Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 10 of 33
Found at i:1353005 original size:10 final size:9
Alignment explanation
Indices: 1352988--1353077 Score: 60
Period size: 9 Copynumber: 10.0 Consensus size: 9
1352978 AAATAATTTT
1352988 TTAAATATA
1 TTAAATATA
1352997 TTAAA-ATA
1 TTAAATATA
* *
1353005 TTAAAAAATCTT
1 TT---AAATATA
1353017 TTAAATATA
1 TTAAATATA
1353026 TTAAA-ATA
1 TTAAATATA
* *
1353034 TTAAAAAAA
1 TTAAATATA
*
1353043 TTAAGTATA
1 TTAAATATA
1353052 TTAAA-ATA
1 TTAAATATA
* * *
1353060 TAAAAAAAA
1 TTAAATATA
1353069 TTAAATATA
1 TTAAATATA
1353078 CTCACGGTAA
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
8 20 0.33
9 35 0.57
11 3 0.05
12 3 0.05
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (9 bp):
TTAAATATA
Found at i:1353028 original size:29 final size:27
Alignment explanation
Indices: 1352986--1353077 Score: 116
Period size: 29 Copynumber: 3.4 Consensus size: 27
1352976 GGAAATAATT
1352986 TTTTAAATATATTAAAATATTAAAAAA
1 TTTTAAATATATTAAAATATTAAAAAA
1353013 TCTTTTAAATATATTAAAATATTAAAAAA
1 --TTTTAAATATATTAAAATATTAAAAAA
* *
1353042 -ATTAAGTATATTAAAATA-TAAAAAA
1 TTTTAAATATATTAAAATATTAAAAAA
**
1353067 AATTAAATATA
1 TTTTAAATATA
1353078 CTCACGGTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
25 7 0.12
26 25 0.42
29 27 0.46
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (27 bp):
TTTTAAATATATTAAAATATTAAAAAA
Found at i:1353053 original size:26 final size:26
Alignment explanation
Indices: 1352988--1353077 Score: 126
Period size: 26 Copynumber: 3.3 Consensus size: 26
1352978 AAATAATTTT
*
1352988 TTAAATATATTAAAATATTAAAAAATCTT
1 TTAAATATATTAAAATATTAAAAAA---A
1353017 TTAAATATATTAAAATATTAAAAAAA
1 TTAAATATATTAAAATATTAAAAAAA
* *
1353043 TTAAGTATATTAAAATATAAAAAAAA
1 TTAAATATATTAAAATATTAAAAAAA
1353069 TTAAATATA
1 TTAAATATA
1353078 CTCACGGTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
26 32 0.56
29 25 0.44
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (26 bp):
TTAAATATATTAAAATATTAAAAAAA
Found at i:1359614 original size:22 final size:23
Alignment explanation
Indices: 1359586--1359640 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
1359576 AACATATATT
1359586 TTTAATATATTAAAA-TATTATA
1 TTTAATATATTAAAATTATTATA
*
1359608 TTTAATATA-AAAAATTATTATA
1 TTTAATATATTAAAATTATTATA
**
1359630 GATAATATATT
1 TTTAATATATT
1359641 TAACAAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTAATATATTAAAATTATTATA
Found at i:1360566 original size:16 final size:16
Alignment explanation
Indices: 1360547--1360577 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1360537 CTAATAATCA
1360547 AAAATATAAATAAATT
1 AAAATATAAATAAATT
*
1360563 AAAATATAACTAAAT
1 AAAATATAAATAAAT
1360578 AAATTAAATT
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:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATAAATAAATT
Found at i:1360592 original size:24 final size:23
Alignment explanation
Indices: 1360552--1360602 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
1360542 AATCAAAAAT
1360552 ATAAATAAATTAAAATATAACTAA
1 ATAAATAAATTAAAATATAAC-AA
* *
1360576 ATAAATTAAATT-TAATATTACAA
1 ATAAA-TAAATTAAAATATAACAA
1360599 ATAA
1 ATAA
1360603 CAAAAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.25
24 12 0.50
25 6 0.25
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAATAAATTAAAATATAACAA
Found at i:1361224 original size:17 final size:17
Alignment explanation
Indices: 1361184--1361225 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1361174 TTTTTATACT
*
1361184 TATATATAAATATATAT
1 TATATATAAATATATAA
*
1361201 TAAATATAAATAT-TAGA
1 TATATATAAATATATA-A
1361218 TATATATA
1 TATATATA
1361226 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
TATATATAAATATATAA
Found at i:1362781 original size:23 final size:23
Alignment explanation
Indices: 1362729--1362782 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1362719 AACATATGGT
1362729 TATAATATTATTAAATTTAAATA
1 TATAATATTATTAAATTTAAATA
* * *
1362752 TAAAATATTTTTATTATTTAAATA
1 TATAATATTATTA-AATTTAAATA
1362776 -ATAATAT
1 TATAATAT
1362783 AAATCATATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATAATATTATTAAATTTAAATA
Found at i:1364167 original size:13 final size:14
Alignment explanation
Indices: 1364143--1364200 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
1364133 ATCAATTTAA
1364143 AATTTAATATAATT
1 AATTTAATATAATT
1364157 AATTT-ATATAATT
1 AATTTAATATAATT
* * *
1364170 ATTTTTAAAATAGAAT
1 A-ATTTAATATA-ATT
1364186 -ATTTAATATAATT
1 AATTTAATATAATT
1364199 AA
1 AA
1364201 AATTATATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
13 11 0.32
14 17 0.50
15 4 0.12
16 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
AATTTAATATAATT
Found at i:1368965 original size:9 final size:10
Alignment explanation
Indices: 1368950--1368995 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
1368940 TTTAAATATA
1368950 ATATTTAATT
1 ATATTTAATT
1368960 -TATTTAATT
1 ATATTTAATT
1368969 -TATTT--TT
1 ATATTTAATT
1368976 ATATTATAATT
1 ATATT-TAATT
1368987 ATATTTAAT
1 ATATTTAAT
1368996 ATAATATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 2 0.06
8 4 0.12
9 15 0.47
10 4 0.12
11 7 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
ATATTTAATT
Found at i:1368998 original size:20 final size:20
Alignment explanation
Indices: 1368950--1369009 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
1368940 TTTAAATATA
*
1368950 ATATTTAATTTATT-TAATT
1 ATATTTAATATATTATAATT
*
1368969 -TATTT-TTATATTATAATT
1 ATATTTAATATATTATAATT
* *
1368987 ATATTTAATATAATATATTT
1 ATATTTAATATATTATAATT
1369007 ATA
1 ATA
1369010 CTTACATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
17 5 0.15
18 10 0.30
19 5 0.15
20 13 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTAATATATTATAATT
Found at i:1369025 original size:31 final size:29
Alignment explanation
Indices: 1368990--1369076 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 29
1368980 TATAATTATA
*
1368990 TTTAATATAATATATTTATACTTACATAAAT
1 TTTAATATAATATATTTATA-TTA-AAAAAT
1369021 TTTAATA-AATTAATAATTTATATTAAAAAAT
1 TTTAATATAA-T-AT-ATTTATATTAAAAAAT
*
1369052 TTTATATATCTATATATTTATATTA
1 TTTA-ATAT-AATATATTTATATTA
1369077 TTTTTTATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
30 2 0.04
31 27 0.56
32 10 0.21
33 8 0.17
34 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTAATATAATATATTTATATTAAAAAAT
Found at i:1369070 original size:17 final size:17
Alignment explanation
Indices: 1369050--1369114 Score: 75
Period size: 17 Copynumber: 4.0 Consensus size: 17
1369040 ATATTAAAAA
*
1369050 ATTTTATA-TA-TCTAT
1 ATTTTATATTATTTTAT
*
1369065 ATATTTATATTATTTTTT
1 AT-TTTATATTATTTTAT
1369083 ATTTTATATTATTTTAT
1 ATTTTATATTATTTTAT
1369100 ATTTTAT-TT-TTTTAT
1 ATTTTATATTATTTTAT
1369115 CATGTAATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
15 8 0.18
16 8 0.18
17 23 0.52
18 5 0.11
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTATATTATTTTAT
Found at i:1369090 original size:25 final size:25
Alignment explanation
Indices: 1369062--1369114 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
1369052 TTTATATATC
1369062 TATA-TATTTATATTATTTT-TTATTT
1 TATATTATTT-TA-TATTTTATTATTT
*
1369087 TATATTATTTTATATTTTATTTTTT
1 TATATTATTTTATATTTTATTATTT
1369112 TAT
1 TAT
1369115 CATGTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 6 0.24
25 14 0.56
26 5 0.20
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (25 bp):
TATATTATTTTATATTTTATTATTT
Found at i:1369099 original size:22 final size:23
Alignment explanation
Indices: 1369064--1369109 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1369054 TATATATCTA
*
