Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 98 of 295
Found at i:29053845 original size:28 final size:27
Alignment explanation
Indices: 29053734--29053885 Score: 173
Period size: 27 Copynumber: 5.6 Consensus size: 27
29053724 GAAATACCCC
*
29053734 AAATACCCTTGATTTGAAAAATTACTG
1 AAATACCCTTGATTTGAAAAATTACAG
*
29053761 AAATACCCTTGATTTGGAAAATTACA-
1 AAATACCCTTGATTTGAAAAATTACAG
29053787 AAAGTACCCTTGATTT-ACAAAATTACAG
1 AAA-TACCCTTGATTTGA-AAAATTACAG
* * *
29053815 AAATACCTTTGACTTTCAAAAATTATAG
1 AAATACCCTTGA-TTTGAAAAATTACAG
* * * *
29053843 AAATACCATTGGTTTGTAAAATTACTG
1 AAATACCCTTGATTTGAAAAATTACAG
*
29053870 AAATACCCTTGGTTTG
1 AAATACCCTTGATTTG
29053886 TAGATTTACC
Statistics
Matches: 108, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
26 3 0.03
27 79 0.73
28 25 0.23
29 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (27 bp):
AAATACCCTTGATTTGAAAAATTACAG
Found at i:29053866 original size:55 final size:53
Alignment explanation
Indices: 29053734--29053880 Score: 179
Period size: 55 Copynumber: 2.7 Consensus size: 53
29053724 GAAATACCCC
**
29053734 AAATACCCTTGATTTGAAAAATTACTGAAATACCCTTGATTTGGAAAATTACA
1 AAATACCCTTGATTTGAAAAATTACTGAAATACCCTTGATTTCAAAAATTACA
* * *
29053787 AAAGTACCCTTGATTT-ACAAAATTACAGAAATACCTTTGACTTTCAAAAATTATA
1 AAA-TACCCTTGATTTGA-AAAATTACTGAAATACCCTTGA-TTTCAAAAATTACA
* * *
29053842 GAAATACCATTGGTTTGTAAAATTACTGAAATACCCTTG
1 -AAATACCCTTGATTTGAAAAATTACTGAAATACCCTTG
29053881 GTTTGTAGAT
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
53 4 0.05
54 32 0.41
55 40 0.51
56 3 0.04
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (53 bp):
AAATACCCTTGATTTGAAAAATTACTGAAATACCCTTGATTTCAAAAATTACA
Found at i:29053904 original size:27 final size:27
Alignment explanation
Indices: 29053851--29053907 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
29053841 AGAAATACCA
** *
29053851 TTGGTTTGTAAAATTACTGAAATACCC
1 TTGGTTTGTAAAATTACCAAAACACCC
* *
29053878 TTGGTTTGTAGATTTACCAAAACACCC
1 TTGGTTTGTAAAATTACCAAAACACCC
29053905 TTG
1 TTG
29053908 TAGGGTGAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (27 bp):
TTGGTTTGTAAAATTACCAAAACACCC
Found at i:29054194 original size:41 final size:41
Alignment explanation
Indices: 29054145--29054267 Score: 185
Period size: 41 Copynumber: 3.0 Consensus size: 41
29054135 GGAGGAAGAA
*
29054145 ATTAAGGATCGCATGGTTGCTTGACAACTGTGGATCCACCG
1 ATTAAGGATCGCATGGTTGCTTGACGACTGTGGATCCACCG
* * *
29054186 ATTGAGGATCGCATGGTTGCTTGATGA-TCGTGGATCCACAG
1 ATTAAGGATCGCATGGTTGCTTGACGACT-GTGGATCCACCG
*
29054227 ATTAAGGATAGCATGGTTGCTTGACGACTGTGGATCCACCG
1 ATTAAGGATCGCATGGTTGCTTGACGACTGTGGATCCACCG
29054268 GTGGCTTTTA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
40 1 0.01
41 70 0.97
42 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.28
Consensus pattern (41 bp):
ATTAAGGATCGCATGGTTGCTTGACGACTGTGGATCCACCG
Found at i:29054495 original size:22 final size:22
Alignment explanation
Indices: 29054414--29054476 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
29054404 TTATCCTGAT
29054414 TATGGCTTTGTGCCAACCTACA
1 TATGGCTTTGTGCCAACCTACA
29054436 TATGGCTTTGTGCCAACCTACA
1 TATGGCTTTGTGCCAACCTACA
*
29054458 TATGGCTCTGTGCCAACCT
1 TATGGCTTTGTGCCAACCT
29054477 GATTATGGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.32
Consensus pattern (22 bp):
TATGGCTTTGTGCCAACCTACA
Found at i:29054722 original size:22 final size:22
Alignment explanation
Indices: 29054697--29054766 Score: 131
Period size: 22 Copynumber: 3.2 Consensus size: 22
29054687 GTTGTTGCGA
*
29054697 TGTTTATGGCTATGTGCTGTCC
1 TGTTTACGGCTATGTGCTGTCC
29054719 TGTTTACGGCTATGTGCTGTCC
1 TGTTTACGGCTATGTGCTGTCC
29054741 TGTTTACGGCTATGTGCTGTCC
1 TGTTTACGGCTATGTGCTGTCC
29054763 TGTT
1 TGTT
29054767 GACTTAGTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.09, C:0.20, G:0.27, T:0.44
Consensus pattern (22 bp):
TGTTTACGGCTATGTGCTGTCC
Found at i:29064398 original size:21 final size:21
Alignment explanation
Indices: 29064365--29064404 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29064355 GAGGTGAGAG
29064365 AAAAATAAAATAAATTAAATT
1 AAAAATAAAATAAATTAAATT
* *
29064386 AAAACTAAGATAAATTAAA
1 AAAAATAAAATAAATTAAA
29064405 AGATTTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (21 bp):
AAAAATAAAATAAATTAAATT
Found at i:29065704 original size:22 final size:21
Alignment explanation
Indices: 29065666--29065706 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
29065656 GAATCCAACC
*
29065666 AAATGCAACAAATATAGCATA
1 AAATGCAACAAAAATAGCATA
*
29065687 AAATGCAGCCAAAAATAGCA
1 AAATGCA-ACAAAAATAGCA
29065707 AATTTATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.56, C:0.17, G:0.12, T:0.15
Consensus pattern (21 bp):
AAATGCAACAAAAATAGCATA
Found at i:29065976 original size:21 final size:21
Alignment explanation
Indices: 29065952--29065991 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29065942 TTTTGCTCTG
29065952 CTCTG-CTGCCATCGCTGCTAC
1 CTCTGCCT-CCATCGCTGCTAC
*
29065973 CTCTGCCTCCCTCGCTGCT
1 CTCTGCCTCCATCGCTGCT
29065992 GCGCAGTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.05, C:0.47, G:0.17, T:0.30
Consensus pattern (21 bp):
CTCTGCCTCCATCGCTGCTAC
Found at i:29066455 original size:13 final size:14
Alignment explanation
Indices: 29066430--29066458 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29066420 TGATGAATTG
29066430 AATTAAACAATTAT
1 AATTAAACAATTAT
29066444 AATTAAAC-ATTAT
1 AATTAAACAATTAT
29066457 AA
1 AA
29066459 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:29066662 original size:16 final size:17
Alignment explanation
Indices: 29066625--29066663 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
29066615 AAAATATTAT
*
29066625 TTAATATTAGAAAGTTA
1 TTAATATTAGAAAGTAA
*
29066642 TTAATATTTGAAAG-AA
1 TTAATATTAGAAAGTAA
29066658 TTAATA
1 TTAATA
29066664 AAATTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (17 bp):
TTAATATTAGAAAGTAA
Found at i:29067742 original size:30 final size:30
Alignment explanation
Indices: 29067708--29067782 Score: 150
Period size: 30 Copynumber: 2.5 Consensus size: 30
29067698 TACATATAAG
29067708 ATTATGTAAGTTATGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGAAATTTGATCTTTAA
29067738 ATTATGTAAGTTATGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGAAATTTGATCTTTAA
29067768 ATTATGTAAGTTATG
1 ATTATGTAAGTTATG
29067783 TATTATGTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.47
Consensus pattern (30 bp):
ATTATGTAAGTTATGAAATTTGATCTTTAA
Found at i:29067783 original size:9 final size:9
Alignment explanation
Indices: 29067769--29067910 Score: 80
Period size: 9 Copynumber: 15.8 Consensus size: 9
29067759 GATCTTTAAA
29067769 TTATGTAAG
1 TTATGTAAG
29067778 TTATGT-A-
1 TTATGTAAG
29067785 TTATGTAAG
1 TTATGTAAG
* *
29067794 TTATGAAAT
1 TTATGTAAG
* *
29067803 TTGATCTTTAAA
1 TT-A--TGTAAG
*
29067815 TTATGTAAC
1 TTATGTAAG
*
29067824 TCATGT-A-
1 TTATGTAAG
29067831 TTATGTAAG
1 TTATGTAAG
*
29067840 TTATGTAAA
1 TTATGTAAG
29067849 TTATGTAAG
1 TTATGTAAG
** *
29067858 TTATAAAAA
1 TTATGTAAG
* *
29067867 TTGATCTTTAAA
1 TT-A--TGTAAG
29067879 TTATGTAAG
1 TTATGTAAG
29067888 TTATGT-A-
1 TTATGTAAG
29067895 TTATGTAAG
1 TTATGTAAG
29067904 TTATGTA
1 TTATGTA
29067911 TTAAATAATA
Statistics
Matches: 103, Mismatches: 18, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
7 17 0.17
8 6 0.06
9 65 0.63
10 2 0.02
11 2 0.02
12 11 0.11
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:29067789 original size:16 final size:16
Alignment explanation
Indices: 29067768--29067913 Score: 88
Period size: 16 Copynumber: 9.2 Consensus size: 16
29067758 TGATCTTTAA
29067768 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
*
29067784 ATTATGTAAGTTATGAA
1 ATTATGTAAGTTATG-T
** **
29067801 ATT-TG-ATCTT-TAA
1 ATTATGTAAGTTATGT
* *
29067814 ATTATGTAACTCATGT
1 ATTATGTAAGTTATGT
29067830 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
*
29067846 AAATTATGTAAGTTAT-A
1 --ATTATGTAAGTTATGT
** * * **
29067863 AAAAT-TGA-TCTTTAA
1 ATTATGTAAGT-TATGT
29067878 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
29067894 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
29067910 ATTA
1 ATTA
29067914 AATAATATTT
Statistics
Matches: 99, Mismatches: 21, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
13 5 0.05
14 7 0.07
15 13 0.13
16 56 0.57
17 4 0.04
18 14 0.14
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:29067790 original size:46 final size:46
Alignment explanation
Indices: 29067738--29067850 Score: 199
Period size: 46 Copynumber: 2.4 Consensus size: 46
29067728 TGATCTTTAA
* *
29067738 ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTTATGT
1 ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
29067784 ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
1 ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
29067830 ATTATGTAAGTTATGTAAATT
1 ATTATGTAAGTTATG-AAATT
29067851 ATGTAAGTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
46 59 0.92
47 5 0.08
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (46 bp):
ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
Found at i:29067818 original size:30 final size:30
Alignment explanation
Indices: 29067784--29067892 Score: 105
Period size: 30 Copynumber: 3.5 Consensus size: 30
29067774 TAAGTTATGT
29067784 ATTATGTAAGTTATGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGAAATTTGATCTTTAA
* * *
29067814 ATTATGTAACTCATG-TATTATGTAAGT-TATGTAA
1 ATTATGTAAGTTATGAAATT-TG--A-TCT-T-TAA
* *
29067848 ATTATGTAAGTTATAAAAATTGATCTTTAA
1 ATTATGTAAGTTATGAAATTTGATCTTTAA
29067878 ATTATGTAAGTTATG
1 ATTATGTAAGTTATG
29067893 TATTATGTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
29 3 0.05
30 32 0.52
31 2 0.03
32 4 0.06
33 2 0.03
34 17 0.27
35 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.45
Consensus pattern (30 bp):
ATTATGTAAGTTATGAAATTTGATCTTTAA
Found at i:29067871 original size:64 final size:63
Alignment explanation
Indices: 29067768--29067910 Score: 234
Period size: 64 Copynumber: 2.3 Consensus size: 63
