Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 6 of 26
Found at i:1061030 original size:16 final size:16
Alignment explanation
Indices: 1060966--1061037 Score: 69
Period size: 15 Copynumber: 4.6 Consensus size: 16
1060956 TTTTAAATTT
1060966 TAATTTAAACTTT-AAA
1 TAATTTAAA-TTTAAAA
*
1060982 -AATATAAATTTAAAA
1 TAATTTAAATTTAAAA
* *
1060997 AAAATTATAATTTAAAA
1 TAATTTA-AATTTAAAA
*
1061014 TAATTTAAATTTTAAA
1 TAATTTAAATTTAAAA
1061030 T-ATTTAAA
1 TAATTTAAA
1061038 ACATAAAATC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
14 3 0.06
15 17 0.36
16 13 0.28
17 14 0.30
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATTTAAATTTAAAA
Found at i:1061416 original size:2 final size:2
Alignment explanation
Indices: 1061409--1061438 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1061399 TTTGTCAATT
1061409 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1061439 GATTTAGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1061944 original size:27 final size:29
Alignment explanation
Indices: 1061891--1061944 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
1061881 TTTTAATGTA
1061891 TTAAAATTATTCAATTTATATAAATATCT
1 TTAAAATTATTCAATTTATATAAATATCT
1061920 TTAAAATT-TT-ATATTTA-ATAAATAT
1 TTAAAATTATTCA-ATTTATATAAATAT
1061945 AAAATTCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.38
28 7 0.29
29 8 0.33
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (29 bp):
TTAAAATTATTCAATTTATATAAATATCT
Found at i:1062915 original size:23 final size:23
Alignment explanation
Indices: 1062889--1062949 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
1062879 TCTGTTGTTC
1062889 AAATTATTATTTA-AATAATATTA
1 AAATTATT-TTTATAATAATATTA
*
1062912 AAATTATTTTTATATTAATATTTA
1 AAATTATTTTTATAATAATA-TTA
*
1062936 TAA--ATTTTTATAAT
1 AAATTATTTTTATAAT
1062950 TAAATTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 14 0.42
23 14 0.42
24 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AAATTATTTTTATAATAATATTA
Found at i:1064292 original size:23 final size:23
Alignment explanation
Indices: 1064262--1064308 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1064252 TAAGCTTTCA
1064262 TGAAAAAGAAGGCTGCACTTAGT
1 TGAAAAAGAAGGCTGCACTTAGT
1064285 TGAAAAAGAAGGCTGCACTTAGT
1 TGAAAAAGAAGGCTGCACTTAGT
1064308 T
1 T
1064309 TAATGTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (23 bp):
TGAAAAAGAAGGCTGCACTTAGT
Found at i:1065245 original size:22 final size:21
Alignment explanation
Indices: 1065203--1065261 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
1065193 AAATTTTAAC
*
1065203 TAAAATATATTAACATAATTA
1 TAAAATATATTAAAATAATTA
1065224 TAAAATTATATTAAAA-ATATTA
1 TAAAA-TATATTAAAATA-ATTA
*
1065246 TAATAA-ATATTTAAAT
1 TAA-AATATATTAAAAT
1065262 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 14 0.44
22 16 0.50
23 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAATATATTAAAATAATTA
Found at i:1070250 original size:23 final size:20
Alignment explanation
Indices: 1070220--1070261 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 20
1070210 TTTTTTATAT
1070220 AAATTTAATTATAAAATATAAA
1 AAATTTAATT-TAAAA-ATAAA
1070242 AAATATTAATTTAAAAATAA
1 AAAT-TTAATTTAAAAATAA
1070262 TAATAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTTAATTTAAAAATAAA
Found at i:1070261 original size:28 final size:30
Alignment explanation
Indices: 1070216--1070280 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
1070206 AATATTTTTT
* **
1070216 ATATAAATTTAATTATAA-AAT-ATAAAAA
1 ATATTAATTTAAAAATAATAATAATAAAAA
*
1070244 ATATTAATTTAAAAATAATAATAATTAAAA
1 ATATTAATTTAAAAATAATAATAATAAAAA
*
1070274 ATTTTAA
1 ATATTAA
1070281 ATCAAATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 15 0.50
29 3 0.10
30 12 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
ATATTAATTTAAAAATAATAATAATAAAAA
Found at i:1070271 original size:16 final size:17
Alignment explanation
Indices: 1070239--1070275 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1070229 TATAAAATAT
*
1070239 AAAA-AATATTAATTTA
1 AAAATAATAATAATTTA
1070255 AAAATAATAATAA-TTA
1 AAAATAATAATAATTTA
1070271 AAAAT
1 AAAAT
1070276 TTTAAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATAATAATAATTTA
Found at i:1070765 original size:5 final size:5
Alignment explanation
Indices: 1070755--1070794 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
1070745 CTATAATTGC
* *
1070755 TTCTT TTCTT TTCCT TTCTT TTC-T TTCTT TTCCT TTCTT T
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT T
1070795 CTTCTTTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (5 bp):
TTCTT
Found at i:1070774 original size:10 final size:10
Alignment explanation
Indices: 1070759--1070794 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
1070749 AATTGCTTCT
1070759 TTTCTTTTCC
1 TTTCTTTTCC
1070769 TTTCTTTT-C
1 TTTCTTTTCC
1070778 TTTCTTTTCC
1 TTTCTTTTCC
1070788 TTTCTTT
1 TTTCTTT
1070795 CTTCTTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTCTTTTCC
Found at i:1072641 original size:19 final size:18
Alignment explanation
Indices: 1072570--1072642 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 18
1072560 GTTAAAATCA
1072570 AAATTTAATATTTTTTTT
1 AAATTTAATATTTTTTTT
* *
1072588 AAA--TAGATCTATTTTTT
1 AAATTTA-ATATTTTTTTT
1072605 --ATTT-ATATTTATTTTTT
1 AAATTTAATA-TT-TTTTTT
1072622 AAATTTAATATTTTTATTT
1 AAATTTAATATTTTT-TTT
1072641 AA
1 AA
1072643 TTCTTCTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 17
0.67 0.06 0.27
Matches are distributed among these distances:
15 3 0.07
16 3 0.07
17 16 0.38
18 6 0.14
19 11 0.26
20 3 0.07
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (18 bp):
AAATTTAATATTTTTTTT
Found at i:1072831 original size:17 final size:17
Alignment explanation
Indices: 1072789--1072831 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1072779 ATAAAAATTT
*
1072789 TTATAAATTAAATTAAA
1 TTATAATTTAAATTAAA
*
1072806 TTATTATTTAAATTACAA
1 TTATAATTTAAATTA-AA
1072824 TT-TAATTT
1 TTATAATTT
1072832 CGCTCATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATAATTTAAATTAAA
Found at i:1072898 original size:30 final size:30
Alignment explanation
Indices: 1072864--1072922 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1072854 TTAAAAAAAA
* *
1072864 AATTT-AATTATATAAATAATAATTTAAATT
1 AATTTAAAATATAAAAATAA-AATTTAAATT
1072894 AATTTAAAATATAAAAATAAAATTTAAAT
1 AATTTAAAATATAAAAATAAAATTTAAAT
1072923 CCAAAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AATTTAAAATATAAAAATAAAATTTAAATT
Found at i:1073034 original size:2 final size:2
Alignment explanation
Indices: 1073027--1073066 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1073017 GCAAACGTGG
1073027 AT 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 AT
1073067 TTGGGTGCTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1075506 original size:21 final size:24
Alignment explanation
Indices: 1075475--1075531 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
1075465 TGACTTGAAT
*
1075475 TAAATA-A-TAAT-AAATATAATA
1 TAAATATATTAATAAAATATAACA
1075496 TAAA-A-ATTAATTAAAATATAACA
1 TAAATATATTAA-TAAAATATAACA
1075519 TAAATATATTAAT
1 TAAATATATTAAT
1075532 TTCTTAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 7 0.23
22 1 0.03
23 13 0.43
24 2 0.07
25 5 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
