Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 4 of 444
Found at i:1068432 original size:19 final size:19
Alignment explanation
Indices: 1068397--1068455 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
1068387 ATTATTTTAC
*
1068397 TATT-TGTA-TTAGAATAA
1 TATTATGTATTTAGTATAA
1068414 TATTATGTATTTAGTATAA
1 TATTATGTATTTAGTATAA
* * * *
1068433 AATTTTTTATTTATTATAA
1 TATTATGTATTTAGTATAA
1068452 -ATTA
1 TATTA
1068456 CATAATATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 4 0.12
18 7 0.21
19 23 0.68
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (19 bp):
TATTATGTATTTAGTATAA
Found at i:1076591 original size:21 final size:21
Alignment explanation
Indices: 1076550--1076591 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1076540 TGGCATTGGT
* *
1076550 TTGTTTTCTTCTTGCTTTAGA
1 TTGTTTTCCTCTTGCTCTAGA
1076571 TTGTTTCTCCTCTTGC-CTAGA
1 TTGTTT-TCCTCTTGCTCTAGA
1076592 AAAAGAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.10, C:0.21, G:0.14, T:0.55
Consensus pattern (21 bp):
TTGTTTTCCTCTTGCTCTAGA
Found at i:1077911 original size:99 final size:99
Alignment explanation
Indices: 1077736--1077930 Score: 300
Period size: 99 Copynumber: 2.0 Consensus size: 99
1077726 AAATGGCTCT
* * *
1077736 AAAGTCTTTAATGTTAGCTCTGGAAGTTGAGACAACCTTAACGCCTCTAACTGATAGCATGCCGT
1 AAAGTCTTTAATGTTAGCTCTGGAAGTTGAGACAACCTTAACGCCTCTAACTGAGAGAATGCCGA
*
1077801 TGTGTGCCTTTCCTCATTGATGAGTCCTTCAAAC
66 TGTATGCCTTTCCTCATTGATGAGTCCTTCAAAC
* * * *
1077835 AAAGTCTTTAATGTTAGCTCTGGAAGTTTAGACAAGCTTAAGGCCTTTAACTGAGAGAATGCCGA
1 AAAGTCTTTAATGTTAGCTCTGGAAGTTGAGACAACCTTAACGCCTCTAACTGAGAGAATGCCGA
* *
1077900 TGTATGTCTTTCCTCGTTGATGAGTCCTTCA
66 TGTATGCCTTTCCTCATTGATGAGTCCTTCA
1077931 GACCAGACTG
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 86 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (99 bp):
AAAGTCTTTAATGTTAGCTCTGGAAGTTGAGACAACCTTAACGCCTCTAACTGAGAGAATGCCGA
TGTATGCCTTTCCTCATTGATGAGTCCTTCAAAC
Found at i:1080369 original size:20 final size:20
Alignment explanation
Indices: 1080344--1080385 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1080334 TGATTGGAGC
1080344 TATTAAATATAATTAA-AATA
1 TATTAAAT-TAATTAATAATA
*
1080364 TATTAAATTATTTAATAATA
1 TATTAAATTAATTAATAATA
1080384 TA
1 TA
1080386 AATAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTAAATTAATTAATAATA
Found at i:1110610 original size:31 final size:32
Alignment explanation
Indices: 1110570--1110638 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
1110560 CTTTCACAAC
1110570 AATTCTCTCTCAATTCTTT-TCAAA-TTCTCTCA
1 AATT-TCTCTCAATT-TTTGTCAAAGTTCTCTCA
* * *
1110602 AATTTCTCTTAATTTTTGTCAAAGTTGTCTCT
1 AATTTCTCTCAATTTTTGTCAAAGTTCTCTCA
1110634 AATTT
1 AATTT
1110639 TTGCAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 3 0.09
31 14 0.44
32 15 0.47
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.51
Consensus pattern (32 bp):
AATTTCTCTCAATTTTTGTCAAAGTTCTCTCA
Found at i:1110623 original size:21 final size:22
Alignment explanation
Indices: 1110599--1110645 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1110589 TCAAATTCTC
1110599 TCAAA-TT-TCTCTTAATTTTTG
1 TCAAAGTTGTCTC-TAATTTTTG
1110620 TCAAAGTTGTCTCTAATTTTTG
1 TCAAAGTTGTCTCTAATTTTTG
1110642 -CAAA
1 TCAAA
1110646 AAAGCTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.38
22 11 0.46
23 4 0.17
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.49
Consensus pattern (22 bp):
TCAAAGTTGTCTCTAATTTTTG
Found at i:1119910 original size:99 final size:99
Alignment explanation
Indices: 1119735--1120026 Score: 386
Period size: 99 Copynumber: 2.9 Consensus size: 99
1119725 AAATGGCTCT
* * * * ** * * * *
1119735 AAAGTCTTTAATGTTAGCTCTGGAAGTTGAGACAACCTTAACGCCTCTAACTGATAGCATGCCGA
1 AAAGTCTTTAATGTCAACTCTGGAAGTTCAGACAAGCTTAATTCCTTTAACTGAGAGAATGCTGA
* * *
1119800 TGTGTGCCTTTCCTCATTGATGAGTCCTTCAAAC
66 TGTATGTCTTTCCTCATGGATGAGTCCTTCAAAC
1119834 AAAGTCTTTAATGTCAACTCTGGAAGTTCAGACAAGCTTAATTCCTTTAACTGAGAGAATGCTGA
1 AAAGTCTTTAATGTCAACTCTGGAAGTTCAGACAAGCTTAATTCCTTTAACTGAGAGAATGCTGA
* ** * *
1119899 TGTATGTCTTTCTTTGTGGTTGCGTCCTTCAAAC
66 TGTATGTCTTTCCTCATGGATGAGTCCTTCAAAC
*
1119933 AAAGTATTTAATGTCAACTCTGGAAGTTCAGACAAGCTTAATTCCTTTAACTGAGAGAATGCTGA
1 AAAGTCTTTAATGTCAACTCTGGAAGTTCAGACAAGCTTAATTCCTTTAACTGAGAGAATGCTGA
** *
1119998 TGTATGTCTTTCCTTGTGGCTGAGTCCTT
66 TGTATGTCTTTCCTCATGGATGAGTCCTT
1120027 TAGGCCGGAC
Statistics
Matches: 171, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 171 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (99 bp):
AAAGTCTTTAATGTCAACTCTGGAAGTTCAGACAAGCTTAATTCCTTTAACTGAGAGAATGCTGA
TGTATGTCTTTCCTCATGGATGAGTCCTTCAAAC
Found at i:1122756 original size:18 final size:17
Alignment explanation
Indices: 1122732--1122786 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 17
1122722 GTAACATAAA
1122732 TAATTTTAAAATTTTAT
1 TAATTTTAAAATTTTAT
*
1122749 TGAATTTTTTAAAATATTAT
1 T-AA--TTTTAAAATTTTAT
*
1122769 TATTTTTAAAAATTTTAT
1 TAATTTT-AAAATTTTAT
1122787 GATTTATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 5 0.16
18 11 0.35
19 1 0.03
20 14 0.45
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TAATTTTAAAATTTTAT
Found at i:1122774 original size:17 final size:19
Alignment explanation
Indices: 1122735--1122786 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
1122725 ACATAAATAA
*
1122735 TTTTAAAATTTTATTGAATT
1 TTTTAAAATATTATT-AATT
1122755 TTTTAAAATATTATT-ATT
1 TTTTAAAATATTATTAATT
* *
1122773 TTTAAAAATTTTAT
1 TTTTAAAATATTAT
1122787 GATTTATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTAAAATATTATTAATT
Found at i:1133918 original size:20 final size:20
Alignment explanation
Indices: 1133888--1133934 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1133878 AAGGAAATTA
* *
1133888 AAAAGATAAATTTTTCCTTGT
1 AAAA-ATAAATATTTCCATGT
1133909 AAAAATAAATATTTCCATGT
1 AAAAATAAATATTTCCATGT
1133929 AAAAAT
1 AAAAAT
1133935 CTAAGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (20 bp):
AAAAATAAATATTTCCATGT
Found at i:1138528 original size:2 final size:2
Alignment explanation
Indices: 1138521--1138563 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1138511 GGGCTAAGTT
1138521 TA TA TA 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 TA TA TA
1138563 T
1 T
1138564 TTCATCTGCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1148211 original size:19 final size:20
Alignment explanation
Indices: 1148175--1148219 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1148165 TTTGCTCTAA
*
1148175 AATAATTAATATATTTTAAT
1 AATATTTAATATATTTTAAT
*
1148195 TATATTTAATA-ATTTTAAT
1 AATATTTAATATATTTTAAT
1148214 AATATT
1 AATATT
1148220 ACTTTATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTTAATATATTTTAAT
Found at i:1149010 original size:16 final size:16
Alignment explanation
Indices: 1148988--1149021 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1148978 GTCATGTGTA
1148988 ATTTTTTTAATATT-T
1 ATTTTTTTAATATTCT
1149003 ATTTTTTTAATATTCT
1 ATTTTTTTAATATTCT
1149019 ATT
1 ATT
1149022 ATACCCCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTTTAATATTCT
Found at i:1150205 original size:3 final size:3
Alignment explanation
Indices: 1150199--1150242 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
1150189 TTATTTTTGA
* * *
1150199 ATT ATT AGT ATT ATT AGT ATT GTT ATT ATT ATT ATT ATGT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT A
1150243 GTATATATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1150211 original size:9 final size:9
Alignment explanation
Indices: 1150199--1150251 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
1150189 TTATTTTTGA
1150199 ATTATTAGT
1 ATTATTAGT
1150208 ATTATTAGT
1 ATTATTAGT
* *
1150217 ATTGTTATT
1 ATTATTAGT
*
1150226 ATTATTATT
1 ATTATTAGT
1150235 ATGTATTAGT
1 AT-TATTAGT
1150245 ATATATT
1 AT-TATT
1150252 CTTGCTTTAC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
9 26 0.68
10 12 0.32
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.58
Consensus pattern (9 bp):
ATTATTAGT
Found at i:1150297 original size:24 final size:24
Alignment explanation
Indices: 1150269--1150347 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 24
1150259 TACACGTGTA
1150269 TATATTATGTAAATGTTTTAATAT
1 TATATTATGTAAATGTTTTAATAT
* *
1150293 TATATTA--TATATGTTTTTCATA-
1 TATATTATGTAAATG-TTTTAATAT
* *
1150315 TATGTTATGTAAATAAATTTTTAATAT
1 TATATTATGTAAAT---GTTTTAATAT
1150342 TATATT
1 TATATT
1150348 TTATATATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
22 11 0.27
23 7 0.17
24 11 0.27
26 7 0.17
27 5 0.12
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (24 bp):
TATATTATGTAAATGTTTTAATAT
Found at i:1150317 original size:46 final size:47
Alignment explanation
Indices: 1150267--1150370 Score: 122
Period size: 46 Copynumber: 2.2 Consensus size: 47
1150257 TTTACACGTG
* *
1150267 TATATATTATGTAAAT-GTTTTAATATTATA-TTATATATGTTTTTCA
1 TATATATTATGTAAATAGTTTTAATATTATATTTATATATATTATT-A
* *
1150313 TATATGTTATGTAAATAAATTTTTAATATTATATTTTATATATATTATTA
1 TATATATTATGTAAAT--AGTTTTAATATTATA-TTTATATATATTATTA
1150363 TATATATT
1 TATATATT
1150371 TTAATATTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
46 15 0.31
49 13 0.27
50 8 0.17
51 12 0.25
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.57
Consensus pattern (47 bp):
TATATATTATGTAAATAGTTTTAATATTATATTTATATATATTATTA
Found at i:1150355 original size:14 final size:15
Alignment explanation
Indices: 1150333--1150406 Score: 50
Period size: 14 Copynumber: 5.1 Consensus size: 15
1150323 GTAAATAAAT
