Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 63 of 128
Found at i:20280658 original size:16 final size:17
Alignment explanation
Indices: 20280624--20280658 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20280614 GTTTGCTTCT
*
20280624 CTGCTGTTTGTTGTGGG
1 CTGCTGTTGGTTGTGGG
20280641 CTGCTGTTGGTT-TGGG
1 CTGCTGTTGGTTGTGGG
20280657 CT
1 CT
20280659 AGGGTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.00, C:0.14, G:0.40, T:0.46
Consensus pattern (17 bp):
CTGCTGTTGGTTGTGGG
Found at i:20280675 original size:18 final size:18
Alignment explanation
Indices: 20280652--20280699 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
20280642 TGCTGTTGGT
20280652 TTGGGCTAGGGTTATTAA
1 TTGGGCTAGGGTTATTAA
* **
20280670 TTGGGCTTGGGTTATTGT
1 TTGGGCTAGGGTTATTAA
20280688 TTGGGCTAGGGT
1 TTGGGCTAGGGT
20280700 AAGTTAGTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.12, C:0.06, G:0.40, T:0.42
Consensus pattern (18 bp):
TTGGGCTAGGGTTATTAA
Found at i:20290360 original size:89 final size:89
Alignment explanation
Indices: 20290209--20290386 Score: 331
Period size: 89 Copynumber: 2.0 Consensus size: 89
20290199 TAAAAAAATT
20290209 CATTTTCATTCTGTTTTAAAAAAACAAAAAAAACCCTCAAAAAAGTTCTCTTCCCCCCAGCTAGT
1 CATTTTCATTCTGTTTTAAAAAAACAAAAAAAACCCTCAAAAAAGTTCTCTTCCCCCCAGCTAGT
*
20290274 TCGGCCTAGGTCGGTCATCGGCCG
66 CCGGCCTAGGTCGGTCATCGGCCG
20290298 CATTTTCATTCTGTTTTAAAAAAACAAAAAAAACCCTCAAAAAAGTTCTC-TCCCACCCAGCTAG
1 CATTTTCATTCTGTTTTAAAAAAACAAAAAAAACCCTCAAAAAAGTTCTCTTCCC-CCCAGCTAG
20290362 TCCGGCCTAGGTCGGTCATCGGCCG
65 TCCGGCCTAGGTCGGTCATCGGCCG
20290387 GTCAATGGCC
Statistics
Matches: 87, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
88 4 0.05
89 83 0.95
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.26
Consensus pattern (89 bp):
CATTTTCATTCTGTTTTAAAAAAACAAAAAAAACCCTCAAAAAAGTTCTCTTCCCCCCAGCTAGT
CCGGCCTAGGTCGGTCATCGGCCG
Found at i:20290670 original size:4 final size:4
Alignment explanation
Indices: 20290661--20290714 Score: 65
Period size: 4 Copynumber: 13.0 Consensus size: 4
20290651 TTTATTTTAG
*
20290661 TAAA TAAA TAAG TAAA TAAA TAAA TAAA TAAA TAACA TATAA -AAA TGAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA-A TA-AA TAAA T-AAA
20290711 TAAA
1 TAAA
20290715 AATATCAACC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
3 2 0.05
4 33 0.75
5 8 0.18
6 1 0.02
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:20292890 original size:22 final size:21
Alignment explanation
Indices: 20292844--20292898 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
20292834 AAAATTTAGT
* *
20292844 ATTTAAAGTTTACTATTTAAG
1 ATTTAAAGTTTACCATTTAAA
*
20292865 ATTTAAAGTTTAGCCCTTTAAA
1 ATTTAAAGTTTA-CCATTTAAA
*
20292887 ATTTAAGGTTTA
1 ATTTAAAGTTTA
20292899 AAATTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (21 bp):
ATTTAAAGTTTACCATTTAAA
Found at i:20292906 original size:22 final size:22
Alignment explanation
Indices: 20292881--20292932 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
20292871 AGTTTAGCCC
20292881 TTTAAAATTTAAGGTTTAAAAT
1 TTTAAAATTTAAGGTTTAAAAT
* * *
20292903 TTTAATATTTAATGTTTAAGAT
1 TTTAAAATTTAAGGTTTAAAAT
20292925 TTATAAAA
1 TT-TAAAA
20292933 AAAATTTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (22 bp):
TTTAAAATTTAAGGTTTAAAAT
Found at i:20292913 original size:15 final size:14
Alignment explanation
Indices: 20292858--20292927 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
20292848 AAAGTTTACT
20292858 ATTTAAGATTTAAA
1 ATTTAAGATTTAAA
* *
20292872 GTTT-AGCCCTTTAAA
1 ATTTAAG--ATTTAAA
*
20292887 ATTTAAGGTTTAAA
1 ATTTAAGATTTAAA
* *
20292901 ATTTTAATATTTAAT
1 A-TTTAAGATTTAAA
*
20292916 GTTTAAGATTTA
1 ATTTAAGATTTA
20292928 TAAAAAAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
13 2 0.05
14 20 0.47
15 19 0.44
16 2 0.05
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (14 bp):
ATTTAAGATTTAAA
Found at i:20300624 original size:60 final size:60
Alignment explanation
Indices: 20300525--20300699 Score: 192
Period size: 60 Copynumber: 2.9 Consensus size: 60
20300515 TTAATATAAC
* * * ***
20300525 ATTTGGTACTTAAACTTAACATTTTTTTTTAATTTGGTACTTAAATTTTTTTTTTTGCACA
1 ATTTGGTACTTAAACTTGACATTTTTTTCTAATTTGGTACTTAAACTTTTTTTGGGGC-CA
* * * * *
20300586 ATTTGGTATTTGAACTTGA-ATTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGGGCCA
1 ATTTGGTACTTAAACTTGACATTTTTTTCTAATTTGGTACTTAAACTTTTTTTGGGGCCA
*
20300645 ATTTGGTACTTAAACTT-AGCATTTTTTTTTCTAATTTGGTACTTAAGCTTTTTTT
1 ATTTGGTACTTAAACTTGA-CA--TTTTTTTCTAATTTGGTACTTAAACTTTTTTT
20300700 AGGTTCAATT
Statistics
Matches: 93, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
58 1 0.01
59 17 0.18
60 31 0.33
61 16 0.17
62 28 0.30
ACGTcount: A:0.23, C:0.11, G:0.13, T:0.53
Consensus pattern (60 bp):
ATTTGGTACTTAAACTTGACATTTTTTTCTAATTTGGTACTTAAACTTTTTTTGGGGCCA
Found at i:20300632 original size:30 final size:30
Alignment explanation
Indices: 20300525--20300632 Score: 94
Period size: 30 Copynumber: 3.6 Consensus size: 30
20300515 TTAATATAAC
**
20300525 ATTTGGTACTTAAACTTAACATTTTTTTTTA
1 ATTTGGTACTTAAACTTAA-ATTTTTTCCTA
***
20300556 ATTTGGTACTTAAA-TTTTTTTTTTTGCAC-A
1 ATTTGGTACTTAAACTTAAATTTTTT-C-CTA
* * *
20300586 ATTTGGTATTTGAACTTGAATTTTTTCCTA
1 ATTTGGTACTTAAACTTAAATTTTTTCCTA
*
20300616 ATTTGGTACCTAAACTT
1 ATTTGGTACTTAAACTT
20300633 TTTTGGGGGC
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
29 7 0.12
30 31 0.52
31 22 0.37
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.53
Consensus pattern (30 bp):
ATTTGGTACTTAAACTTAAATTTTTTCCTA
Found at i:20300710 original size:62 final size:61
Alignment explanation
Indices: 20300525--20300702 Score: 193
Period size: 59 Copynumber: 2.9 Consensus size: 61
20300515 TTAATATAAC
* * **
20300525 ATTTGGTACTTAAACTTAACATTTTTTTT-TAATTTGGTACTTAAATTTTTTTTTTTGCACA
1 ATTTGGTACTTAAACTTAGCATTTTTTTTCTAATTTGGTACTTAAA-CTTTTTTTAGGCACA
* * * * * **
20300586 ATTTGGTATTTGAACTT-G-AATTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGGGC-CA
1 ATTTGGTACTTAAACTTAGCATTTTTTTTCTAATTTGGTACTTAAACTTTTTT-TAGGCACA
*
20300645 ATTTGGTACTTAAACTTAGCATTTTTTTTTCTAATTTGGTACTTAAGCTTTTTTTAGG
1 ATTTGGTACTTAAACTTAGCA-TTTTTTTTCTAATTTGGTACTTAAACTTTTTTTAGG
20300703 TTCAATTTAA
Statistics
Matches: 94, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
59 30 0.32
60 18 0.19
61 18 0.19
62 28 0.30
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.52
Consensus pattern (61 bp):
ATTTGGTACTTAAACTTAGCATTTTTTTTCTAATTTGGTACTTAAACTTTTTTTAGGCACA
Found at i:20306079 original size:10 final size:10
Alignment explanation
Indices: 20306053--20306086 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
20306043 TGTTTCCTAA
*
20306053 ATAATTATTAA
1 ATAATTA-TAC
20306064 ATAATTATAC
1 ATAATTATAC
20306074 ATAATTATAC
1 ATAATTATAC
20306084 ATA
1 ATA
20306087 TTTGTGTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (10 bp):
ATAATTATAC
Found at i:20313528 original size:9 final size:9
Alignment explanation
Indices: 20313514--20313587 Score: 84
Period size: 9 Copynumber: 8.3 Consensus size: 9
20313504 GTTCAGACTA
20313514 AAAAAAATC
1 AAAAAAATC
20313523 AAAAAAATC
1 AAAAAAATC
20313532 -AAAAAATC
1 AAAAAAATC
20313540 AAAAAAAAATC
1 --AAAAAAATC
20313551 -AAAAAATC
1 AAAAAAATC
20313559 AAAAAAA--
1 AAAAAAATC
*
20313566 AATCAAAATC
1 AA-AAAAATC
20313576 AAAAAAATC
1 AAAAAAATC
20313585 AAA
1 AAA
20313588 GTCAAAAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
7 2 0.04
8 20 0.36
9 24 0.43
10 2 0.04
11 8 0.14
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAATC
Found at i:20313529 original size:11 final size:10
Alignment explanation
Indices: 20313513--20313573 Score: 69
Period size: 8 Copynumber: 6.4 Consensus size: 10
20313503 AGTTCAGACT
20313513 AAAAAAAATC
1 AAAAAAAATC
20313523 -AAAAAAATC
1 AAAAAAAATC
20313532 --AAAAAATC
1 AAAAAAAATC
20313540 AAAAAAAAATC
1 -AAAAAAAATC
20313551 --AAAAAATC
1 AAAAAAAATC
20313559 AAAAAAAAATC
1 -AAAAAAAATC
20313570 AAAA
1 AAAA
20313574 TCAAAAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
8 16 0.36
9 9 0.20
10 4 0.09
11 16 0.36
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:20313537 original size:17 final size:17
Alignment explanation
Indices: 20313515--20313587 Score: 96
Period size: 17 Copynumber: 4.2 Consensus size: 17
20313505 TTCAGACTAA
20313515 AAAAAATCAAAAAAATC
1 AAAAAATCAAAAAAATC
20313532 AAAAAATCAAAAAAAAATC
1 AAAAAATC--AAAAAAATC
20313551 AAAAAATCAAAAAAA--
1 AAAAAATCAAAAAAATC
20313566 AATCAAAATCAAAAAAATC
1 AA--AAAATCAAAAAAATC
20313585 AAA
1 AAA
20313588 GTCAAAAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.04
17 29 0.58
19 19 0.38
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAAAATCAAAAAAATC
Found at i:20313537 original size:19 final size:19
Alignment explanation
Indices: 20313515--20313582 Score: 108
Period size: 19 Copynumber: 3.8 Consensus size: 19
20313505 TTCAGACTAA
20313515 AAAAAATC--AAAAAAATC
1 AAAAAATCAAAAAAAAATC
20313532 AAAAAATCAAAAAAAAATC
1 AAAAAATCAAAAAAAAATC
20313551 AAAAAATCAAAAAAAAATC
1 AAAAAATCAAAAAAAAATC
20313570 --AAAATCAAAAAAA
1 AAAAAATCAAAAAAA
20313583 TCAAAGTCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
17 21 0.43
19 28 0.57
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (19 bp):
AAAAAATCAAAAAAAAATC
Found at i:20313592 original size:15 final size:15
Alignment explanation
Indices: 20313517--20313595 Score: 77
Period size: 19 Copynumber: 4.7 Consensus size: 15
20313507 CAGACTAAAA
20313517 AAAATCAAAAAAATC
1 AAAATCAAAAAAATC
20313532 AAAAAATCAAAAAAAAATC
1 --AAAATC--AAAAAAATC
20313551 AAAAAATCAAAAAAAAATC
1 --AAAATC--AAAAAAATC
20313570 AAAATCAAAAAAATC
1 AAAATCAAAAAAATC
*
20313585 AAAGTCAAAAA
1 AAAATCAAAAA
20313596 TAGGAGAAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
15 19 0.32
17 12 0.20
19 28 0.47
ACGTcount: A:0.76, C:0.11, G:0.01, T:0.11
Consensus pattern (15 bp):
AAAATCAAAAAAATC
