Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 13 of 410
Found at i:3339146 original size:26 final size:25
Alignment explanation
Indices: 3339106--3339156 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
3339096 TTAAATAAAA
*
3339106 ATTTAAAAAATATAACAAATCAAATAT
1 ATTTAAAAAACATAA-AAA-CAAATAT
3339133 ATTT-AAAAACATAAAAACAAATAT
1 ATTTAAAAAACATAAAAACAAATAT
3339157 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 9 0.39
27 4 0.17
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (25 bp):
ATTTAAAAAACATAAAAACAAATAT
Found at i:3339176 original size:21 final size:21
Alignment explanation
Indices: 3339119--3339185 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
3339109 TAAAAAATAT
*
3339119 AACAAAT-CAAAT-ATATTTAA
1 AACAAATAAAAATAATA-TTAA
* *
3339139 AA-ACATAAAAACAAATATTAA
1 AACAAATAAAAA-TAATATTAA
*
3339160 AACAAATAAAAATAATACTAA
1 AACAAATAAAAATAATATTAA
3339181 AACAA
1 AACAA
3339186 TTCTTAAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
19 3 0.08
20 5 0.14
21 18 0.49
22 11 0.30
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (21 bp):
AACAAATAAAAATAATATTAA
Found at i:3342684 original size:37 final size:36
Alignment explanation
Indices: 3342630--3342740 Score: 141
Period size: 37 Copynumber: 3.1 Consensus size: 36
3342620 AATAATTCAA
3342630 CCGAAACACATCAATCGCTCATAAGAGCTAATCCAC
1 CCGAAACACATCAATCGCTCATAAGAGCTAATCCAC
* * *
3342666 CCGATAACACGTCAATCGCTCATAAGAGCTAGTCCAA
1 CCGA-AACACATCAATCGCTCATAAGAGCTAATCCAC
* ** * *
3342703 CCGAAACACACCAATTTCTCATTAGAGCTAATCTAC
1 CCGAAACACATCAATCGCTCATAAGAGCTAATCCAC
3342739 CC
1 CC
3342741 CATAACACGC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 30 0.48
37 33 0.52
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.20
Consensus pattern (36 bp):
CCGAAACACATCAATCGCTCATAAGAGCTAATCCAC
Found at i:3342724 original size:36 final size:36
Alignment explanation
Indices: 3342622--3342735 Score: 147
Period size: 36 Copynumber: 3.1 Consensus size: 36
3342612 AGTACACAAA
*
3342622 TAATTCAACCGAAACACATCAATCGCTCATAAGAGC
1 TAATCCAACCGAAACACATCAATCGCTCATAAGAGC
* *
3342658 TAATCCACCCGATAACACGTCAATCGCTCATAAGAGC
1 TAATCCAACCGA-AACACATCAATCGCTCATAAGAGC
* * ** *
3342695 TAGTCCAACCGAAACACACCAATTTCTCATTAGAGC
1 TAATCCAACCGAAACACATCAATCGCTCATAAGAGC
3342731 TAATC
1 TAATC
3342736 TACCCCATAA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
36 33 0.50
37 33 0.50
ACGTcount: A:0.38, C:0.30, G:0.11, T:0.21
Consensus pattern (36 bp):
TAATCCAACCGAAACACATCAATCGCTCATAAGAGC
Found at i:3342775 original size:73 final size:73
Alignment explanation
Indices: 3342622--3342775 Score: 175
Period size: 73 Copynumber: 2.1 Consensus size: 73
3342612 AGTACACAAA
* * * *
3342622 TAATTCAACCGAAACACATCAATCGCTCATAAGAGCTAATCCACCCGATAACACGTCAATCGCTC
1 TAATCCAACCGAAACACACCAATCGCTCATAAGAGCTAATCCACCCCATAACACGCCAATCGCTC
*
3342687 ATAAGAGC
66 AGAAGAGC
* ** * *
3342695 TAGTCCAACCGAAACACACCAATTTCTCATTAGAGCTAATCTACCCCATAACACGCCAAAT-GCT
1 TAATCCAACCGAAACACACCAATCGCTCATAAGAGCTAATCCACCCCATAACACGCC-AATCGCT
* **
3342759 CCGAATTGC
65 CAGAAGAGC
3342768 TAATCCAA
1 TAATCCAA
3342776 TAGAAAACAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
73 63 0.95
74 3 0.05
ACGTcount: A:0.37, C:0.31, G:0.11, T:0.21
Consensus pattern (73 bp):
TAATCCAACCGAAACACACCAATCGCTCATAAGAGCTAATCCACCCCATAACACGCCAATCGCTC
AGAAGAGC
Found at i:3343802 original size:11 final size:12
Alignment explanation
Indices: 3343777--3343803 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3343767 ATTAAACCAA
3343777 TTTTCTTTAATT
1 TTTTCTTTAATT
3343789 TTTTCTTTAATT
1 TTTTCTTTAATT
3343801 TTT
1 TTT
3343804 AACCCCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTTAATT
Found at i:3344544 original size:31 final size:31
Alignment explanation
Indices: 3344506--3344576 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
3344496 GTTTTCATAT
3344506 AACTTGTGAATGCCTATGAATATATAAGTTA
1 AACTTGTGAATGCCTATGAATATATAAGTTA
* *
3344537 AACTTGTGATTGCCTGTGAATATATAAGTTA
1 AACTTGTGAATGCCTATGAATATATAAGTTA
3344568 AACTTGTGA
1 AACTTGTGA
3344577 GTTATTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (31 bp):
AACTTGTGAATGCCTATGAATATATAAGTTA
Found at i:3348517 original size:21 final size:21
Alignment explanation
Indices: 3348476--3348519 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3348466 TACACTATAT
**
3348476 TTTATATTTTTTTACTTAAAG
1 TTTATATTTTTTTACAAAAAG
3348497 TTTA-ATTTTTTTAACAAAAAG
1 TTTATATTTTTTT-ACAAAAAG
3348518 TT
1 TT
3348520 AACATTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTATATTTTTTTACAAAAAG
Found at i:3351167 original size:4 final size:4
Alignment explanation
Indices: 3351158--3351199 Score: 57
Period size: 4 Copynumber: 9.8 Consensus size: 4
3351148 ATTTTAATGT
3351158 TTAA TTAA TTAA TTAAA TTAAA TTAA TTGAA TTAA TTAA TTA
1 TTAA TTAA TTAA TT-AA TT-AA TTAA TT-AA TTAA TTAA TTA
3351200 TTTTAATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 23 0.64
5 13 0.36
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (4 bp):
TTAA
Found at i:3351181 original size:18 final size:18
Alignment explanation
Indices: 3351160--3351196 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3351150 TTTAATGTTT
3351160 AATTAATT-AATTAAATTA
1 AATTAATTGAATT-AATTA
3351178 AATTAATTGAATTAATTA
1 AATTAATTGAATTAATTA
3351196 A
1 A
3351197 TTATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AATTAATTGAATTAATTA
Found at i:3351190 original size:27 final size:29
Alignment explanation
Indices: 3351135--3351199 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 29
3351125 AAGTTAGTTT
*
3351135 TTAATTAAATTAAATTTTAATGTTTAATTAA
1 TTAATTAAATTAAA-TTTAA-GTTGAATTAA
3351166 TTAATTAAATTAAA-TTAA-TTGAATTAA
1 TTAATTAAATTAAATTTAAGTTGAATTAA
3351193 TTAATTA
1 TTAATTA
3351200 TTTTAATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
27 15 0.45
29 4 0.12
31 14 0.42
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
TTAATTAAATTAAATTTAAGTTGAATTAA
Found at i:3351193 original size:31 final size:30
Alignment explanation
Indices: 3351135--3351199 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
3351125 AAGTTAGTTT
*
3351135 TTAATTAAATTAAATTTTAATGTTTAATTAA
1 TTAATTAAATTAAA-TTTAATGATTAATTAA
3351166 TTAATTAAATTAAA-TTAATTGAATTAATTAA
1 TTAATTAAATTAAATTTAA-TG-ATTAATTAA
3351197 TTA
1 TTA
3351200 TTTTAATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.13
30 2 0.06
31 25 0.81
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
TTAATTAAATTAAATTTAATGATTAATTAA
Found at i:3351624 original size:28 final size:28
Alignment explanation
Indices: 3351588--3351645 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
3351578 TAAATTTATG
3351588 AATAATTTTTTTTTAATCTCTAACTGCT
1 AATAATTTTTTTTTAATCTCTAACTGCT
*
3351616 AATAGTTTTTTTTTAATCTCTAACTGCT
1 AATAATTTTTTTTTAATCTCTAACTGCT
3351644 AA
1 AA
3351646 CTATTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (28 bp):
AATAATTTTTTTTTAATCTCTAACTGCT
Found at i:3352574 original size:125 final size:119
Alignment explanation
Indices: 3352347--3352577 Score: 270
Period size: 125 Copynumber: 1.9 Consensus size: 119
3352337 TCTTTTAATG
*
3352347 ATTTATGTTCTTTCTTTACCTGGAAAATTGGGTAATTTGAGGTTCTAAGTTCGGCGGTTCTAATG
1 ATTTATGTTCTTTCTTTACCTGGAAAATTGGGTAATTTGAGCTTCTAAGTTCGGCGGTTCTAATG
*
3352412 ATGGTTCTTTTATGGTAGTATGCTATTATTTATGATTTTTATTTTTTTAAGAATA
66 ATGGTTCATTTATGGTAGTA-GCTATTATTTATGATTTTTATTTTTTTAAGAATA
* * ***
3352467 ATTT-TGTTCTTTTTTTTCCTGGAAAATTGGGTAATTTGAGATTCTTCCATTAAGTTCTTTGGTT
1 ATTTATGTTCTTTCTTTACCTGGAAAATTGGGTAATTTGAG---CTT-C--TAAGTTCGGCGGTT
* *
3352531 CTAATGATTGTTCATTTCT-GTCATGTA-CTATTATTTGATGATTTTTA
60 CTAATGATGGTTCATTTATGGT-A-GTAGCTATTATTT-ATGATTTTTA
3352578 CGTTTTCTTT
Statistics
Matches: 93, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
119 34 0.37
120 4 0.04
122 2 0.02
123 1 0.01
124 11 0.12
125 38 0.41
126 3 0.03
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (119 bp):
ATTTATGTTCTTTCTTTACCTGGAAAATTGGGTAATTTGAGCTTCTAAGTTCGGCGGTTCTAATG
ATGGTTCATTTATGGTAGTAGCTATTATTTATGATTTTTATTTTTTTAAGAATA
Found at i:3379838 original size:16 final size:17
Alignment explanation
Indices: 3379819--3379855 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3379809 TTTTGGTTTT
*
3379819 AAAT-AATTTTAAGTTC
1 AAATCAATTTTAAGTTA
3379835 AAATCAATTTTAAGTTA
1 AAATCAATTTTAAGTTA
3379852 AAAT
1 AAAT
3379856 GATTCGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (17 bp):
AAATCAATTTTAAGTTA
Found at i:3384894 original size:16 final size:15
Alignment explanation
Indices: 3384870--3384909 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
3384860 TAAAAAAGCT
3384870 TAAAAAAGAAAAATA
1 TAAAAAAGAAAAATA
3384885 TAAAACAAGAAAAATTA
1 TAAAA-AAGAAAAA-TA
3384902 TTAAAAAA
1 -TAAAAAA
3384910 AAGTTATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.23
16 8 0.36
17 4 0.18
18 5 0.23
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (15 bp):
TAAAAAAGAAAAATA
Found at i:3384935 original size:15 final size:17
Alignment explanation
Indices: 3384907--3384943 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3384897 AATTATTAAA
*
3384907 AAAAAGTTATAAAG-AT
1 AAAAAGTTAAAAAGTAT
3384923 AAAAA-TTAAAAAGTAT
1 AAAAAGTTAAAAAGTAT
3384939 AAAAA
1 AAAAA
3384944 AAACCCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (17 bp):
AAAAAGTTAAAAAGTAT
