size: 123 Copynumber: 1.8 Consensus size: 123
5792781 AGGAGCTTGA
** * *
5792791 GAAATCAAATAGGAAAATGGATGATACATTAGGCAATGTGAAGGAAGATTGGTCATGTAGGAAGA
1 GAAATCAAATAGGAAAATGGATGATACATTAGGCAATGCAAAGGAAGATGGGTCATGTAAGAAGA
** *
5792856 AATTGTAACGACCCGGCTTTTTTCGGTGTCGAAAAATGCGGTTTCGGAACCCCATTTC
66 AATTGTAACGACCCAACTTTTGTCGGTGTCGAAAAATGCGGTTTCGGAACCCCATTTC
5792914 GAAATCAAATAGGAAAATGGATGATAC-TCTAGGCAATGCAAAGGAAGATGGGTCATGTAAGAAG
1 GAAATCAAATAGGAAAATGGATGATACAT-TAGGCAATGCAAAGGAAGATGGGTCATGTAAGAAG
* *
5792978 AAATTGTAATGACCCAACTTTTGTCGGTGTCGAGAAATG
65 AAATTGTAACGACCCAACTTTTGTCGGTGTCGAAAAATG
5793017 TGATTTCAGA
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
122 1 0.01
123 92 0.99
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (123 bp):
GAAATCAAATAGGAAAATGGATGATACATTAGGCAATGCAAAGGAAGATGGGTCATGTAAGAAGA
AATTGTAACGACCCAACTTTTGTCGGTGTCGAAAAATGCGGTTTCGGAACCCCATTTC
Found at i:5813730 original size:18 final size:18
Alignment explanation
Indices: 5813707--5813748 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5813697 GTCAGGTACT
*
5813707 TATCCTAGCACTTATATG
1 TATCCTAACACTTATATG
*
5813725 TATCCTAACCCTTATATG
1 TATCCTAACACTTATATG
*
5813743 TTTCCT
1 TATCCT
5813749 TTTTCCAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.26, G:0.07, T:0.43
Consensus pattern (18 bp):
TATCCTAACACTTATATG
Found at i:5814826 original size:27 final size:27
Alignment explanation
Indices: 5814796--5814851 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
5814786 TCTTGCAATA
*
5814796 ACTTTCGGAACCATACATGGCCTCCCT
1 ACTTTCAGAACCATACATGGCCTCCCT
5814823 ACTTTCAGAACCATACATGGCCTCCCT
1 ACTTTCAGAACCATACATGGCCTCCCT
5814850 AC
1 AC
5814852 ATTTGGACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.38, G:0.12, T:0.25
Consensus pattern (27 bp):
ACTTTCAGAACCATACATGGCCTCCCT
Found at i:5815490 original size:27 final size:27
Alignment explanation
Indices: 5815460--5815515 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
5815450 TCTTGCAATA
*
5815460 ACTTTCGGAACCATACATGGCCTCCCT
1 ACTTTCAGAACCATACATGGCCTCCCT
5815487 ACTTTCAGAACCATACATGGCCTCCCT
1 ACTTTCAGAACCATACATGGCCTCCCT
5815514 AC
1 AC
5815516 ATTTGGCCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.38, G:0.12, T:0.25
Consensus pattern (27 bp):
ACTTTCAGAACCATACATGGCCTCCCT
Found at i:5816106 original size:663 final size:663
Alignment explanation
Indices: 5814626--5816629 Score: 3711
Period size: 663 Copynumber: 3.0 Consensus size: 663
5814616 AAAGTGCGTC
* *
5814626 AAACGTCCCATAGACGGAAGTCCTATTTCTCAGGACACGATATTGCCCGCCGGTAATACAATGGT
1 AAACGTGCCATAGACGCAAGTCCTATTTCTCAGGACACGATATTGCCCGCCGGTAATACAATGGT
* *
5814691 TCGGTCTGTCAAAATTTGTCACACAAAACCATAGGTAGTTGCGATTGTGACACGCTGTGTGCATG
