Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 146 of 230
Found at i:43037499 original size:46 final size:46
Alignment explanation
Indices: 43037432--43037700 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
43037422 TAAGTGTAGC
* **
43037432 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
43037478 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
43037524 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
43037576 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
43037622 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
43037674 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
43037701 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:43037551 original size:52 final size:52
Alignment explanation
Indices: 43037475--43037694 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
43037465 TAGCTAAAGC
* *
43037475 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
43037528 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
43037580 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
43037626 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
43037678 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
43037695 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:43037597 original size:98 final size:98
Alignment explanation
Indices: 43037432--43037700 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
43037422 TAAGTGTAGC
* * *
43037432 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
43037497 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
43037531 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
43037596 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
43037629 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
43037694 GATCAGA
66 GATCAGA
43037701 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:43048600 original size:18 final size:17
Alignment explanation
Indices: 43048567--43048605 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
43048557 TTTTATAAAT
43048567 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
43048585 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
43048602 TGTG
1 TGTG
43048606 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:43048858 original size:23 final size:23
Alignment explanation
Indices: 43048831--43048952 Score: 172
Period size: 23 Copynumber: 5.3 Consensus size: 23
43048821 AGTATTATTG
43048831 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
43048854 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
43048877 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
43048900 TTCAGTGGTAGCTACTGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
43048923 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
43048946 ATTAGTG
1 ATCAGTG
43048953 TGGCACTTAT
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 85 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:43048883 original size:46 final size:46
Alignment explanation
Indices: 43048831--43048945 Score: 203
Period size: 46 Copynumber: 2.5 Consensus size: 46
43048821 AGTATTATTG
43048831 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
* * *
43048877 ATCAGTGGTAGCTTCAGCTACATTTCAGTGGTAGCTACTGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
43048923 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
43048946 ATTAGTGTGG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:43050732 original size:42 final size:42
Alignment explanation
Indices: 43050683--43050934 Score: 202
Period size: 42 Copynumber: 6.0 Consensus size: 42
43050673 TAAACTCAAA
* *
43050683 GTCATGACCTTTAGCGGCGCTTTTACAAAAACGCCGCTAAAG
1 GTCATGACTTTTAGCGGCACTTTTACAAAAACGCCGCTAAAG
* ** **
43050725 GCCATGACTTTTAGCGGTGCTTTTACAAAAACGCTACTAAAG
1 GTCATGACTTTTAGCGGCACTTTTACAAAAACGCCGCTAAAG
* * * * * *
43050767 GTCATGACTTTTAACGACACTTATACAACAAACACCACTATAG
1 GTCATGACTTTTAGCGGCACTTTTACAA-AAACGCCGCTAAAG
* * * * * *
43050810 GTTATGAC-TTTAGCGGCACTTTTTCCACAAACGACGTTATAG
1 GTCATGACTTTTAGCGGCAC-TTTTACAAAAACGCCGCTAAAG
* * * * * * *
43050852 ATCATGACTTTTAGCGGCATTTTTCCCACAACGCTGCTATA-
1 GTCATGACTTTTAGCGGCACTTTTACAAAAACGCCGCTAAAG
* * *
43050893 GTCATGACTTTTAGCGGCGCTTATCACACAAACGCCGCTAAA
1 GTCATGACTTTTAGCGGCACTT-TTACAAAAACGCCGCTAAA
43050935 AATATATCTT
Statistics
Matches: 163, Mismatches: 43, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
41 19 0.12
42 111 0.68
43 33 0.20
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (42 bp):
GTCATGACTTTTAGCGGCACTTTTACAAAAACGCCGCTAAAG
Found at i:43051726 original size:16 final size:15
Alignment explanation
Indices: 43051716--43051753 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 15
43051706 CATAATTGTT
43051716 ATAAAATATAATTTA
1 ATAAAATATAATTTA
43051731 ATAAATATATAATTTA
1 ATAAA-ATATAATTTA
43051747 ATAAAAT
1 ATAAAAT
43051754 TGTTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAAAATATAATTTA
Found at i:43051825 original size:20 final size:21
Alignment explanation
Indices: 43051786--43051825 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
43051776 AATTTACTAA
*
43051786 TAAAATCATAATATATAATAC
1 TAAAATCATAATATAAAATAC
*
43051807 TAAAAT-ATAATTTAAAATA
1 TAAAATCATAATATAAAATA
43051826 ATTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATCATAATATAAAATAC
Found at i:43051838 original size:26 final size:28
Alignment explanation
Indices: 43051793--43051871 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 28
43051783 TAATAAAATC
43051793 ATAATATATAATACTAAAATATAATTTAA-A
1 ATAATATATAAT--T-AAATATAATTTAATA
*
43051823 ATAAT-TATTATTAAATATAATTTAATA
1 ATAATATATAATTAAATATAATTTAATA
*
43051850 ATAATATATAATTTAATA-AATT
1 ATAATATATAATTAAATATAATT
43051872 CTTATTCTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 13 0.30
27 11 0.25
28 10 0.23
29 5 0.11
30 5 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (28 bp):
ATAATATATAATTAAATATAATTTAATA
Found at i:43060625 original size:17 final size:17
Alignment explanation
Indices: 43060603--43060637 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
43060593 TGTTAAAATT
43060603 AAAAAAAAAAAAGAAAG
1 AAAAAAAAAAAAGAAAG
*
43060620 AAAAAAAAGAAAGAAAG
1 AAAAAAAAAAAAGAAAG
43060637 A
1 A
43060638 TAAGATAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAGAAAG
Found at i:43060642 original size:13 final size:13
Alignment explanation
Indices: 43060607--43060635 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
43060597 AAAATTAAAA
43060607 AAAAAAAAGAAAG
1 AAAAAAAAGAAAG
43060620 AAAAAAAAGAAAG
1 AAAAAAAAGAAAG
43060633 AAA
1 AAA
43060636 GATAAGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:43060732 original size:20 final size:20
Alignment explanation
Indices: 43060707--43060752 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
43060697 TTAAGGGAAA
*
43060707 AAATTTACGGTTTCAGGCGG
1 AAATTTACGGTCTCAGGCGG
*
43060727 AAATTTAGGGTCTCAGGCGG
1 AAATTTACGGTCTCAGGCGG
43060747 AAATTT
1 AAATTT
43060753 TGGGATGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.30
Consensus pattern (20 bp):
AAATTTACGGTCTCAGGCGG
Found at i:43061576 original size:7 final size:7
Alignment explanation
Indices: 43061564--43061692 Score: 73
Period size: 7 Copynumber: 18.1 Consensus size: 7
43061554 ACTAATTAAT
43061564 CTAAACC
1 CTAAACC
43061571 CTAAACC
1 CTAAACC
* *
43061578 TTTAACCC
1 -CTAAACC
43061586 CT-AACTC
1 CTAAAC-C
43061593 CTAAACC
1 CTAAACC
*
43061600 CTAAATC
1 CTAAACC
* *
43061607 ATAAAGC
1 CTAAACC
