Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold401
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: 1910012
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 8 of 13
Found at i:1074715 original size:10 final size:10
Alignment explanation
Indices: 1074700--1074764 Score: 60
Period size: 10 Copynumber: 6.3 Consensus size: 10
1074690 TTTAAAAAAA
1074700 TAAATAAATT
1 TAAATAAATT
1074710 TAAATAAATT
1 TAAATAAATT
*
1074720 TAAA-ATATT
1 TAAATAAATT
* *
1074729 TATTTATAAATA
1 TA--AATAAATT
*
1074741 TAAATAAATC
1 TAAATAAATT
1074751 TAAATAAAATT
1 TAAAT-AAATT
1074762 TAA
1 TAA
1074765 TATTCATATT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
9 6 0.14
10 25 0.57
11 8 0.18
12 5 0.11
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
TAAATAAATT
Found at i:1074747 original size:41 final size:41
Alignment explanation
Indices: 1074684--1074764 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
1074674 AGTTAAAAAT
*
1074684 ATATTTTTTAAAAAAATAAATAAATTTAAAT-AAATTTAAA
1 ATATTTTTTAAAAAAATAAATAAATCTAAATAAAATTTAAA
* *
1074724 ATATTTATTTATAAATATAAATAAATCTAAATAAAATTTAA
1 ATATTT-TTTAAAAAAATAAATAAATCTAAATAAAATTTAA
1074765 TATTCATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 6 0.17
41 22 0.61
42 8 0.22
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (41 bp):
ATATTTTTTAAAAAAATAAATAAATCTAAATAAAATTTAAA
Found at i:1074796 original size:41 final size:38
Alignment explanation
Indices: 1074697--1074796 Score: 96
Period size: 41 Copynumber: 2.5 Consensus size: 38
1074687 TTTTTTAAAA
*
1074697 AAATAAATAAATTTAAATAAATTTAAAATATTTATTTAT
1 AAATAAATAAATATAAATAAATTT-AAATATTTATTTAT
*
1074736 AAATATAAATAAATCTAAATAAAATTT-AATATTCATATTT-T
1 -AA-ATAAATAAATATAAAT-AAATTTAAATATT--TATTTAT
1074777 AAATCAAATAAGATATAAAT
1 AAAT-AAATAA-ATATAAAT
1074797 GATCATTAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
39 2 0.04
40 16 0.31
41 23 0.44
42 11 0.21
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (38 bp):
AAATAAATAAATATAAATAAATTTAAATATTTATTTAT
Found at i:1075403 original size:16 final size:17
Alignment explanation
Indices: 1075377--1075435 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 17
1075367 TTACATAAAA
*
1075377 ATAATAATTAAAATATT
1 ATAAAAATTAAAATATT
* *
1075394 A-AAAAATTAATATAAT
1 ATAAAAATTAAAATATT
*
1075410 ATAAAAATAAAAATA-T
1 ATAAAAATTAAAATATT
*
1075426 ATTAAAATTA
1 ATAAAAATTA
1075436 TTAATATATC
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
16 22 0.65
17 12 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAAAAATTAAAATATT
Found at i:1075424 original size:19 final size:19
Alignment explanation
Indices: 1075371--1075426 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
1075361 TGACTGTTAC
* *
1075371 ATAAAAATAATAATTAAAAT
1 ATAAAAATAA-AAATATAAT
**
1075391 ATTAAAAA-ATTAATATAAT
1 A-TAAAAATAAAAATATAAT
1075410 ATAAAAATAAAAATATA
1 ATAAAAATAAAAATATA
1075427 TTAAAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
18 6 0.21
19 14 0.50
20 2 0.07
21 6 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAAAAATAAAAATATAAT
Found at i:1075444 original size:19 final size:17
Alignment explanation
Indices: 1075389--1075444 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
1075379 AATAATTAAA
1075389 ATATTAAAAAATTAATAT
1 ATATT-AAAAATTAATAT
* *
1075407 A-ATATAAAAATAAAAAT
1 ATAT-TAAAAATTAATAT
1075424 ATATTAAAATTATTAATAT
1 ATATTAAAA--ATTAATAT
1075443 AT
1 AT
1075445 CAAATTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 18 0.60
18 4 0.13
19 8 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATTAAAAATTAATAT
Found at i:1075495 original size:15 final size:18
Alignment explanation
Indices: 1075472--1075516 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
1075462 ATTTATAAAC
*
1075472 ATATTTAAAATAA-AA-A
1 ATATATAAAATAATAATA
1075488 AT-TATAAATATAATAATA
1 ATATATAAA-ATAATAATA
1075506 ATATATAAAAT
1 ATATATAAAAT
1075517 TATCCAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 5 0.21
16 6 0.25
17 2 0.08
18 5 0.21
19 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATATAAAATAATAATA
Found at i:1075681 original size:26 final size:26
Alignment explanation
Indices: 1075651--1075706 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
1075641 TTCATAAATA
1075651 CTTAGCTCCCACGCTTCTTCATTCAC
1 CTTAGCTCCCACGCTTCTTCATTCAC
1075677 CTTAGCTCCCACGCTTCTTCATTCAC
1 CTTAGCTCCCACGCTTCTTCATTCAC
1075703 CTTA
1 CTTA
1075707 TTAATGTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.16, C:0.41, G:0.07, T:0.36
Consensus pattern (26 bp):
CTTAGCTCCCACGCTTCTTCATTCAC
Found at i:1075836 original size:19 final size:20
Alignment explanation
Indices: 1075796--1075837 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1075786 TAAAAATATT
*
1075796 TATTTTAGTTAAATATTTTA
1 TATTTTAGTTAAATATTATA
*
1075816 TATTTTA-TTATATATTATA
1 TATTTTAGTTAAATATTATA
1075835 TAT
1 TAT
1075838 ATAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTTTAGTTAAATATTATA
Found at i:1075893 original size:16 final size:18
Alignment explanation
Indices: 1075858--1075899 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
1075848 TATCAATGTT
*
1075858 TAAATAAAATTATGAATA
1 TAAATATAATTATGAATA
1075876 TAAATATAA-TAT-AATA
1 TAAATATAATTATGAATA
1075892 TAAATATA
1 TAAATATA
1075900 CACAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.52
17 3 0.13
18 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TAAATATAATTATGAATA
Found at i:1076707 original size:17 final size:16
Alignment explanation
Indices: 1076685--1076727 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1076675 TTAATATTCA
1076685 TTTAATTAAAAATTATT
1 TTTAATTAAAAA-TATT
*
1076702 TTTAATT-AATATATT
1 TTTAATTAAAAATATT
1076717 TTATAATTAAA
1 TT-TAATTAAA
1076728 TTTAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 8 0.35
17 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAATTAAAAATATT
Found at i:1076752 original size:19 final size:19
Alignment explanation
Indices: 1076728--1076770 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1076718 TATAATTAAA
1076728 TTTAA-TAAAAATATATTAT
1 TTTAATTAAAAAT-TATTAT
**
1076747 TTTAATTTTAAATTATTAT
1 TTTAATTAAAAATTATTAT
1076766 TTTAA
1 TTTAA
1076771 ATCGAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAATTAAAAATTATTAT
Found at i:1077931 original size:12 final size:12
Alignment explanation
Indices: 1077916--1077958 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
1077906 TATTTTTAAA
1077916 TTTTTATTTATT
1 TTTTTATTTATT
*
1077928 TTTTAATTTATT
1 TTTTTATTTATT
*
1077940 TTTTTAAATTATT
1 TTTTT-ATTTATT
1077953 TTTTTA
1 TTTTTA
1077959 AATTTCATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATTTATT
Found at i:1077944 original size:13 final size:13
Alignment explanation
Indices: 1077916--1077959 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1077906 TATTTTTAAA
1077916 TTTTT-ATTTA-T
1 TTTTTAATTTATT
1077927 TTTTTAATTTATT
1 TTTTTAATTTATT
*
1077940 TTTTTAAATTATT
1 TTTTTAATTTATT
1077953 TTTTTAA
1 TTTTTAA
1077960 ATTTCATTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 5 0.17
12 5 0.17
13 20 0.67
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTAATTTATT
Found at i:1078816 original size:3 final size:3
Alignment explanation
Indices: 1078808--1078854 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1078798 AATTTAATAC
1078808 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1078855 GTTTTGTGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1080870 original size:221 final size:221
Alignment explanation
Indices: 1080487--1080933 Score: 885
Period size: 221 Copynumber: 2.0 Consensus size: 221
1080477 GCTCAAAAAA
1080487 AAAAAAAAATTATAAACAGTTACATTAACTGGAATATGACTGAATATGCTTTAATGGTGTAATAT
1 AAAAAAAAATTATAAACAGTTACATTAACTGGAATATGACTGAATATGCTTTAATGGTGTAATAT
