Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 172 of 195
Found at i:28692279 original size:558 final size:543
Alignment explanation
Indices: 28691240--28692339 Score: 1822
Period size: 558 Copynumber: 2.0 Consensus size: 543
28691230 ATCAAGTTGG
*
28691240 ATGCGAGTTTTGAGCGTTTGTCTTATCTGATTATATATAAATATATGTTTTATTATTCATTTAAT
1 ATGCGAGTTTTGAGCGTTTGTCTTATCTGATCATATATAAATATATGTTTTATTATTCATTTAAT
* *
28691305 TTTATATTTATATATTATTTAAATTATTATTTAATATTTTAATTTAATAAATCCACGTGTCATTT
66 TTTATATTTATATATTATTTAAATTATTATTTAATATCTTAATTTAATAAATCCACGTCTCATTT
28691370 CAATTTGGCTTCATTTTCTTCTTTTCTTTTTCACCATTTCTTTTTTTTTTTTTAAGTTTTTGACT
131 CAATTTGGCTTCATTTTCTTCTTTTCTTTTTCACCATTTCTTTTTTTTTTTTTAAGTTTTTGACT
* *
28691435 TTTTTAATTAGATAAATTTTGTAAAAAAAGTTAATGGATATAAATATGACAAAACAACTCAATCT
196 TTTTTAATTAGATAAATTTTGGAAAAAAAGTTAATGGATATAAATATGACAAAACAACTCAATCC
* *
28691500 CATGGGTTACGATTAATCTTGGTCCAATATTTGTGAATTTTAAAAAAAATCATGATAGGGTTATT
261 CATGGGTTACGATTAATCTCGATCCAATATTTGTGAATTTTAAAAAAAATCATGATAGGGTTATT
*
28691565 CGTTTTTAATTGGGGTTTGGTAAAAGGTGAGTTTAGAATCTTTCATACTGTATTGAGTGTATATA
326 CGTTTTTAATTGGGGTTTGGTAAAAGGTGAGTTTAGAATCTTTCATACTATATTGAGTGTATATA
* *
28691630 TGCATATAATTATTTTTAATTATTTATTTTATTTTATATTTATATATATGTATTATGTTAATTAA
391 TGCATATAATTATTTTTAATTATTTATTTCATTTTATATTTATATATATGTATTATATTAATTAA
28691695 GTTATTATTTAATATTTAAATTTAACAAAAATATTATATTTATAAATAATTAAGATGTAACTCAT
456 GTTATTATTTAATATTTAAATTTAACAAAAATATTATATTTATAAATAATTAAGATGTAACTCAT
28691760 TCATCCATCAATTATATAAATTA
521 TCATCCATCAATTATATAAATTA
* *
28691783 ATGCGAGTTTTGGGTGTTTGTCTTATCTGATCATATATAAATATATGTTTTATTATTCATTTAAT
1 ATGCGAGTTTTGAGCGTTTGTCTTATCTGATCATATATAAATATATGTTTTATTATTCATTTAAT
* *
28691848 TTTATATTTTATATATTATATTATTTAAATTGTTATTTAATATCTTAATTTAATAAATCCATGTC
66 TTTATA---T-T-TA-TATATTATTTAAATTATTATTTAATATCTTAATTTAATAAATCCACGTC
*
28691913 TCATTTCAATTTGGCTTCATTTTCTTCTTTTCTTTTTCACTATTTCCTTTTTTTTTTTTTTAAGT
125 TCATTTCAATTTGGCTTCATTTTCTTCTTTTCTTTTTCACCATTT-C-TTTTTTTTTTTTTAAGT
* *
28691978 TTTTGACTTTTTTAATTAGATAAATTTTGGAAAAAAAGTTAATGGATGTAAATATGACAAAATAA
188 TTTTGACTTTTTTAATTAGATAAATTTTGGAAAAAAAGTTAATGGATATAAATATGACAAAACAA
* * * **
28692043 CTCATATCCCATGGGTTACGATTAATCTCGATCCAATATTTGTGAGTTTTTAAAAAGATTGTGAT
253 CTCA-ATCCCATGGGTTACGATTAATCTCGATCCAATATTTGTGAATTTTAAAAAAAATCATGAT
* ** *
28692108 AGGGTCATTTTTTTTTTTTTTAAATTGGGGTTTGTTAAAAGGTGAGTTTAGAATCTTTCATACTA
317 AGGG-----TTATTCGTTTTT-AATTGGGGTTTGGTAAAAGGTGAGTTTAGAATCTTTCATACTA
*
28692173 TCTTGAGTGTATATATGCATATAATTATTTTTAATTATTTATTTCATTTTATATTTATATATATG
376 TATTGAGTGTATATATGCATATAATTATTTTTAATTATTTATTTCATTTTATATTTATATATATG
28692238 TATTATATTAATTAAGTTATTATTTAATATTTAAATTTAACAAAAATATTATATTTATAAATAAT
441 TATTATATTAATTAAGTTATTATTTAATATTTAAATTTAACAAAAATATTATATTTATAAATAAT
28692303 TAAGATGTAACTCATTCATCCATCAATTATATAAATT
506 TAAGATGTAACTCATTCATCCATCAATTATATAAATT
28692340 TTACTTATTT
Statistics
Matches: 515, Mismatches: 27, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
543 68 0.13
546 1 0.00
547 1 0.00
548 2 0.00
549 89 0.17
550 1 0.00
551 83 0.16
552 56 0.11
557 9 0.02
558 205 0.40
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (543 bp):
ATGCGAGTTTTGAGCGTTTGTCTTATCTGATCATATATAAATATATGTTTTATTATTCATTTAAT
TTTATATTTATATATTATTTAAATTATTATTTAATATCTTAATTTAATAAATCCACGTCTCATTT
CAATTTGGCTTCATTTTCTTCTTTTCTTTTTCACCATTTCTTTTTTTTTTTTTAAGTTTTTGACT
TTTTTAATTAGATAAATTTTGGAAAAAAAGTTAATGGATATAAATATGACAAAACAACTCAATCC
CATGGGTTACGATTAATCTCGATCCAATATTTGTGAATTTTAAAAAAAATCATGATAGGGTTATT
CGTTTTTAATTGGGGTTTGGTAAAAGGTGAGTTTAGAATCTTTCATACTATATTGAGTGTATATA
TGCATATAATTATTTTTAATTATTTATTTCATTTTATATTTATATATATGTATTATATTAATTAA
GTTATTATTTAATATTTAAATTTAACAAAAATATTATATTTATAAATAATTAAGATGTAACTCAT
TCATCCATCAATTATATAAATTA
Found at i:28692643 original size:16 final size:15
Alignment explanation
Indices: 28692609--28692660 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
28692599 GCCTTTTTTC
*
28692609 TTTTTTTCTTT-TTA
1 TTTTTTTGTTTATTA
*
28692623 ATTTTTTGTTCT-TTCA
1 TTTTTTTGTT-TATT-A
28692639 TTTTTTTGTTTATTA
1 TTTTTTTGTTTATTA
28692654 TTTTTTT
1 TTTTTTT
28692661 ATTAAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 8 0.25
15 12 0.38
16 12 0.38
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.81
Consensus pattern (15 bp):
TTTTTTTGTTTATTA
Found at i:28693265 original size:17 final size:20
Alignment explanation
Indices: 28693245--28693285 Score: 61
Period size: 17 Copynumber: 2.2 Consensus size: 20
28693235 ATTTTTTGGG
28693245 TTTTTTCTTT-T-T-CTTTT
1 TTTTTTCTTTATATACTTTT
28693262 TTTTTTCTTTATATACTTTT
1 TTTTTTCTTTATATACTTTT
28693282 TTTT
1 TTTT
28693286 ATTAAATCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.48
18 1 0.05
19 1 0.05
20 9 0.43
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTTCTTTATATACTTTT
Found at i:28693654 original size:17 final size:16
Alignment explanation
Indices: 28693596--28693656 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
28693586 ATATAAAAGT
*
28693596 ATATATT-TTTTATTA
1 ATATATTATTATATTA
* *
28693611 ATTTAATT-TTATATTT
1 ATAT-ATTATTATATTA
28693627 ATATATGTATTATATTA
1 ATATAT-TATTATATTA
28693644 ATATAGTTATTAT
1 ATATA-TTATTAT
28693657 TTGATACCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
15 5 0.14
16 13 0.35
17 18 0.49
18 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATATATTATTATATTA
Found at i:28693793 original size:23 final size:23
Alignment explanation
Indices: 28693753--28693816 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
28693743 TTTCCTTTTC
* *
28693753 CTTTTATTTTTCCT-TTTTGTTCT
1 CTTTTATTTTT-TTATTTTGTTCA
* *
28693776 TTTTTATTTTTTTATTTTTTTCA
1 CTTTTATTTTTTTATTTTGTTCA
**
28693799 CTTTTAGGTTTTTATTTT
1 CTTTTATTTTTTTATTTT
28693817 TTATTAAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.09, C:0.09, G:0.05, T:0.77
Consensus pattern (23 bp):
CTTTTATTTTTTTATTTTGTTCA
Found at i:28698119 original size:13 final size:13
Alignment explanation
Indices: 28698098--28698127 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28698088 ATTCCTTCTA
*
28698098 ATTTTTTGAAGGT
1 ATTTATTGAAGGT
28698111 ATTTATTGAAGGT
1 ATTTATTGAAGGT
28698124 ATTT
1 ATTT
28698128 TTTGTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (13 bp):
ATTTATTGAAGGT
Found at i:28699017 original size:364 final size:362
Alignment explanation
Indices: 28698264--28699128 Score: 1030
Period size: 364 Copynumber: 2.4 Consensus size: 362
28698254 TTTGTATTAT
* * *
28698264 ACGCCTTCAATAATTTTCTTTTAAAAATTATTTGGGATTATTAAAAGCATCTTTTAGTAGAAAAC
1 ACGCCTTTAATAA-TTTCTTTTAAAAATTATTTGGGATTATTAAAGGC-TCTTTTAGTAGAAAAT
* * * * *
28698329 ACATTCAATATTCTACTACTAAAATTTTAAGAGGTTTATTGAAGGCATTTATTCTAAAAAATATC
64 ACCTTTAATATTCTAATACTAAAATTTT-AGGGGTTTATTGAAGGCATTTATTCTAAAAAATAGC
* * * * *
28698394 TTCATTAATTCGTTCTAATTTTTTAAAAAAATTTATTGAAGGTATTTTTTGCATAATACACATTT
128 TTCACTAATTCGCTCTAATTTTTTAAAAAAATTTATTAAAGGTATTTTCTGCATAATACACATTC
* *
28698459 AATAATTCTCTCCATTTTTATCAGTGAATACAAGTGAAGGTAGTTTTCTACTAAAAATACCTTTA
193 AATAATTCTCTCCATTCTTATCAGGGAATACAAGTGAAGGTAGTTTTCTACTAAAAATACCTTTA
*
28698524 ATAATTCACTCAAATTTTTAAGAGAGAATTATTGAAGGCATTTTTTGTATCATACACCTTAAATA
258 ATAATTCACACAAATTTTTAAGAGAGAATTATTGAAGGCATTTTTTGTATCATACACCTTAAATA
*
28698589 ATTTTTGTACAAAATTATTGAAGGTATTTTTTGAGAAAAA
323 ATTTTTGTACAAAATTATCGAAGGTATTTTTTGAGAAAAA
* *
28698629 ATGCCTTTAATAATTTCTTTTTAAAAATTATTT-GGATTATTGAAGGCGTCTTTTAGTAGAAAAT
1 ACGCCTTTAATAATTTC-TTTTAAAAATTATTTGGGATTATTAAAGGC-TCTTTTAGTAGAAAAT
* * *
28698693 GCCTTTAATATTCTAATACTAAAATTTTAGGGGTGTTATTGAATGCGTTTATT-TCAAAAAAT-G
64 ACCTTTAATATTCTAATACTAAAATTTTAGGGGT-TTATTGAAGGCATTTATTCT-AAAAAATAG
* * * * * *
28698756 CATTCACTAATTTGCTCTAATTTTTTGAAAGAATTTGTTAAAGGTGTTTTCTGCATAATACACCT
127 C-TTCACTAATTCGCTCTAATTTTTTAAAAAAATTTATTAAAGGTATTTTCTGCATAATACACAT
* *
28698821 TCAATAATT-TCTTCCATTCTTATCAGGGAATATC-AGTGAAGCG-A-TTTTTTACTAAAAATGC
191 TCAATAATTCTC-TCCATTCTTATCAGGGAATA-CAAGTGAAG-GTAGTTTTCTACTAAAAATAC
* * * **
28698882 CTTTAATAATTTACACCAATTTTTAAGAGA-AATTTATTGAAGGCATTTTTTGTATCGTATGCCT
253 CTTTAATAATTCACACAAATTTTTAAGAGAGAA-TTATTGAAGGCATTTTTTGTATCATACACCT
* * * *
28698946 TCAATAATTTTTGTATAGAATTATCGAAGTGTTTTTTTTTGAGAAAAA
317 TAAATAATTTTTGTACAAAATTATCGAAG-G-TATTTTTTGAGAAAAA
* ** *
28698994 ACGCTTTTAATAATTTCTTTTAAATTTTTTTTGGGATTATTAAAGGCTCTTTTAGTA-AAAAGTA
1 ACGCCTTTAATAATTTCTTTTAAAAATTATTTGGGATTATTAAAGGCTCTTTTAGTAGAAAA-TA
* ** * * * ** *
28699058 CCTTTAATAATCTCTTAGTAAAATTTTAGGAGGATTATTAAAGGTGTTT-TTGCTAGAAAAATAC
65 CCTTTAATATTCTAATACTAAAATTTTAGG-GGTTTATTGAAGGCATTTATT-CTA-AAAAATAG
28699122 CTTCACT
127 CTTCACT
28699129 TATAATTTTT
Statistics
Matches: 427, Mismatches: 56, Indels: 34
0.83 0.11 0.07
Matches are distributed among these distances:
362 2 0.00
363 110 0.26
364 228 0.53
365 86 0.20
366 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (362 bp):
ACGCCTTTAATAATTTCTTTTAAAAATTATTTGGGATTATTAAAGGCTCTTTTAGTAGAAAATAC
CTTTAATATTCTAATACTAAAATTTTAGGGGTTTATTGAAGGCATTTATTCTAAAAAATAGCTTC
ACTAATTCGCTCTAATTTTTTAAAAAAATTTATTAAAGGTATTTTCTGCATAATACACATTCAAT
AATTCTCTCCATTCTTATCAGGGAATACAAGTGAAGGTAGTTTTCTACTAAAAATACCTTTAATA
ATTCACACAAATTTTTAAGAGAGAATTATTGAAGGCATTTTTTGTATCATACACCTTAAATAATT
TTTGTACAAAATTATCGAAGGTATTTTTTGAGAAAAA
Found at i:28701450 original size:16 final size:16
Alignment explanation
Indices: 28701431--28701470 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
28701421 TTGAATTTTG
*
28701431 ATTATTTTATATTTAA
1 ATTATTTTAGATTTAA
*
28701447 ATTATTTTAGATTTGA
1 ATTATTTTAGATTTAA
28701463 ATTATTTT
1 ATTATTTT
28701471 GAATTCTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
ATTATTTTAGATTTAA
Found at i:28714558 original size:16 final size:17
Alignment explanation
Indices: 28714524--28714566 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
28714514 ATTAAATTTA
*
28714524 AATATATAAAATAATTAT
1 AATATAT-ATATAATTAT
*
28714542 AGTATATATATAA-TAT
1 AATATATATATAATTAT
28714558 AATATATAT
1 AATATATAT
28714567 TAAAGAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 11 0.50
17 5 0.23
18 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AATATATATATAATTAT
Found at i:28715286 original size:18 final size:18
Alignment explanation
Indices: 28715246--28715287 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28715236 CATGAATGTT
*
28715246 ATTAAAAAAAAGAAAAGA
1 ATTAAAAAAAAGAAAAAA
* *
28715264 TTTAAAAAAATGAAAAAA
1 ATTAAAAAAAAGAAAAAA
28715282 ATTAAA
1 ATTAAA
28715288 GAAGAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (18 bp):
ATTAAAAAAAAGAAAAAA
Found at i:28719278 original size:33 final size:32
Alignment explanation
Indices: 28719241--28719341 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 32
28719231 AATTATTTAA
*
28719241 TGAAATTTATTTGGGTTTTGGTTTTATGTTTGT
1 TGAAATTTATTT-GGTTTTGGTTATATGTTTGT
* *
28719274 TGAAA---ATTT--TGTTGGTTCTATGTTTGT
