Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, 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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 12 of 138
Found at i:3399074 original size:11 final size:11
Alignment explanation
Indices: 3399058--3399099 Score: 75
Period size: 11 Copynumber: 3.7 Consensus size: 11
3399048 CAAAGAAATA
3399058 AAAAAAAATTC
1 AAAAAAAATTC
3399069 AAAAAAAAATTC
1 -AAAAAAAATTC
3399081 AAAAAAAATTC
1 AAAAAAAATTC
3399092 AAAAAAAA
1 AAAAAAAA
3399100 CCTGGAGCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:3399519 original size:20 final size:20
Alignment explanation
Indices: 3399478--3399522 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3399468 CCGGAAGTCG
*
3399478 GCCGGTTTCTGGGAATATTC
1 GCCGGTTTCTGGGAATACTC
* *
3399498 GCCGGTTTCTGGGATTCCTC
1 GCCGGTTTCTGGGAATACTC
3399518 GCCGG
1 GCCGG
3399523 AAACTGGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.27, G:0.33, T:0.31
Consensus pattern (20 bp):
GCCGGTTTCTGGGAATACTC
Found at i:3399581 original size:31 final size:31
Alignment explanation
Indices: 3399534--3399593 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3399524 AACTGGGCAG
* * *
3399534 GTCGCCGGAAACTTCAAATTTGGCCGGAATT
1 GTCGCCGAAAAATTCAAATTTCGCCGGAATT
*
3399565 GTCGCCGAAAAATTCAAGTTTCGCCGGAA
1 GTCGCCGAAAAATTCAAATTTCGCCGGAA
3399594 AATTCAACCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (31 bp):
GTCGCCGAAAAATTCAAATTTCGCCGGAATT
Found at i:3400597 original size:12 final size:13
Alignment explanation
Indices: 3400580--3400611 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3400570 TGTACAGACT
3400580 AATAATATAT-AA
1 AATAATATATAAA
3400592 AATAAT-TATAAA
1 AATAATATATAAA
3400604 AATAATAT
1 AATAATAT
3400612 TTATAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 14 0.78
13 1 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AATAATATATAAA
Found at i:3400691 original size:14 final size:13
Alignment explanation
Indices: 3400660--3400685 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3400650 AAATTTCGTA
3400660 AAAAAAATTTATT
1 AAAAAAATTTATT
3400673 AAAAAAATTTATT
1 AAAAAAATTTATT
3400686 TTAAAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAAAAATTTATT
Found at i:3402155 original size:17 final size:18
Alignment explanation
Indices: 3402116--3402155 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3402106 TAATTCAAGT
3402116 TTTTAATTAATAATTTAA
1 TTTTAATTAATAATTTAA
3402134 TTTTAATTCAA-AATTT-A
1 TTTTAATT-AATAATTTAA
3402151 TTTTA
1 TTTTA
3402156 TATTTCTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAATTAATAATTTAA
Found at i:3404446 original size:2 final size:2
Alignment explanation
Indices: 3404439--3404481 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3404429 CACTCATAAA
3404439 AG AG AG AG AG 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 AG AG AG AG AG
3404481 A
1 A
3404482 AACACAACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3413721 original size:18 final size:19
Alignment explanation
Indices: 3413698--3413735 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3413688 TTGAAGTTTT
*
3413698 ATAATTTTTAATAT-AAAA
1 ATAATTTTAAATATGAAAA
3413716 ATAATTTTAAATATGAAAA
1 ATAATTTTAAATATGAAAA
3413735 A
1 A
3413736 ATAAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
ATAATTTTAAATATGAAAA
Found at i:3415182 original size:20 final size:20
Alignment explanation
Indices: 3415157--3415198 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3415147 AACTTAGTAG
3415157 GAATTAGGAAAGTTAACACT
1 GAATTAGGAAAGTTAACACT
3415177 GAATTAGGAAAGTTAACACT
1 GAATTAGGAAAGTTAACACT
3415197 GA
1 GA
3415199 GACCAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (20 bp):
GAATTAGGAAAGTTAACACT
Found at i:3419155 original size:12 final size:13
Alignment explanation
Indices: 3419130--3419160 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
3419120 CAATTTATCA
3419130 ATTAAAATTTTTT
1 ATTAAAATTTTTT
3419143 ATTAAAA-TTTTT
1 ATTAAAATTTTTT
3419155 ATTAAA
1 ATTAAA
3419161 TTATTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTAAAATTTTTT
Found at i:3419167 original size:13 final size:12
Alignment explanation
Indices: 3419134--3419167 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3419124 TTATCAATTA
3419134 AAATTTTTTATT
1 AAATTTTTTATT
*
3419146 AAAATTTTTATT
1 AAATTTTTTATT
3419158 AAATTATTTT
1 AAATT-TTTT
3419168 GAATACAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
AAATTTTTTATT
Found at i:3423731 original size:31 final size:31
Alignment explanation
Indices: 3423696--3423754 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
3423686 TAAAATTTTA
* *
3423696 TTTATTAATAAAAT-ATTATCATTTAATTCAT
1 TTTATGAATAAAATGA-TATCATTAAATTCAT
*
3423727 TTTATGAATAAGATGATATCATTAAATT
1 TTTATGAATAAAATGATATCATTAAATT
3423755 TACTATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.96
32 1 0.04
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTATGAATAAAATGATATCATTAAATTCAT
Found at i:3424044 original size:45 final size:47
Alignment explanation
Indices: 3423933--3424044 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 47
3423923 ATATCTCTTT
*
3423933 TATTTAAATTATGTCATATAATTATATTATTAACAAATTAATTATTTAC
1 TATTT-AATTAT-TCATATAATTATATTATTAACAAATTAATTATTCAC
* *
3423982 TATTAAATAATT-A-ATAATTA-ATTTATT-A-AAATTAA-TATTCAC
1 TATTTAATTATTCATATAATTATA-TTATTAACAAATTAATTATTCAC
3424024 TATTTAATTATTACATATAAT
1 TATTTAATTATT-CATATAAT
3424045 ACATAATAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
42 16 0.30
43 7 0.13
44 3 0.06
45 17 0.31
46 1 0.02
47 1 0.02
48 5 0.09
49 4 0.07
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (47 bp):
TATTTAATTATTCATATAATTATATTATTAACAAATTAATTATTCAC
Found at i:3426078 original size:200 final size:205
Alignment explanation
Indices: 3425729--3426130 Score: 634
Period size: 200 Copynumber: 2.0 Consensus size: 205
3425719 CTCGTTTTTC
* * **
3425729 TTTGGTTCTTTTCTTGGTTCACCTCAAAAATTCGTAATCGGATAGTAAATTTGTTTTTACTTTCG
1 TTTGGTTCATTTCTTGATTCACCTCAAAAATTCGTAATCGGATAGTAAATTTGTCATTA-TTTCG
* *
3425794 TTTTTGTTTTAAGTTTGCATTCTCAGCTTTAAACGTGAATGCTGATTCGTTTACCTTGAAGCGGT
65 TTTTTGTTTTAAGTCTGCATTCTCAGCTTTAAACGTGAATGCTGATTCGTTTACCTTGAAGCGAT
* *
3425859 TTGTTGTTTGAGATTTTTACGATCTTTTAATTTGTTTTGATTCGGAATTTGTTACTGATGGCGGT
130 TTGTTGTTTGAGATTTTTACGAGCTGTTAATTTGTTTTGATTCGGAATTTGTTACTGATGGCGGT
3425924 TTAAAACCTTG
195 TTAAAACCTTG
* * *
3425935 TTTGGTTCATTTCTTGATTCACCTC-AAAATTCGTTATCGGATCGTGAA-TT-TCATT-TTT-GT
1 TTTGGTTCATTTCTTGATTCACCTCAAAAATTCGTAATCGGATAGTAAATTTGTCATTATTTCGT
* *
3425995 TTTTGTTTTGAGTCTGCATTCTCAGCTTTAAACGTGAATGCTGATTCGTTTACCTTGAAGCTATT
66 TTTTGTTTTAAGTCTGCATTCTCAGCTTTAAACGTGAATGCTGATTCGTTTACCTTGAAGCGATT
*
3426060 TGTTGTTTTAGATTTTTACGAGCTGTTAATTTGTTTTGATTCGGAATTTGTTACTGATGGCGGTT
131 TGTTGTTTGAGATTTTTACGAGCTGTTAATTTGTTTTGATTCGGAATTTGTTACTGATGGCGGTT
3426125 TAAAAC
196 TAAAAC
3426131 TTTATTTCGC
Statistics
Matches: 182, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
200 131 0.72
201 3 0.02
203 3 0.02
204 2 0.01
205 20 0.11
206 23 0.13
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.47
Consensus pattern (205 bp):
TTTGGTTCATTTCTTGATTCACCTCAAAAATTCGTAATCGGATAGTAAATTTGTCATTATTTCGT
TTTTGTTTTAAGTCTGCATTCTCAGCTTTAAACGTGAATGCTGATTCGTTTACCTTGAAGCGATT
TGTTGTTTGAGATTTTTACGAGCTGTTAATTTGTTTTGATTCGGAATTTGTTACTGATGGCGGTT
TAAAACCTTG
Found at i:3434667 original size:27 final size:27
Alignment explanation
Indices: 3434628--3434683 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
3434618 GTTTTAAGGG
* **
3434628 ATTTGGAATATACTTATGCCTCTTCAC
1 ATTTGGAAGATACTTATGCAGCTTCAC
*
3434655 ATTTTGAAGATACTTATGCAGCTTCAC
1 ATTTGGAAGATACTTATGCAGCTTCAC
3434682 AT
1 AT
3434684 GATCTTATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (27 bp):
ATTTGGAAGATACTTATGCAGCTTCAC
Found at i:3435318 original size:40 final size:40
Alignment explanation
Indices: 3435263--3435342 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
3435253 GCACACGGAA
** *
3435263 TACAATGTCTGTTTTCTCCTTTATTTATTACCCTTAATTT
1 TACAATGTCCATTTTCTCCTTTATTTATTACACTTAATTT
*
3435303 TACAATGTCCATTTTCTCCTTTATTTATTGCACTTAATTT
1 TACAATGTCCATTTTCTCCTTTATTTATTACACTTAATTT
3435343 ATCTTTACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (40 bp):
TACAATGTCCATTTTCTCCTTTATTTATTACACTTAATTT
Found at i:3436492 original size:17 final size:17
Alignment explanation
Indices: 3436453--3436494 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3436443 ACTTTCTATT
3436453 CTTTGAGGCATTTCTAG
1 CTTTGAGGCATTTCTAG
* *
3436470 CGTTGATGCATTT-TATG
1 CTTTGAGGCATTTCTA-G
3436487 CTTTGAGG
1 CTTTGAGG
3436495 TTAGATATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (17 bp):
CTTTGAGGCATTTCTAG
Found at i:3438901 original size:510 final size:510
Alignment explanation
Indices: 3437394--3438946 Score: 1559
Period size: 529 Copynumber: 3.0 Consensus size: 510
3437384 ATGCTTTTTA
* * *
3437394 TCTTCTGGATATTGCAATGTATAAACTTTCTTCTTGGAGTAATATGATTTCTATTTGGATATTGG
1 TCTTCTGGATATTGCAATGTACAAACTATCTTCTTGGAGTAATATGATTTCTATTTGGAGATTGG
* *
