Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013251.1 Kokia drynarioides strain JFW-HI SEQ_128271, 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: 539417
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 114 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:281097 original size:98 final size:98
Alignment explanation
Indices: 280948--281130 Score: 276
Period size: 98 Copynumber: 1.9 Consensus size: 98
280938 AGATGTGGAT
* * *
280948 GGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCCTAAAGATATGAAGGGAAAGATTGAAGCCA
1 GGAAAGGTTGAAGCCACAACGACAAACCTTATACCCTAAAGATATGAAGGGAAAGATTGAAGCCA
* *
281013 CAACGGTAAATTTTATACCCTAGAGATGCAGAG
66 CAAAGGTAAATCTTATACCCTAGAGATGCAGAG
* * * *
281046 GGAAAGGTTGAAGCCACAACGACAAACCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCG
1 GGAAAGGTTGAAGCCACAACGACAAACCTTATACCCTAAAGATATGAAGGGAAAGATTGAAGCCA
*
281111 CAAAGGTGAATCTTATACCC
66 CAAAGGTAAATCTTATACCC
281131 CGGAGATGAG
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
98 75 1.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.19
Consensus pattern (98 bp):
GGAAAGGTTGAAGCCACAACGACAAACCTTATACCCTAAAGATATGAAGGGAAAGATTGAAGCCA
CAAAGGTAAATCTTATACCCTAGAGATGCAGAG
Found at i:281138 original size:49 final size:49
Alignment explanation
Indices: 280921--281130 Score: 206
Period size: 49 Copynumber: 4.3 Consensus size: 49
280911 AAGGAAACAT
* * * * * *
280921 TGAATCCTATACTCTAAAGATGTGGATGGAAAGGTTGAAGCCGCAACGG
1 TGAATCTTATACCCTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGG
* * * * *
280970 CGAACCTTATACCCTAAAGATATGAAGGGAAAGATTGAAGCCACAACGG
1 TGAATCTTATACCCTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGG
* * * * * *
281019 TAAATTTTATACCCTAGAGATG-CAGAGGGAAAGGTTGAAGCCACAACGA
1 TGAATCTTATACCCTAGAGATGTGA-AGGGAAAGATTGAAGCCGCAACGG
** * * *
281068 CAAACCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAAAGG
1 TGAATCTTATACCCTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGG
281117 TGAATCTTATACCC
1 TGAATCTTATACCC
281131 CGGAGATGAG
Statistics
Matches: 128, Mismatches: 31, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
48 1 0.01
49 126 0.98
50 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.20
Consensus pattern (49 bp):
TGAATCTTATACCCTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGG
Found at i:281537 original size:114 final size:114
Alignment explanation
Indices: 281386--282256 Score: 1156
Period size: 114 Copynumber: 7.6 Consensus size: 114
281376 GGGTCGGATT
* *
281386 AAAACAACGAA-ACGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGGCTTCAAATC-C
1 AAAACAACGAAGCCGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATCTC
* *
281449 TATCTTCCTAGTAAGGTACAGAGAAGTGGGTCAAAACAGTATGTTGAATC
66 -ATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAAACAGTATGTTGAATC
* *
281499 AAAACAACGAAGCTGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATCCC
1 AAAACAACGAAGCCGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATCTC
* * * * *
281564 ATATTCCTTGTGAGGTACAGAGAAATGGGTCAAAATAGTATGCTGAATC
66 ATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAAACAGTATGTTGAATC
* * * * *
281613 AAAACAACGAACCCGAGCTCAACGTCCCTGAGAATACAGTGAAGTGGAGTGAGATTTCAAATCTC
1 AAAACAACGAAGCCGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATCTC
*
281678 ATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAAACAGTGTGTTGAATC
66 ATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAAACAGTATGTTGAATC
* * * * *
281727 AAAACAATGAATCCAAGCTCAACATCCTTGAGGATACAGTGGAGTGGAGTAAGACTTCAAATCTC
1 AAAACAACGAAGCCGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATCTC
* * *
281792 ATCTTCCTGGTGAGGTATAGAGAAGTGGGTCAAAATAGTGTGTTGAATC
66 ATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAAACAGTATGTTGAATC
* * * * * * * *
281841 AAAAAAACGAAGTCGAGCTCAATGTCTTTGAGGATATAGTAGAGTGGAGTAAGACTTCAAATCCC
1 AAAACAACGAAGCCGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATCTC
* * *
281906 ATCTTCCTGGTGAGGTATAGAGAAGTAGATCAAAACAGTATGTTGAATC
66 ATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAAACAGTATGTTGAATC
281955 AAAACAACGAAGCCGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATCTC
1 AAAACAACGAAGCCGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATCTC
* * *
282020 ATCTTCCTGGTGAAGTACAGAGAAGTGGGTCAGAACAGTGTGTTGAATC
66 ATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAAACAGTATGTTGAATC
* * * * * * *
282069 AAAATAACGAAGCCAAGCACAATGTCCCTGAGGATACAGTAGAGTGGGGTGAGACTTCAAATCTC
1 AAAACAACGAAGCCGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATCTC
* * *
282134 ATCTTCCTGGTGAGGTACAGTGAAGTGGGTCAAAAC-GATAGGTT-ATATT
66 ATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAAACAG-TATGTTGA-ATC
* ** * * * * * * *
282183 AAAACAACGAAACAAAGCTCAACGTCCCTAAGGTTATAGTGAAGTGGAGTGAGACATCAAATCCC
1 AAAACAACGAAGCCGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATCTC
282248 ATCTTCCTG
66 ATCTTCCTG
282257 TTACACGACA
Statistics
Matches: 666, Mismatches: 88, Indels: 7
0.88 0.12 0.01
Matches are distributed among these distances:
113 13 0.02
114 652 0.98
115 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (114 bp):
AAAACAACGAAGCCGAGCTCAACGTCCTTGAGGATACAGTGGAGTGGAGTGAGACTTCAAATCTC
ATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAAACAGTATGTTGAATC
Found at i:283425 original size:18 final size:18
Alignment explanation
Indices: 283402--283488 Score: 83
Period size: 17 Copynumber: 5.1 Consensus size: 18
283392 CCAATTTTAA
* *
283402 ATTTTAAATTTTTATTTT
1 ATTTTAAATTTTAAATTT
*
283420 ATTTT-AAGTTTAAATTT
1 ATTTTAAATTTTAAATTT
*
283437 ATTTTAAA-TTTAAACTT
1 ATTTTAAATTTTAAATTT
* *
283454 ATTTT-GAGTTTAAATTT
1 ATTTTAAATTTTAAATTT
*
283471 ATTTTGAA-TTTAAATTT
1 ATTTTAAATTTTAAATTT
283488 A
1 A
283489 AAATTTAATT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
16 1 0.02
17 50 0.85
18 8 0.14
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.60
Consensus pattern (18 bp):
ATTTTAAATTTTAAATTT
Found at i:283431 original size:6 final size:6
Alignment explanation
Indices: 283397--283496 Score: 53
Period size: 6 Copynumber: 16.8 Consensus size: 6
283387 TGGACCCAAT
** * * * *
283397 TTTAAA TTTTAAA TTTTTA TTTTAT TTTAAG TTTAAA TTT-AT TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * *
283445 TTTAAA CTT-AT TTTGAG TTTAAA TTT-AT TTTGAA TTTAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
283492 TTTAA
1 TTTAA
283497 TTAAAAGTCC
Statistics
Matches: 71, Mismatches: 18, Indels: 9
0.72 0.18 0.09
Matches are distributed among these distances:
5 11 0.15
6 48 0.68
7 12 0.17
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:283439 original size:17 final size:17
Alignment explanation
Indices: 283417--283488 Score: 101
Period size: 17 Copynumber: 4.2 Consensus size: 17
283407 AAATTTTTAT
283417 TTTATTTTAAGTTTAAA
1 TTTATTTTAAGTTTAAA
*
283434 TTTATTTTAAATTTAAA
1 TTTATTTTAAGTTTAAA
* *
283451 CTTATTTTGAGTTTAAA
1 TTTATTTTAAGTTTAAA
283468 TTTATTTTGAA-TTTAAA
1 TTTATTTT-AAGTTTAAA
283485 TTTA
1 TTTA
283489 AAATTTAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
17 47 0.98
18 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTATTTTAAGTTTAAA
Found at i:283464 original size:34 final size:34
Alignment explanation
Indices: 283418--283484 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
283408 AATTTTTATT
283418 TTATTTTAAGTTTAAATTTATTTTAAATTTAAAC
1 TTATTTTAAGTTTAAATTTATTTTAAATTTAAAC
* *
283452 TTATTTTGAGTTTAAATTTATTTTGAATTTAAA
1 TTATTTTAAGTTTAAATTTATTTTAAATTTAAA
283485 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (34 bp):
TTATTTTAAGTTTAAATTTATTTTAAATTTAAAC
Found at i:285264 original size:28 final size:29
Alignment explanation
Indices: 285221--285336 Score: 96
Period size: 28 Copynumber: 4.0 Consensus size: 29
285211 CCTCGAACTG
*
285221 TCCAGAAATCACATTTTGACCTCCAAACTTT
1 TCCA-AAA-CACATTTTGACCTCTAAACTTT
*
285252 TCCAAAA-GCATTTTGACACT-TAAACTTT
1 TCCAAAACACATTTTGAC-CTCTAAACTTT
*
285280 TCTAAAATCACATTTTGACC-CTAAAC-TT
1 TCCAAAA-CACATTTTGACCTCTAAACTTT
* * * *
285308 TCAAAAATTACATTTTTACCCCTAAACTT
1 TCCAAAA-CACATTTTGACCTCTAAACTT
285337 CAAAAAATTA
Statistics
Matches: 72, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
28 41 0.57
29 14 0.19
30 13 0.18
31 4 0.06
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
TCCAAAACACATTTTGACCTCTAAACTTT
Found at i:285324 original size:29 final size:28
Alignment explanation
Indices: 285272--285624 Score: 287
Period size: 29 Copynumber: 12.0 Consensus size: 28
285262 TTTTGACACT
* * *
285272 TAAACTTTTCTAAAATCACATTTTGACCC
1 TAAAC-TTTCAAAAATTACATTTTTACCC
285301 TAAACTTTCAAAAATTACATTTTTACCCC
1 TAAACTTTCAAAAATTACATTTTTA-CCC
285330 TAAAC-TTCAAAAAATTACATTTTTACCC
1 TAAACTTTC-AAAAATTACATTTTTACCC
* * *
285358 TCAAACTTTCCAAAAATTATAATTTTGCCC
1 T-AAACTTT-CAAAAATTACATTTTTACCC
* * *
285388 TCGAACTTCCAAAAATCACATTTTTACCC
1 T-AAACTTTCAAAAATTACATTTTTACCC
* *
285417 TTAAATTTCTCAAAAATTACATTTTTGCCTC
1 -TAAACTT-TCAAAAATTACATTTTTACC-C
* * * * * *
285448 TGAACTTCCCAAAATCATATTTTTACCAT
1 TAAACTTTCAAAAATTACATTTTTACC-C
*
285477 TAAA-TTTCTTAAAAATTATATTTTTACCCC
1 TAAACTTTC--AAAAATTACATTTTTA-CCC
*
