Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, 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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 79 of 84
Found at i:17085371 original size:124 final size:124
Alignment explanation
Indices: 17085125--17085381 Score: 339
Period size: 124 Copynumber: 2.1 Consensus size: 124
17085115 ATCGAGTATA
* *
17085125 ATCTTTTT-AAACTTCTAAGTATCTTTCTAAATTTTAAAGTTGTGGAGCCTTTGTATGAAAAGAG
1 ATCTTTTTAAAACCTCTAAGTATCTTTCTAAATTTTAAAGTTGTGGAGCCTTTGTATGAAAAGAA
* * * * *
17085189 CTTTTTCAAAATTTGATTTGTAAAATCTCTGAGCATAATCACCAAGTCCTCCGGGCATG
66 CTTTTTCAAAATTCGATTTATAAAACCTCTGAGCATAATCAACAAGTCCTCCGCGCATG
17085248 ATCTTTTTAAAACCTCTAAGTATCTTTCTAAATGTTTAAA-TTGTGGAG-CTTTCGTATGAAATA
1 ATCTTTTTAAAACCTCTAAGTATCTTTCTAAAT-TTTAAAGTTGTGGAGCCTTT-GTATGAAA-A
* *
17085311 -AACTTTTTCAAAATTCGATTTATAAGACCTCT-AGGCATAATCAACAAGTCCAT-TGCGCATG
63 GAACTTTTTCAAAATTCGATTTATAAAACCTCTGA-GCATAATCAACAAGTCC-TCCGCGCATG
17085372 AT-TTTTTAAA
1 ATCTTTTTAAA
17085382 TCTTCTGGGC
Statistics
Matches: 119, Mismatches: 9, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
123 21 0.18
124 90 0.76
125 8 0.07
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (124 bp):
ATCTTTTTAAAACCTCTAAGTATCTTTCTAAATTTTAAAGTTGTGGAGCCTTTGTATGAAAAGAA
CTTTTTCAAAATTCGATTTATAAAACCTCTGAGCATAATCAACAAGTCCTCCGCGCATG
Found at i:17085568 original size:22 final size:21
Alignment explanation
Indices: 17085517--17085568 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
17085507 AGTCATTTGA
* * *
17085517 ACATTATCTATAAATCTTTTG
1 ACATGATCTATAAATCTGTGG
*
17085538 AGCACGATCTATAAATCCTGTGG
1 A-CATGATCTATAAAT-CTGTGG
17085561 ACATGATC
1 ACATGATC
17085569 GGCAAAACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 1 0.04
22 18 0.75
23 5 0.21
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (21 bp):
ACATGATCTATAAATCTGTGG
Found at i:17085666 original size:39 final size:39
Alignment explanation
Indices: 17085590--17085666 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
17085580 TGAGTATCAT
* *
17085590 CTTTAATTTTTAAAGTTGTGTGCCTTTATGCTGGAAGAA
1 CTTTAATTTTTAAAGTTGTGTGCCTCTATGCTAGAAGAA
* * **
17085629 CTTTTATTTTTAAAGTTGTGTGTCTCTATTTTAGAAGA
1 CTTTAATTTTTAAAGTTGTGTGCCTCTATGCTAGAAGA
17085667 GCCTTGGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.48
Consensus pattern (39 bp):
CTTTAATTTTTAAAGTTGTGTGCCTCTATGCTAGAAGAA
Found at i:17091478 original size:2 final size:2
Alignment explanation
Indices: 17091473--17091512 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
17091463 TAGGTCTAAT
* *
17091473 TA TA TA CA TA TA TA TA TA TA TA CA 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
17091513 CAGAGAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:17091494 original size:16 final size:16
Alignment explanation
Indices: 17091473--17091510 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
17091463 TAGGTCTAAT
17091473 TATATACATATATATA
1 TATATACATATATATA
17091489 TATATACATATATATA
1 TATATACATATATATA
17091505 TATATA
1 TATATA
17091511 TACAGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
TATATACATATATATA
Found at i:17095058 original size:18 final size:18
Alignment explanation
Indices: 17095035--17095073 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
17095025 ATATTATAGG
17095035 ATAGACAAACTAAATCTT
1 ATAGACAAACTAAATCTT
17095053 ATAGACAAACTAAATCTT
1 ATAGACAAACTAAATCTT
17095071 ATA
1 ATA
17095074 TATGGTGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.28
Consensus pattern (18 bp):
ATAGACAAACTAAATCTT
Found at i:17096057 original size:17 final size:18
Alignment explanation
Indices: 17096025--17096058 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17096015 TCAAAATGAA
*
17096025 ATTTGTCGATGGCACTTC
1 ATTTGCCGATGGCACTTC
17096043 ATTTGCCGA-GGCACTT
1 ATTTGCCGATGGCACTT
17096059 TTGTAATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (18 bp):
ATTTGCCGATGGCACTTC
Found at i:17097484 original size:16 final size:16
Alignment explanation
Indices: 17097463--17097497 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
17097453 AAAAATACAT
17097463 CAGTTTCTTATGAAAA
1 CAGTTTCTTATGAAAA
17097479 CAGTTTCTTATGAAAA
1 CAGTTTCTTATGAAAA
17097495 CAG
1 CAG
17097498 GTATGTAATA
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:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (16 bp):
CAGTTTCTTATGAAAA
Found at i:17100076 original size:48 final size:48
Alignment explanation
Indices: 17100020--17100116 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
17100010 CAACTTAATC
17100020 AAATAGAATTACAAAGAAACACTTCTAAATATAAGGTTATAGTAGAAG
1 AAATAGAATTACAAAGAAACACTTCTAAATATAAGGTTATAGTAGAAG
* *
17100068 AAATAGAATTGCAAAGAAACACTTCTAAATATAAGGTTATATTAGAAG
1 AAATAGAATTACAAAGAAACACTTCTAAATATAAGGTTATAGTAGAAG
17100116 A
1 A
17100117 TTTAGTAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.26
Consensus pattern (48 bp):
AAATAGAATTACAAAGAAACACTTCTAAATATAAGGTTATAGTAGAAG
Found at i:17101051 original size:3 final size:3
Alignment explanation
Indices: 17101045--17101074 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17101035 ATAATTTTAA
17101045 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17101075 TAAACATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17101461 original size:18 final size:18
Alignment explanation
Indices: 17101421--17101466 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
17101411 GAGTTTATTT
*
17101421 TTAATTTGATAAATAAAA
1 TTAATTTAATAAATAAAA
*
17101439 TTAATTTAATAAATTTAAA
1 TTAATTTAATAAA-TAAAA
17101458 -TAATTTAAT
1 TTAATTTAAT
17101467 TTTTATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TTAATTTAATAAATAAAA
Found at i:17101678 original size:21 final size:20
Alignment explanation
Indices: 17101636--17101681 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
17101626 AATCGATTTC
*
17101636 TAATTAATGATAAATAAATT
1 TAATTAATAATAAATAAATT
17101656 TAATTAATAAATAGAAT-AATT
1 TAATTAAT-AATA-AATAAATT
17101677 TAATT
1 TAATT
17101682 TTAACTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 12 0.52
22 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (20 bp):
TAATTAATAATAAATAAATT
Found at i:17101910 original size:18 final size:18
Alignment explanation
Indices: 17101870--17101915 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
17101860 GAGTTTATTT
*
17101870 TTAATTTGATAAATGAAA
1 TTAATTTAATAAATGAAA
*
17101888 TTAATTTAATAAATTTAAA
1 TTAATTTAATAAA-TGAAA
17101907 -TAATTTAAT
1 TTAATTTAAT
17101916 TTTTATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (18 bp):
TTAATTTAATAAATGAAA
Found at i:17104389 original size:18 final size:19
Alignment explanation
Indices: 17104348--17104392 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
17104338 TAAATAATAA
*
17104348 AATTTTATAAATAAAAAAT
1 AATTTCATAAATAAAAAAT
*
17104367 AATTTCATAAA-AATAAAT
1 AATTTCATAAATAAAAAAT
*
17104385 TATTTCAT
1 AATTTCAT
17104393 TGATCAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTTCATAAATAAAAAAT
Found at i:17104469 original size:17 final size:17
Alignment explanation
Indices: 17104437--17104471 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17104427 TTAATCCATT
17104437 TATAATATAAATATAAA
1 TATAATATAAATATAAA
17104454 TATAA-ATAAATCATAAA
1 TATAATATAAAT-ATAAA
17104471 T
1 T
17104472 TAAGCCCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
TATAATATAAATATAAA
Found at i:17116874 original size:16 final size:16
Alignment explanation
Indices: 17116842--17116879 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17116832 AAATCTCTTA
*
17116842 TAATTATAAATTTTAT
1 TAATTATAAATTCTAT
17116858 TAATTCATAAA-TCTAT
1 TAATT-ATAAATTCTAT
17116874 TAATTA
1 TAATTA
17116880 ATTTAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 14 0.70
17 5 0.25
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTATAAATTCTAT
Found at i:17124184 original size:12 final size:11
Alignment explanation
Indices: 17124168--17124204 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
17124158 TATTTTAAAT
17124168 AATATAAATTA
1 AATATAAATTA
17124179 ATATATAAATTA
1 A-ATATAAATTA
17124191 AATATATAATTA
1 AATATA-AATTA
17124203 AA
1 AA
17124205 AAAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATAAATTA
Found at i:17131327 original size:17 final size:16
Alignment explanation
Indices: 17131283--17131327 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
17131273 TTTGCTTGAG
*
17131283 TAATATTATATTTGCA
