Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 18 of 32
Found at i:9486510 original size:24 final size:26
Alignment explanation
Indices: 9486472--9486533 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 26
9486462 GGCGCGGCCA
9486472 CGCGGC-CGCGCGGCCCCCCG-CGGC-
1 CGCGGCGCGCG-GGCCCCCCGCCGGCG
* *
9486496 CGCGGCGCGCGGGCCGCCGGCCGGCG
1 CGCGGCGCGCGGGCCCCCCGCCGGCG
*
9486522 CGGGGCGCGCGG
1 CGCGGCGCGCGG
9486534 CGCCGGCCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 13 0.41
25 8 0.25
26 11 0.34
ACGTcount: A:0.00, C:0.48, G:0.52, T:0.00
Consensus pattern (26 bp):
CGCGGCGCGCGGGCCCCCCGCCGGCG
Found at i:9486522 original size:19 final size:18
Alignment explanation
Indices: 9486498--9486546 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
9486488 CCCGCGGCCG
9486498 CGGCGCGCGGGCCGCCGGC
1 CGGCGCG-GGGCCGCCGGC
*
9486517 CGGCGCGGGGCGCGCGGCGC
1 CGGCGCGGGGC-CGCCG-GC
9486537 CGGC-CGGGGC
1 CGGCGCGGGGC
9486547 GGGCGCGGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 4 0.15
19 17 0.63
20 6 0.22
ACGTcount: A:0.00, C:0.43, G:0.57, T:0.00
Consensus pattern (18 bp):
CGGCGCGGGGCCGCCGGC
Found at i:9486537 original size:24 final size:23
Alignment explanation
Indices: 9486499--9486567 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
9486489 CCGCGGCCGC
9486499 GGCGCGCGGGCCGCCGGCCGGCGCGG
1 GGCGCGC-GG-CGCCGGCCGGCGC-G
*
9486525 GGCGCGCGGCGCCGGCCGGGGCG
1 GGCGCGCGGCGCCGGCCGGCGCG
*
9486548 GGCGCG-GGCGCGCGGGCGGC
1 GGCGCGCGGCGC-CGGCCGGC
9486568 CCGCCGGCCG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
22 5 0.13
23 13 0.33
24 12 0.31
25 2 0.05
26 7 0.18
ACGTcount: A:0.00, C:0.39, G:0.61, T:0.00
Consensus pattern (23 bp):
GGCGCGCGGCGCCGGCCGGCGCG
Found at i:9486845 original size:30 final size:30
Alignment explanation
Indices: 9486787--9486845 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
9486777 GGCCGCGCTG
*
9486787 TCGGCGACGCGGAGCGCGCGCCGGCCGCGC
1 TCGGCGACGCGGAGCGCGCGCCGCCCGCGC
9486817 TCGGCG-CGCGG-GCGCGCCGCGCGCCCGCG
1 TCGGCGACGCGGAGCGCG-CGC-CGCCCGCG
9486846 GGCGCGCGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 5 0.19
29 8 0.31
30 13 0.50
ACGTcount: A:0.03, C:0.46, G:0.47, T:0.03
Consensus pattern (30 bp):
TCGGCGACGCGGAGCGCGCGCCGCCCGCGC
Found at i:9486991 original size:25 final size:27
Alignment explanation
Indices: 9486941--9486991 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
9486931 TGCAGTCGCG
*
9486941 GGCGCGGCGCGGGCGGCCCGGTCGCCCC
1 GGCGCGGCGCCGGC-GCCCGGTCGCCCC
9486969 GGCGCGGCGCCGGC-CCCGG-CGCC
1 GGCGCGGCGCCGGCGCCCGGTCGCC
9486992 GGGCGCGCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 5 0.23
28 13 0.59
ACGTcount: A:0.00, C:0.49, G:0.49, T:0.02
Consensus pattern (27 bp):
