Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 3 of 16
Found at i:348775 original size:7 final size:8
Alignment explanation
Indices: 348705--348776 Score: 54
Period size: 11 Copynumber: 7.8 Consensus size: 8
348695 TATTTATGTT
348705 ATTTTTTA
1 ATTTTTTA
348713 ATTTTTTCTA
1 A-TTTTT-TA
348723 AGTTTTTTCTA
1 A--TTTTT-TA
348734 ATTTTTCTA
1 ATTTTT-TA
348743 ATTTTTTATAA
1 A-TTTTT-T-A
348754 TATTTTTTA
1 -ATTTTTTA
348763 ATTTTTTA
1 ATTTTTTA
348771 ATTTTT
1 ATTTTT
348777 CTCAATTATT
Statistics
Matches: 57, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
8 15 0.26
9 15 0.26
10 10 0.18
11 16 0.28
12 1 0.02
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (8 bp):
ATTTTTTA
Found at i:348786 original size:29 final size:28
Alignment explanation
Indices: 348705--348796 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 28
348695 TATTTATGTT
*
348705 ATTTTTTAATTTTTTCTAAGTT-TTTTCTA
1 ATTTTTTAATTTTTTC-AA-TTATTTTTTA
*
348734 ATTTTTCTAATTTTTT-ATAATATTTTTTA
1 ATTTTT-TAATTTTTTCA-ATTATTTTTTA
348763 ATTTTTTAATTTTTCTCAATTATTTTTTTA
1 ATTTTTTAATTTTT-TCAATTA-TTTTTTA
348793 ATTT
1 ATTT
348797 CTTAGGTGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
28 10 0.19
29 23 0.43
30 21 0.39
ACGTcount: A:0.24, C:0.05, G:0.01, T:0.70
Consensus pattern (28 bp):
ATTTTTTAATTTTTTCAATTATTTTTTA
Found at i:348790 original size:30 final size:29
Alignment explanation
Indices: 348705--348796 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 29
348695 TATTTATGTT
* *
348705 ATTTTTTAATTTTTTCTAAGT-TTTTTCTA
1 ATTTTTTAATTTTTTC-AATTATTTTTTTA
*
348734 ATTTTTCTAATTTTTT--ATAATATTTTTTA
1 ATTTTT-TAATTTTTTCAATTAT-TTTTTTA
348763 ATTTTTTAATTTTTCTCAATTATTTTTTTA
1 ATTTTTTAATTTTT-TCAATTATTTTTTTA
348793 ATTT
1 ATTT
348797 CTTAGGTGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
27 1 0.02
28 9 0.17
29 19 0.36
30 20 0.38
31 4 0.08
ACGTcount: A:0.24, C:0.05, G:0.01, T:0.70
Consensus pattern (29 bp):
ATTTTTTAATTTTTTCAATTATTTTTTTA
Found at i:349824 original size:13 final size:13
Alignment explanation
Indices: 349806--349840 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
349796 TTTATATTTA
349806 TTTTAATTTTAAT
1 TTTTAATTTTAAT
*
349819 TTTTAATTTTTAT
1 TTTTAATTTTAAT
*
349832 TTATAATTT
1 TTTTAATTT
349841 AAAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:351284 original size:4 final size:4
Alignment explanation
Indices: 351275--351299 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
351265 TTGAGACAAT
351275 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
351300 ATTAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:352419 original size:22 final size:21
Alignment explanation
Indices: 352376--352419 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
352366 TTCCCTATCC
**
352376 TGATTGATTTTTTTTATATTA
1 TGATTGATTTTTTAAATATTA
*
352397 TGATTGAATTTTTTAAATGTTA
1 TGATTG-ATTTTTTAAATATTA
352419 T
1 T
352420 TGATCTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.61
Consensus pattern (21 bp):
TGATTGATTTTTTAAATATTA
Found at i:353536 original size:7 final size:7
Alignment explanation
Indices: 353519--353570 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
353509 GTTTGAAAAC
353519 TTAAA-T
1 TTAAATT
353525 TTAAATT
1 TTAAATT
353532 TTAAAATT
1 TT-AAATT
*
353540 TTAGATT
1 TTAAATT
*
353547 TAAAATT
1 TTAAATT
*
353554 TATAATTT
1 T-TAAATT
353562 TTAAATT
1 TTAAATT
353569 TT
1 TT
353571 TTGTTGAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
6 5 0.14
7 20 0.54
8 12 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:353540 original size:14 final size:14
Alignment explanation
Indices: 353521--353569 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
353511 TTGAAAACTT
353521 AAATTTAAATTTTA
1 AAATTTAAATTTTA
*
353535 AAATTTTAGA-TTTA
1 AAA-TTTAAATTTTA
*
353549 AAATTTATAATTTTT
1 AAATTTA-AATTTTA
353564 AAATTT
1 AAATTT
353570 TTTGTTGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 4 0.14
14 11 0.38
15 14 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
AAATTTAAATTTTA
Found at i:353547 original size:21 final size:21
Alignment explanation
Indices: 353523--353562 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
353513 GAAAACTTAA
*
353523 ATTTAAATTTTAAAATTTTAG
1 ATTTAAAATTTAAAATTTTAG
*
353544 ATTTAAAATTTATAATTTT
1 ATTTAAAATTTAAAATTTT
353563 TAAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTTAAAATTTAAAATTTTAG
Found at i:354311 original size:99 final size:99
Alignment explanation
Indices: 354140--354530 Score: 594
Period size: 99 Copynumber: 4.0 Consensus size: 99
354130 TGTTGTTTCA
* * * *
354140 GTCAGATTTTGTGTAGGCTCTTTCACACCACAGTGTAGTCAAACCTGGTTTCAAATTCATGGGAT
1 GTCAGATTTTGTGTAGGCTCTTCCAAACCACAATGTAGTCAAACCTGGCTTCAAATTCATGGGAT
354205 GGGCAGTCTAATTCGAATGTTCAAACACATTATT
66 GGGCAGTCTAATTCGAATGTTCAAACACATTATT
*
354239 GTCAGATTTTGTGTAGGCTCTTCCAAATCACAATGTAGTCAAACCTGGCTTCAAATTCATGGGAT
1 GTCAGATTTTGTGTAGGCTCTTCCAAACCACAATGTAGTCAAACCTGGCTTCAAATTCATGGGAT
354304 GGGCAGTCTAATTCGAATGTTCAAACACATTATT
66 GGGCAGTCTAATTCGAATGTTCAAACACATTATT
* * *
354338 GTCAGATTTTGTGTAGGCTCTTCCGAACCACAATGTGGTCAAACCTGGCTTCAAATTCATGAGAT
1 GTCAGATTTTGTGTAGGCTCTTCCAAACCACAATGTAGTCAAACCTGGCTTCAAATTCATGGGAT
* *
354403 -GG--G-C-AATTCTAATGTTCAAACACATAATT
66 GGGCAGTCTAATTCGAATGTTCAAACACATTATT
* * * **
354432 GTCAGCTTTTGTGCAGGCTCTTCCAAACCACAATGTAGTCAAACCTGGTTTCAAATTCAACGGAT
1 GTCAGATTTTGTGTAGGCTCTTCCAAACCACAATGTAGTCAAACCTGGCTTCAAATTCATGGGAT
* *
354497 GGGCAGTCTAACTCTAATGTTCAAACACATTATT
66 GGGCAGTCTAATTCGAATGTTCAAACACATTATT
354531 TACTTTTCTC
Statistics
Matches: 266, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
94 80 0.30
95 3 0.01
96 1 0.00
97 1 0.00
98 3 0.01
99 178 0.67
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (99 bp):
GTCAGATTTTGTGTAGGCTCTTCCAAACCACAATGTAGTCAAACCTGGCTTCAAATTCATGGGAT
GGGCAGTCTAATTCGAATGTTCAAACACATTATT
Found at i:354474 original size:193 final size:197
Alignment explanation
Indices: 354140--354530 Score: 594
Period size: 193 Copynumber: 2.0 Consensus size: 197
354130 TGTTGTTTCA
* * * *
354140 GTCAGATTTTGTGTAGGCTCTTTCACACCACAGTGTAGTCAAACCTGGTTTCAAATTCATGGGAT
1 GTCAGATTTTGTGTAGGCTCTTCCACACCACAATGTAGTCAAACCTGGCTTCAAATTCATGAGAT
* * *
354205 GGGCAGTCTAATTCGAATGTTCAAACACATTATTGTCAGATTTTGTGTAGGCTCTTCCAAATCAC
66 GGG-AGTCTAATTCGAATGTTCAAACACATAATTGTCAGATTTTGTGCAGGCTCTTCCAAACCAC
** *
354270 AATGTAGTCAAACCTGGCTTCAAATTCATGGGATGGGCAGTCTAATTCGAATGTTCAAACACATT
130 AATGTAGTCAAACCTGGCTTCAAATTCAACGGATGGGCAGTCTAACTCGAATGTTCAAACACATT
354335 ATT
195 ATT
*
354338 GTCAGATTTTGTGTAGGCTCTTCCGA-ACCACAATGTGGTCAAACCTGGCTTCAAATTCATGAGA
1 GTCAGATTTTGTGTAGGCTCTTCC-ACACCACAATGTAGTCAAACCTGGCTTCAAATTCATGAGA
* *
354402 T-GG-G-C-AATTCTAATGTTCAAACACATAATTGTCAGCTTTTGTGCAGGCTCTTCCAAACCAC
65 TGGGAGTCTAATTCGAATGTTCAAACACATAATTGTCAGATTTTGTGCAGGCTCTTCCAAACCAC
* *
354463 AATGTAGTCAAACCTGGTTTCAAATTCAACGGATGGGCAGTCTAACTCTAATGTTCAAACACATT
130 AATGTAGTCAAACCTGGCTTCAAATTCAACGGATGGGCAGTCTAACTCGAATGTTCAAACACATT
354528 ATT
195 ATT
354531 TACTTTTCTC
Statistics
Matches: 177, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
193 114 0.64
194 1 0.01
195 1 0.01
197 2 0.01
198 58 0.33
199 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (197 bp):
GTCAGATTTTGTGTAGGCTCTTCCACACCACAATGTAGTCAAACCTGGCTTCAAATTCATGAGAT
GGGAGTCTAATTCGAATGTTCAAACACATAATTGTCAGATTTTGTGCAGGCTCTTCCAAACCACA
ATGTAGTCAAACCTGGCTTCAAATTCAACGGATGGGCAGTCTAACTCGAATGTTCAAACACATTA
TT
Found at i:354829 original size:27 final size:28
Alignment explanation
Indices: 354798--354852 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
354788 TATTTTATTA
354798 AATATAAATATAATTTTAATA-ATTTTT
1 AATATAAATATAATTTTAATATATTTTT
* *
354825 AATATAAATGTGATTTTAATATATTTTT
1 AATATAAATATAATTTTAATATATTTTT
354853 TATTATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (28 bp):
AATATAAATATAATTTTAATATATTTTT
Found at i:354846 original size:38 final size:38
Alignment explanation
Indices: 354804--354909 Score: 107
Period size: 36 Copynumber: 2.9 Consensus size: 38
354794 ATTAAATATA
* * *
354804 AATATAATTTTAATAATT-TTTAATATAAATGTGATTTT
1 AATATAATTTT-ATAATTATTTAATATAAATATAAATTT
*
354842 AATAT-ATTTT-TTATTATTTAATATAAATATAAATTT
1 AATATAATTTTATAATTATTTAATATAAATATAAATTT
*
354878 AATAT-ATATTT-T-ATTATTTAATTTAAATATAA
1 AATATAAT-TTTATAATTATTTAATATAAATATAA
354910 TTTTTAATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
35 4 0.07
36 43 0.70
37 9 0.15
38 5 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (38 bp):
