Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 20 of 39
Found at i:2980602 original size:20 final size:21
Alignment explanation
Indices: 2980577--2980621 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2980567 TTATGATCAT
* *
2980577 AAATTATG-TTTTCAACTAGC
1 AAATTAAGCTTTTCAACAAGC
2980597 AAATTAAGCTTTTCAACAAGC
1 AAATTAAGCTTTTCAACAAGC
2980618 AAAT
1 AAAT
2980622 GCAAAACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (21 bp):
AAATTAAGCTTTTCAACAAGC
Found at i:2986909 original size:36 final size:36
Alignment explanation
Indices: 2986860--2986940 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
2986850 ACCAAAACCT
* *
2986860 GTCACTGCTACAATCTAAGTCTCAAAACCAAGCTGA
1 GTCACTACCACAATCTAAGTCTCAAAACCAAGCTGA
* * *
2986896 GTCCCTACCACAATCTGAGTCTCAAAACCAGGCTGA
1 GTCACTACCACAATCTAAGTCTCAAAACCAAGCTGA
2986932 GTCACTACC
1 GTCACTACC
2986941 TTTGTCCCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (36 bp):
GTCACTACCACAATCTAAGTCTCAAAACCAAGCTGA
Found at i:2989271 original size:32 final size:32
Alignment explanation
Indices: 2989230--2989293 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
2989220 TATAAGTTAT
2989230 ATATAGAGGGTTTCCAAAATTTTCGTCGAGGG
1 ATATAGAGGGTTTCCAAAATTTTCGTCGAGGG
*
2989262 ATATAGAGGGTTTCCAAAATTTTCTTCGAGGG
1 ATATAGAGGGTTTCCAAAATTTTCGTCGAGGG
2989294 GTGTTCTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.33
Consensus pattern (32 bp):
ATATAGAGGGTTTCCAAAATTTTCGTCGAGGG
Found at i:2992966 original size:22 final size:20
Alignment explanation
Indices: 2992941--2992991 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2992931 TTTTTTTATT
*
2992941 ATAATTTTTTTAAAAAATGAAA
1 ATAATTTATTT-AAAAA-GAAA
*
2992963 ATAATTTATTTGAAAAGAAA
1 ATAATTTATTTAAAAAGAAA
2992983 ATAATTTAT
1 ATAATTTAT
2992992 GAATTTAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 13 0.48
21 4 0.15
22 10 0.37
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (20 bp):
ATAATTTATTTAAAAAGAAA
Found at i:2993303 original size:16 final size:16
Alignment explanation
Indices: 2993272--2993314 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2993262 TCTAATATTT
*
2993272 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATT-A
2993289 ATAAAA-TTATAATTA
1 ATAAAATTTATAATTA
*
2993304 ATAAATTTTAT
1 ATAAAATTTAT
2993315 TTAAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAAATTTATAATTA
Found at i:2994025 original size:10 final size:9
Alignment explanation
Indices: 2993994--2994032 Score: 55
Period size: 8 Copynumber: 4.4 Consensus size: 9
2993984 AATAGTTAAA
2993994 AATATTTTT
1 AATATTTTT
2994003 AAT-TTTTT
1 AATATTTTT
2994011 -ATATTTTT
1 AATATTTTT
2994019 AATTATTTTT
1 AA-TATTTTT
2994029 AATA
1 AATA
2994033 AAAATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 2 0.07
8 10 0.37
9 6 0.22
10 9 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
AATATTTTT
Found at i:2994549 original size:12 final size:12
Alignment explanation
Indices: 2994532--2994557 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2994522 ACATGAATAT
2994532 ATATACATAAAA
1 ATATACATAAAA
2994544 ATATACATAAAA
1 ATATACATAAAA
2994556 AT
1 AT
2994558 TATCAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (12 bp):
ATATACATAAAA
Found at i:2994629 original size:29 final size:29
Alignment explanation
Indices: 2994530--2994630 Score: 80
Period size: 29 Copynumber: 3.3 Consensus size: 29
2994520 TAACATGAAT
* *
2994530 ATATATACATAAAAATATACATAAAAATTATCA
1 ATATATAAATAAAAATACACAT--AAA-TAT-A
** *
2994563 ATATATAAA-AAATTTACACACAAATATA
1 ATATATAAATAAAAATACACATAAATATA
*
2994591 ATATTTTAAATAAAAATA-ACATAAATATAA
1 ATA-TATAAATAAAAATACACATAAATAT-A
2994621 ATATATAAAT
1 ATATATAAAT
2994631 TTTTTTCTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
28 4 0.07
29 23 0.42
30 12 0.22
32 8 0.15
33 8 0.15
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (29 bp):
ATATATAAATAAAAATACACATAAATATA
Found at i:2994643 original size:4 final size:4
Alignment explanation
Indices: 2994634--2994705 Score: 57
Period size: 4 Copynumber: 19.5 Consensus size: 4
2994624 TATAAATTTT
* * * *
2994634 TTTC TTTC -TTC TTTT TTTT TTTC TTTT TTTC TCTC -TTC TTT- TTT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
2994678 TTT- TTTT TTTC TTTC TTTC -TTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
2994706 CGGGCTGAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
3 17 0.30
4 40 0.70
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTC
Found at i:2994647 original size:7 final size:7
Alignment explanation
Indices: 2994635--2994706 Score: 51
Period size: 7 Copynumber: 10.4 Consensus size: 7
2994625 ATAAATTTTT
2994635 TTCTTTC
1 TTCTTTC
2994642 TTCTTT-
1 TTCTTTC
*
2994648 TT-TTTT
1 TTCTTTC
*
2994654 TTCTTTTT
1 TTC-TTTC
*
2994662 TTCTCTC
1 TTCTTTC
2994669 TTCTTT-
1 TTCTTTC
* *
2994675 TTTTTTT
1 TTCTTTC
*
2994682 TTTTTTC
1 TTCTTTC
2994689 TTTCTTTC
1 -TTCTTTC
2994697 TTCTTTC
1 TTCTTTC
2994704 TTC
1 TTC
2994707 GGGCTGAACC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
5 3 0.06
6 9 0.17
7 29 0.54
8 13 0.24
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTCTTTC
Found at i:2994670 original size:24 final size:22
Alignment explanation
Indices: 2994630--2994695 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 22
2994620 AATATATAAA
*
2994630 TTTTTTTCTTTCTTCTTTTTTT
1 TTTTTTTTTTTCTTCTTTTTTT
2994652 TTTTCTTTTTTTCTCTCTTCTTTTT
1 TTTT-TTTTTTTCT-TCTT-TTTTT
2994677 TTTTTTTTTTTCTTTCTTT
1 TTTTTTTTTTTC-TTCTTT
2994696 CTTCTTTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
22 4 0.10
23 9 0.23
24 16 0.41
25 10 0.26
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (22 bp):
TTTTTTTTTTTCTTCTTTTTTT
Found at i:2994670 original size:27 final size:27
Alignment explanation
Indices: 2994630--2994702 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
2994620 AATATATAAA
2994630 TTTTTTTCTTTCTTCTTTTTTTTTTTC
1 TTTTTTTCTTTCTTCTTTTTTTTTTTC
* *
2994657 TTTTTTTCTCTCTTCTTTTTTTTTTTT
1 TTTTTTTCTTTCTTCTTTTTTTTTTTC
2994684 TTTTCTTTCTTTCTTCTTT
1 TTTT-TTTCTTTCTTCTTT
2994703 CTTCGGGCTG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 29 0.69
28 13 0.31
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (27 bp):
TTTTTTTCTTTCTTCTTTTTTTTTTTC
Found at i:2994842 original size:336 final size:334
Alignment explanation
Indices: 2994435--2995108 Score: 1086
Period size: 336 Copynumber: 2.0 Consensus size: 334
2994425 TATATAAATT
*
2994435 TATTTTATTTTAATAATATAAAAAATAATATAAACACGATATTTATAAAAAATATTTAAAATATA
1 TATTTTATTTTAATAATAGAAAAAATAATATAAACACGATATTTATAAAAAATATTTAAAATATA
2994500 ACATAAAAATAATATGTATATAACATGAATATATATACATA-AAAATATACAT-AAAAATTATCA
66 ACATAAAAATAATATGTATATAACATGAATATATATACATATAAAA-ATACATAAAAAATT-TCA
2994563 ATATATAAAAAATTTACACACAAATATAATATTTTAAATAAAAATAACATAAATATAAATA-TAT
129 ATAT-TAAAAAA-TTACACACAAATATAAT-TTTTAAA-AAAAATAACAT-AA-ATAAATAGTAT
2994627 AAA-TTTTTTTCTTTC-TTCTTTTTTTTTTTCTTTTTTTCTCTCTTCTTTTTTTTTTTTT-TTTC
188 AAATTTTTTTTCTTTCTTTC-TTTTTTTTTTCTTTTTTTCTCT-TTCTTTTTTTTTTTTTCTTTC
*
2994689 TTTCTTTCT-TC-TTTCTTCGGGCTGAACCCAAAAAAAAAAAAGATAGCACGTGTCAGTGTGTGG
251 TTTC-TTCTGTCTTTTC-TCGGGCTGAA-CAAAAAAAAAAAAAGATAGCACGTGTCAGTGTG-GG
2994752 TGTG-T-TGTAGTTGATATTAGA
312 TGTGTTGTGTAGTTGATATTAGA
2994773 TATTTTATTTTAAT-A-AGAAAAAATAATATAAACACGATATTTATAAAAAAATATTTAAAATAT
1 TATTTTATTTTAATAATAGAAAAAATAATATAAACACGATATTTAT-AAAAAATATTTAAAATAT
*
2994836 -ACATAAAAATAATATGTATATAACATGAATATATATATATATAAAAATACATAAAAAATTTCAA
65 AACATAAAAATAATATGTATATAACATGAATATATATACATATAAAAATACATAAAAAATTTCAA
2994900 TATTAAAAAATTACACACAAATATAATTTTTAAAAAAAATAACATAAATAAATAGTATAAATTTT
130 TATTAAAAAATTACACACAAATATAATTTTTAAAAAAAATAACATAAATAAATAGTATAAATTTT
2994965 TTTTCTTTCTTTCTTTTTTTTTTCTTTTTTTCTCTTTCTTTTTTTTTTTTTCTTTCTTTCTTCTG
195 TTTTCTTTCTTTCTTTTTTTTTTCTTTTTTTCTCTTTCTTTTTTTTTTTTTCTTTCTTTCTTCTG
2995030 TCTTTTCTCGGGCTGAACAAAAAAAAAAAAAGATAGCACGTGTCAGTGTGGGTGTGTTTGTGTAG
260 TCTTTTCTCGGGCTGAACAAAAAAAAAAAAAGATAGCACGTGTCAGTGTGGGTGTG-TTGTGTAG
2995095 TTGATATTAGA
324 TTGATATTAGA
2995106 TAT
1 TAT
2995109 ATGTATAGAT
Statistics
Matches: 321, Mismatches: 3, Indels: 29
0.91 0.01 0.08
Matches are distributed among these distances:
330 13 0.04
331 60 0.19
332 66 0.21
333 33 0.10
334 17 0.05
335 7 0.02
336 81 0.25
337 30 0.09
338 14 0.04
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (334 bp):
TATTTTATTTTAATAATAGAAAAAATAATATAAACACGATATTTATAAAAAATATTTAAAATATA
ACATAAAAATAATATGTATATAACATGAATATATATACATATAAAAATACATAAAAAATTTCAAT
ATTAAAAAATTACACACAAATATAATTTTTAAAAAAAATAACATAAATAAATAGTATAAATTTTT
TTTCTTTCTTTCTTTTTTTTTTCTTTTTTTCTCTTTCTTTTTTTTTTTTTCTTTCTTTCTTCTGT
CTTTTCTCGGGCTGAACAAAAAAAAAAAAAGATAGCACGTGTCAGTGTGGGTGTGTTGTGTAGTT
GATATTAGA
Found at i:2995020 original size:4 final size:4
Alignment explanation
Indices: 2994966--2995026 Score: 60
Period size: 4 Copynumber: 16.5 Consensus size: 4
2994956 ATAAATTTTT
* *
2994966 TTTC TTTC TTTC TTT- TTTT TTTC TTT- TTT- TCTC TTTC TTT- TTT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
2995009 TTTT TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TT
2995027 CTGTCTTTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
3 14 0.28
4 36 0.72
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (4 bp):
TTTC
Found at i:2995033 original size:29 final size:29
Alignment explanation
Indices: 2994967--2995035 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
2994957 TAAATTTTTT
*
2994967 TTCTTTCTTTCTTTTTTTTTTCTTTTTTTC
1 TTCTTTCTTT-TTTTTTTTTTCTTTCTTTC
2994997 -TCTTTCTTTTTTTTTTTTTCTTTCTTTC
1 TTCTTTCTTTTTTTTTTTTTCTTTCTTTC
*
2995025 TTCTGTCTTTT
1 TTCTTTCTTTT
2995036 CTCGGGCTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 18 0.50
29 18 0.50
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.81
Consensus pattern (29 bp):
TTCTTTCTTTTTTTTTTTTTCTTTCTTTC
Found at i:2996535 original size:21 final size:21
Alignment explanation
Indices: 2996487--2996535 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2996477 ATATAATACA
*
2996487 ATATAATATGAAAACACAATT
1 ATATAAAATGAAAACACAATT
* * * *
2996508 TTTTAAAATTAAAGCACAATT
1 ATATAAAATGAAAACACAATT
2996529 ATATAAA