GGCGCGGCGCCGGCGCCCGGTCGCCCC
Found at i:9487068 original size:28 final size:28
Alignment explanation
Indices: 9486997--9487068 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
9486987 GCGCCGGGCG
* *
9486997 CGCGGGGGGGCAGC-CGCGGCGCGCGGC
1 CGCGGCGGGGCAGCGCGCGGCGCGCGAC
* *
9487024 TGC-GCGTCGGC-GACGCGCGGCGCGCGAC
1 CGCGGCG-GGGCAG-CGCGCGGCGCGCGAC
9487052 CGCGGCGGGGCAGCGCG
1 CGCGGCGGGGCAGCGCG
9487069 GCCGCCGCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
26 3 0.09
27 6 0.18
28 21 0.62
29 4 0.12
ACGTcount: A:0.06, C:0.38, G:0.54, T:0.03
Consensus pattern (28 bp):
CGCGGCGGGGCAGCGCGCGGCGCGCGAC
Found at i:9488469 original size:16 final size:16
Alignment explanation
Indices: 9488450--9488501 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
9488440 TTTTTAACTC
*
9488450 AAAACAATTAAAATTT
1 AAAATAATTAAAATTT
* *
9488466 AAAATAATTCAAACTT
1 AAAATAATTAAAATTT
* *
9488482 AAAATAATTTAAATTC
1 AAAATAATTAAAATTT
9488498 AAAA
1 AAAA
9488502 ATATGTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATAATTAAAATTT
Found at i:9490564 original size:216 final size:212
Alignment explanation
Indices: 9490207--9491063 Score: 1021
Period size: 216 Copynumber: 4.1 Consensus size: 212
9490197 AGTAGTGTCC
* * *
9490207 CTGAGGGAATTGGTGAGAGTATTAGTAAAACTGAGGGTACTACTTTGAATATGGTGTCAAAGATG
1 CTGAGGGAAATGG-GAGA--ATT-GTAAAATTGAGGGCACTACTTTGAATATGGTGTCAAAGATG
* * * *
9490272 GATGTAGTTCCCGTTGTAGAAAAGGTTTCTCCTCCATTGGCAGCATCTGCCGTTGAAAGTGAAAT
62 GATTTAGTTCCTGATGTAGAAAAGGTTTCTCCTCCATTGGCAGCTTCTGCCGTTGAAAGTGAAAT
* * *
9490337 TACTACTCAATTAGCTTCTTCAGAGT-CTGATTCTAAAACTGAAGTGCCTCATGGTGTTAAGTTC
127 TACTACTCAATTAGCTTCTTCAGAGTCCAG-TTCTAAAATTGAAGTGCCCCATGGTGTTAAGTTC
*
9490401 CAGGAAGAAAATACTGATGCTT
191 CAGGAAGAAAATACTGGTGCTT
*
9490423 CTGAGGGAAATGGCGAGAAAATTGTTAAAATTGAGGGCACTACTTTGAATATGGTGTCGAAGATG
1 CTGAGGGAAATGG-GAG--AATTG-TAAAATTGAGGGCACTACTTTGAATATGGTGTCAAAGATG
**
9490488 GATTTAGTTCCTGATGTAGAAAAGGTTTCTCCTCCAAGGGCAGCTTCTGCCGTTGAAAGTGAAAT
62 GATTTAGTTCCTGATGTAGAAAAGGTTTCTCCTCCATTGGCAGCTTCTGCCGTTGAAAGTGAAAT
* * * * *
9490553 TACTACTCAATTAGATTCTTTAGAGTCCAGTTCTAAAATTGAAGTTCCCCATGGTATTAAGTTTC
127 TACTACTCAATTAGCTTCTTCAGAGTCCAGTTCTAAAATTGAAGTGCCCCATGGTGTTAAGTTCC
*
9490618 AGGAAGAAAATAGTGGTGCTT
192 AGGAAGAAAATACTGGTGCTT
9490639 CTGAGGGAAAT----G----G------TGAGGGCACTACTTTGAATATGGTGTCAAAGATGGATT
1 CTGAGGGAAATGGGAGAATTGTAAAATTGAGGGCACTACTTTGAATATGGTGTCAAAGATGGATT
* * *
9490690 TAGTTCCTGATGTAGAAAATGTTTCTCCTCCATTGGCAGTTTCTGCTGTTGAAAGTGAAATTACT
66 TAGTTCCTGATGTAGAAAAGGTTTCTCCTCCATTGGCAGCTTCTGCCGTTGAAAGTGAAATTACT
* * * * *
9490755 ACTCAATTAGCTTCTTCAGAGTCCAGTTCTACAATTGAAGTCCCCCATGGTCTTAAGTCCCAGAA
131 ACTCAATTAGCTTCTTCAGAGTCCAGTTCTAAAATTGAAGTGCCCCATGGTGTTAAGTTCCAGGA
*