3437459 AAAAGGCTTCTAGCTTCTATGTATATCACCAGTAAAAAGTTT-AAAGCATATGAA-AGGTGAAGA
66 AGAAGGCTTCTAGCTTCTATGTATATCACCAGTAAAAAGTTTAAAAGCATA--AAGAGGTGGAGA
* * *
3437522 TATGAATTCCAAAGTAGATGGATCATAGATGATCATAGATGAGCCTTGTGATTTGGTCTAGAAGC
129 TATGAATT-TAAAGTAGATAGATCATAGATG-----AG-T---CTTTG-GATTTGGTCTAGAAGC
* * *
3437587 -AGAGAATGGCAAGGTCTATTTTGCCCTTGGAATATGTTGTTGATTTTGCAGCTGTCCATGAATA
183 AAG-GAATGACAAGG--TATTTTGCCCTTGGAATATGTTGTTGACTTTGGAGCTGTCCATGAATA
* * * *
3437651 TAATTTGCTGGAGGCAGCTTTTGCCTATTTTGAGCCATAAAAGAGATGACGAGATTGCTTCTCAA
245 TAATTTGTTGGAGGCAGCTTTTGCCTATTTTGAGACATAAAAGAGATGAAGAGATGGCTTCTCAA
* * * **
3437716 GGAAATTGATGAGGTCTTTGGGAAAGGCGTAATTGTAAGGATTTTCCTATTTTTTAAGGTCTCTG
310 -GAAAATGATGAAGTCTTTAGGAAAGGCGTAATTGTAAGGATTTTCCTATTTTTTAAGGTAACTG
* * * * * * * *
3437781 CTTGTAGAACCTTTAATAGGCAAAGATATGAAAACGCCCCT--CATTT-GCATTGCTTGATCATG
374 CTTGTTGAAACGTTATTAGGCAAAGAGATGAAAA--CCCCTGACTTTTAG-ATTGCCTGATCAAG
* * * * * *
3437843 CTACTTAGCTAGTAAAATTATGCTGTTTGAGCCAAGAACTTTTCAAAATCCCATGTGAAATTTAT
436 C-AATTAGC------AACTAGGCTGTTAGAG-C-ATAACTTCTCAAAATCCCATGTGAAATTT-T
* *
3437908 ATATAC-CTATAGATACTTTT
491 -TATGCACTATAGATACATTT
* ** * * ** *
3437928 TCTTCTGTATATTGTGATGTACAAACTGTCTTCTTGGAGTAGTATGATTTCGGTTTGGTGATTGG
1 TCTTCTGGATATTGCAATGTACAAACTATCTTCTTGGAGTAATATGATTTCTATTTGGAGATTGG
* * * *
3437993 AGAAGGCTTCTAACTTTTATG--TGTCACCAGTAAAAAG-TTAAGAA-CATAAAAAGGCAGGAGA
66 AGAAGGCTTCTAGCTTCTATGTATATCACCAGTAAAAAGTTTAA-AAGCAT--AAA-G-A-G-GT
* * * * *
3438054 GCAGAGATATGAATTCTAAAGTAGATAGACCATAAATGAGTCTCTGAATTTGGTCTACAAGCAAG
124 G--GAGATATGAATT-TAAAGTAGATAGATCATAGATGAGTCTTTGGATTTGGTCTAGAAGCAAG
* * * *
3438119 GAA-CAGCAAGGTCTATTTTGCCTTTGGAATATGTTGTTGACTTTGGAGCTGTCCATAAATATTA
186 GAATGA-CAAGG--TATTTTGCCCTTGGAATATGTTGTTGACTTTGGAGCTGTCCATGAATATAA
* ** *
3438183 TTTGTTGGAGGCAGCTTTTACCTATTTTGAGATGTAAAAGAGATGAAGAGATGGCTTCTGAAGAA
248 TTTGTTGGAGGCAGCTTTTGCCTATTTTGAGACATAAAAGAGATGAAGAGATGGCTTCTCAAGAA
* *
3438248 AATTGATGACA-TCTTTAGGGAAGGGGTAATTGTAAGGATTTTCCTATTTTTTAAGGTAACTGCT
313 AA-TGATGA-AGTCTTTAGGAAAGGCGTAATTGTAAGGATTTTCCTATTTTTTAAGGTAACTGCT
* * * *
3438312 TGTTGAAATGTTAATT-GG-TAA-AGATGGAAATGCCCCTGA-TTTTATTGATTGCCTGATCTAG
376 TGTTGAAACGTT-ATTAGGCAAAGAGAT-GAAA-ACCCCTGACTTTTA--GATTGCCTGATCAAG
* * * *
3438373 CAATATAGAAAGTAGGCTGTTAGAGC-TAACTACTCAAAATCCAATGTGAAATTTTTATGCACTG
436 CAAT-TAGCAACTAGGCTGTTAGAGCATAACTTCTCAAAATCCCATGTGAAATTTTTATGCACT-
* *
3438437 CTAGATGCATTT
499 ATAGATACATTT
* * * *
3438449 TCTTCTGGATATTGCAAAGTACAAACTATCCTCTTGGAGTAATATGGTTTCTATTTGAAGATTGG
1 TCTTCTGGATATTGCAATGTACAAACTATCTTCTTGGAGTAATATGATTTCTATTTGGAGATTGG
*
3438514 AGAATGCTTCTAGCTTCTATGTATATCACCAGTAAAAAGTTTAAAAGCATGAAAGAGGTGGAGAT
66 AGAAGGCTTCTAGCTTCTATGTATATCACCAGTAAAAAGTTTAAAAGCAT-AAAGAGGTGGAGAT
* *
3438579 ATGAATTTGAAAGTAGATAGATCATAGATGAGTCTTTGGATTTGATCTGGAAGCAAGGAATGAC-
130 ATGAATTT-AAAGTAGATAGATCATAGATGAGTCTTTGGATTTGGTCTAGAAGCAAGGAATGACA
* * * * *
3438643 A-G-ATTTTGCCCTCGAAATATGTTGTTGACTTTGGAGTTGTCCATGAATATGATTTATTGGA-G
194 AGGTATTTTGCCCTTGGAATATGTTGTTGACTTTGGAGCTGTCCATGAATATAATTTGTTGGAGG
* * *
3438705 CAGCTTTTGCCTGTTTTGCGACATAAAAGAGATGAAGAGATGGCTTCTCAAGAAAATGGTGAAGT
259 CAGCTTTTGCCTATTTTGAGACATAAAAGAGATGAAGAGATGGCTTCTCAAGAAAATGATGAAGT
* *
3438770 CTTTAGGAAAGGCGTAACTGTAAGGATTTTCCTTTTTTTTAAGGTAACTGCTTGTTGAAACGTTA
324 CTTTAGGAAAGGCGTAATTGTAAGGATTTTCCTATTTTTTAAGGTAACTGCTTGTTGAAACGTTA
** *
3438835 TTAGGCAAAGAGATGAAAACACATTGACTTTTAGATTGCCTGATCAAACAAATTAGCAACTAGGC
389 TTAGGCAAAGAGATGAAAAC-CCCTGACTTTTAGATTGCCTGATCAAGC-AATTAGCAACTAGGC
* *
3438900 TGTTAGAGCTAATAACTTCTCAAAATCCCATTTGTAA-TTTTATGCAC
452 TGTTAGAGC--ATAACTTCTCAAAATCCCATGTGAAATTTTTATGCAC
3438947 CCATTGATGC
Statistics
Matches: 849, Mismatches: 128, Indels: 106
0.78 0.12 0.10
Matches are distributed among these distances:
509 4 0.00
510 101 0.12
511 64 0.08
512 71 0.08
513 21 0.02
515 1 0.00
516 2 0.00
517 57 0.07
518 1 0.00
519 6 0.01
520 4 0.00
521 105 0.12
522 1 0.00
523 21 0.02
524 20 0.02
527 8 0.01
528 13 0.02
529 190 0.22
530 22 0.03
531 3 0.00
532 21 0.02
533 3 0.00
534 76 0.09
535 1 0.00
536 1 0.00
537 2 0.00
539 30 0.04
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (510 bp):
TCTTCTGGATATTGCAATGTACAAACTATCTTCTTGGAGTAATATGATTTCTATTTGGAGATTGG
AGAAGGCTTCTAGCTTCTATGTATATCACCAGTAAAAAGTTTAAAAGCATAAAGAGGTGGAGATA
TGAATTTAAAGTAGATAGATCATAGATGAGTCTTTGGATTTGGTCTAGAAGCAAGGAATGACAAG
GTATTTTGCCCTTGGAATATGTTGTTGACTTTGGAGCTGTCCATGAATATAATTTGTTGGAGGCA
GCTTTTGCCTATTTTGAGACATAAAAGAGATGAAGAGATGGCTTCTCAAGAAAATGATGAAGTCT
TTAGGAAAGGCGTAATTGTAAGGATTTTCCTATTTTTTAAGGTAACTGCTTGTTGAAACGTTATT
AGGCAAAGAGATGAAAACCCCTGACTTTTAGATTGCCTGATCAAGCAATTAGCAACTAGGCTGTT
AGAGCATAACTTCTCAAAATCCCATGTGAAATTTTTATGCACTATAGATACATTT
Found at i:3442941 original size:99 final size:97
Alignment explanation
Indices: 3442767--3442960 Score: 262
Period size: 99 Copynumber: 2.0 Consensus size: 97
3442757 TTGATTGATT
* * * *
3442767 TTGTCTTACTGCTGTTAACATATGTTATTTCATTTGTAACTTTAAGATGGTCAATATTTTTCCCC
1 TTGTCTTACTGCTGTTAACACATGTTATTTCATTTATAACTTTAAGATAGTCAATATTTTTCACC
*
3442832 ATCACTTTTGTTTCATGATTCCAAACTCATGG
66 ATCACGTTTGTTTCATGATTCCAAACTCATGG
* * *
3442864 TTGTCTTAAACTGCTGTTCACACATGTTATTTCATTTATAACTTTACGATAGTCAATTTTTTTCA
1 TTGTCTT--ACTGCTGTTAACACATGTTATTTCATTTATAACTTTAAGATAGTCAATATTTTTCA
* * **
3442929 CTATCACGTTTGTTTTATGATTTTAAACTCAT
64 CCATCACGTTTGTTTCATGATTCCAAACTCAT
3442961 ATTCTTCCAC
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
97 7 0.08
99 76 0.92
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.47
Consensus pattern (97 bp):
TTGTCTTACTGCTGTTAACACATGTTATTTCATTTATAACTTTAAGATAGTCAATATTTTTCACC
ATCACGTTTGTTTCATGATTCCAAACTCATGG
Found at i:3446641 original size:17 final size:17
Alignment explanation
Indices: 3446619--3446658 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3446609 ACTTGCTATC
*
3446619 TTTTAAAATTTTAATTA
1 TTTTAAAATTATAATTA
*
3446636 TTTT-AAATTATAATTT
1 TTTTAAAATTATAATTA
3446652 TTTTAAA
1 TTTTAAA
3446659 CTTAATAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAAAATTATAATTA
Found at i:3447698 original size:10 final size:10
Alignment explanation
Indices: 3447683--3447737 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
3447673 AGATCGATAG
3447683 ATATACATAT
1 ATATACATAT
*
3447693 ATATACACAT
1 ATATACATAT
** * *
3447703 ATGCACACAC
1 ATATACATAT
3447713 ATATACATAT
1 ATATACATAT
*
3447723 ATATATATAT
1 ATATACATAT
3447733 ATATA
1 ATATA
3447738 ATTAGTATAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.35
Consensus pattern (10 bp):
ATATACATAT
Found at i:3449214 original size:49 final size:50
Alignment explanation
Indices: 3449157--3449254 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 50
3449147 AAGTTAAGAA
3449157 TATTTTCATGTTTTTTGTTTATCATA-TTAGTTTATTAATTATTTTAAAG
1 TATTTTCATGTTTTTTGTTTATCATATTTAGTTTATTAATTATTTTAAAG
3449206 TATTTTCATGTTTTTTGTTTATCATATTTAGTTTATTAATTATTTTAAA
1 TATTTTCATGTTTTTTGTTTATCATATTTAGTTTATTAATTATTTTAAA
3449255 TATATTTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 26 0.54
50 22 0.46
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (50 bp):
TATTTTCATGTTTTTTGTTTATCATATTTAGTTTATTAATTATTTTAAAG
Found at i:3449233 original size:24 final size:24
Alignment explanation
Indices: 3449156--3449234 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
3449146 AAAGTTAAGA
3449156 ATATTTTCATGTTTTTTGTTTATC
1 ATATTTTCATGTTTTTTGTTTATC
* * * *
3449180 ATATTAGTTTAT-TAATTAT-TTTA-A
1 ATATT--TTCATGT-TTTTTGTTTATC
3449204 AGTATTTTCATGTTTTTTGTTTATC
1 A-TATTTTCATGTTTTTTGTTTATC
3449229 ATATTT
1 ATATTT
3449235 AGTTTATTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
23 7 0.17
24 16 0.40
25 10 0.25
26 7 0.17
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.63
Consensus pattern (24 bp):
ATATTTTCATGTTTTTTGTTTATC
Found at i:3457716 original size:2 final size:2
Alignment explanation
Indices: 3457709--3457736 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3457699 TTAGAAATTC
3457709 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
3457737 TGGTAATAAG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3462645 original size:12 final size:12
Alignment explanation
Indices: 3462630--3462668 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3462620 TCTATTTAAA
3462630 TATATTAAAAAT
1 TATATTAAAAAT
*
3462642 TATATTAAAATAA
1 TATATTAAAA-AT
*
3462655 TATATAAAAAAT
1 TATATTAAAAAT
3462667 TA
1 TA
3462669 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TATATTAAAAAT
Found at i:3462664 original size:25 final size:26
Alignment explanation
Indices: 3462628--3462678 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
3462618 TATCTATTTA
* *
3462628 AATATATTAAAAATT-ATATTAAAAT
1 AATATATAAAAAATTAAAATTAAAAT
3462653 AATATATAAAAAATTAAAATTAAAAT
1 AATATATAAAAAATTAAAATTAAAAT
3462679 TAAAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AATATATAAAAAATTAAAATTAAAAT
Found at i:3465178 original size:373 final size:372
Alignment explanation
Indices: 3464395--3465326 Score: 1207
Period size: 372 Copynumber: 2.5 Consensus size: 372
3464385 CAGGTGCTAT
* * * *