*
43061614 ATAAACC
1 CTAAACC
*
43061621 CTTAACCC
1 C-TAAACC
43061629 CTAAACC
1 CTAAACC
*
43061636 TTAAA-C
1 CTAAACC
*
43061642 CTCAACC
1 CTAAACC
43061649 CTTAAACC
1 C-TAAACC
* *
43061657 ATAAACT
1 CTAAACC
*
43061664 ATAAACC
1 CTAAACC
*
43061671 ATAAACC
1 CTAAACC
* *
43061678 ATAATCC
1 CTAAACC
43061685 CTAAACC
1 CTAAACC
43061692 C
1 C
43061693 ATAATCCATA
Statistics
Matches: 95, Mismatches: 21, Indels: 12
0.74 0.16 0.09
Matches are distributed among these distances:
6 6 0.06
7 70 0.74
8 19 0.20
ACGTcount: A:0.43, C:0.36, G:0.01, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:43061637 original size:14 final size:14
Alignment explanation
Indices: 43061565--43061776 Score: 81
Period size: 14 Copynumber: 14.9 Consensus size: 14
43061555 CTAATTAATC
43061565 TAAACCCTAAACCTT
1 TAAACCCTAAACC-T
* *
43061580 TAACCCCT-AACTCC
1 TAAACCCTAAAC-CT
* *
43061594 TAAACCCTAAATCA
1 TAAACCCTAAACCT
* *
43061608 TAAAGCATAAACCCT
1 TAAACCCTAAA-CCT
*
43061623 TAACCCCTAAACCT
1 TAAACCCTAAACCT
*
43061637 TAAA-CCTCAACCCT
1 TAAACCCT-AAACCT
*
43061651 TAAACCATAAA-CT
1 TAAACCCTAAACCT
* *
43061664 ATAAACCATAAACCA
1 -TAAACCCTAAACCT
* *
43061679 TAATCCCTAAACCCA
1 TAAACCCTAAA-CCT
* * * *
43061694 TAATCCATAATCCA
1 TAAACCCTAAACCT
* ***
43061708 TAAACCTTAAGATAG
1 TAAACCCTAA-ACCT
*
43061723 T-AACTCCTAAACTT
1 TAAAC-CCTAAACCT
* *
43061737 TAAACCATAAACCA
1 TAAACCCTAAACCT
* * *
43061751 TATACCTTAAACCA
1 TAAACCCTAAACCT
43061765 TAAACCCTAAAC
1 TAAACCCTAAAC
43061777 TATAATGATA
Statistics
Matches: 148, Mismatches: 38, Indels: 23
0.71 0.18 0.11
Matches are distributed among these distances:
13 5 0.03
14 101 0.68
15 42 0.28
ACGTcount: A:0.44, C:0.32, G:0.01, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:43061660 original size:43 final size:43
Alignment explanation
Indices: 43061565--43061760 Score: 112
Period size: 43 Copynumber: 4.4 Consensus size: 43
43061555 CTAATTAATC
* * *
43061565 TAAACCCTAAACCTTTAACCCCTAACTCCTAAACCCTAAATCA
1 TAAACCATAAACCCTTAACCCCTAACTCCTAAACCCTAAACCA
* *
43061608 TAAAGCATAAACCCTTAACCCCTAAACCTTAAACCTCAACCCTTAAACCA
1 TAAACCATAAACCCTTAACCCCT-AA-C-T---CCTAAACCC-TAAACCA
* * * * *
43061658 TAAACTATAAA-CCATAAACCATAA-TCCCTAAACCCATAATCCA
1 TAAACCATAAACCCTTAACCCCTAACT-CCTAAACCC-TAAACCA
* **** **
43061701 TAATCCATAAA-CCTTAAGATAGTAACTCCTAAACTTTAAACCA
1 TAAACCATAAACCCTTAA-CCCCTAACTCCTAAACCCTAAACCA
*
43061744 TAAACCATATA-CCTTAA
1 TAAACCATAAACCCTTAA
43061761 ACCATAAACC
Statistics
Matches: 119, Mismatches: 25, Indels: 18
0.73 0.15 0.11
Matches are distributed among these distances:
43 69 0.58
44 13 0.11
45 3 0.03
46 1 0.01
48 2 0.02
49 16 0.13
50 15 0.13
ACGTcount: A:0.44, C:0.31, G:0.02, T:0.23
Consensus pattern (43 bp):
TAAACCATAAACCCTTAACCCCTAACTCCTAAACCCTAAACCA
Found at i:43061701 original size:22 final size:22
Alignment explanation
Indices: 43061645--43061713 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
43061635 CTTAAACCTC
* * *
43061645 AACCCTTAAACCATAAACTATA
1 AACCCATAAACCATAATCCATA
*
43061667 AA-CCATAAACCATAATCCCTA
1 AACCCATAAACCATAATCCATA
*
43061688 AACCCATAATCCATAATCCATA
1 AACCCATAAACCATAATCCATA
43061710 AACC
1 AACC
43061714 TTAAGATAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
21 17 0.43
22 23 0.57
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (22 bp):
AACCCATAAACCATAATCCATA
Found at i:43061747 original size:7 final size:7
Alignment explanation
Indices: 43061737--43061781 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
43061727 TCCTAAACTT
43061737 TAAACCA
1 TAAACCA
43061744 TAAACCA
1 TAAACCA
* *
43061751 TATACCT
1 TAAACCA
43061758 TAAACCA
1 TAAACCA
*
43061765 TAAACCC
1 TAAACCA
*
43061772 TAAACTA
1 TAAACCA
43061779 TAA
1 TAA
43061782 TGATAATTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:43061760 original size:21 final size:21
Alignment explanation
Indices: 43061594--43061776 Score: 102
Period size: 21 Copynumber: 8.6 Consensus size: 21
43061584 CCCTAACTCC
* * * *
43061594 TAAACCCTAAATCATAAAGCA
1 TAAACCATAAACCTTAAACCA
* * * *
43061615 TAAACCCTTAACCCCTAAACCT
1 TAAA-CCATAAACCTTAAACCA
*
43061637 TAAACC-TCAACCCTTAAACCA
1 TAAACCAT-AAACCTTAAACCA
* *
43061658 TAAACTATAAACCATAAACCA
1 TAAACCATAAACCTTAAACCA
* * * *
43061679 TAATCCCTAAACCCATAATCCA
1 TAAACCATAAA-CCTTAAACCA
* *
43061701 TAATCCATAAACCTT-AA-GA
1 TAAACCATAAACCTTAAACCA
* *
43061720 TAGTAACTCCTAAACTTTAAACCA
1 TA--AAC-CATAAACCTTAAACCA
*
43061744 TAAACCATATACCTTAAACCA
1 TAAACCATAAACCTTAAACCA
*
43061765 TAAACCCTAAAC
1 TAAACCATAAAC
43061777 TATAATGATA
Statistics
Matches: 125, Mismatches: 28, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
19 3 0.02
20 2 0.02
21 69 0.55
22 46 0.37
23 2 0.02
24 3 0.02
ACGTcount: A:0.46, C:0.30, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAACCATAAACCTTAAACCA
Found at i:43061781 original size:14 final size:14
Alignment explanation
Indices: 43061594--43061781 Score: 94
Period size: 14 Copynumber: 13.2 Consensus size: 14
43061584 CCCTAACTCC
* *
43061594 TAAACCCTAAATCA
1 TAAACCATAAACCA
* *
43061608 TAAAGCATAAACCCT
1 TAAACCATAAA-CCA
* * *
43061623 TAACCCCTAAACCT
1 TAAACCATAAACCA
* *
43061637 TAAACC-TCAACCCT
1 TAAACCAT-AAACCA
*
43061651 TAAACCATAAACTA
1 TAAACCATAAACCA
43061665 TAAACCATAAACCA
1 TAAACCATAAACCA
* *
43061679 TAATCCCTAAACCCA
1 TAAACCATAAA-CCA
* *
43061694 TAATCCATAATCCA
1 TAAACCATAAACCA
* *
43061708 TAAACC-TTAA-GA
1 TAAACCATAAACCA
* **
43061720 TAGTAACTCCTAAACTT
1 TA--AAC-CATAAACCA
43061737 TAAACCATAAACCA
1 TAAACCATAAACCA
* *
43061751 TATACCTTAAACCA
1 TAAACCATAAACCA
* *
43061765 TAAACCCTAAACTA
1 TAAACCATAAACCA
43061779 TAA
1 TAA
43061782 TGATAATTAA
Statistics
Matches: 133, Mismatches: 32, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
12 3 0.02
13 3 0.02
14 96 0.72
15 26 0.20
16 3 0.02
17 2 0.02
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.23
Consensus pattern (14 bp):
TAAACCATAAACCA
Found at i:43061997 original size:14 final size:14
Alignment explanation
Indices: 43061980--43062013 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
43061970 ACCTTAAATT
* *
43061980 CTAAACCATATACC
1 CTAAACCAAAAACC
43061994 CTAAACCAAAAACC
1 CTAAACCAAAAACC
43062008 CTAAAC
1 CTAAAC
43062014 TATAGTGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CTAAACCAAAAACC
Found at i:43062543 original size:41 final size:41
Alignment explanation
Indices: 43062310--43062546 Score: 201
Period size: 41 Copynumber: 5.8 Consensus size: 41
43062300 GGCTTTTGCG
* * *
43062310 GCGCTTTTTCAAAAACGCCGCTAAAGCTCACGAGCATTAGCT
1 GCGCTTTTTTAAAAACGCCGCTAAAGC-CTCGAGCATTAGCA
* *** ** * *
43062352 GCGCTTATTGGCAAACGCCGCTAAA-AATAGAGCATTAGCG
1 GCGCTTTTTTAAAAACGCCGCTAAAGCCTCGAGCATTAGCA
** * *
43062392 GCGCTTTCCTAAAAACACCGCTAAAATCC-CGAGCATTAGCA
1 GCGCTTTTTTAAAAACGCCGCT-AAAGCCTCGAGCATTAGCA
* * * *
43062433 GTGCTTTCTGAAAAACGCCGCTAAAGCCCCGAGCATTAGC-
1 GCGCTTTTTTAAAAACGCCGCTAAAGCCTCGAGCATTAGCA
* * * * *
43062473 GATGCTTTTTTAAAAACACAGTTAAAGCCTTGAGCATTAGCA
1 G-CGCTTTTTTAAAAACGCCGCTAAAGCCTCGAGCATTAGCA
*
43062515 ACGCTTTTTTAAAAACGCCGCTAAAGCCTCGA
1 GCGCTTTTTTAAAAACGCCGCTAAAGCCTCGA
43062547 AAGCTCAGAA
Statistics
Matches: 152, Mismatches: 38, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
40 31 0.20
41 100 0.66
42 21 0.14
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (41 bp):
GCGCTTTTTTAAAAACGCCGCTAAAGCCTCGAGCATTAGCA
Found at i:43062662 original size:40 final size:39
Alignment explanation
