Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015136.1 Kokia drynarioides strain JFW-HI SEQ_130180, 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: 601175
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 598 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:322311 original size:22 final size:22
Alignment explanation
Indices: 322283--322329 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
322273 TCATGAAACT
322283 TTAAATGGTTAGATCAAGACTC
1 TTAAATGGTTAGATCAAGACTC
322305 TTAAATGGTTAGATCAAGACTC
1 TTAAATGGTTAGATCAAGACTC
322327 TTA
1 TTA
322330 CCTTCTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (22 bp):
TTAAATGGTTAGATCAAGACTC
Found at i:331186 original size:14 final size:15
Alignment explanation
Indices: 331167--331195 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
331157 ATTATTTGTT
331167 TAATTTAGTT-AAAA
1 TAATTTAGTTCAAAA
331181 TAATTTAGTTCAAAA
1 TAATTTAGTTCAAAA
331196 CTATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.41
Consensus pattern (15 bp):
TAATTTAGTTCAAAA
Found at i:331574 original size:21 final size:20
Alignment explanation
Indices: 331498--331570 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
331488 AATTATATTG
* *
331498 TTGTTTTGGTACTACTTTTTG
1 TTGTTTTGGTGCT-CTTTTTA
* *
331519 TTGTTTTGGTGTTGTGTTTTTA
1 TTGTTTTGGTG--CTCTTTTTA
*
331541 CTGTTTTGGTGCTCTTTTTA
1 TTGTTTTGGTGCTCTTTTTA
331561 TTGTTTTGGT
1 TTGTTTTGGT
331571 TGCTGTTTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
20 16 0.38
21 10 0.24
22 15 0.36
23 1 0.02
ACGTcount: A:0.05, C:0.07, G:0.23, T:0.64
Consensus pattern (20 bp):
TTGTTTTGGTGCTCTTTTTA
Found at i:331579 original size:20 final size:20
Alignment explanation
Indices: 331514--331580 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
331504 TGGTACTACT
*
331514 TTTTGTTGTTTTGGTGTTG-TG
1 TTTTATTGTTTT-G-GTTGCTG
* *
331535 TTTTTACTGTTTTGG-TGCTCT
1 -TTTTATTGTTTTGGTTGCT-G
331556 TTTTATTGTTTTGGTTGCTG
1 TTTTATTGTTTTGGTTGCTG
331576 TTTTA
1 TTTTA
331581 GTGCTATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
19 2 0.05
20 20 0.54
21 5 0.14
22 10 0.27
ACGTcount: A:0.04, C:0.06, G:0.24, T:0.66
Consensus pattern (20 bp):
TTTTATTGTTTTGGTTGCTG
Found at i:331602 original size:23 final size:23
Alignment explanation
Indices: 331576--331692 Score: 100
Period size: 23 Copynumber: 5.2 Consensus size: 23
331566 TTGGTTGCTG
331576 TTTTAGTGCTATTTTTATTATTA
1 TTTTAGTGCTATTTTTATTATTA
* * *
331599 TTTTCGTGCTGTTTTTATTGTTA
1 TTTTAGTGCTATTTTTATTATTA
*
331622 TTTTTGTTGCTATTTTT-TTA-TA
1 TTTTAG-TGCTATTTTTATTATTA
* * *
331644 -TTCA-TGCTGTTTTTATTGTTA
1 TTTTAGTGCTATTTTTATTATTA
*
331665 TTTTTGTTGCTATTTTT-TCTATTA
1 TTTTAG-TGCTATTTTTAT-TATTA
331689 TTTT
1 TTTT
331693 TACTGCTGTT
Statistics
Matches: 73, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
19 9 0.12
20 2 0.03
21 4 0.05
22 4 0.05
23 28 0.38
24 26 0.36
ACGTcount: A:0.14, C:0.07, G:0.11, T:0.68
Consensus pattern (23 bp):
TTTTAGTGCTATTTTTATTATTA
Found at i:331657 original size:43 final size:45
Alignment explanation
Indices: 331582--331721 Score: 176
Period size: 43 Copynumber: 3.0 Consensus size: 45
331572 GCTGTTTTAG
*
331582 TGCTATTTTTATTATTATTTTCGTGCTGTTTTTATTGTTATTTTTGT
1 TGCTATTTTT-TTATTA-TTTCATGCTGTTTTTATTGTTATTTTTGT
331629 TGCTATTTTTTTA-TA-TTCATGCTGTTTTTATTGTTATTTTTGT
1 TGCTATTTTTTTATTATTTCATGCTGTTTTTATTGTTATTTTTGT
* ** *
331672 TGCTATTTTTTCTATTATTTTTACTGCTGTTTTGGTTGTTATTTTGGT
1 TGCTATTTTTT-TATTA-TTTCA-TGCTGTTTTTATTGTTATTTTTGT
331720 TG
1 TG
331722 TTTGGATGTT
Statistics
Matches: 83, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
43 38 0.46
44 2 0.02
45 4 0.05
46 3 0.04
47 13 0.16
48 23 0.28
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.66
Consensus pattern (45 bp):
TGCTATTTTTTTATTATTTCATGCTGTTTTTATTGTTATTTTTGT
Found at i:331678 original size:12 final size:12
Alignment explanation
Indices: 331576--331681 Score: 53
Period size: 12 Copynumber: 9.3 Consensus size: 12
331566 TTGGTTGCTG
*
331576 TTTTAGTGCTAT
1 TTTTATTGCTAT
**
331588 TTTTATTATTA-
1 TTTTATTGCTAT
** *
331599 TTTTCGTGCTGT
1 TTTTATTGCTAT
*
331611 TTTTATTGTTAT
1 TTTTATTGCTAT
*
331623 TTTTGTTGCTA-
1 TTTTATTGCTAT
331634 TTTT-TT--TAT
1 TTTTATTGCTAT
* * *
331643 ATTCA-TGCTGT
1 TTTTATTGCTAT
*
331654 TTTTATTGTTAT
1 TTTTATTGCTAT
*
331666 TTTTGTTGCTAT
1 TTTTATTGCTAT
331678 TTTT
1 TTTT
331682 TCTATTATTT
Statistics
Matches: 65, Mismatches: 23, Indels: 12
0.65 0.23 0.12
Matches are distributed among these distances:
8 2 0.03
9 3 0.05
10 2 0.03
11 15 0.23
12 43 0.66
ACGTcount: A:0.13, C:0.07, G:0.12, T:0.68
Consensus pattern (12 bp):
TTTTATTGCTAT
Found at i:331745 original size:21 final size:21
Alignment explanation
Indices: 331686--331745 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 21
331676 ATTTTTTCTA
*
331686 TTATTTTTACTGCTGTTTTGGTTG
1 TTATTTTTA-TGC-G-TTTGGATG
** *
331710 TTATTTTGGT-TGTTTGGATG
1 TTATTTTTATGCGTTTGGATG
331730 TTATTTTTATGCGTTT
1 TTATTTTTATGCGTTT
331746 TTAATTATTG
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
20 15 0.54
21 5 0.18
23 1 0.04
24 7 0.25
ACGTcount: A:0.10, C:0.05, G:0.22, T:0.63
Consensus pattern (21 bp):
TTATTTTTATGCGTTTGGATG
Found at i:332242 original size:20 final size:20
Alignment explanation
Indices: 332190--332252 Score: 90
Period size: 20 Copynumber: 3.0 Consensus size: 20
332180 GTTTTGGTCC
332190 TATTTTTTTTATTGTTTTGG
1 TATTTTTTTTATTGTTTTGG
*
332210 TGTTGTGTTTTTATTGTTTTGG
1 TATT-T-TTTTTATTGTTTTGG
*
332232 TATTTTTTTTACTGTTTTGG
1 TATTTTTTTTATTGTTTTGG
332252 T
1 T
332253 TGCTGTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 18 0.47
21 2 0.05
22 18 0.47
ACGTcount: A:0.08, C:0.02, G:0.19, T:0.71
Consensus pattern (20 bp):
TATTTTTTTTATTGTTTTGG
Found at i:333482 original size:12 final size:12
Alignment explanation
Indices: 333467--333501 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
333457 CAATTCATAT
333467 CACTTTCAATTC
1 CACTTTCAATTC
* *
333479 CACTTTCACTTT
1 CACTTTCAATTC
333491 CACTTTCAATT
1 CACTTTCAATT
333502 TTGATCACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (12 bp):
CACTTTCAATTC
Found at i:335420 original size:23 final size:23
Alignment explanation
Indices: 335390--335463 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
335380 GATGTTATAG
*
335390 TTTTGGTGCTATTTTTTTTACTA
1 TTTTGGTGCTATTTTTTTTATTA
* * *
335413 TTTTGGTGCTGTTTTTATTGTTA
1 TTTTGGTGCTATTTTTTTTATTA
* *
335436 TTTTTGTTGCTATTTTTTCTATTA
1 -TTTTGGTGCTATTTTTTTTATTA
335460 TTTT
1 TTTT
335464 TGCTACTGTT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 23 0.56
24 18 0.44
ACGTcount: A:0.11, C:0.07, G:0.14, T:0.69
Consensus pattern (23 bp):
TTTTGGTGCTATTTTTTTTATTA
Found at i:335440 original size:24 final size:23
Alignment explanation
Indices: 335390--335465 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 23
335380 GATGTTATAG
*
335390 TTTTGGTGCTATTTTTTTTACTA-
1 TTTTGGTGCTA-TTTTTTTATTAT
* *
335413 TTTTGGTGCTGTTTTTATTGTTAT
1 TTTTGGTGCTATTTTT-TTATTAT
*
335437 TTTTGTTGCTATTTTTTCTATTAT
1 TTTTGGTGCTATTTTTT-TATTAT
335461 TTTTG
1 TTTTG
335466 CTACTGTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
22 5 0.11
23 15 0.34
24 24 0.55
ACGTcount: A:0.11, C:0.07, G:0.14, T:0.68
Consensus pattern (23 bp):
TTTTGGTGCTATTTTTTTATTAT
Found at i:335950 original size:22 final size:22
Alignment explanation
Indices: 335904--336007 Score: 104
Period size: 22 Copynumber: 4.7 Consensus size: 22
335894 TATATTGTTG
* * *
335904 TTTTGGTGC-TATTTTTTGCTG
1 TTTTGGTGCTTTTTTTTTACTA
*
335925 TTTTGGTG-TTGTGTTTTTACTA
1 TTTTGGTGCTT-TTTTTTTACTA
* *
335947 TTTTTGTGCTTTTTTTTTTACTG
1 TTTTGGTGC-TTTTTTTTTACTA
335970 TTTTGGTGCTTTTTTTTTACTA
1 TTTTGGTGCTTTTTTTTTACTA
* *
335992 TTTTAGTGCTGTTTTT
1 TTTTGGTGCTTTTTTT
336008 AATAAAAAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
21 9 0.13
22 40 0.59
23 17 0.25
24 2 0.03
ACGTcount: A:0.07, C:0.08, G:0.18, T:0.67
Consensus pattern (22 bp):
TTTTGGTGCTTTTTTTTTACTA
Found at i:335971 original size:45 final size:45
Alignment explanation
Indices: 335915--336007 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
335905 TTTGGTGCTA
* * *
335915 TTTTTTGCTGTTTTGGTG-TTGTGTTTTTACTATTTTTGTGCTTTT
1 TTTTTTACTGTTTTGGTGCTT-TGTTTTTACTATTTTAGTGCTGTT
*
335960 TTTTTTACTGTTTTGGTGCTTTTTTTTTACTATTTTAGTGCTGTT
1 TTTTTTACTGTTTTGGTGCTTTGTTTTTACTATTTTAGTGCTGTT
336005 TTT
1 TTT
336008 AATAAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 41 0.95
46 2 0.05
ACGTcount: A:0.06, C:0.08, G:0.17, T:0.69
Consensus pattern (45 bp):
TTTTTTACTGTTTTGGTGCTTTGTTTTTACTATTTTAGTGCTGTT
Found at i:336807 original size:22 final size:22
Alignment explanation
Indices: 336782--336827 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
336772 TTGACCCATA
*
336782 ATCTTAGGAATATTTTATGTAT
1 ATCTTAGCAATATTTTATGTAT
** *
336804 ATCTTTTCCATATTTTATGTAT
1 ATCTTAGCAATATTTTATGTAT
336826 AT
1 AT
336828 TATTTTCTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (22 bp):
ATCTTAGCAATATTTTATGTAT
Found at i:342828 original size:22 final size:23
Alignment explanation
Indices: 342800--342850 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
342790 ATCTCAGGAA
*
342800 TATTTTATGTATA-TGTTTTCCT
1 TATTTTATGTATATTATTTTCCT
342822 TATTTTATGTATATTATTTTCCT
1 TATTTTATGTATATTATTTTCCT
342845 TGATTT
1 T-ATTT
342851 ACGATAGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 13 0.50
23 9 0.35
24 4 0.15
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.65
