Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, whole genome shotgun sequence
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: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 116 of 129
Found at i:19436727 original size:30 final size:29
Alignment explanation
Indices: 19436668--19436728 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
19436658 TAGTTTTTAA
* *
19436668 AAAATTCAAAAATAAAATGTTTTGTTTTC
1 AAAATTCAAAAATAAAATGATTTGATTTC
* *
19436697 AAAATTCAAAATTCGAAATGATTTGATTTC
1 AAAATTCAAAAAT-AAAATGATTTGATTTC
19436727 AA
1 AA
19436729 GAAAAATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (29 bp):
AAAATTCAAAAATAAAATGATTTGATTTC
Found at i:19438029 original size:19 final size:19
Alignment explanation
Indices: 19438001--19438058 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 19
19437991 TTTCAAGTAT
*
19438001 TTGATTAATAAAAAATTAA
1 TTGATCAATAAAAAATTAA
*
19438020 TTGATCAATAAAAAAATGATTTA
1 TTGATCAAT--AAAAA--ATTAA
19438043 TTGATCAATAAAAAAT
1 TTGATCAATAAAAAAT
19438059 AAGATCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 10 0.30
21 10 0.30
23 13 0.39
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.34
Consensus pattern (19 bp):
TTGATCAATAAAAAATTAA
Found at i:19438155 original size:16 final size:16
Alignment explanation
Indices: 19438125--19438172 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
19438115 AATTTAACAA
19438125 GAAAAAAA-TATTTTAT
1 GAAAAAAACTA-TTTAT
*
19438141 GAAAAAAACTGTTTAT
1 GAAAAAAACTATTTAT
**
19438157 GAGTAAAACTATTTAT
1 GAAAAAAACTATTTAT
19438173 TAATGCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 26 0.96
17 1 0.04
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.35
Consensus pattern (16 bp):
GAAAAAAACTATTTAT
Found at i:19438235 original size:30 final size:30
Alignment explanation
Indices: 19438199--19438285 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
19438189 AATTTTACTT
19438199 ATAAATAATATTATATTAATAAATAATATA
1 ATAAATAATATTATATTAATAAATAATATA
* *
19438229 ATAAATATTATTA-ATT--TAATTAATA-A
1 ATAAATAATATTATATTAATAAATAATATA
* *
19438255 ATATTATAATAATATATTAATAAATAATATA
1 ATA-AATAATATTATATTAATAAATAATATA
19438286 TTAATATCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
26 4 0.09
27 15 0.33
28 3 0.07
29 3 0.07
30 20 0.43
31 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATAAATAATATTATATTAATAAATAATATA
Found at i:19438251 original size:34 final size:37
Alignment explanation
Indices: 19438204--19438308 Score: 119
Period size: 34 Copynumber: 2.9 Consensus size: 37
19438194 TACTTATAAA
19438204 TAATATTATATTAATAAATAATATAATAA-ATATTAT
1 TAATATTATATTAATAAATAATATAATAATATATTAT
*
19438240 TAAT-TTA-ATTAATAAATATTATAATAATATATTAAT
1 TAATATTATATTAATAAATAATATAATAATATATT-AT
* * **
19438276 AAATAATATATTAATATCTTAATA-AATAATATA
1 TAATATTATATTAATA-AATAATATAATAATATA
19438309 AAGAGTAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
34 19 0.33
35 8 0.14
36 9 0.16
37 2 0.03
38 16 0.28
39 4 0.07
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (37 bp):
TAATATTATATTAATAAATAATATAATAATATATTAT
Found at i:19438292 original size:23 final size:23
Alignment explanation
Indices: 19438205--19438308 Score: 111
Period size: 23 Copynumber: 4.4 Consensus size: 23
19438195 ACTTATAAAT
* *
19438205 AATATTATATTAATA-AATAATA
1 AATAATATATTAATATATTAATA
*
19438227 TAATAAATATTATTAATTTAATTAATA
1 -AAT-AATA-TATTAATAT-ATTAATA
* *
19438254 AATATTATAATAATATATTAATA
1 AATAATATATTAATATATTAATA
*
19438277 AATAATATATTAATATCTTAATA
1 AATAATATATTAATATATTAATA
19438300 AATAATATA
1 AATAATATA
19438309 AAGAGTAATA
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
23 39 0.57
24 10 0.15
25 10 0.15
26 3 0.04
27 6 0.09
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (23 bp):
AATAATATATTAATATATTAATA
Found at i:19438307 original size:15 final size:15
Alignment explanation
Indices: 19438205--19438291 Score: 78
Period size: 15 Copynumber: 6.0 Consensus size: 15
19438195 ACTTATAAAT
*
19438205 AATATTATATTAATA
1 AATAATATATTAATA
19438220 AAT-A-ATA-TAATA
1 AATAATATATTAATA
* *
19438232 AATATTATTAATTTAATT
1 AATAATA-T-A-TTAATA
19438250 AATAA-ATATT-AT-
1 AATAATATATTAATA
19438262 AATAATATATTAATA
1 AATAATATATTAATA
19438277 AATAATATATTAATA
1 AATAATATATTAATA
19438292 TCTTAATAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
12 13 0.22
13 10 0.17
14 5 0.08
15 20 0.34
16 2 0.03
17 1 0.02
18 8 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATAATATATTAATA
Found at i:19438368 original size:19 final size:18
Alignment explanation
Indices: 19438334--19438424 Score: 66
Period size: 19 Copynumber: 5.2 Consensus size: 18
19438324 TTTTATTTTA
* *
19438334 AATATTTTTATGTTAACAT
1 AATATTTTAATATTAA-AT
19438353 AATATTTTAATATTAAAT
1 AATATTTTAATATTAAAT
* *
19438371 ATTATTATTAA-AATATAAT
1 AATATT-TTAATATTA-AAT
*
19438390 TAT-TTTTAATATT-AAT
1 AATATTTTAATATTAAAT
*
19438406 -A-ATTTTAATAATAAAT
1 AATATTTTAATATTAAAT
19438422 AAT
1 AAT
19438425 TTCAGTATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
15 10 0.18
16 6 0.11
17 5 0.09
18 14 0.25
19 22 0.39
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (18 bp):
AATATTTTAATATTAAAT
Found at i:19438369 original size:34 final size:36
Alignment explanation
Indices: 19438331--19438425 Score: 92
Period size: 34 Copynumber: 2.7 Consensus size: 36
19438321 TAGTTTTATT
*
19438331 TTAAATATTTTTATGT-TAACATAA-TA-TTTTAATA
1 TTAAATATTTTTAT-TAAAACATAATTATTTTTAATA
* *
19438365 TTAAATATTATTATTAAAATATAATTATTTTTAATA
1 TTAAATATTTTTATTAAAACATAATTATTTTTAATA
* *
19438401 TT-AATAATTTTAATAATAA-ATAATT
1 TTAAATATTTTTATTAA-AACATAATT
19438426 TCAGTATATT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
33 1 0.02
34 19 0.37
35 19 0.37
36 12 0.24
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (36 bp):
TTAAATATTTTTATTAAAACATAATTATTTTTAATA
Found at i:19438410 original size:16 final size:16
Alignment explanation
Indices: 19438351--19438426 Score: 55
Period size: 16 Copynumber: 4.4 Consensus size: 16
19438341 TTATGTTAAC
19438351 ATAATATTTTAATATTAA
1 ATAAT-TTTTAATATT-A
* *
19438369 ATATTATTATTAAAATATA
1 ATA--ATTTTTAATAT-TA
*
19438388 ATTATTTTTAATATTA
1 ATAATTTTTAATATTA
*
19438404 ATAA-TTTTAATAATAA
1 ATAATTTTTAAT-ATTA
19438420 ATAATTT
1 ATAATTT
19438427 CAGTATATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
15 7 0.15
16 12 0.26
17 11 0.24
18 3 0.07
19 10 0.22
20 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATAATTTTTAATATTA
Found at i:19438616 original size:14 final size:14
Alignment explanation
Indices: 19438586--19438614 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19438576 TAAATATTTG
19438586 TTAAAAATTATCTT
1 TTAAAAATTATCTT
19438600 TTAAAAATTA-CTT
1 TTAAAAATTATCTT
19438613 TT
1 TT
19438615 TACGAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAAAAATTATCTT
Found at i:19442385 original size:16 final size:16
Alignment explanation
Indices: 19442366--19442400 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19442356 GCAAGTGTCC
*
19442366 CGTGACTGAAGTCAAA
1 CGTGACAGAAGTCAAA
*
19442382 CGTGACAGGAGTCAAA
1 CGTGACAGAAGTCAAA
19442398 CGT
1 CGT
19442401 TTTTCAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.20, G:0.29, T:0.17
Consensus pattern (16 bp):
CGTGACAGAAGTCAAA
Found at i:19448190 original size:14 final size:15
Alignment explanation
Indices: 19448160--19448196 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
19448150 TTCAATCTCT
19448160 TAAATTATAATACAA
1 TAAATTATAATACAA
*
19448175 TAATTTATAATA-AA
1 TAAATTATAATACAA
19448189 TAAATTAT
1 TAAATTAT
19448197 TCAATCTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATTATAATACAA
Found at i:19448433 original size:20 final size:20
Alignment explanation
Indices: 19448408--19448445 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19448398 ATCAATAAAT
*
19448408 TAAATAATATTATTTATTTA
1 TAAATAATATTAATTATTTA
19448428 TAAATAATATTAATTATT
1 TAAATAATATTAATTATT
19448446 AAAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAATAATATTAATTATTTA
Found at i:19448448 original size:17 final size:17
Alignment explanation
Indices: 19448406--19448448 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 17
19448396 TTATCAATAA
*
19448406 ATTAAATAATATTATTT
1 ATTAAATAATATTAATT
19448423 ATTTATAAATAATATTAATT
1 A--T-TAAATAATATTAATT