Indices: 43062586--43062662 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
43062576 CGCTTCTTGG
* * *
43062586 AAAACGCCGCTAATGCTCTATTTTTAGCGGTATTTTTCA
1 AAAACGCCACTAATGCTCTATTTTTAGCAGCATTTTTCA
*
43062625 AAAAGCGCCACTAATGCTCTATTTTTAGCAGCGTTTTT
1 AAAA-CGCCACTAATGCTCTATTTTTAGCAGCATTTTT
43062663 ATAAATATGC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (39 bp):
AAAACGCCACTAATGCTCTATTTTTAGCAGCATTTTTCA
Found at i:43082284 original size:19 final size:19
Alignment explanation
Indices: 43082260--43082306 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
43082250 ATGTGGTAAG
43082260 CATTCTTCCCAAGCCTTCA
1 CATTCTTCCCAAGCCTTCA
43082279 CATTCTTCCCAAGCCTTCA
1 CATTCTTCCCAAGCCTTCA
43082298 CATTCTTCC
1 CATTCTTCC
43082307 GAATAATAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.19, C:0.43, G:0.04, T:0.34
Consensus pattern (19 bp):
CATTCTTCCCAAGCCTTCA
Found at i:43089738 original size:56 final size:56
Alignment explanation
Indices: 43089633--43089739 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
43089623 ATTAATGTCG
* * * * *
43089633 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
43089689 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
43089740 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
Found at i:43090388 original size:20 final size:20
Alignment explanation
Indices: 43090363--43090417 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
43090353 ACGAGTTAAA
* *
43090363 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
43090383 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
43090403 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
43090418 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:43092664 original size:20 final size:20
Alignment explanation
Indices: 43092641--43092687 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
43092631 GGGTTAAGCT
*
43092641 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
43092661 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
43092681 TGAGCTG
1 TGAGCTG
43092688 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:43099210 original size:48 final size:47
Alignment explanation
Indices: 43099155--43099260 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 47
43099145 TTGTCTTTTC
*
43099155 TTTCTTTTTCAATTT--TCTCTTTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCATCTC-TTTT--TCACATCCTTT-TTCAATCTCAA
*
43099203 TTTCTTTTTCGATTTCATTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCA-TCTCTTTTTCACATCCTTTTTCAATCTCAA
43099251 TTTCTTTTTC
1 TTTCTTTTTC
43099261 CATGACACTC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
48 40 0.77
49 4 0.08
50 4 0.08
51 4 0.08
ACGTcount: A:0.15, C:0.25, G:0.02, T:0.58
Consensus pattern (47 bp):
TTTCTTTTTCAATTTCATCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:43100284 original size:10 final size:9
Alignment explanation
Indices: 43100271--43100306 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
43100261 CTTTTCACTT
43100271 TTTTTTGTTC
1 TTTTTT-TTC
43100281 TTTTTTTTAC
1 TTTTTTTT-C
43100291 TTTTTTTTC
1 TTTTTTTTC
43100300 TTTTTTT
1 TTTTTTT
43100307 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:43100292 original size:22 final size:21
Alignment explanation
Indices: 43100262--43100325 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
43100252 CTCACAAGAC
*
43100262 TTTTCACTTTTTTTTGTTCTTT
1 TTTTCACTTTTTTTTCTT-TTT
*
43100284 TTTTTACTTTTTTTTCTTTTT
1 TTTTCACTTTTTTTTCTTTTT
* *
43100305 TTGCTCACTTCTTTTT-TTTTT
1 TT-TTCACTTTTTTTTCTTTTT
43100326 GAATTTCGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 10 0.28
22 26 0.72
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTCACTTTTTTTTCTTTTT
Found at i:43101874 original size:20 final size:20
Alignment explanation
Indices: 43101851--43101897 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
43101841 GGGTTAAGCT
*
43101851 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
43101871 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
43101891 TGAGCTG
1 TGAGCTG
43101898 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:43106585 original size:20 final size:20
Alignment explanation
Indices: 43106539--43106585 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
43106529 AGCTTGTTTC
*
43106539 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
43106559 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
43106579 CAGCTCA
1 CAGCTCA
43106586 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:43115673 original size:30 final size:30
Alignment explanation
Indices: 43115639--43115735 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
43115629 AGCTCACTCC
43115639 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
43115669 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
43115699 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
43115729 TAGCTCA
1 TAGCTCA
43115736 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:43117463 original size:11 final size:11
Alignment explanation
Indices: 43117449--43117498 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
43117439 GAAGAAATTC
43117449 AAAAAAAATCG
1 AAAAAAAATCG
43117460 AAAAAAAATC-
1 AAAAAAAATCG
**
43117470 AAAAAAAAAGG
1 AAAAAAAATCG
*
43117481 AAAAAAAGT-G
1 AAAAAAAATCG
43117491 AAAAAAAA
1 AAAAAAAA
43117499 AATCGAGTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.80, C:0.04, G:0.10, T:0.06
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:43117471 original size:21 final size:21
Alignment explanation
Indices: 43117447--43117499 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
43117437 GAGAAGAAAT
*
43117447 TCAAAAAAAATCGAAAAAAAA
1 TCAAAAAAAAACGAAAAAAAA
* *
43117468 TCAAAAAAAAAGGAAAAAAAG
1 TCAAAAAAAAACGAAAAAAAA
*
43117489 TGAAAAAAAAA
1 TCAAAAAAAAA
43117500 ATCGAGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.77, C:0.06, G:0.09, T:0.08
Consensus pattern (21 bp):
TCAAAAAAAAACGAAAAAAAA
Found at i:43118443 original size:16 final size:16
Alignment explanation
Indices: 43118424--43118484 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
43118414 AAGAGAAAAC
43118424 AAAG-AAAAGAAAAGAA
1 AAAGAAAAAGAAAAG-A
*
43118440 AAAGAAAAAG-CAAGA
1 AAAGAAAAAGAAAAGA
*
43118455 GAAGAAAAAGAAAATG-
1 AAAGAAAAAGAAAA-GA
*
43118471 AAATAAAAAGAAAA
1 AAAGAAAAAGAAAA
43118485 AGAGGCAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
15 10 0.27
16 21 0.57
17 6 0.16
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAGAAAAAGAAAAGA
Found at i:43118444 original size:6 final size:6
Alignment explanation
Indices: 43118424--43118487 Score: 55
Period size: 6 Copynumber: 10.8 Consensus size: 6
43118414 AAGAGAAAAC
*
43118424 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATG--
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
*
43118471 AAATAA AAAGAA AAAGA
1 AAAGAA AAAGAA AAAGA
43118488 GGCAAGAGGC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
4 2 0.04
5 9 0.18
6 29 0.59
7 3 0.06
8 3 0.06
9 3 0.06
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:43118454 original size:21 final size:21
Alignment explanation
Indices: 43118424--43118487 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
43118414 AAGAGAAAAC
43118424 AAAGAAAAGAAAAGAAAAAGAA
1 AAAG-AAAGAAAAGAAAAAGAA
* *
43118446 AAAGCAAGAGAAGAAAAAGAA
1 AAAGAAAGAAAAGAAAAAGAA
* *
43118467 AATGAAATAAAAAGAAAAAGA
1 AAAGAAA-GAAAAGAAAAAGA
43118488 GGCAAGAGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.03