1 TGAAATTTATTTGGTTTTGGTTATATGTTTGT
* *
28719301 TGAAATTTGTTTAGGTTTTGGTTATATATTTGT
1 TGAAATTTATTT-GGTTTTGGTTATATGTTTGT
*
28719334 TAAAATTT
1 TGAAATTT
28719342 GTTGGTGATA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
27 21 0.38
30 7 0.13
33 27 0.49
ACGTcount: A:0.21, C:0.01, G:0.21, T:0.57
Consensus pattern (32 bp):
TGAAATTTATTTGGTTTTGGTTATATGTTTGT
Found at i:28719317 original size:27 final size:27
Alignment explanation
Indices: 28719257--28719317 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
28719247 TTATTTGGGT
*
28719257 TTTGGTTTTATGTTTGTTGAAAATTT-
1 TTTGGTTCTATGTTTGTTGAAAATTTG
28719283 TGTTGGTTCTATGTTTGTTG-AAATTTG
1 T-TTGGTTCTATGTTTGTTGAAAATTTG
28719310 TTTAGGTT
1 TTT-GGTT
28719318 TTGGTTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 9 0.29
27 22 0.71
ACGTcount: A:0.16, C:0.02, G:0.23, T:0.59
Consensus pattern (27 bp):
TTTGGTTCTATGTTTGTTGAAAATTTG
Found at i:28720525 original size:58 final size:58
Alignment explanation
Indices: 28720461--28720734 Score: 374
Period size: 58 Copynumber: 4.7 Consensus size: 58
28720451 TTATGCAGGA
* * *
28720461 AAAATTGATACTTTCAACTTTTCC-CTAAAAATATTCTTTTGAAATTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTGAAATTTTATTTTCAAGG
** * *
28720519 AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAA-TTTTATTTTCAAGG
*
28720578 AAAATTGATACTTTCAACTTTTCCTCAAAAACCT-TTTTTTTGAAATTTTATTTTAAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTTGAAATTTTATTTTCAAGG
** * *
28720637 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTGAAATTTTGTTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAATTTTATTTTCAAGG
28720695 AAAATTGATACTTTCAACTTTTCC-CAAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTT
28720735 TATTTTTATT
Statistics
Matches: 193, Mismatches: 17, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
57 1 0.01
58 97 0.50
59 84 0.44
60 10 0.05
61 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAATTTTATTTTCAAGG
Found at i:28720598 original size:59 final size:58
Alignment explanation
Indices: 28720461--28720734 Score: 331
Period size: 59 Copynumber: 4.7 Consensus size: 58
28720451 TTATGCAGGA
* * * * *
28720461 AAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTCTTTTGAAATTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCTC-AAAAATATTTTTTTGAAATTTGATTTTCAAGG
* *
28720519 AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAA-TTTGATTTTCAAGG
* * *
28720578 AAAATTGATACTTTCAACTTTTCCTCAAAAACCT-TTTTTTTGAAATTTTATTTTAAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAA--TATTTTTTTGAAATTTGATTTTCAAGG
* ** *
28720637 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTGAAATTTTG-TTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAA-TTTGATTTTCAAGG
*
28720695 AAAATTGATACTTTCAAC-TTTTCCCAAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTTCTC-AAAAATATTTTTTT
28720735 TATTTTTATT
Statistics
Matches: 190, Mismatches: 19, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
57 5 0.03
58 83 0.44
59 91 0.48
60 10 0.05
61 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATTTGATTTTCAAGG
Found at i:28720703 original size:117 final size:116
Alignment explanation
Indices: 28720461--28720754 Score: 382
Period size: 117 Copynumber: 2.5 Consensus size: 116
28720451 TTATGCAGGA
**
28720461 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTCTTTTGAAATTTTAATTTCGAGGAAAATTG
1 AAAATTGATACTTTCAACTTTTCCC-AAAAATATTCTTTTGAAATTTTAATTTAAAGGAAAATTG
** *
28720526 ATACTTTCAACTTTTTTTCAAAAATATTTTTTGGAAACTTTGATTTTCAAGG
65 ATACTTTCAACTTTTCCTCAAAAACATTTTTTGGAAACTTTGATTTTCAAGG
* *
28720578 AAAATTGATACTTTCAACTTTTCCTCAAAAACCT-TTTTTTTGAAATTTTATTTTAAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCC-CAAAAA--TATTCTTTTGAAATTTTAATTTAAAGGAAAAT
* * * *
28720642 TGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTGAAATTTTG-TTTTTAAGG
63 TGATACTTTCAACTTTTCCTCAAAAACATTTTTTGGAAACTTTGATTTTCAAGG
** *
28720695 AAAATTGATACTTTCAACTTTTCCCAAAAAATATT-TTTT-TTATTTTTATTTAAA-GAAAAT
1 AAAATTGATACTTTCAACTTTTCCC-AAAAATATTCTTTTGAAATTTTAATTTAAAGGAAAAT
28720755 AGAATAATAG
Statistics
Matches: 157, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
113 6 0.04
114 11 0.07
115 5 0.03
116 3 0.02
117 66 0.42
118 65 0.41
119 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (116 bp):
AAAATTGATACTTTCAACTTTTCCCAAAAATATTCTTTTGAAATTTTAATTTAAAGGAAAATTGA
TACTTTCAACTTTTCCTCAAAAACATTTTTTGGAAACTTTGATTTTCAAGG
Found at i:28720779 original size:6 final size:6
Alignment explanation
Indices: 28720768--28720826 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
28720758 ATAATAGAAC
* *
28720768 AAAATA AAAATA AAAAAA GGAAAAGT- AAAACA AAAATA AAAAT- AAAATA
1 AAAATA AAAATA AAAATA --AAAA-TA AAAATA AAAATA AAAATA AAAATA
*
28720817 AAGATA AAAA
1 AAAATA AAAA
28720827 GAATATTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
5 5 0.12
6 33 0.79
8 4 0.10
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:28720808 original size:17 final size:17
Alignment explanation
Indices: 28720750--28720826 Score: 61
Period size: 17 Copynumber: 4.6 Consensus size: 17
28720740 TTATTTAAAG
*
28720750 AAAATAGAATAATAGAAC-
1 AAAATA-AA-AATAAAACA
28720768 AAAATAAAAAT-AAA-A
1 AAAATAAAAATAAAACA
** *
28720783 AAAGGAAAAGTAAAACA
1 AAAATAAAAATAAAACA
*
28720800 AAAATAAAAATAAAATA
1 AAAATAAAAATAAAACA
*
28720817 AAGATAAAAA
1 AAAATAAAAA
28720827 GAATATTAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
15 10 0.21
16 6 0.13
17 25 0.53
18 6 0.13
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (17 bp):
AAAATAAAAATAAAACA
Found at i:28720823 original size:11 final size:11
Alignment explanation
Indices: 28720768--28720825 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
28720758 ATAATAGAAC
28720768 AAAATAAAAAT
1 AAAATAAAAAT
*
28720779 AAAA-AAAGGA-
1 AAAATAAA-AAT
*
28720789 AAAGTAAAACA-
1 AAAATAAAA-AT
28720800 AAAATAAAAAT
1 AAAATAAAAAT
*
28720811 AAAATAAAGAT
1 AAAATAAAAAT
28720822 AAAA
1 AAAA
28720826 AGAATATTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
10 7 0.18
11 31 0.82
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:28721731 original size:22 final size:22
Alignment explanation
Indices: 28721699--28721766 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
28721689 AAAATAAATA
28721699 AGATAAA-TAAAAAAAATTAAC
1 AGATAAATTAAAAAAAATTAAC
* *
28721720 AGATAAATTAAAATTAAA-TAAT
1 AGATAAATTAAAA-AAAATTAAC
* *
28721742 AGAT-AATTACATAAATATTAAC
1 AGATAAATTA-AAAAAAATTAAC
28721764 AGA
1 AGA
28721767 AAAAAAGAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
21 14 0.38
22 20 0.54
23 3 0.08
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.26
Consensus pattern (22 bp):
AGATAAATTAAAAAAAATTAAC
Found at i:28722298 original size:42 final size:41
Alignment explanation
Indices: 28722198--28722432 Score: 409
Period size: 42 Copynumber: 5.7 Consensus size: 41
28722188 AAAAAAAAAA
28722198 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAG
28722239 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAG
* *
28722281 TAAATTGCTCATTTAAACAGAGGCACCACGACTTTGAGAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAG
*
28722323 TAAATTGCTCCTTTAAACAGAGGCACCACGACTTTGGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAG
28722365 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAG
28722405 TAAATTGCTCCTCTAAACAGAGGCACCA
1 TAAATTGCTCCTCTAAACAGAGGCACCA
28722433 AAATTGCTCC
Statistics
Matches: 188, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
40 32 0.17
41 38 0.20
42 118 0.63
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (41 bp):
TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAG
Found at i:28722444 original size:27 final size:27
Alignment explanation
Indices: 28722406--28722459 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
28722396 CTTTGAAAGT
28722406 AAATTGCTCCTCTAAACAGAGGCACCA
1 AAATTGCTCCTCTAAACAGAGGCACCA
28722433 AAATTGCTCCTCTAAACAGAGGCACCA
1 AAATTGCTCCTCTAAACAGAGGCACCA
28722460 CGACTTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.19
Consensus pattern (27 bp):
AAATTGCTCCTCTAAACAGAGGCACCA
Found at i:28722492 original size:42 final size:42
Alignment explanation
Indices: 28722433--28722567 Score: 184
Period size: 41 Copynumber: 3.3 Consensus size: 42
28722423 AGAGGCACCA
28722433 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGT
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGT
* * * *
28722475 AAATTGCTCATTTAAACAAAGGCACCACGACTTT-GAAAAAT
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGT
* * *
28722516 AAATTGCTCCTCTAAATAGCGGCACCATGACTTTGG-AAAGT
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGT
*
28722557 AAATTACTCCT
1 AAATTGCTCCT
28722568 TGACAATCAT
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 48 0.60
42 32 0.40
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (42 bp):
AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGT
Found at i:28722556 original size:151 final size:151
Alignment explanation
Indices: 28722282--28722567 Score: 459
Period size: 151 Copynumber: 1.9 Consensus size: 151
28722272 TTGAGAAAGT
* * *
28722282 AAATTGCTCATTTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTTTAAACAGAGGC
1 AAATTGCTCATCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCATTTAAACAAAGGC
* *
28722347 ACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAGTAAATTG
66 ACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAGTAAATTA
28722412 CTCCTCTAAACAGAGGCACCA
131 CTCCTCTAAACAGAGGCACCA
*
28722433 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAAGTAAATTGCTCATTTAAACAAAGG
1 AAATTGCTCATCTAAACAGAGGCACCACGACTTTGAG-AAAGTAAATTGCTCATTTAAACAAAGG
* * *
28722497 CACCACGACTTT-GAAAAATAAATTGCTCCTCTAAATAGCGGCACCATGACTTTGGAAAGTAAAT
65 CACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAGTAAAT
28722561 TACTCCT
129 TACTCCT
28722568 TGACAATCAT
Statistics
Matches: 124, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
150 38 0.31
151 86 0.69
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.24
Consensus pattern (151 bp):
AAATTGCTCATCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCATTTAAACAAAGGC
ACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAGTAAATTA
CTCCTCTAAACAGAGGCACCA
Found at i:28723841 original size:24 final size:25
Alignment explanation
Indices: 28723794--28723861 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 25
28723784 CCCTTTCAGG
*
28723794 TTTTCTCTTTTTTTCATTCATTCATTCTTT
1 TTTTTTCTTTTTTT--TTCA-TCA-TC-TT
28723824 TTTTTTCTTTTTTTTTCATCATCTT
1 TTTTTTCTTTTTTTTTCATCATCTT
28723849 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
28723862 CTCATTTTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 15 0.41
26 2 0.05
27 3 0.08
28 4 0.11
30 13 0.35
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTTTCTTTTTTTTTCATCATCTT
Found at i:28727892 original size:58 final size:59
Alignment explanation
Indices: 28727768--28727915 Score: 248
Period size: 59 Copynumber: 2.5 Consensus size: 59
28727758 TTGTGCAGGA
28727768 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTTGAAATTTTATTTTAAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTTGAAATTTTATTTTAAAGG
*
28727827 AAAATTGATATTTTCAACTTTTCCTCAAAAACC-TTTTTTTGAAATTTTATTTTTAAA-G
1 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTTGAAATTTTA-TTTTAAAGG
28727885 AAAATTGATACTTTCAACTTTTTCC-CAAAAA
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAA
28727916 TATATATTTT
Statistics
Matches: 85, Mismatches: 2, Indels: 5
0.92 0.02 0.05
Matches are distributed among these distances:
58 40 0.47
59 45 0.53
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTTGAAATTTTATTTTAAAGG
Found at i:28727975 original size:23 final size:22
Alignment explanation
Indices: 28727947--28727997 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
28727937 AAAATAGAAT
28727947 AATAAAACAAAATA-AAAAAAAA
1 AATAAAACAAAA-ACAAAAAAAA
*
28727969 AAGTAAAACAAAAACAAAAATAA
1 AA-TAAAACAAAAACAAAAAAAA
28727992 AATAAA
1 AATAAA
28727998 GATAAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.82, C:0.06, G:0.02, T:0.10
Consensus pattern (22 bp):
AATAAAACAAAAACAAAAAAAA
Found at i:28727982 original size:13 final size:12
Alignment explanation
Indices: 28727944--28728069 Score: 56
Period size: 12 Copynumber: 9.5 Consensus size: 12
28727934 AAGAAAATAG
*
28727944 AATAATAAAACAA
1 AATAA-AAAAAAA
28727957 AATAAAAAAAAA
1 AATAAAAAAAAA
28727969 AAGTAAAACAAAAA
1 AA-TAAAA-AAAAA
28727983 CAA-AAATAAAATAA
1 -AATAAA-AAAA-AA
28727997 AGATAAAAAGAATATTA
1 A-ATAAAAA-AA-A--A
***
28728014 AATAAACATAATCT
1 AATAAA-A-AAAAA
*
28728028 AATAAATAAAAA
1 AATAAAAAAAAA
*
28728040 AATAAAAAAATA
1 AATAAAAAAAAA
* *
28728052 AATAAATAAATA
1 AATAAAAAAAAA
28728064 AATAAA
1 AATAAA
28728070 TTCAAAAAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
12 37 0.41
13 17 0.19
14 17 0.19
15 9 0.10
16 5 0.06
17 4 0.04
18 1 0.01
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.17
Consensus pattern (12 bp):
AATAAAAAAAAA
Found at i:28728035 original size:4 final size:4
Alignment explanation
Indices: 28728028--28728070 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
28728018 AACATAATCT
* *
28728028 AATA AATA AAAA AATA AAAA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT
28728071 TCAAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:28728449 original size:20 final size:19
Alignment explanation
Indices: 28728416--28728464 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
28728406 CGGTTGAATG
* *
28728416 TTCATCGGATTCTGGAATTT
1 TTCATCGAAATCTGG-ATTT
*
28728436 TTCATCGAAATCTGGGTTT
1 TTCATCGAAATCTGGATTT
*
28728455 TTCGTCGAAA
1 TTCATCGAAA
28728465 GTTCATCGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.41
Consensus pattern (19 bp):
TTCATCGAAATCTGGATTT
Found at i:28729146 original size:6 final size:6
Alignment explanation
Indices: 28729137--28729211 Score: 52
Period size: 6 Copynumber: 12.5 Consensus size: 6
28729127 ATATAAAATG
*
28729137 ATAATA ATAAAA AT-AAA A-AAAA ATAAAA ATGTGAAATA CA-AAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A--T-AAA-A -ATAAAA ATAAAA
*
28729187 ATAAAA AT-AAA ATGAAA A-AAAA ATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATA
28729212 TAGACTTACC
Statistics
Matches: 57, Mismatches: 2, Indels: 20
0.72 0.03 0.25
Matches are distributed among these distances:
5 18 0.32
6 30 0.53
7 3 0.05
8 1 0.02
9 3 0.05
10 1 0.02
11 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:28729920 original size:16 final size:15
Alignment explanation
Indices: 28729895--28729924 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28729885 ATGGTCAATC
28729895 AATAAAAGGTTTAAT
1 AATAAAAGGTTTAAT
28729910 AATACAAAGGTTTAA
1 AATA-AAAGGTTTAA
28729925 CACTTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.30
Consensus pattern (15 bp):
AATAAAAGGTTTAAT
Found at i:28733973 original size:26 final size:25
Alignment explanation
Indices: 28733939--28733987 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
28733929 TAAAACATGC
28733939 ATCAAAGAATAA-AATAAATTTATCT
1 ATCAAAGAA-AATAATAAATTTATCT
*
28733964 ATCAATAGAAAATTATAAATTTAT
1 ATCAA-AGAAAATAATAAATTTAT
28733988 TTGAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (25 bp):
ATCAAAGAAAATAATAAATTTATCT
Found at i:28735470 original size:15 final size:16
Alignment explanation
Indices: 28735446--28735479 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28735436 GTTTGTAACG
28735446 AAATGCCAT-ATTTTT
1 AAATGCCATAATTTTT
*
28735461 AAATGTCATAATTTTT
1 AAATGCCATAATTTTT
28735477 AAA
1 AAA
28735480 AAAATTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (16 bp):
AAATGCCATAATTTTT
Found at i:28738459 original size:12 final size:12
Alignment explanation
Indices: 28738442--28738466 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28738432 TGATTGGTTC
28738442 TGATGTGAATAT
1 TGATGTGAATAT
28738454 TGATGTGAATAT
1 TGATGTGAATAT
28738466 T
1 T
28738467 CGATATACTA
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:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (12 bp):
TGATGTGAATAT
Found at i:28747209 original size:15 final size:17
Alignment explanation
Indices: 28747182--28747214 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28747172 AACTAAGCAC
28747182 AAAAACAACAAAT-ATA
1 AAAAACAACAAATGATA
28747198 AAAAACAA-AAATGATA
1 AAAAACAACAAATGATA
28747214 A
1 A
28747215 TGGAATCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (17 bp):
AAAAACAACAAATGATA
Found at i:28754671 original size:238 final size:235
Alignment explanation
Indices: 28754058--28754944 Score: 915
Period size: 236 Copynumber: 3.8 Consensus size: 235
28754048 ATCTTGTTGC
*
28754058 CAAA-TTTTAC-CGTCAAATTTATTTGGTG-AAAAATATTTTTGTGACATTTTTTATTTTAGATG
1 CAAACTTTTACTC-TCAAATTTATTTGATGAAAAAATATTTTTGTGACATTTTTTATTTTAGATG
* * *
28754120 ACATTATAATTTTGTCACCAATTTAAAATTTTATTTGTG--ACATTTTTTTGATAAATTTTAGGT
65 ACATTATAATTTTGTCACTAATTTAAAATTTTATTTATGATAAATTTTTTTGATAAATTTTAGGT
** * * * * * *
28754183 GATGTTATTAATTTTTGTCATAAATTGAATACTTTAGTTAACTATTAATGATATTGCAATTTCGT
130 GACATTATTAATTTTTTTCACAAATTGAACACTTTAATTAACTATTAATGACATTGCAATTTCAT
* * *
28754248 CACATCAATGTATGGTGGTATATGACGATAATATAAATGTCA
195 CACATCAATATATGGT-GTATATGATGATAACATAAATGTCA
* * * * * *
28754290 CAAACTTTTATTGTCAAATTTATTTGATG-AGAAATTTTTTTGTGAC-CTTTTTATTTTAGGTGA
1 CAAACTTTTACTCTCAAATTTATTTGATGAAAAAATATTTTTGTGACATTTTTTATTTTAGATGA
* * * * *
28754353 CATT-TAAATTTTGTTACTAATTTAAAATTTTATTTGTGATGAATTTTTTCTAATAGATTTTAGG
66 CATTAT-AATTTTGTCACTAATTTAAAATTTTATTTATGATAAATTTTTT-TGATAAATTTTAGG
** * * *
28754417 TGATGTCATCAATTTTTTTCACAAA-TGAAACACTGTAATTAACTATTAATGACATTGCAATTTC
129 TGACATTATTAATTTTTTTCACAAATTG-AACACTTTAATTAACTATTAATGACATTGCAATTTC
* * * * * *
28754481 ATCACCTTTATTTTATGATAGTATATAATGATAACATAAATGTCA
193 ATCA-CATCAATATATGGT-GTATATGATGATAACATAAATGTCA
* * * * * **
28754526 CAAATTTTTACTCTCAATTTTAATTAGA-GAAAAAATTTTTTTGTGACGTTTTGCATTTTA-ATC
1 CAAACTTTTACTCTCAAATTT-ATTTGATGAAAAAATATTTTTGTGACATTTTTTATTTTAGAT-
* * * * *
28754589 GACGTTATAATTTTCTCACTAATTTAAAATTTTATTTATGAAAAATTTTTTCTGATAAAGTTGAG
64 GACATTATAATTTTGTCACTAATTTAAAATTTTATTTATGATAAATTTTTT-TGATAAATTTTAG
* * * *
28754654 GTGGCATTATTAATTTTTATCACAAATTGAATACTTTAGTTAACTATTAATGACATTGCAATTTC
128 GTGACATTATTAATTTTTTTCACAAATTGAACACTTTAATTAACTATTAATGACATTGCAATTTC
* * * *
28754719 ATCACGTCAATATATGGTGTTATATGATGATAACTTAAAAGTTA
193 ATCACATCAATATATGGTG-TATATGATGATAACATAAATGTCA
* *
28754763 CAAACTTTTAC-CACCAAATTTATTTGATGAAAAAA-ATTTTTATGACATTTTTTATTTTA-AGT
1 CAAACTTTTACTC-TCAAATTTATTTGATGAAAAAATATTTTTGTGACATTTTTTATTTTAGA-T
* * * * *
28754825 GACGTAATAATTTTGTTA-TCAATTTAAAATTTTATCTATGATAAATTTTTTTGATAAATTTTAA
64 GACATTATAATTTTGTCACT-AATTTAAAATTTTATTTATGATAAATTTTTTTGATAAATTTTAG
* * * * *
28754889 GTGACGTTATTAATTTTGTT-AAAAATTGCACACTTTAATTAGCTATTAATGACATT
128 GTGACATTATTAATTTTTTTCACAAATTGAACACTTTAATTAACTATTAATGACATT
28754945 ATAATTTTGT
Statistics
Matches: 541, Mismatches: 95, Indels: 36
0.81 0.14 0.05
Matches are distributed among these distances:
231 1 0.00
232 53 0.10
233 35 0.06
234 40 0.07
235 95 0.18
236 120 0.22
237 75 0.14
238 119 0.22
239 3 0.01
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (235 bp):
CAAACTTTTACTCTCAAATTTATTTGATGAAAAAATATTTTTGTGACATTTTTTATTTTAGATGA
CATTATAATTTTGTCACTAATTTAAAATTTTATTTATGATAAATTTTTTTGATAAATTTTAGGTG
ACATTATTAATTTTTTTCACAAATTGAACACTTTAATTAACTATTAATGACATTGCAATTTCATC
ACATCAATATATGGTGTATATGATGATAACATAAATGTCA
Found at i:28754769 original size:473 final size:469
Alignment explanation
Indices: 28754086--28754944 Score: 1136
Period size: 473 Copynumber: 1.8 Consensus size: 469
28754076 TTATTTGGTG
** *
28754086 AAAAATATTTTTGTGACATTTTTTATTTTAGATGACATTATAATTTTGTCACCAATTTAAAATTT
1 AAAAATATTTTTGTGACATTTTGCATTTTAGATGACATTATAATTTTCTCACCAATTTAAAATTT
* * * * ** * *
28754151 TATTTGTGACATTTTTTTGATAAATTTTAGGTGATGTTATTAATTTTTGTCATAAATTGAATACT
66 TATTTATGAAATTTTTTTGATAAAGTTGAGGTGACATTATTAATTTTTATCACAAATTGAATACT
* * *
28754216 TTAGTTAACTATTAATGATATTGCAATTTCGTCACATCAATGTATGGTGGTATATGACGATAATA
131 TTAGTTAACTATTAATGACATTGCAATTTCATCACATCAATATATGGTGGTATATGACGATAATA
* **** * ** *
28754281 TAAATGTCACAAACTTTTATTGTCAAATTTATTTGATGAGAAATTTTTTTGTGAC-CTTTTTATT
196 TAAAAGTCACAAACTTTTACCACCAAATTTATTTGATGAAAAAAATTTTTATGACACTTTTTATT
* * * * * *
28754345 TTAGGTGACAT-TTAAATTTTGTTA-CTAATTTAAAATTTTATTTGTGATGAATTTTTTCTAATA
261 TTAAGTGACGTAAT-AATTTTGTTATC-AATTTAAAATTTTATCTATGATAAATTTTTT-TAATA
* * * * *
28754408 GATTTTAGGTGATGTCATCAATTTTTTTCACAAA-TGAAACACTGTAATTAACTATTAATGACAT
323 AATTTTAAGTGACGTCATCAATTTTGTT-AAAAATTG-AACACTGTAATTAACTATTAATGACAT
28754472 TGCAATTTCATCACCTTTATTTTATGATAGTATATAATGATAACATAAATGTCACAAATTTTTAC
386 TGCAATTTCATCACCTTTATTTTATGATAGTATATAATGATAACATAAATGTCACAAATTTTTAC
28754537 TCTCAATTTTAATTAGAGA
451 TCTCAATTTTAATTAGAGA
* * * *
28754556 AAAAATTTTTTTGTGACGTTTTGCATTTTA-ATCGACGTTATAATTTTCTCACTAATTTAAAATT
1 AAAAATATTTTTGTGACATTTTGCATTTTAGAT-GACATTATAATTTTCTCACCAATTTAAAATT
*
28754620 TTATTTATGAAAAATTTTTTCTGATAAAGTTGAGGTGGCATTATTAATTTTTATCACAAATTGAA
65 TTATTTATG--AAATTTTTT-TGATAAAGTTGAGGTGACATTATTAATTTTTATCACAAATTGAA
* * *
28754685 TACTTTAGTTAACTATTAATGACATTGCAATTTCATCACGTCAATATATGGTGTTATATGATGAT
127 TACTTTAGTTAACTATTAATGACATTGCAATTTCATCACATCAATATATGGTGGTATATGACGAT
* *
28754750 AACT-TAAAAGTTACAAACTTTTACCACCAAATTTATTTGATGAAAAAAATTTTTATGACATTTT
192 AA-TATAAAAGTCACAAACTTTTACCACCAAATTTATTTGATGAAAAAAATTTTTATGACACTTT
*
28754814 TTATTTTAAGTGACGTAATAATTTTGTTATCAATTTAAAATTTTATCTATGATAAATTTTTTTGA
256 TTATTTTAAGTGACGTAATAATTTTGTTATCAATTTAAAATTTTATCTATGATAAATTTTTTTAA
* * * * *