Found at i:3388011 original size:75 final size:75
Alignment explanation
Indices: 3387932--3388074 Score: 232
Period size: 75 Copynumber: 1.9 Consensus size: 75
3387922 GTATTAAATA
* * * *
3387932 TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTTACACCCAGTGCTAGTCGGGTATACTGACG
1 TGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTACACCAAATGCTAGTCGGGTATACCGACG
3387997 ATAGTAATTG
66 ATAGTAATTG
* *
3388007 TGAGCCTAGCTCTAGTTGGATAAACCAACAATATTTGCACCAAATGCTAGTCGGGTATACCGACG
1 TGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTACACCAAATGCTAGTCGGGTATACCGACG
3388072 ATA
66 ATA
3388075 TCTTCGTCTT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (75 bp):
TGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTACACCAAATGCTAGTCGGGTATACCGACG
ATAGTAATTG
Found at i:3390487 original size:6 final size:6
Alignment explanation
Indices: 3390476--3390504 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3390466 TTTTTCTCGA
3390476 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
3390505 AATTTTTTTA
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:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:3391697 original size:19 final size:19
Alignment explanation
Indices: 3391675--3391756 Score: 72
Period size: 18 Copynumber: 4.7 Consensus size: 19
3391665 TAAGAATAAT
3391675 AAATAAAAATAAATAAATA
1 AAATAAAAATAAATAAATA
*
3391694 AAAT-AAAAT---T-AGTA
1 AAATAAAAATAAATAAATA
3391708 AAATAAAAATAAATAATATA
1 AAATAAAAATAAATAA-ATA
* *
3391728 AAA-AATAAT-AATACATA
1 AAATAAAAATAAATAAATA
3391745 AAAT-AAAATAAA
1 AAATAAAAATAAA
3391757 AGGGGGTGGC
Statistics
Matches: 50, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
14 7 0.14
15 6 0.12
17 10 0.20
18 12 0.24
19 10 0.20
20 5 0.10
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (19 bp):
AAATAAAAATAAATAAATA
Found at i:3391699 original size:5 final size:5
Alignment explanation
Indices: 3391675--3391757 Score: 59
Period size: 5 Copynumber: 16.6 Consensus size: 5
3391665 TAAGAATAAT
* *
3391675 AAATA AAA-A TAAAT- AAATA AAATA AAAT- TAGTA AAATA AAA-A TAAATA
1 AAATA AAATA -AAATA AAATA AAATA AAATA AAATA AAATA AAATA -AAATA
*
3391723 ATATA AAA-A ATAATA ATACATA AAATA AAATA AAA
1 AAATA AAATA A-AATA A-A-ATA AAATA AAATA AAA
3391758 GGGGGTGGCT
Statistics
Matches: 63, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
4 10 0.16
5 43 0.68
6 6 0.10
7 4 0.06
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:3391728 original size:15 final size:15
Alignment explanation
Indices: 3391672--3391757 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 15
3391662 GTATAAGAAT
*
3391672 AATAAATAAAA-ATA
1 AATAAATAAAATAAA
3391686 AATAAATAAAAT-AA
1 AATAAATAAAATAAA
* *
3391700 AATTAGTAAAATAAA
1 AATAAATAAAATAAA
*
3391715 AATAAATAATATAAA
1 AATAAATAAAATAAA
3391730 AA-ATAATAATACAT-AA
1 AATA-AATAA-A-ATAAA
3391746 AATAAAATAAAA
1 AAT-AAATAAAA
3391758 GGGGGTGGCT
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
14 23 0.40
15 22 0.38
16 5 0.09
17 7 0.12
18 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (15 bp):
AATAAATAAAATAAA
Found at i:3391735 original size:22 final size:22
Alignment explanation
Indices: 3391672--3391752 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 22
3391662 GTATAAGAAT
*
3391672 AATAAAT-AAA-AATAAATAAA
1 AATAAATAAAATAAAAAATAAA
* *
3391692 TA-AAATAAAATTAGTAAAATAAA
1 AATAAATAAAA-TA-AAAAATAAA
* *
3391715 AATAAATAATATAAAAAATAAT
1 AATAAATAAAATAAAAAATAAA
*
3391737 AATACATAAAATAAAA
1 AATAAATAAAATAAAA
3391753 TAAAAGGGGG
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
19 4 0.09
20 4 0.09
22 22 0.47
23 10 0.21
24 7 0.15
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (22 bp):
AATAAATAAAATAAAAAATAAA
Found at i:3396804 original size:24 final size:24
Alignment explanation
Indices: 3396777--3396828 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3396767 TTTCTACAAG
* *
3396777 ATTTAGTATTTATTATTATAATAT
1 ATTTAGCATTTATTATCATAATAT
*
3396801 ATTTAGCATTTATTATCATAATTT
1 ATTTAGCATTTATTATCATAATAT
3396825 ATTT
1 ATTT
3396829 GACCTACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (24 bp):
ATTTAGCATTTATTATCATAATAT
Found at i:3398176 original size:29 final size:27
Alignment explanation
Indices: 3398101--3398182 Score: 67
Period size: 30 Copynumber: 2.9 Consensus size: 27
3398091 TTAATTCTAT
*
3398101 TTTAACATAATTATT-ATTAAATAAAA
1 TTTAATATAATTATTAATTAAATAAAA
* * *
3398127 TTTAATAAAATAATATATAATTTAATAACAT
1 TTTAATATAAT--TAT-TAATTAAATAA-AA
*
3398158 TCTTAATATAATTATTAATAAAATA
1 T-TTAATATAATTATTAATTAAATA
3398183 TGAATAAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
26 9 0.21
28 3 0.07
29 9 0.21
30 11 0.26
31 2 0.05
32 9 0.21
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (27 bp):
TTTAATATAATTATTAATTAAATAAAA
Found at i:3404007 original size:53 final size:53
Alignment explanation
Indices: 3403828--3404034 Score: 189
Period size: 53 Copynumber: 3.8 Consensus size: 53
3403818 ATTAGGGTTT
* * * * * *
3403828 AAGGATACCAAGTAAGACCATGCCAAGGCATTGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * * *
3403882 AAGGAAATCATGCAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * *
3403937 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* * * *
3403990 AAGGATACTACGTAAGACCATGTCAAGACATGGAAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
3404035 TAAAAAGGAA
Statistics
Matches: 119, Mismatches: 32, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
53 44 0.37
54 36 0.30
55 39 0.33
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:3411315 original size:53 final size:53
Alignment explanation
Indices: 3411136--3411339 Score: 219
Period size: 53 Copynumber: 3.8 Consensus size: 53
3411126 TAGGGTTTAA
* * * * *
3411136 GATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGCAAG
* * * * * * * *
3411190 GAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGCAAA
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGCAAG
* * *
3411245 GATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGCAAG
* *
3411298 GATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
3411340 TAAAAAGAAA
Statistics
Matches: 121, Mismatches: 27, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
53 46 0.38
54 35 0.29
55 40 0.33
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.21
Consensus pattern (53 bp):
GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGCAAG
Found at i:3411324 original size:108 final size:109
Alignment explanation
Indices: 3411134--3411329 Score: 304
Period size: 108 Copynumber: 1.8 Consensus size: 109
3411124 ATTAGGGTTT
* * * *
3411134 AAGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGCAAGGAAATCATG
1 AAGATACCAAGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTTCACAAGGCAAGGAAACCACG
3411199 TAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGCA
66 TAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGCA
* * * * *
3411243 AAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAG-TTCATAAGGCAAGGATACCACG
1 AAGATACCAAGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTTCACAAGGCAAGGAAACCACG
3411307 TAAGACCATGTCAAGACATGGCA
66 TAAGACCATGTCAAGACATGGCA
3411330 ATGGTAAGTT
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
108 40 0.51
109 38 0.49
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (109 bp):
AAGATACCAAGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTTCACAAGGCAAGGAAACCACG
TAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGCA
Found at i:3415837 original size:2 final size:2
Alignment explanation
Indices: 3415830--3415858 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3415820 GAGTAAACAA
3415830 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3415859 ACCATTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3419804 original size:46 final size:46
Alignment explanation
Indices: 3419737--3420142 Score: 607
Period size: 46 Copynumber: 8.8 Consensus size: 46
3419727 AGTGTGCTCT
*
3419737 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3419783 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3419829 CTGATATGAAATGTGTAAGGCCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3419875 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3419921 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
3419967 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3420013 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** **
3420059 ATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
3420106 ATGATA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC
3420143 TATGACATCA
Statistics
Matches: 340, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
46 299 0.88
47 41 0.12
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3420254 original size:13 final size:13
Alignment explanation
Indices: 3420236--3420290 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
3420226 TATAAGATGG
3420236 AATGGTTATATGA
1 AATGGTTATATGA
* *
3420249 AATGGTTGTGTGA
1 AATGGTTATATGA
*
3420262 AAT-GTTATAGGA
1 AATGGTTATATGA
*
3420274 ATTGGTTATATGGA
1 AATGGTTATAT-GA
3420288 AAT
1 AAT
3420291 ATATGTAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
12 8 0.25
13 20 0.62
14 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (13 bp):
AATGGTTATATGA
Found at i:3421844 original size:29 final size:29