TAAATATATTAATAAAATATAACA
Found at i:1075512 original size:23 final size:25
Alignment explanation
Indices: 1075486--1075532 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
1075476 AAATAATAAT
*
1075486 AAATATAATATAAA-A-ATTAATTA
1 AAATATAACATAAATATATTAATTA
1075509 AAATATAACATAAATATATTAATT
1 AAATATAACATAAATATATTAATT
1075533 TCTTAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 1 0.05
25 7 0.33
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
AAATATAACATAAATATATTAATTA
Found at i:1075578 original size:26 final size:27
Alignment explanation
Indices: 1075536--1075598 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
1075526 ATTAATTTCT
1075536 TAAAAACATATCAAAAT-TTA-TATAAA
1 TAAAAA-ATATCAAAATATTATTATAAA
* *
1075562 TAAAAAATATCTTAAATATTATTATAAT
1 TAAAAAATATC-AAAATATTATTATAAA
*
1075590 TTAAAAATA
1 TAAAAAATA
1075599 AATATAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 5 0.16
26 10 0.32
27 3 0.10
28 13 0.42
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (27 bp):
TAAAAAATATCAAAATATTATTATAAA
Found at i:1075600 original size:23 final size:23
Alignment explanation
Indices: 1075574--1075620 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1075564 AAAAATATCT
*
1075574 TAAATATTAT-TATAATTTAAAAA
1 TAAATATAATATA-AATTTAAAAA
1075597 TAAATATAATATAAATTTAAAAA
1 TAAATATAATATAAATTTAAAAA
1075620 T
1 T
1075621 TATCAAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATATAATATAAATTTAAAAA
Found at i:1075848 original size:2 final size:2
Alignment explanation
Indices: 1075841--1075881 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1075831 CAAACTGGAA
1075841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1075882 GATAGAAGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1080338 original size:2 final size:2
Alignment explanation
Indices: 1080325--1080363 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1080315 AATAGGATAA
*
1080325 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1080364 AGGAAAATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1080711 original size:13 final size:13
Alignment explanation
Indices: 1080693--1080717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1080683 TATATGTAAA
1080693 TAAATATTTAATT
1 TAAATATTTAATT
1080706 TAAATATTTAAT
1 TAAATATTTAAT
1080718 ATTATTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAATATTTAATT
Found at i:1081393 original size:4 final size:4
Alignment explanation
Indices: 1081384--1081409 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1081374 GGTTGCACCA
1081384 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1081410 GATTAGCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1085057 original size:2 final size:2
Alignment explanation
Indices: 1085050--1085080 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1085040 TTTAGCAAGC
1085050 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1085081 AATGTAGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1086152 original size:19 final size:18
Alignment explanation
Indices: 1086128--1086163 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1086118 ATTATGTCAT
1086128 TTTATTTATATAAAAATAA
1 TTTATTTATA-AAAAATAA
*
1086147 TTTATTTTTAAAAAATA
1 TTTATTTATAAAAAATA
1086164 TAATAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATTTATAAAAAATAA
Found at i:1086200 original size:18 final size:18
Alignment explanation
Indices: 1086155--1086188 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1086145 AATTTATTTT
1086155 TAAAA-AATATAATAAAA
1 TAAAATAATATAATAAAA
1086172 TAAAATAATATAATAAA
1 TAAAATAATATAATAAA
1086189 TTAATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAATAATATAATAAAA
Found at i:1086207 original size:16 final size:16
Alignment explanation
Indices: 1086160--1086199 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1086150 ATTTTTAAAA
*
1086160 AATATAATAAAATAAAAT
1 AATATAAT-AAAT-TAAT
1086178 AATATAATAAATTAAT
1 AATATAATAAATTAAT
1086194 AATATA
1 AATATA
1086200 TCAAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 4 0.19
18 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATATAATAAATTAAT
Found at i:1086867 original size:32 final size:33
Alignment explanation
Indices: 1086831--1086894 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
1086821 ATTTGAATAA
1086831 ATTTT-AATATGTTAATTAT-TCATATTATATAG
1 ATTTTAAATATG-TAATTATATCATATTATATAG
*
1086863 ATTTTAAAATATGTATTTATATCATATTATAT
1 ATTTT-AAATATGTAATTATATCATATTATAT
1086895 TTTAAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 5 0.18
33 6 0.21
34 17 0.61
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (33 bp):
ATTTTAAATATGTAATTATATCATATTATATAG
Found at i:1090474 original size:6 final size:6
Alignment explanation
Indices: 1090458--1090497 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
1090448 AATTCCAACG
*
1090458 GGGGAGA GGGGGA GGGGGA GGGGGA GGGGGA TGGGGA GGG
1 GGGG-GA GGGGGA GGGGGA GGGGGA GGGGGA GGGGGA GGG
1090498 AGATTTGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.17, C:0.00, G:0.80, T:0.03
Consensus pattern (6 bp):
GGGGGA
Found at i:1090537 original size:7 final size:7
Alignment explanation
Indices: 1090505--1090539 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1090495 GGGAGATTTG
1090505 AACCTTC
1 AACCTTC
*
1090512 AACCGTC
1 AACCTTC
*
1090519 AACCGTC
1 AACCTTC
1090526 AACCTTC
1 AACCTTC
1090533 AACCTTC
1 AACCTTC
1090540 TATTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.29, C:0.43, G:0.06, T:0.23
Consensus pattern (7 bp):
AACCTTC
Found at i:1090879 original size:2 final size:2
Alignment explanation
Indices: 1090872--1090897 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1090862 CGATCAAATC
1090872 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
1090898 CCTTAATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1091646 original size:3 final size:3
Alignment explanation
Indices: 1091632--1091691 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
1091622 GTGTTTTTGA
* *
1091632 ATT ATT -TT ATT ATT ATT ATT A-T AGTT ATT ATTT GTT ATT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A-TT ATT ATT ATT ATT
*
1091677 ATT TTT ATT ATT ATT
1 ATT ATT ATT ATT ATT
1091692 GGTTTGATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.09
3 39 0.83
4 4 0.09
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1091912 original size:29 final size:30
Alignment explanation
Indices: 1091880--1091977 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 30
1091870 AATTTAATAA
1091880 ATTTATA-TATTTATTTTATATCATATTAT
1 ATTTATATTATTTATTTTATATCATATTAT
*
1091909 ATTTTTATTATTATTATATTTATA-CATATATTAT
1 ATTTATATTA-T-TTAT-TTTATATC--ATATTAT
*
1091943 ATTTAAAATTATTT-TTTTATATCATA-TAT
1 ATTT-ATATTATTTATTTTATATCATATTAT
1091972 ATTTAT
1 ATTTAT
1091978 CTCACTTATC
Statistics
Matches: 57, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
28 1 0.02
29 13 0.23
30 5 0.09
31 7 0.12
32 7 0.12
33 8 0.14
34 12 0.21
35 4 0.07
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (30 bp):
ATTTATATTATTTATTTTATATCATATTAT
Found at i:1091930 original size:46 final size:46
Alignment explanation
Indices: 1091880--1091977 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 46
1091870 AATTTAATAA
* * * * * *
1091880 ATTTATATATTTATTTTATATCATATTATATTTTTATTATTAT-TAT