Consensus pattern (23 bp):
TATTTTATGTATATTATTTTCCT
Found at i:342864 original size:61 final size:61
Alignment explanation
Indices: 342795--342914 Score: 222
Period size: 61 Copynumber: 2.0 Consensus size: 61
342785 CCATAATCTC
* *
342795 AGGAATATTTTATGTATATGTTTTCCTTATTTTATGTATATTATTTTCCTTGATTTACGAT
1 AGGAATATTTTATATATATCTTTTCCTTATTTTATGTATATTATTTTCCTTGATTTACGAT
342856 AGGAATATTTTATATATATCTTTTCCTTATTTTATGTATATTATTTTCCTTGATTTACG
1 AGGAATATTTTATATATATCTTTTCCTTATTTTATGTATATTATTTTCCTTGATTTACG
342915 GTCTAATTGG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.56
Consensus pattern (61 bp):
AGGAATATTTTATATATATCTTTTCCTTATTTTATGTATATTATTTTCCTTGATTTACGAT
Found at i:342888 original size:22 final size:23
Alignment explanation
Indices: 342861--342911 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
342851 ACGATAGGAA
*
342861 TATTTTATATATA-TCTTTTCCT
1 TATTTTATATATATTATTTTCCT
*
342883 TATTTTATGTATATTATTTTCCT
1 TATTTTATATATATTATTTTCCT
342906 TGATTT
1 T-ATTT
342912 ACGGTCTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.48
23 9 0.36
24 4 0.16
ACGTcount: A:0.22, C:0.10, G:0.04, T:0.65
Consensus pattern (23 bp):
TATTTTATATATATTATTTTCCT
Found at i:343996 original size:81 final size:81
Alignment explanation
Indices: 343843--344019 Score: 200
Period size: 81 Copynumber: 2.2 Consensus size: 81
343833 TCCCTACTGC
* * * *
343843 TATTATTTTTTATTTTTCGGTAACTACTTTGCTATTCAATTGCTGGCTCTTCACATCTCTACAAC
1 TATTATTTTTTGTTTTTCGGCAACTACTTTGCTATTCAATTGATGGCTCTTCACATCTATACAAC
*
343908 TATTCCTTGC-TGCTAT
66 TACTCCTT-CTTGCTAT
* * * * * *
343924 TATTATTTTTTGTTTTT-GGACAATTGCTTTGCTATTCAATTGATGGCTCTTGACGTCTATGCAG
1 TATTATTTTTTGTTTTTCGG-CAACTACTTTGCTATTCAATTGATGGCTCTTCACATCTATACAA
*
343988 CTGCTCCTTCTTGCTAT
65 CTACTCCTTCTTGCTAT
344005 TA-T-TTTTTTGTTTTT
1 TATTATTTTTTGTTTTT
344020 TCGATAACTG
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
79 12 0.15
80 4 0.05
81 66 0.80
ACGTcount: A:0.17, C:0.19, G:0.13, T:0.51
Consensus pattern (81 bp):
TATTATTTTTTGTTTTTCGGCAACTACTTTGCTATTCAATTGATGGCTCTTCACATCTATACAAC
TACTCCTTCTTGCTAT
Found at i:352568 original size:17 final size:15
Alignment explanation
Indices: 352537--352582 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
352527 TGGCAATATA
*
352537 TTTCTTT-TCTCTTT
1 TTTCTTTCTTTCTTT
352551 TCTTC-TTCTTTCTTT
1 T-TTCTTTCTTTCTTT
352566 TTTCTTTCTTT-TTT
1 TTTCTTTCTTTCTTT
352580 TTT
1 TTT
352583 ATAAGTGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTTTCTTTCTTT
Found at i:352570 original size:11 final size:11
Alignment explanation
Indices: 352537--352579 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
352527 TGGCAATATA
*
352537 TTTCTTTTCTC
1 TTTCTTTTTTC
*
352548 TTT-TCTTCTTC
1 TTTCT-TTTTTC
352559 TTTCTTTTTTC
1 TTTCTTTTTTC
352570 TTTCTTTTTT
1 TTTCTTTTTT
352580 TTTATAAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 1 0.04
11 25 0.93
12 1 0.04
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:353667 original size:19 final size:21
Alignment explanation
Indices: 353640--353679 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
353630 TTCTCATCAG
353640 ATTCCCCTTC-C-TTTCCTTC
1 ATTCCCCTTCTCATTTCCTTC
*
353659 ATTCTCCTTCTCATTTCCTTC
1 ATTCCCCTTCTCATTTCCTTC
353680 GTCTTTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.07, C:0.42, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTCCCCTTCTCATTTCCTTC
Found at i:371489 original size:71 final size:71
Alignment explanation
Indices: 371355--371506 Score: 169
Period size: 71 Copynumber: 2.1 Consensus size: 71
371345 TGCCAAAAAA
* * * * * * * * * *
371355 CAAAAAATAATAAAAGTAGGGAGTAGTTGCATAGATGTGAAGAGCCATCAATTAAATAACAAAGT
1 CAAAAAAAAATAAAAGTAGGGAGCAATTCCAAAAACGTGAAGAGCCAACAACTAAATAACAAAGC
*
371420 AGTTGC
66 AGTTAC
* * * *
371426 CAAAAAAAAATAACAGTAGGGAGCAATTCCAAAAACGTGAAGGGCCAACAACTGAATAGCAAAGC
1 CAAAAAAAAATAAAAGTAGGGAGCAATTCCAAAAACGTGAAGAGCCAACAACTAAATAACAAAGC
371491 AGTTAC
66 AGTTAC
371497 CAAAAAAAAA
1 CAAAAAAAAA
371507 AAATAGCAGC
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.51, C:0.14, G:0.19, T:0.16
Consensus pattern (71 bp):
CAAAAAAAAATAAAAGTAGGGAGCAATTCCAAAAACGTGAAGAGCCAACAACTAAATAACAAAGC
AGTTAC
Found at i:373071 original size:22 final size:22
Alignment explanation
Indices: 373046--373089 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
373036 TCTCCAGGTT
373046 GTGACATAATGGAGTGCTTGTC
1 GTGACATAATGGAGTGCTTGTC
*
373068 GTGACATAGTGGAGTGCTTGTC
1 GTGACATAATGGAGTGCTTGTC
373090 ACAAAATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.14, G:0.34, T:0.32
Consensus pattern (22 bp):
GTGACATAATGGAGTGCTTGTC
Found at i:383711 original size:7 final size:7
Alignment explanation
Indices: 383693--383730 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
383683 CAAGAGCAAA
383693 CTTCCC-
1 CTTCCCT
383699 CTTCCCT
1 CTTCCCT
383706 CTTCCCT
1 CTTCCCT
383713 CTT-CCT
1 CTTCCCT
*
383719 CTTCCCC
1 CTTCCCT
383726 CTTCC
1 CTTCC
383731 TTGCCAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (7 bp):
CTTCCCT
Found at i:383722 original size:20 final size:20
Alignment explanation
Indices: 383693--383730 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
383683 CAAGAGCAAA
*
383693 CTTCCCCTTCCCTCTTCCCT
1 CTTCCCCTTCCCCCTTCCCT
*
383713 CTTCCTCTTCCCCCTTCC
1 CTTCCCCTTCCCCCTTCC
383731 TTGCCAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (20 bp):
CTTCCCCTTCCCCCTTCCCT
Found at i:383731 original size:13 final size:13
Alignment explanation
Indices: 383696--383731 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
383686 GAGCAAACTT
383696 CCCCTTCCCTCTTC
1 CCCCTT-CCTCTTC
*
383710 CCTCTTCCTCTTC
1 CCCCTTCCTCTTC
383723 CCCCTTCCT
1 CCCCTTCCT
383732 TGCCAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (13 bp):
CCCCTTCCTCTTC
Found at i:386990 original size:19 final size:21
Alignment explanation
Indices: 386966--387005 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
386956 ATCTAAACAT
386966 CAGAAAA-T-ATTAACTTTTC
1 CAGAAAAGTAATTAACTTTTC
*
386985 CAGAAAAGTAATTAATTTTTC
1 CAGAAAAGTAATTAACTTTTC
387006 GAAAACCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (21 bp):
CAGAAAAGTAATTAACTTTTC
Found at i:388969 original size:22 final size:21
Alignment explanation
Indices: 388926--388970 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
388916 AGGAAAACTG
**
388926 TATTTTTATTAATTTAGTTTT
1 TATTTTTATTAATTTAAATTT
*
388947 TATTTTTGTTTAATTTAAATTT
1 TATTTTT-ATTAATTTAAATTT
388969 TA
1 TA
388971 AATTCTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (21 bp):
TATTTTTATTAATTTAAATTT
Found at i:397413 original size:29 final size:28
Alignment explanation
Indices: 397341--397691 Score: 206
Period size: 30 Copynumber: 11.9 Consensus size: 28
397331 ATTTTTAGGC
*
397341 ATTCTAGGGTAAAACA-GTAATTTTTAGAAA
1 ATTCGAGGGTAAAA-ATGTAATTTTT--AAA
* * *
397371 AATCG-GGATCAAAAATGGAATTTTTAAA
1 ATTCGAGGGT-AAAAATGTAATTTTTAAA
397399 CATTCGAGGGT-AAAATGGTAATTTTTGAAA
1 -ATTCGAGGGTAAAAAT-GTAATTTTT-AAA
* * * *
397429 GTTTC-AAGGTCAAAAATGGAATTTTTGGAA
1 -ATTCGAGGGT-AAAAATGTAATTTTT-AAA
* *
397459 TTTCGAGGGTAAAAATGTAATTTTTGGAAG
1 ATTCGAGGGTAAAAATGTAATTTTT--AAA
* * * * *
397489 TTTTGGGGGTCAAAAATGGAATTTTCAGAA
1 ATTCGAGGGT-AAAAATGTAATTTTTA-AA
* * *
397519 GTTTGAAGGTAAAAATGTAATTTTTAGAA
1 ATTCGAGGGTAAAAATGTAATTTTTA-AA
* *
397548 ATTTCGAGGGTAAAAATGTATTTTTTTGAA
1 A-TTCGAGGGTAAAAATGTA-ATTTTTAAA
* *
397578 GTTCAAGGGTAAAAATGTAATTTTTGAAA
1 ATTCGAGGGTAAAAATGTAATTTTT-AAA
* * *
397607 GTTTTGAGGGTAAAAGTGTAATTTTTAGAA
1 -ATTCGAGGGTAAAAATGTAATTTTTA-AA
* * *
397637 GTTTGAGGGTAAAAATGTAATTTTCAAA
1 ATTCGAGGGTAAAAATGTAATTTTTAAA
* *
397665 AGTTTCAAGGGTAAATATGTAATTTTT
1 A--TTCGAGGGTAAAAATGTAATTTTT
397692 GGATAGTTTA
Statistics
Matches: 255, Mismatches: 47, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
28 15 0.06
29 99 0.39
30 118 0.46
31 23 0.09
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (28 bp):
ATTCGAGGGTAAAAATGTAATTTTTAAA
Found at i:397420 original size:59 final size:58
Alignment explanation
Indices: 397323--397484 Score: 159
Period size: 59 Copynumber: 2.7 Consensus size: 58
397313 TTTTGGGGTT
* ** * * *
397323 AAAATAGAATTTTTAGGCATTCTAGGGTAAAACAGTAATTTTTAGAAA-AATC-GGGATCA
1 AAAATGGAATTTTTAAACATTCGAGGGTAAAA-TGTAATTTTT-GAAAGAATCAAGG-TCA
**
397382 AAAATGGAATTTTTAAACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCA
1 AAAATGGAATTTTTAAACATTCGAGGGTAAAAT-GTAATTTTTGAAAGAATCAAGGTCA
* *
397441 AAAATGGAATTTTTGGAA-TTTCGAGGGTAAAAATGTAATTTTTG
1 AAAATGGAATTTTT-AAACATTCGAGGGT-AAAATGTAATTTTTG
397485 GAAGTTTTGG
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
58 4 0.05
59 75 0.85
60 9 0.10
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTTAAACATTCGAGGGTAAAATGTAATTTTTGAAAGAATCAAGGTCA
Found at i:397454 original size:30 final size:29
Alignment explanation
Indices: 397381--397692 Score: 262
Period size: 29 Copynumber: 10.6 Consensus size: 29
397371 AATCGGGATC
* **
397381 AAAAATGGAATTTTT-AAACATTCGAGGGT
1 AAAAATGTAATTTTTGAAAGTTTC-AGGGT
*
397410 -AAAATGGTAATTTTTGAAAGTTTCAAGGT
1 AAAAAT-GTAATTTTTGAAAGTTTCAGGGT
* *
397439 CAAAAATGGAATTTTTGGAA-TTTCGAGGGT
1 -AAAAATGTAATTTTTGAAAGTTTC-AGGGT
* **
397469 AAAAATGTAATTTTTGGAAGTTTTGGGGGT
1 AAAAATGTAATTTTTGAAAG-TTTCAGGGT
* * * *
397499 CAAAAATGGAA-TTTTCAGAAGTTTGAAGGT
1 -AAAAATGTAATTTTTGA-AAGTTTCAGGGT
397529 AAAAATGTAATTTTTAGAAA-TTTCGAGGGT
1 AAAAATGTAATTTTT-GAAAGTTTC-AGGGT
*
397559 AAAAATGTATTTTTTTG-AAG-TTCAAGGGT
1 AAAAATGTA-ATTTTTGAAAGTTTC-AGGGT
*
