Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 176 of 205
Found at i:52315629 original size:30 final size:28
Alignment explanation
Indices: 52315588--52315644 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
52315578 TTATGGGGTT
* *
52315588 TTAGGGGTTAGGGGTTATGCTTTAGGGG
1 TTAGGGGTTAGGAGTTAGGCTTTAGGGG
*
52315616 TTAGGGGATTTAGGAGTTAGGGTTTAGGG
1 TTAGGGG--TTAGGAGTTAGGCTTTAGGG
52315645 TTTCAATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.29
30 17 0.71
ACGTcount: A:0.18, C:0.02, G:0.46, T:0.35
Consensus pattern (28 bp):
TTAGGGGTTAGGAGTTAGGCTTTAGGGG
Found at i:52316683 original size:31 final size:32
Alignment explanation
Indices: 52316648--52316709 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
52316638 TTATTATTGG
*
52316648 ATAAAAAAAT-ACATTTTTTATACCAAATTTT
1 ATAAAAAAATAAAATTTTTTATACCAAATTTT
52316679 ATAAAAAAATAAAATTTTTTATACCAAATTT
1 ATAAAAAAATAAAATTTTTTATACCAAATTT
52316710 ATTATACCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 10 0.34
32 19 0.66
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (32 bp):
ATAAAAAAATAAAATTTTTTATACCAAATTTT
Found at i:52316709 original size:14 final size:14
Alignment explanation
Indices: 52316690--52316723 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
52316680 TAAAAAAATA
*
52316690 AAATTTTTTATACC
1 AAATTTATTATACC
52316704 AAATTTATTATACC
1 AAATTTATTATACC
52316718 AAATTT
1 AAATTT
52316724 CATCCGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTTATTATACC
Found at i:52316827 original size:15 final size:15
Alignment explanation
Indices: 52316809--52316839 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
52316799 TACTTTATAC
52316809 AAAATATATTTAAAT
1 AAAATATATTTAAAT
52316824 AAAATATATTTAAAT
1 AAAATATATTTAAAT
52316839 A
1 A
52316840 TTAGTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATATATTTAAAT
Found at i:52316849 original size:12 final size:11
Alignment explanation
Indices: 52316825--52316886 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 11
52316815 TATTTAAATA
52316825 AAATAT-ATTT
1 AAATATAATTT
*
52316835 AAATATTAGTTT
1 AAATA-TAATTT
*
52316847 AAATAGAATTAAT
1 AAATATAATT--T
52316860 AAATAT-ATTT
1 AAATATAATTT
52316870 AAATATTAATTT
1 AAATA-TAATTT
52316882 AAATA
1 AAATA
52316887 AAATAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 11 0.26
11 5 0.12
12 20 0.48
13 6 0.14
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
AAATATAATTT
Found at i:52320455 original size:24 final size:22
Alignment explanation
Indices: 52320428--52320471 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
52320418 AATTTCAAAA
52320428 ATAAAACATAATATAATATTTACC
1 ATAAAA-ATAA-ATAATATTTACC
*
52320452 ATAAAAATAAATATTATTTA
1 ATAAAAATAAATAATATTTA
52320472 ATTAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAAAAATAAATAATATTTACC
Found at i:52320560 original size:43 final size:43
Alignment explanation
Indices: 52320484--52320636 Score: 195
Period size: 43 Copynumber: 3.6 Consensus size: 43
52320474 TAATTTTTTT
* * **
52320484 TAAAAGTCATG-T-TTTAGCGGCTTTTGTAATAGAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
*
52320525 TAAAGGTCATGATCTTTAGCGGCGCTTT-TGGTAGAAGCGCCGT
1 TAAAGGTCATGATCTTTAGCGGCG-TTTGTGGTAGAAGCGCCGC
* * *
52320568 TAAATGCCATGATCTTTAGTGGCGTTTGTGGTAGAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
*
52320611 TAAAGATCATGATCTTTAGCGGCGTT
1 TAAAGGTCATGATCTTTAGCGGCGTT
52320637 GCCAATAGCG
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
41 10 0.11
42 4 0.04
43 78 0.82
44 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
Found at i:52323546 original size:26 final size:26
Alignment explanation
Indices: 52323499--52323549 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
52323489 AAAATTTTTT
* *
52323499 GAATCGAGTCGAGTGAAATGAAATTC
1 GAATCGAGTCGAATCAAATGAAATTC
*
52323525 GAATCGAGTCGAATCAAGTGAAATT
1 GAATCGAGTCGAATCAAATGAAATT
52323550 TTTAGAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (26 bp):
GAATCGAGTCGAATCAAATGAAATTC
Found at i:52323743 original size:21 final size:21
Alignment explanation
Indices: 52323718--52323773 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
52323708 AAAATTATTG
*
52323718 TTTTAGAATTTTTTTAACTT-
1 TTTTAGAATTTTTTTAAATTC
*
52323738 TCTTTA-TATGTTTTTTAAATTC
1 T-TTTAGAAT-TTTTTTAAATTC
*
52323760 TTTTTGAATTTTTT
1 TTTTAGAATTTTTT
52323774 ATAATTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
20 3 0.11
21 22 0.79
22 3 0.11
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTAGAATTTTTTTAAATTC
Found at i:52323763 original size:11 final size:10
Alignment explanation
Indices: 52323718--52323782 Score: 51
Period size: 11 Copynumber: 6.2 Consensus size: 10
52323708 AAAATTATTG
52323718 TTTTAGAATTT
1 TTTTA-AATTT
*
52323729 TTTTAACTTT
1 TTTTAAATTT
* *
52323739 CTTTATATGTT
1 TTTTAAAT-TT
52323750 TTTTAAATTCT
1 TTTTAAATT-T
*
52323761 TTTTGAA-TT
1 TTTTAAATTT
52323770 TTTTATAATTT
1 TTTTA-AATTT
52323781 TT
1 TT
52323783 AAAAAATATA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
9 5 0.12
10 13 0.31
11 24 0.57
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:52323821 original size:20 final size:19
Alignment explanation
Indices: 52323796--52323864 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 19
52323786 AAATATAAAA
*
52323796 TTTGAAAATTTTATAAATAT
1 TTTG-AAATTTTAAAAATAT
*
52323816 TTTG-AATTTAAAAAATAT
1 TTTGAAATTTTAAAAATAT
*
52323834 TTTGAATTTTTGAAAAATAT
1 TTTGAAATTTT-AAAAATAT
*
52323854 TTTGTAATTTT
1 TTTGAAATTTT
52323865 TTGAGAGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 16 0.39
19 4 0.10
20 21 0.51
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (19 bp):
TTTGAAATTTTAAAAATAT
Found at i:52323823 original size:18 final size:18
Alignment explanation
Indices: 52323802--52323864 Score: 81
Period size: 18 Copynumber: 3.3 Consensus size: 18
52323792 AAAATTTGAA
*
52323802 AATTTTATAAATATTTTG
1 AATTTTAAAAATATTTTG
*
52323820 AATTTAAAAAATATTTTG
1 AATTTTAAAAATATTTTG
52323838 AATTTTTGAAAAATATTTTG
1 AA-TTTT-AAAAATATTTTG
52323858 TAATTTT
1 -AATTTT
52323865 TTGAGAGAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
18 18 0.46
19 3 0.08
20 16 0.41
21 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
AATTTTAAAAATATTTTG
Found at i:52323956 original size:17 final size:18
Alignment explanation
Indices: 52323936--52323969 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52323926 CAATTTGTTA
52323936 TTCGAATTATTC-AAATT
1 TTCGAATTATTCGAAATT
*
52323953 TTCGAGTTATTCGAAAT
1 TTCGAATTATTCGAAAT
52323970 GCAAAATTCA
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:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (18 bp):
TTCGAATTATTCGAAATT
Found at i:52327471 original size:57 final size:56
Alignment explanation
Indices: 52327407--52327534 Score: 134
Period size: 57 Copynumber: 2.2 Consensus size: 56
52327397 CCACTCCCCT
* * *
52327407 AGGCGGTCTAGATCAATTTCTCA-GGATCGT-GCCATGAGAGATGATTATCGCTCTCCC
1 AGGCGGTCTAGATCAATGTC-AAGGGATCGTGGCCA--AAAGATGATTATCGCTCTCCC
* * * *
52327464 AGTCGGTCCAGATCCATGTCAAGGGATCGTGGGGCAAAAGATGATTATCGCTCTCCC
1 AGGCGGTCTAGATCAATGTCAAGGGATCGT-GGCCAAAAGATGATTATCGCTCTCCC
*
52327521 AGGCGATCTAGATC
1 AGGCGGTCTAGATC
52327535 TGTTTCTCGG
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
56 1 0.02
57 54 0.93
59 3 0.05
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (56 bp):
AGGCGGTCTAGATCAATGTCAAGGGATCGTGGCCAAAAGATGATTATCGCTCTCCC
Found at i:52330844 original size:3 final size:3
Alignment explanation
Indices: 52330836--52330874 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
52330826 TCTTTTTACC
52330836 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52330875 AGTTGTAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:52335065 original size:20 final size:21
Alignment explanation
Indices: 52335040--52335085 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
52335030 TTTTTTTTCT
52335040 TATAAAA-ATATTAAAAAAAC
1 TATAAAATATATTAAAAAAAC
*
52335060 TATAAAATTATATTAAAAAAAT
1 TATAAAA-TATATTAAAAAAAC
52335082 TATA
1 TATA
52335086 GACTAGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
22 16 0.70
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TATAAAATATATTAAAAAAAC
Found at i:52343735 original size:14 final size:14
Alignment explanation
Indices: 52343716--52343743 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52343706 ACAATTTATT
52343716 AATATATATTAATA
1 AATATATATTAATA
52343730 AATATATATTAATA
1 AATATATATTAATA
52343744 TATGTAAAAT
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:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:52343817 original size:32 final size:31
Alignment explanation
Indices: 52343777--52343851 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
52343767 ACTTTTCCGA
* * *
52343777 AAAATATTTTCAGGAAATCTGCCAAACAGCAG
1 AAAATATTTTCA-CAAATCTACCAAACACCAG
* *
52343809 AAAATATTTTACACAGATTTACCAAACACCAG
1 AAAATATTTT-CACAAATCTACCAAACACCAG
52343841 AAAATATTTTC
1 AAAATATTTTC
52343852 CAGTTAATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 1 0.03
32 34 0.92
33 2 0.05
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (31 bp):
AAAATATTTTCACAAATCTACCAAACACCAG
Found at i:52360824 original size:314 final size:314
Alignment explanation
Indices: 52360255--52360865 Score: 1159
Period size: 314 Copynumber: 1.9 Consensus size: 314
52360245 TTCGATCAAC
*
52360255 ATGCTTACTAGTGGCCGCTGATCTATCAATAGATTGAATCGGAGCTTTCGAATCCTCCCCTTTAT
1 ATGCTTACTAGTGGCCGCTGATCTATCAATAGATTGAATCGGAGCTTCCGAATCCTCCCCTTTAT
* *
52360320 TGTAGTTGTCATGTATTGTTCGTTAACATTTCTTTCCTTTACAAATATCGATTGTTATATTCTTC
66 TGTAGTTGTCATGTATTGTTCGTTAACACTTCTTTCCTTTACAAATATCGATTGTTATATTCTCC
*
52360385 TGCATGGTTTCCCTTTGTTCTATAACTCGGTTTCCTTGGAATGTTACACTTTCGTCTAACCTTCC
131 TGCATGGTTTCCCTTTGTTCTATAACTCGGTTTCCTTGGAATGTTACACTTTCGTCTAACCCTCC
* *
52360450 TTTTTTCTATCTATAAATTTTTATGCTGACGGAGCTATTCTTTCTCTAGAACTCGCCTGGCCTTT
196 TTTTTTCTATCTATAAATTTTTATGCCGACGGAGCTATTCTTTCTCTAGAACCCGCCTGGCCTTT
52360515 TTTCTCTTAGCCATTTACTTTCAGCAAGTAATTCATTTCTATCTATAAATTTTT