285507 TAAAACTTTCCAAAATTACATTTTTACCC
1 T-AAACTTTCAAAAATTACATTTTTACCC
* *
285536 TAAACTTTCCCAAAATGACATTTTTTACGCC
1 TAAACTTT-CAAAAATTACA-TTTTTAC-CC
* *
285567 TAAAACTTTCTAAAATTACATTTTAACCC
1 T-AAACTTTCAAAAATTACATTTTTACCC
* * *
285596 TAAACTCTCTAAAATTTCATTTTTGACCC
1 TAAACTTTCAAAAATTACATTTTT-ACCC
285625 CCTTTTTTCT
Statistics
Matches: 266, Mismatches: 40, Indels: 36
0.78 0.12 0.11
Matches are distributed among these distances:
28 54 0.20
29 92 0.35
30 90 0.34
31 19 0.07
32 11 0.04
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (28 bp):
TAAACTTTCAAAAATTACATTTTTACCC
Found at i:285402 original size:59 final size:59
Alignment explanation
Indices: 285283--285620 Score: 291
Period size: 59 Copynumber: 5.7 Consensus size: 59
285273 AAACTTTTCT
* * *
285283 AAAATCACATTTTGACCCTAAACTTT-CAAAAATTACATTTTTACCC-CTAAACTTCAA
1 AAAATCACATTTTTACCCTAAACTTTCCAAAAATTACATTTTTGCCCTCTAAACTTCCA
* * * *
285340 AAAATTACATTTTTACCCTCAAACTTTCCAAAAATTATAATTTTGCCCTC-GAACTTCCA
1 AAAATCACATTTTTACCCT-AAACTTTCCAAAAATTACATTTTTGCCCTCTAAACTTCCA
* *
285399 AAAATCACATTTTTACCCTTAAA-TTTCTCAAAAATTACATTTTTG-CCTCTGAACTTCCC
1 AAAATCACATTTTTACCC-TAAACTTTC-CAAAAATTACATTTTTGCCCTCTAAACTTCCA
* * * * *
285458 AAAATCATATTTTTACCATTAAA-TTTCTTAAAAATTATATTTTTACCC-CTAAAACTTTCC-
1 AAAATCACATTTTTACC-CTAAACTTTC-CAAAAATTACATTTTTGCCCTCT-AAAC-TTCCA
* * * * * * *
285518 AAAATTACATTTTTACCCTAAACTTTCCCAAAATGACATTTTTTACGCCT-AAAACTTTCT
1 AAAATCACATTTTTACCCTAAACTTTCCAAAAATTACA-TTTTTGC-CCTCTAAACTTCCA
* * * * *
285578 AAAATTACATTTTAACCCTAAACTCT-CTAAAATTTCATTTTTG
1 AAAATCACATTTTTACCCTAAACTTTCCAAAAATTACATTTTTG
285621 ACCCCCTTTT
Statistics
Matches: 234, Mismatches: 32, Indels: 29
0.79 0.11 0.10
Matches are distributed among these distances:
57 17 0.07
58 20 0.09
59 130 0.56
60 61 0.26
61 6 0.03
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.38
Consensus pattern (59 bp):
AAAATCACATTTTTACCCTAAACTTTCCAAAAATTACATTTTTGCCCTCTAAACTTCCA
Found at i:285734 original size:14 final size:14
Alignment explanation
Indices: 285702--285740 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
285692 TTCATGGTTC
285702 GTAT-TTTATTTTT
1 GTATATTTATTTTT
285715 GTTATATTTATTTTT
1 G-TATATTTATTTTT
285730 GTATATTTATT
1 GTATATTTATT
285741 CATTCGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 1 0.04
14 13 0.54
15 10 0.42
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (14 bp):
GTATATTTATTTTT
Found at i:293739 original size:26 final size:26
Alignment explanation
Indices: 293710--293760 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
293700 AAAATTTGTT
*
293710 CAGTTTTTAT-TTAAACATTTTAAATA
1 CAGTTTTTATATCAAA-ATTTTAAATA
293736 CAGTTTTTATATCAAAATTTTAAAT
1 CAGTTTTTATATCAAAATTTTAAAT
293761 GTATATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (26 bp):
CAGTTTTTATATCAAAATTTTAAATA
Found at i:294776 original size:21 final size:21
Alignment explanation
Indices: 294752--294797 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
294742 AAAATGTAAA
294752 TTTAAAATAT-TTTTAAGATTT
1 TTTAAAATATATTTT-AGATTT
*
294773 TTTAAAATATATTTTATATTT
1 TTTAAAATATATTTTAGATTT
294794 TTTA
1 TTTA
294798 GAATTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTAAAATATATTTTAGATTT
Found at i:295194 original size:21 final size:20
Alignment explanation
Indices: 295156--295204 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
295146 TACGTACGTT
*
295156 TTTTACTTGTTTTATTTACA
1 TTTTATTTGTTTTATTTACA
* *
295176 TTTTATTTGTATTTGTTTATA
1 TTTTATTTGT-TTTATTTACA
*
295197 ATTTATTT
1 TTTTATTT
295205 ACAACTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.69
Consensus pattern (20 bp):
TTTTATTTGTTTTATTTACA
Found at i:295251 original size:97 final size:94
Alignment explanation
Indices: 295135--295326 Score: 339
Period size: 97 Copynumber: 2.0 Consensus size: 94
295125 TATGTCTAAA
*
295135 TTTTCAAAAAATACGTACGTTTTTTACTTGTTTTATTTACATTTTATTTGTATTTGTTTATAATT
1 TTTTCAAAAAATACGTACGTTTTTTAATTGTTTTATTTACATTTTATTTGTATTTGTTTATAA-T
295200 TATTTACAACTTTTTATATTTTTAGGGTTTT
65 TATTTACAACTTTTTATATTTTTA-GGTTTT
*
295231 TTTTCCAAAAAATACTTACGTTTTTTAATTGTTTTATTTACATTTTATTTGTATTTGTTTATAAT
1 TTTT-CAAAAAATACGTACGTTTTTTAATTGTTTTATTTACATTTTATTTGTATTTGTTTATAAT
295296 TATTTACAACTTTTTATATTTTTAGGTTTT
65 TATTTACAACTTTTTATATTTTTAGGTTTT
295326 T
1 T
295327 AGTTGTGATT
Statistics
Matches: 93, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
95 7 0.08
96 29 0.31
97 57 0.61
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (94 bp):
TTTTCAAAAAATACGTACGTTTTTTAATTGTTTTATTTACATTTTATTTGTATTTGTTTATAATT
ATTTACAACTTTTTATATTTTTAGGTTTT
Found at i:297674 original size:38 final size:38
Alignment explanation
Indices: 297621--297695 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
297611 GTTTTTCAAG
* * *
297621 GTGAAACAAGCAGAAAAAGCATGCCCAACTTATGCATT
1 GTGAAACAAGAAGAAAAAGCATACCCAACTTAAGCATT
297659 GTGAAACAAGAAGAAAAAGCATACCCAACTTAAGCAT
1 GTGAAACAAGAAGAAAAAGCATACCCAACTTAAGCAT
297696 ACTTTGGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.16
Consensus pattern (38 bp):
GTGAAACAAGAAGAAAAAGCATACCCAACTTAAGCATT
Found at i:298826 original size:96 final size:96
Alignment explanation
Indices: 298662--298856 Score: 381
Period size: 96 Copynumber: 2.0 Consensus size: 96
298652 TATTTTATTA
*
298662 TCAAACTAGACAATTGTAACTTAACACTGTCAAAGCTTGAAATTAGGAAGAAATAGGGGAATCTT
1 TCAAACTAGACAATTGTAACTTAACACTGCCAAAGCTTGAAATTAGGAAGAAATAGGGGAATCTT
298727 AGTACCATAATCAGGTGGAGGTTCAATCAAG
66 AGTACCATAATCAGGTGGAGGTTCAATCAAG
298758 TCAAACTAGACAATTGTAACTTAACACTGCCAAAGCTTGAAATTAGGAAGAAATAGGGGAATCTT
1 TCAAACTAGACAATTGTAACTTAACACTGCCAAAGCTTGAAATTAGGAAGAAATAGGGGAATCTT
298823 AGTACCATAATCAGGTGGAGGTTCAATCAAG
66 AGTACCATAATCAGGTGGAGGTTCAATCAAG
298854 TCA
1 TCA
298857 TTGTCAGGGT
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (96 bp):
TCAAACTAGACAATTGTAACTTAACACTGCCAAAGCTTGAAATTAGGAAGAAATAGGGGAATCTT
AGTACCATAATCAGGTGGAGGTTCAATCAAG
Found at i:302412 original size:34 final size:35
Alignment explanation
Indices: 302366--302443 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 35
302356 CAATAAGTGA
*
302366 GCCCAGCT-CTAGTTGGATTAA-CCAACGATT-TTGC
1 GCCCAG-TGCTAGTTGGA-TAATCCAACGATTCTGGC
*
302400 GCCCAGTGCTAGTTGGATAATCCGACGATTCTGGC
1 GCCCAGTGCTAGTTGGATAATCCAACGATTCTGGC
*
302435 ACCCAGTGC
1 GCCCAGTGC
302444 CTAGCGGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 4 0.11
34 23 0.61
35 11 0.29
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (35 bp):
GCCCAGTGCTAGTTGGATAATCCAACGATTCTGGC
Found at i:305833 original size:16 final size:18
Alignment explanation
Indices: 305814--305857 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
305804 AATTGAAATA
305814 AATATTTT-T-AATATTT
1 AATATTTTATAAATATTT
*
305830 AATATTTTATAAATTTTT
1 AATATTTTATAAATATTT
*
305848 AATAATTTAT
1 AATATTTTAT
305858 TTAATTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 8 0.33
17 1 0.04
18 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AATATTTTATAAATATTT
Found at i:306168 original size:18 final size:18
Alignment explanation
Indices: 306145--306187 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
306135 AGAATAATTT
306145 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
306163 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
306181 TTAATTA
1 TTAATTA
306188 TACCTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:306412 original size:15 final size:14
Alignment explanation
Indices: 306362--306418 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 14
306352 AATTACTTTT
306362 AATATAAATAATTA
1 AATATAAATAATTA
* * *
306376 AAAAAATAATATTTCA
1 AATATA-AATAATT-A
306392 AATATAAATAATTA
1 AATATAAATAATTA
306406 AATTATAATATAA
1 AA-TATAA-ATAA
306419 AAAAAATAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 7 0.21
15 17 0.52
16 9 0.27
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
AATATAAATAATTA
Found at i:316642 original size:24 final size:21
Alignment explanation
Indices: 316610--316658 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 21
316600 AAATTCAATA
316610 CTATTTTCTCAATCCCTCTCTTCT
1 CTATTTTCTC--TCCCTCT-TTCT
*
316634 CTATTTTCTCTCTCTCTTTCT
1 CTATTTTCTCTCCCTCTTTCT
316655 CTAT
1 CTAT
316659 AACTCCTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 6 0.25
24 10 0.42
ACGTcount: A:0.10, C:0.35, G:0.00, T:0.55
Consensus pattern (21 bp):
CTATTTTCTCTCCCTCTTTCT
Found at i:319172 original size:28 final size:28
Alignment explanation
Indices: 319094--319178 Score: 80
Period size: 34 Copynumber: 2.8 Consensus size: 28
319084 AGCTTGCACC
*
319094 CATTTACACTCATTAGCTTATATATATG
1 CATTTACACTCATCAGCTTATATATATG
* *
319122 CGTTTACGCTTATGCTCGTCAGCTTATATATATG
1 CATTTA--C--A--CTCATCAGCTTATATATATG
*
319156 TATTTACACTCATCAGCTTATAT
1 CATTTACACTCATCAGCTTATAT
319179 GTGTATATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
28 19 0.42
30 2 0.04
32 2 0.04
34 22 0.49
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (28 bp):
CATTTACACTCATCAGCTTATATATATG
Found at i:320515 original size:24 final size:24
Alignment explanation
Indices: 320488--320542 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 24