Found at i:20313641 original size:6 final size:7
Alignment explanation
Indices: 20313602--20313640 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
20313592 AAAATAGGAG
20313602 AAAAAGAA
1 AAAAAG-A
20313610 AAAAAGA
1 AAAAAGA
20313617 AAAAAGA
1 AAAAAGA
20313624 AAAAAG-
1 AAAAAGA
20313630 AAAAAGA
1 AAAAAGA
20313637 AAAA
1 AAAA
20313641 GGAGAGGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.20
7 18 0.60
8 6 0.20
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:20314485 original size:8 final size:8
Alignment explanation
Indices: 20314484--20314516 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
20314474 TGAAAAAATG
20314484 AATGAAAA
1 AATGAAAA
20314492 AATG-AAA
1 AATGAAAA
20314499 AATGAAAAA
1 AATG-AAAA
20314508 AATGAAAA
1 AATGAAAA
20314516 A
1 A
20314517 GTAAAANNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.30
8 9 0.39
9 7 0.30
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AATGAAAA
Found at i:20314522 original size:16 final size:16
Alignment explanation
Indices: 20314484--20314516 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
20314474 TGAAAAAATG
20314484 AATG-AAAAAATGAAA
1 AATGAAAAAAATGAAA
20314499 AATGAAAAAAATGAAA
1 AATGAAAAAAATGAAA
20314515 AA
1 AA
20314517 GTAAAANNNN
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AATGAAAAAAATGAAA
Found at i:20316671 original size:46 final size:46
Alignment explanation
Indices: 20315729--20316654 Score: 1390
Period size: 46 Copynumber: 20.1 Consensus size: 46
20315719 ACAGATCAAT
* *
20315729 GAAGATAGCAGATCTTGTCTTCCTGTGTTTGGCAGCGGAGAAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* * *
20315775 GGAGATAGCAGATCTTATCTTCATGTATTTGGCAGCGGAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* * * *
20315821 GAGGATAGCAGATCTTGTCTTCCTGTAATTGGCAGCAGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
*
20315867 GAAGATAGCAGATCTTGTCTTCCTATATTTGGCAGCGGA-GAGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA-GATC
* * *
20315913 GAAGATAGTAGATCTTATCTTCCTGTATTTGGCAGCAGAAGG-GATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC-GGAGGAGATC
* *
20315959 GAAGATAGCAGATATTGTCTTCCTGTATTTGGCAGCGGAGAAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
*
20316005 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGAAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* *
20316051 GAAGATAGCAGATCTTATCTTCATGTATTTGGCAGCGGAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* * *
20316097 GAGGATAGCAGATCTTGTCTTCCTGTAATTGGCAGCGGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
** * * *
20316143 GAAGATAGCAGATCTTGTCTTTTTGTATTTGGCAGCAGAGGGGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
*
20316189 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* * *
20316235 GAAGATAGTAGATCTTGTCTTTCTGTAATTGGCAGCGGA-GAGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA-GATC
20316281 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* * * *
20316327 GAAGATAGCAGATCTTGTCTTCTTGTATTTGGCAGCAGAGGAGGTT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
*
20316373 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGTAGCGGAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* *
20316419 GAAGATGGTAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
20316465 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* *
20316511 GAAGATAGCAGACCTTGTCTTCCTATATTTGGCAGCGGAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* *
20316557 GAAGATAGCAGACCTTGTCTTCCTGTATTTGGCAGCGAAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* * * * *
20316603 GAATATAGCAGATCTTGTCTTCCTGTATTTAGTAGTGGAGCAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
20316649 GAAGAT
1 GAAGAT
20316655 GGTGAATCTT
Statistics
Matches: 794, Mismatches: 80, Indels: 12
0.90 0.09 0.01
Matches are distributed among these distances:
45 6 0.01
46 783 0.99
47 4 0.01
48 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (46 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
Found at i:20316870 original size:132 final size:132
Alignment explanation
Indices: 20316633--20317044 Score: 689
Period size: 132 Copynumber: 3.1 Consensus size: 132
20316623 TCCTGTATTT
20316633 AGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAG
1 AGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAG
* * * * *
20316698 CCATTAGTCCTATCATCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAAATTCTGTCACCATAA
66 CCATTAGTCCTATCACCCTAAGAAGTAGTGGAGTAGGTTGAAGATTGTAGATTCTGTCACCCTAA
20316763 GC
131 GC
20316765 AGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAG
1 AGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAG
*
20316830 CCATTAGTCCTATCACCCTAAGAAGTAGTGGGGTAGGTTGAAGATTGTAGATTCTGTCACCCTAA
66 CCATTAGTCCTATCACCCTAAGAAGTAGTGGAGTAGGTTGAAGATTGTAGATTCTGTCACCCTAA
20316895 GC
131 GC
20316897 AGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAG
1 AGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAG
* * * ** * * *
20316962 CCATTAGTCCTATCACTCTAAGTAGTAGTGGAGTATGTCAAAGACTGTAGATTCTATCCCCCTAA
66 CCATTAGTCCTATCACCCTAAGAAGTAGTGGAGTAGGTTGAAGATTGTAGATTCTGTCACCCTAA
*
20317027 TC
131 GC
20317029 AGTAGTGGAGCAGATC
1 AGTAGTGGAGCAGATC
20317045 AACAATAACG
Statistics
Matches: 264, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 264 1.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (132 bp):
AGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAG
CCATTAGTCCTATCACCCTAAGAAGTAGTGGAGTAGGTTGAAGATTGTAGATTCTGTCACCCTAA
GC
Found at i:20316917 original size:44 final size:44
Alignment explanation
Indices: 20316707--20317043 Score: 138
Period size: 44 Copynumber: 7.7 Consensus size: 44
20316697 GCCATTAGTC
* * * * *
20316707 CTATCATCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAAATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGATT
* * * * *
20316751 CTGTCACCATAAGCAGTAGTGGAGCAGATCGAAGATGGT-GAAT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGATT
* * * * * * *
20316794 CTTATCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCA-T-TAG-TC
1 C-TATC-ACCCTAA-GCAGTAGTGGAGCAGATTGAAG--ATTGTAGATT
* * * *
20316839 CTATCACCCTAAGAAGTAGTGGGGTAGGTTGAAGATTGTAGATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGATT
* * * *
20316883 CTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGT-GAAT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGATT
* * * * * * *
20316926 CTTATCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCA-T-TAG-TC
1 C-TATC-ACCCTAA-GCAGTAGTGGAGCAGATTGAAG--ATTGTAGATT
* * * ** *
20316971 CTATCACTCTAAGTAGTAGTGGAGTATG-TCAAAGACTGTAGATT
1 CTATCACCCTAAGCAGTAGTGGAGCA-GATTGAAGATTGTAGATT
* *
20317015 CTATCCCCCTAATCAGTAGTGGAGCAGAT
1 CTATCACCCTAAGCAGTAGTGGAGCAGAT
20317044 CAACAATAAC
Statistics
Matches: 203, Mismatches: 68, Indels: 44
0.64 0.22 0.14
Matches are distributed among these distances:
41 2 0.01
42 2 0.01
43 44 0.22
44 110 0.54
45 41 0.20
46 2 0.01
47 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (44 bp):
CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGATT
Found at i:20325892 original size:9 final size:8
Alignment explanation
Indices: 20325878--20325911 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 8
20325868 TCATAAAAAA
20325878 ATTTATTCT
1 ATTTATT-T
20325887 ATTTATTT
1 ATTTATTT
20325895 ATTCTATTT
1 ATT-TATTT
20325904 ATTTATTT
1 ATTTATTT
20325912 CTTACGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 9 0.38
9 15 0.62
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (8 bp):
ATTTATTT
Found at i:20325895 original size:4 final size:4
Alignment explanation
Indices: 20325878--20325911 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
20325868 TCATAAAAAA
20325878 ATTT ATTCT ATTT ATTT ATTCT ATTT ATTT ATTT
1 ATTT ATT-T ATTT ATTT ATT-T ATTT ATTT ATTT
20325912 CTTACGCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:20325896 original size:13 final size:13
Alignment explanation
Indices: 20325878--20325910 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
20325868 TCATAAAAAA
20325878 ATTTATTCTATTT
1 ATTTATTCTATTT
20325891 ATTTATTCTATTT
1 ATTTATTCTATTT
20325904 ATTTATT
1 ATTTATT
20325911 TCTTACGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTATTCTATTT
Found at i:20325993 original size:17 final size:18
Alignment explanation
Indices: 20325971--20326009 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
20325961 GCACATTTTG
20325971 TTATTAT-CATTATTATT-
1 TTATTATGCA-TATTATTA
20325988 TTATTATGCATATTATTA
1 TTATTATGCATATTATTA
20326006 TTAT
1 TTAT
20326010 GATTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
TTATTATGCATATTATTA
Found at i:20326068 original size:3 final size:3
Alignment explanation
Indices: 20325971--20326058 Score: 53
Period size: 3 Copynumber: 30.3 Consensus size: 3
20325961 GCACATTTTG
* * *
20325971 TTA TTA TCA TTA TTA TT- TTA TTA TGCA -TA TTA TTA TTA TGA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA -TTA
* * *
20326016 TTT TTA TTA -TA CTT- TTA -TA TT- TTA TTA TGA GTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20326058 T
1 T
20326059 GCCATTATTA
Statistics
Matches: 64, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
2 11 0.17
3 49 0.77
4 4 0.06
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:20326349 original size:140 final size:141
Alignment explanation
Indices: 20326079--20326361 Score: 559
Period size: 140 Copynumber: 2.0 Consensus size: 141
20326069 CTACAAATTG
20326079 ATGTCGCATTATCATTATTAGCTAGCATGGCATTTTTATCTTACTTTTTTAGTCGATTTTTCATA
1 ATGTCGCATTATCATTATTAGCTAGCATGGCATTTTTATCTTACTTTTTTAGTCGATTTTTCATA
20326144 TTCATTTATTTATCATTCTAATATCATTTCATTTTTCTCATCACTATTTATTCTATTAATTACTA
66 TTCATTTATTTATCATTCTAATATCATTTCATTTTTCTCATCACTATTTATTCTATTAATTACTA
20326209 TGCCGTCATAT
131 TGCCGTCATAT
20326220 ATGTCGCATTA-CATTATTAGCTAGCATGGCATTTTTATCTTACTTTTTTAGTCGATTTTTCATA
