Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005550.1 Hibiscus syriacus cultivar Beakdansim tig00012865_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58141
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1510 original size:25 final size:25
Alignment explanation
Indices: 1480--1528 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1470 TTCCACTCGA
1480 AAAATTAATGTTTTCGACTCGACTC
1 AAAATTAATGTTTTCGACTCGACTC
* * *
1505 AAAATTGATTTTTTCGACTTGACT
1 AAAATTAATGTTTTCGACTCGACT
1529 TGATTCAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (25 bp):
AAAATTAATGTTTTCGACTCGACTC
Found at i:10385 original size:23 final size:23
Alignment explanation
Indices: 10357--10400 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
10347 CAAATACATT
*
10357 AAATAAT-ATATTATTTATTAATA
1 AAATAATAATAATATTT-TTAATA
10380 AAATAATAATAATATTTTTAA
1 AAATAATAATAATATTTTTAA
10401 AATATTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATAATAATAATATTTTTAATA
Found at i:10573 original size:20 final size:19
Alignment explanation
Indices: 10548--10599 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
10538 TTAAAATAAA
10548 ATTAATATATTATTGATTAT
1 ATTAATATATTATT-ATTAT
10568 ATTAAT-TACTTATTATTAT
1 ATTAATATA-TTATTATTAT
*
10587 AATAATATTATTA
1 ATTAATA-TATTA
10600 AAATATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 12 0.43
20 14 0.50
21 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTAATATATTATTATTAT
Found at i:10801 original size:59 final size:60
Alignment explanation
Indices: 10722--10838 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 60
10712 ATTAATTTTA
* * * * * *
10722 TTAATAATTTATTATATTATTAAAATAAAAGTATAATATTATATTATTAA-AAATATAAT
1 TTAATAATTAATAATATTATTAAAATAAAACTAAAATAATATATTAATAATAAATATAAT
* * *
10781 TTAATAATTAATAATTTTATTAAAATGATACTAAAATAATATATTAATAATAAATATA
1 TTAATAATTAATAATATTATTAAAATAAAACTAAAATAATATATTAATAATAAATATA
10839 TAAAATAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
59 41 0.85
60 7 0.15
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (60 bp):
TTAATAATTAATAATATTATTAAAATAAAACTAAAATAATATATTAATAATAAATATAAT
Found at i:11047 original size:12 final size:13
Alignment explanation
Indices: 11019--11062 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
11009 AACATTACTA
*
11019 TATATATATATATT
1 TATAT-TATATAAT
11033 TATATTATA-AAT
1 TATATTATATAAT
11045 TATATTATATAA-
1 TATATTATATAAT
11057 TATATT
1 TATATT
11063 CAGCTATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 17 0.61
13 6 0.21
14 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATATTATATAAT
Found at i:12184 original size:22 final size:22
Alignment explanation
Indices: 12159--12210 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
12149 TTTGTTTCAT
*
12159 TTATTATT-TATTCCTTTTATTA
1 TTATTATTCT-TTCCATTTATTA
**
12181 TTATTATTCTTTGGATTTATTA
1 TTATTATTCTTTCCATTTATTA
12203 TTATTATT
1 TTATTATT
12211 ATTTTATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.67
Consensus pattern (22 bp):
TTATTATTCTTTCCATTTATTA
Found at i:12187 original size:25 final size:27
Alignment explanation
Indices: 12159--12219 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
12149 TTTGTTTCAT
*
12159 TTATTATTT-ATTCCTT-TTATTATTA
1 TTATTATTTGATTCATTATTATTATTA
* *
12184 TTATTCTTTGGATTTATTATTATTATTA
1 TTATTATTT-GATTCATTATTATTATTA
12212 TT-TTATTT
1 TTATTATTT
12220 TATTTTCCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 8 0.28
27 10 0.34
28 11 0.38
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (27 bp):
TTATTATTTGATTCATTATTATTATTA
Found at i:12221 original size:22 final size:23
Alignment explanation
Indices: 12173--12223 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
12163 TATTTATTCC
*
12173 TTTTATTATTATTATTCTTTGGA
1 TTTTATTATTATTATTATTTGGA
*
12196 -TTTATTATTATTATTATTT-TA
1 TTTTATTATTATTATTATTTGGA
12217 TTTTATT
1 TTTTATT
12224 TTCCCTCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTTATTATTATTATTATTTGGA
Found at i:12265 original size:2 final size:2
Alignment explanation
Indices: 12258--12389 Score: 209
Period size: 2 Copynumber: 67.5 Consensus size: 2
12248 AATATTGTAT
* *
12258 TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA T- TA TA T- TCG TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
12297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12339 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12381 TA TA TA TA T
1 TA TA TA TA T
12390 TACCTTTTTA
Statistics
Matches: 124, Mismatches: 1, Indels: 10
0.92 0.01 0.07
Matches are distributed among these distances:
1 4 0.03
2 119 0.96
3 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15466 original size:34 final size:34
Alignment explanation
Indices: 15412--15491 Score: 128
Period size: 34 Copynumber: 2.4 Consensus size: 34
15402 GTCTGCATGT
15412 GCCATGCACGT-CCCCAACACCCCAACACAGGCC
1 GCCATGCACGTCCCCCAACACCCCAACACAGGCC
*
15445 GCCATGCACGTCCCCCAACACCCCAACACAGGTC
1 GCCATGCACGTCCCCCAACACCCCAACACAGGCC
*
15479 GCTATGCAC-TCCC
1 GCCATGCACGTCCC
15492 AGCGACCTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 15 0.34
34 29 0.66
ACGTcount: A:0.25, C:0.50, G:0.15, T:0.10
Consensus pattern (34 bp):
GCCATGCACGTCCCCCAACACCCCAACACAGGCC
Found at i:15516 original size:29 final size:29
Alignment explanation
Indices: 15474--15556 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 29
15464 ACCCCAACAC
*
15474 AGGTCGCTATGCACTCCCAGCGACCTACA
1 AGGTCGCCATGCACTCCCAGCGACCTACA
***
15503 AGGTCGCCATGCACTCCCAGCGACCTTGT
1 AGGTCGCCATGCACTCCCAGCGACCTACA
* * *
15532 AGGTCGCCAAGCAGTCCCGGCGACC
1 AGGTCGCCATGCACTCCCAGCGACC