1 ATTTATACATATATTATATATAAAATTATATTTTTA-TATCATATAT
* *
1091926 ATTTATACATATATTATATTTAAAATTATTTTTTTATATCATATAT
1 ATTTATACATATATTATATATAAAATTATATTTTTATATCATATAT
1091972 ATTTAT
1 ATTTAT
1091978 CTCACTTATC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
45 5 0.12
46 38 0.88
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (46 bp):
ATTTATACATATATTATATATAAAATTATATTTTTATATCATATAT
Found at i:1091931 original size:23 final size:22
Alignment explanation
Indices: 1091880--1091932 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
1091870 AATTTAATAA
1091880 ATTTATATATTTATTTTATATC
1 ATTTATATATTTATTTTATATC
*
1091902 ATATTATATTTTTATTATTATTAT-
1 AT-TTATATATTTATT-TTA-TATC
1091926 ATTTATA
1 ATTTATA
1091933 CATATATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 2 0.07
23 17 0.63
24 5 0.19
25 3 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTTATATATTTATTTTATATC
Found at i:1091940 original size:17 final size:16
Alignment explanation
Indices: 1091779--1091977 Score: 75
Period size: 17 Copynumber: 12.4 Consensus size: 16
1091769 TTTATTTAAT
1091779 TATTTAT-ATATATTAA
1 TATTTATAATATATT-A
1091795 TATATTATATATTATAATTA
1 TAT-TTATA-A-TAT-ATTA
1091815 T-TTTA-AAT-TATTA
1 TATTTATAATATATTA
*
1091828 TATATTTTAAATATATTCA
1 TAT-TTAT-AATATATT-A
*
1091847 TA--AATAATATTATATA
1 TATTTATAATA-TAT-TA
* * * *
1091863 AATTTAAAATTTAATA
1 TATTTATAATATATTA
*
1091879 AATTTAT-ATAT-TTA
1 TATTTATAATATATTA
1091893 T-TTTAT-ATCATATTA
1 TATTTATAAT-ATATTA
* *
1091908 TATTTTTATTATTATTA
1 TATTTATAATA-TATTA
1091925 TATTTATACATATATTA
1 TATTTATA-ATATATTA
*
1091942 TATTTAAAAT-TATT-
1 TATTTATAATATATTA
*
1091956 TTTTTAT-ATCATA-TA
1 TATTTATAAT-ATATTA
1091971 TATTTAT
1 TATTTAT
1091978 CTCACTTATC
Statistics
Matches: 139, Mismatches: 20, Indels: 49
0.67 0.10 0.24
Matches are distributed among these distances:
13 14 0.10
14 12 0.09
15 26 0.19
16 25 0.18
17 36 0.26
18 13 0.09
19 5 0.04
20 5 0.04
21 3 0.02
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTATAATATATTA
Found at i:1092133 original size:18 final size:18
Alignment explanation
Indices: 1092110--1092186 Score: 60
Period size: 18 Copynumber: 4.4 Consensus size: 18
1092100 ATATTACAAT
1092110 TATATTTAAAATATTATA
1 TATATTTAAAATATTATA
1092128 TATATTATAAATATATTA-A
1 TATATT-TAAA-ATATTATA
1092147 TA-A-TT--AATATTATA
1 TATATTTAAAATATTATA
*
1092161 TAAATTTTAATAA-ATT-TA
1 TATA-TTTAA-AATATTATA
1092179 TATATTTA
1 TATATTTA
1092187 TATTATATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 19
0.71 0.01 0.28
Matches are distributed among these distances:
13 6 0.12
14 4 0.08
15 1 0.02
16 1 0.02
17 7 0.14
18 12 0.24
19 10 0.20
20 8 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATTTAAAATATTATA
Found at i:1092142 original size:29 final size:31
Alignment explanation
Indices: 1092097--1092162 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 31
1092087 ATATATTTTT
*
1092097 TATATATTACAATTATATT-TAA-AATATTA
1 TATATATTACAAATATATTATAATAATATTA
*
1092126 TATATATTATAAATATATTAATAATTAATATTA
1 TATATATTACAAATATATT-ATAA-TAATATTA
1092159 TATA
1 TATA
1092163 AATTTTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 17 0.55
31 3 0.10
33 11 0.35
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (31 bp):
TATATATTACAAATATATTATAATAATATTA
Found at i:1092143 original size:11 final size:11
Alignment explanation
Indices: 1092098--1092160 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
1092088 TATATTTTTT
*
1092098 ATATATTACAA
1 ATATATTATAA
*
1092109 TTATATT-TAA
1 ATATATTATAA
1092119 A-ATATTAT--
1 ATATATTATAA
1092127 ATATATTATAA
1 ATATATTATAA
1092138 ATATATTAATAA
1 ATATATT-ATAA
*
1092150 TTAATATTATA
1 AT-ATATTATA
1092161 TAAATTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
8 1 0.02
9 12 0.29
10 3 0.07
11 13 0.31
12 8 0.19
13 5 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
ATATATTATAA
Found at i:1092161 original size:33 final size:33
Alignment explanation
Indices: 1092119--1092194 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
1092109 TTATATTTAA
* *
1092119 AATATTATATATATTATAAATATATTAATA-ATT
1 AATATTATATAAATT-TAAATAAATTAATATATT
* *
1092152 AATATTATATAAATTTTAATAAATTTATATATT
1 AATATTATATAAATTTAAATAAATTAATATATT
*
1092185 TATATTATAT
1 AATATTATAT
1092195 TTTATTTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.30
33 26 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
AATATTATATAAATTTAAATAAATTAATATATT
Found at i:1092485 original size:18 final size:18
Alignment explanation
Indices: 1092435--1092551 Score: 63
Period size: 18 Copynumber: 6.8 Consensus size: 18
1092425 TAATAATAGC
*
1092435 ATATT-TATATTTTT-AT
1 ATATTATATATTTTTAAA
*
1092451 GTATTATA-ATTTATTTAAA
1 ATATTATATA-TT-TTTAAA
*
1092470 ATATTATATATTTTTAAT
1 ATATTATATATTTTTAAA
*
1092488 ATATTA-ATA--ATT--A
1 ATATTATATATTTTTAAA
1092501 ATATTATATAAATTTTTAAA
1 ATATTATAT--ATTTTTAAA
* * **
1092521 AAATTATATATTTATATC
1 ATATTATATATTTTTAAA
1092539 ATATTATAT-TTTT
1 ATATTATATATTTT
1092552 ATCATATTTT
Statistics
Matches: 76, Mismatches: 13, Indels: 23
0.68 0.12 0.21
Matches are distributed among these distances:
13 6 0.08
14 2 0.03
15 2 0.03
16 6 0.08
17 10 0.13
18 30 0.39
19 10 0.13
20 10 0.13
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (18 bp):
ATATTATATATTTTTAAA
Found at i:1092546 original size:16 final size:16
Alignment explanation
Indices: 1092527--1092559 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1092517 TAAAAAATTA
1092527 TATATTTATATCATAT
1 TATATTTATATCATAT
*
1092543 TATATTTTTATCATAT
1 TATATTTATATCATAT
1092559 T
1 T
1092560 TTAATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATTTATATCATAT
Found at i:1092625 original size:36 final size:35
Alignment explanation
Indices: 1092551--1092629 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 35
1092541 ATTATATTTT
* * *
1092551 TATCATATTTTAATTATTATTTTATTTTATACATG
1 TATCATATTTTAATTATTATTTTATGTCATACAAG
* *
1092586 TATCAT-TTTTAAATTTATTATTTTGTGTCATATAAG
1 TATCATATTTT-AA-TTATTATTTTATGTCATACAAG
1092622 TATCATAT
1 TATCATAT
1092630 CTTTTCTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 4 0.11
35 8 0.22
36 23 0.64
37 1 0.03
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.57
Consensus pattern (35 bp):
TATCATATTTTAATTATTATTTTATGTCATACAAG
Found at i:1093300 original size:16 final size:18
Alignment explanation
Indices: 1093281--1093321 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
1093271 TATTATACTT
1093281 AAAAATTAAAT-T-TTAA
1 AAAAATTAAATCTATTAA
*
1093297 AAAAATTAAATCTATTTA
1 AAAAATTAAATCTATTAA
1093315 AAAAATT
1 AAAAATT
1093322 GAGTTGAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.50
17 1 0.05
18 10 0.45
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAATTAAATCTATTAA
Found at i:1093479 original size:19 final size:18
Alignment explanation
Indices: 1093441--1093477 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
1093431 ATAATATGAT
1093441 TATATAAATATTAAAAAA
1 TATATAAATATTAAAAAA
1093459 TATATTAAATTATTAAAAA
1 TATA-TAAA-TATTAAAAA
1093478 TAAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TATATAAATATTAAAAAA
Found at i:1094303 original size:10 final size:10
Alignment explanation
Indices: 1094288--1094323 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1094278 CAAAGATAAG
1094288 ATATTATTAA
1 ATATTATTAA