Alignment explanation
Indices: 3421800--3421890 Score: 146
Period size: 29 Copynumber: 3.1 Consensus size: 29
3421790 TTAACAATCA
*
3421800 AATGCCTCTAAAATAATAACAAAATTAAC
1 AATGCCTTTAAAATAATAACAAAATTAAC
* *
3421829 AATGTCTTTAATATAATAACAAAATTAAC
1 AATGCCTTTAAAATAATAACAAAATTAAC
3421858 AAATGCCTTTAAAATAATAACAAAATTAAC
1 -AATGCCTTTAAAATAATAACAAAATTAAC
3421888 AAT
1 AAT
3421891 AAAATAAGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 29 0.52
30 27 0.48
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (29 bp):
AATGCCTTTAAAATAATAACAAAATTAAC
Found at i:3421875 original size:30 final size:30
Alignment explanation
Indices: 3421798--3421889 Score: 150
Period size: 30 Copynumber: 3.1 Consensus size: 30
3421788 ACTTAACAAT
*
3421798 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
* *
3421828 C-AATGTCTTTAATATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
3421857 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
3421887 CAA
1 CAA
3421890 TAAAATAAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 26 0.46
30 30 0.54
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAACAAAATTAA
Found at i:3425173 original size:46 final size:46
Alignment explanation
Indices: 3425121--3425526 Score: 589
Period size: 46 Copynumber: 8.8 Consensus size: 46
3425111 AGTGTGCTCT
*
3425121 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3425167 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGAAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3425213 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3425259 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCAAGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3425305 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
3425351 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3425397 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** **
3425443 ATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
3425490 ATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC
3425527 TATGACATCA
Statistics
Matches: 339, Mismatches: 20, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
46 297 0.88
47 42 0.12
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3426567 original size:14 final size:15
Alignment explanation
Indices: 3426552--3426599 Score: 62
Period size: 14 Copynumber: 3.1 Consensus size: 15
3426542 AAAAAAAAAA
*
3426552 AAAAAGAAAAAGAAAA
1 AAAAAG-AAAAGAAAG
3426568 AGAAAAGAAAAGAAAG
1 A-AAAAGAAAAGAAAG
3426584 AAAAA-AAAAGAAAG
1 AAAAAGAAAAGAAAG
3426598 AA
1 AA
3426600 TGAAAGAGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 11 0.37
15 4 0.13
16 10 0.33
17 5 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAGAAAG
Found at i:3426604 original size:22 final size:21
Alignment explanation
Indices: 3426541--3426606 Score: 79
Period size: 20 Copynumber: 3.3 Consensus size: 21
3426531 TTGAGTGTTT
3426541 GAAA-AAAAAAAAA-AAAGAA
1 GAAAGAAAAAAAAAGAAAGAA
3426560 -AAAGAAAAAGAAAAG-AA-AA
1 GAAAGAAAAA-AAAAGAAAGAA
3426579 GAAAGAAAAAAAAAGAAAGAA
1 GAAAGAAAAAAAAAGAAAGAA
3426600 TGAAAGA
1 -GAAAGA
3426607 GGGGAATTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
18 3 0.08
19 12 0.30
20 17 0.43
21 2 0.05
22 6 0.15
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (21 bp):
GAAAGAAAAAAAAAGAAAGAA
Found at i:3427010 original size:11 final size:11
Alignment explanation
Indices: 3426994--3427024 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3426984 TTCACAAAAT
3426994 GAAATTTCTGG
1 GAAATTTCTGG
3427005 GAAATTTCTGG
1 GAAATTTCTGG
*
3427016 AAAATTTCT
1 GAAATTTCT
3427025 TCTGAATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (11 bp):
GAAATTTCTGG
Found at i:3427704 original size:12 final size:13
Alignment explanation
Indices: 3427682--3427710 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3427672 TTGTTAGTAA
3427682 AAATAAAATAAAT
1 AAATAAAATAAAT
3427695 AAAT-AAATAAAT
1 AAATAAAATAAAT
3427707 AAAT
1 AAAT
3427711 TTTGAATCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:3430194 original size:46 final size:46
Alignment explanation
Indices: 3430127--3430531 Score: 591
Period size: 46 Copynumber: 8.8 Consensus size: 46
3430117 AGTGTGCTCT
*
3430127 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3430173 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3430219 CTGATATGAAATGTGTAAGGCCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3430265 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3430311 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA-
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
**
3430356 C-GCATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTG-ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3430402 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** **
3430448 ATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
3430495 ATGATA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC
3430532 TATGACATCA
Statistics
Matches: 336, Mismatches: 19, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
44 1 0.00
45 40 0.12
46 253 0.75
47 42 0.12
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3430643 original size:13 final size:13
Alignment explanation
Indices: 3430625--3430679 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
3430615 TATAAGATGG
3430625 AATGGTTATATGA
1 AATGGTTATATGA
* *
3430638 AATGGTTGTGTGA
1 AATGGTTATATGA
*
3430651 AAT-GTTATAGGA
1 AATGGTTATATGA
*
3430663 ATTGGTTATATGGA
1 AATGGTTATAT-GA
3430677 AAT
1 AAT
3430680 ATATGTAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
12 8 0.25
13 20 0.62
14 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (13 bp):
AATGGTTATATGA
Found at i:3432234 original size:29 final size:29
Alignment explanation
Indices: 3432190--3432280 Score: 146
Period size: 29 Copynumber: 3.1 Consensus size: 29
3432180 TTAACAATCA
*
3432190 AATGCCTCTAAAATAATAACAAAATTAAC
1 AATGCCTTTAAAATAATAACAAAATTAAC
* *
3432219 AATGTCTTTAATATAATAACAAAATTAAC
1 AATGCCTTTAAAATAATAACAAAATTAAC
3432248 AAATGCCTTTAAAATAATAACAAAATTAAC
1 -AATGCCTTTAAAATAATAACAAAATTAAC
3432278 AAT
1 AAT
3432281 AAAATAAGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 29 0.52
30 27 0.48
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (29 bp):
AATGCCTTTAAAATAATAACAAAATTAAC
Found at i:3432265 original size:30 final size:30
Alignment explanation
Indices: 3432188--3432279 Score: 150
Period size: 30 Copynumber: 3.1 Consensus size: 30
3432178 ACTTAACAAT
*
3432188 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
* *
3432218 C-AATGTCTTTAATATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
3432247 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
3432277 CAA
1 CAA
3432280 TAAAATAAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 26 0.46
30 30 0.54
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAACAAAATTAA
Found at i:3435530 original size:40 final size:40
Alignment explanation
Indices: 3435485--3435692 Score: 213
Period size: 40 Copynumber: 5.2 Consensus size: 40
3435475 CGGAATACAA
*
3435485 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACATGCACAAATGCCTTCGGGTCTTAGC
* * * *
3435525 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACATGCACAAATGCCTTCGGGTCTTAGC
* * * *
3435565 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACATGCACAAATGCCTTCGGGTCTTAGC
* ** * *
3435605 CCGGATGTAGTCAC-TAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACAT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
3435645 CCGGATATAATTACCA-GCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCA-CATGCACAAATGCCTTCGGGTCTTAGC
3435685 CCGGATAT
1 CCGGATAT
3435693 CATTCAATTG
Statistics
Matches: 140, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
39 1 0.01
40 138 0.99
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAACCACATGCACAAATGCCTTCGGGTCTTAGC
Found at i:3435625 original size:80 final size:80
Alignment explanation
Indices: 3435485--3435691 Score: 240
Period size: 80 Copynumber: 2.6 Consensus size: 80
3435475 CGGAATACAA
* *
3435485 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATG
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAATG
*
3435550 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
* * * *
3435565 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GTCACTAGCACAAT
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACG--ACTAGCACAAA
*
3435628 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
* * ** * *
3435645 CCGGATATAATTACCA-GCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAA-CAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATA
3435692 TCATTCAATT
Statistics
Matches: 107, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
79 2 0.02
80 102 0.95
81 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:3440010 original size:38 final size:38
Alignment explanation
Indices: 3439951--3440058 Score: 189
Period size: 38 Copynumber: 2.8 Consensus size: 38
3439941 TCAATCATGC
*
3439951 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTTCATAAT
*
3439990 ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
3440028 ACTGGGCCGAAGCCTTTTCATATTTCATATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATT
3440059 ACTGGGCCGA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