28754879 TAAATTTTAAGTGACGTTATTAATTTTGTTAAAAATTGCACACTTTAATTAGCTATTAATGACAT
321 TAAATTTTAAGTGACGTCATCAATTTTGTTAAAAATTGAACACTGTAATTAACTATTAATGACAT
28754944 T
386 T
28754945 ATAATTTTGT
Statistics
Matches: 330, Mismatches: 50, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
469 2 0.01
470 62 0.19
472 37 0.11
473 171 0.52
474 56 0.17
475 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (469 bp):
AAAAATATTTTTGTGACATTTTGCATTTTAGATGACATTATAATTTTCTCACCAATTTAAAATTT
TATTTATGAAATTTTTTTGATAAAGTTGAGGTGACATTATTAATTTTTATCACAAATTGAATACT
TTAGTTAACTATTAATGACATTGCAATTTCATCACATCAATATATGGTGGTATATGACGATAATA
TAAAAGTCACAAACTTTTACCACCAAATTTATTTGATGAAAAAAATTTTTATGACACTTTTTATT
TTAAGTGACGTAATAATTTTGTTATCAATTTAAAATTTTATCTATGATAAATTTTTTTAATAAAT
TTTAAGTGACGTCATCAATTTTGTTAAAAATTGAACACTGTAATTAACTATTAATGACATTGCAA
TTTCATCACCTTTATTTTATGATAGTATATAATGATAACATAAATGTCACAAATTTTTACTCTCA
ATTTTAATTAGAGA
Found at i:28758276 original size:6 final size:6
Alignment explanation
Indices: 28758266--28758299 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
28758256 TGCATAGTTT
* *
28758266 ATATAT ATATAT ATATAC ATATAC ATATAC ATAT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATAT
28758300 TTAATTTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (6 bp):
ATATAC
Found at i:28760464 original size:203 final size:201
Alignment explanation
Indices: 28759901--28760642 Score: 841
Period size: 203 Copynumber: 3.7 Consensus size: 201
28759891 TTAATAACGT
* * ** *
28759901 TAATTATGTCACCAATACTGTCATGATTTATCTTTTGTCACTAATATATTAGATTTAATCATTTA
1 TAATTATGTCACCAATACTGTGACGATTTATCTTTCATCACTAATATATTAGATTTTATCATTTA
** * *
28759966 TTTTGTGATAATTATAGCCTTTAATGATG-TTTTTTCATAAATAGCTAACGAAAACTAACGTCAC
66 TTTTGTGACGATTATAGCCTTTAATGATGTTTTTTTTATAAATAGCTGACGAAAACTAACGTCAC
* *
28760030 AAAAAAATAAAGCATAATGTGACATTTGATTTTATTGTCACGTTTGACATTATCTTACAACCATT
131 -AAAAAAT-AAGCATAAAGTGACATTTGATTTTATTGTCACGTTTGACATTATCTTACAATCATT
28760095 TGTGATGA
194 TGTGATGA
* * * * * * *
28760103 TAATTATGTTACCAATACTATGATGATTTACCTTTCATCATTAATTTATCAGA--TTATCATTTA
1 TAATTATGTCACCAATACTGTGACGATTTATCTTTCATCACTAATATATTAGATTTTATCATTTA
* * * * *
28760166 TTTTGTGATGATTATAACCTTTAATAATGTTTTTCTTTATAAATAGCTGAC-AGAAATTAACATC
66 TTTTGTGACGATTATAGCCTTTAATGATGTTTTT-TTTATAAATAGCTGACGA-AAACTAACGTC
* * * * * * ** *
28760230 ATATAAAAAGAAGCATAAGGTGACATTTGATTTTGTTATCACGTTTGATATTGGCTTATAATCAT
129 ACA-AAAAATAAGCATAAAGTGACATTTGATTTTATTGTCACGTTTGACATTATCTTACAATCAT
28760295 TTGTGATGA
193 TTGTGATGA
* * ** *
28760304 TAATTTTGTCACCAATATTGTGACGATTTATCTTTTGTCACTAATATATAAGATTTTATCATTTA
1 TAATTATGTCACCAATACTGTGACGATTTATCTTTCATCACTAATATATTAGATTTTATCATTTA
*
28760369 TTTTGTAACGATTATAGCCTTTAATGATGTTTTTGTTTATAAATAGCTGACGAAAACTAACGTCA
66 TTTTGTGACGATTATAGCCTTTAATGATGTTTTT-TTTATAAATAGCTGACGAAAACTAACGTCA
* ** * *
28760434 CAAAAATTAACGCATAAAGTGATGTTTGATTTTTTTGTCACAG-TAGACATTATCTTACAATCAT
130 CAAAAAATAA-GCATAAAGTGACATTTGATTTTATTGTCAC-GTTTGACATTATCTTACAATCAT
* *
28760498 TGGTAATGA
193 TTGTGATGA
* * * ** * *
28760507 TAATTTTATCACTAATACTGCAACGATTTATCTTTCATCACTAATATATTAGATTTTCTTATTT-
1 TAATTATGTCACCAATACTGTGACGATTTATCTTTCATCACTAATATATTAGATTTTATCATTTA
* * * *
28760571 TATTGTGACGAATATAGCCTTTAATGACT-TTTTTTTTCATAAATAGTTGATGAAAACTAACGTC
66 TTTTGTGACGATTATAGCCTTTAATGA-TGTTTTTTTT-ATAAATAGCTGACGAAAACTAACGTC
28760635 ACAAAAAA
129 ACAAAAAA
28760643 AAAAAAACAT
Statistics
Matches: 453, Mismatches: 76, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
200 35 0.08
201 107 0.24
202 139 0.31
203 170 0.38
204 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.42
Consensus pattern (201 bp):
TAATTATGTCACCAATACTGTGACGATTTATCTTTCATCACTAATATATTAGATTTTATCATTTA
TTTTGTGACGATTATAGCCTTTAATGATGTTTTTTTTATAAATAGCTGACGAAAACTAACGTCAC
AAAAAATAAGCATAAAGTGACATTTGATTTTATTGTCACGTTTGACATTATCTTACAATCATTTG
TGATGA
Found at i:28768371 original size:2 final size:2
Alignment explanation
Indices: 28768358--28768395 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
28768348 GTTCTTGTGG
* *
28768358 AT AT AA AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28768396 CAATTTGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28769329 original size:6 final size:6
Alignment explanation
Indices: 28769318--28769345 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
28769308 GTTTTTGTGA
28769318 GAGAGG GAGAGG GAGAGG GAGAGG GAGA
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGA
28769346 AGAAGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:28769352 original size:18 final size:18
Alignment explanation
Indices: 28769318--28769352 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28769308 GTTTTTGTGA
* *
28769318 GAGAGGGAGAGGGAGAGG
1 GAGAGGGAGAAGAAGAGG
28769336 GAGAGGGAGAAGAAGAG
1 GAGAGGGAGAAGAAGAG
28769353 AAACCTTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (18 bp):
GAGAGGGAGAAGAAGAGG
Found at i:28776377 original size:21 final size:20
Alignment explanation
Indices: 28776340--28776386 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
28776330 AAAGATTTAA
* *
28776340 TTATTGATTTTTTATTAATT
1 TTATTCATTTTTAATTAATT
28776360 TTATTCATATTTTAATTAATT
1 TTATTCAT-TTTTAATTAATT
*
28776381 ATATTC
1 TTATTC
28776387 GAACACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (20 bp):
TTATTCATTTTTAATTAATT
Found at i:28786097 original size:2 final size:2
Alignment explanation
Indices: 28786090--28786127 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28786080 TTGGTCTTTG
28786090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28786128 GAATATGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28786731 original size:34 final size:34
Alignment explanation
Indices: 28786691--28786757 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
28786681 AGAATATGAA
28786691 GATGAAAATGAAGAGCATTCAACTTGGCAAAGAT
1 GATGAAAATGAAGAGCATTCAACTTGGCAAAGAT
*
28786725 GATGAAAATGAAGATCATTCAACTTGGCAAAGA
1 GATGAAAATGAAGAGCATTCAACTTGGCAAAGA
28786758 AGATCAACTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (34 bp):
GATGAAAATGAAGAGCATTCAACTTGGCAAAGAT
Found at i:28787150 original size:22 final size:22
Alignment explanation
Indices: 28787124--28787173 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
28787114 ATTTTACGTT
28787124 AAAGTCATACATAATGACAGTA
1 AAAGTCATACATAATGACAGTA
28787146 AAAGTCATACATAATGACAGTA
1 AAAGTCATACATAATGACAGTA
28787168 AAAGTC
1 AAAGTC
28787174 CTTTAACCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22
Consensus pattern (22 bp):
AAAGTCATACATAATGACAGTA
Found at i:28793441 original size:105 final size:102
Alignment explanation
Indices: 28793254--28793518 Score: 279
Period size: 105 Copynumber: 2.5 Consensus size: 102
28793244 ATATATATAA
* * * * *
28793254 TTTTTATAG-TTTTTATTGTAAAAAAAAGCTCTTAATAAAA-TAAGATGAGAAGATTTTGTGAGA
1 TTTTTGTAGTTTTTTATTATAAAAAAAA-TTCTTAA-AAAAGTAA-A-GAGAAGA-TTTGTTACA
* * *
28793317 TTTTGGAGTAC--AAAGACTACTTTTCTTACATAAGAAATGTAG
61 TTTT-G-GTACAAAAACACTACATTTCTTACATAAGAAATGAAG
* *
28793359 TCTTTTGTAGTTTTTTATTAT-AAAAAATTTTTTAAAAAAGTAAAAAGAGAAGAATTTGTTACAT
1 T-TTTTGTAGTTTTTTATTATAAAAAAAATTCTTAAAAAAGT--AAAGAGAAG-ATTTGTTACAT
*
28793423 TTTGGTACAAAAACACTACATTTCTTATATAAGAAATGAAG
62 TTTGGTACAAAAACACTACATTTCTTACATAAGAAATGAAG
* *
28793464 TTTTTGTAGTTTTTTGTTGTAAAAAAAATTCTTAAAAAAGTAAAGAGAAGATTTG
1 TTTTTGTAGTTTTTTATTATAAAAAAAATTCTTAAAAAAGTAAAGAGAAGATTTG
28793519 GTTAGATTCA
Statistics
Matches: 136, Mismatches: 15, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
102 5 0.04
103 13 0.10
104 22 0.16
105 70 0.51
106 15 0.11
107 11 0.08
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (102 bp):
TTTTTGTAGTTTTTTATTATAAAAAAAATTCTTAAAAAAGTAAAGAGAAGATTTGTTACATTTTG
GTACAAAAACACTACATTTCTTACATAAGAAATGAAG
Found at i:28796857 original size:14 final size:14
Alignment explanation
Indices: 28796838--28796867 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28796828 GTGATGCATA
28796838 CAATAAATGAAATG
1 CAATAAATGAAATG
*
28796852 CAATAAATGCAATG
1 CAATAAATGAAATG
28796866 CA
1 CA
28796868 TGAATTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (14 bp):
CAATAAATGAAATG
Found at i:28797777 original size:24 final size:24
Alignment explanation
Indices: 28797749--28797795 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
28797739 TATATAAAAA
28797749 ATAT-TTTAT-TATT-TATTTAATT
1 ATATATTTATATATTATA-TTAATT
28797771 ATATATTTATATATTATATTAATT
1 ATATATTTATATATTATATTAATT
28797795 A
1 A
28797796 AATTATGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 4 0.18
23 5 0.23
24 11 0.50
25 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATATATTTATATATTATATTAATT
Found at i:28798586 original size:11 final size:10
Alignment explanation
Indices: 28798572--28798613 Score: 52
Period size: 9 Copynumber: 4.2 Consensus size: 10
28798562 CTTTTAAATC
28798572 TTATTTATCTA
1 TTATTTAT-TA
28798583 TTATTTATTTA
1 TTATTTA-TTA
28798594 TTA-TTATTA
1 TTATTTATTA
28798603 TTA-TTATTA
1 TTATTTATTA
28798612 TT
1 TT
28798614 TGCTTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 14 0.47
10 3 0.10
11 12 0.40
12 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (10 bp):
TTATTTATTA
Found at i:28798592 original size:15 final size:14
Alignment explanation
Indices: 28798572--28798614 Score: 63
Period size: 12 Copynumber: 3.1 Consensus size: 14
28798562 CTTTTAAATC
28798572 TTATTTATCTATTAT
1 TTATTTAT-TATTAT
28798587 TTATTTATTATTA-
1 TTATTTATTATTAT
28798600 TTA-TTATTATTAT
1 TTATTTATTATTAT
28798613 TT
1 TT
28798615 GCTTATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 9 0.33
13 5 0.19
14 5 0.19
15 8 0.30
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTTATTATTAT
Found at i:28798883 original size:61 final size:60
Alignment explanation
Indices: 28798712--28799527 Score: 771
Period size: 60 Copynumber: 13.7 Consensus size: 60
28798702 AAAATTATAT
* * * *
28798712 ATATTTTT-AAGAAAAGTTGAAAAGCATCAATTTTTCTTAAAAATAAAATTTTCAAAAAAA
1 ATATTTTTGAGGAAAAGTTG-AAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAAA
* * ** * *
28798772 ATATTTTTGAGGAAGAGTTAAAAACATCAACTTTCCTT-AAAATAAAAATTTCAAAAAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAATTTC-AAAAAAA
* * * *
28798832 ATATTTTTGAGAAAAAGTTTATAGTATCAATTTTTTTTGAAAATAAAAATTTTC-AAAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAA-TTTCAAAAAAA
** * * *
28798892 GCATTTTTGA-GAAAGAATTGAAAGTATTAATTTTTCTCGAAAATAAAAAAAAATTTCAAAAAAA
1 ATATTTTTGAGGAAA-AGTTGAAAGTATCAATTTTTCTTGAAAAT----AAAAATTTC--AAAAA
28798956 AA
59 AA
* * * * * *
28798958 AAATTTTTAAGGAAAATTTGAAAGTATTAATTTTTTTTGAAAATAAAGATTTCAAAAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAAA
* * **
28799018 GGA-ATTTTTGAGGAAAAGTTGATAA-TATCAATTTTTCTTAAAAATAAAAAAATTT-GAAAAGG
1 --ATATTTTTGAGGAAAAGTTGA-AAGTATCAATTTTTCTTGAAAAT--AAAAATTTCAAAAAAA
* * * *