320478 AAAATCAATT
320488 CATTTTATATTACATTTGCACTGA
1 CATTTTATATTACATTTGCACTGA
*
320512 CATTTTATATTACTTTTGCACTGA
1 CATTTTATATTACATTTGCACTGA
320536 CAATTTT
1 C-ATTTT
320543 TACTCTTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.49
Consensus pattern (24 bp):
CATTTTATATTACATTTGCACTGA
Found at i:330327 original size:34 final size:34
Alignment explanation
Indices: 330279--330345 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
330269 GATCCAAAAG
*
330279 AAAAAAAACAATA-TTCTACCATAACAATCGATTC
1 AAAAAAAACAATATTTC-AACATAACAATCGATTC
* *
330313 AAAAGAAACAATATTTCAATATAACAATCGATT
1 AAAAAAAACAATATTTCAACATAACAATCGATT
330346 TAAATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.25
Consensus pattern (34 bp):
AAAAAAAACAATATTTCAACATAACAATCGATTC
Found at i:330351 original size:18 final size:18
Alignment explanation
Indices: 330299--330353 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
330289 ATATTCTACC
*
330299 ATAACAATCGATTCAAA-
1 ATAACAATCGATTTAAAT
* *
330316 AGAAACAAT--ATTTCAAT
1 A-TAACAATCGATTTAAAT
330333 ATAACAATCGATTTAAAT
1 ATAACAATCGATTTAAAT
330351 ATA
1 ATA
330354 TAAACAATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
16 11 0.38
17 2 0.07
18 16 0.55
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (18 bp):
ATAACAATCGATTTAAAT
Found at i:331164 original size:19 final size:19
Alignment explanation
Indices: 331140--331185 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
331130 CAATTATTAA
* *
331140 TATAATTAGAGTTCGCGTG
1 TATAATTAGAGTTCACCTG
331159 TATAATTAGAGTTCACCTG
1 TATAATTAGAGTTCACCTG
331178 TATAATTA
1 TATAATTA
331186 AATACAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (19 bp):
TATAATTAGAGTTCACCTG
Found at i:337072 original size:27 final size:27
Alignment explanation
Indices: 337022--337074 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
337012 TGTCCACTTC
* * *
337022 TCCCAGATTGGTACCTAAAGTTTTTTG
1 TCCCAGATTGATACCCAAACTTTTTTG
*
337049 TCCCAGATTGATACCCGAACTTTTTT
1 TCCCAGATTGATACCCAAACTTTTTT
337075 TTGTCTACTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (27 bp):
TCCCAGATTGATACCCAAACTTTTTTG
Found at i:337411 original size:16 final size:16
Alignment explanation
Indices: 337390--337421 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
337380 CCTTTCATTT
*
337390 TCACCATTGTTTTCCC
1 TCACCATCGTTTTCCC
337406 TCACCATCGTTTTCCC
1 TCACCATCGTTTTCCC
337422 CTTTTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.41, G:0.06, T:0.41
Consensus pattern (16 bp):
TCACCATCGTTTTCCC
Found at i:337445 original size:73 final size:74
Alignment explanation
Indices: 337335--337486 Score: 218
Period size: 73 Copynumber: 2.1 Consensus size: 74
337325 TTCGTTTATG
* *
337335 CCATCGTGTTCCCATTTTTCTTCAAAGAAATTTTAACCC-ATTTTTCCTTTCATTTTCACCATTG
1 CCATCGTGTTCCCATTTTTCTTCAAAGAAATATTAACCCTATTTTTCCTTTCA-TTTCACCATCG
337399 TTTTCCCTCA
65 TTTTCCCTCA
* * * * *
337409 CCATCGTTTTCCCCTTTTT-TTCAAAGAAATATTAACCCTTTTTTTCTTTTGATTTCACCATCGT
1 CCATCGTGTTCCCATTTTTCTTCAAAGAAATATTAACCCTATTTTTCCTTTCATTTCACCATCGT
337473 TTTCCCTCA
66 TTTCCCTCA
337482 CCATC
1 CCATC
337487 ATTTATCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
73 43 0.61
74 27 0.39
ACGTcount: A:0.20, C:0.29, G:0.05, T:0.46
Consensus pattern (74 bp):
CCATCGTGTTCCCATTTTTCTTCAAAGAAATATTAACCCTATTTTTCCTTTCATTTCACCATCGT
TTTCCCTCA
Found at i:342827 original size:20 final size:20
Alignment explanation
Indices: 342794--342908 Score: 119
Period size: 20 Copynumber: 5.8 Consensus size: 20
342784 AATGAAGAAG
342794 TGCCCCTGTATGCACTTCGA
1 TGCCCCTGTATGCACTTCGA
* *
342814 TGCCCTTGTTTGCACTTC-A
1 TGCCCCTGTATGCACTTCGA
*
342833 GTGCCCTTGTATGCA-TTCGA
1 -TGCCCCTGTATGCACTTCGA
* *
342853 TGCCCCTGTTTGCACTTCGG
1 TGCCCCTGTATGCACTTCGA
* * *
342873 TGCCCCTGAAAGCACACTCG-
1 TGCCCCTGTATGCAC-TTCGA
342893 TGCCCCTGTATGCACT
1 TGCCCCTGTATGCACT
342909 CTGATTCCCC
Statistics
Matches: 78, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 16 0.21
20 59 0.76
21 3 0.04
ACGTcount: A:0.14, C:0.34, G:0.21, T:0.31
Consensus pattern (20 bp):
TGCCCCTGTATGCACTTCGA
Found at i:342863 original size:39 final size:40
Alignment explanation
Indices: 342792--342908 Score: 148
Period size: 39 Copynumber: 3.0 Consensus size: 40
342782 GAAATGAAGA
*
342792 AGTGCCCCTGTATGCACTTCGATGCCCTTGTTTGCACTTC
1 AGTGCCCCTGTATGCACTTCGATGCCCCTGTTTGCACTTC
*
342832 AGTGCCCTTGTATGCA-TTCGATGCCCCTGTTTGCACTTC
1 AGTGCCCCTGTATGCACTTCGATGCCCCTGTTTGCACTTC
* * * * *
342871 GGTGCCCCTGAAAGCACACTCG-TGCCCCTGTATGCACT
1 AGTGCCCCTGTATGCAC-TTCGATGCCCCTGTTTGCACT
342909 CTGATTCCCC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 34 0.51
40 30 0.45
41 3 0.04
ACGTcount: A:0.15, C:0.33, G:0.21, T:0.31
Consensus pattern (40 bp):
AGTGCCCCTGTATGCACTTCGATGCCCCTGTTTGCACTTC
Found at i:344896 original size:4 final size:4
Alignment explanation
Indices: 344882--344988 Score: 50
Period size: 4 Copynumber: 26.8 Consensus size: 4
344872 ATTACAGTAA
* *
344882 ACAT AACAT ACAT ACAA ATAT ACAT AACAGT A-A- ACAT AACAT ACAT
1 ACAT -ACAT ACAT ACAT ACAT ACAT -ACA-T ACAT ACAT -ACAT ACAT
* *
344928 A-AT A-AT A-A- ACAT AACAT ACAT A-AT -TAT ATAT ACAT AACAT ACAT
1 ACAT ACAT ACAT ACAT -ACAT ACAT ACAT ACAT ACAT ACAT -ACAT ACAT
344972 AACAAT ACAT ACAT ACA
1 -AC-AT ACAT ACAT ACA
344989 CAAACAGTAA
Statistics
Matches: 84, Mismatches: 5, Indels: 27
0.72 0.04 0.23
Matches are distributed among these distances:
2 2 0.02
3 13 0.15
4 42 0.50
5 24 0.29
6 3 0.04
ACGTcount: A:0.57, C:0.18, G:0.01, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:344908 original size:21 final size:21
Alignment explanation
Indices: 344882--344988 Score: 100
Period size: 21 Copynumber: 5.1 Consensus size: 21
344872 ATTACAGTAA
*
344882 ACATAACATACATACA-AATAT
1 ACATAACATA-ATACATAACAT
344903 ACATAACAGTAA-ACATAACAT
1 ACATAACA-TAATACATAACAT
*
344924 ACATAATAATAA-ACATAACAT
1 ACATAA-CATAATACATAACAT
*
344945 ACATAATTATATATACATAACAT
1 ACATAA-CATA-ATACATAACAT
344968 ACATAAC--AATACAT-ACAT
1 ACATAACATAATACATAACAT
344986 ACA
1 ACA
344989 CAAACAGTAA
Statistics
Matches: 77, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.09
19 6 0.08
20 4 0.05
21 41 0.53
22 4 0.05
23 15 0.19
ACGTcount: A:0.57, C:0.18, G:0.01, T:0.24
Consensus pattern (21 bp):
ACATAACATAATACATAACAT
Found at i:344917 original size:33 final size:33
Alignment explanation
Indices: 344875--344943 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
344865 TACAAATATT
*
344875 ACAGTAAACATAACATACATACA-AATATACATA
1 ACAGTAAACATAACATACATA-ATAATAAACATA
344908 ACAGTAAACATAACATACATAATAATAAACATA
1 ACAGTAAACATAACATACATAATAATAAACATA
344941 ACA
1 ACA
344944 TACATAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.59, C:0.17, G:0.03, T:0.20
Consensus pattern (33 bp):
ACAGTAAACATAACATACATAATAATAAACATA
Found at i:344944 original size:54 final size:53
Alignment explanation
Indices: 344879--344982 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 53
344869 AATATTACAG
344879 TAAACATAACATACATACA-A-ATATACATAACAGTAAACATAAC-ATACATAATAA
1 TAAACATAACATACATA-ATATATATACATAACA-T--ACATAACAATACATAATAA
344933 TAAACATAACATACATAATTATATATACATAACATACATAACAATACATA
1 TAAACATAACATACATAA-TATATATACATAACATACATAACAATACATA
344983 CATACACAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
53 8 0.17
54 24 0.52
55 2 0.04
56 12 0.26
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (53 bp):
TAAACATAACATACATAATATATATACATAACATACATAACAATACATAATAA
Found at i:345160 original size:30 final size:30
Alignment explanation
Indices: 345097--345160 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
345087 CAACAAAAAC
*
345097 AAAAAATAAAAGTTAGATATAATACAACTT
1 AAAAAATAAAAGTTAGATATAATACAACAT
* *
345127 AAAAAATAAAGGTTATATATAATACTAA-AT
1 AAAAAATAAAAGTTAGATATAATAC-AACAT
345157 AAAA
1 AAAA
345161 TAATCAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.27
Consensus pattern (30 bp):
AAAAAATAAAAGTTAGATATAATACAACAT
Found at i:345805 original size:31 final size:28
Alignment explanation
Indices: 345765--345823 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
345755 CGGCGTTAGG
*
345765 GTTTGGTACCAAACTAGTGGACGAAAAAAA
1 GTTTGGTACCAAACT-G-GGACAAAAAAAA
*
345795 GTTTGGGTACCAATCTGGGACAAAAAAAA
1 GTTT-GGTACCAAACTGGGACAAAAAAAA
345824 AAACTTTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 5 0.19
31 10 0.38
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (28 bp):
GTTTGGTACCAAACTGGGACAAAAAAAA
Found at i:364141 original size:62 final size:63
Alignment explanation
Indices: 364044--364170 Score: 229
Period size: 62 Copynumber: 2.0 Consensus size: 63
364034 TTGATGCGGC
*
364044 TTTCAATAAGCATAGAAACAAATCGTGCTCAGAAATTGTC-AGAGTTAAATAGTACGGTGCTA
1 TTTCAATAAGCATAGAAACAAATCGTGCTCAGAAATTGTCAAGAGTTAAACAGTACGGTGCTA
364106 TTTCAATAAGCATAGAAACAAATCGTGCTCAGAAATTGTCATAGAGTTAAACAGTACGGTGCTA
1 TTTCAATAAGCATAGAAACAAATCGTGCTCAGAAATTGTCA-AGAGTTAAACAGTACGGTGCTA
364170 T
1 T
364171 GTTAAAAAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 40 0.65
64 22 0.35
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (63 bp):
TTTCAATAAGCATAGAAACAAATCGTGCTCAGAAATTGTCAAGAGTTAAACAGTACGGTGCTA