66 TCGGTCTGTCAAAATTCGTCACACGAAACCATAGGTAGTTGCGATTGTGACACGCTGTGTGCATG
*
5814756 GTGTTGGCCCGCGCCTTTGCATTGTTAATTTCTTGCAATAACTTTCGGAACCATACATGGCCTCC
131 GTGTTGGCCCGCGCCTTTGCCTTGTTAATTTCTTGCAATAACTTTCGGAACCATACATGGCCTCC
* *
5814821 CTACTTTCAGAACCATACATGGCCTCCCTACATTTGGACTTTATAACACACTGCTCGTTTTGGAA
196 CTACTTTCAGAACCATACATGGCCTCCCTACATTTGGCCTTTATAACTCACTGCTCGTTTTGGAA
5814886 ATAGTGCCGCAAAACGAAAATATGTCTCTCGCACAACCGAGGTTATTGGCAAATGACGCGTTCCT
261 ATAGTGCCGCAAAACGAAAATATGTCTCTCGCACAACCGAGGTTATTGGCAAATGACGCGTTCCT
* *
5814951 TTTAGAACATAATATATGCATTTAGTAAGGTTTGTGGTCATATGACCATAATGTAAGTCGCCATC
326 TTTAGAACATAATTTATGCATTTAGTCAGGTTTGTGGTCATATGACCATAATGTAAGTCGCCATC
5815016 TTATGCTTGTGTCCAGTATTCGAAAGGTATTTTATAGAGGTAGTATGCACCTTGATTGGTAACTG
391 TTATGCTTGTGTCCAGTATTCGAAAGGTATTTTATAGAGGTAGTATGCACCTTGATTGGTAACTG
5815081 AACGCAAAATCCCCAAATATCTCATGAAAACGGTCCTTATTGATCTCGTACCCTACCAATATAAG
456 AACGCAAAATCCCC-AATATCTCATGAAAACGGTCCTTATTGATCTCGTACCCTACCAATATAAG
* * *
5815146 TTGATACAAAAAATTACTTACTACTATCCTATTCAAAATAAATTGAATATTACAAACAAAATTAT
520 TTGATACCAAAAATTACTTACTACTATTCTATTCAAAATAAATTGAATATTACAAACGAAATTAT
*
5815211 ATTAATAGAGATTAAATACCCATGTTGGTTATTTGTCGTCGTTAAATGGTAAATTGATATTGCTC
585 ATTAATAGAGATTAAATACCCATGTTGGTTATTTGTCGTCGTTAAATGGTAAATCGATATTGCTC
5815276 GTAGTAGTTGTACG
650 GTAGTAGTTGTACG
* *
5815290 CAACGTGCCATAGACGCAAGTCCTATTTCTCAGGACACGATATTGCCCACCGGTAATACAATGGT
1 AAACGTGCCATAGACGCAAGTCCTATTTCTCAGGACACGATATTGCCCGCCGGTAATACAATGGT
*
5815355 TCGGTCTGTCAAAATTCGTTACACGAAACCATAGGTAGTTGCGATTGTGACACGCTGTGTGCATG
66 TCGGTCTGTCAAAATTCGTCACACGAAACCATAGGTAGTTGCGATTGTGACACGCTGTGTGCATG
5815420 GTGTTGGCCCGCGCCTTTGCCTTGTTAATTTCTTGCAATAACTTTCGGAACCATACATGGCCTCC
131 GTGTTGGCCCGCGCCTTTGCCTTGTTAATTTCTTGCAATAACTTTCGGAACCATACATGGCCTCC
*
5815485 CTACTTTCAGAACCATACATGGCCTCCCTACATTTGGCCTTTATAACTCACTACTCGTTTTGGAA
196 CTACTTTCAGAACCATACATGGCCTCCCTACATTTGGCCTTTATAACTCACTGCTCGTTTTGGAA
5815550 ATAGTGCCGCAAAACGAAAATATGTCTCTCGCACAACCGAGGTTATTGGCAAATGACGCGTTCCT
261 ATAGTGCCGCAAAACGAAAATATGTCTCTCGCACAACCGAGGTTATTGGCAAATGACGCGTTCCT
5815615 TTTAGAACATAATTTATGCATTTAGTCAGGTTTGTGGTCATATGACCATAATGTAAGTCGCCATC
326 TTTAGAACATAATTTATGCATTTAGTCAGGTTTGTGGTCATATGACCATAATGTAAGTCGCCATC
5815680 TTATGCTTGTGTCCAGTATTCGAAAGGTATTTTATAGAGGTAGTATGCACCTTGATTGGTAACTG
391 TTATGCTTGTGTCCAGTATTCGAAAGGTATTTTATAGAGGTAGTATGCACCTTGATTGGTAACTG
5815745 AACGCAAAATCCCCAATATCTCATGAAAACGGTCCTTATTGATCTCGTACCCTACCAATATAAGT
456 AACGCAAAATCCCCAATATCTCATGAAAACGGTCCTTATTGATCTCGTACCCTACCAATATAAGT
5815810 TGATACCAAAAATTACTTACTACTATTCTATTCAAAATAAATTGAATATTACAAACGAAATTATA
521 TGATACCAAAAATTACTTACTACTATTCTATTCAAAATAAATTGAATATTACAAACGAAATTATA
5815875 TTAATAGAGATTAAATACCCATGTTGGTTATTTGTCGTCGTTAAATGGTAAATCGATATTGCTCG