261 TTTCTCTTAGCCATTTACTTTCAGCAAGTAATTCATTTCTATCTATAAATTTTT
52360569 ATGCTTACTAGTGGCCGCTGATCTATCAATAGATTGAATCGGAGCTTCCGAATCCTCCCCTTTAT
1 ATGCTTACTAGTGGCCGCTGATCTATCAATAGATTGAATCGGAGCTTCCGAATCCTCCCCTTTAT
52360634 TGTAGTTGTCATGTATTGTTCGTTAACACTTCTTTCCTTTACAAATATCGATTGTTATATTCTCC
66 TGTAGTTGTCATGTATTGTTCGTTAACACTTCTTTCCTTTACAAATATCGATTGTTATATTCTCC
52360699 TGCATGGTTTCCCTTTGTTCTATAACTCGGTTTCCTTGGAATGTTACACTTTCGTCTAACCCTCC
131 TGCATGGTTTCCCTTTGTTCTATAACTCGGTTTCCTTGGAATGTTACACTTTCGTCTAACCCTCC
*
52360764 TTTTTTCTATCTATAAATTTTTGTGCCGACGGAGCTATTCTTTCTCTAGAACCCGCCTGGCCTTT
196 TTTTTTCTATCTATAAATTTTTATGCCGACGGAGCTATTCTTTCTCTAGAACCCGCCTGGCCTTT
52360829 TTTCTCTTAGCCATTTACTTTCAGCAAGTAATTCATT
261 TTTCTCTTAGCCATTTACTTTCAGCAAGTAATTCATT
52360866 CCTCATGGGT
Statistics
Matches: 290, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
314 290 1.00
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (314 bp):
ATGCTTACTAGTGGCCGCTGATCTATCAATAGATTGAATCGGAGCTTCCGAATCCTCCCCTTTAT
TGTAGTTGTCATGTATTGTTCGTTAACACTTCTTTCCTTTACAAATATCGATTGTTATATTCTCC
TGCATGGTTTCCCTTTGTTCTATAACTCGGTTTCCTTGGAATGTTACACTTTCGTCTAACCCTCC
TTTTTTCTATCTATAAATTTTTATGCCGACGGAGCTATTCTTTCTCTAGAACCCGCCTGGCCTTT
TTTCTCTTAGCCATTTACTTTCAGCAAGTAATTCATTTCTATCTATAAATTTTT
Found at i:52371909 original size:15 final size:15
Alignment explanation
Indices: 52371886--52371915 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52371876 AAAAGCAAAG
52371886 CAAAATGGAAAAACA
1 CAAAATGGAAAAACA
*
52371901 CAAATTGGAAAAACA
1 CAAAATGGAAAAACA
52371916 TACTTCATTG
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:0.63, C:0.13, G:0.13, T:0.10
Consensus pattern (15 bp):
CAAAATGGAAAAACA
Found at i:52383536 original size:16 final size:17
Alignment explanation
Indices: 52383515--52383550 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
52383505 CATTCCAAAT
52383515 AAACAAGAATCG-AATG
1 AAACAAGAATCGTAATG
*
52383531 AAACAATAATCGTAATG
1 AAACAAGAATCGTAATG
52383548 AAA
1 AAA
52383551 ATCATATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.17
Consensus pattern (17 bp):
AAACAAGAATCGTAATG
Found at i:52392653 original size:49 final size:48
Alignment explanation
Indices: 52392582--52392675 Score: 179
Period size: 49 Copynumber: 1.9 Consensus size: 48
52392572 AGCTAGCGAG
52392582 TAGCTCCTGAATTGATGTATACCAATTGATAGATTCCTAATAAATCGC
1 TAGCTCCTGAATTGATGTATACCAATTGATAGATTCCTAATAAATCGC
52392630 TAGCTTCCTGAATTGATGTATACCAATTGATAGATTCCTAATAAAT
1 TAGC-TCCTGAATTGATGTATACCAATTGATAGATTCCTAATAAAT
52392676 AATTATCTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 4 0.09
49 41 0.91
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (48 bp):
TAGCTCCTGAATTGATGTATACCAATTGATAGATTCCTAATAAATCGC
Found at i:52403526 original size:32 final size:32
Alignment explanation
Indices: 52403490--52403550 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
52403480 TTGTTTTATT
52403490 TTATTTCAAGTGATTTATGAGTTGATGCTATG
1 TTATTTCAAGTGATTTATGAGTTGATGCTATG
52403522 TTATTTCAAGTGATTTATGAGTTGATGCT
1 TTATTTCAAGTGATTTATGAGTTGATGCT
52403551 CTAACATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.48
Consensus pattern (32 bp):
TTATTTCAAGTGATTTATGAGTTGATGCTATG
Found at i:52404024 original size:20 final size:20
Alignment explanation
Indices: 52403999--52404065 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
52403989 GCTAAAGAAA
*
52403999 GTAAATGCAATGGGAAGTAT
1 GTAAATGCAATGGAAAGTAT
*
52404019 GTAAATACAATGGAAAGTAT
1 GTAAATGCAATGGAAAGTAT
*
52404039 GTAAATGCAATGGAAAGTAA
1 GTAAATGCAATGGAAAGTAT
52404059 GTAAATG
1 GTAAATG
52404066 AAAGGGGTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.46, C:0.04, G:0.25, T:0.24
Consensus pattern (20 bp):
GTAAATGCAATGGAAAGTAT
Found at i:52409747 original size:20 final size:20
Alignment explanation
Indices: 52409715--52409788 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
52409705 TATTTGAGCT
*
52409715 AAAGAAAGTAAATGCAATGG
1 AAAGTAAGTAAATGCAATGG
* *
52409735 GAAGTATGTAAATGCAATGG
1 AAAGTAAGTAAATGCAATGG
*
52409755 AAAGTAAGTAAATGCAATGA
1 AAAGTAAGTAAATGCAATGG
52409775 AAAGTAAGTAAATG
1 AAAGTAAGTAAATG
52409789 AAAGGGGTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.51, C:0.04, G:0.24, T:0.20
Consensus pattern (20 bp):
AAAGTAAGTAAATGCAATGG
Found at i:52413432 original size:13 final size:14
Alignment explanation
Indices: 52413411--52413457 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
52413401 CATGTACAGT
*
52413411 CAGATTCAGATA-A
1 CAGAATCAGATATA
*
52413424 CAGAATCAGAAATA
1 CAGAATCAGATATA
*
52413438 TAGAAT-AGATATA
1 CAGAATCAGATATA
52413451 CAGAATC
1 CAGAATC
52413458 CTACCCCTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
13 21 0.78
14 6 0.22
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (14 bp):
CAGAATCAGATATA
Found at i:52425840 original size:42 final size:42
Alignment explanation
Indices: 52425780--52425931 Score: 187
Period size: 42 Copynumber: 3.6 Consensus size: 42
52425770 TAATCTGAAA
* *
52425780 TGTTTCACCGGCATTAAGCCTATTAGACGTAAAGTCTGATAT
1 TGTTTCACCGGCAATAAGCCTACTAGACGTAAAGTCTGATAT
* *
52425822 TGTTTCACTGGCAATAAGCCTACTAGACGTAAAGTCTGAAAT
1 TGTTTCACCGGCAATAAGCCTACTAGACGTAAAGTCTGATAT
* * ** * * *
52425864 TATTTCACCGACCTTAAGCCTGCTATATGTAAAGTCTGATAT
1 TGTTTCACCGGCAATAAGCCTACTAGACGTAAAGTCTGATAT
* *
52425906 TGTTTCACTGGCAATAAGCCTGCTAG
1 TGTTTCACCGGCAATAAGCCTACTAG
52425932 GCGTTAAGCC
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (42 bp):
TGTTTCACCGGCAATAAGCCTACTAGACGTAAAGTCTGATAT
Found at i:52425882 original size:84 final size:84
Alignment explanation
Indices: 52425773--52425947 Score: 244
Period size: 84 Copynumber: 2.1 Consensus size: 84
52425763 AGACATATAA
* * *
52425773 TCTGAAA-TGTTTCACCGGCATTAAGCCTATTAGACGTAAAGTCTGATATTGTTTCACTGGCAAT
1 TCTGAAATTATTTCACCGACATTAAGCCTACTAGACGTAAAGTCTGATATTGTTTCACTGGCAAT
52425837 AAGCCTACTAGACGTAAAG
66 AAGCCTACTAGACGTAAAG
* * * *
52425856 TCTGAAATTATTTCACCGACCTTAAGCCTGCTATATGTAAAGTCTGATATTGTTTCACTGGCAAT
1 TCTGAAATTATTTCACCGACATTAAGCCTACTAGACGTAAAGTCTGATATTGTTTCACTGGCAAT
* * *
52425921 AAGCCTGCTAGGCGTTAAG
66 AAGCCTACTAGACGTAAAG
*
52425940 CCTGAAAT
1 TCTGAAAT
52425948 CTCAATTTCA
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
83 7 0.09
84 73 0.91
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (84 bp):
TCTGAAATTATTTCACCGACATTAAGCCTACTAGACGTAAAGTCTGATATTGTTTCACTGGCAAT
AAGCCTACTAGACGTAAAG
Found at i:52434576 original size:3 final size:3
Alignment explanation
Indices: 52434568--52434605 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
52434558 AAAAAACTAG
52434568 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
52434606 TGAAAAGGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:52437278 original size:14 final size:14
Alignment explanation
Indices: 52437256--52437290 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
52437246 ATGGTATGGG
52437256 TTTATGGGTTTTGGT
1 TTTA-GGGTTTTGGT
52437271 TTTAGGGTTTTGGT
1 TTTAGGGTTTTGGT
*
52437285 TATAGG
1 TTTAGG
52437291 CAAATGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.11, C:0.00, G:0.34, T:0.54
Consensus pattern (14 bp):
TTTAGGGTTTTGGT
Found at i:52437444 original size:22 final size:23
Alignment explanation
Indices: 52437419--52437465 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
52437409 GAGGAAAGTT
52437419 TAAAGAACATAAAAT-AAAAAAA
1 TAAAGAACATAAAATGAAAAAAA
** *
52437441 TAAATTACTTAAAATGAAAAAAA
1 TAAAGAACATAAAATGAAAAAAA
52437464 TA
1 TA
52437466 TGGGGATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.21
Consensus pattern (23 bp):
TAAAGAACATAAAATGAAAAAAA
Found at i:52457751 original size:36 final size:35
Alignment explanation
Indices: 52457711--52457786 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 35
52457701 TGATGGTTGT
52457711 TGTGAAAG-AGAATATGTGGGTATGATATTCATGCCA
1 TGTGAAAGTA-AATATGTGGGTAT-ATATTCATGCCA
* * *
52457747 TGTGACAGTAAATATGTGGGTATATTTTCATTCCA
1 TGTGAAAGTAAATATGTGGGTATATATTCATGCCA
52457782 TGTGA
1 TGTGA
52457787 CAGTGATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 15 0.42
36 20 0.56
37 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (35 bp):
TGTGAAAGTAAATATGTGGGTATATATTCATGCCA
Found at i:52457784 original size:35 final size:36
Alignment explanation
Indices: 52457721--52457790 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 36
52457711 TGTGAAAGAG
52457721 AATATGTGGGTATGATATTCATGCCATGTGACAGTA
1 AATATGTGGGTATGATATTCATGCCATGTGACAGTA
* *
52457757 AATATGTGGGTAT-ATTTTCATTCCATGTGACAGT
1 AATATGTGGGTATGATATTCATGCCATGTGACAGT
52457791 GATTATAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.59
36 13 0.41
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (36 bp):
AATATGTGGGTATGATATTCATGCCATGTGACAGTA
Found at i:52473353 original size:394 final size:393
Alignment explanation
Indices: 52472621--52473401 Score: 1230
Period size: 394 Copynumber: 2.0 Consensus size: 393
52472611 GAAAATTGTT
** *
52472621 TCTCCCAGTTGTAAGAGATCTTAATAATTCCCTTAGGATTCATAGATTTCCCTTAGAAGATATTC
1 TCTCCCAACTGTAAGAGACCTTAATAATTCCCTTAGGATTCATAGATTTCCCTTAGAAGATATTC
* * * *
52472686 AAGTTTCGATTCTTCCAAATTCGTCAAAGAATTAAACTGAAGAAACAGGCCCATACTGAACCTCT
66 AAGTTCCAATTCTTCCAAATTCG-CAAAGAATTAAACCGAAGAAACAGGCCCATACTAAACCTCT
* * * * *
52472751 CGTGCTATTATCTGACTGGTCACGTAGATTACAGAGTAACCATTCCGATAGATTACCGTTGAAGA
130 AGTGCTATTATCCGACTGGTCACATAGATTACAGAGTAACCATTCCGATAGATTACCATTAAAGA
52472816 ACCATCTATGTTGATTAGAAGGGATGACTTGATTCCAAATATCCTTCGCGAACAGGCAATCTCTA
195 ACCATCTATGTTGATTAGAAGGGATGACTTGATTCCAAATATCCTTCGCGAACAGGCAATCTCTA
* * *
52472881 AGGACATGTAAAGCATCCTCAGTATTATAACCACATAAGTGGCATGACTCTTCTTGTCCAATCCC
260 AGGACATGTAAAGCATACTCAATATTATAACCACATAAGTGACATGACTCTTCTTGTCCAATCCC
*
52472946 TCTCCGAACTCTTTCAGAGTTAGTTAATAGTCTTTGTTTAAAGACCAACCAGATGAATTGTCCAA
325 TCTCCGAACTCTTTCAGAGTTAGTTAATAGTCTTTGTTTAAAGACCAACCAGATGAACTGTCCAA
52473011 TCCC
390 TCCC
*
52473015 TCTCCCAACTGTAAGAGACCTTAATAATTTCCC-TCGGATTCATAGATGTT-CCTTAGAAGATAT
1 TCTCCCAACTGTAAGAGACCTTAATAA-TTCCCTTAGGATTCATAGAT-TTCCCTTAGAAGATAT