1080552 TGCTTAATATCTTTATATTTCGGTAGAGTGATATTGCTATCTACTTTCTGATTTTGTTTTATTGG
66 TGCTTAATATCTTTATATTTCGGTAGAGTGATATTGCTATCTACTTTCTGATTTTGTTTTATTGG
1080617 TATCGACTGATTGTTTACTGCAGGTTGCTTTAAAAAAATTATAAACAGTTAAAAATCTAAATCCT
131 TATCGACTGATTGTTTACTGCAGGTTGCTTTAAAAAAATTATAAACAGTTAAAAATCTAAATCCT
1080682 AACAGTCTTTAGACGCATCCACAAAC
196 AACAGTCTTTAGACGCATCCACAAAC
*
1080708 AAAAAAAATTTATAAACAGTTACATTAACTGGAATATGACTGAATATGCTTTAATGGTGTAATAT
1 AAAAAAAAATTATAAACAGTTACATTAACTGGAATATGACTGAATATGCTTTAATGGTGTAATAT
1080773 TGCTTAATATCTTTATATTTCGGTAGAGTGATATTGCTATCTACTTTCTGATTTTGTTTTATTGG
66 TGCTTAATATCTTTATATTTCGGTAGAGTGATATTGCTATCTACTTTCTGATTTTGTTTTATTGG
1080838 TATCGACTGATTGTTTACTGCAGGTTGCTTTAAAAAAATTATAAACAGTTAAAAATCTAAATCCT
131 TATCGACTGATTGTTTACTGCAGGTTGCTTTAAAAAAATTATAAACAGTTAAAAATCTAAATCCT
1080903 AACAGTCTTTAGACGCATCCACAAAC
196 AACAGTCTTTAGACGCATCCACAAAC
1080929 AAAAA
1 AAAAA
1080934 TGTAGATTCT
Statistics
Matches: 225, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
221 225 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (221 bp):
AAAAAAAAATTATAAACAGTTACATTAACTGGAATATGACTGAATATGCTTTAATGGTGTAATAT
TGCTTAATATCTTTATATTTCGGTAGAGTGATATTGCTATCTACTTTCTGATTTTGTTTTATTGG
TATCGACTGATTGTTTACTGCAGGTTGCTTTAAAAAAATTATAAACAGTTAAAAATCTAAATCCT
AACAGTCTTTAGACGCATCCACAAAC
Found at i:1083189 original size:16 final size:17
Alignment explanation
Indices: 1083168--1083200 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1083158 ATGGTGTTCG
*
1083168 ATTTTTTTTTG-GTTTA
1 ATTTTTTATTGAGTTTA
1083184 ATTTTTTATTGAGTTTA
1 ATTTTTTATTGAGTTTA
1083201 GTTTGAGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (17 bp):
ATTTTTTATTGAGTTTA
Found at i:1083937 original size:18 final size:18
Alignment explanation
Indices: 1083914--1083951 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1083904 AACTGAGTTA
1083914 AAAAACTGTTTAAATATT
1 AAAAACTGTTTAAATATT
1083932 AAAAACTGTTTAAATATT
1 AAAAACTGTTTAAATATT
1083950 AA
1 AA
1083952 TGCAATGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (18 bp):
AAAAACTGTTTAAATATT
Found at i:1084012 original size:22 final size:23
Alignment explanation
Indices: 1083969--1084012 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
1083959 TTAACGTGTG
*
1083969 ATATAATATAAAATTTTAAATTTT
1 ATATAATAT-AAAGTTTAAATTTT
*
1083993 ATATAATAT-AAGTTTGAATT
1 ATATAATATAAAGTTTAAATT
1084013 AAAGATCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
24 9 0.50
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
ATATAATATAAAGTTTAAATTTT
Found at i:1085875 original size:16 final size:17
Alignment explanation
Indices: 1085851--1085883 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1085841 AGCACGTTGC
1085851 TTTACAAATATA-CTTT
1 TTTACAAATATATCTTT
*
1085867 TTTATAAATATATCTTT
1 TTTACAAATATATCTTT
1085884 ATTTTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTACAAATATATCTTT
Found at i:1085999 original size:15 final size:17
Alignment explanation
Indices: 1085978--1086052 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 17
1085968 TTTATATAAC
1085978 AATAAATT-TTTATTTT
1 AATAAATTATTTATTTT
1085994 -ATAAATTATTTATTTT
1 AATAAATTATTTATTTT
* *
1086010 AATAAAAATAATTATTTTT
1 AAT-AAATTATTTA-TTTT
* *
1086029 ATTAAATAATTTTATTATT
1 AATAAATTA-TTTATT-TT
1086048 AATAA
1 AATAA
1086053 TAAAAATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
15 7 0.15
16 8 0.17
17 2 0.04
18 14 0.30
19 15 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATAAATTATTTATTTT
Found at i:1086007 original size:16 final size:16
Alignment explanation
Indices: 1085978--1086015 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1085968 TTTATATAAC
1085978 AATAAATTTTTATTTT
1 AATAAATTTTTATTTT
1085994 -ATAAATTATTTATTTT
1 AATAAATT-TTTATTTT
1086010 AATAAA
1 AATAAA
1086016 AATAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 8 0.40
17 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATAAATTTTTATTTT
Found at i:1086028 original size:19 final size:19
Alignment explanation
Indices: 1086006--1086063 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
1085996 AAATTATTTA
1086006 TTTTAATAAAAATAATTAT
1 TTTTAATAAAAATAATTAT
* *
1086025 TTTTATTAAATAAT-TTTAT
1 TTTTAATAAA-AATAATTAT
1086044 TATTAATAATAAAAATAATT
1 T-TT--TAATAAAAATAATT
1086064 TAGATATTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 14 0.47
20 5 0.17
21 3 0.10
22 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTAATAAAAATAATTAT
Found at i:1086226 original size:32 final size:32
Alignment explanation
Indices: 1086188--1086260 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
1086178 AATAAGACAT
* * *
1086188 TAAAAATAATTAAATTATCATATACAATATTA
1 TAAAAATAATTAAAATATAATATAAAATATTA
1086220 TAAAAATAATTAAAATATAATATAAAATATTA
1 TAAAAATAATTAAAATATAATATAAAATATTA
*
1086252 -AAATATAAT
1 TAAAAATAAT
1086261 ATATATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 8 0.22
32 29 0.78
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (32 bp):
TAAAAATAATTAAAATATAATATAAAATATTA
Found at i:1086236 original size:20 final size:20
Alignment explanation
Indices: 1086213--1086263 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
1086203 TATCATATAC
*
1086213 AATATTATA-AAAATAATTAA
1 AATATAATATAAAAT-ATTAA
1086233 AATATAATATAAAATATTAA
1 AATATAATATAAAATATTAA
1086253 AATATAATATA
1 AATATAATATA
1086264 TATAAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AATATAATATAAAATATTAA
Found at i:1086258 original size:15 final size:16
Alignment explanation
Indices: 1086238--1086270 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1086228 ATTAAAATAT
1086238 AATATAAAATAT-TAA
1 AATATAAAATATATAA
*
1086253 AATATAATATATATAA
1 AATATAAAATATATAA
1086269 AA
1 AA
1086271 CTACGTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATATAAAATATATAA
Found at i:1092405 original size:2 final size:2
Alignment explanation
Indices: 1092398--1092434 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1092388 TTGCATTCCT
1092398 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1092435 TATTTCCATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1094297 original size:78 final size:78
Alignment explanation
Indices: 1094165--1094786 Score: 836
Period size: 78 Copynumber: 7.9 Consensus size: 78
1094155 TACCAGAACC
* * * * *
1094165 TGTAGTTAAAGACATCAAGGTTGACAACTTTCCATTTGAAGCTGGGTCGCTAGGAAATTCTGAAG
1 TGTAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCTGGATCGCTAGGAATTTCTGAAG
* *
1094230 TTCCCCTTACAGT
66 TTCCCCTGACGGT
* * *
1094243 TGCAGTTAAAGGCATCAAGGTTGAGAATTTTCCAATTGAAGCTGGATTGCTAGGAATTTCTGAAG
1 TGTAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCTGGATCGCTAGGAATTTCTGAAG
1094308 TTCCCCTGACGGT
66 TTCCCCTGACGGT
* * ** * * * *
1094321 TGTAGTTGAAGGTAAGAAGGTTGAGAATTTTCCAATTGAAGCTGGACCACTAGGATTTTCTGAAG
1 TGTAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCTGGATCGCTAGGAATTTCTGAAG
*
1094386 CTCCCCTGACGGT
66 TTCCCCTGACGGT
* * *
1094399 TGTAG-TAGAAGGCGTCAACATCTTGGTTGACAAGTTTCCAATTGAAGCTGGACCGCTAGGAATT
1 TGTAGTTA-AAGGCATC-A-A----GGTTGACAATTTTCCAATTGAAGCTGGATCGCTAGGAATT
*
1094463 TCTGATGTTCCCCTGACGGT
59 TCTGAAGTTCCCCTGACGGT
* * * * *
1094483 TGCAGTTGAAGGCATCAAGGTTGACAATTTTCCAGTTGAAGCTGGACCGCTAGGAATTTCTGATG
1 TGTAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCTGGATCGCTAGGAATTTCTGAAG
* *
1094548 CTT-CCCTGCCGAT
66 -TTCCCCTGACGGT
*
1094561 TGTAGTTGAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCTGGATCGCTAGGAATTTCTGAAG
1 TGTAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCTGGATCGCTAGGAATTTCTGAAG
1094626 TTCCCCTGACGGT
66 TTCCCCTGACGGT
1094639 TGTAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCTGGATCGCTAGGAATTTCTGAAG
1 TGTAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCTGGATCGCTAGGAATTTCTGAAG
*
1094704 TTTCCCTGACGGT
66 TTCCCCTGACGGT
* *
1094717 TGTAGTTAAAGGCATCAAGGTTGACAATTTTCCATTTGAAG-TGGGATTGCTAGGAATTTCTGAA