1369064 TATATTTATATTATTTTTTATTT
1 TATATTTATATTATATTTTATTT
*
1369087 TATA-TTATTTTATATTTTATTT
1 TATATTTATATTATATTTTATTT
1369109 T
1 T
1369110 TTTATCATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
TATATTTATATTATATTTTATTT
Found at i:1369101 original size:33 final size:31
Alignment explanation
Indices: 1369050--1369112 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
1369040 ATATTAAAAA
1369050 ATTTTATATATCTATATATTTATATTATTTTTT
1 ATTTTATATATCTATATATTT-TATT-TTTTTT
*
1369083 ATTTTATATTAT-TTTATATTTTATTTTTTT
1 ATTTTATA-TATCTATATATTTTATTTTTTT
1369113 ATCATGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 5 0.18
32 4 0.14
33 16 0.57
34 3 0.11
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (31 bp):
ATTTTATATATCTATATATTTTATTTTTTTT
Found at i:1369237 original size:15 final size:15
Alignment explanation
Indices: 1369219--1369269 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
1369209 AAATATTTTA
1369219 AAATTTATATAATAT
1 AAATTTATATAATAT
*
1369234 AAA-TTATTATTATATT
1 AAATTTA-TATAATA-T
1369250 AAAATTTATATAAATAT
1 -AAATTTATAT-AATAT
1369267 AAA
1 AAA
1369270 ATATTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 9 0.31
16 4 0.14
17 7 0.24
18 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTTATATAATAT
Found at i:1369237 original size:33 final size:32
Alignment explanation
Indices: 1369195--1369269 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 32
1369185 AAAATAAAAA
*
1369195 ATAAT-TAAATAATTAAATATTTTAAAATTTAT
1 ATAATATAAATAATT-AATATATTAAAATTTAT
* *
1369227 ATAATATAAATTATTATTATATTAAAATTTAT
1 ATAATATAAATAATTAATATATTAAAATTTAT
1369259 ATAAATATAAA
1 AT-AATATAAA
1369270 ATATTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 22 0.58
33 16 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
ATAATATAAATAATTAATATATTAAAATTTAT
Found at i:1369258 original size:18 final size:18
Alignment explanation
Indices: 1369216--1369271 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 18
1369206 ATTAAATATT
1369216 TTAAAATTTA-TATAATA
1 TTAAAATTTATTATAATA
*
1369233 -T-AAA-TTATTATTATA
1 TTAAAATTTATTATAATA
1369248 TTAAAATTTA-TATAA-A
1 TTAAAATTTATTATAATA
1369264 TATAAAAT
1 T-TAAAAT
1369272 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 3 0.09
15 9 0.28
16 4 0.12
17 13 0.41
18 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAAATTTATTATAATA
Found at i:1369281 original size:16 final size:17
Alignment explanation
Indices: 1369217--1369284 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 17
1369207 TTAAATATTT
1369217 TAAAAT-TTA-TATAATA
1 TAAAATATTATTA-AATA
* *
1369233 TAAATTATTATTATAT-
1 TAAAATATTATTAAATA
1369249 TAAAAT-TTATATAAATA
1 TAAAATATTAT-TAAATA
1369266 TAAAATATT-TTAAATA
1 TAAAATATTATTAAATA
1369282 TAA
1 TAA
1369285 TTATAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 4 0.09
16 23 0.53
17 12 0.28
18 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATATTATTAAATA
Found at i:1376127 original size:6 final size:6
Alignment explanation
Indices: 1376116--1376148 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1376106 GACAAGCACC
*
1376116 AAAAA- AAAAAA AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1376149 CAAAGACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1376533 original size:48 final size:46
Alignment explanation
Indices: 1376452--1376541 Score: 137
Period size: 48 Copynumber: 1.9 Consensus size: 46
1376442 AATCTAAGAT
*
1376452 AATTTAATTTAAATTATTAATTATTAATAAAAAATATTTTTATTAA
1 AATTTAATTTAAATTATTAAATATTAATAAAAAATATTTTTATTAA
1376498 AATTTAATTATAAAATTATATAAATATTAAT-AAAAATATTTTTA
1 AATTTAATT-T-AAATTAT-TAAATATTAATAAAAAATATTTTTA
1376542 AATAATAACA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
46 9 0.22
47 1 0.03
48 20 0.50
49 10 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (46 bp):
AATTTAATTTAAATTATTAAATATTAATAAAAAATATTTTTATTAA
Found at i:1376543 original size:22 final size:22
Alignment explanation
Indices: 1376468--1376545 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
1376458 ATTTAAATTA
*
1376468 TTAATTATTAATAAAAAATATTT
1 TTAAATATTAAT-AAAAATATTT
* *
1376491 TTATTAAAATTTAATTATAAAAT-TAT
1 TTA--AATA-TTAA-TA-AAAATATTT
*
1376517 ATAAATATTAATAAAAATATTT
1 TTAAATATTAATAAAAATATTT
1376539 TTAAATA
1 TTAAATA
1376546 ATAACATAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
21 5 0.12
22 10 0.24
23 7 0.17
24 3 0.07
25 2 0.05
26 9 0.21
27 6 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAATATTAATAAAAATATTT
Found at i:1376576 original size:22 final size:20
Alignment explanation
Indices: 1376525--1376577 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1376515 ATATAAATAT
*
1376525 TAATAAAA-ATATTTTTAAA
1 TAATAAAATAAATTTTTAAA
*
1376544 TAATAACATAAATTTTTAAA
1 TAATAAAATAAATTTTTAAA
1376564 TAAATTAAAATAAA
1 T-AA-TAAAATAAA
1376578 AATATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 7 0.25
20 11 0.39
21 2 0.07
22 8 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TAATAAAATAAATTTTTAAA
Found at i:1376662 original size:20 final size:18
Alignment explanation
Indices: 1376649--1376684 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1376639 AATAATATAT
*
1376649 ATAATTTTAAAATATTAA
1 ATAAATTTAAAATATTAA
1376667 ATAAATTTAAAAT-TTAA
1 ATAAATTTAAAATATTAA
1376684 A
1 A
1376685 CCTTCAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAATTTAAAATATTAA
Found at i:1377084 original size:2 final size:2
Alignment explanation
Indices: 1377079--1377107 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1377069 ATGACCACAC
1377079 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1377108 GCTCCAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1377755 original size:16 final size:17
Alignment explanation
Indices: 1377736--1377768 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1377726 AAAATCGAAA
*
1377736 TAAATTTAA-CAAAAAC
1 TAAATTGAACCAAAAAC
1377752 TAAATTGAACCAAAAAC
1 TAAATTGAACCAAAAAC
1377769 AACTATTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.61, C:0.15, G:0.03, T:0.21
Consensus pattern (17 bp):
TAAATTGAACCAAAAAC
Found at i:1377988 original size:27 final size:24
Alignment explanation
Indices: 1377958--1378017 Score: 59
Period size: 27 Copynumber: 2.4 Consensus size: 24
1377948 CTTTCTTACC
1377958 AATAATTTTTAATTTAATATTATAATA
1 AATAATTTTTAATTT-AT-TTATAA-A
*
1377985 AAT-ATATTATAATTTATTTATAAA
1 AATAAT-TTTTAATTTATTTATAAA
*
1378009 CATAATTTT
1 AATAATTTT
1378018 AATATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
24 5 0.18
25 8 0.29
26 4 0.14
27 11 0.39
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
AATAATTTTTAATTTATTTATAAA
Found at i:1378056 original size:33 final size:33
Alignment explanation
Indices: 1377973--1378059 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 33
1377963 TTTTTAATTT
*
1377973 AATATTATAATA-AATATATTATAATTTATTTATA
1 AATA-TATAATATAATATA-TATAATTTATTTAAA
* * *
1378007 AACATA-ATTTTAATATATATAATTT-TTTAAA
1 AATATATAATATAATATATATAATTTATTTAAA
1378038 AATATATAATATACATATATAT
1 AATATATAATATA-ATATATAT
1378060 CTATAAAGTA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
31 10 0.23
32 14 0.33
33 16 0.37
34 3 0.07
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (33 bp):
AATATATAATATAATATATATAATTTATTTAAA
Found at i:1378158 original size:21 final size:20
Alignment explanation
Indices: 1378104--1378160 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
1378094 CTAATTTATA
1378104 TTAAAAATATAAAA-AATATT
1 TTAAAAA-ATAAAATAATATT
*
1378124 TTATAAAATAAAATAATAATT
1 TTAAAAAATAAAATAAT-ATT
1378145 TTAAAAAATAAAATAA
1 TTAAAAAATAAAATAA
1378161 AATAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 6 0.18