1150333 TTTTA-ATATTA-TA
1 TTTTATATATTATTA
1150346 TTTTATATA-TATTA
1 TTTTATATATTATTA
*
1150360 TTATATATATT-TTAA
1 TTTTATATATTATT-A
*
1150375 TATTAT-TAGTTATATA
1 TTTTATATA-TTAT-TA
* *
1150391 TTTTTTATACTATTA
1 TTTTATATATTATTA
1150406 T
1 T
1150407 ATGTATATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
13 7 0.15
14 17 0.36
15 11 0.23
16 9 0.19
17 3 0.06
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (15 bp):
TTTTATATATTATTA
Found at i:1150363 original size:12 final size:12
Alignment explanation
Indices: 1150295--1150487 Score: 79
Period size: 12 Copynumber: 16.0 Consensus size: 12
1150285 TTTAATATTA
*
1150295 TATTATATATGT
1 TATTATATATAT
* *
1150307 TTTTCATATATGT
1 TATT-ATATATAT
* *
1150320 TATGTAAATAAAT
1 TAT-TATATATAT
*
1150333 TTTTAATATTATAT
1 TATT-ATA-TATAT
1150347 T-TTATATATAT
1 TATTATATATAT
1150358 TATTATATATAT
1 TATTATATATAT
1150370 T-TTA-ATATTAT
1 TATTATATA-TAT
1150381 TAGTTATATAT-T
1 TA-TTATATATAT
1150393 T-TT-TATACTAT
1 TATTATATA-TAT
*
1150404 TA-TATGTATAT
1 TATTATATATAT
1150415 T-TCTA-ATAT-T
1 TAT-TATATATAT
*
1150425 ATATTGTATAT-T
1 -TATTATATATAT
* *
1150437 TCTAATACTATA-
1 TATTATA-TATAT
1150449 TA-TATATATAT
1 TATTATATATAT
1150460 ATATATATATATAT
1 -TAT-TATATATAT
1150474 ATATATATATATAT
1 -TAT-TATATATAT
1150488 GCGTGTGTAA
Statistics
Matches: 141, Mismatches: 16, Indels: 46
0.69 0.08 0.23
Matches are distributed among these distances:
9 4 0.03
10 11 0.08
11 32 0.23
12 37 0.26
13 25 0.18
14 32 0.23
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (12 bp):
TATTATATATAT
Found at i:1150405 original size:43 final size:42
Alignment explanation
Indices: 1150338--1150481 Score: 130
Period size: 43 Copynumber: 3.3 Consensus size: 42
1150328 TAAATTTTTA
* *
1150338 ATATTATAT-TTTATATATATTATTATATATATTT-TAATATT
1 ATATTATATATTT-TTTATACTATTATATATATTTCTAATATT
1150379 ATTAGTTATATATTTTTTATACTATTATATGTATATTTCTAATATT
1 A-TA-TTATATATTTTTTATACTATTATA--TATATTTCTAATATT
* * * * *
1150425 ATATTGTATATTTCTAATACTATATATATATATATATATATATAT
1 ATATTATATATTTTTTATACTAT-TATATATATTTCTA-ATAT-T
1150470 ATATATATATAT
1 ATAT-TATATAT
1150482 ATATATGCGT
Statistics
Matches: 85, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 26 0.31
44 24 0.28
45 18 0.21
46 14 0.16
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (42 bp):
ATATTATATATTTTTTATACTATTATATATATTTCTAATATT
Found at i:1150434 original size:21 final size:21
Alignment explanation
Indices: 1150365--1150449 Score: 84
Period size: 21 Copynumber: 3.9 Consensus size: 21
1150355 TATTATTATA
*
1150365 TATATTT-TAATATTATTAGTTA
1 TATATTTCTAATATTA-TA-TTG
*
1150387 TATATTTTTTATACTATTATA-TG
1 TATA-TTTCTA-A-TATTATATTG
1150410 TATATTTCTAATATTATATTG
1 TATATTTCTAATATTATATTG
*
1150431 TATATTTCTAATACTATAT
1 TATATTTCTAATATTATAT
1150450 ATATATATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
20 7 0.13
21 21 0.38
22 9 0.16
23 8 0.15
24 2 0.04
25 3 0.05
26 5 0.09
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.58
Consensus pattern (21 bp):
TATATTTCTAATATTATATTG
Found at i:1150452 original size:2 final size:2
Alignment explanation
Indices: 1150445--1150487 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1150435 TTTCTAATAC
1150445 TA TA TA 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 TA TA TA
1150487 T
1 T
1150488 GCGTGTGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1150578 original size:11 final size:11
Alignment explanation
Indices: 1150564--1150590 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1150554 GTATGTATTG
1150564 TATATGTTCTA
1 TATATGTTCTA
1150575 TATATGTTCTA
1 TATATGTTCTA
1150586 TATAT
1 TATAT
1150591 TTTAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (11 bp):
TATATGTTCTA
Found at i:1157869 original size:22 final size:22
Alignment explanation
Indices: 1157841--1157884 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1157831 ACCGTCAAGG
1157841 GAGAAGAAAATATTATAGCATC
1 GAGAAGAAAATATTATAGCATC
*
1157863 GAGAAGAAAATATTGTAGCATC
1 GAGAAGAAAATATTATAGCATC
1157885 TATTTCTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (22 bp):
GAGAAGAAAATATTATAGCATC
Found at i:1163375 original size:54 final size:54
Alignment explanation
Indices: 1163255--1163452 Score: 299
Period size: 55 Copynumber: 3.6 Consensus size: 54
1163245 TATTCATGTC
* *
1163255 TTCAAAAGTCAACTCATATTACGAGAGATGAGTTGAGCCCTTTTAAATTCATG-TT
1 TTCAAAAGTCAACTCATATTACGAGAGGTGAGTTGAG-CCTTTT-AATTTATGTTT
* * *
1163310 TTCAAAAGTCAACTCATATTGCAAGAGGTGAGTTGAGCCTTTTAATTTTTGTTT
1 TTCAAAAGTCAACTCATATTACGAGAGGTGAGTTGAGCCTTTTAATTTATGTTT
*
1163364 TTCAAAAGTCAACTCATATTACGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTT
1 TTCAAAAGTCAACTCATATTACGAGAGGTGAGTTGAGCCTTTTAATTTATGTTT
*
1163418 TTCAAAAAGTCAACTCATATTGCGAGAGGTGAGTT
1 TTC-AAAAGTCAACTCATATTACGAGAGGTGAGTT
1163453 TAATTTCTGT
Statistics
Matches: 132, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
53 6 0.05
54 62 0.47
55 64 0.48
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (54 bp):
TTCAAAAGTCAACTCATATTACGAGAGGTGAGTTGAGCCTTTTAATTTATGTTT
Found at i:1163396 original size:109 final size:109
Alignment explanation
Indices: 1163255--1163505 Score: 342
Period size: 109 Copynumber: 2.4 Consensus size: 109
1163245 TATTCATGTC
1163255 TTCAAAAGTCAACTCATATTACGAGAGATGAGTTGAGCCCTTTTAAATTCATG-TTTTC-AAAAG
1 TTCAAAAGTCAACTCATATTACGAGAGATGAGTTGAG-CCTTTTAAATTC-TGTTTTTCAAAAAG
1163318 TCAACTCATATTGCAAGAGGTGAGTTGAGCCTTTTAATTTTTGTTT
64 TCAACTCATATTGCAAGAGGTGAGTTGAGCCTTTTAATTTTTGTTT
* *
1163364 TTCAAAAGTCAACTCATATTACGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAAGTC
1 TTCAAAAGTCAACTCATATTACGAGAGATGAGTTGAGCCTTTTAAATTCTGTTTTTCAAAAAGTC
* *
1163429 AACTCATATTGC--GA---GAGGTGAG---TTTAATTTCTGTTT
66 AACTCATATTGCAAGAGGTGAGTTGAGCCTTTTAATTTTTGTTT
* **
1163465 TTCAAAAAATCAACTCATATTGTGAGAGATGAGTTGAGCCT
1 TTC-AAAAGTCAACTCATATTACGAGAGATGAGTTGAGCCT
1163506 CGGCTCACAT
Statistics
Matches: 131, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
101 16 0.12
102 33 0.25
104 7 0.05
107 4 0.03
108 16 0.12
109 55 0.42
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (109 bp):
TTCAAAAGTCAACTCATATTACGAGAGATGAGTTGAGCCTTTTAAATTCTGTTTTTCAAAAAGTC
AACTCATATTGCAAGAGGTGAGTTGAGCCTTTTAATTTTTGTTT
Found at i:1163478 original size:47 final size:47
Alignment explanation
Indices: 1163350--1163499 Score: 176
Period size: 47 Copynumber: 3.0 Consensus size: 47
1163340 AGTTGAGCCT
* *
1163350 TTTAATTTTTGTTTTTC-AAAAGTCAACTCATATTACGAGAGGTGAGTTGAG
1 TTTAATTTCTGTTTTTCAAAAAGTCAACTCATATTGCGAGA---G-G-TGAG
1163401 CCTTTTAATTTCTGTTTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAG
1 ---TTTAATTTCTGTTTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAG
* * *
1163451 TTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGTGAGAGATGAG
1 TTTAATTTCTGTTTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAG
1163498 TT
1 TT
1163500 GAGCCTCGGC
Statistics
Matches: 90, Mismatches: 5, Indels: 9
0.87 0.05 0.09
Matches are distributed among these distances:
47 46 0.51
50 4 0.04
51 1 0.01
52 1 0.01
54 16 0.18
55 22 0.24
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (47 bp):
TTTAATTTCTGTTTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAG
Found at i:1163673 original size:173 final size:170
Alignment explanation
Indices: 1163451--1163942 Score: 548
Period size: 173 Copynumber: 2.8 Consensus size: 170
1163441 GAGAGGTGAG
* * * *
1163451 TTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGTGAGAGATGAGTTGAGCCTCGGCTCACAT
1 TTTAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGG---ACAC
* *
1163516 GCTGAGG-AATTTTTAATTCCTG-TTTAATTTATACTTTTCAAAAGTCAACTCATATTGCGAGAG
63 GCTGAGGTAA-TTTCAATTTCTGTTTTAATTTATACTTTTCAAAA-TCAACTCATATTGCGAGAG
*
1163579 GTGAGTTGAGCCTCGG-GACACGCTGAAGTATTTTT-GAATTCTG-
126 GTGAGTTGAGCCTCGGCCACACGCTGAAGTATTTTTAG-ATTCTGT
* * * *
1163622 TTTAGTTTATATTTTTCAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGACAC
1 TTTAATTTATATTTTTC--AAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCC-TCGGACAC
* *
1163687 GCTGAGGTAATTTCAATTTCTGTCTTTAATTTCTACTTTTCCAAAATCAACTCATATTGCGAAAG
63 GCTGAGGTAATTTCAATTTCTGT-TTTAATTTATACTTTT-CAAAATCAACTCATATTGCGAGAG
* * * *
1163752 GAGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTTAGTTTCTGTTT
126 GTGAGTTGAGCCTCGGC-CACACGCTGAAGTATTTTTAGATTCTG--T
* * * *
1163800 TTTAATTTCTGTTTTTC--AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGT
1 TTTAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTC-GGACACGC
*
1163863 TGAGGTAATTTCAATTTCTGTTTTTTTTAAATTTATATTTTTCAAAAATCAACTCATATTGCGAG
65 TGAGGTAATTTCAATTTCTG----TTTT-AATTTATACTTTTC-AAAATCAACTCATATTGCGAG
1163928 AGGTGAGTTGAGCCT
124 AGGTGAGTTGAGCCT
1163943 TTTAATTCCT
Statistics
Matches: 272, Mismatches: 29, Indels: 33
0.81 0.09 0.10
Matches are distributed among these distances:
171 34 0.12
172 2 0.01
173 83 0.31
174 67 0.25
175 21 0.08
176 1 0.00
177 4 0.01
178 60 0.22
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (170 bp):
TTTAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGACACGCT
GAGGTAATTTCAATTTCTGTTTTAATTTATACTTTTCAAAATCAACTCATATTGCGAGAGGTGAG
TTGAGCCTCGGCCACACGCTGAAGTATTTTTAGATTCTGT
Found at i:1163814 original size:13 final size:14
Alignment explanation
Indices: 1163784--1163815 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1163774 TGCTGAGGTA
*
1163784 TTTTTAGTTTCTGT
1 TTTTTAATTTCTGT
1163798 TTTTTAATTTCTGT
1 TTTTTAATTTCTGT
1163812 TTTT
1 TTTT
1163816 CAAAATCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.75
Consensus pattern (14 bp):