Found at i:369403 original size:12 final size:12
Alignment explanation
Indices: 369392--369480 Score: 115
Period size: 12 Copynumber: 7.4 Consensus size: 12
369382 CTGAGATTGT
* *
369392 TGCTGTTGTTGT
1 TGCTGCTGTTGC
*
369404 TGATGCTGTTGC
1 TGCTGCTGTTGC
369416 TGCTGCTGTTGC
1 TGCTGCTGTTGC
*
369428 TGCTGCTGCTGC
1 TGCTGCTGTTGC
*
369440 TGCTGCTGCTGC
1 TGCTGCTGTTGC
*
369452 TGTTGCTGTTGC
1 TGCTGCTGTTGC
*
369464 TGCTGCTGCTGC
1 TGCTGCTGTTGC
369476 TGCTG
1 TGCTG
369481 TTGTCGGTGA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 68 1.00
ACGTcount: A:0.01, C:0.24, G:0.34, T:0.42
Consensus pattern (12 bp):
TGCTGCTGTTGC
Found at i:369419 original size:3 final size:3
Alignment explanation
Indices: 369407--369480 Score: 112
Period size: 3 Copynumber: 24.7 Consensus size: 3
369397 TTGTTGTTGA
* * *
369407 TGC TGT TGC TGC TGC TGT TGC TGC TGC TGC TGC TGC TGC TGC TGC TGT
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
*
369455 TGC TGT TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TG
369481 TTGTCGGTGA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.00, C:0.27, G:0.34, T:0.39
Consensus pattern (3 bp):
TGC
Found at i:377892 original size:10 final size:10
Alignment explanation
Indices: 377877--377906 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
377867 AGTGCAGAGA
377877 AAAACTAAAG
1 AAAACTAAAG
377887 AAAACTTAAAG
1 AAAAC-TAAAG
377898 AAAACTAAA
1 AAAACTAAA
377907 CCTAGAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.70, C:0.10, G:0.07, T:0.13
Consensus pattern (10 bp):
AAAACTAAAG
Found at i:382416 original size:28 final size:28
Alignment explanation
Indices: 382382--382489 Score: 126
Period size: 28 Copynumber: 3.9 Consensus size: 28
382372 TAGCAAATGT
*
382382 TCTGTATTCTGGCTAGTAAGAGCATAAC
1 TCTGTATTCTGGCTTGTAAGAGCATAAC
* * * *
382410 TTTGTATTTTGGCTTGTAAGAGCGTACC
1 TCTGTATTCTGGCTTGTAAGAGCATAAC
* * * *
382438 TCTGCATTTTGGCTCGTAAGAGCGTAAC
1 TCTGTATTCTGGCTTGTAAGAGCATAAC
*
382466 TCTGTACTCTGGCTTGTAAGAGCA
1 TCTGTATTCTGGCTTGTAAGAGCA
382490 ATATTCTTGA
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (28 bp):
TCTGTATTCTGGCTTGTAAGAGCATAAC
Found at i:382479 original size:56 final size:56
Alignment explanation
Indices: 382382--382488 Score: 151
Period size: 56 Copynumber: 1.9 Consensus size: 56
382372 TAGCAAATGT
* * * *
382382 TCTGTATTCTGGCTAGTAAGAGCATAACTTTGTATTTTGGCTTGTAAGAGCGTACC
1 TCTGCATTCTGGCTAGTAAGAGCATAACTCTGTACTCTGGCTTGTAAGAGCGTACC
* * *
382438 TCTGCATTTTGGCTCGTAAGAGCGTAACTCTGTACTCTGGCTTGTAAGAGC
1 TCTGCATTCTGGCTAGTAAGAGCATAACTCTGTACTCTGGCTTGTAAGAGC
382489 AATATTCTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 44 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (56 bp):
TCTGCATTCTGGCTAGTAAGAGCATAACTCTGTACTCTGGCTTGTAAGAGCGTACC
Found at i:382509 original size:56 final size:56
Alignment explanation
Indices: 382397--382518 Score: 140
Period size: 56 Copynumber: 2.2 Consensus size: 56
382387 ATTCTGGCTA
* * * * * *
382397 GTAAGAGCATAACTTTGTATTTTGGCTTGTAAGAGCGTACCTCTGCATTTTGGCTC
1 GTAAGAGCGTAACTCTGTACTCTGGCTTGTAAGAGCATACCTCTGCATTTTAGCTC
*
382453 GTAAGAGCGTAACTCTGTACTCTGGCTTGTAAGAGCAATA-TTCTTG-ATTTTAGCTC
1 GTAAGAGCGTAACTCTGTACTCTGGCTTGTAAGAGC-ATACCTC-TGCATTTTAGCTC
*
382509 GAAAGAGCGT
1 GTAAGAGCGT
382519 TATTCTGTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
56 52 0.93
57 4 0.07
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (56 bp):
GTAAGAGCGTAACTCTGTACTCTGGCTTGTAAGAGCATACCTCTGCATTTTAGCTC
Found at i:382543 original size:27 final size:27
Alignment explanation
Indices: 382505--382567 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
382495 CTTGATTTTA
382505 GCTCGAAAGAGCGTTATTCTGTTTATG
1 GCTCGAAAGAGCGTTATTCTGTTTATG
382532 GCTCGAAAGAGCGTTATTCTGTTTATG
1 GCTCGAAAGAGCGTTATTCTGTTTATG
382559 GCTCGAAAG
1 GCTCGAAAG
382568 GAGCATTACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (27 bp):
GCTCGAAAGAGCGTTATTCTGTTTATG
Found at i:386923 original size:17 final size:17
Alignment explanation
Indices: 386901--386946 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
386891 TGGCAATATA
386901 TTTCTTTTCTTTTCTCT
1 TTTCTTTTCTTTTCTCT
*
386918 TTTCTTCTTC-TTCCTCT
1 TTTCTT-TTCTTTTCTCT
386935 TTT-TTTTCTTTT
1 TTTCTTTTCTTTT
386947 TGTGATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 3 0.12
16 4 0.16
17 15 0.60
18 3 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTTTTCTTTTCTCT
Found at i:395273 original size:21 final size:21
Alignment explanation
Indices: 395248--395306 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
395238 ATAGTGCAGA
395248 CTTCTACCGATACAAGTGA-T
1 CTTCTACCGATACAAGTGACT
* * *
395268 AGTTCTACTGATACAAGAGACT
1 -CTTCTACCGATACAAGTGACT
*
395290 CTTCTACCGACACAAGT
1 CTTCTACCGATACAAGT
395307 CTTACTTCTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (21 bp):
CTTCTACCGATACAAGTGACT
Found at i:396322 original size:254 final size:254
Alignment explanation
Indices: 395872--396383 Score: 961
Period size: 254 Copynumber: 2.0 Consensus size: 254
395862 ATTTCACTGG
395872 TAAGCTTTATAACTTAATAAGTTCGCAAGGTTTATCAATTTACCGAATAACATGTGGTAAATGAA
1 TAAGCTTTATAACTTAATAAGTTCGCAAGGTTTATCAATTTACCGAATAACATGTGGTAAATGAA
395937 TATGTAAGTCTGTCGAGATAACACAGGATTGTACTTCAGCGATCGATATTCGTTTTACACCCTGT
66 TATGTAAGTCTGTCGAGATAACACAGGATTGTACTTCAGCGATCGATATTCGTTTTACACCCTGT
*
396002 TGACCCAAAGGTCATTATGCTCATTTTTCTCCCTATTGACCCAAAGGTCATGCCTGTTACCAATA
131 TGACCCAAAGGTCATTATGCTCATTTTTCTCCCTATTGACCCAAAGGTCATGCCTGTTAACAATA
*
396067 TTCGATGCTATTCTTAGCCATCGATACGATATATTTGTTCCCTACAATGCTGCTCATAC
196 TTCGATGCTATTCTTAGCCATCGATACGATATATTTGTTCCCTACAATGCTGCTCACAC
396126 TAAGCTTTATAACTTAATAAGTTCGCAAGGTTTATCAATTTACCGAATAACATGTGGTAAATGAA
1 TAAGCTTTATAACTTAATAAGTTCGCAAGGTTTATCAATTTACCGAATAACATGTGGTAAATGAA
*
396191 TATGTAAGTCTGTCGAGATAACATAGGATTGTACTTCAGCGATCGATATTCGTTTTACACCCTGT
66 TATGTAAGTCTGTCGAGATAACACAGGATTGTACTTCAGCGATCGATATTCGTTTTACACCCTGT
* *
396256 TGACCCAAAGGTCATTATGCTCATTTTTCTCCCTGTTGACCCAAAGGTCATGCTTGTTAACAATA
131 TGACCCAAAGGTCATTATGCTCATTTTTCTCCCTATTGACCCAAAGGTCATGCCTGTTAACAATA
* *
396321 TTCGATGTTATTCTTAGCCATCGATACGGTATATTTGTTCCCTACAATGCTGCTCACAC
196 TTCGATGCTATTCTTAGCCATCGATACGATATATTTGTTCCCTACAATGCTGCTCACAC
396380 TAAG
1 TAAG
396384 TTGACGAGAA
Statistics
Matches: 251, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
254 251 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (254 bp):
TAAGCTTTATAACTTAATAAGTTCGCAAGGTTTATCAATTTACCGAATAACATGTGGTAAATGAA
TATGTAAGTCTGTCGAGATAACACAGGATTGTACTTCAGCGATCGATATTCGTTTTACACCCTGT
TGACCCAAAGGTCATTATGCTCATTTTTCTCCCTATTGACCCAAAGGTCATGCCTGTTAACAATA
TTCGATGCTATTCTTAGCCATCGATACGATATATTTGTTCCCTACAATGCTGCTCACAC
Found at i:401263 original size:14 final size:14
Alignment explanation
Indices: 401227--401263 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
401217 ATTTTTAAAA
*
401227 GATTATTAAGTTTG
1 GATTATTTAGTTTG
401241 G-TT-TTTAGTTTG
1 GATTATTTAGTTTG
401253 GATTATTTAGT
1 GATTATTTAGT
401264 AAAGTGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 9 0.45
13 4 0.20
14 7 0.35
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.57
Consensus pattern (14 bp):
GATTATTTAGTTTG
Found at i:401832 original size:28 final size:28
Alignment explanation
Indices: 401737--401834 Score: 110
Period size: 28 Copynumber: 3.5 Consensus size: 28
401727 TTAGCAAATG
*
401737 CTCTATATTTTGGCTTGTAAGAGCGTAA
1 CTCTATATTCTGGCTTGTAAGAGCGTAA
* * **
401765 CTTTGTATTCTGGCTCATAAGAGCGT-A
1 CTCTATATTCTGGCTTGTAAGAGCGTAA
401792 -TCTATGCATTCTGGCTTGTAAGAGCGTAA
1 CTCTAT--ATTCTGGCTTGTAAGAGCGTAA
*
401821 CTCTATACTCTGGC
1 CTCTATATTCTGGC
401835 CCGCAAGAGT
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
26 3 0.05
27 1 0.02
28 46 0.82
29 1 0.02
30 5 0.09
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (28 bp):
CTCTATATTCTGGCTTGTAAGAGCGTAA
Found at i:401878 original size:28 final size:27
Alignment explanation
Indices: 401829--401957 Score: 74
Period size: 27 Copynumber: 4.7 Consensus size: 27
401819 AACTCTATAC
* * *
401829 TCTGGCCCGCAAGAGTAATATTTTGGA-T
1 TCTGGCTCGAAAGAGTAATATTCT--ATT
**
401857 TCTGGCTCGAAAGAGTGTTATTCTATT
1 TCTGGCTCGAAAGAGTAATATTCTATT
*
401884 TCTGGCTCGAAAGGAGT-AT-TACTATGT
1 TCTGGCTCGAAA-GAGTAATATTCTAT-T
*
401911 TCTGGCTC-AAATGAGCT-ATATTCTGTT
1 TCTGGCTCGAAA-GAG-TAATATTCTATT
401938 T-TGAGCTCGAATA-AGTAATA
1 TCTG-GCTCGAA-AGAGTAATA
401958 ATTTTCTAGG
Statistics
Matches: 82, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
26 15 0.18
27 37 0.45
28 29 0.35
29 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (27 bp):
TCTGGCTCGAAAGAGTAATATTCTATT
Found at i:401892 original size:27 final size:27
Alignment explanation
Indices: 401856--401918 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
401846 ATATTTTGGA
*
401856 TTCTGGCTCGAAA-GAGTGTTATTCTAT-
1 TTCTGGCTCGAAAGGAGTATTA--CTATG
401883 TTCTGGCTCGAAAGGAGTATTACTATG
1 TTCTGGCTCGAAAGGAGTATTACTATG
401910 TTCTGGCTC
1 TTCTGGCTC
401919 AAATGAGCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 4 0.12
27 22 0.67
28 7 0.21
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (27 bp):