20 9 0.27
21 18 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAAAAATAAAATAATATT
Found at i:1378178 original size:26 final size:25
Alignment explanation
Indices: 1378107--1378179 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 25
1378097 ATTTATATTA
1378107 AAAATATAAA-AAATATTTTATAAAAT
1 AAAATA-AAATAAATA-TTTATAAAAT
*
1378133 AAAAT--AAT-AAT-TTTAAAAAAT
1 AAAATAAAATAAATATTTATAAAAT
1378154 AAAATAAAATAAATATTTATCAAAAT
1 AAAATAAAATAAATATTTAT-AAAAT
1378180 TATTTTTACC
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
21 14 0.36
23 8 0.21
24 3 0.08
25 4 0.10
26 10 0.26
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAATAAAATAAATATTTATAAAAT
Found at i:1378767 original size:7 final size:7
Alignment explanation
Indices: 1378755--1378791 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
1378745 ATCCCAGAAT
1378755 AATAATA
1 AATAATA
1378762 AATAAT-
1 AATAATA
1378768 AATAATA
1 AATAATA
1378775 AA-AATA
1 AATAATA
1378781 AATAATA
1 AATAATA
1378788 AATA
1 AATA
1378792 GCATTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AATAATA
Found at i:1378770 original size:13 final size:13
Alignment explanation
Indices: 1378752--1378791 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
1378742 TTGATCCCAG
1378752 AATAATAATAAAT
1 AATAATAATAAAT
1378765 AATAATAATAAA-
1 AATAATAATAAAT
1378777 AATAAATAATAAAT
1 AAT-AATAATAAAT
1378791 A
1 A
1378792 GCATTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 3 0.12
13 21 0.84
14 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:1378780 original size:19 final size:19
Alignment explanation
Indices: 1378752--1378788 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1378742 TTGATCCCAG
*
1378752 AATAATAATAAATAATAAT
1 AATAAAAATAAATAATAAT
1378771 AATAAAAATAAATAATAA
1 AATAAAAATAAATAATAA
1378789 ATAGCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AATAAAAATAAATAATAAT
Found at i:1382052 original size:26 final size:26
Alignment explanation
Indices: 1382006--1382107 Score: 134
Period size: 27 Copynumber: 3.8 Consensus size: 26
1381996 ATAATAAGCT
1382006 ACTATTTTTGACAAACAAAAAAGAATC
1 ACTATTTTTGACAAAC-AAAAAGAATC
* * *
1382033 ACTATTTTTGATAAACAAAAACAACC
1 ACTATTTTTGACAAACAAAAAGAATC
*
1382059 ACCATTTTTGACAAACAAAAAGGAATC
1 ACTATTTTTGACAAACAAAAA-GAATC
1382086 A-TCATTTTTGACAAACAAAAAG
1 ACT-ATTTTTGACAAACAAAAAG
1382108 GGTGGCTTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
26 28 0.43
27 37 0.57
ACGTcount: A:0.50, C:0.17, G:0.08, T:0.25
Consensus pattern (26 bp):
ACTATTTTTGACAAACAAAAAGAATC
Found at i:1383521 original size:27 final size:26
Alignment explanation
Indices: 1383488--1383545 Score: 98
Period size: 27 Copynumber: 2.2 Consensus size: 26
1383478 AACAACAAGT
*
1383488 CACCATTTTTGACAAATAAAAAGGAGC
1 CACCATTTTTGACAAATAAAAA-GAAC
1383515 CACCATTTTTGACAAATAAAAAGAAC
1 CACCATTTTTGACAAATAAAAAGAAC
1383541 CACCA
1 CACCA
1383546 ACAATTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.47, C:0.22, G:0.10, T:0.21
Consensus pattern (26 bp):
CACCATTTTTGACAAATAAAAAGAAC
Found at i:1383912 original size:24 final size:24
Alignment explanation
Indices: 1383882--1383927 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1383872 GTGGTTCCTT
1383882 TTGTTTGTCAAAAATGGTGGCTTG
1 TTGTTTGTCAAAAATGGTGGCTTG
* *
1383906 TTGTTTGTTAAAATTGGTGGCT
1 TTGTTTGTCAAAAATGGTGGCT
1383928 AATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.46
Consensus pattern (24 bp):
TTGTTTGTCAAAAATGGTGGCTTG
Found at i:1386488 original size:18 final size:18
Alignment explanation
Indices: 1386462--1386511 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
1386452 GAAGAGGTTC
* *
1386462 AAACCCAAGAATCATTGG
1 AAACACAAGAACCATTGG
1386480 AAACACAAGAACCATTGG
1 AAACACAAGAACCATTGG
* *
1386498 AGACATAAGAACCA
1 AAACACAAGAACCA
1386512 CTTGCAGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (18 bp):
AAACACAAGAACCATTGG
Found at i:1388277 original size:27 final size:27
Alignment explanation
Indices: 1388236--1388306 Score: 117
Period size: 26 Copynumber: 2.7 Consensus size: 27
1388226 AAAGCCACCA
* *
1388236 TTTTTGTTTGTAAAAAATGGTGGTTC-
1 TTTTTGTTTATAAAAAATGATGGTTCG
1388262 TTTTTGTTTATAAAAAATGATGGTTCG
1 TTTTTGTTTATAAAAAATGATGGTTCG
1388289 TTTTTGTTTATAAAAAAT
1 TTTTTGTTTATAAAAAAT
1388307 ATTGACTTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
26 24 0.57
27 18 0.43
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.51
Consensus pattern (27 bp):
TTTTTGTTTATAAAAAATGATGGTTCG
Found at i:1391861 original size:2 final size:2
Alignment explanation
Indices: 1391856--1391886 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1391846 ATATATATAT
1391856 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1391887 TGCTCAAAAG
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1397066 original size:43 final size:43
Alignment explanation
Indices: 1396965--1397066 Score: 100
Period size: 43 Copynumber: 2.3 Consensus size: 43
1396955 TAATATTTAT
*
1396965 AAATTTTTTTATTAAATAAAATTATAATTAATAAAATTTATTGA
1 AAATTTTTTTA-TAAATAAAATTAAAATTAATAAAATTTATTGA
* * * * **
1397009 AAAATATTTAATAAATAAATTTAAAATTAAGTTTAA-TTATAT-A
1 AAATTTTTTTATAAATAAAATTAAAATTAA-TAAAATTTAT-TGA
1397052 AAATTTTTTTATAAA
1 AAATTTTTTTATAAA
1397067 ATATAAGATT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
43 34 0.74
44 12 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (43 bp):
AAATTTTTTTATAAATAAAATTAAAATTAATAAAATTTATTGA
Found at i:1397098 original size:11 final size:12
Alignment explanation
Indices: 1397066--1397103 Score: 55
Period size: 11 Copynumber: 3.4 Consensus size: 12
1397056 TTTTTTATAA
1397066 AATATAAGAT-T
1 AATATAAGATAT
1397077 AAT-TAAGATAT
1 AATATAAGATAT
1397088 AATATAA-ATAT
1 AATATAAGATAT
1397099 AATAT
1 AATAT
1397104 TAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.24
11 16 0.64
12 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (12 bp):
AATATAAGATAT
Found at i:1397726 original size:10 final size:10
Alignment explanation
Indices: 1397711--1397748 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
1397701 TAAACATAAC
1397711 AATAATAAAA
1 AATAATAAAA
1397721 AATAATGAAAA
1 AATAAT-AAAA
*
1397732 CATAATAAAA
1 AATAATAAAA
1397742 AATAATA
1 AATAATA
1397749 TGAATATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (10 bp):
AATAATAAAA
Found at i:1397938 original size:19 final size:19
Alignment explanation
Indices: 1397916--1397958 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1397906 GACATGAATA
*
1397916 TATAAATATAAAATATATT
1 TATAAATATAAAATAAATT
* *
1397935 TATAAATATTACATAAATT
1 TATAAATATAAAATAAATT
1397954 TATAA
1 TATAA
1397959 TATTATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TATAAATATAAAATAAATT
Found at i:1398062 original size:10 final size:10
Alignment explanation
Indices: 1398003--1398065 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
1397993 TTTTTCTCAT
1398003 ATATATAAAA
1 ATATATAAAA
1398013 ATATA-AATAA
1 ATATATAA-AA
*
1398023 A-ATAAAATAA
1 ATATATAA-AA
* *
1398033 AT-TATTAAT
1 ATATATAAAA
1398042 ATATA-AAAA
1 ATATATAAAA
1398051 ATATATAAAA
1 ATATATAAAA
1398061 ATATA
1 ATATA
1398066 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
9 15 0.35
10 28 0.65
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATATATAAAA
Found at i:1398062 original size:32 final size:32
Alignment explanation
Indices: 1398026--1398091 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 32
1398016 TAAATAAAAT
*
1398026 AAAATA-AAT-TATTAATATATAAAAAATATATA
1 AAAATATAATATATTAA-ATACAAAAAAT-TATA
*
1398058 AAAATATAATATTTTAAATACAAAAAATTATA
1 AAAATATAATATATTAAATACAAAAAATTATA
1398090 AA
1 AA