1 TGTAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCT-GGATCGCTAGGAATTTCTGAA
1094781 GTTCCC
65 GTTCCC
1094787 ACAACAGTCA
Statistics
Matches: 484, Mismatches: 49, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
77 4 0.01
78 408 0.84
79 3 0.01
80 1 0.00
82 1 0.00
83 1 0.00
84 65 0.13
85 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (78 bp):
TGTAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCTGGATCGCTAGGAATTTCTGAAG
TTCCCCTGACGGT
Found at i:1094606 original size:240 final size:234
Alignment explanation
Indices: 1094165--1094786 Score: 872
Period size: 240 Copynumber: 2.6 Consensus size: 234
1094155 TACCAGAACC
* * * *
1094165 TGTAGTTAAAGACATCAAGGTTGACAACTTTCCATTTGAAGCTGGGTCGCTAGGAAATTCTGAAG
1 TGTAGTTAAAGGCATCAAGGTTGACAACTTTCCAATTGAAGCTGGATCGCTAGGAATTTCTGAAG
* * *
1094230 TTCCCCTTACAGTTGCAGTTAAAGGCATCAAGGTTGAGAATTTTCCAATTGAAGCTGGATTGCTA
66 TTCCCCTGACGGTTGCAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCTGGATTGCTA
* * * *
1094295 GGAATTTCTGAAGTTCCCCTGACGGTTGTAGTTGAAGGTAAGAAGGTTGAGAATTTTCCAATTGA
131 GGAATTTCTGAAGTTCCCCTGACGATTGTAGTTGAAGGCAACAAGGTTGACAATTTTCCAATTGA
*
1094360 AGCTGGACCACTAGGATTTTCTGAAGCTCCCCTGACGGT
196 AGCTGGACCACTAGGAATTTCTGAAGCTCCCCTGACGGT
* * *
1094399 TGTAG-TAGAAGGCGTCAACATCTTGGTTGACAAGTTTCCAATTGAAGCTGGACCGCTAGGAATT
1 TGTAGTTA-AAGGCATC-A-A----GGTTGACAACTTTCCAATTGAAGCTGGATCGCTAGGAATT
* * *
1094463 TCTGATGTTCCCCTGACGGTTGCAGTTGAAGGCATCAAGGTTGACAATTTTCCAGTTGAAGCTGG
59 TCTGAAGTTCCCCTGACGGTTGCAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCTGG
** * * *
1094528 ACCGCTAGGAATTTCTGATGCTT-CCCTGCCGATTGTAGTTGAAGGCATCAAGGTTGACAATTTT
124 ATTGCTAGGAATTTCTGAAG-TTCCCCTGACGATTGTAGTTGAAGGCAACAAGGTTGACAATTTT
* * *
1094592 CCAATTGAAGCTGGATCGCTAGGAATTTCTGAAGTTCCCCTGACGGT
188 CCAATTGAAGCTGGACCACTAGGAATTTCTGAAGCTCCCCTGACGGT
*
1094639 TGTAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCTGGATCGCTAGGAATTTCTGAAG
1 TGTAGTTAAAGGCATCAAGGTTGACAACTTTCCAATTGAAGCTGGATCGCTAGGAATTTCTGAAG
* * *
1094704 TTTCCCTGACGGTTGTAGTTAAAGGCATCAAGGTTGACAATTTTCCATTTGAAG-TGGGATTGCT
66 TTCCCCTGACGGTTGCAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCT-GGATTGCT
1094768 AGGAATTTCTGAAGTTCCC
130 AGGAATTTCTGAAGTTCCC
1094787 ACAACAGTCA
Statistics
Matches: 340, Mismatches: 37, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
233 5 0.01
234 126 0.37
235 1 0.00
236 1 0.00
238 1 0.00
239 1 0.00
240 201 0.59
241 4 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (234 bp):
TGTAGTTAAAGGCATCAAGGTTGACAACTTTCCAATTGAAGCTGGATCGCTAGGAATTTCTGAAG
TTCCCCTGACGGTTGCAGTTAAAGGCATCAAGGTTGACAATTTTCCAATTGAAGCTGGATTGCTA
GGAATTTCTGAAGTTCCCCTGACGATTGTAGTTGAAGGCAACAAGGTTGACAATTTTCCAATTGA
AGCTGGACCACTAGGAATTTCTGAAGCTCCCCTGACGGT
Found at i:1098668 original size:2 final size:2
Alignment explanation
Indices: 1098663--1098687 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1098653 GCAAAGTGAA
1098663 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 A
1098688 AGTGAACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1104706 original size:17 final size:18
Alignment explanation
Indices: 1104686--1104723 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1104676 ACACAAAAAC
1104686 ATATATAAAT-AAATAAA
1 ATATATAAATAAAATAAA
* *
1104703 ATATTTATATAAAATAAA
1 ATATATAAATAAAATAAA
1104721 ATA
1 ATA
1104724 ATCAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATATAAATAAAATAAA
Found at i:1108480 original size:35 final size:36
Alignment explanation
Indices: 1108416--1108500 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
1108406 TATTAATAAA
* * *
1108416 ATTAATAATATTATTTTATTATAAAATAATTT-TTTT
1 ATTAATAATA-AATTTTAATATAAAATAATTTAATTT
**
1108452 ATTTTTAATAAATTTTAATA-AAAGATAATTTAATTT
1 ATTAATAATAAATTTTAATATAAA-ATAATTTAATTT
1108488 ATTAATAATAAAT
1 ATTAATAATAAAT
1108501 AAGAAACTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
34 3 0.08
35 15 0.38
36 22 0.55
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (36 bp):
ATTAATAATAAATTTTAATATAAAATAATTTAATTT
Found at i:1108749 original size:19 final size:19
Alignment explanation
Indices: 1108725--1108845 Score: 56
Period size: 19 Copynumber: 6.4 Consensus size: 19
1108715 ATTGCATAAA
1108725 AATATTTATAATATAATAT
1 AATATTTATAATATAATAT
1108744 AATA--T-TAATAT-ATA-
1 AATATTTATAATATAATAT
* * *
1108758 AATATTTAAAAAATTATAT
1 AATATTTATAATATAATAT
* * ** *
1108777 AATATATATTAATTTTTTTAA
1 AATATTTA-TAA-TATAATAT
*
1108798 AATATAATTATAATATAATAA
1 AATAT--TTATAATATAATAT
* *
1108819 AATATATA-AATATGATAT
1 AATATTTATAATATAATAT
1108837 AAATATTTA
1 -AATATTTA
1108846 ATTTATTAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
14 4 0.05
15 3 0.04
16 7 0.09
17 5 0.07
18 11 0.14
19 20 0.26
20 2 0.03
21 19 0.25
22 3 0.04
23 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.45
Consensus pattern (19 bp):
AATATTTATAATATAATAT
Found at i:1108855 original size:57 final size:59
Alignment explanation
Indices: 1108739--1108855 Score: 136
Period size: 59 Copynumber: 2.0 Consensus size: 59
1108729 TTTATAATAT
* * *
1108739 AATATAATATTAATATATAAATATTTAAAAAATTATATAATATATATTAATTTTTTTAA
1 AATATAATATTAATATATAAATATATAAAAAATGATATAATATATATTAATTTTATTAA
*
1108798 AATATAAT-TATAATATAATAAA-ATATATAAATATGATATAA-ATAT-TTAA-TTTATTAA
1 AATATAATAT-TAATAT-ATAAATATATA-AAAAATGATATAATATATATTAATTTTATTAA
1108855 A
1 A
1108856 TTTAAATAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
57 8 0.16
58 5 0.10
59 22 0.43
60 16 0.31
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (59 bp):
AATATAATATTAATATATAAATATATAAAAAATGATATAATATATATTAATTTTATTAA
Found at i:1109412 original size:11 final size:12
Alignment explanation
Indices: 1109395--1109427 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1109385 TATCTTAATA
1109395 ATAAATAAATTT
1 ATAAATAAATTT
1109407 -TAAAT-AATTT
1 ATAAATAAATTT
1109417 ATAAATAAATT
1 ATAAATAAATT
1109428 AAATTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.26
11 10 0.53
12 4 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAAATAAATTT
Found at i:1109463 original size:24 final size:24
Alignment explanation
Indices: 1109431--1109479 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1109421 ATAAATTAAA
* *
1109431 TTTATTAAATTTATATTAAAATTT
1 TTTAATAAATATATATTAAAATTT
*
1109455 TTTAATAAATATATTTTAAAATTT
1 TTTAATAAATATATATTAAAATTT
1109479 T
1 T
1109480 ATCTATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTAATAAATATATATTAAAATTT
Found at i:1109479 original size:22 final size:22
Alignment explanation
Indices: 1109393--1109480 Score: 60
Period size: 24 Copynumber: 4.1 Consensus size: 22
1109383 TATATCTTAA
* * *
1109393 TAATAAATAAATTTTAAATAATT
1 TAATAAATATATATTAAA-ATTT
1109416 T-ATAAATA-A-ATT-AAA-TT
1 TAATAAATATATATTAAAATTT
* *
1109433 TATTAAATTTATATTAAAATTTTT
1 TAATAAATATATATTAAAA--TTT
*
1109457 TAATAAATATATTTTAAAATTT
1 TAATAAATATATATTAAAATTT
1109479 TA
1 TA
1109481 TCTATATTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
17 3 0.06
18 6 0.12
19 3 0.06
20 5 0.10
21 4 0.08
22 12 0.23
23 1 0.02
24 18 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAATAAATATATATTAAAATTT
Found at i:1109492 original size:23 final size:22
Alignment explanation
Indices: 1109431--1109493 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
1109421 ATAAATTAAA
*
1109431 TTTATTAAATTTATATTAAAATTT
1 TTTATTAAATTTATTTTAAAA--T
* *
1109455 TTTAATAAATATATTTTAAAAT
1 TTTATTAAATTTATTTTAAAAT
*
1109477 TTTATCTATATTTATTT
1 TTTAT-TAAATTTATTT
1109494 ATTTAATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
22 5 0.16
23 9 0.28
24 18 0.56
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTATTAAATTTATTTTAAAAT
Found at i:1113342 original size:2 final size:2
Alignment explanation
Indices: 1113330--1113359 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1113320 TTCATGTATG