28799080 ATATTTTTAAGGAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAATTTTCAAAAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAAA
*
28799140 ATATTTTTAAGGAAAAGTT-AAAGTATCAA-TTTTCTTTGAAAATAAAAAATTTC-AAAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTGAAAAT-AAAAATTTCAAAAAAA
* * * *
28799199 ATATTTTTAAGAAAAAGTTAAAAGTATCAATTTTTC-TCAGAAATAAAAA--T---AAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGA-AAATAAAAATTTCAAAAAAA
* * * * *
28799254 ATATTTTTGAGAAAAATTTGAAAGTATC-AGTTTTCTTTGAAAATGAAAATTTCAAGAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTGAAAATAAAAATTTCAAAAAAA
** * * **
28799314 ATATTTTTGAAAAAAAGTTGAAAGTATCGATTTTCCTTGAAAATAAAAATTTCAAATAATG
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAA-AAAA
* * *
28799375 A-ATTTTTGAGGAAAAGTTGAAAATATCAAATTTTCTTGAAAATAAAGATTTCAAAAAAGA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAA-A
*
28799435 A-ATTTTTGAGGTAAAGTTGAAAGTATCAATTTTTCTTGAAAAT-AAAA-TT-AAAAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAAA
** *
28799491 ATATTTTT-AAAAAAAGTT-AAAGTATCAATTTTCCTTG
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTG
28799528 TATAGAAGTA
Statistics
Matches: 635, Mismatches: 84, Indels: 79
0.80 0.11 0.10
Matches are distributed among these distances:
54 6 0.01
55 56 0.09
56 11 0.02
57 14 0.02
58 7 0.01
59 75 0.12
60 286 0.45
61 102 0.16
62 19 0.03
63 11 0.02
64 5 0.01
66 39 0.06
67 4 0.01
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.35
Consensus pattern (60 bp):
ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAAA
Found at i:28810166 original size:58 final size:58
Alignment explanation
Indices: 28810074--28810186 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 58
28810064 TTTCTTAACA
* * * *
28810074 AAAAGAAAAAGAGCTCAAATTGAAGACTCGTAAAGGGCGATTTACGTTAAAAAAAAAG
1 AAAAGAAAAAGAACTCAAATTGAAAACCCATAAAGGGCGATTTACGTTAAAAAAAAAG
* **
28810132 AAAA-AAAAAGAAACTCAAATTGAAAACCCATAAAGGGTGATTTGGGTTAAAAAAA
1 AAAAGAAAAAG-AACTCAAATTGAAAACCCATAAAGGGCGATTTACGTTAAAAAAA
28810187 TTTAAAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 6 0.13
58 41 0.87
ACGTcount: A:0.54, C:0.10, G:0.19, T:0.18
Consensus pattern (58 bp):
AAAAGAAAAAGAACTCAAATTGAAAACCCATAAAGGGCGATTTACGTTAAAAAAAAAG
Found at i:28810338 original size:46 final size:46
Alignment explanation
Indices: 28810251--28810339 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
28810241 TTAAAAAAAA
* ***
28810251 AAAAAAAAAAGCTCAAACTGAAAACCCATAAATGGTGATTTGATTT
1 AAAAAAAAAAGCTCAAACTGAAAACCCATAAAAGACAATTTGATTT
*
28810297 AAAAAAAAAAGCTCAAATTGAAAA-CCAGTAAAAGACAATTTGA
1 AAAAAAAAAAGCTCAAACTGAAAACCCA-TAAAAGACAATTTGA
28810340 GTTCCAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
45 3 0.08
46 34 0.92
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (46 bp):
AAAAAAAAAAGCTCAAACTGAAAACCCATAAAAGACAATTTGATTT
Found at i:28811290 original size:86 final size:86
Alignment explanation
Indices: 28811138--28811306 Score: 225
Period size: 86 Copynumber: 2.0 Consensus size: 86
28811128 ATTTTTAACG
* * * *
28811138 TAGTCCACGTCATTCATTTCAGACTTCGATTCAATCCAAGTCATTATATTTTTGGATTTCGACAT
1 TAGTCCAAGTCATTCATTTCAAACTTCGATTCAAACCAAGTCATTATATTTTTGGATTTAGACAT
28811203 ATGTCAGATTCTTT-TTCGATT
66 ATGTCAGA-TCTTTCTTCGATT
* * * * *
28811224 TAGTCCAAGTCATTCGTTTCAAACTTCGGTTCAAACTAGGTCATTTTATTTTTGGATTTTAG-CA
1 TAGTCCAAGTCATTCATTTCAAACTTCGATTCAAACCAAGTCATTATATTTTTGGA-TTTAGACA
28811288 TATGTCAGATCTTTCTTCG
65 TATGTCAGATCTTTCTTCG
28811307 GCTTAGTCTA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
85 5 0.07
86 63 0.88
87 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (86 bp):
TAGTCCAAGTCATTCATTTCAAACTTCGATTCAAACCAAGTCATTATATTTTTGGATTTAGACAT
ATGTCAGATCTTTCTTCGATT
Found at i:28812331 original size:20 final size:18
Alignment explanation
Indices: 28812320--28812362 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
28812310 ATAAATAAAT
28812320 TAAAATAGAAATCAAAAAA
1 TAAAA-AGAAATCAAAAAA
*
28812339 TAAAAAGAAAATGAAAAAA
1 TAAAAAG-AAATCAAAAAA
28812358 -AAAAA
1 TAAAAA
28812363 CCTGCGGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (18 bp):
TAAAAAGAAATCAAAAAA
Found at i:28813201 original size:16 final size:16
Alignment explanation
Indices: 28813180--28813217 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
28813170 AATCAGAACA
* *
28813180 AAAAAAGAAAGAAGGG
1 AAAAAAGAAAAAAAGG
28813196 AAAAAAGAAAAAAAGG
1 AAAAAAGAAAAAAAGG
28813212 AAAAAA
1 AAAAAA
28813218 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAGG
Found at i:28813201 original size:17 final size:17
Alignment explanation
Indices: 28813179--28813224 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
28813169 GAATCAGAAC
*
28813179 AAAAAAAG-AAAGAAGG
1 AAAAAAAGAAAAAAAGG
*
28813195 GAAAAAAGAAAAAAAGG
1 AAAAAAAGAAAAAAAGG
*
28813212 AAAAAAATAAAAA
1 AAAAAAAGAAAAA
28813225 TATAATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAGG
Found at i:28813232 original size:3 final size:3
Alignment explanation
Indices: 28813217--28813310 Score: 172
Period size: 3 Copynumber: 31.7 Consensus size: 3
28813207 AAAGGAAAAA
*
28813217 AAT AAA AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28813264 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28813311 ATCTAATTGA
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 86 0.98
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28813352 original size:25 final size:25
Alignment explanation
Indices: 28813318--28813380 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
28813308 TAAATCTAAT
*
28813318 TGACCTAAATGGGTCAGAACGGGTA
1 TGACCTAAATGGGTCAGAAAGGGTA
28813343 TGACCTAAATGGGTCAGAAAGGGTA
1 TGACCTAAATGGGTCAGAAAGGGTA
*
28813368 TGACCAAAATGGG
1 TGACCTAAATGGG
28813381 CCCAGTTGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.32, T:0.19
Consensus pattern (25 bp):
TGACCTAAATGGGTCAGAAAGGGTA
Found at i:28814284 original size:118 final size:117
Alignment explanation
Indices: 28813774--28814407 Score: 541
Period size: 118 Copynumber: 5.4 Consensus size: 117
28813764 GAAACCACGG
* * **
28813774 ATCAAGAAGAATGATCTAGATTGAGCCAAGA-CTAAGTGACTGGGATGAAACCATGAGTCAAATA
1 ATCAAGAAGAATGATCTAGACTGAGCCAAGATC-AAGTGACTGAGACAAAACCATGAGTCAAATA
** * * * * * ** *
28813838 AAGCAACCAAGATGGAGTCGAGATCAAAATAGATGA-TCAGGATGGAACCACCA
65 AAGTGACCAAGATCGAGTCAAGGTCAAAATAAATGATTGA-GACAGAACCACAA
* * ** * * * *
28813891 ATCAAGAAAAATGATCTGGACTGAATCAAGATCAGGTGA-TCGAGACAAAACTAAGAGTCAAATG
1 ATCAAGAAGAATGATCTAGACTGAGCCAAGATCAAGTGACT-GAGACAAAACCATGAGTCAAATA
* ** *
28813955 AAGTGACCAAGATCGAGTTAAGGT-AACATATAAATGATCAAGACAGAACCATAA
65 AAGTGACCAAGATCGAGTCAAGGTCAA-A-ATAAATGATTGAGACAGAACCACAA
* * *
28814009 ATC-ATAAGAAATGATCTAGACTGAGCCAAGATCAGGTGA-TCGAGACACAACCATGAGTCAAAA
1 ATCAAGAAG-AATGATCTAGACTGAGCCAAGATCAAGTGACT-GAGACAAAACCATGAGTC-AAA
* * * * * *
28814072 TAAAATGA-CTAGAATCGAGTCAAGGTCAAAATAGATGGTCGAGACAGAACCACGA
63 TAAAGTGACCAAG-ATCGAGTCAAGGTCAAAATAAATGATTGAGACAGAACCACAA
* * * * * * *
28814127 ATCAAGAAGAATGATCTGGATTGAGCCAAGATTAGGTGACTGAAACAAAATCATGAGTCAAATGA
1 ATCAAGAAGAATGATCTAGACTGAGCCAAGATCAAGTGACTGAGACAAAACCATGAGTCAAATAA
* *
28814192 AGTGACCAAGATCGAGTCAAGATCACAAATAAATGATTGAGACAGAACCATAA
66 AGTGACCAAGATCGAGTCAAGGTCA-AAATAAATGATTGAGACAGAACCACAA
* * * * **
28814245 ATCAAGAAGAATGATCTAGACTAAGCCAAGATCAAGTGACTGGGACGAAATCACAAGTCAAAT-A
1 ATCAAGAAGAATGATCTAGACTGAGCCAAGATCAAGTGACTGAGACAAAACCATGAGTCAAATAA
* * * * * *
28814309 AGACGACCAGGACCAAGTCAAGGTCAAAAATAAATGATTGAGA-TGAAACCACGA
66 AG-TGACCAAGATCGAGTCAAGGTC-AAAATAAATGATTGAGACAG-AACCACAA
* *
28814363 ATCATAAGAA-AATGATTTAGACTGAGCCAAGATCAAGTGAGTGAG
1 ATC--AAGAAGAATGATCTAGACTGAGCCAAGATCAAGTGACTGAG
28814408 TTGATGCAAA
Statistics
Matches: 419, Mismatches: 80, Indels: 34
0.79 0.15 0.06
Matches are distributed among these distances:
116 3 0.01
117 97 0.23
118 252 0.60
119 60 0.14
120 7 0.02
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (117 bp):
ATCAAGAAGAATGATCTAGACTGAGCCAAGATCAAGTGACTGAGACAAAACCATGAGTCAAATAA
AGTGACCAAGATCGAGTCAAGGTCAAAATAAATGATTGAGACAGAACCACAA
Found at i:28814306 original size:236 final size:233
Alignment explanation
Indices: 28813774--28814402 Score: 680
Period size: 236 Copynumber: 2.7 Consensus size: 233
28813764 GAAACCACGG
* *
28813774 ATCAAGAAGAATGATCTAGATTGAGCCAAGA-CTAAGTGACTGGGATGAAACCATGAGTCAAATA
1 ATCAAGAAGAATGATCTAGACTGAGCCAAGATC-AAGTGACTGGGACGAAACCATGAGTCAAATA
* * * * * * *
28813838 AAGCAACCA-AGATGGAGTCGAGATCAAAATAGATGATC-AGGATGGAACCACCAATCAAGAAAA
65 AAACGACCAGA-ATCGAGTCAAGGTCAAAATAGATGATCGA-GA-AGAACCACGAATCAAG-AAA
** *
28813901 ATGATCTGGACTGAATCAAGATCAGGTGATCGAGACAAAACTAAGAGTCAAATGAAGTGACCAAG
126 ATGATCTGGACTGAGCCAAGATCAGGTGATCGAAACAAAACTAAGAGTCAAATGAAGTGACCAAG
* * *
28813966 ATCGAGTTAAGGTAACATATAAATGATCAAGACAGAACCATAA
191 ATCGAGTCAAGATAACAAATAAATGATCAAGACAGAACCATAA
* * *
28814009 ATC-ATAAGAAATGATCTAGACTGAGCCAAGATCAGGTGA-TCGAGAC-ACAACCATGAGTCAAA
1 ATCAAGAAG-AATGATCTAGACTGAGCCAAGATCAAGTGACT-GGGACGA-AACCATGAGTC-AA
* * *
28814071 ATAAAATGACTAGAATCGAGTCAAGGTCAAAATAGATGGTCGAGACAGAACCACGAATCAAGAAG
62 ATAAAACGACCAGAATCGAGTCAAGGTCAAAATAGATGATCGAGA-AGAACCACGAATCAAGAA-
* * *
28814136 AATGATCTGGATTGAGCCAAGATTAGGTGA-CTGAAACAAAA-TCATGAGTCAAATGAAGTGACC
125 AATGATCTGGACTGAGCCAAGATCAGGTGATC-GAAACAAAACT-AAGAGTCAAATGAAGTGACC
* **
28814199 AAGATCGAGTCAAGATCACAAATAAATGATTGAGACAGAACCATAA
188 AAGATCGAGTCAAGATAACAAATAAATGATCAAGACAGAACCATAA
* * **
28814245 ATCAAGAAGAATGATCTAGACTAAGCCAAGATCAAGTGACTGGGACGAAATCACAAGTCAAATAA
1 ATCAAGAAGAATGATCTAGACTGAGCCAAGATCAAGTGACTGGGACGAAACCATGAGTCAAATAA
* * * * * * *
28814310 GACGACCAGGACCAAGTCAAGGTCAAAAATAAATGATTGAGATGAAACCACGAATCATAAGAAAA
66 AACGACCAGAATCGAGTCAAGGTC-AAAATAGATGATCGAGAAG-AACCACGAATC--AAGAAAA
* * *
28814375 TGATTTAGACTGAGCCAAGATCAAGTGA
127 TGATCTGGACTGAGCCAAGATCAGGTGA
28814403 GTGAGTTGAT
Statistics
Matches: 327, Mismatches: 50, Indels: 32
0.80 0.12 0.08
Matches are distributed among these distances:
234 6 0.02
235 72 0.22
236 211 0.65
237 33 0.10
238 5 0.02
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.18
Consensus pattern (233 bp):
ATCAAGAAGAATGATCTAGACTGAGCCAAGATCAAGTGACTGGGACGAAACCATGAGTCAAATAA
AACGACCAGAATCGAGTCAAGGTCAAAATAGATGATCGAGAAGAACCACGAATCAAGAAAATGAT
CTGGACTGAGCCAAGATCAGGTGATCGAAACAAAACTAAGAGTCAAATGAAGTGACCAAGATCGA
GTCAAGATAACAAATAAATGATCAAGACAGAACCATAA
Found at i:28825469 original size:20 final size:20
Alignment explanation
Indices: 28825446--28825489 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
28825436 AATATGGGTC
* * *
28825446 AAAATAAACAAATTAAAATA
1 AAAATAAAAAAATAAAAAGA
28825466 AAAATAAAAAAATAAAAAGA
1 AAAATAAAAAAATAAAAAGA
28825486 AAAA
1 AAAA
28825490 GCCTTGCGAC
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:0.82, C:0.02, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAATAAAAAAATAAAAAGA
Found at i:28825477 original size:14 final size:14