1398092 TACAAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 12 0.40
33 13 0.43
34 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (32 bp):
AAAATATAATATATTAAATACAAAAAATTATA
Found at i:1398091 original size:16 final size:16
Alignment explanation
Indices: 1398022--1398097 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 16
1398012 AATATAAATA
1398022 AAATA-AAATAAATTATT
1 AAATACAAA-AAATTA-T
*
1398039 AATATATAAAAAATATAT
1 AA-ATACAAAAAAT-TAT
* * * * *
1398057 AAAAATATAATATTTT
1 AAATACAAAAAATTAT
1398073 AAATACAAAAAATTAT
1 AAATACAAAAAATTAT
1398089 AAATACAAA
1 AAATACAAA
1398098 TATATATTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
16 22 0.47
17 10 0.21
18 10 0.21
19 5 0.11
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATACAAAAAATTAT
Found at i:1398162 original size:17 final size:19
Alignment explanation
Indices: 1398140--1398182 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
1398130 TTCACCGCCT
*
1398140 AAAAAAAGCTT-AAAGT-A
1 AAAAAAAGATTAAAAGTCA
1398157 AAAAAAA-ATTAAAAGTCA
1 AAAAAAAGATTAAAAGTCA
1398175 AAAAAAAG
1 AAAAAAAG
1398183 TCACACGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.09
17 12 0.55
18 8 0.36
ACGTcount: A:0.72, C:0.05, G:0.09, T:0.14
Consensus pattern (19 bp):
AAAAAAAGATTAAAAGTCA
Found at i:1398295 original size:16 final size:15
Alignment explanation
Indices: 1398264--1398355 Score: 54
Period size: 15 Copynumber: 6.4 Consensus size: 15
1398254 TTTAATATTT
*
1398264 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATT-A
1398281 ATAAAATTATAATTA
1 ATAAAATTATAATTA
*
1398296 ATAAAATT-TATTTA
1 ATAAAATTATAATTA
* *
1398310 A-AATATT-TAATAA
1 ATAAAATTATAATTA
* *
1398323 ATAAATTTA-AAGT-
1 ATAAAATTATAATTA
1398336 -TAAAATT-TAATTA
1 ATAAAATTATAATTA
1398349 TATAAAA
1 -ATAAAA
1398356 AATTTATATA
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
12 9 0.16
13 10 0.17
14 12 0.21
15 14 0.24
16 7 0.12
17 6 0.10
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (15 bp):
ATAAAATTATAATTA
Found at i:1398328 original size:26 final size:26
Alignment explanation
Indices: 1398282--1398331 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1398272 TTTAATTAAA
*
1398282 TAAAATTATAATTAATAAAATTTATT
1 TAAAATTATAATAAATAAAATTTATT
*
1398308 TAAAATATTTAATAAAT-AAATTTA
1 TAAAAT-TATAATAAATAAAATTTA
1398332 AAGTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAAATTATAATAAATAAAATTTATT
Found at i:1398480 original size:18 final size:18
Alignment explanation
Indices: 1398457--1398514 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
1398447 ATGACAGAAA
1398457 TATATAAATATAAATATT
1 TATATAAATATAAATATT
1398475 TATATAAA-AT-AA-A-T
1 TATATAAATATAAATATT
1398489 TAT-TAATATATAAATATT
1 TATATAA-ATATAAATATT
1398507 TATATAAA
1 TATATAAA
1398515 AAATATCACG
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.09
14 5 0.15
15 3 0.09
16 4 0.12
17 3 0.09
18 13 0.38
19 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATATAAATATAAATATT
Found at i:1398518 original size:15 final size:15
Alignment explanation
Indices: 1398468--1398520 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
1398458 ATATAAATAT
1398468 AAATATTTATATAAAA
1 AAATATTTATAT-AAA
* *
1398484 TAAATTATTAATAT-AT
1 -AAA-TATTTATATAAA
1398500 AAATATTTATATAAA
1 AAATATTTATATAAA
1398515 AAATAT
1 AAATAT
1398521 CACGAATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 8 0.27
15 10 0.33
16 1 0.03
17 3 0.10
18 8 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATTTATATAAA
Found at i:1400768 original size:21 final size:20
Alignment explanation
Indices: 1400742--1400788 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1400732 ATTAGATAAA
1400742 TAAAAGAA-TTGAGAAAATTT
1 TAAAAGAAGTT-AGAAAATTT
*
1400762 TAGAAAGAAGTTAGAGAATTT
1 TA-AAAGAAGTTAGAAAATTT
1400783 TAAAAG
1 TAAAAG
1400789 GTAGAGAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 16 0.67
22 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (20 bp):
TAAAAGAAGTTAGAAAATTT
Found at i:1401249 original size:141 final size:141
Alignment explanation
Indices: 1400990--1401260 Score: 348
Period size: 141 Copynumber: 1.9 Consensus size: 141
1400980 AAAAAGCCAC
* ** *
1400990 GCAGGACTCGCTGATGCAAGACACGATTCACATGGAGAATCGTTGTTTGTTCCAACGCATCCATG
1 GCAGGACTCGCTGATGCAAGACACGATTCACAGGGAGAATCACTGTTTGTTCCAACGCATCCACG
* * * * * *
1401055 TAGAATTCGCTGTCCTACGTGGTGCGTCCATATAAGATGCGTTGATGATGTCAGCACATCTTACG
66 TAGAATTCGCGGTCCTACATGATGCGTCAATATAAGATGCGCTGATGACGTCAGCACATCTTACG
1401120 AAAGAATCTAT
131 AAAGAATCTAT
* * * * *
1401131 GCAGGACTCGCTGTTGCAAGCCACGATTTACACGGGA-AATCACTGTTTGTTCCAGCGCATCTAC
1 GCAGGACTCGCTGATGCAAGACACGATTCACA-GGGAGAATCACTGTTTGTTCCAACGCATCCAC
* * *
1401195 GTA-AGATTTGCGGTCCTACATGATGCGTCAATATCAGATGCGCTGATGACGTCAGCGCATCTTA
65 GTAGA-ATTCGCGGTCCTACATGATGCGTCAATATAAGATGCGCTGATGACGTCAGCACATCTTA
1401259 CG
129 CG
1401261 TGAAATCGTA
Statistics
Matches: 110, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
140 1 0.01
141 106 0.96
142 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (141 bp):
GCAGGACTCGCTGATGCAAGACACGATTCACAGGGAGAATCACTGTTTGTTCCAACGCATCCACG
TAGAATTCGCGGTCCTACATGATGCGTCAATATAAGATGCGCTGATGACGTCAGCACATCTTACG
AAAGAATCTAT
Found at i:1405639 original size:23 final size:24
Alignment explanation
Indices: 1405595--1405639 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1405585 GTATCACCTG
***
1405595 TTTTAATTTTTATAATTTAAATTT
1 TTTTAATTTTTATAAAAAAAATTT
1405619 TTTTAA-TTTTATAAAAAAAAT
1 TTTTAATTTTTATAAAAAAAAT
1405640 AATTAAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTAATTTTTATAAAAAAAATTT
Found at i:1406109 original size:17 final size:17
Alignment explanation
Indices: 1406079--1406116 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1406069 TACGATATAT
*
1406079 AATA-TAAAATATAATA
1 AATATTAAAAAATAATA
1406095 AATATTAAAAAATAATA
1 AATATTAAAAAATAATA
*
1406112 TATAT
1 AATAT
1406117 GTATAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATATTAAAAAATAATA
Found at i:1406198 original size:16 final size:16
Alignment explanation
Indices: 1406125--1406206 Score: 62
Period size: 16 Copynumber: 4.8 Consensus size: 16
1406115 ATGTATAATA
1406125 TAAATATATTAAATTT
1 TAAATATATTAAATTT
*
1406141 TATATA-ATATAAATTAT
1 TAAATATAT-TAAATT-T
1406158 T-AATATATTAAAATTT
1 TAAATATATT-AAATTT
1406174 ACGTAAATATA-TAATATTT
1 ---TAAATATATTAA-ATTT
1406193 TAAATATAATTAAA
1 TAAATAT-ATTAAA
1406207 ATATAAAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 21
0.70 0.03 0.28
Matches are distributed among these distances:
15 2 0.04
16 23 0.43
17 11 0.21
18 5 0.09
19 6 0.11
20 6 0.11
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (16 bp):
TAAATATATTAAATTT
Found at i:1406247 original size:22 final size:22
Alignment explanation
Indices: 1406206--1406247 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1406196 ATATAATTAA
*
1406206 AATATAAAAATTATATAAACAT
1 AATATAAAAATAATATAAACAT
1406228 AATATAAAATATAATA-AAAC
1 AATATAAAA-ATAATATAAAC
1406248 TGAGCTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (22 bp):
AATATAAAAATAATATAAACAT
Found at i:1407294 original size:2 final size:2
Alignment explanation
Indices: 1407287--1407317 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1407277 TAAGTACTTA
*
1407287 AT AT AT AT AT AT AT TT 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
1407318 GAGAGAGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1407969 original size:22 final size:19
Alignment explanation
Indices: 1407936--1407975 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 19
1407926 TATCTACTTT
1407936 TTAAAAAAACTAGCAATTTC
1 TTAAAAAAACTAG-AATTTC