1 ATGTCGCATTATCATTATTAGCTAGCATGGCATTTTTATCTTACTTTTTTAGTCGATTTTTCATA
20326284 TTCATTTATTTATCATTCTAATATCATTTCATTTTTCTCATCACTATTTATTCTATTAATTACTA
66 TTCATTTATTTATCATTCTAATATCATTTCATTTTTCTCATCACTATTTATTCTATTAATTACTA
20326349 TGCCGTCATAT
131 TGCCGTCATAT
20326360 AT
1 AT
20326362 TCATTCATTT
Statistics
Matches: 142, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
140 131 0.92
141 11 0.08
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (141 bp):
ATGTCGCATTATCATTATTAGCTAGCATGGCATTTTTATCTTACTTTTTTAGTCGATTTTTCATA
TTCATTTATTTATCATTCTAATATCATTTCATTTTTCTCATCACTATTTATTCTATTAATTACTA
TGCCGTCATAT
Found at i:20336564 original size:21 final size:21
Alignment explanation
Indices: 20336539--20336579 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20336529 TATTTTTTTT
20336539 TAATT-TTATGATTTTCATATG
1 TAATTATTATGATTTT-ATATG
*
20336560 TAATTATTATTATTTTATAT
1 TAATTATTATGATTTTATAT
20336580 ATATGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (21 bp):
TAATTATTATGATTTTATATG
Found at i:20336607 original size:20 final size:21
Alignment explanation
Indices: 20336569--20336607 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
20336559 GTAATTATTA
*
20336569 TTATTTTATATATATGTATAT
1 TTATTTTATATATACGTATAT
*
20336590 TTATTTT-TATGTACGTAT
1 TTATTTTATATATACGTAT
20336608 TTATACCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (21 bp):
TTATTTTATATATACGTATAT
Found at i:20339977 original size:44 final size:44
Alignment explanation
Indices: 20339926--20340299 Score: 311
Period size: 44 Copynumber: 8.3 Consensus size: 44
20339916 GCCTATACCC
* * * * *
20339926 CTGAAGTTTCAGTGGAGTAGGTTAAAGCTACGAGTCTTATCTCT
1 CTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCT
* * * * *
20339970 TTGAAGTTGCAGTGGAGCAGAGTGAAGTTACAAATCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCT
* * *
20340014 CTAAAGTTGCAGTGGAGCAGATTAAAGCTGCAAATATTATCTCT
1 CTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCT
* ** * * *
20340058 CTGAAGTTGTAGTGGAATAGATTAAAGCTACAAGTTACGAATCTCATGTCC
1 CTGAAGTTGCAGTGGAGCAGATTAAAGCTAC-----A--AATCTTATCTCT
* * * *
20340109 CTGAAGTTGTAGTGGAGCAAATTGAAGCTACAAATCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCT
* * * *
20340153 CTAAAGTTGCAGTGGAGTAGATTAAAG-TCACAAATATTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTAAAGCT-ACAAATCTTATCTCT
** * * * *
20340197 CTGAAGTTGCAGTGGAATAGATTAAGGTTACAAATCTAATCTAT
1 CTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCT
** * *
20340241 CTGAAGTTGCAGTGGAATAGATTAAAGCGACAAATCATATAC-CT
1 CTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTAT-CTCT
*
20340285 CTGAAGTTACAGTGG
1 CTGAAGTTGCAGTGG
20340300 GTCGGATTAA
Statistics
Matches: 267, Mismatches: 53, Indels: 20
0.79 0.16 0.06
Matches are distributed among these distances:
43 1 0.00
44 227 0.85
45 2 0.01
46 1 0.00
49 1 0.00
51 35 0.13
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCT
Found at i:20340137 original size:95 final size:95
Alignment explanation
Indices: 20339994--20340273 Score: 268
Period size: 95 Copynumber: 3.0 Consensus size: 95
20339984 GAGCAGAGTG
* * * *
20339994 AAGTTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTGCAAATATTATCTCTC
1 AAGTTACAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCTACAAATATTATCTCCC
* *
20340059 TGAAGTTGTAGTGGAATAGATTAAAGCTAC
66 TAAAGTTGCAGTGGAATAGATTAAAGCTAC
* * * * * *
20340089 AAGTTACGAATCTCATGTCCCTGAAGTTGTAGTGGAGCAAATTGAAGCTACAAATCTTATCTCCC
1 AAGTTACAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCTACAAATATTATCTCCC
*
20340154 TAAAGTTGCAGTGGAGTAGATTAAAG-T-C
66 TAAAGTTGCAGTGGAATAGATTAAAGCTAC
* * * ** * * * * * **
20340182 -----ACAAATATTATCTCCCTGAAGTTGCAGTGGAATAGATTAAGGTTACAAATCTAATCTATC
1 AAGTTACAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCTACAAATATTATCTCCC
* *
20340242 TGAAGTTGCAGTGGAATAGATTAAAGCGAC
66 TAAAGTTGCAGTGGAATAGATTAAAGCTAC
20340272 AA
1 AA
20340274 ATCATATACC
Statistics
Matches: 151, Mismatches: 30, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
88 70 0.46
90 1 0.01
93 1 0.01
94 1 0.01
95 78 0.52
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (95 bp):
AAGTTACAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCTACAAATATTATCTCCC
TAAAGTTGCAGTGGAATAGATTAAAGCTAC
Found at i:20340229 original size:139 final size:139
Alignment explanation
Indices: 20339971--20340221 Score: 414
Period size: 139 Copynumber: 1.8 Consensus size: 139
20339961 CTTATCTCTT
* *
20339971 TGAAGTTGCAGTGGAGCAGAGTGAAGTTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGAT
1 TGAAGTTGCAGTGGAGCAAAGTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGAT
* * *
20340036 TAAAGCTGCAAATATTATCTCTCTGAAGTTGTAGTGGAATAGATTAAAGCTACAAGTTACGAATC
66 TAAAGCTACAAATATTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAGTTACGAATC
20340101 TCATGTCCC
131 TCATGTCCC
* * *
20340110 TGAAGTTGTAGTGGAGCAAATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGAT
1 TGAAGTTGCAGTGGAGCAAAGTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGAT
20340175 TAAAG-TCACAAATATTATCTCCCTGAAGTTGCAGTGGAATAGATTAA
66 TAAAGCT-ACAAATATTATCTCCCTGAAGTTGCAGTGGAATAGATTAA
20340222 GGTTACAAAT
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
138 1 0.01
139 102 0.99
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (139 bp):
TGAAGTTGCAGTGGAGCAAAGTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGAT
TAAAGCTACAAATATTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAGTTACGAATC
TCATGTCCC
Found at i:20340246 original size:183 final size:183
Alignment explanation
Indices: 20339924--20340273 Score: 459
Period size: 183 Copynumber: 1.9 Consensus size: 183
20339914 ATGCCTATAC
* ** * * ** *
20339924 CCCTGAAGTTTCAGTGGAGTAGGTTAAAGCTACGAGTCTTATCTCTTTGAAGTTGCAGTGGAGCA
1 CCCTGAAGTTTCAGTGGAGCAAATTAAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCA
* * * * * *
20339989 GAGTGAAGTTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTGCAAATATTAT
66 GAGTAAAGTCACAAATATTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTACAAATATAAT
* * *
20340054 CTCTCTGAAGTTGTAGTGGAATAGATTAAAGCTACAAGTTACGAATCTCATGT
131 CTATCTGAAGTTGCAGTGGAATAGATTAAAGCGACAAGTTACGAATCTCATGT
* *
20340107 CCCTGAAGTTGT-AGTGGAGCAAATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGT
1 CCCTGAAGTT-TCAGTGGAGCAAATTAAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGC
* * * * * *
20340171 AGATTAAAGTCACAAATATTATCTCCCTGAAGTTGCAGTGGAATAGATTAAGGTTACAAATCTAA
65 AGAGTAAAGTCACAAATATTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTACAAATATAA
20340236 TCTATCTGAAGTTGCAGTGGAATAGATTAAAGCGACAA
130 TCTATCTGAAGTTGCAGTGGAATAGATTAAAGCGACAA
20340274 ATCATATACC
Statistics
Matches: 141, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
183 140 0.99
184 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (183 bp):
CCCTGAAGTTTCAGTGGAGCAAATTAAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCA
GAGTAAAGTCACAAATATTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTACAAATATAAT
CTATCTGAAGTTGCAGTGGAATAGATTAAAGCGACAAGTTACGAATCTCATGT
Found at i:20342050 original size:3 final size:3
Alignment explanation
Indices: 20341950--20342040 Score: 68
Period size: 3 Copynumber: 31.3 Consensus size: 3
20341940 CACATTTTTG
* * *
20341950 TTA TTA TCA TTA TTA TTA TT- TTA TTA TGTA -TA TTA GTA TTA TGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* *
20341994 TTTA TTA TTA TTA -TA CTT- TTA -TA TT- TTA TTA TGA GTA TTA TTA
1 -TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20342037 TTA T
1 TTA T
20342041 GCCATTATTA
Statistics
Matches: 69, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
2 12 0.17
3 52 0.75
4 5 0.07
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:20347698 original size:33 final size:33
Alignment explanation
Indices: 20347629--20347707 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
20347619 GTTAATTAAT
* * *
20347629 CTAAACCTTAAACCCTAACCCGACCCTAAATTC
1 CTAAACCTTAAACCCTAACACGACCCCAAATCC
* * *
20347662 CTAATCCTTAAACCCTAACATGACCCCGAATCC
1 CTAAACCTTAAACCCTAACACGACCCCAAATCC
* *
20347695 CTAACCCCTAAAC
1 CTAAACCTTAAAC
20347708 ATTATTTAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.35, C:0.41, G:0.04, T:0.20
Consensus pattern (33 bp):
CTAAACCTTAAACCCTAACACGACCCCAAATCC
Found at i:20347890 original size:14 final size:15
Alignment explanation
Indices: 20347873--20347905 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
20347863 CTTAAATCAG
20347873 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
20347887 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
20347902 AATC
1 AATC
20347906 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:20348144 original size:26 final size:26
Alignment explanation
Indices: 20348109--20348167 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
20348099 TACCCAAAAA
20348109 ATTTTAAAATTATTTTAAATAATAGT
1 ATTTTAAAATTATTTTAAATAATAGT
* *
20348135 TTTTTAAAATTATTTTAAATAATTGT
1 ATTTTAAAATTATTTTAAATAATAGT
20348161 ATTTTAA
1 ATTTTAA
20348168 TTTCTCCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (26 bp):
ATTTTAAAATTATTTTAAATAATAGT
Found at i:20348165 original size:15 final size:15
Alignment explanation
Indices: 20348119--20348167 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
20348109 ATTTTAAAAT
*
20348119 TATTTTAAATAATAG
1 TATTTTAAATAATTG
*
20348134 T-TTTTTAA-AA-T-
1 TATTTTAAATAATTG
20348145 TATTTTAAATAATTG
1 TATTTTAAATAATTG
20348160 TATTTTAA
1 TATTTTAA
20348168 TTTCTCCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
11 1 0.04
12 6 0.22
13 4 0.15
14 7 0.26
15 9 0.33
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (15 bp):
TATTTTAAATAATTG
Found at i:20348620 original size:41 final size:41
Alignment explanation
Indices: 20348549--20348913 Score: 498
Period size: 41 Copynumber: 8.9 Consensus size: 41
20348539 TTTTATTATT
* * * *
20348549 ATTAGCGGCGCTTTTTCAAAAACGCTGCTAAAGGCTCGAGC
