Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 181 of 259
Found at i:58654237 original size:25 final size:25
Alignment explanation
Indices: 58654209--58654256 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
58654199 ATTTAGTTAA
58654209 ATATTACATAA-TAATATAATATAAT
1 ATATTACATAATTAA-ATAATATAAT
**
58654234 ATATTTTATAATTAAATAATATA
1 ATATTACATAATTAAATAATATA
58654257 TTTAAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATTACATAATTAAATAATATAAT
Found at i:58654254 original size:20 final size:22
Alignment explanation
Indices: 58654219--58654259 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
58654209 ATATTACATA
58654219 ATAATATAATATAATATATTTT
1 ATAATATAATATAATATATTTT
58654241 ATAAT-TAA-ATAATATATTT
1 ATAATATAATATAATATATTT
58654260 AAAACATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 3 0.16
22 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATATAATATAATATATTTT
Found at i:58654446 original size:20 final size:21
Alignment explanation
Indices: 58654398--58654450 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
58654388 TAATCCTTAT
*
58654398 ACCTAATTAACCTTAATTTAA
1 ACCTAATTAACCTTAATTAAA
*
58654419 A-CTAAATTCA-CTTAATTAAA
1 ACCT-AATTAACCTTAATTAAA
58654439 ACCTAATTAACC
1 ACCTAATTAACC
58654451 ACTCGATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (21 bp):
ACCTAATTAACCTTAATTAAA
Found at i:58654790 original size:16 final size:16
Alignment explanation
Indices: 58654769--58654800 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
58654759 AAAATAAACT
58654769 CAATTAAACAATGAAA
1 CAATTAAACAATGAAA
58654785 CAATTAAACAATGAAA
1 CAATTAAACAATGAAA
58654801 ATATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (16 bp):
CAATTAAACAATGAAA
Found at i:58656350 original size:14 final size:14
Alignment explanation
Indices: 58656331--58656359 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
58656321 AACTCGAAAG
58656331 ATTGAACATTGGAT
1 ATTGAACATTGGAT
58656345 ATTGAACATTGGAT
1 ATTGAACATTGGAT
58656359 A
1 A
58656360 ATCTTTTTAT
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:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (14 bp):
ATTGAACATTGGAT
Found at i:58657894 original size:22 final size:22
Alignment explanation
Indices: 58657869--58657911 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
58657859 TTCATAATTT
58657869 AGTTCATATATTCTTTCTCATG
1 AGTTCATATATTCTTTCTCATG
58657891 AGTTCATATATTCTTTCTCAT
1 AGTTCATATATTCTTTCTCAT
58657912 ACTTTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.51
Consensus pattern (22 bp):
AGTTCATATATTCTTTCTCATG
Found at i:58659425 original size:15 final size:14
Alignment explanation
Indices: 58659407--58659437 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
58659397 TTAATTTATT
58659407 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
58659422 TAATAATAATCTAA
1 TAATAATAATCTAA
58659436 TA
1 TA
58659438 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:58659448 original size:21 final size:20
Alignment explanation
Indices: 58659424--58659492 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
58659414 AATGCTAATA
58659424 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
58659445 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
58659464 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
58659485 ATAATAAT
1 ATAATAAT
58659493 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:58664551 original size:18 final size:18
Alignment explanation
Indices: 58664517--58664576 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
58664507 ATTGCAATAT
*
58664517 ATATAAAAA-TAATTTAAA
1 ATATAAAAATTTA-TTAAA
58664535 ATATAAAAATTTATTAATA
1 ATATAAAAATTTATTAA-A
* * *
58664554 TGTATATAAATTTATTAAT
1 -ATATAAAAATTTATTAAA
58664573 ATAT
1 ATAT
58664577 GTAAAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 16 0.47
19 3 0.09
20 15 0.44
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
ATATAAAAATTTATTAAA
Found at i:58664576 original size:22 final size:20
Alignment explanation
Indices: 58664536--58664584 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
58664526 TAATTTAAAA
58664536 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
58664556 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
58664576 TGTAAAAAT
1 TATAAAAAT
58664585 AACTTTTACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:58666462 original size:17 final size:17
Alignment explanation
Indices: 58666437--58666479 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
58666427 GGACCCTAAA
*
58666437 AATACTTTTACACGAGT
1 AATAATTTTACACGAGT
* *
58666454 AATAATTTTTACATGGGT
1 AATAA-TTTTACACGAGT
58666472 AATAATTT
1 AATAATTT
58666480 ATCTCCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (17 bp):
AATAATTTTACACGAGT
Found at i:58666465 original size:18 final size:18
Alignment explanation
Indices: 58666442--58666479 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
58666432 CTAAAAATAC
58666442 TTTTACACGAGTAATAAT
1 TTTTACACGAGTAATAAT
* *
58666460 TTTTACATGGGTAATAAT
1 TTTTACACGAGTAATAAT
58666478 TT
1 TT
58666480 ATCTCCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (18 bp):
TTTTACACGAGTAATAAT
Found at i:58688206 original size:14 final size:14
Alignment explanation
Indices: 58688189--58688228 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
58688179 TAGTTCTCTT
58688189 TTTGCTTCATTTGG
1 TTTGCTTCATTTGG
58688203 TTTGCTTCATTTGG
1 TTTGCTTCATTTGG
58688217 TTTGCTTC-TTTG
1 TTTGCTTCATTTG
58688229 TACTGCCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.15
14 22 0.85
ACGTcount: A:0.05, C:0.15, G:0.20, T:0.60
Consensus pattern (14 bp):
TTTGCTTCATTTGG
Found at i:58709335 original size:26 final size:26
Alignment explanation
Indices: 58709298--58709355 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
58709288 TGATACAAAT
*
58709298 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAAGTAAATGTTCCA
* *
58709324 TGATAATGGGTTAAGTAAATGTTTCA
1 TGATAATAGGTTAAGTAAATGTTCCA
58709350 TGATAA
1 TGATAA
58709356 GAATTTCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAAGTAAATGTTCCA
Found at i:58731819 original size:28 final size:28
Alignment explanation
Indices: 58731783--58731839 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
58731773 CTGAAATCAG
*
58731783 AGTAAGCATCAGAAAGTCTAGACACAGA
1 AGTAAGCATCAGAAAGTCTAAACACAGA
58731811 AGTAAGCATCAGAAAGTCTAAACACAGA
1 AGTAAGCATCAGAAAGTCTAAACACAGA
58731839 A
1 A
58731840 CTCCATACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.49, C:0.18, G:0.19, T:0.14
Consensus pattern (28 bp):
AGTAAGCATCAGAAAGTCTAAACACAGA
Found at i:58737271 original size:20 final size:20
Alignment explanation
Indices: 58737233--58737271 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
58737223 AAAAAGCAAG
* *
58737233 AAAAAAACAATGAGAAAATC
1 AAAAAAAAAAGGAGAAAATC
*
58737253 AAAAAAAAAAGGAGTAAAT
1 AAAAAAAAAAGGAGAAAAT
58737272 TACAAAGGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.72, C:0.05, G:0.13, T:0.10
Consensus pattern (20 bp):
AAAAAAAAAAGGAGAAAATC
Found at i:58754268 original size:21 final size:21
Alignment explanation
Indices: 58754242--58754282 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
58754232 ACAAGTACGA
58754242 ATACTTACCGTAAGCAAAATT
1 ATACTTACCGTAAGCAAAATT
*
58754263 ATACTTACCTTAAGCAAAAT
1 ATACTTACCGTAAGCAAAAT
58754283 ATAAACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (21 bp):
ATACTTACCGTAAGCAAAATT
Found at i:58755686 original size:18 final size:18
Alignment explanation
Indices: 58755668--58755861 Score: 217
Period size: 18 Copynumber: 10.8 Consensus size: 18
58755658 TTAGTATTAA
* *
58755668 TCAGTTATTCAGTAATAA
1 TCAGTTATTCAGTAACAG
*
58755686 TCATTTATTCAGTAACAG
1 TCAGTTATTCAGTAACAG
* *
58755704 TCATTTATTCAGTCACAG
1 TCAGTTATTCAGTAACAG
* * * *
58755722 TCAATTATCCAGTAATAA
1 TCAGTTATTCAGTAACAG
*
58755740 TCAGTTATTCAGTAATAG
1 TCAGTTATTCAGTAACAG
* *
58755758 TCATTTATTCAGTCACAG
1 TCAGTTATTCAGTAACAG
* * *
58755776 TCATTTATTCAGTAATAA
1 TCAGTTATTCAGTAACAG
58755794 TCAGTTATTCAGTAACAG
1 TCAGTTATTCAGTAACAG
*
58755812 TCATTTATTCAGTAACAG
1 TCAGTTATTCAGTAACAG
* * *
58755830 TTAATTATTCAGTAGCAG
1 TCAGTTATTCAGTAACAG
58755848 TCAGTTATTCAGTA
1 TCAGTTATTCAGTA
58755862 CCTTTATTTT
Statistics
Matches: 149, Mismatches: 27, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 149 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (18 bp):
TCAGTTATTCAGTAACAG
Found at i:58755738 original size:54 final size:54
Alignment explanation
Indices: 58755672--58755861 Score: 299
Period size: 54 Copynumber: 3.5 Consensus size: 54
58755662 TATTAATCAG
*
58755672 TTATTCAGTAATAATCATTTATTCAGTAACAGTCATTTATTCAGTCACAGTCAA
1 TTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAGTCAA
* * *
58755726 TTATCCAGTAATAATCAGTTATTCAGTAATAGTCATTTATTCAGTCACAGTCAT
1 TTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAGTCAA
* *
58755780 TTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTAACAGTTAA
1 TTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAGTCAA
** *
58755834 TTATTCAGTAGCAGTCAGTTATTCAGTA
1 TTATTCAGTAATAATCAGTTATTCAGTA