397588 AAAAATGTAATTTTTGAAAGTTTTGAGGGT
1 AAAAATGTAATTTTTGAAAG-TTTCAGGGT
* *
397618 AAAAGTGTAATTTTT-AGAAGTTTGAGGGT
1 AAAAATGTAATTTTTGA-AAGTTTCAGGGT
**
397647 AAAAATGTAATTTTCAAAAGTTTCAAGGGT
1 AAAAATGTAATTTTTGAAAGTTTC-AGGGT
*
397677 AAATATGTAATTTTTG
1 AAAAATGTAATTTTTG
397693 GATAGTTTAG
Statistics
Matches: 233, Mismatches: 30, Indels: 39
0.77 0.10 0.13
Matches are distributed among these distances:
28 11 0.05
29 97 0.42
30 97 0.42
31 28 0.12
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (29 bp):
AAAAATGTAATTTTTGAAAGTTTCAGGGT
Found at i:397490 original size:59 final size:59
Alignment explanation
Indices: 397381--397700 Score: 321
Period size: 59 Copynumber: 5.4 Consensus size: 59
397371 AATCGGGATC
** *
397381 AAAAATGGAATTTTTA-AACATTCGAGGGT-AAAATGGTAATTTTTGAAAGTTTCAAGGT
1 AAAAATGGAATTTTTAGAAGTTTCGAGGGTAAAAAT-GTAATTTTTGAAAGTTTCAGGGT
* * **
397439 CAAAAATGGAATTTTTGGAA-TTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGGT
1 -AAAAATGGAATTTTTAGAAGTTTCGAGGGTAAAAATGTAATTTTTGAAAG-TTTCAGGGT
* *
397499 CAAAAATGGAATTTTCAGAAGTTT-GAAGGTAAAAATGTAATTTTTAGAAA-TTTCGAGGGT
1 -AAAAATGGAATTTTTAGAAGTTTCGAGGGTAAAAATGTAATTTTT-GAAAGTTTC-AGGGT
* * * * *
397559 AAAAATGTATTTTTTTGAAG-TTCAAGGGTAAAAATGTAATTTTTGAAAGTTTTGAGGGT
1 AAAAATGGAATTTTTAGAAGTTTCGAGGGTAAAAATGTAATTTTTGAAAG-TTTCAGGGT
* * **
397618 AAAAGTGTAATTTTTAGAAGTTT-GAGGGTAAAAATGTAATTTTCAAAAGTTTCAAGGGT
1 AAAAATGGAATTTTTAGAAGTTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTC-AGGGT
* * *
397677 AAATATGTAATTTTTGGATAGTTT
1 AAAAATGGAATTTTTAGA-AGTTT
397701 AGGGACCTCC
Statistics
Matches: 220, Mismatches: 29, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
58 9 0.04
59 140 0.64
60 65 0.30
61 6 0.03
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (59 bp):
AAAAATGGAATTTTTAGAAGTTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCAGGGT
Found at i:399523 original size:17 final size:17
Alignment explanation
Indices: 399503--399547 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
399493 ATTTAATATC
*
399503 AATTTAAATTTTAATTA
1 AATTTAAATTTGAATTA
**
399520 AATTTAAATTTGCTTTA
1 AATTTAAATTTGAATTA
399537 AATTTAAATTT
1 AATTTAAATTT
399548 AAAAAGATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTGAATTA
Found at i:399526 original size:6 final size:6
Alignment explanation
Indices: 399503--399571 Score: 61
Period size: 6 Copynumber: 11.5 Consensus size: 6
399493 ATTTAATATC
* **
399503 AATTTA AATTTT AA-TTA AATTTA AATTT- GCTTTA AATTTA AATTTAAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT--A
**
399551 AAGATA AATTTA AATTTA AAT
1 AATTTA AATTTA AATTTA AAT
399572 AAACTTAAAC
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
5 7 0.14
6 38 0.78
8 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:406732 original size:28 final size:29
Alignment explanation
Indices: 406671--406732 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
406661 AAATATTGCA
* *
406671 AAAC-ACATTTACATGCCTTATCAACAAG
1 AAACAACATTTACATGCCATATCAACAAC
*
406699 AAACAACATTT-CATGCCATATCAACCAC
1 AAACAACATTTACATGCCATATCAACAAC
*
406727 ATACAA
1 AAACAA
406733 GCCTATTTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (29 bp):
AAACAACATTTACATGCCATATCAACAAC
Found at i:413512 original size:28 final size:28
Alignment explanation
Indices: 413472--413525 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
413462 GGTAACAGGT
413472 ATGACCTTTGGGTCAACAGGGAGTAAGC
1 ATGACCTTTGGGTCAACAGGGAGTAAGC
413500 ATGACCTTTGGGTCAACAGGGAGTAA
1 ATGACCTTTGGGTCAACAGGGAGTAA
413526 ATCGGATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (28 bp):
ATGACCTTTGGGTCAACAGGGAGTAAGC
Found at i:414294 original size:21 final size:22
Alignment explanation
Indices: 414270--414319 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
414260 GATTTGTTTT
414270 GGTAGAAGCT-TCACT-CGTATC
1 GGTAGAAGCTATCA-TACGTATC
*
414291 GGTAGAA-CTATCATAGGTATC
1 GGTAGAAGCTATCATACGTATC
414312 GGTAGAAG
1 GGTAGAAG
414320 TCCGCACTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (22 bp):
GGTAGAAGCTATCATACGTATC
Found at i:414928 original size:13 final size:13
Alignment explanation
Indices: 414910--414935 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
414900 TTTGTAATTA
414910 AATAAATTGTGAT
1 AATAAATTGTGAT
414923 AATAAATTGTGAT
1 AATAAATTGTGAT
414936 TGATGATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
AATAAATTGTGAT
Found at i:415959 original size:30 final size:29
Alignment explanation
Indices: 415921--415984 Score: 110
Period size: 30 Copynumber: 2.2 Consensus size: 29
415911 CATTCCACAT
415921 CTTTATACACACATACATTAATTATGAAC
1 CTTTATACACACATACATTAATTATGAAC
*
415950 CTTTGATACACACGTACATTAATTATGAAC
1 CTTT-ATACACACATACATTAATTATGAAC
415980 CTTTA
1 CTTTA
415985 ATTTTGAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (29 bp):
CTTTATACACACATACATTAATTATGAAC
Found at i:416163 original size:22 final size:22
Alignment explanation
Indices: 416149--416203 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 22
416139 AAAATCAATT
416149 AATTTTTACCATAAAAAATTTA
1 AATTTTTACCATAAAAAATTTA
416171 GAATTTTTACCATAAAAAATTTA
1 -AATTTTTACCATAAAAAATTTA
416194 GAATTTTTAC
1 -AATTTTTAC
416204 TTATGCTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (22 bp):
AATTTTTACCATAAAAAATTTA
Found at i:416166 original size:24 final size:23
Alignment explanation
Indices: 416139--416203 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
416129 TTTTGAAACT
*
416139 AAAATCAATTAATTTTTACCATAA
1 AAAATCAA-GAATTTTTACCATAA
**
416163 AAAATTTAGAATTTTTACCATAA
1 AAAATCAAGAATTTTTACCATAA
**
416186 AAAATTTAGAATTTTTAC
1 AAAATCAAGAATTTTTAC
416204 TTATGCTCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 32 0.84
24 6 0.16
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (23 bp):
AAAATCAAGAATTTTTACCATAA
Found at i:421764 original size:13 final size:14
Alignment explanation
Indices: 421740--421769 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
421730 AATTATATGC
421740 TAATTAATTTTAAT
1 TAATTAATTTTAAT
421754 TAATT-ATTTTAAT
1 TAATTAATTTTAAT
421767 TAA
1 TAA
421770 GTTTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATTAATTTTAAT
Found at i:421792 original size:23 final size:23
Alignment explanation
Indices: 421740--421784 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
421730 AATTATATGC
*
421740 TAATTAATTTTAATTAATTATTT
1 TAATTAAGTTTAATTAATTATTT
421763 TAATTAAGTTTAATT-ATTATTT
1 TAATTAAGTTTAATTAATTATTT
421785 AATCTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TAATTAAGTTTAATTAATTATTT
Found at i:424183 original size:3 final size:3
Alignment explanation
Indices: 424175--424211 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
424165 CCTATCATAC
424175 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
424212 AAGTTATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:425394 original size:25 final size:24
Alignment explanation
Indices: 425366--425414 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
425356 GCGAACTTTG
425366 ATAAATT-CAAATAATTTTAAATTTT
1 ATAAATTACAAAT-ATTTT-AATTTT
*
425391 ATAAATTATAAATATTTTAATTTT
1 ATAAATTACAAATATTTTAATTTT
425415 GAATGAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 12 0.55
26 4 0.18
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
ATAAATTACAAATATTTTAATTTT
Found at i:426061 original size:20 final size:19
Alignment explanation
Indices: 426027--426069 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
426017 AGAGTAGTAC
426027 ATATATATTAATTATTATA
1 ATATATATTAATTATTATA
* *
426046 ATATATTATTATTTATTATT
1 ATATA-TATTAATTATTATA
426066 ATAT
1 ATAT
426070 TGATTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATATATTAATTATTATA
Found at i:426187 original size:27 final size:29
Alignment explanation
Indices: 426126--426189 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
426116 GCTTCTACAT
*
426126 TATATATTATTGTTTATTACTATACCATA
1 TATATATTATAGTTTATTACTATACCATA
*
426155 TCATATATTAATAGTTTA-TA-TATA-TATA
1 T-ATATATT-ATAGTTTATTACTATACCATA
426183 TATATAT
1 TATATAT
426190 GCATAATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 6 0.19
28 4 0.13
29 5 0.16
30 9 0.29
31 7 0.23
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (29 bp):
TATATATTATAGTTTATTACTATACCATA
Found at i:427724 original size:21 final size:21
Alignment explanation
Indices: 427682--427725 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
427672 ATTGAGTTTA
* * *
427682 TTTTATATATATTTACATTAT
1 TTTTACATATATTGACACTAT
*
427703 TTTTACATATATTGCCACTAT
1 TTTTACATATATTGACACTAT
427724 TT
1 TT
427726 ATTTATAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTACATATATTGACACTAT
Found at i:427975 original size:19 final size:19
Alignment explanation
Indices: 427947--427987 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
427937 TGTCCAAGTG
* *
427947 CATAACTAGTATTACATCA
1 CATAACTAGTACTACACCA
*
427966 CATAATTAGTACTACACCA
1 CATAACTAGTACTACACCA
427985 CAT
1 CAT
427988 TTAAGCATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.29
Consensus pattern (19 bp):
CATAACTAGTACTACACCA
Found at i:429260 original size:5 final size:5
Alignment explanation
Indices: 429250--429387 Score: 90
Period size: 5 Copynumber: 27.8 Consensus size: 5
429240 TTAGAACGTG
* * * * *
429250 TCATA TCATA TCATA ACATA ACGA-A T-TTA TCATA TCATAA TGA-A TAATA
1 TCATA TCATA TCATA TCATA TC-ATA TCATA TCATA TCAT-A TCATA TCATA
* * *
429299 TCATA TCATA TCAAAA TGA-A TCATA TCATA TCATAA TGA-A TCATA TCATA
