Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008685.1 Hibiscus syriacus cultivar Beakdansim tig00111708_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3669133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 19
Found at i:215503 original size:64 final size:65
Alignment explanation
Indices: 215430--215591 Score: 161
Period size: 64 Copynumber: 2.5 Consensus size: 65
215420 ATTGTTTGAA
* *** *
215430 GGTGTATCGATGCACAAGTAGTGCATCGATGCACT-CTTTTAATCTAA-AAACATCGAATGCAAT
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAAT-AAACAAACATCGAATGCAAT
215493 T
65 T
* * * *
215494 GGTGCATCGATGCATAAGGCA-TGCATCGATGCA-TCCCAGTAATAAACAAACATCGAATGTATT
1 GGTGCATCGATGCACAA-GTAGTGCATCGATGCACTCCCAGTAATAAACAAACATCGAATGCAAT
215557 T
65 T
** * *
215558 TATGCACCGATGCACATGTAGTGCATCGATGCAC
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCAC
215592 CGATAGGGAA
Statistics
Matches: 78, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
63 5 0.06
64 71 0.91
65 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (65 bp):
GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAATAAACAAACATCGAATGCAATT
Found at i:215587 original size:19 final size:20
Alignment explanation
Indices: 215560--215633 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
215550 ATGTATTTTA
*
215560 TGCACCGATGCAC-ATGTAG
1 TGCATCGATGCACGATGTAG
* *
215579 TGCATCGATGCACCGATAGGGAA
1 TGCATCGATGCA-CGAT--GTAG
*
215602 TGCATCGATACACTG-TGTAG
1 TGCATCGATGCAC-GATGTAG
215622 TGCATCGATGCA
1 TGCATCGATGCA
215634 TACCTTCATT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 11 0.26
20 14 0.33
21 2 0.05
22 2 0.05
23 14 0.33
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (20 bp):
TGCATCGATGCACGATGTAG
Found at i:216595 original size:103 final size:103
Alignment explanation
Indices: 216370--216587 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
216360 GTCGAGGGTC
* *
216370 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAAGTATGGTGAGACATATAC
1 TATGTGGTCCTTCCGGACATATATGTATTCTTTGGAACATATGTGAAGTATGGTGAGACACATAC
* *
216435 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
216473 TATGTGGTCCTTCCGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCCGGACATATATGTATTCTTTGGAACATATGTGAAGTATGGTGAGACACATAC
*
216538 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
216576 TATGTGGTCCTT
1 TATGTGGTCCTT
216588 ATGGACATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCCGGACATATATGTATTCTTTGGAACATATGTGAAGTATGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:216661 original size:23 final size:23
Alignment explanation
Indices: 216604--216669 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
216594 ATTATTATAT
* * *
216604 GGCACTACGATGTAATTCTACGC
1 GGCACTCCGGTGTAATTATACGC
*
216627 GGCACTCCGGTGTAATTATACGT
1 GGCACTCCGGTGTAATTATACGC
** *
216650 GGCACTTTGGTGCAATTATA
1 GGCACTCCGGTGTAATTATA
216670 TGAGCTGTGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (23 bp):
GGCACTCCGGTGTAATTATACGC
Found at i:219915 original size:29 final size:30
Alignment explanation
Indices: 219883--219956 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 30
219873 AAATAACAAA
* *
219883 AAAAATGAGGGATAATGTAT-ATTAACCAT
1 AAAAATGAGGGACAAGGTATAATTAACCAT
*
219912 AAAAATGAGGGGGCAAGGTATAATTAACCAT
1 AAAAATGA-GGGACAAGGTATAATTAACCAT
219943 AAAAAT-AGGGACAA
1 AAAAATGAGGGACAA
219957 ATCAAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 14 0.36
30 10 0.26
31 15 0.38
ACGTcount: A:0.50, C:0.08, G:0.22, T:0.20
Consensus pattern (30 bp):
AAAAATGAGGGACAAGGTATAATTAACCAT
Found at i:228655 original size:2 final size:2
Alignment explanation
Indices: 228648--228692 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
228638 TCTATGACCT
228648 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
228690 TA T
1 TA T
228693 TCTCATGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:233714 original size:20 final size:21
Alignment explanation
Indices: 233661--233722 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
233651 CCAGAACCCC
233661 AGGGGGTATCGGTTCCCCTTCAA
1 AGGGGGTATCGGTT-CCC-TCAA
*
233684 AGGGGGAATCGGTTCCCTC-A
1 AGGGGGTATCGGTTCCCTCAA
* *
233704 TGGGGGTATCGATTCCCTC
1 AGGGGGTATCGGTTCCCTC
233723 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.32, T:0.26
Consensus pattern (21 bp):
AGGGGGTATCGGTTCCCTCAA
Found at i:242676 original size:20 final size:20
Alignment explanation
Indices: 242653--242704 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
242643 TAAATGGGTG
242653 GTATCAATACCAAGAGGTTA
1 GTATCAATACCAAGAGGTTA
*
242673 GTATCGATACCAAGAGGTTA
1 GTATCAATACCAAGAGGTTA
242693 GTATCAATACCA
1 GTATCAATACCA
242705 TAGTATGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (20 bp):
GTATCAATACCAAGAGGTTA
Found at i:243005 original size:20 final size:19
Alignment explanation
Indices: 242980--243057 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
242970 TATCTAGCTC
242980 AAAGGATCGATCCCTTAGCA
1 AAAGGATCGATCCCTT-GCA
* *
243000 AAAGGATTGATCCCTTCGACC
1 AAAGGATCGATCCCTT-G-CA
* *
243021 AAAGGATTGATGCCCTTGAA
1 AAAGGATCGAT-CCCTTGCA
*
243041 AAAGGATCAATCCCTTG
1 AAAGGATCGATCCCTTG
243058 GACAACAGTG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
19 6 0.12
20 25 0.51
21 13 0.27
22 5 0.10
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (19 bp):
AAAGGATCGATCCCTTGCA
Found at i:243044 original size:41 final size:41
Alignment explanation
Indices: 242979--243056 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
242969 TTATCTAGCT
* **
242979 CAAAGGATCGATCCCTTAGCAAAAGGATTGATCCCTTCGAC
1 CAAAGGATCGATCCCTTAGAAAAAGGATCAATCCCTTCGAC
*
243020 CAAAGGATTGATGCCCTT-GAAAAAGGATCAATCCCTT
1 CAAAGGATCGAT-CCCTTAGAAAAAGGATCAATCCCTT
243057 GGACAACAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 27 0.84
42 5 0.16
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (41 bp):
CAAAGGATCGATCCCTTAGAAAAAGGATCAATCCCTTCGAC
Found at i:247213 original size:64 final size:65
Alignment explanation
Indices: 247140--247301 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 65
247130 ATTGTTTGAA
* * * *
247140 GGTGTATCGATGCACAAGTAGTGCATCGATGCACTCTC-TTAATCTAA-AAACATCGAATGCAAT
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAAT-AAACAAACATCGAATGCAAT
247203 T
65 T
* * * *
247204 GGTGCATCGATGCATAAGGCA-TGCATCGATGCA-TCCCAGTAATAAACAAACATCGAATGTATT
1 GGTGCATCGATGCACAA-GTAGTGCATCGATGCACTCCCAGTAATAAACAAACATCGAATGCAAT
247267 T
65 T
** * *
247268 TATGCACCGATGCACAGGTAGTGCATCGATGCAC
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCAC
247302 CGATAGGGAA
Statistics
Matches: 79, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
63 7 0.09
64 70 0.89
65 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (65 bp):
GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAATAAACAAACATCGAATGCAATT
Found at i:248321 original size:103 final size:103
Alignment explanation
Indices: 248088--248305 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
248078 GTTGAGGGTC
248088 TATGTGGTCCTTCGGGACATATATATATTCTTTAGAACATGTGTAAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTAGAACATGTGTAAAGTCTGGTGAGACACATAC
* *
248153 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* * * *
248191 TTTGTGGCCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTAGAACATGTGTAAAGTCTGGTGAGACACATAC
*
248256 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
248294 TATGTGGTCCTT
1 TATGTGGTCCTT
248306 ATGGACATTA
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATATATTCTTTAGAACATGTGTAAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:248379 original size:23 final size:23
Alignment explanation
Indices: 248321--248387 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
248311 CATTATTATA
*
248321 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
* * *
248344 CGGAACTCCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
** *
248367 TGGCACTTTGGTGTAATTATA
1 TGGCACTACGGTGCAATTATA
248388 TGAGCTGTGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:251333 original size:37 final size:36
Alignment explanation
Indices: 251291--251364 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
251281 CATTAAACCT
251291 TTTTAT-ATTTTCAATTTTGTAAAAAAAATTATATAAA
1 TTTTATAATTTT-AATTTTGTAAAAAAAA-TATATAAA
* *
251328 TTTTATGAATTTTAATTTTTTAAATAAAATATATAAA
1 TTTTAT-AATTTTAATTTTGTAAAAAAAATATATAAA
251365 AATATTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 14 0.42
38 14 0.42
39 5 0.15
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (36 bp):
TTTTATAATTTTAATTTTGTAAAAAAAATATATAAA
Found at i:251669 original size:30 final size:30
Alignment explanation
Indices: 251619--251707 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 30
251609 GGAGGTAAAA
* * * *
251619 TATAACTAATCATAAAAAATGAGGGATAATG
1 TATAATTAACCAT-AAAAATGAGGGACAAGG
*
251650 TATAATTAACCATAAAAATGAGGGGGCAAGG
1 TATAATTAACCATAAAAATGA-GGGACAAGG
251681 TATAATTAACCATAAAAAT-AGGGACAA
1 TATAATTAACCATAAAAATGAGGGACAA
251708 ATCAAAATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
29 6 0.12
30 9 0.18
31 36 0.71
ACGTcount: A:0.51, C:0.09, G:0.18, T:0.22
Consensus pattern (30 bp):
TATAATTAACCATAAAAATGAGGGACAAGG
Found at i:258812 original size:44 final size:41
Alignment explanation
Indices: 258717--258821 Score: 106
Period size: 44 Copynumber: 2.5 Consensus size: 41
258707 AAGTTAGAGT
*
258717 CCTCAATTTTAAAGATAAAAGTGAGATTAAAAAAATAGGGA
1 CCTCAATTATAAAGATAAAAGTGAGATTAAAAAAATAGGGA
* * *
258758 CTTCGATTATAAA-ATTAGAAAGTGATATTGAAAAAAATTGAGGG-
1 CCTCAATTATAAAGA-TA-AAAGTGAGATT-AAAAAAA-T-AGGGA
*
258802 CCTCAATTATAAATATAAAA
1 CCTCAATTATAAAGATAAAA
258822 AGTTAATCTA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
40 1 0.02
41 12 0.23
42 10 0.19
43 10 0.19
44 14 0.27
45 5 0.10
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.28
Consensus pattern (41 bp):
CCTCAATTATAAAGATAAAAGTGAGATTAAAAAAATAGGGA