19448443 ATTAAA
1 ATTAAA
19448449 ATAAATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
17 5 0.23
18 1 0.05
19 1 0.05
20 15 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAAATAATATTAATT
Found at i:19448476 original size:26 final size:28
Alignment explanation
Indices: 19448426--19448477 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
19448416 ATTATTTATT
*
19448426 TATAAATAATATTAATTATTAAAATAAA
1 TATAAATAAAATTAATTATTAAAATAAA
*
19448454 TATAAA-AAAATT-ATTTTTAAAATA
1 TATAAATAAAATTAATTATTAAAATA
19448478 TTTATTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.50
27 5 0.23
28 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TATAAATAAAATTAATTATTAAAATAAA
Found at i:19448521 original size:31 final size:31
Alignment explanation
Indices: 19448477--19448545 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
19448467 TTTTTAAAAT
*
19448477 ATTTATTTCATTAATTAAATAATATCATTTA
1 ATTTATTTCATTAATAAAATAATATCATTTA
*
19448508 ATTTACTTT-ATTAATAAAATAATATTATTTA
1 ATTTA-TTTCATTAATAAAATAATATCATTTA
19448539 ATTTATT
1 ATTTATT
19448546 AATAACACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 2 0.06
31 30 0.86
32 3 0.09
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (31 bp):
ATTTATTTCATTAATAAAATAATATCATTTA
Found at i:19449146 original size:23 final size:23
Alignment explanation
Indices: 19449098--19449146 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
19449088 AAATTAATTG
* *
19449098 AATTAATTTTAAATTTTTTAATA
1 AATTAATTTTAAATGTGTTAATA
*
19449121 AATTACTTTTGAAATGTGTTAA-A
1 AATTAATTTT-AAATGTGTTAATA
19449144 AAT
1 AAT
19449147 CTAAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (23 bp):
AATTAATTTTAAATGTGTTAATA
Found at i:19449449 original size:24 final size:25
Alignment explanation
Indices: 19449418--19449467 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
19449408 ATGCTTTACC
19449418 AAAGCATAA-TTC-AATATTGTTTAA
1 AAAGCATAAGTTCAAAT-TTGTTTAA
19449442 AAAGCATAAGTTCAAATTTGTTTAA
1 AAAGCATAAGTTCAAATTTGTTTAA
19449467 A
1 A
19449468 TTTAGTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.38
25 12 0.50
26 3 0.12
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (25 bp):
AAAGCATAAGTTCAAATTTGTTTAA
Found at i:19449504 original size:38 final size:41
Alignment explanation
Indices: 19449436--19449515 Score: 114
Period size: 39 Copynumber: 2.0 Consensus size: 41
19449426 ATTCAATATT
*
19449436 GTTTAAAAAGCATAAGTTCAAATTTGTTT-AAAT-TTAGTA
1 GTTTAAAAAGCATAAGTTCAAATTTCTTTAAAATATTAGTA
19449475 GTTTAAAAAGCATAA-TTC-AATATTCTTTAAAATATTAGTA
1 GTTTAAAAAGCATAAGTTCAAAT-TTCTTTAAAATATTAGTA
19449515 G
1 G
19449516 GTTTTTTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
37 3 0.08
38 8 0.22
39 19 0.51
40 7 0.19
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.40
Consensus pattern (41 bp):
GTTTAAAAAGCATAAGTTCAAATTTCTTTAAAATATTAGTA
Found at i:19456472 original size:2 final size:2
Alignment explanation
Indices: 19456465--19456572 Score: 108
Period size: 2 Copynumber: 54.0 Consensus size: 2
19456455 TTGTATACAC
* * * * *
19456465 AT AT AT AT AC AT AT AT GT AT AT AT AT GT GT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * **
19456507 AT AT GT AT AC AT AC AT AT AT AT GT AT AC AT AT AT AT AT GC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19456549 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
19456573 CGAAACACCT
Statistics
Matches: 86, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (2 bp):
AT
Found at i:19456486 original size:18 final size:16
Alignment explanation
Indices: 19456466--19456572 Score: 119
Period size: 16 Copynumber: 6.7 Consensus size: 16
19456456 TGTATACACA
*
19456466 TATATATACATATATG
1 TATATATATATATATG
* *
19456482 --TATATATATGTGTG
1 TATATATATATATATG
19456496 TATATATATATATATG
1 TATATATATATATATG
*
19456512 TATACATACATATATATG
1 TAT--ATATATATATATG
*
19456530 TATACATATATATATG
1 TATATATATATATATG
* *
19456546 CATATATATATATATA
1 TATATATATATATATG
19456562 TATATATATAT
1 TATATATATAT
19456573 CGAAACACCT
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
14 11 0.15
16 49 0.65
18 15 0.20
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.46
Consensus pattern (16 bp):
TATATATATATATATG
Found at i:19464967 original size:172 final size:172
Alignment explanation
Indices: 19464664--19464991 Score: 439
Period size: 172 Copynumber: 1.9 Consensus size: 172
19464654 ATACTTCTGT
19464664 TAAAAAAACTATGAACAACTATTGCACTAGTAGCAGGAACACATAAATCATATATAAATGAATTA
1 TAAAAAAACTATGAACAACTATTGCACTAGTAGCAGGAACAC--AAATCATATATAAATGAATTA
* * * * * *
19464729 TAAACAAAAATATGAATCACACCTGGTGTTGTCAGTTGATTTCCTTTTAGAAAACCTAAAATCAT
64 TAAAAAAAAAAATGAATAAAACCTGGTGTTCTCAGTTGATTTCCTCTTAGAAAACCTAAAATCAT
*
19464794 GGATACCAAGAAG-AAAGCACTTAGGAGTTAGGATTAGTTAAAAA
129 GGACACCAAGAAGAAAAG-ACTTAGGAGTTAGGATTAGTTAAAAA
* * * *
19464838 TAAAAAAACTATGAATAACTATTGCCCTAGTGATCA-GAACAC-AATCATATACATGAATGAATT
1 TAAAAAAACTATGAACAACTATTGCACTAGT-AGCAGGAACACAAATCATAT--ATAAATGAATT
* * *
19464901 A-AAAAAAAAAAATGAATAAAACCTGTTGTTCTCAGTTGATTTGCTCTTAGAAAACCTGAAATCA
63 ATAAAAAAAAAAATGAATAAAACCTGGTGTTCTCAGTTGATTTCCTCTTAGAAAACCTAAAATCA
*
19464965 TGGACGCCAAGAAGAAAAGACTTAGGA
128 TGGACACCAAGAAGAAAAGACTTAGGA
19464992 TTTGTGAATG
Statistics
Matches: 135, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
171 8 0.06
172 74 0.55
173 15 0.11
174 35 0.26
175 3 0.02
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (172 bp):
TAAAAAAACTATGAACAACTATTGCACTAGTAGCAGGAACACAAATCATATATAAATGAATTATA
AAAAAAAAAATGAATAAAACCTGGTGTTCTCAGTTGATTTCCTCTTAGAAAACCTAAAATCATGG
ACACCAAGAAGAAAAGACTTAGGAGTTAGGATTAGTTAAAAA
Found at i:19470033 original size:2 final size:2
Alignment explanation
Indices: 19470026--19470065 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
19470016 GTCAACGTTT
19470026 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
19470066 AAATCTTACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19471773 original size:27 final size:26
Alignment explanation
Indices: 19471722--19471774 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
19471712 CATTGGGTAA
**
19471722 AATTCATAAAATTTTTAATTTAAAAT
1 AATTCATAAAATTTTTAATAAAAAAT
19471748 AATTCAATACAAA-TTTTAATAAAAAAT
1 AATTC-ATA-AAATTTTTAATAAAAAAT
19471775 TTAATTTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.22
27 15 0.65
28 3 0.13
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.40
Consensus pattern (26 bp):
AATTCATAAAATTTTTAATAAAAAAT
Found at i:19474872 original size:18 final size:18
Alignment explanation
Indices: 19474849--19474888 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
19474839 TTAATAAAAT
* *
19474849 ATTAAAATTTTAATTTTA
1 ATTAAAATTTAAATTTAA
19474867 ATTAAAATTTAAATTTAA
1 ATTAAAATTTAAATTTAA
19474885 ATTA
1 ATTA
19474889 TAATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAAAATTTAAATTTAA
Found at i:19476334 original size:29 final size:29
Alignment explanation
Indices: 19476270--19476328 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
19476260 AATTATATTG
* * *
19476270 AAATGTTTAATGTGATATATAAATTTTAA
1 AAATATTTAATGTGATATAAAAATTATAA
19476299 AAATATTTAATGTGATATAAAAATTATAA
1 AAATATTTAATGTGATATAAAAATTATAA
19476328 A
1 A
19476329 TTTATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (29 bp):
AAATATTTAATGTGATATAAAAATTATAA
Found at i:19477517 original size:2 final size:2
Alignment explanation
Indices: 19477510--19477548 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19477500 GAAGGAAGGA
19477510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19477549 GATAGATTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19484236 original size:21 final size:21
Alignment explanation
Indices: 19484212--19484251 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19484202 AATAACATAA
19484212 AAATAATATATA-ATAATAAAG
1 AAATAATA-ATAGATAATAAAG
*
19484233 AAATAGTAATAGATAATAA
1 AAATAATAATAGATAATAA
19484252 TTAATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (21 bp):
AAATAATAATAGATAATAAAG
Found at i:19485409 original size:23 final size:23
Alignment explanation
Indices: 19485381--19485424 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19485371 CTTTCTTTTC
19485381 CTTTTCCTTTATATCTTTTTCGA
1 CTTTTCCTTTATATCTTTTTCGA
* * *
19485404 CTTTTCTTTTCTTTCTTTTTC
1 CTTTTCCTTTATATCTTTTTC
