Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 171 of 250
Found at i:54813901 original size:13 final size:13
Alignment explanation
Indices: 54813858--54813901 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
54813848 TTGATTTTTG
54813858 AAAAACAGAAATT
1 AAAAACAGAAATT
*
54813871 AAAAGCAGAAATT
1 AAAAACAGAAATT
*
54813884 GAAAACAGAAATT
1 AAAAACAGAAATT
54813897 AAAAA
1 AAAAA
54813902 TACCTCGGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.68, C:0.07, G:0.11, T:0.14
Consensus pattern (13 bp):
AAAAACAGAAATT
Found at i:54814011 original size:73 final size:74
Alignment explanation
Indices: 54813882--54814048 Score: 248
Period size: 73 Copynumber: 2.3 Consensus size: 74
54813872 AAAGCAGAAA
* * * *
54813882 TTGAAAA-CAGAAATTAAAAATACCTCGGCATGCCCTGAGGCTCAGCTCACCTCTCGCAATATGA
1 TTGAAAAGCATAAATTGAAAATACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
54813946 GTTGA-TTT
66 GTTAATTTT
* * *
54813954 TTGAAAAGCATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAGCATAAATTGAAAATACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
54814019 GTTAATTTT
66 GTTAATTTT
54814028 TTGAAAAGCATAAATTGAAAA
1 TTGAAAAGCATAAATTGAAAA
54814049 AACCGAAATT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
72 7 0.08
73 54 0.64
74 23 0.27
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (74 bp):
TTGAAAAGCATAAATTGAAAATACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTAATTTT
Found at i:54814140 original size:91 final size:89
Alignment explanation
Indices: 54813965--54814141 Score: 259
Period size: 91 Copynumber: 2.0 Consensus size: 89
54813955 TGAAAAGCAT
* *
54813965 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCCCAACTCACCTCTCGCAATATGAGTTAATTTTTT
* *
54814030 GAAAAGCATAAATTGAAAAAACCG
66 GAAAAGCAGAAATTAAAAAAACCG
*
54814054 AAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATTGAAAATACCTCAGCGTGT--CCTGAGGCCCAACTCACCTCTCGCAATATGAGTT-AATTT
54814119 TTTG-AAAGACAGAAA-TAAAAAAA
63 TTTGAAAAG-CAGAAATTAAAAAAA
54814142 TCAAAATACC
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
89 22 0.28
91 44 0.56
92 13 0.16
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (89 bp):
AAATTGAAAATACCTCAGCGTGTCCTGAGGCCCAACTCACCTCTCGCAATATGAGTTAATTTTTT
GAAAAGCAGAAATTAAAAAAACCG
Found at i:54826151 original size:25 final size:25
Alignment explanation
Indices: 54826123--54826170 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
54826113 CCAATCTTGG
*
54826123 ATTTCAGGTCAAGTCAGGTTTGAAA
1 ATTTCAGGTCAAGTCAGCTTTGAAA
*
54826148 ATTTCAGTTCAAGTCAGCTTTGA
1 ATTTCAGGTCAAGTCAGCTTTGA
54826171 TTGGTTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (25 bp):
ATTTCAGGTCAAGTCAGCTTTGAAA
Found at i:54847762 original size:16 final size:15
Alignment explanation
Indices: 54847736--54847770 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
54847726 TGATGTGAAT
54847736 AATATAAAATATTAA
1 AATATAAAATATTAA
*
54847751 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
54847767 AATA
1 AATA
54847771 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:54848043 original size:25 final size:25
Alignment explanation
Indices: 54847921--54848138 Score: 107
Period size: 25 Copynumber: 8.9 Consensus size: 25
54847911 TACGTGATAA
* *
54847921 TATTAAAAATATATACACAATATAG
1 TATTAAAGATATATACATAATATAG
* * * *
54847946 TGTAAAAAATACATACATAATATA-
1 TATTAAAGATATATACATAATATAG
*
54847970 -ATTAAA-ATATATACATAAGATAACATG
1 TATTAAAGATATATACAT-A-AT-ATA-G
* * * *
54847997 TAAAATATATATATATAAATAATATAG
1 T--ATTAAAGATATATACATAATATAG
*
54848024 TATTAAAGATATATACATAAAATAG
1 TATTAAAGATATATACATAATATAG
* *
54848049 TA-T-AATATATATACGTAATATAG
1 TATTAAAGATATATACATAATATAG
* * *
54848072 AATT-TAGA-ATATACCTAATATA-
1 TATTAAAGATATATACATAATATAG
* * *
54848094 T-TAAAAGAATATATATATAATATAA
1 TATTAAAG-ATATATACATAATATAG
*
54848119 TATT-AAGAAATATA-ATAATA
1 TATTAAAGATATATACATAATA
54848139 ACAAAAAAAA
Statistics
Matches: 147, Mismatches: 31, Indels: 32
0.70 0.15 0.15
Matches are distributed among these distances:
21 1 0.01
22 11 0.07
23 43 0.29
24 24 0.16
25 47 0.32
26 1 0.01
27 2 0.01
28 2 0.01
29 2 0.01
30 5 0.03
31 9 0.06
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.34
Consensus pattern (25 bp):
TATTAAAGATATATACATAATATAG
Found at i:54848114 original size:24 final size:23
Alignment explanation
Indices: 54848087--54848138 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
54848077 AGAATATACC
*
54848087 TAATATATTA-AAAGAATATATATA
1 TAATATAATATAAAGAA-ATATA-A
*
54848111 TAATATAATATTAAGAAATATAA
1 TAATATAATATAAAGAAATATAA
54848134 TAATA
1 TAATA
54848139 ACAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 14 0.56
25 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (23 bp):
TAATATAATATAAAGAAATATAA
Found at i:54848703 original size:30 final size:30
Alignment explanation
Indices: 54848618--54848716 Score: 135
Period size: 30 Copynumber: 3.3 Consensus size: 30
54848608 GAGGTATAAG
* * *
54848618 TGGTGGTTGAGCAAGTGTGGCTAGTAGAGC
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
54848648 AGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
54848678 TGATGGTGGAGCAAGTGTGGTTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
54848708 TGGTGGTGG
1 TGGTGGTGG
54848717 CAAAGGCTAG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.19, C:0.06, G:0.47, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:54852709 original size:22 final size:25
Alignment explanation
Indices: 54852659--54852717 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 25
54852649 TTCTGTAATT
*
54852659 TAAAAA-AATATTATTTTTACATAA
1 TAAAAATAAAATTATTTTTACATAA
*
54852683 TAAAAATTAAATTATTTTTA-AT-A
1 TAAAAATAAAATTATTTTTACATAA
54852706 -AAAAATAAAATT
1 TAAAAATAAAATT
54852718 TTGGATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 11 0.35
23 1 0.03
24 8 0.26
25 11 0.35
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
TAAAAATAAAATTATTTTTACATAA
Found at i:54855068 original size:29 final size:29
Alignment explanation
Indices: 54855000--54855065 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
54854990 AATCTATATA
* * *
54855000 TTTATAATTTTTAAGGGATAAATTAAATT
1 TTTATTATTTTTAAGGGATAAAATAAAAT
54855029 TTTATTATTTTTAAGGGACTAAAAATAAAAT
1 TTTATTATTTTTAAGGGA-T-AAAATAAAAT
54855060 TTTATT
1 TTTATT
54855066 TTTACTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 17 0.53
30 1 0.03
31 14 0.44
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (29 bp):
TTTATTATTTTTAAGGGATAAAATAAAAT
Found at i:54860738 original size:16 final size:16
Alignment explanation
Indices: 54860717--54860755 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
54860707 CAAAATAAAT
*
54860717 TAAACTTGAAATGATC
1 TAAACTCGAAATGATC
* *
54860733 TGAACTCGAATTGATC
1 TAAACTCGAAATGATC
54860749 TAAACTC
1 TAAACTC
54860756 AAAACAACTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (16 bp):
TAAACTCGAAATGATC
Found at i:54862047 original size:13 final size:13
Alignment explanation
Indices: 54862029--54862055 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54862019 TCAATTGTTG
54862029 TTTCAATTTTTTT
1 TTTCAATTTTTTT
54862042 TTTCAATTTTTTT
1 TTTCAATTTTTTT
54862055 T
1 T
54862056 ATTTAGGTCT
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:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTCAATTTTTTT
Found at i:54862051 original size:12 final size:12
Alignment explanation
Indices: 54862017--54862055 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
54862007 AGAACAGCAA
* *
54862017 TTTCAATTGTTG
1 TTTCAATTTTTT
54862029 TTTCAATTTTTTT
1 TTTCAA-TTTTTT
54862042 TTTCAATTTTTT
1 TTTCAATTTTTT
54862054 TT
1 TT
54862056 ATTTAGGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (12 bp):
TTTCAATTTTTT
Found at i:54862201 original size:19 final size:19
Alignment explanation
Indices: 54862177--54862238 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
54862167 GAGTACTTTA
*
54862177 TTATTTATTTACGTTCAAT
1 TTATTTATTTACGTTTAAT
* *
54862196 TTATTT-TTTTCAATTTAA-
1 TTATTTATTTAC-GTTTAAT
54862214 TTATTTATTTACGTTTAAT
1 TTATTTATTTACGTTTAAT
54862233 TTATTT
1 TTATTT
54862239 TTTCCAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 15 0.43
19 20 0.57
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (19 bp):
TTATTTATTTACGTTTAAT
Found at i:54862219 original size:18 final size:19
Alignment explanation
Indices: 54862193--54862249 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
54862183 ATTTACGTTC
54862193 AATTTATTTTTTTCAATTT
1 AATTTATTTTTTTCAATTT
* *
54862212 AA-TTATTTATTT-ACGTTT
1 AATTTATTTTTTTCA-ATTT
*
54862230 AATTTATTTTTTCCAATTT
1 AATTTATTTTTTTCAATTT
54862249 A
1 A
54862250 TCTTAACGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