Found at i:258824 original size:44 final size:41
Alignment explanation
Indices: 258678--258824 Score: 109
Period size: 41 Copynumber: 3.4 Consensus size: 41
258668 TAGGGATATA
* * ** * *
258678 AATTATAAAAGTAAAAGGTTAGATTGAAAAAGTTAGAGTCCTC
1 AATTATAAAA-TAAAAAGTGAGATT-AAAAAAATAGGGACCTC
* *
258721 AATTTTAAAGAT-AAAAGTGAGATTAAAAAAATAGGGACTTC
1 AATTATAAA-ATAAAAAGTGAGATTAAAAAAATAGGGACCTC
* * *
258762 GATTATAAAATTAGAAAGTGATATTGAAAAAAATTGAGGG-CCTC
1 AATTATAAAA-TAAAAAGTGAGATT-AAAAAAA-T-AGGGACCTC
258806 AATTATAAATATAAAAAGT
1 AATTATAAA-ATAAAAAGT
258825 TAATCTAAGT
Statistics
Matches: 82, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
40 1 0.01
41 20 0.24
42 20 0.24
43 16 0.20
44 20 0.24
45 5 0.06
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.28
Consensus pattern (41 bp):
AATTATAAAATAAAAAGTGAGATTAAAAAAATAGGGACCTC
Found at i:262257 original size:21 final size:20
Alignment explanation
Indices: 262212--262283 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
262202 TATCTAGCTC
262212 AAGGATCGATCCCTTAGCAA
1 AAGGATCGATCCCTTAGCAA
* *
262232 AAGGATCGATCCCTTCGACCA
1 AAGGATCGATCCCTTAG-CAA
262253 AAGGATCGATCCCCTT-G-AA
1 AAGGATCGAT-CCCTTAGCAA
*
262272 AATGATCGATCC
1 AAGGATCGATCC
262284 TTGGACCAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.04
19 10 0.22
20 16 0.35
21 13 0.28
22 5 0.11
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (20 bp):
AAGGATCGATCCCTTAGCAA
Found at i:262373 original size:20 final size:20
Alignment explanation
Indices: 262312--262377 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 20
262302 TAGGAGAAAT
262312 CCCTTGAAAAATGATTATCGAT-
1 CCCTTGAAAAATG---ATCGATC
* *
262334 CCCTTCGACCAAAGGATCGATC
1 CCCTT-GA-AAAATGATCGATC
262356 CCCTTGAAAAATGATCGATC
1 CCCTTGAAAAATGATCGATC
262376 CC
1 CC
262378 TTGGACAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 13 0.35
21 8 0.22
22 10 0.27
23 2 0.05
24 4 0.11
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (20 bp):
CCCTTGAAAAATGATCGATC
Found at i:262406 original size:93 final size:93
Alignment explanation
Indices: 262236--262421 Score: 340
Period size: 93 Copynumber: 2.0 Consensus size: 93
262226 TAGCAAAAGG
262236 ATCGATCCCTTCGACCAAAGGATCGATCCCCTTGAAAATGATCGATCCTTGGACCAACAATGAGT
1 ATCGATCCCTTCGACCAAAGGATCGATCCCCTTGAAAATGATCGATCCTTGGACCAACAATGAGT
262301 TTAGGAGAAATCCCTTG-AAAAATGATT
66 TTAGGAGAAATCCCTTGAAAAAATGATT
262328 ATCGATCCCTTCGACCAAAGGATCGATCCCCTTGAAAAATGATCGATCCCTTGGA-CAACAATGA
1 ATCGATCCCTTCGACCAAAGGATCGATCCCCTTG-AAAATGATCGAT-CCTTGGACCAACAATGA
262392 GTTTAGGAGAAATCCCTTGAAAAAATGATT
64 GTTTAGGAGAAATCCCTTGAAAAAATGATT
262422 GATCCCTCGA
Statistics
Matches: 91, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
92 34 0.37
93 40 0.44
94 17 0.19
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (93 bp):
ATCGATCCCTTCGACCAAAGGATCGATCCCCTTGAAAATGATCGATCCTTGGACCAACAATGAGT
TTAGGAGAAATCCCTTGAAAAAATGATT
Found at i:276162 original size:11 final size:11
Alignment explanation
Indices: 276146--276187 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
276136 GAAAGAGACC
276146 ATTAAATTATT
1 ATTAAATTATT
276157 ATTAAATTA-T
1 ATTAAATTATT
*
276167 A-TAAACTATT
1 ATTAAATTATT
*
276177 AATAAATTATT
1 ATTAAATTATT
276188 TAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 6 0.22
10 4 0.15
11 17 0.63
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTAAATTATT
Found at i:276171 original size:20 final size:20
Alignment explanation
Indices: 276148--276191 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
276138 AAGAGACCAT
* *
276148 TAAATTATTATTAAATTATA
1 TAAACTATTAATAAATTATA
*
276168 TAAACTATTAATAAATTATT
1 TAAACTATTAATAAATTATA
276188 TAAA
1 TAAA
276192 ATAAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAACTATTAATAAATTATA
Found at i:276542 original size:3 final size:3
Alignment explanation
Indices: 276534--276565 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
276524 GATGGCCCAC
276534 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
276566 GGCGACTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:276855 original size:11 final size:11
Alignment explanation
Indices: 276839--276888 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
276829 GAATCGGTAA
276839 AAAACCGGCTG
1 AAAACCGGCTG
276850 AAAACCGG--G
1 AAAACCGGCTG
*
276859 AAAACCGGGGTG
1 AAAACC-GGCTG
276871 --AACCGGCTG
1 AAAACCGGCTG
276880 AAAACCGGC
1 AAAACCGGC
276889 AAAACCAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
9 11 0.33
10 6 0.18
11 15 0.45
12 1 0.03
ACGTcount: A:0.36, C:0.26, G:0.32, T:0.06
Consensus pattern (11 bp):
AAAACCGGCTG
Found at i:276905 original size:30 final size:30
Alignment explanation
Indices: 276840--276905 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
276830 AATCGGTAAA
* *
276840 AAACCGGCTGAAAACCGGGAAAACCGGGGT
1 AAACCGGCTGAAAACCGGCAAAACCAGGGT
* **
276870 GAACCGGCTGAAAACCGGCAAAACCAGTTT
1 AAACCGGCTGAAAACCGGCAAAACCAGGGT
276900 AAACCG
1 AAACCG
276906 CCGGTTCACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.38, C:0.26, G:0.27, T:0.09
Consensus pattern (30 bp):
AAACCGGCTGAAAACCGGCAAAACCAGGGT
Found at i:277155 original size:25 final size:24
Alignment explanation
Indices: 277127--277183 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
277117 TAGAAGTTTG
277127 ATTGAAGCCAAAAAATTTGAGCTCA
1 ATTGAAGCC-AAAAATTTGAGCTCA
* *
277152 ATTGAAGCCTAGAATTTGAGCTCA
1 ATTGAAGCCAAAAATTTGAGCTCA
277176 ATTGAAGC
1 ATTGAAGC
277184 GAAAGAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 21 0.70
25 9 0.30
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (24 bp):
ATTGAAGCCAAAAATTTGAGCTCA
Found at i:279405 original size:22 final size:21
Alignment explanation
Indices: 279380--279420 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
279370 CTCTGCCTAA
279380 AATTTACATTTAATAT-TTTATT
1 AATTTA-A-TTAATATATTTATT
279402 AATTTAATTAATATATTTA
1 AATTTAATTAATATATTTA
279421 AAAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTTAATTAATATATTTATT
Found at i:281353 original size:13 final size:13
Alignment explanation
Indices: 281309--281355 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
281299 ATGTTCTTTG
*
281309 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
281323 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
281335 TTTATTTAAAATAA
1 -ATATTTAAAATAA
281349 ATATTTA
1 ATATTTA
281356 TTTAATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:281367 original size:15 final size:16
Alignment explanation
Indices: 281329--281371 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
281319 CTAAATATTA
281329 AAATAATTTATTTAAAAT
1 AAAT-ATTTATTT-AAAT
281347 AAATATTTATTT-AAT
1 AAATATTTATTTAAAT
*
281362 ATATATTTAT
1 AAATATTTAT
281372 AACAACATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 12 0.50
17 8 0.33
18 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATATTTATTTAAAT
Found at i:282649 original size:12 final size:12
Alignment explanation
Indices: 282632--282656 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
282622 TTAGGGTTAG
282632 GAAACCCTAACT
1 GAAACCCTAACT
282644 GAAACCCTAACT
1 GAAACCCTAACT
282656 G
1 G
282657 TTTTGGGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.32, G:0.12, T:0.16
Consensus pattern (12 bp):
GAAACCCTAACT
Found at i:282724 original size:12 final size:11
Alignment explanation
Indices: 282707--282783 Score: 60
Period size: 9 Copynumber: 7.3 Consensus size: 11
282697 TGGCTTTGTA
282707 ATATTAAATAAT
1 ATATT-AATAAT
282719 ATATTAATAAT
1 ATATTAATAAT
282730 A-A-TAATAATT
1 ATATTAATAA-T
282740 ATAATT-ATAATT
1 AT-ATTAATAA-T
*
282752 ATAATAATAAT
1 ATATTAATAAT
282763 A-ATT-ATAAT
1 ATATTAATAAT
282772 A-A-TAATAAT
1 ATATTAATAAT
282781 ATA
1 ATA
282784 AATAAAATGA
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
8 1 0.02
9 19 0.34
10 6 0.11
11 11 0.20
12 18 0.32
13 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATTAATAAT
Found at i:282729 original size:3 final size:3
Alignment explanation
Indices: 282713--282781 Score: 86
Period size: 3 Copynumber: 23.3 Consensus size: 3
282703 TGTAATATTA
* * * *
282713 AAT AAT -AT ATT AAT AAT AAT AAT AAT TAT AAT TAT AAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
282760 AAT AAT TAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
282782 TAAATAAAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:283347 original size:228 final size:228
Alignment explanation
Indices: 283081--284787 Score: 3288
Period size: 228 Copynumber: 7.5 Consensus size: 228
283071 TAGAATTATG
*
283081 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
283146 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
66 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
*
283211 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
131 CTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
283276 GGCAATGTTGATCCATCAAATGATGAATTCAAA
196 GGCAATGTTGATCCATCAAATGATGAATTCAAA
283309 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
283374 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATT
66 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
283439 CTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
131 CTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
283504 GGCAATGTTGATCCATCAAATGATGAATTCAAA
196 GGCAATGTTGATCCATCAAATGATGAATTCAAA
283537 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
283602 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
66 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
**
283667 CTTCTCATTATGAATTTCTTCTTCCTTCATCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
131 CTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
283732 GGCAATGTTGATCCATCAAATGATGAATTCAAA
196 GGCAATGTTGATCCATCAAATGATGAATTCAAA
283765 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
283830 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATT
66 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