38 55 0.83
39 11 0.17
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (38 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
Found at i:3440016 original size:31 final size:31
Alignment explanation
Indices: 3439974--3440075 Score: 132
Period size: 31 Copynumber: 3.1 Consensus size: 31
3439964 CCTTTTCATA
3439974 TTTCATATTTCATAATACTGGGCCGAAGCCTTTTCAT
1 TTTCATATTTCATAATACTGGGCCGAAG-C----C-T
3440011 GTTTCATATTTCATAATACTGGGCCGAAGCCT
1 -TTTCATATTTCATAATACTGGGCCGAAGCCT
*
3440043 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
3440074 TT
1 TT
3440076 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
31 32 0.51
32 1 0.02
33 1 0.02
37 1 0.02
38 28 0.44
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:3440313 original size:24 final size:24
Alignment explanation
Indices: 3440267--3440385 Score: 154
Period size: 24 Copynumber: 5.0 Consensus size: 24
3440257 GCTTTATCAT
*
3440267 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
3440292 ATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGGGG-CATAAGCCCTTTTA
3440316 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
**
3440339 ATAACTGGGGCATAAGCCCTTTCG
1 ATAACTGGGGCATAAGCCCTTTTA
3440363 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
3440386 TCACTTCCTC
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
23 24 0.28
24 48 0.56
25 13 0.15
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:3440346 original size:47 final size:48
Alignment explanation
Indices: 3440267--3440385 Score: 172
Period size: 47 Copynumber: 2.5 Consensus size: 48
3440257 GCTTTATCAT
*
3440267 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGG-CATAAGCCCTTTCA
*
3440316 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTCG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
3440363 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
3440386 TCACTTCCTC
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
46 2 0.03
47 43 0.65
48 9 0.14
49 12 0.18
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:3440461 original size:20 final size:20
Alignment explanation
Indices: 3440436--3440475 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3440426 TATGATTACC
3440436 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
3440456 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
3440476 CCATATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:3442847 original size:42 final size:42
Alignment explanation
Indices: 3442695--3442853 Score: 140
Period size: 42 Copynumber: 3.6 Consensus size: 42
3442685 GGGTGCCAAA
* * * * * *
3442695 GCCATGTCCCAGACATGGTCTTACATGGGACCACACATTGAT
1 GCCATGTCCCAGACATGGTCTTATACGGGATCTCATATCGAT
* * *
3442737 GCCATATCCCAGATATGGTCTTATAC-GAAGTCTCAAATTAGTTTCGAT
1 GCCATGTCCCAGACATGGTCTTATACGGGA-TCTC--A-TA---TCGAT
* *
3442785 GCCATGCCCCAGACAAGGTCTTATACGGGATCTCATATCGAT
1 GCCATGTCCCAGACATGGTCTTATACGGGATCTCATATCGAT
*
3442827 GCCATGTCCCAAACATGGTCTTATACG
1 GCCATGTCCCAGACATGGTCTTATACG
3442854 AAATCACTTA
Statistics
Matches: 92, Mismatches: 17, Indels: 16
0.74 0.14 0.13
Matches are distributed among these distances:
41 2 0.02
42 53 0.58
44 1 0.01
45 3 0.03
46 1 0.01
48 30 0.33
49 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (42 bp):
GCCATGTCCCAGACATGGTCTTATACGGGATCTCATATCGAT
Found at i:3442869 original size:42 final size:42
Alignment explanation
Indices: 3442781--3442870 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
3442771 AAATTAGTTT
* ** * *
3442781 CGATGCCATGCCCCAGACAAGGTCTTATACGGGATCTCATAT
1 CGATGCCATGCCCCAAACAAGGTCTTATACGAAATCACATAA
* * *
3442823 CGATGCCATGTCCCAAACATGGTCTTATACGAAATCACTTAA
1 CGATGCCATGCCCCAAACAAGGTCTTATACGAAATCACATAA
3442865 CGATGC
1 CGATGC
3442871 TGAAGCCATA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (42 bp):
CGATGCCATGCCCCAAACAAGGTCTTATACGAAATCACATAA
Found at i:3451850 original size:21 final size:21
Alignment explanation
Indices: 3451824--3451879 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
3451814 AATAGAGGTG
*
3451824 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
3451845 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
3451866 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
3451880 AACAACGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:3452269 original size:2 final size:2
Alignment explanation
Indices: 3452262--3452298 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3452252 GTTTTTAATA
*
3452262 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3452299 GTAACATAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3453947 original size:32 final size:32
Alignment explanation
Indices: 3453908--3454035 Score: 211
Period size: 32 Copynumber: 4.0 Consensus size: 32
3453898 CATAAAAAAT
*
3453908 ATCATACATTAGCTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
*
3453940 ATCATACATTAGTTTTGCATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* * *
3453972 ATCATACATTAGGTTCACATATAAAAATGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
3454004 ATCATACATTAGTTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
3454036 CATAGTTATA
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 87 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (32 bp):
ATCATACATTAGTTTTACATATAAAAAAGTAG
Found at i:3458534 original size:25 final size:25
Alignment explanation
Indices: 3458506--3458563 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
3458496 TACAAACTGT
*
3458506 GAATATGGTAGCAAGAAGAAACAGA
1 GAATATGGTAGCAAGAAGAAACAAA
3458531 GAATATGGTAGCAAGAAGAAACAAA
1 GAATATGGTAGCAAGAAGAAACAAA
3458556 GAATATGG
1 GAATATGG
3458564 GAATGAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.52, C:0.07, G:0.28, T:0.14
Consensus pattern (25 bp):
GAATATGGTAGCAAGAAGAAACAAA
Found at i:3465970 original size:501 final size:503
Alignment explanation
Indices: 3465022--3465994 Score: 1567
Period size: 501 Copynumber: 1.9 Consensus size: 503
3465012 TAAGGAGATA
* * * *
3465022 CATGAGATGTGTGCTACATTTGTTGTAGTTCATGCACCTACCTACTTTCCGTTCAAAAAGAATTA
1 CATGAGATGTGTGCTACATTTGCTATAGTTCATGCACCTACCTACTTTCCATTCAAAAAGAAATA
* *
3465087 AGCATTTACAAAATCCAAATCATAATTCAAATATATTCTAGAAATGGTAGAAAAAATTATATTTT
66 AGCACTTACAAAATCCAAATCATAATTCAAATATATTCCAGAAATGGTAGAAAAAATTATATTTT
* * * *
3465152 TTCTGCTTTTTTTATAAAAATGAGAGGATTTATAATTTAATCCTTATACTTTTAAATCTTTTTAT
131 TTCTCCATTTTTTATAAAAATGAGAGAATTTAAAATTTAATCCTTATACTTTTAAATCTTTTTAT
* * * *
3465217 TTGGTCTTAAATGTGATTCTCGTAATATCAAAACATTTTCCAACTTATCCTTATGCCTATTAATT
196 TTGGTCTCAAATGCGATTCTCGTAATACCAAAACATTATCCAACTTATCCTTATGCCTATTAATT
* * *
3465282 AGTACTAAGACACTCATACTTTGATCAAATTGCACTTTTACTCCTCAAACTTTACAAAATTTTTT
261 AGTACT-A-ACACTCATACTTTAATAAAATTACACTTTTACTCCTCAAACTTTACAAAATTTTTT
* *
3465347 GGTTTGGTCCTTTAATCACACTTTCAAGTCTAAAATTCTTTTCATTTATTCTCATATCCAAAATC
324 GGTTTGGTACTTCAATCACACTTTCAAGTCTAAAATTCTTTTCATTTATTCTCATATCCAAAATC
* *
3465412 ACTTTATTTTCATAAGAATTATTTGATTCGAAAAATTTTGCATTTTTCTCGAAAATTCACTGTAT
389 ACTTTATTTTCATAAGAATTATTTGATTCGAAAAATTTTGCATTTTTCTCAAAAATTCACTATAT
3465477 CCACTATCGAAATAGTGTAACGTGTTTAATTGGAAATTTTGGAGTGTTAT
454 CCACTATCGAAATAGTGTAACGTGTTTAATTGGAAATTTTGGAGTGTTAT
* * * *
3465527 CATGAGATGTGTGCTACCTTTGCTATAGTTCATGTACCTGCCTACTTTCTATTCAAAAAGAAATA
1 CATGAGATGTGTGCTACATTTGCTATAGTTCATGCACCTACCTACTTTCCATTCAAAAAGAAATA
* * * *
3465592 AGCACTTATAAAATCCAAAAATTATAATTCAAATGTATTCCATAAATGGTAGAAAAAATTATATT
66 AGCACTTACAAAATCC--AAATCATAATTCAAATATATTCCAGAAATGGTAGAAAAAATTATATT
3465657 TTTTC-CCATTTTTTATAAAAATGAGAGAATTTAAAATTTAATCCTTATACTTTTAAATCTTTTT
129 TTTTCTCCATTTTTTATAAAAATGAGAGAATTTAAAATTTAATCCTTATACTTTTAAATCTTTTT
* *
3465721 ATTTGGTCTCAAATGCGATTCTCGTAATGCCAATACATTATCCAACTTATCCTTATGCCTATTAA
194 ATTTGGTCTCAAATGCGATTCTCGTAATACCAAAACATTATCCAACTTATCCTTATGCCTATTAA
* *
3465786 TTAGTACT-A-ACTCATATTTTAATAAAATTACACTTTTAGTCCTCAAACTTTACAAAA-TTTTT
259 TTAGTACTAACACTCATACTTTAATAAAATTACACTTTTACTCCTCAAACTTTACAAAATTTTTT
*
3465848 GGTTTGGTACTTCAATCACACTTTCAATTCTAAAATTCTTTTCATTTATTCTCATATCCAAAATC
324 GGTTTGGTACTTCAATCACACTTTCAAGTCTAAAATTCTTTTCATTTATTCTCATATCCAAAATC
3465913 ACTTTATTTTCATAAGAATTATTTGATTCGAAAAATTTTGCATTTTTCTCAAAAATTCACTATAT
389 ACTTTATTTTCATAAGAATTATTTGATTCGAAAAATTTTGCATTTTTCTCAAAAATTCACTATAT
*
3465978 CCATTATCGAAATAGTG
454 CCACTATCGAAATAGTG
3465995 CAAAGCATTT
Statistics
Matches: 431, Mismatches: 35, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
501 146 0.34
502 43 0.10
503 1 0.00
505 71 0.16
506 122 0.28
507 48 0.11
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (503 bp):
CATGAGATGTGTGCTACATTTGCTATAGTTCATGCACCTACCTACTTTCCATTCAAAAAGAAATA
AGCACTTACAAAATCCAAATCATAATTCAAATATATTCCAGAAATGGTAGAAAAAATTATATTTT
TTCTCCATTTTTTATAAAAATGAGAGAATTTAAAATTTAATCCTTATACTTTTAAATCTTTTTAT
TTGGTCTCAAATGCGATTCTCGTAATACCAAAACATTATCCAACTTATCCTTATGCCTATTAATT
AGTACTAACACTCATACTTTAATAAAATTACACTTTTACTCCTCAAACTTTACAAAATTTTTTGG
TTTGGTACTTCAATCACACTTTCAAGTCTAAAATTCTTTTCATTTATTCTCATATCCAAAATCAC
TTTATTTTCATAAGAATTATTTGATTCGAAAAATTTTGCATTTTTCTCAAAAATTCACTATATCC
ACTATCGAAATAGTGTAACGTGTTTAATTGGAAATTTTGGAGTGTTAT
Found at i:3469821 original size:60 final size:59
Alignment explanation
Indices: 3469684--3469832 Score: 151
Period size: 60 Copynumber: 2.5 Consensus size: 59
3469674 CTATTCAGAA
* * *
3469684 ATCAGAGT-TAACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAG
1 ATCAGAGTAT-ACTGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTAAAG
* * *
3469744 TATCAGAGTATACTGGGCCTAGCCCATGTCAGTATCAATCTGGGCCGTAGCCCTATTATAAG
1 -ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTA-AAG
* *
3469806 -TC-GAGATATATTGGGCCTTGCCCATAT
1 ATCAGAG-TATACTGGGCCTAGCCCATAT
3469833 TAACACAGTT
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
59 3 0.04
60 50 0.67
61 19 0.25
62 3 0.04
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (59 bp):
ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTAAAG
Found at i:3470253 original size:27 final size:25
Alignment explanation
Indices: 3470216--3470267 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
3470206 TAAACTTACT
*
3470216 CCTTTAGGGTATTACGGTAATTCTA
1 CCTTTAGGGTATTACAGTAATTCTA
*
3470241 CCTTATAGAGGTATTTCAGTAATTCTA
1 CCTT-TAG-GGTATTACAGTAATTCTA
3470268 TCAGTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 3 0.13
27 16 0.70
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (25 bp):
CCTTTAGGGTATTACAGTAATTCTA
Found at i:3472844 original size:44 final size:44
Alignment explanation
Indices: 3472781--3472869 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
3472771 TGGTTAGAAG
*
3472781 ATAAACAAATTAAAAAGATGAATATTTATCAAATTCTAAAACTT
1 ATAAAAAAATTAAAAAGATGAATATTTATCAAATTCTAAAACTT
3472825 ATAAAAAAATTAAAAAGATGAATATTTATCAAATTCTAAAACTT
1 ATAAAAAAATTAAAAAGATGAATATTTATCAAATTCTAAAACTT
3472869 A
1 A
3472870 CTTACGTAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.31
Consensus pattern (44 bp):
ATAAAAAAATTAAAAAGATGAATATTTATCAAATTCTAAAACTT
Found at i:3475309 original size:13 final size:13
Alignment explanation
Indices: 3475291--3475315 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3475281 TCATGTGGAA
3475291 ATGATTGCAAACC
1 ATGATTGCAAACC
3475304 ATGATTGCAAAC
1 ATGATTGCAAAC
3475316 GATTGCATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGATTGCAAACC
Found at i:3484914 original size:18 final size:18
Alignment explanation
Indices: 3484891--3484928 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3484881 TGCCAGGTGC
3484891 GTATCCTAACCCATATAT
1 GTATCCTAACCCATATAT
*
3484909 GTATCCTAACCCTTATAT
1 GTATCCTAACCCATATAT
3484927 GT
1 GT
3484929 TTCTTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (18 bp):
GTATCCTAACCCATATAT
Found at i:3485394 original size:56 final size:56
Alignment explanation
Indices: 3485308--3485413 Score: 194
Period size: 56 Copynumber: 1.9 Consensus size: 56
3485298 ATTGATTTAT
3485308 TTTTGAATATTTTTGTAAAAATTATTTTTATATTGTTTCATTTAATAAATAGGTTC
1 TTTTGAATATTTTTGTAAAAATTATTTTTATATTGTTTCATTTAATAAATAGGTTC
* *
3485364 TTTTGAATATTTTTGTAGAACTTATTTTTATATTGTTTCATTTAATAAAT
1 TTTTGAATATTTTTGTAAAAATTATTTTTATATTGTTTCATTTAATAAAT
3485414 TAGAAGATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (56 bp):
TTTTGAATATTTTTGTAAAAATTATTTTTATATTGTTTCATTTAATAAATAGGTTC
Found at i:3488093 original size:27 final size:28
Alignment explanation
Indices: 3488040--3488093 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
3488030 AATCCTGGGA
* * *
3488040 TATTTTTTTAGATTCATCTACTCGAAAT
1 TATTTTTTCAGAATCATCTACTAGAAAT
*
3488068 TATTTTTTCAGAATCATC-AGTAGAAA
1 TATTTTTTCAGAATCATCTACTAGAAA
3488094 AAAAACGCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (28 bp):
TATTTTTTCAGAATCATCTACTAGAAAT
Found at i:3488703 original size:43 final size:43
Alignment explanation
Indices: 3488654--3488756 Score: 170
Period size: 43 Copynumber: 2.4 Consensus size: 43
3488644 GTTTCAAACT
*
3488654 GATTCGAGAATCGATTAAGAAGGTTGGTTTAGGGTTAGAAATT
1 GATTCGAGAATCGATTAAGAAGGTTGGTTTAGGGTTAGAAATC
* *
3488697 GTTTCGAGAATCGATTAAGAAGGTTTGTTTAGGGTTAGAAATC
1 GATTCGAGAATCGATTAAGAAGGTTGGTTTAGGGTTAGAAATC
*
3488740 GATTCGATAATCGATTA
1 GATTCGAGAATCGATTA
3488757 GGATGGTATT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (43 bp):
GATTCGAGAATCGATTAAGAAGGTTGGTTTAGGGTTAGAAATC
Found at i:3488960 original size:16 final size:16
Alignment explanation
Indices: 3488935--3488966 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3488925 TATTTTTTAT
*
3488935 ATTTAGGGTTATTTTG
1 ATTTAAGGTTATTTTG
3488951 ATTTAAGGTTATTTTG
1 ATTTAAGGTTATTTTG
3488967 GATTCTTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (16 bp):
ATTTAAGGTTATTTTG
Found at i:3489036 original size:6 final size:6
Alignment explanation
Indices: 3488983--3489016 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
3488973 TTCGATTTCA
*
3488983 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTA ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTT
3489017 AGGGATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.68
Consensus pattern (6 bp):
ATTTTG
Found at i:3489551 original size:21 final size:21
Alignment explanation
Indices: 3489526--3489567 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3489516 ACATGGATGA
*
3489526 TACAGATGTAGGTGAACTGTG
1 TACAGAAGTAGGTGAACTGTG
3489547 TACAGAAGTAGGTGAACTGTG
1 TACAGAAGTAGGTGAACTGTG
3489568 CGATAGTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.33, T:0.26
Consensus pattern (21 bp):
TACAGAAGTAGGTGAACTGTG
Found at i:3491272 original size:75 final size:75
Alignment explanation
Indices: 3491149--3491315 Score: 246
Period size: 75 Copynumber: 2.2 Consensus size: 75
3491139 TTAGTGAGTG
* * *
3491149 TTTTTTAATATGCATGCAATGTTTTTTAATCTGTCTGTGTATGATTGTTGGTGAGGTTGGTCA-T
1 TTTTTTAATATGCATGCAATGTTTTTTAATCTATCTGTGTATGATTGTTGGCGAGGATGGT-ATT
**
3491213 ATGTTGTTGAC
65 ATACTGTTGAC
* *
3491224 TTTTTTAATATGCATGCAATGTTTTTTAATTTATCTGTGTATGATTGTTGGCGGGGATGGTATTA
1 TTTTTTAATATGCATGCAATGTTTTTTAATCTATCTGTGTATGATTGTTGGCGAGGATGGTATTA
3491289 TACTGTTGAC
66 TACTGTTGAC
3491299 TATTTTTAATATGCATG
1 T-TTTTTAATATGCATG
3491316 AATTAACTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
74 1 0.01
75 67 0.81
76 15 0.18
ACGTcount: A:0.21, C:0.08, G:0.22, T:0.49
Consensus pattern (75 bp):
TTTTTTAATATGCATGCAATGTTTTTTAATCTATCTGTGTATGATTGTTGGCGAGGATGGTATTA
TACTGTTGAC
Found at i:3491431 original size:28 final size:25
Alignment explanation
Indices: 3491377--3491438 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 25
3491367 CACATGTTGT
3491377 TGACTATTTTTTAATAAGCATGCAG
1 TGACTATTTTTTAATAAGCATGCAG
* *
3491402 TGATTATTTTTTAATAATATGCATGTAG
1 TGACTATTTTTTAAT-A-A-GCATGCAG
3491430 TGACTATTT
1 TGACTATTT
3491439 CTTAGGTGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.45
26 1 0.03
27 1 0.03
28 15 0.48
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.47
Consensus pattern (25 bp):
TGACTATTTTTTAATAAGCATGCAG
Found at i:3491451 original size:2 final size:2
Alignment explanation
Indices: 3491444--3491514 Score: 79
Period size: 2 Copynumber: 35.5 Consensus size: 2
3491434 TATTTCTTAG
* * ** ** *
3491444 GT GT GT GT GT GT GT GT GC GT GT GC GT GT AC GT GT AC GT GC GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
3491486 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
3491515 AGTGATTGTT
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.03, C:0.07, G:0.48, T:0.42
Consensus pattern (2 bp):
GT
Found at i:3495375 original size:21 final size:21
Alignment explanation
Indices: 3495351--3495403 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3495341 CAAGTGGTTG
* *
3495351 CCCCAACTCAACAACAGGATA
1 CCCCAACTCAACAAAAGAATA
* *
3495372 CCCCAAATCAGCAAAAGAATA
1 CCCCAACTCAACAAAAGAATA
3495393 CCCCAACTCAA
1 CCCCAACTCAA
3495404 TAGGAGGCTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.38, G:0.08, T:0.09
Consensus pattern (21 bp):
CCCCAACTCAACAAAAGAATA
Found at i:3497813 original size:2 final size:2
Alignment explanation
Indices: 3497808--3497833 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3497798 TTCTGATACA
3497808 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3497834 TTGCATGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3498810 original size:11 final size:11
Alignment explanation
Indices: 3498794--3498820 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3498784 GAGGTCTTTG
3498794 TTTTTATTTTC
1 TTTTTATTTTC
3498805 TTTTTATTTTC
1 TTTTTATTTTC
3498816 TTTTT
1 TTTTT
3498821 GGGCTTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTTTC
Found at i:3499401 original size:154 final size:153
Alignment explanation
Indices: 3499202--3499490 Score: 438
Period size: 155 Copynumber: 1.9 Consensus size: 153
3499192 ATTTTTTTTT
***
3499202 AAAAGAGAAAGTTTAGATTTTTAAAATAAAAATATATTTTATAGTCATATTAAAGGAAATTTTTA
1 AAAAGAGAAAGTTTAGATTTTTAAAATAAAAATATATTTTATAGTCATATTAAAGGAAAAGCTTA
* * *
3499267 AA-ATTTTAAAATAAAGTTTTGATCTTTTTCAACTATTTTGAAATAAAACTTTGATTTTTAAGAA
66 AATATTTTAAAACAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAACTTTGATTTTTAAGAA
3499331 AAATAGTGTTTTTTTTTAAAAAA
131 AAATAGTGTTTTTTTTTAAAAAA
* *
3499354 AAAAGAGAAAGTTTAGATTTTTTTAAAATAAAAATATGTCTTT-TAGTCATTTTAAAGGAAAAGC
1 AAAAGAGAAAGTTTAGA--TTTTTAAAATAAAAATATAT-TTTATAGTCATATTAAAGGAAAAGC
* **
3499418 TTAAATTTTTTAAAACAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAGTTTTGATTTTTAA
63 TTAAATATTTTAAAACAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAACTTTGATTTTTAA
3499483 GAAAAATA
128 GAAAAATA
3499491 ATAATTTTTT
Statistics
Matches: 122, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
152 17 0.14
154 41 0.34
155 64 0.52
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (153 bp):