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
* * *
20348590 ATCAGCGACGCCTT-TTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCG-CTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
*
20348631 ATTAGCGGCGCTTATCCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
* *
20348672 ATTAGCGGCGCTTCTACAAAAAGGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
*
20348713 ATTAGCGGCGCTTATCCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
* *
20348754 ATTAGCGGCGCTTCTCCAAAAGCGCCGCTAAAGGCCCGAGA
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
* * * *
20348795 ATTAGCGGCGCTTCTCCAAAAGCACCGCTAAAGGGCTGAGC
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
* * *
20348836 ATTAGCGGCGCTTCTTCAAAAGCGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
* * * *
20348877 ATTAGCAGCGCTTTTTCAAAAACGTCGCTAAAGGCCC
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCC
20348914 TAAGGCTTTT
Statistics
Matches: 293, Mismatches: 29, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
40 3 0.01
41 287 0.98
42 3 0.01
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:20349043 original size:40 final size:39
Alignment explanation
Indices: 20348919--20349052 Score: 119
Period size: 40 Copynumber: 3.4 Consensus size: 39
20348909 GGCCCTAAGG
* * *
20348919 CTTTTTGCGGCGCTTTTCAAAAAATGCCGCTAATG-TTTA
1 CTTTTAGCGGCG-TTTTCAAAAAGTGCCGCTAATGCTTGA
* * * * *
20348958 TTTTTAACGGCGTTTCCAAAAAGCGCCGCTAATGCTCGA
1 CTTTTAGCGGCGTTTTCAAAAAGTGCCGCTAATGCTTGA
* *
20348997 CCTTTAGCGGCGTTTTTATAAAAGTGCCGCTAATGCTTGGA
1 CTTTTAGCGGCGTTTTCA-AAAAGTGCCGCTAATGCTT-GA
* *
20349038 -TTTTAGTGGCTTTTT
1 CTTTTAGCGGCGTTTT
20349053 TTGTCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
38 19 0.26
39 24 0.32
40 29 0.39
41 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (39 bp):
CTTTTAGCGGCGTTTTCAAAAAGTGCCGCTAATGCTTGA
Found at i:20354725 original size:31 final size:31
Alignment explanation
Indices: 20354664--20354840 Score: 230
Period size: 31 Copynumber: 5.7 Consensus size: 31
20354654 ATCCAATGCT
* * *
20354664 CAAATC-AATTAGGAAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * * *
20354694 CGAATCAAATTCGGTAATGTACATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
20354725 CAAATCAAATTAGGCAATGAATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * *
20354756 CAAATCGAATTCGACAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
20354787 CAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
20354818 CAAATCAAATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
20354841 AAACATATAC
Statistics
Matches: 125, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
30 5 0.04
31 120 0.96
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCCATATA
Found at i:20355784 original size:9 final size:9
Alignment explanation
Indices: 20355770--20355800 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20355760 GTTAAACGAA
20355770 TCGAGTTAT
1 TCGAGTTAT
*
20355779 TCGAGTTAA
1 TCGAGTTAT
20355788 TCGAGTTAT
1 TCGAGTTAT
20355797 TCGA
1 TCGA
20355801 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:20355870 original size:9 final size:9
Alignment explanation
Indices: 20355853--20355889 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20355843 TGAGTTTTCG
20355853 AATTCGAAT
1 AATTCGAAT
*
20355862 AACTCGAAT
1 AATTCGAAT
20355871 AATTCGAAT
1 AATTCGAAT
20355880 AATTCGAAT
1 AATTCGAAT
20355889 A
1 A
20355890 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:20360301 original size:42 final size:42
Alignment explanation
Indices: 20360206--20360311 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
20360196 CAGGATTGTT
* * * *
20360206 CATAACCATGTGTGGAGGAGGAGCAAGCCCAACAGAATGGTG
1 CATACCCATGTGTGGAGAAGGAACAAGCCCAACAAAATGGTG
* * * *
20360248 TAGACCTATGTGTGGAGAAGGAACAGGCCCAACAAAATGGTG
1 CATACCCATGTGTGGAGAAGGAACAAGCCCAACAAAATGGTG
* *
20360290 CATACCCATGTGCGGGGAAGGA
1 CATACCCATGTGTGGAGAAGGA
20360312 GTAGTCGAGT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.33, C:0.19, G:0.33, T:0.15
Consensus pattern (42 bp):
CATACCCATGTGTGGAGAAGGAACAAGCCCAACAAAATGGTG
Found at i:20364976 original size:119 final size:120
Alignment explanation
Indices: 20364764--20364995 Score: 457
Period size: 119 Copynumber: 1.9 Consensus size: 120
20364754 TTTATATTAA
20364764 AACATTAGTTAAAATTTGATTATAAAATGAATTTTAGTAATTAAAAGAAAACAGATGGTACTACA
1 AACATTAGTTAAAATTTGATTATAAAATGAATTTTAGTAATTAAAAGAAAACAGATGGTACTACA
20364829 AAGGGAGAGAAAAAAAAAGGATATTCTCTTTTCATCTACATCAATTGATTTATAT
66 AAGGGAGAGAAAAAAAAAGGATATTCTCTTTTCATCTACATCAATTGATTTATAT
20364884 AACATTAGTT-AAATTTGATTATAAAATGAATTTTAGTAATTAAAAGAAAACAGATGGTACTACA
1 AACATTAGTTAAAATTTGATTATAAAATGAATTTTAGTAATTAAAAGAAAACAGATGGTACTACA
20364948 AAGGGAGAGAAAAAAAAAGGATATTCTCTTTTCATCTACATCAATTGA
66 AAGGGAGAGAAAAAAAAAGGATATTCTCTTTTCATCTACATCAATTGA
20364996 GGGGAGAAAA
Statistics
Matches: 112, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
119 102 0.91
120 10 0.09
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (120 bp):
AACATTAGTTAAAATTTGATTATAAAATGAATTTTAGTAATTAAAAGAAAACAGATGGTACTACA
AAGGGAGAGAAAAAAAAAGGATATTCTCTTTTCATCTACATCAATTGATTTATAT
Found at i:20365037 original size:119 final size:117
Alignment explanation
Indices: 20364762--20365023 Score: 373
Period size: 119 Copynumber: 2.2 Consensus size: 117
20364752 ATTTTATATT
* *
20364762 AAAACATTAGTTAAAATTTGATTATAAAATGAATTTTAGTAATTAAAAGAAAACAGATGGTACTA
1 AAAACATTAGTT---ATTAGATCATAAAATGAATTTTAGTAATTAAAAGAAAACAGATGGTACTA
*** *
20364827 CAAAGGGAGAGAAAAAAAAAGGATATTCTCTTTTCATCTACATCAATTGATTTAT
63 CAAAGGGAGAGAAAAAAAAAGGATATTCTCTTTTCATCTACATCAATTGAGGGAG
* * *
20364882 ATAACATTAGTTAAATTTGATTATAAAATGAATTTTAGTAATTAAAAGAAAACAGATGGTACTAC
1 AAAACATTAGTT--ATTAGATCATAAAATGAATTTTAGTAATTAAAAGAAAACAGATGGTACTAC
20364947 AAAGGGAGAGAAAAAAAAAGGATATTCTCTTTTCATCTACATCAATTGAGGGGAG
64 AAAGGGAGAGAAAAAAAAAGGATATTCTCTTTTCATCTACATCAATTGA-GGGAG
*
20365002 AAAACATTAGTT-TTAGCTCATA
1 AAAACATTAGTTATTAGATCATA
20365024 GTTTCTTCAT
Statistics
Matches: 132, Mismatches: 9, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
117 7 0.05
119 102 0.77
120 23 0.17
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (117 bp):
AAAACATTAGTTATTAGATCATAAAATGAATTTTAGTAATTAAAAGAAAACAGATGGTACTACAA
AGGGAGAGAAAAAAAAAGGATATTCTCTTTTCATCTACATCAATTGAGGGAG
Found at i:20370417 original size:27 final size:28
Alignment explanation
Indices: 20370383--20370577 Score: 122
Period size: 27 Copynumber: 7.2 Consensus size: 28
20370373 ATGATAACAT
*
20370383 AGGTAGTCCATCGA-GACAGTAAACACG
1 AGGTAGTCCATCTAGGACAGTAAACACG
*
20370410 AGGTAGTCCA-CTAGGATAGTAAACACG
1 AGGTAGTCCATCTAGGACAGTAAACACG
**
20370437 AGGTAGT--ATGCTAGGAC-GTAAACATA
1 AGGTAGTCCAT-CTAGGACAGTAAACACG
* * * *
20370463 AGGTAGTCTA-CCAAGATAGTAAACACG
1 AGGTAGTCCATCTAGGACAGTAAACACG
* **
20370490 AGGTAGT-C-TGCTGGGACAGTAAACATA
1 AGGTAGTCCAT-CTAGGACAGTAAACACG
** * * *
20370517 ATATAGTCCA-CCAGGATAGTAAACACA
1 AGGTAGTCCATCTAGGACAGTAAACACG
* * * *
20370544 ACGTAGTCCA-CCAGGATAGTAAACAAG
1 AGGTAGTCCATCTAGGACAGTAAACACG
20370571 AGGTAGT
1 AGGTAGT
20370578 TTGTTAGGAT
Statistics
Matches: 130, Mismatches: 28, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
25 1 0.01
26 20 0.15
27 107 0.82
28 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (28 bp):
AGGTAGTCCATCTAGGACAGTAAACACG
Found at i:20370467 original size:53 final size:54
Alignment explanation
Indices: 20370397--20370542 Score: 204
Period size: 53 Copynumber: 2.7 Consensus size: 54
20370387 AGTCCATCGA
** *
20370397 GACAGTAAACACGAGGTAGTCCACTAGGATAGTAAACACGAGGTAGTATGCTAG
1 GACAGTAAACATAAGGTAGTCCACCAGGATAGTAAACACGAGGTAGTATGCTAG
* * * *
20370451 GAC-GTAAACATAAGGTAGTCTACCAAGATAGTAAACACGAGGTAGTCTGCTGG
1 GACAGTAAACATAAGGTAGTCCACCAGGATAGTAAACACGAGGTAGTATGCTAG
**
20370504 GACAGTAAACATAATATAGTCCACCAGGATAGTAAACAC
1 GACAGTAAACATAAGGTAGTCCACCAGGATAGTAAACAC
20370543 AACGTAGTCC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 46 0.57
54 34 0.43
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (54 bp):
GACAGTAAACATAAGGTAGTCCACCAGGATAGTAAACACGAGGTAGTATGCTAG
Found at i:20370535 original size:54 final size:53
Alignment explanation
Indices: 20370413--20370551 Score: 188
Period size: 54 Copynumber: 2.6 Consensus size: 53
20370403 AAACACGAGG
* * *
20370413 TAGTCCACTAGGATAGTAAACACGAGGTAGTATGCTAGGACGTAAACATAAGG
1 TAGTCCACCAGGATAGTAAACACGAGGTAGTCTGCTAGGACGTAAACATAAGA
* * * *
20370466 TAGTCTACCAAGATAGTAAACACGAGGTAGTCTGCTGGGACAGTAAACATAATA
1 TAGTCCACCAGGATAGTAAACACGAGGTAGTCTGCTAGGAC-GTAAACATAAGA
* *
20370520 TAGTCCACCAGGATAGTAAACACAACGTAGTC
1 TAGTCCACCAGGATAGTAAACACGAGGTAGTC
20370552 CACCAGGATA
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
53 36 0.49
54 38 0.51
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (53 bp):
TAGTCCACCAGGATAGTAAACACGAGGTAGTCTGCTAGGACGTAAACATAAGA
Found at i:20378237 original size:16 final size:15
Alignment explanation
Indices: 20378210--20378239 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20378200 TAAGTCTGAA
20378210 AAATAAAATAAAAAC
1 AAATAAAATAAAAAC
20378225 AAATAACAATAAAAA
1 AAATAA-AATAAAAA
20378240 TAAAAGATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (15 bp):
AAATAAAATAAAAAC
Found at i:20386213 original size:31 final size:30
Alignment explanation
Indices: 20386155--20386214 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
20386145 AATTGTTCAA
*
20386155 TAACTTAAATAAAAACTCCGAATAGTTTAG
1 TAACTTAAATAAAAACTCCAAATAGTTTAG
*
20386185 TAACTTAAATAAAAACTTTCAAATAGTTTA
1 TAACTTAAATAAAAAC-TCCAAATAGTTTA
20386215 ATGACAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (30 bp):
TAACTTAAATAAAAACTCCAAATAGTTTAG
Found at i:20387741 original size:21 final size:21
Alignment explanation
Indices: 20387717--20387756 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20387707 GCTTAAATAA
20387717 TTTGT-AATTAAGTTACAACTC