17 1 0.03
18 14 0.47
19 14 0.47
20 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (19 bp):
AATTTATTTTTTTCAATTT
Found at i:54862226 original size:37 final size:37
Alignment explanation
Indices: 54862176--54862249 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
54862166 TGAGTACTTT
*
54862176 ATTATTTATTTACGTTCAATTTATTTTTTTCAATTTA
1 ATTATTTATTTACGTTCAATTTATTTTTTCCAATTTA
*
54862213 ATTATTTATTTACGTTTAATTTATTTTTTCCAATTTA
1 ATTATTTATTTACGTTCAATTTATTTTTTCCAATTTA
54862250 TCTTAACGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (37 bp):
ATTATTTATTTACGTTCAATTTATTTTTTCCAATTTA
Found at i:54862249 original size:19 final size:19
Alignment explanation
Indices: 54862193--54862249 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
54862183 ATTTACGTTC
*
54862193 AATTTATTTTTTTCAATTT
1 AATTTATTTTTTACAATTT
*
54862212 AA-TTATTTATTTAC-GTTT
1 AATTTATTT-TTTACAATTT
*
54862230 AATTTATTTTTTCCAATTT
1 AATTTATTTTTTACAATTT
54862249 A
1 A
54862250 TCTTAACGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (19 bp):
AATTTATTTTTTACAATTT
Found at i:54863680 original size:22 final size:22
Alignment explanation
Indices: 54863655--54863696 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
54863645 TGGTCATATA
54863655 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
54863677 ATAATTTATTATTTTAATAA
1 ATAAATTATTAATATAATAA
54863697 TTTATTTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:54863734 original size:13 final size:14
Alignment explanation
Indices: 54863718--54863759 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
54863708 TTTCAATTTT
54863718 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
54863731 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
54863746 ATTTTAAATAATAT
1 ATTTT-AATAATAT
54863760 TATTCACATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:54863744 original size:16 final size:16
Alignment explanation
Indices: 54863722--54863758 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
54863712 AATTTTATTT
54863722 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
54863739 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
54863754 TAATA
1 TAATA
54863759 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:54863811 original size:15 final size:15
Alignment explanation
Indices: 54863791--54863847 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
54863781 ATTCAATATT
54863791 AATATTTTAATAATA
1 AATATTTTAATAATA
*
54863806 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
54863825 AATATATTAATAATA
1 AATATTTTAATAATA
*
54863840 AATGTTTT
1 AATATTTT
54863848 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:54866936 original size:15 final size:15
Alignment explanation
Indices: 54866911--54866947 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
54866901 TGGTTTTTTC
54866911 ATTTTTA-TTGAAAT
1 ATTTTTATTTGAAAT
*
54866925 ATTTTTATTTGATAT
1 ATTTTTATTTGAAAT
54866940 ATTTTTAT
1 ATTTTTAT
54866948 ACATGAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (15 bp):
ATTTTTATTTGAAAT
Found at i:54868516 original size:19 final size:20
Alignment explanation
Indices: 54868478--54868522 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
54868468 TTCTTGTCTG
* *
54868478 AATTTTTTTTTTAAAGACTT
1 AATTTTTATGTTAAAGACTT
54868498 AATTTTTATGTTAAA-ACTT
1 AATTTTTATGTTAAAGACTT
54868517 AATTTT
1 AATTTT
54868523 AGCGTCTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (20 bp):
AATTTTTATGTTAAAGACTT
Found at i:54869111 original size:37 final size:37
Alignment explanation
Indices: 54869070--54869145 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
54869060 ATCGGGTATG
*
54869070 AATTTTGATCTTTCAAATATGTGAATAAATCTAGAGA
1 AATTTTAATCTTTCAAATATGTGAATAAATCTAGAGA
*
54869107 AATTTTAATTTTTCAAATATGTGAATAAATCTAGAGA
1 AATTTTAATCTTTCAAATATGTGAATAAATCTAGAGA
54869144 AA
1 AA
54869146 ATTAATCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (37 bp):
AATTTTAATCTTTCAAATATGTGAATAAATCTAGAGA
Found at i:54871200 original size:39 final size:39
Alignment explanation
Indices: 54871076--54871200 Score: 127
Period size: 39 Copynumber: 3.3 Consensus size: 39
54871066 ATAATTTGTA
*
54871076 ATAATA-ATATATACACAATATGGTATTTAAAAATATAT--
1 ATAATATATATATA-ACTA-ATGGTATTTAAAAATATATAC
* *
54871114 AT-ATATGTATAT-A-TAATAGTATTTAAAAATATATAC
1 ATAATATATATATAACTAATGGTATTTAAAAATATATAC
* * * *
54871150 ATAAGAAATATATAACTAATGGCATTAAAAAATATATAC
1 ATAATATATATATAACTAATGGTATTTAAAAATATATAC
54871189 ATAATATATATA
1 ATAATATATATA
54871201 AAATACATAA
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
34 18 0.26
35 1 0.01
36 3 0.04
37 10 0.14
38 8 0.11
39 30 0.43
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.36
Consensus pattern (39 bp):
ATAATATATATATAACTAATGGTATTTAAAAATATATAC
Found at i:54871985 original size:25 final size:24
Alignment explanation
Indices: 54871955--54872009 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
54871945 GGGGGTTAGG
*
54871955 TTTTTTTTTTTTGGGTTAGGTTTT
1 TTTTTTTTTTTTGGATTAGGTTTT
*
54871979 TTCTTTTTTTTTTTGATTAGGTTTT
1 TT-TTTTTTTTTTGGATTAGGTTTT
54872004 TTTTTT
1 TTTTTT
54872010 GGGAGGGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.05, C:0.02, G:0.15, T:0.78
Consensus pattern (24 bp):
TTTTTTTTTTTTGGATTAGGTTTT
Found at i:54871988 original size:22 final size:21
Alignment explanation
Indices: 54871937--54871987 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 21
54871927 GGTTTCTTGA
*
54871937 TTTTTTTTGGGGGTTAGGTTT
1 TTTTTTTTTGGGGTTAGGTTT
54871958 TTTTTTTTT-GGGTTAGGTTT
1 TTTTTTTTTGGGGTTAGGTTT
54871978 TTTCTTTTTT
1 TTT-TTTTTT
54871988 TTTTTGATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.04, C:0.02, G:0.24, T:0.71
Consensus pattern (21 bp):
TTTTTTTTTGGGGTTAGGTTT
Found at i:54874312 original size:20 final size:20
Alignment explanation
Indices: 54874276--54874314 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54874266 TAATTATAAA
*
54874276 TTTAGATAAATATAATTTAT
1 TTTAGATAAATAAAATTTAT
54874296 TTTA-ATAAATAAAAATTTA
1 TTTAGATAAAT-AAAATTTA
54874315 AATTAGTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TTTAGATAAATAAAATTTAT
Found at i:54875933 original size:14 final size:16
Alignment explanation
Indices: 54875916--54875947 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54875906 CCCAAAAAAA
54875916 TTATAA-TTA-AAATC
1 TTATAATTTACAAATC
54875930 TTATAATTTACAAATC
1 TTATAATTTACAAATC
54875946 TT
1 TT
54875948 TTCTTTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATAATTTACAAATC
Found at i:54879835 original size:14 final size:15
Alignment explanation
Indices: 54879816--54879844 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54879806 TCAATTATTC
54879816 TTTTAAATT-TTTTA
1 TTTTAAATTATTTTA
54879830 TTTTAAATTATTTTA
1 TTTTAAATTATTTTA
54879845 CATAAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTAAATTATTTTA
Found at i:54880258 original size:12 final size:12
Alignment explanation
Indices: 54880241--54880287 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 12
54880231 CACAAAATAT
54880241 ATATATATTAAA
1 ATATATATTAAA
*
54880253 ATATAT-GTAAA
1 ATATATATTAAA
54880264 A-AT-TATTAAA
1 ATATATATTAAA
54880274 AT-TATA-TAAA
1 ATATATATTAAA
54880284 ATAT
1 ATAT
54880288 TCTAAGTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
9 1 0.03
10 14 0.48
11 8 0.28
12 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
ATATATATTAAA
Found at i:54880272 original size:21 final size:20
Alignment explanation
Indices: 54880246--54880284 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
54880236 AATATATATA
*
54880246 TATTAAAATATATGTAAAAAT
1 TATTAAAAT-TATATAAAAAT
54880267 TATTAAAATTATATAAAA
1 TATTAAAATTATATAAAA
54880285 TATTCTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TATTAAAATTATATAAAAAT
Found at i:54890116 original size:18 final size:19
Alignment explanation
Indices: 54890095--54890139 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
54890085 ATTGATTTTT
54890095 TTAATTAAATAAATT-T-AA
1 TTAATTAAA-AAATTCTAAA
*
54890113 TTAATT-GAAAATTCTAAA
1 TTAATTAAAAAATTCTAAA
54890131 TTAATTAAA
1 TTAATTAAA
54890140 GGAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 5 0.23
17 2 0.09
18 14 0.64
19 1 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
TTAATTAAAAAATTCTAAA
Found at i:54890144 original size:22 final size:23
Alignment explanation
Indices: 54890104--54890146 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
54890094 TTTAATTAAA
**
54890104 TAAATTTAATTAATTGAAAATTC
1 TAAATTTAATTAAAGGAAAATTC
54890127 TAAA-TTAATTAAAGGAAAAT
1 TAAATTTAATTAAAGGAAAAT
54890147 ATTAATTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (23 bp):