AAAAGAGAAAGTTTAGATTTTTAAAATAAAAATATATTTTATAGTCATATTAAAGGAAAAGCTTA
AATATTTTAAAACAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAACTTTGATTTTTAAGAA
AAATAGTGTTTTTTTTTAAAAAA
Found at i:3502381 original size:39 final size:39
Alignment explanation
Indices: 3502298--3502384 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
3502288 GGACTTTAGC
* * *
3502298 CCGGACATATTTCCAGCACGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
*
3502337 CCGGATATAATTCCATCACATAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
3502376 CCGGATATA
1 CCGGATATA
3502385 CATCACTGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
Found at i:3503865 original size:27 final size:26
Alignment explanation
Indices: 3503828--3503942 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
3503818 AGCATGGCTG
* *
3503828 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
3503854 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
3503882 CCAGAATAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
3503909 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
3503936 CCAGAAC
1 CCAGAAC
3503943 GCTTCCTCCA
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
26 5 0.06
27 56 0.72
28 17 0.22
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:3503887 original size:54 final size:54
Alignment explanation
Indices: 3503828--3503942 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
3503818 AGCATGGCTG
*
3503828 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * * *
3503882 CCAGAATAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
3503936 CCAGAAC
1 CCAGAAC
3503943 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 35 0.66
55 18 0.34
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:3505590 original size:25 final size:26
Alignment explanation
Indices: 3505556--3505664 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
3505546 CATGAAATTC
3505556 TTATCATGAAACATTTACCTAACC-A
1 TTATCATGAAACATTTACCTAACCTA
*
3505581 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
3505607 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
3505633 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
3505659 TTATCA
1 TTATCA
3505665 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
25 24 0.30
26 57 0.70
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:3509556 original size:19 final size:22
Alignment explanation
Indices: 3509517--3509556 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
3509507 AGAAACCCAA
3509517 CCATATCCAACCGTATACACCC
1 CCATATCCAACCGTATACACCC
3509539 CCATA-CCAACC-T-TACACC
1 CCATATCCAACCGTATACACC
3509557 GTGTGGGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.33, C:0.47, G:0.03, T:0.17
Consensus pattern (22 bp):
CCATATCCAACCGTATACACCC
Found at i:3509654 original size:27 final size:26
Alignment explanation
Indices: 3509617--3509731 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
3509607 AGCATGGCTG
* *
3509617 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
3509643 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
3509671 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
3509698 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
3509725 CCAGAAC
1 CCAGAAC
3509732 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:3509676 original size:54 final size:54
Alignment explanation
Indices: 3509617--3509731 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
3509607 AGCATGGCTG
*
3509617 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
3509671 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
3509725 CCAGAAC
1 CCAGAAC
3509732 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:3511382 original size:26 final size:26
Alignment explanation
Indices: 3511346--3511455 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
3511336 CATGAAATTC
3511346 TTATCATGAAACATTTACCTAAACC-A
1 TTATCATGAAACATTTACCT-AACCTA
*
3511372 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
3511398 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
3511424 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
3511450 TTATCA
1 TTATCA
3511456 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
25 4 0.05
26 77 0.95
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:3514972 original size:13 final size:13
Alignment explanation
Indices: 3514954--3514980 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3514944 TGACAAATCC
3514954 AAATAATTTTCTA
1 AAATAATTTTCTA
3514967 AAATAATTTTCTA
1 AAATAATTTTCTA
3514980 A
1 A
3514981 CTTTTGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATTTTCTA
Found at i:3522715 original size:23 final size:23
Alignment explanation
Indices: 3522688--3522732 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
3522678 TAAATCAAGA
3522688 AAAAAAGAGAA-AACAAAATAAAAC
1 AAAAAAGA-AACAA-AAAATAAAAC
3522712 AAAAAAGAAACAAAAAATAAA
1 AAAAAAGAAACAAAAAATAAA
3522733 TAAAGAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.82, C:0.07, G:0.07, T:0.04
Consensus pattern (23 bp):
AAAAAAGAAACAAAAAATAAAAC
Found at i:3523197 original size:42 final size:42
Alignment explanation
Indices: 3523138--3523435 Score: 349
Period size: 42 Copynumber: 7.3 Consensus size: 42
3523128 AAAGAAAGCA
*
3523138 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
** * ** *
3523180 TTCATTGCATTTAGAGGCTTAGGCATAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* *
3523222 TTTATTGCATTTAGAGGCTCAA--GTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * *
3523262 TTCATTGCA--TAAAGG-CCAGGTGTGGAGATCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
3523301 TTCATTGCA--TAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* ** *
3523341 TTCATTGCATTTTGAGGCCCAAGCATAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * * * * *
3523383 TTTAATGCATTTAAAGGTCCAGGTATGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
3523425 TTCATTGCATT
1 TTCATTGCATT
3523436 GTATATGAAT
Statistics
Matches: 217, Mismatches: 34, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
37 2 0.01
38 5 0.02
39 31 0.14
40 55 0.25
42 124 0.57
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
Found at i:3523324 original size:161 final size:163
Alignment explanation
Indices: 3523138--3523434 Score: 474
Period size: 161 Copynumber: 1.8 Consensus size: 163
3523128 AAAGAAAGCA
* ** *
3523138 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTATTTTTCATTGCATTTAGAGGCTTAGG
1 TTCATTGCA-TTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
* *
3523203 CATAGAGGTCCATTTACTTTTTATTGCATTTAGAGG-CTCAAG-TGGAGGTCCATTTACTTTTCA
65 CATAGAGGTCCATTTACTTTTTAATGCATTTAAAGGTC-CAAGATGGAGGTCCATTTACTTTTCA
3523266 TTGCATAAAGGCCAGGTGTGGAGATCCATTTACTT
129 TTGCATAAAGGCCAGGTGTGGAGATCCATTTACTT
*
3523301 TTCATTGCA-TAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTTGAGGCCCAAGC
1 TTCATTGCATTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAGC
*
3523365 ATAGAGGTCCATTTACTTTTTAATGCATTTAAAGGTCCAGGTATGGAGGTCCATTTACTTTTCAT
66 ATAGAGGTCCATTTACTTTTTAATGCATTTAAAGGTCCAAG-ATGGAGGTCCATTTACTTTTCAT
3523430 TGCAT
130 TGCAT
3523435 TGTATATGAA
Statistics
Matches: 123, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
161 86 0.70
162 1 0.01
163 36 0.29
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (163 bp):
TTCATTGCATTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAGC
ATAGAGGTCCATTTACTTTTTAATGCATTTAAAGGTCCAAGATGGAGGTCCATTTACTTTTCATT
GCATAAAGGCCAGGTGTGGAGATCCATTTACTT
Found at i:3523873 original size:13 final size:13
Alignment explanation
Indices: 3523855--3523879 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3523845 TTACTACTAC
3523855 TATTATTATTAAA
1 TATTATTATTAAA
3523868 TATTATTATTAA
1 TATTATTATTAA
3523880 TATCATTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATTATTAAA
Found at i:3528596 original size:25 final size:24
Alignment explanation
Indices: 3528550--3528596 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
3528540 TGTAACTTAA
*
3528550 TTTATCTTTTTAATTTCCTTTTAT
1 TTTATCTTTTTAATTTCATTTTAT
3528574 TTTATTCTTTTATAA-TTCATTTT
1 TTTA-TCTTTT-TAATTTCATTTT
3528597 TTTACTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 4 0.20
25 13 0.65
26 3 0.15
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTATCTTTTTAATTTCATTTTAT
Found at i:3529036 original size:27 final size:27
Alignment explanation
Indices: 3529006--3529076 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
3528996 TTTAGGGTTT
*
3529006 TTAGGG-TTAGGGTTTTGCTAAAATAAG
1 TTAGGGTTTA-GGTTTTGCTAAAACAAG
*
3529033 TTAGGGTTTA-GTATTTGTTAAAACAAG
1 TTAGGGTTTAGGT-TTTGCTAAAACAAG
3529060 TTAGGGTTTAGAGTTTT
1 TTAGGGTTTAG-GTTTT
3529077 AGTAGTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 2 0.05
27 28 0.74
28 6 0.16
29 2 0.05
ACGTcount: A:0.28, C:0.03, G:0.27, T:0.42
Consensus pattern (27 bp):
TTAGGGTTTAGGTTTTGCTAAAACAAG
Found at i:3529265 original size:22 final size:22
Alignment explanation
Indices: 3529237--3529279 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3529227 CTAGAATTTT
* *
3529237 AAATAAATTAAGTTAGTGTTTA
1 AAATAAATTAAATTAGGGTTTA
3529259 AAATAAATTAAATTAGGGTTT
1 AAATAAATTAAATTAGGGTTT
3529280 CAGGTTTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.40
Consensus pattern (22 bp):
AAATAAATTAAATTAGGGTTTA
Found at i:3529334 original size:34 final size:34