29067758 TGATCTTTAA
* *
29067768 ATTATGTAAGTTATGT-ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
1 ATTATGTAAGTTATGTAATTATGTAAGTTATAAAAATTGATCTTTAAATTATGTAACTCATGT
* *
29067830 ATTATGTAAGTTATGTAAATTATGTAAGTTATAAAAATTGATCTTTAAATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT-AATTATGTAAGTTATAAAAATTGATCTTTAAATTATGTAACTCATGT
29067894 ATTATGTAAGTTATGTA
1 ATTATGTAAGTTATGTA
29067911 TTAAATAATA
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
62 16 0.21
63 1 0.01
64 58 0.77
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (63 bp):
ATTATGTAAGTTATGTAATTATGTAAGTTATAAAAATTGATCTTTAAATTATGTAACTCATGT
Found at i:29069175 original size:25 final size:25
Alignment explanation
Indices: 29069154--29069220 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 25
29069144 CTGGAGAAGC
29069154 AGCAGAGGGATGCCGACGGAGATGT
1 AGCAGAGGGATGCCGACGGAGATGT
* *
29069179 AGAAGAGGGGATGCCGATGGAGATGT
1 AGCAGA-GGGATGCCGACGGAGATGT
*
29069205 AGCAGAGGGCTGCCGA
1 AGCAGAGGGATGCCGA
29069221 TGACGATGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 14 0.38
26 23 0.62
ACGTcount: A:0.28, C:0.15, G:0.45, T:0.12
Consensus pattern (25 bp):
AGCAGAGGGATGCCGACGGAGATGT
Found at i:29069228 original size:25 final size:24
Alignment explanation
Indices: 29069154--29069228 Score: 87
Period size: 26 Copynumber: 3.0 Consensus size: 24
29069144 CTGGAGAAGC
*
29069154 AGCAGAGGGATGCCGACGGAGATGT
1 AGCAGAGGGATGCCGA-TGAGATGT
*
29069179 AGAAGAGGGGATGCCGATGGAGATGT
1 AGCAGA-GGGATGCCGAT-GAGATGT
*
29069205 AGCAGAGGGCTGCCGATGACGATG
1 AGCAGAGGGATGCCGATGA-GATG
29069229 CAGAGGACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
24 2 0.05
25 19 0.44
26 22 0.51
ACGTcount: A:0.28, C:0.15, G:0.44, T:0.13
Consensus pattern (24 bp):
AGCAGAGGGATGCCGATGAGATGT
Found at i:29069234 original size:22 final size:22
Alignment explanation
Indices: 29069206--29069253 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
29069196 TGGAGATGTA
* * *
29069206 GCAGAGGGCTGCCGATGACGAT
1 GCAGAGGACTACCGAAGACGAT
*
29069228 GCAGAGGACTACCGAAGGCGAT
1 GCAGAGGACTACCGAAGACGAT
29069250 GCAG
1 GCAG
29069254 CAGACGTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.40, T:0.10
Consensus pattern (22 bp):
GCAGAGGACTACCGAAGACGAT
Found at i:29071241 original size:18 final size:18
Alignment explanation
Indices: 29071218--29071253 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29071208 TGAGAAAGGC
29071218 TGAGAAAGAAAAGGGAAT
1 TGAGAAAGAAAAGGGAAT
29071236 TGAGAAAGAAAAGGGAAT
1 TGAGAAAGAAAAGGGAAT
29071254 CGGGGGAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.33, T:0.11
Consensus pattern (18 bp):
TGAGAAAGAAAAGGGAAT
Found at i:29071486 original size:40 final size:40
Alignment explanation
Indices: 29071436--29071512 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
29071426 CTTTTTTACA
* * *
29071436 GCGTTTTTATCATAAACACCGTTATTGTTTGCCTTTTGCG
1 GCGTTCTTATCATAAACACCGTTAATGTTTGACTTTTGCG
*
29071476 GCGTTCTTATCATAAACGCCGTTAATGTTTGACTTTT
1 GCGTTCTTATCATAAACACCGTTAATGTTTGACTTTT
29071513 TTATAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.44
Consensus pattern (40 bp):
GCGTTCTTATCATAAACACCGTTAATGTTTGACTTTTGCG
Found at i:29071538 original size:22 final size:20
Alignment explanation
Indices: 29071511--29071567 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 20
29071501 TGTTTGACTT
29071511 TTTTATAATTTTTATATTGAA
1 TTTTATAATTTTTATATT-AA
29071532 TTATTAT-ATCTTTTATATTAA
1 TT-TTATAAT-TTTTATATTAA
29071553 TTTTAAATAATTTTT
1 TTTT--ATAATTTTT
29071568 TTAAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
20 2 0.06
21 8 0.26
22 19 0.61
23 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTATAATTTTTATATTAA
Found at i:29071970 original size:28 final size:29
Alignment explanation
Indices: 29071923--29071992 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 29
29071913 ACATAACCCT
29071923 TAAACCCTT-AACCCCTAACCCCTAACACC-
1 TAAA-CCTTAAACCCCTAACCCCTAA-ACCA
*
29071952 TAAACCTTAAACCCC-AACCCTTAAACCA
1 TAAACCTTAAACCCCTAACCCCTAAACCA
29071980 TAAA-CTATAAACC
1 TAAACCT-TAAACC
29071993 ATAATCCATA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 5 0.14
28 22 0.59
29 10 0.27
ACGTcount: A:0.41, C:0.40, G:0.00, T:0.19
Consensus pattern (29 bp):
TAAACCTTAAACCCCTAACCCCTAAACCA
Found at i:29071978 original size:21 final size:22
Alignment explanation
Indices: 29071925--29072028 Score: 63
Period size: 21 Copynumber: 4.9 Consensus size: 22
29071915 ATAACCCTTA
* *
29071925 AACCCTTAACCCCT-AACCCCT
1 AACCCTTAAACCATAAACCCCT
*
29071946 AACACC-TAAACCTTAAACCCC-
1 AAC-CCTTAAACCATAAACCCCT
**
29071967 AACCCTTAAACCATAAA-CTAT
1 AACCCTTAAACCATAAACCCCT
* * * *
29071988 AAACCATAATCCATAAACCCAT
1 AACCCTTAAACCATAAACCCCT
* * *
29072010 AATCCATAATCCATAAACC
1 AACCCTTAAACCATAAACC
29072029 TTAAAATAGT
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
20 3 0.04
21 36 0.53
22 29 0.43
ACGTcount: A:0.43, C:0.38, G:0.00, T:0.19
Consensus pattern (22 bp):
AACCCTTAAACCATAAACCCCT
Found at i:29071990 original size:14 final size:14
Alignment explanation
Indices: 29071973--29072033 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 14
29071963 CCCCAACCCT
*
29071973 TAAACCATAAACTA
1 TAAACCATAAACCA
*
29071987 TAAACCATAATCCA
1 TAAACCATAAACCA
*
29072001 TAAACCCATAATCCA
1 TAAA-CCATAAACCA
* *
29072016 TAATCCATAAACCT
1 TAAACCATAAACCA
29072030 TAAA
1 TAAA
29072034 ATAGTAACTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
14 27 0.68
15 13 0.32
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCATAAACCA
Found at i:29072011 original size:15 final size:14
Alignment explanation
Indices: 29071973--29072025 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
29071963 CCCCAACCCT
* *
29071973 TAAACCATAAACTA
1 TAAACCATAATCCA
29071987 TAAACCATAATCCA
1 TAAACCATAATCCA
29072001 TAAACCCATAATCCA
1 TAAA-CCATAATCCA
*
29072016 TAATCCATAA
1 TAAACCATAA
29072026 ACCTTAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
14 22 0.63
15 13 0.37
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCATAATCCA
Found at i:29072011 original size:22 final size:22
Alignment explanation
Indices: 29071977--29072028 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
29071967 AACCCTTAAA
*
29071977 CCATAAA-CTATAAACCATAAT
1 CCATAAACCCATAAACCATAAT
*
29071998 CCATAAACCCATAATCCATAAT
1 CCATAAACCCATAAACCATAAT
29072020 CCATAAACC
1 CCATAAACC
29072029 TTAAAATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (22 bp):
CCATAAACCCATAAACCATAAT
Found at i:29072016 original size:7 final size:7
Alignment explanation
Indices: 29071986--29072025 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
29071976 ACCATAAACT
*
29071986 ATAAACC
1 ATAATCC
29071993 ATAATCC
1 ATAATCC
*
29072000 ATAAACCC
1 AT-AATCC
29072008 ATAATCC
1 ATAATCC
29072015 ATAATCC
1 ATAATCC
29072022 ATAA
1 ATAA
29072026 ACCTTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.23
Consensus pattern (7 bp):
ATAATCC
Found at i:29072895 original size:17 final size:18
Alignment explanation
Indices: 29072870--29072903 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29072860 GGGTTATAGT
*
29072870 TTAGTATTTAGG-GTTTG
1 TTAGGATTTAGGAGTTTG
29072887 TTAGGATTTAGGAGTTT
1 TTAGGATTTAGGAGTTT
29072904 ACTATTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (18 bp):
TTAGGATTTAGGAGTTTG
Found at i:29073029 original size:41 final size:40
Alignment explanation
Indices: 29072973--29073140 Score: 176
Period size: 41 Copynumber: 4.1 Consensus size: 40
29072963 GTTATATGAC
*
29072973 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTGT
* * *
29073013 CTTTTAGCGGCGTTTTACCAAAAGTGCCGCTATTTCTCTAT
1 -TTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTGT
* * * * *
29073054 TTGTAGCGGCGTTTTAACAAAAAACGCCACTATTGCTCAGT
1 TTTTAGCGGCGTTTT-ACCAAAAGCGCCGCTATTGCTCTGT
*** *
29073095 TTTTAGCGGCGTTTTTGGTAAAA-CACCGCTATTGCTCTGT
1 TTTTAGCGGCG-TTTTACCAAAAGCGCCGCTATTGCTCTGT
29073135 GTTTTA
1 -TTTTA
29073141 CAATTTTTGC
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
40 28 0.27
41 73 0.70
42 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.36
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTGT
Found at i:29073124 original size:81 final size:81
Alignment explanation
Indices: 29072976--29073132 Score: 183
Period size: 81 Copynumber: 1.9 Consensus size: 81
29072966 ATATGACTTT
* * * * **
29072976 TAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGTCTTTTAGCGGCGTTTTACCAAAAGTGCC
1 TAGCGGCGTTTTACAAAAAACGCCACTAATGCTCAGTCTTTTAGCGGCGTTTTACCAAAAGCACC
*
29073041 GCTATTTCTCTATTTG
66 GCTATTGCTCTATTTG
* ***
29073057 TAGCGGCGTTTTAACAAAAAACGCCACTATTGCTCAGT-TTTTAGCGGCGTTTTTGGTAAAA-CA
1 TAGCGGCGTTTT-ACAAAAAACGCCACTAATGCTCAGTCTTTTAGCGGCG-TTTTACCAAAAGCA
29073120 CCGCTATTGCTCT
64 CCGCTATTGCTCT
29073133 GTGTTTTACA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
81 35 0.56
82 28 0.44
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (81 bp):
TAGCGGCGTTTTACAAAAAACGCCACTAATGCTCAGTCTTTTAGCGGCGTTTTACCAAAAGCACC
GCTATTGCTCTATTTG
Found at i:29073442 original size:7 final size:7
Alignment explanation
Indices: 29073430--29073462 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
29073420 TTTCAATTTC
29073430 ATATTGA
1 ATATTGA
29073437 ATATTGA
1 ATATTGA
29073444 ATATTGA
1 ATATTGA
29073451 ATATTGA
1 ATATTGA
29073458 ATATT
1 ATATT
29073463 TTTTCTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (7 bp):
ATATTGA
Found at i:29073913 original size:10 final size:11
Alignment explanation
Indices: 29073894--29073930 Score: 60
Period size: 10 Copynumber: 3.5 Consensus size: 11
29073884 GTCTCCTCCT
29073894 TTTCTTCTTTC
1 TTTCTTCTTTC
29073905 TTT-TTCTTTC
1 TTTCTTCTTTC
29073915 TTTCTT-TTTC
1 TTTCTTCTTTC
29073925 TTTCTT
1 TTTCTT
29073931 AGTTTGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 20 0.80
11 5 0.20
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTCTTTC
Found at i:29073917 original size:14 final size:14
Alignment explanation
Indices: 29073893--29073930 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