AATATAATTTTATAATTATTTAATATAAATATAAATTT
Found at i:354861 original size:19 final size:19
Alignment explanation
Indices: 354839--354899 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
354829 TAAATGTGAT
*
354839 TTTAATATATTTTTTATTA
1 TTTAATATATATTTTATTA
* * *
354858 TTTAATATA-AATATA-AA
1 TTTAATATATATTTTATTA
354875 TTTAATATATATTTTATTA
1 TTTAATATATATTTTATTA
354894 TTTAAT
1 TTTAAT
354900 TTAAATATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 10 0.30
18 7 0.21
19 16 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTAATATATATTTTATTA
Found at i:354863 original size:36 final size:36
Alignment explanation
Indices: 354822--354927 Score: 142
Period size: 36 Copynumber: 2.9 Consensus size: 36
354812 TTTAATAATT
* *
354822 TTTAATATAAATGTGATTTTAATATATTTTTTATTA
1 TTTAATATAAATATAATTTTAATATATTTTTTATTA
* *
354858 TTTAATATAAATATAAATTTAATATATATTTTATTA
1 TTTAATATAAATATAATTTTAATATATTTTTTATTA
* *
354894 TTTAATTTAAATATAATTTTTAAT-TATTTATTAT
1 TTTAATATAAATATAA-TTTTAATATATTTTTTAT
354928 ATGCATACAT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 55 0.90
37 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (36 bp):
TTTAATATAAATATAATTTTAATATATTTTTTATTA
Found at i:354899 original size:72 final size:68
Alignment explanation
Indices: 354775--354927 Score: 155
Period size: 72 Copynumber: 2.2 Consensus size: 68
354765 ATTTTATTTT
* * * *
354775 TTATTTTTATATTTATTTTATTAAATATAAATATAATTTTAATAATTTTTAATATAAATGTGA-T
1 TTATTTTT-TA-TTATTTAATTAAATATAAATATAATTATAATAATTTTTAATATAAATATAATT
354839 TTTAA
64 TTTAA
* * * *
354844 TATATTTTTTATTATTTAATATAAATATAAATTTAATATATATTTTATTATTTAATTTAAATATA
1 T-TATTTTTTATTATTTAAT-TAAATATAAATATAAT-TATA-ATAATT-TTTAATATAAATATA
354909 ATTTTTAA
61 ATTTTTAA
*
354917 TTATTTATTAT
1 TTATTTTTTAT
354928 ATGCATACAT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
68 8 0.12
69 18 0.26
70 10 0.14
71 4 0.06
72 22 0.32
73 7 0.10
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (68 bp):
TTATTTTTTATTATTTAATTAAATATAAATATAATTATAATAATTTTTAATATAAATATAATTTT
TAA
Found at i:354914 original size:25 final size:25
Alignment explanation
Indices: 354873--354923 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 25
354863 TATAAATATA
354873 AATTTAATATATATTTT-ATTATTT
1 AATTTAATATATATTTTAATTATTT
354897 AATTTAA-ATATAATTTTTAATTATTT
1 AATTTAATATAT-A-TTTTAATTATTT
354923 A
1 A
354924 TTATATGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 4 0.17
24 8 0.33
25 4 0.17
26 8 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
AATTTAATATATATTTTAATTATTT
Found at i:355390 original size:2 final size:2
Alignment explanation
Indices: 355383--355414 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
355373 AAATTCATTT
355383 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
355415 AAATGAAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:355685 original size:25 final size:25
Alignment explanation
Indices: 355644--355691 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
355634 TTAAATATTT
355644 TATAAAAAAAAGTTAAT-TAAAATA
1 TATAAAAAAAAGTTAATATAAAATA
*
355668 TATAAAATAAAATTTAATATAAAA
1 TATAAAA-AAAAGTTAATATAAAA
355692 ATAATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 9 0.43
26 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
TATAAAAAAAAGTTAATATAAAATA
Found at i:355775 original size:16 final size:17
Alignment explanation
Indices: 355725--355775 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 17
355715 TATTATTTAT
355725 TAATATATAATAAATTAAA
1 TAATATATAATAAA--AAA
*
355744 TATTATTATAATAAAAAA
1 TAATA-TATAATAAAAAA
355762 TAATATAT-ATAAAA
1 TAATATATAATAAAA
355776 TTGATTGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 6 0.21
17 3 0.10
18 7 0.24
19 4 0.14
20 9 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAATATATAATAAAAAA
Found at i:369529 original size:24 final size:24
Alignment explanation
Indices: 369485--369531 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
369475 TTGTTTATGT
**
369485 TATTAATTATTTTTAATTAACTTA
1 TATTAATTATTAATAATTAACTTA
369509 TATTAATTATATAATAA-TAACTT
1 TATTAATTAT-TAATAATTAACTT
369532 TTAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTAATTATTAATAATTAACTTA
Found at i:369794 original size:14 final size:14
Alignment explanation
Indices: 369775--369816 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
369765 ATCATGTTGA
369775 AATATTTAATATAT
1 AATATTTAATATAT
*
369789 AATATTT-ATATTT
1 AATATTTAATATAT
*
369802 AAAATTTTAATATAT
1 AATA-TTTAATATAT
369817 TTAATAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 8 0.35
14 10 0.43
15 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATATTTAATATAT
Found at i:369817 original size:17 final size:19
Alignment explanation
Indices: 369795--369837 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
369785 ATATAATATT
369795 TATATTTAA-AATTT-TAA
1 TATATTTAATAATTTATAA
*
369812 TATATTTAATAATTTATAT
1 TATATTTAATAATTTATAA
369831 TATATTT
1 TATATTT
369838 TTATTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.39
18 5 0.22
19 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTTAATAATTTATAA
Found at i:369840 original size:30 final size:28
Alignment explanation
Indices: 369774--369831 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 28
369764 AATCATGTTG
369774 AAATATTTAATATATAATATTTATATTTA
1 AAAT-TTTAATATATAATATTTATATTTA
369803 AAATTTTAATATATTTAATAATTTATATT
1 AAATTTTAATATA--TAAT-ATTTATATT
369832 ATATTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 9 0.35
29 4 0.15
30 4 0.15
31 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AAATTTTAATATATAATATTTATATTTA
Found at i:370027 original size:21 final size:18
Alignment explanation
Indices: 369999--370054 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 18
369989 GGGTAAGGAG
369999 AGAAAAGGAGGGAAAGCGAA
1 AGAAAAGGAGGGAAA--GAA
370019 AGAAAAAGGAGCGAGAAAGAA
1 AG-AAAAGGAG-G-GAAAGAA
*
370040 AGAAAAGGAAGGAAA
1 AGAAAAGGAGGGAAA
370055 AGGGAAGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
18 4 0.12
19 1 0.03
20 9 0.28
21 13 0.41
22 1 0.03
23 4 0.12
ACGTcount: A:0.61, C:0.04, G:0.36, T:0.00
Consensus pattern (18 bp):
AGAAAAGGAGGGAAAGAA
Found at i:370674 original size:21 final size:20
Alignment explanation
Indices: 370633--370679 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
370623 TAATCATTTT
*
370633 TATTTAAAGTTTAAATAATA
1 TATTTAAAGATTAAATAATA
* *
370653 TATTTAAAGAATTAATTCATA
1 TATTTAAAG-ATTAAATAATA
370674 TATTTA
1 TATTTA
370680 CTCACGAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
TATTTAAAGATTAAATAATA
Found at i:371428 original size:34 final size:37
Alignment explanation
Indices: 371358--371445 Score: 84
Period size: 34 Copynumber: 2.6 Consensus size: 37
371348 TCTAAAATTA
*
371358 TATT-AAA-AAATTTAAA--AAAATTATATTAATATT
1 TATTGAAATAAATTTAAATTAAAATAATATTAATATT
* *
371391 TATT-AATTAAATTTAAATTAAAATAATATT-TTA-T
1 TATTGAAATAAATTTAAATTAAAATAATATTAATATT
*
371425 TATTGAAAT-AATTTGAATTAA
1 TATTGAAATAAATTTAAATTAA
371446 TTGAATGAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
33 6 0.13
34 25 0.54
35 5 0.11
36 10 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (37 bp):
TATTGAAATAAATTTAAATTAAAATAATATTAATATT
Found at i:371698 original size:15 final size:16
Alignment explanation
Indices: 371673--371703 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
371663 TATCATATAT
371673 TTTACTATTATTTTTA
1 TTTACTATTATTTTTA
371689 TTTA-TATTATTTTTA
1 TTTACTATTATTTTTA
371704 AAATATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTACTATTATTTTTA
Found at i:372873 original size:24 final size:25
Alignment explanation
Indices: 372846--372894 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
372836 TAATATAATG
*
372846 TATTT-TAATATTTTTAAATTTTTT
1 TATTTATAATATTTTAAAATTTTTT
*
372870 TATTTATATTATTTTAAAATTTTTT
1 TATTTATAATATTTTAAAATTTTTT
372895 AATAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TATTTATAATATTTTAAAATTTTTT
Found at i:374394 original size:16 final size:15
Alignment explanation
Indices: 374370--374418 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
374360 CTTATTTATA
374370 TCATATTTTTTATAAT
1 TCATATTTTTTA-AAT
*
374386 TCATTTTTTTTAAAT
1 TCATATTTTTTAAAT
* *
374401 GCATATTTTTAAAAT
1 TCATATTTTTTAAAT
374416 TCA
1 TCA
374419 ATCTTTATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (15 bp):
TCATATTTTTTAAAT
Found at i:375272 original size:12 final size:13
