Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold336
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: 503701
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.32
Warning! 20849 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:4980 original size:22 final size:22
Alignment explanation
Indices: 4935--4981 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
4925 AGTCGATAGT
* *
4935 TTTTGTAAATATTGAAGCTGAA
1 TTTTGTAAATATTGAAGATAAA
* *
4957 TTTTGTAACTATTGAGGATAAA
1 TTTTGTAAATATTGAAGATAAA
4979 TTT
1 TTT
4982 ATTAAAGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (22 bp):
TTTTGTAAATATTGAAGATAAA
Found at i:7023 original size:22 final size:22
Alignment explanation
Indices: 6992--7033 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6982 TTAGGGTGGT
6992 GGTATAAATTCAAAAATAAAAG
1 GGTATAAATTCAAAAATAAAAG
* **
7014 GGTATTAATTTTAAAATAAA
1 GGTATAAATTCAAAAATAAA
7034 TTGGAAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.02, G:0.12, T:0.31
Consensus pattern (22 bp):
GGTATAAATTCAAAAATAAAAG
Found at i:7490 original size:21 final size:21
Alignment explanation
Indices: 7433--7490 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
7423 TGGGTGGATG
* * *
7433 AGCTCTTATGAGCTTCTGTTC
1 AGCTCTTACGAACTTCTATTC
*
7454 AGCTCTTACAAACTTCTATTC
1 AGCTCTTACGAACTTCTATTC
*
7475 AGCTCTTACGACCTTC
1 AGCTCTTACGAACTTC
7491 AGTTTAGCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (21 bp):
AGCTCTTACGAACTTCTATTC
Found at i:7499 original size:21 final size:21
Alignment explanation
Indices: 7433--7499 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
7423 TGGGTGGATG
* * *
7433 AGCTCTTATGAGCTTCTGTTC
1 AGCTCTTACGAACTTCAGTTC
*
7454 AGCTCTTACAAACTTCTA-TTC
1 AGCTCTTACGAACTTC-AGTTC
* *
7475 AGCTCTTACGACCTTCAGTTT
1 AGCTCTTACGAACTTCAGTTC
7496 AGCT
1 AGCT
7500 TTCAAGCTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (21 bp):
AGCTCTTACGAACTTCAGTTC
Found at i:22818 original size:18 final size:19
Alignment explanation
Indices: 22754--22840 Score: 70
Period size: 19 Copynumber: 4.3 Consensus size: 19
22744 TTTTTTATAT
*
22754 ATTTTTAGAATT-TTTTAGA
1 ATTTTTAAAATTATTTT-GA
22773 ATTTTTAAAAATATAAATTTTGAA
1 ATTTTT-AAAAT-T--ATTTTG-A
*
22797 AATTTTATAAA-TATTTTGA
1 ATTTTTA-AAATTATTTTGA
*
22816 ATTTTTAAAATTATTTTGT
1 ATTTTTAAAATTATTTTGA
22835 ATTTTT
1 ATTTTT
22841 TGTTGAGAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
18 3 0.05
19 26 0.46
20 10 0.18
21 1 0.02
22 1 0.02
23 2 0.04
24 13 0.23
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
ATTTTTAAAATTATTTTGA
Found at i:23290 original size:59 final size:59
Alignment explanation
Indices: 23219--23332 Score: 219
Period size: 59 Copynumber: 1.9 Consensus size: 59
23209 AACTTCAAGC
*
23219 AAGCTCTTGTAACCTAATTTAGGTTAACTATACAATATAAATAGGATATTTTGAGGTTG
1 AAGCTCTTGTAACCTAATGTAGGTTAACTATACAATATAAATAGGATATTTTGAGGTTG
23278 AAGCTCTTGTAACCTAATGTAGGTTAACTATACAATATAAATAGGATATTTTGAG
1 AAGCTCTTGTAACCTAATGTAGGTTAACTATACAATATAAATAGGATATTTTGAG
23333 AGAGAGTGAG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.36
Consensus pattern (59 bp):
AAGCTCTTGTAACCTAATGTAGGTTAACTATACAATATAAATAGGATATTTTGAGGTTG
Found at i:27203 original size:20 final size:21
Alignment explanation
Indices: 27137--27208 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 21
27127 AGTCTAAATG
27137 TTTAAAAAATATATATATGAAA
1 TTTAAAAAATATA-ATATGAAA
*
27159 TTTAAAAAAATCCTAATAGTG---
1 TTT-AAAAAAT-ATAATA-TGAAA
27180 TTTAAAAAATATAA-ATGAAA
1 TTTAAAAAATATAATATGAAA
27200 TTTAAAAAA
1 TTTAAAAAA
27209 ATCCTAACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
17 2 0.05
18 1 0.02
19 3 0.07
20 16 0.38
21 3 0.07
22 3 0.07
23 10 0.24
24 4 0.10
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (21 bp):
TTTAAAAAATATAATATGAAA
Found at i:27203 original size:41 final size:43
Alignment explanation
Indices: 27135--27215 Score: 148
Period size: 41 Copynumber: 1.9 Consensus size: 43
27125 AAAGTCTAAA
27135 TGTTTAAAAAATATATATATGAAATTTAAAAAAATCCTAATAG
1 TGTTTAAAAAATATATATATGAAATTTAAAAAAATCCTAATAG
27178 TGTTTAAAAAATATA-A-ATGAAATTTAAAAAAATCCTAA
1 TGTTTAAAAAATATATATATGAAATTTAAAAAAATCCTAA
27216 CATTATTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 22 0.58
42 1 0.03
43 15 0.39
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (43 bp):
TGTTTAAAAAATATATATATGAAATTTAAAAAAATCCTAATAG
Found at i:27207 original size:21 final size:21
Alignment explanation
Indices: 27137--27210 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 21
27127 AGTCTAAATG
*
27137 TTTAAAAAATATATATATGAAA
1 TTTAAAAAA-ATATAAATGAAA
*
27159 TTTAAAAAAATCCTAATAGTG---
1 TTTAAAAAAAT-ATAA-A-TGAAA
27180 TTT-AAAAAATATAAATGAAA
1 TTTAAAAAAATATAAATGAAA
27200 TTTAAAAAAAT
1 TTTAAAAAAAT
27211 CCTAACATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
17 2 0.05
18 1 0.02
19 3 0.07
20 10 0.24
21 12 0.29
22 11 0.26
23 1 0.02
24 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (21 bp):
TTTAAAAAAATATAAATGAAA
Found at i:30276 original size:15 final size:15
Alignment explanation
Indices: 30253--30295 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
30243 TGTTCATCCC
*
30253 ATACCCAATTCATGA
1 ATACACAATTCATGA
30268 ATACACAATTCATGA
1 ATACACAATTCATGA
30283 ATACACAATTCAT
1 ATACACAATTCAT
30296 ATGTCTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.44, C:0.23, G:0.05, T:0.28
Consensus pattern (15 bp):
ATACACAATTCATGA
Found at i:30318 original size:12 final size:14
Alignment explanation
Indices: 30288--30320 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
30278 CATGAATACA
30288 CAATTCATATGTCT
1 CAATTCATATGTCT
30302 CAATTCATAT-T-T
1 CAATTCATATGTCT
30314 CAATTCA
1 CAATTCA
30321 CTGCACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 1 0.05
14 10 0.53
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.42
Consensus pattern (14 bp):
CAATTCATATGTCT
Found at i:30785 original size:24 final size:24
Alignment explanation
Indices: 30740--30786 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
30730 TATATATACC
30740 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
30764 AATTC-ATCACATAGTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
30787 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:31539 original size:13 final size:13
Alignment explanation
Indices: 31502--31540 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
31492 GACTACTGTT
*
31502 TTTTAATTTTAATA
1 TTTT-ATTTTATTA
*
31516 TGTTATTTTATTA
1 TTTTATTTTATTA
31529 TTTTATTTTATT
1 TTTTATTTTATT
31541 TTATTTCTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 19 0.86
14 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:32367 original size:24 final size:24
Alignment explanation
Indices: 32311--32372 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
32301 AATTAGGTTA
* *
32311 TTATTATTAT-TTTTTTTTTTCTT
1 TTATTATTATATTTTTGTTTTATT
32334 TGTA-TA-TATATTTTTGTTTTATT
1 T-TATTATTATATTTTTGTTTTATT
32357 TTATTATTATATTTTT
1 TTATTATTATATTTTT
32373 ACTCTTCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 5 0.15
23 17 0.52
24 11 0.33
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.76
Consensus pattern (24 bp):
TTATTATTATATTTTTGTTTTATT
Found at i:32413 original size:21 final size:21
Alignment explanation
Indices: 32389--32430 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
32379 CTTAAGTACA
32389 TAGTTATTTAATGATTTTTAG
1 TAGTTATTTAATGATTTTTAG
32410 TAGTTATTTAATGATTTTTAG
1 TAGTTATTTAATGATTTTTAG
32431 CATTTAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (21 bp):
TAGTTATTTAATGATTTTTAG
Found at i:32480 original size:16 final size:16
Alignment explanation
Indices: 32461--32509 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
32451 TTTTATCGTA
32461 TTTCTTATTTATTTAT
1 TTTCTTATTTATTTAT
32477 TTTCTT-TATTA-TTAT
1 TTTCTTAT-TTATTTAT
*
32492 TTTACTTA-ATATTTAT
1 TTT-CTTATTTATTTAT
32508 TT
1 TT
32510 ATTTATGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCTTATTTATTTAT
Found at i:32944 original size:72 final size:72
Alignment explanation
Indices: 32835--32977 Score: 220
Period size: 72 Copynumber: 2.0 Consensus size: 72
32825 TCTTTTCAAA
*
32835 CTCAAGTTTTAAACAATCTCTGAAATTAAAAAGAGATCGTGTCCTAACTTACTGGGCGTGATCCC
1 CTCAAGTTTTAAACAATCTCTGAAATTAAAAAGAGATCGTGTCCTAACTTACTGGGCATGATCCC
32900 TTTTTTC
66 TTTTTTC
*
32907 CTCAAGTTTTAAA-ATGATCTC-GGAATTAAGAAA-AGATCGTGTCCTAACTTACTGGGCATGAT
1 CTCAAGTTTTAAACA--ATCTCTGAAATTAA-AAAGAGATCGTGTCCTAACTTACTGGGCATGAT
32969 CCCTTTTTT
63 CCCTTTTTT
32978 TTAATCCGAG
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
71 1 0.02
72 57 0.86
73 8 0.12
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (72 bp):
CTCAAGTTTTAAACAATCTCTGAAATTAAAAAGAGATCGTGTCCTAACTTACTGGGCATGATCCC
TTTTTTC
Found at i:33632 original size:18 final size:19
Alignment explanation
Indices: 33606--33641 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
33596 TAAACTAAAT
*
33606 TTAACTCCCT-AATTTCAC
1 TTAAATCCCTAAATTTCAC
33624 TTAAATCCCTAAATTTCA
1 TTAAATCCCTAAATTTCA
33642 AAATTTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATCCCTAAATTTCAC
Found at i:34011 original size:5 final size:5
Alignment explanation