15557 AAGCTGGCGA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.20, C:0.39, G:0.25, T:0.16
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCAGCGACCTACA
Found at i:15588 original size:26 final size:26
Alignment explanation
Indices: 15559--15610 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
15549 CGGCGACCAA
15559 GCTGGCGACCAAACTTAACCCTGCTC
1 GCTGGCGACCAAACTTAACCCTGCTC
15585 GCTGGCGACCAAACTTAACCCTGCTC
1 GCTGGCGACCAAACTTAACCCTGCTC
15611 CCTCGTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.38, G:0.19, T:0.19
Consensus pattern (26 bp):
GCTGGCGACCAAACTTAACCCTGCTC
Found at i:15655 original size:23 final size:23
Alignment explanation
Indices: 15625--15668 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
15615 GTGCATGCAT
*
15625 TGCATCCATAGTTGGGAGATTCC
1 TGCATCCATAGCTGGGAGATTCC
15648 TGCATCCATAGCTGGGAGATT
1 TGCATCCATAGCTGGGAGATT
15669 GTAGCCAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (23 bp):
TGCATCCATAGCTGGGAGATTCC
Found at i:18883 original size:12 final size:12
Alignment explanation
Indices: 18866--18890 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18856 AAAACTTATC
18866 ACTTTTGTAAAA
1 ACTTTTGTAAAA
18878 ACTTTTGTAAAA
1 ACTTTTGTAAAA
18890 A
1 A
18891 GAAAGGTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ACTTTTGTAAAA
Found at i:20950 original size:399 final size:396
Alignment explanation
Indices: 20216--21004 Score: 1278
Period size: 399 Copynumber: 2.0 Consensus size: 396
20206 TCCACATTAC
* *
20216 CCCGTTTGGTTGGCCGGTAATCTCATTCCCGGTAATTTTTTATTACCAACAGTAGATTTTTTTGG
1 CCCGTTTGGTTGGCCGATAATCTCATTCCCGGTAATGTTTTATTACCAACAGTAGATTTTTTTGG
* * * *
20281 GTATATTATCGGGAATGTTATTACCCCATTCCCTTATGTATTGTTGGATTACCAGCGTTTTGGAC
66 GTATATTACCGGAAATGTCATTACCCCATTCCCTTAGGTATTGTTGGATTACCAGCGTTTTGGAC
* *
20346 TAAAATGCCCTTAATTTTTTTTCAAAAATATCCTTCTTATGTCATTGAATAATAAAAATTCTACT
131 TAAAATGCCCTTAATTTTTTTTCAAAAATATCATTCTTATGTCATTGAATAATAAAAATTCTACG
* * *
20411 AAGGTTAAATTATAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAATTCTATAATTAAAAT
196 AAGATTAAATTATAAATTGATCCTTAAACTATTTTAGATTTACAAAAAAAGTCTATAATTAAAAT
* **
20476 TTTATATGAAGTTCGGGGGTTAAAATAAAATTTTACCCTTTCATTAAACATTTTTATATTTTCAA
261 TTTATATGAAATTCAAGGGTTAAAATAAAATTTTACCCTTTCATTAAACATTTTTATATTTTCAA
*
20541 TGTTGT-AAAAAAATTATATAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATCT
326 TGTTGTAAAAAAAATTATATAAATTTTATGAATTTAAATTTTTCAAAGAAAATATATAAATATCT
20605 CATTCT
391 CATTCT
* *
20611 CCCGTTTGGTTGGTCGATAGTCTCATTCCCGGTAATGTTTTATTACCAACAGT-GCATTTTTTTT
1 CCCGTTTGGTTGGCCGATAATCTCATTCCCGGTAATGTTTTATTACCAACAGTAG-A--TTTTTT
* *
20675 TGGGTATATTACCGGAAATGTCATTATCCCATTCCCTTAGGTATTGTTGGATTACCGGCGTTTTG
63 TGGGTATATTACCGGAAATGTCATTACCCCATTCCCTTAGGTATTGTTGGATTACCAGCGTTTTG
* * * *
20740 GACT-AAATGTCGTTAATTTTTTTTTCCAAAAATATTATTCTTCTGTCATTGAATAATAAAAATT
128 GACTAAAATGCCCTTAA-TTTTTTTT-CAAAAATATCATTCTTATGTCATTGAATAATAAAAATT
20804 CTACGAAGATTAAATTATAAATTGATCCTTAAACTATTTTAGATTTACAAAAAAAAGTCTATAAT
191 CTACGAAGATTAAATTATAAATTGATCCTTAAACTATTTTAGATTTAC-AAAAAAAGTCTATAAT
20869 TAAAATTTTATATGAAATTCAAGGGTTAAAATAAAATTTTACCCTTTCATTAAACATTTTTATAT
255 TAAAATTTTATATGAAATTCAAGGGTTAAAATAAAATTTTACCCTTTCATTAAACATTTTTATAT
* *
20934 TTTCAATTTTGTAAAAAAAATTATATAAATTTTATGGATTTAAATTTTTCAAAGAAAATATATAA
320 TTTCAATGTTGTAAAAAAAATTATATAAATTTTATGAATTTAAATTTTTCAAAGAAAATATATAA
20999 ATATCT
385 ATATCT
21005 TATAGTGATA
Statistics
Matches: 362, Mismatches: 25, Indels: 9
0.91 0.06 0.02
Matches are distributed among these distances:
394 1 0.00
395 50 0.14
396 10 0.03
397 77 0.21
398 80 0.22
399 88 0.24
400 56 0.15
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (396 bp):
CCCGTTTGGTTGGCCGATAATCTCATTCCCGGTAATGTTTTATTACCAACAGTAGATTTTTTTGG
GTATATTACCGGAAATGTCATTACCCCATTCCCTTAGGTATTGTTGGATTACCAGCGTTTTGGAC
TAAAATGCCCTTAATTTTTTTTCAAAAATATCATTCTTATGTCATTGAATAATAAAAATTCTACG
AAGATTAAATTATAAATTGATCCTTAAACTATTTTAGATTTACAAAAAAAGTCTATAATTAAAAT
TTTATATGAAATTCAAGGGTTAAAATAAAATTTTACCCTTTCATTAAACATTTTTATATTTTCAA
TGTTGTAAAAAAAATTATATAAATTTTATGAATTTAAATTTTTCAAAGAAAATATATAAATATCT
CATTCT
Found at i:26013 original size:11 final size:11
Alignment explanation
Indices: 25992--26027 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
25982 ATATTTATTG
25992 TTATT-ATAAA
1 TTATTAATAAA
26002 TTATTAATAAA
1 TTATTAATAAA
*
26013 TTATTAATATA
1 TTATTAATAAA
26024 TTAT
1 TTAT
26028 GTATCAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTATTAATAAA
Found at i:26148 original size:28 final size:27
Alignment explanation
Indices: 26090--26149 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
26080 TAATTGTATG
* * *
26090 ATTATATATCTATAATTTTTTATTTTG
1 ATTATAGATCTATAATTTTTCATTTTA
26117 ATTATAGATCTATTAATTTTATCA-TTTA
1 ATTATAGATCTA-TAATTTT-TCATTTTA
26145 ATTAT
1 ATTAT
26150 TTAAATGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 11 0.39
28 15 0.54
29 2 0.07
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.58
Consensus pattern (27 bp):
ATTATAGATCTATAATTTTTCATTTTA
Found at i:26376 original size:19 final size:20
Alignment explanation
Indices: 26349--26389 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
26339 GTAATTATTT
*
26349 TAATATTTTAAAATTAATAA
1 TAATATTTTAAAATAAATAA
*
26369 TAAT-TTTTATAATAAATAA
1 TAATATTTTAAAATAAATAA
26388 TA
1 TA
26390 TTAATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATATTTTAAAATAAATAA
Found at i:26394 original size:22 final size:22
Alignment explanation
Indices: 26363--26418 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
26353 ATTTTAAAAT
* *
26363 TAATAATAATTTTTATAATAAA
1 TAATATTAATTATTATAATAAA
*
26385 TAATATTAATTATTATATTAAA
1 TAATATTAATTATTATAATAAA
26407 TAA-ATATAATTA