1 ATATAAA
2996536 CTATATAAAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (21 bp):
ATATAAAATGAAAACACAATT
Found at i:2996611 original size:11 final size:11
Alignment explanation
Indices: 2996583--2996629 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
2996573 TAGAACAAAA
2996583 AAAAATTAAT-T
1 AAAAA-TAATAT
2996594 AAAAATAATAT
1 AAAAATAATAT
*
2996605 AAAAATAACAT
1 AAAAATAATAT
*
2996616 AAATATAATA-
1 AAAAATAATAT
2996626 AAAA
1 AAAA
2996630 CACACAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 7 0.23
11 24 0.77
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:2998503 original size:18 final size:18
Alignment explanation
Indices: 2998480--2998518 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2998470 TCAAAAATAA
2998480 AATTTA-TCATAATATTTT
1 AATTTACTCATAA-ATTTT
*
2998498 AATTTACTTATAAATTTT
1 AATTTACTCATAAATTTT
2998516 AAT
1 AAT
2998519 CCTAATTTAA
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:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTACTCATAAATTTT
Found at i:2999154 original size:14 final size:14
Alignment explanation
Indices: 2999135--2999199 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
2999125 ATTTGAATCT
2999135 ATTTAATTAATTAA
1 ATTTAATTAATTAA
*
2999149 ATTTAATTAATTTA
1 ATTTAATTAATTAA
*
2999163 ATTTAATTTATTTAA
1 ATTTAA-TTAATTAA
*
2999178 TTTTAA--AATTAA
1 ATTTAATTAATTAA
2999190 A--TAATTAATT
1 ATTTAATTAATT
2999200 TGCATTGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
10 3 0.07
12 9 0.21
14 19 0.45
15 11 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTTAATTAATTAA
Found at i:2999156 original size:5 final size:5
Alignment explanation
Indices: 2999135--2999180 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
2999125 ATTTGAATCT
*
2999135 ATTTA A-TTA ATTAA ATTTA A-TTA ATTTA ATTTA ATTT- ATTTA ATTT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTT
2999181 TAAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 12 0.33
5 24 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTTA
Found at i:3000223 original size:19 final size:20
Alignment explanation
Indices: 3000199--3000247 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
3000189 CATGTTTTGG
*
3000199 TTTAATTTAAAATAATGT-T
1 TTTAATTTAAAATAATATAT
3000218 TTTAA-TTAAAATAATATAT
1 TTTAATTTAAAATAATATAT
*
3000237 TTTTATTTAAA
1 TTTAATTTAAA
3000248 TTTAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 10 0.38
20 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTAATTTAAAATAATATAT
Found at i:3000246 original size:20 final size:18
Alignment explanation
Indices: 3000203--3000247 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
3000193 TTTTGGTTTA
*
3000203 ATTTAAAATAATGTTTTT
1 ATTTAAAATAATATTTTT
*
3000221 AATTAAAATAATATATTTTT
1 ATTTAAAAT-A-ATATTTTT
3000241 ATTTAAA
1 ATTTAAA
3000248 TTTAATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 8 0.36
19 1 0.05
20 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
ATTTAAAATAATATTTTT
Found at i:3000248 original size:19 final size:18
Alignment explanation
Indices: 3000199--3000248 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
3000189 CATGTTTTGG
*
3000199 TTTAATTTAAAATAATGTT
1 TTTAATTT-AAATAATATT
*
3000218 TTTAATTAAAATAATATAT
1 TTTAATTTAAATAATAT-T
*
3000237 TTTTATTTAAAT
1 TTTAATTTAAAT
3000249 TTAATTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TTTAATTTAAATAATATT
Found at i:3000274 original size:22 final size:19
Alignment explanation
Indices: 3000244--3000285 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
3000234 TATTTTTATT
3000244 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
3000265 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
3000285 T
1 T
3000286 TTTTTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:3000893 original size:22 final size:22
Alignment explanation
Indices: 3000868--3000916 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
3000858 ATACATACAT
3000868 TTAAAATGAGTTACAAATTAAG
1 TTAAAATGAGTTACAAATTAAG
3000890 TTAAAATGAGTTACAAATTAAG
1 TTAAAATGAGTTACAAATTAAG
3000912 TTAAA
1 TTAAA
3000917 TTTTGACACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.33
Consensus pattern (22 bp):
TTAAAATGAGTTACAAATTAAG
Found at i:3000998 original size:11 final size:10
Alignment explanation
Indices: 3000972--3001004 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
3000962 GGTGGCAGGC
3000972 AAAGGG-GAA
1 AAAGGGAGAA
3000981 AAAGGGAGAA
1 AAAGGGAGAA
3000991 ATAAGGGAGAA
1 A-AAGGGAGAA
3001002 AAA
1 AAA
3001005 AAACTAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.27
10 6 0.27
11 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (10 bp):
AAAGGGAGAA
Found at i:3001533 original size:15 final size:16
Alignment explanation
Indices: 3001497--3001536 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
3001487 TTTAATATTT
*
3001497 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
3001514 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
3001529 ATAAAATT
1 ATAAAATT
3001537 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:3001539 original size:16 final size:17
Alignment explanation
Indices: 3001497--3001539 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
3001487 TTTAATATTT
*
3001497 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
3001514 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
3001529 ATAAAATTTAT
1 ATAAAATTTAT
3001540 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:3001633 original size:35 final size:37
Alignment explanation
Indices: 3001594--3001673 Score: 87
Period size: 35 Copynumber: 2.3 Consensus size: 37
3001584 ATAAAAAATT
* * *
3001594 ATATAAAATATAAGATA-AATTGAAACATAATACAA-
1 ATATAAAATATAAAAAATAATTAAAACATAATACAAC
* *
3001629 ATATAATAT-TAAAAAATAATTAAAATATAATACAAC
1 ATATAAAATATAAAAAATAATTAAAACATAATACAAC
3001665 ATA-AAAATA
1 ATATAAAATA
3001674 ATATGAACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
34 5 0.14
35 28 0.78
36 3 0.08
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (37 bp):
ATATAAAATATAAAAAATAATTAAAACATAATACAAC
Found at i:3002202 original size:21 final size:20
Alignment explanation
Indices: 3002161--3002199 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
3002151 ATTTTAGATT
3002161 TTTTATATTTAAGTTTTTAA
1 TTTTATATTTAAGTTTTTAA
3002181 TTTT-TATTTAA-TTTTTAA
1 TTTTATATTTAAGTTTTTAA
3002199 T
1 T
3002200 AATATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTATATTTAAGTTTTTAA
Found at i:3004647 original size:97 final size:96
Alignment explanation
Indices: 3004485--3004693 Score: 294
Period size: 97 Copynumber: 2.2 Consensus size: 96
3004475 TTGAAAAATA
* * * *
3004485 GGGTTGAAGTATCCTCTCAGAGGAATAGGGTTGGAATGTCCTCGATGATGATAATTTAGGCAAAA
1 GGGTTGAAGTATCCCCTCAGAGGAATAGGGTCGGAATATCCTCGATAATGATAATTTAGGCAAAA
*
3004550 ATAAGTTTTAAATCATGACAAGTTTAAAAAC
66 ATAAGTTTTAAATCATAACAAGTTTAAAAAC
* * * *
3004581 GAGGTTGGAGTATCCCCTCAGAGG-ATTGTGGTCGGAGTATCCTCGATAATGATAATTTAGGTAA
1 G-GGTTGAAGTATCCCCTCAGAGGAATAG-GGTCGGAATATCCTCGATAATGATAATTTAGGCAA
*
3004645 AAATAAGTTTTAAATCATAACAAGTTTAAAAAT
64 AAATAAGTTTTAAATCATAACAAGTTTAAAAAC
3004678 GGGATTGAAGTATCCC
1 GGG-TTGAAGTATCCC
3004694 TTCGGAAGAA
Statistics
Matches: 99, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
96 6 0.06
97 93 0.94
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (96 bp):
GGGTTGAAGTATCCCCTCAGAGGAATAGGGTCGGAATATCCTCGATAATGATAATTTAGGCAAAA
ATAAGTTTTAAATCATAACAAGTTTAAAAAC
Found at i:3006949 original size:51 final size:51
Alignment explanation
Indices: 3006894--3007016 Score: 187
Period size: 51 Copynumber: 2.4 Consensus size: 51
3006884 AATTGCATGC
* * *
3006894 ATGTATCGATACATTGAAGAATGTATCGATAAATTT-GGTCAAAAACTTAGA
1 ATGTATCGATACAATGAAAAATGTATCGATAAATTTGGGTCAAAAAC-CAGA
*
3006945 ATGTATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAAACCAGA
1 ATGTATCGATACAATGAAAAATGTATCGATAAATTTGGGTCAAAAACCAGA
3006996 ATGTATCGATACAAT-AAAAAT
1 ATGTATCGATACAATGAAAAAT
3007017 TTGCTTCGAC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
50 6 0.09
51 51 0.76
52 10 0.15
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACAATGAAAAATGTATCGATAAATTTGGGTCAAAAACCAGA
Found at i:3007058 original size:21 final size:21
Alignment explanation
Indices: 3007034--3007088 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
3007024 GACATGGTCC
3007034 TGTATCGATACATTTCAAATA
1 TGTATCGATACATTTCAAATA
**
3007055 TGTATCGATACA-TTCACTTA
1 TGTATCGATACATTTCAAATA
*
3007075 TGTATTGATACATT
1 TGTATCGATACATT
3007089 ACTATATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTTCAAATA
Found at i:3007101 original size:21 final size:20
Alignment explanation
Indices: 3007034--3007107 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
3007024 GACATGGTCC
* **
3007034 TGTATCGATACATTTCAAATA
1 TGTATTGATACA-TTCACTTA
*
3007055 TGTATCGATACATTCACTTA
1 TGTATTGATACATTCACTTA
3007075 TGTATTGATACATT-ACTATA
1 TGTATTGATACATTCACT-TA
3007095 TTGTATTGATACA
1 -TGTATTGATACA
3007108 ATTTGTTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 3 0.06
20 21 0.44
21 24 0.50
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (20 bp):
TGTATTGATACATTCACTTA
Found at i:3008723 original size:5 final size:5
Alignment explanation
Indices: 3008707--3008735 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3008697 ACAAGAATAC
3008707 ATAAA A-AAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
3008736 GAAAGACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:3009300 original size:22 final size:22
Alignment explanation
Indices: 3009275--3009322 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
3009265 GATGAGAAAA
3009275 CTTTATTTTGGTGACATCTATG
1 CTTTATTTTGGTGACATCTATG
3009297 CTTTATTTTGGTGACATCTATG
1 CTTTATTTTGGTGACATCTATG
3009319 CTTT
1 CTTT
3009323 GGACAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.52
Consensus pattern (22 bp):
CTTTATTTTGGTGACATCTATG
Found at i:3011885 original size:23 final size:23
Alignment explanation
Indices: 3011833--3011902 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 23
3011823 AAAAATATTT
3011833 TATTTAAA-TTTAATTATAAAA-A
1 TATTTAAATTTTAA-TATAAAATA