Indices: 34001--34044 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
33991 TTTGTTTTAT
34001 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
34045 CTTAATTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:35294 original size:72 final size:72
Alignment explanation
Indices: 35177--35319 Score: 234
Period size: 72 Copynumber: 2.0 Consensus size: 72
35167 TCTTTTCAAA
* *
35177 CTCAAGTTTTAAACAATCTCTGAAATTAAAAAGAGATCGTGTCCTAACTTACTGGGCGTGATCCC
1 CTCAAGTTTTAAACAATCTCGGAAATTAAAAAGAGATCGTGTCCTAACTTACTGGGCATGATCCC
35242 TTTTTTC
66 TTTTTTC
**
35249 CTCAAGTTTTAAATGATCTCGGAAATTAAGAAA-AGATCGTGTCCTAACTTACTGGGCATGATCC
1 CTCAAGTTTTAAACAATCTCGGAAATTAA-AAAGAGATCGTGTCCTAACTTACTGGGCATGATCC
35313 CTTTTTT
65 CTTTTTT
35320 TTAATCCGAG
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
72 63 0.95
73 3 0.05
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (72 bp):
CTCAAGTTTTAAACAATCTCGGAAATTAAAAAGAGATCGTGTCCTAACTTACTGGGCATGATCCC
TTTTTTC
Found at i:35974 original size:18 final size:19
Alignment explanation
Indices: 35948--35983 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
35938 TAAACTAAAT
*
35948 TTAACTCCCT-AATTTCAC
1 TTAAATCCCTAAATTTCAC
35966 TTAAATCCCTAAATTTCA
1 TTAAATCCCTAAATTTCA
35984 AAATTTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATCCCTAAATTTCAC
Found at i:36353 original size:5 final size:5
Alignment explanation
Indices: 36343--36386 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
36333 TTTGTTTTAT
36343 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
36387 CTTAATTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:44563 original size:20 final size:20
Alignment explanation
Indices: 44538--44581 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
44528 ATTAACTAAT
44538 TTTTAAAAAT-TAAAAAATTA
1 TTTT-AAAATGTAAAAAATTA
*
44558 TTTTAATATGTAAAAAATTA
1 TTTTAAAATGTAAAAAATTA
44578 TTTT
1 TTTT
44582 TTATATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTTAAAATGTAAAAAATTA
Found at i:46053 original size:19 final size:19
Alignment explanation
Indices: 46029--46066 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
46019 NNNNNNNNNN
46029 ATATCTAAGATTGCATATC
1 ATATCTAAGATTGCATATC
46048 ATATCTAAGATTGCATATC
1 ATATCTAAGATTGCATATC
46067 CCTGAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
ATATCTAAGATTGCATATC
Found at i:49829 original size:98 final size:98
Alignment explanation
Indices: 49660--50504 Score: 1656
Period size: 98 Copynumber: 8.6 Consensus size: 98
49650 ATACAATAAA
* *
49660 ACTTTAAAAGAACA-TCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTAT
1 ACTTTAAAAGAA-AGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTAT
49724 TCCTTTAGAATCCCAAACTCGGAATATTTCCTTT
65 TCCTTTAGAATCCCAAACTCGGAATATTTCCTTT
49758 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
49823 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
49856 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
49921 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
49954 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
50019 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
50052 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
50117 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
50150 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
50215 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
50248 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
50313 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
50346 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
50411 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
50444 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCAC
1 ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCAC
50505 NNNNNNNNNN
Statistics
Matches: 744, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
97 1 0.00
98 743 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (98 bp):
ACTTTAAAAGAAAGTCCGCTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:51968 original size:13 final size:13
Alignment explanation
Indices: 51949--51978 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
51939 TGCAGCATAG
51949 AAAAAAAAGAAAAC
1 AAAAAAAA-AAAAC
51963 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
51976 AAA
1 AAA
51979 GGCTCTCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:58021 original size:83 final size:83
Alignment explanation
Indices: 57882--58042 Score: 313
Period size: 83 Copynumber: 1.9 Consensus size: 83
57872 AAACAAAAAA
57882 AAGGATAACTCCTCAAATACTATCCAAAGGAGTTAATCGAACACTTAATATGCAAACAAGCAAAG
1 AAGGATAACTCCTCAAATACTATCCAAAGGAGTTAATCGAACACTTAATATGCAAACAAGCAAAG
*
57947 GGGGGGGGGGGGGGGGTG
66 AGGGGGGGGGGGGGGGTG
57965 AAGGATAACTCCTCAAATACTATCCAAAGGAGTTAATCGAACACTTAATATGCAAACAAGCAAAG
1 AAGGATAACTCCTCAAATACTATCCAAAGGAGTTAATCGAACACTTAATATGCAAACAAGCAAAG
58030 AGGGGGGGGGGGG
66 AGGGGGGGGGGGG
58043 ATGATGCACC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.17
Consensus pattern (83 bp):
AAGGATAACTCCTCAAATACTATCCAAAGGAGTTAATCGAACACTTAATATGCAAACAAGCAAAG
AGGGGGGGGGGGGGGGTG
Found at i:59073 original size:10 final size:10
Alignment explanation
Indices: 59060--59084 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
59050 AAATTATAAA
59060 AAAAACTTAT
1 AAAAACTTAT
59070 AAAAACTTAT
1 AAAAACTTAT
59080 AAAAA
1 AAAAA
59085 AATCTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAACTTAT
Found at i:59099 original size:20 final size:22
Alignment explanation
Indices: 59040--59104 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
59030 AAGTAGATAT
*
59040 AAACTTATTAAAATTATAAAAA
1 AAACTTATAAAAATTATAAAAA
59062 AAACTTATAAAAACTTATAAAAA
1 AAACTTATAAAAA-TTATAAAAA
* *
59085 AATC-TA-ATAAATTATAAAAA
1 AAACTTATAAAAATTATAAAAA
59105 TCCTAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
20 9 0.23
21 4 0.10
22 14 0.36
23 12 0.31
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (22 bp):
AAACTTATAAAAATTATAAAAA
Found at i:59788 original size:17 final size:17
Alignment explanation
Indices: 59766--59808 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
59756 CAATTTTCAT
59766 ATTTTTAATATATAATA
1 ATTTTTAATATATAATA
* * *
59783 ATTTTTAAAATTTTATA
1 ATTTTTAATATATAATA
59800 ATTTTTAAT
1 ATTTTTAAT
59809 CATTTTTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTTAATATATAATA
Found at i:61861 original size:34 final size:35
Alignment explanation
Indices: 61817--61883 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
61807 CAGTAAAATA
61817 TTTTCCGTAAAATGATTT-CGGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* **
61851 TTTTCTGTAAAATGATTTACTTGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
61884 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:64076 original size:4 final size:4
Alignment explanation
Indices: 64067--64099 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
64057 CTCACTCCTC
64067 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
64100 AAATACTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:64949 original size:18 final size:19
Alignment explanation
Indices: 64913--64959 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
64903 TTTAAATTAA
64913 AAATATATTCAAACCTTA-T
1 AAATAT-TTCAAACCTTATT
**
64932 AAATATTTCAAATTTTATT
1 AAATATTTCAAACCTTATT
64951 AAATCATTT
1 AAAT-ATTT
64960 AAAAAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.38
19 11 0.46
20 4 0.17
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATATTTCAAACCTTATT
Found at i:73511 original size:30 final size:31
Alignment explanation
Indices: 73453--73515 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 31
73443 AAGTTTACAA
73453 GTCCAAAATCAAACTCATGATACCACATTTTAT
1 GTCCAAAATCAAACTCATG--ACCACATTTTAT
*
73486 GTCCAAAATCGAACTCATG-CCACATTTTAT
1 GTCCAAAATCAAACTCATGACCACATTTTAT
73516 ATAATCTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 11 0.38
33 18 0.62
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (31 bp):
GTCCAAAATCAAACTCATGACCACATTTTAT
Found at i:74532 original size:21 final size:21
Alignment explanation
Indices: 74506--74560 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
74496 AGGGTTTAGA
*
74506 CCGTGTGACAG-GGGTACATGG
1 CCGTGTGACAGAGGG-ACATGC
* *
74527 CCGTGTGGCTGAGGGACATGC
1 CCGTGTGACAGAGGGACATGC
74548 CCGTGTGAGCAGA
1 CCGTGTGA-CAGA
74561 CTATATAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.18, C:0.22, G:0.42, T:0.18
Consensus pattern (21 bp):
CCGTGTGACAGAGGGACATGC
Found at i:81408 original size:21 final size:18
Alignment explanation
Indices: 81379--81421 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 18
81369 AATTCATATA
81379 TATTAATATTGGCATATTTTT
1 TATTAATATT-G--TATTTTT
*
81400 TATTCATATTGTATTTTT
1 TATTAATATTGTATTTTT
81418 TATT
1 TATT
81422 GTTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 11 0.52
20 1 0.05
21 9 0.43
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.63
Consensus pattern (18 bp):
TATTAATATTGTATTTTT
Found at i:83761 original size:63 final size:63
Alignment explanation
Indices: 83687--83820 Score: 171
Period size: 63 Copynumber: 2.1 Consensus size: 63
83677 TGCAAGGGTG
* *
83687 ACACGAGTAAGACACACAGGCGTCTGTCCAGGAC-GTGTAACTAACTAAGTTCATATTAGAGTC