Alignment explanation
Indices: 375244--375280 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
375234 CTTCAATTGC
*
375244 CAAAATTTTTATT
1 CAAAATTATTATT
375257 CAAAATTATT-TT
1 CAAAATTATTATT
375269 CAAAA-TATTATT
1 CAAAATTATTATT
375281 AAAGTTTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 4 0.18
12 9 0.41
13 9 0.41
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (13 bp):
CAAAATTATTATT
Found at i:376946 original size:11 final size:11
Alignment explanation
Indices: 376930--376999 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
376920 TTAACATAAT
376930 ATAATAAATTA
1 ATAATAAATTA
376941 ATAATAATATT-
1 ATAATAA-ATTA
* *
376952 ATTATAATTTA
1 ATAATAAATTA
* *
376963 AAAATAAAATA
1 ATAATAAATTA
*
376974 TTAAATAAA-TA
1 AT-AATAAATTA
*
376985 ATTATAAATTA
1 ATAATAAATTA
376996 ATAA
1 ATAA
377000 ATTTTAATTT
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
10 7 0.16
11 28 0.64
12 9 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATAATAAATTA
Found at i:376947 original size:14 final size:14
Alignment explanation
Indices: 376926--376999 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
376916 ATAATTAACA
376926 TAAT-ATAATAAAT
1 TAATAATAATAAAT
*
376939 TAATAATAATATTAT
1 TAATAATAATA-AAT
376954 T-ATAATTTAA-AAA-
1 TAATAA--TAATAAAT
*
376967 TAA-AATATTAAAT
1 TAATAATAATAAAT
* *
376980 AAATAATTATAAAT
1 TAATAATAATAAAT
376994 TAATAA
1 TAATAA
377000 ATTTTAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 15
0.68 0.10 0.22
Matches are distributed among these distances:
11 2 0.04
12 3 0.07
13 9 0.20
14 25 0.54
15 4 0.09
16 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATAATAATAAAT
Found at i:377646 original size:38 final size:38
Alignment explanation
Indices: 377595--377668 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
377585 CTTTGGACAG
* * * *
377595 TAGAGAAGTCATCGACGTCTAAATTGGTTTAGAAAAAT
1 TAGAGAAATCATCGAAGTCTAAATTAGTGTAGAAAAAT
*
377633 TAGAGAAATCATCGAAGTTTAAATTAGTGTAGAAAA
1 TAGAGAAATCATCGAAGTCTAAATTAGTGTAGAAAA
377669 GTAATGTATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.28
Consensus pattern (38 bp):
TAGAGAAATCATCGAAGTCTAAATTAGTGTAGAAAAAT
Found at i:378644 original size:21 final size:24
Alignment explanation
Indices: 378612--378666 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
378602 AATATATTAT
378612 TTTATATTTA-TTG-ATATTT-TAA
1 TTTAT-TTTATTTGCATATTTATAA
378634 TATT-TTTTATTTGCATATTTATAA
1 T-TTATTTTATTTGCATATTTATAA
378658 TTTATTTTA
1 TTTATTTTA
378667 AAATTTCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
21 4 0.14
22 5 0.18
23 10 0.36
24 9 0.32
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTATTTTATTTGCATATTTATAA
Found at i:378717 original size:15 final size:15
Alignment explanation
Indices: 378677--378750 Score: 85
Period size: 15 Copynumber: 4.8 Consensus size: 15
378667 AAATTTCTTA
*
378677 ATAAAATATATATTAT
1 ATAAAATATA-AATAT
*
378693 ATACACATATAAATAT
1 ATA-AAATATAAATAT
*
378709 ATAAAATATAAATTT
1 ATAAAATATAAATAT
*
378724 ATAAATTATAAATAT
1 ATAAAATATAAATAT
*
378739 TTAAAATATAAA
1 ATAAAATATAAA
378751 ATTTTAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
15 33 0.67
16 10 0.20
17 6 0.12
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATATAAATAT
Found at i:378717 original size:23 final size:23
Alignment explanation
Indices: 378680--378750 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
378670 TTTCTTAATA
** *
378680 AAATATATATTATATACACATAT
1 AAATATATAAAATATAAACATAT
**
378703 AAATATATAAAATATAAATTTAT
1 AAATATATAAAATATAAACATAT
*
378726 AAAT-TATAAATATTTAAA-ATAT
1 AAATATATAAA-ATATAAACATAT
378748 AAA
1 AAA
378751 ATTTTAAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
22 12 0.30
23 28 0.70
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATATATAAAATATAAACATAT
Found at i:378734 original size:30 final size:29
Alignment explanation
Indices: 378677--378772 Score: 95
Period size: 30 Copynumber: 3.1 Consensus size: 29
378667 AAATTTCTTA
*
378677 ATAAAATATATATTATATACACATATAAATAT
1 ATAAAATATAAATT-TATA-A-ATATAAATAT
378709 ATAAAATATAAATTTATAAATTATAAATAT
1 ATAAAATATAAATTTATAAA-TATAAATAT
* * *
378739 TTAAAATATAAAATTT-TAAAAATCAAATAA
1 ATAAAATAT-AAATTTATAAATAT-AAATAT
378769 ATAA
1 ATAA
378773 GTATAAAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
29 3 0.05
30 30 0.54
31 10 0.18
32 13 0.23
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (29 bp):
ATAAAATATAAATTTATAAATATAAATAT
Found at i:378766 original size:14 final size:16
Alignment explanation
Indices: 378699--378794 Score: 71
Period size: 15 Copynumber: 6.3 Consensus size: 16
378689 TTATATACAC
*
378699 ATAT-AAATATATAAA
1 ATATAAAATATTTAAA
378714 ATAT-AAAT-TTATAAA
1 ATATAAAATATT-TAAA
*
378729 TTAT-AAATATTTAAA
1 ATATAAAATATTTAAA
378744 ATATAAAAT-TTTAAA
1 ATATAAAATATTTAAA
* **
378759 A-ATCAAATAAAT-AA
1 ATATAAAATATTTAAA
*
378773 GTATAAAATATTTAAAA
1 ATATAAAATATTT-AAA
378790 ATATA
1 ATATA
378795 TTAAATGTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
14 9 0.14
15 42 0.67
16 6 0.10
17 6 0.10
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (16 bp):
ATATAAAATATTTAAA
Found at i:379831 original size:14 final size:14
Alignment explanation
Indices: 379814--379881 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 14
379804 TTTAAGCCTA
379814 TTTAT-ATTATATTT
1 TTTATAATT-TATTT
379828 TTTATAATTTATTT
1 TTTATAATTTATTT
* *
379842 TTTAAAAATATATATT
1 TTT-ATAATTTAT-TT
*
379858 TTTA-AATTTAATT
1 TTTATAATTTATTT
379871 TTTATTAATTT
1 TTTA-TAATTT
379882 TTTATCAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
13 6 0.13
14 18 0.40
15 16 0.36
16 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATAATTTATTT
Found at i:381962 original size:27 final size:27
Alignment explanation
Indices: 381941--381991 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
381931 GTGATGTATG
*
381941 CTAAA-ATGGTGAAAATTATGATGACA
1 CTAAAGATAGTGAAAATTATGATGACA
381967 CTAAAGATAGTGAAAATTATGATGA
1 CTAAAGATAGTGAAAATTATGATGA
381992 TTGAAATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (27 bp):
CTAAAGATAGTGAAAATTATGATGACA
Found at i:389435 original size:33 final size:35
Alignment explanation
Indices: 389356--389442 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 35
389346 GTATAGTAAA
**
389356 AATAAATAATAATTATTTTAAATATTAAATTAAAATT
1 AATAAATAATAAAAATTTTAAATATT--ATTAAAATT
* * *
389393 TATATATAATAAAAATTTTAAAT-TT-TTTAAATT
1 AATAAATAATAAAAATTTTAAATATTATTAAAATT
*
389426 AATAAATAATTAAAATT
1 AATAAATAATAAAAATT
389443 ATATTTTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
33 21 0.50
36 2 0.05
37 19 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (35 bp):
AATAAATAATAAAAATTTTAAATATTATTAAAATT
Found at i:389441 original size:17 final size:17
Alignment explanation
Indices: 389383--389443 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
389373 TTAAATATTA
* *
389383 AATTAAAATTTATATAT
1 AATTAAAATTAATAAAT
* *
389400 AATAAAAATT-TTAAAT
1 AATTAAAATTAATAAAT
** *
389416 TTTTTAAATTAATAAAT
1 AATTAAAATTAATAAAT
389433 AATTAAAATTA
1 AATTAAAATTA
389444 TATTTTTTTC
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
16 10 0.31
17 22 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTAAAATTAATAAAT
Found at i:389699 original size:7 final size:7
Alignment explanation
Indices: 389689--389734 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
389679 ATTCATATAA
389689 AATATTT
1 AATATTT
389696 AATATTT
1 AATATTT
389703 AATATTT
1 AATATTT
389710 -ATATTT
1 AATATTT
389716 -ATATTT
1 AATATTT
*
389722 AAAATTTT
1 AATA-TTT
389730 AATAT
1 AATAT
389735 ATTTAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 12 0.34
7 17 0.49
8 6 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATATTT
Found at i:389715 original size:6 final size:6
Alignment explanation
Indices: 389690--389767 Score: 54
Period size: 6 Copynumber: 12.7 Consensus size: 6
389680 TTCATATAAA
* *
389690 ATATTT AATATTT AATATTT ATATTT ATATTT AAAATTT -TA-AT ATATTT
1 ATATTT -ATATTT -ATATTT ATATTT ATATTT -ATATTT ATATTT ATATTT
* *
389739 AATAATTT ATA-TT ATTTTT ATATCT ATAT
1 -AT-ATTT ATATTT ATATTT ATATTT ATAT
389768 AACTAATACA
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
4 1 0.02
5 7 0.12
6 24 0.41
7 22 0.38
8 4 0.07
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (6 bp):
ATATTT
Found at i:389754 original size:17 final size:18
Alignment explanation
Indices: 389697--389755 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 18