1 TAATAT-TAATTA
26419 ATCATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATATTAATTATTATAATAAA
Found at i:26433 original size:26 final size:26
Alignment explanation
Indices: 26359--26433 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 26
26349 TAATATTTTA
*
26359 AAAT-TAA-TAATAATTTT-TATAAT
1 AAATATAATTAATAATTTTATAAAAT
* * *
26382 AAATA-ATATTAATTATTATATTAAAT
1 AAATATA-ATTAATAATTTTATAAAAT
*
26408 AAATATAATTAATCATTTTATAAAAT
1 AAATATAATTAATAATTTTATAAAAT
26434 TACAATGTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
23 5 0.12
24 1 0.03
25 8 0.20
26 25 0.62
27 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATATAATTAATAATTTTATAAAAT
Found at i:29867 original size:115 final size:115
Alignment explanation
Indices: 29553--29995 Score: 715
Period size: 116 Copynumber: 3.8 Consensus size: 115
29543 CACGTGAAGG
* * *
29553 CCCGGGGGCGTCTTCCATTATTTTGTCAGATAATATGTTATCATTACCCTATTATGTCACTCATG
1 CCCGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
* *
29618 TCCCTCGGGGGCACTATTTATGTCAGTACCCAAAGTGGTGAAAGCGGGTT
66 TCCCTCGGGGGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTT
* ** * *
29668 CCCGGGGGGCGTCTTTTATTATTTTGTCAGAGAATATATTATCATTGCTCTATTATGTCACTCAT
1 CCC-GGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCAT
29733 GTCCCTCGGGGGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTT
65 GTCCCTCGGGGGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTT
* * *
29784 CCCGGGGGCGCCTTCCATTATTTTGTCATATAATTTGTTATCATTGCCCTATTATGTCACTCATG
1 CCCGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
*
29849 TCCCTCGGGAGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTT
66 TCCCTCGGGGGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTT
* *
29899 CCCGGGGGACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGTCCTATTATATCACTCAT
1 CCCGGGGG-CGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCAT
*
29964 GTCCCTCGGGGGCACTATTTATGTCAGTACCC
65 GTCCCTCGGGGGCACTATTCATGTCAGTACCC
29996 CTTCCATTAT
Statistics
Matches: 302, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
115 114 0.38
116 188 0.62
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (115 bp):
CCCGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
TCCCTCGGGGGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTT
Found at i:29962 original size:231 final size:231
Alignment explanation
Indices: 29553--30634 Score: 796
Period size: 231 Copynumber: 4.8 Consensus size: 231
29543 CACGTGAAGG
* *
29553 CCCGGGGGCGTCTTCCATTATTTTGTCAGATAATATGTTATCATTACCCTATTATGTCACTCATG
1 CCCGGGGGCGCCTTCCATTATTTTGTCAGATAATATGTTATCATTGCCCTATTATGTCACTCATG
* * *
29618 TCCCTCGGGGGCACTATTTATGTCAGTACCCAAAGTGGTGAAAGCGGGTTCCCGGGGGGCGTCTT
66 TCCCTCGGGGGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGCGCCTT
** * *
29683 TTATTATTTTGTCAGAGAATATATTATCATTGCTCTATTATGTCACTCATGTCCCTCGGGGGCAC
131 CCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGGCAC
*
29748 TATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTT
196 TATTCATGTCAGTACCCAAAGTGGTGAAAGCGCATT
* *
29784 CCCGGGGGCGCCTTCCATTATTTTGTCATATAATTTGTTATCATTGCCCTATTATGTCACTCATG
1 CCCGGGGGCGCCTTCCATTATTTTGTCAGATAATATGTTATCATTGCCCTATTATGTCACTCATG
* *
29849 TCCCTCGGGAGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGACGCCTT
66 TCCCTCGGGGGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGCGCCTT
* *
29914 CCATTATTTTGTCAGAGAATATGTTATCATTGTCCTATTATATCACTCATGTCCCTCGGGGGCAC
131 CCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGGCAC
* ** * ** *** * *
29979 TATTTATGTCAGTACCCCTTCCATTATTTTTCAGAGAATAT
196 TATTCATGTCAGTA-CCC--AAAGT-GGTGAAAGCGCAT-T
**** * * * * * ** *** *
30020 ---GTTATC-AC-TGC-TCTATTATGTCA-CT--CATGTCCCTCGGGGGCACTATTCATGT---T
1 CCCGGGGGCGCCTTCCAT-TATTTTGTCAGATAATATGT-TATC-ATTGCCCTATT-ATGTCACT
** * ** * * * ******
30073 -A-GTACCCAAAGTGGTG-A--AGGC--G-C-GTTCTC--AG-GG-G---GCGCCTTCCATTATT
62 CATGT-CCC-TCG-GGGGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGG
**** **** * * * ** ** * * * ** * *
30122 TTTTCAGAGAATATGTTATCATTGCCCTA--TTAT-A-T-CAC--TCATGTCCCTCGGGGACACT
124 GCGCCTTCCATTATTTTGTCAGAG-AATATGTTATCATTGCCCTATTATGTCACTC-ATGTCCCT
* ** *
30180 -A---------TTCATGTCAGTACCCTGAGTGGTGAAAGCGCGTT
187 CGGGGGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCATT
* ** * * *
30215 CCCGGGGGGCGCATTTGATTATTTTTTCAGAGAATATCTTATCATTGCCCTATTATGTCACTCAT
1 CCC-GGGGGCGCCTTCCATTATTTTGTCAGATAATATGTTATCATTGCCCTATTATGTCACTCAT
*
30280 GTCCCTCGGGGGCACTATTCATGTCAGTACCCAAAGTGGTAAAAGCGCGTTCCCGGGGGGCGCCT
65 GTCCCTCGGGGGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGCGCCT
* * *
30345 TCCATTATTTTTTCAGATAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGTGCA
130 TCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGGCA
30410 CTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCATT
195 CTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCATT
* *
30447 CCCGGGGGGGGCGTCTTCCATTATTTTTTCAGATAATATGTTATCATTGCCCTATTATGTCACTC
1 CCC---GGGGGCGCCTTCCATTATTTTGTCAGATAATATGTTATCATTGCCCTATTATGTCACTC
* *
30512 ATGTCCCTTGGGGGCACTATTTATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGCGC
63 ATGTCCCTCGGGGGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGCGC
* * *
30577 CTTCCATTATTTTGTTAGAGAATATGTTATTATTGCCCTATTATATCACTCATGTCCC
128 CTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
30635 CCCGAATAAC
Statistics
Matches: 619, Mismatches: 170, Indels: 121
0.68 0.19 0.13
Matches are distributed among these distances:
195 1 0.00
196 5 0.01
197 2 0.00
199 5 0.01
200 11 0.02
201 13 0.02
202 8 0.01
203 5 0.01
204 6 0.01
205 4 0.01
206 4 0.01
208 1 0.00
209 9 0.01
210 8 0.01