1 ACACGGGTAAGACACACAGGCGTCTGTCCAGG-CTGTGTAACTAACTAAGTTCATATTAGAGAC
* * * * * *
83750 ACACGGGTAAGACACACGGGCGTGTGTCCAGGCTGTGTAACTCACTGAGTTTATATTTGAGAC
1 ACACGGGTAAGACACACAGGCGTCTGTCCAGGCTGTGTAACTAACTAAGTTCATATTAGAGAC
*
83813 ACATGGGT
1 ACACGGGT
83821 GTGCACCAGG
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 1 0.02
63 60 0.98
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (63 bp):
ACACGGGTAAGACACACAGGCGTCTGTCCAGGCTGTGTAACTAACTAAGTTCATATTAGAGAC
Found at i:86797 original size:21 final size:21
Alignment explanation
Indices: 86773--86812 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
86763 TTAGGTCCAA
*
86773 TTGTTAATATTGTTAATTTTT
1 TTGTCAATATTGTTAATTTTT
* *
86794 TTGTCAATTTTGTTGATTT
1 TTGTCAATATTGTTAATTT
86813 GACATTTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (21 bp):
TTGTCAATATTGTTAATTTTT
Found at i:87831 original size:5 final size:5
Alignment explanation
Indices: 87821--87845 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
87811 ACTATTTAAA
87821 GATAT GATAT GATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT
87846 AGTAGGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
GATAT
Found at i:90352 original size:14 final size:13
Alignment explanation
Indices: 90331--90361 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
90321 CTTTTTGTTC
90331 TTTCTCTTTTCTT
1 TTTCTCTTTTCTT
90344 TTTCTTCTTTTCTT
1 TTTC-TCTTTTCTT
90358 TTTC
1 TTTC
90362 GCCATATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTCTTTTCTT
Found at i:90361 original size:20 final size:20
Alignment explanation
Indices: 90319--90359 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
90309 TCTCTTTCCC
*
90319 TTCTTTTTGTTCTTTCTCTT
1 TTCTTTTTCTTCTTTCTCTT
90339 TTCTTTTTCTTCTTT-TCTT
1 TTCTTTTTCTTCTTTCTCTT
90358 TT
1 TT
90360 TCGCCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (20 bp):
TTCTTTTTCTTCTTTCTCTT
Found at i:92877 original size:15 final size:15
Alignment explanation
Indices: 92857--92907 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
92847 ACAACATGAT
92857 AACGTAAATGACTAA
1 AACGTAAATGACTAA
* *
92872 AACGTAACAT--TTCA
1 AACGTAA-ATGACTAA
*
92886 AACATAAATGACTAA
1 AACGTAAATGACTAA
92901 AACGTAA
1 AACGTAA
92908 CCTAAGGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 15 0.56
16 2 0.07
ACGTcount: A:0.53, C:0.16, G:0.10, T:0.22
Consensus pattern (15 bp):
AACGTAAATGACTAA
Found at i:94577 original size:20 final size:20
Alignment explanation
Indices: 94539--94579 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
94529 ATTATATAAT
*
94539 GGTTGTTATCATAAATAAAA
1 GGTTGTTATCAGAAATAAAA
94559 GGTTGTTAT-AGAAAGTAAAA
1 GGTTGTTATCAGAAA-TAAAA
94579 G
1 G
94580 TAAAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.44, C:0.02, G:0.22, T:0.32
Consensus pattern (20 bp):
GGTTGTTATCAGAAATAAAA
Found at i:101840 original size:10 final size:10
Alignment explanation
Indices: 101825--101931 Score: 60
Period size: 10 Copynumber: 10.5 Consensus size: 10
101815 CAGGAAAATA
101825 TAAAAATTAT
1 TAAAAATTAT
101835 TAAAAA-TAT
1 TAAAAATTAT
*
101844 CAAAAAATTAT
1 -TAAAAATTAT
* *
101855 T-AAATTTAA
1 TAAAAATTAT
101864 TAAAAACTTA-
1 TAAAAA-TTAT
101874 -AAAATATTAT
1 TAAAA-ATTAT
* *
101884 AAAAAAATAT
1 TAAAAATTAT
* *
101894 TTAAAATTTT
1 TAAAAATTAT
*
101904 ATAAAAATTCT
1 -TAAAAATTAT
101915 TAAAAACTTATT
1 TAAAAA-TTA-T
101927 TAAAA
1 TAAAA
101932 CTTAATTTAA
Statistics
Matches: 74, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
9 17 0.23
10 31 0.42
11 20 0.27
12 6 0.08
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:101917 original size:20 final size:20
Alignment explanation
Indices: 101823--101919 Score: 76
Period size: 20 Copynumber: 4.8 Consensus size: 20
101813 ATCAGGAAAA
*
101823 TATAAAAATTATTAAAAATAT
1 TATAAAAATTATT-AAAATTT
*
101844 CA-AAAAATTATT-AAATTT
1 TATAAAAATTATTAAAATTT
* *
101862 AATAAAAACTTA--AAAATAT
1 TATAAAAA-TTATTAAAATTT
*
101881 TATAAAAAAATATTTAAAATTT
1 TAT-AAAAATTA-TTAAAATTT
*
101903 TATAAAAATTCTTAAAA
1 TATAAAAATTATTAAAA
101920 ACTTATTTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
18 6 0.10
19 14 0.23
20 24 0.40
21 7 0.12
22 9 0.15
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
TATAAAAATTATTAAAATTT
Found at i:102256 original size:2 final size:2
Alignment explanation
Indices: 102249--102274 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
102239 NNNNNNNNNN
102249 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
102275 CAATTTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:103740 original size:14 final size:13
Alignment explanation
Indices: 103714--103756 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
103704 ATAATTTTAA
103714 TTAATTT-TATTT
1 TTAATTTATATTT
103726 TTATATTTATATTT
1 TTA-ATTTATATTT
* *
103740 TTAAATTATAATT
1 TTAATTTATATTT
103753 TTAA
1 TTAA
103757 GAAGTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 3 0.11
13 16 0.59
14 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTAATTTATATTT
Found at i:105454 original size:2 final size:2
Alignment explanation
Indices: 105447--105477 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
105437 TTCTCAAGGT
105447 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
105478 CATTGAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:114039 original size:24 final size:23
Alignment explanation
Indices: 114007--114058 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
113997 GACTTTTTCA
* *
114007 TTTTTCAAATATTTT-TAGTCTTT
1 TTTTTCAAAAATTTTATAAT-TTT
114030 TTTTTCCAAAAATTTTATAATTTT
1 TTTTT-CAAAAATTTTATAATTTT
114054 TTTTT
1 TTTTT
114059 AAATTTTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.20
24 17 0.68
25 3 0.12
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTTCAAAAATTTTATAATTTT
Found at i:114974 original size:77 final size:77
Alignment explanation
Indices: 114847--115074 Score: 429
Period size: 77 Copynumber: 3.0 Consensus size: 77
114837 CAAACAGTAC
* * *
114847 CTGTTGACACTATTTTTTGATGAAACCGGGGTCGACTTGGGTTTTGAAAAATGAAAATGAAAACG
1 CTGTTGACACCATTTTTTGATGAAAACGGGGTCGACTTGGGTTTTGAAAAATGAAAACGAAAACG
114912 GGAGTCGCCTGG
66 GGAGTCGCCTGG
114924 CTGTTGACACCATTTTTTGATGAAAACGGGGTCGACTTGGGTTTTGAAAAATGAAAACGAAAACG
1 CTGTTGACACCATTTTTTGATGAAAACGGGGTCGACTTGGGTTTTGAAAAATGAAAACGAAAACG
114989 GGAGTCGCCTGG
66 GGAGTCGCCTGG
115001 CTGTTGACACCATTTTTTGATGAAAACGGGGTCGACTTGGGTTTTGAAAAATGAAAACGAAAACG
1 CTGTTGACACCATTTTTTGATGAAAACGGGGTCGACTTGGGTTTTGAAAAATGAAAACGAAAACG
115066 GGAGTCGCC
66 GGAGTCGCC
115075 AAGAGGATAT
Statistics
Matches: 148, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
77 148 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (77 bp):
CTGTTGACACCATTTTTTGATGAAAACGGGGTCGACTTGGGTTTTGAAAAATGAAAACGAAAACG
GGAGTCGCCTGG
Found at i:115552 original size:16 final size:16
Alignment explanation
Indices: 115531--115569 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
115521 AATTATGGAG
* *
115531 ATATATGAAAGCGTGT
1 ATATATAAAAGCATGT
*
115547 ATATATAAAAGTATGT
1 ATATATAAAAGCATGT
115563 ATATATA
1 ATATATA
115570 TGTATACGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (16 bp):
ATATATAAAAGCATGT
Found at i:117148 original size:20 final size:21
Alignment explanation
Indices: 117125--117171 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
117115 TTTTTTGGGC
*
117125 TGGGTTTTAATTTT-TCT-TTT
1 TGGGTTGTAATTTTAT-TGTTT
*
117145 TGGGCTGTAATTTTATTGTTT
1 TGGGTTGTAATTTTATTGTTT
117166 TGGGTT
1 TGGGTT
117172 AGGTCTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.11, C:0.04, G:0.23, T:0.62
Consensus pattern (21 bp):
TGGGTTGTAATTTTATTGTTT
Found at i:117642 original size:41 final size:42
Alignment explanation
Indices: 117595--118182 Score: 267
Period size: 44 Copynumber: 13.7 Consensus size: 42
117585 ATTAACGGTC
*
117595 TTCAATCTGCTCCACTGCATCTTCAGGGAGATAAGATT-TGT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTGT
* * * * * *
117636 TACAATCTACTCTACAGTAACTTCAGAGAGATAAGATCTGTGGT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGT-GT
* * * *** *
117680 TTTAATCCGCTCCACTACAACTTCAGGGAGATAAGA-CCAGA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTGT
* * * * *
117721 TGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTGAT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGTG-T
* * * *
117765 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTCT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTG---TGT
* * * * ** *
117810 TTC-GTCTACTCCACTGTAACCTCAGGGAGATAAGA-CCTGA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTGT
* * * *
117850 TGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGAT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGTG-T
* ** * * * * *
117894 TTTAATCCCCTCTACTGTAACTTAAGGGAGATAGGATT-TAT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTGT
** * * * ** *
117935 TTCTTTCGTCTGCTCCACTGTAACCTCAGGAAGATAAGA-CCTGA
1 TTC---AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTGT
* * * * * * *
117979 TGCTATCTACTCTACTGTAACTTTAGAGAGATAAGATCTGTGAT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGTG-T
* * * *
118023 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTCT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTG---TGT