TTTTTAATTTCTGT
Found at i:1163823 original size:88 final size:85
Alignment explanation
Indices: 1163451--1163942 Score: 476
Period size: 86 Copynumber: 5.6 Consensus size: 85
1163441 GAGAGGTGAG
* * *
1163451 TTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGTGAGA-GATGAGTTGAGCCTCGGCTCACA
1 TTTAATTTATATTTTTC-AAAAATCAACTCATATTGCGAGAGGA-GAGTTGAGCCTCGG--CACA
* * *
1163515 TGCTGAGGAATTTTTAATTCCTG-
62 CGCTGAGGTATTTTTAATTTCTGT
* * * *
1163538 TTTAATTTATACTTTTCAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCT
1 TTTAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTCGGCACACGCT
*
1163603 GAAGTATTTTTGAA-TTCTG-
66 GAGGTATTTTT-AATTTCTGT
* * * * *
1163622 TTTAGTTTATATTTTTCAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGACAC
1 TTTAATTTATATTTTTC---AAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTCGGCACAC
* *
1163687 GCTGAGGTAATTTCAATTTCTGT
63 GCTGAGGTATTTTTAATTTCTGT
* * * * *
1163710 CTTTAATTTCTACTTTTCCAAAATCAACTCATATTGCGAAAGGAGAGTTGAGCCTCGGCTCACAT
1 -TTTAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTCGG--CACAC
*
1163775 GCTGAGGTATTTTTAGTTTCTGTTT
63 GCTGAGGTATTTTTAATTTCTG--T
* * *
1163800 TTTAATTTCTGTTTTTC-AAAATCAACTCATATTGCGAGA-AATGAGTTGAGCCTCAGG-ACACG
1 TTTAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGA-GAGTTGAGCCTC-GGCACACG
* * *
1163862 TTGAGGTAATTTCAATTTCTGTTTTT
64 CTGAGGTATTTTTAATTTCTG----T
*
1163888 TTTAAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTT-AATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCT
1163943 TTTAATTCCT
Statistics
Matches: 341, Mismatches: 45, Indels: 35
0.81 0.11 0.08
Matches are distributed among these distances:
84 34 0.10
85 2 0.01
86 93 0.27
87 74 0.22
88 61 0.18
89 43 0.13
90 34 0.10
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (85 bp):
TTTAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTCGGCACACGCT
GAGGTATTTTTAATTTCTGT
Found at i:1164083 original size:140 final size:140
Alignment explanation
Indices: 1163799--1164105 Score: 437
Period size: 140 Copynumber: 2.2 Consensus size: 140
1163789 AGTTTCTGTT
1163799 TTTTAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGTT
1 TTTTAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGTT
*
1163864 GAGGTAATTTCAATTTCTGTTTTTTTTAAATTTATATTTTTCAAAAATCAACTCATATTGCGAGA
66 GAGGTAATTTCAATTTC---TTTTTTTAAATTTATATTTTTCAAAAAACAACTCATATTGCGAGA
1163929 GGTGAGTTGAGCC
128 GGTGAGTTGAGCC
* * * *
1163942 TTTTAATTCCTGTTTTTCAAAAGTCAACTCATATTGCGAGAAGTGAGTTGAGCCT-TGGCCCACG
1 TTTTAATTTCTGTTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG-ACACG
1164006 TGCTGAGGT-ATTTCCAATTTC-TTTTTT-AA-TTA-ATGTTTTCAAAAAACAACTCATATTGCG
64 T--TGAGGTAATTT-CAATTTCTTTTTTTAAATTTATAT-TTTTCAAAAAACAACTCATATTGCG
1164066 AGAGGTGAGTTGAGCC
125 AGAGGTGAGTTGAGCC
*
1164082 TTTTAATTTCTGTTTTCCAAAATC
1 TTTTAATTTCTGTTTTTCAAAATC
1164106 TACTTTTCAA
Statistics
Matches: 151, Mismatches: 7, Indels: 16
0.87 0.04 0.09
Matches are distributed among these distances:
139 4 0.03
140 63 0.42
141 2 0.01
142 6 0.04
143 23 0.15
144 36 0.24
145 4 0.03
146 13 0.09
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (140 bp):
TTTTAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGTT
GAGGTAATTTCAATTTCTTTTTTTAAATTTATATTTTTCAAAAAACAACTCATATTGCGAGAGGT
GAGTTGAGCC
Found at i:1165837 original size:3 final size:3
Alignment explanation
Indices: 1165831--1165877 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
1165821 TTATTTTTGA
* * *
1165831 ATT ATT AGT ATT ATT AGT ATT GTT ATT ATT ATT ATT ATT ATGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
1165877 A
1 A
1165878 GTATATATTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1165948 original size:12 final size:12
Alignment explanation
Indices: 1165933--1165976 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
1165923 AATATTATAT
1165933 TTATATATATTG
1 TTATATATATTG
1165945 TTATATATATT-
1 TTATATATATTG
1165956 TTA-ATATTATTAG
1 TTATATA-TATT-G
1165969 TTATATAT
1 TTATATAT
1165977 TTTTATACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 3 0.11
11 7 0.25
12 11 0.39
13 4 0.14
14 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (12 bp):
TTATATATATTG
Found at i:1165956 original size:22 final size:24
Alignment explanation
Indices: 1165928--1166052 Score: 83
Period size: 23 Copynumber: 5.5 Consensus size: 24
1165918 GTTTTAATAT
1165928 TATATTTATATA-TATT-GTTATA
1 TATATTTATATATTATTAGTTATA
1165950 TATATTT-TAATATTATTAGTTATA
1 TATATTTAT-ATATTATTAGTTATA
* *
1165974 TAT-TTT-TATACTATTA--TATG
1 TATATTTATATATTATTAGTTATA
* *
1165994 TATATTTCTAATATTA-TA-TTGTA
1 TATATTTAT-ATATTATTAGTTATA
* *
1166017 TAT-TTCTA-ATACTATTATTTATA
1 TATATT-TATATATTATTAGTTATA
*
1166040 TATATATATATAT
1 TATATTTATATAT
1166053 ATATATATAT
Statistics
Matches: 81, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
20 6 0.07
21 9 0.11
22 25 0.31
23 28 0.35
24 13 0.16
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (24 bp):
TATATTTATATATTATTAGTTATA
Found at i:1165962 original size:20 final size:21
Alignment explanation
Indices: 1165928--1166064 Score: 91
Period size: 21 Copynumber: 6.2 Consensus size: 21
1165918 GTTTTAATAT
*
1165928 TATATTTATATATATTGTTATA
1 TATATTTATA-ATATTATTATA
1165950 TATATTT-TAATATTATTAGTTA
1 TATATTTATAATATTATTA--TA
* *
1165972 TATATTTTTATACTATTA-TATG
1 TATA--TTTATAATATTATTATA
* *
1165994 TATATTTCTAATATTA-TATTG
1 TATATTTATAATATTATTA-TA
* * *
1166015 TATATTTCTAATACTATTATT
1 TATATTTATAATATTATTATA
*
1166036 TATATATATATATATATATATATA
1 TATATTTATA-ATAT-TAT-TATA
1166060 TATAT
1 TATAT
1166065 ATGTGTGTGT
Statistics
Matches: 94, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
20 20 0.21
21 28 0.30
22 23 0.24
23 3 0.03
24 13 0.14
25 7 0.07
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
TATATTTATAATATTATTATA
Found at i:1165973 original size:42 final size:45
Alignment explanation
Indices: 1165928--1166042 Score: 130
Period size: 44 Copynumber: 2.6 Consensus size: 45
1165918 GTTTTAATAT
*
1165928 TATATTTATATA-TATTGTTATATATATTT-TAATATTATTAGTTA
1 TATATTTATATACTATT-ATATATATATTTCTAATATTATTAGTTA
* * *
1165972 TATATTTTTATACTATTATATGTATATTTCTAATATTA-TA-TTG
1 TATATTTATATACTATTATATATATATTTCTAATATTATTAGTTA
* *
1166015 TATATTTCTAATACTATTATTTATATAT
1 TATATTTAT-ATACTATTATATATATAT
1166043 ATATATATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
43 10 0.16
44 39 0.64
45 12 0.20
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (45 bp):
TATATTTATATACTATTATATATATATTTCTAATATTATTAGTTA
Found at i:1165976 original size:44 final size:43
Alignment explanation
Indices: 1165928--1166066 Score: 122
Period size: 44 Copynumber: 3.1 Consensus size: 43
1165918 GTTTTAATAT
1165928 TATATTTATATA-TATTGTTATATATATTT-TAATATTATTAGTTA
1 TATATTTATATACTATT-TTATATATATTTCTAATATTA-TA-TTA
* * * *
1165972 TATATTTTTATACTATTATATGTATATTTCTAATATTATATTG
1 TATATTTATATACTATTTTATATATATTTCTAATATTATATTA
* * *
1166015 TATATTTCTAATACTATTATT-TATATATATATATATATATATATATA
1 TATATTTAT-ATACTATT-TTATATATATTTCTA-ATAT-TATAT-TA
1166062 TATAT
1 TATAT
1166067 GTGTGTGTAA
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
43 10 0.13
44 40 0.51
45 17 0.22
46 5 0.06
47 6 0.08
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (43 bp):
TATATTTATATACTATTTTATATATATTTCTAATATTATATTA
Found at i:1166018 original size:21 final size:22
Alignment explanation
Indices: 1165928--1166040 Score: 101
Period size: 22 Copynumber: 5.2 Consensus size: 22
1165918 GTTTTAATAT
* * *
1165928 TATATTTATATATATTGTTA-TA
1 TATATTTCTA-ATATTATTATTG
*
1165950 TATATTT-TAATATTATTAGTTA
1 TATATTTCTAATATTATTA-TTG
* *
1165972 TATATTT-TTATACTATTATATG
1 TATATTTCTAATATTATTAT-TG
1165994 TATATTTCTAATATTA-TATTG
1 TATATTTCTAATATTATTATTG
*
1166015 TATATTTCTAATACTATTATT-
1 TATATTTCTAATATTATTATTG
1166036 TATAT
1 TATAT
1166041 ATATATATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
20 8 0.10
21 25 0.32
22 40 0.51
23 6 0.08
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (22 bp):
TATATTTCTAATATTATTATTG
Found at i:1166043 original size:2 final size:2
Alignment explanation
Indices: 1166036--1166066 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1166026 TACTATTATT
1166036 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
1166067 GTGTGTGTAA
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:1166270 original size:2 final size:2
Alignment explanation
Indices: 1166263--1166289 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1166253 CTATATTGTG
1166263 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 T
1166290 TCTTAGTACC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1168978 original size:99 final size:99
Alignment explanation
Indices: 1168807--1169000 Score: 253
Period size: 99 Copynumber: 2.0 Consensus size: 99
1168797 GGCTCTAAAG
* * * * * *
1168807 TCTTTAATGTTAGCTCTGGAAGTTGAGACAACCTTAACACCTCTAACTGATAGCATGCCGATGTC
1 TCTTTAATGTCAACTCTGGAAGTTCAGACAACCTTAACACCTCTAACTGAGAGAATGCCGATGTA
*
1168872 TGCCTTTCCTCGTTGATGAGTCCTTCAGACAAAA
66 TGCCTTTCCTCGTGGATGAGTCCTTCAGACAAAA
* ** * *
1168906 TCTTTAATGTCAACTCTGGAAGTTCAGACAAGCTTAATTCCTTTAACTGAGAGAATGCTGATGTA
1 TCTTTAATGTCAACTCTGGAAGTTCAGACAACCTTAACACCTCTAACTGAGAGAATGCCGATGTA
* * *
1168971 TGTCTTTCCTTGTGGCTGAGTCCTTCAGAC
66 TGCCTTTCCTCGTGGATGAGTCCTTCAGAC
1169001 CGGACTATTT
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (99 bp):
TCTTTAATGTCAACTCTGGAAGTTCAGACAACCTTAACACCTCTAACTGAGAGAATGCCGATGTA
TGCCTTTCCTCGTGGATGAGTCCTTCAGACAAAA
Found at i:1187101 original size:23 final size:22
Alignment explanation