1 TAATAATATATTTGCA
* *
17131299 TGATAATTTATTTGCA
1 TAATAATATATTTGCA
17131315 TAATTAATATATT
1 TAA-TAATATATT
17131328 CATTTGTGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (16 bp):
TAATAATATATTTGCA
Found at i:17131370 original size:45 final size:47
Alignment explanation
Indices: 17131302--17131436 Score: 183
Period size: 47 Copynumber: 3.0 Consensus size: 47
17131292 ATTTGCATGA
* *
17131302 TAATTTATTTGCAT-A--ATTAATATATTCATTTGTGTGATT-TA-T
1 TAATTTATTTGCATGATTATTAATATATTTATTTGTATGATTATATT
*
17131344 TAATATATTTGCATGATTATTAATATATTTATTTGTATGATTATATT
1 TAATTTATTTGCATGATTATTAATATATTTATTTGTATGATTATATT
*
17131391 TAATTTGA-TTGCATGATTATTAATATATTTATTTGCATGATTATAT
1 TAATTT-ATTTGCATGATTATTAATATATTTATTTGTATGATTATAT
17131437 ATTTAATTGC
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
42 13 0.16
43 1 0.01
45 22 0.27
46 2 0.02
47 43 0.52
48 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.54
Consensus pattern (47 bp):
TAATTTATTTGCATGATTATTAATATATTTATTTGTATGATTATATT
Found at i:17131377 original size:24 final size:24
Alignment explanation
Indices: 17131304--17131434 Score: 120
Period size: 24 Copynumber: 5.8 Consensus size: 24
17131294 TTGCATGATA
17131304 ATTTATTTGCAT-A--ATTAATAT
1 ATTTATTTGCATGATTATTAATAT
* **
17131325 ATTCATTTGTGTGATTTATT-A-AT
1 ATTTATTTGCATGA-TTATTAATAT
17131348 A--TATTTGCATGATTATTAATAT
1 ATTTATTTGCATGATTATTAATAT
* *
17131370 ATTTATTTGTATGATTA-T-ATTT
1 ATTTATTTGCATGATTATTAATAT
17131392 AATTTGA-TTGCATGATTATTAATAT
1 -ATTT-ATTTGCATGATTATTAATAT
17131417 ATTTATTTGCATGATTAT
1 ATTTATTTGCATGATTAT
17131435 ATATTTAATT
Statistics
Matches: 87, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
20 5 0.06
21 18 0.21
22 7 0.08
23 19 0.22
24 32 0.37
25 6 0.07
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (24 bp):
ATTTATTTGCATGATTATTAATAT
Found at i:17131446 original size:20 final size:20
Alignment explanation
Indices: 17131366--17131563 Score: 82
Period size: 20 Copynumber: 10.7 Consensus size: 20
17131356 ATGATTATTA
* *
17131366 ATATATTTATTTGTATGATT
1 ATATATTTAATTGCATGATT
*
17131386 ATATTTAATTTGATTGCATGATTATT
1 ATA--T-ATTTAATTGCATG---ATT
*
17131412 AATATATTTATTTGCATGATT
1 -ATATATTTAATTGCATGATT
17131433 ATATATTTAATTGC---A-T
1 ATATATTTAATTGCATGATT
17131449 AT-TA--T--TTGCATGATT
1 ATATATTTAATTGCATGATT
17131464 ATATATTTAATTGCAT-ACTT
1 ATATATTTAATTGCATGA-TT
* ** *
17131484 ATTTACATGATT-CAT-A-T
1 ATATATTTAATTGCATGATT
*
17131501 AT-T-TTTATTTGCATGATT
1 ATATATTTAATTGCATGATT
17131519 ATATATTTAATTGCAT-A-T
1 ATATATTTAATTGCATGATT
17131537 -T-TA--T--TTGCATGATT
1 ATATATTTAATTGCATGATT
17131551 ATATATTTAATTG
1 ATATATTTAATTG
17131564 TATATTTATT
Statistics
Matches: 133, Mismatches: 15, Indels: 60
0.64 0.07 0.29
Matches are distributed among these distances:
11 4 0.03
12 6 0.05
13 2 0.02
14 3 0.02
15 9 0.07
16 13 0.10
17 6 0.05
18 6 0.05
19 7 0.05
20 45 0.34
21 3 0.02
22 1 0.01
23 10 0.08
24 11 0.08
25 1 0.01
26 3 0.02
27 3 0.02
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.54
Consensus pattern (20 bp):
ATATATTTAATTGCATGATT
Found at i:17131457 original size:31 final size:32
Alignment explanation
Indices: 17131419--17131504 Score: 147
Period size: 31 Copynumber: 2.7 Consensus size: 32
17131409 ATTAATATAT
17131419 TTATTTGCATGATTATATATTTAATTGCATA-
1 TTATTTGCATGATTATATATTTAATTGCATAC
17131450 TTATTTGCATGATTATATATTTAATTGCATAC
1 TTATTTGCATGATTATATATTTAATTGCATAC
*
17131482 TTATTTACATGATTCATATATTT
1 TTATTTGCATGATT-ATATATTT
17131505 TTATTTGCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
31 31 0.60
32 13 0.25
33 8 0.15
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.52
Consensus pattern (32 bp):
TTATTTGCATGATTATATATTTAATTGCATAC
Found at i:17131525 original size:22 final size:23
Alignment explanation
Indices: 17131482--17131526 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
17131472 AATTGCATAC
17131482 TTATTTACATGATTCATATATTT
1 TTATTTACATGATTCATATATTT
*
17131505 TTATTTGCATGATT-ATATATTT
1 TTATTTACATGATTCATATATTT
17131527 AATTGCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.58
Consensus pattern (23 bp):
TTATTTACATGATTCATATATTT
Found at i:17131541 original size:32 final size:32
Alignment explanation
Indices: 17131504--17131654 Score: 221
Period size: 32 Copynumber: 4.7 Consensus size: 32
17131494 TTCATATATT
17131504 TTTATTTGCATGATTATATATTTAATTGCATA
1 TTTATTTGCATGATTATATATTTAATTGCATA
*
17131536 TTTATTTGCATGATTATATATTTAATTGTATA
1 TTTATTTGCATGATTATATATTTAATTGCATA
* ** *
17131568 TTTATTTGCATGATTATACATTTAATTATATG
1 TTTATTTGCATGATTATATATTTAATTGCATA
* *
17131600 TTTATTTGTATGATTATAAATTTAATTGCATA
1 TTTATTTGCATGATTATATATTTAATTGCATA
*
17131632 TTTATTTGTATGATTTATATATT
1 TTTATTTGCATGA-TTATATATT
17131655 ATTATTTACA
Statistics
Matches: 108, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
32 100 0.93
33 8 0.07
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.56
Consensus pattern (32 bp):
TTTATTTGCATGATTATATATTTAATTGCATA
Found at i:17131715 original size:24 final size:24
Alignment explanation
Indices: 17131688--17131733 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
17131678 AATTGCATGT
*
17131688 TTGCTTGATTATTAATATATTTGC
1 TTGCATGATTATTAATATATTTGC
*
17131712 TTGCATGATTATTAATTTATTT
1 TTGCATGATTATTAATATATTT
17131734 ACATAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.57
Consensus pattern (24 bp):
TTGCATGATTATTAATATATTTGC
Found at i:17131724 original size:151 final size:150
Alignment explanation
Indices: 17131415--17131709 Score: 403
Period size: 151 Copynumber: 2.0 Consensus size: 150
17131405 GATTATTAAT
* * *
17131415 ATATTTATTTGCATGATTATATATTTAATTGCATATTATTTGCATGATTATATATTTAATTGCAT
1 ATATTTATTTGCATGATTATACATTTAATTACATATTATTTGCATGATTATAAATTTAATTGCAT
* * * *
17131480 ACTTATTTACATGATTCATATATTTTTATTTGCATGATTATATATTTAATTGCATATTTATTTGC
66 ACTTATTTACATGATTCATATATTATTATTTACATAATTATATATTTAATTGCATATTTACTTGC
*
17131545 ATGATTATATATTTAATTGT
131 ATGATTATATATTTAATTGC
* * *
17131565 ATATTTATTTGCATGATTATACATTTAATTATATGTTTATTTGTATGATTATAAATTTAATTGCA
1 ATATTTATTTGCATGATTATACATTTAATTACAT-ATTATTTGCATGATTATAAATTTAATTGCA
* ** * * *
17131630 TATTTATTTGTATGATTTATATATTATTATTTACATAATTATATATTTAATTGCATGTTTGCTTG
65 TACTTATTTACATGATTCATATATTATTATTTACATAATTATATATTTAATTGCATATTTACTTG
*
17131695 -ATTATTAATATATTT
130 CATGATT-ATATATTT
17131710 GCTTGCATGA
Statistics
Matches: 126, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
150 36 0.29
151 90 0.71
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.54
Consensus pattern (150 bp):
ATATTTATTTGCATGATTATACATTTAATTACATATTATTTGCATGATTATAAATTTAATTGCAT
ACTTATTTACATGATTCATATATTATTATTTACATAATTATATATTTAATTGCATATTTACTTGC
ATGATTATATATTTAATTGC
Found at i:17131729 original size:20 final size:20
Alignment explanation
Indices: 17131687--17131749 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
17131677 TAATTGCATG
* *
17131687 TTTGCTTG-ATTATTAATATA
1 TTTGCTTGCATAATTATTA-A
*
17131707 TTTGCTTGCATGATTATTAA
1 TTTGCTTGCATAATTATTAA
** *
17131727 TTTATTTACATAATTATTAA
1 TTTGCTTGCATAATTATTAA
17131747 TTT
1 TTT
17131750 ATTTATTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 28 0.78
21 8 0.22
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.56
Consensus pattern (20 bp):
TTTGCTTGCATAATTATTAA
Found at i:17131792 original size:24 final size:24
Alignment explanation
Indices: 17131687--17131793 Score: 63
Period size: 24 Copynumber: 4.3 Consensus size: 24
17131677 TAATTGCATG
* *
17131687 TTTGCTTGATTATTAATATATTTG
1 TTTGCATGATTATTAATATATTTA
* *
17131711 CTTGCATGATTATTAATTTATTTA
1 TTTGCATGATTATTAATATATTTA
** * * * * *
17131735 CAT-AATTATTAATTTATTTATTTG
1 TTTGCATGATT-ATTAATATATTTA
17131759 TGTGACTGCATGATTATTAATATATTTA
1 T-T---TGCATGATTATTAATATATTTA
17131787 TTTGCAT
1 TTTGCAT
17131794 AATATGATAT
Statistics
Matches: 61, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
23 5 0.08
24 38 0.62
27 1 0.02
28 12 0.20
29 5 0.08
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (24 bp):
TTTGCATGATTATTAATATATTTA
Found at i:17132016 original size:16 final size:16
Alignment explanation
Indices: 17131965--17132026 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
17131955 GAATGGTTAT
17131965 TAATATATTTGCATGGTA
1 TAATATATTTGCAT-G-A
** *
17131983 TTTTATATTATTGAATGA
1 TAATATA-T-TTGCATGA
17132001 TAATATATTTGCATGA
1 TAATATATTTGCATGA
*
17132017 TATTATATTT
1 TAATATATTT
17132027 ACATTATTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