211 1 0.00
212 3 0.00
213 3 0.00
214 4 0.01
215 19 0.03
216 4 0.01
217 18 0.03
218 5 0.01
219 3 0.00
220 3 0.00
221 2 0.00
222 8 0.01
223 10 0.02
224 1 0.00
226 4 0.01
227 4 0.01
228 6 0.01
229 5 0.01
230 9 0.01
231 208 0.34
232 38 0.06
233 2 0.00
234 171 0.28
235 5 0.01
236 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.34
Consensus pattern (231 bp):
CCCGGGGGCGCCTTCCATTATTTTGTCAGATAATATGTTATCATTGCCCTATTATGTCACTCATG
TCCCTCGGGGGCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGCGCCTT
CCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGGCAC
TATTCATGTCAGTACCCAAAGTGGTGAAAGCGCATT
Found at i:30022 original size:84 final size:85
Alignment explanation
Indices: 29910--30079 Score: 281
Period size: 84 Copynumber: 2.0 Consensus size: 85
29900 CCGGGGGACG
*
29910 CCTTCCATTATTTTGTCAGAGAATATGTTATCATTG-TCCTATTATATCACTCATGTCCCTCGGG
1 CCTTCCATTATTTTGTCAGAGAATATGTTATCACTGCT-CTATTATATCACTCATGTCCCTCGGG
*
29974 GGCACTATTTATGTCAGTACC
65 GGCACTATTCATGTCAGTACC
*
29995 CCTTCCATTATTTT-TCAGAGAATATGTTATCACTGCTCTATTATGTCACTCATGTCCCTCGGGG
1 CCTTCCATTATTTTGTCAGAGAATATGTTATCACTGCTCTATTATATCACTCATGTCCCTCGGGG
*
30059 GCACTATTCATGTTAGTACC
66 GCACTATTCATGTCAGTACC
30079 C
1 C
30080 AAAGTGGTGA
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
84 65 0.81
85 15 0.19
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (85 bp):
CCTTCCATTATTTTGTCAGAGAATATGTTATCACTGCTCTATTATATCACTCATGTCCCTCGGGG
GCACTATTCATGTCAGTACC
Found at i:30140 original size:116 final size:116
Alignment explanation
Indices: 29995--30634 Score: 1023
Period size: 116 Copynumber: 5.5 Consensus size: 116
29985 TGTCAGTACC
* *
29995 CCTTCCATTA-TTTTTCAGAGAATATGTTATCACTGCTCTATTATGTCACTCATGTCCCTCGGGG
1 CCTTCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
* * * *
30059 GCACTATTCATGTTAGTACCCAAAGTGGTGAAGGCGCGTTCTCAGGGGGCG
66 GCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGCG
*
30110 CCTTCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTATTATATCACTCATGTCCCTCGGGG
1 CCTTCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
* **
30175 ACACTATTCATGTCAGTACCCTGAGTGGTGAAAGCGCGTTCCCGGGGGGCG
66 GCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGCG
* ** *
30226 CATTTGATTATTTTTTCAGAGAATATCTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
1 CCTTCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
*
30291 GCACTATTCATGTCAGTACCCAAAGTGGTAAAAGCGCGTTCCCGGGGGGCG
66 GCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGCG
* *
30342 CCTTCCATTATTTTTTCAGATAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGT
1 CCTTCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
*
30407 GCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCATTCCCGGGGGGGGCG
66 GCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCC--GGGGGGCG
* * *
30460 TCTTCCATTATTTTTTCAGATAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTTGGGG
1 CCTTCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
*
30525 GCACTATTTATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGCG
66 GCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGCG
* *
30576 CCTTCCATTATTTTGTT-AGAGAATATGTTATTATTGCCCTATTATATCACTCATGTCCC
1 CCTTCCATTATTTT-TTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
30635 CCCGAATAAC
Statistics
Matches: 485, Mismatches: 36, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
115 10 0.02
116 362 0.75
117 2 0.00
118 111 0.23
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (116 bp):
CCTTCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
GCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGCG
Found at i:30162 original size:200 final size:201
Alignment explanation
Indices: 29794--30427 Score: 671
Period size: 200 Copynumber: 3.0 Consensus size: 201
29784 CCCGGGGGCG
* * * *
29794 CCTTCCATTATTTTGTCATATAATTTGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGA
1 CCTTCCATTATTTTGTCAGAGAATATGTTATCACTGCCCTATTATGTCACTCATGTCCCTCGGGA
*
29859 GCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGACGCCTTCCATTATTTT
66 GCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCAGGGGGACGCCTTCCATTATTTT
* * *
29924 GTCAGAGAATATGTTATCATTGTCCTATTATATCACTCATGTCCCTCGGGGGCACTATTTATGTC
131 GTCAGAGAATATGTTATCATTGCCCTATTATATCACTCATGTCCCTCGGGGACACTATTCATGTC
29989 AGTACC
196 AGTACC
* *
29995 CCTTCCATTATTTT-TCAGAGAATATGTTATCACTGCTCTATTATGTCACTCATGTCCCTCGGGG
1 CCTTCCATTATTTTGTCAGAGAATATGTTATCACTGCCCTATTATGTCACTCATGTCCCTCGGGA
* *
30059 GCACTATTCATGTTAGTACCCAAAGTGGTGAAGGCGCGTTCTCAGGGGG-CGCCTTCCATTATTT
66 GCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTC-CAGGGGGACGCCTTCCATTATTT
*
30123 TTTCAGAGAATATGTTATCATTGCCCTATTATATCACTCATGTCCCTCGGGGACACTATTCATGT
130 TGTCAGAGAATATGTTATCATTGCCCTATTATATCACTCATGTCCCTCGGGGACACTATTCATGT
30188 CAGTACC
195 CAGTACC
* * ***** * * * *
30195 CTGAGTGGTGAAAGCGCGTTCCCGGGGGGCGCATTTGATTATTTTTTCAGAGAATATCTTATCAT
1 C---CT--T-----C-CATT---ATTTTG-TCA---GA-GA------------ATATGTTATCAC
* *
30260 TGCCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACCCAAAGTGGTAAAAG
35 TGCCCTATTATGTCACTCATGTCCCTCGGGAGCACTATTCATGTCAGTACCCAAAGTGGTGAAAG
* * * * *
30325 CGCGTTCCCGGGGGGCGCCTTCCATTATTTTTTCAGATAATATGTTATCATTGCCCTATTATGTC
100 CGCGTTCCAGGGGGACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATATC
30390 ACTCATGTCCCTCGGGTG-CACTATTCATGTCAGTACC
165 ACTCATGTCCCTCGGG-GACACTATTCATGTCAGTACC
30427 C
1 C
30428 AAAGTGGTGA
Statistics
Matches: 367, Mismatches: 31, Indels: 39
0.84 0.07 0.09
Matches are distributed among these distances:
200 167 0.46
201 20 0.05
203 1 0.00
205 1 0.00
210 1 0.00
211 3 0.01
216 2 0.01
219 2 0.01
220 1 0.00
231 6 0.02
232 162 0.44