*
1113330 AT AT GT 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 AT AT
1113360 TTATTTGCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1119402 original size:82 final size:82
Alignment explanation
Indices: 1119314--1119472 Score: 309
Period size: 82 Copynumber: 1.9 Consensus size: 82
1119304 ATATATGTTC
*
1119314 ATATTCGGTACTACCTCGAATCCAGATCATGAGAAGCAACAACATACCCATTGCTGGAATGGGAT
1 ATATTCGGTACTACCTCGAATCCAGATCATGAGAAGCAACAACATACCCATTGCAGGAATGGGAT
1119379 AAATAAAAAATATTCAT
66 AAATAAAAAATATTCAT
1119396 ATATTCGGTACTACCTCGAATCCAGATCATGAGAAGCAACAACATACCCATTGCAGGAATGGGAT
1 ATATTCGGTACTACCTCGAATCCAGATCATGAGAAGCAACAACATACCCATTGCAGGAATGGGAT
1119461 AAATAAAAAATA
66 AAATAAAAAATA
1119473 AGTAGTTGAC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (82 bp):
ATATTCGGTACTACCTCGAATCCAGATCATGAGAAGCAACAACATACCCATTGCAGGAATGGGAT
AAATAAAAAATATTCAT
Found at i:1120877 original size:15 final size:15
Alignment explanation
Indices: 1120857--1120889 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1120847 TTTGATATTA
1120857 TAATTATCTTAAATT
1 TAATTATCTTAAATT
*
1120872 TAATTATTTTAAATT
1 TAATTATCTTAAATT
1120887 TAA
1 TAA
1120890 ATAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTATCTTAAATT
Found at i:1120908 original size:16 final size:15
Alignment explanation
Indices: 1120865--1120910 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1120855 TATAATTATC
* **
1120865 TTAAATTTAATTATT
1 TTAAATTTAAATAAA
1120880 TTAAATTTAAATAAA
1 TTAAATTTAAATAAA
1120895 TTAAATTATAAATAAA
1 TTAAATT-TAAATAAA
1120911 ATTTATTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 19 0.70
16 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTAAATTTAAATAAA
Found at i:1124418 original size:15 final size:17
Alignment explanation
Indices: 1124382--1124421 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1124372 GATTGGCATA
1124382 TATTATATAATAATTAT
1 TATTATATAATAATTAT
*
1124399 TATTATTTAA-AATT-T
1 TATTATATAATAATTAT
1124414 TATTATAT
1 TATTATAT
1124422 TTAATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 4 0.19
17 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTATATAATAATTAT
Found at i:1124422 original size:17 final size:18
Alignment explanation
Indices: 1124395--1124451 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
1124385 TATATAATAA
1124395 TTATTATTATTTAA-AATT
1 TTATTA-TATTTAATAATT
1124413 TTATTATATTTAATAATT
1 TTATTATATTTAATAATT
*
1124431 TAATTTATATTT-AT-ATT
1 TTA-TTATATTTAATAATT
1124448 TTAT
1 TTAT
1124452 AATTAATACA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 1 0.03
17 12 0.34
18 14 0.40
19 8 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATTATATTTAATAATT
Found at i:1124431 original size:25 final size:25
Alignment explanation
Indices: 1124409--1124455 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1124399 TATTATTTAA
1124409 AATTT-TA-TTATATTTAATAATTT
1 AATTTATATTTATATTTAATAATTT
*
1124432 AATTTATATTTATATTTTATAATT
1 AATTTATATTTATATTTAATAATT
1124456 AATACAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 14 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
AATTTATATTTATATTTAATAATTT
Found at i:1127215 original size:12 final size:12
Alignment explanation
Indices: 1127198--1127229 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1127188 TAGTGGTGTA
1127198 ATTTATATATAT
1 ATTTATATATAT
1127210 ATTTATATATAT
1 ATTTATATATAT
*
1127222 ATATATAT
1 ATTTATAT
1127230 TTGTTTTGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATATATAT
Found at i:1131379 original size:13 final size:13
Alignment explanation
Indices: 1131363--1131390 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1131353 ATTTTTTAAA
1131363 AATATTTATGTTT
1 AATATTTATGTTT
1131376 AATATTTATGTTT
1 AATATTTATGTTT
1131389 AA
1 AA
1131391 ATATGAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (13 bp):
AATATTTATGTTT
Found at i:1132212 original size:46 final size:41
Alignment explanation
Indices: 1132179--1132264 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
1132169 TTATTTCATA
* * **
1132179 TAAAAATAAATATAATATATATAATTAAATATATTAAAATTT
1 TAAAAAAAAATATAATATACAT-ATTAAATATATTATTATTT
* *
1132221 TAAATAAAAATATAATATACATATTAAATATATTATTATAT
1 TAAAAAAAAATATAATATACATATTAAATATATTATTATTT
1132262 TAA
1 TAA
1132265 TTATATTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
41 19 0.50
42 19 0.50
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (41 bp):
TAAAAAAAAATATAATATACATATTAAATATATTATTATTT
Found at i:1132255 original size:9 final size:9
Alignment explanation
Indices: 1132185--1132319 Score: 72
Period size: 9 Copynumber: 15.6 Consensus size: 9
1132175 CATATAAAAA
*
1132185 TAAATATAA
1 TAAATATAT
*
1132194 TATATATAAT
1 TAAATAT-AT
1132204 TAAATATAT
1 TAAATATAT
*
1132213 TAAA-ATTT
1 TAAATATAT
1132221 TAAATA-A-
1 TAAATATAT
*
1132228 -AAATATAA
1 TAAATATAT
* *
1132236 TATACATAT
1 TAAATATAT
1132245 TAAATATAT
1 TAAATATAT
*
1132254 T-ATTATAT
1 TAAATATAT
*
1132262 TAATTATATT
1 TAAATATA-T
*
1132272 TAAATGTAT
1 TAAATATAT
1132281 TATAATAT-T
1 TA-AATATAT
*
1132290 TACATTATAT
1 TA-AATATAT
1132300 T-AAT-T-T
1 TAAATATAT
*
1132306 TAAATTTAT
1 TAAATATAT
1132315 TAAAT
1 TAAAT
1132320 TAAAATATTT
Statistics
Matches: 97, Mismatches: 17, Indels: 24
0.70 0.12 0.17
Matches are distributed among these distances:
6 7 0.07
7 5 0.05
8 17 0.18
9 48 0.49
10 20 0.21
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (9 bp):
TAAATATAT
Found at i:1132281 original size:27 final size:29
Alignment explanation
Indices: 1132244--1132300 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 29
1132234 AATATACATA
*
1132244 TTAAATATATTATTATA-TTA-ATTATAT
1 TTAAATATATTATAATATTTACATTATAT
*
1132271 TTAAATGTATTATAATATTTACATTATAT
1 TTAAATATATTATAATATTTACATTATAT
1132300 T
1 T
1132301 AATTTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 15 0.58
28 3 0.12
29 8 0.31
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (29 bp):
TTAAATATATTATAATATTTACATTATAT
Found at i:1132890 original size:3 final size:3
Alignment explanation
Indices: 1132882--1132913 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1132872 CCACAAAGTA
*
1132882 AAT AAT AAT AAT AAT AAT AAT AAT AAT CAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1132914 GCAAACAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1133175 original size:15 final size:15
Alignment explanation
Indices: 1133157--1133203 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
1133147 TATAAAAAAT
1133157 TTAAATATATTTTTA
1 TTAAATATATTTTTA
1133172 TTAAATATATATTTATA
1 TTAAATATAT-TTT-TA
* *
1133189 TTTAATATTTTTTTA
1 TTAAATATATTTTTA
1133204 ATTATATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.43
16 6 0.21
17 10 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAAATATATTTTTA
Found at i:1142768 original size:52 final size:46
Alignment explanation
Indices: 1142712--1142835 Score: 106
Period size: 48 Copynumber: 2.5 Consensus size: 46
1142702 TTGAAATTTT
1142712 AATTTAATTTAATTTTTATTATTAAATAATAATTTAAATAAAATTAATAGTA
1 AATTTAATTTAATTTTTATTA--AAAT-ATAATTT-AATAAAATTAA-A-TA
** * *
1142764 AATTT-ATAAAATTTTTACTTAAAATTTAATTTTATAAAATTAAATA
1 AATTTAATTTAATTTTTA-TTAAAATATAATTTAATAAAATTAAATA
* * *
1142810 AATTTATTTTTAATTTATATTTAAAT
1 AATTTA-ATTTAATTTTTATTAAAAT
1142836 CGATAGAATA
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
46 7 0.12
47 7 0.12
48 18 0.30
49 6 0.10
50 4 0.07
51 10 0.17
52 8 0.13
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.51
Consensus pattern (46 bp):
AATTTAATTTAATTTTTATTAAAATATAATTTAATAAAATTAAATA
Found at i:1143130 original size:26 final size:25
Alignment explanation
Indices: 1143079--1143131 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
1143069 TTATCATATG
** **
1143079 AATAATTTTAAAATTAATTATTTTA