19485425 TCTCAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.07, C:0.23, G:0.02, T:0.68
Consensus pattern (23 bp):
CTTTTCCTTTATATCTTTTTCGA
Found at i:19497632 original size:17 final size:17
Alignment explanation
Indices: 19497600--19497640 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
19497590 TTATTAACAT
*
19497600 ACAAATAACCACAGGAAA
1 ACAAA-AACAACAGGAAA
19497618 ACAAAAACAACAGGAAA
1 ACAAAAACAACAGGAAA
*
19497635 AGAAAA
1 ACAAAA
19497641 CTAAATCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.68, C:0.17, G:0.12, T:0.02
Consensus pattern (17 bp):
ACAAAAACAACAGGAAA
Found at i:19498157 original size:17 final size:14
Alignment explanation
Indices: 19498134--19498168 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
19498124 ATAATTTTTT
* *
19498134 ATTATAATTAAATA
1 ATTATAATAAAAAA
19498148 ATTATAATAAAAAA
1 ATTATAATAAAAAA
19498162 ATTATAA
1 ATTATAA
19498169 ATGATATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTATAATAAAAAA
Found at i:19498532 original size:11 final size:11
Alignment explanation
Indices: 19498505--19498540 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
19498495 AGGATGCGAC
19498505 ATAAAAATAAT
1 ATAAAAATAAT
*
19498516 A-CAAAATAAT
1 ATAAAAATAAT
19498526 ATAAAAATAAT
1 ATAAAAATAAT
19498537 ATAA
1 ATAA
19498541 TTTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:19506980 original size:14 final size:13
Alignment explanation
Indices: 19506963--19507000 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
19506953 CATCTATTTA
19506963 AATATAATAAAAAT
1 AATAT-ATAAAAAT
19506977 -A-ATATAAAAAT
1 AATATATAAAAAT
19506988 AATATATAAAAAT
1 AATATATAAAAAT
19507001 TAAAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 8 0.36
12 3 0.14
13 11 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATATATAAAAAT
Found at i:19506983 original size:11 final size:11
Alignment explanation
Indices: 19506969--19506998 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
19506959 TTTAAATATA
19506969 ATAAAAATAAT
1 ATAAAAATAAT
19506980 ATAAAAATAAT
1 ATAAAAATAAT
19506991 ATATAAAA
1 ATA-AAAA
19506999 ATTAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:19515021 original size:26 final size:26
Alignment explanation
Indices: 19514984--19515039 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
19514974 AATATAGTAA
*
19514984 ATAAAATATTATTTTATTTAAAATTT
1 ATAAAATATTATTTAATTTAAAATTT
*
19515010 ATAAAATTTTATTTAATTTAAAATTT
1 ATAAAATATTATTTAATTTAAAATTT
19515036 ATAA
1 ATAA
19515040 GTATCTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATAAAATATTATTTAATTTAAAATTT
Found at i:19522225 original size:96 final size:94
Alignment explanation
Indices: 19521934--19522225 Score: 219
Period size: 96 Copynumber: 3.1 Consensus size: 94
19521924 TTAAATTTTA
*
19521934 TTTTTTATTTCATCATGGCATTTTTTATTACACATAACATGACATTATACTTTTAAAGTTGACAT
1 TTTTTTATTTCATCATGGCATTTTTTATTACACATAACATGACATTATA-TTTTTAAGTTGACAT
19521999 CAACCTTTTTTCTACATAGTTTTTTAAGATT
65 C-ACCTTTTTTCTACATAGTTTTTTAAGATT
* * * **** * * *
19522030 TTTTTAAATTATAAT-ATAG--TTTCTAATATAGTTTTTTATTGAATATTACACTT-TATTTTTT
1 TTTTT-TATT-TCATCATGGCATTT-T--T-TA-TTACACA-T-AACATGACA-TTATATTTTTA
* * * **
19522091 A-TT-TCAT-A--ATTTTTCTACATA--ATTTTACATTTT
56 AGTTGACATCACCTTTTTTCTACATAGTTTTTTA-AGATT
19522124 ATTTTTTATTTCATCATGGCATTTTTTATTACACATAACATGACATTATAGTTTTTAAGTTGACA
1 -TTTTTTATTTCATCATGGCATTTTTTATTACACATAACATGACATTATA-TTTTTAAGTTGACA
19522189 TCGACCTTTTTTCTACATAGTTTTTTAAGATT
64 TC-ACCTTTTTTCTACATAGTTTTTTAAGATT
19522221 TTTTT
1 TTTTT
19522226 AAATTATAAT
Statistics
Matches: 140, Mismatches: 31, Indels: 50
0.63 0.14 0.23
Matches are distributed among these distances:
88 2 0.01
89 9 0.06
90 7 0.05
91 5 0.04
92 5 0.04
93 9 0.06
94 10 0.07
95 21 0.15
96 26 0.19
97 10 0.07
98 9 0.06
99 5 0.04
100 5 0.04
101 6 0.04
102 9 0.06
103 2 0.01
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.53
Consensus pattern (94 bp):
TTTTTTATTTCATCATGGCATTTTTTATTACACATAACATGACATTATATTTTTAAGTTGACATC
ACCTTTTTTCTACATAGTTTTTTAAGATT
Found at i:19522244 original size:191 final size:191
Alignment explanation
Indices: 19521920--19522267 Score: 633
Period size: 191 Copynumber: 1.8 Consensus size: 191
19521910 TAATCATCTG
19521920 AATTTTAAATTTTATTTTTTATTTCATCATGGCATTTTTTATTACACATAACATGACATTATACT
1 AATTTTAAATTTTATTTTTTATTTCATCATGGCATTTTTTATTACACATAACATGACATTATACT
19521985 TTTAAAGTTGACATCAACCTTTTTTCTACATAGTTTTTTAAGATTTTTTTAAATTATAATATAGT
66 TTTAAAGTTGACATCAACCTTTTTTCTACATAGTTTTTTAAGATTTTTTTAAATTATAATATAGT
** *
19522050 TTCTAATATAGTTTTTTATTGAATATTACACTTTATTTTTTATTTCATAATTTTTCTACAT
131 TTCTAATATAAATTTTTATTAAATATTACACTTTATTTTTTATTTCATAATTTTTCTACAT
* *
19522111 AATTTTACATTTTATTTTTTATTTCATCATGGCATTTTTTATTACACATAACATGACATTATAGT
1 AATTTTAAATTTTATTTTTTATTTCATCATGGCATTTTTTATTACACATAACATGACATTATACT
* *
19522176 TTTTAAGTTGACATCGACCTTTTTTCTACATAGTTTTTTAAGATTTTTTTAAATTATAATATAGT
66 TTTAAAGTTGACATCAACCTTTTTTCTACATAGTTTTTTAAGATTTTTTTAAATTATAATATAGT
19522241 TTCTAATATAAATTTTTATTAAATATT
131 TTCTAATATAAATTTTTATTAAATATT
19522268 TTTAATTATT
Statistics
Matches: 150, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
191 150 1.00
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.53
Consensus pattern (191 bp):
AATTTTAAATTTTATTTTTTATTTCATCATGGCATTTTTTATTACACATAACATGACATTATACT
TTTAAAGTTGACATCAACCTTTTTTCTACATAGTTTTTTAAGATTTTTTTAAATTATAATATAGT
TTCTAATATAAATTTTTATTAAATATTACACTTTATTTTTTATTTCATAATTTTTCTACAT
Found at i:19522685 original size:16 final size:16
Alignment explanation
Indices: 19522664--19522708 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
19522654 GTGATAATTT
19522664 TTTATTTTTTATTAAA
1 TTTATTTTTTATTAAA
*
19522680 TTTA-TTTTTATT-TA
1 TTTATTTTTTATTAAA
*
19522694 -GTATTTTTTATTAAA
1 TTTATTTTTTATTAAA
19522709 CAAATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 9 0.38
16 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTATTTTTTATTAAA
Found at i:19522932 original size:18 final size:19
Alignment explanation
Indices: 19522906--19522941 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19522896 TTTTTTTATT
*
19522906 TTTTAAATTTTTTTTAAAA
1 TTTTAAATTTTTATTAAAA
19522925 TTTT-AATTTTTATTAAA
1 TTTTAAATTTTTATTAAA
19522942 TAAATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTAAATTTTTATTAAAA
Found at i:19523290 original size:20 final size:21
Alignment explanation
Indices: 19523262--19523300 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
19523252 TTTATTTATT
*
19523262 AAATAAATT-TTGTAAAAAAA
1 AAATAAATTGATGTAAAAAAA
*
19523282 AAATTAATTGATGTAAAAA
1 AAATAAATTGATGTAAAAA
19523301 TGATAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (21 bp):
AAATAAATTGATGTAAAAAAA
Found at i:19523553 original size:29 final size:29
Alignment explanation
Indices: 19523490--19523561 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
19523480 TTTATTTAAT
*
19523490 TTATATTT-ATATATTATATTAATAAAGA
1 TTATATTTAATATATTATATTAATAAAAA
*
19523518 -TATTATTTAATATTTTA-ATTTAATAAAAA
1 TTA-TATTTAATATATTATA-TTAATAAAAA
19523547 TTATATTTATATATA
1 TTATATTTA-ATATA
19523562 ATTAAGTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 2 0.06
28 6 0.17
29 22 0.61
30 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
TTATATTTAATATATTATATTAATAAAAA
Found at i:19523563 original size:22 final size:22
Alignment explanation
Indices: 19523538--19523580 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
19523528 TATTTTAATT
19523538 TAATAAAAATTAT-ATTTATATA
1 TAAT-AAAATTATAATTTATATA
* *
19523560 TAATTAAGTTATAATTTATAT
1 TAATAAAATTATAATTTATAT
19523581 TAAAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAATAAAATTATAATTTATATA
Found at i:19524505 original size:15 final size:15
Alignment explanation
Indices: 19524487--19524520 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
19524477 AATTTTCTCC
*
19524487 ATATATATTTATATA
1 ATATATATATATATA
*
19524502 ATATATATATATATG
1 ATATATATATATATA
19524517 ATAT
1 ATAT
19524521 TTTGCTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:19524938 original size:49 final size:50
Alignment explanation
Indices: 19524795--19524947 Score: 136
Period size: 49 Copynumber: 3.1 Consensus size: 50
19524785 AAAAGTCAAC
* *
19524795 AAATTCTAGTAAATATAGAAAAAAGTCCATGAATTTATGGCCAAAATGGAA
1 AAATTCTAGTAAATATAGAAAAAAGTCCACGAATTTAAGGCCAAAATGG-A