16 16 0.46
17 1 0.03
18 11 0.31
19 2 0.06
20 5 0.14
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (16 bp):
TAATATATTTGCATGA
Found at i:17132024 original size:18 final size:18
Alignment explanation
Indices: 17131962--17132024 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
17131952 CATGAATGGT
*
17131962 TATTAATATATTTGCATGG
1 TATT-ATATATTTGCATGA
* *
17131981 TATTTTATATTATTGAATGA
1 TATTATATA-T-TTGCATGA
17132001 TA--ATATATTTGCATGA
1 TATTATATATTTGCATGA
17132017 TATTATAT
1 TATTATAT
17132025 TTACATTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
16 9 0.26
17 1 0.03
18 12 0.34
19 5 0.14
20 8 0.23
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
TATTATATATTTGCATGA
Found at i:17132181 original size:17 final size:16
Alignment explanation
Indices: 17132144--17132192 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
17132134 TTATAATATA
17132144 TTTGCATGATA--ATT
1 TTTGCATGATATGATT
*
17132158 TTTGCATGTTATGATT
1 TTTGCATGATATGATT
17132174 TATTGCATGATATGATT
1 T-TTGCATGATATGATT
17132191 TT
1 TT
17132193 ATATTTATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 10 0.33
16 5 0.17
17 15 0.50
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.53
Consensus pattern (16 bp):
TTTGCATGATATGATT
Found at i:17132182 original size:31 final size:30
Alignment explanation
Indices: 17132145--17132230 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 30
17132135 TATAATATAT
17132145 TTGCATGATAATTTTTGCATGTTATGATTTA
1 TTGCATGATAA-TTTTGCATGTTATGATTTA
*
17132176 TTGCATGAT-A---TG-ATTTTAT-ATTTA
1 TTGCATGATAATTTTGCATGTTATGATTTA
* *
17132200 TTGCGTGATAACTTTTGCATGGTATGATTTA
1 TTGCATGATAA-TTTTGCATGTTATGATTTA
17132231 ATATTTATTG
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
24 13 0.30
25 7 0.16
26 2 0.05
29 2 0.05
30 6 0.14
31 14 0.32
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (30 bp):
TTGCATGATAATTTTGCATGTTATGATTTA
Found at i:17135114 original size:9 final size:9
Alignment explanation
Indices: 17135102--17135147 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
17135092 AAAAAATTTT
17135102 AAAAAAAAG
1 AAAAAAAAG
17135111 AAAAAAAAAG
1 -AAAAAAAAG
*
17135121 AAAAAAGAG
1 AAAAAAAAG
*
17135130 AAAGAAAAG
1 AAAAAAAAG
17135139 AAAAGAAAA
1 AAAA-AAAA
17135148 AAATTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 18 0.58
10 13 0.42
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:17135115 original size:10 final size:10
Alignment explanation
Indices: 17135102--17135150 Score: 62
Period size: 10 Copynumber: 4.6 Consensus size: 10
17135092 AAAAAATTTT
17135102 AAAAAAAAGA
1 AAAAAAAAGA
17135112 AAAAAAAAGAA
1 AAAAAAAAG-A
17135123 AAAAGAGAAAGA
1 AAAA-A-AAAGA
*
17135135 AAAGAAAAGA
1 AAAAAAAAGA
17135145 AAAAAA
1 AAAAAA
17135151 TTTTAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 19 0.56
11 6 0.18
12 5 0.15
13 4 0.12
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:17135124 original size:18 final size:19
Alignment explanation
Indices: 17135103--17135142 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
17135093 AAAAATTTTA
17135103 AAAAAAAGA-AAAAAAAAG
1 AAAAAAAGAGAAAAAAAAG
*
17135121 -AAAAAAGAGAAAGAAAAG
1 AAAAAAAGAGAAAAAAAAG
17135139 AAAA
1 AAAA
17135143 GAAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 8 0.42
18 8 0.42
19 3 0.16
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAGAAAAAAAAG
Found at i:17137004 original size:36 final size:36
Alignment explanation
Indices: 17136937--17137077 Score: 142
Period size: 36 Copynumber: 3.9 Consensus size: 36
17136927 ATGATTTTAG
* * *
17136937 ATGTGAA-TCTCTAAGA-TTTTTAATGTTAATCTTGA
1 ATGTGAACT-TCTAAGATTTTTTAATATGAATCTTAA
* * *
17136972 ATATGAATTTTTAAGATTTTTTAATATGAATCTTAA
1 ATGTGAACTTCTAAGATTTTTTAATATGAATCTTAA
* * *
17137008 ATGTTAGCTTCTAAGATTTTTGAATATGAATCTTAA
1 ATGTGAACTTCTAAGATTTTTTAATATGAATCTTAA
* ** *
17137044 AGGTGAACTTCTAAGATTTTCAAATGTGAATCTT
1 ATGTGAACTTCTAAGATTTTTTAATATGAATCTT
17137078 TAGATGTAAA
Statistics
Matches: 87, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
35 12 0.14
36 75 0.86
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (36 bp):
ATGTGAACTTCTAAGATTTTTTAATATGAATCTTAA
Found at i:17137165 original size:18 final size:18
Alignment explanation
Indices: 17137139--17137185 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
17137129 TTTGGAATTA
17137139 TTTGAGACTTTTATGAAT
1 TTTGAGACTTTTATGAAT
*
17137157 TTTGGGACTTTTATGAAT
1 TTTGAGACTTTTATGAAT
*
17137175 TTTGAAACTTT
1 TTTGAGACTTT
17137186 GGCGAATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.51
Consensus pattern (18 bp):
TTTGAGACTTTTATGAAT
Found at i:17137222 original size:18 final size:18
Alignment explanation
Indices: 17137176--17137222 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
17137166 TTTATGAATT
*
17137176 TTGAAACTTTGGCGAATC
1 TTGAAACTTTGGCGAACC
*
17137194 TTGAAACCTTT-GTGAACC
1 TTGAAA-CTTTGGCGAACC
17137212 TTGGAAACTTT
1 TT-GAAACTTT
17137223 ACGAATCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (18 bp):
TTGAAACTTTGGCGAACC
Found at i:17137253 original size:18 final size:18
Alignment explanation
Indices: 17137226--17137261 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17137216 AAACTTTACG
*
17137226 AATCTAGAATGTTTTGCA
1 AATCTAGAATATTTTGCA
*
17137244 AATCTTGAATATTTTGCA
1 AATCTAGAATATTTTGCA
17137262 TTGCATTCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (18 bp):
AATCTAGAATATTTTGCA
Found at i:17137311 original size:32 final size:32
Alignment explanation
Indices: 17137260--17137326 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
17137250 GAATATTTTG
*
17137260 CATTGCATTCACTGTATTCGCTAAAATCATTA
1 CATTGCATTCACTGCATTCGCTAAAATCATTA
* * * * *
17137292 CATTGCATTTATTGCATTCGTTACATTCATTA
1 CATTGCATTCACTGCATTCGCTAAAATCATTA
17137324 CAT
1 CAT
17137327 GTTATGTATG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (32 bp):
CATTGCATTCACTGCATTCGCTAAAATCATTA
Found at i:17137721 original size:43 final size:42
Alignment explanation
Indices: 17137635--17138120 Score: 317
Period size: 43 Copynumber: 11.6 Consensus size: 42
17137625 AGATATCTTT
* *
17137635 CATTTT-TTTTTCAAAGTTTGAAAGCCT-AGTTGTG-GGGAAG
1 CATTTTATTTTTCAAAGTTTCAAAGCCTCAGTTGTGAGAG-AG
* **
17137675 CATTTTAATTTTTCAAAGTTTCAAAGTCTCAACTGTGAGAGAG
1 CATTTT-ATTTTTCAAAGTTTCAAAGCCTCAGTTGTGAGAGAG
*
17137718 CATTTTATTTTTTTTCAAAGTTTCAAAGCCTCAGTTGT-AGGGGAG
1 CATTTTA---TTTTTCAAAGTTTCAAAGCCTCAGTTGTGA-GAGAG
* * *
17137763 TATTTTATTTTTCCAAAGTTTC--A--TTTA--TG-GA-AGAG
1 CATTTTATTTTT-CAAAGTTTCAAAGCCTCAGTTGTGAGAGAG
* * * *
17137798 CATTTTATTTTTCCAAAGTTCCAAAACCTCAGTTGTGGGGGAG
1 CATTTTATTTTT-CAAAGTTTCAAAGCCTCAGTTGTGAGAGAG
* * * *
17137841 CATTTTA--TTACAAAGTTTCAAAGTCTCATTTATGATG-GAG
1 CATTTTATTTTTCAAAGTTTCAAAGCCTCAGTTGTGA-GAGAG
* * *
17137881 CATTTTATTTTTCAAAAGTTCCAAAGCATCGGTTGTGATG-GAG
1 CATTTTATTTTTC-AAAGTTTCAAAGCCTCAGTTGTGA-GAGAG
* * * **
17137924 CATTTTATTTTTTAAAAGTTCCAAAGCCTTAGTTACGAGAGAG
1 CATTTTA-TTTTTCAAAGTTTCAAAGCCTCAGTTGTGAGAGAG
* * * * *
17137967 TATTTTATTTTTAAAAGTTTCAAAGCCTCAATTGTG-GGGTAA
1 CATTTTATTTTTCAAAGTTTCAAAGCCTCAGTTGTGAGAG-AG
* * *
17138009 CATTTTATTTTTCAAAAGTTCCAAAGCCTCAGTTAT-AGGGGAG
1 CATTTTATTTTTC-AAAGTTTCAAAGCCTCAGTTGTGA-GAGAG
* * *
17138052 CATTTTATGTTTTAAAAGTTCCAAAGCCTCAATTGTTGAG-GAG
1 CATTTTAT-TTTTCAAAGTTTCAAAGCCTCAGTTG-TGAGAGAG
* * *
17138095 TATTTAATTCTTTCAAAAGTATCAAA
1 CATTTTATT-TTTC-AAAGTTTCAAA
17138121 CATTTGTCAA
Statistics
Matches: 352, Mismatches: 61, Indels: 62
0.74 0.13 0.13
Matches are distributed among these distances:
35 23 0.07
37 4 0.01
39 4 0.01
40 35 0.10
41 8 0.02
42 67 0.19
43 149 0.42
44 26 0.07
45 36 0.10
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (42 bp):
CATTTTATTTTTCAAAGTTTCAAAGCCTCAGTTGTGAGAGAG
Found at i:17138013 original size:85 final size:85
Alignment explanation
Indices: 17137794--17138114 Score: 305
Period size: 85 Copynumber: 3.8 Consensus size: 85
17137784 CATTTATGGA
* * * * * *
17137794 AGAGCATTTTATTTTTCCAAAGTTCCAAAACCTCAGTTGTGGGGGAGCATTTTA--TTAC-AAAG
1 AGAGCATTTTATTTTT-AAAAGTTCCAAAGCCTCAATTGTGAGGGAACATTTTATTTTTCAAAAG
* * * *
17137856 TTTCAAAGTCTCATTTATGATG
65 TTCCAAAGCCTCAGTTA-GAGG
* ** * * *
17137878 -GAGCATTTTATTTTTCAAAAGTTCCAAAGCATCGGTTGTGATGGAGCATTTTATTTTTTAAAAG
1 AGAGCATTTTATTTTT-AAAAGTTCCAAAGCCTCAATTGTGAGGGAACATTTTATTTTTCAAAAG
*
17137942 TTCCAAAGCCTTAGTTACGA-G
65 TTCCAAAGCCTCAGTTA-GAGG
* *
17137963 AGAGTATTTTATTTTTAAAAGTTTCAAAGCCTCAATTGTG-GGGTAACATTTTATTTTTCAAAAG