1 AATAATTTTAAAATTAAAAAAATTA
1143104 AATAATTTTAAAAATTAAAAAAATTA
1 AATAATTTT-AAAATTAAAAAAATTA
1143130 AA
1 AA
1143132 AAAAATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AATAATTTTAAAATTAAAAAAATTA
Found at i:1144115 original size:20 final size:19
Alignment explanation
Indices: 1144047--1144115 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 19
1144037 AAAAGTTAAG
1144047 AAATAAATATA-AATAATTAT
1 AAATAAATATATAA-AATT-T
*
1144067 AAAT-AATATCATCAAATTT
1 AAATAAATAT-ATAAAATTT
* *
1144086 ATTATTAATATATAAAATTT
1 A-AATAAATATATAAAATTT
1144106 AACATAAATA
1 AA-ATAAATA
1144116 ATACATCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 7 0.18
20 26 0.67
21 6 0.15
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATAAATATATAAAATTT
Found at i:1144845 original size:32 final size:33
Alignment explanation
Indices: 1144779--1144845 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
1144769 CGTTCTGCTT
*
1144779 ACCCTGCTTGTGATCCCTCCGTGGAAAATCACA
1 ACCCTGCTTGTGATCCCTCCATGGAAAATCACA
* * *
1144812 ACCCTGCTTGTGAT-GCTCTATGGAAAATGACA
1 ACCCTGCTTGTGATCCCTCCATGGAAAATCACA
1144844 AC
1 AC
1144846 TAACCCACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (33 bp):
ACCCTGCTTGTGATCCCTCCATGGAAAATCACA
Found at i:1153114 original size:21 final size:20
Alignment explanation
Indices: 1153063--1153114 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
1153053 AATAAATGAT
*
1153063 AATATTTTA-TTAATATTTA
1 AATAATTTATTTAATATTTA
*
1153082 AATAATTT-TTTAATATTATT
1 AATAATTTATTTAATATT-TA
*
1153102 AATTATTTATTTA
1 AATAATTTATTTA
1153115 TTATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 15 0.56
20 8 0.30
21 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
AATAATTTATTTAATATTTA
Found at i:1154446 original size:13 final size:13
Alignment explanation
Indices: 1154423--1154465 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
1154413 GAGAAAATGA
1154423 TTAAA-TTAAAAT
1 TTAAATTTAAAAT
* *
1154435 TTGAGTTTAAAAT
1 TTAAATTTAAAAT
1154448 TTAAATTTAAAAT
1 TTAAATTTAAAAT
1154461 TTAAA
1 TTAAA
1154466 ATTATTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 3 0.12
13 23 0.88
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (13 bp):
TTAAATTTAAAAT
Found at i:1154452 original size:7 final size:7
Alignment explanation
Indices: 1154440--1154468 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1154430 AAAATTTGAG
1154440 TTTAAAA
1 TTTAAAA
1154447 TTT-AAA
1 TTTAAAA
1154453 TTTAAAA
1 TTTAAAA
1154460 TTTAAAA
1 TTTAAAA
1154467 TT
1 TT
1154469 ATTTATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTTAAAA
Found at i:1154521 original size:16 final size:15
Alignment explanation
Indices: 1154491--1154527 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
1154481 ATTTATTTAC
1154491 ATTTAAAAATATAAA
1 ATTTAAAAATATAAA
*
1154506 ATTTAATAAATTTAAA
1 ATTTAA-AAATATAAA
1154522 ATTTAA
1 ATTTAA
1154528 CTTTTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTAAAAATATAAA
Found at i:1163462 original size:2 final size:2
Alignment explanation
Indices: 1163455--1163488 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1163445 TTTTATTAGA
1163455 AT AT AT AT 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 AT AT AT AT
1163489 CTATTGAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1165088 original size:2 final size:2
Alignment explanation
Indices: 1165070--1165123 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
1165060 AAACAAGCAA
1165070 TC TC -C TC T- TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1165109 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
1165124 TAACTTCTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1165568 original size:2 final size:2
Alignment explanation
Indices: 1165561--1165586 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1165551 CACCTCCTGG
1165561 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1165587 GCTTTTCAGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1178990 original size:14 final size:14
Alignment explanation
Indices: 1178973--1179000 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1178963 ATATAAAAAA
1178973 TTATATTTTAATAT
1 TTATATTTTAATAT
1178987 TTATATTTTAATAT
1 TTATATTTTAATAT
1179001 ATATTAAATA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATATTTTAATAT
Found at i:1179062 original size:3 final size:3
Alignment explanation
Indices: 1179054--1179084 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1179044 TTTAATACAC
1179054 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1179085 GCTTTGCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1179957 original size:20 final size:20
Alignment explanation
Indices: 1179932--1179986 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
1179922 GTTTGAGATA
*
1179932 ATGTATCGATAAAATTCTTC
1 ATGTATCGATAAAATTCTGC
* * *
1179952 ATGTATTGAT-ACATTGTGC
1 ATGTATCGATAAAATTCTGC
1179971 ATGTATCGATACAAAT
1 ATGTATCGATA-AAAT
1179987 AGTGGTAGGG
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 15 0.56
20 9 0.33
21 3 0.11
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (20 bp):
ATGTATCGATAAAATTCTGC
Found at i:1180622 original size:3 final size:3
Alignment explanation
Indices: 1180614--1180647 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1180604 TCTCTAATAG
1180614 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1180648 AGGGTCAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1182487 original size:3 final size:3
Alignment explanation
Indices: 1182479--1182509 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1182469 TTATGATATC
1182479 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1182510 CTTTTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1182762 original size:17 final size:17
Alignment explanation
Indices: 1182733--1182805 Score: 68
Period size: 17 Copynumber: 4.6 Consensus size: 17
1182723 ATATGTCAAT
1182733 AAATAAATCATTTATATA
1 AAATAAAT-ATTTATATA
1182751 AAATAAATATTT-T-TA
1 AAATAAATATTTATATA
1182766 AAA-AAAT-TTTA-AT-
1 AAATAAATATTTATATA
***
1182779 TTTTAAATATTTATATA
1 AAATAAATATTTATATA
1182796 AAATAAATAT
1 AAATAAATAT
1182806 AAAACACATA
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
13 3 0.07
14 9 0.21
15 9 0.21
16 3 0.07
17 11 0.26
18 8 0.19
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATAAATATTTATATA
Found at i:1183167 original size:16 final size:17
Alignment explanation
Indices: 1183126--1183173 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1183116 TATATATATA
*
1183126 TATATATAAAATATAAT
1 TATATTTAAAATATAAT
1183143 TATATTTAAAATATTAA-
1 TATATTTAAAATA-TAAT
*
1183160 TA-ATTTAAATTATA
1 TATATTTAAAATATA
1183174 TAAATTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 2 0.07
16 9 0.32
17 14 0.50
18 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATATTTAAAATATAAT
Found at i:1183209 original size:28 final size:28
Alignment explanation
Indices: 1183168--1183256 Score: 91
Period size: 26 Copynumber: 3.4 Consensus size: 28
1183158 AATAATTTAA
**
1183168 ATTATATAAATTTATATATTTATATAAT
1 ATTATATTTATTTATATATTTATATAAT
1183196 ATTTATATTT-TTTAT-TATTT-TATAAT
1 A-TTATATTTATTTATATATTTATATAAT
* *
1183222 A-TATATTTATTT-CATATTTA-ATATT
1 ATTATATTTATTTATATATTTATATAAT
1183247 ATTATATTTA
1 ATTATATTTA
1183257 CCCACATATT
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
24 7 0.13
25 13 0.25
26 15 0.29
27 5 0.10
28 6 0.12
29 6 0.12
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTATATTTATTTATATATTTATATAAT
Found at i:1183227 original size:35 final size:36
Alignment explanation
Indices: 1183178--1183249 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 36
1183168 ATTATATAAA
* **
1183178 TTTATATATTTATATAATATTT-ATATTTTTTATTAT
1 TTTATATATATATAT-ATATTTCATATTTAATATTAT
*
1183214 TTTATA-ATATATATTTATTTCATATTTAATATTAT