1 TCATA TCATA TC-ATA TCATA TCATA TCATA TCAT-A TCATA TCATA TCATA
* * *
429349 TCATA ACATA ACGA-A TCATA TCATA TCATA ACATA TCAT
1 TCATA TCATA TC-ATA TCATA TCATA TCATA TCATA TCAT
429388 GTCCTACCCT
Statistics
Matches: 106, Mismatches: 16, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
4 12 0.11
5 83 0.78
6 11 0.10
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (5 bp):
TCATA
Found at i:429302 original size:20 final size:20
Alignment explanation
Indices: 429254--429379 Score: 119
Period size: 20 Copynumber: 5.8 Consensus size: 20
429244 AACGTGTCAT
* *
429254 ATCATATCATAACATAACGA
1 ATCATATCATATCATAATGA
*
429274 AT-TTATCATATCATAATGAATAA
1 ATCATATCATATCATAATG----A
*
429297 TATCATATCATATCAAAATGA
1 -ATCATATCATATCATAATGA
429318 ATCATATCATATCATAATGA
1 ATCATATCATATCATAATGA
429338 ATCATATCATATCATAACATAACGA
1 ATCATATCATATCAT-A-AT---GA
429363 ATCATATCATATCATAA
1 ATCATATCATATCATAA
429380 CATATCATGT
Statistics
Matches: 89, Mismatches: 6, Indels: 19
0.78 0.05 0.17
Matches are distributed among these distances:
19 13 0.15
20 36 0.40
21 2 0.02
22 2 0.02
23 2 0.02
24 3 0.03
25 31 0.35
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.33
Consensus pattern (20 bp):
ATCATATCATATCATAATGA
Found at i:429311 original size:25 final size:25
Alignment explanation
Indices: 429277--429383 Score: 134
Period size: 25 Copynumber: 4.5 Consensus size: 25
429267 ATAACGAATT
*
429277 TATCATATCATAATGAATAATATCA
1 TATCATATCATAATGAATCATATCA
*
429302 TATCATATC--AA--AATGA-ATCA
1 TATCATATCATAATGAATCATATCA
429322 TATCATATCATAATGAATCATATCA
1 TATCATATCATAATGAATCATATCA
* *
429347 TATCATAACATAACGAATCATATCA
1 TATCATATCATAATGAATCATATCA
*
429372 TATCATAACATA
1 TATCATATCATA
429384 TCATGTCCTA
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.18
21 4 0.05
22 2 0.03
23 2 0.03
24 4 0.05
25 48 0.66
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.33
Consensus pattern (25 bp):
TATCATATCATAATGAATCATATCA
Found at i:430108 original size:49 final size:49
Alignment explanation
Indices: 430055--430292 Score: 243
Period size: 49 Copynumber: 4.9 Consensus size: 49
430045 CACATAGTTC
* * ** *
430055 TGTGCCTCACATAGCCTACCTACACGGGCTACAAAATCGCACAC-ATTCA
1 TGTGCCCCACATAGCCTACCCACACGGGCTACAAAATAACACACGACT-A
** * *
430104 TGTGCCCCACA-AGACCTATTCACACGGGCTACAAAATTACACACGGCCGTA
1 TGTGCCCCACATAG-CCTACCCACACGGGCTACAAAATAACACAC-GAC-TA
* * *
430155 TGT--CTCACAT-GCCTACCCACACGGGCTACAAAATAAGACACGACTG
1 TGTGCCCCACATAGCCTACCCACACGGGCTACAAAATAACACACGACTA
* *
430201 TGTGCCCCACATGGCCTACCCATACGGGCTACAAAATAACACACGACTA
1 TGTGCCCCACATAGCCTACCCACACGGGCTACAAAATAACACACGACTA
* * * *
430250 TGTGCCCTACATGGCCTACCCACACGGGCTACACAATCACACA
1 TGTGCCCCACATAGCCTACCCACACGGGCTACAAAATAACACA
430293 TGTTCGTGTG
Statistics
Matches: 158, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
46 4 0.03
47 2 0.01
48 34 0.22
49 113 0.72
51 4 0.03
52 1 0.01
ACGTcount: A:0.31, C:0.35, G:0.16, T:0.18
Consensus pattern (49 bp):
TGTGCCCCACATAGCCTACCCACACGGGCTACAAAATAACACACGACTA
Found at i:430183 original size:97 final size:97
Alignment explanation
Indices: 430055--430292 Score: 259
Period size: 97 Copynumber: 2.4 Consensus size: 97
430045 CACATAGTTC
* *
430055 TGTGCCTCACATAGCCTACCTACACGGGCTACAAAATCGCACAC-ATTCATGTGCCCCACAAGAC
1 TGTG-CTCACATAGCCTACCCACACGGGCTACAAAATCGCACACGACT-ATGTGCCCCACAAGAC
** * *
430119 CTATTCACACGGGCTACAAAATTACACACGGCCGTA
64 CTACCCACACGGGCTACAAAATAACACAC-GAC-TA
* * * *
430155 TGT-CTCACAT-GCCTACCCACACGGGCTACAAAATAAG-ACACGACTGTGTGCCCCACATGGCC
1 TGTGCTCACATAGCCTACCCACACGGGCTACAAAAT-CGCACACGACTATGTGCCCCACAAGACC
*
430217 TACCCATACGGGCTACAAAATAACACACGACTA
65 TACCCACACGGGCTACAAAATAACACACGACTA
* * * *
430250 TGTGCCCTACATGGCCTACCCACACGGGCTACACAATCACACA
1 TGTGCTC-ACATAGCCTACCCACACGGGCTACAAAATCGCACA
430293 TGTTCGTGTG
Statistics
Matches: 117, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
95 5 0.04
96 4 0.03
97 69 0.59
98 36 0.31
100 3 0.03
ACGTcount: A:0.31, C:0.35, G:0.16, T:0.18
Consensus pattern (97 bp):
TGTGCTCACATAGCCTACCCACACGGGCTACAAAATCGCACACGACTATGTGCCCCACAAGACCT
ACCCACACGGGCTACAAAATAACACACGACTA
Found at i:434657 original size:235 final size:233
Alignment explanation
Indices: 434248--434717 Score: 832
Period size: 235 Copynumber: 2.0 Consensus size: 233
434238 ACAAAAAAAA
*
434248 ACCAGTATTTAGAGAAATAAAAAAAAGTTACCTTCAATGAATAGCTGTAATAGTTAAAGATTATG
1 ACCAGTATTTAGAGAAATAAAAAAAAGTTACCTTCAATGAATAGCTGCAATAGTTAAAGATTATG
434313 TTTGGATGTTAATTACCATAGACCATTGATTCAATCAAATTCGAGTTTAACTTTTACCCATTACA
66 TTTGGATGTTAATTACCATAGACCATTGATTCAATCAAATTCGAGTTTAACTTTTACCCATTACA
*
434378 AGACTTGGAAATGTTAGACAGAGCTGAAGTAGGGTATTTGGATTTGTTAAGAAACAAAGCATGGT
131 AGACTTGGAAATGTTAAACAGAGCTGAAGTAGGGTATTTGGATTTGTTAAGAAACAAAGCATGGT
* * *
434443 AATGGAGAAAAGACAGAGAATTTAGAGGTTGAAATAAC
196 AATGGAGAAAAGAAAGAGAATTCAAAGGTTGAAATAAC
434481 ACCAGTATTTAGAGAAATAAAAAAAAAAGTTACCTTCAATGAATAGCTGCAATAGTTAAAGATTA
1 ACCAGTATTTAGAGAAAT--AAAAAAAAGTTACCTTCAATGAATAGCTGCAATAGTTAAAGATTA
* * *
434546 TGTTTGGATGTTCATTAGCATAGACCATTGATTCAATCAAATTCGAGTTTAACTTTTACCTATTA
64 TGTTTGGATGTTAATTACCATAGACCATTGATTCAATCAAATTCGAGTTTAACTTTTACCCATTA
* *
434611 CAAGACTTGGAAATGTTAAACAGAGCTGAAGTAGGGTATTTGGATTTGTTAAGAAATAGAGCATG
129 CAAGACTTGGAAATGTTAAACAGAGCTGAAGTAGGGTATTTGGATTTGTTAAGAAACAAAGCATG
434676 GTAATGGAGAAAAGAAAGAGAATTCAAAGGTTGAAATAAC
194 GTAATGGAGAAAAGAAAGAGAATTCAAAGGTTGAAATAAC
434716 AC
1 AC
434718 AGGAACCTGT
Statistics
Matches: 225, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
233 18 0.08
235 207 0.92
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (233 bp):
ACCAGTATTTAGAGAAATAAAAAAAAGTTACCTTCAATGAATAGCTGCAATAGTTAAAGATTATG
TTTGGATGTTAATTACCATAGACCATTGATTCAATCAAATTCGAGTTTAACTTTTACCCATTACA
AGACTTGGAAATGTTAAACAGAGCTGAAGTAGGGTATTTGGATTTGTTAAGAAACAAAGCATGGT
AATGGAGAAAAGAAAGAGAATTCAAAGGTTGAAATAAC
Found at i:436447 original size:41 final size:40
Alignment explanation
Indices: 436372--436537 Score: 172
Period size: 41 Copynumber: 4.1 Consensus size: 40
436362 GTTTTTTTAT
* *
436372 AAACACCGCAAAAGGTAA-AGCATTAGCGGTGTTTATGAGA
1 AAACA-CGCAAAAGGTAAGAGCATTAGTGGCGTTTATGAGA
* *
436412 AAACACAGAAAAAGGTAAGAGCATTAGTGGCGTTTACGAGA
1 AAACAC-GCAAAAGGTAAGAGCATTAGTGGCGTTTATGAGA
* * *
436453 AAACGTCGCAAAAGGTAAGAGAATTAGTGGCATTTATGAGA
1 AAAC-ACGCAAAAGGTAAGAGCATTAGTGGCGTTTATGAGA
** ** * *
436494 AAACGTTGCAAAAGGTTGGAGCATTAGTGGTGTTTATGGGA
1 AAAC-ACGCAAAAGGTAAGAGCATTAGTGGCGTTTATGAGA
436535 AAA
1 AAA
436538 AAGCCGCTAA
Statistics
Matches: 107, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.01
40 15 0.14
41 90 0.84
42 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.22
Consensus pattern (40 bp):
AAACACGCAAAAGGTAAGAGCATTAGTGGCGTTTATGAGA
Found at i:436507 original size:82 final size:81
Alignment explanation
Indices: 436378--436569 Score: 197
Period size: 82 Copynumber: 2.3 Consensus size: 81
436368 TTATAAACAC
* **
436378 CGCAAAAGGTAAAGCATTAGCGGTGTTTATGAGAAAACACAGAAAAAGGTAAGAGCATTAGTGGC
1 CGCAAAAGGTAAAGAATTAGCGGCATTTATGAGAAAACACAGAAAAAGGTAAGAGCATTAGTGGC
436443 GTTTACGAGAAAACGT
66 GTTTACGAGAAAACGT
* *** * **
436459 CGCAAAAGGTAAGAGAATTAGTGGCATTTATGAGAAAACGTTGCAAAAGGTTGGAGCATTAGTGG
1 CGCAAAAGGTAA-AGAATTAGCGGCATTTATGAGAAAACACAGAAAAAGGTAAGAGCATTAGTGG
* * * * *
436524 TGTTTATGGGAAAAAAGC
65 CGTTTACGAG-AAAACGT
* *
436542 CGCTAAAGGTTAAGCAA-TAGCGGCATTT
1 CGCAAAAGGTAAAG-AATTAGCGGCATTT
436570 TCCCATAAAC
Statistics
Matches: 90, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
81 12 0.13
82 61 0.68
83 17 0.19
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.22
Consensus pattern (81 bp):
CGCAAAAGGTAAAGAATTAGCGGCATTTATGAGAAAACACAGAAAAAGGTAAGAGCATTAGTGGC
GTTTACGAGAAAACGT
Found at i:438110 original size:43 final size:42
Alignment explanation
Indices: 438040--438160 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
438030 ATAAAGGCAC
* * * *
438040 AAAAAGTA-A-AGCAATAGTGACGTTTATGGGAATAACACCGT
1 AAAAAGTATAGAGCAATAGCGGCGTTTAT-GCAAAAACACCGT
* * *
438081 AAAAGGTATAGAGCAATAGCGGCGCTTATGCAAAAACACTGT
1 AAAAAGTATAGAGCAATAGCGGCGTTTATGCAAAAACACCGT
* * *
438123 AAAAAGTCTAGAGCATTAGCGGCGTTTATAGAAAAAAC
1 AAAAAGTATAGAGCAATAGCGGCGTTTAT-GCAAAAAC
438161 GCCGAAAGTA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 7 0.11
42 36 0.55
43 22 0.34
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (42 bp):
AAAAAGTATAGAGCAATAGCGGCGTTTATGCAAAAACACCGT
Found at i:457620 original size:30 final size:29
Alignment explanation
Indices: 457573--457638 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
457563 TACTTTTTTT
457573 TTTTTAAATTTTAATTAAGTT-TCCAAAA
1 TTTTTAAATTTTAATTAAGTTATCCAAAA
* **
457601 TTTTTAAATATTATTATTAAGTTATTGAAAA
1 TTTTTAAAT-TT-TAATTAAGTTATCCAAAA
457632 TTTTTAA
1 TTTTTAA
457639 TTAAAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 9 0.28
29 2 0.06
30 9 0.28
31 12 0.38
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (29 bp):
TTTTTAAATTTTAATTAAGTTATCCAAAA
Found at i:457721 original size:31 final size:30
Alignment explanation
Indices: 457681--457759 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
457671 TAAAATCTTT
* *
457681 AAAATTTTTGAAAATTTTAATTACAACTAAC
1 AAAAATTTTGAAAATTTT-ATTAAAACTAAC
* * **
457712 AAAAGTTTTGAAAAATCTTATTAAAACTCTC
1 AAAAATTTTG-AAAATTTTATTAAAACTAAC
457743 AAAAATTTT-AAAATTTT
1 AAAAATTTTGAAAATTTT
457760 TTGTTAGAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 7 0.17
31 26 0.65
32 7 0.17
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (30 bp):