Consensus pattern (21 bp):
AAAGAAAGAAAAGAAAAAGAA
Found at i:43118465 original size:37 final size:37
Alignment explanation
Indices: 43118414--43118486 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
43118404 CATTCTTGTA
43118414 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
43118451 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAAAG
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAAAG
43118487 AGGCAAGAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
37 30 0.91
38 3 0.09
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:43118566 original size:11 final size:12
Alignment explanation
Indices: 43118533--43118563 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
43118523 TTGAGAGAAC
*
43118533 TTGAAAAAGCCT
1 TTGAAAAAGCAT
43118545 TTGAAAAAGCAT
1 TTGAAAAAGCAT
43118557 TTGAAAA
1 TTGAAAA
43118564 GCAAAAAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCAT
Found at i:43120765 original size:30 final size:30
Alignment explanation
Indices: 43120731--43120827 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
43120721 AGCTCACTCC
43120731 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
43120761 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
43120791 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
43120821 TAGCTCA
1 TAGCTCA
43120828 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:43123284 original size:6 final size:6
Alignment explanation
Indices: 43123275--43123299 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43123265 GGAGTTTTTT
43123275 TTTTAG TTTTAG TTTTAG TTTTAG T
1 TTTTAG TTTTAG TTTTAG TTTTAG T
43123300 GTTCTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTTAG
Found at i:43130831 original size:13 final size:13
Alignment explanation
Indices: 43130813--43130837 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43130803 TGGTCATCAT
43130813 GGTGTGAACACAA
1 GGTGTGAACACAA
43130826 GGTGTGAACACA
1 GGTGTGAACACA
43130838 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:43134040 original size:14 final size:13
Alignment explanation
Indices: 43134022--43134055 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
43134012 TTTTCAATCA
*
43134022 ATTTTTTTTTTCG
1 ATTTTTTTTTTTG
43134035 ATTTTTTTTTTTG
1 ATTTTTTTTTTTG
43134048 ATTTTTTT
1 ATTTTTTT
43134056 GTTACTCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (13 bp):
ATTTTTTTTTTTG
Found at i:43134133 original size:13 final size:13
Alignment explanation
Indices: 43134115--43134148 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
43134105 TACAACTCAA
43134115 TTTTTTTTTGA-T
1 TTTTTTTTTGACT
43134127 TTTTTTTTTGACT
1 TTTTTTTTTGACT
43134140 TTTTTTTTT
1 TTTTTTTTT
43134149 TTACATTACG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTGACT
Found at i:43136673 original size:6 final size:6
Alignment explanation
Indices: 43136662--43136686 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43136652 AGGAGTTTTT
43136662 TTTTAG TTTTAG TTTTAG TTTTAG T
1 TTTTAG TTTTAG TTTTAG TTTTAG T
43136687 GTTCTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTTAG
Found at i:43141536 original size:20 final size:20
Alignment explanation
Indices: 43141511--43141557 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
43141501 AGCTCGTTTC
43141511 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* *
43141531 CAGCTCATTCGAGCTCAATT
1 CAGCTCACTCGAGCTCAAGT
43141551 CAGCTCA
1 CAGCTCA
43141558 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:43141555 original size:10 final size:10
Alignment explanation
Indices: 43141522--43141559 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
43141512 AGCTCACTCG
*
43141522 AGCTCAAGTC
1 AGCTCAATTC
43141532 AGCTC-ATTC
1 AGCTCAATTC
43141541 GAGCTCAATTC
1 -AGCTCAATTC
43141552 AGCTCAAT
1 AGCTCAAT
43141560 CTTAACCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.72
11 4 0.16
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:43143839 original size:45 final size:45
Alignment explanation
Indices: 43143775--43143962 Score: 322
Period size: 45 Copynumber: 4.2 Consensus size: 45
43143765 CATGAAATTA
*
43143775 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
43143820 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
43143865 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
43143910 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
43143955 AGGAAGCA
1 AGGAAGCA
43143963 CCATGGCCGA
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 136 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:43144798 original size:22 final size:20
Alignment explanation
Indices: 43144755--43144802 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
43144745 AAAAAAAAGA
* *
43144755 GAAATTCAAAAAAAAATTTT
1 GAAATTAAAAAAAAAATATT
43144775 GAAATTAAAAAAAAAAGTGATT
1 GAAATTAAAAAAAAAA-T-ATT
43144797 GAAATT
1 GAAATT
43144803 CATTTTAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 15 0.62
21 1 0.04
22 8 0.33
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.27
Consensus pattern (20 bp):
GAAATTAAAAAAAAAATATT
Found at i:43148623 original size:12 final size:12
Alignment explanation
Indices: 43148583--43148632 Score: 64
Period size: 13 Copynumber: 4.0 Consensus size: 12
43148573 GAGAGTTCGA
43148583 AAAAAAAAATCTG
1 AAAAAAAAAT-TG
**
43148596 AAAAAAAAGAAGG
1 AAAAAAAA-ATTG
43148609 AAAAAAAAATTG
1 AAAAAAAAATTG
43148621 AAAAAAAAATTG
1 AAAAAAAAATTG
43148633 CATACGGTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 14 0.44
13 17 0.53
14 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:43149732 original size:18 final size:18
Alignment explanation
Indices: 43149694--43149735 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
43149684 AAATCGAAAG
* **
43149694 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
43149712 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
43149730 AAAAGA
1 AAAAGA
43149736 GAGTGAGGTC
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:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:43154271 original size:25 final size:26
Alignment explanation
Indices: 43154227--43154277 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
43154217 AAATTAAATA
*
43154227 CCTCACCAAAAAATTCTCAC-CAATT
1 CCTCACAAAAAAATTCTCACACAATT
43154252 CCTCACAAAGAAAATT-TCACACAATT
1 CCTCACAAA-AAAATTCTCACACAATT
43154278 TGGCTTTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.43, C:0.31, G:0.02, T:0.24
Consensus pattern (26 bp):
CCTCACAAAAAAATTCTCACACAATT
Found at i:43154499 original size:17 final size:17
Alignment explanation
Indices: 43154476--43154522 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
43154466 ATTTCAATCA
43154476 CTTTTTTTTTAATTCCGT
1 CTTTTTTTTTAATTCC-T
* *
43154494 -TTTTTTTTGAATTTCT
1 CTTTTTTTTTAATTCCT
43154510 CTTTTTTTTTAAT
1 CTTTTTTTTTAAT
43154523 ACCGAATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 24 0.96
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.72
Consensus pattern (17 bp):
CTTTTTTTTTAATTCCT
Found at i:43155347 original size:45 final size:45
Alignment explanation
Indices: 43155296--43155393 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
43155286 TCGGCCATGG
* * * *
43155296 TGCTTCCTCAATTTGTTTCATAAATTATGCATGATGTTTGCCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
* * *
43155341 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
43155386 TGCTTCCT
1 TGCTTCCT
43155394 GATACGGAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.42