389687 AAAATATTTA
389697 ATATTTAAT-ATTTATATTT
1 ATATTTAATAATTTATA--T
389716 ATATTTAA-AATTT-TAAT
1 ATATTTAATAATTTAT-AT
389733 ATATTTAATAATTTATAT
1 ATATTTAATAATTTATAT
389751 -TATTT
1 ATATTT
389756 TTATATCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 14 0.39
18 8 0.22
19 14 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATTTAATAATTTATAT
Found at i:390161 original size:139 final size:137
Alignment explanation
Indices: 389993--390264 Score: 388
Period size: 139 Copynumber: 2.0 Consensus size: 137
389983 AAGTGAGAAC
* * *
389993 GGAGAAAAAAATAGAAAATTTTATGCAATTGTTTTGGTTTTTTGTTTATATATT-ATTTTT-TGC
1 GGAGAAAAAAAGAAAAAATTTTATGCAATTGTTTTGATTTTTTGTTTATATATTGATTTTTATGC
* * *
390056 ATGGTTAAAGTATTAAAAATTTATTTATTTTTTTAATTATCA-GAATGAAAAATCACATTTATAT
66 --GGTTAAAATATTAAAAATTTATTTATTTTTTT-ATTAT-ATGAACGAAAAATCACATATATAT
390120 TATTTTTGAAG
127 TATTTTTGAAG
* *
390131 GGAGAAAGAAAAGAAAAAATTTTGTGCAATTGTTTTGATTTTTTGTTTATATGTTGATTTTTATG
1 GGAGAAA-AAAAGAAAAAATTTTATGCAATTGTTTTGATTTTTTGTTTATATATTGATTTTTATG
* *
390196 CGTTTAAAATATTAAAATTTTATTTATTTTTTTATTATATGAACGAAAAATCACATATATATTAT
65 CGGTTAAAATATTAAAAATTTATTTATTTTTTTATTATATGAACGAAAAATCACATATATATTAT
390261 TTTT
130 TTTT
390265 CATATCGTGT
Statistics
Matches: 120, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
137 1 0.01
138 39 0.32
139 71 0.59
140 6 0.05
141 3 0.03
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (137 bp):
GGAGAAAAAAAGAAAAAATTTTATGCAATTGTTTTGATTTTTTGTTTATATATTGATTTTTATGC
GGTTAAAATATTAAAAATTTATTTATTTTTTTATTATATGAACGAAAAATCACATATATATTATT
TTTGAAG
Found at i:397983 original size:14 final size:14
Alignment explanation
Indices: 397966--398009 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
397956 CCTATATCAT
*
397966 ATTTTTTATAATTC
1 ATTTTTTAAAATTC
*
397980 ATTTTTTAAAATGC
1 ATTTTTTAAAATTC
397994 ATATTTTTAAAATTC
1 AT-TTTTTAAAATTC
398009 A
1 A
398010 ATCTTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (14 bp):
ATTTTTTAAAATTC
Found at i:398016 original size:14 final size:14
Alignment explanation
Indices: 397968--398016 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
397958 TATATCATAT
* *
397968 TTTTTATAATTCAT
1 TTTTTAAAATTCAA
*
397982 TTTTTAAAATGCATA
1 TTTTTAAAATTCA-A
397997 TTTTTAAAATTCAA
1 TTTTTAAAATTCAA
*
398011 TCTTTA
1 TTTTTA
398017 TTAATTTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (14 bp):
TTTTTAAAATTCAA
Found at i:400891 original size:10 final size:10
Alignment explanation
Indices: 400872--400915 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
400862 AAAAATATTA
*
400872 TTAAAATAAT
1 TTAAATTAAT
400882 TTAAATTAAT
1 TTAAATTAAT
400892 TTAAATTAAT
1 TTAAATTAAT
*
400902 ATAAATTAAAT
1 TTAAATT-AAT
400913 TTA
1 TTA
400916 TTGAATCTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 25 0.83
11 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TTAAATTAAT
Found at i:403027 original size:17 final size:15
Alignment explanation
Indices: 402997--403044 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
402987 TATAATTATT
402997 TTTAAAATA-TAATA
1 TTTAAAATATTAATA
403011 TTTAAAATATTTAA-A
1 TTTAAAATA-TTAATA
403026 TATT-AAATATTAATA
1 T-TTAAAATATTAATA
403041 TTTA
1 TTTA
403045 TAATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 15 0.52
15 9 0.31
16 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTAAAATATTAATA
Found at i:403462 original size:14 final size:14
Alignment explanation
Indices: 403445--403490 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
403435 ACTTATATTA
*
403445 TATTTTTTATAATT
1 TATTTTTTAAAATT
*
403459 TATTTTTTAAAAATA
1 TATTTTTT-AAAATT
403474 TATATTTTTAAAATT
1 TAT-TTTTTAAAATT
403489 TA
1 TA
403491 ATCTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 8 0.30
15 14 0.52
16 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTTTTAAAATT
Found at i:403717 original size:22 final size:21
Alignment explanation
Indices: 403690--403734 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
403680 ACCTGATCCA
*
403690 TTTTTTATTCAAGCTTAATTTT
1 TTTTTTATTCAAGCCT-ATTTT
* *
403712 TTTTTTGTTGAAGCCTATTTT
1 TTTTTTATTCAAGCCTATTTT
403733 TT
1 TT
403735 GGGCATAATA
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:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTTTTATTCAAGCCTATTTT
Found at i:403933 original size:19 final size:19
Alignment explanation
Indices: 403906--403942 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
403896 GGGTATTAAC
403906 TAATATTTTATAAAATTTT
1 TAATATTTTATAAAATTTT
* *
403925 TAATTTTTTTTAAAATTT
1 TAATATTTTATAAAATTT
403943 ATCTTATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TAATATTTTATAAAATTTT
Found at i:406341 original size:27 final size:27
Alignment explanation
Indices: 406311--406365 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
406301 AGTTGCATCA
406311 ATAAAAGTAATAAGAAAGTTATAAACT
1 ATAAAAGTAATAAGAAAGTTATAAACT
* *
406338 ATAAAAGTAGTGAGAAAGTTATAAACT
1 ATAAAAGTAATAAGAAAGTTATAAACT
406365 A
1 A
406366 GTGAGTGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.56, C:0.04, G:0.15, T:0.25
Consensus pattern (27 bp):
ATAAAAGTAATAAGAAAGTTATAAACT
Found at i:406535 original size:11 final size:11
Alignment explanation
Indices: 406519--406545 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
406509 GAGTGCTTTA
406519 GTATAGCAAAC
1 GTATAGCAAAC
406530 GTATAGCAAAC
1 GTATAGCAAAC
406541 GTATA
1 GTATA
406546 AAATTTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (11 bp):
GTATAGCAAAC
Found at i:410801 original size:14 final size:14
Alignment explanation
Indices: 410784--410843 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 14
410774 TTTAAGTCTA
410784 TTTAT-ATTATATTT
1 TTTATAATT-TATTT
410798 TTTATAATTTATTT
1 TTTATAATTTATTT
*
410812 TTTAAAAATATATATTT
1 TTT-ATAAT-T-TATTT
410829 TTTA-AATTTAATTT
1 TTTATAATTT-ATTT
410843 T
1 T
410844 ATTAATTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 1 0.03
14 19 0.47
15 10 0.25
16 2 0.05
17 8 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATAATTTATTT
Found at i:410829 original size:17 final size:16
Alignment explanation
Indices: 410789--410834 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
410779 GTCTATTTAT
*
410789 ATTATATTTTTT-ATA
1 ATTATATTTTTTAAAA
410804 ATT-TATTTTTTAAAA
1 ATTATATTTTTTAAAA
410819 ATATATATTTTTTAAA
1 AT-TATATTTTTTAAA
410835 TTTAATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 8 0.30
15 7 0.26
16 1 0.04
17 11 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATATTTTTTAAAA
Found at i:410835 original size:15 final size:14
Alignment explanation
Indices: 410784--410836 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
410774 TTTAAGTCTA
*
410784 TTTATATTATATTT
1 TTTAAATTATATTT
410798 TTTATAATT-TATTT
1 TTTA-AATTATATTT
410812 TTTAAAAATATATATTT
1 TTT--AAAT-TATATTT
410829 TTTAAATT
1 TTTAAATT
410837 TAATTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
14 13 0.39
15 10 0.30
16 2 0.06
17 8 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTAAATTATATTT
Found at i:412944 original size:27 final size:27
Alignment explanation
Indices: 412923--412973 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
412913 GTGATGTATG
*
412923 CTAAA-ATGGTGAAAATTATGATGACA
1 CTAAAGATAGTGAAAATTATGATGACA
412949 CTAAAGATAGTGAAAATTATGATGA
1 CTAAAGATAGTGAAAATTATGATGA
412974 TTGAAATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (27 bp):
CTAAAGATAGTGAAAATTATGATGACA
Found at i:420415 original size:33 final size:35
Alignment explanation
Indices: 420336--420422 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 35
420326 GTATAGTAAA
**
420336 AATAAATAATAATTATTTTAAATATTAAATTAAAATT
1 AATAAATAATAAAAATTTTAAATATT--ATTAAAATT
* * *
420373 TATATATAATAAAAATTTTAAAT-TT-TTTAAATT
1 AATAAATAATAAAAATTTTAAATATTATTAAAATT
*
420406 AATAAATAATTAAAATT
1 AATAAATAATAAAAATT
420423 ATATTTTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
33 21 0.50
36 2 0.05
37 19 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (35 bp):
AATAAATAATAAAAATTTTAAATATTATTAAAATT
Found at i:420421 original size:17 final size:17
Alignment explanation
Indices: 420363--420423 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
420353 TTAAATATTA
* *
420363 AATTAAAATTTATATAT
1 AATTAAAATTAATAAAT
* *
420380 AATAAAAATT-TTAAAT
1 AATTAAAATTAATAAAT
** *
420396 TTTTTAAATTAATAAAT
1 AATTAAAATTAATAAAT
420413 AATTAAAATTA
1 AATTAAAATTA
420424 TATTTTTTTC
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