*
3011855 TATATAAATTTTAATATAAAATA
1 TATTTAAATTTTAATATAAAATA
*
3011878 TTTTTAAATATTTTAATAATAAAAT
1 TATTT-AA-ATTTTAAT-ATAAAAT
3011903 TAATTCTCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 14 0.35
23 9 0.22
24 2 0.05
25 8 0.20
26 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTTAAATTTTAATATAAAATA
Found at i:3012600 original size:15 final size:15
Alignment explanation
Indices: 3012580--3012663 Score: 60
Period size: 15 Copynumber: 6.1 Consensus size: 15
3012570 GCTGCTGTTT
*
3012580 TTAAATTTAATAATA
1 TTAAATATAATAATA
*
3012595 TTAAATATAATCATA
1 TTAAATATAATAATA
3012610 -TAAATATAA-AATA
1 TTAAATATAATAATA
* *
3012623 --AAAAATTAT-A-A
1 TTAAATATAATAATA
3012634 TTAAA-A-AATAATA
1 TTAAATATAATAATA
3012647 -TAAATATAATAAATA
1 TTAAATATAAT-AATA
3012662 TT
1 TT
3012664 TTAAAATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
11 3 0.06
12 13 0.24
13 8 0.15
14 12 0.22
15 17 0.31
16 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAATATAATAATA
Found at i:3012668 original size:18 final size:18
Alignment explanation
Indices: 3012647--3012732 Score: 54
Period size: 18 Copynumber: 4.6 Consensus size: 18
3012637 AAAAATAATA
3012647 TAAATATAATAAATATTT
1 TAAATATAATAAATATTT
*
3012665 TAAAATTTATATAATAAAAATTAT
1 T--AA---ATATAATAAATATT-T
*
3012689 TAAA-ATATTAAA-ATTT
1 TAAATATAATAAATATTT
3012705 ATATAA-AT-ATAAATATTT
1 -TA-AATATAATAAATATTT
3012723 TAAATATAAT
1 TAAATATAAT
3012733 TATAATATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 22
0.68 0.04 0.28
Matches are distributed among these distances:
16 3 0.06
17 13 0.24
18 18 0.33
19 1 0.02
20 2 0.04
22 2 0.04
23 13 0.24
24 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATATAATAAATATTT
Found at i:3012680 original size:23 final size:24
Alignment explanation
Indices: 3012650--3012694 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
3012640 AATAATATAA
*
3012650 ATATAATAAATATT-TTAAAATTT
1 ATATAATAAAAATTATTAAAATTT
3012673 ATATAATAAAAATTATTAAAAT
1 ATATAATAAAAATTATTAAAAT
3012695 ATTAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATAATAAAAATTATTAAAATTT
Found at i:3012700 original size:32 final size:34
Alignment explanation
Indices: 3012641--3012761 Score: 111
Period size: 34 Copynumber: 3.5 Consensus size: 34
3012631 TAATTAAAAA
* *
3012641 ATAATATAAATATAATAAATATTTTAAAATTTAT
1 ATAATAAAAATATAATAAATATATTAAAATTTAT
*
3012675 ATAATAAAAAT-TATTAAA-ATATTAAAATTTAT
1 ATAATAAAAATATAATAAATATATTAAAATTTAT
* ** * *
3012707 ATAAATATAAATATTTTAAATATAATTATAATATAAT
1 AT-AATAAAAATATAATAAATAT-ATTAAAAT-TTAT
*
3012744 AAAAATAAAAATATAATA
1 -ATAATAAAAATATAATA
3012762 TGAATATAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
32 15 0.21
33 14 0.20
34 16 0.23
35 2 0.03
36 7 0.10
37 15 0.21
38 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
ATAATAAAAATATAATAAATATATTAAAATTTAT
Found at i:3012716 original size:6 final size:6
Alignment explanation
Indices: 3012705--3012771 Score: 50
Period size: 6 Copynumber: 11.2 Consensus size: 6
3012695 ATTAAAATTT
* * *
3012705 ATATAA ATATAA ATATTTTAA ATATAA TTAT-A ATAT-A ATAAAA ATAAAA
1 ATATAA ATATAA ATA---TAA ATATAA ATATAA ATATAA ATATAA ATATAA
*
3012754 ATAT-A ATATGA ATATAA A
1 ATATAA ATATAA ATATAA A
3012772 ATTATAAAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
5 13 0.25
6 32 0.63
9 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:3012717 original size:17 final size:17
Alignment explanation
Indices: 3012665--3012722 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
3012655 ATAAATATTT
3012665 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
3012681 -AAAA-TTAT-TAAAATA
1 TAAAATTTATAT-AAATA
3012696 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
3012714 TAAATATTT
1 TAAA-ATTT
3012723 TAAATATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 4 0.11
15 8 0.23
17 8 0.23
18 13 0.37
19 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:3012767 original size:17 final size:18
Alignment explanation
Indices: 3012597--3012778 Score: 56
Period size: 17 Copynumber: 9.8 Consensus size: 18
3012587 TAATAATATT
*
3012597 AAATATAATCATATAAATATA
1 AAATATAA-AATAT-AATA-A
*
3012618 AAATAAAAAATTATAATTAAA
1 AAATATAAAA-TATAA-T-AA
3012639 AAATAATATAAATATAATAA
1 AAAT-ATA-AAATATAATAA
* * *
3012659 ATATTTTAAAAT-TTAT-A
1 A-AATATAAAATATAATAA
* *
3012676 TAATA-AAAAT-T-ATTA
1 AAATATAAAATATAATAA
* *
3012691 AAATATTAAAAT-TTATAT
1 AAATA-TAAAATATAATAA
**
3012709 AAATAT-AAATATTTTAA
1 AAATATAAAATATAATAA
* *
3012726 ATATAATTATAATATAATAA
1 AAAT-A-TAAAATATAATAA
*
3012746 AAATA-AAAATATAATAT
1 AAATATAAAATATAATAA
*
3012763 GAATATAAAATTATAA
1 AAATATAAAA-TATAA
3012779 AGTCAGTATT
Statistics
Matches: 123, Mismatches: 22, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
14 2 0.02
15 11 0.09
16 6 0.05
17 29 0.24
18 15 0.12
19 11 0.09
20 19 0.15
21 19 0.15
22 8 0.07
23 3 0.02
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.37
Consensus pattern (18 bp):
AAATATAAAATATAATAA
Found at i:3014086 original size:29 final size:29
Alignment explanation
Indices: 3014053--3014120 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
3014043 ATTATATAAG
3014053 ATTTTTTATATT-TTTACTTATTGAAA-TT-
1 ATTTTTT-TATTGTTTAC-TATTGAAACTTA
*
3014081 ATTTTTGGTTATTGTTTACTATTTAAACTTA
1 ATTTTT--TTATTGTTTACTATTGAAACTTA
3014112 ATTTTTTTA
1 ATTTTTTTA
3014121 AAAATATTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
28 6 0.18
29 14 0.41
30 8 0.24
31 6 0.18
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.63
Consensus pattern (29 bp):
ATTTTTTTATTGTTTACTATTGAAACTTA
Found at i:3015017 original size:27 final size:28
Alignment explanation
Indices: 3014952--3015017 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 28
3014942 TTATTTATTG
**
3014952 ATAAAT-TATTTTTATATTTTAATAATAT
1 ATAAATATATTTAAATATTTTAAT-ATAT
*
3014980 ATAAA-A-CTTTAAATATTTTAAT-TAT
1 ATAAATATATTTAAATATTTTAATATAT
3015005 ATAAATATATTTA
1 ATAAATATATTTA
3015018 TTCTATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
25 8 0.26
26 1 0.03
27 17 0.55
28 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAAATATATTTAAATATTTTAATATAT
Found at i:3018452 original size:9 final size:9
Alignment explanation
Indices: 3018438--3018476 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
3018428 CTGAAGTAAA
3018438 TAATAATAT
1 TAATAATAT
3018447 TAATAATAT
1 TAATAATAT
*
3018456 TAATATTAT
1 TAATAATAT
* *
3018465 TATTAAAAT
1 TAATAATAT
3018474 TAA
1 TAA
3018477 CAAATAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TAATAATAT
Found at i:3018567 original size:9 final size:9
Alignment explanation
Indices: 3018553--3018594 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
3018543 ATAAGGTTTT
3018553 TATTAATAA
1 TATTAATAA
*
3018562 TATTAATAT
1 TATTAATAA
*
3018571 TATTATTAA
1 TATTAATAA
*
3018580 AATTAATAA
1 TATTAATAA
3018589 T-TTAAT
1 TATTAAT
3018595 TTATCATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
8 5 0.19
9 22 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TATTAATAA
Found at i:3019011 original size:2 final size:2
Alignment explanation
Indices: 3019004--3019029 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3018994 CTAATCTTAT
3019004 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
3019030 AAGTGACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3019768 original size:45 final size:45
Alignment explanation
Indices: 3019719--3019835 Score: 198
Period size: 45 Copynumber: 2.6 Consensus size: 45
3019709 TTTGTTATTT
3019719 TTTTAATTGGGTTTGGGTTTAAGTTTATATAAATTTTTAGTTGGG
1 TTTTAATTGGGTTTGGGTTTAAGTTTATATAAATTTTTAGTTGGG
* *
3019764 TTTTAATTGGGTTTGGGTTTAAGGTTATATAGATTTTTAGTTGGG
1 TTTTAATTGGGTTTGGGTTTAAGTTTATATAAATTTTTAGTTGGG
**
3019809 TTTTAATTGGGTTTAAGTTTAAGTTTA
1 TTTTAATTGGGTTTGGGTTTAAGTTTA
3019836 AATTTATATT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (45 bp):
TTTTAATTGGGTTTGGGTTTAAGTTTATATAAATTTTTAGTTGGG
Found at i:3024802 original size:5 final size:5
Alignment explanation
Indices: 3024789--3024887 Score: 55
Period size: 5 Copynumber: 19.4 Consensus size: 5
3024779 ATATAATTTA
**
3024789 ATTATT ATTAT ATTTAT ATTAT -TTAT ATTAT AATT-T AAAAAT ATTAT
1 ATTA-T ATTAT A-TTAT ATTAT ATTAT ATTAT -ATTAT -ATTAT ATTAT
* *
3024836 A-TAT -TTAT ATGAT TTTAAAT ATTAT ATTAT ATTAT AATTAT -TTAT
1 ATTAT ATTAT ATTAT ATT--AT ATTAT ATTAT ATTAT -ATTAT ATTAT
*
3024881 TTTAT AT
1 ATTAT AT
3024888 CATTTTGTGA
Statistics
Matches: 74, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
4 14 0.19
5 38 0.51
6 18 0.24
7 4 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:3024803 original size:26 final size:25
Alignment explanation
Indices: 3024756--3024822 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
3024746 CTTTTGATTT
*
3024756 TAATTTAATAATAATAAAATTTGATA
1 TAATTTAATTATAATAAAATTT-ATA
* * *
3024782 TAATTTAATTATTATTATATTTATA
1 TAATTTAATTATAATAAAATTTATA
*
3024807 TTATTTATATTATAAT
1 TAATTTA-ATTATAAT
3024823 TTAAAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 9 0.26
26 25 0.74
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
TAATTTAATTATAATAAAATTTATA
Found at i:3024838 original size:55 final size:57
Alignment explanation
Indices: 3024771--3024876 Score: 132
Period size: 55 Copynumber: 1.9 Consensus size: 57
3024761 TAATAATAAT
* *
3024771 AAAATTTGATATAATTTA-ATTATTATTATAT-TTATATTAT-TTAT-ATTATAATTTA
1 AAAATTTGATAT-ATTTATATGATT-TTAAATATTATATTATATTATAATTATAATTTA
3024826 AAAATATT-ATATATTTATATGATTTTAAATATTATATTATATTATAATTAT
1 AAAAT-TTGATATATTTATATGATTTTAAATATTATATTATATTATAATTAT
3024877 TTATTTTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
54 10 0.23
55 23 0.52
56 6 0.14
57 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (57 bp):
AAAATTTGATATATTTATATGATTTTAAATATTATATTATATTATAATTATAATTTA
Found at i:3024870 original size:27 final size:26
Alignment explanation
Indices: 3024804--3024874 Score: 87
Period size: 25 Copynumber: 2.8 Consensus size: 26
3024794 TATTATATTT
3024804 ATATTAT-TTATATTATAATTTAAAA
1 ATATTATATTATATTATAATTTAAAA
*
3024829 ATATTATA-TAT-TTATATGATTT-TAA
1 ATATTATATTATATTATA--ATTTAAAA
3024854 ATATTATATTATATTATAATT