58755862 CCTTTATTTT
Statistics
Matches: 124, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 124 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (54 bp):
TTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAGTCAA
Found at i:58756261 original size:20 final size:20
Alignment explanation
Indices: 58756236--58756275 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
58756226 TCAATACATA
58756236 TTTCAGCT-AATCATATATTT
1 TTTCAGCTCAAT-ATATATTT
*
58756256 TTTCAGTTCAATATATATTT
1 TTTCAGCTCAATATATATTT
58756276 CAATTCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTCAGCTCAATATATATTT
Found at i:58757121 original size:8 final size:8
Alignment explanation
Indices: 58757103--58757144 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
58757093 AATCCCAATT
58757103 TTTCCTT-
1 TTTCCTTC
58757110 TTTCCTTC
1 TTTCCTTC
58757118 TTTCCTTTC
1 TTTCC-TTC
58757127 TTTTTCCTTC
1 --TTTCCTTC
58757137 TTTCCTTC
1 TTTCCTTC
58757145 CCCTGTTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.23
8 13 0.42
9 3 0.10
10 3 0.10
11 5 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTCCTTC
Found at i:58757131 original size:19 final size:19
Alignment explanation
Indices: 58757107--58757143 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
58757097 CCAATTTTTC
58757107 CTTTTTCCTTCTTTCCTTT
1 CTTTTTCCTTCTTTCCTTT
58757126 CTTTTTCCTTCTTTCCTT
1 CTTTTTCCTTCTTTCCTT
58757144 CCCCTGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (19 bp):
CTTTTTCCTTCTTTCCTTT
Found at i:58759645 original size:13 final size:13
Alignment explanation
Indices: 58759627--58759651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58759617 CTTAATGGGT
58759627 AATTGAACTTGAA
1 AATTGAACTTGAA
58759640 AATTGAACTTGA
1 AATTGAACTTGA
58759652 TATCGAAATT
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
AATTGAACTTGAA
Found at i:58759861 original size:392 final size:391
Alignment explanation
Indices: 58759129--58759922 Score: 1378
Period size: 392 Copynumber: 2.0 Consensus size: 391
58759119 AAGTGATTTT
58759129 TGGAAAAA-T-TAATATTGATCAAGTAAAATAAAACCAATCAAATTAATTACAATTAATATGATA
1 TGGAAAAATTATAATATTGATCAAGTAAAATAAAACCAATCAAATTAATTACAATTAATATGATA
58759192 TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTCAATGGTAATTGAACTTGAAAATTGAACC
66 TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTCAATGGTAATTGAACTTGAAAATTGAACC
*
58759257 TGATATCAAAATTTGGGCCCAAGAACCCAAAACCGAGATCGATACCTAAAAACTAGTTGAATCAA
131 TGATATCAAAATTTGGGCCCAAGAACCCAAAACCGAGATCGATACCTAAAAACTAGTCGAATCAA
* * *
58759322 GTCTGGTACATGAAACTAGGCTTGGACTAGACCGATCGGACCTTCACTAGGCTTGGATCGAATCG
196 GTCTGGTACATGAAACTAGGCTTGGACCAGACCGATCGGACCGTCACTAGGCCTGGATCGAATCG
*
58759387 GCAACAGTCGACCCAGCTCGAGTTTTCGTGAGAGTGTCGTACCTGCGATGGCACCACCAGACACG
261 GCAACAGTCGACCCAGCTCGAGTTTTCGTGAGAGTGTCGCACCTGCGATGGCACCACCAGACACG
** *
58759452 ATGGTGACGGCGATGACGATGACAGCATTCTAGTGGCCAACGGGTGGTCTTTCGATGATTGAGCA
326 ACAGTGACGGCGATGACGATGACAGCATTCTAGTGGCCAACGGGTGGTCCTTCGATGATTGAGCA
58759517 G
391 G
* *
58759518 TGGAAAAATTATAATATTGATCAAGTAAAATTAAATCAATCAAATTAATTACAATTAATATGATA
1 TGGAAAAATTATAATATTGATCAAGTAAAATAAAACCAATCAAATTAATTACAATTAATATGATA
*
58759583 TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTTAATGGGTAATTGAACTTGAAAATTGAAC
66 TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTCAAT-GGTAATTGAACTTGAAAATTGAAC
* * *
58759648 TTGATATCGAAATTTGGGCCCAAGAACCCAAAATCGAGATCGATACCTAAAAACTAGTCGAATCA
130 CTGATATCAAAATTTGGGCCCAAGAACCCAAAACCGAGATCGATACCTAAAAACTAGTCGAATCA
*
58759713 AGTCTGGTACGTGAAACTAGGCTTGGACCAGACCGATCGGACCGTCACTAGGCCTGGATCGAATC
195 AGTCTGGTACATGAAACTAGGCTTGGACCAGACCGATCGGACCGTCACTAGGCCTGGATCGAATC
* * *
58759778 GGCAACAGTCGACCCAGTTCGAGTTTTCGTGAGGGTGTCGCACCTGCGATGGCACCACCGGACAC
260 GGCAACAGTCGACCCAGCTCGAGTTTTCGTGAGAGTGTCGCACCTGCGATGGCACCACCAGACAC
*
58759843 GACAGTG-CTGGCGATGACGATGACAGCATTCTAGTGGCCAGCGGGTGGTCCTTCGATGATTGAG
325 GACAGTGAC-GGCGATGACGATGACAGCATTCTAGTGGCCAACGGGTGGTCCTTCGATGATTGAG
58759907 CAG
389 CAG
58759910 TGGAAAAATTATA
1 TGGAAAAATTATA
58759923 CTCTTACCAG
Statistics
Matches: 382, Mismatches: 19, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
389 8 0.02
390 1 0.00
391 92 0.24
392 281 0.74
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (391 bp):
TGGAAAAATTATAATATTGATCAAGTAAAATAAAACCAATCAAATTAATTACAATTAATATGATA
TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTCAATGGTAATTGAACTTGAAAATTGAACC
TGATATCAAAATTTGGGCCCAAGAACCCAAAACCGAGATCGATACCTAAAAACTAGTCGAATCAA
GTCTGGTACATGAAACTAGGCTTGGACCAGACCGATCGGACCGTCACTAGGCCTGGATCGAATCG
GCAACAGTCGACCCAGCTCGAGTTTTCGTGAGAGTGTCGCACCTGCGATGGCACCACCAGACACG
ACAGTGACGGCGATGACGATGACAGCATTCTAGTGGCCAACGGGTGGTCCTTCGATGATTGAGCA
G
Found at i:58762180 original size:20 final size:21
Alignment explanation
Indices: 58762147--58762187 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
58762137 ATAAAAGTAC
58762147 AATAGGTATCGATACTTTTTG
1 AATAGGTATCGATACTTTTTG
*
58762168 AATA-GTATTGATACTTTTTG
1 AATAGGTATCGATACTTTTTG
58762188 CTTTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.46
Consensus pattern (21 bp):
AATAGGTATCGATACTTTTTG
Found at i:58782639 original size:18 final size:16
Alignment explanation
Indices: 58782607--58782645 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
58782597 TACATGATCA
*
58782607 AAACAAAAAGAATAAG
1 AAACAAAAAGAATAAC
58782623 AAACAAAGAATGAATAAC
1 AAACAAA-AA-GAATAAC
58782641 AAACA
1 AAACA
58782646 GTTACATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 2 0.10
18 11 0.55
ACGTcount: A:0.72, C:0.10, G:0.10, T:0.08
Consensus pattern (16 bp):
AAACAAAAAGAATAAC
Found at i:58782814 original size:15 final size:15
Alignment explanation
Indices: 58782779--58782830 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
58782769 TTAAGAATTT
*
58782779 TATTAAATTAT-ATA
1 TATTTAATTATAATA
58782793 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
58782807 TATTTAATAATAAT-
1 TATTTAATTATAATA
58782821 TATGTTAATT
1 TAT-TTAATT
58782831 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:58782853 original size:120 final size:120
Alignment explanation
Indices: 58782717--58782946 Score: 460
Period size: 120 Copynumber: 1.9 Consensus size: 120
58782707 TTTGAGTAAA
58782717 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
58782782 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
66 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
58782837 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
58782902 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
66 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
58782947 TAAATATGAT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 110 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (120 bp):
TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
Found at i:58782912 original size:61 final size:61
Alignment explanation
Indices: 58782727--58782914 Score: 208
Period size: 61 Copynumber: 3.1 Consensus size: 61
58782717 TTATAGTATC
58782727 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * * * * *
58782788 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAATTTA-TATTTTA-TAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT-ATTAAGAATTTTATTA-AATT
58782847 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
58782908 ATATATT
1 ATATATT
58782915 TTAATTATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 29 0.30
60 26 0.27
61 36 0.37
62 3 0.03
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
Found at i:58782929 original size:16 final size:16
Alignment explanation
Indices: 58782908--58782949 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
58782898 TTATTAAATT
*
58782908 ATATATTTTAATTATA
1 ATATATTTTAATAATA
58782924 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
58782939 AT-TATGTTTAA
1 ATATAT-TTTAA
58782950 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:58782934 original size:15 final size:15
Alignment explanation
Indices: 58782899--58782940 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
58782889 TTAAGAATTT
*
58782899 TATTAAATTAT-ATA
1 TATTTAATTATAATA
58782913 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
58782927 TATTTAATAATAAT
1 TATTTAATTATAAT
58782941 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:58783175 original size:45 final size:43
Alignment explanation
Indices: 58783075--58783184 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
58783065 TTTTCCATTA
58783075 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* * ***
58783114 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
58783159 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
58783185 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 23 0.40
46 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:58783186 original size:16 final size:16
Alignment explanation
Indices: 58783165--58783232 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
58783155 GATTTGCTAT
*
58783165 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
58783181 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