16 10 0.31
17 22 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTAAAATTAATAAAT
Found at i:420679 original size:7 final size:7
Alignment explanation
Indices: 420669--420714 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
420659 ATTCATATAA
420669 AATATTT
1 AATATTT
420676 AATATTT
1 AATATTT
420683 AATATTT
1 AATATTT
420690 -ATATTT
1 AATATTT
420696 -ATATTT
1 AATATTT
*
420702 AAAATTTT
1 AATA-TTT
420710 AATAT
1 AATAT
420715 ATTTAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 12 0.34
7 17 0.49
8 6 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATATTT
Found at i:420734 original size:17 final size:18
Alignment explanation
Indices: 420677--420735 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 18
420667 AAAATATTTA
420677 ATATTTAAT-ATTTATATTT
1 ATATTTAATAATTTATA--T
420696 ATATTTAA-AATTT-TAAT
1 ATATTTAATAATTTAT-AT
420713 ATATTTAATAATTTATAT
1 ATATTTAATAATTTATAT
420731 -TATTT
1 ATATTT
420736 TTTATCTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 14 0.39
18 8 0.22
19 14 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATTTAATAATTTATAT
Found at i:421140 original size:138 final size:136
Alignment explanation
Indices: 420972--421241 Score: 384
Period size: 138 Copynumber: 2.0 Consensus size: 136
420962 AAGTGAGAAC
* * *
420972 GGAGAAAAAAATAGAAATTTTATGCAATTGTTTTGGTTTTTTGTTTATATATT-ATTTTT-TGCA
1 GGAGAAAAAAAGAAAAATTTTATGCAATTGTTTTGATTTTTTGTTTATATATTGATTTTTATGC-
* * *
421035 TGGTTAAAGTATTAAAAATTTATTTATTTTTTTAATTATCA-GAATGAAAAATCACATTTATATT
65 -GGTTAAAATATTAAAAATTTATTTATTTTTTT-ATTAT-ATGAACGAAAAATCACATATATATT
421099 ATTTTTGAAG
127 ATTTTTGAAG
* *
421109 GGAGAAAGAAAAGAAAAATTTTGTGCAATTGTTTTGATTTTTTGTTTATATGTTGATTTTTATGC
1 GGAGAAA-AAAAGAAAAATTTTATGCAATTGTTTTGATTTTTTGTTTATATATTGATTTTTATGC
* *
421174 GTTTAAAATATTAAAATTTTATTTATTTTTTTATTATATGAACGAAAAATCACATATATATTATT
65 GGTTAAAATATTAAAAATTTATTTATTTTTTTATTATATGAACGAAAAATCACATATATATTATT
421239 TTT
130 TTT
421242 CATATCGTGT
Statistics
Matches: 119, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
136 1 0.01
137 39 0.33
138 70 0.59
139 6 0.05
140 3 0.03
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.49
Consensus pattern (136 bp):
GGAGAAAAAAAGAAAAATTTTATGCAATTGTTTTGATTTTTTGTTTATATATTGATTTTTATGCG
GTTAAAATATTAAAAATTTATTTATTTTTTTATTATATGAACGAAAAATCACATATATATTATTT
TTGAAG
Found at i:430360 original size:17 final size:17
Alignment explanation
Indices: 430293--430360 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 17
430283 TTAATATATA
*
430293 ATATTTATAT--TTAAA
1 ATATTTATATAATTAAT
*
430308 AT-TTTGATATATTTAAT
1 ATATTT-ATATAATTAAT
* **
430325 A-ATTTATATTATTTTT
1 ATATTTATATAATTAAT
430341 ATATTTATATAATTAAT
1 ATATTTATATAATTAAT
430358 ATA
1 ATA
430361 AAAAATTATA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
14 3 0.08
15 6 0.15
16 8 0.20
17 23 0.57
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
ATATTTATATAATTAAT
Found at i:430934 original size:28 final size:30
Alignment explanation
Indices: 430876--430935 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
430866 GTTATTTTAT
*
430876 TTTTCATATTACTTTTATGTTGTATCTTAA
1 TTTTCATATTACTTTTATGTTGTATCATAA
*
430906 TTTTCATATT-TTTTTCA-GTT-TATCATAA
1 TTTTCATATTACTTTT-ATGTTGTATCATAA
430934 TT
1 TT
430936 AATTAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 9 0.33
29 7 0.26
30 11 0.41
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTTCATATTACTTTTATGTTGTATCATAA
Found at i:431943 original size:12 final size:12
Alignment explanation
Indices: 431928--431959 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
431918 AATGTCAAAA
*
431928 TTGGCGGCACAG
1 TTGGCAGCACAG
431940 TTGGCAGCACAG
1 TTGGCAGCACAG
431952 TTGGCAGC
1 TTGGCAGC
431960 CTTTGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.25, G:0.38, T:0.19
Consensus pattern (12 bp):
TTGGCAGCACAG
Found at i:432326 original size:13 final size:13
Alignment explanation
Indices: 432308--432334 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
432298 CACAATATAC
432308 TATATAGTCTTTT
1 TATATAGTCTTTT
432321 TATATAGTCTTTT
1 TATATAGTCTTTT
432334 T
1 T
432335 GTTGCACGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (13 bp):
TATATAGTCTTTT
Found at i:437298 original size:10 final size:10
Alignment explanation
Indices: 437279--437322 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
437269 AAAAATATTA
*
437279 TTAAAATAAT
1 TTAAATTAAT
437289 TTAAATTAAT
1 TTAAATTAAT
437299 TTAAATTAAT
1 TTAAATTAAT
*
437309 ATAAATTAAAT
1 TTAAATT-AAT
437320 TTA
1 TTA
437323 TTGAATCTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 25 0.83
11 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TTAAATTAAT
Found at i:439160 original size:25 final size:24
Alignment explanation
Indices: 439123--439171 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
439113 TACCTTTTCC
439123 TTTACGTTCTTTTTTTCTATCTTTA
1 TTTACGTTCTTTTTTTCTAT-TTTA
* * *
439148 TTTAGGTTTTTTTTTTTTATTTTA
1 TTTACGTTCTTTTTTTCTATTTTA
439172 ATATCTGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.12, C:0.08, G:0.06, T:0.73
Consensus pattern (24 bp):
TTTACGTTCTTTTTTTCTATTTTA
Found at i:439200 original size:23 final size:23
Alignment explanation
Indices: 439162--439211 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
439152 GGTTTTTTTT
*
439162 TTTTATTTTAATATCTGAGATTAA
1 TTTTATTTTAAAATCTGAGATT-A
*
439186 TTTTA-TTTAAAATCTGTGATTA
1 TTTTATTTTAAAATCTGAGATTA
439208 TTTT
1 TTTT
439212 CCTCAATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.21
23 14 0.58
24 5 0.21
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.58
Consensus pattern (23 bp):
TTTTATTTTAAAATCTGAGATTA
Found at i:440113 original size:20 final size:19
Alignment explanation
Indices: 440080--440122 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
440070 ACCTGACTCA
*
440080 TTTTTTATTCAAGCTTAATT
1 TTTTTTATTCAAGCCT-ATT
* *
440100 TTTTTTGTTGAAGCCTATT
1 TTTTTTATTCAAGCCTATT
440119 TTTT
1 TTTT
440123 GGGCATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.63
Consensus pattern (19 bp):
TTTTTTATTCAAGCCTATT
Found at i:442730 original size:27 final size:27
Alignment explanation
Indices: 442700--442754 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
442690 AGTTGCATCA
442700 ATAAAAGTAATAAGAAAGTTATAAACT
1 ATAAAAGTAATAAGAAAGTTATAAACT
* *
442727 ATAAAAGTAGTGAGAAAGTTATAAACT
1 ATAAAAGTAATAAGAAAGTTATAAACT
442754 A
1 A
442755 GTGAGTGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.56, C:0.04, G:0.15, T:0.25
Consensus pattern (27 bp):
ATAAAAGTAATAAGAAAGTTATAAACT
Found at i:442924 original size:11 final size:11
Alignment explanation
Indices: 442908--442934 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
442898 GAGTGCTTTA
442908 GTATAGCAAAC
1 GTATAGCAAAC
442919 GTATAGCAAAC
1 GTATAGCAAAC
442930 GTATA
1 GTATA
442935 AAATTTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (11 bp):
GTATAGCAAAC
Found at i:449039 original size:15 final size:16
Alignment explanation
Indices: 449014--449043 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
449004 AAAATTATCT
449014 TACATTTTATTTTACA
1 TACATTTTATTTTACA
449030 TACA-TTTATTTTAC
1 TACATTTTATTTTAC
449044 TTGATCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (16 bp):
TACATTTTATTTTACA
Found at i:450593 original size:14 final size:14
Alignment explanation
Indices: 450570--450617 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
450560 AATATGATTG
*
450570 ATATAAAATATTTA
1 ATATATAATATTTA
450584 ATATATAATATTT-
1 ATATATAATATTTA
* *
450597 ATATTTAAAATTTTA
1 ATATATAATA-TTTA
450612 ATATAT
1 ATATAT
450618 TTAATAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 8 0.29
14 15 0.54
15 5 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATAATATTTA
Found at i:450618 original size:17 final size:19
Alignment explanation
Indices: 450596--450638 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
450586 ATATAATATT
450596 TATATTTAA-AATTT-TAA
1 TATATTTAATAATTTATAA
*
450613 TATATTTAATAATTTATAT
1 TATATTTAATAATTTATAA
450632 TATATTT
1 TATATTT
450639 TTATTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.39
18 5 0.22
19 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTTAATAATTTATAA
Found at i:450641 original size:30 final size:28
Alignment explanation
Indices: 450573--450632 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 28
450563 ATGATTGATA
450573 TAAAATATTTAATATATAATATTTATATT