TAAATTTAATTAAAGGAAAATTC
Found at i:54891548 original size:18 final size:18
Alignment explanation
Indices: 54891525--54891562 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54891515 AACCGGTCTG
**
54891525 ATTAAAAAATTATTAAAA
1 ATTAAAAAAAAATTAAAA
54891543 ATTAAAAAAAAATTAAAA
1 ATTAAAAAAAAATTAAAA
54891561 AT
1 AT
54891563 CTGGTTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATTAAAAAAAAATTAAAA
Found at i:54891920 original size:36 final size:36
Alignment explanation
Indices: 54891873--54891942 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
54891863 ATTCATATTT
*
54891873 AAGCTCTTTCTATATAGTAAGGATAAAAATATAGTG
1 AAGCTCTTTCTATATAATAAGGATAAAAATATAGTG
*
54891909 AAGCTCTTTCTATATAATGAGGATAAAAATATAG
1 AAGCTCTTTCTATATAATAAGGATAAAAATATAG
54891943 CGAAACGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.33
Consensus pattern (36 bp):
AAGCTCTTTCTATATAATAAGGATAAAAATATAGTG
Found at i:54904627 original size:44 final size:43
Alignment explanation
Indices: 54904553--54904710 Score: 133
Period size: 44 Copynumber: 3.6 Consensus size: 43
54904543 CACAGATCTT
* * * * *
54904553 ACCCCATAAGCAGTAGGGGAA-TAGATTGAAGGCAACTAGCTTTA
1 ACCCCCTAAGCAGTAGGGTAACAAG-CTGAAGACAA-TAGCTTTA
* *
54904597 ACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTC-ATAGATCTTA
1 ACCCCCTAAGCAGTAGGGTAACAAGCTGAAG-ACAATAGCT-TTA
* * * * *
54904641 TCACCCTAAGCAGTAGGGAAAC-AGATCGAAGATAATGAGCTTTA
1 ACCCCCTAAGCAGTAGGGTAACAAGCT-GAAGACAAT-AGCTTTA
54904685 ACCCCCTAAGCAGTAGGGTAACAAGC
1 ACCCCCTAAGCAGTAGGGTAACAAGC
54904711 CAAATTTACA
Statistics
Matches: 90, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
43 7 0.08
44 75 0.83
45 8 0.09
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (43 bp):
ACCCCCTAAGCAGTAGGGTAACAAGCTGAAGACAATAGCTTTA
Found at i:54904694 original size:88 final size:86
Alignment explanation
Indices: 54904537--54904745 Score: 251
Period size: 88 Copynumber: 2.4 Consensus size: 86
54904527 CTAGAATCAG
* * * *
54904537 TGAATTCACAGATCTTACCCCATAAGCAGTAGGGGAATAGATTGAAGGCAACTAGCTTTAACCCC
1 TGAATTCACAGATCTTACCCCATAAGCAGTAGGGAAACAGATCGAAGACAACTAGCTTTAACCCC
54904602 CTAAGCAGTAGGGTAACAAGC
66 CTAAGCAGTAGGGTAACAAGC
* *
54904623 TGAAGTTCATAGATCTTATCACCC-TAAGCAGTAGGGAAACAGATCGAAGATAA-TGAGCTTTAA
1 TGAA-TTCACAGATCTTA-C-CCCATAAGCAGTAGGGAAACAGATCGAAGACAACT-AGCTTTAA
54904686 CCCCCTAAGCAGTAGGGTAACAAGC
62 CCCCCTAAGCAGTAGGGTAACAAGC
** * * * *
54904711 CAAATTTACAGACCTTAACCCCCTAAGTAGTAGGG
1 TGAATTCACAGATCTT-ACCCCATAAGCAGTAGGG
54904746 TAATAGGTTG
Statistics
Matches: 105, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
86 7 0.07
87 34 0.32
88 61 0.58
89 3 0.03
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (86 bp):
TGAATTCACAGATCTTACCCCATAAGCAGTAGGGAAACAGATCGAAGACAACTAGCTTTAACCCC
CTAAGCAGTAGGGTAACAAGC
Found at i:54904910 original size:44 final size:43
Alignment explanation
Indices: 54904862--54905016 Score: 152
Period size: 44 Copynumber: 3.5 Consensus size: 43
54904852 TACAAATCTT
*
54904862 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCAACGAGCTTTA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGACAA-GAGCTTTA
* * * *
54904906 ACCCCCTAAGCAGTAGGGTAACA-AGCTGAAGTTCATAGATC-TTA
1 ACCCCCTAAGCAGTAGGGAAACAGATC-GAAG-ACA-AGAGCTTTA
* * * * *
54904950 TCACCCTAGGCAGTAAGGAAACAGATCGAAGATAATGAGCTTTA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGACAA-GAGCTTTA
*
54904994 ACCCCCTAAGCAGTAGGGTAACA
1 ACCCCCTAAGCAGTAGGGAAACA
54905017 AGCCAAATTT
Statistics
Matches: 87, Mismatches: 18, Indels: 12
0.74 0.15 0.10
Matches are distributed among these distances:
42 1 0.01
43 6 0.07
44 72 0.83
45 7 0.08
46 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (43 bp):
ACCCCCTAAGCAGTAGGGAAACAGATCGAAGACAAGAGCTTTA
Found at i:54904963 original size:88 final size:87
Alignment explanation
Indices: 54904857--54905019 Score: 263
Period size: 88 Copynumber: 1.9 Consensus size: 87
54904847 AGATTTACAA
* * *
54904857 ATCTTACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCAACGAGCTTTAACCCCCTAAGCAGTAG
1 ATCTTACACCCTAAGCAGTAAGGAAACAGATCGAAGACAACGAGCTTTAACCCCCTAAGCAGTAG
54904922 GGTAACAAGCTGAAGTTCATAG
66 GGTAACAAGCTGAAGTTCATAG
* * *
54904944 ATCTTATCACCCTAGGCAGTAAGGAAACAGATCGAAGATAATGAGCTTTAACCCCCTAAGCAGTA
1 ATCTTA-CACCCTAAGCAGTAAGGAAACAGATCGAAGACAACGAGCTTTAACCCCCTAAGCAGTA
54905009 GGGTAACAAGC
65 GGGTAACAAGC
54905020 CAAATTTATA
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 6 0.09
88 63 0.91
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (87 bp):
ATCTTACACCCTAAGCAGTAAGGAAACAGATCGAAGACAACGAGCTTTAACCCCCTAAGCAGTAG
GGTAACAAGCTGAAGTTCATAG
Found at i:54905044 original size:43 final size:43
Alignment explanation
Indices: 54904903--54905057 Score: 143
Period size: 44 Copynumber: 3.6 Consensus size: 43
54904893 GCAACGAGCT
* * *
54904903 TTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTCATAGATC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGC-GAAATTAATAGACC
* * * * * * *
54904947 TTATCACCCTAGGCAGTAAGGAAACAGATCGAAGA-TAAT-GAGCT
1 TTAACCCCCTAAGCAGTAGGGTAACA-AGCGAA-ATTAATAGA-CC
* *
54904991 TTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTATAGACC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCGAAATTAATAGACC
*
54905034 TTAACCCCCTAAGTAGTAGGGTAA
1 TTAACCCCCTAAGCAGTAGGGTAA
54905058 TAGGTTGAAA
Statistics
Matches: 86, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
42 1 0.01
43 33 0.38
44 50 0.58
45 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (43 bp):
TTAACCCCCTAAGCAGTAGGGTAACAAGCGAAATTAATAGACC
Found at i:54905107 original size:309 final size:308
Alignment explanation
Indices: 54904548--54905245 Score: 1180
Period size: 309 Copynumber: 2.3 Consensus size: 308
54904538 GAATTCACAG
* * * *
54904548 ATCTTACCCCATAAGCAGTAGGGGAATAGATTGAAGGCAACTAGCTTTAACCCCCTAAGCAGTAG
1 ATCTTACCCCCTAAGCAGTAGGGAAACAGA-TGAAGGCAACGAGCTTTAACCCCCTAAGCAGTAG
*
54904613 GGTAACAAGCTGAAGTTCATAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCGAAGATAATG
65 GGTAACAAGCTGAAGTTCATAGATCTTATCACCCTAAGCAGTAAGGAAACAGATCGAAGATAATG
54904678 AGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAACCCCCTAAGTAGTA
130 AGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAACCCCCTAAGTAGTA
* *
54904743 GGGTAATAGGTTGAAAATTACAGATTTTTTCTCTCTGAAGTTGCAGTGGAACAGATCGAATCCAG
195 GGGTAATAGGTTGAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAATCCAG
* *
54904808 TGAATTTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATTTACAA
260 CGAATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATTTACAA
54904857 ATCTTACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCAACGAGCTTTAACCCCCTAAGCAGTAG
1 ATCTTACCCCCTAAGCAGTAGGGAAACAGAT-GAAGGCAACGAGCTTTAACCCCCTAAGCAGTAG
*
54904922 GGTAACAAGCTGAAGTTCATAGATCTTATCACCCTAGGCAGTAAGGAAACAGATCGAAGATAATG
65 GGTAACAAGCTGAAGTTCATAGATCTTATCACCCTAAGCAGTAAGGAAACAGATCGAAGATAATG
*
54904987 AGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTATAGACCTTAACCCCCTAAGTAGTA
130 AGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAACCCCCTAAGTAGTA
*
54905052 GGGTAATAGGTTGAAAATTACAGATTTTGTCTCCCTGAAGTTGTAGTGGAACAGATCGAATCCAG
195 GGGTAATAGGTTGAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAATCCAG
54905117 CGAATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATTTACAA
260 CGAATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATTTACAA
* * * * * * *
54905166 ATCTTATCACCCTAAGCAGTAGGGAAACAGATTAAAGAAGATGGGCCTTAACCCCCTAAGCAGTA
1 ATCTTA-CCCCCTAAGCAGTAGGGAAACAGATGAAGGCA-ACGAGCTTTAACCCCCTAAGCAGTA
*
54905231 GGGTAACAGGCTGAA
64 GGGTAACAAGCTGAA
54905246 AATCACAGAT
Statistics
Matches: 366, Mismatches: 20, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
308 1 0.00
309 305 0.83
310 60 0.16
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (308 bp):
ATCTTACCCCCTAAGCAGTAGGGAAACAGATGAAGGCAACGAGCTTTAACCCCCTAAGCAGTAGG
GTAACAAGCTGAAGTTCATAGATCTTATCACCCTAAGCAGTAAGGAAACAGATCGAAGATAATGA
GCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAACCCCCTAAGTAGTAG
GGTAATAGGTTGAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAATCCAGC
GAATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATTTACAA
Found at i:54907142 original size:29 final size:27
Alignment explanation
Indices: 54907110--54907177 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
54907100 TATAAATATG
* *
54907110 TATATATGTATACTTTATGTATATATTTT
1 TATATAT-TATA-TGTATATATATATTTT
54907139 TATAAATATTATATGTATATATATATTTT
1 TAT--ATATTATATGTATATATATATTTT
*
54907168 AATATATTAT
1 TATATATTAT
54907178 GTATATTGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 7 0.21
29 19 0.56
30 4 0.12
31 4 0.12
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (27 bp):