1 ATATTATATTATATTATAATT
3024875 ATTTATTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
24 5 0.12
25 23 0.57
26 7 0.17
27 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (26 bp):
ATATTATATTATATTATAATTTAAAA
Found at i:3030376 original size:30 final size:30
Alignment explanation
Indices: 3030352--3030416 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
3030342 AAATTTTACT
*
3030352 ATTTTGAAATTCATTAATTCAAATTATTAA
1 ATTTTAAAATTCATTAATTCAAATTATTAA
* * *
3030382 ATTTTAAAATTTATTAATTTAAAATATTAA
1 ATTTTAAAATTCATTAATTCAAATTATTAA
3030412 TATTT
1 -ATTT
3030417 GTAACTGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (30 bp):
ATTTTAAAATTCATTAATTCAAATTATTAA
Found at i:3030397 original size:17 final size:15
Alignment explanation
Indices: 3030338--3030406 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
3030328 TTTGGAGAAT
* *
3030338 TTTAAAATTTTACTAT
1 TTTAAAA-TTTATTAA
* *
3030354 TTTGAAATTCATTAA
1 TTTAAAATTTATTAA
*
3030369 -TTCAAA-TTATTAAA
1 TTTAAAATTTATT-AA
3030383 TTTTAAAATTTATTAA
1 -TTTAAAATTTATTAA
3030399 TTTAAAAT
1 TTTAAAAT
3030407 ATTAATATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 4 0.10
14 7 0.17
15 13 0.31
16 13 0.31
17 5 0.12
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (15 bp):
TTTAAAATTTATTAA
Found at i:3035535 original size:19 final size:19
Alignment explanation
Indices: 3035498--3035535 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3035488 TTGATTAAGT
*
3035498 TGTTTCTGGAGGAAGTTCA
1 TGTTTCTGGAGGAACTTCA
3035517 TGTTTCT-GAGGAACCTTCA
1 TGTTTCTGGAGGAA-CTTCA
3035536 GATCAGAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (19 bp):
TGTTTCTGGAGGAACTTCA
Found at i:3039293 original size:21 final size:21
Alignment explanation
Indices: 3039263--3039315 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3039253 TTATTAAAAT
*
3039263 TATATCTTTTTCATTTAATAAA
1 TATAT-TTTTTCATTCAATAAA
*
3039285 TATATTTTTTCATTCAATAAG
1 TATATTTTTTCATTCAATAAA
3039306 TATATTTTTT
1 TATATTTTTT
3039316 ACTTAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (21 bp):
TATATTTTTTCATTCAATAAA
Found at i:3039324 original size:21 final size:21
Alignment explanation
Indices: 3039263--3039325 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
3039253 TTATTAAAAT
*
3039263 TATATCTTTTTCATTTAATAAA
1 TATAT-TTTTTCATTAAATAAA
* *
3039285 TATATTTTTTCATTCAATAAG
1 TATATTTTTTCATTAAATAAA
3039306 TATATTTTTT-ACTTAAATAA
1 TATATTTTTTCA-TTAAATAA
3039326 TGATTATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.03
21 31 0.84
22 5 0.14
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.54
Consensus pattern (21 bp):
TATATTTTTTCATTAAATAAA
Found at i:3039949 original size:17 final size:18
Alignment explanation
Indices: 3039929--3039966 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3039919 TAATTAAATT
3039929 ATTGAAT-TAAAAAATAA
1 ATTGAATGTAAAAAATAA
* *
3039946 ATTGATTGTAAAAAATTA
1 ATTGAATGTAAAAAATAA
3039964 ATT
1 ATT
3039967 TTAATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (18 bp):
ATTGAATGTAAAAAATAA
Found at i:3044209 original size:31 final size:31
Alignment explanation
Indices: 3044148--3044211 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
3044138 TAATATATTT
* * *
3044148 AATTTTTAAAAAATAATATTATAATATTTAA
1 AATTTATAAAAAATAATATAAAAATATTTAA
*
3044179 AATTTATAAAAAATATTAATAAAAAT-TTTAA
1 AATTTATAAAAAATAAT-ATAAAAATATTTAA
3044210 AA
1 AA
3044212 AATTATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AATTTATAAAAAATAATATAAAAATATTTAA
Found at i:3044285 original size:19 final size:20
Alignment explanation
Indices: 3044243--3044285 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
3044233 TTTTAATATT
3044243 TTTTTAAAAATATAATGATAA
1 TTTTTAAAAATATAAT-ATAA
3044264 TTTTT-AAAATAATAAT-TAA
1 TTTTTAAAAAT-ATAATATAA
3044283 TTT
1 TTT
3044286 ATTTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
20 5 0.24
21 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTTTAAAAATATAATATAA
Found at i:3044396 original size:16 final size:17
Alignment explanation
Indices: 3044370--3044406 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
3044360 TTTAATAAGT
3044370 ATTTAATTTAAAATATA
1 ATTTAATTTAAAATATA
*
3044387 ATTTAA-TTAAAATTTA
1 ATTTAATTTAAAATATA
3044403 ATTT
1 ATTT
3044407 GATAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAATTTAAAATATA
Found at i:3045769 original size:18 final size:18
Alignment explanation
Indices: 3045737--3045777 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3045727 AATTTTTATA
3045737 AAAATAATATATTAAATAT
1 AAAATAATATATTAAAT-T
*
3045756 AAAAT-ATATTTTAAATT
1 AAAATAATATATTAAATT
3045773 AAAAT
1 AAAAT
3045778 TTAAGTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 10 0.48
19 5 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATAATATATTAAATT
Found at i:3045771 original size:42 final size:39
Alignment explanation
Indices: 3045692--3045772 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 39
3045682 TAAAGTACTA
* *
3045692 TTTATAAAAAAATATAATTAATAAATTATTTTTTAAATT
1 TTTATAAAAAAATATAATTAATAAAATATATTTTAAATT
3045731 TTTATAAAAATAATAT-ATTAAATATAAAATATATTTTAAATT
1 TTTATAAAAA-AATATAATT--A-ATAAAATATATTTTAAATT
3045773 AAAATTTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
39 13 0.36
40 5 0.14
41 1 0.03
42 17 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (39 bp):
TTTATAAAAAAATATAATTAATAAAATATATTTTAAATT
Found at i:3046219 original size:10 final size:10
Alignment explanation
Indices: 3046206--3046236 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3046196 TTTTAATTTT
3046206 TATAAATATA
1 TATAAATATA
*
3046216 TATAATTATA
1 TATAAATATA
3046226 TATAAATATA
1 TATAAATATA
3046236 T
1 T
3046237 TTTAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TATAAATATA
Found at i:3046327 original size:33 final size:33
Alignment explanation
Indices: 3046282--3046357 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
3046272 TTTATTAATT
*
3046282 TTAATTTAATTATTAA-ATTTATCATTATAATAA
1 TTAATTTTATTATTAATA-TTATCATTATAATAA
* * **
3046315 TTAATTTTATTATTATTATTATTATTATAATTT
1 TTAATTTTATTATTAATATTATCATTATAATAA
3046348 TTAATTTTAT
1 TTAATTTTAT
3046358 CATAATCAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 36 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (33 bp):
TTAATTTTATTATTAATATTATCATTATAATAA
Found at i:3046338 original size:21 final size:20
Alignment explanation
Indices: 3046260--3046338 Score: 65
Period size: 21 Copynumber: 4.0 Consensus size: 20
3046250 TTTTAAAAAT
* *
3046260 ATTTTTTTATTT-TTTATTA
1 ATTTTATTATTTAATTATTA
3046279 ATTTTA--ATTTAATTATTA
1 ATTTTATTATTTAATTATTA
* * *
3046297 AATTTATCATTATAATAATTA
1 ATTTTATTATT-TAATTATTA
*
3046318 ATTTTATTATTATTATTATTA
1 ATTTTATTATT-TAATTATTA
3046339 TTATAATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
17 4 0.08
18 11 0.23
19 5 0.10
20 3 0.06
21 25 0.52
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTATTATTTAATTATTA
Found at i:3046357 original size:18 final size:18
Alignment explanation
Indices: 3046273--3046363 Score: 82
Period size: 18 Copynumber: 5.1 Consensus size: 18
3046263 TTTTTATTTT
3046273 TTATTAATTTTAATT-TAA
1 TTATTAATTTT-ATTATAA
3046291 TTATTAAATTTATCATTATAA
1 TTATT-AATTT-T-ATTATAA
* *
3046312 TAATTAATTTTATTATTA
1 TTATTAATTTTATTATAA
3046330 TTATT-A--TTATTATAA
1 TTATTAATTTTATTATAA
* *
3046345 TTTTTAATTTTATCATAA
1 TTATTAATTTTATTATAA
3046363 T
1 T
3046364 CAATCACCTG
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
15 12 0.20
16 1 0.02
17 1 0.02
18 24 0.40
19 6 0.10
20 9 0.15
21 7 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTAATTTTATTATAA
Found at i:3047056 original size:8 final size:8
Alignment explanation
Indices: 3047043--3047069 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3047033 TTTATTACAA
3047043 AAAAATTT
1 AAAAATTT
3047051 AAAAATTT
1 AAAAATTT
3047059 AAAAATTT
1 AAAAATTT
3047067 AAA
1 AAA
3047070 TATTATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAAATTT
Found at i:3047117 original size:28 final size:29
Alignment explanation
Indices: 3047062--3047120 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
3047052 AAAATTTAAA
* * *
3047062 AATTTAAATATTATTAAATATTATTATTT
1 AATTTAAATATTATAAAATAATAATATTT
*
3047091 AATTTAAATTTTA-AAAATAATAATATTT
1 AATTTAAATATTATAAAATAATAATATTT
3047119 AA
1 AA
3047121 ATTATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AATTTAAATATTATAAAATAATAATATTT
Found at i:3047119 original size:23 final size:23
Alignment explanation
Indices: 3047092--3047136 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3047082 TTATTATTTA
*
3047092 ATTTAAATTTTAAAAATAATAAT
1 ATTTAAATTATAAAAATAATAAT
3047115 ATTTAAATTATAAAAATAATAA
1 ATTTAAATTATAAAAATAATAA
3047137 ATATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTTAAATTATAAAAATAATAAT
Found at i:3047123 original size:29 final size:30
Alignment explanation
Indices: 3047061--3047137 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
3047051 AAAAATTTAA
* * *
3047061 AAATTTAAATATTATTAAATATTATTATTT
1 AAATTTAAATATTATAAAATAATAATATTT
*
3047091 -AATTTAAATTTTA-AAAATAATAATATTT
1 AAATTTAAATATTATAAAATAATAATATTT
* *
3047119 AAATTATAAAAATAATAAA
1 AAATT-TAAATATTATAAA
3047138 TATATTTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 12 0.32
29 16 0.43
30 6 0.16
31 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
AAATTTAAATATTATAAAATAATAATATTT
Found at i:3047148 original size:20 final size:20
Alignment explanation
Indices: 3047095--3047164 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 20
3047085 TTATTTAATT
3047095 TAAATTTTAAAAATAATAATA
1 TAAATTTTAAAAATAATAA-A
*
3047116 TTTAAATTATAAAAATAATAAA
1 --TAAATTTTAAAAATAATAAA
* *
3047138 TATATTTTAAAATTATATAAA
1 TAAATTTTAAAAATA-ATAAA
*
3047159 TTAATT
1 TAAATT
3047165 AAATTTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 12 0.30
21 9 0.22
22 1 0.03
23 18 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATTTTAAAAATAATAAA
Found at i:3049393 original size:34 final size:34
Alignment explanation
Indices: 3049351--3049419 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
3049341 GTGAAAGCGA