1094298 ATATTATTAA
1 ATATTATTAA
*
1094308 ATGTTATTAA
1 ATATTATTAA
1094318 A-ATTAT
1 ATATTAT
1094324 ATCTAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (10 bp):
ATATTATTAA
Found at i:1095602 original size:19 final size:18
Alignment explanation
Indices: 1095571--1095607 Score: 65
Period size: 18 Copynumber: 2.0 Consensus size: 18
1095561 AATTAAATTA
1095571 TTTATTTAAATTTAAAAT
1 TTTATTTAAATTTAAAAT
1095589 TTTATTTAATATTTAAAAT
1 TTTATTTAA-ATTTAAAAT
1095608 AATTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTATTTAAATTTAAAAT
Found at i:1097473 original size:3 final size:3
Alignment explanation
Indices: 1097465--1097495 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1097455 AAATAATTTT
1097465 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1097496 AGTAGGGGCT
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):
ATA
Found at i:1102958 original size:21 final size:22
Alignment explanation
Indices: 1102934--1102984 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
1102924 ACCATAATTA
*
1102934 TTGACT-ATTCTTTACCAACCT
1 TTGACTAATTCTTCACCAACCT
1102955 TTGA-TAATTCTTCACCAACCT
1 TTGACTAATTCTTCACCAACCT
1102976 TTGAC-AATT
1 TTGACTAATT
1102985 GAGAGAGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.41
Consensus pattern (22 bp):
TTGACTAATTCTTCACCAACCT
Found at i:1103000 original size:71 final size:71
Alignment explanation
Indices: 1102894--1103029 Score: 186
Period size: 71 Copynumber: 1.9 Consensus size: 71
1102884 TTGACTATTA
*
1102894 TTCATCAACCTTTGACAATCAAGAAAGGTGACCATAATTATTGACTATTCTTT-ACCAACCTTTG
1 TTCACCAACCTTTGACAATCAAGAAAGGTGACCATAATTATTGACTATT-TTTCACCAACCTTTG
1102958 ATAATTC
65 ATAATTC
** * * *
1102965 TTCACCAACCTTTGACAATTGAGAGAGGT-AGCCATAATTATTGATTATTTTTCACCAACTTTTG
1 TTCACCAACCTTTGACAATCAAGAAAGGTGA-CCATAATTATTGACTATTTTTCACCAACCTTTG
1103029 A
65 A
1103030 CAATCGAGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
70 4 0.07
71 53 0.93
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (71 bp):
TTCACCAACCTTTGACAATCAAGAAAGGTGACCATAATTATTGACTATTTTTCACCAACCTTTGA
TAATTC
Found at i:1107575 original size:50 final size:50
Alignment explanation
Indices: 1107388--1107568 Score: 229
Period size: 50 Copynumber: 3.6 Consensus size: 50
1107378 GGGAGAGGAA
* *
1107388 TGTTGATTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGGTCATAAT
1 TGTTGACTATTATTTACCAACCTTTGACAATCGAGAGAGGTGGTCATAAT
* * * *
1107438 TGTTGACGATT-TTTCATCAACATTTGACAATCGAGAGAGGTGGCCATAAT
1 TGTTGACTATTATTT-ACCAACCTTTGACAATCGAGAGAGGTGGTCATAAT
* * * ** *
1107488 TGTTGACAATTATTCACCAACCTTTAACAATCGAGAGAGGTAATAATAAT
1 TGTTGACTATTATTTACCAACCTTTGACAATCGAGAGAGGTGGTCATAAT
*
1107538 TGTTGACTATTATTTACCAACTTTTGACAAT
1 TGTTGACTATTATTTACCAACCTTTGACAAT
1107569 ATAGAGAAGT
Statistics
Matches: 111, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 3 0.03
50 106 0.95
51 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (50 bp):
TGTTGACTATTATTTACCAACCTTTGACAATCGAGAGAGGTGGTCATAAT
Found at i:1107588 original size:50 final size:50
Alignment explanation
Indices: 1107388--1107593 Score: 225
Period size: 50 Copynumber: 4.1 Consensus size: 50
1107378 GGGAGAGGAA
* * *
1107388 TGTTGATTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGGTCATAAT
1 TGTTGACTATTATTTACCAACCTTTGACAATCGAGAGAGGTGATCATAAT
* * * **
1107438 TGTTGACGATT-TTTCATCAACATTTGACAATCGAGAGAGGTGGCCATAAT
1 TGTTGACTATTATTT-ACCAACCTTTGACAATCGAGAGAGGTGATCATAAT
* * * * *
1107488 TGTTGACAATTATTCACCAACCTTTAACAATCGAGAGAGGTAATAATAAT
1 TGTTGACTATTATTTACCAACCTTTGACAATCGAGAGAGGTGATCATAAT
* ** * *
1107538 TGTTGACTATTATTTACCAACTTTTGACAATATAGAGAAGTGATCGTAAT
1 TGTTGACTATTATTTACCAACCTTTGACAATCGAGAGAGGTGATCATAAT
*
1107588 TATTGA
1 TGTTGA
1107594 TTCTAAACAA
Statistics
Matches: 129, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
49 3 0.02
50 124 0.96
51 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (50 bp):
TGTTGACTATTATTTACCAACCTTTGACAATCGAGAGAGGTGATCATAAT
Found at i:1109399 original size:28 final size:28
Alignment explanation
Indices: 1109354--1109407 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
1109344 AATATATTAA
*
1109354 ATATAAATTAAAAGATAAAATTTATTTGT
1 ATATAAATGAAAAGAT-AAATTTATTTGT
*
1109383 ATAT-AATGAAAATATAAATTTATTT
1 ATATAAATGAAAAGATAAATTTATTT
1109408 TTTTAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 10 0.43
28 9 0.39
29 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (28 bp):
ATATAAATGAAAAGATAAATTTATTTGT
Found at i:1109758 original size:20 final size:21
Alignment explanation
Indices: 1109733--1109775 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
1109723 ATTCAAAAAA
*
1109733 AAATTTAAATTTTA-TTATTT
1 AAATTTAAATTTGATTTATTT
1109753 AAATTTAAATTTGATTTATTT
1 AAATTTAAATTTGATTTATTT
1109774 AA
1 AA
1109776 TTATTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AAATTTAAATTTGATTTATTT
Found at i:1109819 original size:33 final size:33
Alignment explanation
Indices: 1109779--1109849 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 33
1109769 TATTTAATTA
1109779 TTTATATTTAATAAAAAAATT-ATAAAAAATATT
1 TTTATATTT-ATAAAAAAATTAATAAAAAATATT
**
1109812 TTTATATTTATAATTAAATTCAAATAAAAAATATT
1 TTTATATTTATAAAAAAATT--AATAAAAAATATT
1109847 TTT
1 TTT
1109850 TAATTATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 9 0.27
33 9 0.27
35 15 0.45
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (33 bp):
TTTATATTTATAAAAAAATTAATAAAAAATATT
Found at i:1110152 original size:59 final size:58
Alignment explanation
Indices: 1110085--1110210 Score: 134
Period size: 59 Copynumber: 2.2 Consensus size: 58
1110075 AATTAAATTA
* * *
1110085 ATTA-ATTAAAAAATAA-ATTATTTATATTAT-TATATATAATAATATA-AAATTATTTTTT
1 ATTATATTAAAAAATAATA-TAATGATATTATGT-TATATAATAAT-TACAAA-TATATTTT
* *
1110143 ATTATATTAATATATAATATAATGATATTATGTTATATAATAATTACAAATATATTTT
1 ATTATATTAAAAAATAATATAATGATATTATGTTATATAATAATTACAAATATATTTT
1110201 ATTTATATTA
1 A-TTATATTA
1110211 TATATAAGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
58 14 0.24
59 42 0.72
60 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (58 bp):
ATTATATTAAAAAATAATATAATGATATTATGTTATATAATAATTACAAATATATTTT
Found at i:1110160 original size:33 final size:32
Alignment explanation
Indices: 1110099--1110217 Score: 108
Period size: 30 Copynumber: 3.8 Consensus size: 32
1110089 ATTAAAAAAT
1110099 AAATTATTTATATTATTATATATAATAATATA
1 AAATTATTTATATTATTATATATAATAATATA
1110131 AAATTATTT-T-TTATTATAT-TAAT-ATATA
1 AAATTATTTATATTATTATATATAATAATATA
* * *
1110159 ATA-TAATGATATTATGT-TATATAATAAT-TA
1 AAATTATTTATATTAT-TATATATAATAATATA
*
1110189 CAAATATATTTTATTTATATTATATATAA
1 -AAAT-TA-TTTATAT-TATTATATATAA
1110218 GATAAATAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
27 3 0.04
28 8 0.12
29 11 0.16
30 16 0.23
31 5 0.07
32 9 0.13
33 2 0.03
34 5 0.07
35 10 0.14
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (32 bp):
AAATTATTTATATTATTATATATAATAATATA
Found at i:1110356 original size:19 final size:19
Alignment explanation
Indices: 1110332--1110371 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1110322 ATTAATTTTA
1110332 AAATTAAGTAAATTAAATT
1 AAATTAAGTAAATTAAATT
** *
1110351 AAATTATTTAAATTTAATT
1 AAATTAAGTAAATTAAATT
1110370 AA
1 AA
1110372 CTTGATCGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AAATTAAGTAAATTAAATT