TATATATTATATGTATATATATATTTT
Found at i:54907153 original size:25 final size:27
Alignment explanation
Indices: 54907125--54907177 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 27
54907115 ATGTATACTT
54907125 TATGTATATAT-T-TTTATAA-ATATTA
1 TATGTATATATATATTT-TAATATATTA
54907150 TATGTATATATATATTTTAATATATTA
1 TATGTATATATATATTTTAATATATTA
54907177 T
1 T
54907178 GTATATTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 11 0.44
26 4 0.16
27 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (27 bp):
TATGTATATATATATTTTAATATATTA
Found at i:54907178 original size:25 final size:24
Alignment explanation
Indices: 54907123--54907183 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
54907113 ATATGTATAC
54907123 TTTATGTATATATTTTTATAAATA
1 TTTATGTATATATTTTTATAAATA
54907147 TTATATGTATATATATATTT-T-AATA
1 TT-TATGTATATAT-T-TTTATAAATA
54907172 TATTATGTATAT
1 T-TTATGTATAT
54907184 TGTGTACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
24 2 0.06
25 25 0.76
26 3 0.09
27 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (24 bp):
TTTATGTATATATTTTTATAAATA
Found at i:54907739 original size:21 final size:21
Alignment explanation
Indices: 54907715--54907756 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
54907705 ATCATTTTCG
*
54907715 TTATCATTGTCAT-TTTTATTT
1 TTAT-ATTGCCATGTTTTATTT
*
54907736 TTATTTTGCCATGTTTTATTT
1 TTATATTGCCATGTTTTATTT
54907757 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (21 bp):
TTATATTGCCATGTTTTATTT
Found at i:54910210 original size:49 final size:48
Alignment explanation
Indices: 54910027--54910215 Score: 148
Period size: 50 Copynumber: 3.8 Consensus size: 48
54910017 TGAGGTCATG
* * * *
54910027 TGTGTAGTACTAAGTGCAGGCTACTATGCATACTC-GATAACTTCGATCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTAC-CAGATAA-TTGGTTCA
** * * **
54910076 CGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAAATGGTTAGG-TCA
1 --TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT-GGTTCA
* * * * *
54910126 CGTATGTAATACTAATTGCAGGCTACTACGTGTACCGGATAATTGGTTGCA
1 --TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTT-CA
*
54910177 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATA
54910216 GCTTTGGCTA
Statistics
Matches: 110, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
49 35 0.32
50 42 0.38
51 33 0.30
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (48 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTTCA
Found at i:54911547 original size:28 final size:26
Alignment explanation
Indices: 54911515--54911579 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
54911505 TGACAACGAG
*
54911515 GTTCACTTTGATACTTATATCATTTTTT
1 GTTCACTTTGATAATTATAT--TTTTTT
* * *
54911543 GTTCATTTTGGTAATTGTATTTTTTT
1 GTTCACTTTGATAATTATATTTTTTT
54911569 GTCTCACTTTG
1 GT-TCACTTTG
54911580 GTACCTAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 8 0.26
27 7 0.23
28 16 0.52
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.58
Consensus pattern (26 bp):
GTTCACTTTGATAATTATATTTTTTT
Found at i:54912200 original size:78 final size:78
Alignment explanation
Indices: 54912071--54912225 Score: 283
Period size: 78 Copynumber: 2.0 Consensus size: 78
54912061 ACCCGACACT
*
54912071 CAAACCCATGGAATTAAGAATTTCTTCTTTTTTAATCTCTATTCGAGGAGTAGGGGCAGATTTAA
1 CAAACCCATGGAATTAAGAATTTCTTCTTTTTTAATCTCTATTCGAGGAGTAGGGGCAGATCTAA
54912136 GGGGTGGCAGGGA
66 GGGGTGGCAGGGA
*
54912149 CAAACCCATGGAATTAAGAATTTCTTCTTTTTTAATCTCTATTCGAGGAGTAGGGGTAGATCTAA
1 CAAACCCATGGAATTAAGAATTTCTTCTTTTTTAATCTCTATTCGAGGAGTAGGGGCAGATCTAA
*
54912214 GGGGTGGTAGGG
66 GGGGTGGCAGGG
54912226 GCCGGCCCAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.32
Consensus pattern (78 bp):
CAAACCCATGGAATTAAGAATTTCTTCTTTTTTAATCTCTATTCGAGGAGTAGGGGCAGATCTAA
GGGGTGGCAGGGA
Found at i:54923147 original size:19 final size:19
Alignment explanation
Indices: 54923123--54923170 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
54923113 AAATTAATTT
54923123 TTTATAAATA-AGTATTTTG
1 TTTATAAATAGA-TATTTTG
* *
54923142 TTTATAACTAGTATATTTTT
1 TTTATAAATAG-ATATTTTG
54923162 TTTATAAAT
1 TTTATAAAT
54923171 TTTAGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 9 0.38
20 14 0.58
21 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTATAAATAGATATTTTG
Found at i:54924245 original size:21 final size:21
Alignment explanation
Indices: 54924221--54924262 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
54924211 TTATAATGTA
54924221 CATTTTTATATTAATAATATG
1 CATTTTTATATTAATAATATG
54924242 CATTTTTATATTAATAATATG
1 CATTTTTATATTAATAATATG
54924263 TAAACTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (21 bp):
CATTTTTATATTAATAATATG
Found at i:54925468 original size:21 final size:20
Alignment explanation
Indices: 54925444--54925485 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
54925434 AAATAAAGTA
54925444 AATAATGAC-AATGATAACAAT
1 AATAAT-ACTAATGATAA-AAT
54925465 AATAATACTAATGATAAAAT
1 AATAATACTAATGATAAAAT
54925485 A
1 A
54925486 TGCACATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (20 bp):
AATAATACTAATGATAAAAT
Found at i:54925742 original size:18 final size:18
Alignment explanation
Indices: 54925735--54925774 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
54925725 TGAATAGATA
54925735 ATAATAAAACAATAATAG
1 ATAATAAAACAATAATAG
*
54925753 ATAATAAAATAATAATAG
1 ATAATAAAACAATAATAG
54925771 -TAAT
1 ATAAT
54925775 GAAGGCATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (18 bp):
ATAATAAAACAATAATAG
Found at i:54925756 original size:15 final size:14
Alignment explanation
Indices: 54925732--54925769 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
54925722 AAATGAATAG
54925732 ATAATAATAA-AACA
1 ATAATAATAATAA-A
54925746 ATAATAGATAATAAA
1 ATAATA-ATAATAAA
54925761 ATAATAATA
1 ATAATAATA
54925770 GTAATGAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.41
15 11 0.50
16 2 0.09
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (14 bp):
ATAATAATAATAAA
Found at i:54929306 original size:22 final size:23
Alignment explanation
Indices: 54929281--54929327 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
54929271 ATTTAGTACC
54929281 TAAGTTTTTACAC-GTTTTTTAA
1 TAAGTTTTTACACTGTTTTTTAA
*
54929303 TAAGTTTTTACACTTTTTTTTAA
1 TAAGTTTTTACACTGTTTTTTAA
54929326 TA
1 TA
54929328 TGGTATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.28, C:0.09, G:0.06, T:0.57
Consensus pattern (23 bp):
TAAGTTTTTACACTGTTTTTTAA
Found at i:54931507 original size:16 final size:16
Alignment explanation
Indices: 54931486--54931521 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
54931476 TCAAAAAGGG
54931486 AAATGAAAATGAAAAA
1 AAATGAAAATGAAAAA
*
54931502 AAATGAAAATGAAAAG
1 AAATGAAAATGAAAAA
54931518 AAAT
1 AAAT
54931522 TTTATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (16 bp):
AAATGAAAATGAAAAA
Found at i:54932281 original size:71 final size:71
Alignment explanation
Indices: 54932165--54932308 Score: 207
Period size: 71 Copynumber: 2.0 Consensus size: 71
54932155 ATGATTTCAT
** * * * *
54932165 ACATATTTGTTGGTTTTACCGACCAGCATAGGGCGCATTTATTGTCGGTTATACCAACTAGTGCT
1 ACATATTTGCCGGTTCTACCGACCAACATAGGGCGCATTTATTGTCAGTTATACCAACCAGTGCT
*
54932230 GGGCAC
66 AGGCAC
* *
54932236 ACATATTTGCCGGTTCTACCGACCAACTTAGGGCGCATTTATTGTCAGTTATACCGACCAGTGCT
1 ACATATTTGCCGGTTCTACCGACCAACATAGGGCGCATTTATTGTCAGTTATACCAACCAGTGCT
54932301 AGGCAC
66 AGGCAC
54932307 AC
1 AC
54932309 TAATTGTTGA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (71 bp):
ACATATTTGCCGGTTCTACCGACCAACATAGGGCGCATTTATTGTCAGTTATACCAACCAGTGCT
AGGCAC
Found at i:54933174 original size:21 final size:21
Alignment explanation
Indices: 54933150--54933191 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
54933140 CGGATTGGAC
54933150 CAAAAAGTAGACCATGTACTA
1 CAAAAAGTAGACCATGTACTA
54933171 CAAAAAGTAGACCATGTACTA
1 CAAAAAGTAGACCATGTACTA
54933192 AGTTAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.19
Consensus pattern (21 bp):
CAAAAAGTAGACCATGTACTA
Found at i:54933744 original size:132 final size:126
Alignment explanation
Indices: 54933508--54933760 Score: 312
Period size: 132 Copynumber: 1.9 Consensus size: 126
54933498 TAACATATTA
* **
54933508 GTTAGATGGTTAGATAGTTGCAATTACATCATTGAGTCTCAAGTTTGATTCTTCTTTTACTCATA
1 GTTAGATGGTTAGATAGTTGCAATTACATCATTGAGTCTCAAGTTTGATTCCTCTACTACTCATA
* *
54933573 TTTTTTTTTCATGTTGCTTCAAGCTTTTTAACATTTTAATTAATGATTTTTAACATATTAGTTTT
66 TTTTTTTTTCACGTTGCTTCAAG--TTTT---ATTTTAATCAAT-ATTTTTAACATATTAGTTTT
54933638 TT
125 TT
* *
54933640 GTTAGATGGTTAGATAGTTGTAATTACATCATTGAGTCTCGAGTTTGATTCCTCTACTACTCGCA
1 GTTAGATGGTTAGATAGTTGCAATTACATCATTGAGTCTCAAGTTTGATTCCTCTACTACT--CA