1 TTTGTCAATTAA-TTACAACTC
*
20387738 TTTGTCTATTAATTACAAC
1 TTTGTCAATTAATTACAAC
20387757 ATTATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (21 bp):
TTTGTCAATTAATTACAACTC
Found at i:20392198 original size:21 final size:21
Alignment explanation
Indices: 20392174--20392216 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20392164 GAATTTAACT
*
20392174 CAATTTAATACAATTCACATC
1 CAATTCAATACAATTCACATC
* *
20392195 CAATTCCATCCAATTCACATC
1 CAATTCAATACAATTCACATC
20392216 C
1 C
20392217 TAGGAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (21 bp):
CAATTCAATACAATTCACATC
Found at i:20392204 original size:10 final size:11
Alignment explanation
Indices: 20392184--20392216 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
20392174 CAATTTAATA
20392184 CAATTCACATC
1 CAATTCACATC
20392195 CAATTC-CATC
1 CAATTCACATC
20392205 CAATTCACATC
1 CAATTCACATC
20392216 C
1 C
20392217 TAGGAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.33, C:0.39, G:0.00, T:0.27
Consensus pattern (11 bp):
CAATTCACATC
Found at i:20402601 original size:30 final size:30
Alignment explanation
Indices: 20402566--20402624 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
20402556 AATTATTTGC
* *
20402566 AAAATTTAGTTAT-TCTTTTTGTAAATATT
1 AAAAATTAGCTATCTCTTTTTGTAAATATT
* *
20402595 AAAAATTGGCTGTCTCTTTTTGTAAATATT
1 AAAAATTAGCTATCTCTTTTTGTAAATATT
20402625 TTTAAGGCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (30 bp):
AAAAATTAGCTATCTCTTTTTGTAAATATT
Found at i:20406130 original size:49 final size:49
Alignment explanation
Indices: 20406010--20406138 Score: 154
Period size: 50 Copynumber: 2.6 Consensus size: 49
20406000 TTATGAGAGG
* *
20406010 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGATATGGCATGGGCA-CGATAGGAGAAC
* * * *
20406060 TCCCATGTAAGACCATATCTGGGATATGGCATTGGTA-GTTCAGGA-AAC
1 TCCCATGTAAGACCATGTCTGGGATATGGCATGGGCACGAT-AGGAGAAC
*
20406108 ATCCTATGTAAGACCATGTCTGGGATATGGC
1 -TCCCATGTAAGACCATGTCTGGGATATGGC
20406139 TTTCGCATGT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
48 5 0.07
49 31 0.45
50 33 0.48
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTGGGATATGGCATGGGCACGATAGGAGAAC
Found at i:20406373 original size:20 final size:20
Alignment explanation
Indices: 20406348--20406386 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
20406338 TGAGTTATTT
20406348 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
20406368 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
20406387 GAAGAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:20422131 original size:101 final size:100
Alignment explanation
Indices: 20421926--20422107 Score: 240
Period size: 101 Copynumber: 1.8 Consensus size: 100
20421916 CGGTTCACAG
* * * **
20421926 AGTAGCCTGCACATATTACTACACATGCGACCATTACCATTTGATACACGTAGTATTCTGCACAT
1 AGTAGCATGCACATAGTACTACACATGCGACCA-TACCATTCGATACACGTAGTAGCCTGCACAT
*
20421991 AGTACTACACACGTGATCGAAACTATCCGGTACGCAT
65 AGTACTACACACGTGATCCAAACTATCCGGTAC-CAT
* * * *
20422028 AGTAGCATGCACATCGTACTACACATGCGACC-TATCATTCCGGTATACGTAGTAGCCTGCACAT
1 AGTAGCATGCACATAGTACTACACATGCGACCATACCATT-CGATACACGTAGTAGCCTGCACAT
20422092 AGTACTACACACGTGA
65 AGTACTACACACGTGA
20422108 CCATCACTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
100 6 0.09
101 35 0.50
102 29 0.41
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (100 bp):
AGTAGCATGCACATAGTACTACACATGCGACCATACCATTCGATACACGTAGTAGCCTGCACATA
GTACTACACACGTGATCCAAACTATCCGGTACCAT
Found at i:20433313 original size:28 final size:28
Alignment explanation
Indices: 20433273--20433328 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
20433263 AGAATGTTAG
*
20433273 TGAAATTCAGAGTTTTCTCATACTTGCT
1 TGAAATTCAGAGTTTTCTCAGACTTGCT
*
20433301 TGAAATTCAGAGTTTTCTCGGACTTGCT
1 TGAAATTCAGAGTTTTCTCAGACTTGCT
20433329 GGCTATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (28 bp):
TGAAATTCAGAGTTTTCTCAGACTTGCT
Found at i:20437090 original size:16 final size:17
Alignment explanation
Indices: 20437064--20437096 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20437054 TATGAGCATA
20437064 AATATGTGAAAAATATG
1 AATATGTGAAAAATATG
*
20437081 AATA-GTGAAACATATG
1 AATATGTGAAAAATATG
20437097 TGTTTAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.03, G:0.18, T:0.27
Consensus pattern (17 bp):
AATATGTGAAAAATATG
Found at i:20437254 original size:22 final size:22
Alignment explanation
Indices: 20437229--20437297 Score: 57
Period size: 26 Copynumber: 3.0 Consensus size: 22
20437219 ATATGCCAGC
20437229 TCATCAGTATCTATGTGGTGGT
1 TCATCAGTATCTATGTGGTGGT
* * * *
20437251 TCATCCATGATGTGTTATGTGATCGT
1 TCAT-CA-G-TAT-CTATGTGGTGGT
*
20437277 TCATCGGTATCTATGTGGTGG
1 TCATCAGTATCTATGTGGTGG
20437298 CTTGTCCACA
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
22 12 0.35
23 4 0.12
24 2 0.06
25 3 0.09
26 13 0.38
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.41
Consensus pattern (22 bp):
TCATCAGTATCTATGTGGTGGT
Found at i:20441921 original size:3 final size:3
Alignment explanation
Indices: 20441913--20441956 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
20441903 CTTGACTTTC
*
20441913 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20441957 TATTTACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:20446725 original size:26 final size:27
Alignment explanation
Indices: 20446672--20446735 Score: 112
Period size: 26 Copynumber: 2.4 Consensus size: 27
20446662 ATAAAAAATA
20446672 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAAC-TTTTTTTATTT
20446700 ACCAAAATATTATAA-TTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTATTT
20446726 ACCAAAATAT
1 ACCAAAATAT
20446736 ACTAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 21 0.58
28 15 0.42
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (27 bp):
ACCAAAATATTATAACTTTTTTTATTT
Found at i:20447237 original size:45 final size:45
Alignment explanation
Indices: 20447187--20447487 Score: 540
Period size: 45 Copynumber: 6.8 Consensus size: 45
20447177 ATTCAAGAAG
*
20447187 TAATAACTCTATTTTAATTTAATAAATTATTCTCATCAAATTACT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
* *
20447232 TAATAACTCCATTTTAATTTAATACACTATTCTCATC--A-T--T
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
20447272 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
20447317 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
20447362 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
20447407 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
20447452 TAATAACTCTATTTTAATTTAATAAACTATTCTCAT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCAT
20447488 TTAATAAACT
Statistics
Matches: 246, Mismatches: 5, Indels: 10
0.94 0.02 0.04
Matches are distributed among these distances:
40 36 0.15
42 2 0.01
43 2 0.01
45 206 0.84
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (45 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
Found at i:20447307 original size:85 final size:88
Alignment explanation
Indices: 20447149--20447487 Score: 534
Period size: 90 Copynumber: 3.9 Consensus size: 88
20447139 TCTAATTAAG
*
20447149 TAATAACTCTATTTTAATTTAATAAACTA-T-TCA--AGA--AGTAATAACTCTATTTTAATTTA
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCA-ATTATTAATAACTCTATTTTAATTTA
*
20447208 ATAAATTATTCTCATCAAATTACT
65 ATAAACTATTCTCATCAAATTACT
* *
20447232 TAATAACTCCATTTTAATTTAATACACTATTCTCATC-A-T-TTAATAACTCTATTTTAATTTAA
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAATTATTAATAACTCTATTTTAATTTAA
20447294 TAAACTATTCTCATCAAATTACT
66 TAAACTATTCTCATCAAATTACT
20447317 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACTTAATAACTCTATTTTAATTT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATC-AATTA-TTAATAACTCTATTTTAATTT
20447382 AATAAACTATTCTCATCAAATTACT
64 AATAAACTATTCTCATCAAATTACT
20447407 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACTTAATAACTCTATTTTAATTT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATC-AATTA-TTAATAACTCTATTTTAATTT
20447472 AATAAACTATTCTCAT
64 AATAAACTATTCTCAT
20447488 TTAATAAACT
Statistics
Matches: 240, Mismatches: 6, Indels: 13
0.93 0.02 0.05
Matches are distributed among these distances:
83 27 0.11
84 1 0.00
85 83 0.35
87 1 0.00
88 1 0.00
90 127 0.53
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.45
Consensus pattern (88 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAATTATTAATAACTCTATTTTAATTTAA
TAAACTATTCTCATCAAATTACT
Found at i:20447506 original size:15 final size:15
Alignment explanation
Indices: 20447466--20447514 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
20447456 AACTCTATTT
20447466 TAATTTAATAAACTATTC
1 TAATTTAATAAAC---TC
*
20447484 TCATTTAATAAACTC
1 TAATTTAATAAACTC
20447499 TAATTTAATAAACTC
1 TAATTTAATAAACTC
20447514 T
1 T
20447515 CTTTTGGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 17 0.59
18 12 0.41
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATTTAATAAACTC
Found at i:20447617 original size:45 final size:45
Alignment explanation
Indices: 20447521--20447687 Score: 205
Period size: 40 Copynumber: 4.0 Consensus size: 45
20447511 CTCTCTTTTG
20447521 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATT-A
1 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
* *
20447565 --AA--TGATGAGAATAGTGTATTAAATTAAAATGGAGTTATTAA
1 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
*
20447606 GTAATTTGATGAGAATAATTTATTAAATTAAAATAGAGTTATT-A
1 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
* *
20447650 CT--TCT--T--GAATAGTTTATTAAATTAAAATAGAGTTATTA
1 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTA
20447688 CTTAATTAGA
Statistics
Matches: 109, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
38 30 0.28
40 36 0.33
41 1 0.01
42 4 0.04
43 2 0.02
44 2 0.02
45 34 0.31
ACGTcount: A:0.44, C:0.01, G:0.15, T:0.40
Consensus pattern (45 bp):
GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