58783197 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
58783213 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
58783229 TACA
1 TACA
58783233 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:58783820 original size:12 final size:12
Alignment explanation
Indices: 58783803--58783829 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
58783793 TTGTCTCTTA
58783803 AGTTTATTCATT
1 AGTTTATTCATT
58783815 AGTTTATTCATT
1 AGTTTATTCATT
58783827 AGT
1 AGT
58783830 ATTTAGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (12 bp):
AGTTTATTCATT
Found at i:58784265 original size:13 final size:13
Alignment explanation
Indices: 58784218--58784266 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
58784208 TTTGGCAATA
58784218 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
58784231 TTTTTAAAAAGTG
1 CTTTTGAAAAGTG
*
58784244 -TTATGGAAAAGTG
1 CTT-TTGAAAAGTG
58784257 CTTTTGAAAA
1 CTTTTGAAAA
58784267 TTTTAGGTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 2 0.07
13 25 0.86
14 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:58785880 original size:24 final size:23
Alignment explanation
Indices: 58785842--58785896 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
58785832 AATACATGTT
*
58785842 CATAATAT-ATATAAAACGTATA
1 CATAATATAATATAAAACATATA
* *
58785864 TATAATATAATATTAAAACATTTA
1 CATAATATAATA-TAAAACATATA
58785888 CATAATATA
1 CATAATATA
58785897 TACACATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 7 0.26
23 3 0.11
24 17 0.63
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (23 bp):
CATAATATAATATAAAACATATA
Found at i:58785973 original size:21 final size:18
Alignment explanation
Indices: 58785929--58785973 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
58785919 AAAAACATAT
58785929 TAATATTAATAATAATAC
1 TAATATTAATAATAATAC
58785947 TAATATTACATAAATATATAC
1 TAATATTA-AT-AATA-ATAC
*
58785968 TTATAT
1 TAATAT
58785974 ATATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 4 0.17
21 9 0.39
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATATTAATAATAATAC
Found at i:58786488 original size:3 final size:3
Alignment explanation
Indices: 58786480--58786549 Score: 92
Period size: 3 Copynumber: 24.0 Consensus size: 3
58786470 GAGTACATAC
* *
58786480 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA GAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
58786528 TAA T-A TCAA TAA T-A TAA -AA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA
58786550 CAAGGATATT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
2 6 0.10
3 51 0.86
4 2 0.03
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:58788686 original size:14 final size:14
Alignment explanation
Indices: 58788663--58788693 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
58788653 GAGTTGATTT
*
58788663 AAAAATATAAATTG
1 AAAAACATAAATTG
58788677 AAAAACATAAATTG
1 AAAAACATAAATTG
58788691 AAA
1 AAA
58788694 TTACCTCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (14 bp):
AAAAACATAAATTG
Found at i:58788694 original size:90 final size:83
Alignment explanation
Indices: 58788524--58788742 Score: 228
Period size: 84 Copynumber: 2.5 Consensus size: 83
58788514 AAAAGTAGAT
* * * * *
58788524 CTCAGCGTGCCCCGAGGCTTAACTTACCTCTCGTAATATGAGTTGATTTTTGAAAAATATAGATT
1 CTCAGCATGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAAATATAAATT
*
58788589 GGAAAAAAACAGAAATTGAAAATAC
65 GG--AAAAA-A-AAA--GAAATTAC
* *
58788614 CTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT-AAAAATATAAATT-
1 CTCAGCATGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAATATAAATTG
58788676 GAAAAACATAAATTGAAATTAC
66 GAAAAA-A-AAA--GAAATTAC
* *
58788698 CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCACAATATGAGTTG
1 CTCAGCATGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
58788743 GTCTTTTTGA
Statistics
Matches: 116, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
84 60 0.52
86 1 0.01
87 12 0.10
88 3 0.03
90 40 0.34
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (83 bp):
CTCAGCATGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAATATAAATTG
GAAAAAAAAAGAAATTAC
Found at i:58788851 original size:14 final size:14
Alignment explanation
Indices: 58788832--58788858 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58788822 TTGATTTTTG
58788832 AAAAGCAGAAATTA
1 AAAAGCAGAAATTA
58788846 AAAAGCAGAAATT
1 AAAAGCAGAAATT
58788859 GAAATTACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAAGCAGAAATTA
Found at i:58788861 original size:82 final size:82
Alignment explanation
Indices: 58788712--58788862 Score: 189
Period size: 82 Copynumber: 1.8 Consensus size: 82
58788702 GCGTGCCCCG
* ** * * * **
58788712 AGGCTCAACTCACCTCTCACAATATGAGTTGGTCTTTTTGAAACTTAATTTGAAAAGTAGATTTT
1 AGGCTCAACTCACCTCTCACAATATGAGTTGGTATTTTTGAAACAGAAATTAAAAAGCAGAAATT
58788777 GAAAAACAGAAATTAAA
66 GAAAAACAGAAATTAAA
*
58788794 AGGCTCAACTCACCTCTCGCAATATGAGTT-G-ATTTTTGAAAAGCAGAAATTAAAAAGCAGAAA
1 AGGCTCAACTCACCTCTCACAATATGAGTTGGTATTTTTG-AAA-CAGAAATTAAAAAGCAGAAA
58788857 TTGAAA
64 TTGAAA
58788863 TTACCTCAGC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
80 6 0.10
81 4 0.07
82 48 0.83
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (82 bp):
AGGCTCAACTCACCTCTCACAATATGAGTTGGTATTTTTGAAACAGAAATTAAAAAGCAGAAATT
GAAAAACAGAAATTAAA
Found at i:58788904 original size:87 final size:88
Alignment explanation
Indices: 58788524--58788923 Score: 387
Period size: 87 Copynumber: 4.6 Consensus size: 88
58788514 AAAAGTAGAT
* * * * *
58788524 CTCAGCGTGCCCCGAGGCTTAACTTACCTCTCGTAATATGAGTTGATTTTTGAAAAATATAGATT
1 CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT
* *
58788589 GGAAAAAAACAGAAATTGAAAATAC
66 -G-AAAAAGCAGAAATTGAAATTAC
* * * *
58788614 CTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTT-AAAAATATAAATT
1 CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT
*
58788676 GAAAAA-CATAAATTGAAATTAC
66 GAAAAAGCAGAAATTGAAATTAC
* * * *
58788698 CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGGTCTTTTTG--AAACTTAAT
1 CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT-G-ATTTTTGAAAAACATAAA
* **
58788761 TTG-AAAAGTAGATTTTGAAA--A-
64 TTGAAAAAGCAGAAATTGAAATTAC
* ** **** * *
58788782 -ACAGAAAT--TAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAAT
1 CTCAG-CGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAAT
58788844 T-AAAAAGCAGAAATTGAAATTAC
65 TGAAAAAGCAGAAATTGAAATTAC
* *
58788867 CTCAGCGTGCCCTGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTGAAAAA
1 CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
58788924 AAAATGGAAT
Statistics
Matches: 248, Mismatches: 46, Indels: 35
0.75 0.14 0.11
Matches are distributed among these distances:
80 6 0.02
81 1 0.00
82 50 0.20
83 3 0.01
84 56 0.23
85 8 0.03
86 8 0.03
87 70 0.28
88 6 0.02
90 40 0.16
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (88 bp):
CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT
GAAAAAGCAGAAATTGAAATTAC
Found at i:58792477 original size:11 final size:12
Alignment explanation
Indices: 58792460--58792490 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
58792450 TAAATGATAT
58792460 TTTATTATTTTA
1 TTTATTATTTTA
58792472 -TTATTATTTTA
1 TTTATTATTTTA
58792483 TTTATTAT
1 TTTATTAT
58792491 ATATAAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:58794685 original size:46 final size:46
Alignment explanation
Indices: 58794632--58794951 Score: 412
Period size: 46 Copynumber: 7.0 Consensus size: 46
58794622 GCTCTCTGAA
* *
58794632 ATGAAATGCGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
58794678 ATGAAATGTA-TAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATG-AGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
58794724 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** ** * *
58794770 GGGAAATGAAAAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
58794816 ATGAAACGAATAAGACCATGGTTGAAAGATACCATGGCAACTTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
58794862 ATGAAAAG-GATAAGACCATGGTTGAAAAATACCATGGCAACATGAC
1 ATGAAATGAG-TAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
58794908 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
58794952 TCAAAGATAA
Statistics
Matches: 241, Mismatches: 28, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
45 1 0.00
46 239 0.99
47 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:58794703 original size:21 final size:21
Alignment explanation
Indices: 58794679--58794750 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
58794669 CAACATGATA
58794679 TGAAATGTATAAGACCATGGT
1 TGAAATGTATAAGACCATGGT
*
58794700 TGAAA-G-ATACCATGACAACATGAT
1 TGAAATGTATA--A-GAC--CATGGT
*
58794724 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTATAAGACCATGGT
58794746 TGAAA
1 TGAAA
58794751 GATACCATGG
Statistics
Matches: 40, Mismatches: 3, Indels: 16
0.68 0.05 0.27
Matches are distributed among these distances:
19 3 0.08
20 1 0.03
21 11 0.28
22 8 0.20
24 8 0.20
25 6 0.15
26 1 0.03
27 2 0.05
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (21 bp):
TGAAATGTATAAGACCATGGT
Found at i:58805761 original size:16 final size:15