AAAAATTTTGAAAATTTTATTAAAACTAAC
Found at i:457901 original size:58 final size:57
Alignment explanation
Indices: 457837--457973 Score: 148
Period size: 58 Copynumber: 2.4 Consensus size: 57
457827 AATATAACAA
* ** * * *
457837 TTGGTACCTAAATTTTTTTTACTCAATTTAGTATTTGAATTTGACATTTTTTCTTAAT
1 TTGGTACCTAAATTTTTTTTACCCAATTTAGTACCTAAACTTGACA-TTTTTCCTAAT
* * * *
457895 TTGGTACCAAAATTTTTTTGGACCCAATTTGGTACCTAAACTTGGCATTTTTCCTAAT
1 TTGGTACCTAAATTTTTTT-TACCCAATTTAGTACCTAAACTTGACATTTTTCCTAAT
* *
457953 TTGATACCTAAGTTTTTTTTA
1 TTGGTACCTAAATTTTTTTTA
457974 AAATTCAATT
Statistics
Matches: 64, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
57 1 0.02
58 44 0.69
59 19 0.30
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.50
Consensus pattern (57 bp):
TTGGTACCTAAATTTTTTTTACCCAATTTAGTACCTAAACTTGACATTTTTCCTAAT
Found at i:458415 original size:23 final size:24
Alignment explanation
Indices: 458385--458430 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
458375 TCATTAATAA
458385 ATAAATGAG-TCATAAACGAGCTC
1 ATAAATGAGCTCATAAACGAGCTC
**
458408 ATAAATGAGCTTTTAAACGAGCT
1 ATAAATGAGCTCATAAACGAGCT
458431 TATTTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (24 bp):
ATAAATGAGCTCATAAACGAGCTC
Found at i:460416 original size:23 final size:23
Alignment explanation
Indices: 460390--460459 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
460380 TTTATTTAAC
*
460390 TTAATCGAACATGTTCGCGAACA
1 TTAATCGAACATGTTCACGAACA
* * **
460413 TTAAACGAATATGTTCATTAACA
1 TTAATCGAACATGTTCACGAACA
* *
460436 TATAATTGAACATGTTTACGAACA
1 T-TAATCGAACATGTTCACGAACA
460460 ATGTTAATGA
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:460570 original size:12 final size:12
Alignment explanation
Indices: 460553--460618 Score: 64
Period size: 12 Copynumber: 5.5 Consensus size: 12
460543 TTAATAAATA
460553 AACGAGTCAATG
1 AACGAGTCAATG
* *
460565 AACGAG-CTTATA
1 AACGAGTC-AATG
460577 AACGAGTCAATG
1 AACGAGTCAATG
* *
460589 AACGAG-CTTATA
1 AACGAGTC-AATG
460601 AACGAGTCAATG
1 AACGAGTCAATG
460613 AACGAG
1 AACGAG
460619 CTTATAAACG
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (12 bp):
AACGAGTCAATG
Found at i:460582 original size:24 final size:24
Alignment explanation
Indices: 460550--460630 Score: 162
Period size: 24 Copynumber: 3.4 Consensus size: 24
460540 TCATTAATAA
460550 ATAAACGAGTCAATGAACGAGCTT
1 ATAAACGAGTCAATGAACGAGCTT
460574 ATAAACGAGTCAATGAACGAGCTT
1 ATAAACGAGTCAATGAACGAGCTT
460598 ATAAACGAGTCAATGAACGAGCTT
1 ATAAACGAGTCAATGAACGAGCTT
460622 ATAAACGAG
1 ATAAACGAG
460631 CTTGTTCGTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (24 bp):
ATAAACGAGTCAATGAACGAGCTT
Found at i:460628 original size:12 final size:12
Alignment explanation
Indices: 460565--460633 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
460555 CGAGTCAATG
460565 AACGAGCTTATA
1 AACGAGCTTATA
* *
460577 AACGAG-TCAATG
1 AACGAGCT-TATA
460589 AACGAGCTTATA
1 AACGAGCTTATA
* *
460601 AACGAG-TCAATG
1 AACGAGCT-TATA
460613 AACGAGCTTATA
1 AACGAGCTTATA
460625 AACGAGCTT
1 AACGAGCTT
460634 GTTCGTGAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (12 bp):
AACGAGCTTATA
Found at i:461845 original size:16 final size:16
Alignment explanation
Indices: 461812--461862 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
461802 AAAACATATA
* *
461812 AAAAAAATAACATCCAA
1 AAAAAAACAACA-ACAA
*
461829 ACAAAAAA-AATAACAA
1 A-AAAAAACAACAACAA
461845 AAAAAAACAACAACAA
1 AAAAAAACAACAACAA
461861 AA
1 AA
461863 GCAGCATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 13 0.45
17 4 0.14
18 6 0.21
ACGTcount: A:0.78, C:0.16, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAAAAACAACAACAA
Found at i:461903 original size:21 final size:21
Alignment explanation
Indices: 461848--461923 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
461838 ATAACAAAAA
**
461848 AAAACAACAACAAAAGCAGCATT
1 AAAACAACAA-AAAA-CAGCACC
* *
461871 AAAATAATAAAAAACAGCACC
1 AAAACAACAAAAAACAGCACC
* * *
461892 AAAACAGCAAAAAATAGTACC
1 AAAACAACAAAAAACAGCACC
461913 AAAACAACAAA
1 AAAACAACAAA
461924 CAAAACAACA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 31 0.72
22 4 0.09
23 8 0.19
ACGTcount: A:0.66, C:0.20, G:0.07, T:0.08
Consensus pattern (21 bp):
AAAACAACAAAAAACAGCACC
Found at i:461936 original size:33 final size:33
Alignment explanation
Indices: 461891--461966 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
461881 AAAACAGCAC
* * *
461891 CAAAACAGCAAAAAATAGTACC-AAAACAACAAA
1 CAAAACAACAAAAAACA-CACCAAAAACAACAAA
461924 CAAAACAACAAAAAACACACCAAAAACAACAAA
1 CAAAACAACAAAAAACACACCAAAAACAACAAA
461957 -AAAACAACAA
1 CAAAACAACAA
461967 TATAATTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 13 0.33
33 26 0.67
ACGTcount: A:0.71, C:0.24, G:0.03, T:0.03
Consensus pattern (33 bp):
CAAAACAACAAAAAACACACCAAAAACAACAAA
Found at i:461937 original size:21 final size:21
Alignment explanation
Indices: 461925--461966 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
461915 AACAACAAAC
* *
461925 AAAACAACAAAAAACACACCA
1 AAAACAACAAAAAAAACAACA
461946 AAAACAAC-AAAAAAACAACA
1 AAAACAACAAAAAAAACAACA
461966 A
1 A
461967 TATAATTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (21 bp):
AAAACAACAAAAAAAACAACA
Found at i:461950 original size:11 final size:10
Alignment explanation
Indices: 461913--461966 Score: 63
Period size: 11 Copynumber: 5.0 Consensus size: 10
461903 AAATAGTACC
461913 AAAACAACAAA
1 AAAACAAC-AA
461924 CAAAACAACAA
1 -AAAACAACAA
*
461935 AAAACACACCA
1 AAAACA-ACAA
461946 AAAACAACAAA
1 AAAACAAC-AA
461957 AAAACAACAA
1 AAAACAACAA
461967 TATAATTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 10 0.26
11 20 0.53
12 8 0.21
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAACAACAA
Found at i:472907 original size:20 final size:21
Alignment explanation
Indices: 472868--472907 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
472858 TTAATTTTCC
*
472868 TATTGTTATTTTCAATAATTT
1 TATTGTTATTTTCAAAAATTT
*
472889 TATT-TTATTTTTAAAAATT
1 TATTGTTATTTTCAAAAATT
472908 CAAATCTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
TATTGTTATTTTCAAAAATTT
Found at i:481213 original size:19 final size:19
Alignment explanation
Indices: 481174--481260 Score: 79
Period size: 19 Copynumber: 4.5 Consensus size: 19
481164 TTTCATCCCA
* *
481174 AAAAAATAAA-AAAATAA-
1 AAAAAAGAAAGAAAAAAAG
* *
481191 AAAAAAGGAAGAGAAAAAG
1 AAAAAAGAAAGAAAAAAAG
481210 AAAAAAGAAAGAAAAAAAG
1 AAAAAAGAAAGAAAAAAAG
*
481229 AAAAACAAAAAGAAAAAAGAAG
1 AAAAA-AGAAAG-AAAAA-AAG
*
481251 GAAAAAGAAA
1 AAAAAAGAAA
481261 AGGAGATGTC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
17 8 0.14
18 5 0.09
19 22 0.39
20 5 0.09
21 9 0.16
22 7 0.12
ACGTcount: A:0.82, C:0.01, G:0.15, T:0.02
Consensus pattern (19 bp):
AAAAAAGAAAGAAAAAAAG
Found at i:481225 original size:31 final size:31
Alignment explanation
Indices: 481190--481256 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
481180 TAAAAAAATA
* * *
481190 AAAAAAAGGAAGAGAAAAAGAAAAAAGAAAG
1 AAAAAAAGAAAAACAAAAAGAAAAAAGAAAG
*
481221 AAAAAAAGAAAAACAAAAAGAAAAAAGAAGG
1 AAAAAAAGAAAAACAAAAAGAAAAAAGAAAG
481252 AAAAA
1 AAAAA
481257 GAAAAGGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (31 bp):
AAAAAAAGAAAAACAAAAAGAAAAAAGAAAG
Found at i:481264 original size:12 final size:11
Alignment explanation
Indices: 481173--481262 Score: 65
Period size: 12 Copynumber: 7.7 Consensus size: 11
481163 ATTTCATCCC
*
481173 AAAAAAATAAA
1 AAAAAAAGAAA
481184 AAAATAAA-AAA
1 AAAA-AAAGAAA
* *
481195 AAGGAAGAGAAAA
1 AA-AAAAAG-AAA
481208 AGAAAAAAGAAA
1 A-AAAAAAGAAA
481220 GAAAAAAAGAAA
1 -AAAAAAAGAAA
481232 AACAAAAAGAAA
1 AA-AAAAAGAAA
* *
481244 AAAGAAGGAAA
1 AAAAAAAGAAA
*
481255 AAGAAAAG
1 AAAAAAAG
481263 GAGATGTCGA
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
11 25 0.40
12 28 0.44
13 9 0.14
14 1 0.02
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:482454 original size:51 final size:51
Alignment explanation
Indices: 482346--482617 Score: 382
Period size: 51 Copynumber: 5.3 Consensus size: 51
482336 AATGACATAG
* ** * * *
482346 AGTCATCAGACCTCTTCTTCCATATAGGAATTCATATACTCACGATGACACTG
1 AGTCATCGGACCT-TTAATCCATAAAGG-ATTCATTTACTCACGATGACACTT
* * *
482399 AGTCATCGGACCTTTAATCCATCATGGATTCATTTACTCACGATGAGACTT
1 AGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTT
* *
482450 AGTCATCGGACCTTTAATCCATAAAGGATTTATTTACTCATGATGACACTT
1 AGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTT
*
482501 AGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTT
1 AGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTT
* * *
482552 AGTCATTGGACTTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTT
1 AGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTT
*
482603 AATCATCGGACCTTT
1 AGTCATCGGACCTTT
482618 TCGTTTATAG
Statistics
Matches: 197, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
51 176 0.89
52 9 0.05
53 12 0.06
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
AGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTT
Found at i:489448 original size:51 final size:51
Alignment explanation
Indices: 489336--489573 Score: 302
Period size: 51 Copynumber: 4.6 Consensus size: 51
489326 TTTTATTTAA
* ** * * *
489336 TACTCACGATGACA-TATAGTTATCAGACCTCTTGTTCCATATAAGAATTCATA
1 TACTCACGATGACACT-TAGTCATCAGACCT-TTAATCCATA-ATGGATTCATT
* *
489389 TACTCACGATGACACTGAGTCATC-GAACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCAG-ACCTTTAATCCATAATGGATTCATT
* * *