Found at i:20447666 original size:38 final size:38
Alignment explanation
Indices: 20447618--20447690 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
20447608 AATTTGATGA
20447618 GAATAATTTATTAAATTAAAATAGAGTTATTACTTCTT
1 GAATAATTTATTAAATTAAAATAGAGTTATTACTTCTT
*
20447656 GAATAGTTTATTAAATTAAAATAGAGTTATTACTT
1 GAATAATTTATTAAATTAAAATAGAGTTATTACTT
20447691 AATTAGAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (38 bp):
GAATAATTTATTAAATTAAAATAGAGTTATTACTTCTT
Found at i:20447678 original size:18 final size:18
Alignment explanation
Indices: 20447619--20447679 Score: 50
Period size: 19 Copynumber: 3.3 Consensus size: 18
20447609 ATTTGATGAG
*
20447619 AATAATTTATTAAATTAA
1 AATAGTTTATTAAATTAA
* ** **
20447637 AATAGAGTTATTACTTCTTG
1 AATAG-TTTATTAAAT-TAA
20447657 AATAGTTTATTAAATTAA
1 AATAGTTTATTAAATTAA
20447675 AATAG
1 AATAG
20447680 AGTTATTACT
Statistics
Matches: 30, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
18 10 0.33
19 14 0.47
20 6 0.20
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (18 bp):
AATAGTTTATTAAATTAA
Found at i:20447692 original size:18 final size:18
Alignment explanation
Indices: 20447633--20447692 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 18
20447623 ATTTATTAAA
20447633 TTAAAATAGAGTTATTAC
1 TTAAAATAGAGTTATTAC
** * *
20447651 TTCTTGAATAG-TTTATTAAA
1 -T-TAAAATAGAGTTATT-AC
20447671 TTAAAATAGAGTTATTAC
1 TTAAAATAGAGTTATTAC
20447689 TTAA
1 TTAA
20447693 TTAGAATTCT
Statistics
Matches: 30, Mismatches: 8, Indels: 7
0.67 0.18 0.16
Matches are distributed among these distances:
18 11 0.37
19 12 0.40
20 7 0.23
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (18 bp):
TTAAAATAGAGTTATTAC
Found at i:20447997 original size:27 final size:27
Alignment explanation
Indices: 20447958--20448033 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
20447948 ATTTTAGTCC
*
20447958 TTTGGCACTATTGGTGCCGCCAATATA
1 TTTGGCACCATTGGTGCCGCCAATATA
* *
20447985 TTTGGCACCATTGGTGCCGCCAATCTC
1 TTTGGCACCATTGGTGCCGCCAATATA
* *
20448012 TTTGGCACCTTTGGTGACGCCA
1 TTTGGCACCATTGGTGCCGCCA
20448034 CAAGTTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.32
Consensus pattern (27 bp):
TTTGGCACCATTGGTGCCGCCAATATA
Found at i:20448102 original size:27 final size:27
Alignment explanation
Indices: 20448071--20448134 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
20448061 TTTTTTTGGT
*
20448071 ATATTTTGGTAAATAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
20448098 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
20448125 ATATTTTGGT
1 ATATTTTGGT
20448135 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:20454456 original size:12 final size:12
Alignment explanation
Indices: 20454439--20454468 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20454429 CTTCACACAC
20454439 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
20454451 CCGTGTGCTAGG
1 CCGTGTGCCAGG
20454463 CCGTGT
1 CCGTGT
20454469 AACTGCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:20456782 original size:22 final size:22
Alignment explanation
Indices: 20456756--20456800 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
20456746 ATTACATGTA
*
20456756 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATACAATTTAATT
*
20456778 TTAATTTTAATACAATTTAATT
1 TTAATTATAATACAATTTAATT
20456800 T
1 T
20456801 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTATAATACAATTTAATT
Found at i:20463638 original size:42 final size:43
Alignment explanation
Indices: 20463536--20463684 Score: 155
Period size: 42 Copynumber: 3.5 Consensus size: 43
20463526 TGTGATTTCG
*
20463536 TGTAAGACCACGTCTGGGAC-GATGGCATCGACT-TGA-GATTAACA
1 TGTAAGACCATGTCTGGGACAG-TGGCATCGA-TAT-ATGATT-ACA
* *
20463580 TGTAAGACCATGTCTGGGACATTGGCATC-ATATATGAATT-CG
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATATATG-ATTACA
* *
20463622 TGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGATTACA
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATATATGATTACA
* *
20463665 TGTAAGACCACGTCTAGGAC
1 TGTAAGACCATGTCTGGGAC
20463685 GATGACATTG
Statistics
Matches: 89, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
42 33 0.37
43 27 0.30
44 29 0.33
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGATATATGATTACA
Found at i:20490239 original size:2 final size:2
Alignment explanation
Indices: 20490234--20490271 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
20490224 TATATATATA
20490234 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
20490272 CAGATCATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:20498882 original size:48 final size:48
Alignment explanation
Indices: 20498811--20498956 Score: 292
Period size: 48 Copynumber: 3.0 Consensus size: 48
20498801 AAATAATAGA
20498811 AAAATGTATATTATTTAAGCTTAGGGAAGAATCAGTTATCATGGGTTT
1 AAAATGTATATTATTTAAGCTTAGGGAAGAATCAGTTATCATGGGTTT
20498859 AAAATGTATATTATTTAAGCTTAGGGAAGAATCAGTTATCATGGGTTT
1 AAAATGTATATTATTTAAGCTTAGGGAAGAATCAGTTATCATGGGTTT
20498907 AAAATGTATATTATTTAAGCTTAGGGAAGAATCAGTTATCATGGGTTT
1 AAAATGTATATTATTTAAGCTTAGGGAAGAATCAGTTATCATGGGTTT
20498955 AA
1 AA
20498957 GTTAAAATGA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 98 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.37
Consensus pattern (48 bp):
AAAATGTATATTATTTAAGCTTAGGGAAGAATCAGTTATCATGGGTTT
Found at i:20500635 original size:54 final size:54
Alignment explanation
Indices: 20500532--20500635 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
20500522 TCAACTCAAT
* *
20500532 GAGTTACACGGTCTAGCACACGGCCTGCGACACAACCATGTGGCACAAGTCAGA
1 GAGTTACACGGTCTAGCACACGGCCTACGACACAACCATGTGACACAAGTCAGA
* * * * *
20500586 GAGTTACACGGTCTGGCACATGGCCTACGACACGACCGTGTGACCCAAGT
1 GAGTTACACGGTCTAGCACACGGCCTACGACACAACCATGTGACACAAGT
20500636 TAGTGAGTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (54 bp):
GAGTTACACGGTCTAGCACACGGCCTACGACACAACCATGTGACACAAGTCAGA
Found at i:20500841 original size:21 final size:21
Alignment explanation
Indices: 20500808--20500847 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
20500798 TATCCTAAAC
*
20500808 TGTTCTTAGGGCCCCAAATGCT
1 TGTTCTTAAGG-CCCAAATGCT
20500830 TGTT-TTAAGGCCCAAATG
1 TGTTCTTAAGGCCCAAATG
20500848 TGAATGCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.33
Consensus pattern (21 bp):
TGTTCTTAAGGCCCAAATGCT
Found at i:20506717 original size:57 final size:57
Alignment explanation
Indices: 20506642--20506755 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 57
20506632 ATTTCCAAAC
* * * *
20506642 CATTTCATTTTGGAGAAAACTACATTCATTTTCAAATGTTTC-CATTTCTCCATTTT
1 CATTTCATTTTGAAGAAAACCACATTCATTTCCAAATGTTTCTCATTTATCCATTTT
20506698 CATTTCCATTTTGAAGAAAACCACATTCATTTCCAAATGTTTCTCATTTATCCATTTT
1 CATTT-CATTTTGAAGAAAACCACATTCATTTCCAAATGTTTCTCATTTATCCATTTT
20506756 TACCATTTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 5 0.10
57 34 0.65
58 13 0.25
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.45
Consensus pattern (57 bp):
CATTTCATTTTGAAGAAAACCACATTCATTTCCAAATGTTTCTCATTTATCCATTTT
Found at i:20509301 original size:4 final size:4
Alignment explanation
Indices: 20509285--20509317 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
20509275 TTTGAATTAC
*
20509285 TAAT TATT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
20509318 GAAGTTCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (4 bp):
TAAT
Found at i:20510333 original size:18 final size:19
Alignment explanation
Indices: 20510307--20510343 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
20510297 AAGGAAAGGT
20510307 AACTAAGTAAGTT-TAGAG
1 AACTAAGTAAGTTCTAGAG
*
20510325 AACTTAGTAAGTTCTAGAG
1 AACTAAGTAAGTTCTAGAG
20510344 TAGGCACTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (19 bp):
AACTAAGTAAGTTCTAGAG
Found at i:20516084 original size:21 final size:20
Alignment explanation
Indices: 20516050--20516093 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
20516040 TTATAACGAC
*
20516050 AAAATAAATTATTTTAATTTAT
1 AAAATAAA-TAATTTAATTT-T
20516072 AAAA-AAATAATTTAATTTT
1 AAAATAAATAATTTAATTTT
20516091 AAA
1 AAA
20516094 TTTTCGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 10 0.48
21 3 0.14
22 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAATAAATAATTTAATTTT
Found at i:20517495 original size:13 final size:13
Alignment explanation
Indices: 20517477--20517501 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20517467 ACTTTATTTG
20517477 TTATTTACTTTAT
1 TTATTTACTTTAT
20517490 TTATTTACTTTA
1 TTATTTACTTTA
20517502 CCACTTTCGG
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTACTTTAT
Found at i:20519105 original size:27 final size:27
Alignment explanation
Indices: 20519075--20519136 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
20519065 AAAGATTGTT
20519075 AAAACTCTTCTAAA-AGAAAACTC-AAGA
1 AAAACTCTTC-AAAGA-AAAACTCAAAGA
*
20519102 AAAATTCCTTCAAAGAAAAACTCAAAGA
1 AAAACT-CTTCAAAGAAAAACTCAAAGA
*
20519130 GAAACTC
1 AAAACTC
20519137 AAAGAGAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.55, C:0.19, G:0.08, T:0.18
Consensus pattern (27 bp):
AAAACTCTTCAAAGAAAAACTCAAAGA
Found at i:20519142 original size:12 final size:12
Alignment explanation
Indices: 20519111--20519144 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
20519101 AAAAATTCCT
*
20519111 TCAAAGAAAAAC
1 TCAAAGAGAAAC
20519123 TCAAAGAGAAAC
1 TCAAAGAGAAAC
20519135 TCAAAGAGAA
1 TCAAAGAGAA
20519145 TTTTATTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.09
Consensus pattern (12 bp):
TCAAAGAGAAAC
Found at i:20520141 original size:10 final size:10
Alignment explanation
Indices: 20520128--20520191 Score: 53
Period size: 10 Copynumber: 6.6 Consensus size: 10
20520118 AAAATATAAA
20520128 AAAAATTATT
1 AAAAATTATT
*
20520138 -AAAATTATA
1 AAAAATTATT
*
20520147 AAAGAACT-TT
1 AAA-AATTATT
**
20520157 AAATTTTA-T
1 AAAAATTATT