Alignment explanation
Indices: 58805737--58805788 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
58805727 AATTAAGACC
58805737 TTTTAAAATTTAAAAA
1 TTTT-AAATTTAAAAA
* *
58805753 TTATTAAATATATAAA
1 TT-TTAAATTTAAAAA
*
58805769 TTTTAAAATTATAAAA
1 TTTTAAATTTA-AAAA
58805785 TTTT
1 TTTT
58805789 TATTAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 7 0.24
16 20 0.69
17 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTAAATTTAAAAA
Found at i:58818832 original size:11 final size:12
Alignment explanation
Indices: 58818802--58818835 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
58818792 CGACCCGCCA
58818802 ATATTAATTTTT
1 ATATTAATTTTT
58818814 ATATTAATTTTT
1 ATATTAATTTTT
58818826 ATA-TAATTTT
1 ATATTAATTTT
58818836 AAAAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:58818858 original size:16 final size:17
Alignment explanation
Indices: 58818837--58818873 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
58818827 TATAATTTTA
*
58818837 AAAAATA-TAATACATC
1 AAAAATACTAAAACATC
58818853 AAAAATACTAAAACATC
1 AAAAATACTAAAACATC
58818870 AAAA
1 AAAA
58818874 TAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAAATACTAAAACATC
Found at i:58818998 original size:30 final size:30
Alignment explanation
Indices: 58818962--58819024 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
58818952 ATTTAACAAG
58818962 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
58818992 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
58819022 CAA
1 CAA
58819025 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:58819109 original size:22 final size:22
Alignment explanation
Indices: 58819062--58819111 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
58819052 TAATAACAAC
* *
58819062 AAAATACTAGCAACATAATAGT
1 AAAATACTAGCAAAATAAGAGT
*
58819084 AAAATAGTAGCAAAATAAGGAG-
1 AAAATACTAGCAAAATAA-GAGT
58819106 AAAATA
1 AAAATA
58819112 ACAAGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.60, C:0.08, G:0.14, T:0.18
Consensus pattern (22 bp):
AAAATACTAGCAAAATAAGAGT
Found at i:58819687 original size:15 final size:15
Alignment explanation
Indices: 58819666--58819701 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
58819656 AGAGTATGAT
58819666 AAAATATTAAAAATA
1 AAAATATTAAAAATA
* *
58819681 TAAATATTTAAAATA
1 AAAATATTAAAAATA
58819696 AAAATA
1 AAAATA
58819702 CGTAACGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATATTAAAAATA
Found at i:58822127 original size:17 final size:19
Alignment explanation
Indices: 58822094--58822128 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
58822084 TAGGATCGTG
58822094 TATTTCTCTAGTAATTTTT
1 TATTTCTCTAGTAATTTTT
58822113 TATTT-TCTA-TAATTTT
1 TATTTCTCTAGTAATTTT
58822129 AAAATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.66
Consensus pattern (19 bp):
TATTTCTCTAGTAATTTTT
Found at i:58824616 original size:22 final size:20
Alignment explanation
Indices: 58824591--58824644 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
58824581 TTTCTTTTTG
58824591 AAAAATAAAATTAATTATATAA
1 AAAAATAAAATTAATT-T-TAA
* *
58824613 AAAAGTAAATTTAATTTTAA
1 AAAAATAAAATTAATTTTAA
58824633 AAAATATAAAAT
1 AAAA-ATAAAAT
58824645 GAGTTATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.26
21 6 0.22
22 14 0.52
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAAATAAAATTAATTTTAA
Found at i:58824642 original size:21 final size:20
Alignment explanation
Indices: 58824586--58824642 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
58824576 CAAGTTTTCT
*
58824586 TTTTGAAAAATA-AAATTAA
1 TTTTAAAAAATATAAATTAA
*
58824605 TTATATAAAAAAGTA-AATTTAA
1 TT-T-TAAAAAA-TATAAATTAA
58824627 TTTTAAAAAATATAAA
1 TTTTAAAAAATATAAA
58824643 ATGAGTTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 4 0.13
20 10 0.32
21 7 0.23
22 10 0.32
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
TTTTAAAAAATATAAATTAA
Found at i:58826735 original size:36 final size:34
Alignment explanation
Indices: 58826671--58826741 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 34
58826661 AGCAATTTAA
*
58826671 TTTTTTTCTTTTATATTCTTTTAACTTTT-CTTC
1 TTTTTTTCTTTTATATTATTTTAACTTTTGCTTC
* *
58826704 TTTTTTTCTGTTTTTATTTATTATTATCTTTTGCTTC
1 TTTTTTTCT-TTTATA-TTATT-TTAACTTTTGCTTC
58826741 T
1 T
58826742 CCCTCTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
33 9 0.29
34 5 0.16
35 4 0.13
36 8 0.26
37 5 0.16
ACGTcount: A:0.11, C:0.13, G:0.03, T:0.73
Consensus pattern (34 bp):
TTTTTTTCTTTTATATTATTTTAACTTTTGCTTC
Found at i:58827005 original size:15 final size:15
Alignment explanation
Indices: 58826985--58827021 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
58826975 ACAACGCGAT
58826985 AACGTAAGTAACTAA
1 AACGTAAGTAACTAA
58827000 AACGTAAGTAACTAA
1 AACGTAAGTAACTAA
58827015 AACGTAA
1 AACGTAA
58827022 TATTTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.19
Consensus pattern (15 bp):
AACGTAAGTAACTAA
Found at i:58830213 original size:18 final size:19
Alignment explanation
Indices: 58830183--58830220 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
58830173 TTTTATTGTA
58830183 TTCTATAATATAATAATAG
1 TTCTATAATATAATAATAG
*
58830202 TTCTAT-ATATAATAGTAG
1 TTCTATAATATAATAATAG
58830220 T
1 T
58830221 ACATTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (19 bp):
TTCTATAATATAATAATAG
Found at i:58830467 original size:20 final size:20
Alignment explanation
Indices: 58830400--58830485 Score: 59
Period size: 20 Copynumber: 4.2 Consensus size: 20
58830390 ATATTATGTA
* *
58830400 ATATTATATATTTTATTATAAT
1 ATATAATATAGTTTATTAT--T
* *
58830422 ATATAATATAATAATAGTTA-T
1 ATATAATATAGT-TTA-TTATT
58830443 ATATAATAGTAGTTT-TTATT
1 ATATAATA-TAGTTTATTATT
* *
58830463 ATATATTATTGTTTATTATT
1 ATATAATATAGTTTATTATT
58830483 ATA
1 ATA
58830486 CTGATTGAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
19 8 0.15
20 16 0.31
21 10 0.19
22 13 0.25
23 2 0.04
24 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
ATATAATATAGTTTATTATT
Found at i:58830546 original size:240 final size:238
Alignment explanation
Indices: 58830153--58830923 Score: 745
Period size: 240 Copynumber: 3.2 Consensus size: 238
58830143 ATATAATGCC
* * *
58830153 ATATAATGTAATACTATATATTTTATTGTATTCTATAATATAATAATAGTTCTATATATAATAGT
1 ATATCATGTAATACTATATATTTTATTATAATCTATAATATAATAATAG-T-TATATATAATAGT
** ** * * * * *
58830218 AG--TACA-T-TAT-TTATTAATTATTATTATATTAGTTGAACTATGTTTTAAGTCCCTATATTT
64 AGTTTTTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAGTCCCTATACTT
* *
58830278 TTCATACATTTGAAAGTTAACCCTCCTACTATATTATATAATGCTATATCACATCATATAGTATA
129 TTCATACATTTAAAAGTTAACCCTCCTACTATATTATATAATGCTATATCATATCATATA-TATA
*
58830343 TAATATAGTAATAGTTTATATATATGTATATATGATTGAACATTATA
193 TAATATA-TAATAGTTTATATATATGTATATATGATTAAACATTATA
* * *
58830390 ATATTATGTAATATTATATATTTTATTATAATATATAATATAATAATAGTTATATATAATAGTAG
1 ATATCATGTAATACTATATATTTTATTATAATCTATAATATAATAATAGTTATATATAATAGTAG
* * *
58830455 TTTTTATTATATATTATTGTTTATTATTATACTGATTGAAATATGCTGTAAGTCCCTATACTATT
66 TTTTTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAGTCCCTATACTTTT
*
58830520 CGA-ACATTTAAAAGTTAACGCTCCTACTATATTATATAATGCTATATCATATC--ATATAT-TA
131 C-ATACATTTAAAAGTTAACCCTCCTACTATATTATATAATGCTATATCATATCATATATATATA
* * * * * *
58830581 ATA-AT--T--TATATATATACGCATAAATTATTAAATATTATA
195 ATATATAATAGTTTATATATATGTATATATGATTAAACATTATA
* * * * *
58830620 ATAGCATGTAATTCTATCTCTTTTATTATAATCTATATTATAATAATAGTTACT-TATAATAGTA
1 ATATCATGTAATACTATATATTTTATTATAATCTATAATATAATAATAGTTA-TATATAATAGTA
58830684 GTACATTATATATTACTTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAG
65 G---------T-TT--TTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAG
* * * * * *
58830749 TCCCTATAGTTTTCATACATTTAAAAATTAGCCCTCCTAC--T-GTATCTAATGCCATATCATAT
118 TCCCTATACTTTTCATACATTTAAAAGTTAACCCTCCTACTATATTATATAATGCTATATCATAT
* * * *
58830811 TATCATATA-AT-ATATATTAATAGTTTATATATATATATGCATCGATGACTAAACATTACA
183 CAT-ATATATATAATATA-TAATAGTTTATATATATGTAT--AT--ATGATTAAACATTATA
* * * * * *
58830871 ATATCAAGTAACACTATATCTTTTATTATGATCTATATTTTAATAATAGTTAT
1 ATATCATGTAATACTATATATTTTATTATAATCTATAATATAATAATAGTTAT
58830924 GTATTTATTA
Statistics
Matches: 438, Mismatches: 62, Indels: 55
0.79 0.11 0.10
Matches are distributed among these distances:
230 81 0.18
231 1 0.00
232 1 0.00
234 1 0.00
235 16 0.04
236 6 0.01
237 49 0.11
238 4 0.01
239 22 0.05
240 93 0.21
241 5 0.01
242 87 0.20
243 1 0.00
245 1 0.00
247 11 0.03
249 1 0.00
250 1 0.00
251 57 0.13
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (238 bp):
ATATCATGTAATACTATATATTTTATTATAATCTATAATATAATAATAGTTATATATAATAGTAG
TTTTTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAGTCCCTATACTTTT
CATACATTTAAAAGTTAACCCTCCTACTATATTATATAATGCTATATCATATCATATATATATAA
TATATAATAGTTTATATATATGTATATATGATTAAACATTATA
Found at i:58830692 original size:16 final size:17
Alignment explanation
Indices: 58830656--58830693 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
58830646 TATAATCTAT
58830656 ATTATAATAATAGTTAC
1 ATTATAATAATAGTTAC
*
58830673 -TTATAATAGTAG-TAC
1 ATTATAATAATAGTTAC