TTCTGGCTCGAAAGGAGTATTACTATG
Found at i:404100 original size:26 final size:26
Alignment explanation
Indices: 404064--404123 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
404054 CTATTTTCTT
404064 AAAATTTTACTAGGGGCAAAATCGTC
1 AAAATTTTACTAGGGGCAAAATCGTC
* * *
404090 AAATTTTTACTAGGGGTAAAATCGTT
1 AAAATTTTACTAGGGGCAAAATCGTC
404116 AAAATTTT
1 AAAATTTT
404124 GTTGGGGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (26 bp):
AAAATTTTACTAGGGGCAAAATCGTC
Found at i:410702 original size:24 final size:24
Alignment explanation
Indices: 410674--410746 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 24
410664 TTTACACTTC
410674 CCAGCTTGCACATGTTTATGCTCG
1 CCAGCTTGCACATGTTTATGCTCG
* ** * ** *
410698 TCAGCTTATATATGCTTTTACACTTG
1 CCAGCTTGCACATG--TTTATGCTCG
410724 CCAGCTTGCACATGTTTATGCTC
1 CCAGCTTGCACATGTTTATGCTC
410747 ATCAACTTAT
Statistics
Matches: 33, Mismatches: 14, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
24 16 0.48
26 17 0.52
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.38
Consensus pattern (24 bp):
CCAGCTTGCACATGTTTATGCTCG
Found at i:410728 original size:50 final size:52
Alignment explanation
Indices: 410624--410855 Score: 283
Period size: 54 Copynumber: 4.4 Consensus size: 52
410614 TTACGCACAT
* * *
410624 CAGCTTGCACACGTTTATGCTCGTTAGC-TATATATATGCGTTTACACTTC-C
1 CAGCTTGCACATGTTTATGCTCGTCAACTTATATATATGCGTTTACAC-TCGC
* * *
410675 CAGCTTGCACATGTTTATGCTCGTCAGC-T-TATATATGCTTTTACACTTGC
1 CAGCTTGCACATGTTTATGCTCGTCAACTTATATATATGCGTTTACACTCGC
* *
410725 CAGCTTGCACATGTTTATGCTCATCAACTTATATATATATGCATTTACACTCGC
1 CAGCTTGCACATGTTTATGCTCGTCAAC-T-TATATATATGCGTTTACACTCGC
* *
410779 CAGCTTGCACATGTTTATGATCATCAACTTATATATATATGCGTTTACACTCGC
1 CAGCTTGCACATGTTTATGCTCGTCAAC-T-TATATATATGCGTTTACACTCGC
* *
410833 CAGCTTGCACACGTTTACGCTCG
1 CAGCTTGCACATGTTTATGCTCG
410856 CTAGCTTGCA
Statistics
Matches: 162, Mismatches: 14, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
49 1 0.01
50 43 0.27
51 27 0.17
53 1 0.01
54 90 0.56
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.37
Consensus pattern (52 bp):
CAGCTTGCACATGTTTATGCTCGTCAACTTATATATATGCGTTTACACTCGC
Found at i:410784 original size:104 final size:106
Alignment explanation
Indices: 410652--410854 Score: 286
Period size: 104 Copynumber: 1.9 Consensus size: 106
410642 GCTCGTTAGC
* * * * *
410652 TATATATATGCGTTTACACTTCCCAGCTTGCACATGTTTATGCTCGTCAGC-T-TATATATGCTT
1 TATATATATGCATTTACACTTCCCAGCTTGCACATGTTTATGATCATCAACTTATATATATGCGT
* * *
410715 TTACACTTGCCAGCTTGCACATGTTTATGCTCATCAACTTA
66 TTACACTCGCCAGCTTGCACACGTTTACGCTCATCAACTTA
410756 TATATATATGCATTTACAC-TCGCCAGCTTGCACATGTTTATGATCATCAACTTATATATATATG
1 TATATATATGCATTTACACTTC-CCAGCTTGCACATGTTTATGATCATCAAC-T-TATATATATG
410820 CGTTTACACTCGCCAGCTTGCACACGTTTACGCTC
63 CGTTTACACTCGCCAGCTTGCACACGTTTACGCTC
410855 GCTAGCTTGC
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
103 2 0.02
104 44 0.51
107 1 0.01
108 39 0.45
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (106 bp):
TATATATATGCATTTACACTTCCCAGCTTGCACATGTTTATGATCATCAACTTATATATATGCGT
TTACACTCGCCAGCTTGCACACGTTTACGCTCATCAACTTA
Found at i:410786 original size:54 final size:54
Alignment explanation
Indices: 410652--410854 Score: 290
Period size: 54 Copynumber: 3.8 Consensus size: 54
410642 GCTCGTTAGC
* *
410652 TATATATATGCGTTTACACTTC-CCAGCTTGCACATGTTTATGCTCGTCAGC---
1 TATATATATGCGTTTACAC-TCGCCAGCTTGCACATGTTTATGCTCATCAACTTA
* *
410703 T-TATATATGCTTTTACACTTGCCAGCTTGCACATGTTTATGCTCATCAACTTA
1 TATATATATGCGTTTACACTCGCCAGCTTGCACATGTTTATGCTCATCAACTTA
* *
410756 TATATATATGCATTTACACTCGCCAGCTTGCACATGTTTATGATCATCAACTTA
1 TATATATATGCGTTTACACTCGCCAGCTTGCACATGTTTATGCTCATCAACTTA
* *
410810 TATATATATGCGTTTACACTCGCCAGCTTGCACACGTTTACGCTC
1 TATATATATGCGTTTACACTCGCCAGCTTGCACATGTTTATGCTC
410855 GCTAGCTTGC
Statistics
Matches: 136, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
49 1 0.01
50 43 0.32
51 1 0.01
53 1 0.01
54 90 0.66
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (54 bp):
TATATATATGCGTTTACACTCGCCAGCTTGCACATGTTTATGCTCATCAACTTA
Found at i:410855 original size:24 final size:24
Alignment explanation
Indices: 410820--410884 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
410810 TATATATATG
*
410820 CGTTTACACTCGCCAGCTTGCACA
1 CGTTTACGCTCGCCAGCTTGCACA
*
410844 CGTTTACGCTCGCTAGCTTGCACA
1 CGTTTACGCTCGCCAGCTTGCACA
*
410868 CGTTTACGCTCGTCAGC
1 CGTTTACGCTCGCCAGC
410885 ATATATATGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.17, C:0.35, G:0.20, T:0.28
Consensus pattern (24 bp):
CGTTTACGCTCGCCAGCTTGCACA
Found at i:410912 original size:50 final size:50
Alignment explanation
Indices: 410844--411310 Score: 504
Period size: 50 Copynumber: 9.1 Consensus size: 50
410834 AGCTTGCACA
* * * *
410844 CGTTTACGCTCGCTAGCTTGCACACGTTTACGCTCGTCAGCATATATATG
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATATATG
* * *
410894 CGTTTATGCTTGCCAGCTTGCACATGTTTACACTCATCAGCTTATATATATATG
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGC---T-TATATATG
** *
410948 CGTTTATGCTTGCCAGCTTGCACACGTTTATTCTCATCAGCTTATATATG
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATATATG
* * *
410998 AGTTTATGCTTGCCAGCTTGCACATGTTTACACTCGTCAGCTTATATATG
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATATATG
* * *
411048 CGTTTATGCTTCCCAGCTTGCACATGTTTACACTCGTCAGCTTATATATATATG
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGC---T-TATATATG
* * * * *
411102 CATTTACGCTCGCCAGCTTGCACACGTTTAAGCTCGTGAGCTTATATATG
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATATATG
* * *
411152 TGTTTATGCTAGCCAGCTTGCACACGTTTACTCTCGTCAGCCTATATATATATG
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAG-C--T-TATATATG
* * ** * * *
411206 CATTTACGCTCACCAGCTTGTACACGTTTATGCTCGTTAGCTTATATATG
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATATATG
* * *
411256 CATTT-TGCTTGCCAGCTTGCACACATTTACGCTCATCAGCTTATATATG
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATATATG
*
411305 CATTTA
1 CGTTTA
411311 ATTTTTTTAA
Statistics
Matches: 355, Mismatches: 49, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
49 41 0.12
50 181 0.51
51 4 0.01
53 3 0.01
54 126 0.35
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37
Consensus pattern (50 bp):
CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATATATG
Found at i:410971 original size:104 final size:100
Alignment explanation
Indices: 410844--411310 Score: 508
Period size: 104 Copynumber: 4.6 Consensus size: 100
410834 AGCTTGCACA
* * * * * *
410844 CGTTTACGCTCGCTAGCTTGCACACGTTTACGCTCGTCAGCATATATATGCGTTTATGCTTGCCA
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCATATATATGCATTTACGCTCGCCA
* *
410909 GCTTGCACATGTTTACACTCATCAGCTTATATATATATG
66 GCTTGCACACGTTTACACTCGTCAGC---T-TATATATG
** * * * *
410948 CGTTTATGCTTGCCAGCTTGCACACGTTTATTCTCATCAGCTTATATATG-AGTTTATGCTTGCC
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCATATATATGCA-TTTACGCTCGCC
*
411012 AGCTTGCACATGTTTACACTCGTCAGCTTATATATG
65 AGCTTGCACACGTTTACACTCGTCAGCTTATATATG
* * *
411048 CGTTTATGCTTCCCAGCTTGCACATGTTTACACTCGTCAGCTTATATATATATGCATTTACGCTC
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGC----ATATATATGCATTTACGCTC
*
411113 GCCAGCTTGCACACGTTTA-AGCTCGTGAGCTTATATATG
62 GCCAGCTTGCACACGTTTACA-CTCGTCAGCTTATATATG
* * *
411152 TGTTTATGCTAGCCAGCTTGCACACGTTTACTCTCGTCAGCCTATATATATATGCATTTACGCTC
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAG-C---ATATATATGCATTTACGCTC
* * ** *
411217 ACCAGCTTGTACACGTTTATGCTCGTTAGCTTATATATG
62 GCCAGCTTGCACACGTTTACACTCGTCAGCTTATATATG
* * * *
411256 CATTT-TGCTTGCCAGCTTGCACACATTTACGCTCATCAGCTTATATATGCATTTA
1 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCATATATATGCATTTA
411311 ATTTTTTTAA
Statistics
Matches: 319, Mismatches: 35, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
99 14 0.04
100 44 0.14
101 1 0.00
102 1 0.00
103 31 0.10
104 226 0.71
105 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37
Consensus pattern (100 bp):
CGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCATATATATGCATTTACGCTCGCCA
GCTTGCACACGTTTACACTCGTCAGCTTATATATG
Found at i:411014 original size:26 final size:25
Alignment explanation
Indices: 410940--411066 Score: 69
Period size: 24 Copynumber: 5.0 Consensus size: 25
410930 TCAGCTTATA
410940 TATATATGCGTTTATGCTTGCCAGCT
1 TATATATG-GTTTATGCTTGCCAGCT
** * * * ***
410966 TGCACA-CGTTTATTCTCATCAGCT
1 TATATATGGTTTATGCTTGCCAGCT
410990 TATATATGAGTTTATGCTTGCCAGCT
1 TATATATG-GTTTATGCTTGCCAGCT
** * ** * *
411016 TGCACAT-GTTTACACTCGTCAGCT
1 TATATATGGTTTATGCTTGCCAGCT
*
411040 TATATATGCGTTTATGCTTCCCAGCT
1 TATATATG-GTTTATGCTTGCCAGCT
411066 T
1 T
411067 GCACATGTTT
Statistics
Matches: 66, Mismatches: 31, Indels: 8
0.63 0.30 0.08
Matches are distributed among these distances:
24 33 0.50
26 33 0.50
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (25 bp):
TATATATGGTTTATGCTTGCCAGCT
Found at i:411035 original size:154 final size:154
Alignment explanation
Indices: 410858--411304 Score: 589
Period size: 154 Copynumber: 2.9 Consensus size: 154
410848 TACGCTCGCT
* *
410858 AGCTTGCACACGTTTACGCTCGTCAGCATATATATGCGTTTATGCTTGCCAGCTTGCACATGTTT