* ** * * * *
19524846 AAAATGGAATCCAAA-AT-GCAAAAAGTCAACAAATTT-AGAGCCAAGAA-GG-
1 AAATTCTAGT--AAATATAGAAAAAAGTCCACGAATTTAAG-GCCAA-AATGGA
*
19524895 AAATTCTAGTAAATATAGAAAAAAGTCCACGAATTTAAGGCCAAAATGAA
1 AAATTCTAGTAAATATAGAAAAAAGTCCACGAATTTAAGGCCAAAATGGA
19524945 AAA
1 AAA
19524948 GTCAACGAAT
Statistics
Matches: 76, Mismatches: 17, Indels: 19
0.68 0.15 0.17
Matches are distributed among these distances:
47 3 0.04
48 4 0.05
49 28 0.37
50 6 0.08
51 28 0.37
52 4 0.05
53 3 0.04
ACGTcount: A:0.52, C:0.12, G:0.16, T:0.20
Consensus pattern (50 bp):
AAATTCTAGTAAATATAGAAAAAAGTCCACGAATTTAAGGCCAAAATGGA
Found at i:19524955 original size:29 final size:30
Alignment explanation
Indices: 19524914--19524977 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
19524904 TAAATATAGA
* *
19524914 AAAAAGTCCACGAATTTAAGGCCAAAAT-G
1 AAAAAGTCAACGAATTCAAGGCCAAAATGG
*
19524943 AAAAAGTCAACGAATTCATGGCCAAAATGG
1 AAAAAGTCAACGAATTCAAGGCCAAAATGG
19524973 AAAAA
1 AAAAA
19524978 ATGGAATCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.52, C:0.16, G:0.17, T:0.16
Consensus pattern (30 bp):
AAAAAGTCAACGAATTCAAGGCCAAAATGG
Found at i:19525780 original size:13 final size:14
Alignment explanation
Indices: 19525762--19525790 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19525752 ATGAACTAAT
19525762 ATAAAAAGAAA-AA
1 ATAAAAAGAAAGAA
19525775 ATAAAAAGAAAGAA
1 ATAAAAAGAAAGAA
19525789 AT
1 AT
19525791 TTACAAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (14 bp):
ATAAAAAGAAAGAA
Found at i:19532665 original size:18 final size:18
Alignment explanation
Indices: 19532644--19532678 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19532634 ATTCATAAAA
19532644 TATACCATTCACATATAT
1 TATACCATTCACATATAT
* *
19532662 TATACTATTCACGTATA
1 TATACCATTCACATATA
19532679 CCAAAAGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (18 bp):
TATACCATTCACATATAT
Found at i:19537658 original size:19 final size:19
Alignment explanation
Indices: 19537634--19537671 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19537624 AATCGGATGT
**
19537634 AAAATTAATTTTAATTTTA
1 AAAATTAAAATTAATTTTA
19537653 AAAATTAAAATTAATTTTA
1 AAAATTAAAATTAATTTTA
19537672 TATTTAAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATTAAAATTAATTTTA
Found at i:19538237 original size:23 final size:24
Alignment explanation
Indices: 19538211--19538269 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
19538201 TTTTAATATA
*
19538211 TTTAATATTAAAATTT-AAAATTT
1 TTTAAAATTAAAATTTCAAAATTT
*
19538234 TTTAAAATTAAAATTTCATAA-TT
1 TTTAAAATTAAAATTTCAAAATTT
*
19538257 TTTAAAATCAAAA
1 TTTAAAATTAAAA
19538270 AGTAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 29 0.91
24 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTAAAATTAAAATTTCAAAATTT
Found at i:19538246 original size:16 final size:17
Alignment explanation
Indices: 19538218--19538249 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19538208 ATATTTAATA
19538218 TTAAAATTTAAAATTTT
1 TTAAAATTTAAAATTTT
19538235 TTAAAA-TTAAAATTT
1 TTAAAATTTAAAATTT
19538250 CATAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAATTTAAAATTTT
Found at i:19538302 original size:13 final size:14
Alignment explanation
Indices: 19538278--19538306 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19538268 AAAGTAAAAA
19538278 AATTTATAAAATAT
1 AATTTATAAAATAT
19538292 AATTT-TAAAATAT
1 AATTTATAAAATAT
19538305 AA
1 AA
19538307 AAAAAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTATAAAATAT
Found at i:19538332 original size:20 final size:20
Alignment explanation
Indices: 19538294--19538331 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
19538284 TAAAATATAA
19538294 TTTTAAAATATAAAAAAAAG
1 TTTTAAAATATAAAAAAAAG
19538314 TTTT-AAATATAAAAAAAA
1 TTTTAAAATATAAAAAAAA
19538332 AAACATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
TTTTAAAATATAAAAAAAAG
Found at i:19544595 original size:52 final size:52
Alignment explanation
Indices: 19544527--19544680 Score: 200
Period size: 54 Copynumber: 2.9 Consensus size: 52
19544517 TACCTAGCGT
* *
19544527 AAATGAAAATTTTTAAAAGTAACTTTTGAATTTTCATTTTTTGATATAACAA
1 AAATGAAAATTATTAAAAGTAACTTTTGAATTTCCATTTTTTGATATAACAA
* * *
19544579 GAATGAAAATTATTAAAAGTAGCTTTTGAATTTCCATTTTTGGATATATAACAA
1 AAATGAAAATTATTAAAAGTAACTTTTGAATTTCCATTTTTTG--ATATAACAA
* ** * *
19544633 AAATGAAAATTGTTAGTAGTAACTTTTTAATTTCCATTTTTTAATATA
1 AAATGAAAATTATTAAAAGTAACTTTTGAATTTCCATTTTTTGATATA
19544681 GAACAATATA
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 43 0.49
54 44 0.51
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (52 bp):
AAATGAAAATTATTAAAAGTAACTTTTGAATTTCCATTTTTTGATATAACAA
Found at i:19560036 original size:16 final size:16
Alignment explanation
Indices: 19560017--19560051 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19560007 TAAAAAACAA
19560017 AAACAAAAAAAAATAG
1 AAACAAAAAAAAATAG
**
19560033 AAACAGCAAAAAATAG
1 AAACAAAAAAAAATAG
19560049 AAA
1 AAA
19560052 ACTGGGGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.77, C:0.09, G:0.09, T:0.06
Consensus pattern (16 bp):
AAACAAAAAAAAATAG
Found at i:19561247 original size:23 final size:24
Alignment explanation
Indices: 19561197--19561248 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
19561187 GATAATAACT
* * *
19561197 AAAAAATATATATTAAAAATGTTT
1 AAAAAATATATAATAAAAATCTTA
*
19561221 AAAAAATA-ATAATAATAATCTTA
1 AAAAAATATATAATAAAAATCTTA
19561244 AAAAA
1 AAAAA
19561249 TTACAACAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAAAATATATAATAAAAATCTTA
Found at i:19561575 original size:13 final size:13
Alignment explanation
Indices: 19561557--19561623 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 13
19561547 TACATAGACC
19561557 GAAACCCTAAATT
1 GAAACCCTAAATT
*
19561570 GAAACCTTAAAACCTT
1 GAAACCCT-AAA--TT
* *
19561586 TAAACCCCAAAATT
1 GAAA-CCCTAAATT
* *
19561600 AAAACCCTAAATC
1 GAAACCCTAAATT
19561613 GAAACCCTAAA
1 GAAACCCTAAA
19561624 ATCTAAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
13 24 0.57
14 8 0.19
16 8 0.19
17 2 0.05
ACGTcount: A:0.49, C:0.27, G:0.04, T:0.19
Consensus pattern (13 bp):
GAAACCCTAAATT
Found at i:19561631 original size:7 final size:7
Alignment explanation
Indices: 19561619--19561677 Score: 57
Period size: 7 Copynumber: 8.1 Consensus size: 7
19561609 AATCGAAACC
19561619 CTAAAAT
1 CTAAAAT
19561626 CTAAAAT
1 CTAAAAT
* *
19561633 TTCAAAT
1 CTAAAAT
19561640 CCTAAAAT
1 -CTAAAAT
19561648 C-AAAAT
1 CTAAAAT
19561654 CTAAAAT
1 CTAAAAT
*
19561661 CCAAAAAT
1 -CTAAAAT
19561669 CTCAAAAT
1 CT-AAAAT
19561677 C
1 C
19561678 CACCAAGCCA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
6 6 0.14
7 19 0.45
8 17 0.40
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.25
Consensus pattern (7 bp):
CTAAAAT
Found at i:19561639 original size:14 final size:14
Alignment explanation
Indices: 19561621--19561676 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
19561611 TCGAAACCCT
19561621 AAAATCTAAAATTTC
1 AAAATCTAAAA-TTC
19561636 -AAATCCTAAAA-TC
1 AAAAT-CTAAAATTC
*
19561649 AAAATCTAAAATCC
1 AAAATCTAAAATTC
19561663 AAAAATCTCAAAAT
1 -AAAATCT-AAAAT
19561677 CCACCAAGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.23
14 9 0.26
15 13 0.37
16 5 0.14
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAATCTAAAATTC
Found at i:19561677 original size:16 final size:15
Alignment explanation
Indices: 19561636--19561679 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
19561626 CTAAAATTTC
19561636 AAATCCTAAAAT-C-A
1 AAAT-CTAAAATCCAA
19561650 AAATCTAAAATCCAA
1 AAATCTAAAATCCAA
19561665 AAATCTCAAAATCCA
1 AAATCT-AAAATCCA
19561680 CCAAGCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 7 0.26
14 5 0.19
15 7 0.26
16 8 0.30
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATCTAAAATCCAA
Found at i:19561735 original size:16 final size:17
Alignment explanation
Indices: 19561704--19561742 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
19561694 TAAACCAAAA
*
19561704 AAAATTCCTTAAAATCC
1 AAAATTCCTAAAAATCC
19561721 AAAATT-CTAAAAATCC
1 AAAATTCCTAAAAATCC
*
19561737 CAAATT
1 AAAATT
19561743 TGATACGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATTCCTAAAAATCC
Found at i:19563763 original size:13 final size:12
Alignment explanation