Alignment explanation
Indices: 3529296--3529364 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
3529286 TAGGGTTTAT
** *
3529296 TAAATTAGGGTT-TATGTTTTTTAAATAGATTAAG
1 TAAATTAGGGTTCTA-GGGTTTTAAATAAATTAAG
3529330 TAAATTAGGGTTCTAGGGTTTTAAATAAATTAAG
1 TAAATTAGGGTTCTAGGGTTTTAAATAAATTAAG
3529364 T
1 T
3529365 TAGGATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.43
Consensus pattern (34 bp):
TAAATTAGGGTTCTAGGGTTTTAAATAAATTAAG
Found at i:3529335 original size:115 final size:112
Alignment explanation
Indices: 3529186--3529581 Score: 485
Period size: 111 Copynumber: 3.6 Consensus size: 112
3529176 AAATTAGGGC
* * *
3529186 TTAGGTTTTATG-GTTTTAAATAGATTAAGTAAATTAGGGTTCTAGAATTTTAAATAAATTAAGT
1 TTAGGGTTTATGTTTTTTAAATAGATTAAGTAAATTAGGGTTCTAGAGTTTTAAATAAATTAAGT
3529250 TAGTGTTTAAAATAAATTAAATTAGGGTTTCAGGTTTAGGGTTTATTAAA
66 TAG-GTTTAAAATAAATTAAATTAGGGTTT--GGTTTAGGGTTTATTAAA
*
3529300 TTAGGGTTTATGTTTTTTAAATAGATTAAGTAAATTAGGGTTCTAGGGTTTTAAATAAATTAAGT
1 TTAGGGTTTATGTTTTTTAAATAGATTAAGTAAATTAGGGTTCTAGAGTTTTAAATAAATTAAGT
* * *
3529365 TAGGATTTTAAATAAATTAAATTAGGG--T--TTT-GGATTTA-GAGAA
66 TAGG-TTTAAAATAAATTAAATTAGGGTTTGGTTTAGGGTTTATTA-AA
*
3529408 TTAGGGCTTATGTTTTTTTTAAAATAGATTAAGTAAATTAGGGTTCTA-AGGTTTTAAATAAATT
1 TTAGGGTTTATG--TTTTTT-AAATAGATTAAGTAAATTAGGGTTCTAGA-GTTTTAAATAAATT
* *
3529472 AAGTTAGGGTTTAAAATAAACTATATTA-GG--T--TTTAGGGTTTATTAAA
62 AAGTTA-GGTTTAAAATAAATTAAATTAGGGTTTGGTTTAGGGTTTATTAAA
* * * *
3529519 TTAGAGTTTATATTTTTTAAATAGATTAAATAAATTAGGGTTCTAGGGTTTTAAATAAATTAA
1 TTAGGGTTTATGTTTTTTAAATAGATTAAGTAAATTAGGGTTCTAGAGTTTTAAATAAATTAA
3529582 AATAGGGATT
Statistics
Matches: 252, Mismatches: 19, Indels: 28
0.84 0.06 0.09
Matches are distributed among these distances:
107 1 0.00
108 61 0.24
109 9 0.04
110 12 0.05
111 80 0.32
112 3 0.01
113 1 0.00
114 12 0.05
115 73 0.29
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (112 bp):
TTAGGGTTTATGTTTTTTAAATAGATTAAGTAAATTAGGGTTCTAGAGTTTTAAATAAATTAAGT
TAGGTTTAAAATAAATTAAATTAGGGTTTGGTTTAGGGTTTATTAAA
Found at i:3529373 original size:22 final size:22
Alignment explanation
Indices: 3529343--3529395 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
3529333 ATTAGGGTTC
*
3529343 TAGGGTTTTAAATAAATTAAGT
1 TAGGGTTTTAAATAAATTAAAT
*
3529365 TAGGATTTTAAATAAATTAAAT
1 TAGGGTTTTAAATAAATTAAAT
3529387 TAGGGTTTT
1 TAGGGTTTT
3529396 GGATTTAGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (22 bp):
TAGGGTTTTAAATAAATTAAAT
Found at i:3529461 original size:111 final size:108
Alignment explanation
Indices: 3529176--3529581 Score: 439
Period size: 115 Copynumber: 3.6 Consensus size: 108
3529166 GGTTTTAAAT
* *
3529176 AAATTAGGGCTTAGGTTTTATGGTTTTAAATAGATTAAGTAAATTAGGGTTCT-AGAATTTTAAA
1 AAATTAGGGCTTATG-TTT-T--TTTTAAATAGATTAAGTAAATTAGGGTTCTAAG-GTTTTAAA
*
3529240 TAAATTAAGTTAGTGTTTAAAATAAATTAAATTAGGGTTTCAGGTTTAGGG
61 TAAATTAAGTTAG-GTTTAAAATAAATTAAATTAGGGTTT-TGGTTTA-GG
* *
3529291 TTTATTAAATTAGGGTTTATG--TTTTTTAAATAGATTAAGTAAATTAGGGTTCTAGGGTTTTAA
1 ------AAATTAGGGCTTATGTTTTTTTTAAATAGATTAAGTAAATTAGGGTTCTAAGGTTTTAA
*
3529354 ATAAATTAAGTTAGGATTTTAAATAAATTAAATTAGGGTTTTGGATTTA-G
60 ATAAATTAAGTTAGG-TTTAAAATAAATTAAATTAGGGTTTTGG-TTTAGG
3529404 AGAATTAGGGCTTATGTTTTTTTTAAAATAGATTAAGTAAATTAGGGTTCTAAGGTTTTAAATAA
1 A-AATTAGGGCTTATGTTTTTTTT-AAATAGATTAAGTAAATTAGGGTTCTAAGGTTTTAAATAA
* * **
3529469 ATTAAGTTAGGGTTTAAAATAAACTATATTA-GGTTTTAGGGTTTATT
64 ATTAAGTTA-GGTTTAAAATAAATTAAATTAGGGTTTT--GGTTTAGG
* * * * *
3529516 AAATTAGAG-TT-TATATTTTTTAAATAGATTAAATAAATTAGGGTTCTAGGGTTTTAAATAAAT
1 AAATTAGGGCTTATGTTTTTTTTAAATAGATTAAGTAAATTAGGGTTCTAAGGTTTTAAATAAAT
3529579 TAA
66 TAA
3529582 AATAGGGATT
Statistics
Matches: 257, Mismatches: 17, Indels: 35
0.83 0.06 0.11
Matches are distributed among these distances:
107 1 0.00
108 56 0.22
109 8 0.03
110 14 0.05
111 75 0.29
112 5 0.02
113 1 0.00
114 3 0.01
115 78 0.30
116 1 0.00
117 1 0.00
118 1 0.00
121 13 0.05
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (108 bp):
AAATTAGGGCTTATGTTTTTTTTAAATAGATTAAGTAAATTAGGGTTCTAAGGTTTTAAATAAAT
TAAGTTAGGTTTAAAATAAATTAAATTAGGGTTTTGGTTTAGG
Found at i:3529506 original size:22 final size:22
Alignment explanation
Indices: 3529456--3529506 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
3529446 TAGGGTTCTA
*
3529456 AGGTTTT-AAATAAATTAAGTT
1 AGGTTTTAAAATAAACTAAGTT
*
3529477 AGGGTTTAAAATAAACTATA-TT
1 AGGTTTTAAAATAAACTA-AGTT
3529499 AGGTTTTA
1 AGGTTTTA
3529507 GGGTTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.24
22 18 0.72
23 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (22 bp):
AGGTTTTAAAATAAACTAAGTT
Found at i:3529607 original size:28 final size:29
Alignment explanation
Indices: 3529543--3529621 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 29
3529533 TTTTAAATAG
* *
3529543 ATTAAATAAATTAGGGTTCTAGGGTTTTAA
1 ATTAATTAAATTAGGGTT-TAGGGTTTAAA
* * *
3529573 ATAAATTAAAATAGGGATTAGGG-TTAAA
1 ATTAATTAAATTAGGGTTTAGGGTTTAAA
3529601 ATTAATTAAATTAGGGTTTAG
1 ATTAATTAAATTAGGGTTTAG
3529622 TTTTTTTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 22 0.54
29 5 0.12
30 14 0.34
ACGTcount: A:0.42, C:0.01, G:0.20, T:0.37
Consensus pattern (29 bp):
ATTAATTAAATTAGGGTTTAGGGTTTAAA
Found at i:3530099 original size:125 final size:127
Alignment explanation
Indices: 3529674--3530176 Score: 705
Period size: 126 Copynumber: 4.0 Consensus size: 127
3529664 CTATTTTTAC
* *
3529674 CCTGAAAAAATAATTTTGAGAAGACATTTCTGAACAAATAGTGTTAAAAACGCTTCAAGCAGGAT
1 CCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGAT
* * * * * * * * *
3529739 GCAATGTCATTAAAA-ATATAGACAAAAGCTCCCACACGAATGCTCTTTTGCTATAGTAGTT
66 GCAATGTCAGTAAAATTTCTAGAAAAAAGCTCCCACATGGACGCTCTTTTTCTACAGTAGTT
*
3529800 CCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAATGCATT-AAGCAGGA
1 CCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGC-TTCAAGCAGGA
* * * * *
3529864 TGCAATGTCAGTAAAAATAC-AGAAAAAAGCTCCCACGTGGACACTCTTTTACTACAGTAGTT
65 TGCAATGTCAGTAAAATTTCTAGAAAAAAGCTCCCACATGGACGCTCTTTTTCTACAGTAGTT
* * * *
3529926 CTTGAAAAAATAATTCTGAGAAGACGTTTCTGAACAAATAGTATCAAAAACGCTTCAAGTAGGAT
1 CCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGAT
* * *
3529991 GCAATGTCAGCAAAATTTCTA-AAAAAAGCTCCCACATGGGCGTTCTTTTTCTACAGTAGTT
66 GCAATGTCAGTAAAATTTCTAGAAAAAAGCTCCCACATGGACGCTCTTTTTCTACAGTAGTT
*
3530052 CCTG-AAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACACTTCAAGCAGGAT
1 CCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGAT
**
3530116 GCAATGTCAGTAAAATTTCT-G-AAAAAGCTCCCATGTGGACGCTCTTTTTCTACAGTAGTT
66 GCAATGTCAGTAAAATTTCTAGAAAAAAGCTCCCACATGGACGCTCTTTTTCTACAGTAGTT
3530176 C
1 C
3530177 AAGCTTGGCC
Statistics
Matches: 334, Mismatches: 38, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
124 36 0.11
125 77 0.23
126 218 0.65
127 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (127 bp):
CCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGAT
GCAATGTCAGTAAAATTTCTAGAAAAAAGCTCCCACATGGACGCTCTTTTTCTACAGTAGTT
Found at i:3530362 original size:9 final size:9
Alignment explanation
Indices: 3530345--3530379 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
3530335 AGTCGCCAAG
*
3530345 TAGATTTTA
1 TAGAATTTA
3530354 TAGAATTTA
1 TAGAATTTA
3530363 TAGAATTTA
1 TAGAATTTA
3530372 TAGAATTT
1 TAGAATTT
3530380 CGTAAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (9 bp):
TAGAATTTA
Found at i:3534337 original size:7 final size:7
Alignment explanation
Indices: 3534327--3534351 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3534317 TTATATACAT
3534327 AATACTA
1 AATACTA
3534334 AATACTA
1 AATACTA
3534341 AATACTA
1 AATACTA
3534348 AATA
1 AATA
3534352 TGAAACGACT
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:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:3535568 original size:21 final size:21
Alignment explanation
Indices: 3535544--3535583 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3535534 CCCTAGGGAG
* *
3535544 AAATTGTAAAGAATTTTTGCT
1 AAATTATAAAGAAATTTTGCT
*
3535565 AAATTATTAAGAAATTTTG
1 AAATTATAAAGAAATTTTG
3535584 TGTGAAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (21 bp):
AAATTATAAAGAAATTTTGCT
Found at i:3536418 original size:18 final size:19
Alignment explanation
Indices: 3536383--3536418 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3536373 CCCCTTCCCC
*
3536383 TTTTTAAAATAAATGTTTT
1 TTTTTAAAATAAAGGTTTT
3536402 TTTTTAAAA-AAAGGTTT
1 TTTTTAAAATAAAGGTTT
3536419 GATCTTGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TTTTTAAAATAAAGGTTTT
Found at i:3537704 original size:30 final size:31
Alignment explanation
Indices: 3537648--3537710 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
3537638 GATAATTTAA
3537648 ATATAAATTATTTAATTTAATTTATTTATAT
1 ATATAAATTATTTAATTTAATTTATTTATAT
* *
3537679 ATATAAA-TATTT-GTTTACTTATATTTATAT
1 ATATAAATTATTTAATTTAATT-TATTTATAT
3537709 AT
1 AT
3537711 TTTTATTAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 6 0.21
30 16 0.55
31 7 0.24
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (31 bp):
ATATAAATTATTTAATTTAATTTATTTATAT
Found at i:3540208 original size:14 final size:15
Alignment explanation
Indices: 3540179--3540219 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
3540169 TGGTTGATGG
3540179 AAATAAAATAATTTC
1 AAATAAAATAATTTC
*