Found at i:1110837 original size:15 final size:15
Alignment explanation
Indices: 1110812--1110844 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
1110802 AAATATATTT
1110812 TTTTAAAAAAA-TAA
1 TTTTAAAAAAATTAA
1110826 TTTTAAATAAAATTAA
1 TTTTAAA-AAAATTAA
1110842 TTT
1 TTT
1110845 ACATTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 4 0.24
16 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTTAAAAAAATTAA
Found at i:1116038 original size:12 final size:12
Alignment explanation
Indices: 1116001--1116040 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1115991 GAATATTTTT
*
1116001 AATAATTTTTAA
1 AATATTTTTTAA
*
1116013 ATTATTTATTTAA
1 AATATTT-TTTAA
1116026 AATATTTTTTAA
1 AATATTTTTTAA
1116038 AAT
1 AAT
1116041 TTATATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AATATTTTTTAA
Found at i:1116047 original size:25 final size:25
Alignment explanation
Indices: 1116001--1116048 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1115991 GAATATTTTT
*
1116001 AATAATTTTTAAATTATTTATTTAA
1 AATAATTTTTAAATTATATATTTAA
*
1116026 AATATTTTTTAAAATT-TATATTT
1 AATAATTTTT-AAATTATATATTT
1116049 TTATATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
AATAATTTTTAAATTATATATTTAA
Found at i:1116749 original size:14 final size:14
Alignment explanation
Indices: 1116730--1116756 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1116720 TGACTGAGCA
1116730 CTGAAGAGGTAGTG
1 CTGAAGAGGTAGTG
1116744 CTGAAGAGGTAGT
1 CTGAAGAGGTAGT
1116757 TGAAAACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.41, T:0.22
Consensus pattern (14 bp):
CTGAAGAGGTAGTG
Found at i:1119358 original size:19 final size:20
Alignment explanation
Indices: 1119320--1119364 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
1119310 GTATAATAAA
1119320 ATTTTAAATAAAAATATATT
1 ATTTTAAATAAAAATATATT
1119340 ATTTT-AATATAAAAT-TATT
1 ATTTTAAATA-AAAATATATT
1119359 ATTTTA
1 ATTTTA
1119365 GACTAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTAAATAAAAATATATT
Found at i:1119371 original size:19 final size:20
Alignment explanation
Indices: 1119320--1119364 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1119310 GTATAATAAA
1119320 ATTTTAA-ATAAAAATATATT
1 ATTTTAATAT-AAAATATATT
1119340 ATTTTAATATAAAAT-TATT
1 ATTTTAATATAAAATATATT
1119359 ATTTTA
1 ATTTTA
1119365 GACTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTAATATAAAATATATT
Found at i:1129812 original size:19 final size:19
Alignment explanation
Indices: 1129788--1129825 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1129778 TATTTTAAAC
1129788 ATTGTTTTTTTTAATCTAT
1 ATTGTTTTTTTTAATCTAT
1129807 ATTGTTTTTTTTAATCTAT
1 ATTGTTTTTTTTAATCTAT
1129826 TTTATCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (19 bp):
ATTGTTTTTTTTAATCTAT
Found at i:1131179 original size:3 final size:3
Alignment explanation
Indices: 1131171--1131202 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1131161 CTTTGCACAG
1131171 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1131203 CAGACAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1131526 original size:2 final size:2
Alignment explanation
Indices: 1131519--1131609 Score: 59
Period size: 2 Copynumber: 47.5 Consensus size: 2
1131509 GCTGTTTGTG
* *
1131519 TA TA TA TA TA TA TA TA TA TA TA AA TA TA T- TT TGA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
* * * *
1131560 -A T- TA TA TA TA TA TT TA TA AA T- TT TA -A TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1131598 TT TA TA TCA TA T
1 TA TA TA T-A TA T
1131610 TTTATTATTT
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
1 6 0.09
2 60 0.87
3 3 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1131567 original size:33 final size:32
Alignment explanation
Indices: 1131519--1131604 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 32
1131509 GCTGTTTGTG
* *
1131519 TATATATATATATATATATATAAATATATTTTGA
1 TATAT-TA-ATATATATATATAAATAAATTTTAA
**
1131553 TATATTAATTATATATATATTTATAAATTTTAA
1 TATATTAA-TATATATATATAAATAAATTTTAA
* *
1131586 TATATTTATATATTTATAT
1 TATATTAATATATATATAT
1131605 CATATTTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 11 0.24
33 29 0.64
34 5 0.11
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (32 bp):
TATATTAATATATATATATAAATAAATTTTAA
Found at i:1131629 original size:20 final size:19
Alignment explanation
Indices: 1131583--1131651 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
1131573 TTATAAATTT
*
1131583 TAATATATTTATATATTTATA
1 TAATAT-TTTATAT-TTTTTA
*
1131604 TCATATTTTATTATTTTTTA
1 TAATATTTTA-TATTTTTTA
1131624 TAATA--TTATATTTTTTA
1 TAATATTTTATATTTTTTA
*
1131641 TTAATTTTTTA
1 -TAATATTTTA
1131652 AAAAAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 9 0.22
18 7 0.17
20 16 0.40
21 8 0.20
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (19 bp):
TAATATTTTATATTTTTTA
Found at i:1131634 original size:38 final size:38
Alignment explanation
Indices: 1131519--1131614 Score: 95
Period size: 43 Copynumber: 2.4 Consensus size: 38
1131509 GCTGTTTGTG
* * * *
1131519 TATATATATATATATATATATAAATATATTTTGATATATTAAT
1 TATATATATATTTATAAATTTTAATATA-TTT-ATATA-T--T
1131562 TATATATATATTTATAAATTTTAATATATTTATATATT
1 TATATATATATTTATAAATTTTAATATATTTATATATT
1131600 TATATCATAT-TTTAT
1 TATAT-ATATATTTAT
1131615 TATTTTTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
38 11 0.23
39 4 0.08
40 1 0.02
41 5 0.10
42 3 0.06
43 24 0.50
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (38 bp):
TATATATATATTTATAAATTTTAATATATTTATATATT
Found at i:1132170 original size:19 final size:18
Alignment explanation
Indices: 1132139--1132178 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1132129 TATAATTAAA
*
1132139 TTTAAATAAAAATATTAT
1 TTTAAATAAAAATAATAT
*
1132157 TTTAATTAATAAATAATAT
1 TTTAAATAA-AAATAATAT
1132176 TTT
1 TTT
1132179 TAATCAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAAAATAATAT
Found at i:1132582 original size:27 final size:29
Alignment explanation
Indices: 1132552--1132606 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1132542 TGAATTTATA
1132552 ACTATAATT-AA-TACTATAACAAAATTT
1 ACTATAATTAAATTACTATAACAAAATTT
*
1132579 ACTATAATTAAATTACTATAATAAAATT
1 ACTATAATTAAATTACTATAACAAAATT
1132607 ATCTTACGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.36
28 2 0.08
29 14 0.56
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (29 bp):
ACTATAATTAAATTACTATAACAAAATTT
Found at i:1132596 original size:14 final size:14
Alignment explanation
Indices: 1132563--1132607 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
1132553 CTATAATTAA
*
1132563 TACTATAACAAAATT
1 TACTATAATAAAA-T
*
1132578 TACTATAATTAAAT
1 TACTATAATAAAAT
1132592 TACTATAATAAAAT
1 TACTATAATAAAAT
1132606 TA
1 TA
1132608 TCTTACGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (14 bp):
TACTATAATAAAAT
Found at i:1132987 original size:18 final size:17
Alignment explanation
Indices: 1132955--1132988 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1132945 AAAATGTAAG
1132955 TAAAATATGCATATTTA
1 TAAAATATGCATATTTA
*
1132972 TAAAATTATTCATATTT
1 TAAAA-TATGCATATTT
1132989 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
TAAAATATGCATATTTA
Found at i:1133008 original size:17 final size:19
Alignment explanation