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
Found at i:43163862 original size:45 final size:45
Alignment explanation
Indices: 43163812--43163952 Score: 273
Period size: 45 Copynumber: 3.1 Consensus size: 45
43163802 ACTCGTATCA
43163812 CTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATG
1 CTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATG
43163857 CTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATG
1 CTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATG
*
43163902 CTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAATG
1 CTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATG
43163947 CTTCCT
1 CTTCCT
43163953 TAATTTCATG
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 95 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (45 bp):
CTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATG
Found at i:43166917 original size:15 final size:14
Alignment explanation
Indices: 43166881--43166922 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
43166871 TCTATTGAGC
43166881 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
43166895 GAGAAAAATAAAAA
1 GAGAAAAAGAAAAA
*
43166909 GAGTGAAAAGAAAA
1 GAG-AAAAAGAAAA
43166923 GAAAGAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:43172345 original size:13 final size:14
Alignment explanation
Indices: 43172324--43172376 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
43172314 GATATCAAGT
*
43172324 TGAAAAAAAATTCG
1 TGAAAAAAATTTCG
43172338 TGAAAAAAATTTCG
1 TGAAAAAAATTTCG
43172352 TGAAAAAAAAATTTTCG
1 TG--AAAAAAA-TTTCG
43172369 TGAAAAAA
1 TGAAAAAA
43172377 GAAGAAGCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
14 15 0.43
15 6 0.17
16 7 0.20
17 7 0.20
ACGTcount: A:0.57, C:0.06, G:0.13, T:0.25
Consensus pattern (14 bp):
TGAAAAAAATTTCG
Found at i:43172360 original size:17 final size:17
Alignment explanation
Indices: 43172340--43172376 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
43172330 AAAATTCGTG
43172340 AAAAAAATTTCGTGAAA
1 AAAAAAATTTCGTGAAA
*
43172357 AAAAAATTTTCGTGAAA
1 AAAAAAATTTCGTGAAA
43172374 AAA
1 AAA
43172377 GAAGAAGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.24
Consensus pattern (17 bp):
AAAAAAATTTCGTGAAA
Found at i:43174840 original size:14 final size:13
Alignment explanation
Indices: 43174813--43174854 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
43174803 AAAAAAATAT
43174813 AAAAAATTCGAAA
1 AAAAAATTCGAAA
*
43174826 AAAAAATTTGAAA
1 AAAAAATTCGAAA
43174839 AAAAAATT--AAA
1 AAAAAATTCGAAA
43174850 AAAAA
1 AAAAA
43174855 GTTTTTATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 8 0.29
13 20 0.71
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (13 bp):
AAAAAATTCGAAA
Found at i:43174913 original size:13 final size:13
Alignment explanation
Indices: 43174895--43174919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43174885 ATTTAGTATT
43174895 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
43174908 GAAGAAAAAAAA
1 GAAGAAAAAAAA
43174920 TTCGGAATTA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAAAA
Found at i:43174935 original size:30 final size:30
Alignment explanation
Indices: 43174892--43174968 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 30
43174882 TGTATTTAGT
* **
43174892 ATTGAAGAAAAAAAAAGAAGAAAAAAAATTCGGA
1 ATTGAA-AAAAAAAAAGAAAAAAA--AA-TCAAA
43174926 ATT-AAAAAAAAAAAGAAAAAAAAATCAAA
1 ATTGAAAAAAAAAAAGAAAAAAAAATCAAA
43174955 ATTGAAAAAAAAAA
1 ATTGAAAAAAAAAA
43174969 GTGATTGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 6 0.15
30 12 0.31
32 16 0.41
33 2 0.05
34 3 0.08
ACGTcount: A:0.75, C:0.03, G:0.10, T:0.12
Consensus pattern (30 bp):
ATTGAAAAAAAAAAAGAAAAAAAAATCAAA
Found at i:43174942 original size:29 final size:29
Alignment explanation
Indices: 43174899--43174969 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
43174889 AGTATTGAAG
* **
43174899 AAAAAAAAAGAAGAAAAAAAATTCGGAATT
1 AAAAAAAAA-AAGAAAAAAAAATCAAAATT
43174929 AAAAAAAAAAAGAAAAAAAAATCAAAATT
1 AAAAAAAAAAAGAAAAAAAAATCAAAATT
*
43174958 GAAAAAAAAAAG
1 AAAAAAAAAAAG
43174970 TGATTGAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 28 0.76
30 9 0.24
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (29 bp):
AAAAAAAAAAAGAAAAAAAAATCAAAATT
Found at i:43175947 original size:18 final size:18
Alignment explanation
Indices: 43175926--43175963 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
43175916 AAAGCAAAAA
43175926 GAGATTGA-AAAAGAAATT
1 GAGATTGAGAAAA-AAATT
43175944 GAGATTGAGAAAAAAATT
1 GAGATTGAGAAAAAAATT
43175962 GA
1 GA
43175964 AAAAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (18 bp):
GAGATTGAGAAAAAAATT
Found at i:43183747 original size:14 final size:15
Alignment explanation
Indices: 43183728--43183766 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
43183718 TATTGATGCA
43183728 TAAATTAAG-TTCTT
1 TAAATTAAGCTTCTT
*
43183742 TAAATTATGCTTCTT
1 TAAATTAAGCTTCTT
43183757 T-AATTAAGCT
1 TAAATTAAGCT
43183767 AGTTGCTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (15 bp):
TAAATTAAGCTTCTT
Found at i:43190319 original size:12 final size:12
Alignment explanation
Indices: 43190304--43190328 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43190294 TTTTTTTCGA
43190304 TTTTTTTGAATT
1 TTTTTTTGAATT
43190316 TTTTTTTGAATT
1 TTTTTTTGAATT
43190328 T
1 T
43190329 CTTCTCTTTT
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:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:43191410 original size:20 final size:20
Alignment explanation
Indices: 43191364--43191410 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
43191354 AGCTCGTTTC
*
43191364 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
43191384 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
43191404 CAGCTCA
1 CAGCTCA
43191411 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:43193378 original size:20 final size:20
Alignment explanation
Indices: 43193331--43193378 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
43193321 AGTAAGCTCG
43193331 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
43193351 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
43193371 GTTGAGCT
1 GTTGAGCT
43193379 GGATGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:43202302 original size:18 final size:16
Alignment explanation
Indices: 43202276--43202314 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
43202266 GTATGCAATA
43202276 TTTTTTTTTCAAATTTT
1 TTTTTTTTTC-AATTTT
*
43202293 TTTTTCTTTTCGATTTT
1 TTTTT-TTTTCAATTTT
43202310 TTTTT
1 TTTTT
43202315 GATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTTTTTCAATTTT
Found at i:43204929 original size:4 final size:4
Alignment explanation
Indices: 43204920--43204950 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
43204910 AAGTTTTATT
*
43204920 TTTA TTTA TTTA TTTA TTTA TTTA CTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
43204951 TAAATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:43213131 original size:10 final size:11
Alignment explanation
Indices: 43213115--43213143 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
43213105 AAGAAGTGAG
43213115 CAAAAAAAGAA
1 CAAAAAAAGAA
43213126 -AAAAAAAGAA
1 CAAAAAAAGAA
43213136 CAAAAAAA
1 CAAAAAAA
43213144 AGTGAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (11 bp):
CAAAAAAAGAA
Found at i:43214146 original size:6 final size:6
Alignment explanation