* * *
118068 TTC-GTCTGCTCCACTGCAACTTTAGGGAGATAAGAGTG-GAT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTG-T
* * * * *
118109 GT-GATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGT-GT
* ** * *
118152 TTTAATCCACTCCACTGTAACTTTAGGGAGA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGA
118183 CAGGATTATC
Statistics
Matches: 395, Mismatches: 123, Indels: 55
0.69 0.21 0.10
Matches are distributed among these distances:
40 3 0.01
41 144 0.36
42 4 0.01
43 13 0.03
44 223 0.56
45 6 0.02
46 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (42 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTGT
Found at i:117835 original size:129 final size:129
Alignment explanation
Indices: 117688--118189 Score: 745
Period size: 129 Copynumber: 3.9 Consensus size: 129
117678 GTTTTAATCC
** * * * *
117688 GCTCCACTACAACTTCAGGGAGATAAGACCAGATGCGATCTGCTCTACTACAACTTCAGAGAGAT
1 GCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGAT
*
117753 AAGATCTGTGATTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTCTTTCGTCT
66 AAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTCTTTCGTCT
* *
117817 ACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTGCTCTACTGCAACTTCAGAGAGAT
1 GCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGAT
* * * *
117882 AAGATCTGTGATTTTAATCCCCTCTACTGTAACTTAAGGGAGATAGGATTTATTTCTTTCGTCT
66 AAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTCTTTCGTCT
* * * *
117946 GCTCCACTGTAACCTCAGGAAGATAAGACCTGATGCTATCTACTCTACTGTAACTTTAGAGAGAT
1 GCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGAT
*
118011 AAGATCTGTGATTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTCTTTCGTCT
66 AAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTCTTTCGTCT
* * * * *
118075 GCTCCACTGCAACTTTAGGGAGATAAGA-GTGGATGTGATCTACTCTACTGCAACTTCAGAGAGA
1 GCTCCACTGTAACCTCAGGGAGATAAGACCT-GATGCGATCTACTCTACTGCAACTTCAGAGAGA
* * * *
118139 TAAGATCTGTGGTTTTAATCCACTCCACTGTAACTTTAGGGAGACAGGATT
65 TAAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATT
118190 ATCGGCTTCA
Statistics
Matches: 336, Mismatches: 36, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
128 1 0.00
129 335 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (129 bp):
GCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGAT
AAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTCTTTCGTCT
Found at i:117858 original size:85 final size:85
Alignment explanation
Indices: 117769--118182 Score: 274
Period size: 85 Copynumber: 4.8 Consensus size: 85
117759 TGTGATTTTA
* * * *
117769 ATCTGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTCTTTCGTCTACTCCACTGTAACCTCA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGATTTCTTTCATCTACTCCACTGTAACTTTA
*
117834 GGGAGATAAGACCTGA-TGCG
66 GGGAGATAAGA-GTGATTGCG
* * * * * ** *
117854 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG-TGAT-TTTAATCCCCTCTACTGTAACTT
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGAT-TGAT-TTCTTTCATCTACTCCACTGTAACTT
* * * * *
117917 AAGGGAGATAGGATTTATTTCTTTCG
64 TAGGGAGATAAGAGTGA----TTGCG
* * * * *
117943 -TCTGCTCCACTGTAACCTCAGGAAGATAAGACCTGA-TGC--T-ATCTACTCTACTGTAACTTT
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGA-TTGATTTCTTTCATCTACTCCACTGTAACTTT
* ***
118003 AGAGAGATAAGATCTGTGATTTTA
65 AGGGAGATAAGA---GTGATTGCG
* * * *
118027 ATCTGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAACTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGATTTCTTTCATCTACTCCACTGTAACTTTA
*
118092 GGGAGATAAGAGTGGA-TGTG
66 GGGAGATAAGAGT-GATTGCG
* * * * * * *
118112 ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTG-TGGT-TTTAATCCACTCCACTGTAACTT
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGAT-TGAT-TTCTTTCATCTACTCCACTGTAACTT
118175 TAGGGAGA
64 TAGGGAGA
118183 CAGGATTATC
Statistics
Matches: 252, Mismatches: 56, Indels: 42
0.72 0.16 0.12
Matches are distributed among these distances:
84 8 0.03
85 174 0.69
86 9 0.04
87 1 0.00
88 57 0.23
89 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (85 bp):
ATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGATTTCTTTCATCTACTCCACTGTAACTTTA
GGGAGATAAGAGTGATTGCG
Found at i:118265 original size:227 final size:227
Alignment explanation
Indices: 117975--118795 Score: 1373
Period size: 227 Copynumber: 3.6 Consensus size: 227
117965 AAGATAAGAC
* * **
117975 CTGATGCT-ATCTACTCTACTGTAACTTTAGAGAGATAAGATC-TGTGATTTTAATCTGCTCCAC
1 CTGATG-TGATCTACTCTACTGTAACTTCAGAGAGATAAGATCAT-TTATTTTAATCCACTCCAC
* * * *
118038 TGTAACTTCAGGGAGATAGGATTGA-TTTCTTTCGTCTGCTCCACTGCAACTTTAGGGAGATAAG
64 TGTAACTTCAGAGAGATAGGATT-ACTTTCTTTCGTCTGCTCCACTGTAACCTCAGGGAGATAAG
* * * *
118102 A-GTGGATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCA
128 ACCT-GATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCA
* * *
118166 CTGTAACTTTAGGGAGACAGGATTATCGGCTTCAAT
192 CTGTAACTTCAGGGAGATAGGATTATCAGCTTCAAT
* *
118202 CTGATGTGATCTATTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTA
1 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTG
118267 TAACTTCAGAGAGATAGGATTACTTTCTTTCGTCTGCTCCACTGTAACCTCAGGGAGATAAGACC
66 TAACTTCAGAGAGATAGGATTACTTTCTTTCGTCTGCTCCACTGTAACCTCAGGGAGATAAGACC
*
118332 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTACACTGT
131 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGT
118397 AACTTCAGGGAGATAGGATTATCAGCTTCAAT
196 AACTTCAGGGAGATAGGATTATCAGCTTCAAT
* *
118429 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATTAGATCCTTTATTTTAATCCACTCCACTG
1 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTG
118494 TAACTTCAGAGAGATAGGATTACTTTCTTTCGTCTGCTCCACTGTAACCTCAGGGAGATAAGACC
66 TAACTTCAGAGAGATAGGATTACTTTCTTTCGTCTGCTCCACTGTAACCTCAGGGAGATAAGACC
118559 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGT
131 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGT
*
118624 AACTTCAGGGAGATAGGATTATCAGTTTCAAT
196 AACTTCAGGGAGATAGGATTATCAGCTTCAAT
*
118656 GTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAG-TCATTTATTTTAATCCACTCCACTG
1 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTG
118720 TAACTTCAGAGAGATAGGATTACTTTCTTTCGTCTGCTCCACTGTAACCTCAGGGAGATAAGACC
66 TAACTTCAGAGAGATAGGATTACTTTCTTTCGTCTGCTCCACTGTAACCTCAGGGAGATAAGACC
118785 TGATGCGATCT
131 TGATGCGATCT
118796 GATTCACCAA
Statistics
Matches: 563, Mismatches: 27, Indels: 9
0.94 0.05 0.02
Matches are distributed among these distances:
226 102 0.18
227 459 0.82
228 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (227 bp):
CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTG
TAACTTCAGAGAGATAGGATTACTTTCTTTCGTCTGCTCCACTGTAACCTCAGGGAGATAAGACC
TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGT
AACTTCAGGGAGATAGGATTATCAGCTTCAAT
Found at i:118286 original size:98 final size:98
Alignment explanation
Indices: 118106--118288 Score: 278
Period size: 98 Copynumber: 1.9 Consensus size: 98
118096 GATAAGAGTG
* *
118106 GATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTGTA
1 GATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTATA
* *
118171 ACTTTAGGGAGACAGGATTATCGGCTTCAATCT
66 ACTTCAGAGAGACAGGATTATCGGCTTCAATCT
* * *
118204 GATGTGATCTATTCTACTGTAACTTCAGAGAGATAAGATCAT-TTATTTTAATCCACTCCACTAT
1 GATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATC-TGTGATTTTAATCCACTCCACTAT
*
118268 AACTTCAGAGAGATAGGATTA
65 AACTTCAGAGAGACAGGATTA
118289 CTTTCTTTCG
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
98 75 0.99
99 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (98 bp):
GATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTATA
ACTTCAGAGAGACAGGATTATCGGCTTCAATCT
Found at i:118400 original size:44 final size:43
Alignment explanation
Indices: 118210--118735 Score: 287
Period size: 44 Copynumber: 11.7 Consensus size: 43
118200 ATCTGATGTG
* * *
118210 ATCTATTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATC-TTGATTTTA
* * * *
118254 ATCCACTCCACTATAACTTCAGAGAGATAGGATTACTT--TCTTTC
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGA-T-CTTGAT-TTTA
* * * * * ***
118298 GTCTGCTCCACTGTAACCTCAGGGAGATAAGA-CCTGA-TGCG
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCTTGATTTTA
*
118339 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCT-TGATTTTA
* * * * * *
118383 ATCCACTACACTGTAACTTCAGGGAGATAGGATTATCAGCTTCAATCTGATGTG
1 ATCTACTCCACTGTAACTTCAGAGAGATA--A-GAT---CTT-GAT-T--T-TA
* * *
118437 ATCTACTCTACTGTAACTTCAGAGAGATTAGATCCTTTATTTTA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGAT-CTTGATTTTA
* * *
118481 ATCCACTCCACTGTAACTTCAGAGAGATAGGATTACTT--TCTTTC
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGA-T-CTTGAT-TTTA
* * * * * ***
118525 GTCTGCTCCACTGTAACCTCAGGGAGATAAGA-CCTGA-TGCG
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCTTGATTTTA
*
118566 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCT-TGATTTTA
* * * * *
118610 ATCCACTCCACTGTAACTTCAGGGAGATAGGATTATCAGTTTCAATGTGATGTG
1 ATCTACTCCACTGTAACTTCAGAGAGATA--A-GATC---TT-GAT-T--T-TA
* *
118664 ATCTACTCTACTGTAACTTCAGAGAGATAAG-TCATTTATTTTA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATC-TTGATTTTA
*
118707 ATCCACTCCACTGTAACTTCAGAGAGATA
1 ATCTACTCCACTGTAACTTCAGAGAGATA