**
3049351 TTTATGATATTGTAATTAACCTTTAATGTGAATT
1 TTTATGATATTACAATTAACCTTTAATGTGAATT
* *
3049385 TTTATGATATTACAATTAGCCTTTCATGTGAATT
1 TTTATGATATTACAATTAACCTTTAATGTGAATT
3049419 T
1 T
3049420 AAGTCAACAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (34 bp):
TTTATGATATTACAATTAACCTTTAATGTGAATT
Found at i:3054336 original size:27 final size:27
Alignment explanation
Indices: 3054283--3054336 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3054273 AGTACCAAAG
*
3054283 ATAGTCAAGGGTGACTTTAACTATCAA
1 ATAGTCAAGGGTGACTTTAAATATCAA
* *
3054310 ATAGTTAAGGGTGACTTTAAATGTCAA
1 ATAGTCAAGGGTGACTTTAAATATCAA
3054337 TTTTCAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (27 bp):
ATAGTCAAGGGTGACTTTAAATATCAA
Found at i:3058418 original size:2 final size:2
Alignment explanation
Indices: 3058400--3058450 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
3058390 TGAAAACAGT
* * *
3058400 TA TA TA CA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3058442 TA TA TA TA T
1 TA TA TA TA T
3058451 GGACTTAGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3059337 original size:24 final size:23
Alignment explanation
Indices: 3059294--3059454 Score: 72
Period size: 22 Copynumber: 7.1 Consensus size: 23
3059284 TACAGGTAAA
*
3059294 AAAATTAAAATATAATATAATAT
1 AAAATTAAAATATAACATAATAT
3059317 AAAA-TAATAATATTAACATAATAT
1 AAAATTAA-AATA-TAACATAATAT
* *
3059341 AAATTTATAAATAT-A-TTAATAT
1 AAAATTA-AAATATAACATAATAT
* *
3059363 ATAATAAAAATTATTAACAT-AT-T
1 AAAATTAAAA-TA-TAACATAATAT
*
3059386 AAAATT--TATATAA-ATACATAT
1 AAAATTAAAATATAACATA-ATAT
* * * *
3059407 -TACTTTAAATATAATTATAATAT
1 AAAATTAAAATATAA-CATAATAT
* * *
3059430 AAAAATAATAT-TAATATAATAT
1 AAAATTAAAATATAACATAATAT
3059452 AAA
1 AAA
3059455 TATATTAATA
Statistics
Matches: 104, Mismatches: 18, Indels: 33
0.67 0.12 0.21
Matches are distributed among these distances:
18 2 0.02
19 3 0.03
20 7 0.07
21 5 0.05
22 32 0.31
23 22 0.21
24 25 0.24
25 7 0.07
26 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAATTAAAATATAACATAATAT
Found at i:3059351 original size:8 final size:8
Alignment explanation
Indices: 3059301--3059366 Score: 50
Period size: 8 Copynumber: 8.2 Consensus size: 8
3059291 AAAAAAATTA
3059301 AAATATAAT
1 AAATAT-AT
3059310 ATAATATA-
1 A-AATATAT
3059318 AAATA-AT
1 AAATATAT
3059325 -AATAT-T
1 AAATATAT
3059331 AACATAATAT
1 AA-AT-ATAT
*
3059341 AAATTTAT
1 AAATATAT
3059349 AAATATAT
1 AAATATAT
*
3059357 TAATATAT
1 AAATATAT
3059365 AA
1 AA
3059367 TAAAAATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
6 6 0.13
7 5 0.11
8 21 0.46
9 6 0.13
10 8 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (8 bp):
AAATATAT
Found at i:3059366 original size:29 final size:29
Alignment explanation
Indices: 3059334--3059400 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 29
3059324 TAATATTAAC
* *
3059334 ATAATATAAATTTATAAATATATTAATAT
1 ATAATATAAATTTATAAACATATTAAAAT
* *
3059363 ATAATA-AAAATTATTAACATATTAAAAT
1 ATAATATAAATTTATAAACATATTAAAAT
*
3059391 -TTATATAAAT
1 ATAATATAAAT
3059401 ACATATTACT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 4 0.13
28 21 0.68
29 6 0.19
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (29 bp):
ATAATATAAATTTATAAACATATTAAAAT
Found at i:3059392 original size:46 final size:47
Alignment explanation
Indices: 3059277--3059395 Score: 131
Period size: 46 Copynumber: 2.6 Consensus size: 47
3059267 AAATATTATG
*
3059277 AAAATATT-ACAGGTAA-AAAAATTA-AAATATAATATAATATAAAATA
1 AAAATATTAACA--TAATAAAATTTATAAATATAATATAATATAAAATA
* *
3059323 ATAATATTAACATAATATAAATTTATAAATAT-AT-TAATATATAATA
1 AAAATATTAACATAATA-AAATTTATAAATATAATATAATATAAAATA
*
3059369 AAAATTATTAACATATTAAAATTTATA
1 AAAA-TATTAACATAATAAAATTTATA
3059396 TAAATACATA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
45 3 0.05
46 31 0.49
47 23 0.37
48 6 0.10
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.36
Consensus pattern (47 bp):
AAAATATTAACATAATAAAATTTATAAATATAATATAATATAAAATA
Found at i:3059430 original size:11 final size:11
Alignment explanation
Indices: 3059414--3059475 Score: 65
Period size: 11 Copynumber: 5.7 Consensus size: 11
3059404 TATTACTTTA
*
3059414 AATATAATTAT
1 AATATAAATAT
*
3059425 AATATAAAAAT
1 AATATAAATAT
*
3059436 AATATTAATAT
1 AATATAAATAT
3059447 AATATAAATAT
1 AATATAAATAT
*
3059458 ATTAATAAAT-T
1 AAT-ATAAATAT
3059469 AA-ATAAA
1 AATATAAA
3059476 ATTGAAACCC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
9 5 0.12
11 32 0.74
12 6 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATAAATAT
Found at i:3059437 original size:17 final size:17
Alignment explanation
Indices: 3059392--3059448 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
3059382 TATTAAAATT
* *
3059392 TATATAAATACATATTAC
1 TATAAAAATA-ATATTAA
* *
3059410 TTTAAATATAAT-TATAA
1 TATAAAAATAATAT-TAA
3059427 TATAAAAATAATATTAA
1 TATAAAAATAATATTAA
3059444 TATAA
1 TATAA
3059449 TATAAATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
16 1 0.03
17 22 0.71
18 8 0.26
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
TATAAAAATAATATTAA
Found at i:3059471 original size:17 final size:19
Alignment explanation
Indices: 3059301--3059473 Score: 66
Period size: 20 Copynumber: 9.3 Consensus size: 19
3059291 AAAAAAATTA
*
3059301 AAATATAATATAATATAAAAT
1 AAATAT-AT-TAATATAATAT
*
3059322 -AATAATATTAACATAATAT
1 AAAT-ATATTAATATAATAT
*
3059341 AAATTTA-TAA-AT-ATAT
1 AAATATATTAATATAATAT
* *
3059357 TAATATA-TAATAAAAATTAT
1 AAATATATTAAT-ATAA-TAT
* * * *
3059377 TAACATATTAAAATTTATAT
1 AAATATATTAATA-TAATAT
* *
3059397 AAATACATATTACTTTAA-AT
1 AAAT--ATATTAATATAATAT
3059417 ATAAT-TA-TAATAT-A-A-
1 A-AATATATTAATATAATAT
3059432 AAATAATATTAATATAATAT
1 AAAT-ATATTAATATAATAT
3059452 AAATATATTAATA-AAT-T
1 AAATATATTAATATAATAT
3059469 AAATA
1 AAATA
3059474 AAATTGAAAC
Statistics
Matches: 117, Mismatches: 18, Indels: 38
0.68 0.10 0.22
Matches are distributed among these distances:
14 3 0.03
15 1 0.01
16 16 0.14
17 18 0.15
18 10 0.09
19 22 0.19
20 30 0.26
21 11 0.09
22 6 0.05
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATATATTAATATAATAT
Found at i:3059471 original size:56 final size:56
Alignment explanation
Indices: 3059295--3059478 Score: 151
Period size: 56 Copynumber: 3.3 Consensus size: 56
3059285 ACAGGTAAAA
* * *
3059295 AAATTAAAATATAA-TATAATATAAAATAATAATATTAACATAATATAAATTTATAAAT
1 AAATT-AAATATAATTATAATAT-AAA-AATAATATTAAAATAATATAAATATATTAAT
* * * ** * * * *
3059353 ATATTAATATATAATAAAAAT-TATTAA-CATATTAAAATTTATATAAATACA-TATT
1 AAATTAA-ATATAATTATAATATAAAAATAATATTAAAA-TAATATAAATATATTAAT
** *
3059408 ACTTTAAATATAATTATAATATAAAAATAATATTAATATAATATAAATATATTAAT
1 AAATTAAATATAATTATAATATAAAAATAATATTAAAATAATATAAATATATTAAT
*
3059464 AAATTAAATAAAATT
1 AAATTAAATATAATT
3059479 GAAACCCAAA
Statistics
Matches: 94, Mismatches: 26, Indels: 14
0.70 0.19 0.10
Matches are distributed among these distances:
54 11 0.12
55 30 0.32
56 35 0.37
57 3 0.03
58 11 0.12
59 4 0.04
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (56 bp):
AAATTAAATATAATTATAATATAAAAATAATATTAAAATAATATAAATATATTAAT
Found at i:3060117 original size:18 final size:17
Alignment explanation
Indices: 3060075--3060120 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
3060065 ATCATTTATC
* *
3060075 AATTATTTTTTACTTAA
1 AATTATTTTTAACTCAA
3060092 AA-TATTTTTAACTACAA
1 AATTATTTTTAACT-CAA
3060109 AATTATTTTTAA
1 AATTATTTTTAA
3060121 TTATTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 10 0.40
17 6 0.24
18 9 0.36
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTATTTTTAACTCAA
Found at i:3060638 original size:20 final size:22
Alignment explanation
Indices: 3060595--3060639 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
3060585 GCACTAAATT
*
3060595 ATTTAAATAATAATAATTAATTA
1 ATTTAAATAAAAATAATT-ATTA
3060618 ATTTAAATAAAAAT-ATT-TTA
1 ATTTAAATAAAAATAATTATTA
3060638 AT
1 AT
3060640 AAATTATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
22 3 0.14
23 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTAAATAAAAATAATTATTA
Found at i:3060736 original size:16 final size:16
Alignment explanation
Indices: 3060715--3060746 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3060705 AATTCAAATA
*
3060715 TAATTTAATATTAATT
1 TAATTTAATAGTAATT
3060731 TAATTTAATAGTAATT
1 TAATTTAATAGTAATT
3060747 AAAAATAATT
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:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TAATTTAATAGTAATT
Found at i:3061348 original size:45 final size:46
Alignment explanation
Indices: 3061262--3061359 Score: 171
Period size: 45 Copynumber: 2.2 Consensus size: 46
3061252 AAATTAGACA
3061262 AACTTATTTTTACTATATTTAAAAAAAAATAATGCAATGAGACTTG
1 AACTTATTTTTACTATATTTAAAAAAAAATAATGCAATGAGACTTG
* *
3061308 AACTTATTTTTACTATATTT-TAAAAAAATTATGCAATGAGACTTG
1 AACTTATTTTTACTATATTTAAAAAAAAATAATGCAATGAGACTTG
3061353 AACTTAT
1 AACTTAT
3061360 AACCTTTTAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 30 0.60
46 20 0.40
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (46 bp):
AACTTATTTTTACTATATTTAAAAAAAAATAATGCAATGAGACTTG
Found at i:3061744 original size:29 final size:27
Alignment explanation
Indices: 3061712--3061791 Score: 81
Period size: 29 Copynumber: 2.9 Consensus size: 27
3061702 TATTTAATTT
*
3061712 AAATAAATTCTTATATTTTTATTTCACT-C
1 AAATAAATTCTTA-ATTTTAATTT-A-TAC
* *
3061741 AAATAAACTCATAAATTTTAATTTATAC
1 AAATAAATTC-TTAATTTTAATTTATAC
*
3061769 AAAAAAATTCTTAATTTTAATTT
1 AAATAAATTCTTAATTTTAATTT
3061792 TTTTCAAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
27 13 0.30
28 10 0.23
29 18 0.42
30 2 0.05
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATAAATTCTTAATTTTAATTTATAC
Found at i:3061811 original size:28 final size:27
Alignment explanation
Indices: 3061694--3061811 Score: 74
Period size: 28 Copynumber: 4.1 Consensus size: 27
3061684 TCCTATTTTG
* * *
3061694 AATTTTATTATTTAATTTAAATAAATTCTT
1 AATTTTA--ATTT-ATTCAAATAAACTATT
* * *
3061724 ATATTTTTATTTCACTCAAATAAACTCATA
1 A-ATTTTAATTT-ATTCAAATAAACT-ATT
* * * *
3061754 AATTTTAATTTATACAAAAAAATTCTT
1 AATTTTAATTTATTCAAATAAACTATT
*
3061781 AATTTTAATTTTTTTCAAATAAACTATT