233 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.34
Consensus pattern (201 bp):
CCTTCCATTATTTTGTCAGAGAATATGTTATCACTGCCCTATTATGTCACTCATGTCCCTCGGGA
GCACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCCAGGGGGACGCCTTCCATTATTTT
GTCAGAGAATATGTTATCATTGCCCTATTATATCACTCATGTCCCTCGGGGACACTATTCATGTC
AGTACC
Found at i:30842 original size:23 final size:23
Alignment explanation
Indices: 30816--30878 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
30806 ATGTGAAGTT
30816 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
*
30839 TGAATGAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
* *
30862 TGGATAAATTGAATAAA
1 TGAATAAATTGGATAAA
30879 TGTGAAGTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (23 bp):
TGAATAAATTGGATAAAATGTTA
Found at i:30935 original size:23 final size:23
Alignment explanation
Indices: 30819--30941 Score: 98
Period size: 23 Copynumber: 5.6 Consensus size: 23
30809 TGAAGTTTGA
*
30819 ATAAATTGGATAAAATGTTATGA
1 ATAAATTGGATAAAATGTTATGG
*
30842 ATGAATTGGATAAAATGTTATGG
1 ATAAATTGGATAAAATGTTATGG
* * *
30865 ATAAATTGAAT-AAATGTGAAGTG
1 ATAAATTGGATAAAATGTTATG-G
* * *
30888 ATCAGTTGG-T----TGTT-TGA
1 ATAAATTGGATAAAATGTTATGG
*
30905 ATATATTGGATAAAATGTTATGG
1 ATAAATTGGATAAAATGTTATGG
*
30928 ATAAATTGAATAAA
1 ATAAATTGGATAAA
30942 TGTGAAGTGA
Statistics
Matches: 75, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
17 6 0.08
18 2 0.03
19 3 0.04
22 13 0.17
23 51 0.68
ACGTcount: A:0.42, C:0.01, G:0.21, T:0.36
Consensus pattern (23 bp):
ATAAATTGGATAAAATGTTATGG
Found at i:30938 original size:63 final size:63
Alignment explanation
Indices: 30846--31026 Score: 326
Period size: 63 Copynumber: 2.9 Consensus size: 63
30836 TTATGAATGA
30846 ATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTTGTTTGAATAT
1 ATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTTGTTTGAATAT
* *
30909 ATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGTTTTTTTGAATAT
1 ATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTTGTTTGAATAT
* *
30972 ATTAGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGT
1 ATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTTGT
31027 GAGCATGAGA
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 112 1.00
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.39
Consensus pattern (63 bp):
ATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTTGTTTGAATAT
Found at i:31111 original size:14 final size:14
Alignment explanation
Indices: 31092--31136 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
31082 TGATAAGTTG
31092 GTTTTAATGTATAT
1 GTTTTAATGTATAT
31106 GTTTTAATGTATAT
1 GTTTTAATGTATAT
*
31120 GTTTCAATGTATAT
1 GTTTTAATGTATAT
31134 GTT
1 GTT
31137 ATCAATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.56
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:31816 original size:21 final size:21
Alignment explanation
Indices: 31792--31858 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
31782 GGTGTCATAA
* *
31792 AACCTTACGGGCTAGGCATGT
1 AACCTGACGGGCTAGGAATGT
* * *
31813 AACCTGGCAGGCTAGGAATAT
1 AACCTGACGGGCTAGGAATGT
31834 AACCCTGA-GGGCTAGGAATGT
1 AA-CCTGACGGGCTAGGAATGT
31855 AACC
1 AACC
31859 CTGCGGAGAT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
20 2 0.05
21 31 0.84
22 4 0.11
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.19
Consensus pattern (21 bp):
AACCTGACGGGCTAGGAATGT
Found at i:33664 original size:21 final size:19
Alignment explanation
Indices: 33638--33725 Score: 64
Period size: 18 Copynumber: 4.9 Consensus size: 19
33628 TTAGTACAAA
*
33638 AAATAATTAATTAACTAATTT
1 AAATAAATAA-TAA-TAATTT
33659 AAATAAATAATAATAA-TT
1 AAATAAATAATAATAATTT
*
33677 ATATAAAT-AT--T-ATTT
1 AAATAAATAATAATAATTT
* *
33692 TAATAAAAAATAAT-ATTT
1 AAATAAATAATAATAATTT
*
33710 ATATAAAT-ATAATAAT
1 AAATAAATAATAATAAT
33726 AAAAAATATA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
14 1 0.02
15 8 0.15
16 2 0.04
17 7 0.13
18 21 0.39
19 3 0.06
20 3 0.06
21 9 0.17
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATAAATAATAATAATTT
Found at i:33684 original size:18 final size:17
Alignment explanation
Indices: 33661--33725 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
33651 ACTAATTTAA
33661 ATAAATAATAATAATTAT
1 ATAAAT-ATAATAATTAT
* *
33679 ATAAATATTAT-TTTA-
1 ATAAATATAATAATTAT
* *
33694 ATAAAAAATAATATTTAT
1 AT-AAATATAATAATTAT
33712 ATAAATATAATAAT
1 ATAAATATAATAAT
33726 AAAAAATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
15 2 0.05
16 10 0.26
17 18 0.47
18 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATATAATAATTAT
Found at i:33704 original size:33 final size:33
Alignment explanation
Indices: 33655--33719 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
33645 TAATTAACTA
*
33655 ATTTAAATAAATAATAATAATTATATAAATATT
1 ATTTAAATAAAAAATAATAATTATATAAATATT
* *
33688 ATTTTAATAAAAAATAATATTTATATAAATAT
1 ATTTAAATAAAAAATAATAATTATATAAATAT
33720 AATAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
ATTTAAATAAAAAATAATAATTATATAAATATT
Found at i:33717 original size:15 final size:15
Alignment explanation
Indices: 33667--33718 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
33657 TTAAATAAAT
*
33667 AATAATAATTATATA
1 AATAATATTTATATA
* *
33682 AATATTATTTTAATAAAA
1 AATAATA-TTT-AT-ATA
33700 AATAATATTTATATA
1 AATAATATTTATATA
33715 AATA
1 AATA
33719 TAATAATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 12 0.41
16 4 0.14
17 5 0.17
18 8 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAATATTTATATA
Found at i:33726 original size:30 final size:32
Alignment explanation
Indices: 33660--33733 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 32