*
52473078 TCAAGTTCCAATTCTTCCTAAATTTC-CAAAGAATTAAACCGAAGAAATAGGCCCATACTAAACC
64 TCAAGTTCCAATTCTTCC-AAA-TTCGCAAAGAATTAAACCGAAGAAACAGGCCCATACTAAACC
* *
52473142 TCTAGTGCTATTATCCGTCTGGTCACATAGATTAGAGAGTAACCATTCCGATAGATTACCATTAA
127 TCTAGTGCTATTATCCGACTGGTCACATAGATTACAGAGTAACCATTCCGATAGATTACCATTAA
* * *
52473207 AGAACCATCTATGTTTATTAGAAGGGATGACTTGATTCCAAATATCCTTTGTGAA-AGGGCAATC
192 AGAACCATCTATGTTGATTAGAAGGGATGACTTGATTCCAAATATCCTTCGCGAACA-GGCAATC
*
52473271 TCTAAGGACATGTAAAGCATATTCAATATTATAACCACATAAGTGACATGACTCTTCTTGTCCAA
256 TCTAAGGACATGTAAAGCATACTCAATATTATAACCACATAAGTGACATGACTCTTCTTGTCCAA
* *
52473336 TCCCTCTCC-AGACTCTTTTAGAGTTAGTTAATAGTCTTTGTTTAAAGACCAACTAGATGAACTG
321 TCCCTCTCCGA-ACTCTTTCAGAGTTAGTTAATAGTCTTTGTTTAAAGACCAACCAGATGAACTG
52473400 TC
385 TC
52473402 TGACTCTTTG
Statistics
Matches: 355, Mismatches: 26, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
393 2 0.01
394 340 0.96
395 10 0.03
396 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (393 bp):
TCTCCCAACTGTAAGAGACCTTAATAATTCCCTTAGGATTCATAGATTTCCCTTAGAAGATATTC
AAGTTCCAATTCTTCCAAATTCGCAAAGAATTAAACCGAAGAAACAGGCCCATACTAAACCTCTA
GTGCTATTATCCGACTGGTCACATAGATTACAGAGTAACCATTCCGATAGATTACCATTAAAGAA
CCATCTATGTTGATTAGAAGGGATGACTTGATTCCAAATATCCTTCGCGAACAGGCAATCTCTAA
GGACATGTAAAGCATACTCAATATTATAACCACATAAGTGACATGACTCTTCTTGTCCAATCCCT
CTCCGAACTCTTTCAGAGTTAGTTAATAGTCTTTGTTTAAAGACCAACCAGATGAACTGTCCAAT
CCC
Found at i:52475212 original size:19 final size:19
Alignment explanation
Indices: 52475162--52475201 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
52475152 ATGGGTTCAA
52475162 ACCAATTTTTGAATTAATT
1 ACCAATTTTTGAATTAATT
52475181 ACCAATTTTTGAATTAATT
1 ACCAATTTTTGAATTAATT
52475200 AC
1 AC
52475202 TATTTTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (19 bp):
ACCAATTTTTGAATTAATT
Found at i:52475394 original size:42 final size:43
Alignment explanation
Indices: 52475347--52475430 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
52475337 ATCCTAGAAC
* *
52475347 AAAAAGAATTTAAAAA-AGGAGAAGATAATCTTGGGTTGTTGA
1 AAAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGTTGTTGA
52475389 AAAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGTTGTTG
1 AAAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGTTGTTG
52475431 GATTTACCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 16 0.41
43 23 0.59
ACGTcount: A:0.49, C:0.02, G:0.25, T:0.24
Consensus pattern (43 bp):
AAAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGTTGTTGA
Found at i:52479445 original size:21 final size:20
Alignment explanation
Indices: 52479408--52479451 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
52479398 ACCAATGCCA
* *
52479408 AAAAAAAAGGATTCAAAGAG
1 AAAAAAAAGAATTCAAAAAG
*
52479428 AAAAAAAATAATTACAAAAAG
1 AAAAAAAAGAATT-CAAAAAG
52479449 AAA
1 AAA
52479452 TCCCCTAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.73, C:0.05, G:0.11, T:0.11
Consensus pattern (20 bp):
AAAAAAAAGAATTCAAAAAG
Found at i:52482029 original size:12 final size:11
Alignment explanation
Indices: 52482012--52482046 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
52482002 AACAAATCCT
52482012 CTCTCATATTTC
1 CTCTCA-ATTTC
52482024 CTCTCAA-TTC
1 CTCTCAATTTC
52482034 CTCTCAATTTC
1 CTCTCAATTTC
52482045 CT
1 CT
52482047 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:52482059 original size:22 final size:22
Alignment explanation
Indices: 52482029--52482084 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
52482019 ATTTCCTCTC
52482029 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
*
52482052 AATTCTCTCAGTTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
52482074 AATTCTCTCAA
1 AATTCTCTCAA
52482085 ATCCATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:52482948 original size:7 final size:7
Alignment explanation
Indices: 52482938--52482962 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52482928 ATTCGATTGA
52482938 TATTTAG
1 TATTTAG
52482945 TATTTAG
1 TATTTAG
52482952 TATTTAG
1 TATTTAG
52482959 TATT
1 TATT
52482963 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:52484166 original size:23 final size:22
Alignment explanation
Indices: 52484134--52484696 Score: 189
Period size: 23 Copynumber: 23.8 Consensus size: 22
52484124 TTATTTGATG
* *
52484134 TAATAAAAACCCTAACCTAATT
1 TAATTAAAACCCTAACCTAAAT
52484156 TAACCTT-AAACCCTAACCTAAAT
1 TAA--TTAAAACCCTAACCTAAAT
52484179 TAATTAAAAACCCTAACCTTAACCTAATT
1 TAATT-AAAACCCTAACC-T-A---AA-T
* *
52484208 TAATTAAAAATCCTAACCTAATT
1 TAATT-AAAACCCTAACCTAAAT
*
52484231 TAATTAAAAACCCTAACCTAATT
1 TAATT-AAAACCCTAACCTAAAT
* *
52484254 TAATTAAAAACTCTAAACC---CT
1 TAATT-AAAACCCT-AACCTAAAT
*
52484275 TAATTAAAACCCTAACCTAATT
1 TAATTAAAACCCTAACCTAAAT
52484297 TAATTAAATACCCTAACCT-AA-
1 TAATTAAA-ACCCTAACCTAAAT
*
52484318 T--TT-AAACCCTAAACCCTAATT
1 TAATTAAAACCCT-AA-CCTAAAT
* *
52484339 TAATTAAAAATCCTAACATTCACCTAATT
1 TAATT-AAAA-CC---C--TAACCTAAAT
*
52484368 TAATTAAAAACCCTAACCTAATT
1 TAATT-AAAACCCTAACCTAAAT
*
52484391 TAATTAAAAACCCTAAACC---CT
1 TAATT-AAAACCCT-AACCTAAAT
52484412 TAATTAAAAACCCTAACCTCAACCTAATT
1 TAATT-AAAACCCTAACCT--A---AA-T
*
52484441 TAATTAAAAACCCTAACCTAATT
1 TAATT-AAAACCCTAACCTAAAT
*
52484464 TAATTAAAAACCCTAAACCCTTAAT
1 TAATT-AAAACCCT-AA-CCTAAAT
* * *
52484489 TAA-AAACTCTAACCTTAACCTAATT
1 TAATTAA----AACCCTAACCTAAAT
52484514 TAATTAAAAACCCTAACCT-AA-
1 TAATT-AAAACCCTAACCTAAAT
*
52484535 T--TT-AAACCCTAAACCCTAATT
1 TAATTAAAACCCT-AA-CCTAAAT
*
52484556 TAATAAAAAACCCTAACCTTAACTTAATT
1 TAAT-TAAAACCCTAACC-T-A---AA-T
*
52484585 TAATTAAAAACCCTAACCTAATT
1 TAATT-AAAACCCTAACCTAAAT
*
52484608 TAATTAAAAACCCTAAACC---CT
1 TAATT-AAAACCCT-AACCTAAAT
* * *
52484629 TAATTAAAAATCCTAATCTAATT
1 TAATT-AAAACCCTAACCTAAAT
*
52484652 TAAACCTT-AAACCCTAAACCCTAATT
1 T-AA--TTAAAACCCT-AA-CCTAAAT
52484678 TAATTAAAAACCCTAACCT
1 TAATT-AAAACCCTAACCT
52484697 TAACGTAATG
Statistics
Matches: 432, Mismatches: 36, Indels: 145
0.70 0.06 0.24
Matches are distributed among these distances:
17 12 0.03
18 6 0.01
19 14 0.03
20 16 0.04
21 41 0.09
22 14 0.03
23 152 0.35
24 32 0.07
25 40 0.09
26 13 0.03
27 10 0.02
28 7 0.02
29 73 0.17
30 1 0.00
31 1 0.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATTAAAACCCTAACCTAAAT
Found at i:52484201 original size:29 final size:29
Alignment explanation
Indices: 52484164--52484249 Score: 112
Period size: 29 Copynumber: 3.2 Consensus size: 29
52484154 TTTAACCTTA
* *
52484164 AACCCTAACCTAAATTAATTAAAAACCCT
1 AACCTTAACCTAATTTAATTAAAAACCCT
52484193 AACCTTAACCTAATTTAATTAAAAA---T
1 AACCTTAACCTAATTTAATTAAAAACCCT
52484219 --CC-TAACCTAATTTAATTAAAAACCCT
1 AACCTTAACCTAATTTAATTAAAAACCCT
52484245 AACCT
1 AACCT
52484250 AATTTAATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
23 20 0.41
24 2 0.04
26 2 0.04
28 2 0.04
29 23 0.47
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (29 bp):
AACCTTAACCTAATTTAATTAAAAACCCT
Found at i:52484440 original size:50 final size:50
Alignment explanation
Indices: 52484382--52484479 Score: 153
Period size: 50 Copynumber: 1.9 Consensus size: 50
52484372 TAAAAACCCT
52484382 AACCTAATTTAATTAAAAACCCTAAACC-CTTAATTAAAAACCCTAACCTC
1 AACCTAATTTAATTAAAAACCCT-AACCACTTAATTAAAAACCCTAACCTC
*
52484432 AACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
1 AACCTAATTTAATTAAAAACCCTAACC--ACTTAATTAAAAACCCTAA
52484480 ACCCTTAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
49 4 0.09
50 23 0.52
52 17 0.39
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (50 bp):
AACCTAATTTAATTAAAAACCCTAACCACTTAATTAAAAACCCTAACCTC
Found at i:52484444 original size:29 final size:28
Alignment explanation
Indices: 52484411--52484534 Score: 128
Period size: 29 Copynumber: 4.8 Consensus size: 28
52484401 CCCTAAACCC
52484411 TTAATTAAAAACCCTAACCTCAACCTAAT
1 TTAATTAAAAACCCTAACCT-AACCTAAT
52484440 TTAATTAAAAA--C---CCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAACCTAAT
*
52484463 TTAATTAAAAACCCT-A---AACC---C
1 TTAATTAAAAACCCTAACCTAACCTAAT
*
52484484 TTAATTAAAAACTCTAACCTTAACCTAAT
1 TTAATTAAAAACCCTAACC-TAACCTAAT
52484513 TTAATTAAAAACCCTAACCTAA
1 TTAATTAAAAACCCTAACCTAA
52484535 TTTAAACCCT
Statistics
Matches: 79, Mismatches: 4, Indels: 25
0.73 0.04 0.23
Matches are distributed among these distances:
21 14 0.18
22 1 0.01
23 19 0.24
24 7 0.09
25 1 0.01
26 4 0.05
27 1 0.01
28 3 0.04
29 29 0.37
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (28 bp):
TTAATTAAAAACCCTAACCTAACCTAAT
Found at i:52484446 original size:73 final size:73
Alignment explanation
Indices: 52484288--52484644 Score: 467
Period size: 73 Copynumber: 4.9 Consensus size: 73
52484278 TTAAAACCCT
* **** * *
52484288 AACCTAATTTAATTAAATACCCTAACCTAATTTAAACCCTAAACCCT-AA--TTTAATTAAAAAT
1 AACCTAATTTAATTAAAAACCCTAACCTAATTT-AATTAAAAACCCTAAACCCTTAATTAAAAAC
*
52484350 CCTAACATTC
65 CCTAAC-CTC
52484360 -ACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACC
1 AACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACC
52484424 CTAACCTC
66 CTAACCTC
*
52484432 AACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACT
1 AACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACC
*
52484497 CTAACCTT
66 CTAACCTC
**** * *
52484505 AACCTAATTTAATTAAAAACCCTAACCTAATTTAAACCCTAAACCCT-AA--TTTAATAAAAAAC
1 AACCTAATTTAATTAAAAACCCTAACCTAATTT-AATTAAAAACCCTAAACCCTTAATTAAAAAC
*
52484567 CCTAACCTT
65 CCTAACCTC
* *
52484576 AACTTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAATC
1 AACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACC
52484641 CTAA
66 CTAA
52484645 TCTAATTTAA
Statistics
Matches: 252, Mismatches: 25, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
70 18 0.07
71 86 0.34
72 2 0.01
73 137 0.54
74 9 0.04
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (73 bp):
AACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACC
CTAACCTC
Found at i:52484552 original size:19 final size:17
Alignment explanation
Indices: 52484521--52484558 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
52484511 ATTTAATTAA