1 AATTTTAA-TTTATTCAAATAAACTATT
3061809 AAT
1 AAT
3061812 GTAATTATTC
Statistics
Matches: 66, Mismatches: 19, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
27 9 0.14
28 26 0.39
29 23 0.35
30 3 0.05
31 5 0.08
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.49
Consensus pattern (27 bp):
AATTTTAATTTATTCAAATAAACTATT
Found at i:3062682 original size:3 final size:3
Alignment explanation
Indices: 3062674--3062714 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
3062664 TTAGAAACAC
*
3062674 CTT CTT CTT CCT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
3062715 ATTCCTCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:3064296 original size:18 final size:16
Alignment explanation
Indices: 3064275--3064359 Score: 54
Period size: 15 Copynumber: 5.4 Consensus size: 16
3064265 ATTTTAATAT
3064275 ATATAATAAATTATTAA
1 ATATAA-AAATTATTAA
*
3064292 TATATTAAAATTTATATAA
1 -ATA-TAAAAATTAT-TAA
*
3064311 ATATAAATATT-TTAA
1 ATATAAAAATTATTAA
*
3064326 ATAT---AATTATTAT
1 ATATAAAAATTATTAA
* *
3064339 ATATTAAAA-TAATAA
1 ATATAAAAATTATTAA
3064354 ATATAA
1 ATATAA
3064360 TACATGTATA
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 7 0.13
15 16 0.30
16 3 0.06
17 6 0.11
18 12 0.23
19 6 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATAAAAATTATTAA
Found at i:3064325 original size:26 final size:28
Alignment explanation
Indices: 3064257--3064330 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 28
3064247 TTTCTTTGTT
* *
3064257 ATTA-AAAAATTTTAATATATATAATAA
1 ATTATAAATATTTTAAAATATATAATAA
* * *
3064284 ATTATTAATATATTAAAATTTAT-ATAA
1 ATTATAAATATTTTAAAATATATAATAA
3064311 A-TATAAATATTTT-AAATATA
1 ATTATAAATATTTTAAAATATA
3064331 ATTATTATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
25 6 0.16
26 10 0.26
27 9 0.24
28 13 0.34
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTATAAATATTTTAAAATATATAATAA
Found at i:3067830 original size:13 final size:13
Alignment explanation
Indices: 3067801--3067839 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3067791 ATTTTCAATG
3067801 ATAAATTT-T-AT
1 ATAAATTTATAAT
3067812 -TAAATTTATAAT
1 ATAAATTTATAAT
3067824 ATAAATTTATAA-
1 ATAAATTTATAAT
3067836 ATAA
1 ATAA
3067840 GAAGGAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.28
11 1 0.04
12 6 0.24
13 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAAATTTATAAT
Found at i:3067830 original size:23 final size:25
Alignment explanation
Indices: 3067784--3067831 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
3067774 ATTATCATGG
3067784 TATTAAAATTTTCAATGATAAATTT
1 TATTAAAATTTTCAATGATAAATTT
3067809 TATT-AAATTTAT-AAT-ATAAATTT
1 TATTAAAATTT-TCAATGATAAATTT
3067832 ATAAATAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.36
24 9 0.41
25 5 0.23
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
TATTAAAATTTTCAATGATAAATTT
Found at i:3067943 original size:17 final size:18
Alignment explanation
Indices: 3067912--3067946 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3067902 TTATGAAATT
3067912 TTATATATTGGATATAAAG
1 TTATATATT-GATATAAAG
3067931 TTATATATT-ATATAAA
1 TTATATATTGATATAAA
3067947 TAATTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (18 bp):
TTATATATTGATATAAAG
Found at i:3068157 original size:22 final size:22
Alignment explanation
Indices: 3068111--3068158 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
3068101 CTTTTAACAG
*
3068111 AATTAGAATTCTTATTTATAAA
1 AATTAGAATTCTTATTCATAAA
3068133 AATTATGAATT-TTA-TCATAAGA
1 AATTA-GAATTCTTATTCATAA-A
3068155 AATT
1 AATT
3068159 CATTTAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 5 0.22
22 13 0.57
23 5 0.22
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (22 bp):
AATTAGAATTCTTATTCATAAA
Found at i:3068319 original size:25 final size:25
Alignment explanation
Indices: 3068272--3068320 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
3068262 AATATCAAGG
* * *
3068272 TATTAAAATTTTTAATGATAAATTC
1 TATTAAAATTTATAATAAAAAATTC
*
3068297 TATTAATATTTATAATAAAAAATT
1 TATTAAAATTTATAATAAAAAATT
3068321 GTAAATGATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
TATTAAAATTTATAATAAAAAATTC
Found at i:3069301 original size:2 final size:2
Alignment explanation
Indices: 3069294--3069318 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3069284 AGATACATGC
3069294 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3069319 CACATACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3070816 original size:19 final size:20
Alignment explanation
Indices: 3070792--3070837 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
3070782 AAATTTATTT
3070792 AATTAAATTCTTTTA-ATA-A
1 AATTAAATT-TTTTACATATA
*
3070811 AATT-AATTTTTTACTTATA
1 AATTAAATTTTTTACATATA
3070830 AATTAAAT
1 AATTAAAT
3070838 AAATTTTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 9 0.39
20 3 0.13
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTAAATTTTTTACATATA
Found at i:3071859 original size:15 final size:16
Alignment explanation
Indices: 3071834--3071867 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3071824 ATTCGATTCG
3071834 ATTTAATTTTAAAATA
1 ATTTAATTTTAAAATA
*
3071850 ATTTAA-TTTAATATA
1 ATTTAATTTTAAAATA
3071865 ATT
1 ATT
3071868 ATTAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTAATTTTAAAATA
Found at i:3071903 original size:22 final size:22
Alignment explanation
Indices: 3071877--3071932 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 22
3071867 TATTAAATAT
3071877 TAATAAATTTTAAATAAAAAAA
1 TAATAAATTTTAAATAAAAAAA
* * *
3071899 TAAT--ATTATAGATAAAATAA
1 TAATAAATTTTAAATAAAAAAA
3071919 T-ATAAATTTATAAA
1 TAATAAATTT-TAAA
3071933 AAATTAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
19 2 0.08
20 14 0.54
21 3 0.12
22 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
TAATAAATTTTAAATAAAAAAA
Found at i:3072219 original size:18 final size:19
Alignment explanation
Indices: 3072178--3072221 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
3072168 TTAAAATGTT
* *
3072178 ATATATTTATATAAATTTTG
1 ATATA-TTATATAAATTATA
3072198 ATATATTA-ATAAATTATA
1 ATATATTATATAAATTATA
3072216 ATATAT
1 ATATAT
3072222 AAATTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.64
19 3 0.14
20 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATATTATATAAATTATA
Found at i:3072590 original size:31 final size:31
Alignment explanation
Indices: 3072501--3072605 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 31
3072491 ATTTAAATTA
* * *
3072501 AAAT-AGGTCTTAATTTTTAA-CTTATATTT
1 AAATAAGGTTTTAATTTTTAATCATATATCT
* * *
3072530 AAATAAGTTTTTAATCTTT-ATCATGTATCT
1 AAATAAGGTTTTAATTTTTAATCATATATCT
3072560 AAATAAGGTTTTAATATTTTAATC-TATATCT
1 AAATAAGGTTTTAAT-TTTTAATCATATATCT
**
3072591 AAATAAACTTTTAAT
1 AAATAAGGTTTTAAT
3072606 ATAAATTAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 5 0.08
30 31 0.51
31 22 0.36
32 3 0.05
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.49
Consensus pattern (31 bp):
AAATAAGGTTTTAATTTTTAATCATATATCT
Found at i:3073741 original size:7 final size:7
Alignment explanation
Indices: 3073694--3073759 Score: 52
Period size: 7 Copynumber: 9.6 Consensus size: 7
3073684 TGTATCAAAA
*
3073694 AATACAT
1 AATATAT
3073701 AATATA-
1 AATATAT
3073707 AAT-TATT
1 AATATA-T
3073714 AATATAT
1 AATATAT
3073721 CAA-ATAT
1 -AATATAT
3073728 CATATATAT
1 -A-ATATAT
3073737 AATATAT
1 AATATAT
3073744 AA-ATAT
1 AATATAT
3073750 AAT-TAT
1 AATATAT
3073756 AATA
1 AATA
3073760 AAATGTAACA
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
5 2 0.04
6 15 0.30
7 23 0.46
8 6 0.12
9 4 0.08
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (7 bp):
AATATAT
Found at i:3073749 original size:31 final size:29
Alignment explanation
Indices: 3073693--3073750 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 29
3073683 ATGTATCAAA
*
3073693 AAATACATAATATAAATTATTAATATATC
1 AAATACATAATATAAATTATAAATATATC
3073722 AAATATCAT-ATATATAATATATAAATATA
1 AAATA-CATAATATA-AAT-TATAAATATA
3073751 ATTATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 10 0.40
30 6 0.24
31 9 0.36
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (29 bp):
AAATACATAATATAAATTATAAATATATC
Found at i:3080138 original size:12 final size:13
Alignment explanation
Indices: 3080119--3080150 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3080109 TCAAAAATTA
3080119 ATTAAAAAATATT
1 ATTAAAAAATATT
*
3080132 TTTAAAAAATATT
1 ATTAAAAAATATT
3080145 ATTAAA
1 ATTAAA
3080151 TATCAGATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTAAAAAATATT
Found at i:3081842 original size:96 final size:94
Alignment explanation
Indices: 3081739--3081927 Score: 220
Period size: 96 Copynumber: 2.0 Consensus size: 94
3081729 TCAAACTTTA
* * * * * *
3081739 GGCAATATGGTTAACTTTTT-TCATTTGATTTTATCTA-AAGTTTACTTTTATTTTTTTTTTTTA
1 GGCAATATGATTAACTTTTTAT-ATTTGACTTTATCTATAA-TCTAATTTTA--CTTGTTTTTTA
* *
3081802 ACTTTTAATTTTGACTTTTAAAACAAGTCTCTC
62 ACTTTTAATTTTAACTTCTAAAACAAGTCTCTC
* *
3081835 GGCAATATGATTGACTTTTTATATTTGACTTTGTCTATAATCTAATTTTACTTGTTTTTTAACTT
1 GGCAATATGATTAACTTTTTATATTTGACTTTATCTATAATCTAATTTTACTTGTTTTTTAACTT
* *
3081900 TTGATTTTAACTTCTAAAATAAGTCTCT
66 TTAATTTTAACTTCTAAAACAAGTCTCT
3081928 TTTTATTCAA
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
94 37 0.47
96 39 0.49
97 3 0.04
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (94 bp):
GGCAATATGATTAACTTTTTATATTTGACTTTATCTATAATCTAATTTTACTTGTTTTTTAACTT
TTAATTTTAACTTCTAAAACAAGTCTCTC
Found at i:3084034 original size:657 final size:658
Alignment explanation
Indices: 3082692--3085069 Score: 4099
Period size: 658 Copynumber: 3.6 Consensus size: 658
3082682 CATTTCCACT
3082692 AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTTCCTACATTT
1 AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTTCC-ACATTT
* * *
3082757 AGAACATATCTAATTAGGCCATGGCTATAGTAATGGATTAATCTTGTAAAAATTTTTATAACGAT
65 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAACGAT
* * *
3082822 CTTGATGTATTTTTGCAAAAGTCCAATTGAATATTTTTTTCATAATAGAAATATCTTCTAATGAT
130 CCTGATGTATTTTTGCAAAAGTCCAATTGGATATTTTTTTCATAATAGAAATATCTCCTAATGAT
*