Indices: 43214130--43214270 Score: 72
Period size: 6 Copynumber: 23.3 Consensus size: 6
43214120 CCAATGAGTG
* * * * * *
43214130 AGAAAA GGAAAA AGAAAT TGAAAA AGAAAT TG--AA AG-AAA ACAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
* * * * * *
43214175 AGAAAA CGAAAA AGAAAA AGAAAT TGCAAA AGAAAA AGAAAT CGAAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AG-AAAA
** * * *
43214224 AGTGAG AGAAAA AGAAAA TAAAGAAA AGAAAA TTGAAAA AGAAAA AG
1 AGAAAA AGAAAA AGAAAA -AGA-AAA AGAAAA -AGAAAA AGAAAA AG
43214271 CGAAAAAAGA
Statistics
Matches: 95, Mismatches: 34, Indels: 12
0.67 0.24 0.09
Matches are distributed among these distances:
4 2 0.02
5 3 0.03
6 74 0.78
7 13 0.14
8 3 0.03
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.08
Consensus pattern (6 bp):
AGAAAA
Found at i:43214158 original size:18 final size:18
Alignment explanation
Indices: 43214131--43214270 Score: 97
Period size: 18 Copynumber: 7.7 Consensus size: 18
43214121 CAATGAGTGA
*
43214131 GAAAAGGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATT
**
43214149 GAAAAAGAAATTGAAA--
1 GAAAAAGAAAAAGAAATT
* **
43214165 G-AAAACAAAAAGAAAAC
1 GAAAAAGAAAAAGAAATT
43214182 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATT
* *
43214200 GCAAAAGAAAAAGAAATC
1 GAAAAAGAAAAAGAAATT
** * **
43214218 GAAAAAAGTGAGAGAAAAA
1 G-AAAAAGAAAAAGAAATT
*
43214237 GAAAATAAAGAAAAGAAAATT
1 GAAAA-AGA-AAAAG-AAATT
43214258 GAAAAAGAAAAAG
1 GAAAAAGAAAAAG
43214271 CGAAAAAAGA
Statistics
Matches: 91, Mismatches: 24, Indels: 13
0.71 0.19 0.10
Matches are distributed among these distances:
15 11 0.12
16 1 0.01
17 1 0.01
18 47 0.52
19 18 0.20
20 5 0.05
21 8 0.09
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.08
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATT
Found at i:43214322 original size:33 final size:33
Alignment explanation
Indices: 43214285--43214347 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
43214275 AAAAGAAATT
43214285 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
43214318 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
43214348 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:43225433 original size:12 final size:12
Alignment explanation
Indices: 43225418--43225448 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
43225408 TTCTTTTTGC
43225418 TTTTCAAAGGCT
1 TTTTCAAAGGCT
43225430 TTTTCAAAGGCT
1 TTTTCAAAGGCT
43225442 TTTTCAA
1 TTTTCAA
43225449 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:43225541 original size:37 final size:37
Alignment explanation
Indices: 43225498--43225568 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
43225488 CTTGCCTCTC
43225498 TTTTCTTTTTATTTAATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTATTTAATTTTCTTTGTT-TTCTCTTGCT
* **
43225535 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTATTTAATTTTCTTTGTTTTCTCTT
43225569 TACAAGAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 28 0.93
38 2 0.07
ACGTcount: A:0.04, C:0.17, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTATTTAATTTTCTTTGTTTTCTCTTGCT
Found at i:43225554 original size:16 final size:16
Alignment explanation
Indices: 43225496--43225558 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
43225486 CTCTTGCCTC
*
43225496 TCTTTTCTTTTTATTT
1 TCTTTTCTTTTTCTTT
** *
43225512 AATTTTCTTTTTCTTC
1 TCTTTTCTTTTTCTTT
*
43225528 TC-TTGCTTTTTCTTTT
1 TCTTTTCTTTTTC-TTT
43225544 TCTTTTC-TTTTCTTT
1 TCTTTTCTTTTTCTTT
43225559 GTTTTCTCTT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
15 12 0.33
16 21 0.58
17 3 0.08
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (16 bp):
TCTTTTCTTTTTCTTT
Found at i:43226501 original size:12 final size:11
Alignment explanation
Indices: 43226486--43226526 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 11
43226476 TTTAACTCGA
43226486 TTTTTTTTTCAC
1 TTTTTTTTT-AC
43226498 TTTTTTTTT-C
1 TTTTTTTTTAC
43226508 TTTTTTTTTGA-
1 TTTTTTTTT-AC
43226519 TTTTTTTT
1 TTTTTTTT
43226527 GAATTTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.37
11 8 0.30
12 9 0.33
ACGTcount: A:0.05, C:0.07, G:0.02, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTAC
Found at i:43232113 original size:21 final size:23
Alignment explanation
Indices: 43232068--43232114 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
43232058 TCACCTGCAA
* *
43232068 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
43232091 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
43232112 TAA
1 TAA
43232115 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:43237325 original size:11 final size:12
Alignment explanation
Indices: 43237295--43237323 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
43237285 TTGGAGTAAC
43237295 AAAAAAA-TCAA
1 AAAAAAATTCAA
43237306 AAAAAAATTCAA
1 AAAAAAATTCAA
43237318 AAAAAA
1 AAAAAA
43237324 TTTTTGATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:43237386 original size:24 final size:25
Alignment explanation
Indices: 43237335--43237392 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
43237325 TTTTGATTGA
**
43237335 AAAAAAAATTCAAACAAAAAAAGTG
1 AAAAAAAATTCAAACAAAAAAAAAG
* *
43237360 AAAAAAAA-TCGAGCAAAAAAAAAG
1 AAAAAAAATTCAAACAAAAAAAAAG
43237384 AAAAGAAAA
1 AAAA-AAAA
43237393 AAAAAGGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.76, C:0.07, G:0.10, T:0.07
Consensus pattern (25 bp):
AAAAAAAATTCAAACAAAAAAAAAG
Found at i:43239810 original size:18 final size:18
Alignment explanation
Indices: 43239789--43239823 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43239779 AGAAAAGAAA
43239789 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
43239807 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
43239824 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:43245064 original size:12 final size:12
Alignment explanation
Indices: 43245047--43245091 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
43245037 AAAGCAAACC
43245047 AATTTTTTTTTG
1 AATTTTTTTTTG
43245059 AATTTTTTTTTG
1 AATTTTTTTTTG
*
43245071 AA-TTTTTTTCG
1 AATTTTTTTTTG
43245082 AATTTTTTTT
1 AATTTTTTTT
43245092 GAAGAAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:43245066 original size:11 final size:11
Alignment explanation
Indices: 43245050--43245094 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
43245040 GCAAACCAAT
43245050 TTTTTTTTGAA
1 TTTTTTTTGAA
43245061 TTTTTTTTTGAA
1 -TTTTTTTTGAA
*
43245073 TTTTTTTCGAA
1 TTTTTTTTGAA
43245084 TTTTTTTTGAA
1 TTTTTTTTGAA
43245095 GAAACTACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.71
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:43246129 original size:21 final size:23
Alignment explanation
Indices: 43246084--43246130 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
43246074 TCACTTGCAA
* *
43246084 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
43246107 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
43246128 TAA
1 TAA
43246131 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:43253859 original size:16 final size:16
Alignment explanation
Indices: 43253838--43253873 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
43253828 AAAAAAATTC
43253838 GAAAAAAAATCGAAAA
1 GAAAAAAAATCGAAAA
*
43253854 GAAAAAAAATTGAAAA
1 GAAAAAAAATCGAAAA
43253870 -AAAA
1 GAAAA
43253874 TTGTATACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.78, C:0.03, G:0.11, T:0.08
Consensus pattern (16 bp):
GAAAAAAAATCGAAAA