20520166 AAAAATTATT
1 AAAAATTATT
*
20520176 AAAAAATATT
1 AAAAATTATT
20520186 AAAAAT
1 AAAAAT
20520192 CATAAANNNN
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
9 16 0.40
10 21 0.52
11 3 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
AAAAATTATT
Found at i:20520592 original size:31 final size:29
Alignment explanation
Indices: 20520544--20520601 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
20520534 TTGATAAATT
*
20520544 ATTTTTTTATAAATTCTATAAAATTTTATG
1 ATTTTTTAATAAATTCTA-AAAATTTTATG
* *
20520574 ATTTTTTAATTAATTTCTAATAATTTTA
1 ATTTTTTAA-TAAATTCTAAAAATTTTA
20520602 ATAAATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (29 bp):
ATTTTTTAATAAATTCTAAAAATTTTATG
Found at i:20520621 original size:20 final size:19
Alignment explanation
Indices: 20520564--20520621 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
20520554 AAATTCTATA
20520564 AAATTTTATGATTTTTTAAT
1 AAATTTTATGA-TTTTTAAT
* *
20520584 TAATTTCTAAT-AATTTTAAT
1 AAATTT-T-ATGATTTTTAAT
20520604 AAATTTTGATGATTTTTA
1 AAATTTT-ATGATTTTTA
20520622 TAAGGGTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 3 0.10
20 23 0.77
21 2 0.07
22 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (19 bp):
AAATTTTATGATTTTTAAT
Found at i:20521283 original size:16 final size:16
Alignment explanation
Indices: 20521253--20521290 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
20521243 ACTTTTTATT
20521253 TTTTAGATTTAGGGTTA
1 TTTT-GATTTAGGGTTA
*
20521270 TTTTGATTTGGGGTTA
1 TTTTGATTTAGGGTTA
20521286 TTTTG
1 TTTTG
20521291 GTTATTTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (16 bp):
TTTTGATTTAGGGTTA
Found at i:20521315 original size:6 final size:6
Alignment explanation
Indices: 20521306--20521339 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
20521296 TTCGATTTCA
* *
20521306 ATTTTG ATTTCG ATTTTG ATTTTG ATTTCG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTT
20521340 AGGGTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62
Consensus pattern (6 bp):
ATTTTG
Found at i:20521317 original size:18 final size:18
Alignment explanation
Indices: 20521294--20521449 Score: 93
Period size: 18 Copynumber: 8.6 Consensus size: 18
20521284 TATTTTGGTT
20521294 ATTTCGATTTCAATTTTG
1 ATTTCGATTTCAATTTTG
**
20521312 ATTTCGATTTTGATTTTG
1 ATTTCGATTTCAATTTTG
20521330 ATTTCGATTT-AGGGTTATTTTG
1 ATTTCGATTTCA-----ATTTTG
** * **
20521352 GGTT--ATTTAAATTTCA
1 ATTTCGATTTCAATTTTG
* ** *
20521368 ATTTTGATTTTGATTCTG
1 ATTTCGATTTCAATTTTG
* * *
20521386 ATTTTGATTTCGATTTCG
1 ATTTCGATTTCAATTTTG
*
20521404 ATTTTGATTTCAATTTTG
1 ATTTCGATTTCAATTTTG
*
20521422 ATTTCGATTTCGATTTTG
1 ATTTCGATTTCAATTTTG
*
20521440 ATTTCAATTT
1 ATTTCGATTT
20521450 TGGTTTTATT
Statistics
Matches: 108, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
16 6 0.06
18 89 0.82
20 4 0.04
21 1 0.01
22 8 0.07
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.57
Consensus pattern (18 bp):
ATTTCGATTTCAATTTTG
Found at i:20521370 original size:62 final size:61
Alignment explanation
Indices: 20521269--20521401 Score: 203
Period size: 62 Copynumber: 2.2 Consensus size: 61
20521259 ATTTAGGGTT
* * ** *
20521269 ATTTTGATTTGGGGTTATTTTGGTTATTTCGATTTCAATTTTGATTTCGATTTTGATTTTG
1 ATTTCGATTTAGGGTTATTTTGGTTATTTAAATTTCAATTTTGATTTCGATTCTGATTTTG
*
20521330 ATTTCGATTTAGGGTTATTTTGGGTTATTTAAATTTCAATTTTGATTTTGATTCTGATTTTG
1 ATTTCGATTTAGGGTTATTTT-GGTTATTTAAATTTCAATTTTGATTTCGATTCTGATTTTG
20521392 ATTTCGATTT
1 ATTTCGATTT
20521402 CGATTTTGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
61 19 0.29
62 46 0.71
ACGTcount: A:0.19, C:0.05, G:0.18, T:0.58
Consensus pattern (61 bp):
ATTTCGATTTAGGGTTATTTTGGTTATTTAAATTTCAATTTTGATTTCGATTCTGATTTTG
Found at i:20521377 original size:6 final size:6
Alignment explanation
Indices: 20521368--20521443 Score: 89
Period size: 6 Copynumber: 12.7 Consensus size: 6
20521358 TTAAATTTCA
* * * **
20521368 ATTTTG ATTTTG ATTCTG ATTTTG ATTTCG ATTTCG ATTTTG ATTTCA
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
* *
20521416 ATTTTG ATTTCG ATTTCG ATTTTG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTT
20521444 CAATTTTGGT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.18, C:0.08, G:0.14, T:0.59
Consensus pattern (6 bp):
ATTTTG
Found at i:20521449 original size:6 final size:6
Alignment explanation
Indices: 20521362--20521449 Score: 79
Period size: 6 Copynumber: 14.7 Consensus size: 6
20521352 GGTTATTTAA
* * * * *
20521362 ATTTCA ATTTTG ATTTTG A-TTCTG ATTTTG ATTTCG ATTTCG ATTTTG
1 ATTTCG ATTTCG ATTTCG ATTTC-G ATTTCG ATTTCG ATTTCG ATTTCG
* * * *
20521410 ATTTCA ATTTTG ATTTCG ATTTCG ATTTTG ATTTCA ATTT
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTT
20521450 TGGTTTTATT
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
5 2 0.03
6 62 0.94
7 2 0.03
ACGTcount: A:0.20, C:0.09, G:0.12, T:0.58
Consensus pattern (6 bp):
ATTTCG
Found at i:20521451 original size:12 final size:12
Alignment explanation
Indices: 20521294--20521443 Score: 97
Period size: 12 Copynumber: 12.3 Consensus size: 12
20521284 TATTTTGGTT
* *
20521294 ATTTCGATTTCA
1 ATTTTGATTTCG
20521306 ATTTTGATTTCG
1 ATTTTGATTTCG
*
20521318 ATTTTGATTTTG
1 ATTTTGATTTCG
* *
20521330 ATTTCGATTTAGGG
1 ATTTTGATTT--CG
**
20521344 TTATTTTGGGTT--
1 --ATTTTGATTTCG
** *
20521356 ATTTAAATTTCA
1 ATTTTGATTTCG
*
20521368 ATTTTGATTTTG
1 ATTTTGATTTCG
* *
20521380 ATTCTGATTTTG
1 ATTTTGATTTCG
*
20521392 ATTTCGATTTCG
1 ATTTTGATTTCG
*
20521404 ATTTTGATTTCA
1 ATTTTGATTTCG
20521416 ATTTTGATTTCG
1 ATTTTGATTTCG
* *
20521428 ATTTCGATTTTG
1 ATTTTGATTTCG
20521440 ATTT
1 ATTT
20521444 CAATTTTGGT
Statistics
Matches: 107, Mismatches: 25, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
10 6 0.06
12 93 0.87
14 1 0.01
16 7 0.07
ACGTcount: A:0.20, C:0.07, G:0.15, T:0.57
Consensus pattern (12 bp):
ATTTTGATTTCG
Found at i:20521843 original size:61 final size:61
Alignment explanation
Indices: 20521748--20521882 Score: 225
Period size: 61 Copynumber: 2.2 Consensus size: 61
20521738 GTTAAAGTGT
* * *
20521748 TTGGTTATTGTTTGTCATGTGCTTGACAGAAATGGTTGTGTTTGTATTAAATTACTTTGTA
1 TTGGTTATTGTCTGCCATGTGCATGACAGAAATGGTTGTGTTTGTATTAAATTACTTTGTA
*
20521809 TTGGTTATTGTCTGCCATGTGCATGACAGAAATGGTTGTGTTTGTATTAAATTATTTTGTA
1 TTGGTTATTGTCTGCCATGTGCATGACAGAAATGGTTGTGTTTGTATTAAATTACTTTGTA
*
20521870 TTAGTTATTGTCT
1 TTGGTTATTGTCT
20521883 TATAGAAATG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.21, C:0.07, G:0.22, T:0.49
Consensus pattern (61 bp):
TTGGTTATTGTCTGCCATGTGCATGACAGAAATGGTTGTGTTTGTATTAAATTACTTTGTA
Found at i:20523920 original size:96 final size:97
Alignment explanation
Indices: 20523743--20523964 Score: 349
Period size: 96 Copynumber: 2.3 Consensus size: 97
20523733 TGTCTATGAC
* *
20523743 TATTTTTT-TTAATATGCATGCAGTGATTGTTAGTGTGTATGACTGTTTTTTTTAATATACATGT
1 TATTTTTTAATAATATGCATGCAGTGATTGTTAGTGTGTATGACTGATTTTTTTAATATACATGT
20523807 TGTTGACTATTTCTTAATATGCATGCAGTGAG
66 TGTTGACTATTTCTTAATATGCATGCAGTGAG
*
20523839 TATTTTTTAATAATATGCATGCAGTGATTGTTGGTGTGTATGACT-ATTTTTTTAATATACATGT
1 TATTTTTTAATAATATGCATGCAGTGATTGTTAGTGTGTATGACTGATTTTTTTAATATACATGT
* *
20523903 TGTTGACTTTTTTTTAATATGCATGCAGTGAG
66 TGTTGACTATTTCTTAATATGCATGCAGTGAG
*
20523935 TATTTTTTTTTAATAATATGCATGTAGTGA
1 TA---TTTTTTAATAATATGCATGCAGTGA
20523965 CTTTTTTTAG
Statistics
Matches: 116, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
96 58 0.50
97 34 0.29
99 24 0.21
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.50
Consensus pattern (97 bp):
TATTTTTTAATAATATGCATGCAGTGATTGTTAGTGTGTATGACTGATTTTTTTAATATACATGT
TGTTGACTATTTCTTAATATGCATGCAGTGAG
Found at i:20523952 original size:31 final size:28
Alignment explanation
Indices: 20523910--20523972 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 28
20523900 TGTTGTTGAC
*
20523910 TTTTTTTTAATATGCATGCAGTGAGTATT
1 TTTTTTTTAATATGCATGCAGTGACT-TT
*
20523939 TTTTTTTAATAATATGCATGTAGTGACTTT
1 TTTTTTT--TAATATGCATGCAGTGACTTT
20523969 TTTT
1 TTTT
20523973 AGGTAGGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 7 0.23
30 6 0.20
31 17 0.57
ACGTcount: A:0.24, C:0.06, G:0.14, T:0.56
Consensus pattern (28 bp):
TTTTTTTTAATATGCATGCAGTGACTTT
Found at i:20523969 original size:28 final size:27
Alignment explanation
Indices: 20523875--20523972 Score: 89
Period size: 28 Copynumber: 3.6 Consensus size: 27
20523865 ATTGTTGGTG
20523875 TGTA-TGACTATTTTTTTAATATA--CA
1 TGTAGTGACT-TTTTTTTAATATATGCA
*
20523900 TGTTGTTGACTTTTTTTTAATATGCATGCA
1 TGTAG-TGACTTTTTTTTAATAT--ATGCA
*
20523930 -GTGAGT-ATTTTTTTTTAATAATATGCA
1 TGT-AGTGACTTTTTTTTAAT-ATATGCA
20523957 TGTAGTGACTTTTTTT
1 TGTAGTGACTTTTTTT
20523973 AGGTAGGTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
25 3 0.05
26 12 0.20
27 13 0.22
28 23 0.39
29 5 0.08
30 3 0.05
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.54
Consensus pattern (27 bp):
TGTAGTGACTTTTTTTTAATATATGCA
Found at i:20523973 original size:27 final size:25
Alignment explanation
Indices: 20523875--20523972 Score: 81
Period size: 26 Copynumber: 3.6 Consensus size: 25
20523865 ATTGTTGGTG
*
20523875 TGTA-TGACTATTTTTTTAATATACA
1 TGTAGTGACT-TTTTTTTAATATGCA
*
20523900 TGTTGTTGACTTTTTTTTAATATGCA
1 TGTAG-TGACTTTTTTTTAATATGCA
* *
20523926 TGCAGTGAGTATTTTTTTTTAATAATATGCA
1 TGTAGT--G-A-CTTTTTTT--TAATATGCA
20523957 TGTAGTGACTTTTTTT
1 TGTAGTGACTTTTTTT
20523973 AGGTAGGTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
25 4 0.07
26 17 0.29
27 13 0.22
28 2 0.03
29 8 0.14
31 14 0.24
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.54
Consensus pattern (25 bp):
TGTAGTGACTTTTTTTTAATATGCA
Found at i:20525467 original size:36 final size:36
Alignment explanation
Indices: 20525415--20525497 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
20525405 GGTTAGCCAT
* * *
20525415 ATATACCATCAGCCATGTATAACAATATAAGCAACA
1 ATATACCAGCACCCATGTATAACAACATAAGCAACA