9490820 AGAAAATAATGGTGCTT
196 AGAAAATACTGGTGCTT
* *
9490837 CTGAGGGAAATGGTGAGAATGTTGGTAAATTTGA-GGCTACTATTTTGAATATGGTGTCAAAGAT
1 CTGAGGGAAATGG-GAGAA--TT-GTAAAATTGAGGGC-ACTACTTTGAATATGGTGTCAAAGAT
* * * * **
9490901 CGATTTAGTTCCTGATGTAGAAAAGGTTTCTCCTCCATTGGCAGCTTATGCTGTCGAAAGTGCTA
61 GGATTTAGTTCCTGATGTAGAAAAGGTTTCTCCTCCATTGGCAGCTTCTGCCGTTGAAAGTGAAA
* * * * * *
9490966 TTAC-ATCTCAATTAGCTTCTTTAGAGT-CTGCTTCTGAAAGTGAAGTGCCTCACGGTGTTAAGT
126 TTACTA-CTCAATTAGCTTCTTCAGAGTCCAG-TTCTAAAATTGAAGTGCCCCATGGTGTTAAGT
* *
9491029 TCCAGGAAGAAAACACTGGTACTT
189 TCCAGGAAGAAAATACTGGTGCTT
* *
9491053 CTAATGGAAAT
1 CTGAGGGAAAT
9491064 CTTGAAAGTA
Statistics
Matches: 556, Mismatches: 60, Indels: 50
0.83 0.09 0.08
Matches are distributed among these distances:
198 181 0.33
203 1 0.00
205 1 0.00
210 1 0.00
211 1 0.00
215 7 0.01
216 361 0.65
217 2 0.00
218 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32
Consensus pattern (212 bp):
CTGAGGGAAATGGGAGAATTGTAAAATTGAGGGCACTACTTTGAATATGGTGTCAAAGATGGATT
TAGTTCCTGATGTAGAAAAGGTTTCTCCTCCATTGGCAGCTTCTGCCGTTGAAAGTGAAATTACT
ACTCAATTAGCTTCTTCAGAGTCCAGTTCTAAAATTGAAGTGCCCCATGGTGTTAAGTTCCAGGA
AGAAAATACTGGTGCTT
Found at i:9490793 original size:198 final size:201
Alignment explanation
Indices: 9490453--9491041 Score: 731
Period size: 198 Copynumber: 2.9 Consensus size: 201
9490443 ATTGTTAAAA
*
9490453 TTGAGGGCACTACTTTGAATATGGTGTCGAAGATGGATTTAGTTCCTGATGTAGAAAAGGTTTCT
1 TTGAGGGCACTACTTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATGTAGAAAAGGTTTCT
** * *
9490518 CCTCCAAGGGCAGCTTCTGCCGTTGAAAGTGAAATTACTACTCAATTAGATTCTTTAGAGTCCAG
66 CCTCCATTGGCAGCTTCTGCTGTTGAAAGTGAAATTACTACTCAATTAGCTTCTTTAGAGTCCAG
* * *
9490583 TTCTAAAATTGAAGTTCCCCATGGTATTAAGTTTCAGGAAGAAAATAGTGGTGCTTCTGAGGGAA
131 TTCT-AAATTGAAGTCCCCCATGGTATTAAGTTCCAGGAAGAAAATAATGGTGCTTCTGAGGGAA
9490648 A-T-G-G
195 AGTAGAG
*
9490652 -TGAGGGCACTACTTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATGTAGAAAATGTTTCT
1 TTGAGGGCACTACTTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATGTAGAAAAGGTTTCT
* *
9490716 CCTCCATTGGCAGTTTCTGCTGTTGAAAGTGAAATTACTACTCAATTAGCTTCTTCAGAGTCCAG
66 CCTCCATTGGCAGCTTCTGCTGTTGAAAGTGAAATTACTACTCAATTAGCTTCTTTAGAGTCCAG
* * *
9490781 TTCTACAATTGAAGTCCCCCATGGTCTTAAGTCCCAGAAAGAAAATAATGGTGCTTCTGAGGGAA
131 TTCTA-AATTGAAGTCCCCCATGGTATTAAGTTCCAGGAAGAAAATAATGGTGCTTCTGAGGGAA
9490846 ATGGTGAGAATG
195 A--GT-AG-A-G
* *
9490858 TTGGTAAATTTGAGGCTACTATTTTGAATATGGTGTCAAAGATCGATTTAGTTCCTGATGTAGAA
1 TT-G---A---G-GGC-ACTACTTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATGTAGAA
* * **
9490923 AAGGTTTCTCCTCCATTGGCAGCTTATGCTGTCGAAAGTGCTATTAC-ATCTCAATTAGCTTCTT
57 AAGGTTTCTCCTCCATTGGCAGCTTCTGCTGTTGAAAGTGAAATTACTA-CTCAATTAGCTTCTT
* * * * * *