283895 CTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
131 CTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
283960 GGCAATGTTGATCCATCAAATGATGAATTCAAA
196 GGCAATGTTGATCCATCAAATGATGAATTCAAA
283993 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
284058 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
66 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
**
284123 CTTCTCATTATGAATTTCTTCTTCCTTCATCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
131 CTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
284188 GGCAATGTTGATCCATCAAATGATGAATTCAAA
196 GGCAATGTTGATCCATCAAATGATGAATTCAAA
284221 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
284286 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATT
66 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
284351 CTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
131 CTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
284416 GGCAATGTTGATCCATCAAATGATGAATTCAAA
196 GGCAATGTTGATCCATCAAATGATGAATTCAAA
284449 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
284514 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
66 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
284579 CTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
131 CTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
284644 GGCAATGTTGATCCATCAAATGATGAATTCAAA
196 GGCAATGTTGATCCATCAAATGATGAATTCAAA
284677 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
284742 TTATGAACTTCTCTGGCAATGTTGATCCATCAAGTGATGGATTTGA
66 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGA
284788 ATCTTTGCTA
Statistics
Matches: 1458, Mismatches: 21, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
228 1458 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (228 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
CTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
GGCAATGTTGATCCATCAAATGATGAATTCAAA
Found at i:285984 original size:83 final size:83
Alignment explanation
Indices: 285509--285969 Score: 850
Period size: 83 Copynumber: 5.6 Consensus size: 83
285499 GTAGTTCCTA
*
285509 CCAAACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
285574 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * *
285592 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
285657 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
** *
285675 TTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCATCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
285740 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
285758 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCCATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
285823 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
285841 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
285906 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
285924 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
285970 TGGCCAATTT
Statistics
Matches: 363, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 363 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:287144 original size:13 final size:12
Alignment explanation
Indices: 287125--287174 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
287115 ACCCTCCTTT
287125 TTCTTTTTTTTC
1 TTCTTTTTTTTC
287137 -TCTCTTTTTTTC
1 TTCT-TTTTTTTC
*
287149 TT-TTTTTTTTT
1 TTCTTTTTTTTC
*
287160 TTCTTTCTTTTC
1 TTCTTTTTTTTC
287172 TTC
1 TTC
287175 AAGCATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
11 12 0.38
12 19 0.59
13 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTCTTTTTTTTC
Found at i:287171 original size:9 final size:9
Alignment explanation
Indices: 287123--287173 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
287113 TGACCCTCCT
*
287123 TTTTCTTTT
1 TTTTCTTTC
*
287132 TTTTCTCTC
1 TTTTCTTTC
287141 TTTT-TTTC
1 TTTTCTTTC
* *
287149 TTTTTTTTT
1 TTTTCTTTC
287158 TTTTCTTTC
1 TTTTCTTTC
287167 TTTTCTT
1 TTTTCTT
287174 CAAGCATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 7 0.20
9 28 0.80
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:298526 original size:13 final size:13
Alignment explanation
Indices: 298482--298528 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
298472 CTGTTCTTTG
*
298482 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
298496 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
298508 TTTATTTAAAATAA
1 -ATATTTAAAATAA
298522 ATATTTA
1 ATATTTA
298529 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:299893 original size:3 final size:3
Alignment explanation
Indices: 299877--299947 Score: 60
Period size: 3 Copynumber: 24.7 Consensus size: 3
299867 TGTAATATTA
* * * * *
299877 AAT AAT -AT ATT AAT AAT AAT AAT TAT TAT AAT TAT AAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
299924 AAT AAT -AT AAAT AA- AAT AA- AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT AA
299948 AAAATGAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
2 8 0.15
3 45 0.82
4 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:300802 original size:32 final size:32
Alignment explanation
Indices: 300758--300837 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
300748 ATATTCATGT
* *
300758 GGGTCGGGTTTTTTT-TAAAAAAATCAG-GGTC
1 GGGTCGGATTTTTTTAAAAAAAAATC-GTGGTC
*
300789 GGGTCGGATTTTTTTAAAAAAAAATCGTGTTC
1 GGGTCGGATTTTTTTAAAAAAAAATCGTGGTC
*
300821 GGATCGGATTTTTTTAA
1 GGGTCGGATTTTTTTAA
300838 GTTTGATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
31 15 0.35
32 28 0.65
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
GGGTCGGATTTTTTTAAAAAAAAATCGTGGTC
Found at i:301721 original size:21 final size:21
Alignment explanation
Indices: 301679--301721 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
301669 TTTCTGGGCT
* *
301679 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
301700 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
301721 A
1 A
301722 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:301773 original size:20 final size:20
Alignment explanation
Indices: 301748--301785 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
301738 GAATGCTAGA
301748 GGGGAATCGATACCCCCAGG
1 GGGGAATCGATACCCCCAGG
*
301768 GGGGAATCGATTCCCCCA
1 GGGGAATCGATACCCCCA
301786 TAATGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.32, G:0.32, T:0.13
Consensus pattern (20 bp):
GGGGAATCGATACCCCCAGG
Found at i:303056 original size:31 final size:30
Alignment explanation
Indices: 302972--303071 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 30
302962 GAGTCGAGGG
* * *
302972 TACCTATGTTCTACGGAACATATGGACGGAA
1 TACCTATGTTTTA-GGAACATATGGACAGTA
*
303003 TTACCTATGTCTTT-CGAGACATATGGACAGTA
1 -TACCTATGT-TTTAGGA-ACATATGGACAGTA
* *
303035 TACCTATGTTTTAAGGAACATATGGATAGTT
1 TACCTATGTTTT-AGGAACATATGGACAGTA
303066 TACCTA
1 TACCTA
303072 GGTTCTTCGG
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
30 3 0.05
31 29 0.51
32 23 0.40
33 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (30 bp):
TACCTATGTTTTAGGAACATATGGACAGTA
Found at i:303116 original size:30 final size:30
Alignment explanation
Indices: 303082--303424 Score: 659
Period size: 30 Copynumber: 11.4 Consensus size: 30
303072 GGTTCTTCGG
*
303082 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
303112 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
303142 GACCTCTGGATAGTTATCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
303172 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
303202 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
303232 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
303262 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
303292 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
303322 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
303352 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
303382 GACCTCTGGATAGTTATCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
303412 GACCTCTGGATAG
1 GACCTCTGGATAG
303425 GTCCTTCGGA
Statistics
Matches: 309, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 309 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:306398 original size:21 final size:21
Alignment explanation
Indices: 306356--306398 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
306346 TTTCTGGGCT
* *
306356 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
306377 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
306398 A
1 A
306399 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:306450 original size:20 final size:20
Alignment explanation
Indices: 306425--306462 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
306415 GAATGCTAGA
306425 GGGGAATCGATACCCCCAGG
1 GGGGAATCGATACCCCCAGG
*
306445 GGGGAATCGATTCCCCCA
1 GGGGAATCGATACCCCCA
306463 TAATGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.32, G:0.32, T:0.13
Consensus pattern (20 bp):
GGGGAATCGATACCCCCAGG
Found at i:307730 original size:31 final size:30
Alignment explanation
Indices: 307646--307745 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 30
307636 GAGTCGAGGG
* * *
307646 TACCTATGTTCTACGGAACATATGGACGGAA
1 TACCTATGTTTTA-GGAACATATGGACAGTA
*
307677 TTACCTATGTCTTT-CGAGACATATGGACAGTA
1 -TACCTATGT-TTTAGGA-ACATATGGACAGTA
* *
307709 TACCTATGTTTTAAGGAACATATGGATAGTT
1 TACCTATGTTTT-AGGAACATATGGACAGTA
307740 TACCTA
1 TACCTA
307746 GGTTCTTCAG
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
30 3 0.05
31 29 0.51
32 23 0.40
33 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (30 bp):
TACCTATGTTTTAGGAACATATGGACAGTA
Found at i:307790 original size:30 final size:30
Alignment explanation
Indices: 307731--308038 Score: 553
Period size: 30 Copynumber: 10.2 Consensus size: 30
307721 AAGGAACATA
* * * * *
307731 TGGATAGTTTACCTAGGTTCTTCAGGACCTA
1 TGGATAG-TTACCGAGGATCTTTATGACCTC
307762 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