586 TTAATAGAGATTAAATACCCATGTTGGTTATTTGTCGTCGTTAAATGGTAAATCGATATTGCTCG
5815940 TAGTAGTTGTACG
651 TAGTAGTTGTACG
5815953 AAACGTGCCATAGACGCAAGTCCTATTTCTCAGGACACGATATTGCCCGCCGGTAATACAATGGT
1 AAACGTGCCATAGACGCAAGTCCTATTTCTCAGGACACGATATTGCCCGCCGGTAATACAATGGT
5816018 TCGGTCTGTCAAAATTCGTCACACGAAACCATAGGTAGTTGCGATTGTGACACGCTGTGTGCATG
66 TCGGTCTGTCAAAATTCGTCACACGAAACCATAGGTAGTTGCGATTGTGACACGCTGTGTGCATG
* * *
5816083 GTGTTGGCCCACGCCTCTGCCTTGTTAATTTCTTGCAATAATTTTCGGAACCATACATGGCCTCC
131 GTGTTGGCCCGCGCCTTTGCCTTGTTAATTTCTTGCAATAACTTTCGGAACCATACATGGCCTCC
*
5816148 CTACTTTCAGAACCATACATGGCCTCCCTACATTTGGCCTTTATAACTCACTGCTCGTTTTGGGA
196 CTACTTTCAGAACCATACATGGCCTCCCTACATTTGGCCTTTATAACTCACTGCTCGTTTTGGAA
* * *
5816213 GTAGTACCGCAAAACGAAAATATGTCTCTCGCACAACCGAGGTTATTGGCAAATGACGCGTTCTT
261 ATAGTGCCGCAAAACGAAAATATGTCTCTCGCACAACCGAGGTTATTGGCAAATGACGCGTTCCT
* *
5816278 TTTAGAACATAATTTATGCATTTAGTCAGGTTTGTGGTCATATGACCATATTGTAGGTCGCCATC
326 TTTAGAACATAATTTATGCATTTAGTCAGGTTTGTGGTCATATGACCATAATGTAAGTCGCCATC
*
5816343 TTGTGCTTGTGTCCAGTATTCGAAAGGTATTTTATAGAGGTAGTATGCACCTTGATTGGTAACTG
391 TTATGCTTGTGTCCAGTATTCGAAAGGTATTTTATAGAGGTAGTATGCACCTTGATTGGTAACTG
5816408 AACGCAAAATCCCCAATATCTCATGAAAACGGTCCTTATTGATCTCGTACCCTACCAATATAAGT
456 AACGCAAAATCCCCAATATCTCATGAAAACGGTCCTTATTGATCTCGTACCCTACCAATATAAGT
5816473 TGATACCAAAAATTACTTACTACTATTCTATTCAAAATAAATTGAATATTACAAACGAAATTATA
521 TGATACCAAAAATTACTTACTACTATTCTATTCAAAATAAATTGAATATTACAAACGAAATTATA
* * *
5816538 TTAATAGAGATTAAATACCCATGTTGGTTATTTATTGTCGTTAAATGATAAATCGATATTGCTCG
586 TTAATAGAGATTAAATACCCATGTTGGTTATTTGTCGTCGTTAAATGGTAAATCGATATTGCTCG
5816603 TAGTAGTTGTACG
651 TAGTAGTTGTACG
* *
5816616 CAACGTGCCTTAGA
1 AAACGTGCCATAGA
5816630 TAATAACGAT
Statistics
Matches: 1304, Mismatches: 36, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
663 848 0.65
664 456 0.35
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (663 bp):
AAACGTGCCATAGACGCAAGTCCTATTTCTCAGGACACGATATTGCCCGCCGGTAATACAATGGT
TCGGTCTGTCAAAATTCGTCACACGAAACCATAGGTAGTTGCGATTGTGACACGCTGTGTGCATG
GTGTTGGCCCGCGCCTTTGCCTTGTTAATTTCTTGCAATAACTTTCGGAACCATACATGGCCTCC
CTACTTTCAGAACCATACATGGCCTCCCTACATTTGGCCTTTATAACTCACTGCTCGTTTTGGAA
ATAGTGCCGCAAAACGAAAATATGTCTCTCGCACAACCGAGGTTATTGGCAAATGACGCGTTCCT
TTTAGAACATAATTTATGCATTTAGTCAGGTTTGTGGTCATATGACCATAATGTAAGTCGCCATC
TTATGCTTGTGTCCAGTATTCGAAAGGTATTTTATAGAGGTAGTATGCACCTTGATTGGTAACTG
AACGCAAAATCCCCAATATCTCATGAAAACGGTCCTTATTGATCTCGTACCCTACCAATATAAGT
TGATACCAAAAATTACTTACTACTATTCTATTCAAAATAAATTGAATATTACAAACGAAATTATA
TTAATAGAGATTAAATACCCATGTTGGTTATTTGTCGTCGTTAAATGGTAAATCGATATTGCTCG
TAGTAGTTGTACG
Found at i:5816163 original size:27 final size:27
Alignment explanation
Indices: 5816125--5816178 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