52484521 AAACCCTAACCTAATTT
1 AAACCCTAACCTAATTT
52484538 AAACCCTAAACCCTAATTT
1 AAACCCT-AA-CCTAATTT
52484557 AA
1 AA
52484559 TAAAAAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 10 0.53
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (17 bp):
AAACCCTAACCTAATTT
Found at i:52484559 original size:144 final size:145
Alignment explanation
Indices: 52484221--52484644 Score: 532
Period size: 144 Copynumber: 3.0 Consensus size: 145
52484211 TTAAAAATCC
** * *
52484221 TAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACTCTAAACCCTTAAT-TAAAA-
1 TAACCTAATTTAATTAAAAACCCTAACCTAATTTAACCAAAAACCCTAAA-CCTTAATAAAAAAC
* **** *
52484284 -C---CCT-AACCTAATTTAATTAAATACCCTAACCTAATTTAAACCCTAAACCCT-AA--TTTA
65 CCTAACCTCAACCTAATTTAATTAAAAACCCTAACCTAATTT-AATTAAAAACCCTAAACCCTTA
52484341 ATTAAAAATCCTAACAT
129 ATTAAAAATCCTAACAT
* ** *
52484358 TCACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAAC
1 TAACCTAATTTAATTAAAAACCCTAACCTAATTTAACCAAAAACCCTAAA-CCTTAATAAAAAAC
52484423 CCTAACCTCAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAA
65 CCTAACCTCAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAA
*
52484488 TTAAAAA-CTCTAACCT
130 TTAAAAATC-CTAACAT
** *
52484504 TAACCTAATTTAATTAAAAACCCTAACCTAATTTAAACCCTAAACCCT-AA-TTTAATAAAAAAC
1 TAACCTAATTTAATTAAAAACCCTAACCTAATTT-AACCAAAAACCCTAAACCTTAATAAAAAAC
* *
52484567 CCTAACCTTAACTTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAA
65 CCTAACCTCAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAA
52484632 TTAAAAATCCTAA
130 TTAAAAATCCTAA
52484645 TCTAATTTAA
Statistics
Matches: 255, Mismatches: 19, Indels: 19
0.87 0.06 0.06
Matches are distributed among these distances:
137 56 0.22
138 4 0.02
140 1 0.00
143 12 0.05
144 119 0.47
145 2 0.01
146 52 0.20
147 9 0.04
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (145 bp):
TAACCTAATTTAATTAAAAACCCTAACCTAATTTAACCAAAAACCCTAAACCTTAATAAAAAACC
CTAACCTCAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAAT
TAAAAATCCTAACAT
Found at i:52484593 original size:29 final size:28
Alignment explanation
Indices: 52484551--52484612 Score: 97
Period size: 29 Copynumber: 2.2 Consensus size: 28
52484541 CCCTAAACCC
52484551 TAATTTAATAAAAAACCCTAACCTTAACT
1 TAATTTAATAAAAAACCCTAACC-TAACT
* *
52484580 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATAAAAAACCCTAACCTAACT
52484608 TAATT
1 TAATT
52484613 AAAAACCCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (28 bp):
TAATTTAATAAAAAACCCTAACCTAACT
Found at i:52484595 original size:217 final size:210
Alignment explanation
Indices: 52484222--52484644 Score: 711
Period size: 217 Copynumber: 2.0 Consensus size: 210
52484212 TAAAAATCCT
*
52484222 AACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACTCTAAACCCTTAATTAAAACCC
1 AACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAACCC
* * *
52484287 TAACCTAATTTAATTAAATACCCTAACCTAATTTAAACCCTAAACCCTAATTTAATTAAAAATCC
66 TAACCTAATTTAATTAAAAACCCTAACCTAATTTAAACCCTAAACCCTAATTTAATAAAAAACCC
*
52484352 TAACATTCACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATT
131 TAACATTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATT
52484417 AAAAACCCTAACCTC
196 AAAAACCCTAACCTC
52484432 AACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACT
1 AACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATT-AAAA--
52484497 CTAACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAAACCCTAAACCCTAATTTAATAA
63 C---CC-TAACCTAATTTAATTAAAAACCCTAACCTAATTTAAACCCTAAACCCTAATTTAATAA
* *
52484562 AAAACCCTAACCTTAACTTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACC
124 AAAACCCTAACATTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACC
*
52484627 CTTAATTAAAAATCCTAA
189 CTTAATTAAAAACCCTAA
52484645 TCTAATTTAA
Statistics
Matches: 198, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
210 57 0.29
211 4 0.02
213 1 0.01
216 2 0.01
217 134 0.68
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.30
Consensus pattern (210 bp):
AACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAACCC
TAACCTAATTTAATTAAAAACCCTAACCTAATTTAAACCCTAAACCCTAATTTAATAAAAAACCC
TAACATTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATT
AAAAACCCTAACCTC
Found at i:52484633 original size:21 final size:22
Alignment explanation
Indices: 52484584--52484644 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
52484574 TTAACTTAAT
*
52484584 TTAATTAAAAACCCT-AACCTAAT
1 TTAATTAAAAACCCTAAACC--AC
52484607 TTAATTAAAAACCCTAAACC-C
1 TTAATTAAAAACCCTAAACCAC
*
52484628 TTAATTAAAAATCCTAA
1 TTAATTAAAAACCCTAA
52484645 TCTAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.46
23 15 0.43
24 4 0.11
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (22 bp):
TTAATTAAAAACCCTAAACCAC
Found at i:52484851 original size:116 final size:116
Alignment explanation
Indices: 52484702--52484912 Score: 368
Period size: 116 Copynumber: 1.8 Consensus size: 116
52484692 AACCTTAACG
*
52484702 TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
1 TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTCTACATAATTTGATA
*
52484767 ATTTTATTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
* * * *
52484818 TAATGTTAGATTTGGAAAAATGTTTTGATTGGTACTAACAATTAATAATTCTATATAATTTGATA
1 TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTCTACATAATTTGATA
52484883 ATTTTACTAACCATTAATACAATTTTTTGA
66 ATTTTACTAACCATTAATACAATTTTTTGA
52484913 TGTTATACAA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 89 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (116 bp):
TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTCTACATAATTTGATA
ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
Found at i:52487799 original size:126 final size:126
Alignment explanation
Indices: 52487574--52487801 Score: 420
Period size: 126 Copynumber: 1.8 Consensus size: 126
52487564 CCCAAACATG
* *
52487574 CTACTGTAGCAAAAGCGCGTCCACGATGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTGC
* *
52487639 TAGAAGCGATTTTATATTATTTTCTCAGAAACGTCAAAAAAATAATTATTTCTTCTGTGAC
66 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAAAAAAATAATTATTTCTTCTGTGAC
52487700 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTGC
52487765 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAA
52487802 CTCGAAATTA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 98 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTGC
TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAAAAAAATAATTATTTCTTCTGTGAC
Found at i:52492611 original size:42 final size:42
Alignment explanation
Indices: 52492508--52492613 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
52492498 ATGCCACAGG
* * * *
52492508 GCCTGAACACACGCCTATGTCCTTGCTCGTGTGGCTCACACA
1 GCCTGGACACACGCCCATGTCCTTGCTCGTATGACTCACACA
* * *
52492550 GCCTGGAAACACACTCATGTCCTTGCTCGTATGACTCACACA
1 GCCTGGACACACGCCCATGTCCTTGCTCGTATGACTCACACA
* * *
52492592 TCTTGGGCACACGCCCATGTCC
1 GCCTGGACACACGCCCATGTCC
52492614 CTGGCCGTGT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.24
Consensus pattern (42 bp):
GCCTGGACACACGCCCATGTCCTTGCTCGTATGACTCACACA
Found at i:52496881 original size:28 final size:27
Alignment explanation
Indices: 52496850--52496915 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
52496840 GAGCCCTATT
*
52496850 CAATAACAGTACAGTATGGGCCTTAGCC
1 CAAT-ACAGTACAATATGGGCCTTAGCC
* * *
52496878 CAATACAATAATAATGTGGGCCTTAGCC
1 CAATACAGT-ACAATATGGGCCTTAGCC
52496906 CAATACAGTA
1 CAATACAGTA
52496916 TTGGTACAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
27 5 0.16
28 27 0.84
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (27 bp):
CAATACAGTACAATATGGGCCTTAGCC
Found at i:52499548 original size:51 final size:48
Alignment explanation
Indices: 52499456--52499550 Score: 120
Period size: 51 Copynumber: 1.9 Consensus size: 48
52499446 CTTCACCATC
* *
52499456 GTCTTCAACATTTTTCCTGACTACTTTCTCTTTCGTTTTCTTTGAATT
1 GTCTTCAACATTTTTCCTGACTACTTTCTATATCGTTTTCTTTGAATT
*
52499504 GTCTTCAACATTTTTCATTCATGTCT-CTTTCTATATCGTTTTCTTTG
1 GTCTTCAACATTTTTC---C-TGACTACTTTCTATATCGTTTTCTTTG
52499551 CCATCTCTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
48 16 0.40
51 20 0.50
52 4 0.10
ACGTcount: A:0.15, C:0.22, G:0.08, T:0.55
Consensus pattern (48 bp):
GTCTTCAACATTTTTCCTGACTACTTTCTATATCGTTTTCTTTGAATT
Found at i:52500457 original size:26 final size:26
Alignment explanation
Indices: 52500428--52500493 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
52500418 GGATCAACAT
*
52500428 AAAATGTCCATCAAAATACAACCATC
1 AAAATGTCCATCAAAATAAAACCATC
* * *
52500454 AAAATGATCTAACAAAATAAAACCATT
1 AAAATG-TCCATCAAAATAAAACCATC
* *
52500481 AAATTATCCATCA
1 AAAATGTCCATCA
52500494 TATGTTAACT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
26 11 0.35
27 20 0.65
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.23
Consensus pattern (26 bp):
AAAATGTCCATCAAAATAAAACCATC
Found at i:52500513 original size:35 final size:35
Alignment explanation
Indices: 52500469--52500585 Score: 164
Period size: 35 Copynumber: 3.3 Consensus size: 35
52500459 GATCTAACAA
*
52500469 AATAAAACCATTAAATTATCCATCATATGTTAACT
1 AATAAAACCATCAAATTATCCATCATATGTTAACT
* *
52500504 AACT-AAACCATCAAATTATCCATCGTATGTTAACAA
1 AA-TAAAACCATCAAATTATCCATCATATGTTAAC-T
*
52500540 AATAAAACCATCAAATTATCCATGATATGTTAACT
1 AATAAAACCATCAAATTATCCATCATATGTTAACT
*
52500575 AATGAAACCAT
1 AATAAAACCAT
52500586 ATTGACATTA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 41 0.57
36 31 0.43
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (35 bp):
AATAAAACCATCAAATTATCCATCATATGTTAACT
Found at i:52500555 original size:36 final size:36
Alignment explanation
Indices: 52500463--52500573 Score: 163
Period size: 36 Copynumber: 3.1 Consensus size: 36
52500453 CAAAATGATC
* *
52500463 TAACAAAATAAAACCATTAAATTATCCATCATATGT
1 TAACAAAATAAAACCATCAAATTATCCATCGTATGT
* *
52500499 TAACTAACT-AAACCATCAAATTATCCATCGTATGT
1 TAACAAAATAAAACCATCAAATTATCCATCGTATGT
52500534 TAACAAAATAAAACCATCAAATTATCCAT-GATATGT
1 TAACAAAATAAAACCATCAAATTATCCATCG-TATGT