1 AGAGCATTTTATTTTTAAAAGTTCCAAAGCCTCAATTGTGAGGG-AACATTTTATTTTTCAAAAG
*
17138027 TTCCAAAGCCTCAGTTATAGG
65 TTCCAAAGCCTCAGTTAGAGG
* ** *
17138048 GGAGCATTTTATGTTTTAAAAGTTCCAAAGCCTCAATTGTTGA-GGAGTATTTAATTCTTTCAAA
1 AGAGCATTTTAT-TTTTAAAAGTTCCAAAGCCTCAATTG-TGAGGGAACATTTTATT-TTTCAAA
17138112 AGT
63 AGT
17138115 ATCAAACATT
Statistics
Matches: 198, Mismatches: 29, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
83 47 0.24
84 3 0.02
85 68 0.34
86 66 0.33
87 14 0.07
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (85 bp):
AGAGCATTTTATTTTTAAAAGTTCCAAAGCCTCAATTGTGAGGGAACATTTTATTTTTCAAAAGT
TCCAAAGCCTCAGTTAGAGG
Found at i:17138096 original size:128 final size:127
Alignment explanation
Indices: 17137795--17138120 Score: 349
Period size: 128 Copynumber: 2.5 Consensus size: 127
17137785 ATTTATGGAA
* * * * *
17137795 GAGCATTTTATTTTTCCAAAGTTCCAAAACCTCAGTTGTGGGGGAGCATTTTA---TTACAAAGT
1 GAGCATTTTATTTTT-AAAAGTTCCAAAGCCTCAGTTGTCGAGGAGTATTTTATTTTTA-AAAGT
* * * * * * *
17137857 TTCAAAGTCTCATTTATGATGGAGCATTTTATTTTTCAAAAGTTCCAAAGCATCGGTTGTGATG
64 TTCAAAGCCTCAATTATGAGGGAACATTTTATTTTTCAAAAGTTCCAAAGCATCAGTTATGAGG
* *
17137921 GAGCATTTTATTTTTTAAAAGTTCCAAAGCCTTAGTT-ACGAGAGAGTATTTTATTTTTAAAAGT
1 GAGCATTTTA-TTTTTAAAAGTTCCAAAGCCTCAGTTGTCGAG-GAGTATTTTATTTTTAAAAGT
* *
17137985 TTCAAAGCCTCAATTGTG-GGGTAACATTTTATTTTTCAAAAGTTCCAAAGCCTCAGTTAT-AGG
64 TTCAAAGCCTCAATTATGAGGG-AACATTTTATTTTTCAAAAGTTCCAAAGCATCAGTTATGA-G
17138048 G
127 G
* * *
17138049 GAGCATTTTATGTTTTAAAAGTTCCAAAGCCTCAATTGTTGAGGAGTATTTAATTCTTTCAAAAG
1 GAGCATTTTAT-TTTTAAAAGTTCCAAAGCCTCAGTTGTCGAGGAGTATTTTATT-TTT-AAAAG
*
17138114 TATCAAA
63 TTTCAAA
17138121 CATTTGTCAA
Statistics
Matches: 167, Mismatches: 22, Indels: 18
0.81 0.11 0.09
Matches are distributed among these distances:
125 2 0.01
126 37 0.22
127 9 0.05
128 99 0.59
129 9 0.05
130 11 0.07
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (127 bp):
GAGCATTTTATTTTTAAAAGTTCCAAAGCCTCAGTTGTCGAGGAGTATTTTATTTTTAAAAGTTT
CAAAGCCTCAATTATGAGGGAACATTTTATTTTTCAAAAGTTCCAAAGCATCAGTTATGAGG
Found at i:17138396 original size:16 final size:16
Alignment explanation
Indices: 17138361--17138406 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
17138351 TTAAACCCTA
* *
17138361 AATTTTATTTGTATTTT
1 AATTTT-TTTTTAGTTT
17138378 AATTTTTTTTTAGTTT
1 AATTTTTTTTTAGTTT
17138394 AATTTTTTGTTTA
1 AATTTTTT-TTTA
17138407 ATTTTGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.72
Consensus pattern (16 bp):
AATTTTTTTTTAGTTT
Found at i:17139086 original size:17 final size:17
Alignment explanation
Indices: 17139045--17139121 Score: 75
Period size: 17 Copynumber: 4.3 Consensus size: 17
17139035 TGCATGACTA
17139045 ATATTATATTTGCATAAT
1 ATATT-TATTTGCATAAT
*
17139063 A-ATTTATTTGCCTAAT
1 ATATTTATTTGCATAAT
17139079 ATATTTATTTGCATGATTAAT
1 ATATTTATTTGC---A-TAAT
*
17139100 ATATTTATTTGTATAAT
1 ATATTTATTTGCATAAT
*
17139117 TTATT
1 ATATT
17139122 ATTATATTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
16 12 0.24
17 21 0.42
18 2 0.04
21 15 0.30
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (17 bp):
ATATTTATTTGCATAAT
Found at i:17139099 original size:21 final size:21
Alignment explanation
Indices: 17139075--17139205 Score: 95
Period size: 21 Copynumber: 5.9 Consensus size: 21
17139065 TTTATTTGCC
17139075 TAATATATTTATTTGCATGAT
1 TAATATATTTATTTGCATGAT
* *
17139096 TAATATATTTATTTGTATAAT
1 TAATATATTTATTTGCATGAT
*
17139117 TTAT-TATTATATTTGCATGATTAT
1 TAATATATT-TATTTGCATG---AT
* *
17139141 TAATATATTTATTTGTATGGT
1 TAATATATTTATTTGCATGAT
*
17139162 TATATTTAATTTGA-TTGCATGATTTT
1 TA-ATAT-ATTT-ATTTGCATGA---T
*
17139188 TAATATATTTAATTGCAT
1 TAATATATTTATTTGCAT
17139206 ATTTATTTGC
Statistics
Matches: 86, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
20 4 0.05
21 33 0.38
22 3 0.03
23 11 0.13
24 25 0.29
25 7 0.08
26 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (21 bp):
TAATATATTTATTTGCATGAT
Found at i:17139152 original size:45 final size:43
Alignment explanation
Indices: 17139080--17139337 Score: 142
Period size: 44 Copynumber: 5.9 Consensus size: 43
17139070 TTGCCTAATA
17139080 TATTTATTTGCATG---ATTAATATATTTATTTGTATAATTTAT
1 TATTTATTTGCATGATTATTAATATATTTATTTGTAT-ATTTAT
*
17139121 TATTATATTTGCATGATTATTAATATATTTATTTGTATGGTTATATT
1 TATT-TATTTGCATGATTATTAATATATTTATTTGTAT-ATT-TA-T
* **
17139168 TAATTTGA-TTGCATGATTTTTAATATATTTA-----AT-TGCA-
1 T-ATTT-ATTTGCATGATTATTAATATATTTATTTGTATATTTAT
* *
17139205 TATTTATTTGCATGATTTATATATTATTATTTGCATGATTATATATTTAAT
1 TATTTATTTGCATGA-TTAT-TAATA-TATTT--AT--TTGTATATTT-AT
* * * * ** *
17139256 TGTATGTTTGCATGATTATTAATATATTTACTTACATAATTAT
1 TATTTATTTGCATGATTATTAATATATTTATTTGTATATTTAT
* * * *
17139299 TAATCTATTTACATTATTATTAATTTATTTATTTGTATA
1 T-ATTTATTTGCATGATTATTAATATATTTATTTGTATA
17139338 ATTGTATGAT
Statistics
Matches: 167, Mismatches: 25, Indels: 47
0.70 0.10 0.20
Matches are distributed among these distances:
35 1 0.01
36 12 0.07
37 4 0.02
38 4 0.02
39 6 0.04
40 1 0.01
41 5 0.03
42 12 0.07
43 3 0.02
44 36 0.22
45 22 0.13
46 3 0.02
47 25 0.15
48 11 0.07
49 5 0.03
50 5 0.03
51 12 0.07
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (43 bp):
TATTTATTTGCATGATTATTAATATATTTATTTGTATATTTAT
Found at i:17139155 original size:24 final size:24
Alignment explanation
Indices: 17139075--17139205 Score: 102
Period size: 24 Copynumber: 5.8 Consensus size: 24
17139065 TTTATTTGCC
17139075 TAATATATTTATTTGCATG---AT
1 TAATATATTTATTTGCATGATTAT
*
17139096 TAATATATTTATTTG--T-ATAAT
1 TAATATATTTATTTGCATGATTAT
*
17139117 TTAT-TATTATATTTGCATGATTAT
1 TAATATATT-TATTTGCATGATTAT
* *
17139141 TAATATATTTATTTGTATGGTTA-
1 TAATATATTTATTTGCATGATTAT
* *
17139164 T-ATTTAATTTGA-TTGCATGATTTT
1 TAATAT-ATTT-ATTTGCATGATTAT
*
17139188 TAATATATTTAATTGCAT
1 TAATATATTTATTTGCAT
17139206 ATTTATTTGC
Statistics
Matches: 87, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
19 1 0.01
20 4 0.05
21 26 0.30
22 3 0.03
23 15 0.17
24 31 0.36
25 7 0.08
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (24 bp):
TAATATATTTATTTGCATGATTAT
Found at i:17139196 original size:47 final size:45
Alignment explanation
Indices: 17139080--17139212 Score: 136
Period size: 47 Copynumber: 3.0 Consensus size: 45
17139070 TTGCCTAATA
17139080 TATT-TATTTGCATG---ATTAATATATTTATTTGTATAATTTAT
1 TATTATATTTGCATGATTATTAATATATTTATTTGTATAATTTAT
**
17139121 TATTATATTTGCATGATTATTAATATATTTATTTGTATGGTTATATT
1 TATTATATTTGCATGATTATTAATATATTTATTTGTATAATT-TA-T
* * *
17139168 TAATT-TGA-TTGCATGATTTTTAATATATTTAATTGCAT-ATTTAT
1 T-ATTAT-ATTTGCATGATTATTAATATATTTATTTGTATAATTTAT
17139212 T
1 T
17139213 TGCATGATTT
Statistics
Matches: 78, Mismatches: 6, Indels: 13
0.80 0.06 0.13
Matches are distributed among these distances:
41 4 0.05
42 10 0.13
44 2 0.03
45 24 0.31
46 4 0.05
47 30 0.38
48 4 0.05
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (45 bp):
TATTATATTTGCATGATTATTAATATATTTATTTGTATAATTTAT
Found at i:17139249 original size:22 final size:23
Alignment explanation
Indices: 17139208--17139251 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
17139198 AATTGCATAT
17139208 TTATTTGCATGATTTATATATTA
1 TTATTTGCATGATTTATATATTA
17139231 TTATTTGCATGA-TTATATATT
1 TTATTTGCATGATTTATATATT
17139252 TAATTGTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.57
Consensus pattern (23 bp):
TTATTTGCATGATTTATATATTA
Found at i:17139312 original size:20 final size:20
Alignment explanation
Indices: 17139287--17139329 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17139277 ATATATTTAC
17139287 TTACATAATTATTAATCTAT
1 TTACATAATTATTAATCTAT
* *
17139307 TTACATTATTATTAATTTAT
1 TTACATAATTATTAATCTAT
17139327 TTA
1 TTA
17139330 TTTGTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (20 bp):
TTACATAATTATTAATCTAT
Found at i:17139331 original size:24 final size:23
Alignment explanation
Indices: 17139270--17139332 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 23
17139260 TGTTTGCATG
* *
17139270 ATTATTAATATATTTACTTACAT
1 ATTATTAATTTATTTATTTACAT
* *
17139293 A--ATT-ATTAATCTATTTACATT
1 ATTATTAATTTATTTATTTACA-T
17139314 ATTATTAATTTATTTATTT
1 ATTATTAATTTATTTATTT
17139333 GTATAATTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
20 11 0.37
21 5 0.17
23 4 0.13
24 10 0.33
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTATTAATTTATTTATTTACAT
Found at i:17139597 original size:18 final size:18
Alignment explanation