489440 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCATAATGGATTCATT
*
489491 TACTCACGATGACACTTTGTCATCAGACCTTTAATCCATAAAT-GATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCAT-AATGGATTCATT
489542 TACTCACGATGACACTTAGTCATCAGACCTTT
1 TACTCACGATGACACTTAGTCATCAGACCTTT
489574 TCGTTTATAG
Statistics
Matches: 164, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
51 128 0.78
52 11 0.07
53 24 0.15
54 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCAGACCTTTAATCCATAATGGATTCATT
Found at i:491626 original size:49 final size:48
Alignment explanation
Indices: 491555--491973 Score: 222
Period size: 49 Copynumber: 8.6 Consensus size: 48
491545 TGGAAATAAA
*
491555 GGGAAAAGTTGAGGCCGCAACGGCGAACCAGGTACCTTAGAAACATGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCA-GTACCTTAGAAACATGAT
* * * * *
491604 GGGAAAGGTTGAGGCCGTAACGGCAAATCC-GATACCAT-GAAGATATGAA
1 GGGAAAGGTTGAGGCCGCAACGGCGAA-CCAG-TACCTTAGAA-ACATGAT
* * * * *
491653 GGGAAAGATTGAGGCCACAGCGGTGAACCCTGTACCTTAGAAGACATGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAA-CCAGTACCTTAGAA-ACATGAT
* * * * * * * * * *
491703 GGGAAAGATCGAGGTCGCAACGGCAGATCTATTACCAT-GGAA-ATAAA
1 GGGAAAGGTTGAGGCCGCAACGGC-GAACCAGTACCTTAGAAACATGAT
* * * * * *
491750 GGGAAACGTCGAGGTCGCAACGGCGAGCCTGGTACCTTAGAAACGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAACC-AGTACCTTAGAAACATGAT
* * ** * * *
491799 GAGAAAGGTTGAGGCCGTAACGATGAACCTTGTCCCTTA-AAAGATG-T
1 GGGAAAGGTTGAGGCCGCAACGGCGAACC-AGTACCTTAGAAACATGAT
* * * * * * * * *
491846 GAAGGGAAGGATCGAGGCCGCAACGGTGGATCTAGTACCAT-GAAAATATAAA
1 G--GGAAAGG-TTGAGGCCGCAACGG-CGAACCAGTACCTTAG-AAACATGAT
* *
491898 GGGAAAGGTTGAGGCCACAACAGCGAACCTAGTACCTTAGAAACATGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAACC-AGTACCTTAGAAACATGAT
* * *
491947 AGGAAAGATTGAAGCCGCAACGGCGAA
1 GGGAAAGGTTGAGGCCGCAACGGCGAA
491974 TCTTATACCT
Statistics
Matches: 270, Mismatches: 82, Indels: 36
0.70 0.21 0.09
Matches are distributed among these distances:
46 3 0.01
47 32 0.12
48 16 0.06
49 147 0.54
50 61 0.23
51 10 0.04
52 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.30, T:0.16
Consensus pattern (48 bp):
GGGAAAGGTTGAGGCCGCAACGGCGAACCAGTACCTTAGAAACATGAT
Found at i:491904 original size:195 final size:195
Alignment explanation
Indices: 491511--491918 Score: 464
Period size: 195 Copynumber: 2.1 Consensus size: 195
491501 ATCATTTCTC
* *
491511 AAAGATCGAGGCCGCAACGGGAGATATAGTACCATGGAAATAAAGGGAAAAGTTGAGGCCGCAAC
1 AAAGATCGAGGCCGCAACGGCAGATATAGTACCATGGAAATAAAGGGAAAAGTCGAGGCCGCAAC
* *
491576 GGCGAACCAGGTACCTTAGAAACATGATGGGAAAGGTTGAGGCCGTAACGGCAAATCCGATACCA
66 GGCGAACCAGGTACCTTAGAAACATGATGAGAAAGGTTGAGGCCGTAACGACAAATCCGATACCA
* * * * * * *
491641 TGAAGATATGAAGGGAAAGATTGAGGCCACAGCGGTGAACCCTGTACCTTAGAAGACATGATGGG
131 TAAAGATATGAAGGGAAAGATCGAGGCCACAACGGTGAACCCTGTACCATAGAAAACATAAAGGG
* * * * *
491706 AAAGATCGAGGTCGCAACGGCAGATCTATTACCATGGAAATAAAGGGAAACGTCGAGGTCGCAAC
1 AAAGATCGAGGCCGCAACGGCAGATATAGTACCATGGAAATAAAGGGAAAAGTCGAGGCCGCAAC
* * * ** *
491771 GGCGAGCCTGGTACCTTAGAAACGTGATGAGAAAGGTTGAGGCCGTAACGATGAA-CCTTG-TCC
66 GGCGAACCAGGTACCTTAGAAACATGATGAGAAAGGTTGAGGCCGTAACGACAAATCC--GATAC
* * * * * * *
491834 CTTAAAAGATGTGAAGGGAAGGATCGAGGCCGCAACGGTGGA-TCTAGTACCAT-GAAAATATAA
129 CAT-AAAGATATGAAGGGAAAGATCGAGGCCACAACGGTGAACCCT-GTACCATAGAAAACATAA
491897 AGGG
192 AGGG
* * *
491901 AAAGGTTGAGGCCACAAC
1 AAAGATCGAGGCCGCAAC
491919 AGCGAACCTA
Statistics
Matches: 176, Mismatches: 33, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
194 2 0.01
195 136 0.77
196 38 0.22
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.16
Consensus pattern (195 bp):
AAAGATCGAGGCCGCAACGGCAGATATAGTACCATGGAAATAAAGGGAAAAGTCGAGGCCGCAAC
GGCGAACCAGGTACCTTAGAAACATGATGAGAAAGGTTGAGGCCGTAACGACAAATCCGATACCA
TAAAGATATGAAGGGAAAGATCGAGGCCACAACGGTGAACCCTGTACCATAGAAAACATAAAGGG
Found at i:492489 original size:27 final size:28
Alignment explanation
Indices: 492454--492517 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 28
492444 TTTGGAGATT
*
492454 TTTTCATTAAT-TAATTAGTTAAATA-TTA
1 TTTT-ATTAATAT-ATTACTTAAATATTTA
*
492482 TTTTATTAATATTTTACTTAAATATTTA
1 TTTTATTAATATATTACTTAAATATTTA
492510 TTATTATT
1 TT-TTATT
492518 TTATTTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 16 0.52
28 10 0.32
29 5 0.16
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTTATTAATATATTACTTAAATATTTA
Found at i:492507 original size:13 final size:11
Alignment explanation
Indices: 492480--492522 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
492470 AGTTAAATAT
492480 TATTTTATTAA
1 TATTTTATTAA
492491 TATTTTACTTAA
1 TATTTTA-TTAA
*
492503 -ATATTTATTAT
1 TAT-TTTATTAA
492514 TATTTTATT
1 TATTTTATT
492523 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:495005 original size:96 final size:93
Alignment explanation
Indices: 494873--495117 Score: 337
Period size: 96 Copynumber: 2.6 Consensus size: 93
494863 AGTGGGTCGG
* * * **
494873 GTCAAAACAACTAAGAAGAGCTCAACGTCCTTGAGGTTATAGTGGAGTGGAGTGAGTCTTCAAAT
1 GTCAAAACAA--AACAA-AGCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAAACTTCAAAT
494938 CTCATCTTCCTGGTGAGGTACAAAGAAGTGA
63 CTCATCTTCCTGGTGAGGTACAAAGAAGTGA
* *
494969 GTCAAAATAATGAAGCAAAGCTCAATGTCCCTGAGGTTACAGTGGAGTGGAGTGAAACTTCAAAT
1 GTCAAAACAA--AA-CAAAGCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAAACTTCAAAT
* *
495034 CTCATCTTCCTGGTGAGGTATAGAGAAGTGA
63 CTCATCTTCCTGGTGAGGTACAAAGAAGTGA
* *
495065 GTCAAAACAAAACAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAA
1 GTCAAAACAAAACAAAGCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAA
495118 GTAGCAAATC
Statistics
Matches: 133, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
93 38 0.29
94 2 0.02
96 91 0.68
97 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (93 bp):
GTCAAAACAAAACAAAGCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAAACTTCAAATCTC
ATCTTCCTGGTGAGGTACAAAGAAGTGA
Found at i:495455 original size:76 final size:76
Alignment explanation
Indices: 495268--495551 Score: 435
Period size: 76 Copynumber: 3.8 Consensus size: 76
495258 AATGAAGCGG
* * *
495268 TCATCTTCTTGATAAGATACAGAGAAATAGACCAAAATCAATGAAGCAGAGCTCAATGTGAGTGA
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAATCAATGAAGCAGAGCTCAATGTGAGTGA
495333 AACTTC-AACC
66 AACTTCAAACC
* * *
495343 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAATGAATGAAGCGGAGCTCAATTTGAGTGA
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAATCAATGAAGCAGAGCTCAATGTGAGTGA
495408 AACTTCAAACC
66 AACTTCAAACC
* * * *
495419 CCATCTTCCTGATGAGATATAGAGAAGTAGACCAAAATCAATGAAACGGAGCTCAATGTGAGTGA
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAATCAATGAAGCAGAGCTCAATGTGAGTGA
495484 AACTTCAAACC
66 AACTTCAAACC
* * * *
495495 TTATCTTCCTGATGAGATACAGAGAAGTAAACAAAAATCAATGAAGTAGAGCTCAAT
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAATCAATGAAGCAGAGCTCAAT
495552 AAAAGTAGAC
Statistics
Matches: 189, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
75 65 0.34
76 124 0.66
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (76 bp):
TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAATCAATGAAGCAGAGCTCAATGTGAGTGA
AACTTCAAACC
Found at i:497212 original size:29 final size:28
Alignment explanation
Indices: 497158--497212 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
497148 TAAAAGTTTG
**
497158 GTTTTGACCCTAAGTTTTCAAAAATTAC
1 GTTTTGACCCTAAACTTTCAAAAATTAC
*
497186 GTTTTGACCCATAAACTTTCCAAAATT
1 GTTTTGACCC-TAAACTTTCAAAAATT
497213 TAATTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (28 bp):
GTTTTGACCCTAAACTTTCAAAAATTAC
Found at i:497668 original size:26 final size:24
Alignment explanation
Indices: 497638--497685 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
497628 CAATCTCGTC
497638 AATTACGTGCATTCATATTTTTATTT
1 AATTACGTG--TTCATATTTTTATTT
* *
497664 AATTATGTGTTCATTTTTTTAT
1 AATTACGTGTTCATATTTTTAT
497686 ATTTTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
26 8 0.40
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.58
Consensus pattern (24 bp):
AATTACGTGTTCATATTTTTATTT
Found at i:498616 original size:29 final size:27
Alignment explanation
Indices: 498583--498644 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
498573 ATAAACTATA
*
498583 AAAAATTGTAAAAAAAATAAATATAATAT
1 AAAAATTG--AAAAAAATAAATACAATAT
* * *
498612 AAAAATTGAGAAAAATATATACAATCT
1 AAAAATTGAAAAAAATAAATACAATAT
498639 AAAAAT
1 AAAAAT
498645 ATATATGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 21 0.72
29 8 0.28
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (27 bp):
AAAAATTGAAAAAAATAAATACAATAT
Found at i:498728 original size:41 final size:38
Alignment explanation
Indices: 498680--498756 Score: 93
Period size: 38 Copynumber: 1.9 Consensus size: 38
498670 AAAATGGAAA
498680 GAAATAATAAACAATATATAAATAATAT-AAAAAATATATGT
1 GAAATAAT-AA-AATATATAAA-AA-ATCAAAAAATATATGT
* *
498721 GAAATAATTAAATATATAAAAAATCAGAAAATATAT
1 GAAATAATAAAATATATAAAAAATCAAAAAATATAT
498757 AAAATCTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 2 0.06
38 12 0.36
39 10 0.30
40 1 0.03
41 8 0.24
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.29
Consensus pattern (38 bp):
GAAATAATAAAATATATAAAAAATCAAAAAATATATGT
Found at i:498744 original size:19 final size:19
Alignment explanation
Indices: 498692--498760 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
498682 AATAATAAAC
498692 AATATATAAATAATATAA-AA
1 AATATATAAA-AA-ATAAGAA