118736 GGATTACTTT
Statistics
Matches: 363, Mismatches: 82, Indels: 75
0.70 0.16 0.14
Matches are distributed among these distances:
41 60 0.17
42 2 0.01
43 36 0.10
44 167 0.46
45 8 0.02
46 4 0.01
47 8 0.02
48 4 0.01
49 5 0.01
50 9 0.02
51 4 0.01
52 2 0.01
53 2 0.01
54 52 0.14
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (43 bp):
ATCTACTCCACTGTAACTTCAGAGAGATAAGATCTTGATTTTA
Found at i:118500 original size:98 final size:98
Alignment explanation
Indices: 118331--118515 Score: 309
Period size: 98 Copynumber: 1.9 Consensus size: 98
118321 GAGATAAGAC
118331 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTACACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTACACTG
*
118396 TAACTTCAGGGAGATAGGATTATCAGCTTCAAT
66 TAACTTCAGAGAGATAGGATTATCAGCTTCAAT
* * * *
118429 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATTAGATCCT-TTATTTTAATCCACTCCACT
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTGTGATTTTAATCCACTACACT
118493 GTAACTTCAGAGAGATAGGATTA
65 GTAACTTCAGAGAGATAGGATTA
118516 CTTTCTTTCG
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 79 0.98
99 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (98 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTACACTG
TAACTTCAGAGAGATAGGATTATCAGCTTCAAT
Found at i:118738 original size:97 final size:98
Alignment explanation
Indices: 118559--118741 Score: 316
Period size: 97 Copynumber: 1.9 Consensus size: 98
118549 AGATAAGACC
118559 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGT
*
118624 AACTTCAGGGAGATAGGATTATCAGTTTCAATG
66 AACTTCAGAGAGATAGGATTATCAGTTTCAATG
* *
118657 TGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAG-TCAT-TTATTTTAATCCACTCCACTG
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC-TGTGATTTTAATCCACTCCACTG
118720 TAACTTCAGAGAGATAGGATTA
65 TAACTTCAGAGAGATAGGATTA
118742 CTTTCTTTCG
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
97 43 0.53
98 38 0.47
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (98 bp):
TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGT
AACTTCAGAGAGATAGGATTATCAGTTTCAATG
Found at i:119340 original size:14 final size:14
Alignment explanation
Indices: 119321--119349 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
119311 AATCTAAGGG
119321 TAGAAATATGTGGC
1 TAGAAATATGTGGC
119335 TAGAAATATGTGGC
1 TAGAAATATGTGGC
119349 T
1 T
119350 TTTCCTCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (14 bp):
TAGAAATATGTGGC
Found at i:120323 original size:6 final size:6
Alignment explanation
Indices: 120307--120341 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
120297 GCCTCTCCAT
*
120307 TTTTCA TTTTTCA TTTTCA TTTTCA GTTTCA TTTT
1 TTTTCA -TTTTCA TTTTCA TTTTCA TTTTCA TTTT
120342 TTTTGACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.69
Consensus pattern (6 bp):
TTTTCA
Found at i:121278 original size:6 final size:6
Alignment explanation
Indices: 121269--121388 Score: 68
Period size: 6 Copynumber: 20.2 Consensus size: 6
121259 TTTCTTTTTC
* * * * **
121269 TCATTT TCATTT TCATTT TCATTT TGATCT TGATTT TGATTT TTTTTCT
1 TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT TCATT-T
* ** * * **
121318 TCTTTCT TC-TTT TTGTTT T--TTT T-ATTT TGATTTT TGATTT TTTTTT
1 TCATT-T TCATTT TCATTT TCATTT TCATTT TCA-TTT TCATTT TCATTT
121364 TCATTT TCATTT TCATTT TCATTT T
1 TCATTT TCATTT TCATTT TCATTT T
121389 GACTTTGACT
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
4 4 0.04
5 6 0.06
6 73 0.74
7 15 0.15
ACGTcount: A:0.12, C:0.11, G:0.05, T:0.72
Consensus pattern (6 bp):
TCATTT
Found at i:121409 original size:6 final size:6
Alignment explanation
Indices: 121271--121412 Score: 67
Period size: 6 Copynumber: 23.8 Consensus size: 6
121261 TCTTTTTCTC
* * * * * * *
121271 ATTTTC ATTTTC ATTTTC ATTTTG ATCTTG ATTTTG ATTTTT TTTCTTC
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATT-TTG
* * * * * *
121320 TTTCTTC TTTTTG -TTTT- -TTTT- ATTTTG ATTTTTG ATTTTT TTTTTC
1 ATT-TTG ATTTTG ATTTTG ATTTTG ATTTTG A-TTTTG ATTTTG ATTTTG
* * * * *
121366 ATTTTC ATTTTC ATTTTC ATTTTG ACTTTG ACTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
121413 TCTTTTTCTT
Statistics
Matches: 118, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
4 4 0.03
5 8 0.07
6 88 0.75
7 18 0.15
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (6 bp):
ATTTTG
Found at i:125690 original size:20 final size:19
Alignment explanation
Indices: 125639--125691 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
125629 AGGGTACGTG
125639 TATATATAT-ATATAGATA
1 TATATATATAATATAGATA
* * *
125657 GATCATAAAAAATATAGATA
1 TAT-ATATATAATATAGATA
125677 TTATATATATAATAT
1 -TATATATATAATAT
125692 GAAAACGCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
18 2 0.08
19 4 0.15
20 18 0.69
21 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.40
Consensus pattern (19 bp):
TATATATATAATATAGATA
Found at i:125798 original size:5 final size:5
Alignment explanation
Indices: 125788--125816 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
125778 ATAATAATTT
125788 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
125817 CAATAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:126938 original size:20 final size:21
Alignment explanation
Indices: 126915--126961 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
126905 TTTTTTGGGC
*
126915 TGGGTTTTAATTTT-TCT-TTT
1 TGGGTTGTAATTTTAT-TGTTT
*
126935 TGGGCTGTAATTTTATTGTTT
1 TGGGTTGTAATTTTATTGTTT
126956 TGGGTT
1 TGGGTT
126962 AGGTCTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.11, C:0.04, G:0.23, T:0.62
Consensus pattern (21 bp):
TGGGTTGTAATTTTATTGTTT
Found at i:127573 original size:20 final size:20
Alignment explanation
Indices: 127546--127593 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
127536 TAAAGTTTTG
*
127546 TTTA-TTTTTTATT-TTTATT
1 TTTAGTTTTTTATTCTTT-CT
*
127565 TTTAGTTTTTTCTTCTTTCT
1 TTTAGTTTTTTATTCTTTCT
127585 TTTAGTTTT
1 TTTAGTTTT
127594 AAAAAACGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 18 0.72
21 3 0.12
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.79
Consensus pattern (20 bp):
TTTAGTTTTTTATTCTTTCT
Found at i:128314 original size:11 final size:12
Alignment explanation
Indices: 128266--128314 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
128256 TTATTAATTC
128266 ATTATTTTTAAT
1 ATTATTTTTAAT
128278 ATTA-TTTTAAT
1 ATTATTTTTAAT
*
128289 ATTGA--CTTAAT
1 ATT-ATTTTTAAT
128300 ATTATTTTTAA-
1 ATTATTTTTAAT
128311 ATTA
1 ATTA
128315 ATTATTAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 1 0.03
11 22 0.69
12 9 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (12 bp):
ATTATTTTTAAT
Found at i:130534 original size:10 final size:11
Alignment explanation
Indices: 130519--130567 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
130509 AACTAAATCC
130519 TTTCTCTC-AA
1 TTTCTCTCAAA
*
130529 TTTCTCTCTAA
1 TTTCTCTCAAA
*
130540 TATTCTATCAAA
1 T-TTCTCTCAAA
*
130552 TTCCTCTCAAA
1 TTTCTCTCAAA
130563 TTTCT
1 TTTCT
130568 ATTTAAAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
10 8 0.25
11 15 0.47
12 9 0.28
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (11 bp):
TTTCTCTCAAA
Found at i:132807 original size:124 final size:125
Alignment explanation
Indices: 132566--132977 Score: 684
Period size: 125 Copynumber: 3.3 Consensus size: 125
132556 CCAAACATGT
* * *
132566 TACTGTAGCAAAAAACGCGTCCACATGGGAGCGATTTCA-AAACTTCTTCTGATAAAGCATCCTG
1 TACTGTAGC-AAAAGCGCATCCACGTGGGAGCGATTTCAGAAA-TTCTTCTGATAAAGCATCCTG
132630 CTTGAAGCG-TTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACC
64 CTTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACC
* *
132691 TACTGTAGCAAAAGCGCATCCACGTGGGAACGATTTCAGAAATTCTTCTGATAAAGCATCTTGCT
1 TACTGTAGCAAAAGCGCATCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCT
* * *
132756 TCAAGTGTTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTTCAGGACC
66 TGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACC
*
132816 TACTGTAGCAAAAGTGCATCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCT
1 TACTGTAGCAAAAGCGCATCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCT
* *
132881 TGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACT
66 TGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACC
*
132941 TACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
1 TACTGTAGCAAAAGCGCATCCACGTGGGAGCGATTTC
132978 CTTAATAAAT
Statistics
Matches: 267, Mismatches: 18, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
124 52 0.19
125 215 0.81
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (125 bp):
TACTGTAGCAAAAGCGCATCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCT
TGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACC
Found at i:133163 original size:8 final size:9
Alignment explanation
Indices: 133143--133171 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
133133 ATTTTTCTCC
133143 AAAACCCTA
1 AAAACCCTA
133152 AAAACCCTA
1 AAAACCCTA
133161 AAAACCC-A
1 AAAACCCTA
133169 AAA
1 AAA
133172 TCTAACGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.62, C:0.31, G:0.00, T:0.07
Consensus pattern (9 bp):
AAAACCCTA
Found at i:143000 original size:14 final size:13