3464395 TGTCACGGACCTAAGGAAGAGTCTTGAATCTCACATCGAATATAATAAGAGGGTCATTGGGGTAT
1 TGTCACGGACCTAAGGAAGAGTCCTGAATCTCACATCGAACATAATAGGAGGGTCCTTGGGGTAT
* * * * * * *
3464460 ATAAA-GGTTCACACCACTTCCGT-CTTATGAGGTGTCTTTTGTAGGATAAAACCGTGAGGTCAA
66 AAAAAGGGTTCACACCACCT-CTTCCTTGTGAGGCGTTTTTTGTAGGATAAAACCGTGAGG-CCA
* * * * *
3464523 GAGGGGCTAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGTAGGTAGACTGATCTAGGACA
129 GGGGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCATGGTACGTAGACTGATCCAGGACA
* * * *
3464588 TCGGAATGGTGAATGCCCAGGTCCCGGAGCCGTGCAGGTTCAGAGCTTAAGTCTCGACCCGTGAC
194 CCGAAATGGTGAATGCCCAGGTCCCGAAGCCGCGCAGGTTCAGAGCTTAAGTCTCGACCCGTGAC
* * * *
3464653 AAGTGGTATCAGAGCCAACCCTAAACCGTTCGATCCACGCCAAGCACCTCGAGAGAGGTAAGTAG
259 AAGTGGTATCAGAGCCAACCCTAAACCGTTCAATCCACGCCAAGCACCTCAAGAGAGGCAAGCAG
* * *
3464718 GGTGGCTAGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGGGAGAA
324 GGTGGCTAGCCTCCGTAACGAGGACGTCACGAGGTTGAGTGCGGGAGAA
* *
3464767 TATCACGGACCTAAGGAAGAGTCCTGAATCTCACATCGAACATAATAGGAGGTTCCTTGGGGTAT
1 TGTCACGGACCTAAGGAAGAGTCCTGAATCTCACATCGAACATAATAGGAGGGTCCTTGGGGTAT
*
3464832 AAAAAGGGTTCACACCACCTCTTCCTTGTGAGGCGTTTTTTGTAGGATAAAATCGTGAGGCCAGG
66 AAAAAGGGTTCACACCACCTCTTCCTTGTGAGGCGTTTTTTGTAGGATAAAACCGTGAGGCCAGG
* * *
3464897 GGGAGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCATGG-CCGTCAGGCTGATCCGGGACA
131 GGG-GCCAGAGCGGACAATACCTCACAAGGGTGTGAACCATGGTACGT-AGACTGATCCAGGACA
* *
3464961 CCGAAATGGTGAATGCCCAGGTTCC-AAGTCGCGC-GAGTTCAGAGCTTAAGTCTCGACCCGTGA
194 CCGAAATGGTGAATGCCCAGGTCCCGAAGCCGCGCAG-GTTCAGAGCTTAAGTCTCGACCCGTGA
* * * *
3465024 CAAGTGGTATCAGAGTCAGCCCTAAACCGTTCAATCCACGCCAAGCACCTCAAGGGAGGCAGGCA
258 CAAGTGGTATCAGAGCCAACCCTAAACCGTTCAATCCACGCCAAGCACCTCAAGAGAGGCAAGCA
* * *
3465089 GGGTGG-TCAGCTTCTGTAACGAGGACGTCACGAGGTTGAGTGTGGGAGAAA
323 GGGTGGCT-AGCCTCCGTAACGAGGACGTCACGAGGTTGAGTGCGGGAG-AA
* * *
3465140 TGTCACGGACCTAAGAAAGAGTCCTGAATCTCACATCGAACAAAATAGGAGGGTCAC-TGGAGTA
1 TGTCACGGACCTAAGGAAGAGTCCTGAATCTCACATCGAACATAATAGGAGGGTC-CTTGGGGTA
* * * *
3465204 T-ATAAGGGTTCACACCACCT-TCGCCTTGTGAGACATTTTTTGTAGGATAAAACCGTGAGGCCA
65 TAAAAAGGGTTCACACCACCTCT-TCCTTGTGAGGCGTTTTTTGTAGGATAAAACCGTGAGGCCA
* * * ** *
3465267 GGAGGGGATCAGAGCGGATAATACCTCACAAGAGTGTGAACCATGACAGGTAGACTGATC
129 GG-GGGG-CCAGAGCGGACAATACCTCACAAGGGTGTGAACCATGGTACGTAGACTGATC
3465327 TGGGACGTCA
Statistics
Matches: 489, Mismatches: 59, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
371 3 0.01
372 261 0.53
373 222 0.45
374 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (372 bp):
TGTCACGGACCTAAGGAAGAGTCCTGAATCTCACATCGAACATAATAGGAGGGTCCTTGGGGTAT
AAAAAGGGTTCACACCACCTCTTCCTTGTGAGGCGTTTTTTGTAGGATAAAACCGTGAGGCCAGG
GGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCATGGTACGTAGACTGATCCAGGACACC
GAAATGGTGAATGCCCAGGTCCCGAAGCCGCGCAGGTTCAGAGCTTAAGTCTCGACCCGTGACAA
GTGGTATCAGAGCCAACCCTAAACCGTTCAATCCACGCCAAGCACCTCAAGAGAGGCAAGCAGGG
TGGCTAGCCTCCGTAACGAGGACGTCACGAGGTTGAGTGCGGGAGAA
Found at i:3466182 original size:13 final size:13
Alignment explanation
Indices: 3466164--3466188 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3466154 GATTAATAAT
3466164 TTTTTAATTTTTA
1 TTTTTAATTTTTA
3466177 TTTTTAATTTTT
1 TTTTTAATTTTT
3466189 CCACTCTCGC
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTAATTTTTA
Found at i:3472776 original size:19 final size:20
Alignment explanation
Indices: 3472739--3472780 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
3472729 AAATTTTTTT
3472739 ATTAAAATTGATTAAATAAAA
1 ATTAAAATTGA-TAAATAAAA
3472760 ATTAAAATTGA-AAATAAAA
1 ATTAAAATTGATAAATAAAA
3472779 AT
1 AT
3472781 AATAGATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
ATTAAAATTGATAAATAAAA
Found at i:3484466 original size:61 final size:62
Alignment explanation
Indices: 3484371--3484497 Score: 238
Period size: 61 Copynumber: 2.1 Consensus size: 62
3484361 ACTATGCTGA
3484371 ATGGCAGTTGTCAGATGAATTGAACTACTTTAACCTAGACTTCAGCTCACATGTCATCAA-T
1 ATGGCAGTTGTCAGATGAATTGAACTACTTTAACCTAGACTTCAGCTCACATGTCATCAACT
*
3484432 ATGGCAGTTGTCAGATGAATTGAATTACTTTAACCTAGACTTCAGCTCACATGTCATCAACT
1 ATGGCAGTTGTCAGATGAATTGAACTACTTTAACCTAGACTTCAGCTCACATGTCATCAACT
3484494 ATGG
1 ATGG
3484498 ACCATGGAGT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
61 59 0.92
62 5 0.08
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (62 bp):
ATGGCAGTTGTCAGATGAATTGAACTACTTTAACCTAGACTTCAGCTCACATGTCATCAACT
Found at i:3488838 original size:14 final size:15
Alignment explanation
Indices: 3488812--3488849 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3488802 CCCGTAAGTT
*
3488812 TTTAATATTTATTTA
1 TTTAATTTTTATTTA
*
3488827 TTT-ATTTTTATTTG
1 TTTAATTTTTATTTA
3488841 TTTAATTTT
1 TTTAATTTT
3488850 CCGGATGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTAATTTTTATTTA
Found at i:3497176 original size:3 final size:3
Alignment explanation
Indices: 3497168--3497239 Score: 58
Period size: 3 Copynumber: 24.0 Consensus size: 3
3497158 AAGAAAACCT
* * * * *
3497168 TGA TGA TGA TGA GGA TGA GGA -GA TGTC TGGA -GA TGA TGG GGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TG-A T-GA TGA TGA TGA TGA TGA
*
3497213 AGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA
3497240 GGACCATAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
2 4 0.07
3 48 0.89
4 1 0.02
5 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.40, T:0.26
Consensus pattern (3 bp):
TGA
Found at i:3503088 original size:85 final size:85
Alignment explanation
Indices: 3502978--3503136 Score: 309
Period size: 85 Copynumber: 1.9 Consensus size: 85
3502968 AAGCTCACCC
*
3502978 TAAAGGTTAATTATTGAATGTTTGAACTAAGATTCAGGTAGCATAAATGAGGTTTTAGTATGTAG
1 TAAAGGTTAATTATTGAATGCTTGAACTAAGATTCAGGTAGCATAAATGAGGTTTTAGTATGTAG
3503043 AGATATAGCCGAGCTCTATA
66 AGATATAGCCGAGCTCTATA
3503063 TAAAGGTTAATTATTGAATGCTTGAACTAAGATTCAGGTAGCATAAATGAGGTTTTAGTATGTAG
1 TAAAGGTTAATTATTGAATGCTTGAACTAAGATTCAGGTAGCATAAATGAGGTTTTAGTATGTAG
3503128 AGATATAGC
66 AGATATAGC
3503137 AGAAAACTTT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.34
Consensus pattern (85 bp):
TAAAGGTTAATTATTGAATGCTTGAACTAAGATTCAGGTAGCATAAATGAGGTTTTAGTATGTAG
AGATATAGCCGAGCTCTATA
Found at i:3507246 original size:115 final size:115
Alignment explanation
Indices: 3507041--3507253 Score: 282
Period size: 115 Copynumber: 1.9 Consensus size: 115
3507031 ATTCAGGCAC
* * **
3507041 TTGAGACGCAAAGCATTAATTAAAGCGCGTCTGCTCGAAAACCGTGGTAATGTTTATACTTGCTC
1 TTGAGAAGCAAAGCATCAATTAAAGCGCGTCTGCTCGAAAACCGTGGTAATGTTTATACTCACTC
3507106 CTTAAGGAAAGGAAGCGAATCCACCAAAAACACCATTCCGGCGTTCTCAT
66 CTTAAGGAAAGGAAGCGAATCCACCAAAAACACCATTCCGGCGTTCTCAT
* ** * * * * *
3507156 TTGAGAAGCGAAGCATCAATTGGAGCGCGTCTGCTCGAAAACCGTTGTAATTTTTGTAGTCACTG
1 TTGAGAAGCAAAGCATCAATTAAAGCGCGTCTGCTCGAAAACCGTGGTAATGTTTATACTCACTC
* * * *
3507221 CTTAGGGGACGGAAGCGAATGCACCAAAAACAC
66 CTTAAGGAAAGGAAGCGAATCCACCAAAAACAC
3507254 ATGTTACTTT
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
115 82 1.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (115 bp):
TTGAGAAGCAAAGCATCAATTAAAGCGCGTCTGCTCGAAAACCGTGGTAATGTTTATACTCACTC
CTTAAGGAAAGGAAGCGAATCCACCAAAAACACCATTCCGGCGTTCTCAT
Found at i:3509053 original size:16 final size:16
Alignment explanation
Indices: 3509032--3509066 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3509022 CGTTCAATGT
*
3509032 TAATACTAATAGCTTA
1 TAATACTAATAGCCTA
3509048 TAATACTAATAGCCTA
1 TAATACTAATAGCCTA
3509064 TAA
1 TAA
3509067 GCAATTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (16 bp):
TAATACTAATAGCCTA
Found at i:3511336 original size:126 final size:126
Alignment explanation
Indices: 3511111--3511361 Score: 439
Period size: 126 Copynumber: 2.0 Consensus size: 126
3511101 ACTAGTGAAA
*
3511111 ATCCTATCTCTGTCAGAAACAATGATATTAGGTATTCCATGCAACTTGTACACATTATCTAGATA
1 ATCCTATCTCTATCAGAAACAATGATATTAGGTATTCCATGCAACTTGTACACATTATCTAGATA
* * * *
3511176 TGCTTGAGTAATTGTAATGGCAGTGAAAGAATGAGCCTAAGTGATAAAATGGGCATATTTT
66 GGCTTGAGCAACTGTAATGGCAATGAAAGAATGAGCCTAAGTGATAAAATGGGCATATTTT
*
3511237 ATCCTATCTCTATCAGAAACAATGGTATTAGGTATTCCATGCAACTTGTACACATTATCTAGATA
1 ATCCTATCTCTATCAGAAACAATGATATTAGGTATTCCATGCAACTTGTACACATTATCTAGATA
*
3511302 GGCTTGAGCAACTGTAATGGCAATGAAATAATGAGCCTAAGTGATAAAATGGGCATATTT
66 GGCTTGAGCAACTGTAATGGCAATGAAAGAATGAGCCTAAGTGATAAAATGGGCATATTT
3511362 ACTTAACCTA
Statistics
Matches: 118, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 118 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (126 bp):
ATCCTATCTCTATCAGAAACAATGATATTAGGTATTCCATGCAACTTGTACACATTATCTAGATA
GGCTTGAGCAACTGTAATGGCAATGAAAGAATGAGCCTAAGTGATAAAATGGGCATATTTT
Found at i:3514149 original size:277 final size:277
Alignment explanation
Indices: 3513655--3514209 Score: 1031
Period size: 277 Copynumber: 2.0 Consensus size: 277
3513645 CCAAGAATAT
3513655 TACTGATTGGTTCTTGATTCGACCATATAATCTCATGGTCATATGACTTTCAACTCCAATTAAAG
1 TACTGATTGGTTCTTGATTCGACCATATAATCTCATGGTCATATGACTTTCAACTCCAATTAAAG
* *
3513720 CATGTAAGGAGATGACATGCATGTTCTGTAATTCATGGTCTTCCTTTTTAATCTTCTCTAAATTG