58830688 ATTATA
1 ATTATA
58830694 TATTACTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (17 bp):
ATTATAATAATAGTTAC
Found at i:58830741 original size:242 final size:248
Alignment explanation
Indices: 58830458--58830922 Score: 597
Period size: 242 Copynumber: 1.9 Consensus size: 248
58830448 ATAGTAGTTT
*
58830458 TTATTATATATTATTGTTTATTATTATACTGATTGAAATATGCTGTAAGTCCCTATACTATTCGA
1 TTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTGTAAGTCCCTATACTATTC-A
* *
58830523 -ACATTTAAAAGTTAACGCTCCTACTATAT-T-AT-ATAATGC-TA-TATCATAT-CATATATTA
65 TACATTTAAAAATTAACCCTCCTACTATATCTAATCAT-AT-CATATTATCATATACATATATTA
* * * * * ** *
58830581 ATA-ATT-TATATATATACGCATAAATTATTAAATATTATAATAGCATGTAATTCTATCTCTTTT
128 ATAGATTATATATATATACGCATAAATGACTAAACATTACAATAGCAAGTAACACTATATCTTTT
58830644 ATTATAATCTATATTATAATAATAGTTACTTATAATAGTAGTACATTATATATTAC
193 ATTATAATCTATATTATAATAATAGTTACTTATAATAGTAGTACATTATATATTAC
* * *
58830700 TTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAGTCCCTATAGTTTTCAT
1 TTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTGTAAGTCCCTATACTATTCAT
* * *
58830765 ACATTTAAAAATTAGCCCTCCTACTGTATCTAATGCCATATCATATTATCATATAATATATATTA
66 ACATTTAAAAATTAACCCTCCTACTATATCTAAT--CATATCATATTATCATAT-ACATATATTA
* * ** *
58830830 ATAGTTTATATATATATATGCATCGATGACTAAACATTACAATATCAAGTAACACTATATCTTTT
128 ATAGATTATATATATATACGCATAAATGACTAAACATTACAATAGCAAGTAACACTATATCTTTT
* *
58830895 ATTATGATCTATATTTTAATAATAGTTA
193 ATTATAATCTATATTATAATAATAGTTA
58830923 TGTATTTATT
Statistics
Matches: 187, Mismatches: 24, Indels: 15
0.83 0.11 0.07
Matches are distributed among these distances:
241 1 0.01
242 84 0.45
243 1 0.01
244 2 0.01
245 1 0.01
246 4 0.02
247 10 0.05
249 11 0.06
250 2 0.01
251 71 0.38
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (248 bp):
TTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTGTAAGTCCCTATACTATTCAT
ACATTTAAAAATTAACCCTCCTACTATATCTAATCATATCATATTATCATATACATATATTAATA
GATTATATATATATACGCATAAATGACTAAACATTACAATAGCAAGTAACACTATATCTTTTATT
ATAATCTATATTATAATAATAGTTACTTATAATAGTAGTACATTATATATTAC
Found at i:58830973 original size:27 final size:28
Alignment explanation
Indices: 58830904--58830982 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 28
58830894 TATTATGATC
* *
58830904 TATATTTTAATAATAGTTATGTATTTAT
1 TATATTTTAGTAATAGTTATATATTTAT
58830932 TAATATTTTTAGTAATAGTTATATA-TTAT
1 T-ATA-TTTTAGTAATAGTTATATATTTAT
*
58830961 T-TATTTTACGTAATAGTAATAT
1 TATATTTTA-GTAATAGTTATAT
58830983 TCTAATTTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
26 5 0.11
27 14 0.31
28 1 0.02
29 8 0.18
30 17 0.38
ACGTcount: A:0.37, C:0.01, G:0.08, T:0.54
Consensus pattern (28 bp):
TATATTTTAGTAATAGTTATATATTTAT
Found at i:58836155 original size:17 final size:16
Alignment explanation
Indices: 58836135--58836180 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
58836125 AAAGTAAAAC
*
58836135 AAAAGAAAAAGAGATAG
1 AAAAGAAACAGAGAT-G
58836152 AAAAGAAACAGA-ATG
1 AAAAGAAACAGAGATG
*
58836167 AAACGAAACAGAGA
1 AAAAGAAACAGAGA
58836181 GCAAGGAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 12 0.46
16 3 0.12
17 11 0.42
ACGTcount: A:0.67, C:0.07, G:0.22, T:0.04
Consensus pattern (16 bp):
AAAAGAAACAGAGATG
Found at i:58837864 original size:6 final size:6
Alignment explanation
Indices: 58837853--58837877 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58837843 CTGTGTACCG
58837853 TACTGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT T
58837878 CCGGCTTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TACTGT
Found at i:58838039 original size:18 final size:18
Alignment explanation
Indices: 58837994--58838169 Score: 126
Period size: 18 Copynumber: 9.7 Consensus size: 18
58837984 TAACTGATTA
58837994 TTACTGAAT-ATTGACTG
1 TTACTGAATAATTGACTG
* *
58838011 TTACCGGATAATTGACTG
1 TTACTGAATAATTGACTG
* * * *
58838029 TTACTGAATAACTAAATA
1 TTACTGAATAATTGACTG
58838047 TTACTGAATAATTGA-TCG
1 TTACTGAATAATTGACT-G
* *
58838065 TTACTGAATAACTGATTG
1 TTACTGAATAATTGACTG
* *
58838083 TCACTGAACGAA-TGACTG
1 TTACTGAA-TAATTGACTG
* * *
58838101 TTATTGAATAACTTAATTG
1 TTACTGAATAA-TTGACTG
* *
58838120 TTACTGAATACCTCCTGA-TT
1 TTACTGAATA-AT--TGACTG
58838140 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
*
58838158 TTACTGGATAAT
1 TTACTGAATAAT
58838170 CGATCAATTG
Statistics
Matches: 122, Mismatches: 27, Indels: 19
0.73 0.16 0.11
Matches are distributed among these distances:
17 13 0.11
18 78 0.64
19 18 0.15
20 11 0.09
21 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:58838090 original size:54 final size:53
Alignment explanation
Indices: 58837982--58838090 Score: 130
Period size: 54 Copynumber: 2.0 Consensus size: 53
58837972 AAAGGTATAA
* * * * *
58837982 AATAACTGATTATTACTGAATATTGACTGTTACCGGATAATTGACTGTTACTG
1 AATAACTAAATATTACTGAATATTGACTGTTACCGAATAACTGACTGTCACTG
* *
58838035 AATAACTAAATATTACTGAATAATTGA-TCGTTACTGAATAACTGATTGTCACTG
1 AATAACTAAATATTACTGAAT-ATTGACT-GTTACCGAATAACTGACTGTCACTG
58838089 AA
1 AA
58838091 CGAATGACTG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
53 20 0.43
54 27 0.57
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (53 bp):
AATAACTAAATATTACTGAATATTGACTGTTACCGAATAACTGACTGTCACTG
Found at i:58838231 original size:22 final size:22
Alignment explanation
Indices: 58838188--58838238 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
58838178 TGATCGATAC
** *
58838188 TGAATAACTGGTTATTATTGAA
1 TGAATAACTGACTATTACTGAA
*
58838210 TGAATAACTGACTGTTACTGAA
1 TGAATAACTGACTATTACTGAA
*
58838232 TAAATAA
1 TGAATAA
58838239 TTGTTCTGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (22 bp):
TGAATAACTGACTATTACTGAA
Found at i:58842061 original size:22 final size:22
Alignment explanation
Indices: 58842036--58842077 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
58842026 GTAATTACAC
* * *
58842036 ATAAAATATATATTATATTAAA
1 ATAAAAAATAGATTAAATTAAA
58842058 ATAAAAAATAGATTAAATTA
1 ATAAAAAATAGATTAAATTA
58842078 TATGTAAAAC
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:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAAAAAATAGATTAAATTAAA
Found at i:58849273 original size:18 final size:17
Alignment explanation
Indices: 58849245--58849282 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
58849235 GTTCAGAAAG
58849245 AAAGATAAAAAGTAAAAAA
1 AAAGATAAAAA--AAAAAA
58849264 AAAG-TAAAAAAAAAAA
1 AAAGATAAAAAAAAAAA
58849280 AAA
1 AAA
58849283 ACGTACATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.47
18 6 0.32
19 4 0.21
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAGATAAAAAAAAAAA
Found at i:58849278 original size:12 final size:11
Alignment explanation
Indices: 58849251--58849277 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
58849241 AAAGAAAGAT
58849251 AAAAAGTAAAA
1 AAAAAGTAAAA
58849262 AAAAAGTAAAA
1 AAAAAGTAAAA
58849273 AAAAA
1 AAAAA
58849278 AAAAAACGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAAGTAAAA
Found at i:58852546 original size:46 final size:43
Alignment explanation
Indices: 58852496--58852584 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 43
58852486 CGCTGTAATG
58852496 GAATAGAACTGTAATAAGTAATTCAATTG-TTTGGTTGAATGAAATA
1 GAATAGAACTGTAAT-AGT-ATTC--TTGATTTGGTTGAATGAAATA
*
58852542 GAATAGAACTGTAATGGTATTCTTGTATTTGGTTGAATGAAAT
1 GAATAGAACTGTAATAGTATTCTTG-ATTTGGTTGAATGAAAT
58852585 GATGTTGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
42 3 0.08
44 20 0.50
45 2 0.05
46 15 0.38
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.37
Consensus pattern (43 bp):
GAATAGAACTGTAATAGTATTCTTGATTTGGTTGAATGAAATA
Found at i:58852760 original size:16 final size:18
Alignment explanation
Indices: 58852691--58852754 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 18
58852681 ATTATTATTA
58852691 AATTTAATA-ATAAATAAT
1 AATTTAATACATAAAT-AT
58852709 AATTTAATCACATTTAAATAT
1 AATTTAAT-ACA--TAAATAT
*
58852730 AA-TTATTAC-TAAATAT
1 AATTTAATACATAAATAT
58852746 AATTTAATA
1 AATTTAATA
58852755 AAAATAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
16 9 0.23
17 5 0.13
18 8 0.21
19 3 0.08
20 5 0.13
21 4 0.10
22 5 0.13
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTTAATACATAAATAT
Found at i:58854190 original size:63 final size:63
Alignment explanation
Indices: 58854091--58854216 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
58854081 CATGGAGATT
* *
58854091 TTCTTATCACATCAAGAATGAGGCGCATCTTAATAGAGTTTGAATTACCAAATTTAAGTTATA
1 TTCTTATCACATCAAGAAGGAGGCGCAGCTTAATAGAGTTTGAATTACCAAATTTAAGTTATA
* *
58854154 TTCTTATCACATCGAGAAGGAGGTGCAGCTTAATAGAGTTTGAATTACCAAATTTAAGTTATA
1 TTCTTATCACATCAAGAAGGAGGCGCAGCTTAATAGAGTTTGAATTACCAAATTTAAGTTATA
58854217 AATTAGGTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (63 bp):
TTCTTATCACATCAAGAAGGAGGCGCAGCTTAATAGAGTTTGAATTACCAAATTTAAGTTATA
Found at i:58856492 original size:21 final size:22
Alignment explanation
Indices: 58856448--58856498 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
58856438 TTTCCTGCAT
58856448 TTAAACACATTAAATTGAACTTA
1 TTAAACACATTAAA-TGAACTTA
* *
58856471 TTAAACACATTTAA-GCACTTA
1 TTAAACACATTAAATGAACTTA