1 AGCTTGCACACGTTTACACTCGTCAGCATATATATGCGTTTATGCTTACCAGCTTGCACATGTTT
* * **
410923 ACACTCATCAGCTTATATATATATGCGTTTATGCTTGCCAGCTTGCACACGTTTATTCTCATCAG
66 ACACTCGTCAGCTTATATATATATGCATTTATGCTTGCCAGCTTGCACACGTTTAAGCTCATCAG
*
410988 CTTATATATGAGTTTATGCTTGCC
131 CTTATATATGAGTTTATGCTAGCC
* * *
411012 AGCTTGCACATGTTTACACTCGTCAGCTTATATATGCGTTTATGCTTCCCAGCTTGCACATGTTT
1 AGCTTGCACACGTTTACACTCGTCAGCATATATATGCGTTTATGCTTACCAGCTTGCACATGTTT
* * * *
411077 ACACTCGTCAGCTTATATATATATGCATTTACGCTCGCCAGCTTGCACACGTTTAAGCTCGTGAG
66 ACACTCGTCAGCTTATATATATATGCATTTATGCTTGCCAGCTTGCACACGTTTAAGCTCATCAG
*
411142 CTTATATATGTGTTTATGCTAGCC
131 CTTATATATGAGTTTATGCTAGCC
* * * * * *
411166 AGCTTGCACACGTTTACTCTCGTCAGCCTATATATATATGCATTTACGCTCACCAGCTTGTACAC
1 AGCTTGCACACGTTTACACTCGTCAG-C---ATATATATGCGTTTATGCTTACCAGCTTGCACAT
** * * *
411231 GTTTATGCTCGTTAGC---T-TATATATGCATTT-TGCTTGCCAGCTTGCACACATTTACGCTCA
62 GTTTACACTCGTCAGCTTATATATATATGCATTTATGCTTGCCAGCTTGCACACGTTTAAGCTCA
411291 TCAGCTTATATATG
127 TCAGCTTATATATG
411305 CATTTAATTT
Statistics
Matches: 257, Mismatches: 32, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
153 38 0.15
154 177 0.69
155 2 0.01
158 40 0.16
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (154 bp):
AGCTTGCACACGTTTACACTCGTCAGCATATATATGCGTTTATGCTTACCAGCTTGCACATGTTT
ACACTCGTCAGCTTATATATATATGCATTTATGCTTGCCAGCTTGCACACGTTTAAGCTCATCAG
CTTATATATGAGTTTATGCTAGCC
Found at i:411088 original size:24 final size:24
Alignment explanation
Indices: 411011--411090 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
411001 TTATGCTTGC
411011 CAGCTTGCACATGTTTACACTCGT
1 CAGCTTGCACATGTTTACACTCGT
** * ** *
411035 CAGCTTATATATGCGTTTATGCTTC-C
1 CAGCTTGCACAT--GTTTACAC-TCGT
411061 CAGCTTGCACATGTTTACACTCGT
1 CAGCTTGCACATGTTTACACTCGT
411085 CAGCTT
1 CAGCTT
411091 ATATATATAT
Statistics
Matches: 40, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
23 2 0.05
24 21 0.52
26 15 0.38
27 2 0.05
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (24 bp):
CAGCTTGCACATGTTTACACTCGT
Found at i:446771 original size:35 final size:35
Alignment explanation
Indices: 446725--446798 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
446715 CTTTGCGGAG
*
446725 TAACACGTGTACAATGGATGGGGTTAATTGTAGCC
1 TAACACGTGTACAATGGATGGGGTTAATTGCAGCC
446760 TAACACGTGTACAATGGATGGGGTTAATTGCAGCC
1 TAACACGTGTACAATGGATGGGGTTAATTGCAGCC
446795 TAAC
1 TAAC
446799 TCCCTCTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (35 bp):
TAACACGTGTACAATGGATGGGGTTAATTGCAGCC
Found at i:454241 original size:1 final size:1
Alignment explanation
Indices: 454231--454325 Score: 55
Period size: 1 Copynumber: 95.0 Consensus size: 1
454221 CAATTTATTC
* * * * * * *** * *
454231 TTTTTCTTTTTTCTTTTTTCTTTTTCTCTTTTTTTTTTTTTGTTTTTCANTTTTCTTTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
454296 TTTCTTTTTCTCTTTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
454326 CAAGTGACTG
Statistics
Matches: 66, Mismatches: 28, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.01, C:0.12, G:0.02, T:0.84
Consensus pattern (1 bp):
T
Found at i:454243 original size:7 final size:7
Alignment explanation
Indices: 454231--454325 Score: 115
Period size: 7 Copynumber: 13.6 Consensus size: 7
454221 CAATTTATTC
454231 TTTTTCT
1 TTTTTCT
454238 TTTTTCT
1 TTTTTCT
454245 TTTTTCT
1 TTTTTCT
454252 TTTTCTCT
1 TTTT-TCT
454260 TTTTT-T
1 TTTTTCT
454266 TTTTT-T
1 TTTTTCT
*
454272 GTTTTTCA
1 -TTTTTCT
*
454280 NTTTTCT
1 TTTTTCT
454287 TTTTTCT
1 TTTTTCT
454294 TTTTTCT
1 TTTTTCT
454301 TTTTCTCT
1 TTTT-TCT
454309 TTTTT-T
1 TTTTTCT
*
454315 TTTTTGT
1 TTTTTCT
454322 TTTT
1 TTTT
454326 CAAGTGACTG
Statistics
Matches: 79, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
6 13 0.16
7 52 0.66
8 14 0.18
ACGTcount: A:0.01, C:0.12, G:0.02, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:454288 original size:49 final size:47
Alignment explanation
Indices: 454232--454327 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 47
454222 AATTTATTCT
454232 TTTTCTTTTTTCTTTTTTCTTTTTCTCTTTTTTTTTTTTTGTTTTTCA
1 TTTTCTTTTTTCTTTTTTCTTTTTCTC-TTTTTTTTTTTTGTTTTTCA
454280 NTTTTCTTTTTTCTTTTTTCTTTTTCTCTTTTTTTTTTTTGTTTTTCA
1 -TTTTCTTTTTTCTTTTTTCTTTTTCTCTTTTTTTTTTTTGTTTTTCA
454328 AGTGACTGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 20 0.43
49 27 0.57
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.82
Consensus pattern (47 bp):
TTTTCTTTTTTCTTTTTTCTTTTTCTCTTTTTTTTTTTTGTTTTTCA
Found at i:455873 original size:28 final size:28
Alignment explanation
Indices: 455840--455923 Score: 168
Period size: 28 Copynumber: 3.0 Consensus size: 28
455830 TGAACTTTCA
455840 TTAGTACCTTTGCTATTTGGGTTTCTAT
1 TTAGTACCTTTGCTATTTGGGTTTCTAT
455868 TTAGTACCTTTGCTATTTGGGTTTCTAT
1 TTAGTACCTTTGCTATTTGGGTTTCTAT
455896 TTAGTACCTTTGCTATTTGGGTTTCTAT
1 TTAGTACCTTTGCTATTTGGGTTTCTAT
455924 CGATGCATCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.54
Consensus pattern (28 bp):
TTAGTACCTTTGCTATTTGGGTTTCTAT
Found at i:455885 original size:16 final size:16
Alignment explanation
Indices: 455840--455913 Score: 56
Period size: 16 Copynumber: 5.1 Consensus size: 16
455830 TGAACTTTCA
455840 TTAGTACCTTTGCTAT
1 TTAGTACCTTTGCTAT
**
455856 TT-G--GGTTT-CTAT
1 TTAGTACCTTTGCTAT
455868 TTAGTACCTTTGCTAT
1 TTAGTACCTTTGCTAT
**
455884 TT-G--GGTTT-CTAT
1 TTAGTACCTTTGCTAT
455896 TTAGTACCTTTGCTAT
1 TTAGTACCTTTGCTAT
455912 TT
1 TT
455914 GGGTTTCTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
12 12 0.29
13 8 0.19
15 8 0.19
16 14 0.33
ACGTcount: A:0.15, C:0.15, G:0.16, T:0.54
Consensus pattern (16 bp):
TTAGTACCTTTGCTAT
Found at i:472360 original size:20 final size:20
Alignment explanation
Indices: 472318--472381 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
472308 TACTTGAAGA
* * * *
472318 TGTTTGAACTTCGATGTCTC
1 TGTTTGCACTTCGGTGCCCC
* *
472338 TGTTTGCATTTTGGTGCCCC
1 TGTTTGCACTTCGGTGCCCC
*
472358 TG-TTGCACTTCGGTTCCCC
1 TGTTTGCACTTCGGTGCCCC
472377 TGTTT
1 TGTTT
472382 AACATCTTTG
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.08, C:0.25, G:0.22, T:0.45
Consensus pattern (20 bp):
TGTTTGCACTTCGGTGCCCC
Found at i:473284 original size:55 final size:55
Alignment explanation
Indices: 473204--473321 Score: 164
Period size: 55 Copynumber: 2.1 Consensus size: 55
473194 AGTGAGTTAT
* *
473204 ACAGTCTGGGGCACGAGCTGAGACACGATCGTGTGTCCCTACTTCAAATGATCAC
1 ACAGTCTGGGGCACAAGCTGAGACACGATCATGTGTCCCTACTTCAAATGATCAC
* * * * * *
473259 ACGGTCTGGGGCACAAGTTGGGACACGATCATGTGTCCCTATTTCGAATGCTCAC
1 ACAGTCTGGGGCACAAGCTGAGACACGATCATGTGTCCCTACTTCAAATGATCAC
473314 ACAGTCTG
1 ACAGTCTG
473322 AACAAAAGTC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (55 bp):
ACAGTCTGGGGCACAAGCTGAGACACGATCATGTGTCCCTACTTCAAATGATCAC
Found at i:473968 original size:123 final size:121
Alignment explanation
Indices: 473693--474060 Score: 501
Period size: 123 Copynumber: 3.0 Consensus size: 121
473683 TTCTACTATC
* * * *
473693 TTTTCTTTTATTTTAATATCTCATATTAAAATAGAAATATATATCTTTAGAGAAATATATGAAAG
1 TTTTCTTTTA-TATAATATCTCATATTAAAATGGAAATAT-T-CCTTTA-AAAAATATATGAAAG
* *
473758 GTTTATTAAAACATTATATACTTTTCCAAAAAGGATATTAACTTCCATG---T-ATATTCAA
62 GTTTATTAAAACATTATAT-CTTTTCC-AAAAGGATATTAACTTTCATGTTTTAATATTTAA
* *
473816 TTTTCTTTTATATAATATCTCATATTAAAATGGAAATGTTCCTTTACAAAAATATATGGAAGGTT
1 TTTTCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTA-AAAAATATATGAAAGGTT
* *
473881 TATTAAAACATTATATCCTTTCCAAAAGAATATTAACTTTCATGTTTTTAATATTTAA
65 TATTAAAACATTATATCTTTTCCAAAAGGATATTAACTTTCATG-TTTTAATATTTAA
*
473939 TTTTCTTTTATATAATATCTAATATTAAAATGGAAATATTCCTTTAAAGAAATATATGAAAGGTT
1 TTTTCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAA-AAATATATGAAAGGTT
* * *
474004 TATTAAAACATTATATATTTTCCAAAGGGATATTATCTTTCATGTTTTAATATTTAA
65 TATTAAAACATTATATCTTTTCCAAAAGGATATTAACTTTCATGTTTTAATATTTAA
474061 CGAAATCATT
Statistics
Matches: 220, Mismatches: 19, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
118 19 0.09
119 6 0.03
120 37 0.17
121 1 0.00
122 42 0.19
123 115 0.52
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (121 bp):
TTTTCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAAAATATATGAAAGGTTT
ATTAAAACATTATATCTTTTCCAAAAGGATATTAACTTTCATGTTTTAATATTTAA
Found at i:474133 original size:106 final size:106
Alignment explanation
Indices: 473988--474207 Score: 359
Period size: 106 Copynumber: 2.1 Consensus size: 106
473978 TCCTTTAAAG
** * *
473988 AAATATATGAAAGGTTTATTAAAACATTATATATTTTCCAAAGGGATATTATCTTTCATGTTTTA
1 AAAT-TATGAAAGGTTTATTAAAACATTATATACCTTCCAAAAGGATATTAACTTTCATGTTTTA
* *
474053 ATATTTAACGAAATCATTATAATTAATAATTATAATTATGTT
65 ATATTTAACGAAATCATCATAATTAATAATTATAATTACGTT
* *
474095 AAATTATGGAAGGTTTATTAAAACATTATATCCCTTCCAAAAGGATATTAACTTTCATGTTTTAA
1 AAATTATGAAAGGTTTATTAAAACATTATATACCTTCCAAAAGGATATTAACTTTCATGTTTTAA
474160 TATTTAACGAAATCATCATAATTAATAATTATAATTACGTT
66 TATTTAACGAAATCATCATAATTAATAATTATAATTACGTT
474201 AAATTAT
1 AAATTAT
474208 ATTCAGTAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
106 101 0.96
107 4 0.04
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (106 bp):