66 CATGTAAGGAGATGACATGCATGTTCTGTAATTCATGGTCTTCCTTCTTAATCTTCTCCAAATTG
*
3513785 TTTACACAATCACAAAACTCTTCAATATCATTATTATTGTTTTCCCTTTCCTCAGTAAACATCTG
131 TTTACACAATCACAAAACTCTTCAATATCATTATTATTGTCTTCCCTTTCCTCAGTAAACATCTG
3513850 GTACAATTGAGCCTTGACACACCTATGACCTGATGTAAACTTAATCCAACACCACATACAAAGTC
196 GTACAATTGAGCCTTGACACACCTATGACCTGATGTAAACTTAATCCAACACCACATACAAAGTC
3513915 CTTTCTTCCTCTTGTCA
261 CTTTCTTCCTCTTGTCA
*
3513932 TACTGATTGGTTCTTGATTCGACCATATAATCTCATGGTCATATGAGTTTCAACTCCAATTAAAG
1 TACTGATTGGTTCTTGATTCGACCATATAATCTCATGGTCATATGACTTTCAACTCCAATTAAAG
*
3513997 CATGTAAAGGAGATGACATGCTTGTTCTGTAATTCATGGTCTTCC-TCTTAATCTTCTCCAAATT
66 CATGT-AAGGAGATGACATGCATGTTCTGTAATTCATGGTCTTCCTTCTTAATCTTCTCCAAATT
*
3514061 GTTTACACAATCACAGAACTCTTCAATATCATTATTATTGTCTTCCCTTTCCTCAGTAAACATCT
130 GTTTACACAATCACAAAACTCTTCAATATCATTATTATTGTCTTCCCTTTCCTCAGTAAACATCT
*
3514126 GGTACAATTGAGCCTTGACACACCTATGACCTGGTGTAAACTTAATCCAACACCACATACAAAGT
195 GGTACAATTGAGCCTTGACACACCTATGACCTGATGTAAACTTAATCCAACACCACATACAAAGT
3514191 CCTTTCTTCCTCTTGTCA
260 CCTTTCTTCCTCTTGTCA
3514209 T
1 T
3514210 TTGTTTCCTC
Statistics
Matches: 270, Mismatches: 7, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
277 232 0.86
278 38 0.14
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (277 bp):
TACTGATTGGTTCTTGATTCGACCATATAATCTCATGGTCATATGACTTTCAACTCCAATTAAAG
CATGTAAGGAGATGACATGCATGTTCTGTAATTCATGGTCTTCCTTCTTAATCTTCTCCAAATTG
TTTACACAATCACAAAACTCTTCAATATCATTATTATTGTCTTCCCTTTCCTCAGTAAACATCTG
GTACAATTGAGCCTTGACACACCTATGACCTGATGTAAACTTAATCCAACACCACATACAAAGTC
CTTTCTTCCTCTTGTCA
Found at i:3527194 original size:99 final size:99
Alignment explanation
Indices: 3527010--3527209 Score: 301
Period size: 99 Copynumber: 2.0 Consensus size: 99
3527000 AAACCTCTTT
* * *
3527010 TAAACAAAGTTAAAAATTCCCTTTGAAAAGAATGAAGTCTATCTGGTTTAAATGATCCGAATTTG
1 TAAAAAAAGTTAAAAATCCCCTTTGAAAAGAATGAAGGCTATCTGGTTTAAATGATCCGAATTTG
* * *
3527075 TTTCAGTACGTAATATTTTATTATTATTTCCTGC
66 TTTCAGTACATAATAATTTATTATCATTTCCTGC
* * *
3527109 TAAAAAAAGTTAAAAATCCCCTTTGAAAAGCATGAAGGCTATCTGTTTTAAATGATCTGAATTTG
1 TAAAAAAAGTTAAAAATCCCCTTTGAAAAGAATGAAGGCTATCTGGTTTAAATGATCCGAATTTG
* *
3527174 TTTCAGTACATATTAATTTATTATCGTTTCCTGC
66 TTTCAGTACATAATAATTTATTATCATTTCCTGC
3527208 TA
1 TA
3527210 TTTGTTCCAG
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 90 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (99 bp):
TAAAAAAAGTTAAAAATCCCCTTTGAAAAGAATGAAGGCTATCTGGTTTAAATGATCCGAATTTG
TTTCAGTACATAATAATTTATTATCATTTCCTGC
Found at i:3539343 original size:45 final size:45
Alignment explanation
Indices: 3539293--3539383 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
3539283 TTTTCTACCA
*
3539293 GAACCAATTTCTGAAGT-TTTTTCTCAGCTGGTTATACCCATATGG
1 GAACCAATTTCTAAAGTGTTTTTCT-AGCTGGTTATACCCATATGG
*
3539338 GAACCAATTTCTAAAGTGTTTTTGTAGCTGGTTATACCCATATGG
1 GAACCAATTTCTAAAGTGTTTTTCTAGCTGGTTATACCCATATGG
3539383 G
1 G
3539384 GTATCAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 37 0.86
46 6 0.14
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (45 bp):
GAACCAATTTCTAAAGTGTTTTTCTAGCTGGTTATACCCATATGG
Found at i:3545462 original size:2 final size:2
Alignment explanation
Indices: 3545455--3545496 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3545445 GTGAAAGTTC
3545455 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3545497 GTGTGTGATC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3551120 original size:157 final size:157
Alignment explanation
Indices: 3550867--3551184 Score: 636
Period size: 157 Copynumber: 2.0 Consensus size: 157
3550857 AGATTTGCAG
3550867 GGGCGTGAACTCGTGTTCCCTTAGAGAGACTCAAATGGGAAATTCTTTCTTTCTCATTTTTATTT
1 GGGCGTGAACTCGTGTTCCCTTAGAGAGACTCAAATGGGAAATTCTTTCTTTCTCATTTTTATTT
3550932 TAATTTTATTTTTGATGGAAAGAGAACGTGGGGAATTACTATTTCAATATATATAATAAGAAAAA
66 TAATTTTATTTTTGATGGAAAGAGAACGTGGGGAATTACTATTTCAATATATATAATAAGAAAAA
3550997 AATAACTGAAAAATAAGAAAAGAGAAA
131 AATAACTGAAAAATAAGAAAAGAGAAA
3551024 GGGCGTGAACTCGTGTTCCCTTAGAGAGACTCAAATGGGAAATTCTTTCTTTCTCATTTTTATTT
1 GGGCGTGAACTCGTGTTCCCTTAGAGAGACTCAAATGGGAAATTCTTTCTTTCTCATTTTTATTT
3551089 TAATTTTATTTTTGATGGAAAGAGAACGTGGGGAATTACTATTTCAATATATATAATAAGAAAAA
66 TAATTTTATTTTTGATGGAAAGAGAACGTGGGGAATTACTATTTCAATATATATAATAAGAAAAA
3551154 AATAACTGAAAAATAAGAAAAGAGAAA
131 AATAACTGAAAAATAAGAAAAGAGAAA
3551181 GGGC
1 GGGC
3551185 ATTGTGGGTA
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 161 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (157 bp):
GGGCGTGAACTCGTGTTCCCTTAGAGAGACTCAAATGGGAAATTCTTTCTTTCTCATTTTTATTT
TAATTTTATTTTTGATGGAAAGAGAACGTGGGGAATTACTATTTCAATATATATAATAAGAAAAA
AATAACTGAAAAATAAGAAAAGAGAAA
Found at i:3557512 original size:20 final size:20
Alignment explanation
Indices: 3557487--3557526 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
3557477 TAATTTTTGT
3557487 TTATAA-ATTTGTAAATAAAC
1 TTATAATATTT-TAAATAAAC
3557507 TTATAATTATTTTAAATAAA
1 TTATAA-TATTTTAAATAAA
3557527 TTGTGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
TTATAATATTTTAAATAAAC
Found at i:3557697 original size:32 final size:33
Alignment explanation
Indices: 3557641--3557705 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
3557631 TATTTCTTCG
3557641 TTAGATAAAGATGATATTAATTAGATGAAATTTT
1 TTAGATAAAGATGA-ATTAATTAGATGAAATTTT
3557675 TTAGATAAAGATG-ATTAATTAGATGAAATTT
1 TTAGATAAAGATGAATTAATTAGATGAAATTT
3557706 GTCGAAAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 18 0.58
34 13 0.42
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (33 bp):
TTAGATAAAGATGAATTAATTAGATGAAATTTT
Found at i:3559831 original size:2 final size:2
Alignment explanation
Indices: 3559826--3559857 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3559816 CTCTCTGGCA
3559826 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
3559858 GCAATTTTAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3560119 original size:22 final size:22
Alignment explanation
Indices: 3560093--3560135 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3560083 TGTATATTTA
*
3560093 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
3560115 TATTTGTATCCCTAGAATTAA
1 TATTTGTATCCCTAGAATTAA
3560136 AGACAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:3561636 original size:41 final size:41
Alignment explanation
Indices: 3561583--3561666 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
3561573 CCACAAAAAC
3561583 AATATGCTAAACTTGGAAGACTTCACTAGGAAATTTTCAAA
1 AATATGCTAAACTTGGAAGACTTCACTAGGAAATTTTCAAA
3561624 AATATGCTAAACTTGGAAGACTTCACTAGGAAATTTTCAAA
1 AATATGCTAAACTTGGAAGACTTCACTAGGAAATTTTCAAA
3561665 AA
1 AA
3561667 GGTTTCAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (41 bp):
AATATGCTAAACTTGGAAGACTTCACTAGGAAATTTTCAAA
Found at i:3562873 original size:2 final size:2
Alignment explanation
Indices: 3562866--3562897 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3562856 GTATACAAGG
3562866 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
3562898 TGTAGCCAAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3564633 original size:122 final size:122
Alignment explanation
Indices: 3564416--3564660 Score: 472
Period size: 122 Copynumber: 2.0 Consensus size: 122
3564406 ATGAGAAAGG
3564416 AATATTATTCATAAGACAGGATTTTAACCATATTTAATGCATTCATACCTATGACCAGTATACAA
1 AATATTATTCATAAGACAGGATTTTAACCATATTTAATGCATTCATACCTATGACCAGTATACAA
*
3564481 TTATCAGACTTTGTATGACTACTGCAATGACTTTTACAACCTTTGTCTTTTGTTGGT
66 TTATCAGACTTTGTATGACTACTGCAATGACTTTGACAACCTTTGTCTTTTGTTGGT
*
3564538 AATATTATTCATAAGACAGGATTTTAACCATATTTAATGCATTCATACCTATGACCGGTATACAA
1 AATATTATTCATAAGACAGGATTTTAACCATATTTAATGCATTCATACCTATGACCAGTATACAA
3564603 TTATCAGACTTTGTATGACTACTGCAATGACTTTGACAACCTTTGTCTTTTGTTGGT
66 TTATCAGACTTTGTATGACTACTGCAATGACTTTGACAACCTTTGTCTTTTGTTGGT
3564660 A
1 A
3564661 GAATCATGTG
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 121 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (122 bp):
AATATTATTCATAAGACAGGATTTTAACCATATTTAATGCATTCATACCTATGACCAGTATACAA
TTATCAGACTTTGTATGACTACTGCAATGACTTTGACAACCTTTGTCTTTTGTTGGT
Found at i:3566996 original size:10 final size:10
Alignment explanation
Indices: 3566981--3567010 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3566971 TGAGCCTATT
3566981 AAAGAAGCTA
1 AAAGAAGCTA
3566991 AAAGAAGCT-
1 AAAGAAGCTA
3567000 AAAGAAGCTA
1 AAAGAAGCTA
3567010 A
1 A
3567011 GGACCAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.60, C:0.10, G:0.20, T:0.10
Consensus pattern (10 bp):
AAAGAAGCTA
Found at i:3567003 original size:9 final size:9
Alignment explanation
Indices: 3566980--3567010 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
3566970 ATGAGCCTAT
3566980 TAAAGAAGC
1 TAAAGAAGC
3566989 TAAAAGAAGC
1 T-AAAGAAGC
3566999 TAAAGAAGC
1 TAAAGAAGC
3567008 TAA
1 TAA
3567011 GGACCAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.58, C:0.10, G:0.19, T:0.13
Consensus pattern (9 bp):
TAAAGAAGC
Found at i:3569211 original size:22 final size:22
Alignment explanation
Indices: 3569185--3569228 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3569175 TGTATATTTA