Found at i:43273254 original size:23 final size:21
Alignment explanation
Indices: 43273204--43273254 Score: 50
Period size: 23 Copynumber: 2.3 Consensus size: 21
43273194 CTCGTCTTTG
*
43273204 TCTTTTGTTTCTTTTTCTAAC
1 TCTTTTCTTTCTTTTTCTAAC
43273225 TCATTTTCTCTTCTTTCTTC-AAC
1 TC-TTTTCT-TTCTTT-TTCTAAC
43273248 TTCTTTT
1 -TCTTTT
43273255 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.24, G:0.02, T:0.65
Consensus pattern (21 bp):
TCTTTTCTTTCTTTTTCTAAC
Found at i:43273269 original size:18 final size:18
Alignment explanation
Indices: 43273248--43273286 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
43273238 TTTCTTCAAC
* *
43273248 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
43273266 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
43273284 TTC
1 TTC
43273287 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:43277056 original size:23 final size:21
Alignment explanation
Indices: 43277006--43277056 Score: 50
Period size: 23 Copynumber: 2.3 Consensus size: 21
43276996 CTCGTCTTTG
*
43277006 TCTTTTGTTTCTTTTTCTAAC
1 TCTTTTCTTTCTTTTTCTAAC
43277027 TCATTTTCTCTTCTTTCTTC-AAC
1 TC-TTTTCT-TTCTTT-TTCTAAC
43277050 TTCTTTT
1 -TCTTTT
43277057 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.24, G:0.02, T:0.65
Consensus pattern (21 bp):
TCTTTTCTTTCTTTTTCTAAC
Found at i:43277071 original size:18 final size:18
Alignment explanation
Indices: 43277050--43277088 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
43277040 TTTCTTCAAC
* *
43277050 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
43277068 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
43277086 TTC
1 TTC
43277089 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:43286018 original size:30 final size:30
Alignment explanation
Indices: 43285943--43286019 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
43285933 TCAGCTCACA
*
43285943 AGCTAAACCTTAGCTCAACTTCAGCTTAGG
1 AGCTAAACCTTAGCTCAACTTCAGCTAAGG
* * * *
43285973 AGTTTAACCTCAGCTCAACTTTAGCTCAAGG
1 AGCTAAACCTTAGCTCAACTTCAGCT-AAGG
*
43286004 -GCTAAAGCTTAGCTCA
1 AGCTAAACCTTAGCTCA
43286020 TTTTATCTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
30 34 0.92
31 3 0.08
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (30 bp):
AGCTAAACCTTAGCTCAACTTCAGCTAAGG
Found at i:43296011 original size:22 final size:22
Alignment explanation
Indices: 43295983--43296026 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
43295973 TTTTAAACCA
43295983 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
43296005 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
43296027 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:43302924 original size:23 final size:22
Alignment explanation
Indices: 43302872--43302924 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
43302862 TCCACGTCTT
*
43302872 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
43302894 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
43302917 TTTCTTTT
1 TTTCTTTT
43302925 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:43309991 original size:23 final size:22
Alignment explanation
Indices: 43309939--43309991 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
43309929 TCCACGTCTT
*
43309939 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
43309961 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
43309984 TTTCTTTT
1 TTTCTTTT
43309992 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:43317698 original size:18 final size:18
Alignment explanation
Indices: 43317677--43317711 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43317667 TTTTTCTTTT
43317677 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
43317695 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
43317712 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:43318660 original size:11 final size:11
Alignment explanation
Indices: 43318646--43318680 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
43318636 TTTTTTTTCC
*
43318646 TTTTTTTCG-A
1 TTTTTTTTGAA
43318656 TTTTTTTTGAA
1 TTTTTTTTGAA
43318667 TTTTTTTTGAA
1 TTTTTTTTGAA
43318678 TTT
1 TTT
43318681 CTTCTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:43318774 original size:10 final size:11
Alignment explanation
Indices: 43318759--43318787 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
43318749 CAACTCAAAT
43318759 TTTTTTTTGA-
1 TTTTTTTTGAC
43318769 TTTTTTTTGAC
1 TTTTTTTTGAC
43318780 TTTTTTTT
1 TTTTTTTT
43318788 CGTTACGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:43320565 original size:20 final size:20
Alignment explanation
Indices: 43320519--43320565 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
43320509 AGCTCGTTTC
*
43320519 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
43320539 CAACTCAGTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
43320559 CAGCTCA
1 CAGCTCA
43320566 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.15, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:43322129 original size:10 final size:10
Alignment explanation
Indices: 43322114--43322153 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
43322104 AGAAGTGAGC
43322114 AAAAAAAGAA
1 AAAAAAAGAA
43322124 AAAAAAAGTAA
1 AAAAAAAG-AA
*
43322135 AAAAAGAACAA
1 AAAAA-AAGAA
43322146 AAAAAAAG
1 AAAAAAAG
43322154 TGAAAAGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 10 0.38
11 14 0.54
12 2 0.08
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:43322159 original size:23 final size:22
Alignment explanation
Indices: 43322098--43322159 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
43322088 GAAATTCAAA
* *
43322098 AAAAAAAGAAGTGAGCAAAAAAAG
1 AAAAAAA-AAGTGA-AAAAAAAAC
43322122 AAAAAAAAAGT-AAAAAAAGAAC
1 AAAAAAAAAGTGAAAAAAA-AAC
43322144 AAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
43322160 GTCTTGTGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 5 0.15
22 14 0.41
23 8 0.24
24 7 0.21
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (22 bp):
AAAAAAAAAGTGAAAAAAAAAC
Found at i:43325027 original size:20 final size:20
Alignment explanation
Indices: 43324981--43325027 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
43324971 AGCTCGTTTC
*
43324981 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
43325001 CTA-CTCATTCAAGCTCAATT
1 C-AGCTCACTCAAGCTCAAGT
43325021 CAGCTCA
1 CAGCTCA
43325028 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.28, C:0.34, G:0.13, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:43328433 original size:15 final size:15
Alignment explanation
Indices: 43328415--43328443 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43328405 AAAAAGAAGG
43328415 AAAAAAAAATTGCAA
1 AAAAAAAAATTGCAA
43328430 AAAAAAAAATTGCA
1 AAAAAAAAATTGCA
43328444 TACGGTCTAG
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:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAAAAAAATTGCAA
Found at i:43330698 original size:24 final size:25
Alignment explanation
Indices: 43330671--43330724 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
43330661 ATGAGTGATA
*
43330671 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
43330695 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
43330719 AAAAAA
1 AAAAAA
43330725 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:43337815 original size:14 final size:13
Alignment explanation
Indices: 43337794--43337844 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 13