3082887 TTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAAACCTTTAAAAAATTTTT
195 TTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAAACCTTTAAAAAATTTCT
* * * * * *
3082952 GACATCTTAATTTCTAAGGTTTTTTTTATAACCTAATTTTGATTGTAATTTCTTGACTTAAAGTT
260 AACATCTTAATTTCTAAGG-TTTTTTCATAACCTGATTTCGATTATACTTTCTTGACTTAAAGTT
* * * *
3083017 CATGTTTAGTTTTATTTTGATGTAACCAATTTTTAAATCTAAGTTTTAGAATTCTTTAAATTTAA
324 CATGTTTAGTTTTATTTTGATGCAACCAATTTTGAAATCTAAATTTTAAAATTCTTTAAATTTAA
*
3083082 AAATCAAATTTTACATAATATAGTTAGCTTTTTACGATTGAGTTTGTTTACAGTTTACTTTTATT
389 AAGTCAAATTTTACATAATATAGTTAGCTTTTTACGATTGAGTTTGTTTACAGTTTACTTTTATT
3083147 TTTTAGTTGACTTTTAATTTTGACTTTTAAAATAAATCTTTTTTTATTCAAATGACCTTAATAAC
454 TTTTAGTTGACTTTTAATTTTGACTTTTAAAATAAATCTTTTTTTATTCAAATGACCTTAATAAC
* *
3083212 CATTCACATTTCTTCAAGAGATTTATATAAGTAAATTTTCATCATACTCAAATTCTCAAGACTTA
519 CATTCACATTTCTTCAAGAGATTTATATGAGTCAATTTTCATCATACTCAAATTCTCAAGACTTA
* *
3083277 ATTTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAACTAAGCTCAAATACTTTGTTT
584 ATTTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAATTAAGCTCAAATGCTTTGTTT
3083342 AATCAAACTA
649 AATCAAACTA
* *
3083352 AACTACCTAAATAGAAGTGACCATTGCACACTTAATTGAATGGATAGGCAAAATTTCCAACATTT
1 AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTTCC-ACATTT
3083417 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAACGAT
65 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAACGAT
*
3083482 CCTGATGTATTTTTGCAAAAGTCCAATTGGAT-TTTTTTTCATAATAGAAATATCTCATAATGAT
130 CCTGATGTATTTTTGCAAAAGTCCAATTGGATATTTTTTTCATAATAGAAATATCTCCTAATGAT
* *
3083546 TTCTCATTGAAAAATTTGAAATCTTTTATCCTAAACCCATCGGATTAAACCTTTAAAAAATTTCT
195 TTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAAACCTTTAAAAAATTTCT
* * * * *
3083611 AACATCTTAATTTCTAAAGTTTTTTCATAACTTGATTTCGATTTTACTTTCTTAACTTAACGTTC
260 AACATCTTAATTTCTAAGGTTTTTTCATAACCTGATTTCGATTATACTTTCTTGACTTAAAGTTC
3083676 ATGTTTAGTTTTATTTTGATGCAACCAATTTTGAAATCTAAATTTTAAAATTCTTTAAATTTAAA
325 ATGTTTAGTTTTATTTTGATGCAACCAATTTTGAAATCTAAATTTTAAAATTCTTTAAATTTAAA
*
3083741 AGTCAAATTTTACATAATATAGTTAGCTTTTTACGATTGAGTTTGTTTGCAGTTTACTTTTATTT
390 AGTCAAATTTTACATAATATAGTTAGCTTTTTACGATTGAGTTTGTTTACAGTTTACTTTTATTT
3083806 TTTAGTTGACTTTTAATTTTGACTTTTAAAATAAATC-TTTTTTATTCAAATGACCTTAATAACC
455 TTTAGTTGACTTTTAATTTTGACTTTTAAAATAAATCTTTTTTTATTCAAATGACCTTAATAACC
* * *
3083870 ATTCAAATTTCTTCAAGAGATTTATATGAGTCAATTTTCACCATACTCAGATTCTCAAGACTTAA
520 ATTCACATTTCTTCAAGAGATTTATATGAGTCAATTTTCATCATACTCAAATTCTCAAGACTTAA
*
3083935 TTTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAATTAAGCTCAAATGCTTTGTTTC
585 TTTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAATTAAGCTCAAATGCTTTGTTTA
3084000 ATCAAACTA
650 ATCAAACTA
3084009 AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTTCTCACATTT
1 AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTTC-CACATTT
*
3084074 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTATAAAAATTTTTATAACGAT
65 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAACGAT
*
3084139 CCTGATGTATTTTTGCAAAAGTTCAATTGGATATTTTTTTCATAATAGAAATATCTCCTAATGAT
130 CCTGATGTATTTTTGCAAAAGTCCAATTGGATATTTTTTTCATAATAGAAATATCTCCTAATGAT
*
3084204 TTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAGACCTTTAAAAAATTTCT
195 TTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAAACCTTTAAAAAATTTCT
3084269 AACATCTTAATTTCTAAGGTTTTTTCATAACCTGATTTCGATTATACTTTCTTGACTTAAAGTTC
260 AACATCTTAATTTCTAAGGTTTTTTCATAACCTGATTTCGATTATACTTTCTTGACTTAAAGTTC
* *
3084334 ATGTTTAGTTTTATTTTGATGCAATCAATTTTGAAATCTGAATTTTAAAATTCTTTAAATTTAAA
325 ATGTTTAGTTTTATTTTGATGCAACCAATTTTGAAATCTAAATTTTAAAATTCTTTAAATTTAAA
* *
3084399 AGTCAAACTTTACATAATATAGTTGGCTTTTTACGATTGAGTTTGTTTACAGTTTACTTTTATTT
390 AGTCAAATTTTACATAATATAGTTAGCTTTTTACGATTGAGTTTGTTTACAGTTTACTTTTA-TT
*
3084464 TTTTAGTTGACTTTTAATTTTGACTTCTAAAATAAATCTTTTTTTATTCAAATGACCTTAATAAC
454 TTTTAGTTGACTTTTAATTTTGACTTTTAAAATAAATCTTTTTTTATTCAAATGACCTTAATAAC
3084529 CATTCACATTTCTTCAAGAGATTTATATGAGTCAATTTTCATCATACTCAAATTCTCAAGACTTA
519 CATTCACATTTCTTCAAGAGATTTATATGAGTCAATTTTCATCATACTCAAATTCTCAAGACTTA
3084594 ATTTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAATTAAGCTCAAATGCTTTGTTT
584 ATTTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAATTAAGCTCAAATGCTTTGTTT
3084659 AATCAAACTA
649 AATCAAACTA
*
3084669 AACTACCTAAATAGAAGTGACCATTGGACACTTAATTGAATGGATAAGCAAAATTTCCCACATTT
1 AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTT-CCACATTT
*
3084734 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAAAGAT
65 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAACGAT
** *
3084799 TTTGATGTATTTTTGCAAAAGTTCAATTGGATATTTTTTTTCATAATAGAAATATCTCCTAATGA
130 CCTGATGTATTTTTGCAAAAGTCCAATTGGATA-TTTTTTTCATAATAGAAATATCTCCTAATGA
* *
3084864 TTTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAGACCTTTAAAAAATTTT
194 TTTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAAACCTTTAAAAAATTTC
* * * *
3084929 TGACATCTTAATTTCTAAGGTTTTTTCATAACTTGATTTTGATTATATTTTCTTGACTTAAAGTT
259 TAACATCTTAATTTCTAAGGTTTTTTCATAACCTGATTTCGATTATACTTTCTTGACTTAAAGTT
* *
3084994 CATGTTTAGTTTTATTTTGATGCAACCAATTTTGAAAATCT-GAGTTTAAAA------AAATTTA
324 CATGTTTAGTTTTATTTTGATGCAACCAATTTTG-AAATCTAAATTTTAAAATTCTTTAAATTTA
3085052 AAAGTCAAATTTTACATA
388 AAAGTCAAATTTTACATA
3085070 TAATATGAGT
Statistics
Matches: 1637, Mismatches: 74, Indels: 19
0.95 0.04 0.01
Matches are distributed among these distances:
655 24 0.01
657 314 0.19
658 475 0.29
659 148 0.09
660 472 0.29
661 198 0.12
662 6 0.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (658 bp):
AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTTCCACATTTA
GCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAACGATC
CTGATGTATTTTTGCAAAAGTCCAATTGGATATTTTTTTCATAATAGAAATATCTCCTAATGATT
TCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAAACCTTTAAAAAATTTCTA
ACATCTTAATTTCTAAGGTTTTTTCATAACCTGATTTCGATTATACTTTCTTGACTTAAAGTTCA
TGTTTAGTTTTATTTTGATGCAACCAATTTTGAAATCTAAATTTTAAAATTCTTTAAATTTAAAA
GTCAAATTTTACATAATATAGTTAGCTTTTTACGATTGAGTTTGTTTACAGTTTACTTTTATTTT
TTAGTTGACTTTTAATTTTGACTTTTAAAATAAATCTTTTTTTATTCAAATGACCTTAATAACCA
TTCACATTTCTTCAAGAGATTTATATGAGTCAATTTTCATCATACTCAAATTCTCAAGACTTAAT
TTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAATTAAGCTCAAATGCTTTGTTTAA
TCAAACTA
Found at i:3084786 original size:660 final size:659
Alignment explanation
Indices: 3082692--3085069 Score: 4110
Period size: 660 Copynumber: 3.6 Consensus size: 659
3082682 CATTTCCACT
*
3082692 AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTTCCTACATTT
1 AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTTCCCACATTT
* * *
3082757 AGAACATATCTAATTAGGCCATGGCTATAGTAATGGATTAATCTTGTAAAAATTTTTATAACGAT
66 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAACGAT
* * *
3082822 CTTGATGTATTTTTGCAAAAGTCCAATTGAATATTTTTTTCATAATAGAAATATCTTCTAATGAT
131 CCTGATGTATTTTTGCAAAAGTCCAATTGGATATTTTTTTCATAATAGAAATATCTCCTAATGAT
*
3082887 TTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAAACCTTTAAAAAATTTTT
196 TTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAAACCTTTAAAAAATTTCT
* * * * * *
3082952 GACATCTTAATTTCTAAGGTTTTTTTTATAACCTAATTTTGATTGTAATTTCTTGACTTAAAGTT
261 AACATCTTAATTTCTAAGG-TTTTTTCATAACCTGATTTCGATTATACTTTCTTGACTTAAAGTT
* * *
3083017 CATGTTTAGTTTTATTTTGATGTAACCAATTTTTAAATCT-AAGTTTTAGAATTCTTTAAATTTA
325 CATGTTTAGTTTTATTTTGATGCAACCAATTTTGAAATCTGAA-TTTTAAAATTCTTTAAATTTA
*
3083081 AAAATCAAATTTTACATAATATAGTTAGCTTTTTACGATTGAGTTTGTTTACAGTTTACTTTTAT
389 AAAGTCAAATTTTACATAATATAGTTAGCTTTTTACGATTGAGTTTGTTTACAGTTTACTTTTAT
3083146 TTTTTAGTTGACTTTTAATTTTGACTTTTAAAATAAATCTTTTTTTATTCAAATGACCTTAATAA
454 TTTTTAGTTGACTTTTAATTTTGACTTTTAAAATAAATCTTTTTTTATTCAAATGACCTTAATAA
* *
3083211 CCATTCACATTTCTTCAAGAGATTTATATAAGTAAATTTTCATCATACTCAAATTCTCAAGACTT
519 CCATTCACATTTCTTCAAGAGATTTATATGAGTCAATTTTCATCATACTCAAATTCTCAAGACTT
* *
3083276 AATTTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAACTAAGCTCAAATACTTTGTT
584 AATTTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAATTAAGCTCAAATGCTTTGTT
3083341 TAATCAAACTA
649 TAATCAAACTA
* * *
3083352 AACTACCTAAATAGAAGTGACCATTGCACACTTAATTGAATGGATAGGCAAAATTTCCAACATTT
1 AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTTCCCACATTT
3083417 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAACGAT
66 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAACGAT
*
3083482 CCTGATGTATTTTTGCAAAAGTCCAATTGGAT-TTTTTTTCATAATAGAAATATCTCATAATGAT
131 CCTGATGTATTTTTGCAAAAGTCCAATTGGATATTTTTTTCATAATAGAAATATCTCCTAATGAT
* *
3083546 TTCTCATTGAAAAATTTGAAATCTTTTATCCTAAACCCATCGGATTAAACCTTTAAAAAATTTCT
196 TTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAAACCTTTAAAAAATTTCT
* * * * *
3083611 AACATCTTAATTTCTAAAGTTTTTTCATAACTTGATTTCGATTTTACTTTCTTAACTTAACGTTC
261 AACATCTTAATTTCTAAGGTTTTTTCATAACCTGATTTCGATTATACTTTCTTGACTTAAAGTTC
*
3083676 ATGTTTAGTTTTATTTTGATGCAACCAATTTTGAAATCTAAATTTTAAAATTCTTTAAATTTAAA
326 ATGTTTAGTTTTATTTTGATGCAACCAATTTTGAAATCTGAATTTTAAAATTCTTTAAATTTAAA
*
3083741 AGTCAAATTTTACATAATATAGTTAGCTTTTTACGATTGAGTTTGTTTGCAGTTTACTTTTATTT
391 AGTCAAATTTTACATAATATAGTTAGCTTTTTACGATTGAGTTTGTTTACAGTTTACTTTTATTT
3083806 TTTAGTTGACTTTTAATTTTGACTTTTAAAATAAATC-TTTTTTATTCAAATGACCTTAATAACC
456 TTTAGTTGACTTTTAATTTTGACTTTTAAAATAAATCTTTTTTTATTCAAATGACCTTAATAACC
* * *
3083870 ATTCAAATTTCTTCAAGAGATTTATATGAGTCAATTTTCACCATACTCAGATTCTCAAGACTTAA
521 ATTCACATTTCTTCAAGAGATTTATATGAGTCAATTTTCATCATACTCAAATTCTCAAGACTTAA
*
3083935 TTTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAATTAAGCTCAAATGCTTTGTTTC
586 TTTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAATTAAGCTCAAATGCTTTGTTTA
3084000 ATCAAACTA
651 ATCAAACTA
*
3084009 AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTTCTCACATTT
1 AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTTCCCACATTT
*
3084074 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTATAAAAATTTTTATAACGAT
66 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAACGAT
*
3084139 CCTGATGTATTTTTGCAAAAGTTCAATTGGATATTTTTTTCATAATAGAAATATCTCCTAATGAT
131 CCTGATGTATTTTTGCAAAAGTCCAATTGGATATTTTTTTCATAATAGAAATATCTCCTAATGAT
*