Indices: 17139543--17139642 Score: 73
Period size: 18 Copynumber: 5.5 Consensus size: 18
17139533 GTTATTAATG
*
17139543 TATTTGCATGATATTTTA
1 TATTTGCATGATATTATA
* *
17139561 TATTATTGAATG--ATGATA
1 TA-T-TTGCATGATATTATA
17139579 TATTTGCATGATATTATA
1 TATTTGCATGATATTATA
* *
17139597 TATTTACATGATTGTTAT-
1 TATTTGCATGA-TATTATA
*
17139615 TA-TTGCATAATAATTAATA
1 TATTTGCATGAT-ATT-ATA
17139634 TATTTGCAT
1 TATTTGCAT
17139643 AACATTTTTG
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
16 7 0.11
17 9 0.14
18 27 0.43
19 8 0.13
20 12 0.19
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (18 bp):
TATTTGCATGATATTATA
Found at i:17139757 original size:69 final size:66
Alignment explanation
Indices: 17139682--17139901 Score: 223
Period size: 69 Copynumber: 3.2 Consensus size: 66
17139672 TCTAGGTATG
* * *
17139682 ATATTATTCCATGATATT-TGGTATGA-TTTATAATATATTTGCATAATAATTTTTGCATGGTAT
1 ATATTATTGCATGATATTATGGTATGATTTTAT-AT-TA-TTGCATAAT--TTATTGCATGATAT
17139745 GATTTT
61 GATTTT
* *
17139751 ATATTATTGTATGATTTATTGCATGGTGTGATTTTATATTATTGCATAATTTATTGCATGATATG
1 ATATTATTGCATGA--TATT--ATGGTATGATTTTATATTATTGCATAATTTATTGCATGATATG
17139816 ATTTT
62 ATTTT
* *
17139821 AT-TTATTGCATGATTTATTGCATGATATGATTTTAT-TTATTGCATGATTTATTGCATGATATG
1 ATATTATTGCATGA--TATT--ATGGTATGATTTTATATTATTGCATAATTTATTGCATGATATG
17139884 ATTTT
62 ATTTT
17139889 ATATTTATTGCAT
1 ATA-TTATTGCAT
17139902 AATAACTTTA
Statistics
Matches: 134, Mismatches: 9, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
68 33 0.25
69 43 0.32
70 29 0.22
71 4 0.03
72 9 0.07
73 2 0.01
74 9 0.07
75 5 0.04
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.52
Consensus pattern (66 bp):
ATATTATTGCATGATATTATGGTATGATTTTATATTATTGCATAATTTATTGCATGATATGATTT
T
Found at i:17139771 original size:12 final size:12
Alignment explanation
Indices: 17139754--17139880 Score: 81
Period size: 12 Copynumber: 11.0 Consensus size: 12
17139744 TGATTTTATA
*
17139754 TTATTGTATGAT
1 TTATTGCATGAT
*
17139766 TTATTGCATGGT
1 TTATTGCATGAT
* **
17139778 GTGATTTTAT-A-
1 -TTATTGCATGAT
*
17139789 TTATTGCATAAT
1 TTATTGCATGAT
17139801 TTATTGCATGAT
1 TTATTGCATGAT
* *
17139813 ATGATT---TTAT
1 -TTATTGCATGAT
17139823 TTATTGCATGAT
1 TTATTGCATGAT
17139835 TTATTGCATGAT
1 TTATTGCATGAT
* *
17139847 ATGATT---TTAT
1 -TTATTGCATGAT
17139857 TTATTGCATGAT
1 TTATTGCATGAT
17139869 TTATTGCATGAT
1 TTATTGCATGAT
17139881 ATGATTTTAT
Statistics
Matches: 86, Mismatches: 18, Indels: 22
0.68 0.14 0.17
Matches are distributed among these distances:
9 8 0.09
10 12 0.14
11 1 0.01
12 51 0.59
13 14 0.16
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.53
Consensus pattern (12 bp):
TTATTGCATGAT
Found at i:17139773 original size:35 final size:35
Alignment explanation
Indices: 17139730--17139901 Score: 269
Period size: 34 Copynumber: 5.0 Consensus size: 35
17139720 TTGCATAATA
* *
17139730 ATTT-TTGCATGGTATGATTTTATATTATTGTATG
1 ATTTATTGCATGATATGATTTTATATTATTGCATG
* * *
17139764 ATTTATTGCATGGTGTGATTTTATATTATTGCATA
1 ATTTATTGCATGATATGATTTTATATTATTGCATG
17139799 ATTTATTGCATGATATGATTTTAT-TTATTGCATG
1 ATTTATTGCATGATATGATTTTATATTATTGCATG
17139833 ATTTATTGCATGATATGATTTTAT-TTATTGCATG
1 ATTTATTGCATGATATGATTTTATATTATTGCATG
17139867 ATTTATTGCATGATATGATTTTATATTTATTGCAT
1 ATTTATTGCATGATATGATTTTATA-TTATTGCAT
17139902 AATAACTTTA
Statistics
Matches: 129, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
34 71 0.55
35 49 0.38
36 9 0.07
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.53
Consensus pattern (35 bp):
ATTTATTGCATGATATGATTTTATATTATTGCATG
Found at i:17139819 original size:17 final size:17
Alignment explanation
Indices: 17139799--17139887 Score: 78
Period size: 17 Copynumber: 5.2 Consensus size: 17
17139789 TTATTGCATA
17139799 ATTTATTGCATGATATG
1 ATTTATTGCATGATATG
* *
17139816 ATTTTATT-TATTG-CATG
1 A-TTTATTGCA-TGATATG
17139833 ATTTATTGCATGATATG
1 ATTTATTGCATGATATG
* *
17139850 ATTTTATT-TATTG-CATG
1 A-TTTATTGCA-TGATATG
17139867 ATTTATTGCATGATATG
1 ATTTATTGCATGATATG
17139884 ATTT
1 ATTT
17139888 TATATTTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
16 16 0.29
17 24 0.43
18 16 0.29
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.53
Consensus pattern (17 bp):
ATTTATTGCATGATATG
Found at i:17143524 original size:31 final size:30
Alignment explanation
Indices: 17143489--17143546 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
17143479 CGATGTGACA
*
17143489 AAGAAATGAATTCAGGTAAATGAATTCAAGT
1 AAGAAATGAATTCA-ATAAATGAATTCAAGT
17143520 AAGAAATGAATTCAATAAATGAATTCA
1 AAGAAATGAATTCAATAAATGAATTCA
17143547 TGGATTCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.26
Consensus pattern (30 bp):
AAGAAATGAATTCAATAAATGAATTCAAGT
Found at i:17143528 original size:17 final size:17
Alignment explanation
Indices: 17143489--17143534 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 17
17143479 CGATGTGACA
*
17143489 AAGAAATGAATTCAGGT
1 AAGAAATGAATTCAAGT
17143506 ---AAATGAATTCAAGT
1 AAGAAATGAATTCAAGT
17143520 AAGAAATGAATTCAA
1 AAGAAATGAATTCAA
17143535 TAAATGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 13 0.52
17 12 0.48
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.24
Consensus pattern (17 bp):
AAGAAATGAATTCAAGT
Found at i:17143541 original size:13 final size:13
Alignment explanation
Indices: 17143492--17143546 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 13
17143482 TGTGACAAAG
*
17143492 AAATGAATTCAGGT
1 AAATGAATTCA-AT
17143506 AAATGAATTCAAGT
1 AAATGAATTCAA-T
17143520 AAGAAATGAATTCAAT
1 ---AAATGAATTCAAT
17143536 AAATGAATTCA
1 AAATGAATTCA
17143547 TGGATTCTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 11 0.31
14 12 0.33
16 1 0.03
17 12 0.33
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27
Consensus pattern (13 bp):
AAATGAATTCAAT
Found at i:17145370 original size:24 final size:24
Alignment explanation
Indices: 17145343--17145393 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
17145333 CATTAATCTG
*
17145343 TCTACTGA-AGAGAGAAGAAAATTA
1 TCTACTGATAG-GAGAAAAAAATTA
17145367 TCTACTGATAGGAGAAAAAAATTA
1 TCTACTGATAGGAGAAAAAAATTA
17145391 TCT
1 TCT
17145394 TTTAAACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (24 bp):
TCTACTGATAGGAGAAAAAAATTA
Found at i:17147479 original size:12 final size:12
Alignment explanation
Indices: 17147462--17147492 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
17147452 ATTTGAAAAT
17147462 TATAAATACAAA
1 TATAAATACAAA
17147474 TATAAATACAAA
1 TATAAATACAAA
*
17147486 TACAAAT
1 TATAAAT
17147493 TGAAATATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (12 bp):
TATAAATACAAA
Found at i:17147802 original size:15 final size:15
Alignment explanation
Indices: 17147782--17147902 Score: 91
Period size: 16 Copynumber: 7.7 Consensus size: 15
17147772 TTCGAGTGAG
*
17147782 TTTGAGTTGAATAAT
1 TTTGATTTGAATAAT
* * *
17147797 TTTGAGTTCAGATTAT
1 TTTGATTTGA-ATAAT
*
17147813 ATTTGATTTGAATTAT
1 -TTTGATTTGAATAAT
17147829 TTTAGATTTGAATAAT
1 TTT-GATTTGAATAAT
* *
17147845 TTTGATTTGAGTTAT
1 TTTGATTTGAATAAT
*
17147860 TTTGGATTTAAATAAT
1 TTT-GATTTGAATAAT
17147876 TTT-ATGTTTGAATCAAT
1 TTTGA--TTTGAAT-AAT
*
17147893 TTAGATTTGA
1 TTTGATTTGA
17147903 GTTTTTTTAA
Statistics
Matches: 86, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
14 1 0.01
15 25 0.29
16 46 0.53
17 13 0.15
18 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.52
Consensus pattern (15 bp):
TTTGATTTGAATAAT
Found at i:17147852 original size:31 final size:31
Alignment explanation
Indices: 17147814--17147902 Score: 108
Period size: 31 Copynumber: 2.8 Consensus size: 31
17147804 TCAGATTATA
17147814 TTTGATTTGAATTATTTTAGATTTGAATAAT
1 TTTGATTTGAATTATTTTAGATTTGAATAAT
* * *
17147845 TTTGATTTGAGTTATTTTGGATTTAAATAAT
1 TTTGATTTGAATTATTTTAGATTTGAATAAT
* *
17147876 TTT-ATGTTTGAATCAATTTAGATTTGA
1 TTTGA--TTTGAATTATTTTAGATTTGA
17147903 GTTTTTTTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 1 0.02
31 31 0.65
32 16 0.33
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (31 bp):
TTTGATTTGAATTATTTTAGATTTGAATAAT
Found at i:17147919 original size:47 final size:46
Alignment explanation
Indices: 17147827--17147937 Score: 109
Period size: 48 Copynumber: 2.3 Consensus size: 46
17147817 GATTTGAATT
* *
17147827 ATTTTAGATTTGAATAATTTTGATTTGAGTTATTTTGGATTTAAATA
1 ATTTTAGATTTGAATAATTTAGATTTGAGTTATTTTAGA-TTAAATA
*
17147874 ATTTTATG-TTTGAATCAATTTAGATTTGAGTTTTTTTAAGA-TAAATTTA
1 ATTTTA-GATTTGAAT-AATTTAGATTTGAGTTATTTT-AGATTAAA--TA