1 TAAAAT-TTTAATATATAATATTTATATT
450602 TAAAATTTTAATATATTTAATAATTTATATT
1 TAAAATTTTAATATA--TAAT-ATTTATATT
450633 ATATTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 9 0.32
29 6 0.21
30 4 0.14
31 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TAAAATTTTAATATATAATATTTATATT
Found at i:451745 original size:21 final size:23
Alignment explanation
Indices: 451710--451771 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 23
451700 GTAATTAATA
451710 AATATCAATATAATTTAAAAAATT
1 AATA-CAATATAATTTAAAAAATT
*
451734 AATA-AA-ATAA-TT-ATAAATT
1 AATACAATATAATTTAAAAAATT
*
451753 AATACAATTTAATTTAAAA
1 AATACAATATAATTTAAAA
451772 TTATTTCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
19 10 0.32
20 4 0.13
21 7 0.23
22 4 0.13
23 2 0.06
24 4 0.13
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (23 bp):
AATACAATATAATTTAAAAAATT
Found at i:451761 original size:28 final size:28
Alignment explanation
Indices: 451702--451754 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
451692 TAATTTTTGT
*
451702 AATTAATAAATATCAATATAATTTAAAA
1 AATTAATAAATATCAATATAAATTAAAA
451730 AATTAATAAA-AT-AATTATAAATTAA
1 AATTAATAAATATCAA-TATAAATTAA
451755 TACAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 2 0.09
27 11 0.48
28 10 0.43
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (28 bp):
AATTAATAAATATCAATATAAATTAAAA
Found at i:451772 original size:21 final size:21
Alignment explanation
Indices: 451710--451774 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
451700 GTAATTAATA
451710 AATATCAATATAATTTAAAAAATT
1 AATA-CAATATAATTT--AAAATT
451734 AATA-AA-ATAA-TTATAAATT
1 AATACAATATAATTTA-AAATT
*
451753 AATACAATTTAATTTAAAATT
1 AATACAATATAATTTAAAATT
451774 A
1 A
451775 TTTCTACTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
18 1 0.03
19 9 0.25
20 4 0.11
21 13 0.36
22 5 0.14
24 4 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
AATACAATATAATTTAAAATT
Found at i:454007 original size:24 final size:24
Alignment explanation
Indices: 453961--454005 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
453951 ACATATTTAT
453961 TAATTTATTTTATAAATATAAATA
1 TAATTTATTTTATAAATATAAATA
453985 TAATTTATTATT-TAAAT-TAAA
1 TAATTTATT-TTATAAATATAAA
454006 ATTCATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 4 0.20
24 14 0.70
25 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATTTATTTTATAAATATAAATA
Found at i:454318 original size:2 final size:2
Alignment explanation
Indices: 454311--454344 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
454301 TGTTATGAAA
454311 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
454345 GGATATCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:456719 original size:151 final size:151
Alignment explanation
Indices: 456524--456813 Score: 395
Period size: 150 Copynumber: 1.9 Consensus size: 151
456514 GTCATATTGT
* * *
456524 AACTTAAAAATCTAAAATTTATTCTAATTGATTCATATAATTATTTTTAAAATATAACATTCAAG
1 AACTTAAAAATCTAAAATTAATTCTAATTAATTCATATAATTATTTTTAAAATATAACATTCAAA
* * * *
456589 ATATTTGAAAAAAAAAATATTGACATTTGTAATTTCTTTTTCTATTTTTATATTACAATTTTATT
66 ATATTT-AAAAAAAAAATATTGACATTTATAATTTATTTCTCTATTTTCATATTACAATTTTATT
456654 TACAAAAAAAAAGTTACAATGC
130 TACAAAAAAAAAGTTACAATGC
* * *
456676 AACTTAAAAAT-TCAAACTTAATT-TAATTAATTCATATAATTATTTTTAAAATATAATATTTAA
1 AACTTAAAAATCT-AAAATTAATTCTAATTAATTCATATAATTATTTTTAAAATATAACATTCAA
* * * * * *
456739 AATATTTAAAAAACAAATATTTATATTTATAATTTATTTCTCTATTTTCATGTTATAATTTTTTT
65 AATATTTAAAAAAAAAATATTGACATTTATAATTTATTTCTCTATTTTCATATTACAATTTTATT
*
456804 TATAAAAAAA
130 TACAAAAAAA
456814 GTATAATCTC
Statistics
Matches: 120, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
150 57 0.47
151 44 0.37
152 19 0.16
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (151 bp):
AACTTAAAAATCTAAAATTAATTCTAATTAATTCATATAATTATTTTTAAAATATAACATTCAAA
ATATTTAAAAAAAAAATATTGACATTTATAATTTATTTCTCTATTTTCATATTACAATTTTATTT
ACAAAAAAAAAGTTACAATGC
Found at i:457048 original size:67 final size:67
Alignment explanation
Indices: 456940--457076 Score: 204
Period size: 67 Copynumber: 2.0 Consensus size: 67
456930 AAAATTAAAA
* * *
456940 AAAAAAAAAAGACATGTGCCTTTTGGACCAAAGAAAATATTGTCAAAGACTTTTACACATCAGA-
1 AAAAAAAAAAGACATGTGCCTTTTGGACCAAAGAAAATATTGCCAAAGACCTTTACACATAAGAG
457004 AC
66 AC
* * *
457006 AAAAAAAAAAGGCATGTGCCTTTTTGGATCAAAGAAAGTATTGCCAAAGACCTTTACACATAAGA
1 AAAAAAAAAAGACATGTGCC-TTTTGGACCAAAGAAAATATTGCCAAAGACCTTTACACATAAGA
457071 GAC
65 GAC
457074 AAA
1 AAA
457077 GCATATTAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 19 0.30
67 39 0.62
68 5 0.08
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (67 bp):
AAAAAAAAAAGACATGTGCCTTTTGGACCAAAGAAAATATTGCCAAAGACCTTTACACATAAGAG
AC
Found at i:458237 original size:4 final size:4
Alignment explanation
Indices: 458228--458252 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
458218 TGATTAGTAC
458228 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
458253 TAATGTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:458764 original size:160 final size:160
Alignment explanation
Indices: 458495--458816 Score: 590
Period size: 160 Copynumber: 2.0 Consensus size: 160
458485 TAAATGGCTC
458495 TTTCAACATAAACTCAGACAATGCTGGTTTGGACATAAATACCAAAATGGACACCTTGACTGATG
1 TTTCAACATAAACTCAGACAATGCTGGTTTGGACATAAATACCAAAATGGACACCTTGACTGATG
*
458560 CATCCATAGGAACGTGGAAAGAAATTTTGATAAAACTTTCAACCATGATGAGGCAGAAGCTATAC
66 CATCCATAGGAACGTGGAAAGAAATTTTGATAAAACTTTCAACCATGATGAGGCAGAAGCCATAC
458625 GCAGCATTCCACTGGCGAGGATCAATCCAG
131 GCAGCATTCCACTGGCGAGGATCAATCCAG
* *
458655 TTTCGACATAAACTCAGACAATGCTGGTTTGGACATAAATACCAAAATGGACACCTTGATTGATG
1 TTTCAACATAAACTCAGACAATGCTGGTTTGGACATAAATACCAAAATGGACACCTTGACTGATG
458720 CATCCATAGGAACGTGGAAAGAAATTTTGATAAAACTTTCAACCATGATGAGGCAGAAGCCATAC
66 CATCCATAGGAACGTGGAAAGAAATTTTGATAAAACTTTCAACCATGATGAGGCAGAAGCCATAC
* * *
458785 GCAGCATTCTATTGGCGATGATCAATCCAG
131 GCAGCATTCCACTGGCGAGGATCAATCCAG
458815 TT
1 TT
458817 AATGAATTGA
Statistics
Matches: 156, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
160 156 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (160 bp):
TTTCAACATAAACTCAGACAATGCTGGTTTGGACATAAATACCAAAATGGACACCTTGACTGATG
CATCCATAGGAACGTGGAAAGAAATTTTGATAAAACTTTCAACCATGATGAGGCAGAAGCCATAC
GCAGCATTCCACTGGCGAGGATCAATCCAG
Found at i:469394 original size:21 final size:21
Alignment explanation
Indices: 469369--469419 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
469359 TACTTTGTAG
469369 GTTTTTTAAT-GAAATAAGTA
1 GTTTTTTAATAGAAATAAGTA
* *
469389 GTTTTTTATTAGATATAAGTA
1 GTTTTTTAATAGAAATAAGTA
469410 GTTTTCTTAA
1 GTTTT-TTAA
469420 GAATTGGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 9 0.35
21 14 0.54
22 3 0.12
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (21 bp):
GTTTTTTAATAGAAATAAGTA
Found at i:477442 original size:2 final size:2
Alignment explanation
Indices: 477435--477464 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
477425 GGTTTGGCAC
477435 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
477465 TGAATGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:478805 original size:22 final size:22
Alignment explanation
Indices: 478780--478844 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
478770 AAAAAAAAAA
*
478780 AAACTAAAAATAATTAAAATTT
1 AAACTAGAAATAATTAAAATTT
478802 AAACTAGAAATAATTAAAA-TT
1 AAACTAGAAATAATTAAAATTT
478823 AAACTAGAAATAATTTAAAATT
1 AAACTAGAAATAA-TTAAAATT
478845 GAGAATATCT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 15 0.38
22 24 0.60
23 1 0.03
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (22 bp):
AAACTAGAAATAATTAAAATTT
Found at i:479124 original size:16 final size:17
Alignment explanation
Indices: 479103--479164 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 17
479093 TATTATAATC
479103 ATATTTA-AAATATTTT
1 ATATTTATAAATATTTT
479119 ATATTTATATAA-ATTTT
1 ATATTTATA-AATATTTT
* *
479136 A-ATATATAAATAATTT
1 ATATTTATAAATATTTT
479152 ATATTATATAAAT
1 ATATT-TATAAAT
479165 TTAAAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 2 0.05
16 18 0.47
17 9 0.24
18 9 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTTATAAATATTTT
Found at i:479143 original size:14 final size:16
Alignment explanation
Indices: 479114--479166 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 16
479104 TATTTAAAAT
479114 ATTTTATATTTATATAA
1 ATTTTATA-TTATATAA
479131 ATTTTA-A-TATATAA
1 ATTTTATATTATATAA
479145 ATAATTTATATTATATAA
1 AT--TTTATATTATATAA