43337784 ATAGGTACGT
43337794 AAAAAAAAAGAGTTCG
1 AAAAAAAAA-A-TT-G
43337810 AAAAAAAAAATTG
1 AAAAAAAAAATTG
43337823 --AAAAAAAATTG
1 AAAAAAAAAATTG
43337834 AAAGAAAAAAA
1 AAA-AAAAAAA
43337845 AATTGCATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 11 0.34
13 2 0.06
14 9 0.28
15 1 0.03
16 9 0.28
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.12
Consensus pattern (13 bp):
AAAAAAAAAATTG
Found at i:43337828 original size:10 final size:11
Alignment explanation
Indices: 43337812--43337842 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
43337802 AGAGTTCGAA
43337812 AAAAAAAATTG
1 AAAAAAAATTG
43337823 AAAAAAAATTG
1 AAAAAAAATTG
43337834 AAAGAAAAA
1 AAA-AAAAA
43337843 AAAATTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:43340090 original size:17 final size:17
Alignment explanation
Indices: 43340058--43340107 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 17
43340048 GCGAAAATAC
43340058 AAAAGAAAAGAAAAATGAT
1 AAAA-AAAAG-AAAATGAT
43340077 AAAAAAAAGAAAAT--T
1 AAAAAAAAGAAAATGAT
* *
43340092 CAAAAAAAGAGAATGA
1 AAAAAAAAGAAAATGA
43340108 AAAGAGAGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 13 0.48
17 5 0.19
18 5 0.19
19 4 0.15
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.10
Consensus pattern (17 bp):
AAAAAAAAGAAAATGAT
Found at i:43347573 original size:13 final size:13
Alignment explanation
Indices: 43347544--43347583 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
43347534 AACCGACCAA
*
43347544 TTTGTTCATATCCC
1 TTTGTTCCTA-CCC
43347558 TTTGTTCCTACCC
1 TTTGTTCCTACCC
43347571 TTTCGTTCCTACC
1 TTT-GTTCCTACC
43347584 ATTCCGTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.10, C:0.35, G:0.07, T:0.47
Consensus pattern (13 bp):
TTTGTTCCTACCC
Found at i:43358691 original size:20 final size:20
Alignment explanation
Indices: 43358666--43358720 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
43358656 TGTGGTTCAA
*
43358666 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
43358686 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
* *
43358706 GTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
43358721 TTTAACTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:43360761 original size:12 final size:11
Alignment explanation
Indices: 43360720--43360760 Score: 73
Period size: 11 Copynumber: 3.6 Consensus size: 11
43360710 AAAAAAAAGG
43360720 AAAAAAATTCGA
1 AAAAAAATTC-A
43360732 AAAAAAATTCA
1 AAAAAAATTCA
43360743 AAAAAAATTCA
1 AAAAAAATTCA
43360754 AAAAAAA
1 AAAAAAA
43360761 AATTGTATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:43363301 original size:20 final size:20
Alignment explanation
Indices: 43363276--43363330 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
43363266 TGTGGTTCAA
* *
43363276 CTCATTCGAGCTCAGGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
43363296 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
43363316 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
43363331 TTTAACTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:43365747 original size:14 final size:14
Alignment explanation
Indices: 43365725--43365760 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
43365715 TAGAAAGAGG
*
43365725 GGTACGAATGAAAT
1 GGTAGGAATGAAAT
43365739 GGTAGGAATGAAAT
1 GGTAGGAATGAAAT
43365753 GGTAGGAA
1 GGTAGGAA
43365761 CAAAGGGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.03, G:0.36, T:0.19
Consensus pattern (14 bp):
GGTAGGAATGAAAT
Found at i:43366808 original size:20 final size:20
Alignment explanation
Indices: 43366785--43366838 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
43366775 AGTTTTTCCC
*
43366785 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
43366805 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
43366825 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
43366839 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:43366820 original size:30 final size:30
Alignment explanation
Indices: 43366785--43366858 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
43366775 AGTTTTTCCC
43366785 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
43366815 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
43366845 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
43366859 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:43366848 original size:20 final size:20
Alignment explanation
Indices: 43366785--43366849 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
43366775 AGTTTTTCCC
* * * *
43366785 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
43366805 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
43366824 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
43366845 AGCTC
1 AGCTC
43366850 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:43369564 original size:13 final size:13
Alignment explanation
Indices: 43369546--43369570 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43369536 TAACCTACAA
43369546 AATTAAATAACAT
1 AATTAAATAACAT
43369559 AATTAAATAACA
1 AATTAAATAACA
43369571 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:43369840 original size:20 final size:21
Alignment explanation
Indices: 43369795--43369850 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
43369785 AAAAAGGAAT
* * *
43369795 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAATGAGCTAAATAC
43369816 GAGCTCAAATGAGCTAAA-AC
1 GAGCTCAAATGAGCTAAATAC
*
43369836 GAGCTCAAGTGAGCT
1 GAGCTCAAATGAGCT
43369851 GATGGGAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.18
Consensus pattern (21 bp):
GAGCTCAAATGAGCTAAATAC
Found at i:43371824 original size:12 final size:11
Alignment explanation
Indices: 43371809--43371850 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
43371799 GAAAAAAACC
43371809 GAAAAAAAATTT
1 GAAAAAAAA-TT
43371821 GAAAAAAAATT
1 GAAAAAAAATT
*
43371832 CAAAAAAAA-T
1 GAAAAAAAATT
43371842 GAAAAAAAA
1 GAAAAAAAA
43371851 GTGATTTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.32
11 10 0.36
12 9 0.32
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.14
Consensus pattern (11 bp):
GAAAAAAAATT
Found at i:43372822 original size:26 final size:27
Alignment explanation
Indices: 43372756--43372822 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
43372746 ACATTCTTGT
*
43372756 AAAGAGAAAACAAAG-AAAAGAAAAGCA
1 AAAGA-AAAAGAAAGAAAAAGAAAAGCA
* *
43372783 AAAGCAAAAG-AAGAAAAAGAAAA-CG
1 AAAGAAAAAGAAAGAAAAAGAAAAGCA
*
43372808 AAATAAAAAGAAAGA
1 AAAGAAAAAGAAAGA
43372823 GAGGCAAGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
25 12 0.36
26 17 0.52
27 4 0.12
ACGTcount: A:0.75, C:0.06, G:0.18, T:0.01
Consensus pattern (27 bp):
AAAGAAAAAGAAAGAAAAAGAAAAGCA
Found at i:43372902 original size:11 final size:12
Alignment explanation
Indices: 43372870--43372900 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
43372860 TTGAGAGAAC
43372870 TTGAAAAAGCCT
1 TTGAAAAAGCCT
43372882 TTGAAAAAGCCT
1 TTGAAAAAGCCT
43372894 TTGAAAA
1 TTGAAAA
43372901 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:43381641 original size:14 final size:14
Alignment explanation
Indices: 43381619--43381663 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
43381609 TTAAAGAAGC
43381619 AACTCATTAAATTA
1 AACTCATTAAATTA
*
43381633 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
43381646 AACTCATTTAATTA
1 AACTCATTAAATTA
43381660 AACT
1 AACT
43381664 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Done.