Indices: 1132955--1133009 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 19
1132945 AAAATGTAAG
* *
1132955 TAAAA-TATGCATA-TTTA
1 TAAAATTATTCATATTTTT
1132972 TAAAATTATTCATATTTTT
1 TAAAATTATTCATATTTTT
*
1132991 TAAAATT-TT-ATCTTTTT
1 TAAAATTATTCATATTTTT
1133008 TA
1 TA
1133010 TTTTAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 14 0.42
18 9 0.27
19 10 0.30
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (19 bp):
TAAAATTATTCATATTTTT
Found at i:1133771 original size:18 final size:18
Alignment explanation
Indices: 1133721--1133775 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
1133711 AAATTTTAAC
* *
1133721 TTTATTTATTTTAAAATA
1 TTTATATATCTTAAAATA
* **
1133739 TTTATATTTGATAAAATA
1 TTTATATATCTTAAAATA
*
1133757 TTTGTATATCTTAAAATA
1 TTTATATATCTTAAAATA
1133775 T
1 T
1133776 AAATATAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (18 bp):
TTTATATATCTTAAAATA
Found at i:1134212 original size:3 final size:3
Alignment explanation
Indices: 1134166--1134196 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1134156 CCATTAAACA
1134166 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1134197 TCTTTGAAAT
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):
TAT
Found at i:1134964 original size:50 final size:49
Alignment explanation
Indices: 1134820--1134975 Score: 168
Period size: 50 Copynumber: 3.1 Consensus size: 49
1134810 ACCTAGAGTT
* * *
1134820 AACAATTATGATCACTTTCTTTTATTGTCAAAGGTTGATGAAGAATCGTA
1 AACAATTATGATCA-TCTCTTTTATTGTCAAAGGTTGATGAAAAATCGTC
* * * * *
1134870 AATAATTATGGTCACCTCCTTCTATTGTTAAAGGTTGATGAAAAATCGTC
1 AACAATTATGATCATCT-CTTTTATTGTCAAAGGTTGATGAAAAATCGTC
* ** * *
1134920 AACAATTATGATCATCTCTTTATATTGTCAAAGATCAATAAAAAATAGTC
1 AACAATTATGATCATCTCTTT-TATTGTCAAAGGTTGATGAAAAATCGTC
1134970 AACAAT
1 AACAAT
1134976 ATCAATAACT
Statistics
Matches: 86, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
49 4 0.05
50 82 0.95
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (49 bp):
AACAATTATGATCATCTCTTTTATTGTCAAAGGTTGATGAAAAATCGTC
Found at i:1135290 original size:10 final size:9
Alignment explanation
Indices: 1135275--1135364 Score: 64
Period size: 9 Copynumber: 10.2 Consensus size: 9
1135265 AAAAATTAAA
1135275 ATATAATAT
1 ATATAATAT
1135284 GATATAA-AT
1 -ATATAATAT
1135293 ATATAAT-T
1 ATATAATAT
* *
1135301 ATTTTAAAAT
1 A-TATAATAT
*
1135311 ATATATTAT
1 ATATAATAT
1135320 ATA-AAT-T
1 ATATAATAT
1135327 AT-TAATAT
1 ATATAATAT
* *
1135335 ATATAAAAA
1 ATATAATAT
*
1135344 ATATATATAA
1 ATATA-ATAT
1135354 ATATAATAT
1 ATATAATAT
1135363 AT
1 AT
1135365 TTTTAATATA
Statistics
Matches: 63, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
7 6 0.10
8 13 0.21
9 28 0.44
10 16 0.25
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (9 bp):
ATATAATAT
Found at i:1135298 original size:18 final size:16
Alignment explanation
Indices: 1135271--1135364 Score: 83
Period size: 17 Copynumber: 5.9 Consensus size: 16
1135261 ATAAAAAAAT
1135271 TAAAATATAATATGATA
1 TAAAATATAATAT-ATA
*
1135288 TAAATATATAAT-TATTT
1 TAAA-ATATAATATA-TA
1135305 TAAAATAT-ATATTATA
1 TAAAATATAATA-TATA
*
1135321 TAAATTATTAATATATA
1 TAAAATA-TAATATATA
1135338 T-AAA-A-AATATATA
1 TAAAATATAATATATA
1135351 T-AAATATAATATAT
1 TAAAATATAATATAT
1135365 TTTTAATATA
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
13 12 0.18
14 1 0.02
15 10 0.15
16 14 0.22
17 18 0.28
18 10 0.15
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (16 bp):
TAAAATATAATATATA
Found at i:1135342 original size:33 final size:32
Alignment explanation
Indices: 1135271--1135364 Score: 99
Period size: 33 Copynumber: 3.0 Consensus size: 32
1135261 ATAAAAAAAT
* *
1135271 TAAAATATAATATGATATAAATATATAAT-TATTT
1 TAAAATAT-ATATTATATAAATAT-TAATATA-TA
1135305 TAAAATATATATTATATAAATTATTAATATATA
1 TAAAATATATATTATATAAA-TATTAATATATA
1135338 TAAAA-A-ATA-TATATAAATA-TAATATAT
1 TAAAATATATATTATATAAATATTAATATAT
1135365 TTTTAATATA
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
28 8 0.14
29 2 0.04
30 8 0.14
31 3 0.05
32 1 0.02
33 21 0.38
34 13 0.23
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (32 bp):
TAAAATATATATTATATAAATATTAATATATA
Found at i:1147116 original size:6 final size:6
Alignment explanation
Indices: 1147073--1147099 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1147063 ATGTTTAATT
1147073 TATTTA TATTTA TATTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TAT
1147100 AAAATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:1147931 original size:3 final size:3
Alignment explanation
Indices: 1147923--1147969 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1147913 TTGCCCAAAA
1147923 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1147970 ATGCCCTTTG
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1150550 original size:14 final size:15
Alignment explanation
Indices: 1150533--1150561 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1150523 ACTCAATTAA
1150533 TTATAAAAT-TATTT
1 TTATAAAATGTATTT
1150547 TTATAAAATGTATTT
1 TTATAAAATGTATTT
1150562 AATATGATTA
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:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATAAAATGTATTT
Found at i:1150775 original size:2 final size:2
Alignment explanation
Indices: 1150768--1150794 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1150758 CATGTTAATG
1150768 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1150795 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1152430 original size:23 final size:23
Alignment explanation
Indices: 1152398--1152445 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1152388 TATATTCAAT
*
1152398 ATAAATATAATACGATAAA-ATAA
1 ATAAACATAATACGA-AAACATAA
1152421 ATAAACATAATACGAAAACATAA
1 ATAAACATAATACGAAAACATAA
1152444 AT
1 AT
1152446 TGTCAAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.23
Consensus pattern (23 bp):
ATAAACATAATACGAAAACATAA
Found at i:1153114 original size:3 final size:3
Alignment explanation
Indices: 1153106--1153133 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1153096 CATGTTTCAC
1153106 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1153134 GGGACAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1154365 original size:32 final size:33
Alignment explanation
Indices: 1154305--1154370 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
1154295 TTCAACGATT
1154305 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
* *
1154338 TGTATTGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1154370 T
1 T
1154371 ATAAGCTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.61
33 12 0.39
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1154427 original size:13 final size:13
Alignment explanation
Indices: 1154409--1154433 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1154399 ACATTTCAAA
1154409 TGTATCGATACAT
1 TGTATCGATACAT
1154422 TGTATCGATACA
1 TGTATCGATACA
1154434 CTGATCTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1154570 original size:52 final size:53
Alignment explanation
Indices: 1154444--1154571 Score: 222
Period size: 53 Copynumber: 2.4 Consensus size: 53
1154434 CTGATCTTTA
1154444 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATCAAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATCAAAATG
*