54933705 TTTGTATTTTTTATTTCACGTTGCTTCAAG-TTT-TTTTAATCAATATTTTTAACATA
64 ----TATTTTTT-TTTCACGTTGCTTCAAGTTTTATTTTAATCAATATTTTTAACATA
54933761 CTAGCTCTGT
Statistics
Matches: 107, Mismatches: 7, Indels: 15
0.83 0.05 0.12
Matches are distributed among these distances:
131 12 0.11
132 66 0.62
134 2 0.02
136 3 0.03
138 8 0.07
139 16 0.15
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (126 bp):
GTTAGATGGTTAGATAGTTGCAATTACATCATTGAGTCTCAAGTTTGATTCCTCTACTACTCATA
TTTTTTTTTCACGTTGCTTCAAGTTTTATTTTAATCAATATTTTTAACATATTAGTTTTTT
Found at i:54934923 original size:25 final size:27
Alignment explanation
Indices: 54934882--54934940 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
54934872 GTAGAAAGGG
54934882 TTTAAAATAAACTATATA-AAAT-AAT
1 TTTAAAATAAACTATATATAAATCAAT
* *
54934907 TTTAAAAT-AAGTAATATATAAGTCAAT
1 TTTAAAATAAACT-ATATATAAATCAAT
54934934 TTTAAAA
1 TTTAAAA
54934941 ATAATAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 3 0.10
25 13 0.45
26 3 0.10
27 10 0.34
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (27 bp):
TTTAAAATAAACTATATATAAATCAAT
Found at i:54934950 original size:28 final size:27
Alignment explanation
Indices: 54934887--54934950 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
54934877 AAGGGTTTAA
54934887 AATAAACTATATAAAATAATTTTAAAAT
1 AATAAA-TATATAAAATAATTTTAAAAT
*
54934915 AAGT-AATATAT-AAGTCAATTTTAAAAAT
1 AA-TAAATATATAAAAT-AATTTT-AAAAT
54934943 AATAAATA
1 AATAAATA
54934951 AGAATTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
26 3 0.10
27 12 0.39
28 15 0.48
29 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (27 bp):
AATAAATATATAAAATAATTTTAAAAT
Found at i:54939202 original size:26 final size:26
Alignment explanation
Indices: 54939172--54939279 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
54939162 TGAAATTCCC
*
54939172 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
54939198 ATCATGGAACATTTACCTAACTCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
54939224 ATAATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
54939250 ATCATGGTACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
54939276 ATCA
1 ATCA
54939280 ATTTGTATCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:54939805 original size:16 final size:16
Alignment explanation
Indices: 54939784--54939838 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 16
54939774 TTGATGATAT
54939784 TTTTTAATTATTTTTA
1 TTTTTAATTATTTTTA
54939800 TTTTTAATTAATTAATTTTTTA
1 --TTT--TTAATT-A-TTTTTA
54939822 TTTTTAATTATTTTTA
1 TTTTTAATTATTTTTA
54939838 T
1 T
54939839 AATCATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 7 0.21
17 1 0.03
18 9 0.27
20 9 0.27
21 1 0.03
22 6 0.18
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTAATTATTTTTA
Found at i:54939822 original size:22 final size:20
Alignment explanation
Indices: 54939753--54939831 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 20
54939743 TTTCAATCTT
54939753 TTTTTATTTTTAATTAATGT-
1 TTTTTATTTTTAATTAAT-TA
*
54939773 TTTGATGATATTTT--TTAATTA
1 TTT--TTAT-TTTTAATTAATTA
54939794 TTTTTATTTTTAATTAATTAA
1 TTTTTATTTTTAATTAATT-A
54939815 TTTTTTATTTTTAATTA
1 -TTTTTATTTTTAATTA
54939832 TTTTTATAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
18 4 0.08
19 3 0.06
20 10 0.20
21 9 0.18
22 19 0.39
23 4 0.08
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (20 bp):
TTTTTATTTTTAATTAATTA
Found at i:54940137 original size:14 final size:14
Alignment explanation
Indices: 54940118--54940154 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
54940108 CCAAAAAAAA
54940118 ACACAGACACACAG
1 ACACAGACACACAG
54940132 ACACAG--ACACAG
1 ACACAGACACACAG
*
54940144 ACACACACACA
1 ACACAGACACA
54940155 TATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 11 0.55
14 9 0.45
ACGTcount: A:0.51, C:0.38, G:0.11, T:0.00
Consensus pattern (14 bp):
ACACAGACACACAG
Found at i:54940143 original size:12 final size:12
Alignment explanation
Indices: 54940124--54940154 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54940114 AAAAACACAG
54940124 ACACACAGACAC
1 ACACACAGACAC
*
54940136 AGACACAGACAC
1 ACACACAGACAC
54940148 ACACACA
1 ACACACA
54940155 TATATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.39, G:0.10, T:0.00
Consensus pattern (12 bp):
ACACACAGACAC
Found at i:54941246 original size:29 final size:28
Alignment explanation
Indices: 54941179--54941253 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
54941169 ACGGGGTTTA
*
54941179 ATTAAAATTTTCAAAAAAATTTTGGGTTT
1 ATTAAAATTTT-AAAAAAATTTTGGGCTT
* * * *
54941208 AATAAGATTTTATAAATATTTTGGGGCTT
1 ATTAAAATTTTAAAAAAATTTT-GGGCTT
54941237 ATTAAAATTTTAAAAAA
1 ATTAAAATTTTAAAAAA
54941254 TTCTTAGAGA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
28 9 0.25
29 27 0.75
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.43
Consensus pattern (28 bp):
ATTAAAATTTTAAAAAAATTTTGGGCTT
Found at i:54941303 original size:32 final size:32
Alignment explanation
Indices: 54941267--54941345 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 32
54941257 TTAGAGAATT
* *
54941267 ATTGAGATTTTTTAAAAATACCGGAAGGTTTG
1 ATTGAGAATTTTTAAAAATACCGGAAGGCTTG
* ***
54941299 ATTGA-AATTTTTAAAACTTTTGGAAGGCTTG
1 ATTGAGAATTTTTAAAAATACCGGAAGGCTTG
54941330 ATT-AGAATTTTTAAAA
1 ATTGAGAATTTTTAAAA
54941346 GTTTTAAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.03
31 34 0.85
32 5 0.12
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.41
Consensus pattern (32 bp):
ATTGAGAATTTTTAAAAATACCGGAAGGCTTG
Found at i:54944709 original size:19 final size:18
Alignment explanation
Indices: 54944665--54944719 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
54944655 TTAAATTCTC
54944665 ATTTTTTATAATTTATTT
1 ATTTTTTATAATTTATTT
**
54944683 -TGAATTTATATATTTATTT
1 AT-TTTTTATA-ATTTATTT
54944702 ATTTTTTATAATTT-TTT
1 ATTTTTTATAATTTATTT
54944719 A
1 A
54944720 CGTAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 5 0.17
18 10 0.33
19 14 0.47
20 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTTTTATAATTTATTT
Found at i:54947930 original size:24 final size:24
Alignment explanation
Indices: 54947902--54947985 Score: 80
Period size: 24 Copynumber: 3.3 Consensus size: 24
54947892 ATAAATTCAA
54947902 TTATTAATACTATTAAAATTTCTT
1 TTATTAATACTATTAAAATTTCTT
* * *
54947926 TTATTAAATTCAAGTTAATTACAATTTC-A
1 TTATT-AA-T--A-CT-ATTAAAATTTCTT
54947955 TTATTAATACTATTAAAATTTCTT
1 TTATTAATACTATTAAAATTTCTT
54947979 TTATTAA
1 TTATTAA
54947986 ATTAAAGTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
23 10 0.21
24 13 0.28
25 3 0.06
26 1 0.02
27 1 0.02
28 3 0.06
29 6 0.13
30 10 0.21
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.51
Consensus pattern (24 bp):
TTATTAATACTATTAAAATTTCTT
Found at i:54947952 original size:30 final size:29
Alignment explanation
Indices: 54947913--54948015 Score: 92
Period size: 30 Copynumber: 3.7 Consensus size: 29
54947903 TATTAATACT
54947913 ATTAAAATTTCTTTTATTAAATTCAAGTTA
1 ATTAAAATTTCTTTTATTAAATT-AAGTTA
* * *
54947943 ATTACAATTTC-ATTATT-AA-T-A-CT-
1 ATTAAAATTTCTTTTATTAAATTAAGTTA
54947966 ATTAAAATTTCTTTTATTAAATTAAAGTTA
1 ATTAAAATTTCTTTTATTAAATT-AAGTTA
* * *
54947996 ATTACAATGTCTTTTTTTAA
1 ATTAAAATTTCTTTTATTAA
54948016 TTATATAGCT
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
23 10 0.18
24 6 0.11
25 3 0.05
26 1 0.02
27 1 0.02
28 3 0.05
29 6 0.11
30 27 0.47
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (29 bp):
ATTAAAATTTCTTTTATTAAATTAAGTTA
Found at i:54947966 original size:53 final size:53
Alignment explanation
Indices: 54947901--54948003 Score: 197
Period size: 53 Copynumber: 1.9 Consensus size: 53
54947891 TATAAATTCA
*
54947901 ATTATTAATACTATTAAAATTTCTTTTATTAAATTCAAGTTAATTACAATTTC
1 ATTATTAATACTATTAAAATTTCTTTTATTAAATTAAAGTTAATTACAATTTC
54947954 ATTATTAATACTATTAAAATTTCTTTTATTAAATTAAAGTTAATTACAAT
1 ATTATTAATACTATTAAAATTTCTTTTATTAAATTAAAGTTAATTACAAT
54948004 GTCTTTTTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.49
Consensus pattern (53 bp):
ATTATTAATACTATTAAAATTTCTTTTATTAAATTAAAGTTAATTACAATTTC
Found at i:54947989 original size:29 final size:29
Alignment explanation
Indices: 54947904--54947990 Score: 82
Period size: 23 Copynumber: 3.2 Consensus size: 29
54947894 AAATTCAATT
54947904 ATTAATACTATTAAAATTTCTTTTATTAA
1 ATTAATACTATTAAAATTTCTTTTATTAA
*
54947933 ATTCAAGT--TAATTACAATTTC----ATT--
1 ATT-AA-TACT-ATTAAAATTTCTTTTATTAA
54947957 ATTAATACTATTAAAATTTCTTTTATTAA
1 ATTAATACTATTAAAATTTCTTTTATTAA
54947986 ATTAA
1 ATTAA
54947991 AGTTAATTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 22
0.65 0.03 0.32
Matches are distributed among these distances:
22 1 0.02
23 12 0.27
24 4 0.09
26 3 0.07
27 3 0.07
29 9 0.20
30 12 0.27