3540194 AAATAAAGT-ATTTC
1 AAATAAAATAATTTC
*
3540208 -AATAAAAAAATT
1 AAATAAAATAATT
3540220 AACTGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 6 0.27
14 8 0.36
15 8 0.36
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (15 bp):
AAATAAAATAATTTC
Found at i:3547618 original size:23 final size:22
Alignment explanation
Indices: 3547569--3547622 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
3547559 TGTTTGATTA
3547569 TAAA-ATA-TTTAAATTAGTTT
1 TAAATATATTTTAAATTAGTTT
3547589 TAAAATATATTTTAAATTAGTGTAT
1 T-AAATATATTTTAAATTAGT-T-T
3547614 T-AATATATT
1 TAAATATATT
3547623 AAAATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 1 0.03
21 3 0.10
22 3 0.10
23 19 0.66
24 1 0.03
25 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (22 bp):
TAAATATATTTTAAATTAGTTT
Found at i:3552160 original size:21 final size:21
Alignment explanation
Indices: 3552134--3552174 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3552124 AGACGAGCGA
* *
3552134 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3552155 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3552175 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3555529 original size:38 final size:38
Alignment explanation
Indices: 3555478--3555550 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
3555468 TTAAATGGCT
3555478 TAATTGCTAACATGTCTTTAGATTAATTGTCATTTAAG
1 TAATTGCTAACATGTCTTTAGATTAATTGTCATTTAAG
3555516 TAATTGCTAACATGTCTTTAGATTAATTGTCATTT
1 TAATTGCTAACATGTCTTTAGATTAATTGTCATTT
3555551 CAGGCATTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (38 bp):
TAATTGCTAACATGTCTTTAGATTAATTGTCATTTAAG
Found at i:3556149 original size:43 final size:43
Alignment explanation
Indices: 3556088--3556183 Score: 192
Period size: 43 Copynumber: 2.2 Consensus size: 43
3556078 ATCTAGAAAT
3556088 TATAGTTGCATGGAGGAAACGAGCAAGTGAGATGACAAGCTCG
1 TATAGTTGCATGGAGGAAACGAGCAAGTGAGATGACAAGCTCG
3556131 TATAGTTGCATGGAGGAAACGAGCAAGTGAGATGACAAGCTCG
1 TATAGTTGCATGGAGGAAACGAGCAAGTGAGATGACAAGCTCG
3556174 TATAGTTGCA
1 TATAGTTGCA
3556184 AGGGCTTTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.34, C:0.14, G:0.31, T:0.21
Consensus pattern (43 bp):
TATAGTTGCATGGAGGAAACGAGCAAGTGAGATGACAAGCTCG
Found at i:3556828 original size:42 final size:42
Alignment explanation
Indices: 3556781--3556867 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
3556771 CCTCATACTT
3556781 AGTCGATTTAAGCAATTGGGCAAATTTCGAATTAAATGTTTA
1 AGTCGATTTAAGCAATTGGGCAAATTTCGAATTAAATGTTTA
3556823 AGTCGATTTAAGCAATTGGGCAAATTTCGAATTAAATGTTTA
1 AGTCGATTTAAGCAATTGGGCAAATTTCGAATTAAATGTTTA
3556865 AGT
1 AGT
3556868 ATATAAATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (42 bp):
AGTCGATTTAAGCAATTGGGCAAATTTCGAATTAAATGTTTA
Found at i:3557785 original size:16 final size:15
Alignment explanation
Indices: 3557760--3557807 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
3557750 CTATTTTAAG
3557760 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
3557775 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
3557792 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
3557807 T
1 T
3557808 ATTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:3558713 original size:18 final size:19
Alignment explanation
Indices: 3558690--3558729 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
3558680 TTCCTTTAAA
3558690 TTATTTCAT-TATTTA-TTT
1 TTATTTCATCT-TTTACTTT
3558708 TTATTTCATCTTTTACTTT
1 TTATTTCATCTTTTACTTT
3558727 TTA
1 TTA
3558730 CCTTTTACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTCATCTTTTACTTT
Found at i:3560231 original size:27 final size:27
Alignment explanation
Indices: 3560193--3560247 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3560183 TTCATGCGCA
3560193 GGTTAAGTATCATTTGATTTGTATGTC
1 GGTTAAGTATCATTTGATTTGTATGTC
3560220 GGTTAAGTATCATTTGATTTGTATGTC
1 GGTTAAGTATCATTTGATTTGTATGTC
3560247 G
1 G
3560248 ATTCAGCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.47
Consensus pattern (27 bp):
GGTTAAGTATCATTTGATTTGTATGTC
Found at i:3568945 original size:11 final size:11
Alignment explanation
Indices: 3568871--3568947 Score: 50
Period size: 11 Copynumber: 6.9 Consensus size: 11
3568861 AAAAATTCAG
3568871 AATAAAATAAT
1 AATAAAATAAT
*
3568882 AAAAAAATAAT
1 AATAAAATAAT
* ** *
3568893 AA-GAGCTGAT
1 AATAAAATAAT
3568903 AAATAAAAT-AT
1 -AATAAAATAAT
**
3568914 AATAAAAATTTGT
1 AAT-AAAA-TAAT
3568927 AATAAAATAAT
1 AATAAAATAAT
3568938 AATAAAATAA
1 AATAAAATAA
3568948 AAAGAGCTCT
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
10 7 0.14
11 32 0.64
12 7 0.14
13 4 0.08
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:3571346 original size:62 final size:63
Alignment explanation
Indices: 3571226--3571368 Score: 155
Period size: 62 Copynumber: 2.3 Consensus size: 63
3571216 ATCACACGGT
* * *
3571226 CTGGGCACACGCCCGTGTGCCTTGGCCGTGTGATCTTAAAGCACAAACAATGAATTACATAGC
1 CTGGGCACACACCCGTGTGCCCTGGCCGTGTGATCTTAAAGCACAAACAATGAATTACACAGC
* * * * * * *
3571289 CTGGGCACACACCTGTGT-CCCTGGCTGTGTGGTTTTTAAA-CACAAACAGTGAGTTACACGGC
1 CTGGGCACACACCCGTGTGCCCTGGCCGTGT-GATCTTAAAGCACAAACAATGAATTACACAGC
* *
3571351 CTGGGCACAAATCCGTGT
1 CTGGGCACACACCCGTGT
3571369 AAACCCTGCA
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
62 43 0.65
63 23 0.35
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (63 bp):
CTGGGCACACACCCGTGTGCCCTGGCCGTGTGATCTTAAAGCACAAACAATGAATTACACAGC
Found at i:3576231 original size:17 final size:19
Alignment explanation
Indices: 3576189--3576232 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3576179 ATGAAATTTT
*
3576189 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
3576208 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
3576226 AA-TATTA
1 AATTATTA
3576233 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:3578059 original size:28 final size:28
Alignment explanation
Indices: 3578027--3578095 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
3578017 GCGTAGATCA
3578027 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
3578055 CGAAATTACCCCTAAAGAGCATAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
3578083 CGATA-TACCCCTA
1 CGAAATTACCCCTA
3578096 GGGTTTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 8 0.21
28 31 0.79
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:3579567 original size:62 final size:62
Alignment explanation
Indices: 3579485--3579687 Score: 199
Period size: 62 Copynumber: 3.3 Consensus size: 62
3579475 GACACGGGAG
* * * * * *
3579485 TGTAGCCAGGCCGTGTAACTCACTGTTGGTGCTTAAAAACCACGCAGCCAGGGGCCCGGGCA
1 TGTACCCAGGCCGTGTAACTCACTGTTTGTGCTTAAAAACCACACAGCCAGGGACACAGGCA
* * * * *
3579547 TGTGCCCAGGCCGTGTAACTCACTATTTGCGCTTAAAAACCACACGGCCAGGGACACAGGCG
1 TGTACCCAGGCCGTGTAACTCACTGTTTGTGCTTAAAAACCACACAGCCAGGGACACAGGCA
* * ** * * * * **
3579609 TGTACCCAGGCCGTATAATTGTCTGTTTGTGCTTAAAGATCACACGGCCAAGGCACACAGGTG
1 TGTACCCAGGCCGTGTAACTCACTGTTTGTGCTTAAAAACCACACAGCC-AGGGACACAGGCA
*
3579672 TGTGCCCAGGCCGTGT
1 TGTACCCAGGCCGTGT
3579688 GACAAGAGGT
Statistics
Matches: 116, Mismatches: 24, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
62 91 0.78
63 25 0.22
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.21
Consensus pattern (62 bp):
TGTACCCAGGCCGTGTAACTCACTGTTTGTGCTTAAAAACCACACAGCCAGGGACACAGGCA
Found at i:3582476 original size:15 final size:16
Alignment explanation
Indices: 3582456--3582485 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3582446 CCTATAATTT
3582456 TTTTTTTGTA-TTTTA
1 TTTTTTTGTACTTTTA
3582471 TTTTTTTGTACTTTT
1 TTTTTTTGTACTTTT
3582486 TCCATCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.10, C:0.03, G:0.07, T:0.80
Consensus pattern (16 bp):
TTTTTTTGTACTTTTA
Found at i:3583330 original size:17 final size:18
Alignment explanation
Indices: 3583308--3583342 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3583298 AAAACTCCTA
*
3583308 AATAATT-TAAAATATTT
1 AATAATTATAAAAAATTT
3583325 AATAATTATAAAAAATTT
1 AATAATTATAAAAAATTT
3583343 TGAATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAATTATAAAAAATTT
Found at i:3597839 original size:41 final size:41
Alignment explanation
Indices: 3597782--3597863 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
3597772 AGATAGTTCG
3597782 GTATAGGACCGGGAACATTTAATAACTTTAAAAAAATTCCT
1 GTATAGGACCGGGAACATTTAATAACTTTAAAAAAATTCCT
3597823 GTATAGGACCGGGAACATTTAATAACTTTAAAAAAATTCCT
1 GTATAGGACCGGGAACATTTAATAACTTTAAAAAAATTCCT
3597864 TACTTAGAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (41 bp):
GTATAGGACCGGGAACATTTAATAACTTTAAAAAAATTCCT
Found at i:3602703 original size:17 final size:17
Alignment explanation
Indices: 3602681--3602769 Score: 64
Period size: 17 Copynumber: 5.4 Consensus size: 17
3602671 GTAGATAAAC
3602681 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
*
3602698 ATTAAAATAACCACTTTAAT
1 ATTAAATTAA--A-TTTAAT
3602718 ATTAAATTAAA---AAT
1 ATTAAATTAAATTTAAT
* * *
3602732 AAT-ATTTAGA--TAAGT
1 ATTAAATTAAATTTAA-T
3602747 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
3602764 ATTAAA
1 ATTAAA
3602770 CTATTAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
13 5 0.09
14 7 0.12
15 3 0.05
16 5 0.09
17 16 0.29
18 4 0.07
19 1 0.02
20 15 0.27
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.40
Consensus pattern (17 bp):
ATTAAATTAAATTTAAT
Done.