Alignment explanation
Indices: 28825460--28825489 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28825450 TAAACAAATT
*
28825460 AAAATAAAAATAAA
1 AAAATAAAAAGAAA
28825474 AAAATAAAAAGAAA
1 AAAATAAAAAGAAA
28825488 AA
1 AA
28825490 GCCTTGCGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (14 bp):
AAAATAAAAAGAAA
Found at i:28825893 original size:22 final size:22
Alignment explanation
Indices: 28825868--28825916 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
28825858 TCCTAAACCC
28825868 AAAAAAA-CCTAAAAAATTCCAA
1 AAAAAAATCCTAAAAAATT-CAA
* *
28825890 AAAAAAATCTTGAAAAATTCAA
1 AAAAAAATCCTAAAAAATTCAA
28825912 AAAAA
1 AAAAA
28825917 TTCCTAGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.69, C:0.12, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAAAAATCCTAAAAAATTCAA
Found at i:28826333 original size:7 final size:7
Alignment explanation
Indices: 28826321--28826359 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
28826311 ATCAGAATAG
28826321 AAAAAGA
1 AAAAAGA
28826328 AAAAAGGAA
1 AAAAA-G-A
28826337 AAAAAGA
1 AAAAAGA
*
28826344 AGAAAGA
1 AAAAAGA
28826351 AAAAAGA
1 AAAAAGA
28826358 AA
1 AA
28826360 TGAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 20 0.71
8 2 0.07
9 6 0.21
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:28826342 original size:16 final size:14
Alignment explanation
Indices: 28826321--28826359 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
28826311 ATCAGAATAG
28826321 AAAAAGAAAAAAGGAA
1 AAAAAGAAAAAA-G-A
*
28826337 AAAAAGAAGAAAGA
1 AAAAAGAAAAAAGA
28826351 AAAAAGAAA
1 AAAAAGAAA
28826360 TGAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 11 0.52
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAGA
Found at i:28826357 original size:11 final size:11
Alignment explanation
Indices: 28826323--28826365 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
28826313 CAGAATAGAA
28826323 AAAGAAAAAAGG
1 AAAGAAAAAA-G
28826335 AAA-AAAAGAAG
1 AAAGAAAA-AAG
28826346 AAAGAAAAAAG
1 AAAGAAAAAAG
28826357 AAATGAAAA
1 AAA-GAAAA
28826366 TATAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 14 0.50
12 14 0.50
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:28826375 original size:3 final size:3
Alignment explanation
Indices: 28826367--28826487 Score: 128
Period size: 3 Copynumber: 40.3 Consensus size: 3
28826357 AAATGAAAAT
*
28826367 ATA ATA ATA ATA ATA ATA ATA ATGGA ATA GA-A A-A ATA A-A GTA A-A
1 ATA ATA ATA ATA ATA ATA ATA AT--A ATA -ATA ATA ATA ATA ATA ATA
*
28826411 A-A AGA AGTA A-A GATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA A-TA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28826456 ATA ATA ATA ATA ATA ATA ATA ATA TATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA A
28826488 ATCTAATTGG
Statistics
Matches: 105, Mismatches: 3, Indels: 20
0.82 0.02 0.16
Matches are distributed among these distances:
2 9 0.09
3 86 0.82
4 7 0.07
5 3 0.03
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:28831289 original size:51 final size:51
Alignment explanation
Indices: 28831183--28831280 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
28831173 ATTTTATATA
* *
28831183 ATTTTAATATGAATTGATTTTAAAATTAAATTTCAAAAATCTCTCAACATT
1 ATTTTAATATGAATTGATTTTAAAATTAAATCTAAAAAATCTCTCAACATT
* * *
28831234 ATTTTAATGTGAATTGATTTTGAAATTAAATCTAAAAAATCTTTCAA
1 ATTTTAATATGAATTGATTTTAAAATTAAATCTAAAAAATCTCTCAA
28831281 TTTCATTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (51 bp):
ATTTTAATATGAATTGATTTTAAAATTAAATCTAAAAAATCTCTCAACATT
Found at i:28833451 original size:16 final size:16
Alignment explanation
Indices: 28833430--28833491 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
28833420 TTTAAGTTAA
28833430 ATAAATCTAATTATTT
1 ATAAATCTAATTATTT
*
28833446 ATAAATTTAATTATTT
1 ATAAATCTAATTATTT
* * **
28833462 ATGAATTTTTTATATTT
1 ATAAATCTAAT-TATTT
*
28833479 ATGAATCTAATTA
1 ATAAATCTAATTA
28833492 ATTGTGAGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
16 25 0.66
17 13 0.34
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
ATAAATCTAATTATTT
Found at i:28844744 original size:6 final size:6
Alignment explanation
Indices: 28844728--28844761 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
28844718 GTTTTGCAAG
* *
28844728 TTTTTC CTTTTC TTTTTC TTTTTC TTTTTA TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
28844762 CTGTTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:28844824 original size:3 final size:3
Alignment explanation
Indices: 28844806--28844862 Score: 89
Period size: 3 Copynumber: 19.0 Consensus size: 3
28844796 ATTTTTGTGC
*
28844806 TAT TTT TAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28844852 T-T TAT TAT TAT
1 TAT TAT TAT TAT
28844863 CACTAGTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:28852178 original size:40 final size:40
Alignment explanation
Indices: 28852123--28852207 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 40
28852113 GCCTCTCAAA
* *
28852123 TTTTTAACATTTAAAGTTCGTTGCCTCTAGTGAGAGGAGC
1 TTTTTAACATTTAAAGTTCATTGCCTCTAGTCAGAGGAGC
* * *
28852163 TTTTTAACATTTAAAGTTTATTGCTTCTGGTCAGAGGAGC
1 TTTTTAACATTTAAAGTTCATTGCCTCTAGTCAGAGGAGC
28852203 TTTTT
1 TTTTT
28852208 TAATTTCAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.44
Consensus pattern (40 bp):
TTTTTAACATTTAAAGTTCATTGCCTCTAGTCAGAGGAGC
Found at i:28852351 original size:39 final size:38
Alignment explanation
Indices: 28852298--28852705 Score: 343
Period size: 39 Copynumber: 10.6 Consensus size: 38
28852288 CTCTCAGATT
*
28852298 TTTG-AATTTAAAGTTTGTTGCCTTTGGTGAGAAGAGCC
1 TTTGAAATTTAAAGTTTGTTGCCTTTGGTTA-AAGAGCC
*
28852336 TTTGAAATTTAAAGTTTGTTGCTTTTGGTTAAAGGAG-C
1 TTTGAAATTTAAAGTTTGTTGCCTTTGGTTAAA-GAGCC
* * *
28852374 TTTTATCATTTAAAGTTTGTTGCCTTTAGTTAAAGGAG-C
1 TTTGA-AATTTAAAGTTTGTTGCCTTTGGTTAAA-GAGCC
* *
28852413 TTTTAACATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTT
1 TTTGAA-ATTTAAAGTTTGTTGCCTTTGGTTAAA-GAGC-C
* * *
28852454 TTTG-AATTTAAAGTTTATTGCATTTGGTTAAAAGAGCT
1 TTTGAAATTTAAAGTTTGTTGCCTTTGGTT-AAAGAGCC
* * * *
28852492 TTTG-AATTTAAAGTTTGTTGCCTCTGGTGAGAGGAGCT
1 TTTGAAATTTAAAGTTTGTTGCCTTTGGTTA-AAGAGCC
*
28852530 TTTGAAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTT
1 TTTGAAATTTAAAGTTTGTTGCCTTTGGTTAAA-GAGC-C
* * * * *
28852570 TTTG-AATTTAAAATTTGTTGCCTCTAGTGAGAAAAGCC
1 TTTGAAATTTAAAGTTTGTTGCCTTTGGTTA-AAGAGCC
*
28852608 TTT-AGAATTTAAAATTTGTTGCCTTTGGTTAAATGAG-C
1 TTTGA-AATTTAAAGTTTGTTGCCTTTGGTTAAA-GAGCC
* * * *
28852646 TTTTATCACTTAAAGTTTGTTGCC-TCGG-TAAGAGAAGCC
1 TTTGA-AATTTAAAGTTTGTTGCCTTTGGTTAA-AG-AGCC
*
28852685 TTTTG-GATTTAAAGTTTGTTG
1 -TTTGAAATTTAAAGTTTGTTG
28852706 TCTCTTGTGA
Statistics
Matches: 312, Mismatches: 38, Indels: 40
0.80 0.10 0.10
Matches are distributed among these distances:
37 5 0.02
38 77 0.25
39 213 0.68
40 14 0.04
41 3 0.01
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (38 bp):
TTTGAAATTTAAAGTTTGTTGCCTTTGGTTAAAGAGCC
Found at i:28852432 original size:78 final size:77
Alignment explanation
Indices: 28852302--28852740 Score: 426
Period size: 78 Copynumber: 5.6 Consensus size: 77
28852292 CAGATTTTTG
* * * * *
28852302 AATTTAAAGTTTGTTGCCTTTGGTGAGAA-GAGCCTTTGAAATTTAAAGTTTGTTGCTTTTGGTT
1 AATTTAAAGTTTGTTGCCTTTGGTTA-AAGGAG-CTTTTAAATTTAAAGTTTGTTGCCTCTGGTG
28852366 AAAGGAGCTTTTAT
64 AAAGGAGCTTTTAT
* * * *
28852380 CATTTAAAGTTTGTTGCCTTTAGTTAAAGGAGCTTTTAACATTTAAAGTTTGTTGCCTTTGGTTA
1 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTAA-ATTTAAAGTTTGTTGCCTCTGGTGA
28852445 AAGGAGCTTTT-T
65 AAGGAGCTTTTAT
* * * *
28852457 GAATTTAAAGTTTATTGCATTTGGTTAAAAGAGCTTTTGAATTTAAAGTTTGTTGCCTCTGGTGA
1 -AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTAAATTTAAAGTTTGTTGCCTCTGGTGA
*
28852522 GAGGAGCTTTTGA-
65 AAGGAGCTTTT-AT
* * *
28852535 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGAATTTAAAATTTGTTGCCTCTAGTGA
1 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGC-TTTTAAATTTAAAGTTTGTTGCCTCTGGTGA
* * *
28852600 GAA-AAGCCTTTAG
65 -AAGGAGCTTTTAT
* * * *
28852613 AATTTAAAATTTGTTGCCTTTGGTTAAATGAGCTTTTATCACTTAAAGTTTGTTGCCTC-GGT-A
1 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTA-AATTTAAAGTTTGTTGCCTCTGGTGA
* *
28852676 AGAGAAGCCTTTT-G
65 A-AGGAG-CTTTTAT
* * * * * *
28852690 GATTTAAAGTTTGTTGTCTCTT-GTGAGATGAGCTTTTTTAATTTAAAGTTT
1 AATTTAAAGTTTGTTGCCT-TTGGTTAAAGGAGC-TTTTAAATTTAAAGTTT
28852741 CATAGCCTCT
Statistics
Matches: 309, Mismatches: 38, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
75 1 0.00
76 2 0.01
77 118 0.38
78 187 0.61
79 1 0.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (77 bp):
AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTAAATTTAAAGTTTGTTGCCTCTGGTGAA
AGGAGCTTTTAT
Found at i:28852628 original size:194 final size:194
Alignment explanation
Indices: 28852297--28852740 Score: 576
Period size: 194 Copynumber: 2.3 Consensus size: 194
28852287 TCTCTCAGAT
* * *
28852297 TTTTGAATTTAAAGTTTGTTGCCTTTGGTGAGAAGAGCCTTTGAAATTTAAAGTTTGTTGCTTTT
1 TTTTGAATTTAAAGTTTGTTGCCTCTGGTGAGAAGAGCTTTTGAAATTTAAAGTTTGTTGCCTTT
* * * * * *
28852362 GGTTAAAGGAGCTTTTATCATTTAAAGTTTGTTGCCTTTAGTTAAAGGAGCTTTTAACATTTAAA
66 GGTTAAAGGAGCTTTTATAATTTAAAATTTGTTGCCTCTAGTGAAAGAAGCCTTTAACATTTAAA
* * * *
28852427 GTTTGTTGCCTTTGGTTAAAGGAGCTTTT-TGAATTTAAAGTTTATTGCATTTGGTTAAAAG-AG
131 ATTTGTTGCCTTTGGTTAAAGGAGCTTTTAT-AACTTAAAGTTTATTGC-CTCGG-TAAAAGAAG
28852490 -C
193 CC
*
28852491 TTTTGAATTTAAAGTTTGTTGCCTCTGGTGAGAGGAGCTTTTGAAATTTAAAGTTTGTTGCCTTT
1 TTTTGAATTTAAAGTTTGTTGCCTCTGGTGAGAAGAGCTTTTGAAATTTAAAGTTTGTTGCCTTT
28852556 GGTTAAAGGAGCTTTT-TGAATTTAAAATTTGTTGCCTCTAGTGAGAA-AAGCCTTTAGA-ATTT
66 GGTTAAAGGAGCTTTTAT-AATTTAAAATTTGTTGCCTCTAGTGA-AAGAAGCCTTTA-ACATTT
* * * *
28852618 AAAATTTGTTGCCTTTGGTTAAATGAGCTTTTATCACTTAAAGTTTGTTGCCTCGGTAAGAGAAG
128 AAAATTTGTTGCCTTTGGTTAAAGGAGCTTTTATAACTTAAAGTTTATTGCCTCGGTAAAAGAAG
28852683 CC
193 CC
* * * * **
28852685 TTTTGGATTTAAAGTTTGTTGTCTCTTGTGAGATGAGCTTTTTTAATTTAAAGTTT
1 TTTTGAATTTAAAGTTTGTTGCCTCTGGTGAGAAGAGCTTTTGAAATTTAAAGTTT
28852741 CATAGCCTCT
Statistics
Matches: 220, Mismatches: 24, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
192 5 0.02
193 6 0.03
194 205 0.93
195 4 0.02
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (194 bp):
TTTTGAATTTAAAGTTTGTTGCCTCTGGTGAGAAGAGCTTTTGAAATTTAAAGTTTGTTGCCTTT
GGTTAAAGGAGCTTTTATAATTTAAAATTTGTTGCCTCTAGTGAAAGAAGCCTTTAACATTTAAA
ATTTGTTGCCTTTGGTTAAAGGAGCTTTTATAACTTAAAGTTTATTGCCTCGGTAAAAGAAGCC
Found at i:28853470 original size:50 final size:52
Alignment explanation
Indices: 28853407--28853511 Score: 133
Period size: 50 Copynumber: 2.1 Consensus size: 52
28853397 TCGTCGGAAA
** *
28853407 CTAGAAATTTTTGAATTTTTCGACGA-CGTTGAATTTTT-TGACACCAAAAT
1 CTAGAAAAGTTTGAATTTTTCGACGATCGTTGAATTTTTCAGACACCAAAAT