1407956 TTAAAAAATTACTAGAATTT
1 TTAAAAAA--ACTAGAATTT
1407976 AAAAAGCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (19 bp):
TTAAAAAAACTAGAATTTC
Found at i:1408988 original size:23 final size:23
Alignment explanation
Indices: 1408955--1409009 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
1408945 GTGCTAAATT
1408955 ATAATATAAATAAAATATATTT-A
1 ATAATA-AAATAAAATATATTTAA
**
1408978 ATAAATAAAATATGATATATTTAA
1 AT-AATAAAATAAAATATATTTAA
1409002 ATAATAAA
1 ATAATAAA
1409010 TGGGTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 21 0.75
24 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAATAAAATAAAATATATTTAA
Found at i:1410467 original size:16 final size:17
Alignment explanation
Indices: 1410448--1410491 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1410438 AACCTCATAT
*
1410448 TAAAATATAAT-ATAGA
1 TAAAATATAATAATAAA
*
1410464 TAAAATATTATAATAAA
1 TAAAATATAATAATAAA
*
1410481 TAAAAAATAAT
1 TAAAATATAAT
1410492 TTTAGATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
TAAAATATAATAATAAA
Found at i:1410685 original size:21 final size:22
Alignment explanation
Indices: 1410643--1410687 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1410633 TATTAAATAT
* *
1410643 TATTTTATATTAATATTTTAAA
1 TATTTTATAATAATAATTTAAA
1410665 TATTTTATAATAA-AATTTAAA
1 TATTTTATAATAATAATTTAAA
1410686 TA
1 TA
1410688 AAAATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTTATAATAATAATTTAAA
Found at i:1410720 original size:3 final size:3
Alignment explanation
Indices: 1410712--1410740 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1410702 TTTATCTTAG
1410712 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1410741 GCTTTCGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1411990 original size:18 final size:18
Alignment explanation
Indices: 1411963--1412001 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1411953 AATGTAAATT
*
1411963 TTTTATTTTTA-TTTTTAC
1 TTTTACTTTTACTTTTT-C
1411981 TTTTACTTTTACTTTTTC
1 TTTTACTTTTACTTTTTC
1411999 TTT
1 TTT
1412002 CTTGTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTACTTTTACTTTTTC
Found at i:1412001 original size:12 final size:12
Alignment explanation
Indices: 1411963--1412001 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1411953 AATGTAAATT
* *
1411963 TTTTATTTTTAT
1 TTTTACTTTTAC
1411975 TTTTACTTTTAC
1 TTTTACTTTTAC
*
1411987 TTTTACTTTTTC
1 TTTTACTTTTAC
1411999 TTT
1 TTT
1412002 CTTGTCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTACTTTTAC
Found at i:1412163 original size:28 final size:28
Alignment explanation
Indices: 1412133--1412189 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
1412123 TTAAATTAAA
1412133 TTTTAGATAAATTTTTATTAAAAATATAT
1 TTTTAGATAAA-TTTTATTAAAAATATAT
**
1412162 TTTTATTTAAATTTTATTATAAAATATA
1 TTTTAGATAAATTTTATTA-AAAATATA
1412190 AATATTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TTTTAGATAAATTTTATTAAAAATATAT
Found at i:1412526 original size:28 final size:30
Alignment explanation
Indices: 1412491--1412550 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
1412481 TTTGGAAGCA
*
1412491 TTTTAAATTT-TT-A-AAAAATTAAATGTTT
1 TTTTAAATTTGTTGACAAAAAATAAAT-TTT
1412519 TTTTAAATTTGTTGACAAAAAATAAATTTT
1 TTTTAAATTTGTTGACAAAAAATAAATTTT
1412549 TT
1 TT
1412551 AAAAGAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 10 0.36
29 2 0.07
30 6 0.21
31 10 0.36
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (30 bp):
TTTTAAATTTGTTGACAAAAAATAAATTTT
Found at i:1412695 original size:22 final size:22
Alignment explanation
Indices: 1412634--1412698 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
1412624 ATAAATTCAA
*
1412634 ATAAGTAACTAAGTTTTTTTTATT
1 ATAAG-AA-TAAGTTTTTTTAATT
* *
1412658 ATAATAATAATATTTTTTTAATT
1 ATAAGAATAA-GTTTTTTTAATT
* *
1412681 CTTAGAATAAGTTTTTTT
1 ATAAGAATAAGTTTTTTT
1412699 GAGAAACATA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
22 10 0.30
23 19 0.58
24 4 0.12
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (22 bp):
ATAAGAATAAGTTTTTTTAATT
Found at i:1413651 original size:74 final size:73
Alignment explanation
Indices: 1413500--1413755 Score: 272
Period size: 74 Copynumber: 3.5 Consensus size: 73
1413490 TTTAAGCTTC
* *
1413500 TACAAATAAAAATAAATAATATC-CAAAAATTTAAACTCATGCAATCA-ACTCAAAAATAA-ATT
1 TACAAATAAAAATAAATTATATCATAAAAATTTAAACTCATGCAATCATACTCAAAAA-AATATT
1413562 TAAA-TTTT
65 TAAACTTTT
* * * * * * *
1413570 TATAAATAAAAATGAATTATATGATTAAAAATATAAACTTATGTAATCATACCCAAAAAACATAT
1 TACAAATAAAAATAAATTATATCA-TAAAAATTTAAACTCATGCAATCATACTCAAAAAA-ATAT
1413635 TTAAACTTTT
64 TTAAACTTTT
* * * * *
1413645 TA-AAATAAAAATAAATTATACCATAAAAATTTAAACTCGTACAAGCATATCTAAAAAAATATAT
1 TACAAATAAAAATAAATTATATCATAAAAATTTAAACTCATGCAATCATA-CTCAAAAAA-ATAT
*
1413709 TTAAAC-TTC
64 TTAAACTTTT
* *
1413718 TACAAATAAAAATAAATTATATCCTAAAAATTTTAACT
1 TACAAATAAAAATAAATTATATCATAAAAATTTAAACT
1413756 TGTATAATCA
Statistics
Matches: 153, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
70 19 0.12
72 21 0.14
73 33 0.22
74 74 0.48
75 6 0.04
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.32
Consensus pattern (73 bp):
TACAAATAAAAATAAATTATATCATAAAAATTTAAACTCATGCAATCATACTCAAAAAAATATTT
AAACTTTT
Found at i:1413773 original size:74 final size:74
Alignment explanation
Indices: 1413489--1413775 Score: 264
Period size: 74 Copynumber: 3.9 Consensus size: 74
1413479 TTAAATAAAA
* * *
1413489 ATTTAAGCTTCTACAAATAAAAATAAATAATATCC-AAAAATTTAAACTCATGCAATC--AACT-
1 ATTTAAACTTCTACAAATAAAAATAAATTATATCCTAAAAATTTAAACTCATACAATCATAACTA
* *
1413550 CAAAAATAA
66 AAAAAATAT
* * * * ** * * ** *
1413559 ATTTAAATTTTTATAAATAAAAATGAATTATATGATTAAAAATATAAACTTATGTAATCAT-ACC
1 ATTTAAACTTCTACAAATAAAAATAAATTATAT-CCTAAAAATTTAAACTCATACAATCATAACT
* *
1413623 CAAAAAACAT
65 AAAAAAATAT
* * * *
1413633 ATTTAAACTTTTTA-AAATAAAAATAAATTATA-CCATAAAAATTTAAACTCGTACAAGCATATC
1 ATTTAAAC-TTCTACAAATAAAAATAAATTATATCC-TAAAAATTTAAACTCATACAATCATAAC
1413696 TAAAAAAATAT
64 TAAAAAAATAT
* ** *
1413707 ATTTAAACTTCTACAAATAAAAATAAATTATATCCTAAAAATTTTAACTTGTATAATCATAACTA
1 ATTTAAACTTCTACAAATAAAAATAAATTATATCCTAAAAATTTAAACTCATACAATCATAACTA
1413772 AAAA
66 AAAA
1413776 TAAATAACTA
Statistics
Matches: 172, Mismatches: 35, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
70 27 0.16
72 19 0.11
73 25 0.15
74 94 0.55
75 7 0.04
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.32
Consensus pattern (74 bp):
ATTTAAACTTCTACAAATAAAAATAAATTATATCCTAAAAATTTAAACTCATACAATCATAACTA
AAAAAATAT
Found at i:1413784 original size:14 final size:14
Alignment explanation
Indices: 1413765--1413794 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1413755 TTGTATAATC
1413765 ATAACTAAAAATAA
1 ATAACTAAAAATAA
1413779 ATAACTAAAAATAA
1 ATAACTAAAAATAA
1413793 AT
1 AT
1413795 TTAAACTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAACTAAAAATAA
Found at i:1413793 original size:20 final size:20
Alignment explanation
Indices: 1413770--1413822 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
1413760 TAATCATAAC
1413770 TAAAAATAAATAACTAAAAA
1 TAAAAATAAATAACTAAAAA
** * *
1413790 TAAATTTAAACT-TCTACAAA
1 TAAAAATAAA-TAACTAAAAA
1413810 TAAAAATAAATAA
1 TAAAAATAAATAA
1413823 TATCTTAATT
Statistics
Matches: 24, Mismatches: 7, Indels: 4
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAAATAAATAACTAAAAA
Found at i:1413963 original size:14 final size:14
Alignment explanation
Indices: 1413944--1413992 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
1413934 ATTAGTTTGT
1413944 AAAAATATATTTTA
1 AAAAATATATTTTA
*
1413958 AAAAATGCT-TTTTA
1 AAAAAT-ATATTTTA
1413972 AAAAA-ATTATTTTA
1 AAAAATA-TATTTTA
1413986 AAAAATA
1 AAAAATA