1 TTTATATATATATATATATTTCATATTTAATATTAT
1183249 T
1 T
1183250 ATATTTACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
34 5 0.16
35 20 0.65
36 6 0.19
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (36 bp):
TTTATATATATATATATATTTCATATTTAATATTAT
Found at i:1189233 original size:79 final size:79
Alignment explanation
Indices: 1189102--1189254 Score: 234
Period size: 79 Copynumber: 1.9 Consensus size: 79
1189092 TGGTATCACC
* * *
1189102 AAGATGCATTTGATTCAATGTAATTGTGATGACATGCATTATACAAGTGAATCAAGAAGGAATTC
1 AAGATGCATTTGATTCAATGTAATTGTAATGAAATGCATTATACAAGAGAATCAAGAAGGAATTC
1189167 TGTATTTTTCCTTT
66 TGTATTTTTCCTTT
*** * *
1189181 AAGATGCATTTGATTGTCTGTAATTGTAATGAAATGCATTATATAAGAGAATCAAGAAGGGATTC
1 AAGATGCATTTGATTCAATGTAATTGTAATGAAATGCATTATACAAGAGAATCAAGAAGGAATTC
1189246 TGTATTTTT
66 TGTATTTTT
1189255 TTTTTTTTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 66 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (79 bp):
AAGATGCATTTGATTCAATGTAATTGTAATGAAATGCATTATACAAGAGAATCAAGAAGGAATTC
TGTATTTTTCCTTT
Found at i:1195781 original size:22 final size:23
Alignment explanation
Indices: 1195739--1195781 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1195729 TAGAAATTAA
*
1195739 TTTAAAAATAAAAAAGTAAAATT
1 TTTAAAAATAAAAAAGAAAAATT
*
1195762 TTTAAAAAT-AATAAGAAAAA
1 TTTAAAAATAAAAAAGAAAAA
1195782 AATTAAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (23 bp):
TTTAAAAATAAAAAAGAAAAATT
Found at i:1195782 original size:23 final size:22
Alignment explanation
Indices: 1195739--1195780 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1195729 TAGAAATTAA
1195739 TTTAAAAATAAAAAAGTAAAATT
1 TTTAAAAATAAAAAAG-AAAATT
*
1195762 TTTAAAAAT-AATAAGAAAA
1 TTTAAAAATAAAAAAGAAAA
1195781 AAATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 5 0.28
23 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (22 bp):
TTTAAAAATAAAAAAGAAAATT
Found at i:1196545 original size:2 final size:2
Alignment explanation
Indices: 1196533--1196566 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1196523 CCACAAAACA
*
1196533 AT AT GT AT 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 AT AT AT AT
1196567 CCTTCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1200761 original size:2 final size:2
Alignment explanation
Indices: 1200756--1200792 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1200746 TTTTTTTAAA
*
1200756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1200793 GATTTCAGTT
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:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1202787 original size:23 final size:24
Alignment explanation
Indices: 1202753--1202800 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
1202743 ATTTTATCAG
1202753 TTTATTTTTATTT-AATT-AATTT
1 TTTATTTTTATTTCAATTGAATTT
1202775 TTTATTTTTTATTTCAATTGAATTT
1 TTTA-TTTTTATTTCAATTGAATTT
1202800 T
1 T
1202801 AACTCTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.17
23 9 0.39
24 4 0.17
25 6 0.26
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTATTTTTATTTCAATTGAATTT
Found at i:1203189 original size:19 final size:20
Alignment explanation
Indices: 1203155--1203194 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1203145 GTCTAATGAC
1203155 AAAATTAAATAAAAAA-TTA
1 AAAATTAAATAAAAAACTTA
* *
1203174 AAAATTAATTATAAAACTTA
1 AAAATTAAATAAAAAACTTA
1203194 A
1 A
1203195 TCAAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATTAAATAAAAAACTTA
Found at i:1203933 original size:19 final size:19
Alignment explanation
Indices: 1203905--1203989 Score: 66
Period size: 19 Copynumber: 4.3 Consensus size: 19
1203895 TGAATTTAAA
*
1203905 TTTTAATATTTATAAATAT
1 TTTTATTATTTATAAATAT
1203924 TTTTATTA-TTATAAATAAAT
1 TTTTATTATTTATAAAT--AT
* * *
1203944 TTTAATAATTTATATATAT
1 TTTTATTATTTATAAATAT
*
1203963 TTTAATTATATT-TAAAGTTAT
1 TTTTATTAT-TTATAAA--TAT
1203984 TTTTAT
1 TTTTAT
1203990 AAAAATTTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
18 8 0.15
19 20 0.38
20 10 0.19
21 15 0.28
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (19 bp):
TTTTATTATTTATAAATAT
Found at i:1204053 original size:25 final size:23
Alignment explanation
Indices: 1204025--1204071 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1204015 TATTATATAA
*
1204025 ATTTTAAAATATTTATTTTTATATT
1 ATTTT-AAA-ATTTAATTTTATATT
*
1204050 ATTTTATAATTTAATTTTATAT
1 ATTTTAAAATTTAATTTTATAT
1204072 CATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 2 0.10
25 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTTTAAAATTTAATTTTATATT
Found at i:1204061 original size:23 final size:24
Alignment explanation
Indices: 1204035--1204080 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1204025 ATTTTAAAAT
* *
1204035 ATTTATTTTTATATTAT-TTTATA
1 ATTTAATTTTATATCATATTTATA
1204058 ATTTAATTTTATATCATATTTAT
1 ATTTAATTTTATATCATATTTAT
1204081 TTATTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTTAATTTTATATCATATTTATA
Found at i:1204094 original size:19 final size:19
Alignment explanation
Indices: 1204066--1204103 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1204056 TAATTTAATT
1204066 TTATATCATATT-TATTTA
1 TTATATCATATTATATTTA
1204084 TTATAATCATATTATATTTA
1 TTAT-ATCATATTATATTTA
1204104 ATATTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATATCATATTATATTTA
Found at i:1204448 original size:3 final size:3
Alignment explanation
Indices: 1204440--1204464 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1204430 GACGCCCACA
1204440 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1204465 TTGAAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1204688 original size:20 final size:21
Alignment explanation
Indices: 1204628--1204690 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
1204618 GTTGATATAT
1204628 TAAATAATAATTTTT-AATAAA
1 TAAATAAT-ATTTTTAAATAAA
* *
1204649 TATAAAAATATTATAATAAATAAA
1 TA-AATAATATT-T-TTAAATAAA
1204673 -AAATAATATTTTTAAATA
1 TAAATAATATTTTTAAATA
1204691 TGATACGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
20 6 0.18
21 6 0.18
22 14 0.41
23 2 0.06
24 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATAATATTTTTAAATAAA
Found at i:1205292 original size:18 final size:18
Alignment explanation
Indices: 1205279--1205326 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
1205269 AATTATTTAT
*
1205279 ATATTAAATTTTATATAA
1 ATATAAAATTTTATATAA
*
1205297 ATATAAAATTTTTTA-AA
1 ATATAAAATTTTATATAA
1205314 CATAATAAAATTT
1 -AT-ATAAAATTT
1205327 ATGAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 2 0.08
18 15 0.58
19 9 0.35
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATAAAATTTTATATAA
Found at i:1205956 original size:27 final size:25
Alignment explanation
Indices: 1205910--1205979 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 25
1205900 GTTAAATTAA
*
1205910 ATTATT-ATTTAATAATAAAAATAT
1 ATTATTAATATAATAATAAAAATAT
* *
1205934 TTTATTTAAATATAATTATAAAAATAT
1 ATTA-TT-AATATAATAATAAAAATAT
*
1205961 ATTATTAATATAAAAATAA
1 ATTATTAATATAATAATAA
1205980 TTTTTAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
24 3 0.08
25 13 0.35
26 2 0.05
27 19 0.51
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTATTAATATAATAATAAAAATAT
Found at i:1205986 original size:18 final size:19
Alignment explanation
Indices: 1205950--1205989 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1205940 TAAATATAAT
1205950 TATAAAAATATATTATTAA
1 TATAAAAATATATTATTAA
*
1205969 TATAAAAATA-ATTTTTAA
1 TATAAAAATATATTATTAA
1205987 TAT
1 TAT
1205990 TTCATTTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATAAAAATATATTATTAA
Found at i:1208235 original size:13 final size:13
Alignment explanation
Indices: 1208207--1208255 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
1208197 ACTCAAAGGA
**
1208207 TAAAAATTATAAT