29073883 TGTCTCCTCC
29073893 TTTTC-TTCTTTCT
1 TTTTCTTTCTTTCT
29073906 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
29073920 TTTTCTTTCTT
1 TTTTCTTTCTT
29073931 AGTTTGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:29077505 original size:32 final size:32
Alignment explanation
Indices: 29077464--29077527 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
29077454 ACATGTCCAA
*
29077464 AGAAATCACAAATTAGCCCCTAACTTCCACCT
1 AGAAATCACAAATTAGCCCATAACTTCCACCT
29077496 AGAAATCACAAATTAGCCCATAACTTCCACCT
1 AGAAATCACAAATTAGCCCATAACTTCCACCT
29077528 TGATTGTCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.39, C:0.33, G:0.06, T:0.22
Consensus pattern (32 bp):
AGAAATCACAAATTAGCCCATAACTTCCACCT
Found at i:29093256 original size:21 final size:21
Alignment explanation
Indices: 29093226--29093265 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29093216 TAACAGGACC
*
29093226 GCTGATGTGGCAAGTTAACTA
1 GCTGACGTGGCAAGTTAACTA
*
29093247 GCTGACGTGGCCAGTTAAC
1 GCTGACGTGGCAAGTTAAC
29093266 CTGCCACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (21 bp):
GCTGACGTGGCAAGTTAACTA
Found at i:29094638 original size:30 final size:31
Alignment explanation
Indices: 29094572--29094640 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
29094562 ACTATTAGTC
* *
29094572 AGTGACTGTTTTGTCACTTTTTTATAACGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
*
29094603 AGTGACTGTTTTGTTA-TTTTTCA-AAAGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
29094632 AGGTGACTG
1 A-GTGACTG
29094641 AAATGAAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 6 0.18
30 13 0.38
31 15 0.44
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.48
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTTCATAAAGTT
Found at i:29096054 original size:15 final size:15
Alignment explanation
Indices: 29096034--29096066 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
29096024 TATTACATGA
29096034 TTTGATTATT-ATAAT
1 TTTGATT-TTGATAAT
29096049 TTTGATTTTGATAAT
1 TTTGATTTTGATAAT
29096064 TTT
1 TTT
29096067 TTTAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (15 bp):
TTTGATTTTGATAAT
Found at i:29097546 original size:2 final size:2
Alignment explanation
Indices: 29097539--29097615 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
29097529 AGGGAGGAAA
29097539 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29097581 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29097616 TAATAACAGC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29122087 original size:27 final size:26
Alignment explanation
Indices: 29122048--29122114 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
29122038 GGGACCAATT
* * * *
29122048 TGCTCACATGAGCTGACATATCTAGGC
1 TGCTCACACGAGCT-ACAAACCAAGGC
* *
29122075 TGCTCACACGAGCTTCAAACCAAGGT
1 TGCTCACACGAGCTACAAACCAAGGC
29122101 TGCTCACACGAGCT
1 TGCTCACACGAGCT
29122115 TAGTTTGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 21 0.62
27 13 0.38
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (26 bp):
TGCTCACACGAGCTACAAACCAAGGC
Found at i:29126709 original size:33 final size:33
Alignment explanation
Indices: 29126666--29126836 Score: 175
Period size: 33 Copynumber: 5.2 Consensus size: 33
29126656 GTGTACGTTT
* **
29126666 CTTTCCAAATGGTACACACAAAGTATACCTTTC
1 CTTTTCAAATGGTACACACAAAGTATACCTAAC
* * **
29126699 CTTTTCAAATGGTATACACTAAGTATACCTTTC
1 CTTTTCAAATGGTACACACAAAGTATACCTAAC
*
29126732 CTTTTCAAATGGTATACACAAAGTATACCTAAC
1 CTTTTCAAATGGTACACACAAAGTATACCTAAC
* * * ** *
29126765 ATTTCCAAGT-GTACACACAAAGTGCACATAAC
1 CTTTTCAAATGGTACACACAAAGTATACCTAAC
* * *
29126797 CTTTTCAAGT-GTACACACAAAGTGTACATAAC
1 CTTTTCAAATGGTACACACAAAGTATACCTAAC
29126829 CTTTTCAA
1 CTTTTCAA
29126837 GTGTACCATT
Statistics
Matches: 122, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
32 55 0.45
33 67 0.55
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (33 bp):
CTTTTCAAATGGTACACACAAAGTATACCTAAC
Found at i:29126806 original size:32 final size:32
Alignment explanation
Indices: 29126677--29126842 Score: 152
Period size: 32 Copynumber: 5.1 Consensus size: 32
29126667 TTTCCAAATG
* * ** *
29126677 GTACACACAAAGTATACCTTTCCTTTTCAAAT
1 GTACACACAAAGTGTACATAACCTTTTCAAGT
* * * * ** *
29126709 GGTATACACTAAGTATACCTTTCCTTTTCAAAT
1 -GTACACACAAAGTGTACATAACCTTTTCAAGT
* * * * *
29126742 GGTATACACAAAGTATACCTAACATTTCCAAGT
1 -GTACACACAAAGTGTACATAACCTTTTCAAGT
*
29126775 GTACACACAAAGTGCACATAACCTTTTCAAGT
1 GTACACACAAAGTGTACATAACCTTTTCAAGT
29126807 GTACACACAAAGTGTACATAACCTTTTCAAGT
1 GTACACACAAAGTGTACATAACCTTTTCAAGT
29126839 GTAC
1 GTAC
29126843 CATTTGGGTA
Statistics
Matches: 118, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
32 61 0.52
33 57 0.48
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.31
Consensus pattern (32 bp):
GTACACACAAAGTGTACATAACCTTTTCAAGT
Found at i:29138226 original size:17 final size:17
Alignment explanation
Indices: 29138187--29138233 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
29138177 TTCACCCCCA
* *
29138187 TCCTTTCTTTTCCACTTT
1 TCCTTTCTATT-CTCTTT
*
29138205 T-CTTTCTCTTCTCTTT
1 TCCTTTCTATTCTCTTT
29138221 TCCTTTCTATTCT
1 TCCTTTCTATTCT
29138234 ATTCTTCTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 6 0.24
17 18 0.72
18 1 0.04
ACGTcount: A:0.04, C:0.32, G:0.00, T:0.64
Consensus pattern (17 bp):
TCCTTTCTATTCTCTTT
Found at i:29144506 original size:17 final size:17
Alignment explanation
Indices: 29144481--29144516 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29144471 TAGAATTGGG
* *
29144481 TTGAGAAAATTATTTAA
1 TTGACAAAATTAATTAA
29144498 TTGACAAAATTAATTAA
1 TTGACAAAATTAATTAA
29144515 TT
1 TT
29144517 AAAATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (17 bp):
TTGACAAAATTAATTAA
Found at i:29150896 original size:40 final size:40
Alignment explanation
Indices: 29150841--29151012 Score: 191
Period size: 40 Copynumber: 4.3 Consensus size: 40
29150831 ACGCTTGGAC
* * * * *
29150841 AAAAAACGCCGCTATAGATTGAGTATTAGTGATGCTTTCT
1 AAAAAACGCCGCTATAGATCGAGCATTAGCGGTGCTTTTT
* * * *
29150881 AAAAAACGCTGCTATAGGTCGACCATTAGCGGCGCTTTTT
1 AAAAAACGCCGCTATAGATCGAGCATTAGCGGTGCTTTTT
* *
29150921 GAAAAACGCCGCTATAGATCGAGCACTAGCGGTGCTTTTT
1 AAAAAACGCCGCTATAGATCGAGCATTAGCGGTGCTTTTT
* * * * *
29150961 CAAAAACACTGCTATAGATCGAGCTTTAGCGGTGCTTTGT
1 AAAAAACGCCGCTATAGATCGAGCATTAGCGGTGCTTTTT
*
29151001 AAAAAAAGCCGC
1 AAAAAACGCCGC
29151013 AAAAACATTT
Statistics
Matches: 107, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 107 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (40 bp):
AAAAAACGCCGCTATAGATCGAGCATTAGCGGTGCTTTTT
Found at i:29151481 original size:15 final size:14
Alignment explanation
Indices: 29151444--29151482 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
29151434 GTAGTTAGGA
*
29151444 GTTAGGGGTTAAGG
1 GTTAGGGTTTAAGG
29151458 GTTATGGGTTTAAGG
1 GTTA-GGGTTTAAGG
29151473 GTTTAGGGTT
1 G-TTAGGGTT
29151483 ATATTTTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 15 0.68
16 3 0.14
ACGTcount: A:0.18, C:0.00, G:0.44, T:0.38
Consensus pattern (14 bp):
GTTAGGGTTTAAGG
Found at i:29156531 original size:69 final size:69
Alignment explanation
Indices: 29156458--29156603 Score: 168
Period size: 69 Copynumber: 2.1 Consensus size: 69
29156448 TTGTGAACCC
* * * * *
29156458 TAAAATGAT-GATTAAGAGCTTTTAACTCTCACTAATTGTTTGGGGCTACAGTGTTTAACCTGCA
1 TAAAATGATAG-TTAAGAGCTTTTAACTATCACTAACTATTTGAGGCTACAGTGCTTAACCTGCA
29156522 AGCCA
65 AGCCA
* * * * ** *
29156527 TAAAATTATAGTTGATAGCTTTTAACTATCGCTAACTATTTGAGGCTGTAGTGCTTAACCTGCGA
1 TAAAATGATAGTTAAGAGCTTTTAACTATCACTAACTATTTGAGGCTACAGTGCTTAACCTGCAA
29156592 GCCA
66 GCCA
29156596 TAAAATGA
1 TAAAATGA
29156604 CACTCGCTAA
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
69 62 0.98
70 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (69 bp):
TAAAATGATAGTTAAGAGCTTTTAACTATCACTAACTATTTGAGGCTACAGTGCTTAACCTGCAA
GCCA
Found at i:29156668 original size:121 final size:121
Alignment explanation
Indices: 29156489--29156726 Score: 300
Period size: 121 Copynumber: 2.0 Consensus size: 121
29156479 TTAACTCTCA
* * * *
29156489 CTAATTGTTTGGGGCTACAGTGTTTAACCTGCAAGCCATAAAATTATAGTTGATAGCTTTTAACT
1 CTAATTGTTTAGGGCTACACTGTTTAACCTGCAAGCCATAAAATTACAGTTGAGAGCTTTTAACT
* * * *
29156554 ATCGCTAACTATTTGAGGCTGTAGTGCTT-AACCTGCGAGCCATAAAATGACACTCG
66 ATCACTAACTATTTAAGGCTGCAGTG-TTCAACCTACGAGCCATAAAATGACACTCG
* * * *
29156610 CTAATTGTTTAGGGTTGCACTGTTTAACTTGCAAGTCATAAAATTACAGCTTG-GAGCTTTTAAC
1 CTAATTGTTTAGGGCTACACTGTTTAACCTGCAAGCCATAAAATTACAG-TTGAGAGCTTTTAAC
* * * *
29156674 TCTCACTAATTATTTAAGGTTGCCGTGTTCAACCTACGAGCCATAAAATGACA
65 TATCACTAACTATTTAAGGCTGCAGTGTTCAACCTACGAGCCATAAAATGACA
29156727 GCTAGGAGCT
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
120 2 0.02
121 94 0.95
122 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (121 bp):
CTAATTGTTTAGGGCTACACTGTTTAACCTGCAAGCCATAAAATTACAGTTGAGAGCTTTTAACT
ATCACTAACTATTTAAGGCTGCAGTGTTCAACCTACGAGCCATAAAATGACACTCG
Found at i:29156728 original size:69 final size:69
Alignment explanation
Indices: 29156610--29156895 Score: 326
Period size: 69 Copynumber: 4.1 Consensus size: 69
29156600 ATGACACTCG
* * * *
29156610 CTAATTGTTTAGGGTTGCAC-TGTTTAACTTGCAAGTCATAAAATTACAGCTTGGAGCTTTTAAC
1 CTAATTGTTTAGGGTTGC-CGTGTTTAACCTACAAGCCATAAAATGACAGCTTGGAGCTTTTAAC
29156674 TCTCA
65 TCTCA
* * * * *
29156679 CTAATTATTTAAGGTTGCCGTGTTCAACCTACGAGCCATAAAATGACAGCTAGGAGCTTTTAACT
1 CTAATTGTTTAGGGTTGCCGTGTTTAACCTACAAGCCATAAAATGACAGCTTGGAGCTTTTAACT
29156744 CTCA
66 CTCA
* * * * * *
29156748 CTAATTGTTTGGGGCTGCGGTGTTTAACCTGCAAGCCATGAAATGACAG-TTGAGAGTTTTTAAC
1 CTAATTGTTTAGGGTTGCCGTGTTTAACCTACAAGCCATAAAATGACAGCTTG-GAGCTTTTAAC
*
29156812 TATCA
65 TCTCA
* * * *
29156817 CAAATTGTTTAGGGTTG-CGATGTTTAACCTATAAGCCATAAAATGATAGCTTAGAGCTTTTAAC
1 CTAATTGTTTAGGGTTGCCG-TGTTTAACCTACAAGCCATAAAATGACAGCTTGGAGCTTTTAAC
*
29156881 TCTCG
65 TCTCA
*
29156886 CTAACTGTTT
1 CTAATTGTTT
29156896 TGTTTTTTAA
Statistics
Matches: 178, Mismatches: 35, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