1413993 AAAATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 1 0.03
14 26 0.90
15 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (14 bp):
AAAAATATATTTTA
Found at i:1417900 original size:26 final size:24
Alignment explanation
Indices: 1417864--1417917 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
1417854 AAATTTTTTA
*
1417864 TTAAAATTTAATTTTAA-AATATTT
1 TTAAAATTTAA-TGTAATAATATTT
1417888 TTAAAATTATTAATGTAATAATATTT
1 TTAAAA-T-TTAATGTAATAATATTT
1417914 TTAA
1 TTAA
1417918 TGTTGACCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 6 0.23
25 5 0.19
26 15 0.58
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTAAAATTTAATGTAATAATATTT
Found at i:1418382 original size:21 final size:19
Alignment explanation
Indices: 1418356--1418403 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
1418346 TAATTTTAAA
1418356 AAATATTTGTTTTGATCACAT
1 AAATATTT-TTTTGATCAC-T
*
1418377 AAATATTATTTTTTATCACT
1 AAATATT-TTTTTGATCACT
1418397 -AATATTT
1 AAATATTT
1418404 ATAAATATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 1 0.04
19 6 0.24
20 1 0.04
21 16 0.64
22 1 0.04
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.52
Consensus pattern (19 bp):
AAATATTTTTTTGATCACT
Found at i:1418843 original size:2 final size:2
Alignment explanation
Indices: 1418836--1418863 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1418826 GATATCATAA
1418836 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
1418864 GCGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1420909 original size:2 final size:2
Alignment explanation
Indices: 1420902--1420937 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1420892 AATGAGAATT
1420902 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1420938 ACACTCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1421546 original size:2 final size:2
Alignment explanation
Indices: 1421539--1421571 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1421529 TATTTGATGT
1421539 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
1421572 TGTTATTATC
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:1422409 original size:28 final size:30
Alignment explanation
Indices: 1422366--1422421 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
1422356 TTTAAATTAG
*
1422366 TAAAAAAATTTAAAATGATATAAATTTTTT
1 TAAAAAAATTTAAAATAATATAAATTTTTT
*
1422396 TAAAAAAA-TT-AAATAATATGAATTTT
1 TAAAAAAATTTAAAATAATATAAATTTT
1422422 AAATCAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.58
29 2 0.08
30 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (30 bp):
TAAAAAAATTTAAAATAATATAAATTTTTT
Found at i:1423892 original size:6 final size:6
Alignment explanation
Indices: 1423883--1423911 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1423873 GAACTAAAAC
1423883 TAGAAA TAGAAA TAGAAA TAGAAA TAGAA
1 TAGAAA TAGAAA TAGAAA TAGAAA TAGAA
1423912 GTTAGTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
TAGAAA
Found at i:1424142 original size:2 final size:2
Alignment explanation
Indices: 1424135--1424176 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1424125 GTGTAAAAGA
1424135 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1424176 A
1 A
1424177 AAAAAGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1424306 original size:3 final size:3
Alignment explanation
Indices: 1424298--1424335 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1424288 ATATCTTTAT
*
1424298 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1424336 TCTATTTCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1424316 original size:9 final size:9
Alignment explanation
Indices: 1424302--1424341 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
1424292 CTTTATTTAT
1424302 TATTATTAC
1 TATTATTAC
*
1424311 TATTATTAT
1 TATTATTAC
*
1424320 TATTATTAT
1 TATTATTAC
*
1424329 TATTATTTC
1 TATTATTAC
1424338 TATT
1 TATT
1424342 TCGTTTTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (9 bp):
TATTATTAC
Found at i:1430905 original size:13 final size:13
Alignment explanation
Indices: 1430879--1430917 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
1430869 ATATTTATAT
1430879 TTAAAAAT--ATA
1 TTAAAAATAAATA
1430890 TTAAAAATAAATA
1 TTAAAAATAAATA
*
1430903 TTAAATATAAATA
1 TTAAAAATAAATA
1430916 TT
1 TT
1430918 TAAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.32
13 17 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAAATAAATA
Found at i:1430922 original size:14 final size:14
Alignment explanation
Indices: 1430883--1430928 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
1430873 TTATATTTAA
*
1430883 AAATATATTAAAAAT
1 AAATAT-TTAAATAT
1430898 AAATA-TTAAATAT
1 AAATATTTAAATAT
*
1430911 AAATATTTAAATAA
1 AAATATTTAAATAT
1430925 AAAT
1 AAAT
1430929 GAAGGTAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 12 0.43
14 11 0.39
15 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATATTTAAATAT
Found at i:1437337 original size:2 final size:2
Alignment explanation
Indices: 1437330--1437354 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1437320 CTTGTTTTCT
1437330 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1437355 ATGACGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1439019 original size:38 final size:38
Alignment explanation
Indices: 1438880--1439026 Score: 152
Period size: 38 Copynumber: 3.9 Consensus size: 38
1438870 ATCAGCCACT
* ** * *
1438880 AGCCAATTCCAAATTGAATTCTCTAGTCGTTAGCCACCG
1 AGCCAATTTCAAATTGAATTCTCTAACCGTTAGTC-GCG
* ** * * *
1438919 A-CCAATTTCAAATTAAATTCTCTAGTCATCAGTCGCC
1 AGCCAATTTCAAATTGAATTCTCTAACCGTTAGTCGCG
*
1438956 AGTCAATTTCAAATTGAATTCTCTAACCGTTAGTCGCG
1 AGCCAATTTCAAATTGAATTCTCTAACCGTTAGTCGCG
* *
1438994 AGCCAATTTCAAAATGAATTCTCTAACTGTTAG
1 AGCCAATTTCAAATTGAATTCTCTAACCGTTAG
1439027 CCAATTCAAT
Statistics
Matches: 90, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
37 2 0.02
38 87 0.97
39 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (38 bp):
AGCCAATTTCAAATTGAATTCTCTAACCGTTAGTCGCG
Found at i:1443582 original size:38 final size:38
Alignment explanation
Indices: 1443540--1443614 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
1443530 TCTAGCTACC
* * * *
1443540 AGCCACCGGTCAATTCCAAATTGAATTTTTTAGTCGTT
1 AGCCACCGATCAATTCCAAATTAAATTCTCTAGTCGTT
*
1443578 AGCCACCGATCAATTCTAAATTAAATTCTCTAGTCGT
1 AGCCACCGATCAATTCCAAATTAAATTCTCTAGTCGT
1443615 CAGTCGTCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (38 bp):
AGCCACCGATCAATTCCAAATTAAATTCTCTAGTCGTT
Found at i:1444038 original size:17 final size:17
Alignment explanation
Indices: 1444018--1444053 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1444008 TATATGATAT
*
1444018 TTTAAATTATAATTTAA
1 TTTAAATTAAAATTTAA
*
1444035 TTTAATTTAAAATTTAA
1 TTTAAATTAAAATTTAA
1444052 TT
1 TT
1444054 AATAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAATTAAAATTTAA
Found at i:1444066 original size:29 final size:27
Alignment explanation
Indices: 1444034--1444092 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 27
1444024 TTATAATTTA
1444034 ATTTAATTTAAAATTTAATTAATAAAAAT
1 ATTTAATTT-AAATTTAATT-ATAAAAAT
*
1444063 ATTTTTATTTAAATTTAATTATAAAAAT
1 A-TTTAATTTAAATTTAATTATAAAAAT
1444091 AT
1 AT
1444093 ATAAATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 1 0.04
28 9 0.32
29 11 0.39
30 7 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTAATTTAAATTTAATTATAAAAAT
Found at i:1444098 original size:22 final size:22
Alignment explanation
Indices: 1444072--1444114 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1444062 TATTTTTATT
1444072 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1444094 TAAATATTAATATAAAAATAT