1 TAAAAATTATTTT
1208220 TAAAAATTATTTT
1 TAAAAATTATTTT
* *
1208233 TAATAGTTATTTT
1 TAAAAATTATTTT
*
1208246 TTAAAATTAT
1 TAAAAATTAT
1208256 GTGTCTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
TAAAAATTATTTT
Found at i:1209941 original size:4 final size:4
Alignment explanation
Indices: 1209934--1209958 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1209924 TTCTCTTTTG
1209934 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
1209959 ATGGCTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:1210531 original size:21 final size:21
Alignment explanation
Indices: 1210502--1210542 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1210492 TATAATTTAC
1210502 ATAAAT-AAATAATAAAATATG
1 ATAAATAAAATAA-AAAATATG
*
1210523 ATAATTAAAATAAAAAATAT
1 ATAAATAAAATAAAAAATAT
1210543 AAATTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
ATAAATAAAATAAAAAATATG
Found at i:1214090 original size:20 final size:20
Alignment explanation
Indices: 1214042--1214102 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1214032 ATTAAGTATT
* *
1214042 ATTATATTAAAATATATAA-A
1 ATTATAATAAAATA-AAAATA
**
1214062 ATATATAATATTATAAAAATA
1 AT-TATAATAAAATAAAAATA
1214083 ATTATAATAAAATAAAAATA
1 ATTATAATAAAATAAAAATA
1214103 TATGAATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 21 0.64
21 12 0.36
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTATAATAAAATAAAAATA
Found at i:1214286 original size:2 final size:2
Alignment explanation
Indices: 1214279--1214316 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1214269 TAATAAACTA
1214279 AT AT AT AT AT AT 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 AT AT AT AT AT AT
1214317 TAAAACTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1214798 original size:22 final size:21
Alignment explanation
Indices: 1214773--1214819 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1214763 TATCCAACCA
1214773 TAATATCAATCGC-ACCAATAAC
1 TAATATCAA-CGCTA-CAATAAC
*
1214795 TAATTTCAACGCTACAATAAC
1 TAATATCAACGCTACAATAAC
1214816 TAAT
1 TAAT
1214820 CTTCGTATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.45, C:0.23, G:0.04, T:0.28
Consensus pattern (21 bp):
TAATATCAACGCTACAATAAC
Found at i:1226938 original size:157 final size:159
Alignment explanation
Indices: 1226630--1226949 Score: 509
Period size: 157 Copynumber: 2.0 Consensus size: 159
1226620 GTTTCATCCA
* * *
1226630 CTTGAAACATAGGCAATAAAGAGCTGGGCCATTGGGTTAATGAGCTGAATTTTTTTTTTGTATTT
1 CTTGAAACATAGGCAAT--AGAGCTGAGCCATTGGGTTAATGAGCTGAATTTTTTTTTTGCATCT
*
1226695 TTGTAGCAATGGCTCTTCTGGTGTTTCGAGAATATCTAGCACATGTGGATCTTATCGATCGATCT
64 TTGTAGCAAGGGCTCTTCTGGTGTTTCGAGAATATCTAGCACATGTGGATCTTATCGATCGATCT
* *
1226760 ATTTACAAATTAGTCAAAAATGAATTATTGG
129 ATCTACAAATTAATCAAAAATGAATTATTGG
*
1226791 CTTGAAACATAGGGAAT-GAGCTGAGCCATTGGGTTAATGAGCTG-ATTTTTTTTTTGCATCTTT
1 CTTGAAACATAGGCAATAGAGCTGAGCCATTGGGTTAATGAGCTGAATTTTTTTTTTGCATCTTT
* *
1226854 GTGGCAAGGGCTCTTTTGGTGTTTCGAGAATATCTAGCACATGTGGATCTTATCGATCGATCTAT
66 GTAGCAAGGGCTCTTCTGGTGTTTCGAGAATATCTAGCACATGTGGATCTTATCGATCGATCTAT
**
1226919 CTACAAATTAATCTCAAATGAATTATTGG
131 CTACAAATTAATCAAAAATGAATTATTGG
1226948 CT
1 CT
1226950 AGGTTGATAA
Statistics
Matches: 148, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
157 106 0.72
158 26 0.18
161 16 0.11
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (159 bp):
CTTGAAACATAGGCAATAGAGCTGAGCCATTGGGTTAATGAGCTGAATTTTTTTTTTGCATCTTT
GTAGCAAGGGCTCTTCTGGTGTTTCGAGAATATCTAGCACATGTGGATCTTATCGATCGATCTAT
CTACAAATTAATCAAAAATGAATTATTGG
Found at i:1227061 original size:20 final size:20
Alignment explanation
Indices: 1227036--1227077 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1227026 TTTATAAAAA
*
1227036 ATTT-AAATATTTTTATTTTT
1 ATTTAAAATA-TTATATTTTT
1227056 ATTTAAAATATTATATTTTT
1 ATTTAAAATATTATATTTTT
1227076 AT
1 AT
1227078 ATATTTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTAAAATATTATATTTTT
Found at i:1227113 original size:21 final size:21
Alignment explanation
Indices: 1227095--1227134 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1227085 TGACATATTA
1227095 ATATT-TTATTTTAT-TATAT
1 ATATTATTATTTTATATATAT
1227114 ATATTCATTATTTTATATATA
1 ATATT-ATTATTTTATATATA
1227135 AGAGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATTATTATTTTATATATAT
Found at i:1227231 original size:37 final size:38
Alignment explanation
Indices: 1227190--1227266 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 38
1227180 ATTTAAAATA
*
1227190 TTATAAATCTATGTAATATTTATAAATTTT-T-TTATAT
1 TTATAAATCTATATAATATTTAT-AATTTTATATTATAT
* * * *
1227227 TTATATATTTATATCATATTTATTATTTTATATTATAT
1 TTATAAATCTATATAATATTTATAATTTTATATTATAT
1227265 TT
1 TT
1227267 TAATTATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
36 5 0.15
37 20 0.61
38 8 0.24
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (38 bp):
TTATAAATCTATATAATATTTATAATTTTATATTATAT
Found at i:1227247 original size:19 final size:19
Alignment explanation
Indices: 1227205--1227266 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
1227195 AATCTATGTA
* *
1227205 ATATTTATAAATTT-TTTT
1 ATATTTATATATTTATATT
*
1227223 ATATTTATATATTTATATC
1 ATATTTATATATTTATATT
1227242 ATATTTAT-TATTTTATATT
1 ATATTTATATA-TTTATATT
1227261 ATATTT
1 ATATTT
1227267 TAATTATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 15 0.39
19 23 0.61
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
ATATTTATATATTTATATT
Found at i:1227274 original size:21 final size:19
Alignment explanation
Indices: 1227223--1227276 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
1227213 AAATTTTTTT
1227223 ATATTTA-TATATTTATATC
1 ATATTTATTAT-TTTATATC
*
1227242 ATATTTATTATTTTATATT
1 ATATTTATTATTTTATATC
1227261 ATATTTTAATTATTTT
1 ATA-TTT-ATTATTTT
1227277 TTAATTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 17 0.55
20 6 0.19
21 8 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
ATATTTATTATTTTATATC
Found at i:1227309 original size:24 final size:24
Alignment explanation
Indices: 1227221--1227309 Score: 78
Period size: 24 Copynumber: 3.7 Consensus size: 24
1227211 ATAAATTTTT
*
1227221 TTATATTTATATATTTATA-TCATA
1 TTAT-TTTTTATATTTATATTCATA
*
1227245 TTTATTATTTTATA-TTATATT-TTAA
1 -TTATT-TTTTATATTTATATTCAT-A
*
1227270 TTATTTTTTA-ATTTTATATTCGTA
1 TTATTTTTTATA-TTTATATTCATA
1227294 TTATTTTTTATATTTA
1 TTATTTTTTATATTTA
1227310 ATGTATTAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
22 1 0.02
23 5 0.09
24 34 0.63
25 14 0.26
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.66
Consensus pattern (24 bp):
TTATTTTTTATATTTATATTCATA
Found at i:1227411 original size:21 final size:21
Alignment explanation
Indices: 1227385--1227440 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1227375 TAGATATTTG
1227385 TATTATATTTATGTTATTTTT
1 TATTATATTTATGTTATTTTT
* *
1227406 TATTATGTTT-TAATTATTTTT
1 TATTATATTTAT-GTTATTTTT
1227427 TATT-TATATTATGT
1 TATTATAT-TTATGT
1227441 CATATTGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 3 0.11
21 24 0.86
22 1 0.04
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (21 bp):
TATTATATTTATGTTATTTTT
Found at i:1227433 original size:11 final size:11
Alignment explanation
Indices: 1227392--1227433 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1227382 TTGTATTATA
1227392 TTTATGTTATTT
1 TTTAT-TTATTT
*
1227404 TTTA-TTATGT
1 TTTATTTATTT
*
1227414 TTTAATTATTT
1 TTTATTTATTT
1227425 TTTATTTAT
1 TTTATTTAT
1227434 ATTATGTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 9 0.35
11 13 0.50
12 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (11 bp):
TTTATTTATTT
Found at i:1227657 original size:23 final size:21
Alignment explanation
Indices: 1227610--1227660 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
1227600 AATATTCGTG
*
1227610 TTATTTTTTATATTTAAAATA