Indices: 1187061--1187116 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1187051 AAAAGCTATC
* *
1187061 TACAAATCAAAT-CTCTAACAT
1 TACAAATCATATGTTCTAACAT
*
1187082 TACAGAATCATATGTTCTAAGAT
1 TACA-AATCATATGTTCTAACAT
*
1187105 TACATATCATAT
1 TACAAATCATAT
1187117 CTAAAATTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 4 0.14
22 14 0.48
23 11 0.38
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (22 bp):
TACAAATCATATGTTCTAACAT
Found at i:1187116 original size:22 final size:23
Alignment explanation
Indices: 1187074--1187116 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1187064 AAATCAAATC
1187074 TCTAACATTACAGAATCATATGT
1 TCTAACATTACAGAATCATATGT
* *
1187097 TCTAAGATTACA-TATCATAT
1 TCTAACATTACAGAATCATAT
1187117 CTAAAATTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (23 bp):
TCTAACATTACAGAATCATATGT
Found at i:1187764 original size:18 final size:18
Alignment explanation
Indices: 1187741--1187775 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1187731 AGAAAATATG
1187741 TTGCTGCAACATGCATAA
1 TTGCTGCAACATGCATAA
*
1187759 TTGCTGCAGCATGCATA
1 TTGCTGCAACATGCATA
1187776 CAAGCTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (18 bp):
TTGCTGCAACATGCATAA
Found at i:1190262 original size:3 final size:3
Alignment explanation
Indices: 1190254--1190299 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1190244 ACGAATGAAT
1190254 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1190300 AAGAACAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1203791 original size:40 final size:40
Alignment explanation
Indices: 1203683--1203892 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
1203673 CGGGATTTAA
* * * * *
1203683 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
1203723 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1203763 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1203803 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1203843 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1203883 CCGGATATAT
1 CCGGATATAT
1203893 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:1211196 original size:2 final size:2
Alignment explanation
Indices: 1211189--1211220 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1211179 ATTGAATACC
1211189 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
1211221 CAAAAGCTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1214804 original size:17 final size:17
Alignment explanation
Indices: 1214782--1214870 Score: 54
Period size: 17 Copynumber: 4.8 Consensus size: 17
1214772 TAAAACATTT
1214782 TTAAAAATTAAAAAATA
1 TTAAAAATTAAAAAATA
*
1214799 TTAAAAATTTATATAAACT-
1 TTAAAAA-TTA-A-AAAATA
*
1214818 TATAACAACTATAAAAATATA
1 T-TAA-AAAT-TAAAAA-ATA
* **
1214839 TATAAAATTTAAAAAACC
1 T-TAAAAATTAAAAAATA
1214857 TTAAAAATTAAAAA
1 TTAAAAATTAAAAA
1214871 TCATAAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
17 19 0.33
18 5 0.09
19 11 0.19
20 13 0.23
21 9 0.16
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAAAATTAAAAAATA
Found at i:1214815 original size:29 final size:29
Alignment explanation
Indices: 1214783--1214865 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
1214773 AAAACATTTT
1214783 TAAAAATTAAAAAATATTAAAAATTTATA
1 TAAAAATTAAAAAATATTAAAAATTTATA
* * *
1214812 T-AAACTTATAACAACTA-TAAAAATATATA
1 TAAAAATTA-AA-AAATATTAAAAATTTATA
* **
1214841 TAAAATTTAAAAAACCTTAAAAATT
1 TAAAAATTAAAAAATATTAAAAATT
1214866 AAAAATCATA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
28 8 0.19
29 24 0.57
30 10 0.24
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (29 bp):
TAAAAATTAAAAAATATTAAAAATTTATA
Found at i:1214890 original size:10 final size:10
Alignment explanation
Indices: 1214800--1214890 Score: 50
Period size: 10 Copynumber: 9.5 Consensus size: 10
1214790 TAAAAAATAT
*
1214800 TAAAAATTTA
1 TAAAAACTTA
*
1214810 TATAAACTTA
1 TAAAAACTTA
*
1214820 TAACAAC-TA
1 TAAAAACTTA
1214829 TAAAAA-TATA
1 TAAAAACT-TA
*
1214839 TATAAAATTTA
1 TA-AAAACTTA
*
1214850 -AAAAACCT-
1 TAAAAACTTA
1214858 TAAAAA-TTA
1 TAAAAACTTA
* *
1214867 -AAAATCATA
1 TAAAAACTTA
*
1214876 AAAAAACTTA
1 TAAAAACTTA
1214886 TAAAA
1 TAAAA
1214891 TAATAAAACA
Statistics
Matches: 60, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
8 5 0.08
9 19 0.32
10 29 0.48
11 6 0.10
12 1 0.02
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAAAACTTA
Found at i:1214896 original size:20 final size:18
Alignment explanation
Indices: 1214859--1214898 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1214849 AAAAAACCTT
*
1214859 AAAAATTAAAAATCATAA
1 AAAAATTAAAAATAATAA
1214877 AAAAACTTATAAAATAATAA
1 AAAAA-TTA-AAAATAATAA
1214897 AA
1 AA
1214899 CATATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 3 0.16
20 11 0.58
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATTAAAAATAATAA
Found at i:1214902 original size:27 final size:26
Alignment explanation
Indices: 1214848--1214902 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1214838 ATATAAAATT
* *
1214848 TAAAAAACCTTAAAAATTAAAAATCA
1 TAAAAAAACTTAAAAATTAAAAAACA
1214874 TAAAAAAACTTATAAAA-TAATAAAACA
1 TAAAAAAACTTA-AAAATTAA-AAAACA
1214901 TA
1 TA
1214903 TTTAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (26 bp):
TAAAAAAACTTAAAAATTAAAAAACA
Found at i:1215516 original size:19 final size:19
Alignment explanation
Indices: 1215494--1215562 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 19
1215484 ATTGTATATT
1215494 TTTTATAATATTTTACAAG
1 TTTTATAATATTTTACAAG
* * * *
1215513 TTTTATGATTTTTTTATAAT
1 TTTTAT-AATATTTTACAAG
*
1215533 TTTTATAAT-TTATACAAG
1 TTTTATAATATTTTACAAG
*
1215551 -TATATAATATTT
1 TTTTATAATATTT
1215563 GTAATATTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
17 7 0.18
18 8 0.21
19 8 0.21
20 15 0.39
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTTATAATATTTTACAAG
Found at i:1215535 original size:9 final size:9
Alignment explanation
Indices: 1215488--1215626 Score: 50
Period size: 9 Copynumber: 14.6 Consensus size: 9
1215478 ATTAATATTG
*
1215488 TATATTTTT
1 TATAATTTT
1215497 TATAATATTT
1 TATAAT-TTT
* *
1215507 TACAAGTTT
1 TATAATTTT
*
1215516 TATGATTTTTT
1 TAT-A-ATTTT
1215527 TATAATTTT
1 TATAATTTT
*
1215536 TATAATTTA
1 TATAATTTT
* * *
1215545 TACAA-GTA
1 TATAATTTT
1215553 TATAATATTT
1 TATAAT-TTT
1215563 GTA-ATATTTT
1 -TATA-ATTTT
*
1215573 TAGAATTTT
1 TATAATTTT
*
1215582 T-TGAGTTTT
1 TAT-AATTTT
* *
1215591 AATAATATT
1 TATAATTTT
1215600 TATAAGTTTTT
1 TATAA--TTTT
1215611 TATGAATTATT
1 TAT-AATT-TT
1215622 TATAA
1 TATAA
1215627 GTTTCCTTAA
Statistics
Matches: 96, Mismatches: 20, Indels: 27
0.67 0.14 0.19
Matches are distributed among these distances:
8 6 0.06
9 47 0.49
10 20 0.21
11 21 0.22
12 2 0.02
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (9 bp):
TATAATTTT
Found at i:1225083 original size:33 final size:33
Alignment explanation
Indices: 1224997--1225085 Score: 110
Period size: 33 Copynumber: 2.7 Consensus size: 33
1224987 TATGTACACC
* **
1224997 TTGTGTGTA-CACTTGGAAATGTTAGGTATACT
1 TTGTGTGTACCACTTGGAAAGGAAAGGTATACT
* *
1225029 TTGTGTATACCA-TATGAAAAGGAAAGGTATACT
1 TTGTGTGTACCACT-TGGAAAGGAAAGGTATACT
1225062 TTGTGTGTACCACTTGGAAAGGAA
1 TTGTGTGTACCACTTGGAAAGGAA
1225086 TGTACACCTC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
32 9 0.19
33 37 0.79
34 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (33 bp):
TTGTGTGTACCACTTGGAAAGGAAAGGTATACT
Found at i:1227557 original size:89 final size:90
Alignment explanation
Indices: 1227456--1227638 Score: 314
Period size: 91 Copynumber: 2.0 Consensus size: 90
1227446 TGTATTGCCC
*
1227456 ATTCTATTGACTTTGGGGACTTAGTGGATGAA-ATTTTTTTTCGGCACTTTTGCAGGTAATTTCC
1 ATTCTATTGACTTGGGGGACTTAGTGGATGAATATTTTTTTTCGGCACTTTTGCAGGTAATTTCC
*
1227520 AAAAAGGAGGTTATAAAATCAAGTA
66 AAAAAAGAGGTTATAAAATCAAGTA
* *
1227545 ATTCTATTGACTTGGGGGACTTAGTGGATGAATTTTTTTTTTTGGGCACTTTTGCAGGTAATTTC
1 ATTCTATTGACTTGGGGGACTTAGTGGATGAA-TATTTTTTTTCGGCACTTTTGCAGGTAATTTC
1227610 CAAAAAAGAGGTTATAAAATCAAGTA
65 CAAAAAAGAGGTTATAAAATCAAGTA
1227636 ATT
1 ATT
1227639 AATCTAAACT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 31 0.35
91 57 0.65
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (90 bp):
ATTCTATTGACTTGGGGGACTTAGTGGATGAATATTTTTTTTCGGCACTTTTGCAGGTAATTTCC
AAAAAAGAGGTTATAAAATCAAGTA
Found at i:1230825 original size:10 final size:10
Alignment explanation
Indices: 1230812--1230861 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
1230802 CTAAAAAAAC
1230812 TTTAAAAATA
1 TTTAAAAATA
1230822 TTTAAAAATTA
1 TTTAAAAA-TA
**
1230833 TAAAAAAATA
1 TTTAAAAATA
*
1230843 TTTAAAATTA
1 TTTAAAAATA
*
1230853 TTAAAAAAT
1 TTTAAAAAT
1230862 TAGAAAAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
10 24 0.75
11 8 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TTTAAAAATA
Found at i:1230838 original size:20 final size:20
Alignment explanation
Indices: 1230815--1230877 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
1230805 AAAAAACTTT
1230815 AAAAATATTTAAAAATTATAA
1 AAAAATATTTAAAAATTAT-A
1230836 AAAAATATTT-AAAATTATTA
1 AAAAATATTTAAAAATTA-TA
**
1230856 AAAAAT-TAGAAAAATTATA
1 AAAAATATTTAAAAATTATA
1230875 AAA
1 AAA
1230878 TCATAAAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 6 0.16
20 21 0.55
21 11 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAAATATTTAAAAATTATA
Found at i:1230847 original size:31 final size:30
Alignment explanation
Indices: 1230803--1230869 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
1230793 TGTCGTCATC