31 1 0.02
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.49
Consensus pattern (29 bp):
ATTAATACTATTAAAATTTCTTTTATTAA
Found at i:54948063 original size:16 final size:16
Alignment explanation
Indices: 54948042--54948074 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54948032 TATTTTTCTT
54948042 AATTTTAAAATATTGC
1 AATTTTAAAATATTGC
54948058 AATTTTAAAATATTGC
1 AATTTTAAAATATTGC
54948074 A
1 A
54948075 TCAATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (16 bp):
AATTTTAAAATATTGC
Found at i:54949888 original size:17 final size:19
Alignment explanation
Indices: 54949866--54949903 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
54949856 TTAAAAAATT
54949866 ATAAAAAT-A-TTTAAAAA
1 ATAAAAATGATTTTAAAAA
54949883 AT-AAAATGATTTTAAAAA
1 ATAAAAATGATTTTAAAAA
54949901 ATA
1 ATA
54949904 TATAAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.28
17 3 0.17
18 10 0.56
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
ATAAAAATGATTTTAAAAA
Found at i:54951086 original size:19 final size:20
Alignment explanation
Indices: 54951048--54951088 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
54951038 ATTTAGTTGA
*
54951048 AAAAATTTAAAAATTATTAT
1 AAAAATTCAAAAATTATTAT
*
54951068 AAAAATTCAATAATT-TTAT
1 AAAAATTCAAAAATTATTAT
54951087 AA
1 AA
54951089 TTTTTAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATTCAAAAATTATTAT
Found at i:54951617 original size:30 final size:31
Alignment explanation
Indices: 54951583--54951640 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
54951573 ATTATTATAT
*
54951583 AAATTATAAAT-T-TAATTATTGAAAATAAAC
1 AAATTAAAAATGTCTAATTA-TGAAAATAAAC
*
54951613 AAATTAAAAATGTCTTATTATGAAAATA
1 AAATTAAAAATGTCTAATTATGAAAATA
54951641 TAGCTTACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.42
31 9 0.38
32 5 0.21
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.36
Consensus pattern (31 bp):
AAATTAAAAATGTCTAATTATGAAAATAAAC
Found at i:54953085 original size:16 final size:16
Alignment explanation
Indices: 54953060--54953090 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54953050 ATAGATCATT
*
54953060 AAAATTTTAAAAATTA
1 AAAATATTAAAAATTA
54953076 AAAATATTAAAAATT
1 AAAATATTAAAAATT
54953091 TAGTTCAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATATTAAAAATTA
Found at i:54954349 original size:20 final size:20
Alignment explanation
Indices: 54954324--54954373 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
54954314 TGGCTTAAAA
54954324 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
54954344 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
54954361 GTGGTAGTGGATT
1 TTGGTAGTGGATT
54954374 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:54958979 original size:20 final size:20
Alignment explanation
Indices: 54958954--54959003 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
54958944 TGGCTTAAAA
54958954 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
54958974 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
54958991 GTGGTAGTGGATT
1 TTGGTAGTGGATT
54959004 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:54965964 original size:17 final size:16
Alignment explanation
Indices: 54965925--54965973 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
54965915 TTAATAATTA
*
54965925 AATTTAATTAAAAAAG
1 AATTAAATTAAAAAAG
54965941 AATTAAATTAACAAAAG
1 AATTAAATTAA-AAAAG
*
54965958 ATATAAATATTAAAAA
1 A-ATTAA-ATTAAAAA
54965974 TTAAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 10 0.36
17 6 0.21
18 7 0.25
19 5 0.18
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (16 bp):
AATTAAATTAAAAAAG
Found at i:54965969 original size:19 final size:16
Alignment explanation
Indices: 54965930--54965973 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
54965920 AATTAAATTT
*
54965930 AATTAAAAAAGAATTA
1 AATTAAAAAAGAATAA
54965946 AATTAACAAAAGATATAA
1 AATTAA-AAAAGA-ATAA
54965964 ATATTAAAAA
1 A-ATTAAAAA
54965974 TTAAATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 6 0.25
17 6 0.25
18 7 0.29
19 5 0.21
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (16 bp):
AATTAAAAAAGAATAA
Found at i:54966584 original size:18 final size:18
Alignment explanation
Indices: 54966553--54966587 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54966543 TCATTATAGC
* *
54966553 TATGTTTATGAATTTTGA
1 TATGTATATAAATTTTGA
54966571 TATGTATATAAATTTTG
1 TATGTATATAAATTTTG
54966588 TTGTTTTAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.54
Consensus pattern (18 bp):
TATGTATATAAATTTTGA
Found at i:54973677 original size:35 final size:35
Alignment explanation
Indices: 54973629--54973787 Score: 162
Period size: 35 Copynumber: 4.6 Consensus size: 35
54973619 ACTCTTTGTT
* * *
54973629 TTGGTGTGTTTCGGTTGGAGTAGCTCTTATGAGCA
1 TTGGTGTGCTTCGGATGGATTAGCTCTTATGAGCA
* * * * **
54973664 TTAGTGTACTTCGGAGGGATTATCTCTTACAAGCA
1 TTGGTGTGCTTCGGATGGATTAGCTCTTATGAGCA
* *
54973699 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
1 TTGGTGTGCTTCGGATGGATTAGCTCTTATGAGCA
* *
54973734 ---GTGTGTTTCGGATGGATTGGCTCTTATGAGCA
1 TTGGTGTGCTTCGGATGGATTAGCTCTTATGAGCA
*
54973766 TCTGGTGTGCTTCGGTTGGATT
1 T-TGGTGTGCTTCGGATGGATT
54973788 GTTGATGTAC
Statistics
Matches: 101, Mismatches: 19, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
32 30 0.30
35 55 0.54
36 16 0.16
ACGTcount: A:0.16, C:0.13, G:0.32, T:0.38
Consensus pattern (35 bp):
TTGGTGTGCTTCGGATGGATTAGCTCTTATGAGCA
Found at i:54973711 original size:70 final size:67
Alignment explanation
Indices: 54973629--54973785 Score: 188
Period size: 70 Copynumber: 2.3 Consensus size: 67
54973619 ACTCTTTGTT
* *
54973629 TTGGTGTGTTTCGGTTGGAGTAGCTCTTATGAGCATTAGTGTACTTCGGAGGGATTATCTCTTAC
1 TTGGTGTGTTTCGGTTGGAGTAGCTCTTATGAGCAGT-GTGT--TTCGGAGGGATTAGCTCTTAC
54973694 AAGCA
63 AAGCA
** * * * **
54973699 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCAGTGTGTTTCGGATGGATTGGCTCTTATGAG
1 TTGGTGTGTTTCGGTTGGAGTAGCTCTTATGAGCAGTGTGTTTCGGAGGGATTAGCTCTTACAAG
54973764 CA
66 CA
*
54973766 TCTGGTGTGCTTCGGTTGGA
1 T-TGGTGTGTTTCGGTTGGA
54973786 TTGTTGATGT
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
67 22 0.30
68 15 0.20
69 4 0.05
70 33 0.45
ACGTcount: A:0.17, C:0.13, G:0.32, T:0.38
Consensus pattern (67 bp):
TTGGTGTGTTTCGGTTGGAGTAGCTCTTATGAGCAGTGTGTTTCGGAGGGATTAGCTCTTACAAG
CA
Found at i:54974183 original size:26 final size:26
Alignment explanation
Indices: 54974149--54974221 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 26
54974139 ATTTCGAGCC
* *
54974149 ATAATCAATAAGCTCCTCTTGAGCTG
1 ATAAACAATAAGCTCCTATTGAGCTG
*
54974175 ATAAACAATAAGCT-TTATTGAGCTG
1 ATAAACAATAAGCTCCTATTGAGCTG
* *
54974200 --AAACGATAAGCT-CTATCGAGCT
1 ATAAACAATAAGCTCCTATTGAGCT
54974222 AAACAGTAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 19 0.46
25 9 0.22
26 13 0.32
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (26 bp):
ATAAACAATAAGCTCCTATTGAGCTG
Found at i:54974257 original size:23 final size:23
Alignment explanation
Indices: 54974183--54974257 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
54974173 TGATAAACAA
* * *
54974183 TAAGCTTTATTGAGCTGAAACGA
1 TAAGCTCTATCGAGCTGAAACGG
*
54974206 TAAGCTCTATCGAGCT-AAACAG
1 TAAGCTCTATCGAGCTGAAACGG
54974228 TAAGCTC-ATACGAGCTGAAACGG
1 TAAGCTCTAT-CGAGCTGAAACGG
54974251 TAAGCTC
1 TAAGCTC
54974258 CAGCTGTGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
21 2 0.04
22 17 0.38
23 26 0.58
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (23 bp):
TAAGCTCTATCGAGCTGAAACGG
Found at i:54978759 original size:37 final size:37
Alignment explanation
Indices: 54978717--54978808 Score: 141
Period size: 37 Copynumber: 2.5 Consensus size: 37
54978707 TTGTTATTAA
*
54978717 ATTTTAATA-AGATTATTATTAAAAATAATTTAATCAT
1 ATTTTAATATA-ATTATTATTAAAAATAATTTAATAAT
*
54978754 ATTTTAATATAATTATTATTAAATATAATTTAATAAT
1 ATTTTAATATAATTATTATTAAAAATAATTTAATAAT
54978791 ATTTTTAATATAATTATT
1 A-TTTTAATATAATTATT
54978809 TTTATATTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
37 34 0.67
38 17 0.33
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (37 bp):
ATTTTAATATAATTATTATTAAAAATAATTTAATAAT
Found at i:54978838 original size:25 final size:25
Alignment explanation
Indices: 54978808--54978860 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 25
54978798 ATATAATTAT
54978808 TTTTATATT-AAATTATATTAAAATA
1 TTTTAT-TTCAAATTATATTAAAATA
54978833 TTTTATTTCAAATTATATTAAAATA
1 TTTTATTTCAAATTATATTAAAATA
54978858 TTT
1 TTT
54978861 CAAAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTATTTCAAATTATATTAAAATA
Found at i:54980516 original size:40 final size:40
Alignment explanation
Indices: 54980459--54980554 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