1 TAAATATTAATATAAAAATAT
1444115 TTTTTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1444103 original size:29 final size:29
Alignment explanation
Indices: 1444038--1444103 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
1444028 AATTTAATTT
* *
1444038 AATTTAAAATTTAATTAATAAAAATATTTT
1 AATTT-AAATTTAATTAATAAAAATATATA
*
1444068 TATTTAAATTTAATT-ATAAAAATATATA
1 AATTTAAATTTAATTAATAAAAATATATA
1444096 AATATTAA
1 AAT-TTAA
1444104 TATAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 13 0.42
29 14 0.45
30 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTTAAATTTAATTAATAAAAATATATA
Found at i:1444123 original size:18 final size:18
Alignment explanation
Indices: 1444100--1444135 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1444090 TATATAAATA
1444100 TTAATATAAAAATATTTT
1 TTAATATAAAAATATTTT
**
1444118 TTAATATGTAAATATTTT
1 TTAATATAAAAATATTTT
1444136 GAATAATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTAATATAAAAATATTTT
Found at i:1444979 original size:19 final size:19
Alignment explanation
Indices: 1444955--1445003 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1444945 TTTAGACTTA
1444955 TTTAAAAAATATATTTTAT
1 TTTAAAAAATATATTTTAT
**
1444974 TTTAAAATGTATATTTTAT
1 TTTAAAAAATATATTTTAT
*
1444993 TATAAAAAATA
1 TTTAAAAAATA
1445004 AATAAATAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TTTAAAAAATATATTTTAT
Found at i:1445429 original size:28 final size:25
Alignment explanation
Indices: 1445374--1445430 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 25
1445364 TTTTTTATAA
**
1445374 ATTTATTTTTTAAATTTAATATTTT
1 ATTTATTTTTTAAATTTAATAAATT
1445399 ATTTATTTTTTAAAAATATTAATAAATT
1 ATTTATTTTTT--AAAT-TTAATAAATT
1445427 ATTT
1 ATTT
1445431 TAATTTTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 11 0.41
27 4 0.15
28 12 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTTATTTTTTAAATTTAATAAATT
Found at i:1446367 original size:11 final size:11
Alignment explanation
Indices: 1446351--1446391 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
1446341 TGTTAATTTA
1446351 TATATTTATAT
1 TATATTTATAT
1446362 TATATTTATAT
1 TATATTTATAT
1446373 TAT-TTTATA-
1 TATATTTATAT
*
1446382 TATTTTTATA
1 TATATTTATA
1446392 AATTTTGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 3 0.10
10 12 0.41
11 14 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1446388 original size:10 final size:10
Alignment explanation
Indices: 1446347--1446402 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
1446337 TACATGTTAA
1446347 TTTATATATT
1 TTTATATATT
* *
1446357 TATAT-TATA
1 TTTATATATT
1446366 TTTATAT-TAT
1 TTTATATAT-T
1446376 TTTATATATT
1 TTTATATATT
*
1446386 TTTATAAATT
1 TTTATATATT
*
1446396 TTGATAT
1 TTTATAT
1446403 GTTAATAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
9 8 0.22
10 27 0.75
11 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTATATATT
Found at i:1446402 original size:18 final size:18
Alignment explanation
Indices: 1446381--1446433 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 18
1446371 ATTATTTTAT
1446381 ATATTTTTATAAATTTTG
1 ATATTTTTATAAATTTTG
* *
1446399 ATATGTTAAT-AA-TTTG
1 ATATTTTTATAAATTTTG
*
1446415 -TA-TTATATAAATTTTG
1 ATATTTTTATAAATTTTG
1446431 ATA
1 ATA
1446434 CGATTATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 7
0.69 0.13 0.18
Matches are distributed among these distances:
14 3 0.11
15 4 0.15
16 8 0.30
17 4 0.15
18 8 0.30
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (18 bp):
ATATTTTTATAAATTTTG
Found at i:1446510 original size:31 final size:29
Alignment explanation
Indices: 1446454--1446514 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 29
1446444 TACAAATAAT
*
1446454 ATAATTAATATTTATATTATTTTTATATA
1 ATAATTAATATTTATATTATATTTATATA
1446483 ATAATT-ATATTTAATATCTTATATTTATATA
1 ATAATTAATATTT-ATA--TTATATTTATATA
1446514 A
1 A
1446515 ATTTTGATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 6 0.21
29 9 0.32
31 13 0.46
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (29 bp):
ATAATTAATATTTATATTATATTTATATA
Found at i:1446574 original size:28 final size:26
Alignment explanation
Indices: 1446488--1446618 Score: 92
Period size: 28 Copynumber: 5.0 Consensus size: 26
1446478 ATATAATAAT
*
1446488 TATA-TTTAATATCTTATAT-TTATA
1 TATATTTTAATATATTATATATTATA
* *
1446512 TAAATTTTGATATATTAATAATATTATA
1 TATATTTTAATATATT-AT-ATATTATA
*
1446540 TAGATTTTAATATATTATATATTA-A
1 TATATTTTAATATATTATATATTATA
* * *
1446565 TATCATATTT-ATATTTTTTATATTTTA
1 TAT-AT-TTTAATATATTATATATTATA
*
1446592 TCATATTTTATATTATATTTTA-ATTAT
1 T-ATATTTTA-A-TATATTATATATTAT
1446619 TTGTATATTT
Statistics
Matches: 85, Mismatches: 11, Indels: 18
0.75 0.10 0.16
Matches are distributed among these distances:
24 3 0.04
25 12 0.14
26 25 0.29
27 11 0.13
28 26 0.31
29 8 0.09
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (26 bp):
TATATTTTAATATATTATATATTATA
Found at i:1446625 original size:22 final size:21
Alignment explanation
Indices: 1446535--1446627 Score: 59
Period size: 22 Copynumber: 4.3 Consensus size: 21
1446525 ATTAATAATA
*
1446535 TTATA-TAGATTTTAATATATT
1 TTATATTATATTTT-ATATATT
* ** *
1446556 ATATATTAATATCATATTTATAT
1 TTATATTA-TATTTTATATAT-T
1446579 TT-T-TTATATTTTATCATATT
1 TTATATTATATTTTAT-ATATT
1446599 TTATATTATATTTTA-ATTATT
1 TTATATTATATTTTATA-TATT
1446620 TGTATATT
1 T-TATATT
1446628 TTGTATGATG
Statistics
Matches: 55, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
20 10 0.18
21 16 0.29
22 24 0.44
23 5 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATATTATATTTTATATATT
Found at i:1446633 original size:9 final size:9
Alignment explanation
Indices: 1446502--1446604 Score: 63
Period size: 10 Copynumber: 11.3 Consensus size: 9
1446492 TTTAATATCT
1446502 TATATTTATA
1 TATATTT-TA
*
1446512 TAAATTTTGA
1 TATATTTT-A
*
1446522 TATA-TTAA
1 TATATTTTA
*
1446530 TAATATTATA
1 T-ATATTTTA
*
1446540 TAGATTTTA
1 TATATTTTA
*
1446549 -ATATATTA
1 TATATTTTA
*
1446557 TATA-TTAA
1 TATATTTTA
1446565 TATCATATTTA
1 TAT-AT-TTTA
1446576 TAT-TTTT-
1 TATATTTTA
1446583 TATATTTTA
1 TATATTTTA
1446592 TCATATTTTA
1 T-ATATTTTA
1446602 TAT
1 TAT
1446605 TATATTTTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
7 3 0.04
8 20 0.28
9 20 0.28
10 22 0.31
11 6 0.08
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (9 bp):
TATATTTTA
Found at i:1446761 original size:19 final size:18
Alignment explanation
Indices: 1446735--1446781 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
1446725 TAATTATATT
* *
1446735 TAAAATATTTTATATTTA
1 TAAAATATTATATATTAA
*
1446753 TATAAATATGATATATTAA
1 TA-AAATATTATATATTAA
1446772 TAAAATATTA
1 TAAAATATTA
1446782 AATAAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TAAAATATTATATATTAA
Found at i:1446805 original size:17 final size:18
Alignment explanation
Indices: 1446783--1446820 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1446773 AAAATATTAA
1446783 ATAAATTTATAATAT-TT
1 ATAAATTTATAATATATT
*
1446800 ATAAATTTATATTATATT
1 ATAAATTTATAATATATT
1446818 ATA
1 ATA
1446821 TTTTTATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAAATTTATAATATATT
Found at i:1448380 original size:13 final size:13
Alignment explanation
Indices: 1448362--1448386 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1448352 AATGATTGAA
1448362 TATAATTTTTTAT
1 TATAATTTTTTAT
1448375 TATAATTTTTTA
1 TATAATTTTTTA
1448387 CCCAAATTTG
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:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATAATTTTTTAT
Found at i:1450758 original size:23 final size:25
Alignment explanation