307792 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
307822 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
307852 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
307882 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
307912 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
307942 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
307972 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
308002 TGGATAGTTATCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
308032 TGGATAG
1 TGGATAG
308039 GTCCTTCGGA
Statistics
Matches: 271, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
30 264 0.97
31 7 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:310571 original size:20 final size:20
Alignment explanation
Indices: 310546--310780 Score: 192
Period size: 20 Copynumber: 11.7 Consensus size: 20
310536 GATTTTCCAT
* *
310546 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
310566 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
310586 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
310605 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
310627 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
310647 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
310668 AATCGCAACGAC-AATACGTA
1 AATCGCAACG-CGAATACGTA
*
310688 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
**
310708 AATCGCAACAAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * * *
310728 AATCACAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
310748 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
310768 AATCGCAACGCGA
1 AATCGCAACGCGA
310781 TTTTTAAAGC
Statistics
Matches: 178, Mismatches: 28, Indels: 18
0.79 0.12 0.08
Matches are distributed among these distances:
18 1 0.01
19 4 0.02
20 129 0.72
21 42 0.24
22 2 0.01
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:310638 original size:41 final size:41
Alignment explanation
Indices: 310607--310697 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
310597 GATTCTGACT
** *
310607 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* *
310648 ATCGCAACGACAATACGTAAAATCGCAACGAC-AATACGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACG-CGTATCCGTAA
310689 ATCGCAACG
1 ATCGCAACG
310698 CGTATCTGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 43 0.98
42 1 0.02
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.16
Consensus pattern (41 bp):
ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:311062 original size:34 final size:36
Alignment explanation
Indices: 311015--311116 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
311005 TTTCGTCCTA
*
311015 CTAGGATTGAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
311050 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
311085 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
311117 GTTCTACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:311722 original size:16 final size:18
Alignment explanation
Indices: 311701--311735 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
311691 TTTACTCATT
311701 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
311717 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
311735 T
1 T
311736 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:314412 original size:8 final size:8
Alignment explanation
Indices: 314399--314437 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
314389 GAACATTTCG
*
314399 TGCATTCT
1 TGCATTTT
314407 TGCA-TTT
1 TGCATTTT
314414 TGCATTTT
1 TGCATTTT
*
314422 TGCCTTTT
1 TGCATTTT
314430 TGCATTTT
1 TGCATTTT
314438 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:315629 original size:10 final size:10
Alignment explanation
Indices: 315606--315676 Score: 51
Period size: 10 Copynumber: 7.4 Consensus size: 10
315596 AACAAAAAAG
*
315606 AAAAGAAGC-
1 AAAAAAAGCA
315615 AAAAAAAGCA
1 AAAAAAAGCA
*
315625 AAAAAAAACA
1 AAAAAAAGCA
315635 AAGAAAAAG-A
1 AA-AAAAAGCA
* *
315645 GAAACAAG--
1 AAAAAAAGCA
* *
315653 AACAAAAGGA
1 AAAAAAAGCA
315663 AAAAAAAGCA
1 AAAAAAAGCA
315673 AAAA
1 AAAA
315677 TCAAAAAAGA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
8 5 0.10
9 13 0.27
10 25 0.52
11 5 0.10
ACGTcount: A:0.77, C:0.08, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAGCA
Found at i:315644 original size:38 final size:38
Alignment explanation
Indices: 315600--315674 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
315590 ATCAAGAACA
*
315600 AAAAAGA-AAAGAAGCAAAAAAAGCAAAAAAAAACAAAG
1 AAAAAGAGAAACAAG-AAAAAAAGCAAAAAAAAACAAAG
* * *
315638 AAAAAGAGAAACAAGAACAAAAGGAAAAAAAAGCAAA
1 AAAAAGAGAAACAAGAAAAAAAGCAAAAAAAAACAAA
315675 AATCAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 26 0.81
39 6 0.19
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (38 bp):
AAAAAGAGAAACAAGAAAAAAAGCAAAAAAAAACAAAG
Found at i:316342 original size:22 final size:22
Alignment explanation
Indices: 316317--316365 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
316307 CCATCAATCT
* *
316317 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
316339 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
316361 TTTGA
1 TTTGA
316366 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:317335 original size:71 final size:73
Alignment explanation
Indices: 317252--317575 Score: 212
Period size: 72 Copynumber: 4.6 Consensus size: 73
317242 ATTTTTCTTA
* * * * * *
317252 AAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTAG-AA-GAGTTTTATCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCATCTATCTTGAGACAG
*
317314 TTTCCCTTG
65 TTTCCCTTC
* * *
317323 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCATCTATCTTGAGACAGT
317387 TTCCCTTC
66 TTCCCTTC
* * * *
317395 AAATAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA----A--TAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCATCTATCTTGAGACA-G
* * *
317451 TTTTCTTTG
65 TTTCCCTTC
* * ** * * * ** *
317460 AAACAAATTCTGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAAC-AAATTTCATCTATCTTGAGACAG
* *
317524 TTTCTCTTG
65 TTTCCCTTC
* * *
317533 AAAC-AATTTTCGTCTATCTTGAGACAG-TTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTAGAAACAAA
317576 ACCTTTGAAT
Statistics
Matches: 202, Mismatches: 37, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
64 2 0.01
65 45 0.22
66 5 0.02
70 8 0.04
71 25 0.12
72 76 0.38
73 39 0.19
74 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCATCTATCTTGAGACAGT
TTCCCTTC
Found at i:317342 original size:36 final size:36
Alignment explanation
Indices: 317294--317575 Score: 303
Period size: 36 Copynumber: 8.0 Consensus size: 36
317284 ACTAGAAGAG
*
317294 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
317330 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * *
317366 TTTCGTCTATCTTGAGACAGTTTCCCTTCAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
317402 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
317438 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
* * ** * *
317467 TTCTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
317504 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
317539 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
317576 ACCTTTGAAT
Statistics
Matches: 203, Mismatches: 31, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 139 0.68
37 35 0.17
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:317533 original size:102 final size:102
Alignment explanation
Indices: 317350--317538 Score: 274
Period size: 102 Copynumber: 1.9 Consensus size: 102
317340 CTTGAGACAG
*
317350 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTCAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTCAAATAAATTTTGTCTCTCTT
317415 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* ** * * *
317452 TTTCT-TTGAAACAAA-TTCTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 TTTCTCTTGAAACAAATTTC-GTCTACCTTGAGACAGTTTCCCTT-CAAATAAATTTTGTCTCTC
*
317515 TTGAGACAGTTTCTCTTGAAACAA
64 TTGAGACAGTTTCCCTTGAAACAA
317539 TTTTCGTCTA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
100 3 0.04
101 30 0.39
102 44 0.57
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTCAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:317572 original size:138 final size:137
Alignment explanation
Indices: 317314--317638 Score: 436
Period size: 138 Copynumber: 2.4 Consensus size: 137
317304 CTTGAGACAG
*
317314 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
* *
317379 GAGACAGTTTCCCTTCAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTCAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
*
317444 GAATATG
131 GAATATA
* * * * * * * *
317451 TTTTCTTTGAAACAAATTCTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * * *
317516 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACCT
65 TGAGACAGTTTCCCTTCAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAACAT
*
317580 TTGAATTTA
129 TTGAATATA
* * * *
317589 TTTCCCCTAAAACAAATTTTATCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
317639 CAAAATCTTC
Statistics
Matches: 160, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
137 50 0.31
138 110 0.69
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTCAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
GAATATA
Found at i:317668 original size:67 final size:68
Alignment explanation
Indices: 317550--317706 Score: 203
Period size: 68 Copynumber: 2.4 Consensus size: 68
317540 TTTCGTCTAT
* **
317550 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTTATC
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTATC
317612 TCC
66 TCC
* * * * *
317615 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTATC
317680 TCC
66 TCC
* *
317683 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
317707 ACAGATATCT
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 28 0.36
68 31 0.40