3084204 TTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAGACCTTTAAAAAATTTCT
196 TTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAAACCTTTAAAAAATTTCT
3084269 AACATCTTAATTTCTAAGGTTTTTTCATAACCTGATTTCGATTATACTTTCTTGACTTAAAGTTC
261 AACATCTTAATTTCTAAGGTTTTTTCATAACCTGATTTCGATTATACTTTCTTGACTTAAAGTTC
*
3084334 ATGTTTAGTTTTATTTTGATGCAATCAATTTTGAAATCTGAATTTTAAAATTCTTTAAATTTAAA
326 ATGTTTAGTTTTATTTTGATGCAACCAATTTTGAAATCTGAATTTTAAAATTCTTTAAATTTAAA
* *
3084399 AGTCAAACTTTACATAATATAGTTGGCTTTTTACGATTGAGTTTGTTTACAGTTTACTTTTATTT
391 AGTCAAATTTTACATAATATAGTTAGCTTTTTACGATTGAGTTTGTTTACAGTTTACTTTTA-TT
*
3084464 TTTTAGTTGACTTTTAATTTTGACTTCTAAAATAAATCTTTTTTTATTCAAATGACCTTAATAAC
455 TTTTAGTTGACTTTTAATTTTGACTTTTAAAATAAATCTTTTTTTATTCAAATGACCTTAATAAC
3084529 CATTCACATTTCTTCAAGAGATTTATATGAGTCAATTTTCATCATACTCAAATTCTCAAGACTTA
520 CATTCACATTTCTTCAAGAGATTTATATGAGTCAATTTTCATCATACTCAAATTCTCAAGACTTA
3084594 ATTTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAATTAAGCTCAAATGCTTTGTTT
585 ATTTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAATTAAGCTCAAATGCTTTGTTT
3084659 AATCAAACTA
650 AATCAAACTA
*
3084669 AACTACCTAAATAGAAGTGACCATTGGACACTTAATTGAATGGATAAGCAAAATTTCCCACATTT
1 AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTTCCCACATTT
*
3084734 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAAAGAT
66 AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAACGAT
** *
3084799 TTTGATGTATTTTTGCAAAAGTTCAATTGGATATTTTTTTTCATAATAGAAATATCTCCTAATGA
131 CCTGATGTATTTTTGCAAAAGTCCAATTGGATA-TTTTTTTCATAATAGAAATATCTCCTAATGA
* *
3084864 TTTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAGACCTTTAAAAAATTTT
195 TTTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAAACCTTTAAAAAATTTC
* * * *
3084929 TGACATCTTAATTTCTAAGGTTTTTTCATAACTTGATTTTGATTATATTTTCTTGACTTAAAGTT
260 TAACATCTTAATTTCTAAGGTTTTTTCATAACCTGATTTCGATTATACTTTCTTGACTTAAAGTT
*
3084994 CATGTTTAGTTTTATTTTGATGCAACCAATTTTGAAAATCTG-AGTTTAAAA------AAATTTA
325 CATGTTTAGTTTTATTTTGATGCAACCAATTTTG-AAATCTGAATTTTAAAATTCTTTAAATTTA
3085052 AAAGTCAAATTTTACATA
389 AAAGTCAAATTTTACATA
3085070 TAATATGAGT
Statistics
Matches: 1637, Mismatches: 75, Indels: 17
0.95 0.04 0.01
Matches are distributed among these distances:
655 24 0.01
657 314 0.19
658 472 0.29
659 150 0.09
660 473 0.29
661 197 0.12
662 7 0.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (659 bp):
AACTACCTAAATAGAAGTGACCATTGTACACTTAATTGAATGGATAAGCAAAATTTCCCACATTT
AGCACATGTCTAATTAGGCCATGGCTATGGTAATGGATTAATCTTGTAAAAATTTTTATAACGAT
CCTGATGTATTTTTGCAAAAGTCCAATTGGATATTTTTTTCATAATAGAAATATCTCCTAATGAT
TTCTCATTGAAAAAATTGAAATCTTTTATCCCAAACCCATCGGATTAAACCTTTAAAAAATTTCT
AACATCTTAATTTCTAAGGTTTTTTCATAACCTGATTTCGATTATACTTTCTTGACTTAAAGTTC
ATGTTTAGTTTTATTTTGATGCAACCAATTTTGAAATCTGAATTTTAAAATTCTTTAAATTTAAA
AGTCAAATTTTACATAATATAGTTAGCTTTTTACGATTGAGTTTGTTTACAGTTTACTTTTATTT
TTTAGTTGACTTTTAATTTTGACTTTTAAAATAAATCTTTTTTTATTCAAATGACCTTAATAACC
ATTCACATTTCTTCAAGAGATTTATATGAGTCAATTTTCATCATACTCAAATTCTCAAGACTTAA
TTTCAGTTTTTCAAATCTAGCACTTACTCTCTAAATTAAATAATTAAGCTCAAATGCTTTGTTTA
ATCAAACTA
Found at i:3087235 original size:8 final size:8
Alignment explanation
Indices: 3087222--3087358 Score: 62
Period size: 8 Copynumber: 17.5 Consensus size: 8
3087212 ATTTAAAATA
3087222 TTATATAT
1 TTATATAT
3087230 TTATATAAAT
1 TTATAT--AT
3087240 ATTA-ATAT
1 -TTATATAT
*
3087248 ATTA-AAAT
1 -TTATATAT
3087256 TTA--TAT
1 TTATATAT
3087262 T-ATATAT
1 TTATATAT
* *
3087269 ATATATTT
1 TTATATAT
3087277 TTATATAT
1 TTATATAT
3087285 TTATATAT
1 TTATATAT
*
3087293 TCATATTAT
1 TTATA-TAT
3087302 ATTA-ATAT
1 -TTATATAT
3087310 TTATAT-T
1 TTATATAT
*
3087317 ATATTATAT
1 TTA-TATAT
3087326 TTA-A-A-
1 TTATATAT
*
3087331 TTATTTTAT
1 TTA-TATAT
3087340 TT-TATAT
1 TTATATAT
*
3087347 TTATATAA
1 TTATATAT
3087355 TTAT
1 TTAT
3087359 TCTGGACCAA
Statistics
Matches: 100, Mismatches: 13, Indels: 32
0.69 0.09 0.22
Matches are distributed among these distances:
5 4 0.04
6 4 0.04
7 19 0.19
8 55 0.55
9 9 0.09
10 6 0.06
11 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (8 bp):
TTATATAT
Found at i:3087283 original size:10 final size:10
Alignment explanation
Indices: 3087223--3087353 Score: 73
Period size: 10 Copynumber: 13.4 Consensus size: 10
3087213 TTTAAAATAT
3087223 TATATATTTA
1 TATATATTTA
*
3087233 TATAAATATTA
1 TATATAT-TTA
3087244 -ATATA-TTA
1 TATATATTTA
3087252 -A-A-ATTTA
1 TATATATTTA
*
3087259 TAT-TATATA
1 TATATATTTA
*
3087268 TATATATTTT
1 TATATATTTA
3087278 TATATA-TT-
1 TATATATTTA
*
3087286 TATATATTCA
1 TATATATTTA
*
3087296 TATTATATTAA
1 TA-TATATTTA
*
3087307 TATTTATATTA
1 TATATAT-TTA
3087318 TATTATATTTA
1 TA-TATATTTA
*
3087329 AAT-TATTTTA
1 TATATA-TTTA
*
3087339 TTTTATATTTA
1 -TATATATTTA
3087350 TATA
1 TATA
3087354 ATTATTCTGG
Statistics
Matches: 93, Mismatches: 14, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
6 1 0.01
7 4 0.04
8 11 0.12
9 12 0.13
10 34 0.37
11 25 0.27
12 6 0.06
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (10 bp):
TATATATTTA
Found at i:3087304 original size:11 final size:10
Alignment explanation
Indices: 3087219--3087352 Score: 70
Period size: 11 Copynumber: 13.4 Consensus size: 10
3087209 CATATTTAAA
3087219 ATATTATA-T
1 ATATTATATT
*
3087228 AT-TTATATAA
1 ATATTATAT-T
3087238 ATATTA-A-T
1 ATATTATATT
*
3087246 ATATTAAAATTT
1 ATATT-ATA-TT
3087258 ATATTATA-T
1 ATATTATATT
3087267 ATA-TATATT
1 ATATTATATT
3087276 -T-TTATA-T
1 ATATTATATT
*
3087283 ATTTATATATT
1 ATAT-TATATT
3087294 CATATTATATT
1 -ATATTATATT
3087305 AATATTTATATT
1 -ATA-TTATATT
3087317 ATATTATATTT
1 ATATTATA-TT
* *
3087328 AAATTATTTT
1 ATATTATATT
*
3087338 ATTTTATATTT
1 ATATTATA-TT
3087349 ATAT
1 ATAT
3087353 AATTATTCTG
Statistics
Matches: 97, Mismatches: 11, Indels: 32
0.69 0.08 0.23
Matches are distributed among these distances:
7 1 0.01
8 20 0.21
9 9 0.09
10 20 0.21
11 31 0.32
12 16 0.16
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (10 bp):
ATATTATATT
Found at i:3087315 original size:41 final size:38
Alignment explanation
Indices: 3087226--3087352 Score: 93
Period size: 41 Copynumber: 3.3 Consensus size: 38
3087216 AAAATATTAT
**
3087226 ATATTTATATAAATATTAATATATTAAA--AT-TTATATTA
1 ATATTTATATTTATATT-ATAT-TTAAATTATATTAT-TTA
* *
3087264 TATATATATATTTTTA-TATATTTATATATTCATATTATATTA
1 -ATATTTATATTTATATTATATTTA-A-ATT-ATATTAT-TTA
* *
3087306 ATATTTATA-TTATATTATATTTAAATTATTTTATTTT
1 ATATTTATATTTATATTATATTTAAATTATATTATTTA
3087343 ATATTTATAT
1 ATATTTATAT
3087353 AATTATTCTG
Statistics
Matches: 72, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
36 3 0.04
37 16 0.22
38 8 0.11
39 14 0.19
40 5 0.07
41 18 0.25
42 8 0.11
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (38 bp):
ATATTTATATTTATATTATATTTAAATTATATTATTTA
Found at i:3087328 original size:16 final size:16
Alignment explanation
Indices: 3087256--3087352 Score: 87
Period size: 16 Copynumber: 6.1 Consensus size: 16
3087246 ATATTAAAAT
3087256 TTATATTATATATATATA
1 TTATATT-TATAT-TATA
3087274 TT-T-TTATATATT-TA
1 TTATATT-TATATTATA
*
3087288 -TATATTCATATTATA
1 TTATATTTATATTATA
3087303 TTAATATTTATATTATA
1 TT-ATATTTATATTATA
* *
3087320 TTATATTTAAATTATT
1 TTATATTTATATTATA
3087336 TTAT-TTTATATTTATA
1 TTATATTTATA-TTATA
3087352 T
1 T
3087353 AATTATTCTG
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
13 1 0.01
14 8 0.12
15 10 0.15
16 30 0.45
17 16 0.24
18 2 0.03
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATATTTATATTATA
Found at i:3087347 original size:54 final size:54
Alignment explanation
Indices: 3087220--3087325 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
3087210 ATATTTAAAA
* *
3087220 TATTATATATTTATATAAAT-ATTAATATATTAAAATTTATATTATATATATATAT
1 TATTATATATTTATAT-ATTCA-TATTATATTAAAATTTATATTATATATATATAT
* *
3087275 TTTTATATATTTATATATTCATATTATATTAATATTTATATTATAT-TATAT
1 TATTATATATTTATATATTCATATTATATTAAAATTTATATTATATATATAT
3087326 TTAAATTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
53 5 0.11
54 25 0.54
55 16 0.35
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (54 bp):
TATTATATATTTATATATTCATATTATATTAAAATTTATATTATATATATATAT
Found at i:3087351 original size:6 final size:6
Alignment explanation
Indices: 3087219--3087352 Score: 86
Period size: 6 Copynumber: 22.7 Consensus size: 6
3087209 CATATTTAAA
** * * *
3087219 ATATTAT ATATTT ATATAA ATATTAAT ATATTA AAATTT ATATTAT ATATAT
1 ATATT-T ATATTT ATATTT ATATT--T ATATTT ATATTT ATATT-T ATATTT
* *
3087271 ATATTT -T-TAT ATATTT ATATATT CATA-TT ATATTA ATATTT ATA-TT
1 ATATTT ATATTT ATATTT ATAT-TT -ATATTT ATATTT ATATTT ATATTT
*
3087317 ATA-TT ATATTT A-AATT AT-TTT AT-TTT ATATTT ATAT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATAT
3087353 AATTATTCTG
Statistics
Matches: 100, Mismatches: 16, Indels: 23
0.72 0.12 0.17
Matches are distributed among these distances:
4 2 0.02
5 28 0.28
6 50 0.50
7 12 0.12
8 8 0.08
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (6 bp):
ATATTT
Found at i:3087358 original size:35 final size:36
Alignment explanation
Indices: 3087202--3087358 Score: 110
Period size: 35 Copynumber: 4.3 Consensus size: 36
3087192 ATATAATGTG
* * * **
3087202 ATATAATCATATTTAAAATATTATATATTTATATAA
1 ATATAATTATATTTAAATTATTTTATATTTATATTT
* *
3087238 ATATTAA-TATATTAAAATTTATATTATATATATATATTT
1 ATA-TAATTATATTTAAA-TTAT-TT-TATATTTATATTT
* *
3087277 -T-T-A-TATATTTATATATTCATATTATATTAATATTT
1 ATATAATTATATTTA-A-ATT-ATTTTATATTTATATTT
3087312 ATATTATATTATATTTAAATTATTTTAT-TTTATATTT
1 ATA-TA-ATTATATTTAAATTATTTTATATTTATATTT
3087349 ATATAATTAT
1 ATATAATTAT
3087359 TCTGGACCAA
Statistics
Matches: 95, Mismatches: 13, Indels: 27
0.70 0.10 0.20
Matches are distributed among these distances:
35 24 0.25
36 19 0.20
37 20 0.21
38 9 0.09
39 13 0.14
40 2 0.02
41 8 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (36 bp):
ATATAATTATATTTAAATTATTTTATATTTATATTT
Found at i:3087628 original size:2 final size:2
Alignment explanation
Indices: 3087623--3087665 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
3087613 ACACACACAC
3087623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
3087666 TGCACTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.