AAATTATGAAAGGTTTATTAAAACATTATATACCTTCCAAAAGGATATTAACTTTCATGTTTTAA
TATTTAACGAAATCATCATAATTAATAATTATAATTACGTT
Found at i:486559 original size:12 final size:12
Alignment explanation
Indices: 486544--486574 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
486534 ATTATGATTT
486544 CAACAATGAATC
1 CAACAATGAATC
486556 CAACAATGAATC
1 CAACAATGAATC
486568 CAACAAT
1 CAACAAT
486575 CCAAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.26, G:0.06, T:0.16
Consensus pattern (12 bp):
CAACAATGAATC
Found at i:487063 original size:120 final size:120
Alignment explanation
Indices: 486845--487203 Score: 486
Period size: 120 Copynumber: 3.0 Consensus size: 120
486835 CTTACATAAA
* * *
486845 CTATAATCCAGAATTTCATCCTCATGTTTGTATCAACTCTGTTACCAGTATATGATGCTGATCAC
1 CTATAATCTAGAATTTCATTCTCATGTTTGTATCAACTCTGTTACCAGTATACGATGCTGATCAC
* *
486910 AAGAGCTATCGAGGATTCGCAACATATGCGGTACCCTAGCCATCGATACAGTATG
66 ACGAGCTATCGAGGAATCGCAACATATGCGGTACCCTAGCCATCGATACAGTATG
* * *
486965 CTATAATCTAGAATTTCATTGTCATGTTTGTATCAACTCTATTACCAGTATACGATGCTGCTCAC
1 CTATAATCTAGAATTTCATTCTCATGTTTGTATCAACTCTGTTACCAGTATACGATGCTGATCAC
* * * * *
487030 ACTAGCTATCGAGGACTCGCAACATATGTGGTACCCCAACCATCGATACAGTATG
66 ACGAGCTATCGAGGAATCGCAACATATGCGGTACCCTAGCCATCGATACAGTATG
* * * * * * * *
487085 CTACAATCTATAATTTCATTCTCATGTCTATATCAACTCTGTTACTAGTATACAATGTTGTTCAC
1 CTATAATCTAGAATTTCATTCTCATGTTTGTATCAACTCTGTTACCAGTATACGATGCTGATCAC
* * *
487150 ACGAGCTGTCGAGGAATCGCAACATATGCGATA-CCTCAGCCATCGATACGGTAT
66 ACGAGCTATCGAGGAATCGCAACATATGCGGTACCCT-AGCCATCGATACAGTAT
487204 CTGTGCATAT
Statistics
Matches: 208, Mismatches: 30, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
119 2 0.01
120 206 0.99
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (120 bp):
CTATAATCTAGAATTTCATTCTCATGTTTGTATCAACTCTGTTACCAGTATACGATGCTGATCAC
ACGAGCTATCGAGGAATCGCAACATATGCGGTACCCTAGCCATCGATACAGTATG
Found at i:489558 original size:8 final size:8
Alignment explanation
Indices: 489545--489579 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
489535 CATATGACCA
489545 ATACACAC
1 ATACACAC
489553 ATACACAC
1 ATACACAC
*
489561 ACACACAC
1 ATACACAC
*
489569 ACACACAC
1 ATACACAC
489577 ATA
1 ATA
489580 TATATATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.51, C:0.40, G:0.00, T:0.09
Consensus pattern (8 bp):
ATACACAC
Found at i:489560 original size:2 final size:2
Alignment explanation
Indices: 489547--489577 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
489537 TATGACCAAT
*
489547 AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
489578 TATATATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.45, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:490188 original size:28 final size:28
Alignment explanation
Indices: 490157--490224 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
490147 ATCGCCCTTT
*
490157 CGAGCCAAAATGCAGAATAATGCTCACA
1 CGAGCCAAAATACAGAATAATGCTCACA
* * * **
490185 CGAGCCAGAATACAGAGTCATGCTCTTA
1 CGAGCCAAAATACAGAATAATGCTCACA
*
490213 CGAGCCAGAATA
1 CGAGCCAAAATA
490225 TAGAGTTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (28 bp):
CGAGCCAAAATACAGAATAATGCTCACA
Found at i:490275 original size:55 final size:56
Alignment explanation
Indices: 490184--490312 Score: 188
Period size: 55 Copynumber: 2.3 Consensus size: 56
490174 TAATGCTCAC
* * *
490184 ACGAGCCAGAATACAGAGTCATGCTCTTACGAGCCAGAATATAGAGTTATGCTTTT
1 ACGAGCCAGAATACAGAGTCATACTCTTACAAGCCAGAATATAGAGTTATGCTCTT
* *
490240 ACGAGCCAG-ATATAGAGTTATACTCTTACAAGCCAGAATATAGAGTTATGCTCTT
1 ACGAGCCAGAATACAGAGTCATACTCTTACAAGCCAGAATATAGAGTTATGCTCTT
**
490295 ACGAGATAGAATACAGAG
1 ACGAGCCAGAATACAGAG
490313 AAATTCTCAA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
55 48 0.75
56 16 0.25
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (56 bp):
ACGAGCCAGAATACAGAGTCATACTCTTACAAGCCAGAATATAGAGTTATGCTCTT
Found at i:490312 original size:28 final size:28
Alignment explanation
Indices: 490184--490299 Score: 180
Period size: 28 Copynumber: 4.2 Consensus size: 28
490174 TAATGCTCAC
* *
490184 ACGAGCCAGAATACAGAGTCATGCTCTT
1 ACGAGCCAGAATATAGAGTTATGCTCTT
*
490212 ACGAGCCAGAATATAGAGTTATGCTTTT
1 ACGAGCCAGAATATAGAGTTATGCTCTT
*
490240 ACGAGCCAG-ATATAGAGTTATACTCTT
1 ACGAGCCAGAATATAGAGTTATGCTCTT
*
490267 ACAAGCCAGAATATAGAGTTATGCTCTT
1 ACGAGCCAGAATATAGAGTTATGCTCTT
490295 ACGAG
1 ACGAG
490300 ATAGAATACA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 24 0.30
28 55 0.70
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (28 bp):
ACGAGCCAGAATATAGAGTTATGCTCTT
Found at i:494204 original size:347 final size:347
Alignment explanation
Indices: 493569--494249 Score: 1193
Period size: 347 Copynumber: 2.0 Consensus size: 347
493559 TTATTTAAAT
493569 AGAGTTTGTTCACACAAATAGGACAACCTTACGACTCATTAAGATATCCAAAATGGACAACTTGA
1 AGAGTTTGTTCACACAAATAGGACAACCTTACGACTCATTAAGATATCCAAAATGGACAACTTGA
*
493634 ACAACCTTAATTCAGACAGTATTTTGACTTACTTAAACATCAATATAAACAACATAAATACATCA
66 ACAACCTTAATTCAGAAAGTATTTTGACTTACTTAAACATCAATATAAACAACATAAATACATCA
*
493699 TCCAAACATCATAAATCACAACCTTCAGACACCATATCTTGCAGCGTTTAACACATAAATTTTCA
131 TCCAAACATCATAAATCACAACCTTCAGACACCATATCTTGCAGCGTTTAACAAATAAATTTTCA
*
493764 GCTTACTATCATCTTAAATTCGCATCCATTTGGACATCATTAATTAACATTTAACAATTTAGTCT
196 GCTTACTATCATCATAAATTCGCATCCATTTGGACATCATTAATTAACATTTAACAATTTAGTCT
* *
493829 CAGACTATTCAGACCATTTAATTTTCCTGATCACTTGGGCGGTTTTTATTTAATATCCAGACAAT
261 CAGACTAATCAGACCATTTAATTTTCCTGATCACTTGGGCAGTTTTTATTTAATATCCAGACAAT
493894 AGTAAACAATCTCCATTCAAAC
326 AGTAAACAATCTCCATTCAAAC
* *
493916 AGAGTTTGTTCACACAAATAGGACAACTTTACGACTCATTAAGATATCCAAAATGGACAGCTTGA
1 AGAGTTTGTTCACACAAATAGGACAACCTTACGACTCATTAAGATATCCAAAATGGACAACTTGA
493981 ACAACCTTAATTCAGAAAGTATTTTGACTTACTTAAACATCAATATAAACAACATAAATACATCA
66 ACAACCTTAATTCAGAAAGTATTTTGACTTACTTAAACATCAATATAAACAACATAAATACATCA
* * *
494046 TTCAAACATCATAAATCACAGCCTTTAGACACCATATCTTGCAGCGTTTAACAAATAAATTTTCA
131 TCCAAACATCATAAATCACAACCTTCAGACACCATATCTTGCAGCGTTTAACAAATAAATTTTCA
* *
494111 GCTTACTATTATCATAAATTCTCATCCATTTGGACATCATTAATTAACATTTAACAATTTAGTCT
196 GCTTACTATCATCATAAATTCGCATCCATTTGGACATCATTAATTAACATTTAACAATTTAGTCT
* * ** *
494176 CATG-CTAATCAGGCCATTTAATTTTCCTGGTCACTTGGGCAGTTTTTATTTAATATTTAGACGA
261 CA-GACTAATCAGACCATTTAATTTTCCTGATCACTTGGGCAGTTTTTATTTAATATCCAGACAA
494240 TAGTAAACAA
325 TAGTAAACAA
494250 CCATCGATCG
Statistics
Matches: 316, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
347 315 1.00
348 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.32
Consensus pattern (347 bp):
AGAGTTTGTTCACACAAATAGGACAACCTTACGACTCATTAAGATATCCAAAATGGACAACTTGA
ACAACCTTAATTCAGAAAGTATTTTGACTTACTTAAACATCAATATAAACAACATAAATACATCA
TCCAAACATCATAAATCACAACCTTCAGACACCATATCTTGCAGCGTTTAACAAATAAATTTTCA
GCTTACTATCATCATAAATTCGCATCCATTTGGACATCATTAATTAACATTTAACAATTTAGTCT
CAGACTAATCAGACCATTTAATTTTCCTGATCACTTGGGCAGTTTTTATTTAATATCCAGACAAT
AGTAAACAATCTCCATTCAAAC
Found at i:501111 original size:46 final size:46
Alignment explanation
Indices: 501050--501138 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
501040 CTTCATGCAT
501050 TTATTTCACATCAAGTACATGTATTTTTATCATTTTAGCAATTTAG
1 TTATTTCACATCAAGTACATGTATTTTTATCATTTTAGCAATTTAG
* *
501096 TTATTTCGCATCAAGTACATGTATTTTTATTATTTTAGCAATT
1 TTATTTCACATCAAGTACATGTATTTTTATCATTTTAGCAATT
501139 ATTCCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.49
Consensus pattern (46 bp):
TTATTTCACATCAAGTACATGTATTTTTATCATTTTAGCAATTTAG
Found at i:506412 original size:28 final size:28
Alignment explanation
Indices: 506319--506481 Score: 130
Period size: 28 Copynumber: 5.8 Consensus size: 28
506309 CAAAATAATA
* * *
506319 CTCTTTCGAGCCAGAATATAGA-ATATCG
1 CTCTTACGAGCCAGAATACAGAGTTAT-G
* * * * * *
506347 CCCTTTCAAGCCAGATTACAGAATAATG
1 CTCTTACGAGCCAGAATACAGAGTTATG
** * * *
506375 CTCACACGAGCTAGAATATAGAGTCATG
1 CTCTTACGAGCCAGAATACAGAGTTATG
* *
506403 CTCTTACGAGCTAGAATACATAGTTATG
1 CTCTTACGAGCCAGAATACAGAGTTATG
* *
506431 CTCTTAGGAGCCAAAATACAGAGTTATG
1 CTCTTACGAGCCAGAATACAGAGTTATG
* *
506459 CTCTTACGAACCAGAATATAGAG
1 CTCTTACGAGCCAGAATACAGAG
506482 AAATTCTCAA
Statistics
Matches: 105, Mismatches: 29, Indels: 2
0.77 0.21 0.01
Matches are distributed among these distances:
28 103 0.98
29 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (28 bp):
CTCTTACGAGCCAGAATACAGAGTTATG
Found at i:508244 original size:19 final size:19
Alignment explanation
Indices: 508220--508261 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
508210 TACGAAAGAT
*
508220 CAAATGTTTCGTGAGAGAA
1 CAAATGTTTCATGAGAGAA
508239 CAAATGTTTCATGAGAGAA
1 CAAATGTTTCATGAGAGAA
508258 CAAA
1 CAAA
508262 GCACATTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (19 bp):
CAAATGTTTCATGAGAGAA
Found at i:509640 original size:28 final size:27
Alignment explanation
Indices: 509603--509681 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 27
509593 AACAAGATGA
*
509603 ATAAAATATTTTTTAAATAT-AATTTAAT
1 ATAAAATATTTTTTAAATATCAA--AAAT
*
509631 ATAAAATATTATTTTCAAATTTCAAAAAT
1 ATAAAATATT-TTTT-AAATATCAAAAAT
509660 ATAAAATAATTTTTTTAAATAT
1 ATAAAAT-A-TTTTTTAAATAT