52500570 TAAC
1 TAAC
52500574 TAATGAAACC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
35 32 0.48
36 35 0.52
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.30
Consensus pattern (36 bp):
TAACAAAATAAAACCATCAAATTATCCATCGTATGT
Found at i:52503847 original size:4 final size:4
Alignment explanation
Indices: 52503833--52503925 Score: 91
Period size: 4 Copynumber: 22.5 Consensus size: 4
52503823 AATAAACCTA
*
52503833 ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A-A-
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
52503879 ACAATT ATAT ACAT AACAT ACAT AGTAT ACAT ACAT AACAA ACAT AC
1 AC-A-T ACAT ACAT -ACAT ACAT A-CAT ACAT ACAT -ACAT ACAT AC
52503926 TAATAGACAT
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
2 1 0.01
3 1 0.01
4 60 0.81
5 11 0.15
6 1 0.01
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:52503944 original size:63 final size:62
Alignment explanation
Indices: 52503814--52504022 Score: 212
Period size: 63 Copynumber: 3.4 Consensus size: 62
52503804 CATACATATA
* * * * *
52503814 ATAAACAATAATAAACCTAACATGCATACATACATACAT-ACATACATACATACAT--ACATAC
1 ATAAACAATAATATACATAACATACATATATACATACATAACAAACATAC-TA-ATAGACATAC
* *
52503875 ATAAACAATTATATACATAACATACATAGTATACATACATAACAAACATACTAATAGACATCC
1 ATAAACAATAATATACATAACATACATA-TATACATACATAACAAACATACTAATAGACATAC
* *** * *
52503938 ATAAACAACAATATTTGTAACATACATAATATACATACATAACAGACATACTAACATG-CATAC
1 ATAAACAATAATATACATAACATACAT-ATATACATACATAACAAACATACTAATA-GACATAC
52504001 ATAAA-AAGTAATATACATAACA
1 ATAAACAA-TAATATACATAACA
52504023 GATTGACCTT
Statistics
Matches: 122, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
61 26 0.21
62 14 0.11
63 80 0.66
64 2 0.02
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.24
Consensus pattern (62 bp):
ATAAACAATAATATACATAACATACATATATACATACATAACAAACATACTAATAGACATAC
Found at i:52503947 original size:25 final size:26
Alignment explanation
Indices: 52503845--52504004 Score: 72
Period size: 25 Copynumber: 6.4 Consensus size: 26
52503835 ATGCATACAT
*
52503845 ACATACATACAT--ACATACAT-ACAT
1 ACATACATA-ATAGACATACATAACAA
* *
52503869 ACATACATAA-ACA-AT-TATATACATA
1 ACATACATAATAGACATACATA-ACA-A
* *
52503894 ACATACATAGTATACATACATAACAA
1 ACATACATAATAGACATACATAACAA
*
52503920 ACATAC-TAATAGACATCCATAA-ACA
1 ACATACATAATAGACATACATAACA-A
* ** * *
52503945 ACAATA-TTTGTA-ACATACATAATAT
1 AC-ATACATAATAGACATACATAACAA
* *
52503970 ACATACATAACAGACATAC-TAACAT
1 ACATACATAATAGACATACATAACAA
*
52503995 GCATACATAA
1 ACATACATAA
52504005 AAAGTAATAT
Statistics
Matches: 104, Mismatches: 18, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
22 2 0.02
23 3 0.03
24 17 0.16
25 52 0.50
26 22 0.21
27 5 0.05
28 3 0.03
ACGTcount: A:0.52, C:0.20, G:0.03, T:0.25
Consensus pattern (26 bp):
ACATACATAATAGACATACATAACAA
Found at i:52503999 original size:12 final size:13
Alignment explanation
Indices: 52503957--52504004 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
52503947 AATATTTGTA
* *
52503957 ACATACATAATAT
1 ACATACATAACAG
52503970 ACATACATAACAG
1 ACATACATAACAG
52503983 ACATAC-TAACATG
1 ACATACATAACA-G
52503996 -CATACATAA
1 ACATACATAA
52504005 AAAGTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.52, C:0.21, G:0.04, T:0.23
Consensus pattern (13 bp):
ACATACATAACAG
Found at i:52507019 original size:44 final size:44
Alignment explanation
Indices: 52506936--52507510 Score: 667
Period size: 44 Copynumber: 13.0 Consensus size: 44
52506926 ATAAGACTTG
* * *
52506936 TATCTTCGATCTGCTTCAGTGTCGATACAGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCA-TGTCAATACATGAAGACAAGATCTGC
***
52506981 TATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCAT
1 TATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCTGC
52507025 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
*
52507069 TATC-CCTGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
1 TATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCTGC
* **
52507113 TATC-TCTGATCTACTTCATGTCAATACATGAAGTCAAGATCTAT
1 TATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCTGC
* *
52507157 TATCTTCGATCTACTTCATGTCAATACATGAAGATAATATCTGC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
* * ***
52507201 TATC-CCTAATCTACTTCATGTCAATACATGACA-ACAAGATCCAT
1 TATCTTC-GATCTACTTCATGTCAATACATGA-AGACAAGATCTGC
*** * ***
52507245 TATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCA-TGTCAATACATGAAGACAAGATCTGC
* * * ***
52507290 TATC-TCTGCTCTACTCCATGTCACTACATGAAGACAAGATCCAT
1 TATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCTGC
52507334 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
* *** *
52507378 TTTCTTCGATCTACTTCACACCAATACACGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
* * *
52507422 TTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
* * *
52507466 TTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
52507510 T
1 T
52507511 GCTTTTCAAC
Statistics
Matches: 456, Mismatches: 63, Indels: 23
0.84 0.12 0.04
Matches are distributed among these distances:
43 2 0.00
44 405 0.89
45 49 0.11
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (44 bp):
TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
Found at i:52508820 original size:14 final size:13
Alignment explanation
Indices: 52508805--52508850 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
52508795 AGCCTCTCCA
52508805 TTTTACTTTTTCC
1 TTTTACTTTTTCC
*
52508818 ATTTTTCATTTTTCC
1 -TTTTAC-TTTTTCC
52508833 TTTTCACTTTTTCC
1 TTTT-ACTTTTTCC
52508847 TTTT
1 TTTT
52508851 TTCATTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 20 0.71
15 8 0.29
ACGTcount: A:0.09, C:0.22, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTACTTTTTCC
Found at i:52508858 original size:21 final size:21
Alignment explanation
Indices: 52508819--52508859 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52508809 ACTTTTTCCA
*
52508819 TTTTTCATTTTTCCTTTTCAC
1 TTTTTCATTTTTCCATTTCAC
* *
52508840 TTTTTCCTTTTTTCATTTCA
1 TTTTTCATTTTTCCATTTCA
52508860 TCATTTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTCATTTTTCCATTTCAC
Found at i:52509786 original size:18 final size:18
Alignment explanation
Indices: 52509760--52509803 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
52509750 TGGTTTGGCA
*
52509760 GAAAAAATCCAAAAAAAT
1 GAAAGAATCCAAAAAAAT
**
52509778 GAAAGAATCGTAAAAAAT
1 GAAAGAATCCAAAAAAAT
52509796 GAAAGAAT
1 GAAAGAAT
52509804 ATTTGCTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (18 bp):
GAAAGAATCCAAAAAAAT
Found at i:52513608 original size:26 final size:26
Alignment explanation
Indices: 52513545--52513611 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
52513535 CTTAAAAAAA
*
52513545 TATATATTAAAAATATGCATATATAT
1 TATATATAAAAAATATGCATATATAT
* *
52513571 TATATATAAAAAATATGCGTATGTA-
1 TATATATAAAAAATATGCATATATAT
* *
52513596 TATGTATAGAAAATAT
1 TATATATAAAAAATAT
52513612 AATAGTAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 14 0.39
26 22 0.61
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (26 bp):
TATATATAAAAAATATGCATATATAT
Found at i:52518874 original size:34 final size:34
Alignment explanation
Indices: 52518825--52518903 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
52518815 GGATTTGTTT
* * ** *
52518825 TGATCTGATACATGTTTCTGAAAATATTAGATTC
1 TGATATGATATATGTTTCTGAAAATAGGACATTC
**
52518859 TGATATGATATATGTTTCTGGTAATAGGACATTC
1 TGATATGATATATGTTTCTGAAAATAGGACATTC
52518893 TGATATGATAT
1 TGATATGATAT
52518904 TTGTATATGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.42
Consensus pattern (34 bp):
TGATATGATATATGTTTCTGAAAATAGGACATTC
Found at i:52519989 original size:29 final size:29
Alignment explanation
Indices: 52519957--52520021 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
52519947 AGCAACACCA
*
52519957 AAGTGAAATATCATAATAGAATGACACTG
1 AAGTGAAATAGCATAATAGAATGACACTG
*** * *
52519986 AAGTGCTTTAGCATAATAGAGTGGCACTG
1 AAGTGAAATAGCATAATAGAATGACACTG
52520015 AAGTGAA
1 AAGTGAA
52520022 TTAACAGAAC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.25
Consensus pattern (29 bp):
AAGTGAAATAGCATAATAGAATGACACTG
Found at i:52521038 original size:15 final size:16
Alignment explanation
Indices: 52521018--52521050 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
52521008 AACCATTAAG
52521018 TAAAATAATT-TAAAA
1 TAAAATAATTCTAAAA
52521033 TAAAATAATTCTAAAA
1 TAAAATAATTCTAAAA
52521049 TA
1 TA
52521051 TTCTAACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATAATTCTAAAA
Found at i:52524978 original size:35 final size:35
Alignment explanation
Indices: 52524938--52525041 Score: 102
Period size: 35 Copynumber: 2.9 Consensus size: 35
52524928 AATAATGTTT
* *
52524938 TGTGCCTAGCACTAGTCGGATACACTGACAATAGG
1 TGTGCCTAGCACTAGTCGGATAAACCGACAATAGG
* * *
52524973 TGTGCCTAGCACTGGTCGGGTAAACCGACAATA-T
1 TGTGCCTAGCACTAGTCGGATAAACCGACAATAGG
* * * *
52525007 TTTGCACCCAACACTAGTCGGATAAACCGATAATA
1 TGTG--CCTAGCACTAGTCGGATAAACCGACAATA
52525042 TCAAATGTGG
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
34 3 0.05
35 29 0.52
36 24 0.43
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (35 bp):
TGTGCCTAGCACTAGTCGGATAAACCGACAATAGG
Found at i:52527094 original size:6 final size:6
Alignment explanation
Indices: 52527085--52527111 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52527075 TAATGATGCA
52527085 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
52527112 AAAAAGGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:52533175 original size:17 final size:15
Alignment explanation
Indices: 52533153--52533186 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
52533143 AACAAATATT
52533153 TTAAAATTATTAAAAAA
1 TTAAAATTA--AAAAAA
52533170 TTAAAATTAAAAAAA
1 TTAAAATTAAAAAAA
52533185 TT
1 TT
52533187 GATACAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAAAATTAAAAAAA
Found at i:52533211 original size:18 final size:19
Alignment explanation
Indices: 52533173--52533212 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
52533163 TAAAAAATTA
* *