5816115 TTGCAATAAT
*
5816125 TTTCGGAACCATACATGGCCTCCCTAC
1 TTTCAGAACCATACATGGCCTCCCTAC
5816152 TTTCAGAACCATACATGGCCTCCCTAC
1 TTTCAGAACCATACATGGCCTCCCTAC
5816179 ATTTGGCCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.37, G:0.13, T:0.26
Consensus pattern (27 bp):
TTTCAGAACCATACATGGCCTCCCTAC
Found at i:5818849 original size:125 final size:126
Alignment explanation
Indices: 5818627--5818882 Score: 363
Period size: 125 Copynumber: 2.0 Consensus size: 126
5818617 GGCCAAACAT
* * * *
5818627 GAACTACTGTAGAAAAAGAGCGTCGACATGAGAGCTTTTTTTAGTAATTTTGCTGACGGTGTATC
1 GAACTACTGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTTAGTAATTTTGCTAACAGTGCATC
* * * * *
5818692 TTGCTTGAAGCGTTTTTTACATTATTTGTTCAGAAACGTCTTCTCAAAATTA-TTTTTCAG
66 CTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAAACGTATTCTCAAAATTATTTTTTCAA
* * * *
5818752 GAACTACTGTAGAAAAATAGTGTCCACTTGGGAGCTTTTTTCT-GTAATTTTGCTAACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTT-TAGTAATTTTGCTAACAGTGCAT
*
5818816 CCTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTCAA
65 CCTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAAACGTATTCTCAAAATTATTTTTTCAA
5818878 GAACT
1 GAACT
5818883 GTAGAAAAAA
Statistics
Matches: 115, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
125 102 0.89
126 13 0.11
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTTAGTAATTTTGCTAACAGTGCATC
CTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAAACGTATTCTCAAAATTATTTTTTCAA
Found at i:5819001 original size:34 final size:34
Alignment explanation
Indices: 5818963--5819044 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
5818953 TAAAAAAATT
5818963 TAAACCCTAATTTAATTAATTT-TCTTAAAAACAC
1 TAAACCCTAATTTAATTAATTTAT-TTAAAAACAC
* * * *
5818997 TAAACCTTAATTTAATTAATTTATTTTAAACCCC
1 TAAACCCTAATTTAATTAATTTATTTAAAAACAC
*
5819031 TAAATCCTAATTTA
1 TAAACCCTAATTTA
5819045 TATTTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 40 0.98
35 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (34 bp):
TAAACCCTAATTTAATTAATTTATTTAAAAACAC
Found at i:5819154 original size:15 final size:15
Alignment explanation
Indices: 5819130--5819168 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5819120 TTATTTTAAC
* * *
5819130 AAAACTCTAACCCTA
1 AAAACCCTAAACCAA
5819145 AAAACCCTAAACCAA
1 AAAACCCTAAACCAA
5819160 AAAACCCTA
1 AAAACCCTA
5819169 GGGACTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.33, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAACCCTAAACCAA
Found at i:5819154 original size:42 final size:42
Alignment explanation
Indices: 5819072--5819150 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
5819062 AACACAGAAC
*
5819072 CCTAAATTATTTTAACAAAACCCTAAACCCTACAAACCTAAG