*
3569185 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
3569207 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
3569229 GAAGATTTAG
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:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:3569632 original size:18 final size:18
Alignment explanation
Indices: 3569609--3569651 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
3569599 ATGTTCTTTG
3569609 GGTAAAGTTTCTAGTTCA
1 GGTAAAGTTTCTAGTTCA
*
3569627 GGTAAAGTTTCTAGTTTA
1 GGTAAAGTTTCTAGTTCA
3569645 GGTAAAG
1 GGTAAAG
3569652 CTTCCGGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (18 bp):
GGTAAAGTTTCTAGTTCA
Found at i:3573103 original size:22 final size:22
Alignment explanation
Indices: 3573077--3573120 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3573067 TGTATATTTA
*
3573077 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
3573099 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
3573121 GAAGATTTAG
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:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:3587316 original size:22 final size:22
Alignment explanation
Indices: 3587291--3587334 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3587281 TATATATTTA
*
3587291 TATTTATATCTCTAGAATTAAG
1 TATTTATATCCCTAGAATTAAG
*
3587313 TATTTGTATCCCTAGAATTAAG
1 TATTTATATCCCTAGAATTAAG
3587335 GACAGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TATTTATATCCCTAGAATTAAG
Found at i:3587525 original size:24 final size:24
Alignment explanation
Indices: 3587477--3587525 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
3587467 ATATACATTT
3587477 AGTTTTACTCTTAATTTTTCACAC
1 AGTTTTACTCTTAATTTTTCACAC
* *
3587501 AGTTTTATTTCTTAGTTTTTC-CAC
1 AGTTTTA-CTCTTAATTTTTCACAC
3587525 A
1 A
3587526 AAATGTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.53
Consensus pattern (24 bp):
AGTTTTACTCTTAATTTTTCACAC
Found at i:3591813 original size:15 final size:15
Alignment explanation
Indices: 3591789--3591838 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3591779 AAATAAAACA
*
3591789 TTAAAATATTTAAAT
1 TTAAATTATTTAAAT
3591804 TTAAATTATTT-AA-
1 TTAAATTATTTAAAT
*
3591817 TAATAATTAATTTAAAT
1 TTA-AATT-ATTTAAAT
3591834 TTAAA
1 TTAAA
3591839 ATTTATTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 2 0.07
14 6 0.21
15 14 0.50
16 4 0.14
17 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAAATTATTTAAAT
Found at i:3594669 original size:2 final size:2
Alignment explanation
Indices: 3594662--3594689 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3594652 CATAAACTGT
3594662 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
3594690 AATGAGATCG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3597162 original size:15 final size:14
Alignment explanation
Indices: 3597133--3597192 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
3597123 TTAAATTAAT
3597133 TTTAAAT-TT-AAA
1 TTTAAATATTCAAA
*
3597145 TTTAAATGTATCAAA
1 TTTAAATAT-TCAAA
*
3597160 TTTGAAATATTTAAA
1 TTT-AAATATTCAAA
3597175 TTTAAAATAATTCAAA
1 TTT-AAAT-ATTCAAA
3597191 TT
1 TT
3597193 CAAAACTATC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 7 0.18
13 1 0.03
14 1 0.03
15 17 0.44
16 13 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (14 bp):
TTTAAATATTCAAA
Found at i:3597182 original size:7 final size:6
Alignment explanation
Indices: 3597096--3597180 Score: 57
Period size: 6 Copynumber: 13.3 Consensus size: 6
3597086 GAACTTGAAT
* * * *
3597096 AATTTAA AATTTT AATTCA AAATTA AA-TTA AA-TTA ATTTTA AATTTA
1 AATTT-A AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
3597143 AATTTA AATGTATCA AATTTGAA ATATTTA AATTTA AA
1 AATTTA AAT-T-T-A AATTT--A A-ATTTA AATTTA AA
3597181 ATAATTCAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
5 9 0.14
6 34 0.53
7 9 0.14
8 4 0.06
9 8 0.12
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:3604418 original size:91 final size:91
Alignment explanation
Indices: 3604291--3604473 Score: 314
Period size: 91 Copynumber: 2.0 Consensus size: 91
3604281 ACTTAAATAT
3604291 TCTGATGTAGAATGCAGTACTCTTATGCATATTTTGCTATCGT-TTGCCAACTAAGCTTGGTGAA
1 TCTGATGTAGAATGCAGTACTCTTATGCATATTTTGCTA-CGTCTTGCCAACTAAGCTTGGTGAA
3604355 TATCTTGATATCTTTTAGTTGTCCTAA
65 TATCTTGATATCTTTTAGTTGTCCTAA
* *
3604382 TCTGATGTAGAATGCAGTACTCTTATGCATTTTTTGCTACGTCTTGCCAATTAAGCTTGGTGAAT
1 TCTGATGTAGAATGCAGTACTCTTATGCATATTTTGCTACGTCTTGCCAACTAAGCTTGGTGAAT
* *
3604447 ATCTTGATGTCTTTTATTTGTCCTAA
66 ATCTTGATATCTTTTAGTTGTCCTAA
3604473 T
1 T
3604474 TGACGAGGGT
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
90 3 0.03
91 84 0.97
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.43
Consensus pattern (91 bp):
TCTGATGTAGAATGCAGTACTCTTATGCATATTTTGCTACGTCTTGCCAACTAAGCTTGGTGAAT
ATCTTGATATCTTTTAGTTGTCCTAA
Found at i:3608204 original size:22 final size:22
Alignment explanation
Indices: 3608161--3608205 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3608151 CTTCTTCAAG
* * *
3608161 AAATTCTCATGTTACTATAAAA
1 AAATTCTCATATCACTACAAAA
*
3608183 AAATTCTCATATCACTCCAAAA
1 AAATTCTCATATCACTACAAAA
3608205 A
1 A
3608206 TATGGGATGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATTCTCATATCACTACAAAA
Found at i:3614100 original size:19 final size:18
Alignment explanation
Indices: 3614070--3614123 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
3614060 TTCATGATCA
3614070 TATAAA-AATAAATATAT
1 TATAAATAATAAATATAT
*
3614087 TCATAAATAATAAATAAAT
1 T-ATAAATAATAAATATAT
*
3614106 TATAACTAAATAAATATA
1 TATAAAT-AATAAATATA
3614124 AATAAACCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 1 0.03
18 10 0.32
19 20 0.65
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
TATAAATAATAAATATAT
Found at i:3614256 original size:22 final size:22
Alignment explanation
Indices: 3614228--3614269 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3614218 TAGTATTATT
3614228 ATAAACGAACAATAAATAAACA
1 ATAAACGAACAATAAATAAACA
*
3614250 ATAAACGAATAATAAATAAA
1 ATAAACGAACAATAAATAAA
3614270 TAAAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.69, C:0.10, G:0.05, T:0.17
Consensus pattern (22 bp):
ATAAACGAACAATAAATAAACA
Found at i:3614280 original size:11 final size:11
Alignment explanation
Indices: 3614266--3614300 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3614256 GAATAATAAA
3614266 TAAATAAAATT
1 TAAATAAAATT
*
3614277 TAAATAAACTT
1 TAAATAAAATT
*
3614288 TAAATAAATTT
1 TAAATAAAATT
3614299 TA
1 TA
3614301 TATTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATAAAATT
Found at i:3614737 original size:3 final size:3
Alignment explanation
Indices: 3614729--3614779 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
3614719 TATCTAATTT
*
3614729 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3614777 ATA
1 ATA
3614780 TATGTTATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3615452 original size:13 final size:14
Alignment explanation
Indices: 3615434--3615479 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3615424 ACGAATTTTA
3615434 TATAATTT-TAAAT
1 TATAATTTATAAAT
*
3615447 TATAATTTATTAAT
1 TATAATTTATAAAT
*
3615461 TAT-ATTATAAAAAT
1 TATAATT-TATAAAT
3615475 TATAA
1 TATAA
3615480 ATGATATACT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 11 0.41
14 15 0.56
15 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATAATTTATAAAT
Found at i:3636383 original size:17 final size:17
Alignment explanation
Indices: 3636363--3636395 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3636353 ATATCAAAAT
3636363 AAAA-TAAAAATTAATTG
1 AAAATTAAAAA-TAATTG
3636380 AAAATTAAAAATAATT
1 AAAATTAAAAATAATT
3636396 TAAACAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AAAATTAAAAATAATTG
Found at i:3649329 original size:147 final size:147
Alignment explanation
Indices: 3649107--3649373 Score: 398
Period size: 147 Copynumber: 1.8 Consensus size: 147
3649097 CAATGGTCTC
* * *
3649107 CTTGTTTTGAACAACTTCAGAATCCTGATCCAATTGGTTCACAGCCATACCTGGATTTTGATGCG
1 CTTGTTTTCAACAACTTCAAAATCCTGATCCAAATGGTTCACAGCCATACCTGGATTTTGATGCG
* *
3649172 ACTGTACAGTTGAATTATCTTCAGAGGGAAGGTCATCACCAATCATTTTCACATCTTCGCCTATG
66 ACTGTACAGTTGAATTATCTTCAGAGGGAAGGGCATCACCAATCATTTGCACATCTTCGCCTATG
3649237 GAATCACCTCTAGCCTT
131 GAATCACCTCTAGCCTT
3649254 CTTGTTTTCAACCAA-TTCAAAATCCTGATCCAAATGGTTCAACA-CCATA-CTGGGATTTTGAT
1 CTTGTTTTCAA-CAACTTCAAAATCCTGATCCAAATGGTTC-ACAGCCATACCT-GGATTTTGAT
* * *
3649316 GTGAC-GATACAGTTGAATTATCTTCAGATGGAAGGGCATCACCGATCATTTGCACATC
63 GCGACTG-TACAGTTGAATTATCTTCAGAGGGAAGGGCATCACCAATCATTTGCACATC
3649374 ATCACCTCTA
Statistics
Matches: 108, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
146 3 0.03
147 99 0.92
148 6 0.06
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (147 bp):
CTTGTTTTCAACAACTTCAAAATCCTGATCCAAATGGTTCACAGCCATACCTGGATTTTGATGCG
ACTGTACAGTTGAATTATCTTCAGAGGGAAGGGCATCACCAATCATTTGCACATCTTCGCCTATG
GAATCACCTCTAGCCTT
Found at i:3649529 original size:132 final size:133
Alignment explanation
Indices: 3649239--3649537 Score: 372
Period size: 132 Copynumber: 2.3 Consensus size: 133