*** **
498712 AATATATGTGAAATAATTA
1 AATATATAAAAAATAAGAA
*
498731 AATATATAAAAAATCAGAA
1 AATATATAAAAAATAAGAA
498750 AATATATAAAA
1 AATATATAAAA
498761 TCTAATTATA
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
18 4 0.11
19 27 0.71
20 7 0.18
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (19 bp):
AATATATAAAAAATAAGAA
Found at i:498782 original size:116 final size:112
Alignment explanation
Indices: 498660--498897 Score: 268
Period size: 116 Copynumber: 2.1 Consensus size: 112
498650 TGTCAAATAT
* *
498660 TAAAATTATAAAAATGGAAAGAAA-TAATAAACAAT-ATATAAATAATA-TAAAAAATATATGTG
1 TAAAATTATAAAAATGGAAAGAAAGT-ATAAAAAATCATATAAATAA-ACTAAAAAATATATAT-
* *
498722 AAATAATTAAATATATAAAAAATCAGAA-AATATATAAAATCTAATTATATACA
63 -AATAATTAAATATATAAAAAATCAGAACAACATATAAAATCCAA--A-ATACA
* * ** **
498775 TATAAATTATTAAAATGGAAAGAAAGTATAAAAAATCATATATATAAACTCTAATTTATATATAA
1 TA-AAATTATAAAAATGGAAAGAAAGTATAAAAAATCATATAAATAAACTAAAAAATATATATAA
* *
498840 TAATTAAATATATAAAAATTTAGAACAACATATAAAATCCAAAATACA
65 TAATTAAATATATAAAAAATCAGAACAACATATAAAATCCAAAATACA
498888 TAAAATTATA
1 TAAAATTATA
498898 TATACAAGAT
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
112 7 0.07
113 7 0.07
114 1 0.01
115 27 0.26
116 44 0.42
117 19 0.18
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (112 bp):
TAAAATTATAAAAATGGAAAGAAAGTATAAAAAATCATATAAATAAACTAAAAAATATATATAAT
AATTAAATATATAAAAAATCAGAACAACATATAAAATCCAAAATACA
Found at i:499489 original size:2 final size:2
Alignment explanation
Indices: 499484--499525 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
499474 AATATATGTG
499484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
499526 AAATAATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:509170 original size:20 final size:20
Alignment explanation
Indices: 509145--509192 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
509135 TTTTTGTTGT
509145 AATTAGGTTTAGGGTTTCT-A
1 AATTAGGTTTA-GGTTTCTAA
*
509165 AATTAGGGTTTAGGTTTTTAA
1 AATTA-GGTTTAGGTTTCTAA
509186 AATTAGG
1 AATTAGG
509193 GTTTTAGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.29, C:0.02, G:0.25, T:0.44
Consensus pattern (20 bp):
AATTAGGTTTAGGTTTCTAA
Found at i:509176 original size:21 final size:21
Alignment explanation
Indices: 509145--509196 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
509135 TTTTTGTTGT
509145 AATTA-GGTTTAGGGTTTCT-A
1 AATTAGGGTTTA-GGTTTCTAA
*
509165 AATTAGGGTTTAGGTTTTTAA
1 AATTAGGGTTTAGGTTTCTAA
509186 AATTAGGGTTT
1 AATTAGGGTTT
509197 TAGTATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (21 bp):
AATTAGGGTTTAGGTTTCTAA
Found at i:509205 original size:21 final size:21
Alignment explanation
Indices: 509164--509205 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
509154 TAGGGTTTCT
*
509164 AAATTAGGGTTTAGGTTTTTA
1 AAATTAGGGTTTAGGTATTTA
509185 AAATTAGGGTTTTA-GTATTTA
1 AAATTAGGG-TTTAGGTATTTA
509206 TTTTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (21 bp):
AAATTAGGGTTTAGGTATTTA
Found at i:511781 original size:27 final size:26
Alignment explanation
Indices: 511743--511825 Score: 100
Period size: 27 Copynumber: 3.3 Consensus size: 26
511733 TTAAAAAATT
*
511743 TAATTAAATTATAAAAATAATATAAAA
1 TAATTAAATTATAAAAATAAAAT-AAA
511770 TAATTAAATTATAAAAATAAAATAAA
1 TAATTAAATTATAAAAATAAAATAAA
* * *
511796 TAA-TAAATAAT-ATAATAAAATTAA
1 TAATTAAATTATAAAAATAAAATAAA
511820 -AATTAA
1 TAATTAA
511826 CTCTTACCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
23 2 0.04
24 14 0.27
25 7 0.14
26 6 0.12
27 22 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
TAATTAAATTATAAAAATAAAATAAA
Found at i:512006 original size:10 final size:11
Alignment explanation
Indices: 511980--512012 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
511970 TTAAAGAGAT
511980 ATTGAGAGAAA
1 ATTGAGAGAAA
511991 ATTGAGAGAAA
1 ATTGAGAGAAA
*
512002 A-TGAGTGAAA
1 ATTGAGAGAAA
512012 A
1 A
512013 ATAAAAGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.55, C:0.00, G:0.27, T:0.18
Consensus pattern (11 bp):
ATTGAGAGAAA
Found at i:517672 original size:14 final size:15
Alignment explanation
Indices: 517644--517682 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
517634 ATAAAATAGG
517644 AAATAATAAATTTTAA
1 AAATAA-AAATTTTAA
517660 AAATAAAAA-TTTAA
1 AAATAAAAATTTTAA
517674 AAGATAAAA
1 AA-ATAAAA
517683 TTAACTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.32
15 9 0.41
16 6 0.27
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAATAAAAATTTTAA
Found at i:518400 original size:19 final size:18
Alignment explanation
Indices: 518344--518409 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 18
518334 AAATTATAAA
*
518344 AATAAAAATAAATAAAAATT
1 AATAAAAAT--ATAAAATTT
* *
518364 -ATAAAAATTATTAGATTT
1 AATAAAAA-TATAAAATTT
518382 CAATAAAAATATAAAATTT
1 -AATAAAAATATAAAATTT
*
518401 ATTAAAAAT
1 AATAAAAAT
518410 CAGAATTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
18 14 0.38
19 15 0.41
20 8 0.22
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AATAAAAATATAAAATTT
Found at i:518644 original size:12 final size:12
Alignment explanation
Indices: 518627--518651 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
518617 AAAAATCAAT
518627 AAAAATTATAAA
1 AAAAATTATAAA
518639 AAAAATTATAAA
1 AAAAATTATAAA
518651 A
1 A
518652 TGCTTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:518687 original size:11 final size:10
Alignment explanation
Indices: 518671--518838 Score: 67
Period size: 9 Copynumber: 17.6 Consensus size: 10
518661 TATTACGATA
518671 ATTTTTATAAT
1 ATTTTTAT-AT
*
518682 ATTTTTTTAT
1 ATTTTTATAT
*
518692 GAATTTTATAT
1 -ATTTTTATAT
518703 -TTCTTTATAT
1 ATT-TTTATAT
*
518713 TTTTTTATA-
1 ATTTTTATAT
*
518722 ATTTTT-TAGG
1 ATTTTTATA-T
* * *
518732 A-CTATA-AA
1 ATTTTTATAT
518740 AT-TTTATA-
1 ATTTTTATAT
*
518748 ATTTATTCTAT
1 ATTT-TTATAT
518759 ATTTTTATAT
1 ATTTTTATAT
518769 ATTTTTATA-
1 ATTTTTATAT
*
518778 ATTTTTA-AG
1 ATTTTTATAT
518787 ATTTTTATA-
1 ATTTTTATAT
** *
518796 A-AATTATAC
1 ATTTTTATAT
518805 ACTTTTTATA-
1 A-TTTTTATAT
*
518815 ATTTTTA-CT
1 ATTTTTATAT
518824 ATTTTTATA-
1 ATTTTTATAT
518833 ATTTTT
1 ATTTTT
518839 TTCTAATTTT
Statistics
Matches: 122, Mismatches: 17, Indels: 38
0.69 0.10 0.21
Matches are distributed among these distances:
8 14 0.11
9 46 0.38
10 36 0.30
11 26 0.21
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:518744 original size:58 final size:56
Alignment explanation
Indices: 518676--518783 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 56
518666 CGATAATTTT
* * * * *
518676 TATAATATTTTTTTATGAATTTTATATTTCTTTATATTTTTTTATAATTTTTTAGGAC
1 TATAAAATTTTATAATGAATTCTATA-TT-TTTATATATTTTTATAATTTTTTAGGAC
**
518734 TATAAAATTTTATAATTTATTCTATATTTTTATATATTTTTATAATTTTT
1 TATAAAATTTTATAATGAATTCTATATTTTTATATATTTTTATAATTTTT
518784 AAGATTTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
56 21 0.49
57 2 0.05
58 20 0.47
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (56 bp):
TATAAAATTTTATAATGAATTCTATATTTTTATATATTTTTATAATTTTTTAGGAC
Found at i:518781 original size:9 final size:9
Alignment explanation
Indices: 518741--518838 Score: 85
Period size: 9 Copynumber: 10.4 Consensus size: 9
518731 GACTATAAAA
518741 TTTTATAAT
1 TTTTATAAT
*
518750 TTATTCTATAT
1 TT-TTATA-AT
518761 TTTTATATAT
1 TTTTATA-AT
518771 TTTTATAAT
1 TTTTATAAT
518780 TTTTA-AGAT
1 TTTTATA-AT
518789 TTTTATAA-
1 TTTTATAAT
**
518797 AATTATACACT
1 TTTTATA-A-T
518808 TTTTATAAT
1 TTTTATAAT
518817 TTTTACT-AT
1 TTTTA-TAAT
518826 TTTTATAAT
1 TTTTATAAT
518835 TTTT
1 TTTT
518839 TTCTAATTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
8 7 0.09
9 37 0.50
10 21 0.28
11 9 0.12
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:518838 original size:28 final size:28
Alignment explanation
Indices: 518741--518852 Score: 81
Period size: 28 Copynumber: 4.0 Consensus size: 28
518731 GACTATAAAA
*
518741 TTTTATAATTTATTCTAT-ATTTTTATATAT
1 TTTTATAATTT-TT-TATAATTTTTA-CTAT
*
518771 TTTTATAA-TTTTTA-AGATTTTTA-TAA
1 TTTTATAATTTTTTATA-ATTTTTACTAT
** *
518797 AATTATACACTTTTTATAATTTTTACTAT
1 TTTTATA-ATTTTTTATAATTTTTACTAT
*
518826 TTTTATAATTTTTTTCTAA-TTTTACTA
1 TTTTATAA-TTTTTTATAATTTTTACTA
518853 AAATTTAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
26 7 0.10
27 3 0.04
28 31 0.46
29 18 0.27
30 8 0.12
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (28 bp):
TTTTATAATTTTTTATAATTTTTACTAT
Found at i:518905 original size:24 final size:23
Alignment explanation
Indices: 518867--518911 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
518857 TTAAATATAT
518867 TTTTATTAAAATTTAATTTTTAGC
1 TTTTATTAAAATTT-ATTTTTAGC
**
518891 TTTTATTAATTTTTATTTTTA
1 TTTTATTAAAATTTATTTTTA
518912 TCATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTATTAAAATTTATTTTTAGC
Found at i:518910 original size:16 final size:16
Alignment explanation
Indices: 518879--518923 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
518869 TTATTAAAAT
*
518879 TTAATTTTTAGCTTTTA
1 TTAATTTTTA-TTTTTA
518896 TTAATTTTTATTTTTA
1 TTAATTTTTATTTTTA
* *
518912 TCATTTTTTATT
1 TTAATTTTTATT
518924 ACATGTCATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (16 bp):
TTAATTTTTATTTTTA
Found at i:519906 original size:23 final size:24
Alignment explanation
Indices: 519857--519900 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
519847 AAATTTCAAT
519857 AAATAAAACAAATATTAAATATCA
1 AAATAAAACAAATATTAAATATCA
*
519881 AAATAAAA-TAATA-TAAATAT
1 AAATAAAACAAATATTAAATAT