1 CCTAAATTATTTTAACAAAACCCTAAACCCTAAAAACCTAAG
*
5819114 CCTAAATTATTTTAACAAAACTCT-AACCCTAAAAACC
1 CCTAAATTATTTTAACAAAACCCTAAACCCTAAAAACC
5819151 CTAAACCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 12 0.34
42 23 0.66
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (42 bp):
CCTAAATTATTTTAACAAAACCCTAAACCCTAAAAACCTAAG
Found at i:5822772 original size:43 final size:42
Alignment explanation
Indices: 5822698--5822778 Score: 117
Period size: 43 Copynumber: 1.9 Consensus size: 42
5822688 TCTTTTCTAA
*
5822698 AAATTAATTAAATTAGGGTTTAGGGGATTTAAATAAATAAAT
1 AAATTAATTAAATTAGGGTTTAGGGGATTTAAAAAAATAAAT
* **
5822740 AAATTAAATTAAATTAGGGTTTAGTGTTTTTAAAAAAAT
1 AAATT-AATTAAATTAGGGTTTAGGGGATTTAAAAAAAT
5822779 TTATTAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 5 0.15
43 29 0.85
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (42 bp):
AAATTAATTAAATTAGGGTTTAGGGGATTTAAAAAAATAAAT
Found at i:5822788 original size:34 final size:36
Alignment explanation
Indices: 5822747--5822818 Score: 112
Period size: 34 Copynumber: 2.1 Consensus size: 36
5822737 AATAAATTAA
5822747 ATTAAATTAGGGTTTAGTGTTTTTAAAAA-AAT-TT
1 ATTAAATTAGGGTTTAGTGTTTTTAAAAATAATATT
* *
5822781 ATTAAATTAGTGTTTAGTTTTTTTAAAAATAATATT
1 ATTAAATTAGGGTTTAGTGTTTTTAAAAATAATATT
5822817 AT
1 AT
5822819 GTTTAGGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 27 0.79
35 3 0.09
36 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (36 bp):
ATTAAATTAGGGTTTAGTGTTTTTAAAAATAATATT
Found at i:5822829 original size:33 final size:31
Alignment explanation
Indices: 5822752--5822836 Score: 82
Period size: 34 Copynumber: 2.5 Consensus size: 31
5822742 ATTAAATTAA
5822752 ATTAGGGTTTAGTGTTTTTAAAAAAATTTATT
1 ATTA-GGTTTAGTGTTTTTAAAAAAATTTATT
*
5822784 AAATTAGTGTTTAGTTTTTTTAAAAATAATATTATGT
1 --ATTAG-GTTTAGTGTTTTTAAAAA-AAT-TTAT-T
*
5822821 -TTAGGTTTAGGGTTTT
1 ATTAGGTTTAGTGTTTT
5822837 CAGAAAATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
33 11 0.25
34 25 0.57
35 3 0.07
36 4 0.09
37 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (31 bp):
ATTAGGTTTAGTGTTTTTAAAAAAATTTATT
Found at i:5823062 original size:126 final size:125
Alignment explanation
Indices: 5822872--5823265 Score: 492
Period size: 126 Copynumber: 3.1 Consensus size: 125
5822862 TTTTGTTTTT
* *
5822872 TTTTTCTACAGTAGTTCTTGAAAAAATAA-TTTGAGAATACGGTTCTGAACAAATAGTG-CGAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTC-AAA
* * * *
5822935 AACGCTTCAAGCAGGATGTACTGTCAGCAAAATTACTGAAAAAAGCTCTCACATAGACACTT
65 AACGCTTCAAGCAGGATGAACTGTCAGCAAAATTACTGAAAAAAGCTC-CACGTAGACGCTC
* *
5822997 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGA-GGTTTCTGAATAACTAGTGTCAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGG-TTCTGAACAAATAGTGTCAAA