Alignment explanation
Indices: 142977--143007 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
142967 TCGATTAAAC
142977 TAAATAAATCGAA
1 TAAATAAATCGAA
142990 TAAATTAAATCGAA
1 TAAA-TAAATCGAA
143004 TAAA
1 TAAA
143008 CTGGTGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (13 bp):
TAAATAAATCGAA
Found at i:152994 original size:31 final size:29
Alignment explanation
Indices: 152929--152994 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
152919 ATGATAACGT
** *
152929 AAGTGACTAAAACGTAATATTTCAAACAT
1 AAGTGACTAAAACGTAATATGACAAACAA
* *
152958 GAGTGACTAAAATGTAATATGAGACAAACAA
1 AAGTGACTAAAACGTAATAT--GACAAACAA
152989 AAGTGA
1 AAGTGA
152995 TTATTTTTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
29 18 0.62
31 11 0.38
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.23
Consensus pattern (29 bp):
AAGTGACTAAAACGTAATATGACAAACAA
Found at i:153654 original size:11 final size:11
Alignment explanation
Indices: 153638--153663 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
153628 TGATCTTATT
153638 AAAAATTATAA
1 AAAAATTATAA
153649 AAAAATTATAA
1 AAAAATTATAA
153660 AAAA
1 AAAA
153664 CAATAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:153784 original size:19 final size:19
Alignment explanation
Indices: 153702--153792 Score: 96
Period size: 19 Copynumber: 4.8 Consensus size: 19
153692 TTAATAAGAA
153702 TATAAAAATTATAAAA-TT
1 TATAAAAATTATAAAATTT
* * *
153720 TATTAACAATTAGAAATTTT
1 TA-TAAAAATTATAAAATTT
* **
153740 TATAAAAATCATAAAAAAT
1 TATAAAAATTATAAAATTT
*
153759 TGT-AAAATTATAAAATTT
1 TATAAAAATTATAAAATTT
153777 TATAAAAATTATAAAA
1 TATAAAAATTATAAAA
153793 AAATTACTGA
Statistics
Matches: 56, Mismatches: 14, Indels: 5
0.75 0.19 0.07
Matches are distributed among these distances:
18 16 0.29
19 36 0.64
20 4 0.07
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
TATAAAAATTATAAAATTT
Found at i:153797 original size:38 final size:39
Alignment explanation
Indices: 153702--153794 Score: 120
Period size: 37 Copynumber: 2.5 Consensus size: 39
153692 TTAATAAGAA
* * *
153702 TATAAAAATTAT-AAAATTTATTAACAATTAGAAATTTT
1 TATAAAAATTATAAAAAATTAGTAACAATTAGAAAATTT
* *
153740 TATAAAAATCATAAAAAATT-GTAA-AATTATAAAATTT
1 TATAAAAATTATAAAAAATTAGTAACAATTAGAAAATTT
153777 TATAAAAATTATAAAAAA
1 TATAAAAATTATAAAAAA
153795 ATTACTGACC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 28 0.58
38 14 0.29
39 6 0.12
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (39 bp):
TATAAAAATTATAAAAAATTAGTAACAATTAGAAAATTT
Found at i:154140 original size:88 final size:88
Alignment explanation
Indices: 154007--154174 Score: 232
Period size: 88 Copynumber: 1.9 Consensus size: 88
153997 AAAAAAATTA
* *
154007 TTAATTGCTTTTTCTGAAAAAGTTTGAGGCGGTCTTTTTGCATTTTGAAAGTTCAAGTACCCAAT
1 TTAACTGCTTTTTCTGAAAAAGTTTGAGGCGGTCTTTTTGCATTTTGAAAGTTCAAGTACCCAAA
154072 TGAGTGCAAAAAAAAGTAGGGAC
66 TGAGTGCAAAAAAAAGTAGGGAC
* * * * *
154095 TTAACTGCTTTTT-TGAAAAGGTTTGAGAGC-TTTTTTTATGCATTTTGAAAGTTTAAGTACCTA
1 TTAACTGCTTTTTCTGAAAAAGTTTGAG-GCGGTCTTTT-TGCATTTTGAAAGTTCAAGTACCCA
*
154158 AATGAGTGTAAAAAAAA
64 AATGAGTGCAAAAAAAA
154175 AAAGAGTTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
87 18 0.26
88 52 0.74
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (88 bp):
TTAACTGCTTTTTCTGAAAAAGTTTGAGGCGGTCTTTTTGCATTTTGAAAGTTCAAGTACCCAAA
TGAGTGCAAAAAAAAGTAGGGAC
Found at i:154195 original size:88 final size:86
Alignment explanation
Indices: 154007--154195 Score: 186
Period size: 88 Copynumber: 2.2 Consensus size: 86
153997 AAAAAAATTA
* *
154007 TTAATTGC-TTTTTCTGAAAAAGTTTGAGGCGGTCTTTTTGCATTTTGAAAGTTCAAGTACCCAA
1 TTAATTACTTTTTTTTGAAAAAGTTTGAGGCGGTCTTTTTGCATTTTGAAAGTTCAAGTACCCAA
* **
154071 TTGAGTGCAAAAAAAAGTAGG
66 ATGAGTGCAAAAAAAAAAAGG
* * * * * * *
154092 -GACTTAACTGCTTTTTTGAAAAGGTTTGAGAGC-TTTTTTTATGCATTTTGAAAGTTTAAGTAC
1 TTAATT-ACT-TTTTTTTGAAAAAGTTTGAG-GCGGTCTTTT-TGCATTTTGAAAGTTCAAGTAC
* *
154155 CTAAATGAGTGTAAAAAAAAAAAGAG
62 CCAAATGAGTGCAAAAAAAAAAAG-G
154181 TTAATTACTTTTTTT
1 TTAATTACTTTTTTT
154196 AAAAAAATTT
Statistics
Matches: 80, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
84 3 0.04
85 1 0.01
87 22 0.28
88 47 0.59
89 4 0.05
90 3 0.04
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (86 bp):
TTAATTACTTTTTTTTGAAAAAGTTTGAGGCGGTCTTTTTGCATTTTGAAAGTTCAAGTACCCAA
ATGAGTGCAAAAAAAAAAAGG
Found at i:159595 original size:6 final size:6
Alignment explanation
Indices: 159584--159613 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
159574 GCTTTATTGC
159584 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
159614 TGCACCAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:164374 original size:6 final size:6
Alignment explanation
Indices: 164363--164396 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
164353 AGATGATGAG
164363 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAG
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAG
164397 CAAGCATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:167962 original size:18 final size:18
Alignment explanation
Indices: 167939--167975 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
167929 CTCTAAAATC
167939 ACATGCAAAAACAAGACT
1 ACATGCAAAAACAAGACT
*
167957 ACATGCATAAACAAGACT
1 ACATGCAAAAACAAGACT
167975 A
1 A
167976 AAAAATGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.22, G:0.11, T:0.14
Consensus pattern (18 bp):
ACATGCAAAAACAAGACT
Found at i:176951 original size:24 final size:24
Alignment explanation
Indices: 176882--176951 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 24
176872 ATTTCCCCTC
176882 TTTTCCTTCTTTCTCCTT-TGTTTA
1 TTTTCCTTCTTTCT-CTTCTGTTTA
* * *
176906 -TTTCCTTTTTTTTCTAAC-GTTTA
1 TTTTCCTTCTTTCTCT-TCTGTTTA
*
176929 TTTTCCTTCTTTGTCTTCTGTTT
1 TTTTCCTTCTTTCTCTTCTGTTT
176952 TCTCTCGTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
22 2 0.06
23 17 0.47
24 17 0.47
ACGTcount: A:0.06, C:0.21, G:0.06, T:0.67
Consensus pattern (24 bp):
TTTTCCTTCTTTCTCTTCTGTTTA
Found at i:180449 original size:24 final size:24
Alignment explanation
Indices: 180417--180464 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
180407 ATAGCCGACA
180417 AGAAATTAATCTTTGTTATGAACT
1 AGAAATTAATCTTTGTTATGAACT
180441 AGAAATTAATCTTTGTTATGAACT
1 AGAAATTAATCTTTGTTATGAACT
180465 TTCTCTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (24 bp):
AGAAATTAATCTTTGTTATGAACT
Found at i:183382 original size:6 final size:6
Alignment explanation
Indices: 183373--183412 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
183363 CCAAGACATA
183373 ACTTTG ACTTTG ACTTTG ACTTTG ACTTTG ACTTTG ACTT
1 ACTTTG ACTTTG ACTTTG ACTTTG ACTTTG ACTTTG ACTT
183413 GTTCAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.50
Consensus pattern (6 bp):
ACTTTG
Found at i:190577 original size:13 final size:13
Alignment explanation
Indices: 190559--190584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
190549 ACTGTTTTGC
190559 CTTGTTCCTCAAA
1 CTTGTTCCTCAAA
190572 CTTGTTCCTCAAA
1 CTTGTTCCTCAAA
190585 GAGAATGAGA
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:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (13 bp):
CTTGTTCCTCAAA
Found at i:191664 original size:13 final size:13
Alignment explanation
Indices: 191646--191670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
191636 GAATTACTAT
191646 GTATGAAAATTTC
1 GTATGAAAATTTC
191659 GTATGAAAATTT
1 GTATGAAAATTT
191671 GATCGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (13 bp):
GTATGAAAATTTC
Found at i:192882 original size:13 final size:12
Alignment explanation
Indices: 192855--192888 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
192845 AATTTTACAA
192855 AAAAATTTC-TT
1 AAAAATTTCGTT
192866 AAAAATTTCGTT
1 AAAAATTTCGTT
192878 CAAAAATTTCG
1 -AAAAATTTCG
192889 ACATTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (12 bp):
AAAAATTTCGTT
Found at i:193802 original size:20 final size:21
Alignment explanation
Indices: 193774--193813 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
193764 ATTTAATTCA
*
193774 ATATTTTGACA-TTATTTGAT
1 ATATGTTGACATTTATTTGAT
*
193794 ATATGTTGAGATTTATTTGA
1 ATATGTTGACATTTATTTGA
193814 ACATAGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.53
Consensus pattern (21 bp):
ATATGTTGACATTTATTTGAT
Found at i:194016 original size:69 final size:70
Alignment explanation
Indices: 193928--194125 Score: 294
Period size: 69 Copynumber: 2.8 Consensus size: 70
193918 GAGTACATTG
193928 AATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCACCG-TA
1 AATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTG-TGATTCCACCGATA
193992 T-TTTA
65 TCTTTA
* * *
193997 AATGTGAAA-GGGGTCGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCAACCGAT
1 AATAT-AAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTG-TGATTCCACCGAT
*
194061 ATCTTTG
64 ATCTTTA
*
194068 AATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAAGGGTTGCTAAGTGTCGATTCC
1 AATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGT-GATTCC
194126 TCGATTCATT
Statistics
Matches: 115, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
69 54 0.47
70 10 0.09
71 51 0.44