52533173 AAATTAAAAAAATTGATAC
1 AAATTAAAAAAATAGACAC
52533192 AAATTAAAAAAATAG-CAC
1 AAATTAAAAAAATAGACAC
52533210 AAA
1 AAA
52533213 GTATATGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (19 bp):
AAATTAAAAAAATAGACAC
Found at i:52542817 original size:35 final size:34
Alignment explanation
Indices: 52542727--52542825 Score: 110
Period size: 34 Copynumber: 2.9 Consensus size: 34
52542717 AATCCGCGAA
* *
52542727 AGAGTTTGCGCCCAACACTAGTCGGATAAATCGAC
1 AGAGGTTGC-CCCAACACTAGTCAGATAAATCGAC
* * * *
52542762 AAATGTGTG-CCCAGCACTAGTCAGATAAATTGAC
1 AGAGGT-TGCCCCAACACTAGTCAGATAAATCGAC
52542796 AGAGGTTGCACCCAACACTAGTCAGATAAA
1 AGAGGTTGC-CCCAACACTAGTCAGATAAA
52542826 CTAACGAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
33 2 0.04
34 26 0.50
35 22 0.42
36 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.20
Consensus pattern (34 bp):
AGAGGTTGCCCCAACACTAGTCAGATAAATCGAC
Found at i:52543048 original size:143 final size:143
Alignment explanation
Indices: 52542731--52543049 Score: 399
Period size: 143 Copynumber: 2.2 Consensus size: 143
52542721 CGCGAAAGAG
* * * * *
52542731 TTTGCGCCCAACACTAGTCGGATAAATCGACAAATGTGTGCCCAGCACTAGTCAGATAAATTGAC
1 TTTGCGCCCAGCGCTAGTCGAATAAATCGACGAATGTGTGCCCAGCACTAGTCAGATAAACTGAC
* *
52542796 AGAGGTTGCACCCAACACTAGTCAGATAAACTAACGAATAATTAGTGAGCCCAACTCTAGTTGGA
66 AGAAGTTGCACCCAACACTAATCAGATAAACTAACGAATAATTAGTGAGCCCAACTCTAGTTGGA
*
52542861 TAAATCAACGATA
131 TAAACCAACGATA
** * * * *
52542874 TTTTTGCACAGCGCTAG-CCAGATAAACCGACGAATGTGTGCCCAGCGCTAGTCAGATAAACTGA
1 TTTGCGCCCAGCGCTAGTCGA-ATAAATCGACGAATGTGTGCCCAGCACTAGTCAGATAAACTGA
* * * * * * *
52542938 -TGAAAGTTGCGCCCAGCACTAATCGGATAAACTAACTAATAATTAGTGAGCCTAGCTCTAGTTG
65 CAG-AAGTTGCACCCAACACTAATCAGATAAACTAACGAATAATTAGTGAGCCCAACTCTAGTTG
52543002 GATAAACCAACGATA
129 GATAAACCAACGATA
* *
52543017 TTTGCGCCCAGCGCTAGTTGAACAAATCGACGA
1 TTTGCGCCCAGCGCTAGTCGAATAAATCGACGA
52543050 TGTCAATTAC
Statistics
Matches: 145, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
142 2 0.01
143 142 0.98
144 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (143 bp):
TTTGCGCCCAGCGCTAGTCGAATAAATCGACGAATGTGTGCCCAGCACTAGTCAGATAAACTGAC
AGAAGTTGCACCCAACACTAATCAGATAAACTAACGAATAATTAGTGAGCCCAACTCTAGTTGGA
TAAACCAACGATA
Found at i:52549746 original size:47 final size:47
Alignment explanation
Indices: 52549690--52549784 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
52549680 TTTATTTTGA
52549690 GTATGATCCTACTAATTTGAGCTATTTATGATTTTTTATGTTGTAGG
1 GTATGATCCTACTAATTTGAGCTATTTATGATTTTTTATGTTGTAGG
52549737 GTATGATCCTACTAATTTGAGCTATTTATGATTTTTTATGTTGTAGG
1 GTATGATCCTACTAATTTGAGCTATTTATGATTTTTTATGTTGTAGG
52549784 G
1 G
52549785 ACTAAATTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.23, C:0.08, G:0.20, T:0.48
Consensus pattern (47 bp):
GTATGATCCTACTAATTTGAGCTATTTATGATTTTTTATGTTGTAGG
Found at i:52551161 original size:33 final size:33
Alignment explanation
Indices: 52551118--52551195 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
52551108 AGCTAATGTG
*
52551118 CTTGATTTCCAACAGCAGATACAACGACAAACT
1 CTTGATTTCCAACAGCAAATACAACGACAAACT
* * * *
52551151 GTTGATTTCCAGCAGTAAATACAACGGCAAACT
1 CTTGATTTCCAACAGCAAATACAACGACAAACT
52551184 CTTGATTTCCAA
1 CTTGATTTCCAA
52551196 AAGGAAACAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (33 bp):
CTTGATTTCCAACAGCAAATACAACGACAAACT
Found at i:52552589 original size:6 final size:6
Alignment explanation
Indices: 52552578--52552627 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
52552568 GGTAACCCAA
* *
52552578 TTTTAT TTTTAT TTTTA- TTTTAT TTATAT ATTTA- TTTTATT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT
52552625 TTT
1 TTT
52552628 CTTGCATGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 9 0.24
6 23 0.62
7 5 0.14
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:52552599 original size:17 final size:17
Alignment explanation
Indices: 52552577--52552627 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
52552567 AGGTAACCCA
52552577 ATTTTATTTTTATTTTT
1 ATTTTATTTTTATTTTT
* *
52552594 ATTTTATTTATATATTT
1 ATTTTATTTTTATTTTT
52552611 ATTTTATTTTTTATTTT
1 ATTTTA-TTTTTATTTT
52552628 CTTGCATGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 21 0.72
18 8 0.28
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
ATTTTATTTTTATTTTT
Found at i:52552627 original size:5 final size:5
Alignment explanation
Indices: 52552577--52552620 Score: 52
Period size: 5 Copynumber: 8.0 Consensus size: 5
52552567 AGGTAACCCA
52552577 ATTTT ATTTTT ATTTTT ATTTT ATTTAT ATATTT ATTTT ATTTT
1 ATTTT A-TTTT A-TTTT ATTTT ATTT-T AT-TTT ATTTT ATTTT
52552621 TTATTTTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 17 0.47
6 17 0.47
7 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:52553589 original size:18 final size:19
Alignment explanation
Indices: 52553554--52553595 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
52553544 ATATATTATT
52553554 AAGAAAAAAAGAAGGAAAA
1 AAGAAAAAAAGAAGGAAAA
52553573 AAGAAAAGAAA-AA-GAAAA
1 AAGAAAA-AAAGAAGGAAAA
52553591 AAGAA
1 AAGAA
52553596 GTAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.45
19 9 0.41
20 3 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAAGAAGGAAAA
Found at i:52556048 original size:40 final size:39
Alignment explanation
Indices: 52556017--52556226 Score: 233
Period size: 40 Copynumber: 5.3 Consensus size: 39
52556007 GGACTAAGAT
* *
52556017 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
52556057 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
52556097 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* ** *
52556137 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGAT-ACAAATCCGGGTTAAGTC
* * * * *
52556177 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
52556216 CCGAAGGCATT
1 CCGAAGGCATT
52556227 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
39 33 0.22
40 117 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:52556180 original size:120 final size:120
Alignment explanation
Indices: 52555964--52556226 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
52555954 TTGAATGCTG
* *
52555964 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
52556028 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
52556084 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * * * *
52556147 TCGTGCGAGTTGTTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
52556203 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
52556227 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 38 0.32
120 73 0.61
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:52556246 original size:79 final size:80
Alignment explanation
Indices: 52556017--52556261 Score: 228
Period size: 80 Copynumber: 3.1 Consensus size: 80
52556007 GGACTAAGAT
* * * * * * * ** *
52556017 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGA-GATAC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-GC
52556080 TAAATCCGGGTTAAGTC
64 TAAATCCGGGTTAAGTC
* * * ** ** *
52556097 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
52556162 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
52556177 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
52556241 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
52556255 CCGAAGG
1 CCGAAGG
52556262 TACGTGATTT
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
78 14 0.10
79 46 0.33
80 75 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:52558737 original size:14 final size:13
Alignment explanation
Indices: 52558720--52558759 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
52558710 AATACAAAAC
52558720 TTTTTTCTTTTTCT
1 TTTTTTCTTTTT-T
52558734 TTTTTTCTTTCTTT
1 TTTTTTCTTT-TTT
52558748 TTTTTT-TTTTTT
1 TTTTTTCTTTTTT
52558760 GAGTCATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 3 0.12
14 17 0.68
15 2 0.08
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:52558757 original size:18 final size:18
Alignment explanation
Indices: 52558723--52558756 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52558713 ACAAAACTTT
52558723 TTTCTTTTTCTTTTTTTC
1 TTTCTTTTTCTTTTTTTC
52558741 TTTCTTTTT-TTTTTTT
1 TTTCTTTTTCTTTTTTT
52558757 TTTGAGTCAT
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTCTTTTTCTTTTTTTC
Found at i:52558840 original size:22 final size:22
Alignment explanation
Indices: 52558812--52558881 Score: 131
Period size: 22 Copynumber: 3.2 Consensus size: 22
52558802 TAGTTCGGTA
52558812 CTAAAGTAGAAAATAACGTATC
1 CTAAAGTAGAAAATAACGTATC
52558834 CTAAAGTAGAAAATAACGTATC
1 CTAAAGTAGAAAATAACGTATC
*
52558856 CTAAAGTAGAAAATAACTTATC
1 CTAAAGTAGAAAATAACGTATC
52558878 CTAA
1 CTAA
52558882 TATTCTTCAA
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:0.50, C:0.14, G:0.11, T:0.24
Consensus pattern (22 bp):
CTAAAGTAGAAAATAACGTATC
Found at i:52570924 original size:30 final size:29
Alignment explanation
Indices: 52570884--52570960 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 29
52570874 TTGGTTGGAA
* *
52570884 AAAAATAAAAAAAATATATATT-AACTTATG
1 AAAAAGAAAAAAAATAT-TATTAAAATT-TG
52570914 AAAAAGAAAAAAAA-ATTATTAAAATTTG
1 AAAAAGAAAAAAAATATTATTAAAATTTG
*
52570942 TAAAAGAAGAAAAAATATT
1 AAAAAGAA-AAAAAATATT
52570961 TGTTTATGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.32
29 12 0.29
30 16 0.39
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.26
Consensus pattern (29 bp):
AAAAAGAAAAAAAATATTATTAAAATTTG
Found at i:52570933 original size:28 final size:29
Alignment explanation
Indices: 52570884--52570959 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 29
52570874 TTGGTTGGAA
* *
52570884 AAAAATAAAAAAAATATATATT-AACTTATG
1 AAAAAGAAAAAAAA-ATATATTAAAATT-TG
52570914 AAAAAGAAAAAAAAAT-TATTAAAATTTG
1 AAAAAGAAAAAAAAATATATTAAAATTTG
* *
52570942 TAAAAGAAGAAAAAATAT
1 AAAAAGAAAAAAAAATAT
52570960 TTGTTTATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 20 0.50
29 7 0.17
30 13 0.32
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (29 bp):
AAAAAGAAAAAAAAATATATTAAAATTTG