479163 ATTT
1 ATTT
479167 AAAAATATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
14 9 0.28
16 7 0.22
17 7 0.22
18 9 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:479148 original size:18 final size:17
Alignment explanation
Indices: 479130--479164 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
479120 TATTTATATA
479130 AATTTTAATATATAAAT
1 AATTTTAATATATAAAT
*
479147 AATTTATATTATATAAAT
1 AATTT-TAATATATAAAT
479165 TTAAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTTAATATATAAAT
Found at i:479387 original size:3 final size:3
Alignment explanation
Indices: 479374--479408 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
479364 ATATGGAACA
479374 AAT ACAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
479409 GTTGTAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:482442 original size:18 final size:17
Alignment explanation
Indices: 482409--482490 Score: 55
Period size: 18 Copynumber: 4.8 Consensus size: 17
482399 ATTTTAAATT
*
482409 TTTTTAATTTTAAGTTTA
1 TTTTTAAGTTTAAG-TTA
*
482427 TTTTTAAGTTTGAGTTA
1 TTTTTAAGTTTAAGTTA
* *
482444 TTATTTTAGTTTCAAGTCA
1 TT-TTTAAGTTT-AAGTTA
482463 -TTTTACA-TTT-AGATTA
1 TTTTTA-AGTTTAAG-TTA
482479 -TTTTAAGTTTAA
1 TTTTTAAGTTTAA
482491 TTCATTTTGA
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
15 3 0.06
16 10 0.20
17 12 0.24
18 22 0.43
19 4 0.08
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.59
Consensus pattern (17 bp):
TTTTTAAGTTTAAGTTA
Found at i:484646 original size:28 final size:25
Alignment explanation
Indices: 484597--484658 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 25
484587 CTGTGGTTCA
484597 AAATTTTTTTAATTTATATTAAATT
1 AAATTTTTTTAATTTATATTAAATT
484622 AAATTTATTTT-ATTT-TA-TAAATT
1 AAATTT-TTTTAATTTATATTAAATT
484645 AAATTATTATTTAA
1 AAATT-TT-TTTAA
484659 AATATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
23 12 0.36
24 6 0.18
25 11 0.33
26 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
AAATTTTTTTAATTTATATTAAATT
Found at i:484733 original size:21 final size:21
Alignment explanation
Indices: 484709--484756 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
484699 ATAATTACAT
**
484709 TTAAATAAAAAATAATTTTTA
1 TTAAATAAAAAATAATTTAAA
*
484730 TTAAATAAATAATAATTTAAA
1 TTAAATAAAAAATAATTTAAA
484751 TTAAAT
1 TTAAAT
484757 TAAATTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAATAAAAAATAATTTAAA
Found at i:486993 original size:18 final size:20
Alignment explanation
Indices: 486953--486993 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
486943 AAGTGAAAAG
**
486953 TTTTATAAATTTTATTTTTA
1 TTTTATAAATTTTATTTAGA
486973 TTTTAT-AA-TTTATTTAGA
1 TTTTATAAATTTTATTTAGA
486991 TTT
1 TTT
486994 ATTTATTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 11 0.58
19 2 0.11
20 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTATAAATTTTATTTAGA
Found at i:487181 original size:22 final size:23
Alignment explanation
Indices: 487135--487181 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
487125 CGATGCATGG
* *
487135 TTAATATTTTAATATATATATAA
1 TTAATATTTTAATATATAAAAAA
*
487158 TTAAT-TTTTAATTTATAAAAAA
1 TTAATATTTTAATATATAAAAAA
487180 TT
1 TT
487182 TTATATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAATATTTTAATATATAAAAAA
Found at i:488196 original size:16 final size:14
Alignment explanation
Indices: 488175--488208 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
488165 ATTTGAGATA
488175 AAAAAAAGAGAAATAG
1 AAAAAAAGA-AAA-AG
488191 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
488205 AAAA
1 AAAA
488209 TGATAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 3 0.17
16 9 0.50
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:488200 original size:14 final size:15
Alignment explanation
Indices: 488176--488208 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
488166 TTTGAGATAA
*
488176 AAAAAAGAGAAATAG
1 AAAAAAGAGAAAAAG
488191 AAAAAA-AGAAAAAG
1 AAAAAAGAGAAAAAG
488205 AAAA
1 AAAA
488209 TGATAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAAAAGAGAAAAAG
Found at i:489208 original size:18 final size:19
Alignment explanation
Indices: 489161--489208 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
489151 CTATAAACGA
489161 ATTTA-TAATTTATATATCT
1 ATTTATTAATTTATATA-CT
* *
489180 ATTGATGAATTTATATA-T
1 ATTTATTAATTTATATACT
489198 ATTTATTAATT
1 ATTTATTAATT
489209 AATAGTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 10 0.42
19 4 0.17
20 10 0.42
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (19 bp):
ATTTATTAATTTATATACT
Found at i:489668 original size:176 final size:176
Alignment explanation
Indices: 489235--489927 Score: 960
Period size: 176 Copynumber: 4.0 Consensus size: 176
489225 GACTCAATGA
* *
489235 ATTTATGTATCTATTAATTAATATTATAAAAAATTCTTGAAGAATAAAATTTTAAAAAAAAAGTT
1 ATTTATATATCTATTAATTAATATTATAAAAAATTCTTGAAGAACAAAA-TTTAAAAAAAAAGTT
* * *
489300 AAAGTAAACTCTAAATAATTTATT-AGAAAAATAAATAAAATTATTAATTAATATTGTAAAAAAT
65 AAAGCAAACTCTTAATAATTTATTGA-AAAAATAAATAAAATTATTAATTAATATTATAAAAAAT
* * *
489364 TTATTGATTT--TAAAAATCTTT-AAAAAACCCATAATAAACACTAGC
129 TTATTGATTTAAAAAAAATCTTTAAAAAAATCCATAATAAACATTAGC
489409 ATTTATATATCTATTAATTAATATTATAAAAAATTCTTGAAGAACAAAA-TTAAAAAAAAAGTTA
1 ATTTATATATCTATTAATTAATATTATAAAAAATTCTTGAAGAACAAAATTTAAAAAAAAAGTTA
489473 AAGCAAACTCTTAATAATTTATTGAAAAAATAAATAAAATTATTAATTAATATTATAAAAAATTT
66 AAGCAAACTCTTAATAATTTATTGAAAAAATAAATAAAATTATTAATTAATATTATAAAAAATTT
* *
489538 ATTGATTTAAAAAAAATCTTTAAAAAAATTCATAATAAACATTAAC
131 ATTGATTTAAAAAAAATCTTTAAAAAAATCCATAATAAACATTAGC
* *
489584 ATTTATATATCTATTAATTAATATTATAAAAAAATCTTGAATAACAAAATTTAAAAAAAAAGTTA
1 ATTTATATATCTATTAATTAATATTATAAAAAATTCTTGAAGAACAAAATTTAAAAAAAAAGTTA
*
489649 AAGCAAACTCTTAATAATTTATTGAAAAAATAAATAAAATTATTAATTAATATTATAAAAAAATT
66 AAGCAAACTCTTAATAATTTATTGAAAAAATAAATAAAATTATTAATTAATATTATAAAAAATTT
* * *
489714 ATTGATTTAAAAAAAATCTTTGAAAAAATTCATAATAAATATTAGC
131 ATTGATTTAAAAAAAATCTTTAAAAAAATCCATAATAAACATTAGC
* * * * *
489760 ATCTAT-GA-C-A--AA--AA-ACTAT------TT-TTTATA-TACAAAATTTAAAAAAAAAGTT
1 ATTTATATATCTATTAATTAATATTATAAAAAATTCTTGA-AGAACAAAATTTAAAAAAAAAGTT
* *
489809 AAAGCAAACTCTTAATAATTTATTGAAAAAATAAATAAAATTATCAATTAATATTATAAAAAGTT
65 AAAGCAAACTCTTAATAATTTATTGAAAAAATAAATAAAATTATTAATTAATATTATAAAAAATT
* * * *
489874 TATTGATTTCAAAAAAATATTTGAAAAAGATCCATAATAAACATTACC
130 TATTGATTTAAAAAAAATCTTT-AAAAAAATCCATAATAAACATTAGC
489922 ATTTAT
1 ATTTAT
489928 GTTAAAAAAA
Statistics
Matches: 479, Mismatches: 33, Indels: 26
0.89 0.06 0.05
Matches are distributed among these distances:
161 106 0.22
162 27 0.06
168 4 0.01
169 2 0.00
171 2 0.00
172 83 0.17
173 2 0.00
174 58 0.12
175 68 0.14
176 127 0.27
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.35
Consensus pattern (176 bp):
ATTTATATATCTATTAATTAATATTATAAAAAATTCTTGAAGAACAAAATTTAAAAAAAAAGTTA
AAGCAAACTCTTAATAATTTATTGAAAAAATAAATAAAATTATTAATTAATATTATAAAAAATTT
ATTGATTTAAAAAAAATCTTTAAAAAAATCCATAATAAACATTAGC
Found at i:489812 original size:161 final size:162
Alignment explanation
Indices: 489627--489951 Score: 528
Period size: 161 Copynumber: 2.0 Consensus size: 162
489617 ATCTTGAATA
489627 ACAAAATTTAAAAAAAAAGTTAAAGCAAACTCTTAATAATTTATTGAAAAAATAAATAAAATTAT
1 ACAAAATTTAAAAAAAAAGTTAAAGCAAACTCTTAATAATTTATTGAAAAAATAAATAAAATTAT
* * * *
489692 TAATTAATATTATAAAAAAATTATTGATTTAAAAAAAATCTTTGAAAAA-ATTCATAATAAATAT
66 CAATTAATATTATAAAAAAATTATTGATTTAAAAAAAATATTTGAAAAAGATCCATAATAAACAT
* *
489756 TAGCATCTATG-ACAAAAAACTATTTTTTATAT
131 TACCATCTATGTA-AAAAAACTATATTTTATAT
489788 ACAAAATTTAAAAAAAAAGTTAAAGCAAACTCTTAATAATTTATTGAAAAAATAAATAAAATTAT
1 ACAAAATTTAAAAAAAAAGTTAAAGCAAACTCTTAATAATTTATTGAAAAAATAAATAAAATTAT
** *
489853 CAATTAATATTATAAAAAGTTTATTGATTTCAAAAAAATATTTGAAAAAGATCCATAATAAACAT
66 CAATTAATATTATAAAAAAATTATTGATTTAAAAAAAATATTTGAAAAAGATCCATAATAAACAT
*
489918 TACCATTTATGTTAAAAAAACTATATTTTATAT
131 TACCATCTATG-TAAAAAAACTATATTTTATAT
489951 A
1 A
489952 TATTACTAGT
Statistics
Matches: 151, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
161 109 0.72
162 22 0.15
163 19 0.13
164 1 0.01
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (162 bp):
ACAAAATTTAAAAAAAAAGTTAAAGCAAACTCTTAATAATTTATTGAAAAAATAAATAAAATTAT
CAATTAATATTATAAAAAAATTATTGATTTAAAAAAAATATTTGAAAAAGATCCATAATAAACAT
TACCATCTATGTAAAAAAACTATATTTTATAT
Found at i:489869 original size:337 final size:343
Alignment explanation
Indices: 489235--489927 Score: 960