** * *
28853457 CTAGAAAAGTTTGAATTTTTTTATGATCGTTGAATTTTTCAGCCACCAAAAT
1 CTAGAAAAGTTTGAATTTTTCGACGATCGTTGAATTTTTCAGACACCAAAAT
28853509 CTA
1 CTA
28853512 AGGATCTTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
50 21 0.46
51 12 0.26
52 13 0.28
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (52 bp):
CTAGAAAAGTTTGAATTTTTCGACGATCGTTGAATTTTTCAGACACCAAAAT
Found at i:28853840 original size:12 final size:12
Alignment explanation
Indices: 28853825--28853854 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28853815 TTTAGATTTA
*
28853825 TTTTATGTTATT
1 TTTTATGCTATT
28853837 TTTTATGCTATT
1 TTTTATGCTATT
28853849 TTTTAT
1 TTTTAT
28853855 ATAATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.73
Consensus pattern (12 bp):
TTTTATGCTATT
Found at i:28853977 original size:16 final size:16
Alignment explanation
Indices: 28853948--28853993 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
28853938 GATAAAAATG
28853948 AAACTAAAATAAAATAA
1 AAACTAAAA-AAAATAA
* *
28853965 AAACTTAAAAAAATAT
1 AAACTAAAAAAAATAA
28853981 AAA-TAAAAAAAAT
1 AAACTAAAAAAAAT
28853994 TTAATAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 9 0.35
16 9 0.35
17 8 0.31
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (16 bp):
AAACTAAAAAAAATAA
Found at i:28854146 original size:14 final size:13
Alignment explanation
Indices: 28854114--28854147 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
28854104 ATAAATAATA
*
28854114 AATTGTTTAAATG
1 AATTTTTTAAATG
28854127 AATTTTTTAAATG
1 AATTTTTTAAATG
28854140 CAATTTTT
1 -AATTTTT
28854148 AGAGAAAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (13 bp):
AATTTTTTAAATG
Found at i:28869446 original size:17 final size:17
Alignment explanation
Indices: 28869424--28869457 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28869414 TTCCCGGTCC
28869424 TTTTTGAATAAACAGCA
1 TTTTTGAATAAACAGCA
28869441 TTTTTGAATAAACAGCA
1 TTTTTGAATAAACAGCA
28869458 AAGAAACAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TTTTTGAATAAACAGCA
Found at i:28870740 original size:2 final size:2
Alignment explanation
Indices: 28870733--28870768 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
28870723 AGATTAACAC
*
28870733 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28870769 TGAATGCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28874715 original size:16 final size:17
Alignment explanation
Indices: 28874686--28874718 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28874676 TATAATATTA
28874686 TAAATCATTAGTATTTT
1 TAAATCATTAGTATTTT
28874703 TAAATCATT-GTATTTT
1 TAAATCATTAGTATTTT
28874719 GTGTTATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (17 bp):
TAAATCATTAGTATTTT
Found at i:28875495 original size:2 final size:2
Alignment explanation
Indices: 28875488--28875524 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
28875478 CGTAATGCTT
28875488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28875525 AATAAACACT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28876560 original size:24 final size:24
Alignment explanation
Indices: 28876495--28876560 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 24
28876485 GAATGAACAA
*
28876495 TAAAATTAAAAATAATAATAGAAG
1 TAAAATTAATAATAATAATAGAAG
* *
28876519 TAAAATTAATTATTATAATAATATAAT
1 TAAAATTAA-TA--ATAATAATAGAAG
*
28876546 TAAAATTAATGATAA
1 TAAAATTAATAATAA
28876561 AATGTGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 13 0.37
25 1 0.03
26 1 0.03
27 20 0.57
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.35
Consensus pattern (24 bp):
TAAAATTAATAATAATAATAGAAG
Found at i:28876793 original size:23 final size:24
Alignment explanation
Indices: 28876746--28876799 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
28876736 TTACTAATAA
28876746 ATTATATAATAATAAAATTTATTT
1 ATTATATAATAATAAAATTTATTT
*
28876770 ATTATATAATAA-AAATTTTATTT
1 ATTATATAATAATAAAATTTATTT
28876793 ATTATAT
1 ATTATAT
28876800 TAAATCACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTATATAATAATAAAATTTATTT
Found at i:28877657 original size:9 final size:9
Alignment explanation
Indices: 28877645--28877678 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
28877635 TATTTTTTCT
28877645 TAAAATATA
1 TAAAATATA
28877654 TAAAATATA
1 TAAAATATA
28877663 TTAATAATATA
1 -TAA-AATATA
28877674 TAAAA
1 TAAAA
28877679 AAATTTTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 11 0.48
10 6 0.26
11 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAATATA
Found at i:28877858 original size:19 final size:19
Alignment explanation
Indices: 28877826--28877866 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28877816 AACATATAAT
*
28877826 AAAAATAAATGTTTGGTTGA
1 AAAAACAAATGTTTGGTT-A
28877846 AAAAACAAA-GTTTGGTTA
1 AAAAACAAATGTTTGGTTA
28877864 AAA
1 AAA
28877867 TTTTTACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.29
Consensus pattern (19 bp):
AAAAACAAATGTTTGGTTA
Found at i:28878207 original size:9 final size:9
Alignment explanation
Indices: 28878180--28878213 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
28878170 AAAAATCTTT
28878180 TTTTATATA
1 TTTTATATA
28878189 TTATTAATATA
1 TT-TT-ATATA
28878200 TTTTATATA
1 TTTTATATA
28878209 TTTTA
1 TTTTA
28878214 AGAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 12 0.52
10 4 0.17
11 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTATATA
Found at i:28889958 original size:59 final size:58
Alignment explanation
Indices: 28889884--28890038 Score: 188
Period size: 59 Copynumber: 2.6 Consensus size: 58
28889874 TGCTTTTATA
* * * *
28889884 TAAAAAAAATTGATACTTTCAACTTTTCTTTAAAA-TTTTTTCTTGATAATTTTTATTT
1 TAAAGAAAATTGATACTTTCAACTTTTCGTCAAAATTTTTTTCTTGA-AATTTTAATTT
*
28889942 CTAAAGAAAATTGATACTTTCAACTTTTCGTCAAAATGTTTTTTTTTTGAAATTTTAATTT
1 -TAAAGAAAATTGATACTTTCAACTTTTCGTCAAAA--TTTTTTTCTTGAAATTTTAATTT
* *
28890003 T-AAGAAAAATTGATATTTTCAACTTTTCCTCAAAAT
1 TAAAG-AAAATTGATACTTTCAACTTTTCGTCAAAAT
28890039 ACTTTTTGAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
58 1 0.01
59 35 0.41
60 29 0.34
61 10 0.12
62 10 0.12
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (58 bp):
TAAAGAAAATTGATACTTTCAACTTTTCGTCAAAATTTTTTTCTTGAAATTTTAATTT
Found at i:28890016 original size:60 final size:59
Alignment explanation
Indices: 28889886--28890038 Score: 195
Period size: 60 Copynumber: 2.6 Consensus size: 59
28889876 CTTTTATATA
* * *
28889886 AAAAAAATTGATACTTTCAACTTTTCTTTAAAA-TTTTTTCTTGATAATTTTTATTTCT
1 AAAAAAATTGATACTTTCAACTTTTCCTCAAAATTTTTTTCTTGATAATTTTAATTTCT
* *
28889944 AAAGAAAATTGATACTTTCAACTTTTCGTCAAAATGTTTTTTTTTTGA-AATTTTAATTT-T
1 AAA-AAAATTGATACTTTCAACTTTTCCTCAAAA--TTTTTTTCTTGATAATTTTAATTTCT
*
28890004 AAGAAAAATTGATATTTTCAACTTTTCCTCAAAAT
1 AA-AAAAATTGATACTTTCAACTTTTCCTCAAAAT
28890039 ACTTTTTGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
58 4 0.05
59 28 0.33
60 31 0.37
61 11 0.13
62 10 0.12
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (59 bp):
AAAAAAATTGATACTTTCAACTTTTCCTCAAAATTTTTTTCTTGATAATTTTAATTTCT
Found at i:28890530 original size:18 final size:18
Alignment explanation
Indices: 28890507--28890554 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
28890497 CATAGATTGC
28890507 TTTCTTTCTTCTCTCTCT
1 TTTCTTTCTTCTCTCTCT
* * *
28890525 TTTCTTTTTTTTTTCTCT
1 TTTCTTTCTTCTCTCTCT
28890543 TTT-TTTC-TCTCT
1 TTTCTTTCTTCTCT
28890555 AAAAGATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 3 0.12
17 3 0.12
18 18 0.75
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTCTTTCTTCTCTCTCT
Found at i:28890978 original size:16 final size:16
Alignment explanation
Indices: 28890957--28890991 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
28890947 CGAAAAATTG
28890957 ATAAAAAAAAGATAAA
1 ATAAAAAAAAGATAAA
28890973 ATAAAAAAAAGATAAA
1 ATAAAAAAAAGATAAA
28890989 ATA
1 ATA
28890992 TATATATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (16 bp):
ATAAAAAAAAGATAAA
Found at i:28891038 original size:24 final size:24
Alignment explanation
Indices: 28891010--28891055 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
28891000 CTAATAGATA
28891010 ATTAATAGATAAATAATAAAAAAT
1 ATTAATAGATAAATAATAAAAAAT
28891034 ATTAATAGATAAATAATAAAAA
1 ATTAATAGATAAATAATAAAAA
28891056 TTATATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (24 bp):
ATTAATAGATAAATAATAAAAAAT
Found at i:28891069 original size:24 final size:24
Alignment explanation
Indices: 28891010--28891075 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
28891000 CTAATAGATA
*
28891010 ATTAATAGATAAATAATAAAAAAT
1 ATTAATAAATAAATAATAAAAAAT
* *
28891034 ATTAATAGATAAATAATAAAAATT
1 ATTAATAAATAAATAATAAAAAAT
28891058 A-TATATAAAT-AATAATAA
1 ATTA-ATAAATAAATAATAA
28891076 TAATAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
23 10 0.26
24 29 0.74
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (24 bp):
ATTAATAAATAAATAATAAAAAAT
Found at i:28891071 original size:3 final size:3
Alignment explanation
Indices: 28891001--28891084 Score: 55
Period size: 3 Copynumber: 26.0 Consensus size: 3
28890991 ATATATATAC
*
28891001 TAA TAGA TAA TTAA TAGA TAAA TAA TAA -AA -AA TAT TAA TAGA TAAA
1 TAA TA-A TAA -TAA TA-A T-AA TAA TAA TAA TAA TAA TAA TA-A T-AA
* *
28891047 TAA TAA AAA TTA TATA TAAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A T-AA TAA TAA TAA TAA TAA TAA
28891085 ATACAAATAC
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
2 4 0.06
3 41 0.62
4 18 0.27
5 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:28892204 original size:14 final size:14
Alignment explanation
Indices: 28892185--28892215 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28892175 TTATTCTTAA
28892185 TTTATTAGTTAATT
1 TTTATTAGTTAATT
*
28892199 TTTATTATTTAATT
1 TTTATTAGTTAATT
28892213 TTT
1 TTT
28892216 TACCAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTATTAGTTAATT
Found at i:28892536 original size:16 final size:17
Alignment explanation
Indices: 28892505--28892537 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28892495 ATCTAACAAA
28892505 TATAAATATTTTAATATG
1 TATAAATA-TTTAATATG
28892523 TATAAATA-TTAATAT
1 TATAAATATTTAATAT
28892538 AAAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TATAAATATTTAATATG
Found at i:28894813 original size:11 final size:12
Alignment explanation
Indices: 28894779--28894818 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
28894769 TTGATATATT
*
28894779 TTTTAAATAGACA
1 TTTTAAATA-AAA
28894792 TTTTAAATAAAA
1 TTTTAAATAAAA
28894804 TTTT-AATAAAA
1 TTTTAAATAAAA
28894815 TTTT
1 TTTT
28894819 TACTATTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 11 0.42
12 6 0.23
13 9 0.35
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (12 bp):
TTTTAAATAAAA
Found at i:28894868 original size:28 final size:28
Alignment explanation