1 TTATTTTTTACATTTAAAATA
1227631 TTATATTTTTACATATTAATAAT-
1 TTAT-TTTTTACAT-TTAA-AATA
1227654 TTATTTT
1 TTATTTT
1227661 ATTTTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.15
22 11 0.42
23 8 0.31
24 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTTTTTACATTTAAAATA
Found at i:1227758 original size:11 final size:11
Alignment explanation
Indices: 1227736--1227777 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1227726 TGGTAAGATG
1227736 AAAAGAAAAGAA
1 AAAAG-AAAGAA
*
1227748 AAAAGAGAGAA
1 AAAAGAAAGAA
1227759 AAAA-AAAGAA
1 AAAAGAAAGAA
1227769 AGAAAGAAA
1 A-AAAGAAA
1227778 ATTTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 6 0.23
11 12 0.46
12 8 0.31
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAGAAAGAA
Found at i:1227759 original size:21 final size:22
Alignment explanation
Indices: 1227735--1227775 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1227725 TTGGTAAGAT
*
1227735 GAAAAGAAAAGAAA-AAAGAGA
1 GAAAAAAAAAGAAAGAAAGAGA
1227756 GAAAAAAAAAGAAAGAAAGA
1 GAAAAAAAAAGAAAGAAAGA
1227776 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (22 bp):
GAAAAAAAAAGAAAGAAAGAGA
Found at i:1227765 original size:14 final size:15
Alignment explanation
Indices: 1227737--1227778 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
1227727 GGTAAGATGA
1227737 AAAGAAAAGAAAAAAG
1 AAAG-AAAGAAAAAAG
*
1227753 AGAGAAA-AAAAAAG
1 AAAGAAAGAAAAAAG
1227767 AAAGAAAGAAAA
1 AAAGAAAGAAAA
1227779 TTTTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 13 0.57
15 7 0.30
16 3 0.13
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAAAG
Found at i:1228801 original size:36 final size:38
Alignment explanation
Indices: 1228736--1228810 Score: 100
Period size: 36 Copynumber: 2.0 Consensus size: 38
1228726 AAATCAATCG
* *
1228736 AAATATATAATACTATTATTGACATATAAAAAATTATAT
1 AAATATATAATAC-ATTATTGACACATAAAAAATAATAT
*
1228775 AAATTTATAATA-ATT-TTGACACATAAAAAATAATAT
1 AAATATATAATACATTATTGACACATAAAAAATAATAT
1228811 GAACACATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 19 0.58
37 3 0.09
39 11 0.33
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (38 bp):
AAATATATAATACATTATTGACACATAAAAAATAATAT
Found at i:1229549 original size:21 final size:23
Alignment explanation
Indices: 1229507--1229554 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1229497 TAAGAAAAAA
**
1229507 TTTTTATATATTTGTATATATAT
1 TTTTTATATAAATGTATATATAT
1229530 TTTTTATATAAAT-TAT-TATAT
1 TTTTTATATAAATGTATATATAT
1229551 TTTT
1 TTTT
1229555 ATAATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 3 0.13
23 11 0.48
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTATATAAATGTATATATAT
Found at i:1229910 original size:16 final size:17
Alignment explanation
Indices: 1229868--1229910 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1229858 TTTAATATTT
*
1229868 ATAAAATTTTTAATGAA
1 ATAAAATTTATAATGAA
*
1229885 ATAAAA-TTATAAT-TA
1 ATAAAATTTATAATGAA
1229900 ATAAAATTTAT
1 ATAAAATTTAT
1229911 TTAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
ATAAAATTTATAATGAA
Found at i:1230638 original size:14 final size:14
Alignment explanation
Indices: 1230615--1230644 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1230605 GATCACCAGA
*
1230615 TATATGTAAAATTT
1 TATATATAAAATTT
1230629 TATATATAAAATTT
1 TATATATAAAATTT
1230643 TA
1 TA
1230645 ATACTTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
TATATATAAAATTT
Found at i:1231171 original size:12 final size:12
Alignment explanation
Indices: 1231154--1231219 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
1231144 GATCTAAAAG
*
1231154 TTTATATTATTA
1 TTTATATTAATA
1231166 TTTATATTAATA
1 TTTATATTAATA
* * *
1231178 TTAAAAATTAAATT
1 TT-TATATT-AATA
*
1231192 TTTATTTTAATA
1 TTTATATTAATA
* *
1231204 TTTATAATAAAA
1 TTTATATTAATA
1231216 TTTA
1 TTTA
1231220 AATAAAAAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
12 29 0.71
13 7 0.17
14 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTATATTAATA
Found at i:1231215 original size:32 final size:33
Alignment explanation
Indices: 1231160--1231222 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
1231150 AAAGTTTATA
* *
1231160 TTATTATTTATATTAATATTAAAAATTAAATTT
1 TTATTATTAATATTAATAATAAAAATTAAATTT
* *
1231193 TTATT-TTAATATTTATAATAAAATTTAAAT
1 TTATTATTAATATTAATAATAAAAATTAAAT
1231223 AAAAAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TTATTATTAATATTAATAATAAAAATTAAATTT
Found at i:1231216 original size:26 final size:26
Alignment explanation
Indices: 1231166--1231218 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1231156 TATATTATTA
*
1231166 TTTATATTAATATTAAAAATTAAATT
1 TTTATATTAATATTAAAAATAAAATT
* * *
1231192 TTTATTTTAATATTTATAATAAAATT
1 TTTATATTAATATTAAAAATAAAATT
1231218 T
1 T
1231219 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTATATTAATATTAAAAATAAAATT
Found at i:1236428 original size:29 final size:29
Alignment explanation
Indices: 1236374--1236429 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1236364 AATAATGTAA
* *
1236374 TAAATATTATATATATTTTATTTTTATTT
1 TAAATATTATATATATTTAATATTTATTT
*
1236403 TAAATTTTA-ATATATTTAATAATTTAT
1 TAAATATTATATATATTTAAT-ATTTAT
1236430 ATTATATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TAAATATTATATATATTTAATATTTATTT
Found at i:1239910 original size:24 final size:24
Alignment explanation
Indices: 1239880--1239926 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1239870 TTAGAGGTAC
1239880 TTATAGATTAAGTTATTTATTTAT
1 TTATAGATTAAGTTATTTATTTAT
1239904 TTATAGATTAAGTTATTTATTTA
1 TTATAGATTAAGTTATTTATTTA
1239927 AAATTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (24 bp):
TTATAGATTAAGTTATTTATTTAT
Found at i:1239993 original size:19 final size:18
Alignment explanation
Indices: 1239962--1240005 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
1239952 TAAAGATTTT
1239962 AAAA-AAATATTAAGTTTAA
1 AAAATAAATATTAAG--TAA
1239981 AAAATAAAT-TTAAGTAA
1 AAAATAAATATTAAGTAA
1239998 AAAATAAA
1 AAAATAAA
1240006 ATTTGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.46
19 9 0.38
20 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
AAAATAAATATTAAGTAA
Found at i:1240015 original size:17 final size:17
Alignment explanation
Indices: 1239977--1240017 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
1239967 AATATTAAGT
1239977 TTAAAAAATAAATTTAAG
1 TTAAAAAATAAATTT-AG
1239995 -TAAAAAATAAAATTT-G
1 TTAAAAAAT-AAATTTAG
1240011 TTAAAAA
1 TTAAAAA
1240018 GTAACCAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.05
17 14 0.67
18 6 0.29
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
TTAAAAAATAAATTTAG
Found at i:1240669 original size:6 final size:6
Alignment explanation
Indices: 1240658--1240731 Score: 53
Period size: 6 Copynumber: 11.7 Consensus size: 6
1240648 ATATATAATG
* *
1240658 ATATAA ATATAA ATATAAA AAATTAA GATATATT ATATAA ATAT-- ATATAA
1 ATATAA ATATAA ATAT-AA ATA-TAA -ATATA-A ATATAA ATATAA ATATAA
*
1240708 TATATAC ATATTAA ATATAA ATAT
1 -ATATAA ATA-TAA ATATAA ATAT
1240732 TTTTAGAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
4 4 0.07
6 24 0.44
7 23 0.43
8 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:1240676 original size:28 final size:28
Alignment explanation
Indices: 1240644--1240731 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 28
1240634 ATTTGATATG
1240644 ATAAATATATAATGATATAAATATAAAT
1 ATAAATATATAATGATATAAATATAAAT
* *
1240672 ATAAA-AAATTAA-GATATATTATATAAATAT
1 ATAAATATA-TAATGATATA-AATAT-AA-AT
1240702 ATATAATATATACAT-AT-TAAATATAAAT
1 ATA-AATATATA-ATGATATAAATATAAAT
1240730 AT
1 AT
1240732 TTTTAGAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
27 8 0.17
28 16 0.33
29 4 0.08
30 9 0.19
31 6 0.12
32 5 0.10
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (28 bp):
ATAAATATATAATGATATAAATATAAAT
Done.