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTATC
TCC
Found at i:318535 original size:105 final size:105
Alignment explanation
Indices: 318350--319286 Score: 1452
Period size: 105 Copynumber: 9.0 Consensus size: 105
318340 GCACTCGAGG
* * * *
318350 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
*
318415 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
318456 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
318521 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
318561 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
318626 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
318666 CAACGCAAGTTCAACTTCATGACGAAGGGACCGTTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
318731 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
318771 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
318836 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
318876 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
318941 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
318981 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTAAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
319046 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
319086 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAAA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
319146 TTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * ** * *
319186 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAT
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* ** *
319251 AACCAATTTCAACTTCATGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
319287 TGGAACAATG
Statistics
Matches: 781, Mismatches: 44, Indels: 12
0.93 0.05 0.01
Matches are distributed among these distances:
100 80 0.10
101 3 0.00
102 3 0.00
103 4 0.01
104 3 0.00
105 614 0.79
106 74 0.09
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:319881 original size:34 final size:36
Alignment explanation
Indices: 319834--319935 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
319824 TTTCGTCCTA
*
319834 CTAGGATTGAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
319869 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
319904 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
319936 GTTCTACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:320385 original size:2 final size:2
Alignment explanation
Indices: 320380--320410 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
320370 TTAGTGTTAT
320380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
320411 TTCCTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:320549 original size:16 final size:18
Alignment explanation
Indices: 320528--320562 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
320518 TTTACTCATT
320528 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
320544 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
320562 T
1 T
320563 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:321378 original size:20 final size:20
Alignment explanation
Indices: 321353--321442 Score: 68
Period size: 20 Copynumber: 4.8 Consensus size: 20
321343 TTCTAAACTT
*
321353 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
*
321373 AAAATCGTAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
321393 ACTATCGC-A-ACG---A-G
1 AAAATCGCAACACGAAAATG
* *
321407 AGAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
321426 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
321443 CCAAAATCGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 7 0.13
15 2 0.04
16 2 0.04
18 4 0.07
19 15 0.27
20 25 0.45
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:321433 original size:19 final size:19
Alignment explanation
Indices: 321409--321453 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
321399 GCAACGAGAG
**
321409 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
321428 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
321447 AATCGCA
1 AATCGCA
321454 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:321490 original size:14 final size:14
Alignment explanation
Indices: 321471--321527 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
321461 TTTCATTTCG
321471 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
321485 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
321504 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
321518 CGTTGCGATT
1 CGTTGCGATT
321528 TTCATTTCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:321496 original size:33 final size:33
Alignment explanation
Indices: 321454--321575 Score: 181
Period size: 33 Copynumber: 3.5 Consensus size: 33
321444 CAAAATCGCA
321454 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
321487 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
321520 TTGCGATTTTCATTTCCGCGTTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGCG------ATTCTCTCG
321560 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
321576 AACCAAAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
33 48 0.59
34 9 0.11
39 1 0.01
40 24 0.29
ACGTcount: A:0.10, C:0.24, G:0.19, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:321543 original size:20 final size:19
Alignment explanation
Indices: 321449--321575 Score: 130
Period size: 20 Copynumber: 7.1 Consensus size: 19
321439 GAAACCAAAA
*
321449 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
321468 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
321482 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
321501 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
321515 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
321534 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
321554 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
321574 TC
1 TC
321576 AACCAAAAGA
Statistics
Matches: 90, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
14 20 0.22
16 6 0.07
17 6 0.07
19 23 0.26
20 34 0.38
21 1 0.01
ACGTcount: A:0.10, C:0.24, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:321696 original size:25 final size:26
Alignment explanation
Indices: 321642--321698 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
321632 TTATGTTTAT
*
321642 TGTTTATGGTATATCTTCACATTGTA
1 TGTTTATGGTATATCTTAACATTGTA
*
321668 -GTTTTTGGTATATC-TAAC-TTGGTA
1 TGTTTATGGTATATCTTAACATT-GTA
321692 TGTTTAT
1 TGTTTAT
321699 TATTTTTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 2 0.08
24 6 0.23
25 18 0.69
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.53
Consensus pattern (26 bp):
TGTTTATGGTATATCTTAACATTGTA
Found at i:323431 original size:94 final size:94
Alignment explanation
Indices: 323270--323648 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
323260 TAGATTGCTT
* * *
323270 AGTAAATTTATTTGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
323335 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
323364 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
323429 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
323458 AGTAAATTTGTTCGGTTGCTGTCAA-TCTGCTAAAATGTGTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
323522 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
323551 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
323616 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
323644 AGTAA
1 AGTAA
323649 TGCAATCCAT
Statistics
Matches: 271, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
93 116 0.43
94 155 0.57
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:323612 original size:187 final size:187
Alignment explanation
Indices: 323270--323648 Score: 645
Period size: 187 Copynumber: 2.0 Consensus size: 187
323260 TAGATTGCTT
* * * *
323270 AGTAAATTTATTTGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAATGTGTATTCTTTAACACTGTGAAGTTAAT
323335 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC
*
323400 TGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
323458 AGTAAATTTGTTCGGTTGCTGTCAAT-CTGCTAAAATGTGTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAATGTGTATTCTTTAACACTGTGAAGTTAAT
*
323522 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAA
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-AAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAA
*
323586 CTGTGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
130 CTGTGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
323644 AGTAA
1 AGTAA
323649 TGCAATCCAT
Statistics
Matches: 181, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
186 26 0.14
187 132 0.73
188 23 0.13
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (187 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAATGTGTATTCTTTAACACTGTGAAGTTAAT
ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC
TGTGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:323752 original size:19 final size:19
Alignment explanation
Indices: 323696--323820 Score: 116
Period size: 19 Copynumber: 6.7 Consensus size: 19
323686 TAGTTTACTT
* *
323696 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
323716 TCGCAACGTGAAAAATGACTA
1 TCGCAACGCG--AAATGAAAA
323737 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
323756 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
323770 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
**
323789 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
323808 TCGCAACGCGAAA
1 TCGCAACGCGAAA
323821 CTATAATCGC
Statistics
Matches: 86, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 47 0.55
20 8 0.09
21 12 0.14
22 3 0.03
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:323854 original size:19 final size:19
Alignment explanation
Indices: 323832--323933 Score: 88
Period size: 19 Copynumber: 5.5 Consensus size: 19
323822 TATAATCGCG
323832 TTGCGATTTTCATTTCTCA
1 TTGCGATTTTCATTTCTCA
323851 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCTCA
* *