54980449 ATGACAAAGA
54980459 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
54980500 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
54980540 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
54980555 GAAAGAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:54987784 original size:13 final size:13
Alignment explanation
Indices: 54987766--54987791 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54987756 CACTTGATAA
54987766 GGTTTCCTAAAAG
1 GGTTTCCTAAAAG
54987779 GGTTTCCTAAAAG
1 GGTTTCCTAAAAG
54987792 TATTCTCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GGTTTCCTAAAAG
Found at i:54999871 original size:264 final size:264
Alignment explanation
Indices: 54999400--54999933 Score: 960
Period size: 264 Copynumber: 2.0 Consensus size: 264
54999390 GAGTCATGAG
*
54999400 ATTTTGAGTTATGGCTCAGTTTGTGTTATCTGTTGTCTGCCTTTGAATAATTCTGGTGTATTTGA
1 ATTTTGAGTTATGGCTCAGTTTGTGTTATCTGTTGTCTGCCTTTGAATAATTCTGGTATATTTGA
* *
54999465 TTTTCTTTTTTTGATCCTACTGCTTGTTACTCTCTCTTATCTCAGACACTTCTGTCTGATTACTG
66 TTTTCTTTTTTCGATCCTACTGCTTGTTACTCTCTCTCATCTCAGACACTTCTGTCTGATTACTG
* *
54999530 TTTTTAGAAGAATTATTTAAAAGGTTTTGGTTTAGAGGAAATAGTGGACCGTTACCTCTGTTATT
131 TTTTTAGAACAATTATTTAAAAGGTTTTGGTTTAGAGGAAATAGTGGACCGTTACCTCTGCTATT
*
54999595 ATCCACTACATTGTCATTTGTGGTCACGATCCACCGCTATTGATGTGAAATTTGTTCACACCACT
196 ATCCACTACATTGTCATTTGTGGCCACGATCCACCGCTATTGATGTGAAATTTGTTCACACCACT
54999660 ATTA
261 ATTA
54999664 ATTTTGAGTTATGGCTCAGTTTGTGTTATCTGTTGTCTGCCTTTGAATAATTCTGGTATATTTGA
1 ATTTTGAGTTATGGCTCAGTTTGTGTTATCTGTTGTCTGCCTTTGAATAATTCTGGTATATTTGA
* *
54999729 TTTTCTTTTTTCGATCCTACTGCTTGTTACTCTCTCTCATCTCAGACTCTTCTGTCTGATTATTG
66 TTTTCTTTTTTCGATCCTACTGCTTGTTACTCTCTCTCATCTCAGACACTTCTGTCTGATTACTG
*
54999794 TTTTTAGAACAATTATTTAAAAGGTTTTGGTTTAGAGGAAATAGTGGACTGTTACCTCTGCTATT
131 TTTTTAGAACAATTATTTAAAAGGTTTTGGTTTAGAGGAAATAGTGGACCGTTACCTCTGCTATT
**
54999859 ATCCTTTACATTGTCATTTGTGGCCACGATCCACCGCTATTGATGTGAAATTTGTTCACACCACT
196 ATCCACTACATTGTCATTTGTGGCCACGATCCACCGCTATTGATGTGAAATTTGTTCACACCACT
54999924 ATTA
261 ATTA
*
54999928 AATTTG
1 ATTTTG
54999934 GTGGCAGACA
Statistics
Matches: 258, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
264 258 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (264 bp):
ATTTTGAGTTATGGCTCAGTTTGTGTTATCTGTTGTCTGCCTTTGAATAATTCTGGTATATTTGA
TTTTCTTTTTTCGATCCTACTGCTTGTTACTCTCTCTCATCTCAGACACTTCTGTCTGATTACTG
TTTTTAGAACAATTATTTAAAAGGTTTTGGTTTAGAGGAAATAGTGGACCGTTACCTCTGCTATT
ATCCACTACATTGTCATTTGTGGCCACGATCCACCGCTATTGATGTGAAATTTGTTCACACCACT
ATTA
Found at i:55005205 original size:14 final size:14
Alignment explanation
Indices: 55005186--55005217 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
55005176 ATAACTCTCT
*
55005186 AAATTTTGAAATGA
1 AAATTTTAAAATGA
55005200 AAATTTTAAAATGA
1 AAATTTTAAAATGA
55005214 AAAT
1 AAAT
55005218 ATATCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (14 bp):
AAATTTTAAAATGA
Found at i:55008086 original size:37 final size:37
Alignment explanation
Indices: 55008036--55008112 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
55008026 AAATTCGAGA
55008036 GTTAAATTTTGTTTTAGTTTGAAGTTTATAACAATAT
1 GTTAAATTTTGTTTTAGTTTGAAGTTTATAACAATAT
55008073 GTTAAATTTTGTTTTAGTTTGAAGTTTATAACAATAT
1 GTTAAATTTTGTTTTAGTTTGAAGTTTATAACAATAT
55008110 GTT
1 GTT
55008113 CTTATTTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (37 bp):
GTTAAATTTTGTTTTAGTTTGAAGTTTATAACAATAT
Found at i:55008545 original size:36 final size:36
Alignment explanation
Indices: 55008498--55008569 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
55008488 TTAAAAGTGG
*
55008498 GCAAATAAGGACAATTAGTTATGACGTTAATTTTTT
1 GCAAATAAGGACAATTAATTATGACGTTAATTTTTT
55008534 GCAAATAAGGACAATTAATTATGACGTTAATTTTTT
1 GCAAATAAGGACAATTAATTATGACGTTAATTTTTT
55008570 TTCTGTCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (36 bp):
GCAAATAAGGACAATTAATTATGACGTTAATTTTTT
Found at i:55008708 original size:51 final size:51
Alignment explanation
Indices: 55008647--55008768 Score: 174
Period size: 51 Copynumber: 2.4 Consensus size: 51
55008637 ATGTAAATGT
* *
55008647 TGACAG-ATGTGTAAATTTTGCAGGTTAAATTTGTTAAATCAGAATCAAGC
1 TGACAGAATGTGTAAATTTTGCAGGTTAAATTTGTTAAATCAAAATCAAAC
* * * *
55008697 TGACAGAATGTGTAAATGTTGCAGGTTAAATTTGTTAAATTAAAATTAAAT
1 TGACAGAATGTGTAAATTTTGCAGGTTAAATTTGTTAAATCAAAATCAAAC
*
55008748 TGACAAAATGTGTAAATTTTG
1 TGACAGAATGTGTAAATTTTG
55008769 AGGGCAAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 6 0.10
51 57 0.90
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (51 bp):
TGACAGAATGTGTAAATTTTGCAGGTTAAATTTGTTAAATCAAAATCAAAC
Found at i:55011197 original size:27 final size:26
Alignment explanation
Indices: 55011135--55011206 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
55011125 GCTCTAATTG
*
55011135 GATTAAGAAAATATTTTATATTTTTAA
1 GATTAA-AAAATATTTTTTATTTTTAA
**
55011162 TCTTCAAAAAATATTTTTTATTTTTAA
1 GATT-AAAAAATATTTTTTATTTTTAA
*
55011189 GATTAAAAAATCTTTTTT
1 GATTAAAAAATATTTTTT
55011207 CAAAAGTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 13 0.34
27 23 0.61
28 2 0.05
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (26 bp):
GATTAAAAAATATTTTTTATTTTTAA
Found at i:55015370 original size:55 final size:55
Alignment explanation
Indices: 55015286--55015417 Score: 255
Period size: 55 Copynumber: 2.4 Consensus size: 55
55015276 TTTCTTATCC
*
55015286 TTGAACTTGACAATTAAGTTTACTTCGGTACATGTTTTTTAGTCCATTTTGGCAT
1 TTGAACTTGACAATTAAGTTTACTTCGGTACATGTTTTTTAGTCCATTTTGACAT
55015341 TTGAACTTGACAATTAAGTTTACTTCGGTACATGTTTTTTAGTCCATTTTGACAT
1 TTGAACTTGACAATTAAGTTTACTTCGGTACATGTTTTTTAGTCCATTTTGACAT
55015396 TTGAACTTGACAATTAAGTTTA
1 TTGAACTTGACAATTAAGTTTA
55015418 TTTTTTTATC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 76 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.45
Consensus pattern (55 bp):
TTGAACTTGACAATTAAGTTTACTTCGGTACATGTTTTTTAGTCCATTTTGACAT
Found at i:55021551 original size:12 final size:12
Alignment explanation
Indices: 55021534--55021566 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
55021524 ATAAAAAAAG
55021534 TTTATTTTATTT
1 TTTATTTTATTT
55021546 TTTATTTTATTT
1 TTTATTTTATTT
55021558 TTTAATTTT
1 TTT-ATTTT
55021567 TAAGTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:55021574 original size:20 final size:20
Alignment explanation
Indices: 55021538--55021581 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
55021528 AAAAAGTTTA
* *
55021538 TTTTATTTTTTATTTTAT-T
1 TTTTATTTTTAAGTTTATAT
55021557 TTTTAATTTTTAAGTTTATAT
1 TTTT-ATTTTTAAGTTTATAT
55021578 TTTT
1 TTTT
55021582 TGTTCAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTATTTTTAAGTTTATAT
Found at i:55027976 original size:19 final size:20
Alignment explanation
Indices: 55027954--55027991 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55027944 TAACAAAATT
55027954 AATAAAAG-AAAAAATATAC
1 AATAAAAGTAAAAAATATAC
* *
55027973 AATAACAGTAAAAGATATA
1 AATAAAAGTAAAAAATATA
55027992 ATATAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.18
Consensus pattern (20 bp):
AATAAAAGTAAAAAATATAC
Found at i:55047427 original size:20 final size:21
Alignment explanation
Indices: 55047404--55047448 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
55047394 TTTTGAGCAA
55047404 TTTAA-TTTTTTTTATGT-TCT
1 TTTAACTTTTTTTTAT-TATCT
55047424 TTTAACTTTTTTTTATTATCT
1 TTTAACTTTTTTTTATTATCT
55047445 TTTA
1 TTTA
55047449 CTTCTCCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTAACTTTTTTTTATTATCT
Found at i:55051215 original size:21 final size:23
Alignment explanation
Indices: 55051189--55051233 Score: 76
Period size: 21 Copynumber: 2.0 Consensus size: 23
55051179 TTTCATCTAT
55051189 AGATAATTAATTA-A-AAAAATA
1 AGATAATTAATTATATAAAAATA
55051210 AGATAATTAATTATATAAAAATA
1 AGATAATTAATTATATAAAAATA
55051233 A
1 A
55051234 ATTTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 13 0.59
22 1 0.05
23 8 0.36
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (23 bp):
AGATAATTAATTATATAAAAATA
Found at i:55054559 original size:20 final size:21
Alignment explanation
Indices: 55054521--55054559 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
55054511 TGATTTGATT
55054521 AAATTTGTGATTAAATTAGTG
1 AAATTTGTGATTAAATTAGTG
*
55054542 AAATTTGT-ATTAATTTAG
1 AAATTTGTGATTAAATTAG
55054560 ATCAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (21 bp):
AAATTTGTGATTAAATTAGTG
Found at i:55054928 original size:43 final size:43
Alignment explanation
Indices: 55054835--55055006 Score: 131
Period size: 43 Copynumber: 4.0 Consensus size: 43
55054825 AGATGTGATC
*
55054835 ACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATT
1 ACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGAGATT
* * **
55054878 ACGTGTAAGACCGTGTCTGGGACATTGTTATCGTTAATT-A-ATT
1 ACATGTAAGACCATGTCTGGGACATTGGCATCG-T-ATTGAGATT
* * * * * *
55054921 TCATGTAAGACCCTGTATGGGACAGTGGCATCAATATGTG-G-TA
1 ACATGTAAGACCATGTCTGGGACATTGGCATC-GTAT-TGAGATT
* * * *
55054964 ACATGTAAGACCATATCTGGGATA-TGGCATTGTA-TGAGCTT
1 ACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGAGATT
55055005 AC
1 AC
55055007 GTGATTTCGA
Statistics
Matches: 99, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
39 2 0.02
40 1 0.01
41 5 0.05
42 8 0.08
43 78 0.79
44 2 0.02
45 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (43 bp):
ACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGAGATT
Found at i:55056213 original size:46 final size:46
Alignment explanation
Indices: 55056092--55056222 Score: 174
Period size: 46 Copynumber: 2.8 Consensus size: 46
55056082 TTTGACATGA
* * * * *
55056092 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGT
*
55056138 CGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
* *
55056184 TGCCATGGTATCTTTCAACCATGGTCTTATACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCAT
55056223 TTCAAAGAGC
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
45 5 0.07
46 70 0.93
ACGTcount: A:0.19, C:0.24, G:0.15, T:0.43
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
Found at i:55058087 original size:11 final size:11
Alignment explanation
Indices: 55058071--55058126 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
55058061 CTTTATATAC
55058071 TAATAAAATAA
1 TAATAAAATAA
55058082 TAATAAAATAA
1 TAATAAAATAA
* * **
55058093 TGA-AATATCT
1 TAATAAAATAA
* *
55058103 TACTAAAATAT
1 TAATAAAATAA
55058114 TAATAAAATAA
1 TAATAAAATAA
55058125 TA
1 TA
55058127 TTTATCTAAT
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
10 5 0.15
11 29 0.85
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:55058142 original size:43 final size:41
Alignment explanation
Indices: 55058071--55058154 Score: 96
Period size: 43 Copynumber: 2.0 Consensus size: 41
55058061 CTTTATATAC
*
55058071 TAATAAAATAATAATAAAATAATGAAATATCTTACTAAAATAT
1 TAATAAAATAATAATAAAATAATGAAATA-ATTA-TAAAATAT
* * ** *
55058114 TAATAAAATAATATTTATCTAATTAAATAATTATAAAATAT
1 TAATAAAATAATAATAAAATAATGAAATAATTATAAAATAT
55058155 CAAAATATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 8 0.23
42 3 0.09
43 24 0.69
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (41 bp):
TAATAAAATAATAATAAAATAATGAAATAATTATAAAATAT
Found at i:55064110 original size:36 final size:38
Alignment explanation
Indices: 55064063--55064155 Score: 109
Period size: 39 Copynumber: 2.5 Consensus size: 38
55064053 CAAAAAAGTT
* * *
55064063 TAGATCTCATTATAATC-CGAGAATCTGCAAC-AATGC
1 TAGATCTCATTATAATCTCAAGAATCTACAACAAATAC
**
55064099 TAGATCTCATTATGTTACTCAAGAATCTACAACAAATAC
1 TAGATCTCATTATAAT-CTCAAGAATCTACAACAAATAC
*
55064138 TAGATCTCGTTATAATCT
1 TAGATCTCATTATAATCT
55064156 ATAATAATCT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
36 14 0.30
37 1 0.02
38 14 0.30
39 17 0.37
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (38 bp):
TAGATCTCATTATAATCTCAAGAATCTACAACAAATAC
Found at i:55065140 original size:16 final size:16
Alignment explanation
Indices: 55065119--55065178 Score: 99
Period size: 16 Copynumber: 3.9 Consensus size: 16
55065109 TTATACTATA
55065119 ATTAATCTTTAATTAC
1 ATTAATCTTTAATTAC
55065135 ATTAATCTTTAATTAC
1 ATTAATCTTTAATTAC
55065151 ATTAATCTTTAATTAC
1 ATTAATCTTTAATTAC
55065167 -TTAA-C-TTAATTA
1 ATTAATCTTTAATTA
55065179 ATTTAATCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.16
14 1 0.02
15 4 0.09
16 32 0.73
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATCTTTAATTAC
Found at i:55065155 original size:32 final size:28
Alignment explanation
Indices: 55065117--55065186 Score: 95
Period size: 32 Copynumber: 2.3 Consensus size: 28
55065107 TTTTATACTA
55065117 TAATTAATCTTTAATTACATTAATCTTTAAT
1 TAATTAATCTTTAATTAC-TTAA-C-TTAAT
55065148 TACATTAATCTTTAATTACTTAACTTAAT
1 TA-ATTAATCTTTAATTACTTAACTTAAT
55065177 TAATTTAATC
1 TAA-TTAATC
55065187 ATGTTTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
28 1 0.03
29 13 0.35
30 1 0.03
31 6 0.16
32 16 0.43
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (28 bp):
TAATTAATCTTTAATTACTTAACTTAAT
Found at i:55065633 original size:35 final size:35
Alignment explanation
Indices: 55065582--55065655 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
55065572 AACTCAAGAG
55065582 TTTAAATATCAAACTAGATTACGACAATGAAATAA
1 TTTAAATATCAAACTAGATTACGACAATGAAATAA
*
55065617 TTTATATATCAAACTAGATTACGACAATGAAATAA
1 TTTAAATATCAAACTAGATTACGACAATGAAATAA
55065652 TTTA
1 TTTA
55065656 GGTAACAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (35 bp):
TTTAAATATCAAACTAGATTACGACAATGAAATAA
Found at i:55067032 original size:31 final size:31
Alignment explanation
Indices: 55066994--55067054 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
55066984 TCGAGGTAAG
55066994 TTCATGTAACTTGAATTATATTCTTAAATGC
1 TTCATGTAACTTGAATTATATTCTTAAATGC
55067025 TTCATGTAACTTGAATTATATTCTTAAATG
1 TTCATGTAACTTGAATTATATTCTTAAATG
55067055 TTTGAAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (31 bp):
TTCATGTAACTTGAATTATATTCTTAAATGC
Found at i:55067983 original size:23 final size:24
Alignment explanation
Indices: 55067942--55067998 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
55067932 CCCAACAATC
55067942 AAACCCAAATATACCCTAACCCTA
1 AAACCCAAATATACCCTAACCCTA
55067966 AAACCC-AATA-ACCACTAACCC-A
1 AAACCCAAATATACC-CTAACCCTA
55067988 AGAA-CCAAATA
1 A-AACCCAAATA
55067999 CTTAGCCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 7 0.23
23 17 0.57
24 6 0.20
ACGTcount: A:0.51, C:0.35, G:0.02, T:0.12
Consensus pattern (24 bp):
AAACCCAAATATACCCTAACCCTA
Found at i:55068511 original size:17 final size:18
Alignment explanation
Indices: 55068489--55068524 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55068479 ACAGAGGTGA
*
55068489 TTTTCTTT-TTTTTTTTC
1 TTTTCTTTGTTTTGTTTC
55068506 TTTTCTTTGTTTTGTTTC
1 TTTTCTTTGTTTTGTTTC
55068524 T
1 T
55068525 AGGTTTATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (18 bp):
TTTTCTTTGTTTTGTTTC
Found at i:55068711 original size:11 final size:11
Alignment explanation
Indices: 55068695--55068719 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55068685 CTCCCCTCTC
55068695 TCTTTTTTTTT
1 TCTTTTTTTTT
55068706 TCTTTTTTTTT
1 TCTTTTTTTTT
55068717 TCT
1 TCT
55068720 CTTCTGCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:55069004 original size:30 final size:31
Alignment explanation
Indices: 55068945--55069009 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
55068935 GATTTTTTTA
* *
55068945 TTTTCAATTTAGCCCCACAATTTGTTGCGC-
1 TTTTCAATTTAGCCCCACAATCTGCTGCGCG
*
55068975 TTTTCAATTTGGCCCC-CAATGCTGCTGCGCG
1 TTTTCAATTTAGCCCCACAAT-CTGCTGCGCG
55069006 TTTT
1 TTTT
55069010 GATTGAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 4 0.13
30 22 0.73
31 4 0.13
ACGTcount: A:0.15, C:0.28, G:0.17, T:0.40
Consensus pattern (31 bp):
TTTTCAATTTAGCCCCACAATCTGCTGCGCG
Found at i:55069216 original size:17 final size:18
Alignment explanation
Indices: 55069186--55069232 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
55069176 CTGTTATTTA
* *
55069186 TTATTATTAATTATAATCT
1 TTATTA-TATTTATAATAT
*
55069205 TTA-TATATTTATTATAT
1 TTATTATATTTATAATAT
55069222 TTATTATATTT
1 TTATTATATTT
55069233 TATATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 12 0.50
18 9 0.38
19 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATTATATTTATAATAT
Found at i:55069220 original size:9 final size:9
Alignment explanation
Indices: 55069180--55069232 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 9
55069170 CATTTTCTGT
55069180 TATTTATTA
1 TATTTATTA
*
55069189 TTATTAATTA
1 -TATTTATTA
55069199 TAATCTT-TATA
1 T-AT-TTAT-TA
55069210 TATTTATTA
1 TATTTATTA
55069219 TATTTATTA
1 TATTTATTA
55069228 TATTT
1 TATTT
55069233 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 19 0.51
10 14 0.38
11 4 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (9 bp):
TATTTATTA
Found at i:55069228 original size:20 final size:20
Alignment explanation
Indices: 55069180--55069241 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
55069170 CATTTTCTGT
*
55069180 TATTTATTAT-TATTAATTA
1 TATTTATTATATATTTATTA
*
55069199 TAATCT-TTATATATTTATTA
1 T-ATTTATTATATATTTATTA
55069219 TATTTATTATAT-TTTATATA
1 TATTTATTATATATTTAT-TA
55069239 TAT
1 TAT
55069242 AGTAGTGTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
19 13 0.36
20 23 0.64
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTATTATATATTTATTA
Done.