Indices: 28894829--28894883 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
28894819 TACTATTAAG
*
28894829 TAAATATTAATCAAATTTAATTATAAAA
1 TAAACATTAATCAAATTTAATTATAAAA
28894857 TAAACATTAATCAAATTTAATTATAAA
1 TAAACATTAATCAAATTTAATTATAAA
28894884 TAGTACTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAACATTAATCAAATTTAATTATAAAA
Found at i:28896437 original size:57 final size:55
Alignment explanation
Indices: 28896283--28896445 Score: 182
Period size: 55 Copynumber: 2.9 Consensus size: 55
28896273 ATAACTTTTT
* * *
28896283 ATATCACCATAAAAAGAAAACTCAAATATCACTATTAAGAAAATGCAAATAAGTTCGG
1 ATATCACC--AAAAA-AAGACTCGAATATCACTATTAAGAAAATGCAAATGAGTTCGG
* * * *
28896341 ATATCACCACAAAAAGACTCGAATATCACTATCAAGAAAATGTAAATGATTTCGG
1 ATATCACCAAAAAAAGACTCGAATATCACTATTAAGAAAATGCAAATGAGTTCGG
* * * *
28896396 ATATCACTAAATAAGAATACTTGAATATCACCATTAAGAAAATGCAAATG
1 ATATCACCAAA-AA-AAGACTCGAATATCACTATTAAGAAAATGCAAATG
28896446 TAGAGAAAAA
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
55 45 0.51
56 6 0.07
57 30 0.34
58 8 0.09
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (55 bp):
ATATCACCAAAAAAAGACTCGAATATCACTATTAAGAAAATGCAAATGAGTTCGG
Found at i:28896578 original size:42 final size:42
Alignment explanation
Indices: 28896515--28896636 Score: 176
Period size: 42 Copynumber: 2.9 Consensus size: 42
28896505 TTGAAAATGT
*
28896515 CTTGGATATCACCACCAAGAAAATGAAATTCAAACTTTAACA
1 CTTGGATATCACCACCGAGAAAATGAAATTCAAACTTTAACA
*
28896557 CTTGGATATCACCACCGAGAAAATGTAATTTC-AACTTTAACA
1 CTTGGATATCACCACCGAGAAAATG-AAATTCAAACTTTAACA
* *
28896599 CTTGGATATTACCACTGA-AAAGATGAAATTCAAACTTT
1 CTTGGATATCACCACCGAGAAA-ATGAAATTCAAACTTT
28896637 TAATGCTCGA
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
41 8 0.11
42 59 0.82
43 5 0.07
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (42 bp):
CTTGGATATCACCACCGAGAAAATGAAATTCAAACTTTAACA
Found at i:28898319 original size:25 final size:26
Alignment explanation
Indices: 28898291--28898340 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
28898281 TTTGTTTTTG
28898291 TTTTTCATCAT-TTTC-ACTTTTGCTC
1 TTTTTCA-CATATTTCAACTTTTGCTC
*
28898316 TTTTTGACATATTTCAACTTTTGCT
1 TTTTTCACATATTTCAACTTTTGCT
28898341 GGAATATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 10 0.45
26 9 0.41
ACGTcount: A:0.16, C:0.20, G:0.06, T:0.58
Consensus pattern (26 bp):
TTTTTCACATATTTCAACTTTTGCTC
Found at i:28903882 original size:22 final size:21
Alignment explanation
Indices: 28903857--28903911 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
28903847 CTACTTGTGA
*
28903857 TTTTATTATTATTGT-TATTATT
1 TTTTATTATTATT-TAT-TTAAT
28903879 TTTTATTTATGTATTTATTTAAT
1 TTTTA-TTAT-TATTTATTTAAT
28903902 TTTTATTATT
1 TTTTATTATT
28903912 TATTCGAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 1 0.03
22 9 0.31
23 14 0.48
24 5 0.17
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTTATTATTATTTATTTAAT
Found at i:28903915 original size:22 final size:23
Alignment explanation
Indices: 28903857--28903915 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
28903847 CTACTTGTGA
*
28903857 TTTTATTA-TTATTGTTATTATT
1 TTTTATTATTTATTGTTATTAAT
*
28903879 TTTTATTTATGTA-T-TTATTTAAT
1 TTTTA-TTATTTATTGTTA-TTAAT
28903902 TTTTATTATTTATT
1 TTTTATTATTTATT
28903916 CGAAGTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
22 14 0.47
23 14 0.47
24 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (23 bp):
TTTTATTATTTATTGTTATTAAT
Found at i:28904283 original size:21 final size:22
Alignment explanation
Indices: 28904246--28904298 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
28904236 CCTTAAATTA
28904246 ATAAAATATTATTTTTTAAAAAT
1 ATAAAATATTA-TTTTTAAAAAT
*
28904269 ATAAAATATTATTTTT-TAAAT
1 ATAAAATATTATTTTTAAAAAT
28904290 AT-AAATATT
1 ATAAAATATT
28904299 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 7 0.24
21 6 0.21
22 5 0.17
23 11 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAAATATTATTTTTAAAAAT
Found at i:28904307 original size:30 final size:30
Alignment explanation
Indices: 28904271--28904327 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
28904261 TTAAAAATAT
* * *
28904271 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATCATTATATAAATATAAATATTTA
*
28904301 AAAATATCATTATATAAATATATATAT
1 AAAATATCATTATATAAATATAAATAT
28904328 AAATAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (30 bp):
AAAATATCATTATATAAATATAAATATTTA
Found at i:28904322 original size:8 final size:8
Alignment explanation
Indices: 28904288--28904344 Score: 51
Period size: 8 Copynumber: 7.1 Consensus size: 8
28904278 TATTTTTTAA
28904288 ATATAAAT
1 ATATAAAT
* *
28904296 ATTTAAAA
1 ATATAAAT
* *
28904304 ATATCATT
1 ATATAAAT
28904312 ATATAAAT
1 ATATAAAT
*
28904320 ATATATAT
1 ATATAAAT
*
28904328 AAATAAAT
1 ATATAAAT
*
28904336 AAATAAAT
1 ATATAAAT
28904344 A
1 A
28904345 ATTAATTAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATAAAT
Found at i:28904333 original size:4 final size:4
Alignment explanation
Indices: 28904314--28904360 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
28904304 ATATCATTAT
* * * *
28904314 ATAA ATAT ATAT ATAA ATAA ATAA ATAA ATAA TTAA TTAA A-AA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
28904361 TTTTTTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 3 0.08
4 35 0.92
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (4 bp):
ATAA
Found at i:28904425 original size:16 final size:16
Alignment explanation
Indices: 28904404--28904436 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28904394 TTTTAGGCAT
28904404 ACCCGAACCCGACCCG
1 ACCCGAACCCGACCCG
*
28904420 ACCCGACCCCGACCCG
1 ACCCGAACCCGACCCG
28904436 A
1 A
28904437 AACCCGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.58, G:0.18, T:0.00
Consensus pattern (16 bp):
ACCCGAACCCGACCCG
Found at i:28906022 original size:3 final size:3
Alignment explanation
Indices: 28906014--28906050 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
28906004 TAATTAATGA
28906014 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
28906051 TTTGCTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:28906596 original size:13 final size:13
Alignment explanation
Indices: 28906578--28906602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28906568 GTCCTCCATT
28906578 TCTCTCCCTCTTC
1 TCTCTCCCTCTTC
28906591 TCTCTCCCTCTT
1 TCTCTCCCTCTT
28906603 TCAACAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (13 bp):
TCTCTCCCTCTTC
Found at i:28908359 original size:130 final size:133
Alignment explanation
Indices: 28908213--28908521 Score: 377
Period size: 130 Copynumber: 2.3 Consensus size: 133
28908203 ATGAAGAAGA
* * *
28908213 TTTTTATTTAAGAAAAATTGATACTTTCAACTTTTAT-TTAAAAATGTTTCTTTTGAAATATAT-
1 TTTTTATTTAA-AAAAATTGATACTTTCAACTTTTATCTTAAAAATATATATTTTGAAATATATA
* *
28908276 T-TTTGAAAACTTTTTATTTTCTAAGGAAAATTGATA-GTT-CTTTTCCTTAAAAC-C-CTATTT
65 TATTT-AAAAATTTTTATTTTCTAAGAAAAATTGATACGTTACTTTTCCTTAAAACTCTCT-TTT
28908336 TTATTATT
128 TTA-T-TT
* *
28908344 TTTTTATTTAAAAAAATTGATACTTTCAA-TTTTTTCTTAAAAATATATATTTTTAAATATATAT
1 TTTTTATTTAAAAAAATTGATACTTTCAACTTTTATCTTAAAAATATATATTTTGAAATATATAT
*
28908408 AGTTTAAAAATTTTTATTTTCTAAGAAAAATTGATACTTTCAACTTTTCCTTAAAACTCTCTTTT
66 A-TTTAAAAATTTTTATTTTCTAAGAAAAATTGATACGTT--ACTTTTCCTTAAAACTCTCTTTT
28908473 TTATTT
128 TTATTT
*
28908479 TTTTTATTTAAAAAAAAATTGATACTTT-AACTTTT-TCTCAAAA
1 TTTTTATTT--AAAAAAATTGATACTTTCAACTTTTATCTTAAAA
28908522 CCTTTATTTT
Statistics
Matches: 156, Mismatches: 9, Indels: 21
0.84 0.05 0.11
Matches are distributed among these distances:
129 5 0.03
130 40 0.26
131 12 0.08
132 29 0.19
133 5 0.03
135 11 0.07
136 24 0.15
137 28 0.18
138 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.51
Consensus pattern (133 bp):
TTTTTATTTAAAAAAATTGATACTTTCAACTTTTATCTTAAAAATATATATTTTGAAATATATAT
ATTTAAAAATTTTTATTTTCTAAGAAAAATTGATACGTTACTTTTCCTTAAAACTCTCTTTTTTA
TTT
Found at i:28908495 original size:58 final size:57
Alignment explanation
Indices: 28908417--28908563 Score: 165
Period size: 56 Copynumber: 2.5 Consensus size: 57
28908407 TAGTTTAAAA
* * *
28908417 ATTTTTATTTTCTAAGAAAAATTGATACTTTCAACTTTTCCTTAAAACTCTCTT-TTTTATT
1 ATTTTTATTTT-AAAAAAAAATTGATACTTT-AACTTTTCCTCAAAAC-CT-TTATTTT-TT
* *
28908478 TTTTTTA-TTTAAAAAAAAATTGATACTTTAACTTTTTCTCAAAACCTTTATTTTTT
1 ATTTTTATTTTAAAAAAAAATTGATACTTTAACTTTTCCTCAAAACCTTTATTTTTT
*
28908534 ATTTTTATTTT-AAGAAAAATTGATATCTTT
1 ATTTTTATTTTAAAAAAAAATTGATA-CTTT
28908564 TTTTAGTAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
56 23 0.30
57 13 0.17
58 14 0.18
59 17 0.22
60 3 0.04
61 6 0.08
ACGTcount: A:0.33, C:0.11, G:0.03, T:0.53
Consensus pattern (57 bp):
ATTTTTATTTTAAAAAAAAATTGATACTTTAACTTTTCCTCAAAACCTTTATTTTTT
Found at i:28909639 original size:16 final size:16
Alignment explanation
Indices: 28909626--28909656 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28909616 ATAATAAAAG
28909626 TAAAAATAAATAAATA
1 TAAAAATAAATAAATA
*
28909642 TAACAATAAATAAAT
1 TAAAAATAAATAAAT
28909657 TTGATTAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAATAAATAAATA
Found at i:28910155 original size:16 final size:16
Alignment explanation
Indices: 28910136--28910168 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28910126 AATAAACTAA
28910136 CTATCAAAAGAAAAAT
1 CTATCAAAAGAAAAAT
28910152 CTATCAAAAGAAAAAT
1 CTATCAAAAGAAAAAT
28910168 C
1 C
28910169 CATGGCTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.15, G:0.06, T:0.18
Consensus pattern (16 bp):
CTATCAAAAGAAAAAT
Found at i:28911105 original size:32 final size:35
Alignment explanation
Indices: 28911069--28911144 Score: 86
Period size: 38 Copynumber: 2.2 Consensus size: 35
28911059 TAATTAGAAT
28911069 GAATTTGAATT-TAGTTTGA-TTATT-ATCGAGTC
1 GAATTTGAATTATAGTTTGATTTATTAATCGAGTC
*
28911101 GAATTTTAATTCGAATAGTTTGATTTATTAATCGAGTC
1 GAATTTGAATT---ATAGTTTGATTTATTAATCGAGTC
*
28911139 CAATTT
1 GAATTT
28911145 AAATATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
32 10 0.28
36 8 0.22
37 5 0.14
38 13 0.36
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (35 bp):
GAATTTGAATTATAGTTTGATTTATTAATCGAGTC
Found at i:28911207 original size:10 final size:10
Alignment explanation
Indices: 28911194--28911223 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28911184 ATCAAATTTT
28911194 TATATTTTAA
1 TATATTTTAA
28911204 TATATTTTAA
1 TATATTTTAA
28911214 T-TATTTTAA
1 TATATTTTAA
28911223 T
1 T
28911224 TGATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:28920515 original size:2 final size:2
Alignment explanation
Indices: 28920508--28920549 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
28920498 TAAAACACAT
28920508 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
28920550 AANNNNNNNN
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.