1154497 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTAT-GAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATCAAAATG
* *
1154549 TATCGATACATACAAGCAAATTT
1 TATCGATACATGCAGGCAAATTT
1154572 TCATATTTCG
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 26 0.36
53 46 0.64
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (53 bp):
TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATCAAAATG
Found at i:1156703 original size:24 final size:26
Alignment explanation
Indices: 1156676--1156725 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1156666 TCAAAAAATT
1156676 ATTCAT-CG-GGGACACTCCAACCCC
1 ATTCATCCGAGGGACACTCCAACCCC
*
1156700 ATTCTTCCGAGGGACACTCCAACCCC
1 ATTCATCCGAGGGACACTCCAACCCC
1156726 GTTTTCAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.22
25 2 0.09
26 16 0.70
ACGTcount: A:0.24, C:0.42, G:0.16, T:0.18
Consensus pattern (26 bp):
ATTCATCCGAGGGACACTCCAACCCC
Found at i:1158788 original size:2 final size:2
Alignment explanation
Indices: 1158781--1158811 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1158771 TCGTACACGT
1158781 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 T
1158812 TCCCGCCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1159357 original size:2 final size:2
Alignment explanation
Indices: 1159352--1159384 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1159342 CGCGTGTGTG
1159352 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 T
1159385 CTTATCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1162707 original size:2 final size:2
Alignment explanation
Indices: 1162700--1162734 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1162690 AACAAACAAG
* *
1162700 TA TA TA TA TA TA TA TA TA TA TA TT TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1162735 TCACAGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:1165697 original size:12 final size:12
Alignment explanation
Indices: 1165655--1165700 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
1165645 GGATAATTTT
1165655 AAATATAATA-A
1 AAATATAATATA
*
1165666 AAAAATAAT-TA
1 AAATATAATATA
*
1165677 ATA-ATAATATA
1 AAATATAATATA
1165688 AAATATAATATA
1 AAATATAATATA
1165700 A
1 A
1165701 TATAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 5 0.17
11 15 0.52
12 9 0.31
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATATAATATA
Found at i:1165702 original size:17 final size:17
Alignment explanation
Indices: 1165656--1165715 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 17
1165646 GATAATTTTA
*
1165656 AATATAATAAAAAAATAATT
1 AATATAAT-ATAAAAT-A-T
1165676 AATAATAATATAAAATAT
1 AAT-ATAATATAAAATAT
*
1165694 AATATAATATAAAAAAT
1 AATATAATATAAAATAT
1165711 AATAT
1 AATAT
1165716 TAATTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 18 0.49
18 4 0.11
19 1 0.03
20 9 0.24
21 5 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATATAATATAAAATAT
Found at i:1166828 original size:9 final size:9
Alignment explanation
Indices: 1166816--1166845 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1166806 CATTATACTA
1166816 ATTAAAAAT
1 ATTAAAAAT
*
1166825 ATTAAAAAA
1 ATTAAAAAT
1166834 ATTAAAAAT
1 ATTAAAAAT
1166843 ATT
1 ATT
1166846 TTTATTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:1170480 original size:48 final size:48
Alignment explanation
Indices: 1170427--1170534 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 48
1170417 AACACCATCC
* * * *
1170427 CCACCACCGATGATGCTTTCAAAAGGCTCAGGACCATTACCCCCACCA
1 CCACCACCCATGATGCTTCCAAAAGGATCAGGACCAATACCCCCACCA
* *
1170475 CCACCACCCATGATGCTTCCCAAAGGATCAGGACCAATGCCCCCACCA
1 CCACCACCCATGATGCTTCCAAAAGGATCAGGACCAATACCCCCACCA
* *
1170523 CCAACATCCATG
1 CCACCACCCATG
1170535 TCACCTGCGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.30, C:0.42, G:0.14, T:0.15
Consensus pattern (48 bp):
CCACCACCCATGATGCTTCCAAAAGGATCAGGACCAATACCCCCACCA
Found at i:1172529 original size:39 final size:38
Alignment explanation
Indices: 1172473--1172550 Score: 88
Period size: 38 Copynumber: 2.0 Consensus size: 38
1172463 TATAAATCAA
*
1172473 TTTTATTATTTAAAAAT-ATTAATTAAATTTAAATAAATT
1 TTTTATTATTTAAAAATAAATAA-T-AATTTAAATAAATT
* *
1172512 TTTTATT-TTTATTAAATAAATAATAATTTAAATTAATT
1 TTTTATTATTTA-AAAATAAATAATAATTTAAATAAATT
1172550 T
1 T
1172551 AAATTATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
38 18 0.53
39 12 0.35
40 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (38 bp):
TTTTATTATTTAAAAATAAATAATAATTTAAATAAATT
Found at i:1172550 original size:10 final size:11
Alignment explanation
Indices: 1172535--1172584 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 11
1172525 AAATAAATAA
1172535 TAATTTAAA-T
1 TAATTTAAATT
1172545 TAATTTAAA-T
1 TAATTTAAATT
1172555 T-A-TTAAATTT
1 TAATTTAAA-TT
1172565 TATATTTAAATT
1 TA-ATTTAAATT
1172577 TAATTTAA
1 TAATTTAA
1172585 TATGAAGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 5 0.14
9 1 0.03
10 13 0.37
11 6 0.17
12 5 0.14
13 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TAATTTAAATT
Found at i:1173056 original size:33 final size:34
Alignment explanation
Indices: 1172960--1173056 Score: 90
Period size: 35 Copynumber: 2.8 Consensus size: 34
1172950 AAAAAAATGT
*
1172960 GAAAAATAAGCTTATTTAATATATTATTAATTTAAA
1 GAAAAA-AA-CTTATTTTATATATTATTAATTTAAA
* * * *
1172996 AAATAAAAAATT-TATTTATTTATTTATT-ATTTTAA
1 GAA-AAAAACTTAT-TTTATATA-TTATTAATTTAAA
1173031 GAAAAAAACTTATTTTATATATTATT
1 GAAAAAAACTTATTTTATATATTATT
1173057 TTTATTGAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
33 5 0.10
34 15 0.31
35 17 0.35
36 9 0.18
37 3 0.06
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (34 bp):
GAAAAAAACTTATTTTATATATTATTAATTTAAA
Found at i:1176278 original size:15 final size:15
Alignment explanation
Indices: 1176260--1176309 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1176250 AGTACAATTT
1176260 TAATATTTTTATATA
1 TAATATTTTTATATA
* *
1176275 TAATAATTTTAAATA
1 TAATATTTTTATATA
*
1176290 TATATATTTTAATATA
1 TA-ATATTTTTATATA
1176306 -AATA
1 TAATA
1176310 ATATAACCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 3 0.10
15 16 0.55
16 10 0.34
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATATTTTTATATA
Found at i:1177879 original size:14 final size:15
Alignment explanation
Indices: 1177862--1177894 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1177852 ATTTATTATC
*
1177862 AAATTTTTA-TTAAA
1 AAATTTATACTTAAA
1177876 AAATTTATACTTAAA
1 AAATTTATACTTAAA
1177891 AAAT
1 AAAT
1177895 AAAAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATTTATACTTAAA
Found at i:1177947 original size:23 final size:22
Alignment explanation
Indices: 1177874--1177959 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 22
1177864 ATTTTTATTA
* *
1177874 AAAAATTTATACTTAAAAA-AT
1 AAAAATTTAAATTTAAAAATAT
* * **
1177895 AAAAAATTAAA-ATATGAATAT
1 AAAAATTTAAATTTAAAAATAT
1177916 AAAAATTTAAATTTAAAAATATT
1 AAAAATTTAAATTTAAAAATA-T
* * *
1177939 AAAATTTTATATTTTAAAATA
1 AAAAATTTAAATTTAAAAATA
1177960 ATTATAAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
20 4 0.08
21 21 0.42
22 6 0.12
23 19 0.38
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (22 bp):
AAAAATTTAAATTTAAAAATAT
Found at i:1177963 original size:24 final size:23
Alignment explanation
Indices: 1177911--1177968 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
1177901 TTAAAATATG