33650 AACTAATTTA
* *
33660 AATAAATAATAATAATTATATAAATATTATTTT
1 AATAAAAAATAATAATTATATAAATATTA-TAT
*
33693 AATAAAAAATAATATTTATATAAATA-TA-AT
1 AATAAAAAATAATAATTATATAAATATTATAT
33723 AATAAAAAATA
1 AATAAAAAATA
33734 TAACAACTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 12 0.32
32 2 0.05
33 24 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (32 bp):
AATAAAAAATAATAATTATATAAATATTATAT
Found at i:45694 original size:21 final size:19
Alignment explanation
Indices: 45670--45729 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 19
45660 ATTAATATTA
45670 AAAATATTTATTTTAGGTAG
1 AAAA-ATTTATTTTAGGTAG
* * *
45690 TAAAATTAATATTTCGGTAG
1 AAAAATTTAT-TTTAGGTAG
45710 AAAAAATTATATTTTAGGTA
1 -AAAAATT-TATTTTAGGTA
45730 ACGTTCTACC
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 5 0.16
20 11 0.35
21 13 0.42
22 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.42
Consensus pattern (19 bp):
AAAAATTTATTTTAGGTAG
Found at i:50401 original size:16 final size:16
Alignment explanation
Indices: 50380--50413 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
50370 TTATGTAAGT
*
50380 ACATAATCCTTTTATC
1 ACATAATCCTTATATC
50396 ACATAATCCTTATATC
1 ACATAATCCTTATATC
50412 AC
1 AC
50414 TTGGCTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (16 bp):
ACATAATCCTTATATC
Found at i:56200 original size:174 final size:177
Alignment explanation
Indices: 56000--57618 Score: 1207
Period size: 176 Copynumber: 9.6 Consensus size: 177
55990 ATACAAATGA
* *
56000 AAAATGTATCGATCTATAACAATAT-A-AG-TAAATATATGACAAAA-CGGTCTCAAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAGCTAAA-ATATGACAAAACCGGTCTCAAAATGAAAA
* * * * *
56061 ACCGGTAAAACGCTACCGGATAAGTTGAAAGTGTCAATAGTTTAATATAAGTATCGACACTTTCT
65 ACAGGTAAAA--CTACCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTTCT
56126 GAATTTAAA-AG-AGAAGTTATAGCGCCTAAAAAGTGTCGAAATTTTATG
128 GAATTTAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGAAATTTTATG
*
56174 AAAATGTATCGATCCATAATAATATAACAGCTAAAATATGACAAAACCGGTCTC-AAATGAAAAA
1 AAAATGTATCGATCCATAACAATATAACAGCTAAAATATGACAAAACCGGTCTCAAAATGAAAAA
*
56238 CAGGTAAAACTATCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTTCTGAA
66 CAGGTAAAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTTCTGAA
*
56303 TTTAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGAAACTTTATG
131 TTTAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGAAATTTTATG
*
56350 AAAATGTATCGATCTATAACAATATAACAGCTAAAAATATGACAAAACCGGTCTCAAAATGATAA
1 AAAATGTATCGATCCATAACAATATAACAGCT-AAAATATGACAAAACCGGTCTCAAAATGA-AA
*
56415 AACATGTAAATAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTTC
64 AACAGGT-AA-AACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTTC
* **
56480 TGAATTTAAAAGAGAAGAAGTTATAGCGCCT--AAAG-GTCGATATTTTAAA
127 TGAATTT-AAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGAAATTTTATG
* * * * *
56529 AAAATGTATTGATTCATAACTA-ATAACAG-TAAAA-AT-----------TCTAAAAATGACAAA
1 AAAATGTATCGATCCATAACAATATAACAGCTAAAATATGACAAAACCGGTCTCAAAATGAAAAA
* * * * * *
56580 CCGGTAAAACGA-TATCGAATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCT
66 CAGG-TAAA--ACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTTCT
* * * *
56644 GAATTTAAAAGAGAAGAAGTTATAGCGCCTAGAACGTGTCGACACTTTATG
128 GAATTT-AAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGAAATTTTATG
* * * *
56695 CAAATGTATCGATCCATAACAATAT-ACAACCTAAAATATGACAAAATCAGTCTC-AAATGACAA
1 AAAATGTATCGATCCATAACAATATAAC-AGCTAAAATATGACAAAACCGGTCTCAAAATGA-AA
**
56758 AACAGGTAAAAACTACCATATATGTTGAAAGTGTCGATACTTTAATATAA-TATCGACACTTT-T
64 AACAGGT-AAAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTTCT
* *
56821 GGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTATCG--A---TACT-
128 -GAATTT-AAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGAAATTTTA-TG
* * ** *
56868 ----T-TATCGATCCATAACAATATAACAGGTAAAAATAGGACAAAACATGTCTAAAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAGCT-AAAATATGACAAAACCGGTCTCAAAATGA-AA
* * * *
56928 AACCGGTAAAACGATACC-GATATGTAGAAAGTGTCGATAATTT-ATATAAGTATCGACACTTT-
64 AACAGGTAAAAC--TACCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTTC
* * *
56990 TGGAATTTAAA-AG-AGAAGTTAT--CGCCTATAAAGTGTCGATACTTTA--
127 T-GAATTTAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGAAATTTTATG
* * *
57036 AAAAAGTATCGATCCGTAAC-ATATAACAGGTAAAAATATGAC-AAACCGG--T-AAAA-G----
1 AAAATGTATCGATCCATAACAATATAACAGCT-AAAATATGACAAAACCGGTCTCAAAATGAAAA
* * *
57091 --A--T---A--A-CGGATATGTTGAAAGTGTCGATAATTAAATATAAATATCGACACTTT-TGG
65 ACAGGTAAAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTTCT-G
* * * *
57145 AATTTAAA-AGAAGAAGTTATAACACCTACAAAGTGTCG--A-TCTAT-
129 AATTTAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGAAATTTTATG
** * **
57189 AACAA--TAAAGGT--AGGAC-A-A-AACATGTCTAAAA-ATGACAAAACCGG--------T--A
1 AA-AATGTATCGATCCATAACAATATAACA-G-CTAAAATATGACAAAACCGGTCTCAAAATGAA
* * * *
57236 AAAC--G----A-TACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATAGACACTTT-T
63 AAACAGGTAAAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTTCT
* * * **
57293 GGAATTTAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAA
128 -GAATTTAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGAAATTTTATG
* * * *
57344 AAAATGTATCGATCCGTAACAATATAGCAGGTAAAAATATGAC-AAATCGG--------T--AAA
1 AAAATGTATCGATCCATAACAATATAACAGCT-AAAATATGACAAAACCGGTCTCAAAATGAAAA
* *
57398 A-A-G----A-TACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT-TGG
65 ACAGGTAAAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTTCT-G
* * *
57455 AATTTAAAAGAGAAGAAGTTATAGCACCTAAAAA-TGTCGATACTTTT-TAA