*
58856492 TTGAACA
1 TTAAACA
58856499 TGCACTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.48
23 13 0.52
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (22 bp):
TTAAACACATTAAATGAACTTA
Found at i:58859713 original size:24 final size:24
Alignment explanation
Indices: 58859678--58859739 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
58859668 CACTTTTTCC
58859678 TTTC-TTTT-TTTTTCAAT-TTTT
1 TTTCTTTTTCTTTTTCAATCTTTT
*
58859699 TTGTCTTTTTCTTTTTCACTCTTTT
1 TT-TCTTTTTCTTTTTCAATCTTTT
* *
58859724 TTTCTTGTACTTTTTC
1 TTTCTTTTTCTTTTTC
58859740 TTTCACTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 2 0.06
23 4 0.12
24 20 0.59
25 6 0.18
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.74
Consensus pattern (24 bp):
TTTCTTTTTCTTTTTCAATCTTTT
Found at i:58865539 original size:41 final size:41
Alignment explanation
Indices: 58865411--58865543 Score: 135
Period size: 41 Copynumber: 3.2 Consensus size: 41
58865401 TAGCGGCGTT
* * * *
58865411 TGCAAAAGGTCAAGCATTAGCAATGTTTATGAAAAAAAATGC
1 TGCAAAAGATCAAGCATTAGCGACGTTTATG-ATAAAAATGC
* * * **
58865453 CGC-AAAGGTCAAGCATTAGCGGCGTTTATGATAAAAGCGAC
1 TGCAAAAGATCAAGCATTAGCGACGTTTATGATAAAAATG-C
* *
58865494 -GCAAAAGATCAAACATTAGCGACATTTATGATAAAAATGC
1 TGCAAAAGATCAAGCATTAGCGACGTTTATGATAAAAATGC
58865534 TGCAAAAGAT
1 TGCAAAAGAT
58865544 ACATTGCAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
40 9 0.12
41 64 0.85
42 2 0.03
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (41 bp):
TGCAAAAGATCAAGCATTAGCGACGTTTATGATAAAAATGC
Found at i:58865726 original size:22 final size:22
Alignment explanation
Indices: 58865687--58865732 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
58865677 TGATTTAGGG
* *
58865687 TTTATGGTTTGGGGTTTAGTGT
1 TTTATAGTTAGGGGTTTAGTGT
*
58865709 TTTATAGTTAGGGTTTTAGTGT
1 TTTATAGTTAGGGGTTTAGTGT
58865731 TT
1 TT
58865733 AAGGTTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (22 bp):
TTTATAGTTAGGGGTTTAGTGT
Found at i:58865943 original size:21 final size:21
Alignment explanation
Indices: 58865919--58865971 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
58865909 CAGTTGAGGA
* *
58865919 TTTATGATTTATGATTTAGAG
1 TTTAGGATTTAAGATTTAGAG
*
58865940 TTTAGGGTTTAAGATTTAGAG
1 TTTAGGATTTAAGATTTAGAG
* *
58865961 TTCAGGCTTTA
1 TTTAGGATTTA
58865972 GGGTTTAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.04, G:0.23, T:0.47
Consensus pattern (21 bp):
TTTAGGATTTAAGATTTAGAG
Found at i:58865978 original size:21 final size:21
Alignment explanation
Indices: 58865926--58865971 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
58865916 GGATTTATGA
* * *
58865926 TTTATGATTTAGAGTTTAGGG
1 TTTAAGATTTAGAGTTCAGGC
58865947 TTTAAGATTTAGAGTTCAGGC
1 TTTAAGATTTAGAGTTCAGGC
58865968 TTTA
1 TTTA
58865972 GGGTTTAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.46
Consensus pattern (21 bp):
TTTAAGATTTAGAGTTCAGGC
Found at i:58866491 original size:112 final size:117
Alignment explanation
Indices: 58866351--58866576 Score: 336
Period size: 112 Copynumber: 2.0 Consensus size: 117
58866341 AATGATGCCA
***
58866351 TTTTAATGCTTTGTGGAATTGGCGGCACTAGCTAATAAACGCCGCAATAGATAAGAATTAGCGGT
1 TTTTAATGCTTTGTGGAATTAAAGGCACTAGCTAATAAACGCCGCAATAGATAAGAATTAGCGGT
*
58866416 GCTTTTT-AAAAA-A-TGC-CAATTTTTTT-AATTAAATGGAAACGTCGCTG
66 GCTTTTTGAAAAACACTGCAAAATTTTTTTAAATTAAATGGAAACGTCGCTG
* * * *
58866463 TTTTAATGCTTTTTGGAATTAAATGCACTAGCTAATAAACGCTGCAATAGATAAGAATTAGTGGT
1 TTTTAATGCTTTGTGGAATTAAAGGCACTAGCTAATAAACGCCGCAATAGATAAGAATTAGCGGT
*
58866528 GCTTTTTGAAAAACACTGCAAAATTTTTTTAAATTGAATGGAAACGTCG
66 GCTTTTTGAAAAACACTGCAAAATTTTTTTAAATTAAATGGAAACGTCG
58866577 TCATTTTAGC
Statistics
Matches: 100, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
112 65 0.65
113 5 0.05
114 1 0.01
115 3 0.03
116 9 0.09
117 17 0.17
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (117 bp):
TTTTAATGCTTTGTGGAATTAAAGGCACTAGCTAATAAACGCCGCAATAGATAAGAATTAGCGGT
GCTTTTTGAAAAACACTGCAAAATTTTTTTAAATTAAATGGAAACGTCGCTG
Found at i:58868890 original size:9 final size:9
Alignment explanation
Indices: 58868876--58869070 Score: 139
Period size: 9 Copynumber: 21.9 Consensus size: 9
58868866 TTCTTTAAAA
58868876 TTACATAAC
1 TTACATAAC
*
58868885 TTACATACC
1 TTACATAAC
58868894 TTACATAA-
1 TTACATAAC
* * *
58868902 ATATATATC
1 TTACATAAC
*
58868911 ATATCATAAC
1 TTA-CATAAC
*
58868921 TTACATACC
1 TTACATAAC
*
58868930 TCACATAAC
1 TTACATAAC
* *
58868939 ATACCTAAC
1 TTACATAAC
*
58868948 TTACGTAAC
1 TTACATAAC
58868957 TTACATAA-
1 TTACATAAC
58868965 -TACATAA-
1 TTACATAAC
* * *
58868972 ATATATATC
1 TTACATAAC
* *
58868981 ATATCATAAA
1 TTA-CATAAC
58868991 TGT-CATAAC
1 T-TACATAAC
58869000 TTACATAAC
1 TTACATAAC
*
58869009 TTACATAAT
1 TTACATAAC
58869018 TTACATAAC
1 TTACATAAC
*
58869027 TTACATAAT
1 TTACATAAC
*
58869036 TTTCATAAC
1 TTACATAAC
* *
58869045 TTACATTAT
1 TTACATAAC
58869054 TTACATAAC
1 TTACATAAC
*
58869063 TGACATAA
1 TTACATAA
58869071 ATAAATGTCA
Statistics
Matches: 144, Mismatches: 35, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
7 7 0.05
8 11 0.08
9 116 0.81
10 9 0.06
11 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (9 bp):
TTACATAAC
Found at i:58868975 original size:70 final size:70
Alignment explanation
Indices: 58868876--58869035 Score: 214
Period size: 70 Copynumber: 2.3 Consensus size: 70
58868866 TTCTTTAAAA
* * *
58868876 TTACATAACTTACATACCTTACATAAATATATATCATATCATAACT-TACATACCTCACATAACA
1 TTACATAACTTACATA--ATACATAAATATATATCATATCATAAATGT-CATAACTCACATAACA
*
58868940 TACCTAAC
63 TACATAAC
* * *
58868948 TTACGTAACTTACATAATACATAAATATATATCATATCATAAATGTCATAACTTACATAACTTAC
1 TTACATAACTTACATAATACATAAATATATATCATATCATAAATGTCATAACTCACATAACATAC
*
58869013 ATAAT
66 ATAAC
58869018 TTACATAACTTACATAAT
1 TTACATAACTTACATAAT
58869036 TTTCATAACT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
70 62 0.79
71 1 0.01
72 15 0.19
ACGTcount: A:0.44, C:0.20, G:0.01, T:0.34
Consensus pattern (70 bp):
TTACATAACTTACATAATACATAAATATATATCATATCATAAATGTCATAACTCACATAACATAC
ATAAC
Found at i:58870776 original size:12 final size:12
Alignment explanation
Indices: 58870759--58870794 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
58870749 AAGATCGATG
*
58870759 GATGAATCTGAT
1 GATGAATCTAAT
58870771 GATGAATCTAAT
1 GATGAATCTAAT
58870783 GATGAATCTAAT
1 GATGAATCTAAT
58870795 AAAGAGGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.33
Consensus pattern (12 bp):
GATGAATCTAAT
Found at i:58871549 original size:21 final size:20
Alignment explanation
Indices: 58871525--58871563 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
58871515 AATGCACGTG
*
58871525 ATATTAAACATGATAATAATA
1 ATATTAAACACGA-AATAATA
58871546 ATATTAAACACGAAATAA
1 ATATTAAACACGAAATAA
58871564 AATCATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (20 bp):
ATATTAAACACGAAATAATA
Found at i:58871751 original size:14 final size:12
Alignment explanation
Indices: 58871724--58871795 Score: 65
Period size: 14 Copynumber: 5.7 Consensus size: 12
58871714 ATATGTACAT
58871724 AATATATATAAA
1 AATATATATAAA
58871736 AATATAGTATTAAA
1 AATATA-TA-TAAA
* *
58871750 AATATATA-CAT
1 AATATATATAAA
*
58871761 AATATAAAGTTAAA
1 AATATATA--TAAA
58871775 AATAATATATAAA
1 AAT-ATATATAAA
58871788 AATATATA
1 AATATATA
58871796 CATAATATCT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
11 8 0.17
12 11 0.23
13 11 0.23
14 14 0.29
15 4 0.08
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (12 bp):
AATATATATAAA
Found at i:58871794 original size:38 final size:37
Alignment explanation
Indices: 58871702--58871803 Score: 127
Period size: 37 Copynumber: 2.7 Consensus size: 37
58871692 AGGTGCATTA
* * * *
58871702 ATAGAATTGAAAATATGTACATAATATATATAAAAAT
1 ATAGTATTAAAAATATATACATAATATAAATAAAAAT
58871739 ATAGTATTAAAAATATATACATAATATAAAGTTAAAAAT
1 ATAGTATTAAAAATATATACATAATATAAA--TAAAAAT
58871778 A-A-TATATAAAAATATATACATAATAT
1 ATAGTAT-TAAAAATATATACATAATAT
58871804 CTATTAAAAG
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
37 29 0.50
38 21 0.36
39 8 0.14
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (37 bp):
ATAGTATTAAAAATATATACATAATATAAATAAAAAT
Found at i:58871964 original size:3 final size:3
Alignment explanation
Indices: 58871943--58872106 Score: 56
Period size: 3 Copynumber: 54.7 Consensus size: 3
58871933 AACTAATACC
* * *
58871943 AAT AAT AGT AAA AACT AAT AAT -AT AAT -AT AAT -AT AA- AAT AAA
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
58871985 AAT AA- AGA- AAT AAT AGT AAT AAT -AT GAAG ATT AAT AAT AGT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
* * * * * *
58872029 AGT AAC AAT AAT GAT AAT ATAT ATGT ACAT GAAT AGT ACT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT A-AT A-AT -AAT AAT AAT AAT AAT AAT
* **
58872078 AAT ACT AA- AAT AATT AAT TTT AAT AAT AA
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AA
58872107 AGTAATTAAA
Statistics
Matches: 116, Mismatches: 32, Indels: 26
0.67 0.18 0.15
Matches are distributed among these distances:
2 14 0.12
3 86 0.74
4 15 0.13
5 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:58872008 original size:26 final size:24