323865 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCTCA
* *
323884 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCTCA
** *
323903 TTGCGATAGTCATTTTTCA
1 TTGCGATTTTCATTTCTCA
323922 CGTTGCGATTTT
1 --TTGCGATTTT
323934 AAGTTCCAGA
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
14 11 0.16
16 3 0.04
17 3 0.04
19 42 0.63
21 8 0.12
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCA
Found at i:323877 original size:12 final size:13
Alignment explanation
Indices: 323843--323878 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
323833 TGCGATTTTC
323843 ATTTCTCATTGCG
1 ATTTCTCATTGCG
323856 ATTCTCTCATTGCG
1 ATT-TCTCATTGCG
323870 ATTT-TCATT
1 ATTTCTCATT
323879 TCGCGTTGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.23
13 4 0.18
14 13 0.59
ACGTcount: A:0.17, C:0.22, G:0.11, T:0.50
Consensus pattern (13 bp):
ATTTCTCATTGCG
Found at i:324410 original size:21 final size:21
Alignment explanation
Indices: 324386--324453 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
324376 TCATTCCTCG
324386 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
324407 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
324428 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
324449 AGAGT
1 AGAGT
324454 TCGATTCACA
Statistics
Matches: 33, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 2 0.06
21 30 0.91
22 1 0.03
ACGTcount: A:0.24, C:0.35, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:325809 original size:14 final size:14
Alignment explanation
Indices: 325790--325825 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
325780 ATTGTTTAAT
325790 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
325804 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
325818 TGATTTGT
1 TGATTTGT
325826 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:325954 original size:19 final size:19
Alignment explanation
Indices: 325932--326030 Score: 58
Period size: 19 Copynumber: 5.7 Consensus size: 19
325922 AAAAATGACT
325932 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
325951 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
325965 ATCGCAATGCGAAATTAAA
1 ATCGCAATGCGAAATGAAA
* *
325984 ATTGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
325998 ATCACAATGCGAAACT-AAA
1 ATCGCAATGCGAAA-TGAAA
*
326017 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
326031 CTAAATTCGC
Statistics
Matches: 60, Mismatches: 9, Indels: 22
0.66 0.10 0.24
Matches are distributed among these distances:
14 18 0.30
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.50
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:325974 original size:33 final size:32
Alignment explanation
Indices: 325932--326025 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 32
325922 AAAAATGACT
* *
325932 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
*
325965 ATCGCAATGCGAAATTAAAATTGCAACGACAAA
1 ATCGCAATGCGAAA-TAAAATCGCAACGACAAA
*
325998 ATCACAATGCGAAACTAAAATCGCAACG
1 ATCGCAATGCGAAA-TAAAATCGCAACG
326026 CGAAACTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 53 0.98
34 1 0.02
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.15
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGACAAA
Found at i:326047 original size:19 final size:19
Alignment explanation
Indices: 325964--326040 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 19
325954 GCAACGAGAG
*
325964 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAACTAA
*
325983 AATTGCAA--CG--AC-AA
1 AATCGCAATGCGAAACTAA
*
325997 AATCACAATGCGAAACTAA
1 AATCGCAATGCGAAACTAA
*
326016 AATCGCAACGCGAAACTAA
1 AATCGCAATGCGAAACTAA
*
326035 ATTCGC
1 AATCGC
326041 GTTGCGATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
14 8 0.17
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 31 0.67
ACGTcount: A:0.47, C:0.22, G:0.14, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAACTAA
Found at i:326145 original size:20 final size:19
Alignment explanation
Indices: 326119--326172 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
326109 TGCGATTTTT
326119 ATTTCGCATTGCGATAGTC
1 ATTTCGCATTGCGATAGTC
* **
326138 ATTTTCGCGTTGCGATTTTC
1 A-TTTCGCATTGCGATAGTC
326158 ATTTCGCATTGCGAT
1 ATTTCGCATTGCGAT
326173 TCTCTCGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (19 bp):
ATTTCGCATTGCGATAGTC
Found at i:326195 original size:33 final size:33
Alignment explanation
Indices: 326040--326182 Score: 196
Period size: 33 Copynumber: 4.2 Consensus size: 33
326030 ACTAAATTCG
* *
326040 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
326073 CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
*
326106 CGTTGCGATTTTTATTTCGCATTGCGATAGTCATTTTCG
1 CGTTGCGATTTTTATTTCGCATTGCGAT--TC----TCT
*
326145 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
326178 CGTTG
1 CGTTG
326183 TGATAGTAAT
Statistics
Matches: 99, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
33 66 0.67
35 2 0.02
37 2 0.02
39 29 0.29
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
Found at i:326195 original size:72 final size:73
Alignment explanation
Indices: 326073--326213 Score: 212
Period size: 72 Copynumber: 1.9 Consensus size: 73
326063 GCGATTCCCT
* ** * *
326073 CGTTGCGATTTTTATTTCGCATTGCGATTCTCTCGTTGCGATTTTTATTT-CGCATTGCGATAGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCATTGCGATAGA
326137 CATTTTCG
66 CATTTTCG
* *
326145 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGTGATAGTAATTTCCGCGTTGCGATAGA
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCATTGCGATAGA
326210 CATT
66 CATT
326214 AAGATGATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
72 45 0.74
73 16 0.26
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.44
Consensus pattern (73 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCATTGCGATAGA
CATTTTCG
Found at i:328747 original size:24 final size:24
Alignment explanation
Indices: 328720--328773 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
328710 CTGAAACACC
328720 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
328744 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
328768 ATCAAA
1 ATCAAA
328774 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:329647 original size:20 final size:19
Alignment explanation
Indices: 329626--329845 Score: 95
Period size: 20 Copynumber: 10.9 Consensus size: 19
329616 GCGATAGTCA
329626 GAATCTCGTTGCGATTTAC
1 GAATCTCGTTGCGATTTAC
* * *
329645 AGATTCGCATTGCGATTTAC
1 -GAATCTCGTTGCGATTTAC
*
329665 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
* * *
329685 GGATACGCATTGCGATTTAC
1 GAAT-CTCGTTGCGATTTAC
*
329705 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
*
329725 -AGATACGCGTTGCGATTTAC
1 GA-AT-CTCGTTGCGATTTAC
* *
329745 GTATTGTCGTTGCGATTTTAC
1 G-AATCTCGTTGCGA-TTTAC
* * *
329766 GTATTGTTGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* * * *
329786 GGATACACATTGTGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
* *
329807 GGATACTCGTTGCGATAGT-C
1 GAAT-CTCGTTGCGAT-TTAC
*
329827 AGAATCGCGTTGCGATTTA
1 -GAATCTCGTTGCGATTTA
329846 TATGTTCGCG
Statistics
Matches: 151, Mismatches: 34, Indels: 30
0.70 0.16 0.14
Matches are distributed among these distances:
18 2 0.01
19 5 0.03
20 100 0.66
21 42 0.28
22 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (19 bp):
GAATCTCGTTGCGATTTAC
Found at i:329758 original size:60 final size:60
Alignment explanation
Indices: 329631--329822 Score: 203
Period size: 60 Copynumber: 3.2 Consensus size: 60
329621 AGTCAGAATC
* * *
329631 TCGTTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGGATACG
1 TCGTTGCGATTTAC-GTATTCTCGTTGCGATTTACG-ATACGCATTGCGATTTACGGATACG
* * * *
329692 -CATTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTAT-TG
1 TCGTTGCGATTTACGTATTCTCGTTGCGATTTAC-GATACGCATTGCGATTTACGGATACG
* * * *
329751 TCGTTGCGATTTTACGTATTGTTGTTGCGATTTACGGATACACATTGTGATTTTACGGATAC-
1 TCGTTGCGA-TTTACGTATTCTCGTTGCGATTTAC-GATACGCATTGCGA-TTTACGGATACG
329813 TCGTTGCGAT
1 TCGTTGCGAT
329823 AGTCAGAATC
Statistics
Matches: 109, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
59 2 0.02
60 54 0.50
61 36 0.33
62 17 0.16
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (60 bp):
TCGTTGCGATTTACGTATTCTCGTTGCGATTTACGATACGCATTGCGATTTACGGATACG
Found at i:329766 original size:21 final size:20
Alignment explanation
Indices: 329631--329786 Score: 135
Period size: 20 Copynumber: 7.8 Consensus size: 20
329621 AGTCAGAATC
329631 TCGTTGCGATTTACAG-ATTCG
1 TCGTTGCGATTTAC-GTATT-G
*
329652 -CATTGCGATTTACGTATTCG
1 TCGTTGCGATTTACGTATT-G
* * *
329672 -CATTGCGATTTACGGATACG
1 TCGTTGCGATTTACGTAT-TG
* *
329692 -CATTGCGATTTACGTATTC
1 TCGTTGCGATTTACGTATTG
*
329711 TCGTTGCGATTTACAG-ATACG
1 TCGTTGCGATTTAC-GTAT-TG
329732 -CGTTGCGATTTACGTATTG
1 TCGTTGCGATTTACGTATTG
329751 TCGTTGCGATTTTACGTATTG
1 TCGTTGCGA-TTTACGTATTG
*
329772 TTGTTGCGATTTACG
1 TCGTTGCGATTTACG
329787 GATACACATT
Statistics
Matches: 116, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
19 3 0.03
20 93 0.80
21 20 0.17
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGTTGCGATTTACGTATTG
Found at i:329819 original size:41 final size:40
Alignment explanation
Indices: 329629--329822 Score: 192
Period size: 40 Copynumber: 4.8 Consensus size: 40
329619 ATAGTCAGAA
* * * *
329629 TCTCGTTGCGATTTACAGATTCGCATTGCGATTTACGTAT
1 TCTCATTGCGATTTACGGATACGCGTTGCGATTTACGTAT
* *
329669 TCGCATTGCGATTTACGGATACGCATTGCGATTTACGTAT
1 TCTCATTGCGATTTACGGATACGCGTTGCGATTTACGTAT
* *
329709 TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTAT
1 TCTCATTGCGATTTACGGATACGCGTTGCGATTTACGTAT
* * * * * *
329749 TGTCGTTGCGATTTTACGTAT-TGTTGTTGCGATTTACGGAT
1 TCTCATTGCGA-TTTACGGATACG-CGTTGCGATTTACGTAT
* * * *
329790 ACACATTGTGATTTTACGGATACTCGTTGCGAT
1 TCTCATTGCGA-TTTACGGATACGCGTTGCGAT
329823 AGTCAGAATC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
40 83 0.65
41 45 0.35