* *
17147923 AGTTTGGATTTGAAT
1 ATTTTAGATTTGAAT
17147938 TAATCAAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
47 17 0.32
48 21 0.40
49 15 0.28
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.52
Consensus pattern (46 bp):
ATTTTAGATTTGAATAATTTAGATTTGAGTTATTTTAGATTAAATA
Found at i:17148438 original size:78 final size:78
Alignment explanation
Indices: 17148309--17148462 Score: 308
Period size: 78 Copynumber: 2.0 Consensus size: 78
17148299 TATGATCTTG
17148309 ATGGGAGGGGCAATTACGTAAAAATTTGAACTCCTTTGACGTGGAATCTATGCAAATAAATTACA
1 ATGGGAGGGGCAATTACGTAAAAATTTGAACTCCTTTGACGTGGAATCTATGCAAATAAATTACA
17148374 AAGACGAAGAATT
66 AAGACGAAGAATT
17148387 ATGGGAGGGGCAATTACGTAAAAATTTGAACTCCTTTGACGTGGAATCTATGCAAATAAATTACA
1 ATGGGAGGGGCAATTACGTAAAAATTTGAACTCCTTTGACGTGGAATCTATGCAAATAAATTACA
17148452 AAGACGAAGAA
66 AAGACGAAGAA
17148463 ACAGGAGGAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (78 bp):
ATGGGAGGGGCAATTACGTAAAAATTTGAACTCCTTTGACGTGGAATCTATGCAAATAAATTACA
AAGACGAAGAATT
Found at i:17152793 original size:29 final size:29
Alignment explanation
Indices: 17152751--17152819 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
17152741 TTAGTAAAGG
* *
17152751 AAGATAGACTTAAGCTCTGTCTCTCTTTC
1 AAGATAGACTTAAGCTCTGTATCTATTTC
* *
17152780 AAGATCGACTTAAGTTCTGTATCTATTTC
1 AAGATAGACTTAAGCTCTGTATCTATTTC
*
17152809 AAGACAGACTT
1 AAGATAGACTT
17152820 GTGGAGGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.36
Consensus pattern (29 bp):
AAGATAGACTTAAGCTCTGTATCTATTTC
Found at i:17154519 original size:29 final size:29
Alignment explanation
Indices: 17154477--17154545 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
17154467 CAGGACTTAG
*
17154477 ATTATACTAATCTTGTTTGCCTACTATGT
1 ATTATACAAATCTTGTTTGCCTACTATGT
* * *
17154506 ATTATACAAATCTTGTTTGCTTGCTGTGT
1 ATTATACAAATCTTGTTTGCCTACTATGT
*
17154535 ATTATGCAAAT
1 ATTATACAAAT
17154546 ACTTTCTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.46
Consensus pattern (29 bp):
ATTATACAAATCTTGTTTGCCTACTATGT
Found at i:17155300 original size:12 final size:12
Alignment explanation
Indices: 17155283--17155308 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17155273 TTTGGTGGGA
17155283 AAGGCTCATAAT
1 AAGGCTCATAAT
17155295 AAGGCTCATAAT
1 AAGGCTCATAAT
17155307 AA
1 AA
17155309 AATCATTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (12 bp):
AAGGCTCATAAT
Found at i:17158833 original size:22 final size:21
Alignment explanation
Indices: 17158772--17158833 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 21
17158762 AAAGTAAAAG
* *
17158772 AAAATTAATAAAAAGTTATTTT
1 AAAATTAAAAAAAAG-AATTTT
*
17158794 AAAATATAAAAAGTAAGAATTTT
1 AAAAT-TAAAAA-AAAGAATTTT
17158817 AAATATTAAAAAAAAGA
1 AAA-ATTAAAAAAAAGA
17158834 CATAATTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 9 0.27
23 19 0.58
24 5 0.15
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (21 bp):
AAAATTAAAAAAAAGAATTTT
Found at i:17159322 original size:2 final size:2
Alignment explanation
Indices: 17159310--17159341 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
17159300 TTTTCAGTTG
*
17159310 GA GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17159342 CCTTTCACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17160112 original size:4 final size:4
Alignment explanation
Indices: 17160103--17160127 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17160093 TCTCTCTGTA
17160103 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
17160128 GTTCAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:17160286 original size:23 final size:23
Alignment explanation
Indices: 17160260--17160309 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
17160250 TAACATGGGT
*
17160260 TTTTGTTTAGTTATA-ATTTTTTA
1 TTTTATTTAGTTATATA-TTTTTA
* *
17160283 TTTTATTTATTTATTTATTTTTA
1 TTTTATTTAGTTATATATTTTTA
17160306 TTTT
1 TTTT
17160310 CTCTAGATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTATTTAGTTATATATTTTTA
Found at i:17161009 original size:2 final size:2
Alignment explanation
Indices: 17161004--17161035 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17160994 ATATATATAT
17161004 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17161036 GTGTACATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17168819 original size:42 final size:42
Alignment explanation
Indices: 17168760--17168844 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
17168750 AACTTGAAAA
*
17168760 ACAACTGAACTAATGAACTAGTTGGCCTTTATAATAAATTTT
1 ACAACTGAAATAATGAACTAGTTGGCCTTTATAATAAATTTT
17168802 ACAACTGAAATAATGAACTAGTTGGCCTTTATAATAAATTTT
1 ACAACTGAAATAATGAACTAGTTGGCCTTTATAATAAATTTT
17168844 A
1 A
17168845 TGTTGAAGAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (42 bp):
ACAACTGAAATAATGAACTAGTTGGCCTTTATAATAAATTTT
Found at i:17168921 original size:14 final size:15
Alignment explanation
Indices: 17168902--17168930 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17168892 GTAAAAAAGA
17168902 AGTTTGTGCA-CTTT
1 AGTTTGTGCAGCTTT
17168916 AGTTTGTGCAGCTTT
1 AGTTTGTGCAGCTTT
17168931 TTCATTAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.48
Consensus pattern (15 bp):
AGTTTGTGCAGCTTT
Found at i:17170429 original size:22 final size:22
Alignment explanation
Indices: 17170401--17170444 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17170391 CTAAATCTTC
*
17170401 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
17170423 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
17170445 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:17174329 original size:22 final size:22
Alignment explanation
Indices: 17174301--17174344 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17174291 CTAAATCTTC
*
17174301 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
17174323 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
17174345 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:17175812 original size:21 final size:21
Alignment explanation
Indices: 17175786--17175830 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
17175776 ATGGAATATG
*
17175786 TTGAAATAATTTCATGAGCTT
1 TTGAAATAATTTAATGAGCTT
17175807 TTGAAATAATTTAATGAGCTT
1 TTGAAATAATTTAATGAGCTT
17175828 TTG
1 TTG
17175831 TTCTTGGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (21 bp):
TTGAAATAATTTAATGAGCTT
Found at i:17178671 original size:2 final size:2
Alignment explanation
Indices: 17178664--17178692 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17178654 TGGTAGGTTT
17178664 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
17178693 CTATTCTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:17181042 original size:2 final size:2
Alignment explanation
Indices: 17181035--17181073 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17181025 AACTTGAACT
17181035 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17181074 TGGCTTAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17191541 original size:15 final size:15
Alignment explanation
Indices: 17191523--17191552 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17191513 TTTAATATTT
*
17191523 TAATAATATTTTAAA
1 TAATAATATATTAAA
17191538 TAATAATATATTAAA
1 TAATAATATATTAAA
17191553 ATAAAAGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATAATATATTAAA
Found at i:17195191 original size:21 final size:21
Alignment explanation
Indices: 17195167--17195207 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
17195157 ATGTTATAAG
*
17195167 ACTTAGTCTAATTCATCATTA
1 ACTTAATCTAATTCATCATTA
17195188 ACTTAATCTAATTCATCATT
1 ACTTAATCTAATTCATCATT
17195208 TTCTCTAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.02, T:0.44
Consensus pattern (21 bp):
ACTTAATCTAATTCATCATTA
Found at i:17195256 original size:16 final size:16
Alignment explanation
Indices: 17195235--17195276 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
17195225 TGAAAGCTAG
17195235 AATTGAAAAAAAATAT
1 AATTGAAAAAAAATAT
17195251 AATTG-AAAAAAATAT
1 AATTGAAAAAAAATAT
*
17195266 AAGTGAAAAAA
1 AATTGAAAAAA
17195277 TTATCATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (16 bp):
AATTGAAAAAAAATAT
Found at i:17200735 original size:23 final size:22
Alignment explanation
Indices: 17200688--17200737 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
17200678 TTAATGTCTT
17200688 AAAACCCATAATGATTTTGTAAA
1 AAAACCCATAATGA-TTTGTAAA
*
17200711 AAAACCCATAATG-TTTGCTATA