1177911 AATA-TAAAAATTTAAATTTAAA
1 AATATTAAAAATTTAAATTTAAA
* * *
1177933 AATATTAAAATTTTATATTTTAA
1 AATATTAAAAATTTAAATTTAAA
1177956 AATAATTATAAAA
1 AAT-ATTA-AAAA
1177969 AAGTAGTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 4 0.14
23 18 0.62
24 4 0.14
25 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATTAAAAATTTAAATTTAAA
Found at i:1184817 original size:19 final size:17
Alignment explanation
Indices: 1184772--1184847 Score: 68
Period size: 17 Copynumber: 4.3 Consensus size: 17
1184762 TATGAATCAT
1184772 TAAATATTAAAATATATA
1 TAAATA-TAAAATATATA
1184790 TAAATATAAAATATAT-
1 TAAATATAAAATATATA
1184806 TGAACATGAT-AAAT-TATA
1 T-AA-AT-ATAAAATATATA
*
1184824 TAAATATAATAAAAATATA
1 TAAATAT-A-AAATATATA
1184843 TAAAT
1 TAAAT
1184848 TATTAAATTA
Statistics
Matches: 49, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.04
16 3 0.06
17 17 0.35
18 16 0.33
19 11 0.22
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAATATAAAATATATA
Found at i:1185622 original size:3 final size:3
Alignment explanation
Indices: 1185616--1185698 Score: 69
Period size: 3 Copynumber: 27.0 Consensus size: 3
1185606 AACAACTATT
1185616 ATA ATAA ATA AGTA ATA ATA ATA ATA ATA ATA A-A TATA ATA ATA ATA
1 ATA AT-A ATA A-TA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
* * * * * * *
1185663 ATG ATG ATG GTA ATA ATT ATA ATT ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1185699 TGATACAGTG
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
2 1 0.02
3 58 0.88
4 7 0.11
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1185697 original size:21 final size:21
Alignment explanation
Indices: 1185616--1185698 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
1185606 AACAACTATT
*
1185616 ATAATAAATAAGTAATAATAATA
1 ATAAT-AATAA-TGATAATAATA
1185639 ATAATAATAAAT-ATAATAATA
1 ATAATAAT-AATGATAATAATA
* * * *
1185660 ATAATGATGATGGTAATAATT
1 ATAATAATAATGATAATAATA
*
1185681 ATAATTATAATGATAATA
1 ATAATAATAATGATAATA
1185699 TGATACAGTG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.04
21 38 0.75
22 4 0.08
23 7 0.14
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (21 bp):
ATAATAATAATGATAATAATA
Found at i:1186582 original size:19 final size:19
Alignment explanation
Indices: 1186555--1186594 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1186545 AAATATTAAA
*
1186555 AATCTATTTTTTTAATTTT
1 AATCAATTTTTTTAATTTT
*
1186574 AATCAATTTTTTTACTTTT
1 AATCAATTTTTTTAATTTT
1186593 AA
1 AA
1186595 ACTTTTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (19 bp):
AATCAATTTTTTTAATTTT
Found at i:1187099 original size:6 final size:6
Alignment explanation
Indices: 1187090--1187139 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
1187080 AATACTTCTT
1187090 TTAATA TTAATA TTAATA TTAATA -T-A-A TTAATA TTAATA TTAATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
1187135 TTAAT
1 TTAAT
1187140 GATGATGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
3 1 0.02
4 2 0.05
5 2 0.05
6 36 0.88
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:1187119 original size:21 final size:21
Alignment explanation
Indices: 1187095--1187135 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1187085 TTCTTTTAAT
1187095 ATTAATATTAATATTAATATA
1 ATTAATATTAATATTAATATA
1187116 ATTAATATTAATATTAATAT
1 ATTAATATTAATATTAATAT
1187136 TAATGATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAATATTAATATTAATATA
Found at i:1187419 original size:14 final size:12
Alignment explanation
Indices: 1187395--1187438 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
1187385 ATATAAATTT
*
1187395 TTATAATTTAAA
1 TTATTATTTAAA
1187407 TTATTTTATTTAAA
1 TTA--TTATTTAAA
1187421 TTATTATTTAAA
1 TTATTATTTAAA
*
1187433 TAATTA
1 TTATTA
1187439 AAAATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 17 0.61
14 11 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATTATTTAAA
Found at i:1187419 original size:35 final size:35
Alignment explanation
Indices: 1187379--1187458 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
1187369 ATTGAATTAA
** * *
1187379 ATTTAAATATAAATTTTTATAATTTAAATTA-TTTT
1 ATTTAAAT-TAAATTTAAATAATTAAAAATATTTTT
*
1187414 ATTTAAATTATTATTTAAATAATTAAAAATATTTTT
1 ATTTAAATTA-AATTTAAATAATTAAAAATATTTTT
1187450 ATTTAAATT
1 ATTTAAATT
1187459 TAAAACTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
34 2 0.05
35 23 0.61
36 13 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (35 bp):
ATTTAAATTAAATTTAAATAATTAAAAATATTTTT
Found at i:1191634 original size:19 final size:19
Alignment explanation
Indices: 1191612--1191648 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1191602 TGATAATACC
*
1191612 AAAAAAATAAAAAAAATTA
1 AAAAAAAGAAAAAAAATTA
*
1191631 AAAAAAAGAAAAGAAATT
1 AAAAAAAGAAAAAAAATT
1191649 GTCTTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAATTA
Found at i:1192424 original size:24 final size:24
Alignment explanation
Indices: 1192396--1192449 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1192386 AGATTGATCT
1192396 ATTAAATTAA-AATAACATAATTTA
1 ATTAAATTAATAATAA-ATAATTTA
* * *
1192420 ATTAATTTAATATTGAATAATTTA
1 ATTAAATTAATAATAAATAATTTA
1192444 ATTAAA
1 ATTAAA
1192450 AATTAATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTAAATTAATAATAAATAATTTA
Found at i:1193006 original size:22 final size:21
Alignment explanation
Indices: 1192968--1193043 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 21
1192958 TATTTTTATT
1192968 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
*
1192989 TAAATATTAA-TATAAAAATAATT
1 TAAAT-TTAATTAT-AAAAT-ATA
* * *
1193012 TTAATTTTATTATTAAATAATAA
1 TAAATTTAATTATAAAAT-AT-A
1193035 TAAATTTAA
1 TAAATTTAA
1193044 ATGTTTAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
21 8 0.19
22 19 0.44
23 16 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:1193282 original size:3 final size:3
Alignment explanation
Indices: 1193276--1193313 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1193266 ATTTATTTAT
1193276 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 TT
1193314 TCAATTCCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1195674 original size:19 final size:19
Alignment explanation
Indices: 1195650--1195689 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1195640 CATAATATAT
1195650 TTTTTAAATAAATTAAATA
1 TTTTTAAATAAATTAAATA
**
1195669 TTTTTAAATTTATTAAATA
1 TTTTTAAATAAATTAAATA
1195688 TT
1 TT
1195690 ATATTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTTAAATAAATTAAATA
Found at i:1195686 original size:24 final size:24
Alignment explanation
Indices: 1195658--1195713 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1195648 ATTTTTTAAA
*
1195658 TAAATTAAATATTTTTAAATTTAT
1 TAAATTAAATATTTTAAAATTTAT
*
1195682 TAAA-TATTATATTTTAAAATTTAT
1 TAAATTA-AATATTTTAAAATTTAT
*
1195706 TAATTTAA
1 TAAATTAA
1195714 TTTGATTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.08
24 22 0.85
25 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TAAATTAAATATTTTAAAATTTAT
Found at i:1196003 original size:3 final size:3
Alignment explanation
Indices: 1195995--1196031 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1195985 GGCTATGAAC
1195995 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1196032 GGTGACAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Done.