3649229 CGCCTATGGA
* * *
3649239 ATCACCTCTAGCCTTCTTGTTTTCAACCAATTCAAAATCCTGATCCAAATGGTTCAACACCATAC
1 ATCACCTCTAGCCTCCTTG-TTTCAACCAATTCAAAATCCAGATCCAAATGGTTCAACACCATAA
** ** *
3649304 TGGGATTTTGATGTGACGATACAGTTGAATTATCTTCAGATGGAAGGGCATCACCGATCATTTGC
65 TGGGATTTTGATGCAACGATACAACTGAATTATCTTCAGATGGAAGGG-ATCACCAATCATTTGC
3649369 ACATC
129 ACATC
* * * *
3649374 ATCACCTCTAGCCTCC-T-TTTCAACCAGTTCAGAATCCAGATCCAACTGGTTCAACATCATAAT
1 ATCACCTCTAGCCTCCTTGTTTCAACCAATTCAAAATCCAGATCCAAATGGTTCAACACCATAAT
* * **
3649437 GGGATTTTGATGCAATGATGCAACTGAATTATCTTGGGATGGAA-GG-TCACCAATCATTTGCAC
66 GGGATTTTGATGCAACGATACAACTGAATTATCTTCAGATGGAAGGGATCACCAATCATTTGCAC
3649500 ATC
131 ATC
* * *
3649503 ATCAACTCCAGCCTCCTTGTTCTCAACCATTTCAA
1 ATCACCTCTAGCCTCCTTGTT-TCAACCAATTCAA
3649538 CATTCGTTTC
Statistics
Matches: 141, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
129 33 0.23
130 1 0.01
131 4 0.03
132 87 0.62
134 1 0.01
135 15 0.11
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (133 bp):
ATCACCTCTAGCCTCCTTGTTTCAACCAATTCAAAATCCAGATCCAAATGGTTCAACACCATAAT
GGGATTTTGATGCAACGATACAACTGAATTATCTTCAGATGGAAGGGATCACCAATCATTTGCAC
ATC
Found at i:3658781 original size:18 final size:17
Alignment explanation
Indices: 3658748--3658782 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3658738 TTTTATTTCA
3658748 AAATTTAAATTCAAATT
1 AAATTTAAATTCAAATT
*
3658765 AAATTTATAATTGAAATT
1 AAATTTA-AATTCAAATT
3658783 CTAAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATTTAAATTCAAATT
Found at i:3660696 original size:2 final size:2
Alignment explanation
Indices: 3660689--3660717 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3660679 TATGTTCGAG
3660689 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3660718 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3666844 original size:16 final size:15
Alignment explanation
Indices: 3666817--3666864 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 15
3666807 TTTCCCCACA
3666817 TTTTTAAGTTTTATTT
1 TTTTTAA-TTTTATTT
*
3666833 TTTTATAATTTTATTA
1 TTTT-TAATTTTATTT
3666849 TTTTTAATTATTATTT
1 TTTTTAATT-TTATTT
3666865 GCACACAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 5 0.18
16 20 0.71
17 3 0.11
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTTAATTTTATTT
Found at i:3666978 original size:26 final size:24
Alignment explanation
Indices: 3666922--3666980 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 24
3666912 AAAATTTGAG
3666922 TAAAATTTAAAAAAATTTCTCACT
1 TAAAATTTAAAAAAATTTCTCACT
*
3666946 TATAAATTTATTAAAAAATTTACT-ATT
1 TA-AAATTTA--AAAAAATTT-CTCACT
3666973 TAAAATTT
1 TAAAATTT
3666981 CTAAGAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 2 0.07
25 7 0.23
26 6 0.20
27 13 0.43
28 2 0.07
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAATTTAAAAAAATTTCTCACT
Found at i:3668347 original size:43 final size:43
Alignment explanation
Indices: 3668294--3668387 Score: 113
Period size: 43 Copynumber: 2.3 Consensus size: 43
3668284 GATTTAACAC
* *
3668294 TTTGAAAAATATAAAAACTCCTTTCAACAGAGGCTCAACAACT
1 TTTGAAAAATATAAAAACTCCTTTAAACAAAGGCTCAACAACT
* * * *
3668337 TTTGACAAATATATAAGCTTCTTTAAACAAAGGCT---CAACT
1 TTTGAAAAATATAAAAACTCCTTTAAACAAAGGCTCAACAACT
3668377 TTTGAAAAATA
1 TTTGAAAAATA
3668388 AATATGATCT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 15 0.34
43 29 0.66
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.30
Consensus pattern (43 bp):
TTTGAAAAATATAAAAACTCCTTTAAACAAAGGCTCAACAACT
Found at i:3668681 original size:17 final size:16
Alignment explanation
Indices: 3668661--3668708 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3668651 AAAAATTTAC
3668661 AAGACTTTCAAATTCGA
1 AAGA-TTTCAAATTCGA
* *
3668678 AAGAATTCAAATTCGT
1 AAGATTTCAAATTCGA
*
3668694 AATATTTTCAAATTC
1 AAGA-TTTCAAATTC
3668709 ATAGGATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (16 bp):
AAGATTTCAAATTCGA
Found at i:3669193 original size:109 final size:107
Alignment explanation
Indices: 3669009--3669300 Score: 401
Period size: 108 Copynumber: 2.7 Consensus size: 107
3668999 CAGAATTTCG
* *
3669009 TCCAAAATTTTAAAGCTTCTTATTCGAGTTCAAAGATTTACATTCGATAAATTTTAAGAGTTTCA
1 TCCAAAATTTCAAAGCTTCTTATTCGAGTTCAAA-ATTCACATT-GATAAATTTT-AGAGTTTCA
*
3669074 CATCTAAATTCAAAGGTTCTCATTCAAAAAATTTTAGAGGTTCACAT
63 CATCTAAATTCAAAGGTTCTCATTCAAAAAATTTAAGA-GTTCAC-T
*
3669121 T-CAAAATTTCAAA-CTTCTTATTCGAGTTCAAATATTCACATCTGATAGATTTTAGAGTTTCAC
1 TCCAAAATTTCAAAGCTTCTTATTCGAGTTCAAA-ATTCACAT-TGATAAATTTTAGAGTTTCAC
*
3669184 ATCTAAATTCAAAGGTTCTCATTCAAAAAATTTAAGAGTTTACT
64 ATCTAAATTCAAAGGTTCTCATTCAAAAAATTTAAGAGTTCACT
* * * *
3669228 TCCAAAATTTCAAAGTTTCTCATT-AAGTTTAAAATTTCACATTTGATAAATTTTAGAGTTTCAC
1 TCCAAAATTTCAAAGCTTCTTATTCGAGTTCAAAA-TTCACA-TTGATAAATTTTAGAGTTTCAC
3669292 ATCTAAATT
64 ATCTAAATT
3669301 TACATGTTCT
Statistics
Matches: 164, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
107 3 0.02
108 59 0.36
109 54 0.33
110 35 0.21
111 12 0.07
112 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (107 bp):
TCCAAAATTTCAAAGCTTCTTATTCGAGTTCAAAATTCACATTGATAAATTTTAGAGTTTCACAT
CTAAATTCAAAGGTTCTCATTCAAAAAATTTAAGAGTTCACT
Found at i:3669310 original size:108 final size:111
Alignment explanation
Indices: 3669009--3669300 Score: 409
Period size: 109 Copynumber: 2.7 Consensus size: 111
3668999 CAGAATTTCG
* * *
3669009 TCCAAAATTTTAAAGCTTCTTATTCGAGTTCAAAGATTT-ACATTCGATAAATTTTAAGAGTTTC
1 TCCAAAATTTCAAAGCTTCTTATTCGAGTTTAAA-ATTTCACATTTGATAAATTTT-AGAGTTTC
*
3669073 ACATCTAAATTCAAAGGTTCTCATTCAAAAAATTTTAGAGGTTCACAT
64 ACATCTAAATTCAAAGGTTCTCATTCAAAAAATTTAAGAGGTTCACAT
* * *
3669121 T-CAAAATTTCAAA-CTTCTTATTCGAG-TTCAAATATTCACATCTGATAGATTTTAGAGTTTCA
1 TCCAAAATTTCAAAGCTTCTTATTCGAGTTTAAAAT-TTCACATTTGATAAATTTTAGAGTTTCA
*
3669183 CATCTAAATTCAAAGGTTCTCATTCAAAAAATTTAAGA-GTTTAC-T
65 CATCTAAATTCAAAGGTTCTCATTCAAAAAATTTAAGAGGTTCACAT
* * *
3669228 TCCAAAATTTCAAAGTTTCTCATT-AAGTTTAAAATTTCACATTTGATAAATTTTAGAGTTTCAC
1 TCCAAAATTTCAAAGCTTCTTATTCGAGTTTAAAATTTCACATTTGATAAATTTTAGAGTTTCAC
3669292 ATCTAAATT
66 ATCTAAATT
3669301 TACATGTTCT
Statistics
Matches: 161, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
107 2 0.01
108 57 0.35
109 64 0.40
110 26 0.16
111 11 0.07
112 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (111 bp):
TCCAAAATTTCAAAGCTTCTTATTCGAGTTTAAAATTTCACATTTGATAAATTTTAGAGTTTCAC
ATCTAAATTCAAAGGTTCTCATTCAAAAAATTTAAGAGGTTCACAT
Found at i:3670552 original size:18 final size:18
Alignment explanation
Indices: 3670531--3670589 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
3670521 CAATTTAAGT
*
3670531 CTTTTTTTATGTTTTTCA
1 CTTTTTTTATATTTTTCA
*
3670549 C-TTTTTTATTTTTTTCA
1 CTTTTTTTATATTTTTCA
* *
3670566 -TATTTCTCATATTTTTCA
1 CT-TTTTTTATATTTTTCA
3670584 CTTTTT
1 CTTTTT
3670590 CAATTTCATT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
17 15 0.45
18 17 0.52
19 1 0.03
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.71
Consensus pattern (18 bp):
CTTTTTTTATATTTTTCA
Found at i:3670553 original size:17 final size:17
Alignment explanation
Indices: 3670533--3670589 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
3670523 ATTTAAGTCT
*
3670533 TTTTTTATGTTTTTCAC
1 TTTTTTATATTTTTCAC
*
3670550 TTTTTTATTTTTTTCA-
1 TTTTTTATATTTTTCAC
*
3670566 TATTTCTCATATTTTTCAC
1 T-TTT-TTATATTTTTCAC
3670585 TTTTT
1 TTTTT
3670590 CAATTTCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.03
17 19 0.56
18 13 0.38
19 1 0.03
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTTTATATTTTTCAC
Found at i:3670554 original size:9 final size:8
Alignment explanation
Indices: 3670532--3670628 Score: 51
Period size: 9 Copynumber: 11.8 Consensus size: 8
3670522 AATTTAAGTC
*
3670532 TTTTTTTA
1 TTTTTTCA
3670540 TGTTTTTCA
1 T-TTTTTCA
3670549 CTTTTTT-A
1 -TTTTTTCA
3670557 TTTTTTTCA
1 -TTTTTTCA
*
3670566 TATTTCTCA
1 T-TTTTTCA
3670575 TATTTTTCA
1 T-TTTTTCA
*
3670584 CTTTTTCA
1 TTTTTTCA
*
3670592 --ATTTCA
1 TTTTTTCA
3670598 TTTTTT--
1 TTTTTTCA
3670604 TTCATTTTCA
1 TT--TTTTCA
3670614 TTTTTTCA
1 TTTTTTCA
3670622 CTTTTTT
1 -TTTTTT
3670629 TCATCCATCA
Statistics
Matches: 71, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
6 7 0.10
8 29 0.41
9 32 0.45
10 3 0.04
ACGTcount: A:0.14, C:0.13, G:0.01, T:0.71
Consensus pattern (8 bp):
TTTTTTCA
Found at i:3670602 original size:14 final size:14
Alignment explanation
Indices: 3670579--3670621 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
3670569 TTCTCATATT
*
3670579 TTTCACTTTTTCAA
1 TTTCATTTTTTCAA
*
3670593 TTTCATTTTTTTTCAT
1 TTTCA--TTTTTTCAA
3670609 TTTCATTTTTTCA
1 TTTCATTTTTTCA
3670622 CTTTTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 13 0.52
16 12 0.48
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTCATTTTTTCAA
Found at i:3670604 original size:16 final size:16
Alignment explanation
Indices: 3670585--3670619 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3670575 TATTTTTCAC
3670585 TTTTTCAATTTCATTT
1 TTTTTCAATTTCATTT
*
3670601 TTTTTCATTTTCATTT
1 TTTTTCAATTTCATTT
3670617 TTT
1 TTT