Found at i:52571452 original size:19 final size:21
Alignment explanation
Indices: 52571430--52571474 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
52571420 TTAGTAATAG
*
52571430 TAATATTTAAT-T-TTTTTTA
1 TAATACTTAATATATTTTTTA
52571449 TAATACTTAATATATTTTTTA
1 TAATACTTAATATATTTTTTA
*
52571470 AAATA
1 TAATA
52571475 AGTGATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.45
20 1 0.05
21 11 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TAATACTTAATATATTTTTTA
Found at i:52571810 original size:42 final size:42
Alignment explanation
Indices: 52571668--52572000 Score: 352
Period size: 43 Copynumber: 7.9 Consensus size: 42
52571658 TTTTAGAAAT
* * *
52571668 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTT-TCCAC
* *
52571711 AAATGCCGCTATAGATCAGGACCTTTAGCGGCGCATTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGC-TTTTCCAC
** ** * *
52571754 AAACATCGCTATAGATCGGGACCATTAGCGGCGCTTTTTCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCAC
**
52571796 AAACGCCATTATAGATCAAGACCTTTAGCGGCGC-TTTCCGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCC-AC
* *
52571838 AAACGCCACTATA-ACTCAAGACCTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTATAGA-TCAAGACCTTTAGCGGCGCTTTT-CCAC
* *
52571881 AAACGCCGCTATAGATCAAGACCTTTATCGGTGCTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGC-TTTTCCAC
* * **
52571924 AAACGTCGCTAT-GTCTCAAGACCTTTAATGGCGCTTTTCCCAC
1 AAACGCCGCTATAG-ATCAAGACCTTTAGCGGCGCTTTT-CCAC
* *
52571967 AAACGCCGCTATAGAACAA-A-CTTTAGCGACGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
52572001 CTCGTTAAAC
Statistics
Matches: 245, Mismatches: 35, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
41 16 0.07
42 73 0.30
43 145 0.59
44 11 0.04
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCAC
Found at i:52571959 original size:170 final size:169
Alignment explanation
Indices: 52571668--52572000 Score: 420
Period size: 170 Copynumber: 2.0 Consensus size: 169
52571658 TTTTAGAAAT
* * * * *
52571668 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTACCCACAAATGCCGCTATAGATCAGGAC
1 AAACGCCACTATAGACCAAGACCTTTAGCGGCGCTTTACCCAAAAACGCCGCTATAGATCAAGAC
** * *
52571733 CTTTAGCGGCGCATTTTCCACAAACATCGCTATAGATCGGGACCATTAGCGGCGCTTTT-TCACA
66 CTTTAGCGGCGCATTTTCCACAAACATCGCTATAGATCAAGACCATTAACGGCGCTTTTCCCACA
* * *
52571797 AACGCCATTATAGATCAAGACCTTTAGCGGCGCTTTCCGAC
131 AACGCCACTATAGAACAA-A-CTTTAGCGACGCTTTCCGAC
*
52571838 AAACGCCACTATA-ACTCAAGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAGATCAAGA
1 AAACGCCACTATAGAC-CAAGACCTTTAGCGGCGCTTTACCCAAAAACGCCGCTATAGATCAAGA
* * * * * * *
52571902 CCTTTATCGGTGCTTTTTCCACAAACGTCGCTAT-GTCTCAAGACCTTTAATGGCGCTTTTCCCA
65 CCTTTAGCGGCGCATTTTCCACAAACATCGCTATAG-ATCAAGACCATTAACGGCGCTTTTCCCA
*
52571966 CAAACGCCGCTATAGAACAAACTTTAGCGACGCTT
129 CAAACGCCACTATAGAACAAACTTTAGCGACGCTT
52572001 CTCGTTAAAC
Statistics
Matches: 139, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
169 16 0.12
170 104 0.75
171 19 0.14
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (169 bp):
AAACGCCACTATAGACCAAGACCTTTAGCGGCGCTTTACCCAAAAACGCCGCTATAGATCAAGAC
CTTTAGCGGCGCATTTTCCACAAACATCGCTATAGATCAAGACCATTAACGGCGCTTTTCCCACA
AACGCCACTATAGAACAAACTTTAGCGACGCTTTCCGAC
Found at i:52573029 original size:40 final size:40
Alignment explanation
Indices: 52572974--52573053 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
52572964 TTAGGAGAGG
52572974 ATCGAATGTAGCAAACATAGTGTCCAAAAGTAGGTCTGAA
1 ATCGAATGTAGCAAACATAGTGTCCAAAAGTAGGTCTGAA
*
52573014 ATCGAATGTAGCAAACATAGTGTCCAGAAGTAGGTCTGAA
1 ATCGAATGTAGCAAACATAGTGTCCAAAAGTAGGTCTGAA
52573054 TCCGGAATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.23
Consensus pattern (40 bp):
ATCGAATGTAGCAAACATAGTGTCCAAAAGTAGGTCTGAA
Found at i:52575793 original size:27 final size:27
Alignment explanation
Indices: 52575763--52575849 Score: 99
Period size: 27 Copynumber: 3.2 Consensus size: 27
52575753 CTTAAATAAT
52575763 TTAAACTATAATCATAATTTTAATATA
1 TTAAACTATAATCATAATTTTAATATA
* *
52575790 TTAAAAT-TAAT-ATTATCTCTTAA-ATAA
1 TTAAACTATAATCATAAT-T-TTAATAT-A
52575817 TTTAAACTATAATCATAATTTTAATATA
1 -TTAAACTATAATCATAATTTTAATATA
52575845 TTAAA
1 TTAAA
52575850 ATTAATATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
25 4 0.08
26 7 0.14
27 16 0.33
28 11 0.22
29 7 0.14
30 4 0.08
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (27 bp):
TTAAACTATAATCATAATTTTAATATA
Found at i:52575804 original size:55 final size:55
Alignment explanation
Indices: 52575745--52575865 Score: 242
Period size: 55 Copynumber: 2.2 Consensus size: 55
52575735 AAAATGGATT
52575745 TATTATCTCTTAAATAATTTAAACTATAATCATAATTTTAATATATTAAAATTAA
1 TATTATCTCTTAAATAATTTAAACTATAATCATAATTTTAATATATTAAAATTAA
52575800 TATTATCTCTTAAATAATTTAAACTATAATCATAATTTTAATATATTAAAATTAA
1 TATTATCTCTTAAATAATTTAAACTATAATCATAATTTTAATATATTAAAATTAA
52575855 TATTATCTCTT
1 TATTATCTCTT
52575866 TTACAATTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (55 bp):
TATTATCTCTTAAATAATTTAAACTATAATCATAATTTTAATATATTAAAATTAA
Found at i:52575821 original size:28 final size:28
Alignment explanation
Indices: 52575745--52575865 Score: 96
Period size: 27 Copynumber: 4.4 Consensus size: 28
52575735 AAAATGGATT
*
52575745 TATTATCTCTTAA-ATAATTTAAACTATAA
1 TATTATCTCTTAATAT-A-TTAAAATATAA
*
52575774 TCATAAT-T-TTAATATATTAAAAT-TAA
1 T-ATTATCTCTTAATATATTAAAATATAA
*
52575800 TATTATCTCTTAA-ATAATTTAAACTATAA
1 TATTATCTCTTAATAT-A-TTAAAATATAA
*
52575829 TCATAAT-T-TTAATATATTAAAAT-TAA
1 T-ATTATCTCTTAATATATTAAAATATAA
52575855 TATTATCTCTT
1 TATTATCTCTT
52575866 TTACAATTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
25 8 0.11
26 12 0.16
27 19 0.26
28 16 0.22
29 11 0.15
30 8 0.11
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (28 bp):
TATTATCTCTTAATATATTAAAATATAA
Found at i:52576107 original size:121 final size:126
Alignment explanation
Indices: 52575861--52576113 Score: 308
Period size: 130 Copynumber: 2.0 Consensus size: 126
52575851 TTAATATTAT
* *
52575861 CTCTTTTACAATTATATAAGAAATTATTTAATATATAAATTAAGAAACACCAATTAATCTAAACT
1 CTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAAAAAACACCAATTAATCTAAACT
* *
52575926 CTAAACCCCTACCCCCTACATCTTAAACCTTAAATCATAAAACATAAACCTTAAACCCCTAACCC
66 CTAAACCCCGACCCCCGACATCTTAAACCTTAAATCAT-AAACAT--A-CTTAAACCCCTAACCC
* * *
52575991 CTCTTTTACAATTATATAAGAACTTAATTAATATATAAATTAAAAAATACTAATTAATCTAAAC-
1 CTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAAAAAACACCAATTAATCTAAACT
52576055 CTTAAA-CCCGA-CCCCGA-ATCTCTAAATCC-TAAATCACT-AAC-T-CTT-AACCCCTAACCC
66 C-TAAACCCCGACCCCCGACATCT-TAAA-CCTTAAATCA-TAAACATACTTAAACCCCTAACCC
52576112 CT
1 CT
52576114 AACCACTAAC
Statistics
Matches: 112, Mismatches: 7, Indels: 17
0.82 0.05 0.12
Matches are distributed among these distances:
121 14 0.12
122 3 0.03
126 1 0.01
127 7 0.06
128 16 0.14
129 8 0.07
130 63 0.56
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.30
Consensus pattern (126 bp):
CTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAAAAAACACCAATTAATCTAAACT
CTAAACCCCGACCCCCGACATCTTAAACCTTAAATCATAAACATACTTAAACCCCTAACCC
Found at i:52576109 original size:7 final size:7
Alignment explanation
Indices: 52576099--52576129 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
52576089 CACTAACTCT
52576099 TAACCCC
1 TAACCCC
52576106 TAACCCC
1 TAACCCC
*
52576113 TAACCAC
1 TAACCCC
52576120 TAACCCC
1 TAACCCC
52576127 TAA
1 TAA
52576130 ACTTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.35, C:0.48, G:0.00, T:0.16
Consensus pattern (7 bp):
TAACCCC
Found at i:52576116 original size:14 final size:14
Alignment explanation
Indices: 52576089--52576129 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
52576079 AATCCTAAAT
* *
52576089 CACTAACTCTTAAC
1 CACTAACCCCTAAC
*
52576103 CCCTAACCCCTAAC
1 CACTAACCCCTAAC
52576117 CACTAACCCCTAA
1 CACTAACCCCTAA
52576130 ACTTTATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.34, C:0.46, G:0.00, T:0.20
Consensus pattern (14 bp):
CACTAACCCCTAAC
Found at i:52576250 original size:126 final size:119
Alignment explanation
Indices: 52576018--52576256 Score: 293
Period size: 126 Copynumber: 1.9 Consensus size: 119
52576008 AAGAACTTAA
* * * *
52576018 TTAATATATAAATTAAAAAATACTAATTAATCTAAACCTTAAACCCGACCCCGAATCTCTAAATC
1 TTAATATATAAATAAAAAAATACTAATTAATCTAAACCCTAAACCCGACACCGAATCTATAAATC
* *
52576083 CTAAATCACTAACTCTTAACCCCTAACCCCTAACCACTAACCCCTAAACTTTAT
66 CTAAATCACTAACTCATAACCCCTAACCACTAACCACTAACCCCTAAACTTTAT
*
52576137 TTAATATATAAATCAAAAAAATACTAATTAATCTAAACCCTAAACCCTAACTTGACATCGAATCT
1 TTAATATATAAAT-AAAAAAATACTAATTAATCTAAACCCTAAA-CC---C--GACACCGAATCT
* * *
52576202 ATAAA-CCTTAAATTC-CTAACTCATAATCTCTAACCACTAACCCCTAACCCCTAAA
59 ATAAATCC-TAAA-TCACTAACTCATAACCCCTAACCACTAACCACTAACCCCTAAA
52576257 TCACAACCCT
Statistics
Matches: 101, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
119 13 0.13
120 28 0.28
121 2 0.02
124 1 0.01
125 2 0.02
126 53 0.52
127 2 0.02
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.28
Consensus pattern (119 bp):
TTAATATATAAATAAAAAAATACTAATTAATCTAAACCCTAAACCCGACACCGAATCTATAAATC
CTAAATCACTAACTCATAACCCCTAACCACTAACCACTAACCCCTAAACTTTAT
Found at i:52576831 original size:41 final size:41
Alignment explanation
Indices: 52576774--52576983 Score: 321
Period size: 41 Copynumber: 5.1 Consensus size: 41
52576764 CGCTAATGCT
* * * **
52576774 CTAAAAGCCTGAGCATTAGCGCCGCTTTTTCAAAATTGCCG
1 CTAAAAGCCTAAGCATTAGCGGCGCTTTTTTAAAAACGCCG
*
52576815 CTAAAAGCCTAAGCATTCGCGGCGCTTTTTTAAAAACGCCG
1 CTAAAAGCCTAAGCATTAGCGGCGCTTTTTTAAAAACGCCG
*
52576856 CTAAAAGCCTGAGCATTAGCGGCGCTTTTTTAAAAACGCCG
1 CTAAAAGCCTAAGCATTAGCGGCGCTTTTTTAAAAACGCCG
* *
52576897 CTAAAAGCCTAAGCATTAGCGGTGCTTTTTTAAAAACGCCA
1 CTAAAAGCCTAAGCATTAGCGGCGCTTTTTTAAAAACGCCG
* *
52576938 CTAAAAGCCTAAGCATTAGCGGCGCTTTTTCAAAAACACCG
1 CTAAAAGCCTAAGCATTAGCGGCGCTTTTTTAAAAACGCCG
52576979 CTAAA
1 CTAAA
52576984 GCCCCAAAAT
Statistics
Matches: 154, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 154 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (41 bp):