20525451 ATATACCAGCACCCATGTATAACAACATAAGCAACA
1 ATATACCAGCACCCATGTATAACAACATAAGCAACA
20525487 ATATACCAGCA
1 ATATACCAGCA
20525498 ACAATATTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.47, C:0.25, G:0.08, T:0.19
Consensus pattern (36 bp):
ATATACCAGCACCCATGTATAACAACATAAGCAACA
Found at i:20525514 original size:36 final size:36
Alignment explanation
Indices: 20525432--20525518 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
20525422 ATCAGCCATG
* * * * *
20525432 TATAACAATATAAGCAACAATATACCAGCACCCATG
1 TATAAAAACATAAGCAACAATATACCAGCAACAATA
*
20525468 TATAACAACATAAGCAACAATATACCAGCAACAATA
1 TATAAAAACATAAGCAACAATATACCAGCAACAATA
20525504 T-TACAAAACATAAGC
1 TATA-AAAACATAAGC
20525519 TGGTTTTTAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
35 2 0.04
36 43 0.96
ACGTcount: A:0.52, C:0.23, G:0.07, T:0.18
Consensus pattern (36 bp):
TATAAAAACATAAGCAACAATATACCAGCAACAATA
Found at i:20525864 original size:3 final size:3
Alignment explanation
Indices: 20525856--20525921 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
20525846 ATCTCCATTT
*
20525856 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
20525904 TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC
20525922 ACTAACCCTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:20526287 original size:15 final size:14
Alignment explanation
Indices: 20526260--20526286 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20526250 TTGTATTGTA
20526260 AAATATTAAAAAAT
1 AAATATTAAAAAAT
20526274 AAATATTAAAAAA
1 AAATATTAAAAAA
20526287 AAGACACCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATATTAAAAAAT
Found at i:20528237 original size:3 final size:3
Alignment explanation
Indices: 20528229--20528259 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
20528219 TCCATGATCC
20528229 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
20528260 CACAACAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:20530861 original size:75 final size:75
Alignment explanation
Indices: 20530782--20530922 Score: 282
Period size: 75 Copynumber: 1.9 Consensus size: 75
20530772 AAAATTTTTT
20530782 TAATTAAAAAATAATATGGACAGGTCTAAAATGAGTTGGGGTTAGTCTTTTGCAAATATGGATAG
1 TAATTAAAAAATAATATGGACAGGTCTAAAATGAGTTGGGGTTAGTCTTTTGCAAATATGGATAG
20530847 GGTTGGAAAA
66 GGTTGGAAAA
20530857 TAATTAAAAAATAATATGGACAGGTCTAAAATGAGTTGGGGTTAGTCTTTTGCAAATATGGATAG
1 TAATTAAAAAATAATATGGACAGGTCTAAAATGAGTTGGGGTTAGTCTTTTGCAAATATGGATAG
20530922 G
66 G
20530923 TTTGAACAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (75 bp):
TAATTAAAAAATAATATGGACAGGTCTAAAATGAGTTGGGGTTAGTCTTTTGCAAATATGGATAG
GGTTGGAAAA
Found at i:20531005 original size:17 final size:17
Alignment explanation
Indices: 20530980--20531013 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20530970 TAAACATAAA
20530980 ATATGTTAATATCATCT
1 ATATGTTAATATCATCT
* *
20530997 ATATTTTAATATTATCT
1 ATATGTTAATATCATCT
20531014 TTAAATAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (17 bp):
ATATGTTAATATCATCT
Found at i:20531695 original size:3 final size:3
Alignment explanation
Indices: 20531687--20531739 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
20531677 CATATGGCAA
20531687 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20531735 AAT AA
1 AAT AA
20531740 ATAGTAACAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20534041 original size:24 final size:24
Alignment explanation
Indices: 20534014--20534072 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
20534004 GCAAGCTGTG
20534014 GCTGCTGCTGCAACTGGG-GCA-TCT
1 GCTGCTGCTGCAACTGGGAG-AGT-T
* * *
20534038 GCTGTTGTTGCAGCTGGGAGAGTT
1 GCTGCTGCTGCAACTGGGAGAGTT
20534062 GCTGCTGCTGC
1 GCTGCTGCTGC
20534073 TGCTGTTGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.10, C:0.24, G:0.37, T:0.29
Consensus pattern (24 bp):
GCTGCTGCTGCAACTGGGAGAGTT
Found at i:20534100 original size:39 final size:39
Alignment explanation
Indices: 20534043--20534272 Score: 150
Period size: 39 Copynumber: 6.0 Consensus size: 39
20534033 CATCTGCTGT
*
20534043 TGTTGCAGCTG-GGAGAGTTGCTGCTGCTGCTGCTGTTGC
1 TGTTGCAGCTGTGG-GAGCTGCTGCTGCTGCTGCTGTTGC
* * * * ***
20534082 TGTTGCAGCTGAGGGAGTTGTTGCTGTTGCAAATG-TG-
1 TGTTGCAGCTGTGGGAGCTGCTGCTGCTGCTGCTGTTGC
** * * ** * * * *
20534119 -GGAGCGGCTGTTGCTGCTGCGGCTGTTGCTGCTGCTGT
1 TGTTGCAGCTGTGGGAGCTGCTGCTGCTGCTGCTGTTGC
* *
20534157 TGTTGCAGCTGTGGAAGCTGCTGCTGCTGCTGCTGTTGT
1 TGTTGCAGCTGTGGGAGCTGCTGCTGCTGCTGCTGTTGC
20534196 TGTTGCAGCTGTGGGAGCTGCTGCTG-TGGCAT-CTGTTGC
1 TGTTGCAGCTGTGGGAGCTGCTGCTGCT-GC-TGCTGTTGC
* * ** *
20534235 TGTTGTAGCAGTGGCTGCAT-CTGTTGCTGCTGCTGTTG
1 TGTTGCAGCTGTGGGAGC-TGCTGCTGCTGCTGCTGTTG
20534273 ATGCTGGCTT
Statistics
Matches: 148, Mismatches: 34, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
36 21 0.14
37 2 0.01
38 4 0.03
39 116 0.78
40 5 0.03
ACGTcount: A:0.08, C:0.19, G:0.38, T:0.35
Consensus pattern (39 bp):
TGTTGCAGCTGTGGGAGCTGCTGCTGCTGCTGCTGTTGC
Found at i:20534121 original size:24 final size:24
Alignment explanation
Indices: 20534076--20534122 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20534066 CTGCTGCTGC
**
20534076 TGTTGCTGTTGCAGCTGAGGGAGT
1 TGTTGCTGTTGCAAATGAGGGAGT
*
20534100 TGTTGCTGTTGCAAATGTGGGAG
1 TGTTGCTGTTGCAAATGAGGGAG
20534123 CGGCTGTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.11, G:0.40, T:0.34
Consensus pattern (24 bp):
TGTTGCTGTTGCAAATGAGGGAGT
Found at i:20534142 original size:15 final size:15
Alignment explanation
Indices: 20534122--20534167 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
20534112 AAATGTGGGA
20534122 GCGGCTGTTGCTGCT
1 GCGGCTGTTGCTGCT
20534137 GCGGCTGTTGCTGCT
1 GCGGCTGTTGCTGCT
* * *
20534152 GCTGTTGTTGCAGCT
1 GCGGCTGTTGCTGCT
20534167 G
1 G
20534168 TGGAAGCTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.02, C:0.24, G:0.39, T:0.35
Consensus pattern (15 bp):
GCGGCTGTTGCTGCT
Found at i:20534191 original size:15 final size:15
Alignment explanation
Indices: 20534125--20534222 Score: 63
Period size: 15 Copynumber: 6.3 Consensus size: 15
20534115 TGTGGGAGCG
*
20534125 GCTGTTGCTGCTGCG
1 GCTGTTGCTGCTGCT
20534140 GCTGTTGCTGCTGCT
1 GCTGTTGCTGCTGCT
* *
20534155 GTTGTTGCAGCTG-T
1 GCTGTTGCTGCTGCT
*
20534169 GGAAGCTGCTGCTGCTGCT
1 ----GCTGTTGCTGCTGCT
* * *
20534188 GCTGTTGTTGTTGCA
1 GCTGTTGCTGCTGCT
* **
20534203 GCTGTGGGAGCTGCT
1 GCTGTTGCTGCTGCT
20534218 GCTGT
1 GCTGT
20534223 GGCATCTGTT
Statistics
Matches: 63, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
14 1 0.02
15 51 0.81
18 10 0.16
19 1 0.02
ACGTcount: A:0.05, C:0.21, G:0.38, T:0.36
Consensus pattern (15 bp):
GCTGTTGCTGCTGCT
Found at i:20534252 original size:114 final size:113
Alignment explanation
Indices: 20534036--20534272 Score: 282
Period size: 114 Copynumber: 2.1 Consensus size: 113
20534026 ACTGGGGCAT
* *
20534036 CTGCTGTTGTTGCAGCTGGGAGAGTTGCTGCTGCTGCTGCTGTTGCTGTTGCAGCTGAGGGAGTT
1 CTGCTGTTGTTGCAGCTGGGAGAGCTGCTGCTGCTGCTGCTGTTGCTGTTGCAGCTGAGGGAGCT
* * * * *
20534101 GTTGCTGTTGCAAATGTGGGAGCGGCTGTTGCTGCTGCGGCTGTTGCTG
66 GCTGCTGTGGC-AATCTGGGAGCGGCTGTAGCTGCTGCAGCTGTTGCTG
* *
20534150 CTGCTGTTGTTGCAGCTGTGGA-AGCTGCTGCTGCTGCTGCTGTTGTTGTTGCAGCTGTGGGAGC
1 CTGCTGTTGTTGCAGCTG-GGAGAGCTGCTGCTGCTGCTGCTGTTGCTGTTGCAGCTGAGGGAGC
** * * *
20534214 TGCTGCTGTGGC-ATCT-GTTGCTGTTGTAGCAGTGGCTGCATCTGTTGCTG
65 TGCTGCTGTGGCAATCTGGGAGCGGCTGTAGC--T-GCTGCAGCTGTTGCTG
20534264 CTGCTGTTG
1 CTGCTGTTG
20534273 ATGCTGGCTT
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
111 9 0.09
112 3 0.03
113 1 0.01
114 89 0.85
115 3 0.03
ACGTcount: A:0.08, C:0.19, G:0.38, T:0.35
Consensus pattern (113 bp):
CTGCTGTTGTTGCAGCTGGGAGAGCTGCTGCTGCTGCTGCTGTTGCTGTTGCAGCTGAGGGAGCT
GCTGCTGTGGCAATCTGGGAGCGGCTGTAGCTGCTGCAGCTGTTGCTG
Found at i:20546447 original size:55 final size:55
Alignment explanation
Indices: 20546383--20546486 Score: 127
Period size: 55 Copynumber: 1.9 Consensus size: 55
20546373 CATTCGAAGT
* ** *
20546383 AGGGACACACAGTCATGTCTTAGCTCGTGTGTTCGCCCGTGTGAGTATTTGAAAA
1 AGGGACACACAGTCATGTCATAGCTCGTGTGCCCGACCGTGTGAGTATTTGAAAA
* ** * *
20546438 AGGGCCACACAGTTGTGTCATAGGTCGTGTGCCCGACCGTGTGGGTATT
1 AGGGACACACAGTCATGTCATAGCTCGTGTGCCCGACCGTGTGAGTATT
20546487 CGATGTTGGG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 40 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (55 bp):
AGGGACACACAGTCATGTCATAGCTCGTGTGCCCGACCGTGTGAGTATTTGAAAA
Found at i:20547631 original size:41 final size:41
Alignment explanation
Indices: 20547586--20547665 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
20547576 GTTAAAGTTA
*
20547586 CCTGATTTAC-TACACCAGTATGAAGCCTGCTAGGCTCAAGG
1 CCTGA-TTACATACACCAGTATAAAGCCTGCTAGGCTCAAGG
* * * *
20547627 CCTGATTACATGCACCGGTATAAAGCCTGTTAGGTTCAA
1 CCTGATTACATACACCAGTATAAAGCCTGCTAGGCTCAA
20547666 AACCCGATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 4 0.12
41 29 0.88
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (41 bp):
CCTGATTACATACACCAGTATAAAGCCTGCTAGGCTCAAGG
Found at i:20548953 original size:10 final size:10
Alignment explanation
Indices: 20548938--20548970 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
20548928 GTGAGCGCTC
20548938 AATTGAATCG
1 AATTGAATCG
*
20548948 AATTGAATTG
1 AATTGAATCG
20548958 AATTGAATCG
1 AATTGAATCG
20548968 AAT
1 AAT
20548971 GAAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (10 bp):
AATTGAATCG
Found at i:20549531 original size:28 final size:28
Alignment explanation
Indices: 20549494--20549552 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
20549484 GGGAGGAAGT
*
20549494 AAAAGTTTTGGGGAAAAGCAAAAGGAAA
1 AAAAATTTTGGGGAAAAGCAAAAGGAAA
** * *
20549522 AAAAATTTTGGGGGGAAGTAAAAGGGAA
1 AAAAATTTTGGGGAAAAGCAAAAGGAAA
20549550 AAA
1 AAA
20549553 TTTTAGCGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.53, C:0.02, G:0.31, T:0.15
Consensus pattern (28 bp):
AAAAATTTTGGGGAAAAGCAAAAGGAAA
Done.