Indices: 19563747--19563777 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
19563737 AAAAGAGATG
19563747 AAAAAAAAAAGCA
1 AAAAAAAAAAG-A
19563760 AAAAAAAAAAGA
1 AAAAAAAAAAGA
19563772 AAAAAA
1 AAAAAA
19563778 GATATTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.90, C:0.03, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:19565163 original size:4 final size:4
Alignment explanation
Indices: 19565139--19565209 Score: 65
Period size: 4 Copynumber: 17.8 Consensus size: 4
19565129 GTGCATTCTC
* * *
19565139 TCAT TCGT TCAT TCTT TCAT TCAT TTAT AT-AT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT -TCAT TCAT TCAT TCAT TCAT
* *
19565187 TCAT CCAT TTAT GT-AT TCAT TCA
1 TCAT TCAT TCAT -TCAT TCAT TCA
19565210 ATTTAATGCA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
3 2 0.04
4 51 0.93
5 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.03, T:0.52
Consensus pattern (4 bp):
TCAT
Found at i:19565182 original size:32 final size:32
Alignment explanation
Indices: 19565139--19565209 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
19565129 GTGCATTCTC
* * *
19565139 TCATTCGTTCATTCTTTCATTCATTTATATAT
1 TCATTCATTCATTCATTCATCCATTTATATAT
*
19565171 TCATTCATTCATTCATTCATCCATTTATGTAT
1 TCATTCATTCATTCATTCATCCATTTATATAT
19565203 TCATTCA
1 TCATTCA
19565210 ATTTAATGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.24, C:0.21, G:0.03, T:0.52
Consensus pattern (32 bp):
TCATTCATTCATTCATTCATCCATTTATATAT
Found at i:19566828 original size:1 final size:1
Alignment explanation
Indices: 19566822--19566864 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
19566812 AAATGCCTTG
* ** *
19566822 AAAAAAAAAACAAAAAAAAGTAAAAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19566865 GAGAGTTTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.02, G:0.05, T:0.02
Consensus pattern (1 bp):
A
Found at i:19566850 original size:14 final size:13
Alignment explanation
Indices: 19566822--19566864 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
19566812 AAATGCCTTG
*
19566822 AAAAAAA-AAACA
1 AAAAAAAGAAAAA
19566834 AAAAAAAGTAAAAA
1 AAAAAAAG-AAAAA
19566848 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
19566861 AAAA
1 AAAA
19566865 GAGAGTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 7 0.25
13 9 0.32
14 12 0.43
ACGTcount: A:0.91, C:0.02, G:0.05, T:0.02
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:19567061 original size:18 final size:18
Alignment explanation
Indices: 19567040--19567081 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
19567030 ATATCAAATA
* *
19567040 GCAATATTTTTTTCTAGG
1 GCAATATTCTTTTCTAAG
19567058 GCAATATTCTTTTCTAAG
1 GCAATATTCTTTTCTAAG
19567076 GCAATA
1 GCAATA
19567082 AACCATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (18 bp):
GCAATATTCTTTTCTAAG
Found at i:19568080 original size:15 final size:15
Alignment explanation
Indices: 19568060--19568097 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
19568050 TGAAAGGAAC
19568060 GAAAGAATAAAAAAA
1 GAAAGAATAAAAAAA
*
19568075 GAAAGAA-AGAAAAA
1 GAAAGAATAAAAAAA
19568089 GAAATGAAT
1 GAAA-GAAT
19568098 GGGTGGAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (15 bp):
GAAAGAATAAAAAAA
Found at i:19568086 original size:23 final size:23
Alignment explanation
Indices: 19568038--19568086 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
19568028 AAAAAATGCA
* *
19568038 AAAGAAAAAAAATGAAAGGAACG
1 AAAGAAAAAAAAAGAAAGGAAAG
19568061 AAAGAATAAAAAAAGAAA-GAAAG
1 AAAGAA-AAAAAAAGAAAGGAAAG
19568084 AAA
1 AAA
19568087 AAGAAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (23 bp):
AAAGAAAAAAAAAGAAAGGAAAG
Found at i:19568463 original size:6 final size:6
Alignment explanation
Indices: 19568438--19568476 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
19568428 AAAAAAAATC
*
19568438 AAATAA AAA-AA AGAAAAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA A-AATAA AAATAA AAATAA AAATAA AAA
19568477 CGGCTCTAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 3 0.10
6 24 0.80
7 3 0.10
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (6 bp):
AAATAA
Found at i:19569063 original size:63 final size:64
Alignment explanation
Indices: 19568964--19569103 Score: 160
Period size: 63 Copynumber: 2.2 Consensus size: 64
19568954 AAAAAAACTC
* * *
19568964 AAGCCCAGTTTAGCTGACACCAATAAAGTCTTAAGCTAAGATTA-TTTGGCAC-TAATAAAATTT
1 AAGCCCAGTTTATCTGACACCAATAAAGTCTTAAGCTAAGATTAGCTT-ACACTTAATAAAATTT
* * * * * *
19569027 AAGCCCAGTTTATCT-AGCACCAATGAAGTTTTAAGCTCAGTTTAGCTTACCCTTAATGAAATTT
1 AAGCCCAGTTTATCTGA-CACCAATAAAGTCTTAAGCTAAGATTAGCTTACACTTAATAAAATTT
19569091 AAGCCCAGTTTAT
1 AAGCCCAGTTTAT
19569104 TTGGCCATCA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 39 0.60
64 25 0.38
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.32
Consensus pattern (64 bp):
AAGCCCAGTTTATCTGACACCAATAAAGTCTTAAGCTAAGATTAGCTTACACTTAATAAAATTT
Found at i:19569192 original size:33 final size:33
Alignment explanation
Indices: 19569048--19569266 Score: 133
Period size: 33 Copynumber: 6.7 Consensus size: 33
19569038 ATCTAGCACC
* * * *
19569048 AATGAAGTTTTAAG-CTCAGTTTAGCTTACCCTT
1 AATGAAATTTTAAGCCT-AGTTTACCTGACCCTA
* ** * * *
19569081 AATGAAA-TTTAAGCCCAGTTTATTTGGCCATC
1 AATGAAATTTTAAGCCTAGTTTACCTGACCCTA
* * * * *
19569113 AATAAAATTTTAGGCAC-AATTTAGCTGGCCCCT-
1 AATGAAATTTTAAGC-CTAGTTTACCT-GACCCTA
* * * *
19569146 AAGGAAATCTTAAGCCTAGTTTACCTGACCATT
1 AATGAAATTTTAAGCCTAGTTTACCTGACCCTA
* * *
19569179 AACGAAATTTTAAGCCTAGTTTATCTGACCCCA
1 AATGAAATTTTAAGCCTAGTTTACCTGACCCTA
** * *
19569212 AATGAGGTTTTAAGCCTAGTTTAGCTGACCCTC
1 AATGAAATTTTAAGCCTAGTTTACCTGACCCTA
*
19569245 AATGAAA-TTTAAGCCCAGTTTA
1 AATGAAATTTTAAGCCTAGTTTA
19569267 TCTGGCTCCA
Statistics
Matches: 142, Mismatches: 38, Indels: 13
0.74 0.20 0.07
Matches are distributed among these distances:
32 41 0.29
33 96 0.68
34 5 0.04
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Consensus pattern (33 bp):
AATGAAATTTTAAGCCTAGTTTACCTGACCCTA
Found at i:19570002 original size:22 final size:22
Alignment explanation
Indices: 19569955--19570013 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
19569945 TCTGTAAGAC
* * *
19569955 CTCCGAGCATAATTTCTAAGAT
1 CTCCAAGCATAATTTCTAAAAA
19569977 CTCCAAGCATAATCTT-TAAAAA
1 CTCCAAGCATAAT-TTCTAAAAA
**
19569999 CTCCTGGCATAATTT
1 CTCCAAGCATAATTT
19570014 TGATTCGTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (22 bp):
CTCCAAGCATAATTTCTAAAAA
Found at i:19570076 original size:132 final size:132
Alignment explanation
Indices: 19569834--19570079 Score: 318
Period size: 132 Copynumber: 1.9 Consensus size: 132
19569824 AACTTTTGAG
* * * * * *
19569834 ATTTGTAAGACCTCCGAGCATAATCTTTAAGACCTTTGGGCATAATTTCAATTTGTGATGTTATC
1 ATTTCTAAGACCTCCAAGCATAATCTTTAAAAACTCTGGGCATAATTTCAATTCGTGATGTTATC
* * *
19569899 CCGATCGATTCTTTATCTTTTGACTTACGGTGTTATCCTAGTCGATTCTGTAAGACCTCCGAGCA
66 CCAATCAATTCTTTATCTTTTGACTTACAGTGTTATCCTAGTCGATTCTGTAAGACCTCCGAGCA
19569964 TA
131 TA
* ** *
19569966 ATTTCTAAGATCTCCAAGCATAATCTTTAAAAACTCCT-GGCATAATTTTGATTCGTGGTGTTAT
1 ATTTCTAAGACCTCCAAGCATAATCTTTAAAAACT-CTGGGCATAATTTCAATTCGTGATGTTAT
*
19570030 CCCAATCAATTCTTTAT-TTCTCT-ACTTGCAGTGTTATCCTAGTCGATTCT
65 CCCAATCAATTCTTTATCTT-T-TGACTTACAGTGTTATCCTAGTCGATTCT
19570080 TTACTTCTCG
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
131 2 0.02
132 93 0.96
133 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (132 bp):
ATTTCTAAGACCTCCAAGCATAATCTTTAAAAACTCTGGGCATAATTTCAATTCGTGATGTTATC
CCAATCAATTCTTTATCTTTTGACTTACAGTGTTATCCTAGTCGATTCTGTAAGACCTCCGAGCA
TA
Found at i:19570150 original size:74 final size:74
Alignment explanation
Indices: 19570072--19570254 Score: 210
Period size: 74 Copynumber: 2.5 Consensus size: 74
19570062 GTTATCCTAG
19570072 TCGATTCTTTACTTCTCGACTCGTAGTGTTGTCCCAATCACTTTCTTACTTTTT-AACTTGCGAT
1 TCGATTCTTTACTTCTCGACTCGTAGTGTTGTCCCAATCACTTTCTTA-TTTTTCAACTTGCGAT
* *
19570136 CTTGTCCTGA
65 ATTGTCCCGA
* * * * * * * *
19570146 TCGATTCTTTACTTTTCAACT--TACGGTGTTATCTCGATCATTTTTTTATTTTTCGACTTGCGA
1 TCGATTCTTTACTTCTCGACTCGTA--GTGTTGTCCCAATCACTTTCTTATTTTTCAACTTGCGA
19570209 TATTGTCCCGA
64 TATTGTCCCGA
* *
19570220 TCGATTCTTTACTTCTTGACTCGCAGTGTTGTCCC
1 TCGATTCTTTACTTCTCGACTCGTAGTGTTGTCCC
19570255 GGTTGTTTTC
Statistics
Matches: 88, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