509682 TTTAAAGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
28 10 0.23
29 19 0.44
30 10 0.23
31 4 0.09
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (27 bp):
ATAAAATATTTTTTAAATATCAAAAAT
Found at i:509715 original size:23 final size:24
Alignment explanation
Indices: 509684--509740 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
509674 TTAAATATTT
*
509684 TAAAGTATTTTAACATAA-ACATA
1 TAAAATATTTTAACATAAGACATA
* *
509707 TAAAATATTTTAATATAAGTTCATA
1 TAAAATATTTTAACATAAG-ACATA
509732 TAAAATATT
1 TAAAATATT
509741 AATTTTTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 16 0.55
25 13 0.45
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (24 bp):
TAAAATATTTTAACATAAGACATA
Found at i:509777 original size:20 final size:20
Alignment explanation
Indices: 509729--509777 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
509719 ATATAAGTTC
*
509729 ATATAAAATATTAATTTTTG
1 ATATAAAATATTAATTTTTA
* *
509749 ATAGAAAATATTATTTTTTA
1 ATATAAAATATTAATTTTTA
*
509769 ATATTAAAT
1 ATATAAAAT
509778 TGATATGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
ATATAAAATATTAATTTTTA
Found at i:510348 original size:22 final size:24
Alignment explanation
Indices: 510292--510377 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 24
510282 TATAATTATT
*
510292 TTTATATTAAATTATATTAAAAAC
1 TTTATTTTAAATTATATTAAAAAC
510316 TTTTTTATTTTAAATTATATTAAAAAC
1 ---TTTATTTTAAATTATATTAAAAAC
* *
510343 TTTTTTAATTTAAATTAT-TTCAAATAC
1 ---TTTATTTTAAATTATATT-AAAAAC
510370 TTTATTTT
1 TTTATTTT
510378 TATATTTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
24 7 0.13
26 2 0.04
27 45 0.83
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTATTTTAAATTATATTAAAAAC
Found at i:510372 original size:27 final size:27
Alignment explanation
Indices: 510290--510360 Score: 117
Period size: 27 Copynumber: 2.6 Consensus size: 27
510280 AATATAATTA
510290 TTTTT-ATATTAAATTATATTAAAAACT
1 TTTTTAAT-TTAAATTATATTAAAAACT
*
510317 TTTTTATTTTAAATTATATTAAAAACT
1 TTTTTAATTTAAATTATATTAAAAACT
510344 TTTTTAATTTAAATTAT
1 TTTTTAATTTAAATTAT
510361 TTCAAATACT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 40 0.98
28 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTTTAATTTAAATTATATTAAAAACT
Found at i:512409 original size:14 final size:14
Alignment explanation
Indices: 512387--512422 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
512377 GCGACTACGT
512387 TGTTATTTGTATTA
1 TGTTATTTGTATTA
*
512401 TGTTTTTTGTATTA
1 TGTTATTTGTATTA
512415 TGTTATTT
1 TGTTATTT
512423 CACTAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (14 bp):
TGTTATTTGTATTA
Found at i:516195 original size:22 final size:23
Alignment explanation
Indices: 516154--516202 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
516144 GTATTTGTTA
516154 TGTAATCTTTAGAAGATATGATT
1 TGTAATCTTTAGAAGATATGATT
516177 CTGTAATC-TTAG-AGATATGATT
1 -TGTAATCTTTAGAAGATATGATT
516199 TGTA
1 TGTA
516203 GATAGCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 4 0.16
22 10 0.40
23 4 0.16
24 7 0.28
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (23 bp):
TGTAATCTTTAGAAGATATGATT
Found at i:529403 original size:161 final size:161
Alignment explanation
Indices: 529138--529467 Score: 624
Period size: 161 Copynumber: 2.0 Consensus size: 161
529128 CATTATTCTT
*
529138 TTTTACTGCTCTCATTAGTTCAAATTATTCTTGCTTATATATCATTGTTTAACTGGGGGAACCTG
1 TTTTACTGCTCTCATTAGTTCAAATTATTCTTGCTTATATATCATTGTTTAACTGGGGGAACCCG
*
529203 TATCACTTTGTGAAATGGACTTGATGACTTCTATTTGGTGCAATCAATCCTTTTAACTTTTTAAT
66 TATCACATTGTGAAATGGACTTGATGACTTCTATTTGGTGCAATCAATCCTTTTAACTTTTTAAT
*
529268 TTGGTTTGATTGAGCTATTCACTTTAATCTG
131 TTGGTTTGATCGAGCTATTCACTTTAATCTG
*
529299 TTTTACTTCTCTCATTAGTTCAAATTATTCTTGCTTATATATCATTGTTTAACTGGGGGAACCCG
1 TTTTACTGCTCTCATTAGTTCAAATTATTCTTGCTTATATATCATTGTTTAACTGGGGGAACCCG
529364 TATCACATTGTGAAATGGACTTGATGACTTCTATTTGGTGCAATCAATCCTTTTAACTTTTTAAT
66 TATCACATTGTGAAATGGACTTGATGACTTCTATTTGGTGCAATCAATCCTTTTAACTTTTTAAT
529429 TTGGTTTGATCGAGCTATTCACTTTAATCTG
131 TTGGTTTGATCGAGCTATTCACTTTAATCTG
529460 TTTTACTG
1 TTTTACTG
529468 GTACTGAGTT
Statistics
Matches: 164, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
161 164 1.00
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (161 bp):
TTTTACTGCTCTCATTAGTTCAAATTATTCTTGCTTATATATCATTGTTTAACTGGGGGAACCCG
TATCACATTGTGAAATGGACTTGATGACTTCTATTTGGTGCAATCAATCCTTTTAACTTTTTAAT
TTGGTTTGATCGAGCTATTCACTTTAATCTG
Found at i:532707 original size:31 final size:31
Alignment explanation
Indices: 532666--532761 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 31
532656 TAACTTTAAA
*
532666 AGTACTGGGACCAAATCTAAAATTCTATACG
1 AGTACAGGGACCAAATCTAAAATTCTATACG
*
532697 AGTACAGGG-----A-CTAAAACTT-TA-A-A
1 AGTACAGGGACCAAATCTAAAA-TTCTATACG
*
532720 AGTACTGGGACCAAATCTAAAATTCTATACG
1 AGTACAGGGACCAAATCTAAAATTCTATACG
532751 AGTACAGGGAC
1 AGTACAGGGAC
532762 TAACATCGCA
Statistics
Matches: 50, Mismatches: 5, Indels: 20
0.67 0.07 0.27
Matches are distributed among these distances:
23 8 0.16
24 1 0.02
25 8 0.16
26 3 0.06
28 3 0.06
29 8 0.16
30 1 0.02
31 18 0.36
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.23
Consensus pattern (31 bp):
AGTACAGGGACCAAATCTAAAATTCTATACG
Found at i:532721 original size:54 final size:54
Alignment explanation
Indices: 532657--532764 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
532647 TTGAATTTTT
532657 AACTTTAAAAGTACTGGGACCAAATCTAAAATTCTATACGAGTACAGGGACTAA
1 AACTTTAAAAGTACTGGGACCAAATCTAAAATTCTATACGAGTACAGGGACTAA
532711 AACTTTAAAAGTACTGGGACCAAATCTAAAATTCTATACGAGTACAGGGACTAA
1 AACTTTAAAAGTACTGGGACCAAATCTAAAATTCTATACGAGTACAGGGACTAA
532765 CATCGCATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (54 bp):
AACTTTAAAAGTACTGGGACCAAATCTAAAATTCTATACGAGTACAGGGACTAA
Found at i:536162 original size:13 final size:13
Alignment explanation
Indices: 536146--536208 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
536136 TTAATTACAT
536146 TGTTAAATTCTTC
1 TGTTAAATTCTTC
* *
536159 TGTTAAATTGTTAG
1 TGTTAAATTCTT-C
* *
536173 TGTGTTAATTACAT-
1 TGT-TAAATT-CTTC
536187 TGTTAAATTCTTC
1 TGTTAAATTCTTC
536200 TGTTAAATT
1 TGTTAAATT
536209 GTTAGTGTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
12 2 0.05
13 25 0.64
14 6 0.15
15 5 0.13
16 1 0.03
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (13 bp):
TGTTAAATTCTTC
Found at i:536181 original size:41 final size:41
Alignment explanation
Indices: 536136--536220 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
536126 TTAGGTTCAA
536136 TTAATTACATTGTTAAATTCTTCTGTTAAATTGTTAGTGTG
1 TTAATTACATTGTTAAATTCTTCTGTTAAATTGTTAGTGTG
536177 TTAATTACATTGTTAAATTCTTCTGTTAAATTGTTAGTGTG
1 TTAATTACATTGTTAAATTCTTCTGTTAAATTGTTAGTGTG
536218 TTA
1 TTA
536221 GTGTGACATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.52
Consensus pattern (41 bp):
TTAATTACATTGTTAAATTCTTCTGTTAAATTGTTAGTGTG
Found at i:537274 original size:20 final size:20
Alignment explanation
Indices: 537249--537290 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
537239 TTTATGATTG
537249 TTGAATTTGGAGATTTTAGA
1 TTGAATTTGGAGATTTTAGA
*
537269 TTGAATTTGGAGATTTTGGA
1 TTGAATTTGGAGATTTTAGA
537289 TT
1 TT
537291 TTGGGTGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (20 bp):
TTGAATTTGGAGATTTTAGA
Found at i:537339 original size:14 final size:15
Alignment explanation
Indices: 537322--537360 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
537312 TTTTGGATAA
537322 GATTTTTTATTT-GG
1 GATTTTTTATTTAGG
537336 GATTTTTT-TTTAGG
1 GATTTTTTATTTAGG
537350 G-TTTTTTATTT
1 GATTTTTTATTT
537361 TGGAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.13, C:0.00, G:0.18, T:0.69
Consensus pattern (15 bp):
GATTTTTTATTTAGG
Found at i:538014 original size:9 final size:9
Alignment explanation
Indices: 538000--538091 Score: 51
Period size: 9 Copynumber: 10.9 Consensus size: 9
537990 TATTTTAATA
538000 TAATAATTT
1 TAATAATTT
538009 TAATAATTT
1 TAATAATTT
538018 T-AT-ATTT
1 TAATAATTT
*
538025 CAA-AATATAAT
1 TAATAAT-T--T
538036 ATAATAATTT
1 -TAATAATTT
538046 TAATAATTT
1 TAATAATTT
538055 T-AT-ATTT
1 TAATAATTT
*
538062 CAA-AA---
1 TAATAATTT
*
538067 AAATAATTT
1 TAATAATTT
538076 TAATAATTT
1 TAATAATTT
538085 TAA-AATT
1 TAATAATT
538092 ATTTGTTGAT
Statistics
Matches: 65, Mismatches: 5, Indels: 27
0.67 0.05 0.28
Matches are distributed among these distances:
5 2 0.03
6 2 0.03
7 8 0.12
8 13 0.20
9 32 0.49
10 1 0.02
11 1 0.02
12 3 0.05
13 3 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (9 bp):
TAATAATTT
Found at i:538036 original size:37 final size:38
Alignment explanation
Indices: 537995--538091 Score: 153
Period size: 37 Copynumber: 2.6 Consensus size: 38
537985 AAATATATTT
*
537995 TAATATAATAATTTTAATAATTTTATATTTC-AAAATA
1 TAATATAATAATTTTAATAATTTTATATTTCAAAAAAA
538032 TAATATAATAATTTTAATAATTTTATATTTCAAAAAAA
1 TAATATAATAATTTTAATAATTTTATATTTCAAAAAAA
*
538070 TAATTTTAATAATTTTAA-AATT
1 TAA-TATAATAATTTTAATAATT
538092 ATTTGTTGAT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
37 31 0.55
38 12 0.21
39 13 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (38 bp):
TAATATAATAATTTTAATAATTTTATATTTCAAAAAAA
Done.