Alignment explanation
Indices: 58871943--58872008 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 24
58871933 AACTAATACC
* *
58871943 AATAATAGTAAAAACTAATAATATAA
1 AATAATAGT-AAAA-TAAAAATAAAA
*
58871969 TATAATA-TAAAATAAAAATAAAGA
1 AATAATAGTAAAATAAAAATAAA-A
58871993 AATAATAGTAATAATA
1 AATAATAGTAA-AATA
58872009 TGAAGATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 8 0.24
24 11 0.33
25 4 0.12
26 10 0.30
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (24 bp):
AATAATAGTAAAATAAAAATAAAA
Found at i:58873021 original size:21 final size:22
Alignment explanation
Indices: 58872982--58873022 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
58872972 TAGGTATTGA
* *
58872982 GTTATGGGTTTAAGTGTAATGG
1 GTTACGGGTTTAAGGGTAATGG
58873004 GTTACGGG-TTAAGGGTAAT
1 GTTACGGGTTTAAGGGTAAT
58873023 TAGTTTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.02, G:0.37, T:0.37
Consensus pattern (22 bp):
GTTACGGGTTTAAGGGTAATGG
Found at i:58877198 original size:43 final size:43
Alignment explanation
Indices: 58877127--58877296 Score: 205
Period size: 43 Copynumber: 4.0 Consensus size: 43
58877117 TGCCAAAGTT
* * * *
58877127 AGCGACGTTTGTGGTAAAAGCGCCGCTAAAGATCATGTTCTTC
1 AGCGGCGTTTGCGATAAAAGCGCCGCTAAAGGTCATGTTCTTC
* * *
58877170 AACGGCGTTTGCAATAAAAGCGCTGCTAAAGGTCATGTTCTTC
1 AGCGGCGTTTGCGATAAAAGCGCCGCTAAAGGTCATGTTCTTC
* * * *
58877213 AGCGGCGTTTGCGATAAAAGTGCCGTTAAAGGTCATGTTATTT
1 AGCGGCGTTTGCGATAAAAGCGCCGCTAAAGGTCATGTTCTTC
* * * *
58877256 AGCGGCGTTTGTGATAAAAGTGCCGCTAAAAGTTATGTTCT
1 AGCGGCGTTTGCGATAAAAGCGCCGCTAAAGGTCATGTTCT
58877297 AATAGTTTTT
Statistics
Matches: 108, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 108 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
AGCGGCGTTTGCGATAAAAGCGCCGCTAAAGGTCATGTTCTTC
Found at i:58878151 original size:24 final size:22
Alignment explanation
Indices: 58878124--58878173 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
58878114 AATTCTTTTA
58878124 TTTTCCTTTTTTACATTATTTC-TC
1 TTTTCC-TTTTT-CATT-TTTCTTC
*
58878148 TTTTTCTTTTTCATTTTTCTTC
1 TTTTCCTTTTTCATTTTTCTTC
58878170 TTTT
1 TTTT
58878174 ATATTATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 4 0.17
22 10 0.42
23 5 0.21
24 5 0.21
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTCCTTTTTCATTTTTCTTC
Found at i:58878157 original size:22 final size:22
Alignment explanation
Indices: 58878132--58878173 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
58878122 TATTTTCCTT
58878132 TTTTACATTATTTC-TCTTTTTC
1 TTTTACATT-TTTCTTCTTTTTC
*
58878154 TTTTTCATTTTTCTTCTTTT
1 TTTTACATTTTTCTTCTTTT
58878174 ATATTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTACATTTTTCTTCTTTTTC
Found at i:58878972 original size:31 final size:30
Alignment explanation
Indices: 58878900--58878957 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
58878890 ATATTTTATA
*
58878900 TATCATTATATTAATAATTTAAATATCATT
1 TATCATTATATTAAAAATTTAAATATCATT
58878930 TATCATTATATTAAAAATTTAAA-ATCAT
1 TATCATTATATTAAAAATTTAAATATCAT
58878958 ATTTTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (30 bp):
TATCATTATATTAAAAATTTAAATATCATT
Found at i:58883244 original size:15 final size:15
Alignment explanation
Indices: 58883195--58883245 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
58883185 TACCCATATC
58883195 TTTGACTTTCCAATA
1 TTTGACTTTCCAATA
** *
58883210 TTTTGA-TACCCATATC
1 -TTTGACTTTCCA-ATA
58883226 TTTGACTTTCCAATA
1 TTTGACTTTCCAATA
58883241 TTTGA
1 TTTGA
58883246 TACCCATATC
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (15 bp):
TTTGACTTTCCAATA
Found at i:58883247 original size:30 final size:30
Alignment explanation
Indices: 58883183--58883297 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
58883173 CCAAAATCTC
58883183 GATACCCATATCTTTGACTTTCCAATATTTT
1 GATACCCATATCTTTGACTTTCCAATA-TTT
58883214 GATACCCATATCTTTGACTTTCCAATATTT
1 GATACCCATATCTTTGACTTTCCAATATTT
* *
58883244 GATACCCATATCTTTGACTTTCTATTATTT
1 GATACCCATATCTTTGACTTTCCAATATTT
*
58883274 GATACCCATATCTTTGATTTTCCA
1 GATACCCATATCTTTGACTTTCCA
58883298 TAAATATGGA
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 53 0.66
31 27 0.34
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (30 bp):
GATACCCATATCTTTGACTTTCCAATATTT
Found at i:58887907 original size:16 final size:17
Alignment explanation
Indices: 58887883--58887934 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
58887873 CTCGATACCC
58887883 ATATATTTGACTTTCCA
1 ATATATTTGACTTTCCA
* *
58887900 ATAT-TTTGA--TACCC
1 ATATATTTGACTTTCCA
*
58887914 ATATCTTTGACTTTCCA
1 ATATATTTGACTTTCCA
58887931 ATAT
1 ATAT
58887935 TTGATACCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 7 0.25
15 5 0.18
16 5 0.18
17 11 0.39
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (17 bp):
ATATATTTGACTTTCCA
Found at i:58887940 original size:30 final size:30
Alignment explanation
Indices: 58887867--58887990 Score: 167
Period size: 30 Copynumber: 4.1 Consensus size: 30
58887857 TTTATTATGT
* *
58887867 CAATATCTCGATACCCATATATTTGACTTTC
1 CAATAT-TTGATACCCATATCTTTGACTTTC
58887898 CAATATTTTGATACCCATATCTTTGACTTTC
1 CAATA-TTTGATACCCATATCTTTGACTTTC
* *
58887929 CAATATTTGATACCCATATCTTTGATTTTT
1 CAATATTTGATACCCATATCTTTGACTTTC
* * *
58887959 TATTATTTGATACCCATATCTTTGATTTTC
1 CAATATTTGATACCCATATCTTTGACTTTC
58887989 CA
1 CA
58887991 TAAATATGGA
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
30 51 0.61
31 32 0.38
32 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (30 bp):
CAATATTTGATACCCATATCTTTGACTTTC
Found at i:58887952 original size:15 final size:15
Alignment explanation
Indices: 58887876--58887954 Score: 63
Period size: 15 Copynumber: 5.2 Consensus size: 15
58887866 TCAATATCTC
58887876 GATACCCATATATTT
1 GATACCCATATATTT
**
58887891 GACTTTCCA-ATATTTT
1 GA-TACCCATATA-TTT
*
58887907 GATACCCATATCTTT
1 GATACCCATATATTT
**
58887922 GACTTTCCA-ATATTT
1 GA-TACCCATATATTT
*
58887937 GATACCCATATCTTT
1 GATACCCATATATTT
58887952 GAT
1 GAT
58887955 TTTTTATTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
14 4 0.08
15 29 0.60
16 15 0.31
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.43
Consensus pattern (15 bp):
GATACCCATATATTT
Found at i:58888051 original size:16 final size:18
Alignment explanation
Indices: 58888026--58888066 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
58888016 TTTTAAAAAC
*
58888026 ATTTTGTAA-TTA-TATT
1 ATTTTTTAATTTATTATT
58888042 ATTTTTTAATTTATTATT
1 ATTTTTTAATTTATTATT
58888060 ATTTTTT
1 ATTTTTT
58888067 TGAAAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 3 0.14
18 11 0.50
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTTTAATTTATTATT
Found at i:58889251 original size:18 final size:18
Alignment explanation
Indices: 58889225--58889268 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
58889215 AATAGAAGTG
*
58889225 ATAAGTATACATTTAAA-A
1 ATAATTATA-ATTTAAATA
*
58889243 ATAATTATAATTTAAATT
1 ATAATTATAATTTAAATA
58889261 ATAATTAT
1 ATAATTAT
58889269 TAGTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
ATAATTATAATTTAAATA
Found at i:58891064 original size:44 final size:45
Alignment explanation
Indices: 58891003--58891091 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 45
58890993 ACATGAATTT
*
58891003 TCCTGTCTCCAATGCCATA-TATAATATGGACTTACATGGCTCAA
1 TCCTGTCTCCAAAGCCATATTATAATATGGACTTACATGGCTCAA
*
58891047 TCCTGTCTCCAAAGCCATATTTCTAATATGGACTTACATGGCTCA
1 TCCTGTCTCCAAAGCCATA-TTATAATATGGACTTACATGGCTCA
58891092 TTTCTGTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 18 0.44
46 23 0.56
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (45 bp):
TCCTGTCTCCAAAGCCATATTATAATATGGACTTACATGGCTCAA
Found at i:58898469 original size:46 final size:44
Alignment explanation
Indices: 58898365--58898472 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
58898355 TGTCTTTGAC
** * * *
58898365 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
58898409 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
58898455 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
58898473 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:58900476 original size:47 final size:47
Alignment explanation
Indices: 58900401--58900561 Score: 187
Period size: 47 Copynumber: 3.4 Consensus size: 47
58900391 CTGCTTGTGT
* * * * * *
58900401 TTGTGGATGAACCACTAGTTGAGCAGATGACTGCCAACTGAAATACA
1 TTGTGGATAAACCACTGGTCGAGCAGATGACTACCGACTAAAATACA
* * * **
58900448 TTGTGGATAAATCACTGGTCGAGTAGATGACTACTGACTAAAATATG
1 TTGTGGATAAACCACTGGTCGAGCAGATGACTACCGACTAAAATACA
* * * *
58900495 CTGTAGATAAACTACTGGTCGAGCAGATGTCTACCGACTAAAATACA
1 TTGTGGATAAACCACTGGTCGAGCAGATGACTACCGACTAAAATACA
58900542 TTGTGGATAAACCACTGGTC
1 TTGTGGATAAACCACTGGTC
58900562 AAGAAGATAA
Statistics
Matches: 91, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
47 91 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (47 bp):
TTGTGGATAAACCACTGGTCGAGCAGATGACTACCGACTAAAATACA
Found at i:58913450 original size:24 final size:24
Alignment explanation
Indices: 58913406--58913453 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