72 2 0.02
73 5 0.06
74 80 0.91
76 1 0.01
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.46
Consensus pattern (74 bp):
TCGATTCTTTACTTCTCGACTCGTAGTGTTGTCCCAATCACTTTCTTATTTTTCAACTTGCGATA
TTGTCCCGA
Found at i:19570252 original size:37 final size:37
Alignment explanation
Indices: 19570023--19570255 Score: 115
Period size: 37 Copynumber: 6.3 Consensus size: 37
19570013 TTGATTCGTG
* * * *
19570023 GTGTTATCCCAATCAATTCTTTATTTCTCT-ACTTGCA
1 GTGTTGTCCCGATCGATTCTTTACTTCT-TGACTTGCA
* * * * *
19570060 GTGTTAT-CCTAGTCGATTCTTTACTTCTCGACTCGTA
1 GTGTTGTCCCGA-TCGATTCTTTACTTCTTGACTTGCA
* * *
19570097 GTGTTGTCCCAATC-ACTT-TCTTACTTTTTAACTTGC-
1 GTGTTGTCCCGATCGA-TTCT-TTACTTCTTGACTTGCA
* * * * *
19570133 GATCTTGTCCTGATCGATTCTTTACTT-TTCAACTTACG
1 G-TGTTGTCCCGATCGATTCTTTACTTCTT-GACTTGCA
* * * *
19570171 GTGTTATCTCGATC-ATTTTTTTA-TTTTTCGACTTGC-
1 GTGTTGTCCCGATCGA-TTCTTTACTTCTT-GACTTGCA
* *
19570207 GATATTGTCCCGATCGATTCTTTACTTCTTGACTCGCA
1 G-TGTTGTCCCGATCGATTCTTTACTTCTTGACTTGCA
19570245 GTGTTGTCCCG
1 GTGTTGTCCCG
19570256 GTTGTTTTCT
Statistics
Matches: 149, Mismatches: 31, Indels: 32
0.70 0.15 0.15
Matches are distributed among these distances:
36 12 0.08
37 125 0.84
38 12 0.08
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.45
Consensus pattern (37 bp):
GTGTTGTCCCGATCGATTCTTTACTTCTTGACTTGCA
Found at i:19570751 original size:118 final size:118
Alignment explanation
Indices: 19570543--19570777 Score: 452
Period size: 118 Copynumber: 2.0 Consensus size: 118
19570533 GGTGCCTTGC
* *
19570543 AAGGCACCACTGGTCACCCACTCCACTGCCAGCACCATAGCCTTGTCCCAACCATACCTTGTACT
1 AAGGCACCACTGGCCACCCACTCCACTGCCAGCACCATAGCCTTGTCCCAACCATACCCTGTACT
19570608 GCTAGAACCCTCACTAACCACCACCTACTCCACTCATCTCCCAATCACTGAGT
66 GCTAGAACCCTCACTAACCACCACCTACTCCACTCATCTCCCAATCACTGAGT
19570661 AAGGCACCACTGGCCACCCACTCCACTGCCAGCACCATAGCCTTGTCCCAACCATACCCTGTACT
1 AAGGCACCACTGGCCACCCACTCCACTGCCAGCACCATAGCCTTGTCCCAACCATACCCTGTACT
19570726 GCTAGAACCCTCACTAACCACCACCTACTCCACTCATCTCCCAATCACTGAG
66 GCTAGAACCCTCACTAACCACCACCTACTCCACTCATCTCCCAATCACTGAG
19570778 CCCCTTTAAA
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 115 1.00
ACGTcount: A:0.26, C:0.43, G:0.11, T:0.19
Consensus pattern (118 bp):
AAGGCACCACTGGCCACCCACTCCACTGCCAGCACCATAGCCTTGTCCCAACCATACCCTGTACT
GCTAGAACCCTCACTAACCACCACCTACTCCACTCATCTCCCAATCACTGAGT
Found at i:19572246 original size:29 final size:29
Alignment explanation
Indices: 19572203--19572274 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 29
19572193 CTGAAACCTT
19572203 AAAATCCAAAATTTC-AAATCCTAAAAT-C
1 AAAATCCAAAATTTCAAAATCC-AAAATCC
*
19572231 AAAATCCCAAACTTTCAAAATCCAAAATCC
1 AAAAT-CCAAAATTTCAAAATCCAAAATCC
19572261 AAAAATCTCAAAAT
1 -AAAATC-CAAAAT
19572275 CCCCCAAGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 5 0.14
29 14 0.38
30 8 0.22
31 10 0.27
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (29 bp):
AAAATCCAAAATTTCAAAATCCAAAATCC
Found at i:19572258 original size:7 final size:7
Alignment explanation
Indices: 19572203--19572276 Score: 53
Period size: 8 Copynumber: 10.0 Consensus size: 7
19572193 CTGAAACCTT
19572203 AAAATCC
1 AAAATCC
*
19572210 AAAATTTC
1 AAAA-TCC
19572218 -AAATCC
1 AAAATCC
19572224 TAAAAT-C
1 -AAAATCC
19572231 AAAATCCC
1 AAAAT-CC
* *
19572239 AAACTTTC
1 AAA-ATCC
19572247 AAAATCC
1 AAAATCC
19572254 AAAATCC
1 AAAATCC
19572261 AAAAATCTC
1 -AAAATC-C
19572270 AAAATCC
1 AAAATCC
19572277 CCCAAGCCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
6 7 0.13
7 18 0.34
8 26 0.49
9 2 0.04
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.22
Consensus pattern (7 bp):
AAAATCC
Found at i:19572258 original size:23 final size:23
Alignment explanation
Indices: 19572225--19572276 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
19572215 TTCAAATCCT
* * *
19572225 AAAAT-CAAAATCCCAAACTTTC
1 AAAATCCAAAATCCAAAAATCTC
19572247 AAAATCCAAAATCCAAAAATCTC
1 AAAATCCAAAATCCAAAAATCTC
19572270 AAAATCC
1 AAAATCC
19572277 CCCAAGCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (23 bp):
AAAATCCAAAATCCAAAAATCTC
Found at i:19583931 original size:2 final size:2
Alignment explanation
Indices: 19583924--19583971 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
19583914 AGAAATTGTA
* * * *
19583924 AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19583966 AT AT AT
1 AT AT AT
19583972 GTATGTATAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19583958 original size:22 final size:22
Alignment explanation
Indices: 19583933--19583980 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
19583923 AATATATATA
* *
19583933 TATATATATGTATGTATGTATG
1 TATATATATATATATATGTATG
19583955 TATATATATATATATATGTATG
1 TATATATATATATATATGTATG
19583977 TATA
1 TATA
19583981 GATTAGACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (22 bp):
TATATATATATATATATGTATG
Found at i:19583958 original size:26 final size:26
Alignment explanation
Indices: 19583925--19583980 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
19583915 GAAATTGTAA
19583925 TATATATATATATATATGTATGTATG
1 TATATATATATATATATGTATGTATG
* *
19583951 TATGTATATATATATATATATGTATG
1 TATATATATATATATATGTATGTATG
19583977 TATA
1 TATA
19583981 GATTAGACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (26 bp):
TATATATATATATATATGTATGTATG
Found at i:19585020 original size:54 final size:54
Alignment explanation
Indices: 19584960--19585064 Score: 201
Period size: 54 Copynumber: 1.9 Consensus size: 54
19584950 TCCATAATGG
19584960 AGGTAATGTTCTAAATCATCATTGATTTAATTCCCAAAAATTAAAAAAAAATTT
1 AGGTAATGTTCTAAATCATCATTGATTTAATTCCCAAAAATTAAAAAAAAATTT
*
19585014 AGGTAATGTTCTAAGTCATCATTGATTTAATTCCCAAAAATTAAAAAAAAA
1 AGGTAATGTTCTAAATCATCATTGATTTAATTCCCAAAAATTAAAAAAAAA
19585065 AATTTAGCTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (54 bp):
AGGTAATGTTCTAAATCATCATTGATTTAATTCCCAAAAATTAAAAAAAAATTT
Found at i:19590008 original size:51 final size:51
Alignment explanation
Indices: 19589953--19590051 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
19589943 CAGAAATGAG
*
19589953 GAGCAAAGCAGAGTTACAAAGCAAGTTCAAGAACTACATGTCGAAGCCGAT
1 GAGCAAAGCAGAGTTACAAAGCAAGTTCAAGAACTACATGTCAAAGCCGAT
* * * * *
19590004 GAGCAAGGCAGAGTTACAAAGTAAGTTGAGGCACTACATGTCAAAGCC
1 GAGCAAAGCAGAGTTACAAAGCAAGTTCAAGAACTACATGTCAAAGCC
19590052 TAAGAGAGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.16
Consensus pattern (51 bp):
GAGCAAAGCAGAGTTACAAAGCAAGTTCAAGAACTACATGTCAAAGCCGAT
Found at i:19593684 original size:16 final size:16
Alignment explanation
Indices: 19593663--19593695 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19593653 ATTAAGGTGA
19593663 AATAATA-TGTAATATT
1 AATAATAGT-TAATATT
19593679 AATAATAGTTAATATT
1 AATAATAGTTAATATT
19593695 A
1 A
19593696 CTTATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
AATAATAGTTAATATT
Found at i:19593962 original size:22 final size:22
Alignment explanation
Indices: 19593937--19593994 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
19593927 GCTTAATTAC
19593937 TTATAAATAAATATAT-TTTTAA
1 TTATAAATAAATATATATTTT-A
* *
19593959 TTATTAATTCAAT-TATATTTTA
1 TTA-TAAATAAATATATATTTTA
19593981 TTATGAAATAAATA
1 TTAT-AAATAAATA
19593995 AAATATTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
21 1 0.04
22 16 0.57
23 11 0.39
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTATAAATAAATATATATTTTA
Found at i:19596200 original size:138 final size:138
Alignment explanation
Indices: 19595952--19596226 Score: 453
Period size: 138 Copynumber: 2.0 Consensus size: 138
19595942 ATCGAACATA
* *
19595952 ATAGGAAGGTCACTGGGGTATATAAGGGTTCACCTCATCTCTTCCTTGTGAGGCACCTTTTGTAA
1 ATAGGAAGGTCACTGAGGTATATAAGGGTTCACCTCATCTCTTCCTTGTGAGACACCTTTTGTAA
* * * *
19596017 GATAAAATCGTGAGGGCAGGGGGCCAGAGCGGATAATATCTCACAAGGGTGTGAATCTTGACGAT
66 GACAAAATCGTAAGGGCAGGGGGCCAGAGCGGATAATATCTCACAAGGGTATGAACCTTGACGAT
19596082 CAAGCTGG
131 CAAGCTGG
*
19596090 ATAGGAAGGTCACTGAGGTATATAAGGGTTCACAC-CATCTCTTTCTTGTGAGACACCTTTTGTA
1 ATAGGAAGGTCACTGAGGTATATAAGGGTTCAC-CTCATCTCTTCCTTGTGAGACACCTTTTGTA
* *
19596154 GGACAAAATCGTAAGGGCAGGGGGCCAGAGCGGATAATATCTCACAAGGGTATGAACCTTGGCGA
65 AGACAAAATCGTAAGGGCAGGGGGCCAGAGCGGATAATATCTCACAAGGGTATGAACCTTGACGA
19596219 TCAAGCTG
130 TCAAGCTG
19596227 ATCCGGAACG
Statistics