Period size: 337 Copynumber: 2.0 Consensus size: 343
489225 GACTCAATGA
* * *
489235 ATTTATGTATCTATTAATTAATATTATAAAAAATTCTTGAAGAATAAAATTTTAAAAAAAAAGTT
1 ATTTATATATCTATTAATTAATATTATAAAAAAATCTTGAAGAACAAAATTTTAAAAAAAAAGTT
* * *
489300 AAAGTAAACTCTAAATAATTTATTAGAAAAATAAATAAAATTATTAATTAATATTGTAAAAAATT
66 AAAGCAAACTCTAAATAATTTATTAGAAAAATAAATAAAATTATTAATTAATATTATAAAAAAAT
* * *
489365 TATTGATTTTAAAAATCTTTAAAAAACCCATAATAAACACTAGCATTTATATATCTATTAATTAA
131 TATTGATTTAAAAAATCTTTAAAAAACCCATAATAAACACTAGCATCTATAGATCTA-TAA-TAA
*
489430 TATTATAAAAAATTCTTGAAGAACAAAATTAAAAAAAAAGTTAAAGCAAACTCTTAATAATTTAT
194 TACTAT-----ATTCTTGAAGAACAAAATTAAAAAAAAAGTTAAAGCAAACTCTTAATAATTTAT
* *
489495 TGAAAAAATAAATAAAATTATTAATTAATATTATAAAAAATTTATTGATTTAAAAAAAATCTTT-
254 TGAAAAAATAAATAAAATTATCAATTAATATTATAAAAAATTTATTGATTTAAAAAAAATATTTG
*
489559 AAAAAAATTCATAATAAACATTAAC
319 AAAAAAATCCATAATAAACATTAAC
*
489584 ATTTATATATCTATTAATTAATATTATAAAAAAATCTTGAATAACAAAA-TTTAAAAAAAAAGTT
1 ATTTATATATCTATTAATTAATATTATAAAAAAATCTTGAAGAACAAAATTTTAAAAAAAAAGTT
*
489648 AAAGCAAACTCTTAATAATTTATT-GAAAAAATAAATAAAATTATTAATTAATATTATAAAAAAA
66 AAAGCAAACTCTAAATAATTTATTAG-AAAAATAAATAAAATTATTAATTAATATTATAAAAAAA
** * *
489712 TTATTGATTTAAAAAAAATCTTTGAAAAAATTCATAATAAATATTAGCATCTAT-GA-C-A-AA-
130 TTATTGATTT--AAAAAATCTTT-AAAAAACCCATAATAAACACTAGCATCTATAGATCTATAAT
* *
489772 AA-ACTAT-TT-TTTATA-TACAAAATTTAAAAAAAAAGTTAAAGCAAACTCTTAATAATTTATT
192 AATACTATATTCTTGA-AGAACAAAA-TTAAAAAAAAAGTTAAAGCAAACTCTTAATAATTTATT
* *
489833 GAAAAAATAAATAAAATTATCAATTAATATTATAAAAAGTTTATTGATTTCAAAAAAATATTTGA
255 GAAAAAATAAATAAAATTATCAATTAATATTATAAAAAATTTATTGATTTAAAAAAAATATTTGA
* *
489898 AAAAGATCCATAATAAACATTACC
320 AAAAAATCCATAATAAACATTAAC
489922 ATTTAT
1 ATTTAT
489928 GTTAAAAAAA
Statistics
Matches: 312, Mismatches: 25, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
336 9 0.03
337 100 0.32
338 28 0.09
343 4 0.01
344 2 0.01
346 2 0.01
347 1 0.00
348 84 0.27
349 46 0.15
350 11 0.04
351 25 0.08
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.35
Consensus pattern (343 bp):
ATTTATATATCTATTAATTAATATTATAAAAAAATCTTGAAGAACAAAATTTTAAAAAAAAAGTT
AAAGCAAACTCTAAATAATTTATTAGAAAAATAAATAAAATTATTAATTAATATTATAAAAAAAT
TATTGATTTAAAAAATCTTTAAAAAACCCATAATAAACACTAGCATCTATAGATCTATAATAATA
CTATATTCTTGAAGAACAAAATTAAAAAAAAAGTTAAAGCAAACTCTTAATAATTTATTGAAAAA
ATAAATAAAATTATCAATTAATATTATAAAAAATTTATTGATTTAAAAAAAATATTTGAAAAAAA
TCCATAATAAACATTAAC
Found at i:490399 original size:6 final size:6
Alignment explanation
Indices: 490365--490398 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
490355 TGTTTTTTAT
*
490365 ATATAG ATATAG ATATAG ATATAG ATATGG ATAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
490399 GTCTTAGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:491194 original size:39 final size:39
Alignment explanation
Indices: 491151--491231 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
491141 AGGCAGTCGC
491151 TAAAAGCAAAAATCTTACATGTCCTAAAGCATGAAACTT
1 TAAAAGCAAAAATCTTACATGTCCTAAAGCATGAAACTT
* *
491190 TAAAAGCAAAAGTCTTACATGTCCTAAAGCATTAAACTT
1 TAAAAGCAAAAATCTTACATGTCCTAAAGCATGAAACTT
491229 TAA
1 TAA
491232 GAGGATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (39 bp):
TAAAAGCAAAAATCTTACATGTCCTAAAGCATGAAACTT
Found at i:491806 original size:106 final size:107
Alignment explanation
Indices: 491599--491793 Score: 247
Period size: 103 Copynumber: 1.9 Consensus size: 107
491589 ATTAAAATTT
*
491599 ACTCTATTTTTTTATATCTAATGATCAAGTTCTAAAGACATAAATTATACCCGATTTATTTTAAA
1 ACTCTATTTTTTTATATCTAATGATCAAGTTCTAAAAACATAAATTATACCC-ATTTATTTTAAA
* *
491664 AACTTTAATTAAATTTAAGATTTTTTTTAAAAATTTAACGTCG
65 AACTTTAATAAAATTTAAAATTTTTTTTAAAAATTTAACGTCG
* * * * * * *
491707 ACTCTA-TTTTTTATAT-TAGTGATCGAGTTCTAAAAATATAAGTTATA-TC-TTTTTTTTAAGA
1 ACTCTATTTTTTTATATCTAATGATCAAGTTCTAAAAACATAAATTATACCCATTTATTTTAAAA
491768 A-TATTAATAAAATTTAAAATTTTTTT
66 ACT-TTAATAAAATTTAAAATTTTTTT
491794 AAATATAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
102 1 0.01
103 32 0.42
105 1 0.01
106 26 0.34
107 10 0.13
108 6 0.08
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (107 bp):
ACTCTATTTTTTTATATCTAATGATCAAGTTCTAAAAACATAAATTATACCCATTTATTTTAAAA
ACTTTAATAAAATTTAAAATTTTTTTTAAAAATTTAACGTCG
Found at i:492408 original size:2 final size:2
Alignment explanation
Indices: 492401--492435 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
492391 GACTCACAAG
492401 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
492436 TATTAAGTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:493168 original size:19 final size:19
Alignment explanation
Indices: 493144--493183 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
493134 AAAAAAAATT
493144 ATTTAAAT-TTAATTATAAA
1 ATTTAAATATTAA-TATAAA
493163 ATTTAAATATTAATATAAA
1 ATTTAAATATTAATATAAA
493182 AT
1 AT
493184 ATTTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATATTAATATAAA
Found at i:493296 original size:18 final size:18
Alignment explanation
Indices: 493273--493312 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
493263 TATAAATTGA
* *
493273 AAATACTCAATTATAAAT
1 AAATACTAAATCATAAAT
493291 AAATACTAAATCATAAAT
1 AAATACTAAATCATAAAT
493309 AAAT
1 AAAT
493313 CAAAAGAAAT
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:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATACTAAATCATAAAT
Found at i:493524 original size:6 final size:6
Alignment explanation
Indices: 493514--493549 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
493504 AAATAAAATA
*
493514 AAATTT GAATTT AAATTT AAATTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
493550 TATTTAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:493528 original size:18 final size:18
Alignment explanation
Indices: 493507--493546 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
493497 AAAAATAAAA
*
493507 TAAAATAAAATTTGAATT
1 TAAAATAAAATTTAAATT
* *
493525 TAAATTTAAATTTAAATT
1 TAAAATAAAATTTAAATT
493543 TAAA
1 TAAA
493547 TTTTATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TAAAATAAAATTTAAATT
Found at i:493873 original size:6 final size:6
Alignment explanation
Indices: 493858--493902 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
493848 AGAACCCATG
* * * *
493858 TATACA TATATG TATACA TATATA TATATG TATATA TATATA TAT
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TAT
493903 TATGAAGTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (6 bp):
TATATA
Found at i:493884 original size:18 final size:18
Alignment explanation
Indices: 493858--493902 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
493848 AGAACCCATG
*
493858 TATACATATATGTATACA
1 TATATATATATGTATACA
*
493876 TATATATATATGTATATA
1 TATATATATATGTATACA
493894 TATATATAT
1 TATATATAT
493903 TATGAAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (18 bp):
TATATATATATGTATACA
Found at i:495855 original size:2 final size:2
Alignment explanation
Indices: 495848--495877 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
495838 TTGATGTAGC
495848 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
495878 AACAATTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:496551 original size:15 final size:15
Alignment explanation
Indices: 496531--496560 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
496521 TGGGTTCGCC
496531 AGAGAAGAATGAGTT
1 AGAGAAGAATGAGTT
*
496546 AGAGAATAATGAGTT
1 AGAGAAGAATGAGTT
496561 CCCCAGGGAG
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:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (15 bp):
AGAGAAGAATGAGTT
Found at i:502542 original size:15 final size:16
Alignment explanation
Indices: 502522--502553 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
502512 ATTAAAAAAT
502522 AATTAAATATAT-TTA
1 AATTAAATATATATTA
502537 AATTAAATATATATTA
1 AATTAAATATATATTA
502553 A
1 A
502554 TATTCAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTAAATATATATTA
Found at i:503103 original size:34 final size:36
Alignment explanation
Indices: 503048--503120 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 36
503038 GCAGTTCTAG
*
503048 TGTTACCCAGTGCTTGGATT-AAACTTAAAAGGTGA
1 TGTTACCCAGTGCTTGGATTAAAACTTAAAAGGTAA
503083 TGTTACCCAGT-CTTGGATTAAAACTTAAAAGGTAA
1 TGTTACCCAGTGCTTGGATTAAAACTTAAAAGGTAA
503118 TGT
1 TGT
503121 CCTAGTTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 8 0.22
35 28 0.78
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (36 bp):
TGTTACCCAGTGCTTGGATTAAAACTTAAAAGGTAA
Done.