129 AATTT-AAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGA-AATTTTAT-G
** * *
57505 AAAATGTATCGATCCATAGTAATATAACAGGTAAAATATATGACAAAACCGGTCTAAAAATGATA
1 AAAATGTATCGATCCATAACAATATAACAGCT-AAA-ATATGACAAAACCGGTCTCAAAATGA-A
* * *
57570 AATC-GGTAAAGCGCATACCAGATATGTTGAAAGTGTCGATACTTTAATA
63 AAACAGGTAAA--AC-TACCGGATATGTTGAAAGTGTCGATACTTTAATA
57619 AGTACGCGTA
Statistics
Matches: 1213, Mismatches: 118, Indels: 219
0.78 0.08 0.14
Matches are distributed among these distances:
148 10 0.01
149 14 0.01
150 59 0.05
151 51 0.04
152 38 0.03
153 13 0.01
154 7 0.01
155 17 0.01
156 4 0.00
158 3 0.00
159 2 0.00
160 81 0.07
161 70 0.06
162 8 0.01
163 91 0.08
164 11 0.01
165 18 0.01
166 30 0.02
167 14 0.01
168 32 0.03
169 37 0.03
170 59 0.05
171 10 0.01
172 21 0.02
173 15 0.01
174 84 0.07
175 6 0.00
176 101 0.08
177 35 0.03
178 64 0.05
179 75 0.06
180 18 0.01
181 60 0.05
182 23 0.02
183 32 0.03
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (177 bp):
AAAATGTATCGATCCATAACAATATAACAGCTAAAATATGACAAAACCGGTCTCAAAATGAAAAA
CAGGTAAAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTTCTGAA
TTTAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGAAATTTTATG
Found at i:56871 original size:178 final size:178
Alignment explanation
Indices: 56565--57618 Score: 605
Period size: 160 Copynumber: 6.3 Consensus size: 178
56555 CAGTAAAAAT
* *
56565 TCTAAAAATGAC-AAACCGGTAAAACGATATCGAATATGTTGAAAGTGTCGATAATTTAATATAA
1 TCTAAAAATGACAAAACAGGTAAAAC-ATACCG-ATATGTTGAAAGTGTCGATAATTTAATATAA
* * *
56629 GTATCGACACTTTCT-GAATTTAAAAGAGAAGAAGTTATAGCGCCTAGAACGTGTCGACACTTTA
64 GTATCGACACTTT-TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTA
*
56693 TGCAAATGTATCGATCCATAACAATAT-ACAACCT-AAAATATGACAAAATCA-G
128 T--AAATGTATCGATCCATAACAATATAAC-ACCTAAAAATAGGACAAAA-CATG
* * *
56745 TCT-CAAATGACAAAACAGGTAAAA-ACTACCATATATGTTGAAAGTGTCGATACTTTAATATAA
1 TCTAAAAATGACAAAACAGGTAAAACA-TACC-GATATGTTGAAAGTGTCGATAATTTAATATAA
*
56808 -TATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTATCGATAC----T
64 GTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
**
56868 ---T-TATCGATCCATAACAATATAACAGGTAAAAATAGGACAAAACATG
129 AAATGTATCGATCCATAACAATATAACACCTAAAAATAGGACAAAACATG
* *
56914 TCTAAAAATGACAAAACCGGTAAAACGATACCGATATGTAGAAAGTGTCGATAATTT-ATATAAG
1 TCTAAAAATGACAAAACAGGTAAAAC-ATACCGATATGTTGAAAGTGTCGATAATTTAATATAAG
*
56978 TATCGACACTTTTGGAATTT-AAA-AG-AGAAGTTAT--CGCCTATAAAGTGTCGATACTTTAAA
65 TATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTATA
* * ** * *
57038 AAAGTATCGATCCGTAAC-ATATAACAGGTAAAAATATGAC-AAAC-CG
130 AATGTATCGATCCATAACAATATAACACCTAAAAATAGGACAAAACATG
* * * *** * *
57084 -GT-AAAA-G--ATAAC-GG----ATATGTTGAAAGTGTCGATAA-T-T--A-AA--T-ATA-AA
1 TCTAAAAATGACAAAACAGGTAAAACATACCGATA-TGTTGA-AAGTGTCGATAATTTAATATAA
* * *
57130 -TATCGACACTTTTGGAATTT-AAA-AGAAGAAGTTATAACACCTACAAAGTGTCGAT-CTATAA
64 GTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACT-T--
* * * * *
57191 CAATAAAGGTA-GGA--CAAAAC-ATGT-----CTAAAAAT--GACAAAAC---
126 -TATAAATGTATCGATCCATAACAATATAACACCTAAAAATAGGACAAAACATG
** * *
57231 -C-------GGTAAAAC--G--ATAC---CAGATATGTTGAAAGTGTCGATAATTTAATATAAGT
1 TCTAAAAATGACAAAACAGGTAAAACATACCGATATGTTGAAAGTGTCGATAATTTAATATAAGT
* *
57281 ATAGACACTTTTGGAATTT-AAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAA
66 ATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTT--AT
* * ** * *
57345 AAATGTATCGATCCGTAACAATATAGCAGGTAAAAATATGACAAATC--G
129 AAATGTATCGATCCATAACAATATAACACCTAAAAATAGGACAAAACATG
* *
57393 -GTAAAAA-G-------A--T---AC---CGGATATGTTGAAAGTGTCGATAATTTAATATAAGT
1 TCTAAAAATGACAAAACAGGTAAAACATACCGATATGTTGAAAGTGTCGATAATTTAATATAAGT
* *
57441 ATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCACCTA-AAAATGTCGATACTTTTTAA
66 ATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATAC--TTT-A
* ** ** * **
57505 AAAATGTATCGATCCATAGTAATATAACAGGTAAAATATATGACAAAACCGG
128 TAAATGTATCGATCCATAACAATATAACACCTAAAA-ATAGGACAAAACATG
* * * *
57557 TCTAAAAATGATAAATC-GGTAAAGCGCATACCAGATATGTTGAAAGTGTCGATACTTTAATA
1 TCTAAAAATGACAAAACAGGTAAA--ACATACC-GATATGTTGAAAGTGTCGATAATTTAATA
57619 AGTACGCGTA
Statistics
Matches: 706, Mismatches: 75, Indels: 183
0.73 0.08 0.19
Matches are distributed among these distances:
140 2 0.00
141 6 0.01
142 5 0.01
143 1 0.00
144 5 0.01
145 3 0.00
147 1 0.00
148 6 0.01
149 6 0.01
150 36 0.05
151 32 0.05
152 27 0.04
153 15 0.02
154 9 0.01
155 24 0.03
156 2 0.00
157 3 0.00
158 7 0.01
159 13 0.02
160 74 0.10
161 66 0.09
162 14 0.02
164 3 0.00
165 29 0.04
166 1 0.00
167 10 0.01
168 30 0.04
169 30 0.04
170 62 0.09
171 8 0.01
172 22 0.03
173 13 0.02
174 2 0.00
177 1 0.00
178 54 0.08
179 41 0.06
180 14 0.02
182 1 0.00
183 28 0.04
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (178 bp):
TCTAAAAATGACAAAACAGGTAAAACATACCGATATGTTGAAAGTGTCGATAATTTAATATAAGT
ATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTATAA
ATGTATCGATCCATAACAATATAACACCTAAAAATAGGACAAAACATG
Found at i:56995 original size:170 final size:163
Alignment explanation
Indices: 56701--57035 Score: 446
Period size: 170 Copynumber: 2.0 Consensus size: 163
56691 TATGCAAATG
* *
56701 TATCGATCCATAACAATATACAACCTAAAATATGACAAAATCAGTCTCAAATGACAAAACAGGTA
1 TATCGATCCATAACAATATACAACCTAAAATAGGACAAAATCAGTCTAAAATGACAAAACAGGTA
* * *
56766 AAAACTACCATATATGTTGAAAGTGTCGATACTTTAATATAATATCGACACTTTTGGAATTTAAA
66 AAAACTACCAGATATGTAGAAAGTGTCGATAATTTAATATAATATCGACACTTTTGGAATTT-AA
56831 AGAGAAGAAGTTATAGCGCCTATAAAGTATCGATACTT
130 A-AG-AGAAGTTAT--CGCCTATAAAGTATCGATACTT
** *
56869 TATCGATCCATAACAATATA-ACAGGTAAAAATAGGACAAAA-CATGTCTAAAAATGACAAAACC