519901 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 4 0.21
24 8 0.42
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (24 bp):
AAATAAAACAAATATTAAATATCA
Found at i:523331 original size:30 final size:28
Alignment explanation
Indices: 523297--523383 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 28
523287 CAATAAAAGC
523297 AAATTCAACAGCAATTATTAAAAATTATAG
1 AAATTCAA-AG-AATTATTAAAAATTATAG
* * * *
523327 AAATTTAAA-AATAATTAAAAATAATAA
1 AAATTCAAAGAATTATTAAAAATTATAG
* *
523354 AAAATCAAAGAAATTATAAAAAAATTATAG
1 AAATTCAAAG-AATTAT-TAAAAATTATAG
523384 GAATATATTA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
27 22 0.50
29 6 0.14
30 16 0.36
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (28 bp):
AAATTCAAAGAATTATTAAAAATTATAG
Found at i:524068 original size:9 final size:9
Alignment explanation
Indices: 524054--524078 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
524044 ATGAGATTTA
524054 AATATTTTT
1 AATATTTTT
524063 AATATTTTT
1 AATATTTTT
524072 AATATTT
1 AATATTT
524079 AATTGAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
AATATTTTT
Found at i:525344 original size:45 final size:45
Alignment explanation
Indices: 525280--525367 Score: 176
Period size: 45 Copynumber: 2.0 Consensus size: 45
525270 TTTCGACAAG
525280 ATTAATTGATTCGTAATGACTTAAATGTCATCGATTGATCCGAAT
1 ATTAATTGATTCGTAATGACTTAAATGTCATCGATTGATCCGAAT
525325 ATTAATTGATTCGTAATGACTTAAATGTCATCGATTGATCCGA
1 ATTAATTGATTCGTAATGACTTAAATGTCATCGATTGATCCGA
525368 TTATCACCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (45 bp):
ATTAATTGATTCGTAATGACTTAAATGTCATCGATTGATCCGAAT
Found at i:527592 original size:15 final size:15
Alignment explanation
Indices: 527572--527601 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
527562 TAATCCTTCT
*
527572 TCCTATCCTTCTCAC
1 TCCTATCCTTATCAC
527587 TCCTATCCTTATCAC
1 TCCTATCCTTATCAC
527602 CTCTTTCCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (15 bp):
TCCTATCCTTATCAC
Found at i:537471 original size:58 final size:58
Alignment explanation
Indices: 537396--537888 Score: 386
Period size: 58 Copynumber: 8.7 Consensus size: 58
537386 AAAGGTTTAT
* * * * *
537396 CACAAAGACATTTCTTTAACAAAGATCGCCACAAATGCTTTCCTGTCCACAGTTTTGC
1 CACAAAGGCATTCCTTTAACAAAGATCACCACAAAGGCTTTCCTGTCCAGAGTTTTGC
* ** * ** * *
537454 CACAAAGACATTCCTTTAACAAAGATTTCCACAAAAGCTTTATTGTCTAGAGTGTTGC
1 CACAAAGGCATTCCTTTAACAAAGATCACCACAAAGGCTTTCCTGTCCAGAGTTTTGC
* * * * * * *
537512 CATAAAGG-AGTTACTTTAACAGAGATCTCCATAAAGGC--T--T-T-----GTTGTAC
1 CACAAAGGCA-TTCCTTTAACAAAGATCACCACAAAGGCTTTCCTGTCCAGAGTTTTGC
* * * * * * *
537560 CACAAAGGCAAT-CTTTAATAGAGATCACCACAAAGGTTTTTCTGTCTAGAGTTTTGT
1 CACAAAGGCATTCCTTTAACAAAGATCACCACAAAGGCTTTCCTGTCCAGAGTTTTGC
* * * * *
537617 CAAAAAGGCATTCCTTTAACATAGAT-ACCCACAAAGGCTTTCCTTTCCAAAGTTTTTC
1 CACAAAGGCATTCCTTTAACAAAGATCA-CCACAAAGGCTTTCCTGTCCAGAGTTTTGC
* ** * * *
537675 CACGAAGGTGTTCCTTTAACATAA-ATCACGACAAAGGCTTTCCTTTCCAAAAGTTTTGC
1 CACAAAGGCATTCCTTTAACA-AAGATCACCACAAAGGCTTTCCTGTCC-AGAGTTTTGC
* * * * * *
537734 CATAAAGGCGTTCCTTTAATAGAGATCACCACAAAGGCTTTACTGTCCAGATTTTTG-
1 CACAAAGGCATTCCTTTAACAAAGATCACCACAAAGGCTTTCCTGTCCAGAGTTTTGC
* * * * *
537791 CACAAAGGCATTCCTTTAACAGAGATCACCATAAAGTCTTTCTTGTCTAGAGTTTTGC
1 CACAAAGGCATTCCTTTAACAAAGATCACCACAAAGGCTTTCCTGTCCAGAGTTTTGC
**
537849 CACAAAGGCATTCCTTTAACAAAGATCATGACAAAGGCTT
1 CACAAAGGCATTCCTTTAACAAAGATCACCACAAAGGCTT
537889 CTTTATTAGT
Statistics
Matches: 346, Mismatches: 70, Indels: 38
0.76 0.15 0.08
Matches are distributed among these distances:
47 21 0.06
48 12 0.03
49 2 0.01
51 1 0.00
52 1 0.00
53 1 0.00
54 1 0.00
56 1 0.00
57 64 0.18
58 193 0.56
59 49 0.14
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (58 bp):
CACAAAGGCATTCCTTTAACAAAGATCACCACAAAGGCTTTCCTGTCCAGAGTTTTGC
Found at i:537485 original size:29 final size:29
Alignment explanation
Indices: 537396--537488 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
537386 AAAGGTTTAT
* **
537396 CACAAAGACATTTCTTTAACAAAGATCGC
1 CACAAAGACATTCCTTTAACAAAGATTTC
* * * * *
537425 CACAAATG-CTTTCCTGT-CCACAGTTTTGC
1 CACAAA-GACATTCCTTTAACAAAGATTT-C
537454 CACAAAGACATTCCTTTAACAAAGATTTC
1 CACAAAGACATTCCTTTAACAAAGATTTC
537483 CACAAA
1 CACAAA
537489 AGCTTTATTG
Statistics
Matches: 47, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
28 6 0.13
29 33 0.70
30 8 0.17
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.27
Consensus pattern (29 bp):
CACAAAGACATTCCTTTAACAAAGATTTC
Found at i:537677 original size:29 final size:29
Alignment explanation
Indices: 537645--537750 Score: 76
Period size: 29 Copynumber: 3.6 Consensus size: 29
537635 ACATAGATAC
537645 CCACAAAGGCTTTCCTTTCCAAAGTTTTT
1 CCACAAAGGCTTTCCTTTCCAAAGTTTTT
* ***
537674 CCACGAAGG-TGTTCCTTT--AACA-TAAAT
1 CCACAAAGGCT-TTCCTTTCCAA-AGTTTTT
*
537701 CACGACAAAGGCTTTCCTTTCCAAAAGTTTTG
1 C-C-ACAAAGGCTTTCCTTTCC-AAAGTTTTT
* *
537733 CCATAAAGGCGTTCCTTT
1 CCACAAAGGCTTTCCTTT
537751 AATAGAGATC
Statistics
Matches: 57, Mismatches: 11, Indels: 17
0.67 0.13 0.20
Matches are distributed among these distances:
27 5 0.09
28 3 0.05
29 28 0.49
30 15 0.26
31 2 0.04
32 4 0.07
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (29 bp):
CCACAAAGGCTTTCCTTTCCAAAGTTTTT
Found at i:537865 original size:174 final size:175
Alignment explanation
Indices: 537572--537888 Score: 444
Period size: 174 Copynumber: 1.8 Consensus size: 175
537562 CAAAGGCAAT
* * *
537572 CTTTAATAGAGATCACCACAAAGGTTTTTCTGTCTAGAGTTTTGTCAAAAAGGCATTCCTTTAAC
1 CTTTAATAGAGATCACCACAAAGGCTTTACTGTCCAGAGTTTTGTCAAAAAGGCATTCCTTTAAC
* * * **
537637 ATAGATACCCACAAAGGCTTTCCTTTCCAAAGTTTTTCCACGAAGGTGTTCCTTTAACATAA-AT
66 AGAGATACCCACAAAGGCTTTCCTTTCCAAAGTTTTGCCACAAAGGCATTCCTTTAACA-AAGAT
537701 CACGACAAAGGCTTTCCTTTCCAAAAGTTTTGCCATAAAGGCGTTC
130 CACGACAAAGGCTTTCCTTTCCAAAAGTTTTGCCATAAAGGCGTTC
* *
537747 CTTTAATAGAGATCACCACAAAGGCTTTACTGTCCAGATTTTTG-CACAAAGGCATTCCTTTAAC
1 CTTTAATAGAGATCACCACAAAGGCTTTACTGTCCAGAGTTTTGTCAAAAAGGCATTCCTTTAAC
* * * *
537811 AGAGAT-CACCATAAAGTCTTT-CTTGTCTAGAGTTTTGCCACAAAGGCATTCCTTTAACAAAGA
66 AGAGATAC-CCACAAAGGCTTTCCTT-TCCAAAGTTTTGCCACAAAGGCATTCCTTTAACAAAGA
*
537874 TCATGACAAAGGCTT
129 TCACGACAAAGGCTT
537889 CTTTATTAGT
Statistics
Matches: 124, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
173 6 0.05
174 78 0.63
175 40 0.32
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (175 bp):
CTTTAATAGAGATCACCACAAAGGCTTTACTGTCCAGAGTTTTGTCAAAAAGGCATTCCTTTAAC
AGAGATACCCACAAAGGCTTTCCTTTCCAAAGTTTTGCCACAAAGGCATTCCTTTAACAAAGATC
ACGACAAAGGCTTTCCTTTCCAAAAGTTTTGCCATAAAGGCGTTC
Found at i:541490 original size:9 final size:10
Alignment explanation
Indices: 541468--541530 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 10
541458 TCTCTCAATT
541468 TTTTTAATAA
1 TTTTTAATAA
541478 TTTTTAAT--
1 TTTTTAATAA
*
541486 GTTTTAATACA
1 TTTTTAATA-A
541497 TTTTTCAATAA
1 TTTTT-AATAA
541508 -TTTT-ATAA
1 TTTTTAATAA
*
541516 TTTTT-ATTA
1 TTTTTAATAA
541525 TTTTTA
1 TTTTTA
541531 CAACGTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
8 11 0.25
9 12 0.27
10 12 0.27
11 5 0.11
12 4 0.09
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:541662 original size:9 final size:10
Alignment explanation
Indices: 541617--541662 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
541607 ATAAAATTCC
541617 TATA-TTTTA
1 TATATTTTTA
541626 TAT-TTTATTA
1 TATATTT-TTA
541636 TA-ATTTTTA
1 TATATTTTTA
541645 TATATTTTTA
1 TATATTTTTA
541655 -ATATTTTT
1 TATATTTTT
541663 TTCTAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 18 0.55
10 15 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATATTTTTA
Found at i:541663 original size:10 final size:9
Alignment explanation
Indices: 541621--541663 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
541611 AATTCCTATA
541621 TTTTATATT
1 TTTTATATT
541630 TTATTATAATT
1 TT-TTAT-ATT
541641 TTTATATATT
1 TTT-TATATT
*
541651 TTTAATATT
1 TTTTATATT
541660 TTTT
1 TTTT
541664 TCTAAATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 10 0.34
10 11 0.38
11 8 0.28
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATATT
Found at i:541724 original size:19 final size:20
Alignment explanation
Indices: 541702--541748 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
541692 ATTTTTTACA
*
541702 ATTTTTTTAAAAAAA-TTAT
1 ATTTTTATAAAAAAATTTAT
541721 A-TTTTATAAAAAAATTTAT
1 ATTTTTATAAAAAAATTTAT
541740 ATATTTTAT
1 AT-TTTTAT
541749 TGCTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 12 0.50
19 6 0.25
21 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTTATAAAAAAATTTAT
Found at i:542693 original size:16 final size:18
Alignment explanation
Indices: 542672--542704 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
542662 TTTTTGAAAC
542672 TATTT-AATATA-CAAAA
1 TATTTAAATATATCAAAA
542688 TATTTAAATATATCAAA
1 TATTTAAATATATCAAA
542705 TGAATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
TATTTAAATATATCAAAA
Found at i:542744 original size:33 final size:31
Alignment explanation
Indices: 542685--542753 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 31
542675 TTAATATACA
**
542685 AAAT-ATTTAAATATATCAAATGAATTAAATT
1 AAATAATTTAAATATAAAAAATGAATT-AATT
*
542716 AAATAATTTCAAATATAAAAAATTAATTAATT
1 AAATAATTT-AAATATAAAAAATGAATTAATT
*
542748 ATATAA
1 AAATAA
542754 AATACTCATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 4 0.12
32 13 0.41
33 15 0.47
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (31 bp):
AAATAATTTAAATATAAAAAATGAATTAATT
Done.