3670620 CACTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTCAATTTCATTT
Found at i:3670639 original size:25 final size:24
Alignment explanation
Indices: 3670593--3670639 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3670583 ACTTTTTCAA
* **
3670593 TTTCATTTTTTTTCATTTTCATTT
1 TTTCACTTTTTTTCATCATCATTT
3670617 TTTCACTTTTTTTCATCCATCAT
1 TTTCACTTTTTTTCAT-CATCAT
3670640 AAATCTCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTCACTTTTTTTCATCATCATTT
Found at i:3677010 original size:2 final size:2
Alignment explanation
Indices: 3677003--3677037 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3676993 AGCTATACCT
3677003 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 T
3677038 GAATGAGTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3677211 original size:13 final size:14
Alignment explanation
Indices: 3677188--3677216 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3677178 TTTGGATACC
3677188 AAAAAACAAATTTG
1 AAAAAACAAATTTG
3677202 AAAAAA-AAATTTG
1 AAAAAACAAATTTG
3677215 AA
1 AA
3677217 GGAAACCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.21
Consensus pattern (14 bp):
AAAAAACAAATTTG
Found at i:3678909 original size:2 final size:2
Alignment explanation
Indices: 3678904--3678936 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3678894 GTGGGCGTGT
*
3678904 GA GA GA GA GT GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3678937 GGAGGAAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.03
Consensus pattern (2 bp):
GA
Found at i:3680528 original size:9 final size:9
Alignment explanation
Indices: 3680516--3680542 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3680506 TTAATTTTTG
3680516 AATCAAATT
1 AATCAAATT
3680525 AATCAAATT
1 AATCAAATT
3680534 AATCAAATT
1 AATCAAATT
3680543 TTAACAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (9 bp):
AATCAAATT
Found at i:3680823 original size:9 final size:9
Alignment explanation
Indices: 3680725--3680827 Score: 54
Period size: 9 Copynumber: 11.7 Consensus size: 9
3680715 TATTAATTGA
*
3680725 TTAATTAAA
1 TTAATTAAT
*
3680734 ATAATTAAT
1 TTAATTAAT
* *
3680743 TGAATAAAT
1 TTAATTAAT
3680752 TTAATTTAAT
1 TTAA-TTAAT
*
3680762 TTAATTGA-
1 TTAATTAAT
3680770 TTAATT--T
1 TTAATTAAT
*
3680777 TTAAATTTA-
1 TT-AATTAAT
*
3680786 TAAATTAAAT
1 TTAATT-AAT
*
3680796 TTGATTAA-
1 TTAATTAAT
* *
3680804 TAAAATAAT
1 TTAATTAAT
3680813 TTAATTAAT
1 TTAATTAAT
3680822 TTAATT
1 TTAATT
3680828 TTAAATAATT
Statistics
Matches: 69, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
7 2 0.03
8 19 0.28
9 36 0.52
10 12 0.17
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.50
Consensus pattern (9 bp):
TTAATTAAT
Found at i:3680836 original size:15 final size:15
Alignment explanation
Indices: 3680812--3680842 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3680802 AATAAAATAA
*
3680812 TTTAATTAATTTAAT
1 TTTAAATAATTTAAT
3680827 TTTAAATAATTTAAT
1 TTTAAATAATTTAAT
3680842 T
1 T
3680843 CAAAATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAATAATTTAAT
Found at i:3681513 original size:29 final size:30
Alignment explanation
Indices: 3681460--3681518 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
3681450 AAATATAAAA
* *
3681460 TATAATTTTTTAATTTTATTTAATC-TATT
1 TATAATTTTTTAAATTTATTAAATCATATT
3681489 TATAATTTTTTAAAATTT-TTAAATCATATT
1 TATAATTTTTT-AAATTTATTAAATCATATT
3681519 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (30 bp):
TATAATTTTTTAAATTTATTAAATCATATT
Found at i:3681530 original size:24 final size:24
Alignment explanation
Indices: 3681489--3681553 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
3681479 TTAATCTATT
*
3681489 TATAATTTTTTAAAATTTTTAAATCA
1 TATAA-TTTTT-ATATTTTTAAATCA
* * * *
3681515 TATTATTTTTATATTTTTTATTTA
1 TATAATTTTTATATTTTTAAATCA
3681539 TATAATTTTTATATT
1 TATAATTTTTATATT
3681554 GTATTTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 24 0.73
25 5 0.15
26 4 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
TATAATTTTTATATTTTTAAATCA
Found at i:3681533 original size:26 final size:25
Alignment explanation
Indices: 3681504--3681576 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 25
3681494 TTTTTTAAAA
3681504 TTTTTAAATCATATTATTTTTATAT-
1 TTTTTAAAT-ATATTATTTTTATATG
** *
3681529 TTTTTATTTATATAATTTTTATATTG
1 TTTTTAAATATATTATTTTTATA-TG
*
3681555 TATTTTAAA-ATATTATATTTAT
1 T-TTTTAAATATATTATTTTTAT
3681577 TAAAAAATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
24 13 0.34
25 8 0.21
26 12 0.32
27 5 0.13
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (25 bp):
TTTTTAAATATATTATTTTTATATG
Found at i:3681535 original size:15 final size:15
Alignment explanation
Indices: 3681517--3681550 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3681507 TTAAATCATA
* *
3681517 TTATTTTTATATTTT
1 TTATTTATATAATTT
3681532 TTATTTATATAATTT
1 TTATTTATATAATTT
3681547 TTAT
1 TTAT
3681551 ATTGTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTATATAATTT
Found at i:3681583 original size:19 final size:20
Alignment explanation
Indices: 3681547--3681585 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3681537 TATATAATTT
**
3681547 TTATATTGTATTTTAAAATA
1 TTATATTGTATTAAAAAATA
3681567 TTATATT-TATTAAAAAATA
1 TTATATTGTATTAAAAAATA
3681586 AGTTTGTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TTATATTGTATTAAAAAATA
Found at i:3682971 original size:29 final size:26
Alignment explanation
Indices: 3682929--3682998 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 26
3682919 ATAGAAAATG
*
3682929 AAATTAATTTTAATTAGATTAAAAAAATAA
1 AAATT-ATTATAATTA-ATT-AAAAAA-AA
* *
3682959 AAATTATTATAATTAATTTAATAAAA
1 AAATTATTATAATTAATTAAAAAAAA
*
3682985 AATTTATTATAATT
1 AAATTATTATAATT
3682999 TTGATTGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 15 0.42
27 4 0.11
28 3 0.08
29 9 0.25
30 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (26 bp):
AAATTATTATAATTAATTAAAAAAAA
Found at i:3683196 original size:23 final size:24
Alignment explanation
Indices: 3683170--3683219 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
3683160 TAATAATAAT
* *
3683170 ATTATTATAATTGTGA-TTAAAAA
1 ATTATTATAATTATAATTTAAAAA
3683193 ATTATTATAATTATAATTTAAAAA
1 ATTATTATAATTATAATTTAAAAA
3683217 ATT
1 ATT
3683220 TTAATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
ATTATTATAATTATAATTTAAAAA
Found at i:3688117 original size:24 final size:24
Alignment explanation
Indices: 3688096--3688141 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3688086 GATAAAATTT
* *
3688096 TATAATTTAAGTGATTATAAATAG
1 TATAAATTAAGTGATTACAAATAG
3688120 TATAAATTAAGTGATTACAAAT
1 TATAAATTAAGTGATTACAAAT
3688142 CACATATTTA
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:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (24 bp):
TATAAATTAAGTGATTACAAATAG
Found at i:3688592 original size:9 final size:9
Alignment explanation
Indices: 3688579--3688622 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
3688569 AGTATAATGT
3688579 AAAA-ATTA
1 AAAATATTA
3688587 ACAAA-ATTA
1 A-AAATATTA
3688596 AAAATATTA
1 AAAATATTA
3688605 AAAATATTA
1 AAAATATTA
3688614 AAAATATTA
1 AAAATATTA
3688623 TTTATAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
8 4 0.12
9 30 0.88
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAATATTA
Found at i:3695448 original size:6 final size:6
Alignment explanation
Indices: 3695437--3695468 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3695427 GTATGGCGAC
3695437 GTGACG GTGACG GTGACG GTGACG GTGACG GT
1 GTGACG GTGACG GTGACG GTGACG GTGACG GT
3695469 TTCTGCAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.50, T:0.19
Consensus pattern (6 bp):
GTGACG
Found at i:3696177 original size:12 final size:12
Alignment explanation
Indices: 3696153--3696186 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
3696143 TTTATATAAA
3696153 AATTAATTT-TTT
1 AATT-ATTTATTT
3696165 AATTATTTATTT
1 AATTATTTATTT
3696177 AATTATTTAT
1 AATTATTTAT
3696187 ATTTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
AATTATTTATTT
Found at i:3696180 original size:20 final size:20
Alignment explanation
Indices: 3696155--3696213 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
3696145 TATATAAAAA
*
3696155 TTAATTTTTTA-ATTATTTAT
1 TTAATTATTTATATT-TTTAT
3696175 TTAATTATTTATATTTTTATAT
1 TTAATTATTTATA-TTTT-TAT
*
3696197 TTTATATATTTATATTT
1 TTAAT-TATTTATATTT
3696214 AAAAAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 10 0.30
21 3 0.09
22 12 0.36
23 8 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTAATTATTTATATTTTTAT
Found at i:3696202 original size:15 final size:15
Alignment explanation
Indices: 3696182--3696213 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3696172 TATTTAATTA
*
3696182 TTTATATTTTTATAT
1 TTTATATATTTATAT
3696197 TTTATATATTTATAT
1 TTTATATATTTATAT
3696212 TT
1 TT
3696214 AAAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATATATTTATAT
Found at i:3697103 original size:26 final size:26
Alignment explanation
Indices: 3697050--3697099 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3697040 TTTGAAATTA
*