58913396 ACACATAAAT
*
58913406 AAATAAAATATAATAATAATACTA
1 AAATAAAATATAATAAAAATACTA
*
58913430 AAATAAAGTA-AATAAAAAATACTA
1 AAATAAAATATAAT-AAAAATACTA
58913454 TATATAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (24 bp):
AAATAAAATATAATAAAAATACTA
Found at i:58913949 original size:13 final size:13
Alignment explanation
Indices: 58913933--58914003 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
58913923 AATATTAGCA
58913933 AATATATGTACAT
1 AATATATGTACAT
* *
58913946 AATATATATATA-
1 AATATATGTACAT
* *
58913958 AAAATATATACAT
1 AATATATGTACAT
* *
58913971 AATATA-GTATTAA
1 AATATATGTA-CAT
58913984 AATATATGTACAT
1 AATATATGTACAT
58913997 AATATAT
1 AATATAT
58914004 ACTTATTAGA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
12 12 0.27
13 30 0.67
14 3 0.07
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (13 bp):
AATATATGTACAT
Found at i:58913997 original size:26 final size:26
Alignment explanation
Indices: 58913932--58914004 Score: 114
Period size: 25 Copynumber: 2.8 Consensus size: 26
58913922 TAATATTAGC
58913932 AAATATATGTACATAATATATATATA
1 AAATATATGTACATAATATATATATA
*
58913958 AAA-ATATATACATAATATAGTAT-TA
1 AAATATATGTACATAATATA-TATATA
58913983 AAATATATGTACATAATATATA
1 AAATATATGTACATAATATATA
58914005 CTTATTAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
25 22 0.51
26 21 0.49
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (26 bp):
AAATATATGTACATAATATATATATA
Found at i:58914598 original size:11 final size:11
Alignment explanation
Indices: 58914584--58914617 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
58914574 AAGAAAAAAA
58914584 GAAGAGAGAAG
1 GAAGAGAGAAG
58914595 GAAGAGAGAAG
1 GAAGAGAGAAG
*
58914606 GGAGAGAGAAG
1 GAAGAGAGAAG
58914617 G
1 G
58914618 GTGGGGAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAAG
Found at i:58915052 original size:26 final size:26
Alignment explanation
Indices: 58915023--58915131 Score: 182
Period size: 26 Copynumber: 4.2 Consensus size: 26
58915013 TGGTACAAAT
58915023 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
58915049 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
58915075 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
58915101 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
58915127 TGATA
1 TGATA
58915132 GGCATTTCAT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:58917232 original size:137 final size:137
Alignment explanation
Indices: 58916916--58917475 Score: 1023
Period size: 137 Copynumber: 4.1 Consensus size: 137
58916906 GAGTAGTCTC
58916916 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
58916981 TGTTATCTGAATAAAGGGCTAA-GCCTAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
58917045 ACTGTTA
131 ACTGTTA
58917052 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
58917117 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
*
58917182 ACTTTTA
131 ACTGTTA
58917189 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
58917254 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
58917319 ACTGTTA
131 ACTGTTA
* * *
58917326 CCAAAATGGGCTTGCATATGTTTATTGATGTTGCATGTATTTTAAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
58917391 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
58917456 ACTGTTA
131 ACTGTTA
**
58917463 CCTGAATGGGCTT
1 CCCAAATGGGCTT
58917476 AGGCCCAATG
Statistics
Matches: 411, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
136 86 0.21
137 325 0.79
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:58919432 original size:18 final size:18
Alignment explanation
Indices: 58919405--58919439 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
58919395 ATAAAATTTT
58919405 ATAGGCCCAATATATTAG
1 ATAGGCCCAATATATTAG
*
58919423 ATAGGTCCAATATATTA
1 ATAGGCCCAATATATTA
58919440 CGTAAGCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (18 bp):
ATAGGCCCAATATATTAG
Found at i:58919450 original size:18 final size:18
Alignment explanation
Indices: 58919409--58919455 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
58919399 AATTTTATAG
*
58919409 GCCCAATATATTAGATAG
1 GCCCAATATATTAGATAA
*
58919427 GTCCAATATATTACG-TAA
1 GCCCAATATATTA-GATAA
*
58919445 GCCCAAAATAT
1 GCCCAATATAT
58919456 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (18 bp):
GCCCAATATATTAGATAA
Found at i:58933426 original size:12 final size:12
Alignment explanation
Indices: 58933409--58933434 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58933399 TTTTTATATA
58933409 TTATTTAGAATT
1 TTATTTAGAATT
58933421 TTATTTAGAATT
1 TTATTTAGAATT
58933433 TT
1 TT
58933435 TAAATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (12 bp):
TTATTTAGAATT
Found at i:58933446 original size:19 final size:22
Alignment explanation
Indices: 58933391--58933446 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
58933381 AATTTAAAAA
*
58933391 ATTT-GAA-TTTTTTATATATT
1 ATTTAGAATTTTTTTAGATATT
58933411 ATTTAGAATTTTATTTAGA-ATT
1 ATTTAGAATTTT-TTTAGATATT
58933433 -TTTA-AATTTTTTTA
1 ATTTAGAATTTTTTTA
58933447 AAAAATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.12
20 10 0.31
21 7 0.22
22 6 0.19
23 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (22 bp):
ATTTAGAATTTTTTTAGATATT
Found at i:58933499 original size:12 final size:12
Alignment explanation
Indices: 58933484--58933512 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
58933474 AATATTTTGA
58933484 ATTTTAAAAATT
1 ATTTTAAAAATT
58933496 ATTTTAAAAATT
1 ATTTTAAAAATT
58933508 ATTTT
1 ATTTT
58933513 GATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTTAAAAATT
Found at i:58935856 original size:21 final size:21
Alignment explanation
Indices: 58935830--58935869 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
58935820 CACCTGCAAC
*
58935830 AAAAAGTATCAATACTTTTTG
1 AAAAAGTATCAATAATTTTTG
*
58935851 AAAAAGTATCGATAATTTT
1 AAAAAGTATCAATAATTTT
58935870 ATCATTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (21 bp):
AAAAAGTATCAATAATTTTTG
Found at i:58938101 original size:25 final size:23
Alignment explanation
Indices: 58938049--58938103 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
58938039 TATAAATAGT
58938049 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
58938072 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
58938097 AATAGTG
1 AATAGTG
58938104 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:58938260 original size:77 final size:81
Alignment explanation
Indices: 58938129--58938315 Score: 195
Period size: 77 Copynumber: 2.3 Consensus size: 81
58938119 ATGTTAAGAT
* * * * * *
58938129 ATATATAATATATACATATGTATAAAATAGATATAAAAAAATATGTACATAATATAGTGTAAAAA
1 ATATAAAATATATACATAAGTATAAAATAGATAGAAAAAAATATATAAATAATATAGTATAAAAA
*
58938194 ATACATACATAATATA
66 ATACATACATAAAATA
* * * *
58938210 AT-TAAAATATATACATAAG-ATAACAT-G-TAGAAAAGAATATATAAATAATATAGTATTAAAG
1 ATATAAAATATATACATAAGTATAAAATAGATAGAAAAAAATATATAAATAATATAGTATAAAAA
*
58938271 ATATATACATAAAATA
66 ATACATACATAAAATA
* *
58938287 GTATAATATATATATACGTAA-TATAAAAT
1 ATATAA-A-ATATATACATAAGTATAAAAT
58938316 TTAGAATATA
Statistics
Matches: 87, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
77 42 0.48
78 4 0.05
79 7 0.08
80 32 0.37
81 2 0.02
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (81 bp):
ATATAAAATATATACATAAGTATAAAATAGATAGAAAAAAATATATAAATAATATAGTATAAAAA
ATACATACATAAAATA
Found at i:58938274 original size:25 final size:25
Alignment explanation
Indices: 58938169--58938377 Score: 107
Period size: 25 Copynumber: 8.6 Consensus size: 25
58938159 ATATAAAAAA
* * * * *
58938169 ATATGTACATAATATAGTGTAAAAA
1 ATATATACATAATATAATATTAAAG
*
58938194 ATACATACATAATAT-A-ATTAAA-
1 ATATATACATAATATAATATTAAAG
* *
58938216 ATATATACATAAGATAACATGTAGAAAAG
1 ATATATACATAATATAATAT-T---AAAG
* *
58938245 AATATATAAATAATATAGTATTAAAG
1 -ATATATACATAATATAATATTAAAG
* * *
58938271 ATATATACATAAAATAGTA-TAATAT
1 ATATATACATAATATAATATTAA-AG
* * *
58938296 ATATATACGTAATATAAAATT-TAG
1 ATATATACATAATATAATATTAAAG
* *
58938320 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATACATAATATAATATTAAAG
*
58938342 A-ATATATATAATATAATATT-AAG
1 ATATATACATAATATAATATTAAAG
*
58938365 AAATATA-ATAATA
1 ATATATACATAATA
58938378 ACAAAAAAAA
Statistics
Matches: 143, Mismatches: 27, Indels: 30
0.71 0.14 0.15
Matches are distributed among these distances:
21 1 0.01
22 28 0.20
23 29 0.20
24 13 0.09
25 47 0.33
26 5 0.03
28 3 0.02
29 1 0.01
30 16 0.11
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (25 bp):
ATATATACATAATATAATATTAAAG
Found at i:58938370 original size:22 final size:22
Alignment explanation
Indices: 58938305--58938377 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
58938295 TATATATACG
* *
58938305 TAATATAAAATTTAG-AATATA
1 TAATATAATATTAAGAAATATA
* *
58938326 CCTAATATATTA-AAAGAATATATA
1 --TAATATAATATTAAGAA-ATATA
58938350 TAATATAATATTAAGAAATATAA
1 TAATATAATATTAAGAAATAT-A
58938373 TAATA
1 TAATA
58938378 ACAAAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
22 15 0.38
23 20 0.50
24 5 0.12
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (22 bp):
TAATATAATATTAAGAAATATA
Done.