68 4 0.02
69 172 0.97
70 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (69 bp):
CTAATTGTTTAGGGTTGCCGTGTTTAACCTACAAGCCATAAAATGACAGCTTGGAGCTTTTAACT
CTCA
Found at i:29158923 original size:41 final size:40
Alignment explanation
Indices: 29158878--29158967 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
29158868 AAACAGGTTT
*
29158878 TTAGCGGCGTTTGAACGAAAAACGCCACTATAG-ATCGAGCA
1 TTAGCGGCGTTT-AACGAAAAACGCCACTAAAGAAT-GAGCA
** **
29158919 TTAGCGGCGTTTTTCTTAAAACGCCACTAAAGAATGAGCA
1 TTAGCGGCGTTTAACGAAAAACGCCACTAAAGAATGAGCA
29158959 TTAGCGGCG
1 TTAGCGGCG
29158968 CTTTTTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 29 0.67
41 14 0.33
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.23
Consensus pattern (40 bp):
TTAGCGGCGTTTAACGAAAAACGCCACTAAAGAATGAGCA
Found at i:29158947 original size:40 final size:41
Alignment explanation
Indices: 29158896--29158973 Score: 124
Period size: 40 Copynumber: 1.9 Consensus size: 41
29158886 GTTTGAACGA
*
29158896 AAAACGCCACTATAG-ATCGAGCATTAGCGGCG-TTTTTCTT
1 AAAACGCCACTAAAGAAT-GAGCATTAGCGGCGCTTTTTCTT
29158936 AAAACGCCACTAAAGAATGAGCATTAGCGGCGCTTTTT
1 AAAACGCCACTAAAGAATGAGCATTAGCGGCGCTTTTT
29158974 AAAAAGCGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 28 0.80
41 7 0.20
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (41 bp):
AAAACGCCACTAAAGAATGAGCATTAGCGGCGCTTTTTCTT
Found at i:29159284 original size:39 final size:39
Alignment explanation
Indices: 29159189--29159289 Score: 107
Period size: 40 Copynumber: 2.5 Consensus size: 39
29159179 CTTTTTGTGG
* * *
29159189 CTTTAGTGGCGCTTTTTAAAAAATGCCGCTATAAATTCAC
1 CTTTAGCGGCG-TTTTTAAAAAACGCCGCTATAAACTCAC
* *
29159229 CTTTAGCTGTGC-TTTTTAAAAAACGCCGCTA-ATACTCAAT
1 CTTTAGC-G-GCGTTTTTAAAAAACGCCGCTATAAACTC-AC
29159269 CTTTAGCGGCGTTTTTAAAAA
1 CTTTAGCGGCGTTTTTAAAAA
29159290 CTCCACAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
38 2 0.04
39 15 0.29
40 32 0.62
41 1 0.02
42 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (39 bp):
CTTTAGCGGCGTTTTTAAAAAACGCCGCTATAAACTCAC
Found at i:29160356 original size:17 final size:18
Alignment explanation
Indices: 29160328--29160362 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
29160318 AATGAATAAT
*
29160328 ATTTTCCATAATCTTTAA
1 ATTTTCCATAATATTTAA
29160346 ATTTT-CATAATATTTAA
1 ATTTTCCATAATATTTAA
29160363 TTATTTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTCCATAATATTTAA
Found at i:29163416 original size:22 final size:22
Alignment explanation
Indices: 29163389--29163432 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29163379 GATTAATATT
*
29163389 TTATATTTAATATTTATAAATA
1 TTATATATAATATTTATAAATA
* *
29163411 TTATATATAATTTTTTTAAATA
1 TTATATATAATATTTATAAATA
29163433 AAAATAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATATATAATATTTATAAATA
Found at i:29164695 original size:43 final size:43
Alignment explanation
Indices: 29164613--29164803 Score: 211
Period size: 43 Copynumber: 4.4 Consensus size: 43
29164603 TTAAAATTTT
* ** * ** *
29164613 ATGACCTTTAGCGGCGTTTTTAAGAGAAGCATTGCTAAAGGTC
1 ATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCTGTTAAAGGTC
*
29164656 ATGATCTTTAGCGGCGTTTGTGGGAAAAGCGCTGTTAAAGGTC
1 ATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCTGTTAAAGGTC
* *
29164699 ATGACCTTTAGCGGCGTTTGTGGGAAAAGCGTTGCTAAAGGTC
1 ATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCTGTTAAAGGTC
*** * * * *
29164742 ATGACCTTTAGTAACATTTGTGGGAAAAGAGCCGTTAAAGGTT
1 ATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCTGTTAAAGGTC
**
29164785 ATGACCTTTAATGGCGTTT
1 ATGACCTTTAGCGGCGTTT
29164804 CCTATAGCGT
Statistics
Matches: 124, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 124 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (43 bp):
ATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCTGTTAAAGGTC
Found at i:29164713 original size:86 final size:86
Alignment explanation
Indices: 29164613--29164803 Score: 247
Period size: 86 Copynumber: 2.2 Consensus size: 86
29164603 TTAAAATTTT
* * * ** *
29164613 ATGACCTTTAGCGGCGTTTTTAAGAGAAGCATTGCTAAAGGTCATGATCTTTAGCGGCGTTTGTG
1 ATGACCTTTAGCGGCGTTTGTAAGAAAAGCATTGCTAAAGGTCATGACCTTTAGCAACATTTGTG
* *
29164678 GGAAAAGCGCTGTTAAAGGTC
66 GGAAAAGAGCCGTTAAAGGTC
** * *
29164699 ATGACCTTTAGCGGCGTTTGTGGGAAAAGCGTTGCTAAAGGTCATGACCTTTAGTAACATTTGTG
1 ATGACCTTTAGCGGCGTTTGTAAGAAAAGCATTGCTAAAGGTCATGACCTTTAGCAACATTTGTG
*
29164764 GGAAAAGAGCCGTTAAAGGTT
66 GGAAAAGAGCCGTTAAAGGTC
**
29164785 ATGACCTTTAATGGCGTTT
1 ATGACCTTTAGCGGCGTTT
29164804 CCTATAGCGT
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 90 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (86 bp):
ATGACCTTTAGCGGCGTTTGTAAGAAAAGCATTGCTAAAGGTCATGACCTTTAGCAACATTTGTG
GGAAAAGAGCCGTTAAAGGTC
Found at i:29188304 original size:29 final size:29
Alignment explanation
Indices: 29188263--29188320 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
29188253 AAAGATATCC
29188263 TCCTCGAGGGATTGAAGCTTTATTATTGA
1 TCCTCGAGGGATTGAAGCTTTATTATTGA
29188292 TCCTCGAGGGATTGAAGCTTTATTATTGA
1 TCCTCGAGGGATTGAAGCTTTATTATTGA
29188321 AGGACTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (29 bp):
TCCTCGAGGGATTGAAGCTTTATTATTGA
Found at i:29189506 original size:6 final size:6
Alignment explanation
Indices: 29189495--29189525 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
29189485 ACGCTAGAAG
29189495 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
29189526 AGGTAAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:29205101 original size:18 final size:19
Alignment explanation
Indices: 29205075--29205113 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
29205065 TTATATGTAT
29205075 TGACAATTTTTG-AAAGCA
1 TGACAATTTTTGTAAAGCA
*
29205093 TGACTATTTTTGTAAAGCA
1 TGACAATTTTTGTAAAGCA
29205112 TG
1 TG
29205114 TTTGACATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (19 bp):
TGACAATTTTTGTAAAGCA
Found at i:29208402 original size:81 final size:82
Alignment explanation
Indices: 29208246--29208445 Score: 203
Period size: 80 Copynumber: 2.5 Consensus size: 82
29208236 AATACTCAAT
* * *
29208246 ATCTCGCACACTAAGTGCCAAAGCAT-GACTGAAGCTATTATAATTTCGCACACTAAGTGCCTTT
1 ATCTCGCACACTAAGTGCCATA-TATAG-CTGAAGCTATTACAATTTCGCACACTAAGTGCCTTT
*
29208310 CATAGCTGAAGCTATCTC-
64 CATAGCCGAAGCTATCTCG
* * *
29208328 AGTCTCGCACACTAAGTGCCATATATAGCTGAAGCTATTCCGA-TTCGTACACTAAGTG-CTTTA
1 A-TCTCGCACACTAAGTGCCATATATAGCTGAAGCTATTACAATTTCGCACACTAAGTGCCTTT-
* *
29208391 TATAGCCGAAGCTATTTCG
64 CATAGCCGAAGCTATCTCG
* ** **
29208410 AT-TTGCACACTAAGTGCTTTATATAGCCAAAGCTAT
1 ATCTCGCACACTAAGTGCCATATATAGCTGAAGCTAT
29208446 CTCGATACGC
Statistics
Matches: 100, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
80 33 0.33
81 30 0.30
82 16 0.16
83 21 0.21
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (82 bp):
ATCTCGCACACTAAGTGCCATATATAGCTGAAGCTATTACAATTTCGCACACTAAGTGCCTTTCA
TAGCCGAAGCTATCTCG
Found at i:29208451 original size:40 final size:40
Alignment explanation
Indices: 29208290--29208466 Score: 189
Period size: 40 Copynumber: 4.4 Consensus size: 40
29208280 CTATTATAAT
* *
29208290 TTCGCACACTAAGTGCCTTT-CATAGCTGAAGCTATCTC-A
1 TTCGCACACTAAGTG-CTTTATATAGCCGAAGCTATCTCGA
** *
29208329 GTCTCGCACACTAAGTGCCATATATAGCTGAAGCTAT-TCCGA
1 -T-TCGCACACTAAGTGCTTTATATAGCCGAAGCTATCT-CGA
* *
29208371 TTCGTACACTAAGTGCTTTATATAGCCGAAGCTATTTCGA
1 TTCGCACACTAAGTGCTTTATATAGCCGAAGCTATCTCGA
* *
29208411 TTTGCACACTAAGTGCTTTATATAGCCAAAGCTATCTCGA
1 TTCGCACACTAAGTGCTTTATATAGCCGAAGCTATCTCGA
* * *
29208451 TACGCAAATTAAGTGC
1 TTCGCACACTAAGTGC
29208467 CAAACATAAC
Statistics
Matches: 117, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
40 85 0.73
41 31 0.26
42 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (40 bp):
TTCGCACACTAAGTGCTTTATATAGCCGAAGCTATCTCGA
Found at i:29210018 original size:14 final size:14
Alignment explanation
Indices: 29209999--29210039 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
29209989 AAAGAAAGAA
29209999 AAACAAATAGAAAG
1 AAACAAATAGAAAG
*
29210013 AAACAAA-AGCAA-
1 AAACAAATAGAAAG
29210025 AAACGAAATAGAAAG
1 AAAC-AAATAGAAAG
29210040 GGAAAGGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 4 0.18
13 7 0.32
14 11 0.50
ACGTcount: A:0.71, C:0.10, G:0.15, T:0.05
Consensus pattern (14 bp):
AAACAAATAGAAAG
Found at i:29210996 original size:41 final size:40
Alignment explanation
Indices: 29210952--29211086 Score: 143
Period size: 40 Copynumber: 3.4 Consensus size: 40
29210942 GACTTCGAGT
*
29210952 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAA-TTATTACTTCGGATTAATC
* * * *
29210993 CGATAAGACATTGGGTGCCAA-T-TTACTTCGGTTTAA-C
1 CGATGAGACACTGGGTGTCAATTATTACTTCGGATTAATC
* *
29211030 CGATGAGACACTGGGCGTCAATCTATTACTTCGAATT-ATC
1 CGATGAGACACTGGGTGTCAAT-TATTACTTCGGATTAATC
* *
29211070 CGATGAGGCACTAGGTG
1 CGATGAGACACTGGGTG
29211087 CCAAATTGGT
Statistics
Matches: 76, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
37 17 0.22
38 13 0.17
39 3 0.04
40 25 0.33
41 18 0.24
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTATTACTTCGGATTAATC
Found at i:29214300 original size:46 final size:46
Alignment explanation
Indices: 29214233--29214505 Score: 368
Period size: 46 Copynumber: 5.9 Consensus size: 46
29214223 GTGTGCTCTG
** *
29214233 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGAAACC
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACC
**
29214279 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACC
29214325 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACC
* *
29214371 TGATATGAAATGAATAAGACTATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACC
*** * * *
29214417 TGACGGGAAATGAATAAGACCATGGTTGAAAGATACCATGACAGCG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACC
* * * * *
29214463 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
29214506 TCATGTCAAA
Statistics
Matches: 208, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.00
46 207 1.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACC
Found at i:29227278 original size:16 final size:17
Alignment explanation
Indices: 29227259--29227292 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
29227249 CTTCGAGAAG
29227259 CTCAAGCT-TGTTCTGA
1 CTCAAGCTCTGTTCTGA
29227275 CTCAAGCTCCTGTTCTGA
1 CTCAAGCT-CTGTTCTGA
29227293 TGCAGCCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (17 bp):
CTCAAGCTCTGTTCTGA
Found at i:29229244 original size:30 final size:30
Alignment explanation
Indices: 29229208--29229267 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
29229198 TTCTTTTAAG
*
29229208 GGGTAGAGTTATAACGCCCTGAATAATTTA
1 GGGTAGAGTTATAACACCCTGAATAATTTA
29229238 GGGTAGAGTTATAACACCCTGAATAATTTA
1 GGGTAGAGTTATAACACCCTGAATAATTTA
29229268 TTCCTATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (30 bp):
GGGTAGAGTTATAACACCCTGAATAATTTA
Found at i:29230799 original size:12 final size:12
Alignment explanation
Indices: 29230778--29230811 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29230768 TATATATTTT
*
29230778 AAAATTATATAA
1 AAAATAATATAA
29230790 AAAATAATATAA
1 AAAATAATATAA
*
29230802 AAATTAATAT
1 AAAATAATAT
29230812 GGGCGGGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:29232261 original size:21 final size:23
Alignment explanation
Indices: 29232237--29232279 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29232227 ATAAATATTT
29232237 TATT-AATTAA-ATAAGATTTAA
1 TATTAAATTAATATAAGATTTAA
*
29232258 TATTAAATTAATATAATATTTA
1 TATTAAATTAATATAAGATTTA
29232280 TCAAGTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TATTAAATTAATATAAGATTTAA
Found at i:29233692 original size:100 final size:100
Alignment explanation
Indices: 29233519--29233718 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
29233509 ATACTCATTT
29233519 AGCCAATGCTTTTAAAGACAACAACTTACATTTTGAATAGAGTACCTACTAAAACAGCTGCAAAA
1 AGCCAATGCTTTTAAAGACAACAACTTACATTTTGAATAGAGTACCTACTAAAACAGCTGCAAAA
29233584 ACACCTTATGAGCTTTGGACAAGTCAAAAGCCTAG
66 ACACCTTATGAGCTTTGGACAAGTCAAAAGCCTAG
29233619 AGCCAATGCTTTTAAAGACAACAACTTACATTTTGAATAGAGTACCTACTAAAACAGCTGCAAAA
1 AGCCAATGCTTTTAAAGACAACAACTTACATTTTGAATAGAGTACCTACTAAAACAGCTGCAAAA
29233684 ACACCTTATGAGCTTTGGACAAGTCAAAAGCCTAG
66 ACACCTTATGAGCTTTGGACAAGTCAAAAGCCTAG
29233719 TCTAAAGCAC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (100 bp):
AGCCAATGCTTTTAAAGACAACAACTTACATTTTGAATAGAGTACCTACTAAAACAGCTGCAAAA
ACACCTTATGAGCTTTGGACAAGTCAAAAGCCTAG
Found at i:29247819 original size:27 final size:27
Alignment explanation
Indices: 29247771--29247822 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
29247761 AATAATGACA
* *
29247771 ATATTAATAATGAAAAATAATAATAAT
1 ATATTAATAATAAAAAAAAATAATAAT
29247798 ATATTAATAA-AAATAAAAAATAATA
1 ATATTAATAATAAA-AAAAAATAATA
29247823 CGTTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (27 bp):
ATATTAATAATAAAAAAAAATAATAAT
Found at i:29247819 original size:30 final size:32
Alignment explanation
Indices: 29247783--29247867 Score: 86
Period size: 38 Copynumber: 2.6 Consensus size: 32
29247773 ATTAATAATG
29247783 AAAAATAATAATAATATATTAAT-A-AAAATA
1 AAAAATAATAATAATATATTAATGATAAAATA
29247813 AAAAATAATACGTTAATAATGATATTAATGATAAAATA
1 AAAAAT-A-A---TAATAAT-ATATTAATGATAAAATA
*
29247851 GAAAATAATAAT-ATATA
1 AAAAATAATAATAATATA
29247868 AGGATGATGA
Statistics
Matches: 46, Mismatches: 1, Indels: 15
0.74 0.02 0.24
Matches are distributed among these distances:
30 6 0.13
31 4 0.09
32 3 0.07
33 4 0.09
35 7 0.15
36 9 0.20
37 2 0.04
38 11 0.24
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.31
Consensus pattern (32 bp):
AAAAATAATAATAATATATTAATGATAAAATA
Found at i:29247831 original size:38 final size:38
Alignment explanation
Indices: 29247791--29247860 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
29247781 TGAAAAATAA
29247791 TAATAAT-ATATTAAT-A-AAAATAAAAAATAATACGT
1 TAATAATGATATTAATGATAAAATAAAAAATAATACGT
*
29247826 TAATAATGATATTAATGATAAAATAGAAAATAATA
1 TAATAATGATATTAATGATAAAATAAAAAATAATA
29247861 ATATATAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 7 0.23
36 8 0.26
37 1 0.03
38 15 0.48
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.31
Consensus pattern (38 bp):
TAATAATGATATTAATGATAAAATAAAAAATAATACGT
Found at i:29247832 original size:27 final size:25
Alignment explanation
Indices: 29247770--29247834 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
29247760 AAATAATGAC
*
29247770 AATATTAATAATGAAAAATAATAAT
1 AATATTAATAATGAAAAATAAAAAT
*
29247795 AATA-TATTAAT-AAAAATAAAAAAT
1 AATATTAATAATGAAAAAT-AAAAAT
29247819 AATACGTTAATAATGA
1 AATA--TTAATAATGA
29247835 TATTAATGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 6 0.19
24 15 0.47
25 4 0.12
27 6 0.19
28 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (25 bp):
AATATTAATAATGAAAAATAAAAAT
Found at i:29247895 original size:3 final size:3
Alignment explanation
Indices: 29247889--29248288 Score: 64
Period size: 3 Copynumber: 133.7 Consensus size: 3
29247879 AGTATGTAGG
* * * *
29247889 TAA TAA TAA TAA -AA TAA TAA TAG TAA TAA TAA TAG TAG TAA -ATG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * *
29247933 TAA -AA AAA AAA T-A TAA GGTAA TGAA -AA TAA TATA GAA TTAA TTAA
1 TAA TAA TAA TAA TAA TAA --TAA T-AA TAA TAA TA-A TAA -TAA -TAA
* * * ** *
29247978 T-T TAA TAA T-A TGA TAA TAA TAG TAA TAA TAA -AA TAA TGC TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * ** * ** *
29248023 TAA TCA TAA -ATA TAA TAG TAA CGA TAA AAA TAA TAA TAA CGA CAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
29248068 CAA -AA TAGA -AGA TAA TAA TAA T-A TAT TAA TAA -ACT TAA TAA T-A
1 TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
** * * * * * *
29248111 TGC TAA TAA TAA AAA TAA AAA TAA AAA TAA AAA GTTAA TAA TGA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA --TAA TAA TAA TAA
* * * * * * * * *
29248158 TAC TGA TAG TAC TGA T-A TGAA -AA AAA TAG TAA TGA TAA T-A TAT
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
29248201 TAA TAA TAA TAG TAGA AAA TAA TAA TAAA TAA TAA TAA TAA TGA CAG
1 TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* * *
29248248 TTA TAA TGAA -CA TAA TAA TAC TAA TAA TAAA TAA T-A TAA TA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
29248289 GTAAATACAA
Statistics
Matches: 280, Mismatches: 82, Indels: 70
0.65 0.19 0.16
Matches are distributed among these distances:
2 31 0.11
3 219 0.78
4 25 0.09
5 5 0.02
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:29248223 original size:13 final size:13
Alignment explanation
Indices: 29248192--29248241 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
29248182 AATAGTAATG
*
29248192 ATAATATATTAATA
1 ATAATA-ATAAATA
*
29248206 ATAATAGTAGAA-A
1 ATAATAATA-AATA
29248219 ATAATAATAAATA
1 ATAATAATAAATA
29248232 ATAATAATAA
1 ATAATAATAA
29248242 TGACAGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 2 0.06
13 21 0.68
14 8 0.26
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
ATAATAATAAATA
Found at i:29248964 original size:22 final size:22
Alignment explanation
Indices: 29248918--29248964 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
29248908 GTTTATTACT
* *
29248918 AAAATATATAAAAAAAATAGTA
1 AAAATATATAAAAAAAAGAGCA
29248940 AAAATATA-AATAAAAAAGAGCA
1 AAAATATATAA-AAAAAAGAGCA
29248962 AAA
1 AAA
29248965 TGGAACACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (22 bp):
AAAATATATAAAAAAAAGAGCA
Found at i:29249885 original size:44 final size:43
Alignment explanation
Indices: 29249837--29250285 Score: 173
Period size: 44 Copynumber: 10.2 Consensus size: 43
29249827 TACCTTGGGA
29249837 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCA-CGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * ** * * *
29249881 AGATATGATCTGCA-ATTTTCAGCCTGCTCCACTGCTTCTCAGGG
1 AGATAAGAT-T-CACGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
29249925 AGATAAGACTAATGGCTTAAATTTGCTTCCCCACTAC--CTT-GGG
1 AGATAAGATTCACGTCTTCAATCTGC-T--CCACTACTGCTTAGGG
* *
29249968 AAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 -AGATAAGATTC-ACGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * *
29250013 AGATATGATCTGCA-ATCTTCAACCTGCTCCACTGCTGCTCAGGG
1 AGATAAGAT-T-CACGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * * *
29250057 AGGTAAAATT-A-GTGGCTTAAATCTGCTTCTCTACTACCTCAGGA
1 AGATAAGATTCACGT--CTTCAATCTGCTCCACTACT-GCTTAGGG
* * * * *
29250101 AGATAAGATTCACCATCTTCGATCCGCTCCACCATTGCTTAGGG
1 AGATAAGATTCA-CGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * **
29250145 AGATAAGATCTGTA-ATCTTCAGTCTGCTCCACTGTTGCTTAGGG
1 AGATAAGAT-T-CACGTCTTCAATCTGCTCCACTACTGCTTAGGG
** * * * * * *
29250189 AGATAAGGCT-A-GTGGCTTAAATCTGCTTCC-CCACTACCTCGGAA
1 AGATAAGATTCACGT--CTTCAATCTGC-TCCACTACTGCTTAGG-G
** * *
29250233 AGATAAGATTTGTCGTCTTCGATCTGCTCCATTACTGCTTAGGG
1 AGATAAGA-TTCACGTCTTCAATCTGCTCCACTACTGCTTAGGG
29250277 AGATAAGAT
1 AGATAAGAT
29250286 CTGTGAATTC
Statistics
Matches: 288, Mismatches: 88, Indels: 59
0.66 0.20 0.14
Matches are distributed among these distances:
41 4 0.01
42 8 0.03
43 43 0.15
44 174 0.60
45 46 0.16
46 10 0.03
47 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (43 bp):
AGATAAGATTCACGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:29249902 original size:132 final size:132
Alignment explanation
Indices: 29249705--29250288 Score: 724
Period size: 132 Copynumber: 4.4 Consensus size: 132
29249695 TGCTTCATGG
* * * * * *
29249705 AGATAAGATTCGCCATCTTTGATCTGCTCCACTGCTACTCAGGGAGATAAGATCTACAATCTTCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCA
* * * * * * * *
29249770 GCTTGC-CCTACTGCTACTTAGGGAGATAAAGCTAGTGACTTAAATCTAC-GCCCCTGCTACCTT
66 GCCTGCTCC-ACTGCTGCTCAGGGAGATAAAGCTAGTGGCTTAAATCTGCTTCCCC-ACTACCTC
29249833 GGGA
129 GGGA
* * * *
29249837 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGGAGATATGATCTGCAATTTTCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCA
* * * *
29249902 GCCTGCTCCACTGCTTCTCAGGGAGAT-AAGACTAATGGCTTAAATTTGCTTCCCCACTACCTTG
66 GCCTGCTCCACTGCTGCTCAGGGAGATAAAG-CTAGTGGCTTAAATCTGCTTCCCCACTACCTCG
29249966 GGA
130 GGA
*