3697050 ATAAAATATTATTATTTAATATAAAT
1 ATAAAATATTATTAATTAATATAAAT
3697076 ATAAAA-ATTATATAATTAAT-TAAA
1 ATAAAATATTAT-TAATTAATATAAA
3697100 ATATTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
ATAAAATATTATTAATTAATATAAAT
Found at i:3698251 original size:12 final size:12
Alignment explanation
Indices: 3698236--3698278 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 12
3698226 ATTTTTAATA
3698236 TAAATATAAAAT
1 TAAATATAAAAT
3698248 TAAATATATATATAT
1 TAAATATA-A-A-AT
3698263 ATAAATATAAAAT
1 -TAAATATAAAAT
3698276 TAA
1 TAA
3698279 TTAATTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 11 0.41
13 3 0.11
14 2 0.07
15 3 0.11
16 8 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:3698593 original size:18 final size:19
Alignment explanation
Indices: 3698570--3698610 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
3698560 AACCAAATTA
3698570 TATATATATTTT-AATTTT
1 TATATATATTTTAAATTTT
3698588 TATATATATTTTAAATTTT
1 TATATATATTTTAAATTTT
3698607 TATA
1 TATA
3698611 AAATAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATATATTTTAAATTTT
Found at i:3699472 original size:31 final size:31
Alignment explanation
Indices: 3699437--3699499 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
3699427 TAATATGTTT
* *
3699437 TTTTTACAATGGCAAATATTTAATTTTTCCA
1 TTTTTACAATGGCAAATATGTAATTTTACCA
3699468 TTTTTACAATGGCAAATATGTAATTTTACCA
1 TTTTTACAATGGCAAATATGTAATTTTACCA
3699499 T
1 T
3699500 GCTTAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (31 bp):
TTTTTACAATGGCAAATATGTAATTTTACCA
Found at i:3701727 original size:34 final size:33
Alignment explanation
Indices: 3701677--3701741 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
3701667 AATATTTAAG
* *
3701677 TAAATTTTTTTTGAAAATGAATTTTTGATAAATT
1 TAAAATTTTCTTGAAAATGAATTTTT-ATAAATT
**
3701711 TAAAATTTTCTTGAAAATTTATTTTTATAAA
1 TAAAATTTTCTTGAAAATGAATTTTTATAAA
3701742 AAGTTATAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 5 0.19
34 22 0.81
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (33 bp):
TAAAATTTTCTTGAAAATGAATTTTTATAAATT
Found at i:3708178 original size:40 final size:40
Alignment explanation
Indices: 3708118--3708197 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
3708108 CTCCACGCAG
3708118 AGGGCAATCCTCACACCAATAGCCTCCAAACCTACTTCCT
1 AGGGCAATCCTCACACCAATAGCCTCCAAACCTACTTCCT
*
3708158 AGGGTAATCCTCACACCAATAGCCTCCAAACCTACTTCCT
1 AGGGCAATCCTCACACCAATAGCCTCCAAACCTACTTCCT
3708198 CTGTCTGCCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.30, C:0.39, G:0.10, T:0.21
Consensus pattern (40 bp):
AGGGCAATCCTCACACCAATAGCCTCCAAACCTACTTCCT
Found at i:3708293 original size:21 final size:21
Alignment explanation
Indices: 3708233--3708295 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
3708223 TGAATTAACA
3708233 ATAAAATTAAAAATAATAATAATG
1 ATAAAATTAAAAAT--T-ATAATG
* ** *
3708257 ATGAAATTAATTATTATAATT
1 ATAAAATTAAAAATTATAATG
3708278 ATAAAATTAAAAATTATA
1 ATAAAATTAAAAATTATA
3708296 TATATGTTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 20 0.62
22 1 0.03
24 11 0.34
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (21 bp):
ATAAAATTAAAAATTATAATG
Found at i:3712197 original size:2 final size:2
Alignment explanation
Indices: 3712190--3712224 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3712180 AGTTTCTTTA
3712190 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3712225 CGGTAGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3715511 original size:23 final size:22
Alignment explanation
Indices: 3715485--3715532 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3715475 TATTATTATC
*
3715485 TTTAAAAGATGATATTTAATAAT
1 TTTAAAAGATAATATTT-ATAAT
**
3715508 TTTAAAATTTAATATTTATAAT
1 TTTAAAAGATAATATTTATAAT
3715530 TTT
1 TTT
3715533 TTTATTAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTAAAAGATAATATTTATAAT
Found at i:3717938 original size:30 final size:30
Alignment explanation
Indices: 3717904--3718048 Score: 106
Period size: 30 Copynumber: 4.7 Consensus size: 30
3717894 TGAAAATAAG
3717904 ATAAAAATAATTTATAATTTTAATAGAATT
1 ATAAAAATAATTTATAATTTTAATAGAATT
3717934 ATAAAAATATATTT-TAATTTT--TA-AA-T
1 ATAAAAATA-ATTTATAATTTTAATAGAATT
* *** *
3717960 A-AATATAATAATTTAAAATACAAGACGTGAAAATAAT
1 ATAA-A-AATAATTTATAATTTTA-A--T-AGAAT--T
3717997 ATAAAAATAATTTATAATTTTAATAGAATT
1 ATAAAAATAATTTATAATTTTAATAGAATT
3718027 ATAAAAATATATTT-TAATTTTA
1 ATAAAAATA-ATTTATAATTTTA
3718049 TATCAAGATA
Statistics
Matches: 90, Mismatches: 9, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
25 2 0.02
26 7 0.08
27 9 0.10
28 2 0.02
30 34 0.38
31 8 0.09
32 5 0.06
33 2 0.02
34 2 0.02
35 1 0.01
36 13 0.14
37 3 0.03
38 2 0.02
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (30 bp):
ATAAAAATAATTTATAATTTTAATAGAATT
Found at i:3718022 original size:93 final size:93
Alignment explanation
Indices: 3717863--3718047 Score: 352
Period size: 93 Copynumber: 2.0 Consensus size: 93
3717853 CTCTCCTTGC
*
3717863 AAATAAATATAATAATTTAAAATGCAAGACGTGAAAATAAGATAAAAATAATTTATAATTTTAAT
1 AAATAAATATAATAATTTAAAATACAAGACGTGAAAATAAGATAAAAATAATTTATAATTTTAAT
3717928 AGAATTATAAAAATATATTTTAATTTTT
66 AGAATTATAAAAATATATTTTAATTTTT
*
3717956 AAATAAATATAATAATTTAAAATACAAGACGTGAAAATAATATAAAAATAATTTATAATTTTAAT
1 AAATAAATATAATAATTTAAAATACAAGACGTGAAAATAAGATAAAAATAATTTATAATTTTAAT
3718021 AGAATTATAAAAATATATTTTAATTTT
66 AGAATTATAAAAATATATTTTAATTTT
3718048 ATATCAAGAT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (93 bp):
AAATAAATATAATAATTTAAAATACAAGACGTGAAAATAAGATAAAAATAATTTATAATTTTAAT
AGAATTATAAAAATATATTTTAATTTTT
Found at i:3721421 original size:21 final size:22
Alignment explanation
Indices: 3721377--3721421 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
3721367 AATATATTAT
*
3721377 TTATTTTAATAAATATAATAAAA
1 TTATTTT-ATAAAAATAATAAAA
*
3721400 TTATTTT-TAAAAATAATTAAA
1 TTATTTTATAAAAATAATAAAA
3721421 T
1 T
3721422 ATCCTTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTATTTTATAAAAATAATAAAA
Found at i:3721598 original size:23 final size:25
Alignment explanation
Indices: 3721554--3721602 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
3721544 TAGTATAAAT
*
3721554 TTTTTTTAATCGTAAATTATAATAA
1 TTTTTTTAATCGTAAATCATAATAA
3721579 TTTTTTTAATC-T-AATCATAATAA
1 TTTTTTTAATCGTAAATCATAATAA
3721602 T
1 T
3721603 AATAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 11 0.48
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (25 bp):
TTTTTTTAATCGTAAATCATAATAA
Found at i:3721603 original size:26 final size:25
Alignment explanation
Indices: 3721554--3721605 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
3721544 TAGTATAAAT
*
3721554 TTTTTTTAATCGTAAATTATAATAA
1 TTTTTTTAATCGTAAATAATAATAA
3721579 TTTTTTTAATC-TAATCATAATAATAA
1 TTTTTTTAATCGTAA--ATAATAATAA
3721605 T
1 T
3721606 AATTATTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 3 0.12
25 11 0.46
26 10 0.42
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTTTTTAATCGTAAATAATAATAA
Found at i:3722566 original size:17 final size:17
Alignment explanation
Indices: 3722546--3722595 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
3722536 TTCATTATAT
3722546 TATTAATTTAATTTAAA
1 TATTAATTTAATTTAAA
*
3722563 TATTAATTTTA-TTAAA
1 TATTAATTTAATTTAAA
* *
3722579 -ATTCATTTAATATAAA
1 TATTAATTTAATTTAAA
3722595 T
1 T
3722596 TTTTTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 8 0.30
16 9 0.33
17 10 0.37
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAATTTAATTTAAA
Found at i:3722574 original size:26 final size:25
Alignment explanation
Indices: 3722545--3722610 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
3722535 GTTCATTATA
*
3722545 TTATTAATTTAATTTAAATATTAATT
1 TTATTAATTTAATTT-AATATAAATT
* *
3722571 TTATTAAAATTCATTTAATATAAATT
1 TTATT-AATTTAATTTAATATAAATT
*
3722597 TTTTTAATTATAAT
1 TTATTAATT-TAAT
3722611 CATAATTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 3 0.09
26 21 0.66
27 8 0.25
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATTAATTTAATTTAATATAAATT
Found at i:3726127 original size:25 final size:27
Alignment explanation
Indices: 3726093--3726155 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 27
3726083 ACTTTAAATA
*
3726093 TAAAATATATTTTTTAT-TA-A-AATTT
1 TAAATTATATTTTTT-TGTATACAATTT
3726118 TAAATTATATTTTTTTGTATACAATTT
1 TAAATTATATTTTTTTGTATACAATTT
3726145 TAATATTATAT
1 TAA-ATTATAT
3726156 CATAATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 1 0.03
25 16 0.48
26 1 0.03
27 8 0.24
28 7 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
TAAATTATATTTTTTTGTATACAATTT
Found at i:3730917 original size:27 final size:27
Alignment explanation
Indices: 3730879--3730932 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
3730869 TCGAACAAAC
*
3730879 AAAGCTAAAGGAATGATGCCATGATAA
1 AAAGCTAAAGGAATGACGCCATGATAA
*
3730906 AAAGCTGAAGGAATGACGCCATGATAA
1 AAAGCTAAAGGAATGACGCCATGATAA
3730933 GCGAAGGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.46, C:0.13, G:0.24, T:0.17
Consensus pattern (27 bp):
AAAGCTAAAGGAATGACGCCATGATAA
Done.