1 TATCGATCCATAACAATATACA-ACCT-AAAATAGGACAAAATCA-GTCT-AAAATGACAAAACA
56932 GGT-AAAACGATACC-GATATGTAGAAAGTGTCGATAATTT-ATATAAGTATCGACACTTTTGGA
62 GGTAAAAAC--TACCAGATATGTAGAAAGTGTCGATAATTTAATATAA-TATCGACACTTTTGGA
*
56994 ATTTAAAAGAGAAGTTATCGCCTATAAAGTGTCGATACTT
124 ATTTAAAAGAGAAGTTATCGCCTATAAAGTATCGATACTT
57034 TA
1 TA
57036 AAAAAGTATC
Statistics
Matches: 151, Mismatches: 9, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
165 23 0.15
167 10 0.07
168 26 0.17
169 31 0.21
170 57 0.38
171 4 0.03
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (163 bp):
TATCGATCCATAACAATATACAACCTAAAATAGGACAAAATCAGTCTAAAATGACAAAACAGGTA
AAAACTACCAGATATGTAGAAAGTGTCGATAATTTAATATAATATCGACACTTTTGGAATTTAAA
AGAGAAGTTATCGCCTATAAAGTATCGATACTT
Found at i:57266 original size:150 final size:152
Alignment explanation
Indices: 56917--57500 Score: 691
Period size: 160 Copynumber: 3.8 Consensus size: 152
56907 AAACATGTCT
*
56917 AAAA-ATGACAAAACCGGTAAAACGATACC-GATATGTAGAAAGTGTCGATAATTT-ATATAAGT
1 AAAATATGAC-AAACCGGTAAAACGATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGT
*
56979 ATCGACACTTTTGGAATTTAAA-AG-AGAAGTTAT--CGCCTATAAAGTGTCGATACTTT-AAA-
65 ATCGACACTTTTGGAATTTAAAGAGAAGAAGTTATAGCACCTATAAAGTGTCGATACTTTAAAAT
57038 AAA-GTATCGATCCGTAACATATAACAGGTA
130 AAAGGTA--G---CG--ACA-ATAACAGGTA
* * *
57068 AAAATATGACAAACCGGTAAAA-GATAACGGATATGTTGAAAGTGTCGATAATTAAATATAAATA
1 AAAATATGACAAACCGGTAAAACGATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTA
* * *
57132 TCGACACTTTTGGAATTTAAA-AGAAGAAGTTATAACACCTACAAAGTGTCGAT-CTATAACAAT
66 TCGACACTTTTGGAATTTAAAGAGAAGAAGTTATAGCACCTATAAAGTGTCGATACTTTAA-AAT
* *
57195 AAAGGTAG-GACAA-AACATGTCT
130 AAAGGTAGCGACAATAACAGGT-A
*
57217 AAAA-ATGACAAAACCGGTAAAACGATACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGT
1 AAAATATGAC-AAACCGGTAAAACGATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGT
* *
57281 ATAGACACTTTTGGAATTTAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAA-
65 ATCGACACTTTTGGAATTTAAAGAGAAGAAGTTATAGCACCTATAAAGTGTCGATACTTTAAAAT
*
57345 AAATGTATCGATCCGTAACAATATAGCAGGTA
130 AAAGGTA--G---CG--ACAATA-A-CAGGTA
* *
57377 AAAATATGACAAATCGGTAAAAAGATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTA
1 AAAATATGACAAACCGGTAAAACGATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTA
*
57442 TCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCACCTA-AAAATGTCGATACTTT
66 TCGACACTTTTGGAATTT-AAAGAGAAGAAGTTATAGCACCTATAAAGTGTCGATACTTT
57501 TTAAAAAATG
Statistics
Matches: 378, Mismatches: 27, Indels: 47
0.84 0.06 0.10
Matches are distributed among these distances:
148 11 0.03
149 17 0.04
150 72 0.19
151 70 0.19
152 43 0.11
153 9 0.02
154 3 0.01
155 17 0.04
156 4 0.01
157 3 0.01
158 7 0.02
159 1 0.00
160 89 0.24
161 32 0.08
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.27
Consensus pattern (152 bp):
AAAATATGACAAACCGGTAAAACGATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTA
TCGACACTTTTGGAATTTAAAGAGAAGAAGTTATAGCACCTATAAAGTGTCGATACTTTAAAATA
AAGGTAGCGACAATAACAGGTA
Found at i:57455 original size:310 final size:301
Alignment explanation
Indices: 56777--57495 Score: 1003
Period size: 310 Copynumber: 2.3 Consensus size: 301
56767 AAACTACCAT
* *
56777 ATATGTTGAAAGTGTCGATACTTTAATAT-AATATCGACACTTTTGGAATTTAAAAGAGAAGAAG
1 ATATGTTGAAAGTGTCGATAATTAAATATAAATATCGACACTTTTGGAATTTAAAAGAGAAGAAG
* * *
56841 TTATAGCGCCTATAAAGTATCGATACTTTATCGATCCATAACAATATAACAGGTAAAAATAGGAC
66 TTATAACACCTA-AAA--AT-G--------TCGATCTATAAC-A-ATAA-AGG------TAGGAC
56906 AAAACATGTCTAAAAATGACAAAACCGGTAAAACGATACCGATATGTAGAAAGTGTCGATAATTT
110 AAAACATGTCTAAAAATGACAAAACCGGTAAAACGATACCGATATGTAGAAAGTGTCGATAATTT
*
56971 ATATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGTTATCGCCTATAAAGTGTCGATACTTTA
175 ATATAAGTATAGACACTTTTGGAATTTAAAAGAGAAGTTATCGCCTATAAAGTGTCGATACTTTA
57036 AAAAAGTATCGATCCGTAACATATAACAGGTAAAAATATGACAAACCGGTAAAAGATAACGG
240 AAAAAGTATCGATCCGTAACATATAACAGGTAAAAATATGACAAACCGGTAAAAGATAACGG
57098 ATATGTTGAAAGTGTCGATAATTAAATATAAATATCGACACTTTTGGAATTT-AAA-AGAAGAAG
1 ATATGTTGAAAGTGTCGATAATTAAATATAAATATCGACACTTTTGGAATTTAAAAGAGAAGAAG
*
57161 TTATAACACCTACAAAGTGTCGATCTATAACAATAAAGGTAGGACAAAACATGTCTAAAAATGAC
66 TTATAACACCTA-AAAATGTCGATCTATAACAATAAAGGTAGGACAAAACATGTCTAAAAATGAC
*
57226 AAAACCGGTAAAACGATACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATAGACACTT
130 AAAACCGGTAAAACGATACC-GATATGTAGAAAGTGTCGATAATTT-ATATAAGTATAGACACTT
57291 TTGGAATTTAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATGTATCGA
193 TTGGAATTTAAA-AG-AGAAGTTAT--CGCCTATAAAGTGTCGATACTTT-AAAAAA-GTATCGA
* * *
57356 TCCGTAACAATATAGCAGGTAAAAATATGACAAATCGGTAAAAAGATACCGG
252 TCCGTAAC-ATATAACAGGTAAAAATATGACAAACCGGT-AAAAGATAACGG
* *
57408 ATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAG
1 ATATGTTGAAAGTGTCGATAATTAAATATAAATATCGACACTTTTGGAATTTAAAAGAGAAGAAG
*
57473 TTATAGCACCTAAAAATGTCGAT
66 TTATAACACCTAAAAATGTCGAT
57496 ACTTTTTAAA
Statistics
Matches: 369, Mismatches: 16, Indels: 36
0.88 0.04 0.09
Matches are distributed among these distances:
300 46 0.12
301 24 0.07
302 29 0.08
303 2 0.01
304 9 0.02
306 26 0.07
307 10 0.03
308 16 0.04
309 39 0.11
310 61 0.17
311 13 0.04
312 19 0.05
317 1 0.00
318 1 0.00
320 21 0.06
321 30 0.08
322 22 0.06
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.27
Consensus pattern (301 bp):
ATATGTTGAAAGTGTCGATAATTAAATATAAATATCGACACTTTTGGAATTTAAAAGAGAAGAAG
TTATAACACCTAAAAATGTCGATCTATAACAATAAAGGTAGGACAAAACATGTCTAAAAATGACA
AAACCGGTAAAACGATACCGATATGTAGAAAGTGTCGATAATTTATATAAGTATAGACACTTTTG
GAATTTAAAAGAGAAGTTATCGCCTATAAAGTGTCGATACTTTAAAAAAGTATCGATCCGTAACA
TATAACAGGTAAAAATATGACAAACCGGTAAAAGATAACGG
Done.