* * * ** *
5823061 AACGCTTCAAGAAAGGGTGAACTGTCAGTAAAATTACTG-AAAAATTTCCCACGTGGACGCTC
65 AACGCTTCAAG-CAGGATGAACTGTCAGCAAAATTACTGAAAAAAGCT-CCACGTAGACGCTC
* *
5823123 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGATGGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
** * * * *
5823188 ACATTTCAAGCAAGATGCATTGTCAGCAAAATTGA-TGAAAAAAGCTCCAACGTCGACGCTC
66 ACGCTTCAAGCAGGATGAACTGTCAGCAAAATT-ACTGAAAAAAGCTCC-ACGTAGACGCTC
5823249 TTTTTCTACAGTAGTTC
1 TTTTTCTACAGTAGTTC
5823266 ATGTTTGGCT
Statistics
Matches: 232, Mismatches: 28, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
125 51 0.22
126 154 0.66
127 27 0.12
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (125 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGAACTGTCAGCAAAATTACTGAAAAAAGCTCCACGTAGACGCTC
Found at i:5838882 original size:44 final size:46
Alignment explanation
Indices: 5838798--5838886 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 46
5838788 TTCGCTGTAA
* *
5838798 TGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGGAT
1 TGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGATTGAATGGAT
5838844 TGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGATTGAATGGA
1 TGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGATTGAATGGA
5838887 ATAGAGGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 21 0.51
45 3 0.07
46 17 0.41
ACGTcount: A:0.26, C:0.04, G:0.31, T:0.38
Consensus pattern (46 bp):
TGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGATTGAATGGAT
Found at i:5838887 original size:39 final size:42
Alignment explanation
Indices: 5838796--5838901 Score: 128
Period size: 46 Copynumber: 2.5 Consensus size: 42
5838786 GGTTCGCTGT
* *
5838796 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGA
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGATTGA
5838838 ATGGATTGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGATTG-
1 A---A-TGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGATTGA
*
5838881 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
5838902 CATAAGGAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
39 16 0.29
40 2 0.04
42 1 0.02
43 1 0.02
44 15 0.27
45 4 0.07
46 17 0.30
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (42 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGATTGA
Found at i:5839118 original size:26 final size:26
Alignment explanation
Indices: 5839085--5839136 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
5839075 TAATACTATA
5839085 AAATATAATTTAA-AATAATTCTTATT
1 AAATATAATTTAATAA-AATTCTTATT
5839111 AAATATAATTTAATAAAATTCTTATT
1 AAATATAATTTAATAAAATTCTTATT
5839137 CTTATATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATATAATTTAATAAAATTCTTATT
Done.