* *
1230803 TAAAAAAACTTTAAAAATATTTAAAAATTA
1 TAAAAAAAATTTAAAAATATTAAAAAATTA
*
1230833 TAAAAAAATATTTAAAATTATTAAAAAATTA
1 TAAAAAAA-ATTTAAAAATATTAAAAAATTA
*
1230864 GAAAAA
1 TAAAAA
1230870 TTATAAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (30 bp):
TAAAAAAAATTTAAAAATATTAAAAAATTA
Found at i:1231266 original size:20 final size:18
Alignment explanation
Indices: 1231235--1231287 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 18
1231225 TTTTTTCTAT
*
1231235 TTTTAATTATTTTTGTAA
1 TTTTAAATATTTTTGTAA
1231253 TTATTAAATAATTTTTTGTAA
1 TT-TTAAAT-A-TTTTTGTAA
*
1231274 TTTTATATATTTTT
1 TTTTAAATATTTTT
1231288 TCATTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 7 0.23
19 6 0.20
20 6 0.20
21 11 0.37
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (18 bp):
TTTTAAATATTTTTGTAA
Found at i:1231268 original size:21 final size:19
Alignment explanation
Indices: 1231225--1231288 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
1231215 ATAATTTCAT
* * *
1231225 TTTTTTCTATTTTTAATTA
1 TTTTTTGTAATTTTAAATA
1231244 -TTTTTGTAATTATTAAATAA
1 TTTTTTGTAATT-TTAAAT-A
*
1231264 TTTTTTGTAATTTTATATA
1 TTTTTTGTAATTTTAAATA
1231283 TTTTTT
1 TTTTTT
1231289 CATTTTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
18 9 0.24
19 12 0.32
20 6 0.16
21 11 0.29
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTTTGTAATTTTAAATA
Found at i:1231784 original size:3 final size:3
Alignment explanation
Indices: 1231776--1231808 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1231766 TTAAATTGAC
1231776 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1231809 TTTCCTTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:1234576 original size:42 final size:42
Alignment explanation
Indices: 1234529--1234620 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
1234519 TAATAAGAAG
*
1234529 ATAACACTGTTGTGTAAGTGTAAATAGTAAATTAACAACAAA
1 ATAACACTGTTGTGTAAGTGTAAACAGTAAATTAACAACAAA
* *
1234571 ATAACACTGTTGTGTAAGTGTAACCAGTAAATTAATAACAAA
1 ATAACACTGTTGTGTAAGTGTAAACAGTAAATTAACAACAAA
1234613 ATAACACT
1 ATAACACT
1234621 TCTATTGGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (42 bp):
ATAACACTGTTGTGTAAGTGTAAACAGTAAATTAACAACAAA
Found at i:1246878 original size:14 final size:14
Alignment explanation
Indices: 1246853--1246887 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
1246843 ATTCACTATG
1246853 CATTTATATTATTAA
1 CATTT-TATTATTAA
1246868 CATTTTATTATTAA
1 CATTTTATTATTAA
1246882 CATTTT
1 CATTTT
1246888 CTAGACAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (14 bp):
CATTTTATTATTAA
Found at i:1253037 original size:6 final size:6
Alignment explanation
Indices: 1253022--1253057 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
1253012 ATGTCGACCA
1253022 CCAT-G CCATAG CCATAG CCATAG CCATAG CCATAG C
1 CCATAG CCATAG CCATAG CCATAG CCATAG CCATAG C
1253058 ATATGGATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.31, C:0.36, G:0.17, T:0.17
Consensus pattern (6 bp):
CCATAG
Found at i:1254519 original size:14 final size:15
Alignment explanation
Indices: 1254494--1254522 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1254484 AACAATCAAC
1254494 AGAACAAAAAGAAAA
1 AGAACAAAAAGAAAA
1254509 AGAAC-AAAAGAAAA
1 AGAACAAAAAGAAAA
1254523 GAGCTAAATA
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:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (15 bp):
AGAACAAAAAGAAAA
Found at i:1254582 original size:14 final size:14
Alignment explanation
Indices: 1254565--1254593 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1254555 CAAATTTCAT
1254565 CATTTAAATCATTG
1 CATTTAAATCATTG
1254579 CATTTAAATCATTG
1 CATTTAAATCATTG
1254593 C
1 C
1254594 CTATTGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (14 bp):
CATTTAAATCATTG
Found at i:1255975 original size:2 final size:2
Alignment explanation
Indices: 1255968--1255995 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1255958 TCAAGATTAG
1255968 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
1255996 GAGATTATAC
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:1258324 original size:5 final size:5
Alignment explanation
Indices: 1258287--1258320 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1258277 CATCAGAGGC
* *
1258287 CATGG CATGG CATGG CATGG CATGA CATGA CATG
1 CATGG CATGG CATGG CATGG CATGG CATGG CATG
1258321 ACATAATACG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (5 bp):
CATGG
Found at i:1272447 original size:7 final size:7
Alignment explanation
Indices: 1272435--1272469 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
1272425 GAATTCATGT
1272435 TTGTCAA
1 TTGTCAA
1272442 TTGTCAA
1 TTGTCAA
1272449 TTGTCAA
1 TTGTCAA
1272456 TTGTCAA
1 TTGTCAA
1272463 TTGTCAA
1 TTGTCAA
1272470 CTGCGATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (7 bp):
TTGTCAA
Found at i:1272480 original size:21 final size:21
Alignment explanation
Indices: 1272434--1272481 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1272424 GGAATTCATG
*
1272434 TTTGTCAATTGTCAATTGTCA
1 TTTGTCAATTGTCAACTGTCA
*
1272455 ATTGTCAATTGTCAACTG-CGA
1 TTTGTCAATTGTCAACTGTC-A
1272476 TTTGTC
1 TTTGTC
1272482 TACTTTCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (21 bp):
TTTGTCAATTGTCAACTGTCA
Found at i:1272916 original size:20 final size:20
Alignment explanation
Indices: 1272874--1272916 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1272864 TTAAATAATT
*
1272874 TTAACTATAAAAAATATTAA
1 TTAACTATAAAAAATACTAA
* * *
1272894 TTAATTATATAAAATACTCA
1 TTAACTATAAAAAATACTAA
1272914 TTA
1 TTA
1272917 TTTAACAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAACTATAAAAAATACTAA
Found at i:1275090 original size:16 final size:16
Alignment explanation
Indices: 1275071--1275102 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1275061 TGATAATTTG
*
1275071 TTTACATTAGAATTCA
1 TTTACATTAAAATTCA
1275087 TTTACATTAAAATTCA
1 TTTACATTAAAATTCA
1275103 GATGACATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (16 bp):
TTTACATTAAAATTCA
Found at i:1283189 original size:51 final size:51
Alignment explanation
Indices: 1283113--1283218 Score: 203
Period size: 51 Copynumber: 2.1 Consensus size: 51
1283103 GTTCGATTCT
1283113 GAAATTGACCACCAAACCATTATAAAGAAAGTTAATTATAATAATTTTTCA
1 GAAATTGACCACCAAACCATTATAAAGAAAGTTAATTATAATAATTTTTCA
*
1283164 GAAATTGACCACCAAACCATTATAAAGAAATTTAATTATAATAATTTTTCA
1 GAAATTGACCACCAAACCATTATAAAGAAAGTTAATTATAATAATTTTTCA
1283215 GAAA
1 GAAA
1283219 GATCCTTTCT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (51 bp):
GAAATTGACCACCAAACCATTATAAAGAAAGTTAATTATAATAATTTTTCA
Found at i:1286861 original size:32 final size:32
Alignment explanation
Indices: 1286818--1286896 Score: 122
Period size: 35 Copynumber: 2.4 Consensus size: 32
1286808 ATCAGGCGAT
*
1286818 CACATCGCGATGTCAAGCTCTCAACGTTGTGA
1 CACATCACGATGTCAAGCTCTCAACGTTGTGA
1286850 CACATCACGATGATGTCAAGCTCTCAACGTTGTGA
1 CACATCAC---GATGTCAAGCTCTCAACGTTGTGA
1286885 CACATCACGATG
1 CACATCACGATG
1286897 ATGTCAAGTC
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
32 11 0.26
35 32 0.74
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (32 bp):
CACATCACGATGTCAAGCTCTCAACGTTGTGA
Found at i:1286871 original size:35 final size:35
Alignment explanation
Indices: 1286826--1286904 Score: 158
Period size: 35 Copynumber: 2.3 Consensus size: 35
1286816 ATCACATCGC
1286826 GATGTCAAGCTCTCAACGTTGTGACACATCACGAT
1 GATGTCAAGCTCTCAACGTTGTGACACATCACGAT
1286861 GATGTCAAGCTCTCAACGTTGTGACACATCACGAT
1 GATGTCAAGCTCTCAACGTTGTGACACATCACGAT
1286896 GATGTCAAG
1 GATGTCAAG
1286905 TCAAGTAGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (35 bp):
GATGTCAAGCTCTCAACGTTGTGACACATCACGAT
Found at i:1303989 original size:50 final size:50
Alignment explanation
Indices: 1303914--1304013 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
1303904 ATGGTGTAAC
1303914 TTAATTTTTCTTTTGACATCATCACCATGTCCTGTTCCTAAGAAGATTGG
1 TTAATTTTTCTTTTGACATCATCACCATGTCCTGTTCCTAAGAAGATTGG
1303964 TTAATTTTTCTTTTGACATCATCACCATGTCCTGTTCCTAAGAAGATTGG
1 TTAATTTTTCTTTTGACATCATCACCATGTCCTGTTCCTAAGAAGATTGG
1304014 CATCATCCTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (50 bp):
TTAATTTTTCTTTTGACATCATCACCATGTCCTGTTCCTAAGAAGATTGG
Found at i:1308139 original size:10 final size:11
Alignment explanation
Indices: 1308123--1308160 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1308113 CATCTATTTG
1308123 ATATTTTTAAA
1 ATATTTTTAAA
*
1308134 AT-TTTTTTAA
1 ATATTTTTAAA
*
1308144 ATATTTTTAAT
1 ATATTTTTAAA
1308155 ATATTT
1 ATATTT
1308161 AAGAGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTTTTAAA
Found at i:1311956 original size:17 final size:17
Alignment explanation
Indices: 1311934--1311966 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1311924 ACCCAACTCT
1311934 CTCTTATTACTTGCCAA
1 CTCTTATTACTTGCCAA
1311951 CTCTTATTACTTGCCA
1 CTCTTATTACTTGCCA
1311967 GGTTGGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.30, G:0.06, T:0.42
Consensus pattern (17 bp):
CTCTTATTACTTGCCAA
Found at i:1314759 original size:22 final size:22
Alignment explanation
Indices: 1314731--1314775 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1314721 AACTTGTTCT
1314731 AAAGATGAAAACCACAATACCC
1 AAAGATGAAAACCACAATACCC
1314753 AAAGATGAAAACCACAATACCC
1 AAAGATGAAAACCACAATACCC
1314775 A
1 A
1314776 CAGAAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.27, G:0.09, T:0.09
Consensus pattern (22 bp):
AAAGATGAAAACCACAATACCC
Found at i:1323409 original size:90 final size:90