1 AAAACCCATAATGATTTG-TAAA
17200733 AAAAC
1 AAAAC
17200738 ATTACCCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 8 0.32
23 13 0.52
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (22 bp):
AAAACCCATAATGATTTGTAAA
Found at i:17203650 original size:22 final size:23
Alignment explanation
Indices: 17203601--17203651 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
17203591 ATTTTTTATA
*
17203601 TAATTTATCTATAAAAATTAATT
1 TAATTTATCAATAAAAATTAATT
* *
17203624 T-ATTTATCAATAAATA-TATTT
1 TAATTTATCAATAAAAATTAATT
17203645 TAATTTA
1 TAATTTA
17203652 AAATTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 5 0.21
22 18 0.75
23 1 0.04
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATTTATCAATAAAAATTAATT
Found at i:17203670 original size:24 final size:23
Alignment explanation
Indices: 17203634--17203679 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
17203624 TATTTATCAA
17203634 TAAATATATTTTAATT-TAAAATT
1 TAAATATATTTT-ATTATAAAATT
17203657 TAAATTATATTTTATTATAAAAT
1 TAAA-TATATTTTATTATAAAAT
17203680 AAATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATATATTTTATTATAAAATT
Found at i:17204018 original size:15 final size:15
Alignment explanation
Indices: 17203998--17204027 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17203988 TTTAATATTT
*
17203998 TAATAATATTTTAAA
1 TAATAATATATTAAA
17204013 TAATAATATATTAAA
1 TAATAATATATTAAA
17204028 ATAAAAGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATAATATATTAAA
Found at i:17210931 original size:46 final size:46
Alignment explanation
Indices: 17210870--17210959 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
17210860 ATTTTCTAGT
17210870 ACTGGATTTTACCTAAATTACTAAGACTTATTCAACATCTTTCCGA
1 ACTGGATTTTACCTAAATTACTAAGACTTATTCAACATCTTTCCGA
* *
17210916 ACTGGAGTTTT-CCTAAATTACTGAGACTTATTCAACTTCTTTCC
1 ACTGGA-TTTTACCTAAATTACTAAGACTTATTCAACATCTTTCC
17210960 AAAGAATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 37 0.90
47 4 0.10
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (46 bp):
ACTGGATTTTACCTAAATTACTAAGACTTATTCAACATCTTTCCGA
Found at i:17211130 original size:17 final size:17
Alignment explanation
Indices: 17211108--17211140 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
17211098 AACATTAATG
17211108 AATACTGTTACCTCCTA
1 AATACTGTTACCTCCTA
17211125 AATACTGTTACCTCCT
1 AATACTGTTACCTCCT
17211141 GTGAATAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.30, G:0.06, T:0.36
Consensus pattern (17 bp):
AATACTGTTACCTCCTA
Found at i:17212543 original size:17 final size:17
Alignment explanation
Indices: 17212517--17212549 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
17212507 GAAAATCTTT
17212517 AAAAAAAAATT-ATTTC
1 AAAAAAAAATTCATTTC
17212533 AAAAAATAAATTCATTT
1 AAAAAA-AAATTCATTT
17212550 AATGAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAAAAAATTCATTTC
Found at i:17213162 original size:173 final size:174
Alignment explanation
Indices: 17212865--17213210 Score: 443
Period size: 173 Copynumber: 2.0 Consensus size: 174
17212855 AGTATTTGTT
* * *
17212865 ATAATGTACATCGCAATGTGAATCTTTATTTTTTATTTTAAAATAACAATTATTTATTAAATAAA
1 ATAATATACATCGCAATGTGAATATTTATTTTTTATTTTAAAATAACAATTATATATTAAATAAA
* * *
17212930 TGATTATTTATTATAAAATAATTGAAATTAATAAAATATATATTAACCAGAATTTGCATGGATA-
66 TGATTATATATTATAAAATAATT-AAA-TAATAAAATACATATTAACCAGAATTTGCAT-GAAAG
17212994 TAGAAAGTTTATCTCATATCAAAATA-ATTATTTGATTAACATATAG
128 TAGAAAGTTTATCTCATATCAAAATATATTATTTGATTAACATATAG
* * *
17213040 ATAATATACATCGCAATTTGAATATTTATTTTTTATTTATTTTAAAATAATAATTGTATATTAAA
1 ATAATATACATCGCAATGTGAATATTTA---TTT-TTTATTTTAAAATAACAATTATATATTAAA
* * * *
17213105 TATATGA-TATATATTATAAAATAATT-AA-AAT-TAATACATATTAATCGGAATTTGCATGAAA
62 TAAATGATTATATATTATAAAATAATTAAATAATAAAATACATATTAACCAGAATTTGCATGAAA
* * *
17213166 GTATAAAGTTTATCTTATGTCAAAATATATTATTTGATTAACATA
127 GTAGAAAGTTTATCTCATATCAAAATATATTATTTGATTAACATA
17213211 AATTTAAATT
Statistics
Matches: 149, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
172 3 0.02
173 45 0.30
174 20 0.13
175 25 0.17
176 2 0.01
178 21 0.14
179 33 0.22
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (174 bp):
ATAATATACATCGCAATGTGAATATTTATTTTTTATTTTAAAATAACAATTATATATTAAATAAA
TGATTATATATTATAAAATAATTAAATAATAAAATACATATTAACCAGAATTTGCATGAAAGTAG
AAAGTTTATCTCATATCAAAATATATTATTTGATTAACATATAG
Found at i:17213850 original size:19 final size:20
Alignment explanation
Indices: 17213817--17213859 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
17213807 AAAATGTATA
17213817 TTTATAATATTTTAAAATTG
1 TTTATAATATTTTAAAATTG
*
17213837 TTTATAAT-TTTTAAAATTT
1 TTTATAATATTTTAAAATTG
17213856 TTTA
1 TTTA
17213860 AAAATTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTATAATATTTTAAAATTG
Found at i:17213863 original size:11 final size:10
Alignment explanation
Indices: 17213826--17213867 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
17213816 ATTTATAATA
17213826 TTTTAAAATT
1 TTTTAAAATT
* *
17213836 GTTTATAA-T
1 TTTTAAAATT
17213845 TTTTAAAATT
1 TTTTAAAATT
17213855 TTTTAAAAATT
1 TTTT-AAAATT
17213866 TT
1 TT
17213868 GTTTTAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 7 0.27
10 11 0.42
11 8 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:17213867 original size:19 final size:19
Alignment explanation
Indices: 17213825--17213867 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
17213815 TATTTATAAT
*
17213825 ATTTTAAAATTGTTTATAA
1 ATTTTAAAATTGTTTAAAA
* *
17213844 TTTTTAAAATTTTTTAAAA
1 ATTTTAAAATTGTTTAAAA
17213863 ATTTT
1 ATTTT
17213868 GTTTTAATAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTAAAATTGTTTAAAA
Found at i:17214113 original size:14 final size:14
Alignment explanation
Indices: 17214096--17214125 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17214086 TATTTAACCC
17214096 AAAATATATATATA
1 AAAATATATATATA
*
17214110 AAAATATATTTATA
1 AAAATATATATATA
17214124 AA
1 AA
17214126 GTGGCGTGAA
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATATATATATA
Found at i:17215385 original size:14 final size:13
Alignment explanation
Indices: 17215368--17215399 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
17215358 TATGTGATGA
17215368 AATTTTTAATTTTT
1 AATTTTTAA-TTTT
17215382 AATTTTTAATTTT
1 AATTTTTAATTTT
17215395 AATTT
1 AATTT
17215400 ATTTATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATTTTTAATTTT
Found at i:17215387 original size:6 final size:7
Alignment explanation
Indices: 17215368--17215399 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
17215358 TATGTGATGA
17215368 AATTTTT
1 AATTTTT
17215375 AATTTTT
1 AATTTTT
17215382 AATTTTT
1 AATTTTT
17215389 AA-TTTT
1 AATTTTT
17215395 AATTT
1 AATTT
17215400 ATTTATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:17217786 original size:24 final size:23
Alignment explanation
Indices: 17217744--17217793 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
17217734 TTATATATTA
*
17217744 TTAATTTTTATCAATTTATTGAT
1 TTAATTTTTATCAAATTATTGAT
* *
17217767 TTAATTTTTTATTAAATTATTTAT
1 TTAA-TTTTTATCAAATTATTGAT
17217791 TTA
1 TTA
17217794 TTTATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
TTAATTTTTATCAAATTATTGAT
Found at i:17218326 original size:19 final size:18
Alignment explanation
Indices: 17218284--17218326 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
17218274 ACACATATTT
*
17218284 TATTTTTATTTTTAATTA
1 TATTTTTATTTTTAAATA
*
17218302 TCTTTTTATTTTTTAAATA
1 TATTTTTA-TTTTTAAATA
17218321 TATTTT
1 TATTTT
17218327 AAAAAATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTTTTATTTTTAAATA
Found at i:17219474 original size:25 final size:26
Alignment explanation
Indices: 17219411--17219476 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 26
17219401 TTTTAAAATT
* *
17219411 TTTTATTCATT-TTGATTCGTTTATA
1 TTTTATTTATTATTTATTCGTTTATA
** *
17219436 TTTT-TTTAAAATTTATTTGTTTA-A
1 TTTTATTTATTATTTATTCGTTTATA
17219460 TTTTATTTATTATTTAT
1 TTTTATTTATTATTTAT
17219477 AAATATATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
24 8 0.25
25 24 0.75
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (26 bp):
TTTTATTTATTATTTATTCGTTTATA
Found at i:17219493 original size:11 final size:12
Alignment explanation
Indices: 17219461--17219536 Score: 59
Period size: 11 Copynumber: 6.4 Consensus size: 12
17219451 TTTGTTTAAT
*
17219461 TTTATTTAT-TA
1 TTTATATATATA
17219472 TTTATAAATATATA
1 TTTAT--ATATATA
*
17219486 TTT-TATATATG