Matches: 127, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
138 126 0.99
139 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (138 bp):
ATAGGAAGGTCACTGAGGTATATAAGGGTTCACCTCATCTCTTCCTTGTGAGACACCTTTTGTAA
GACAAAATCGTAAGGGCAGGGGGCCAGAGCGGATAATATCTCACAAGGGTATGAACCTTGACGAT
CAAGCTGG
Found at i:19596574 original size:18 final size:19
Alignment explanation
Indices: 19596526--19596574 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
19596516 TTTTTTGATT
* *
19596526 AAATTT-ATATCAAATTTT
1 AAATTTAATATTAAATTTC
19596544 AAATTTTAA-ATTAAA-TTC
1 AAA-TTTAATATTAAATTTC
19596562 AAATTTAATATTA
1 AAATTTAATATTA
19596575 TATAAATCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 5 0.19
18 12 0.46
19 8 0.31
20 1 0.04
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTTAATATTAAATTTC
Found at i:19600398 original size:2 final size:2
Alignment explanation
Indices: 19600391--19600434 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
19600381 CTAGAGACTT
*
19600391 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GC GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19600433 GA
1 GA
19600435 AGGAGAATGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19601877 original size:15 final size:15
Alignment explanation
Indices: 19601852--19601893 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
19601842 AAATAATATA
19601852 TAAAAATTTAATAAAT-
1 TAAAAA-TTAA-AAATC
19601868 TAAAAATTAAAAATC
1 TAAAAATTAAAAATC
*
19601883 TATAAATTAAA
1 TAAAAATTAAA
19601894 TCAAATCGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 14 0.58
16 6 0.25
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAAATTAAAAATC
Found at i:19610118 original size:19 final size:20
Alignment explanation
Indices: 19610082--19610121 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19610072 TATTTTTTTA
*
19610082 TTTTATTAAATTTATTAAAT
1 TTTTATTAAAATTATTAAAT
*
19610102 TTTTTTTAAAATT-TTAAAT
1 TTTTATTAAAATTATTAAAT
19610121 T
1 T
19610122 ATATTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTATTAAAATTATTAAAT
Found at i:19610154 original size:13 final size:11
Alignment explanation
Indices: 19610120--19610163 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
19610110 AAATTTTAAA
19610120 TTATATTATTT
1 TTATATTATTT
*
19610131 TTATATCATTT
1 TTATATTATTT
19610142 ATTCATATTATTT
1 -TT-ATATTATTT
*
19610155 TTGTATTAT
1 TTATATTAT
19610164 ATCACCTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 16 0.57
12 4 0.14
13 8 0.29
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (11 bp):
TTATATTATTT
Found at i:19612621 original size:16 final size:16
Alignment explanation
Indices: 19612602--19612632 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
19612592 CCAACTATTT
19612602 TTGTTTGTCTCTATCA
1 TTGTTTGTCTCTATCA
19612618 TTGTTTGTCTCTATC
1 TTGTTTGTCTCTATC
19612633 TGCCAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.19, G:0.13, T:0.58
Consensus pattern (16 bp):
TTGTTTGTCTCTATCA
Found at i:19612937 original size:28 final size:28
Alignment explanation
Indices: 19612884--19612970 Score: 95
Period size: 28 Copynumber: 3.0 Consensus size: 28
19612874 TATTACAAAT
* *
19612884 AATTTTTAAATTATT-ATATAATATTTA
1 AATTTTAAAATTTTTAATATAATATTTA
19612911 AATTTTAAAATTTTTAATATAATATTTA
1 AATTTTAAAATTTTTAATATAATATTTA
* *
19612939 AATTATAAATTTATTTATTAATATGATATTTA
1 AATTTTAAA---ATTT-TTAATATAATATTTA
19612971 TTTTTAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
27 13 0.25
28 20 0.39
31 4 0.08
32 14 0.27
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
AATTTTAAAATTTTTAATATAATATTTA
Found at i:19612945 original size:14 final size:14
Alignment explanation
Indices: 19612900--19612951 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
19612890 TAAATTATTA
19612900 TATAATATTTAAAT
1 TATAATATTTAAAT
* * *
19612914 TTTAAAATTTTTAA-
1 TATAATA-TTTAAAT
19612928 TATAATATTTAAAT
1 TATAATATTTAAAT
19612942 TATAA-ATTTA
1 TATAATATTTA
19612952 TTTATTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 10 0.33
14 15 0.50
15 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATAATATTTAAAT
Found at i:19612948 original size:35 final size:35
Alignment explanation
Indices: 19612884--19612950 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
19612874 TATTACAAAT
*
19612884 AATTTTTAAATTATTATATAATATTTAAATTTTAA
1 AATTTTTAAATTAATATATAATATTTAAATTTTAA
*
19612919 AATTTTT-AATATAATATTTAA-ATTATAAATTT
1 AATTTTTAAAT-TAATATATAATATT-TAAATTT
19612951 ATTTATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 6 0.21
35 22 0.79
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
AATTTTTAAATTAATATATAATATTTAAATTTTAA
Found at i:19612979 original size:18 final size:19
Alignment explanation
Indices: 19612947--19612983 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
19612937 TAAATTATAA
19612947 ATTTATTTATTAATATGAT
1 ATTTATTTATTAATATGAT
19612966 ATTTATTT-TTAATATGAT
1 ATTTATTTATTAATATGAT
19612984 TAATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
ATTTATTTATTAATATGAT
Found at i:19613068 original size:27 final size:26
Alignment explanation
Indices: 19613030--19613080 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
19613020 CCTCTAAATA
* * *
19613030 ATATATTAATTAATAAATTTTTAATC
1 ATATATCAATTAAAAAAATTTTAATC
19613056 ATATATCACATTAAAAAAATTTTAA
1 ATATATCA-ATTAAAAAAATTTTAA
19613081 ATATAAATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATATCAATTAAAAAAATTTTAATC
Found at i:19618107 original size:2 final size:2
Alignment explanation
Indices: 19618100--19618137 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
19618090 CAAAAACTTT
* *
19618100 TA TA TA TA TA TA TA TA TA TA CA TA TA TA T- TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19618138 TATTTATAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:19620056 original size:23 final size:22
Alignment explanation
Indices: 19620026--19620081 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
19620016 TCTCTGTCCT
*
19620026 AATT-TTTTTTAGTTTTTATTAA
1 AATTATTTTTT-GCTTTTATTAA
*
19620048 AATTATTTTCTTGCTTTTATTAT
1 AATTATTTT-TTGCTTTTATTAA
*
19620071 TATTATTTTTT
1 AATTATTTTTT
19620082 TATGAAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 6 0.21
23 21 0.72
24 2 0.07
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.70
Consensus pattern (22 bp):
AATTATTTTTTGCTTTTATTAA
Found at i:19621907 original size:14 final size:16
Alignment explanation
Indices: 19621868--19621900 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
19621858 ATACTTGAGT
19621868 TTAAATT-TTATTAAA
1 TTAAATTATTATTAAA
19621883 TTAAATTTATTATTAAA
1 TTAAA-TTATTATTAAA
19621900 T
1 T
19621901 AATTATTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 2 0.12
17 9 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAATTATTATTAAA
Found at i:19621980 original size:18 final size:19
Alignment explanation
Indices: 19621949--19622003 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
19621939 TCGAATCGAT
*
19621949 TTTAATCAATTTAATTATAA
1 TTTAATTAATTTAATTAT-A
*
19621969 TTT-ATT-ATTTAATAATA
1 TTTAATTAATTTAATTATA
19621986 TTTAATTAATTTAATTAT
1 TTTAATTAATTTAATTAT
19622004 TTATTAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 4 0.13
18 12 0.40
19 11 0.37
20 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAATTAATTTAATTATA
Found at i:19622008 original size:31 final size:31
Alignment explanation
Indices: 19621959--19622040 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
19621949 TTTAATCAAT
*
19621959 TTAATTATAATT-TATTATTTAATAATATTTAA
1 TTAATT-TAATTAT-TTATTTAATAAAATTTAA
*
19621991 TTAATTTAATTATTTATTAAATAAAATTTAA
1 TTAATTTAATTATTTATTTAATAAAATTTAA
* *
19622022 TTAAATTAATTATTAATTT
1 TTAATTTAATTATTTATTT
19622041 TTTCATATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
31 37 0.84
32 7 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
TTAATTTAATTATTTATTTAATAAAATTTAA
Found at i:19630940 original size:6 final size:6
Alignment explanation
Indices: 19630929--19630957 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
19630919 CGACTTTCCT
19630929 CCTCCA CCTCCA CCTCCA CCTCCA CCTCC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCC
19630958 GGCTCCACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.69, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTCCA
Found at i:19632327 original size:2 final size:2
Alignment explanation
Indices: 19632320--19632354 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
19632310 TTAGCTTTAT
19632320 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19632355 GGGTTGACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19632567 original size:20 final size:21
Alignment explanation
Indices: 19632531--19632582 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
19632521 CTCGAAATTA
19632531 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
19632553 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
19632574 AT-AAATATT
1 ATAAAATATT
19632583 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:19632573 original size:21 final size:22
Alignment explanation
Indices: 19632531--19632582 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
19632521 CTCGAAATTA
19632531 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
19632553 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
19632574 AT-AAATATT
1 ATAAAATATT
19632583 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:19634887 original size:21 final size:22
Alignment explanation
Indices: 19634853--19634938 Score: 74
Period size: 22 Copynumber: 4.0 Consensus size: 22
19634843 ATTAATTCAA
* *
19634853 TTTAAAATTAATAAAATAT-TAT
1 TTTAAAAAT-ATAAAATATAAAT
19634875 TTTAAAAATAT-AAATATAAAT
1 TTTAAAAATATAAAATATAAAT
* *
19634896 TTAAATAAATATAAAATATATAAA
1 TTTAA-AAATATAAAATATA-AAT
19634920 TTT-AAAAT-TAAAAT-TAAAT
1 TTTAAAAATATAAAATATAAAT
19634939 AAATAATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
19 2 0.04
20 8 0.15
21 14 0.26
22 18 0.33
23 8 0.15
24 4 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAAATATAAAATATAAAT
Found at i:19634941 original size:31 final size:31
Alignment explanation
Indices: 19634877--19634939 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
19634867 AATATTATTT
*
19634877 TAAAA-ATATAAATATAAATTTAAATAAATA
1 TAAAATATATAAATATAAATTAAAATAAATA
*
19634907 TAAAATATATAAATTTAAAATTAAAATTAAATA
1 TAAAATATATAAATAT-AAATTAAAA-TAAATA
19634940 AATAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 5 0.18
31 9 0.32
32 8 0.29
33 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
TAAAATATATAAATATAAATTAAAATAAATA
Found at i:19634944 original size:26 final size:25
Alignment explanation
Indices: 19634890--19634944 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
19634880 AAATATAAAT
*
19634890 ATAAATTTAAATAAATATAAAATAT
1 ATAAATTTAAATAAATATAAAATAA
*
19634915 ATAAATTTAAAATTAAA-ATTAAATAA
1 ATAAATTT-AAA-TAAATATAAAATAA
19634941 ATAA
1 ATAA
19634945 TAAAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.31
26 14 0.54
27 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAAATTTAAATAAATATAAAATAA
Found at i:19635504 original size:34 final size:33
Alignment explanation
Indices: 19635464--19635540 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 33
19635454 ATCCGACTCG
* **
19635464 AAATTAATAAAATATTATTTTAAATATAAATATA
1 AAATTAATAAAATATAAAATTAAATATAAA-ATA
*
19635498 AAATTAA-ATAAATATAAAATTAAATATAAAATT
1 AAATTAATA-AAATATAAAATTAAATATAAAATA
*
19635531 AAATAAATAA
1 AAATTAATAA
19635541 TTAAAAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
33 10 0.28
34 26 0.72
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (33 bp):
AAATTAATAAAATATAAAATTAAATATAAAATA
Found at i:19635510 original size:16 final size:16
Alignment explanation
Indices: 19635489--19635539 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
19635479 TATTTTAAAT
19635489 ATAAATATAAAATTAA
1 ATAAATATAAAATTAA
19635505 ATAAATATAAAA-T--
1 ATAAATATAAAATTAA
19635518 -TAAATATAAAATTAA
1 ATAAATATAAAATTAA
19635533 ATAAATA
1 ATAAATA
19635540 ATTAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 11 0.35
13 1 0.03
15 1 0.03
16 18 0.58
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAATATAAAATTAA
Found at i:19635521 original size:28 final size:29
Alignment explanation
Indices: 19635485--19635539 Score: 103
Period size: 28 Copynumber: 1.9 Consensus size: 29
19635475 ATATTATTTT
19635485 AAATATAAATATAAAATTAAATAAATATA
1 AAATATAAATATAAAATTAAATAAATATA
19635514 AAAT-TAAATATAAAATTAAATAAATA
1 AAATATAAATATAAAATTAAATAAATA
19635540 ATTAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 22 0.85
29 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (29 bp):
AAATATAAATATAAAATTAAATAAATATA
Found at i:19635542 original size:12 final size:12
Alignment explanation
Indices: 19635483--19635545 Score: 71
Period size: 12 Copynumber: 5.4 Consensus size: 12
19635473 AAATATTATT
19635483 TTAAATAT-AAA
1 TTAAATATAAAA
*
19635494 TATAAA-ATTAAA
1 T-TAAATATAAAA
19635506 -TAAATATAAAA
1 TTAAATATAAAA
19635517 TTAAATATAAAA
1 TTAAATATAAAA
19635529 TTAAATA-AATAA
1 TTAAATATAA-AA
19635541 TTAAA
1 TTAAA
19635546 AAAATAATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
10 4 0.09
11 10 0.22
12 32 0.70
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TTAAATATAAAA
Found at i:19636573 original size:31 final size:31
Alignment explanation
Indices: 19636513--19636573 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
19636503 TCATGAATAT
* *
19636513 ATTTTATTATTAAATAATTTACTATTATTTA
1 ATTTTAATATTAAATAATTTAATATTATTTA
19636544 ATTTTAAT-TTAAA-AATATTAATATATATTT
1 ATTTTAATATTAAATAAT-TTAATAT-TATTT
19636574 TAAAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 3 0.12
30 11 0.42
31 12 0.46
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (31 bp):
ATTTTAATATTAAATAATTTAATATTATTTA
Found at i:19636594 original size:22 final size:21
Alignment explanation
Indices: 19636551--19636599 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
19636541 TTAATTTTAA
19636551 TTTAAAAATATTAATATATAT
1 TTTAAAAATATTAATATATAT
*
19636572 TTTAAAATATTTTAATA-ATTAT
1 TTTAAAA-ATATTAATATA-TAT
19636594 TTTAAA
1 TTTAAA
19636600 TTAAATAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAAAAATATTAATATATAT
Found at i:19636916 original size:18 final size:17
Alignment explanation
Indices: 19636893--19637071 Score: 80
Period size: 18 Copynumber: 10.9 Consensus size: 17
19636883 AATTTTACTT
19636893 ATAAATAATATTATATAA
1 ATAAATAATATTATAT-A
19636911 ATAAATAATA-TACTAT-
1 ATAAATAATATTA-TATA
*
19636927 -TAATATAATA-TA-CTA
1 ATAA-ATAATATTATATA
* *
19636942 ATAAATAATATTAAAAA
1 ATAAATAATATTATATA
* *
19636959 ATATTATAATA-TAT-TC
1 ATA-AATAATATTATATA
19636975 ATAAAATAATATTATATTA
1 AT-AAATAATATTATA-TA
* *
19636994 ATAAATATTATTACA-A
1 ATAAATAATATTATATA
19637010 AT--A-AATATTATACTA
1 ATAAATAATATTATA-TA
** *
19637025 ATGTATTA-ATT-T-TA
1 ATAAATAATATTATATA
19637039 ATAAATAATATTATATTA
1 ATAAATAATATTATA-TA
* *
19637057 ATACATCATATTATA
1 ATAAATAATATTATA
19637072 ATATATTAAT
Statistics
Matches: 122, Mismatches: 19, Indels: 40
0.67 0.10 0.22
Matches are distributed among these distances:
13 7 0.06
14 9 0.07
15 15 0.12
16 26 0.21
17 16 0.13
18 46 0.38
19 3 0.02
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
ATAAATAATATTATATA
Found at i:19636936 original size:16 final size:15
Alignment explanation
Indices: 19636910--19636952 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 15
19636900 ATATTATATA
19636910 AATAAATAATATACT
1 AATAAATAATATACT
*
19636925 ATTAATATAATATACT
1 AATAA-ATAATATACT
19636941 AATAAATAATAT
1 AATAAATAATAT
19636953 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (15 bp):
AATAAATAATATACT
Found at i:19636946 original size:49 final size:49
Alignment explanation
Indices: 19636893--19637059 Score: 141
Period size: 49 Copynumber: 3.4 Consensus size: 49
19636883 AATTTTACTT
19636893 ATAAATAATATTATATAAATAAATAATATACT-ATTAATATAATATACTA
1 ATAAATAATATTATATAAATAAATAATATACTAATTAATATAATAT-CTA
* * * * *
19636942 ATAAATAATATTA-AAAAATATTATAATATATTCA-TAAAATAATAT-TA
1 ATAAATAATATTATATAAATA-AATAATATACTAATTAATATAATATCTA
* * * *
19636989 TATTAATAAATATTATTACAAATAAATATTATACTAATGT-AT-TAAT-TTTA
1 -ATAAAT-AATATTA-TATAAATAAATAATATACTAAT-TAATATAATATCTA
*
19637039 ATAAATAATATTATATTAATA
1 ATAAATAATATTATATAAATA
19637060 CATCATATTA
Statistics
Matches: 95, Mismatches: 14, Indels: 20
0.74 0.11 0.16
Matches are distributed among these distances:
47 8 0.08
48 18 0.19
49 45 0.47
50 16 0.17
51 7 0.07
52 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (49 bp):
ATAAATAATATTATATAAATAAATAATATACTAATTAATATAATATCTA
Done.