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (70 bp):
AATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTGATTCCACCGATAT
CTTTA
Found at i:194219 original size:33 final size:33
Alignment explanation
Indices: 194181--194305 Score: 124
Period size: 33 Copynumber: 3.5 Consensus size: 33
194171 ATGTGAAAGG
194181 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
194214 GGTTGCTAAGTGCTGATTCCACCGTATCATTGAATATGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG----ATT-CAT-TG---GT
* *
194257 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
194290 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
194306 ACCCACCGAT
Statistics
Matches: 76, Mismatches: 6, Indels: 20
0.75 0.06 0.20
Matches are distributed among these distances:
33 37 0.49
34 3 0.04
36 2 0.03
37 1 0.01
38 5 0.07
39 2 0.03
40 2 0.03
42 3 0.04
43 21 0.28
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:194290 original size:76 final size:75
Alignment explanation
Indices: 194105--194313 Score: 321
Period size: 76 Copynumber: 2.8 Consensus size: 75
194095 TTCCCCCAAA
* *
194105 GGGTTGCTAAGTG-TCGATTCCTCGATTCATTGGTGGTTGCTAAGTGCTAATCCCACCGTATCTT
1 GGGTTGCTAAGTGCT-GATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
*
194169 AAATGTGAAAG
65 AAATATGAAAG
*
194180 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCATT
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC-TT
*
194245 GAATATGAAAG
65 AAATATGAAAG
* * *
194256 GGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAACCCACCG
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCG
194314 ATAACGGTTG
Statistics
Matches: 123, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
75 57 0.46
76 66 0.54
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.31
Consensus pattern (75 bp):
GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTTA
AATATGAAAG
Found at i:196141 original size:75 final size:75
Alignment explanation
Indices: 196005--196147 Score: 173
Period size: 75 Copynumber: 1.9 Consensus size: 75
195995 GCTTACATAT
* * * * * *
196005 ATGTATATGTTCTTTTATTGAATTTAGGAAGGACATTTATATAAGTTTATATGAGACTCGATTAT
1 ATGTATATGTTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTGTATATGAAACTCGATTAT
196070 GTAGGTATAC
66 GTAGGTATAC
* * *
196080 ATGTATATGTTCTTGTAATGAATTTAAGTATGAAATTTATAT-A-TGTATATGGAAAATTCGATT
1 ATGTATATGTTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTGTATAT-G-AAACTCGATT
196143 ATGTA
64 ATGTA
196148 TATATATTCA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 6 0.11
74 2 0.04
75 49 0.86
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.43
Consensus pattern (75 bp):
ATGTATATGTTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTGTATATGAAACTCGATTAT
GTAGGTATAC
Found at i:196275 original size:41 final size:41
Alignment explanation
Indices: 196227--196330 Score: 129
Period size: 41 Copynumber: 2.5 Consensus size: 41
196217 TGATCGAATG
* * * *
196227 TTTCAGACTTTACGTCTAGCA-ACTTTGATGCCGGTGAAAGA
1 TTTCAGACTTTAAGTCTAGCAGAC-TTAATGCCAGTGAAACA
*
196268 TTTCAGACTTTATGTCTAGCAGACTTAATGCCAGTGAAACA
1 TTTCAGACTTTAAGTCTAGCAGACTTAATGCCAGTGAAACA
* *
196309 ATTCAGACTATAAGTCTAGCAG
1 TTTCAGACTTTAAGTCTAGCAG
196331 GCTAAAAGCC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 53 0.96
42 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (41 bp):
TTTCAGACTTTAAGTCTAGCAGACTTAATGCCAGTGAAACA
Found at i:198554 original size:15 final size:15
Alignment explanation
Indices: 198534--198578 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
198524 TCGTAATTTT
198534 ATTAAATAATTTAAG
1 ATTAAATAATTTAAG
198549 ATTAAAT--TTT---
1 ATTAAATAATTTAAG
198559 ATTAAATAATTTAAG
1 ATTAAATAATTTAAG
198574 ATTAA
1 ATTAA
198579 TATTTGATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
10 7 0.28
12 3 0.12
13 3 0.12
15 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (15 bp):
ATTAAATAATTTAAG
Found at i:198556 original size:25 final size:25
Alignment explanation
Indices: 198528--198583 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
198518 AATTTTTCGT
198528 AATTTTATTAAATAATTTAAGATTA
1 AATTTTATTAAATAATTTAAGATTA
198553 AATTTTATTAAATAATTTAAGATTA
1 AATTTTATTAAATAATTTAAGATTA
198578 ATATTT
1 A-ATTT
198584 GATGTATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 26 0.87
26 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
AATTTTATTAAATAATTTAAGATTA
Found at i:200832 original size:11 final size:11
Alignment explanation
Indices: 200816--200846 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
200806 TGAAAATTTG
200816 AAATTCAAATA
1 AAATTCAAATA
200827 AAATTCAAATA
1 AAATTCAAATA
200838 AAATATCAA
1 AAAT-TCAA
200847 TTTAAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATTCAAATA
Found at i:200836 original size:24 final size:23
Alignment explanation
Indices: 200769--200836 Score: 57
Period size: 24 Copynumber: 2.9 Consensus size: 23
200759 ATATAAATAA
* *
200769 AAATTCAAATAAACTTTAA-TTG
1 AAATTCAAATAAAATTAAATTTG
* * *
200791 AAAGTTCCAATGAAATGAAAATTTG
1 AAA-TTCAAATAAAAT-TAAATTTG
200816 AAATTCAAATAAAATTCAAAT
1 AAATTCAAATAAAATT-AAAT
200837 AAAATATCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
22 3 0.09
23 9 0.26
24 16 0.47
25 6 0.18
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (23 bp):
AAATTCAAATAAAATTAAATTTG
Found at i:200898 original size:35 final size:35
Alignment explanation
Indices: 200858--200966 Score: 114
Period size: 35 Copynumber: 3.1 Consensus size: 35
200848 TTAAAGCAAT
*
200858 ATTTATCAAATTACAATTTAAATATATGAATAAAA
1 ATTTATAAAATTACAATTTAAATATATGAATAAAA
* * * *
200893 ATTTATAATAAATATAATTTAAATA-AAGAA-AGCAAT
1 ATTTATAA-AATTACAATTTAAATATATGAATA--AAA
* *
200929 ATTTATTAAATTACAATTTAAATATATAAATAAAA
1 ATTTATAAAATTACAATTTAAATATATGAATAAAA
200964 ATT
1 ATT
200967 CAAATAAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
34 1 0.02
35 30 0.52
36 26 0.45
37 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (35 bp):
ATTTATAAAATTACAATTTAAATATATGAATAAAA
Found at i:200913 original size:36 final size:37
Alignment explanation
Indices: 200865--200974 Score: 115
Period size: 36 Copynumber: 3.1 Consensus size: 37
200855 AATATTTATC
200865 AAATTACAATTTAAATATATGAATAAAAATTTATAAT
1 AAATTACAATTTAAATATATGAATAAAAATTTATAAT
* * *
200902 AAA-TATAATTTAAATA-AAGAA-AGCAATATTTAT--T
1 AAATTACAATTTAAATATATGAATA--AAAATTTATAAT
* *
200936 AAATTACAATTTAAATATATAAATAAAAATTCA-AAT
1 AAATTACAATTTAAATATATGAATAAAAATTTATAAT
200972 AAA
1 AAA
200975 ATTTAATTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
34 5 0.09
35 22 0.38
36 27 0.47
37 4 0.07
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (37 bp):
AAATTACAATTTAAATATATGAATAAAAATTTATAAT
Found at i:203914 original size:11 final size:11
Alignment explanation
Indices: 203900--203930 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
203890 TGAAAATTTG
203900 AAATTCAAATA
1 AAATTCAAATA
203911 AAATTCAAATA
1 AAATTCAAATA
203922 AAATATCAA
1 AAAT-TCAA
203931 TTTAAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATTCAAATA
Found at i:203920 original size:24 final size:23
Alignment explanation
Indices: 203853--203920 Score: 57
Period size: 24 Copynumber: 2.9 Consensus size: 23
203843 ATATAAATAA
* *
203853 AAATTCAAATAAACTTTAA-TTG
1 AAATTCAAATAAAATTAAATTTG
* * *
203875 AAAGTTCCAATTAAATGAAAATTTG
1 AAA-TTCAAATAAAAT-TAAATTTG
203900 AAATTCAAATAAAATTCAAAT
1 AAATTCAAATAAAATT-AAAT
203921 AAAATATCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
22 3 0.09
23 9 0.26
24 16 0.47
25 6 0.18
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (23 bp):
AAATTCAAATAAAATTAAATTTG
Found at i:203982 original size:35 final size:35
Alignment explanation
Indices: 203942--204050 Score: 114
Period size: 35 Copynumber: 3.1 Consensus size: 35
203932 TTAAAGCAAT
*
203942 ATTTATCAAATTACAATTTAAATATATGAATAAAA
1 ATTTATAAAATTACAATTTAAATATATGAATAAAA
* * * *
203977 ATTTATAATAAATATAATTTAAATA-AAGAA-AGCAAT
1 ATTTATAA-AATTACAATTTAAATATATGAATA--AAA
* *
204013 ATTTATTAAATTACAATTTAAATATATAAATAAAA
1 ATTTATAAAATTACAATTTAAATATATGAATAAAA
204048 ATT
1 ATT
204051 CAAATAAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
34 1 0.02
35 30 0.52
36 26 0.45
37 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (35 bp):
ATTTATAAAATTACAATTTAAATATATGAATAAAA
Found at i:203997 original size:36 final size:37
Alignment explanation
Indices: 203949--204058 Score: 115
Period size: 36 Copynumber: 3.1 Consensus size: 37
203939 AATATTTATC
203949 AAATTACAATTTAAATATATGAATAAAAATTTATAAT
1 AAATTACAATTTAAATATATGAATAAAAATTTATAAT
* * *
203986 AAA-TATAATTTAAATA-AAGAA-AGCAATATTTAT--T
1 AAATTACAATTTAAATATATGAATA--AAAATTTATAAT
* *
204020 AAATTACAATTTAAATATATAAATAAAAATTCA-AAT
1 AAATTACAATTTAAATATATGAATAAAAATTTATAAT
204056 AAA
1 AAA
204059 ATTTAATTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
34 5 0.09
35 22 0.38
36 27 0.47
37 4 0.07
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (37 bp):
AAATTACAATTTAAATATATGAATAAAAATTTATAAT
Found at i:207067 original size:3 final size:3
Alignment explanation
Indices: 207061--207107 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
207051 TATGGTCTTA
* *
207061 TAT TAT TAA TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