1 TTTATATATATA
*
17219497 TTTATAAATATA
1 TTTATATATATA
*
17219509 TTTATTTA-ATA
1 TTTATATATATA
* *
17219520 TTTATAAATAAA
1 TTTATATATATA
17219532 TTTAT
1 TTTAT
17219537 TTAATTTAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
11 23 0.45
12 19 0.37
13 4 0.08
14 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (12 bp):
TTTATATATATA
Found at i:17219520 original size:27 final size:24
Alignment explanation
Indices: 17219461--17219539 Score: 101
Period size: 23 Copynumber: 3.3 Consensus size: 24
17219451 TTTGTTTAAT
17219461 TTTATTTAT-TATTTATAAATATA
1 TTTATTTATATATTTATAAATATA
*
17219484 TATT-TTATATATGTTTATAAATATA
1 T-TTATT-TATATATTTATAAATATA
*
17219509 TTTATTTA-ATATTTATAAATAAA
1 TTTATTTATATATTTATAAATATA
17219532 TTTATTTA
1 TTTATTTA
17219540 ATTTAATCGA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
23 24 0.49
24 9 0.18
25 16 0.33
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (24 bp):
TTTATTTATATATTTATAAATATA
Found at i:17220234 original size:18 final size:18
Alignment explanation
Indices: 17220202--17220240 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
17220192 CGTAAGCCTC
* *
17220202 TTGCTTTTTCCTTTATTT
1 TTGCTTTTTACTTTATGT
*
17220220 TTGCTTTTTATTTTATGT
1 TTGCTTTTTACTTTATGT
17220238 TTG
1 TTG
17220241 AATTTCAGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.10, G:0.10, T:0.72
Consensus pattern (18 bp):
TTGCTTTTTACTTTATGT
Found at i:17225654 original size:2 final size:2
Alignment explanation
Indices: 17225647--17225671 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17225637 TCAAATAATT
17225647 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17225672 TCAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17226303 original size:34 final size:34
Alignment explanation
Indices: 17226261--17226339 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
17226251 AAATATTGGT
* * *
17226261 TTTTTAAAAATTTAATTTC-AAAATATTATAATAC
1 TTTTTAAAAATGTAATTTCGAAAAT-TAATAACAC
*
17226295 TTTTTAAAAATGTATTTTCGAAAATTAATAACAC
1 TTTTTAAAAATGTAATTTCGAAAATTAATAACAC
*
17226329 TTATTAAAAAT
1 TTTTTAAAAAT
17226340 ACATTTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 34 0.87
35 5 0.13
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (34 bp):
TTTTTAAAAATGTAATTTCGAAAATTAATAACAC
Found at i:17226449 original size:23 final size:24
Alignment explanation
Indices: 17226423--17226469 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
17226413 AATGTAATAA
17226423 AAAAGTT-ATTATTAAAAAATTAT
1 AAAAGTTAATTATTAAAAAATTAT
*
17226446 AAAATTTAAAATTATTAAAAAATT
1 AAAAGTT--AATTATTAAAAAATT
17226470 TTATTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
26 14 0.70
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAAGTTAATTATTAAAAAATTAT
Found at i:17228852 original size:30 final size:29
Alignment explanation
Indices: 17228816--17228884 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
17228806 TCAAATTAAT
17228816 TTAACCCTTAAACATCTATCTTCACCCAA
1 TTAACCCTTAAACATCTATCTTCACCCAA
* * * *
17228845 TTGAACCCTCATACATCTATTTTCACTCAA
1 TT-AACCCTTAAACATCTATCTTCACCCAA
17228875 TTAAGCCCTT
1 TTAA-CCCTT
17228885 GATTGGACGG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 4 0.12
30 29 0.88
ACGTcount: A:0.30, C:0.32, G:0.03, T:0.35
Consensus pattern (29 bp):
TTAACCCTTAAACATCTATCTTCACCCAA
Found at i:17230574 original size:3 final size:3
Alignment explanation
Indices: 17230566--17230597 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
17230556 TGAAGAGTAC
*
17230566 GAG GAG GAG GAG GAG GAG GAA GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
17230598 AGCTACAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:17230902 original size:2 final size:2
Alignment explanation
Indices: 17230885--17230925 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
17230875 CTTGTGGCTT
*
17230885 TA TA T- TA TA CA 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
17230926 AATCTAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17236550 original size:2 final size:2
Alignment explanation
Indices: 17236543--17236573 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17236533 ACAAGCAACC
17236543 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17236574 GTTCCTGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17237883 original size:30 final size:30
Alignment explanation
Indices: 17237849--17237907 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
17237839 TATTCTTTAA
* *
17237849 TTACTATAAAATTTAAAGTATAATAGTAAT
1 TTACTATAAAATTAAAAATATAATAGTAAT
* *
17237879 TTACTCTAAACTTAAAAATATAATAGTAA
1 TTACTATAAAATTAAAAATATAATAGTAA
17237908 ATTATGTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (30 bp):
TTACTATAAAATTAAAAATATAATAGTAAT
Found at i:17242219 original size:17 final size:17
Alignment explanation
Indices: 17242197--17242229 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17242187 CTAATGAATG
17242197 ATGAACTATAAGCAAAT
1 ATGAACTATAAGCAAAT
*
17242214 ATGAACTATAATCAAA
1 ATGAACTATAAGCAAA
17242230 ATAAAGAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.12, G:0.09, T:0.24
Consensus pattern (17 bp):
ATGAACTATAAGCAAAT
Found at i:17256200 original size:2 final size:2
Alignment explanation
Indices: 17256193--17256220 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17256183 AACTAACAAT
17256193 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
17256221 AGAGAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:17258960 original size:19 final size:18
Alignment explanation
Indices: 17258927--17258962 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17258917 AATTTTAGCA
*
17258927 ATATAAAATATTAAAATG
1 ATATAAAAAATTAAAATG
17258945 ATATAATAAAATTAAAAT
1 ATATAA-AAAATTAAAAT
17258963 AATAATGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
ATATAAAAAATTAAAATG
Found at i:17265619 original size:3 final size:3
Alignment explanation
Indices: 17265611--17265636 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17265601 AGGGACGAGG
17265611 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
17265637 TTTATAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:17269052 original size:69 final size:69
Alignment explanation
Indices: 17268941--17269077 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 69
17268931 TTAAGTAGGT
* *
17268941 TTTAAATTGCCAATTGCTGAGATTTTGGAATATTAATTTTGAGATTTATCCCTCCAGTTCTCTTG
1 TTTAAATTGCAAATTGCTGAGACTTTGGAATATTAATTTTGAGATTTATCCCTCCAGTTCTCTTG
17269006 GGTA
66 GGTA
17269010 TTTAAATTGCAAATTGCTGAGACTTTGGAATATTAATTTTGAGATTTATCCCTCCAGTTCTCTTG
1 TTTAAATTGCAAATTGCTGAGACTTTGGAATATTAATTTTGAGATTTATCCCTCCAGTTCTCTTG
17269075 GGT
66 GGT
17269078 TGTCTCTCCT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.43
Consensus pattern (69 bp):
TTTAAATTGCAAATTGCTGAGACTTTGGAATATTAATTTTGAGATTTATCCCTCCAGTTCTCTTG
GGTA
Found at i:17269893 original size:70 final size:71
Alignment explanation
Indices: 17269755--17269893 Score: 219
Period size: 70 Copynumber: 2.0 Consensus size: 71
17269745 TTCAGATCAC
* * * *
17269755 TTAGTTTCTTTTTGCAAAAACAAAAACCATTTTTTTGTCATTTGAAAATCTAAAGTACATATGCA
1 TTAGTTTCTTTTTCCAAAAACAAAAAACATTTTTATGTCATTCGAAAATCTAAAGTACATATGCA
17269820 AGACAT
66 AGACAT
17269826 TTAGTTTCTTTTTCCAAAAACAAAAAACA-TTTTATGTCATTCGAAAATCTAAAGTA-AGTATGC
1 TTAGTTTCTTTTTCCAAAAACAAAAAACATTTTTATGTCATTCGAAAATCTAAAGTACA-TATGC
17269889 AAGAC
65 AAGAC
17269894 GTCGTCTATT
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
69 1 0.02
70 35 0.56
71 27 0.43
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (71 bp):
TTAGTTTCTTTTTCCAAAAACAAAAAACATTTTTATGTCATTCGAAAATCTAAAGTACATATGCA
AGACAT
Found at i:17271946 original size:14 final size:15
Alignment explanation
Indices: 17271920--17271948 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17271910 TTAGTACATC
17271920 TATGATCTGTTGTTT
1 TATGATCTGTTGTTT
17271935 TATGAT-TGTTGTTT
1 TATGATCTGTTGTTT
17271949 ATGTTTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.03, G:0.21, T:0.62
Consensus pattern (15 bp):
TATGATCTGTTGTTT
Found at i:17272687 original size:14 final size:15
Alignment explanation
Indices: 17272668--17272705 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
17272658 TTAGGTATTG
17272668 TGCCTAAGACCATT-
1 TGCCTAAGACCATTA
17272682 TGCCTAAGACCATTA
1 TGCCTAAGACCATTA
*
17272697 GGCCTAAGA
1 TGCCTAAGA
17272706 TGAGGGGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (15 bp):
TGCCTAAGACCATTA
Done.