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (40 bp):
TCTCATTGCGATTTACGGATACGCGTTGCGATTTACGTAT
Found at i:334181 original size:66 final size:66
Alignment explanation
Indices: 334007--334215 Score: 283
Period size: 66 Copynumber: 3.2 Consensus size: 66
333997 ATAGTCACTT
* * ** ** * * *
334007 CACCTTATGCACCATAAAGGTACACAAGTCTCATTGAGTGATAAGTACAATATTCAATTATCACT
1 CACCTCATGCACCACAAAGGTACATGAGTCTCATTGAGTGATTTGTATAGTATTCAATTATCATT
334072 C
66 C
* *
334073 CACCCCATGCACCACAAAGATACATGAGTCTCATTGAGTGATTTGTATAGTATTCAATTATCATT
1 CACCTCATGCACCACAAAGGTACATGAGTCTCATTGAGTGATTTGTATAGTATTCAATTATCATT
*
334138 T
66 C
**
334139 CACCTCATGCACCACAAAGGTACATGAGTCTCATTGAGTGATTTGTATAGTATTCAACAATCATT
1 CACCTCATGCACCACAAAGGTACATGAGTCTCATTGAGTGATTTGTATAGTATTCAATTATCATT
334204 C
66 C
*
334205 CACCTCGTGCA
1 CACCTCATGCA
334216 TCATTGACTA
Statistics
Matches: 125, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 125 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (66 bp):
CACCTCATGCACCACAAAGGTACATGAGTCTCATTGAGTGATTTGTATAGTATTCAATTATCATT
C
Found at i:346537 original size:29 final size:29
Alignment explanation
Indices: 346491--346548 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
346481 TTTCAACTTC
*
346491 AAATAAAATATTTCATTTATA-AAATCATA
1 AAATAAAATATTTAATTTATATAAA-CATA
346520 AAATGAAAATA-TTAATTTATATAAACATA
1 AAAT-AAAATATTTAATTTATATAAACATA
346549 CATCAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (29 bp):
AAATAAAATATTTAATTTATATAAACATA
Found at i:354261 original size:40 final size:40
Alignment explanation
Indices: 354186--354261 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
354176 TTTGTGGCCG
**
354186 CTAGATAACTTTGCATCGACTGGCTTCCTATTTTTCATTT
1 CTAGATAACTTTGCATCGACTGGCTTCAAATTTTTCATTT
354226 CTAGAGTAACTTTGCATCGACT-G-TTCAAATATTTTC
1 CTAGA-TAACTTTGCATCGACTGGCTTCAAAT-TTTTC
354262 TGATATTCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 5 0.16
40 11 0.34
41 16 0.50
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (40 bp):
CTAGATAACTTTGCATCGACTGGCTTCAAATTTTTCATTT
Found at i:360258 original size:20 final size:20
Alignment explanation
Indices: 360220--360259 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
360210 GTGATATTTT
*
360220 TATTTTTTTAATGATAAAAA
1 TATTTTTTTAATGAAAAAAA
360240 TATTATTTTTAAT-AAAAAAA
1 TATT-TTTTTAATGAAAAAAA
360260 ACTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TATTTTTTTAATGAAAAAAA
Found at i:360259 original size:21 final size:20
Alignment explanation
Indices: 360220--360260 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
360210 GTGATATTTT
* *
360220 TATTTTTTTAATGATAAAAA
1 TATTTTTTTAATAAAAAAAA
360240 TATTATTTTTAATAAAAAAAA
1 TATT-TTTTTAATAAAAAAAA
360261 CTTAATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TATTTTTTTAATAAAAAAAA
Found at i:361033 original size:13 final size:12
Alignment explanation
Indices: 360993--361030 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
360983 CACTCTTCCT
360993 TTTTCT-TCATC
1 TTTTCTCTCATC
361004 TTTTCTCT-ATC
1 TTTTCTCTCATC
*
361015 TTTTCTCTCTTC
1 TTTTCTCTCATC
361027 TTTT
1 TTTT
361031 TCTATCAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 17 0.71
12 7 0.29
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTCTCTCATC
Found at i:361034 original size:22 final size:22
Alignment explanation
Indices: 360993--361036 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
360983 CACTCTTCCT
360993 TTTTCTTCATCTTTTCTCTATC
1 TTTTCTTCATCTTTTCTCTATC
*
361015 TTTTCTCTCTTCTTTT-TCTATC
1 TTTTCT-TCATCTTTTCTCTATC
361037 AAGTTAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTCTTCATCTTTTCTCTATC
Found at i:363467 original size:21 final size:21
Alignment explanation
Indices: 363443--363554 Score: 124
Period size: 21 Copynumber: 5.3 Consensus size: 21
363433 GACTATCGCA
363443 TTGCGATTTATTCCAAGTTCG
1 TTGCGATTTATTCCAAGTTCG
** *
363464 TTGCGA--TCGTCGAAGTTCG
1 TTGCGATTTATTCCAAGTTCG
*
363483 CATTGCGATTTATTCCAAATTCG
1 --TTGCGATTTATTCCAAGTTCG
363506 TTGCGA--TATTCCAAGTTTGCG
1 TTGCGATTTATTCCAAG-TT-CG
363527 TTGCGATTTATTCCAAGTTCG
1 TTGCGATTTATTCCAAGTTCG
363548 TTGCGAT
1 TTGCGAT
363555 AGTCCAAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
19 18 0.24
20 2 0.03
21 35 0.47
22 2 0.03
23 18 0.24
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (21 bp):
TTGCGATTTATTCCAAGTTCG
Found at i:363485 original size:42 final size:42
Alignment explanation
Indices: 363438--363561 Score: 194
Period size: 42 Copynumber: 3.0 Consensus size: 42
363428 ACTTCGACTA
* *
363438 TCGCATTGCGATTTATTCCAAGTTCGTTGCGATCGTCGAAGT
1 TCGCATTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGT
* *
363480 TCGCATTGCGATTTATTCCAAATTCGTTGCGATATTCCAAGT
1 TCGCATTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGT
* *
363522 TTGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
1 TCGCATTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
363562 AATCGCAACG
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (42 bp):
TCGCATTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGT
Found at i:363679 original size:6 final size:6
Alignment explanation
Indices: 363647--363689 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
363637 GACACGTATT
* *
363647 ACCACG ACAACG ACAACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
363690 CGAGACGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:364500 original size:110 final size:110
Alignment explanation
Indices: 364367--364587 Score: 417
Period size: 110 Copynumber: 2.0 Consensus size: 110
364357 CACAATAAAA
364367 ACACTTCAATGACACTTGAAGAAGGTTATTGCACCTATCCAAGCTTAAAGATCAAGAGAAAA-GA
1 ACACTTCAATGACACTTGAAGAAGGTTATTGCACCTATCCAAGCTTAAAGATCAAGAGAAAATG-
364431 GTTTACATTCTTATTTCCTTCATTTTTCTCTTGTACATAAGTGTAT
65 GTTTACATTCTTATTTCCTTCATTTTTCTCTTGTACATAAGTGTAT
364477 ACACTTCAATGACACTTGAAGAAGGTTATTGCACCTATCCAAGCTTAAAGATCAAGAGAAAATGG
1 ACACTTCAATGACACTTGAAGAAGGTTATTGCACCTATCCAAGCTTAAAGATCAAGAGAAAATGG
*
364542 TTTTCATTCTTATTTCCTTCATTTTTCTCTTGTACATAAGTGTAT
66 TTTACATTCTTATTTCCTTCATTTTTCTCTTGTACATAAGTGTAT
364587 A
1 A
364588 GAGCTTAATT
Statistics
Matches: 109, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
110 108 0.99
111 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (110 bp):
ACACTTCAATGACACTTGAAGAAGGTTATTGCACCTATCCAAGCTTAAAGATCAAGAGAAAATGG
TTTACATTCTTATTTCCTTCATTTTTCTCTTGTACATAAGTGTAT
Found at i:369247 original size:16 final size:16
Alignment explanation
Indices: 369226--369256 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
369216 TGGAGTTGTA
369226 TTGAGACTTTAGTTTT
1 TTGAGACTTTAGTTTT
369242 TTGAGACTTTAGTTT
1 TTGAGACTTTAGTTT
369257 ATCGTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.55
Consensus pattern (16 bp):
TTGAGACTTTAGTTTT
Found at i:373615 original size:19 final size:19
Alignment explanation
Indices: 373579--373617 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
373569 TACAAAAGTT
*
373579 TCGATACTTTATATCATTA
1 TCGATACTTTATAGCATTA
373598 TCGATACTTT-TAAGCATTA
1 TCGATACTTTAT-AGCATTA
373617 T
1 T
373618 GGACTGCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (19 bp):
TCGATACTTTATAGCATTA
Found at i:373777 original size:20 final size:20
Alignment explanation
Indices: 373739--373777 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
373729 ACCAAAAACA
* *
373739 AGTATCGATATTATCCCTAT
1 AGTATCGATACTATACCTAT
*
373759 AGTATCGATACTCTACCTA
1 AGTATCGATACTATACCTA
373778 AAGAAGTCAT
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:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (20 bp):
AGTATCGATACTATACCTAT
Found at i:384649 original size:44 final size:43
Alignment explanation
Indices: 384562--384788 Score: 248
Period size: 44 Copynumber: 5.2 Consensus size: 43
384552 ATTTTATGAA
* *
384562 ATTGAAAAAA-TAGAGGCCTTAATTATAAAGGTAGAAATTGAG
1 ATTGAAAAAATTAGAGGCCTCAATTATAAAGGTAGAAAGTGAG
*
384604 ATCGAAAAAATTAGAGGCCTCAATTAATAAAGGTAGAAAGTGAG
1 ATTGAAAAAATTAGAGGCCTCAATT-ATAAAGGTAGAAAGTGAG
* *
384648 ATTGAAAAAACTTA-AGGGCCTCAATTATAAAGTTAAAAAAGTGAG
1 ATTGAAAAAA-TTAGA-GGCCTCAATTATAAAGGT-AGAAAGTGAG
* * * *
384693 AAT-AAAAAATTAG-GGACTTCAATTATAAAGGTATAAA-TCAAG
1 ATTGAAAAAATTAGAGG-CCTCAATTATAAAGGTAGAAAGT-GAG
* * *
384735 ATTGAAAAAACTTAGGGGCCTCAATTGTAAAGGTAGAAAGCGAG
1 ATTGAAAAAA-TTAGAGGCCTCAATTATAAAGGTAGAAAGTGAG
384779 ATTGAAAAAA
1 ATTGAAAAAA
384789 AACCTAAGGG
Statistics
Matches: 156, Mismatches: 17, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
41 1 0.01
42 19 0.12
43 36 0.23
44 74 0.47
45 26 0.17
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.23
Consensus pattern (43 bp):
ATTGAAAAAATTAGAGGCCTCAATTATAAAGGTAGAAAGTGAG
Found at i:384787 original size:87 final size:88
Alignment explanation
Indices: 384562--384788 Score: 268
Period size: 87 Copynumber: 2.6 Consensus size: 88
384552 ATTTTATGAA
* * * *
384562 ATTGAAAAAA--TAGAGGCCTTAATTATAAAGGTAGAAATTGAGATCGAAAAAATTAGAGGCCTC
1 ATTGAAAAAACTTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAATTAGAGGCCTC
*
384625 AATTAATAAAGGTAGAAAGTGAG
66 AATTAATAAAGGTAGAAAGTAAG
* * * * *
384648 ATTGAAAAAACTTAAGGGCCTCAATTATAAAGTTAAAAAAGTGAGAAT-AAAAAATTAG-GGACT
1 ATTGAAAAAACTTAGGGGCCTCAATTATAAAGGT-AGAAAGTGAGATTGAAAAAATTAGAGG-CC
*
384711 TCAATT-ATAAAGGTATAAA-TCAAG
64 TCAATTAATAAAGGTAGAAAGT-AAG
* *
384735 ATTGAAAAAACTTAGGGGCCTCAATTGTAAAGGTAGAAAGCGAGATTGAAAAAA
1 ATTGAAAAAACTTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAA
384789 AACCTAAGGG
Statistics
Matches: 118, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
86 21 0.18
87 53 0.45
88 35 0.30
89 9 0.08
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.23
Consensus pattern (88 bp):
ATTGAAAAAACTTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAATTAGAGGCCTC
AATTAATAAAGGTAGAAAGTAAG
Found at i:387444 original size:15 final size:15
Alignment explanation
Indices: 387424--387471 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
387414 GGCCGAGTAT