29249969 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATATGATCTGCAATCTTCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCA
* * ** * * *
29250034 ACCTGCTCCACTGCTGCTCAGGGAGGTAAAATTAGTGGCTTAAATCTGCTTCTCTACTACCTCAG
66 GCCTGCTCCACTGCTGCTCAGGGAGATAAAGCTAGTGGCTTAAATCTGCTTCCCCACTACCTCGG
29250099 GA
131 GA
* * * * * *
29250101 AGATAAGATTCACCATCTTCGATCCGCTCCACCATTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCA
* * * *
29250166 GTCTGCTCCACTGTTGCTTAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCCACTACCTCGG
66 GCCTGCTCCACTGCTGCTCAGGGAGATAAAGCTAGTGGCTTAAATCTGCTTCCCCACTACCTCGG
*
29250231 AA
131 GA
* * *
29250233 AGATAAGATTTGTCGTCTTCGATCTGCTCCATTACTGCTTAGGGAGATAAGATCTG
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
29250289 TGAATTCACC
Statistics
Matches: 388, Mismatches: 60, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
131 3 0.01
132 377 0.97
133 8 0.02
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (132 bp):
AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCA
GCCTGCTCCACTGCTGCTCAGGGAGATAAAGCTAGTGGCTTAAATCTGCTTCCCCACTACCTCGG
GA
Found at i:29254621 original size:11 final size:11
Alignment explanation
Indices: 29254605--29254630 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29254595 TTTTATGGGG
29254605 ACGCAATATCA
1 ACGCAATATCA
29254616 ACGCAATATCA
1 ACGCAATATCA
29254627 ACGC
1 ACGC
29254631 TTAACCCAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.31, G:0.12, T:0.15
Consensus pattern (11 bp):
ACGCAATATCA
Found at i:29258158 original size:23 final size:23
Alignment explanation
Indices: 29258132--29258176 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29258122 TGGGTATGTG
*
29258132 ATGACTTTATCTT-ATAAATATGC
1 ATGAATTTATCTTGA-AAATATGC
29258155 ATGAATTTATCTTGAAAATATG
1 ATGAATTTATCTTGAAAATATG
29258177 TTGAATTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (23 bp):
ATGAATTTATCTTGAAAATATGC
Found at i:29262147 original size:15 final size:15
Alignment explanation
Indices: 29262118--29262147 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29262108 TTCTACTATA
29262118 ATTATATTTCTATTT
1 ATTATATTTCTATTT
*
29262133 ATTATATTTTTATTT
1 ATTATATTTCTATTT
29262148 CTATTTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTATATTTCTATTT
Found at i:29262346 original size:25 final size:24
Alignment explanation
Indices: 29262285--29262346 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
29262275 TATAATGCTC
* *
29262285 ATTTCAAATTTTTATACATTATTT
1 ATTTCAAATTTTCATACATTATGT
*
29262309 ACTTT-AATATTTTCATATATTATGT
1 A-TTTCAA-ATTTTCATACATTATGT
29262334 ATTTCAAACTTTT
1 ATTTCAAA-TTTT
29262347 TTCCACACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTCAAATTTTCATACATTATGT
Found at i:29269973 original size:30 final size:30
Alignment explanation
Indices: 29269915--29269974 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
29269905 TTCCCGAGCC
*
29269915 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAGTGTAATTATACAAAAGTT
* *
29269945 TAGGGGCAAAAGTGTAATTTTACCAAAGTT
1 TAGGGGCAAAAGTGTAATTATACAAAAGTT
29269975 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAATTATACAAAAGTT
Found at i:29270453 original size:46 final size:46
Alignment explanation
Indices: 29270403--29270575 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
29270393 TGGTTGAGCA
29270403 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
29270449 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
29270494 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
29270542 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
29270576 GGGGCAGGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:29270559 original size:93 final size:93
Alignment explanation
Indices: 29270400--29270570 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
29270390 GGATGGTTGA
* *
29270400 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
29270465 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
29270493 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
29270558 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
29270571 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:29273566 original size:15 final size:15
Alignment explanation
Indices: 29273546--29273601 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
29273536 GTATCTTGGG
29273546 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
29273561 TTTCTTTACTCTGGA
1 TTTCTTTATTCTGGA
*
29273576 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
29273591 TTTCTTTATTC
1 TTTCTTTATTC
29273602 GGTTTCCTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
14 2 0.06
15 32 0.89
16 2 0.06
ACGTcount: A:0.12, C:0.18, G:0.11, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:29275577 original size:30 final size:30
Alignment explanation
Indices: 29275519--29275578 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29275509 TTCCCGAGCC
*
29275519 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAGTGTAATTATACAAAAGTT
* * *
29275549 TAGGGGCAAAAGTTTAATTTTACCAAAGTT
1 TAGGGGCAAAAGTGTAATTATACAAAAGTT
29275579 CGTATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAATTATACAAAAGTT
Found at i:29276054 original size:46 final size:46
Alignment explanation
Indices: 29276004--29276176 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
29275994 TGGTTGAGCA
29276004 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
29276050 TCCGAACTCGTTGAGTTGAGTTCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
29276095 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
29276143 CCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
29276177 GGGGCAGGTT
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 59 0.57
47 28 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:29276160 original size:93 final size:93
Alignment explanation
Indices: 29276001--29276171 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
29275991 GGATGGTTGA
* *
29276001 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
29276066 TGAGTTCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
29276094 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTTGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
29276159 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
29276172 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:29277796 original size:178 final size:178
Alignment explanation
Indices: 29277490--29278206 Score: 1078
Period size: 178 Copynumber: 4.0 Consensus size: 178
29277480 GGGGCATTAC
* * *
29277490 AAGCAGACTGAAAATTATAGATCTTATCTCCATATATCGGCTATAGAGCAGATCGAAAATGGCGA
1 AAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGA
*
29277555 GTCTTATCTCCATGTATCGATTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGC
66 GTCTTATCTCCATGTATCGGTTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGC
* * *
29277620 AAGAGAGCAAGTTGAAGATACAGGTATTATCTTCCTGAGGTAGCAAGG
131 AAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGG
*
29277668 AAGCAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATC-AGAAATGGCG
1 AAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGA-AAATGGCG
* * * * *
29277732 AGTCTTATCCCCATGTATCGGCTATAGAGTAGATTTTAGCCATCAGCCTTATCTCTCTGAGGTAG
65 AGTCTTATCTCCATGTATCGGTTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAG
* * *
29277797 CAAGAAAGCAGGTTGAAGATGCAAGTCTTATCTTTCTGAGGTAGCAAGG
130 CAAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGG
*
29277846 AAGCAGACTGAAAATTACAGATCTTATCTCTATGTATCGGCTATGGAGCAGATCGAAAATGGCGA
1 AAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGA
* * * *
29277911 GTCTTATCTCCATGTATCGGTTATGAAGTAGATTTTAGCCACTAGCTTTATCTCTCTGAGGTAGC
66 GTCTTATCTCCATGTATCGGTTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGC
* ** * *
29277976 AAGAGAGTAGGTTGAAGATACAAGTCTTATCTTTTTAAGGTACCAAGG
131 AAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGG
* * * * *
29278024 AAGCAGACTGAAAATTACAGATTTTA-CATCCATGTATAGGCTATGGAGTAGATCAAAAATGGCA
1 AAGCAGACTGAAAATTACAGATCTTATC-TCCATGTATCGGCTATGGAGCAGATCGAAAATGGCG
* * * *
29278088 AGTCTTATCTCCATGTATCGGTAATGGAGCAAATTTTAGCCACCGGCCTTATATCTCTGAGGTAG
65 AGTCTTATCTCCATGTATCGGTTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAG
*
29278153 CAAGAGAGCAGGTCGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGG
130 CAAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGG
29278202 AAGCA
1 AAGCA
29278207 AATTAAACAT
Statistics
Matches: 485, Mismatches: 51, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
177 2 0.00
178 482 0.99
179 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (178 bp):
AAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGA
GTCTTATCTCCATGTATCGGTTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGC
AAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGG
Found at i:29278270 original size:44 final size:44
Alignment explanation
Indices: 29278222--29278375 Score: 125
Period size: 44 Copynumber: 3.5 Consensus size: 44
29278212 AACATTTCAA
29278222 ATCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAAATTACAG
1 ATCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAAATTACAG
* * ** * * ***
29278266 ATCTTATCTCCCTAAGCAGTAGCGG-AGTAGATCGAAGACGGTA-AG
1 ATCTTAACCCCCTAAGCAGTAG-GGTAACAGGT-TAA-AAATTACAG
* * **
29278311 -CCTTAACCCCCTAAGCAATAGGGTAACAGGTTGCAAATTACAG
1 ATCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAAATTACAG
* *
29278354 ATCTTATCTCCCTAAGCAGTAG
1 ATCTTAACCCCCTAAGCAGTAG
29278376 TGGAGCAGAT
Statistics
Matches: 78, Mismatches: 26, Indels: 12
0.67 0.22 0.10
Matches are distributed among these distances:
42 3 0.04
43 4 0.05
44 62 0.79
45 6 0.08
46 3 0.04
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (44 bp):
ATCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAAATTACAG
Found at i:29278326 original size:88 final size:88
Alignment explanation
Indices: 29278224--29278391 Score: 291
Period size: 88 Copynumber: 1.9 Consensus size: 88
29278214 CATTTCAAAT
*
29278224 CTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGTAGC
1 CTTAACCCCCTAAGCAATAGGGTAACAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGTAGC
*
29278289 GGAGTAGATCGAAGACGGTAAGC
66 GGAGCAGATCGAAGACGGTAAGC
** *
29278312 CTTAACCCCCTAAGCAATAGGGTAACAGGTTGCAAATTACAGATCTTATCTCCCTAAGCAGTAGT
1 CTTAACCCCCTAAGCAATAGGGTAACAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGTAGC
29278377 GGAGCAGATCGAAGA
66 GGAGCAGATCGAAGA
29278392 ACTCCCTAAG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 75 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (88 bp):
CTTAACCCCCTAAGCAATAGGGTAACAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGTAGC
GGAGCAGATCGAAGACGGTAAGC
Found at i:29278462 original size:76 final size:76
Alignment explanation
Indices: 29278319--29278462 Score: 209
Period size: 76 Copynumber: 1.9 Consensus size: 76
29278309 AGCCTTAACC
* * *
29278319 CCCTAAGCAATAGGGTAACAGGTTGCAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
1 CCCTAAGCAATAGGGTAACAGGCTGCAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAACAG
29278384 ATCGAAGAACT
66 ATCGAAGAACT
* * * *
29278395 CCCTAAGCAGA-AGGGTAATAGGCTGGAAATTACAGATCTTATCTCTCTAAGCAGTAGCGGAATA
1 CCCTAAGCA-ATAGGGTAACAGGCTGCAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAACA
29278459 GATC
65 GATC
29278463 AAAAATGGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
76 59 0.98
77 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (76 bp):
CCCTAAGCAATAGGGTAACAGGCTGCAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAACAG
ATCGAAGAACT
Found at i:29278565 original size:88 final size:88
Alignment explanation
Indices: 29278395--29278711 Score: 472
Period size: 88 Copynumber: 3.6 Consensus size: 88
29278385 TCGAAGAACT
* * * * * *
29278395 CCCTAAGCAGAAGGGTAATAGGCTGGAAATTACAGATCTTATCTCTCTAAGCAGTAGCGGAATAG
1 CCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAATAGCGGAACAA
* * * *
29278460 ATCAAAAATGGTAAGCCTTAACC
66 ATCGAAGACGGTGAGCCTTAACC
* * *
29278483 CCCTAAGCAGTAGGGTAGCAGGCTGGAAATTACAGATCTTATCTCCCTAAGTAATAGTGGAACAA
1 CCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAATAGCGGAACAA
29278548 ATCGAAGACGGTGAGCCTTAACC
66 ATCGAAGACGGTGAGCCTTAACC
*
29278571 CCCTAAGCAATAGGGTAACAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAATAGCGGAACAA
1 CCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAATAGCGGAACAA
*
29278636 ATTGAAGACGGTGAGCCTTAACC
66 ATCGAAGACGGTGAGCCTTAACC
* * *
29278659 CCCTAAGAAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCACCCTAAGCA
1 CCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTCCCTAAGCA
29278712 GTAGTGGAGC
Statistics
Matches: 207, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 207 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (88 bp):
CCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAATAGCGGAACAA
ATCGAAGACGGTGAGCCTTAACC
Found at i:29278766 original size:44 final size:44
Alignment explanation
Indices: 29278393--29278759 Score: 177
Period size: 44 Copynumber: 8.3 Consensus size: 44
29278383 GATCGAAGAA
* * *
29278393 CTCCCTAAGCAGAAGGGTAATAGGCTGGAA-ATTACAGATCTTAT
1 CTCCCTAAGCAGTAGGG-AACAGACTGGAAGATTACAGATCTTAT
* * ** * * *
29278437 CTCTCTAAGCAGTAGCGGAATAGA-TCAAAAATGGTA-AG-CCTTAA
1 CTCCCTAAGCAGTAG-GGAACAGACTGGAAGAT--TACAGATCTTAT
* * *
29278481 CCCCCTAAGCAGTAGGGTAGCAGGCTGGAA-ATTACAGATCTTAT
1 CTCCCTAAGCAGTAGGG-AACAGACTGGAAGATTACAGATCTTAT
* * * * * * * *
29278525 CTCCCTAAGTAATAGTGGAACA-AATCGAAGACGGT-GAG-CCTTAA
1 CTCCCTAAGCAGTAG-GGAACAGACTGGAAGA--TTACAGATCTTAT
* * *
29278569 CCCCCTAAGCAATAGGGTAACAGGCTGGAA-ATTACAGATCTTAT
1 CTCCCTAAGCAGTAGGG-AACAGACTGGAAGATTACAGATCTTAT
* * * * * * *
29278613 CTCCCTAAGCAATAGCGGAACA-AATTGAAGACGGT-GAG-CCTTAA
1 CTCCCTAAGCAGTAG-GGAACAGACTGGAAGA--TTACAGATCTTAT
* * * *
29278657 CCCCCTAAGAAGTAGGGTAACAGGCT-GAAAATTACAGATCTTAT
1 CTCCCTAAGCAGTAGGG-AACAGACTGGAAGATTACAGATCTTAT
* *
29278701 CACCCTAAGCAGTAGTGGAGCAGACT-GAAGATTACAGATCTTAT
1 CTCCCTAAGCAGTAG-GGAACAGACTGGAAGATTACAGATCTTAT
29278745 CTCCCTAAGCAGTAG
1 CTCCCTAAGCAGTAG
29278760 TGGAGCAAAT
Statistics
Matches: 238, Mismatches: 60, Indels: 50
0.68 0.17 0.14
Matches are distributed among these distances:
42 4 0.02
43 23 0.10
44 185 0.78
45 22 0.09
46 4 0.02
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (44 bp):
CTCCCTAAGCAGTAGGGAACAGACTGGAAGATTACAGATCTTAT
Found at i:29278775 original size:44 final size:44
Alignment explanation
Indices: 29278681--29278768 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
29278671 GGGTAACAGG
* *
29278681 CTGAAAATTACAGATCTTATCACCCTAAGCAGTAGTGGAGCAGA
1 CTGAAGATTACAGATCTTATCACCCTAAGCAGTAGTGGAGCAAA
*
29278725 CTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAA
1 CTGAAGATTACAGATCTTATCACCCTAAGCAGTAGTGGAGCAAA
29278769 TCGAAGACAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (44 bp):
CTGAAGATTACAGATCTTATCACCCTAAGCAGTAGTGGAGCAAA
Found at i:29279620 original size:22 final size:22
Alignment explanation
Indices: 29279575--29279620 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
29279565 CATTCAAGAT
* *
29279575 AAATAATATATAAAACTTTTAA
1 AAATAATATATAAAACATTCAA
29279597 AAATAATATAT-AAACAATTCAA
1 AAATAATATATAAAAC-ATTCAA
29279619 AA
1 AA
29279621 TATATAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATAATATATAAAACATTCAA
Found at i:29279870 original size:17 final size:15
Alignment explanation
Indices: 29279838--29279884 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 15
29279828 ATAGAAAGAA
29279838 AAATATAATAAATAG
1 AAATATAATAAATAG
29279853 AAATATAATAATAGTAG
1 AAATATAATAA-A-TAG
29279870 AAATATAAATAAATA
1 AAATAT-AATAAATA
29279885 AATAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 11 0.38
16 3 0.10
17 10 0.34
18 5 0.17
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (15 bp):
AAATATAATAAATAG
Found at i:29284100 original size:84 final size:84
Alignment explanation
Indices: 29283916--29284520 Score: 809
Period size: 85 Copynumber: 7.1 Consensus size: 84
29283906 TTACCCTACT
* * * * * * * **
29283916 GTTAAGGCTCACTATCCTCGATCTACTCTATTACTGCTTAGGGAGATAAGATCTGTA-ACTCAGC
1 GTTAAGGCTCGCTGTCTTCGATCTGCTCCACTACTGTTTA-GG-GATAAGATCTGTATTTTCAGC
* *
29283980 CTGTTACCCTATTGTTTAGGG
64 CTGTTACCCTACTGCTTAGGG
* *
29284001 GTTAAGGCTCACTGTCTTCGATCTGCTCTACTACTGTTTAGGGATAAGATCTGTATTTTCAGCCT
1 GTTAAGGCTCGCTGTCTTCGATCTGCTCCACTACTGTTTAGGGATAAGATCTGTATTTTCAGCCT
29284066 GTTACCCTACTGCTTAGGG
66 GTTACCCTACTGCTTAGGG
* *
29284085 GTTAAGGCTCGCTGTCTTCGATATGCTCCATTACTGTTTAGGGATAAGATCTGTATTTTCCAGCC
1 GTTAAGGCTCGCTGTCTTCGATCTGCTCCACTACTGTTTAGGGATAAGATCTGTATTTT-CAGCC
*
29284150 TGTTACCCTACTACTTA-GG
65 TGTTACCCTACTGCTTAGGG
** * *
29284169 GTTAAGGCTTACCGTCTTCGATCTGCTCCACTATTGTTTAGGGATAAGATCTGTATTTTCCAGCC
1 GTTAAGGCTCGCTGTCTTCGATCTGCTCCACTACTGTTTAGGGATAAGATCTGTATTTT-CAGCC
29284234 TGTTACCCTACTGCTTAGAGG
65 TGTTACCCTACTGCTTAG-GG
* * * * * * *
29284255 GTTAAGGCTTGCTATCTTCAATCTGCTCCACTATTGTTTAGGGATAAGATCTATATTTCCATCCT
1 GTTAAGGCTCGCTGTCTTCGATCTGCTCCACTACTGTTTAGGGATAAGATCTGTATTTTCAGCCT
29284320 GTTACCCTACTGCTTAGGGG
66 GTTACCCTACTGCTTA-GGG
* * * * *
29284340 GTTAAGGCTCGTTGTCTTTGATCTGTTCCACTACTGTTTAGGGATAAGATCTGTATTTTTAGCTT
1 GTTAAGGCTCGCTGTCTTCGATCTGCTCCACTACTGTTTAGGGATAAGATCTGTATTTTCAGCCT
*
29284405 GTTACCCTATTGCTTAGGGG
66 GTTACCCTACTGCTTA-GGG
* *
29284425 GTTAAGGCTCGCTGTCTTCGATCTGTTCCACTACTGTTTAGGGATAAGATCTGTATTTTTAGCCT
1 GTTAAGGCTCGCTGTCTTCGATCTGCTCCACTACTGTTTAGGGATAAGATCTGTATTTTCAGCCT
29284490 GTTACCCTACTGCTTAGGGG
66 GTTACCCTACTGCTTA-GGG
29284510 GTTAAGGCTCG
1 GTTAAGGCTCG
29284521 TATCTTCAGC
Statistics
Matches: 470, Mismatches: 45, Indels: 10
0.90 0.09 0.02
Matches are distributed among these distances:
83 13 0.03
84 158 0.34
85 243 0.52
86 56 0.12
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (84 bp):
GTTAAGGCTCGCTGTCTTCGATCTGCTCCACTACTGTTTAGGGATAAGATCTGTATTTTCAGCCT
GTTACCCTACTGCTTAGGG
Found at i:29284169 original size:42 final size:42
Alignment explanation
Indices: 29284031--29284508 Score: 170
Period size: 42 Copynumber: 11.3 Consensus size: 42
29284021 ATCTGCTCTA
*
29284031 CTACTGTTTAGGGATAAGATCTGTATTTT-CAGCCTGTTACC
1 CTACTGCTTAGGGATAAGATCTGTATTTTCCAGCCTGTTACC
* * * * * ** *
29284072 CTACTGCTTAGGGGTTAAG-GCTCGCTGTCTTCGA-TATGCT-CC
1 CTACTGCTTA-GGGATAAGATCT-G-TATTTTCCAGCCTGTTACC
* *
29284114 ATTACTGTTTAGGGATAAGATCTGTATTTTCCAGCCTGTTACC
1 -CTACTGCTTAGGGATAAGATCTGTATTTTCCAGCCTGTTACC
* * * * * * *
29284157 CTACTACTTAGGGTTAAG-GCT-TACCGTCTTCGA-TCTGCT-CC
1 CTACTGCTTAGGGATAAGATCTGTA---TTTTCCAGCCTGTTACC
* *
29284198 ACTATTGTTTAGGGATAAGATCTGTATTTTCCAGCCTGTTACC
1 -CTACTGCTTAGGGATAAGATCTGTATTTTCCAGCCTGTTACC
* * * ** *
29284241 CTACTGCTTAGAGGGTTAAG-GCTTGCTATCTT-CAATCTGCT-CC
1 CTACTGCTT--AGGGATAAGATC-TG-TATTTTCCAGCCTGTTACC
* * * *
29284284 ACTATTGTTTAGGGATAAGATCTATA-TTTCCATCCTGTTACC
1 -CTACTGCTTAGGGATAAGATCTGTATTTTCCAGCCTGTTACC
* * ** *
29284326 CTACTGCTTAGGGGGTTAAG-GCTCGT-TGTCTTTGA-TCTGTT-CC
1 CTACTGCTTA--GGGATAAGATCT-GTAT-T-TTCCAGCCTGTTACC
* * *
29284369 ACTACTGTTTAGGGATAAGATCTGTATTTT-TAGCTTGTTACC
1 -CTACTGCTTAGGGATAAGATCTGTATTTTCCAGCCTGTTACC
* * * * * * *
29284411 CTATTGCTTAGGGGGTTAAG-GCTCGCTGTCTTCGA-TCTGTT-CC
1 CTACTGCTTA--GGGATAAGATCT-G-TATTTTCCAGCCTGTTACC
* *
29284454 ACTACTGTTTAGGGATAAGATCTGTATTTT-TAGCCTGTTACC
1 -CTACTGCTTAGGGATAAGATCTGTATTTTCCAGCCTGTTACC
29284496 CTACTGCTTAGGG
1 CTACTGCTTAGGG
29284509 GGTTAAGGCT
Statistics
Matches: 307, Mismatches: 86, Indels: 88
0.64 0.18 0.18
Matches are distributed among these distances:
40 6 0.02
41 77 0.25
42 101 0.33
43 57 0.19
44 57 0.19
45 9 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
CTACTGCTTAGGGATAAGATCTGTATTTTCCAGCCTGTTACC
Found at i:29284381 original size:44 final size:44
Alignment explanation
Indices: 29284318--29284521 Score: 139
Period size: 41 Copynumber: 4.8 Consensus size: 44
29284308 TATTTCCATC
29284318 CTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTTGTCTTTGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTTGTCTTTGAT
* * * *
29284362 CTGTT-CCACTACTGTTTA--GGGATAA-GATCTGTAT-T-TTT-AG
1 CTGTTACC-CTACTGCTTAGGGGGTTAAGGCTC-GT-TGTCTTTGAT
* * *