207108 AATAAAGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:212148 original size:21 final size:21
Alignment explanation
Indices: 212107--212150 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
212097 AAACATTATA
*
212107 AAAATTGTAAAAATGAGAAAT
1 AAAATTGTAAAAATGAAAAAT
*
212128 AAAATTTTAAAAAAT-AAAAAT
1 AAAATTGT-AAAAATGAAAAAT
212149 AA
1 AA
212151 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (21 bp):
AAAATTGTAAAAATGAAAAAT
Found at i:213890 original size:2 final size:2
Alignment explanation
Indices: 213852--213876 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
213842 TCTTATAACC
213852 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 T
213877 TTTGGTGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:218411 original size:15 final size:14
Alignment explanation
Indices: 218375--218413 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
218365 ATATTTAGTG
218375 AATATTTATTGTTGA
1 AATA-TTATTGTTGA
*
218390 GATATTATTGGTTGA
1 AATATTATT-GTTGA
218405 AATATTATT
1 AATATTATT
218414 TTATTATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (14 bp):
AATATTATTGTTGA
Found at i:240003 original size:241 final size:241
Alignment explanation
Indices: 239580--240061 Score: 955
Period size: 241 Copynumber: 2.0 Consensus size: 241
239570 ATAATAAACA
239580 TAGTATAAAACGCACGGGACTCACCTGATTTGGCGACAAAATTAGGGTCGAAAGTCGAAACCCAA
1 TAGTATAAAACGCACGGGACTCACCTGATTTGGCGACAAAATTAGGGTCGAAAGTCGAAACCCAA
239645 ACGAAGTAGTTCTTTCTTATTTTAATTTCTATCGCAATTTGTCAACTACTTATTTTTTTTTTTCA
66 ACGAAGTAGTTCTTTCTTATTTTAATTTCTATCGCAATTTGTCAACTACTTATTTTTTTTTTTCA
239710 AAACAAAATCTTGACTTTCTTCTTCCTTTCTTTACCTCGTAGACACACTCCCAAAAACAGGGAAA
131 AAACAAAATCTTGACTTTCTTCTTCCTTTCTTTACCTCGTAGACACACTCCCAAAAACAGGGAAA
*
239775 AAAAAAAAAAAAAGAGCCTGCGCAAGGGGGGGTTGAGAGTTGGAAT
196 AAAAAAAAAAAAAGAGCCTGCGCAAGGGGGAGTTGAGAGTTGGAAT
239821 TAGTATAAAACGCACGGGACTCACCTGATTTGGCGACAAAATTAGGGTCGAAAGTCGAAACCCAA
1 TAGTATAAAACGCACGGGACTCACCTGATTTGGCGACAAAATTAGGGTCGAAAGTCGAAACCCAA
239886 ACGAAGTAGTTCTTTCTTATTTTAATTTCTATCGCAATTTGTCAACTACTTATTTTTTTTTTTCA
66 ACGAAGTAGTTCTTTCTTATTTTAATTTCTATCGCAATTTGTCAACTACTTATTTTTTTTTTTCA
239951 AAACAAAATCTTGACTTTCTTCTTCCTTTCTTTACCTCGTAGACACACTCCCAAAAACAGGGAAA
131 AAACAAAATCTTGACTTTCTTCTTCCTTTCTTTACCTCGTAGACACACTCCCAAAAACAGGGAAA
240016 AAAAAAAAAAAAAGAGCCTGCGCAAGGGGGAGTTGAGAGTTGGAAT
196 AAAAAAAAAAAAAGAGCCTGCGCAAGGGGGAGTTGAGAGTTGGAAT
240062 AGATGGGTCG
Statistics
Matches: 240, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
241 240 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (241 bp):
TAGTATAAAACGCACGGGACTCACCTGATTTGGCGACAAAATTAGGGTCGAAAGTCGAAACCCAA
ACGAAGTAGTTCTTTCTTATTTTAATTTCTATCGCAATTTGTCAACTACTTATTTTTTTTTTTCA
AAACAAAATCTTGACTTTCTTCTTCCTTTCTTTACCTCGTAGACACACTCCCAAAAACAGGGAAA
AAAAAAAAAAAAAGAGCCTGCGCAAGGGGGAGTTGAGAGTTGGAAT
Found at i:255896 original size:15 final size:16
Alignment explanation
Indices: 255876--255912 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
255866 ACAAAATCAA
*
255876 ATAAAA-TTACATTGT
1 ATAAAAGTTACATTAT
255891 ATAAAAGTTACATTAT
1 ATAAAAGTTACATTAT
255907 ATAAAA
1 ATAAAA
255913 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (16 bp):
ATAAAAGTTACATTAT
Found at i:256123 original size:60 final size:60
Alignment explanation
Indices: 256030--256151 Score: 190
Period size: 60 Copynumber: 2.0 Consensus size: 60
256020 ATACTAAACT
* * * * * *
256030 AAACACAACAATTTATAGCTTAATCCTAAATTACTAATAAATTAATTTTTAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAAAAAATTAATTATAAAATAATTAC
256090 AAACACAAAAATTTATAACATAATCCTAAATTACTAAAAAATTAATTATAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAAAAAATTAATTATAAAATAATTAC
256150 AA
1 AA
256152 TATTCATACA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAAAAAATTAATTATAAAATAATTAC
Found at i:256169 original size:21 final size:22
Alignment explanation
Indices: 256139--256186 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
256129 AATTAATTAT
256139 AAAATAATTACAATATTCATAC
1 AAAATAATTACAATATTCATAC
256161 AAAA-AATTACAATATTCATAC
1 AAAATAATTACAATATTCATAC
256182 AAAAT
1 AAAAT
256187 TATCCATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATAATTACAATATTCATAC
Found at i:259178 original size:3 final size:3
Alignment explanation
Indices: 259172--259205 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
259162 TGGTGGGGAA
*
259172 GAT GAT GAT GAT GAT GAT GAT GAT GAT TAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
259206 GTGAGAGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
GAT
Found at i:262286 original size:21 final size:19
Alignment explanation
Indices: 262262--262307 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
262252 ACATTTTGCT
262262 AAATTGTCATTTTTTTTTATA
1 AAATTGT-ATTTTTTTTTA-A
*
262283 AAATTTGTTTTTTTTTTTAA
1 AAA-TTGTATTTTTTTTTAA
262303 AAATT
1 AAATT
262308 AGTCTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 2 0.09
20 4 0.17
21 13 0.57
22 4 0.17
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (19 bp):
AAATTGTATTTTTTTTTAA
Found at i:265375 original size:21 final size:21
Alignment explanation
Indices: 265350--265393 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
265340 ATAGTTTAAA
*
265350 AAAAGTAATTCTATTCATCCT
1 AAAAGCAATTCTATTCATCCT
265371 AAAAGCAATTCTATTCATCCT
1 AAAAGCAATTCTATTCATCCT
265392 AA
1 AA
265394 CATGTTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (21 bp):
AAAAGCAATTCTATTCATCCT
Found at i:267325 original size:23 final size:23
Alignment explanation
Indices: 267299--267351 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
267289 CAAATTCCTC
267299 ATGTAAAGAAGCATGACACAAAA
1 ATGTAAAGAAGCATGACACAAAA
*
267322 ATGTTAAGAAGCATGACACAAAA
1 ATGTAAAGAAGCATGACACAAAA
*
267345 GTGTAAA
1 ATGTAAA
267352 CCAAGTGTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.53, C:0.11, G:0.19, T:0.17
Consensus pattern (23 bp):
ATGTAAAGAAGCATGACACAAAA
Found at i:269899 original size:24 final size:26
Alignment explanation
Indices: 269863--269912 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
269853 TATGGTTTGA
*
269863 TAAATGATAATCAACTATCAATTCAT
1 TAAATGATAATCAAATATCAATTCAT
*
269889 TAAAT-AT-ATCAAATTTCAATTCAT
1 TAAATGATAATCAAATATCAATTCAT
269913 CATATTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
25 2 0.09
26 5 0.23
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (26 bp):
TAAATGATAATCAAATATCAATTCAT
Found at i:270750 original size:10 final size:10
Alignment explanation
Indices: 270737--270779 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
270727 AAAATTAGCC
270737 TAATTAACTA
1 TAATTAACTA
270747 TAATTAACTA
1 TAATTAACTA
*
270757 -AACTTAATTA
1 TAA-TTAACTA
270767 TAATTAA-TA
1 TAATTAACTA
270776 TAAT
1 TAAT
270780 CAGTGGATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 8 0.27
10 20 0.67
11 2 0.07
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATTAACTA
Found at i:288502 original size:21 final size:21
Alignment explanation
Indices: 288478--288546 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
288468 ACGAAATAAA
288478 ATTTTGAGAAACCCGAATGAG
1 ATTTTGAGAAACCCGAATGAG
* **
288499 ATTTT-AGATTGA-TGGAATGAG
1 ATTTTGAGA--AACCCGAATGAG
*
288520 ATTTTGAGAAACCCGGATGAG
1 ATTTTGAGAAACCCGAATGAG
288541 ATTTTG
1 ATTTTG
288547 GAGGTAATGG
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
20 4 0.11
21 29 0.78
22 4 0.11
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (21 bp):
ATTTTGAGAAACCCGAATGAG
Found at i:293149 original size:143 final size:148
Alignment explanation
Indices: 292918--293307 Score: 384
Period size: 159 Copynumber: 2.6 Consensus size: 148
292908 TTAGTAAAGT
** * ** *
292918 TACATAAAATTTGAAATGTATTAATTTAGTGTGTTTTTATTATATAAATTTAGTAAAAAATTCTC
1 TACATAATGTTTGAAATGTATTATTTTAGTGTG-TTTT-TTATATAAATTTAGTAAAAAACCCTT
* * * * * *
292983 ATTTTGACCCTTTGTTCG-GTTTTTA-TTAC---TT-T-TAAAAAATATATTATTTTCGTGTCTA
64 ATTTTGGCCATTTGTTCGTATTTTTATTTACGTTTTATATAAAAAATATAATATTGTCGT-ACTA
*
293041 T-TTATTTTATTTTATTTTAG
128 TATTATTTTATATTATTTTAG
293061 TACATAATGTTTGAAATGTATTATTTTAGTGTG-TTTTTATATAAATTTAGTAAAAAAAACCCTT
1 TACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGT--AAAAAACCCTT
* * *
293125 ATTTTGGCCTTTTATTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATAATATT
64 ATTTTGGCCATTTGTTCGTA--TTT-TTATTTAC-G-TTTTA-TA---T-AAAAAATATAATATT
* * *
293190 TTCGTATTTTATTATTTTATATTATTTTAG
119 GTCGTACTATATTATTTTATATTATTTTAG
* *
293220 TACATAATGTTTGAAATGTATTATTTTTGTGTGTTTTTTATATAAATTTAGTGAAAAACCCTTAT
1 TACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGTAAAAAACCCTTAT
*
293285 TTTGGCAATTTGTTCGTATTTTT
66 TTTGGCCATTTGTTCGTATTTTT
293308 CTCTTTTTTT
Statistics
Matches: 205, Mismatches: 21, Indels: 30
0.80 0.08 0.12
Matches are distributed among these distances:
140 15 0.07
141 3 0.01
142 23 0.11
143 30 0.15
145 3 0.01
146 3 0.01
147 3 0.01
152 2 0.01
154 1 0.00
155 2 0.01
156 3 0.01
158 30 0.15
159 69 0.34
160 18 0.09
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (148 bp):
TACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGTAAAAAACCCTTAT
TTTGGCCATTTGTTCGTATTTTTATTTACGTTTTATATAAAAAATATAATATTGTCGTACTATAT
TATTTTATATTATTTTAG
Done.