CTAAAAGCCTAAGCATTAGCGGCGCTTTTTTAAAAACGCCG
Found at i:52579541 original size:6 final size:6
Alignment explanation
Indices: 52579520--52579553 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
52579510 AAATAAAGAC
52579520 AATTAA AATTGCAA AATTAA AATTAA AATTAA AA
1 AATTAA AATT--AA AATTAA AATTAA AATTAA AA
52579554 ACTTTTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.77
8 6 0.23
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (6 bp):
AATTAA
Found at i:52586370 original size:15 final size:16
Alignment explanation
Indices: 52586350--52586379 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52586340 GATTTGAAGA
52586350 ATGAGGGAT-ATTGAG
1 ATGAGGGATGATTGAG
52586365 ATGAGGGATGATTGA
1 ATGAGGGATGATTGA
52586380 AATGGAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.40, T:0.27
Consensus pattern (16 bp):
ATGAGGGATGATTGAG
Found at i:52588352 original size:63 final size:63
Alignment explanation
Indices: 52588274--52588414 Score: 178
Period size: 63 Copynumber: 2.3 Consensus size: 63
52588264 AATATCTCTC
** * * * *
52588274 ACACGGCCTGGACACACGTTCATGTCTCTGGCCTGTGTGACTCTAATTC-CAAAACAATGAGTT
1 ACACGGCCTGGACACACGACCATGTCCCTGGCCCGTGGGACACTAATTCAC-AAACAATGAGTT
* * *
52588337 ACATGGCCTGGACACACGACCGTGTCCCTGGCCCGTGGGACACTAATTCACAAACAGTGAGTT
1 ACACGGCCTGGACACACGACCATGTCCCTGGCCCGTGGGACACTAATTCACAAACAATGAGTT
52588400 ACACGGCCTGG-CACA
1 ACACGGCCTGGACACA
52588415 TGGTTATGTG
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
62 4 0.06
63 62 0.93
64 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (63 bp):
ACACGGCCTGGACACACGACCATGTCCCTGGCCCGTGGGACACTAATTCACAAACAATGAGTT
Found at i:52588930 original size:14 final size:14
Alignment explanation
Indices: 52588911--52588957 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
52588901 TGTGAAAACC
52588911 AAAAAGAATAAGAG
1 AAAAAGAATAAGAG
52588925 AAAAAGAAT-A-A-
1 AAAAAGAATAAGAG
*
52588936 TAAAAGAATAAGAG
1 AAAAAGAATAAGAG
52588950 AAAAAGAA
1 AAAAAGAA
52588958 CGAACGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 8 0.29
12 2 0.07
13 2 0.07
14 16 0.57
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAAAGAATAAGAG
Found at i:52589339 original size:4 final size:4
Alignment explanation
Indices: 52589330--52589383 Score: 108
Period size: 4 Copynumber: 13.5 Consensus size: 4
52589320 TTGTGGGCGT
52589330 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
52589378 GATA GA
1 GATA GA
52589384 ATGCCTAAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (4 bp):
GATA
Found at i:52590001 original size:28 final size:28
Alignment explanation
Indices: 52589961--52590018 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
52589951 CAAATCAAAA
52589961 GTAGTTTAAATACTTGAGATTTGTATAG
1 GTAGTTTAAATACTTGAGATTTGTATAG
52589989 GTAGTTTAAATACTTGAGATTTGTATAG
1 GTAGTTTAAATACTTGAGATTTGTATAG
52590017 GT
1 GT
52590019 TTTATACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.43
Consensus pattern (28 bp):
GTAGTTTAAATACTTGAGATTTGTATAG
Found at i:52590025 original size:24 final size:26
Alignment explanation
Indices: 52589969--52590026 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 26
52589959 AAGTAGTTTA
52589969 AATACTTGAGATTTGTATAGGTAGTTT
1 AATACTTGAGATTTGTATAGGTA-TTT
52589996 AAATACTTGAGATTTGTATAGGT-TTT
1 -AATACTTGAGATTTGTATAGGTATTT
52590022 -ATACT
1 AATACT
52590027 AAGAGTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.17
26 3 0.10
28 22 0.73
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (26 bp):
AATACTTGAGATTTGTATAGGTATTT
Found at i:52595777 original size:17 final size:17
Alignment explanation
Indices: 52595754--52595795 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
52595744 TAAGTAAAAT
*
52595754 AAAATAAAGCAAAGTAA
1 AAAATAAAGCAAAGAAA
* *
52595771 TAAATAAAGTAAAGAAA
1 AAAATAAAGCAAAGAAA
52595788 AAAATAAA
1 AAAATAAA
52595796 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.14
Consensus pattern (17 bp):
AAAATAAAGCAAAGAAA
Found at i:52602192 original size:44 final size:44
Alignment explanation
Indices: 52602129--52602214 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
52602119 CCTATCCGTG
*
52602129 AACACCTTATCCTGAACCGGTCTGGATTGTGAGGTCGAGAGATA
1 AACACCTTATCCTGAACCGGTCTGGACTGTGAGGTCGAGAGATA
52602173 AACACCTTA-CCTTGAACCGGTCTGGACTGTGAGGTCGAGAGA
1 AACACCTTATCC-TGAACCGGTCTGGACTGTGAGGTCGAGAGA
52602215 AAAATAGTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 2 0.05
44 38 0.95
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (44 bp):
AACACCTTATCCTGAACCGGTCTGGACTGTGAGGTCGAGAGATA
Found at i:52607809 original size:46 final size:46
Alignment explanation
Indices: 52607742--52607832 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
52607732 CAATCTCTTG
52607742 TCATTTATTGAGGACAATGTATTGATTAAGTGGGGGATATAACTAC
1 TCATTTATTGAGGACAATGTATTGATTAAGTGGGGGATATAACTAC
52607788 TCATTTATTGAGGACAATGTATTGATTAAGTGGGGGATATAACTA
1 TCATTTATTGAGGACAATGTATTGATTAAGTGGGGGATATAACTA
52607833 GCCTGGTCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (46 bp):
TCATTTATTGAGGACAATGTATTGATTAAGTGGGGGATATAACTAC
Found at i:52638006 original size:114 final size:113
Alignment explanation
Indices: 52637825--52638042 Score: 244
Period size: 114 Copynumber: 1.9 Consensus size: 113
52637815 ACTTCACAAA
** * *
52637825 TTTATCGATACATTTTTCGGTATCAATACGAAAATGGCATTCTACTTTTCAAAATGTTTACCAAG
1 TTTATCGATACATTTTTCAATATCAATACGAAAATGACATTCTAC-TTTCAAAAGGTTTACCAAG
* * * *
52637890 TATCAAT-CTGGTATTGATACCTCTTGTTAGGTATCGATAATGGTATACT
65 TATCAATAC-GGTATCGATAACTCATATTAGGTATCGATAATGGTATACT
* * * *
52637939 TTTATCGATATATTTTTCAATATCAATATGAAATTGACATTCTAAC-TTCCAAAGGATTT-CTCA
1 TTTATCGATACATTTTTCAATATCAATACGAAAATGACATTCT-ACTTTCAAAAGG-TTTAC-CA
**
52638002 AGTATTGATACGGTATCGATAACTCATATTAGGTATCGATA
63 AGTATCAATACGGTATCGATAACTCATATTAGGTATCGATA
52638043 GAATTTTCTA
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
113 8 0.09
114 75 0.87
115 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (113 bp):
TTTATCGATACATTTTTCAATATCAATACGAAAATGACATTCTACTTTCAAAAGGTTTACCAAGT
ATCAATACGGTATCGATAACTCATATTAGGTATCGATAATGGTATACT
Found at i:52640264 original size:18 final size:18
Alignment explanation
Indices: 52640241--52640320 Score: 115
Period size: 18 Copynumber: 4.4 Consensus size: 18
52640231 GATGATGTCA
52640241 ATATTGATGCTAGTGACG
1 ATATTGATGCTAGTGACG
52640259 ATATTGATGCTAGTGACG
1 ATATTGATGCTAGTGACG
52640277 ATATTGATGCTAGTGACG
1 ATATTGATGCTAGTGACG
* * * *
52640295 CTATTGGTGATAGTGGCG
1 ATATTGATGCTAGTGACG
*
52640313 CTATTGAT
1 ATATTGAT
52640321 CGTGACCTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (18 bp):
ATATTGATGCTAGTGACG
Found at i:52640564 original size:18 final size:18
Alignment explanation
Indices: 52640524--52640566 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
52640514 GTTCAAGGTG
52640524 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
52640542 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
52640560 TAATTAA
1 TAATTAA
52640567 AAACTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:52642003 original size:21 final size:22
Alignment explanation
Indices: 52641976--52642039 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 22
52641966 CAGAAGCAGT
*
52641976 ATACGACACATAAAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
** *
52641998 A-ACGACACACGTGGTGCCT-A
1 ATACGACACATATAGTGCCTGA
52642018 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
52642040 TCGGCAAAGC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:52642913 original size:12 final size:12
Alignment explanation
Indices: 52642896--52642929 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
52642886 TAAACCCTAA
52642896 TTTTTCCTTTTC
1 TTTTTCCTTTTC
52642908 TTTTT-CTTTTC
1 TTTTTCCTTTTC
52642919 TTCTTTCCTTT
1 TT-TTTCCTTT
52642930 CTCCCTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 8 0.40
13 4 0.20
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTCCTTTTC
Found at i:52643208 original size:13 final size:13
Alignment explanation
Indices: 52643192--52643234 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
52643182 ATAGAAAGCC
52643192 ATAATAATAATTA
1 ATAATAATAATTA
*
52643205 ATAATTATAATT-
1 ATAATAATAATTA
52643217 ATAATAATAAATTA
1 ATAATAAT-AATTA
52643231 ATAA
1 ATAA
52643235 CAAAATCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 7 0.27
13 15 0.58
14 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATAATAATTA
Found at i:52644102 original size:40 final size:41
Alignment explanation
Indices: 52644047--52644142 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 41
52644037 ATCCACTAGC
* * *
52644047 ACCTCCCA-TAGTACCACCCACACCATGATTCCTAATGGTA
1 ACCTCCCACGAGTACCACCCACACCATGATTCCTAACGATA
***
52644087 ACCTCCCACGA-TACCACCCATGGCATGATTCCTAACGATA
1 ACCTCCCACGAGTACCACCCACACCATGATTCCTAACGATA
*
52644127 ACCTTCCACGAGTACC
1 ACCTCCCACGAGTACC
52644143 TTTCGCAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
40 42 0.89
41 5 0.11
ACGTcount: A:0.29, C:0.39, G:0.11, T:0.21
Consensus pattern (41 bp):
ACCTCCCACGAGTACCACCCACACCATGATTCCTAACGATA
Found at i:52644174 original size:39 final size:39
Alignment explanation
Indices: 52644125--52644292 Score: 110
Period size: 39 Copynumber: 4.3 Consensus size: 39
52644115 TTCCTAACGA
*
52644125 TAACCTTCCACGAGTACCTTTCGCAATACCCTCCCACGG
1 TAACCATCCACGAGTACCTTTCGCAATACCCTCCCACGG
* * * ***
52644164 TAACCATCCACAAATACCTCTT-GCGATACCCTCCCATAA
1 TAACCATCCACGAGTACCT-TTCGCAATACCCTCCCACGG
* * *** * * * *
52644203 TAACAATCCAGGAGTACCACCCGCGATACCTTCCAATGG
1 TAACCATCCACGAGTACCTTTCGCAATACCCTCCCACGG
* * *
52644242 TAACCATCCACGAGTA-C-TACCCACAGTACCCTCCCACTG
1 TAACCATCCACGAGTACCTTTCGCA-A-TACCCTCCCACGG
52644281 -AACCATCCACGA
1 TAACCATCCACGA
52644293 TATAACTCAT
Statistics
Matches: 97, Mismatches: 28, Indels: 9
0.72 0.21 0.07
Matches are distributed among these distances:
37 2 0.02
38 14 0.14
39 79 0.81
40 2 0.02
ACGTcount: A:0.30, C:0.39, G:0.11, T:0.20
Consensus pattern (39 bp):
TAACCATCCACGAGTACCTTTCGCAATACCCTCCCACGG
Done.