387424 ATATATTTAAATTAA
1 ATATATTTAAATTAA
* *
387439 ATATA-TAAATATTAT
1 ATATATTTAA-ATTAA
387454 ATATATTTAAATTTAA
1 ATATATTTAAA-TTAA
387470 AT
1 AT
387472 TAAATTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
14 3 0.12
15 15 0.58
16 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATTTAAATTAA
Found at i:389684 original size:153 final size:153
Alignment explanation
Indices: 389406--389718 Score: 608
Period size: 153 Copynumber: 2.0 Consensus size: 153
389396 AGTTAATTGC
*
389406 TGAAGGTCGGCATTCCTTGTTTGGTGAACAATCTAGCAAGCTCTAGTTCCATTCCAAATTTCTGT
1 TGAAGATCGGCATTCCTTGTTTGGTGAACAATCTAGCAAGCTCTAGTTCCATTCCAAATTTCTGT
389471 AAGAAAATACTAGGAACTGGTGGATGTTTTACTTGTACTATTTTAAGAACTGCTTTCTTGGAAGC
66 AAGAAAATACTAGGAACTGGTGGATGTTTTACTTGTACTATTTTAAGAACTGCTTTCTTGGAAGC
389536 ATATTATGTGATTTCTGACTTTA
131 ATATTATGTGATTTCTGACTTTA
389559 TGAAGATCGGCATTCCTTGTTTGGTGAACAATCTAGCAAGCTCTAGTTCCATTCCAAATTTCTGT
1 TGAAGATCGGCATTCCTTGTTTGGTGAACAATCTAGCAAGCTCTAGTTCCATTCCAAATTTCTGT
389624 AAGAAAATACTAGGAACTGGTGGATGTTTTACTTGTACTATTTTAAGAACTGCTTTCTTGGAAGC
66 AAGAAAATACTAGGAACTGGTGGATGTTTTACTTGTACTATTTTAAGAACTGCTTTCTTGGAAGC
389689 ATATTATGTGATTTCTGACTTTA
131 ATATTATGTGATTTCTGACTTTA
*
389712 CGAAGAT
1 TGAAGAT
389719 TCTCTAGTAA
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 158 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (153 bp):
TGAAGATCGGCATTCCTTGTTTGGTGAACAATCTAGCAAGCTCTAGTTCCATTCCAAATTTCTGT
AAGAAAATACTAGGAACTGGTGGATGTTTTACTTGTACTATTTTAAGAACTGCTTTCTTGGAAGC
ATATTATGTGATTTCTGACTTTA
Found at i:394529 original size:41 final size:41
Alignment explanation
Indices: 394484--394564 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
394474 TGCTTCCTGC
* *
394484 AATTGATATTTGTAATTGTTGAAACGATAGAGATAGTGGGT
1 AATTGATAATTGTAATTGTTGAAACGATAGAGACAGTGGGT
*
394525 AATTGATAATTGTAATTGTTGAAACGGTAGAGACAGTGGG
1 AATTGATAATTGTAATTGTTGAAACGATAGAGACAGTGGG
394565 GAAAGAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (41 bp):
AATTGATAATTGTAATTGTTGAAACGATAGAGACAGTGGGT
Found at i:395543 original size:34 final size:34
Alignment explanation
Indices: 395497--395579 Score: 150
Period size: 34 Copynumber: 2.4 Consensus size: 34
395487 GAGATGGGAT
395497 TCCAC-TAGAATCACTTTCAGTGATAACGATATCG
1 TCCACATA-AATCACTTTCAGTGATAACGATATCG
395531 TCCACATAAATCACTTTCAGTGATAACGATATCG
1 TCCACATAAATCACTTTCAGTGATAACGATATCG
395565 TCCACATAAATCACT
1 TCCACATAAATCACT
395580 AATAGGATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
34 46 0.96
35 2 0.04
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (34 bp):
TCCACATAAATCACTTTCAGTGATAACGATATCG
Found at i:399076 original size:62 final size:62
Alignment explanation
Indices: 398999--399137 Score: 251
Period size: 62 Copynumber: 2.2 Consensus size: 62
398989 GGGCTTGACC
*
398999 AGTATCGATACTATGCTACATGATATTGATACCACTGTGTAAAGTAGTATTGGTACCCCTTT
1 AGTATCGATACTATGCTACATGATATTGATACCACTGTGTAAAGTAGTATTGGTACCCCTTG
*
399061 AGTATCAATACTATGCTACATGATATTGATACCACTGTGTAAAGTAGTATTGGTACCCCTTG
1 AGTATCGATACTATGCTACATGATATTGATACCACTGTGTAAAGTAGTATTGGTACCCCTTG
399123 AGTATCGATATCTAT
1 AGTATCGATA-CTAT
399138 TTTGCATTAT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
62 69 0.95
63 4 0.05
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (62 bp):
AGTATCGATACTATGCTACATGATATTGATACCACTGTGTAAAGTAGTATTGGTACCCCTTG
Found at i:405413 original size:74 final size:74
Alignment explanation
Indices: 405237--405451 Score: 378
Period size: 74 Copynumber: 2.9 Consensus size: 74
405227 CTGAGCATAA
*
405237 AATCTAATTGAAACTTATAAGGGATGTAACATGTGATGATTGCCAATTTTTATTAGGT-AGGCAT
1 AATCTAATTGAAACTTATAAGGGATGTAACAGGTGATGATTGCCAATTTTTATTAGGTAAGGCAT
405301 CCGACTAAT
66 CCGACTAAT
* *
405310 AATCTAATTGAAACTTATAAGGGATGTAACAGGTTATTATTGCCAATTTTTATTAGGTAAGGCAT
1 AATCTAATTGAAACTTATAAGGGATGTAACAGGTGATGATTGCCAATTTTTATTAGGTAAGGCAT
405375 CCGACTAAT
66 CCGACTAAT
*
405384 AATCTAATTGAAACTTTTAAGGGATGTAACAGGTGATGATTGCCAATTTTTATTAGGTCAAGGCA
1 AATCTAATTGAAACTTATAAGGGATGTAACAGGTGATGATTGCCAATTTTTATTAGGT-AAGGCA
405449 TCC
65 TCC
405452 TACCATTAGT
Statistics
Matches: 134, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
73 55 0.41
74 70 0.52
75 9 0.07
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (74 bp):
AATCTAATTGAAACTTATAAGGGATGTAACAGGTGATGATTGCCAATTTTTATTAGGTAAGGCAT
CCGACTAAT
Found at i:408980 original size:20 final size:21
Alignment explanation
Indices: 408955--409047 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
408945 TTTTCCCAAT
*
408955 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
408975 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
408996 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
409016 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
409037 TCGCAATGCGA
1 TCGCAATGCGA
409048 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:409000 original size:41 final size:41
Alignment explanation
Indices: 408955--409047 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
408945 TTTTCCCAAT
408955 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
408996 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
409037 TCGCAATGCGA
1 TCGCAATGCGA
409048 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:409060 original size:41 final size:41
Alignment explanation
Indices: 408974--409108 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
408964 GAATAAGTAA
** *
408974 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
409015 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
409056 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
409097 TTCGCAACGCGA
1 ATCGCAACGCGA
409109 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:409061 original size:20 final size:20
Alignment explanation
Indices: 409036--409129 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
409026 AATTGGGAAA
*
409036 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
409056 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
409077 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
409097 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
409117 TTCGCAACGCGAT
1 ATCGCAACGCGAT
409130 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:409707 original size:19 final size:19
Alignment explanation
Indices: 409683--409727 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
409673 GCAACGAGAT
* *
409683 AATCGCAACGTGAAATAAA
1 AATCGCAACGCGAAACAAA
*
409702 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
409721 AATCGCA
1 AATCGCA
409728 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:409745 original size:19 final size:19
Alignment explanation
Indices: 409723--409873 Score: 177
Period size: 19 Copynumber: 8.1 Consensus size: 19
409713 GAAACCAAAA
*
409723 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
409742 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
409761 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
409780 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
409800 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
409816 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
409833 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
409852 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
409872 TC
1 TC
409874 AACCAAAAGA
Statistics
Matches: 114, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 65 0.57
20 35 0.31
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:409800 original size:39 final size:38
Alignment explanation
Indices: 409723--409873 Score: 177
Period size: 39 Copynumber: 4.1 Consensus size: 38
409713 GAAACCAAAA
*
409723 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
409761 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
409800 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
409833 TCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
409872 TC
1 TC
409874 AACCAAAAGA
Statistics
Matches: 94, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
33 27 0.29
35 1 0.01
36 1 0.01
37 1 0.01
38 21 0.22
39 43 0.46
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:411810 original size:14 final size:14
Alignment explanation
Indices: 411791--411826 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
411781 ATTGTTTAAT
411791 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
411805 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
411819 TGATTTGT
1 TGATTTGT
411827 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:412028 original size:19 final size:19
Alignment explanation
Indices: 412006--412156 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
411996 CGAAATTAAA
412006 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
412025 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
412040 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
412058 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
412072 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
412091 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
412106 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
** ** *
412124 TTCGTATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
412143 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
412157 GGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 28 0.30
16 6 0.06
17 6 0.06
19 44 0.47
20 9 0.10
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:412052 original size:33 final size:32
Alignment explanation
Indices: 412010--412136 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
412000 ATTAAATTCG
412010 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
412043 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
412076 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
412109 CGTTGCGATTTTCATTTCGTATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
412137 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Done.