Alignment explanation
Indices: 1323256--1323432 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 90
1323246 CTGTGGACCT
* * *
1323256 CTTAAATTTTAGTTACTGAATTTTTGAGCTTACGTTATGCCCTATGTACTAGACTTGTTTTGGGT
1 CTTAAATTTTAGTTACTGAATTTTTGAGCTTACGTTATACCCCATGTACTAGACTTATTTTGGGT
* *
1323321 CTTCATTTAGTTAGTTAGATAGGTC
66 CATCATTTAATTAGTTAGATAGGTC
1323346 CTTAAATTTTAGTTACTGAATTTTTGAGCTTACGTTATACCCCATGTACTAGACTTATTTTGGGT
1 CTTAAATTTTAGTTACTGAATTTTTGAGCTTACGTTATACCCCATGTACTAGACTTATTTTGGGT
1323411 CATCATTTAATTAGTTAGATAG
66 CATCATTTAATTAGTTAGATAG
1323433 ACCCTTTCGT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.45
Consensus pattern (90 bp):
CTTAAATTTTAGTTACTGAATTTTTGAGCTTACGTTATACCCCATGTACTAGACTTATTTTGGGT
CATCATTTAATTAGTTAGATAGGTC
Found at i:1324332 original size:20 final size:20
Alignment explanation
Indices: 1324307--1324352 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1324297 GATATATCCA
1324307 TTTGGTGAAAATACTCTGAT
1 TTTGGTGAAAATACTCTGAT
1324327 TTTGGTGAAAATACTCTGAT
1 TTTGGTGAAAATACTCTGAT
1324347 TTTGGT
1 TTTGGT
1324353 TAAAGATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (20 bp):
TTTGGTGAAAATACTCTGAT
Found at i:1331687 original size:32 final size:32
Alignment explanation
Indices: 1331642--1331712 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1331632 TCCCAATTGG
*
1331642 TAATTAAAATCAATGCT-TAATTAAGCCTTGATT
1 TAATT-AAATCAATGCTAT-ATTAAGCCTCGATT
*
1331675 TAATTAAATCAATGCTATATTAAGGCTCGATT
1 TAATTAAATCAATGCTATATTAAGCCTCGATT
1331707 TAATTA
1 TAATTA
1331713 TCTAATTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
32 29 0.83
33 6 0.17
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (32 bp):
TAATTAAATCAATGCTATATTAAGCCTCGATT
Found at i:1336533 original size:6 final size:6
Alignment explanation
Indices: 1336522--1336553 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1336512 ACCTAGACTC
1336522 TTCTTT TTCTTT TTCTTT TT-TTT TT-TTT TTCT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCT
1336554 AAAGTATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTCTTT
Found at i:1337809 original size:125 final size:126
Alignment explanation
Indices: 1337655--1337898 Score: 409
Period size: 127 Copynumber: 1.9 Consensus size: 126
1337645 TCCTGTTTAT
*
1337655 TTCTAACGTTTCTTTCTCCTTTCTTAACTACTG-TTTTCCCCTTCTTTTCAAATATTTTCCTTCT
1 TTCTAACGTTCCTTTCTCCTTTCTTAACTACTGTTTTTCCCCTTCTTTTCAAATATTTTCCTTCT
* * *
1337719 CTCCTGTTTTCTATCTCCCGGGCTCCTTTCTTGTCCTTTCTTTCTTCACACACTCCCTTAC
66 CTCCTGTTTTCTATCTCCCAGCCTCCGTTCTTGTCCTTTCTTTCTTCACACACTCCCTTAC
*
1337780 TTCTAACGTTCCTTTCTCCTTTCTTAACTACTGTTTTTTTCCCTTCTTTTCAAATATTTTCCTTC
1 TTCTAACGTTCCTTTCTCCTTTCTTAACTACTG-TTTTTCCCCTTCTTTTCAAATATTTTCCTTC
* *
1337845 TCTCCTGTTTTCTTTCTTCCAGCCTCCGTTCTTGTCCTTTCTTTCTTCACACAC
65 TCTCCTGTTTTCTATCTCCCAGCCTCCGTTCTTGTCCTTTCTTTCTTCACACAC
1337899 ACAAATACGG
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
125 32 0.29
127 78 0.71
ACGTcount: A:0.11, C:0.33, G:0.05, T:0.51
Consensus pattern (126 bp):
TTCTAACGTTCCTTTCTCCTTTCTTAACTACTGTTTTTCCCCTTCTTTTCAAATATTTTCCTTCT
CTCCTGTTTTCTATCTCCCAGCCTCCGTTCTTGTCCTTTCTTTCTTCACACACTCCCTTAC
Found at i:1343994 original size:27 final size:27
Alignment explanation
Indices: 1343942--1343998 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1343932 ATATCCTACA
* *
1343942 CCAGGGATATCCCGCTTTTAGGATATC
1 CCAGGGATATCCCGCATTCAGGATATC
*
1343969 CCAGGGATATCCCG-ATTCGGGTATATC
1 CCAGGGATATCCCGCATTCAGG-ATATC
1343996 CCA
1 CCA
1343999 TTCCAAGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (27 bp):
CCAGGGATATCCCGCATTCAGGATATC
Found at i:1345343 original size:2 final size:2
Alignment explanation
Indices: 1345336--1345360 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1345326 ATGCCACTCA
1345336 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1345361 TGGGTGGGGT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1348730 original size:39 final size:39
Alignment explanation
Indices: 1348684--1348766 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
1348674 CCACCGGCAA
*
1348684 CCACCATCTTCGTTCACCAGTCAGGCAGTCACCACCGGT
1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT
* * * *
1348723 CCACCATCATCGTTCATCAGTCATGTAGTCACCATCGGT
1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT
1348762 CCACC
1 CCACC
1348767 CGTCACCACC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.23
Consensus pattern (39 bp):
CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT
Found at i:1351223 original size:16 final size:16
Alignment explanation
Indices: 1351202--1351232 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1351192 ATTTGGCTTA
1351202 CTGTTTCCCTCTTTTT
1 CTGTTTCCCTCTTTTT
*
1351218 CTGTTTTCCTCTTTT
1 CTGTTTCCCTCTTTT
1351233 GTATATATTA
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:0.00, C:0.29, G:0.06, T:0.65
Consensus pattern (16 bp):
CTGTTTCCCTCTTTTT
Found at i:1353238 original size:16 final size:16
Alignment explanation
Indices: 1353188--1353238 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
1353178 GTAAGTACTG
1353188 TGTTATTTGGTTAGCT
1 TGTTATTTGGTTAGCT
*
1353204 TGATATTTGGTTAGCT
1 TGTTATTTGGTTAGCT
* *
1353220 TGTTATTGGGTTGGCT
1 TGTTATTTGGTTAGCT
1353236 TGT
1 TGT
1353239 GTCGCAGCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.12, C:0.06, G:0.29, T:0.53
Consensus pattern (16 bp):
TGTTATTTGGTTAGCT
Found at i:1357551 original size:21 final size:21
Alignment explanation
Indices: 1357512--1357551 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1357502 TTTATTTAAA
*
1357512 AATATAAATGATATAGAATAT
1 AATATAAATGAAATAGAATAT
*
1357533 AATATAAATGAAATGGAAT
1 AATATAAATGAAATAGAAT
1357552 TACTGATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (21 bp):
AATATAAATGAAATAGAATAT
Found at i:1359992 original size:103 final size:103
Alignment explanation
Indices: 1359872--1360069 Score: 396
Period size: 103 Copynumber: 1.9 Consensus size: 103
1359862 TATGGCATTG
1359872 TTGTGTGTTTTCTAATAGAATCGAAAGTAAGAGACACTGGGCTCAATTAACATCAATTTTAACTA
1 TTGTGTGTTTTCTAATAGAATCGAAAGTAAGAGACACTGGGCTCAATTAACATCAATTTTAACTA
1359937 GAACATGGTCATATTTAGAGTGAAAAGTCTAGATAAAA
66 GAACATGGTCATATTTAGAGTGAAAAGTCTAGATAAAA
1359975 TTGTGTGTTTTCTAATAGAATCGAAAGTAAGAGACACTGGGCTCAATTAACATCAATTTTAACTA
1 TTGTGTGTTTTCTAATAGAATCGAAAGTAAGAGACACTGGGCTCAATTAACATCAATTTTAACTA
1360040 GAACATGGTCATATTTAGAGTGAAAAGTCT
66 GAACATGGTCATATTTAGAGTGAAAAGTCT
1360070 TGCATTTTAT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (103 bp):
TTGTGTGTTTTCTAATAGAATCGAAAGTAAGAGACACTGGGCTCAATTAACATCAATTTTAACTA
GAACATGGTCATATTTAGAGTGAAAAGTCTAGATAAAA
Found at i:1366415 original size:36 final size:36
Alignment explanation
Indices: 1366368--1366440 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1366358 TGATAATCAG
1366368 TCATAAATTCCTATTAGCAGTTTGACAGTTTCCTCC
1 TCATAAATTCCTATTAGCAGTTTGACAGTTTCCTCC
1366404 TCATAAATTCCTATTAGCAGTTTGACAGTTTCCTCC
1 TCATAAATTCCTATTAGCAGTTTGACAGTTTCCTCC
1366440 T
1 T
1366441 TTTTTTCTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.40
Consensus pattern (36 bp):
TCATAAATTCCTATTAGCAGTTTGACAGTTTCCTCC
Found at i:1384171 original size:79 final size:80
Alignment explanation
Indices: 1384054--1384811 Score: 284
Period size: 87 Copynumber: 9.6 Consensus size: 80
1384044 GTTTTATTTC
* * *
1384054 AAAATTCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGCTGGGGTAATTTT-AATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACG-TGGAGTAATTTTCAATTT
1384118 CTG-TTGTCAAAAAAA
65 CTGTTTGTCAAAAAAA
* * * * * *
1384133 AAAAATCAACTCGTATTGCGAGCGGTGAGTTGAGCCTCAAGACATGTTGAGTTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTGGAGTAATTTTCAATTTC
*
1384198 TGTTTTTC----AAA
66 TGTTTGTCAAAAAAA
* * * * *
1384209 AAAAATCAGCTCATATTGCGAGAGATGAGTTGAACCTCAAGACGC-T-GAGGT-GTTTTCCATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTGGA-GTAATTTTCAATTT
* * **
1384271 TTGTTCT-TTAATTTATGTGTTTCAA
65 CTGTT-TGTCAA---A------AAAA
* * **
1384296 AAAAATCAGCTCATATTGCGA-ATGGTGAGTTGAGCCTCGGGACACGCT-GAGGTAA-TTTCAAT
1 AAAAATCAACTCATATTGCGAGA-GGTGAGTTGAACCTCAAGACACG-TGGA-GTAATTTTCAAT
1384358 TTCTGTTT-TC-------
63 TTCTGTTTGTCAAAAAAA
* * * ** * *
1384368 AAAATTCAACTTATATTGAGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT-ATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTGGA-GTAATTTTCAATTT
1384432 CTGTTT-TC--AAAAA
65 CTGTTTGTCAAAAAAA
* * * * * *
1384445 AAAAACCAACTTATATTGCGAGAGGTAAGTTGAGCCTC-AGTTCACATGCTGAGGT-ATTTTCAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAG-ACACGTG--GA-GTAATTTTCAA
1384508 TTTCTGTCTT-TC----AAA
62 TTTCTGT-TTGTCAAAAAAA
* * * * * ***
1384523 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACT-GAGGTATTTTTTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCA-A-GACAC-GTGGA-GTAATTTTCAA
** * ******
1384587 TTTCAATTTAT-ATTTTTC
62 TTTCTGTTTGTCAAAAAAA
* ** ** * ** **
1384605 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGAGTCACATATCGAGGCATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACACGTGGAGTAATTTTCAATT
***
1384670 TCTGCTTT-TCAAGTTAAGTTTC
64 TCTG-TTTGTCAA---AA--AAA
* *
1384692 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGT-ATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTGGA-GTAATTTTCAATTT
**
1384756 CTGTTT-T----TTAA
65 CTGTTTGTCAAAAAAA
*
1384767 AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACAC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACAC
1384812 TGAGGTGTTT
Statistics
Matches: 529, Mismatches: 96, Indels: 112
0.72 0.13 0.15
Matches are distributed among these distances:
71 2 0.00
72 58 0.11
73 1 0.00
74 16 0.03
75 48 0.09
76 43 0.08
77 36 0.07
78 53 0.10
79 78 0.15
80 12 0.02
81 11 0.02
82 45 0.09
84 4 0.01
85 18 0.03
86 2 0.00
87 82 0.16
88 2 0.00
89 18 0.03
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (80 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTGGAGTAATTTTCAATTTC
TGTTTGTCAAAAAAA
Found at i:1384247 original size:76 final size:76
Alignment explanation
Indices: 1384054--1384251 Score: 229
Period size: 79 Copynumber: 2.6 Consensus size: 76
1384044 GTTTTATTTC
* * *
1384054 AAAATTCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGCTGGGGTAATTTTAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGCTGGAGTAATTTTAATTTC
1384119 TGTTGTCAAAAAAA
66 TGTTGTC---AAAA
* * * * * *
1384133 AAAAATCAACTCGTATTGCGAGCGGTGAGTTGAGCCTCAAGACATG-TTGAGTTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGCTGGAGTAATTTT-AATTT
*
1384197 CTGTTTTTC-AAA
65 CTG-TTGTCAAAA
* *
1384209 AAAAATCAGCTCATATTGCGAGAGATGAGTTGAACCTCAAGAC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC
1384252 GCTGAGGTGT
Statistics
Matches: 102, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
76 41 0.40
78 9 0.09
79 48 0.47
80 4 0.04
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (76 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGCTGGAGTAATTTTAATTTC
TGTTGTCAAAA
Found at i:1384833 original size:73 final size:74
Alignment explanation
Indices: 1384692--1384839 Score: 235
Period size: 75 Copynumber: 2.0 Consensus size: 74
1384682 GTTAAGTTTC
*
1384692 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACG-TGAGGTATTTTCAATTTC
*
1384757 TGTTTTTTAA
65 TGTTCTTTAA
* * *
1384767 AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACAC-TGAGGTGTTTTCCATTTCT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTGAGGTATTTTCAATTTCT
1384831 GTTCTTTAA
66 GTTCTTTAA
1384840 TTTCTGTGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
73 25 0.37
75 43 0.63
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (74 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTGAGGTATTTTCAATTTCT
GTTCTTTAA
Found at i:1384948 original size:92 final size:90
Alignment explanation
Indices: 1384746--1385005 Score: 255
Period size: 91 Copynumber: 2.9 Consensus size: 90
1384736 CGTTGAGGTA
** * * * * * *
1384746 TTTTCAATTTCTGTTTTTTAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCT-CA--AG
1 TTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTAGATCAC
* * * * *
1384808 ACACTGAGGTGTTTTCCATTTCTGT
66 ACACCGAGGTATTTTCAATTCCCGT
**
1384833 TCTTT-AATTTCTGTGTTTCAAAAAAAAT-AAGCTCATATTGCGA-ATGGTGAGTTGAGCCTT-G
1 T-TTTCAATTTCTGCCTTTC-AAAAAAATCAA-CTCATATTGCGAGA-GGTGAGTTGAG-CTTAG
*
1384894 ACTCACACGCCGAGGTATTTTCAATTCCCGT
61 A-TCACACACCGAGGTATTTTCAATTCCCGT
1384925 TTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCA
1 TTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTT-AGATCA
*
1384990 CACACTGAGGTATTTT
65 CACACCGAGGTATTTT
1385006 TTTTCAATTT
Statistics
Matches: 143, Mismatches: 17, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
87 15 0.10
88 33 0.23
89 3 0.02
90 3 0.02
91 51 0.36
92 38 0.27
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (90 bp):
TTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTAGATCAC
ACACCGAGGTATTTTCAATTCCCGT
Found at i:1385116 original size:72 final size:72
Alignment explanation
Indices: 1384926--1385496 Score: 671
Period size: 72 Copynumber: 7.7 Consensus size: 72
1384916 AATTCCCGTT
* * *
1384926 TTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCAC
1 TTTCAATTTCTG-TTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GA-GAC
* *
1384991 ACACTGAGGTATTTTT
61 ACGCTGAGGTA----A
* * * *
1385007 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGACACGC
1 TTTCAATTTCT-GTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACGC
1385072 TGAGGTAA
65 TGAGGTAA
* *
1385080 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCC
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACGCT
1385145 GAGGTAA
66 GAGGTAA
* * ** *
1385152 TTTCAA--TCTGTTTTTAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCT
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACGCT
1385215 GAGGTAA
66 GAGGTAA
* ** * * *
1385222 TTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTT
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACGCT
1385287 GAGGTAA
66 GAGGTAA
* ** * *
1385294 TTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTT
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACGCT
*
1385359 GAGGTAT
66 GAGGTAA
* *
1385366 TTTCAATTTCTGTTTTCAAAAAAATCAACTTATATTGTGAGAGGTGAGTTGAGCCTCG-GTTCAC
1 TTTCAATTTCTGTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAG---AC
* *
1385430 ATGCTGAGGTAT
61 ACGCTGAGGTAA
1385442 TTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 TTTCAATTTCTGT-TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1385497 TTCAGATCAC
Statistics
Matches: 446, Mismatches: 35, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
70 63 0.14
72 212 0.48
73 11 0.02
74 33 0.07
76 25 0.06
77 51 0.11
78 1 0.00
79 36 0.08
81 14 0.03
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (72 bp):
TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACGCT
GAGGTAA
Found at i:1385291 original size:142 final size:143
Alignment explanation
Indices: 1384926--1385496 Score: 626
Period size: 142 Copynumber: 3.9 Consensus size: 143
1384916 AATTCCCGTT
* *
1384926 TTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTC-AGATCA
1 TTTCAATTTCTG-TTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGA-CA
* * * * * **
1384990 CACACTGAGGTATTTTTTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
62 CGC-C-GAGGTA----ATTTCAA-TTCTGTTTTT-AAAATTCAACTCATATTGCGAGAAATGAGT
***
1385055 TGAGCCTTGGGACACGCTGAGGTAA
119 TGAGCCTCAAGACACGCTGAGGTAA
**
1385080 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCC
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCC
1385145 GAGGTAATTTCAA-TCTGTTTTTAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGA
66 GAGGTAATTTCAATTCTGTTTTTAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGA
1385209 CACGCTGAGGTAA
131 CACGCTGAGGTAA
* ** * **
1385222 TTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTT
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCC
*
1385287 GAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG
66 GAGGTAATTTCAA-TTCTGTTTTTAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG
* *
1385352 ACACGTTGAGGTAT
130 ACACGCTGAGGTAA
* * *
1385366 TTTCAATTTCTGTTTTCAAAAAAATCAACTTATATTGTGAGAGGTGAGTTGAGCCTC-GGTTCAC
1 TTTCAATTTCTGTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG---AC
* * * * * **
1385430 ATGCTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
61 ACGCCGAGGTAATTTCAA-TTCTGT-TTT--TAAAATTCAACTCATATTGCGAGAAATGAGTTGA
1385495 GC
122 GC
1385497 TTCAGATCAC
Statistics
Matches: 368, Mismatches: 38, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
142 119 0.32
143 7 0.02
144 78 0.21
145 7 0.02
146 32 0.09
148 24 0.07
149 9 0.02
150 1 0.00
151 73 0.20
152 2 0.01
153 4 0.01
154 12 0.03
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (143 bp):
TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCC
GAGGTAATTTCAATTCTGTTTTTAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGA
CACGCTGAGGTAA
Found at i:1385327 original size:214 final size:216
Alignment explanation
Indices: 1384926--1385494 Score: 676
Period size: 214 Copynumber: 2.6 Consensus size: 216
1384916 AATTCCCGTT
* * *
1384926 TTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCAC
1 TTTCAA-TTCTG--TTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-A-GAC
* * *
1384991 ACACTGAGGTATTTTTTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
61 ACGCTGAGGTA----TTTTCAATTTCT-GTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
* *** *
1385056 GAGCCTTGGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAG
121 GAACCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAA
* **
1385121 GTGAGTTGAGCCTCGGGACACGCCGAGGTAA
186 ATGAGTTGAGCCTCAAGACACGCCGAGGTAA
* * **
1385152 TTTCAA-TCTGTTTT-TAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCT
1 TTTCAATTCTGTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCT
* * **
1385215 GAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAG
66 GAGGTATTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAG
* *
1385280 ACACGTTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAG
131 ACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAG
** *
1385345 CCTCAAGACACGTTGAGGTAT
196 CCTCAAGACACGCCGAGGTAA
* * *
1385366 TTTCAATTTCTGTTTTCAAAAAAATCAACTTATATTGTGAGAGGTGAGTTGAGCCTC-GGTTCAC
1 TTTCAA-TTCTGTTTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG---AC
*
1385430 ATGCTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
61 ACGCTGAGGTATTTTCAATTTCTGT-TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1385495 GCTTCAGATC
Statistics
Matches: 294, Mismatches: 39, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
214 122 0.41
215 10 0.03
216 8 0.03
217 1 0.00
218 33 0.11
219 12 0.04
220 26 0.09
221 39 0.13
222 3 0.01
223 30 0.10
224 4 0.01
226 6 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (216 bp):
TTTCAATTCTGTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCT
GAGGTATTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAG
ACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAG
CCTCAAGACACGCCGAGGTAA
Found at i:1386997 original size:2 final size:2