Indices: 1450732--1450780 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1450722 AAGTTTTTTT
* *
1450732 ATTTTTTAA-TATAT-TATAATATA
1 ATTTATTAATTATATATAAAATATA
1450755 ATTTATTAATTATATATAAAATATA
1 ATTTATTAATTATATATAAAATATA
1450780 A
1 A
1450781 AATAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 5 0.23
25 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTATTAATTATATATAAAATATA
Found at i:1451546 original size:14 final size:16
Alignment explanation
Indices: 1451517--1451548 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1451507 ATAAAATAAA
1451517 AAAATCTATATATATT
1 AAAATCTATATATATT
1451533 AAAAT-TAT-TATATT
1 AAAATCTATATATATT
1451547 AA
1 AA
1451549 TTATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATCTATATATATT
Found at i:1451595 original size:13 final size:15
Alignment explanation
Indices: 1451523--1451618 Score: 60
Period size: 15 Copynumber: 6.6 Consensus size: 15
1451513 TAAAAAAATC
* *
1451523 TATATATATTAAAAT
1 TATATATATTATATT
1451538 TAT-TATATTA-A-T
1 TATATATATTATATT
* * *
1451550 TATATTTA-AATATG
1 TATATATATTATATT
1451564 TA-ATATTATATATATT
1 TATATA-TAT-TATATT
* *
1451580 T-TAAATATTTTATT
1 TATATATATTATATT
1451594 TATATATATTATATT
1 TATATATATTATATT
1451609 TATATTATAT
1 TATA-TATAT
1451619 CTAAAAATAT
Statistics
Matches: 62, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
12 5 0.08
13 7 0.11
14 17 0.27
15 21 0.34
16 12 0.19
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (15 bp):
TATATATATTATATT
Found at i:1451596 original size:24 final size:23
Alignment explanation
Indices: 1451523--1451603 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 23
1451513 TAAAAAAATC
* *
1451523 TATATATATTAAAATTATTATATT
1 TATATATATTTAAA-TATTTTATT
* * *
1451547 AAT-TATATTTAAATATGTAATAT
1 TATATATATTTAAATATTTTAT-T
1451570 TATATATATTTTAAATATTTTATT
1 TATATATA-TTTAAATATTTTATT
1451594 TATATATATT
1 TATATATATT
1451604 ATATTTATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
22 5 0.11
23 14 0.30
24 15 0.33
25 12 0.26
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (23 bp):
TATATATATTTAAATATTTTATT
Found at i:1451605 original size:9 final size:9
Alignment explanation
Indices: 1451523--1451618 Score: 52
Period size: 9 Copynumber: 11.6 Consensus size: 9
1451513 TAAAAAAATC
1451523 TATATATAT
1 TATATATAT
1451532 TA-A-A-AT
1 TATATATAT
1451538 TAT-TATAT
1 TATATATAT
1451546 TA-ATTATAT
1 TATA-TATAT
*
1451555 T-TAAATA-
1 TATATATAT
*
1451562 TGTA-ATAT
1 TATATATAT
1451570 TATATATAT
1 TATATATAT
* *
1451579 TTTAAATAT
1 TATATATAT
1451588 T-T-TAT-T
1 TATATATAT
1451594 TATATATAT
1 TATATATAT
1451603 TATATTTATAT
1 TATA--TATAT
1451614 TATAT
1 TATAT
1451619 CTAAAAATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 28
0.67 0.05 0.28
Matches are distributed among these distances:
6 6 0.09
7 9 0.13
8 17 0.25
9 27 0.40
11 9 0.13
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (9 bp):
TATATATAT
Found at i:1451616 original size:24 final size:24
Alignment explanation
Indices: 1451523--1451616 Score: 79
Period size: 24 Copynumber: 4.0 Consensus size: 24
1451513 TAAAAAAATC
1451523 TATATATATTA-AAAT-TATTATAT
1 TATATATATTATAAATATATTAT-T
* *
1451546 TA-ATTATATT-TAAATATGTAATAT
1 TATA-TATATTATAAATATATTAT-T
* *
1451570 TATATATATTTTAAATATTTTATT
1 TATATATATTATAAATATATTATT
**
1451594 TATATATATTATATTTATATTAT
1 TATATATATTATAAATATATTAT
1451617 ATCTAAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
22 1 0.02
23 12 0.21
24 34 0.59
25 11 0.19
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (24 bp):
TATATATATTATAAATATATTATT
Found at i:1453037 original size:14 final size:16
Alignment explanation
Indices: 1453007--1453041 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
1452997 ATATTAATTT
1453007 AATTAAAATTAATAAA
1 AATTAAAATTAATAAA
1453023 AATTAAAA-T-ATAAA
1 AATTAAAATTAATAAA
1453037 AATTA
1 AATTA
1453042 TATTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
15 1 0.05
16 8 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATTAAAATTAATAAA
Found at i:1454364 original size:18 final size:19
Alignment explanation
Indices: 1454331--1454367 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1454321 ATAATGAGAT
1454331 ATAAAATAAAATAAATATA
1 ATAAAATAAAATAAATATA
*
1454350 ATAAAA-AATATAAATATA
1 ATAAAATAAAATAAATATA
1454368 TCAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAAAATAAAATAAATATA
Found at i:1454460 original size:17 final size:18
Alignment explanation
Indices: 1454428--1454474 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
1454418 AATATAATAA
1454428 AAAATATATAAATATATT
1 AAAATATATAAATATATT
*
1454446 AAAATTTATAATATATAATT
1 AAAATATATAA-ATAT-ATT
1454466 -AAATATATA
1 AAAATATATA
1454475 TTTTTACTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.40
19 12 0.48
20 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATATATAAATATATT
Found at i:1454931 original size:27 final size:27
Alignment explanation
Indices: 1454892--1454979 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
1454882 TATTAAAAAA
*
1454892 ATAATTAT-TAATATATTAAAATTTAT
1 ATAAATATATAATATATTAAAATTTAT
* * *
1454918 ATAAATATATAATATTTTAAAAATAAGT
1 ATAAATATATAATATATTAAAATTTA-T
* * * *
1454946 ATAAA-ATAAAAAATATTTAACTATTAT
1 ATAAATATATAATATATTAAAAT-TTAT
1454973 ATAAATA
1 ATAAATA
1454980 CACATAATAA
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
26 7 0.15
27 31 0.66
28 9 0.19
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (27 bp):
ATAAATATATAATATATTAAAATTTAT
Found at i:1456024 original size:16 final size:16
Alignment explanation
Indices: 1455990--1456062 Score: 69
Period size: 16 Copynumber: 4.4 Consensus size: 16
1455980 AAAAATTCGA
1455990 AATATAAATAATTATAT
1 AATATAAA-AATTATAT
*
1456007 AATATAAAAATAATAT
1 AATATAAAAATTATAT
* *
1456023 AAAATAAAATTTATAT
1 AATATAAAAATTATAT
1456039 AAATATATAATAATT-TA-
1 -AATATA-AA-AATTATAT
1456056 AATATAA
1 AATATAA
1456063 TTAAAAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
15 1 0.02
16 26 0.55
17 13 0.28
18 4 0.09
19 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATAAAAATTATAT
Found at i:1456037 original size:32 final size:33
Alignment explanation
Indices: 1455989--1456062 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 33
1455979 AAAAAATTCG
*
1455989 AAATATAAATAATTATAT-AATATAAAAATAATAT
1 AAATATAAA-ATTTATATAAATAT-AAAATAATAT
* *
1456023 AAA-ATAAAATTTATATAAATATATAATAATTT
1 AAATATAAAATTTATATAAATATAAAATAATAT
1456055 AAATATAA
1 AAATATAA
1456063 TTAAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 18 0.51
33 14 0.40
34 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (33 bp):
AAATATAAAATTTATATAAATATAAAATAATAT
Found at i:1456073 original size:20 final size:20
Alignment explanation
Indices: 1456014--1456083 Score: 54
Period size: 20 Copynumber: 3.4 Consensus size: 20
1456004 TATAATATAA
1456014 AAAT-AATATAAAATAAAATTT
1 AAATAAATAT-AAA-AAAATTT
* * *
1456035 ATATAAATATATAATAATTT
1 AAATAAATATAAAAAAATTT
1456055 AAATATAAT-TAAAAAAATTAT
1 AAATA-AATATAAAAAAATT-T
*
1456076 AAGTAAAT
1 AAATAAAT
1456084 TGAATCTACA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
20 21 0.54
21 13 0.33
22 5 0.13
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (20 bp):
AAATAAATATAAAAAAATTT
Found at i:1464832 original size:21 final size:20
Alignment explanation
Indices: 1464808--1464862 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1464798 TTTTTTATGA
*
1464808 TTTTATATTTATATTAATTAT
1 TTTTA-ATTTATATTAATTAG
* *
1464829 TTTTCATTGATAATTAATTAG
1 TTTTAATTTAT-ATTAATTAG
*
1464850 TTTTAAGTTATAT
1 TTTTAATTTATAT
1464863 ATTTAACATT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTAATTTATATTAATTAG
Done.