29284402 CTTGTTACCCTATTGCTTAGGGGGTTAAGGCTCGCTGTCTTCGAT
1 C-TGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTTGTCTTTGAT
* * * *
29284447 CTGTT-CCACTACTGTTTA--GGGATAA-GATCTGTAT-T-TTT-AGC
1 CTGTTACC-CTACTGCTTAGGGGGTTAAGGCTC-GT-TGTCTTTGA-T
29284488 CTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGT
29284522 ATCTTCAGCT
Statistics
Matches: 120, Mismatches: 21, Indels: 39
0.67 0.12 0.22
Matches are distributed among these distances:
40 3 0.03
41 37 0.31
42 22 0.18
43 22 0.18
44 34 0.28
45 2 0.02
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.39
Consensus pattern (44 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTTGTCTTTGAT
Found at i:29284953 original size:33 final size:33
Alignment explanation
Indices: 29284915--29284980 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
29284905 AATGTCATGA
29284915 GAATGATTTTTAAAATCTTAAAGTGTCATCACT
1 GAATGATTTTTAAAATCTTAAAGTGTCATCACT
29284948 GAATGATTTTTAAAATCTTAAAGTGTCATCACT
1 GAATGATTTTTAAAATCTTAAAGTGTCATCACT
29284981 CGTTATCCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (33 bp):
GAATGATTTTTAAAATCTTAAAGTGTCATCACT
Found at i:29289180 original size:5 final size:5
Alignment explanation
Indices: 29289170--29289210 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
29289160 ATGATACAAT
*
29289170 AATGC AATGC AATGC AATGC AAATGC -ATGG AATG- AATGC AA
1 AATGC AATGC AATGC AATGC -AATGC AATGC AATGC AATGC AA
29289211 AAGAAAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
4 7 0.22
5 20 0.62
6 5 0.16
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (5 bp):
AATGC
Found at i:29291012 original size:21 final size:23
Alignment explanation
Indices: 29290965--29291018 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
29290955 CATTCAAGAT
**
29290965 AAAATAATATATAAAACTTTTTA
1 AAAATAATATATAAAACTAATTA
*
29290988 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
29291009 AAAAT-ATATA
1 AAAATAATATA
29291019 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:29291248 original size:21 final size:21
Alignment explanation
Indices: 29291219--29291271 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
29291209 ATATTAGTAT
29291219 ATAAATAGAAATAAAAATATA
1 ATAAATAGAAATAAAAATATA
* * *
29291240 ATAAGTAGAAATATAAATA-G
1 ATAAATAGAAATAAAAATATA
*
29291260 ATAAATAAAAAT
1 ATAAATAGAAAT
29291272 TAGACAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.25
Consensus pattern (21 bp):
ATAAATAGAAATAAAAATATA
Found at i:29291271 original size:14 final size:14
Alignment explanation
Indices: 29291248--29291330 Score: 55
Period size: 14 Copynumber: 5.8 Consensus size: 14
29291238 TAATAAGTAG
*
29291248 AAATATAAATAGAT
1 AAATAAAAATAGAT
*
29291262 AAATAAAAATTAGAC
1 AAATAAAAA-TAGAT
*
29291277 AAATAATAATAGTATT
1 AAATAAAAATAG-A-T
*
29291293 AGAATAACAA-A-AT
1 A-AATAAAAATAGAT
*
29291306 AAATATAAATAGA-
1 AAATAAAAATAGAT
29291319 AACATAAAAATA
1 AA-ATAAAAATA
29291331 ATAGCAATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
12 6 0.11
13 5 0.09
14 21 0.39
15 13 0.24
16 2 0.04
17 7 0.13
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.24
Consensus pattern (14 bp):
AAATAAAAATAGAT
Found at i:29292390 original size:19 final size:20
Alignment explanation
Indices: 29292366--29292412 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
29292356 TTGTAAAATT
* *
29292366 TAATGCACATG-ATGTGATG
1 TAATGCAAATGCATGAGATG
29292385 TAATGCAAATGCATGAGATG
1 TAATGCAAATGCATGAGATG
29292405 -AATGCAAA
1 TAATGCAAA
29292413 ACTAAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (20 bp):
TAATGCAAATGCATGAGATG
Found at i:29296433 original size:3 final size:3
Alignment explanation
Indices: 29296211--29296423 Score: 61
Period size: 3 Copynumber: 71.0 Consensus size: 3
29296201 AGTATGTAGG
* ** *
29296211 TAA TAA TAA TAA -AA TAA TAA TAG TAA TAA TAA TCG TAG TAA -ATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * *
29296255 TAA AAA GAA -AA TATA TAA GGTAA TGAA -AA TAA TACA GAA TTAA TTAA
1 TAA TAA TAA TAA TA-A TAA --TAA T-AA TAA TAA TA-A TAA -TAA -TAA
* * ** *
29296302 T-T TAA TAA T-A TAA TAA TAG TAA TAA TAA -AA TAA TGC TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * ** * * * *
29296347 TCA TAA -ATA TAA TAG TAA CGA TAA AAA TAA TAA TAA CAA CAA CAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
29296392 -AA TAGA -AGA TAA TAA TAA TAA T-A TAT TAA TAA
1 TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA
29296424 ACTTAATAAT
Statistics
Matches: 157, Mismatches: 33, Indels: 40
0.68 0.14 0.17
Matches are distributed among these distances:
2 17 0.11
3 120 0.76
4 17 0.11
5 3 0.02
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:29296449 original size:6 final size:6
Alignment explanation
Indices: 29296438--29296466 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29296428 AATAATATGC
29296438 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
29296467 GGTTAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:29296570 original size:15 final size:16
Alignment explanation
Indices: 29296544--29296578 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
29296534 TAATGAAAAT
29296544 AATAATACTAATAATA
1 AATAATACTAATAATA
*
29296560 AATAATA-TAATAGTA
1 AATAATACTAATAATA
29296575 AATA
1 AATA
29296579 CAAAACTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAATACTAATAATA
Found at i:29300708 original size:13 final size:13
Alignment explanation
Indices: 29300669--29300713 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
29300659 AGTTCTTAAT
29300669 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* * *
29300682 TGCTGTGGAAAAG
1 TGCTTTTGAGAAG
*
29300695 TACTTTTGAGAAG
1 TGCTTTTGAGAAG
29300708 TGCTTT
1 TGCTTT
29300714 GAAAAAATTT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.24, C:0.09, G:0.29, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:29306142 original size:30 final size:32
Alignment explanation
Indices: 29306092--29306152 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
29306082 TGGCTTAACC
*
29306092 AAAATTCAATTTAAAATAT-AAAAATATTTTT
1 AAAATTCAAATTAAAATATAAAAAATATTTTT
*
29306123 AAAATT-AAATTAAATTATAAAAAATATTTT
1 AAAATTCAAATTAAAATATAAAAAATATTTT
29306153 AAATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (32 bp):
AAAATTCAAATTAAAATATAAAAAATATTTTT
Found at i:29307994 original size:14 final size:14
Alignment explanation
Indices: 29307977--29308004 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29307967 TTTTTTAAAT
29307977 TACACATGAAAAAC
1 TACACATGAAAAAC
29307991 TACACATGAAAAAC
1 TACACATGAAAAAC
29308005 CTTAACTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.21, G:0.07, T:0.14
Consensus pattern (14 bp):
TACACATGAAAAAC
Found at i:29308559 original size:58 final size:58
Alignment explanation
Indices: 29308485--29308616 Score: 165
Period size: 58 Copynumber: 2.3 Consensus size: 58
29308475 TGGAAGATGT
* *
29308485 TAGATATGTTGCTATATATTATAAATTTTATTATCCATATAAAATATTATTATATAAA
1 TAGATATGTTGCTATATATTATAAATTTTAGTATCCATATAAAATATTATCATATAAA
* * * *** * *
29308543 TTGATATGTTGGTATATATTATAGATTTTAGTATTTGTATAAAATATTCTCATATAAG
1 TAGATATGTTGCTATATATTATAAATTTTAGTATCCATATAAAATATTATCATATAAA
*
29308601 TAGATATGTTGTTATA
1 TAGATATGTTGCTATA
29308617 ATAAGATTTT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.48
Consensus pattern (58 bp):
TAGATATGTTGCTATATATTATAAATTTTAGTATCCATATAAAATATTATCATATAAA
Found at i:29308654 original size:20 final size:20
Alignment explanation
Indices: 29308594--29308670 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
29308584 AAATATTCTC
*
29308594 ATATAAGTAGATATGTTGTT
1 ATATAAATAGATATGTTGTT
* * *
29308614 ATA-ATA-AGATTTTGGTAGTT
1 ATATAAATAGA-TAT-GTTGTT
29308634 ATATAAATAGATATGTTGTT
1 ATATAAATAGATATGTTGTT
**
29308654 ATATATTTAGATATGTT
1 ATATAAATAGATATGTT
29308671 ATATATTATA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
18 3 0.07
19 3 0.07
20 31 0.70
21 4 0.09
22 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (20 bp):
ATATAAATAGATATGTTGTT
Found at i:29308688 original size:24 final size:23
Alignment explanation
Indices: 29308632--29308689 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 23
29308622 ATTTTGGTAG
*
29308632 TTATATAAATAGATATGTTGTTA
1 TTATATAAATAGATATGTTATTA
*
29308655 -TATAT--TTAGATATGTTATATA
1 TTATATAAATAGATATGTTAT-TA
29308676 TTATATAAATAGAT
1 TTATATAAATAGAT
29308690 TTCGGAACCG
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 11 0.39
21 2 0.07
22 10 0.36
24 5 0.18
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (23 bp):
TTATATAAATAGATATGTTATTA
Found at i:29308874 original size:40 final size:42
Alignment explanation
Indices: 29308778--29308879 Score: 138
Period size: 40 Copynumber: 2.5 Consensus size: 42
29308768 TATTGAAATT
*
29308778 CCAACTTTGTAACCAAATACTTTGTAATTGTGCGTAGGTGTAC
1 CCAACTTTGTAACCAAATACTTTGTAATTATGCGTA-GTGTAC
* *
29308821 CCAACTTTATAACCAAATAC-TTGT-TTATATGCGT-GTGTAC
1 CCAACTTTGTAACCAAATACTTTGTAAT-TATGCGTAGTGTAC
29308861 CCAACTTTGTAACCAAATA
1 CCAACTTTGTAACCAAATA
29308880 TTAAAATTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
40 24 0.44
41 1 0.02
42 10 0.19
43 19 0.35
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (42 bp):
CCAACTTTGTAACCAAATACTTTGTAATTATGCGTAGTGTAC
Found at i:29310653 original size:18 final size:17
Alignment explanation
Indices: 29310632--29310665 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
29310622 ACAAGTTGTG
29310632 ATAATTATACATTTAAAA
1 ATAATTATA-ATTTAAAA
29310650 ATAATTATAATTTAAA
1 ATAATTATAATTTAAA
29310666 TTTGCAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTATAATTTAAAA
Found at i:29316210 original size:14 final size:16
Alignment explanation
Indices: 29316191--29316222 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29316181 CATAAAGTAC
29316191 AATAAA-CC-ACAATT
1 AATAAATCCAACAATT
29316205 AATAAATCCAACAATT
1 AATAAATCCAACAATT
29316221 AA
1 AA
29316223 GTACCACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 2 0.12
16 8 0.50
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (16 bp):
AATAAATCCAACAATT
Done.