Alignment explanation
Indices: 1386992--1387022 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1386982 TAAATACTAT
1386992 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
1387023 TTTTTTTTTT
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:1387000 original size:39 final size:39
Alignment explanation
Indices: 1386928--1387002 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
1386918 TTTATATATA
* * *
1386928 TTATGTATATATTTTTTAATGCCATTAGTTATATATTTC
1 TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
*
1386967 TTATGTATATATTCTTAAATACTATTA-TATATATAT
1 TTATGTATATATTCTTAAATACCATTAGT-TATATAT
1387003 ATATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 30 0.97
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (39 bp):
TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
Found at i:1387142 original size:2 final size:2
Alignment explanation
Indices: 1387130--1387165 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1387120 TTTTATGTAC
* *
1387130 AT AT GT AT AT AT AT AC 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
1387166 TTGTACATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1387217 original size:15 final size:15
Alignment explanation
Indices: 1387197--1387227 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1387187 ATTATTGTTG
1387197 TATATTTTTTATGTA
1 TATATTTTTTATGTA
1387212 TATATTTTTTATGTA
1 TATATTTTTTATGTA
1387227 T
1 T
1387228 GTTTCCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATATTTTTTATGTA
Found at i:1398497 original size:13 final size:13
Alignment explanation
Indices: 1398479--1398504 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1398469 CTGTTTCTTC
1398479 CATTTTTGCTATT
1 CATTTTTGCTATT
1398492 CATTTTTGCTATT
1 CATTTTTGCTATT
1398505 TTGCTCTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (13 bp):
CATTTTTGCTATT
Found at i:1401399 original size:10 final size:10
Alignment explanation
Indices: 1401377--1401409 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
1401367 ATTATGTTTC
1401377 TTTTTATAA-
1 TTTTTATAAT
1401386 TTTTTATAAT
1 TTTTTATAAT
1401396 TTTTTATATAT
1 TTTTTATA-AT
1401407 TTT
1 TTT
1401410 GTGTGATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 8 0.36
11 5 0.23
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:1405933 original size:22 final size:22
Alignment explanation
Indices: 1405908--1405952 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1405898 ATAATCTTTG
1405908 AATTACAAGTAAAAGTAAGCTA
1 AATTACAAGTAAAAGTAAGCTA
1405930 AATTACAAGTAAAAGTAAGCTA
1 AATTACAAGTAAAAGTAAGCTA
1405952 A
1 A
1405953 CATTTCAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (22 bp):
AATTACAAGTAAAAGTAAGCTA
Found at i:1407418 original size:51 final size:51
Alignment explanation
Indices: 1407305--1407458 Score: 237
Period size: 51 Copynumber: 3.1 Consensus size: 51
1407295 AAATGGTGCA
*
1407305 TCTCTTTTGCCTCAAT-TGCACAATCCATACTC-TTTGACTTCTTCTTC-TC-
1 TCTCTTTTGCCTCAATCAG-ACAATCCATACTCTTTTG-CTTCTTCTTCTTCT
1407354 -CTCTTTTGCCTCAATCAGACAATCCATACTCTTTTGCTTCTTCTTCTTCT
1 TCTCTTTTGCCTCAATCAGACAATCCATACTCTTTTGCTTCTTCTTCTTCT
*
1407404 TCTCTTTTGCCTCAATCAGACAATCCATACTCTTTGGCTTCTTCTTCTTCT
1 TCTCTTTTGCCTCAATCAGACAATCCATACTCTTTTGCTTCTTCTTCTTCT
1407455 TCTC
1 TCTC
1407459 GTCAAATGAA
Statistics
Matches: 98, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
48 38 0.39
49 7 0.07
51 53 0.54
ACGTcount: A:0.16, C:0.32, G:0.06, T:0.45
Consensus pattern (51 bp):
TCTCTTTTGCCTCAATCAGACAATCCATACTCTTTTGCTTCTTCTTCTTCT
Found at i:1410713 original size:72 final size:73
Alignment explanation
Indices: 1410595--1410775 Score: 202
Period size: 72 Copynumber: 2.5 Consensus size: 73
1410585 TCCCAGAAAT
* * ** * *
1410595 TCTACGAAGACCCGAAAAACCTAAAGAGCCTGAAGAGTTCCGTCCATATTCATCGAAATACTCTT
1 TCTACCAAGACCCGAAAAACCTAAAGAGCCTGAAAAGCCCCATCCATATTCATCGAAATACTATT
*
1410660 T-CTACCC
66 TCCCACCC
* * ** *
1410667 TCTACCGAGACCCGAAAAACCTAAAGAGCCTGAAAAGCCCCATCCATGTTCATCGTCATCCTATT
1 TCTACCAAGACCCGAAAAACCTAAAGAGCCTGAAAAGCCCCATCCATATTCATCGAAATACTATT
1410732 TCCCCCACCC
66 T--CCCACCC
* * *
1410742 TTTACCAAGACCCAAAAAACCTAAAGCGCCTGAA
1 TCTACCAAGACCCGAAAAACCTAAAGAGCCTGAA
1410776 GCGAAAAAAG
Statistics
Matches: 90, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
72 55 0.61
75 35 0.39
ACGTcount: A:0.34, C:0.33, G:0.13, T:0.20
Consensus pattern (73 bp):
TCTACCAAGACCCGAAAAACCTAAAGAGCCTGAAAAGCCCCATCCATATTCATCGAAATACTATT
TCCCACCC
Found at i:1410787 original size:18 final size:18
Alignment explanation
Indices: 1410764--1410802 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1410754 CAAAAAACCT
1410764 AAAGCGCCTGAAGCGAAA
1 AAAGCGCCTGAAGCGAAA
*
1410782 AAAGCGCCTGAAGTGAAA
1 AAAGCGCCTGAAGCGAAA
1410800 AAA
1 AAA
1410803 AAAAACGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.18, G:0.26, T:0.08
Consensus pattern (18 bp):
AAAGCGCCTGAAGCGAAA
Found at i:1418483 original size:40 final size:40
Alignment explanation
Indices: 1418439--1418515 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
1418429 TACCTCTAAG
* * *
1418439 CATGAAAGGAAGTCGACATAGCTCTGGGCATGTTATGGTT
1 CATGAAAGGAAATCGACAAAGCTCGGGGCATGTTATGGTT
* *
1418479 CATGAAAGGAAATTGGCAAAGCTCGGGGCATGTTATG
1 CATGAAAGGAAATCGACAAAGCTCGGGGCATGTTATG
1418516 ATTAACTTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.25
Consensus pattern (40 bp):
CATGAAAGGAAATCGACAAAGCTCGGGGCATGTTATGGTT
Found at i:1423602 original size:17 final size:17
Alignment explanation
Indices: 1423580--1423613 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1423570 TTGACAAAAC
1423580 CTCCTGGTGTGAGAATT
1 CTCCTGGTGTGAGAATT
1423597 CTCCTGGTGTGAGAATT
1 CTCCTGGTGTGAGAATT
1423614 TGAAAGCTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (17 bp):
CTCCTGGTGTGAGAATT
Found at i:1428229 original size:15 final size:15
Alignment explanation
Indices: 1428209--1428238 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1428199 ATAATTCTAA
*
1428209 TAATTATCTTAATAT
1 TAATTATCCTAATAT
1428224 TAATTATCCTAATAT
1 TAATTATCCTAATAT
1428239 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:1428819 original size:9 final size:9
Alignment explanation
Indices: 1428805--1428839 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
1428795 TTAATATGAC
1428805 TTTTTTTCT
1 TTTTTTTCT
1428814 TTTTTTTCT
1 TTTTTTTCT
1428823 TTTTTTTCT
1 TTTTTTTCT
1428832 TCTTTTTT
1 T-TTTTTT
1428840 ATAGAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 19 0.76
10 6 0.24
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:1429792 original size:5 final size:5
Alignment explanation
Indices: 1429742--1429798 Score: 57
Period size: 5 Copynumber: 11.4 Consensus size: 5
1429732 AATAATAAAT
*
1429742 AATAA AAT-- AATAA GATAA AAT-A AATAAA AATAAA AATAA AATAA AATAAA
1 AATAA AATAA AATAA AATAA AATAA AAT-AA AAT-AA AATAA AATAA AAT-AA
1429792 AATAA AA
1 AATAA AA
1429799 ATTGGGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
3 3 0.07
4 4 0.09
5 23 0.51
6 15 0.33
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:1429793 original size:22 final size:21
Alignment explanation
Indices: 1429735--1429800 Score: 87
Period size: 22 Copynumber: 2.9 Consensus size: 21
1429725 ATCTGAAAAT
1429735 AATAAATAATAAAATAATAAGATAA
1 AATAAAT-A-AAAATAA-AA-ATAA
1429760 AATAAATAAAAATAAAAATAA
1 AATAAATAAAAATAAAAATAA
1429781 AATAAAATAAAAATAAAAAT
1 AAT-AAATAAAAATAAAAAT
1429801 TGGGTTGCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.17
22 18 0.45
23 7 0.17
24 1 0.03
25 7 0.17
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (21 bp):
AATAAATAAAAATAAAAATAA
Found at i:1429797 original size:28 final size:28
Alignment explanation
Indices: 1429730--1429800 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
1429720 TTAATATCTG
* * *
1429730 AAAATAATAAATAATAA-AATAATAAGAT
1 AAAATAA-AAATAAAAATAAAAATAAAAT
1429758 AAAAT--AAATAAAAATAAAAATAAAAT
1 AAAATAAAAATAAAAATAAAAATAAAAT
1429784 AAAATAAAAATAAAAAT
1 AAAATAAAAATAAAAAT
1429801 TGGGTTGCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 8 0.22
26 14 0.38
28 15 0.41
ACGTcount: A:0.77, C:0.00, G:0.01, T:0.21
Consensus pattern (28 bp):
AAAATAAAAATAAAAATAAAAATAAAAT
Found at i:1429798 original size:16 final size:16
Alignment explanation
Indices: 1429735--1429798 Score: 76
Period size: 16 Copynumber: 3.8 Consensus size: 16
1429725 ATCTGAAAAT
1429735 AATAAATAATAAAATAA
1 AATAAA-AATAAAATAA
*
1429752 TAAGATAAAAT-AAATAAA
1 -AATA-AAAATAAAAT-AA
1429770 AATAAAAATAAAATAA
1 AATAAAAATAAAATAA
1429786 AATAAAAATAAAA
1 AATAAAAATAAAA
1429799 ATTGGGTTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
16 20 0.49
17 11 0.27
18 8 0.20
19 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (16 bp):
AATAAAAATAAAATAA
Found at i:1433547 original size:20 final size:20
Alignment explanation
Indices: 1433509--1433556 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1433499 TAAATTCTAA
* **
1433509 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
1433529 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
1433549 AAA-ATAAA
1 AAAGATAAA
1433557 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:1433581 original size:27 final size:26
Alignment explanation
Indices: 1433551--1433613 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
1433541 AGATAATTAA
1433551 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
1433578 AATAACTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
1433605 AATATAAAT
1 AATA-AAAT
1433614 AAAATGGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Done.