9490987 TAGAGT-CTGCTTCTGAAAGTGAAGTGCCTCACGGTGTTAAGTTCCAGGAAGAAAA
121 TAGAGTCCAG-TTCT-AAATTGAAGTCCCCCATGGTATTAAGTTCCAGGAAGAAAA
9491042 CACTGGTACT
Statistics
Matches: 337, Mismatches: 31, Indels: 27
0.85 0.08 0.07
Matches are distributed among these distances:
197 1 0.00
198 179 0.53
201 1 0.00
203 1 0.00
206 1 0.00
207 1 0.00
208 1 0.00
211 1 0.00
214 1 0.00
215 6 0.02
216 143 0.42
217 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (201 bp):
TTGAGGGCACTACTTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATGTAGAAAAGGTTTCT
CCTCCATTGGCAGCTTCTGCTGTTGAAAGTGAAATTACTACTCAATTAGCTTCTTTAGAGTCCAG
TTCTAAATTGAAGTCCCCCATGGTATTAAGTTCCAGGAAGAAAATAATGGTGCTTCTGAGGGAAA
GTAGAG
Found at i:9491029 original size:414 final size:414
Alignment explanation
Indices: 9490238--9491041 Score: 1166
Period size: 414 Copynumber: 1.9 Consensus size: 414
9490228 TTAGTAAAAC
* *
9490238 TGAGGGTACTACTTTGAATATGGTGTCAAAGATGGATGTAGTTCCCGTTGTAGAAAAGGTTTCTC
1 TGAGGGCACTACTTTGAATATGGTGTCAAAGATGGATGTAGTTCCCGATGTAGAAAAGGTTTCTC
*
9490303 CTCCATTGGCAGCATCTGCCGTTGAAAGTGAAATTACTACTCAATTAGCTTCTTCAGAGTCTGAT
66 CTCCATTGGCAGCATCTGCCGTTGAAAGTGAAATTACTACTCAATTAGCTTCTTCAGAGTCAGAT
* * * * * *
9490368 TCTAAAACTGAAGTGCCTCATGGTGTTAAGTTCCAGGAAGAAAATACTGATGCTTCTGAGGGAAA
131 TCTAAAACTGAAGTCCCCCATGGTCTTAAGTCCCAGAAAGAAAATAATGATGCTTCTGAGGGAAA
* * *
9490433 TGGCGAGAAAATTGTTAAAATTGAGGGCACTACTTTGAATATGGTGTCGAAGATGGATTTAGTTC
196 TGGCGAGAAAATTGGTAAAATTGAGGGCACTACTTTGAATATGGTGTCAAAGATCGATTTAGTTC
* *
9490498 CTGATGTAGAAAAGGTTTCTCCTCCAAGGGCAGCTTCTGCCGTTGAAAGTGAAATTACTACTCAA
261 CTGATGTAGAAAAGGTTTCTCCTCCAAGGGCAGCTTATGCCGTCGAAAGTGAAATTACTACTCAA
* * * *
9490563 TTAGATTCTTTAGAGTCCAGTTCTAAAATTGAAGTTCCCCATGGTATTAAGTTTCAGGAAGAAAA
326 TTAGATTCTTTAGAGTCCAGTTCTAAAAGTGAAGTGCCCCACGGTATTAAGTTCCAGGAAGAAAA
9490628 TAGTGGTGCTTCTGAGGGAAATGG
391 TAGTGGTGCTTCTGAGGGAAATGG
* * *
9490652 TGAGGGCACTACTTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATGTAGAAAATGTTTCTC
1 TGAGGGCACTACTTTGAATATGGTGTCAAAGATGGATGTAGTTCCCGATGTAGAAAAGGTTTCTC
** *
9490717 CTCCATTGGCAGTTTCTGCTGTTGAAAGTGAAATTACTACTCAATTAGCTTCTTCAGAGTCCAG-
66 CTCCATTGGCAGCATCTGCCGTTGAAAGTGAAATTACTACTCAATTAGCTTCTTCAGAGT-CAGA
* * *
9490781 TTCTACAATTGAAGTCCCCCATGGTCTTAAGTCCCAGAAAGAAAATAATGGTGCTTCTGAGGGAA
130 TTCTAAAACTGAAGTCCCCCATGGTCTTAAGTCCCAGAAAGAAAATAATGATGCTTCTGAGGGAA
* ** * *
9490846 ATGGTGAGAATGTTGGTAAATTTGA-GGCTACTATTTTGAATATGGTGTCAAAGATCGATTTAGT
195 ATGGCGAGAAAATTGGTAAAATTGAGGGC-ACTACTTTGAATATGGTGTCAAAGATCGATTTAGT
** * **
9490910 TCCTGATGTAGAAAAGGTTTCTCCTCCATTGGCAGCTTATGCTGTCGAAAGTGCTATTAC-ATCT
259 TCCTGATGTAGAAAAGGTTTCTCCTCCAAGGGCAGCTTATGCCGTCGAAAGTGAAATTACTA-CT
* * * * *
9490974 CAATTAGCTTCTTTAGAGT-CTGCTTCTGAAAGTGAAGTGCCTCACGGTGTTAAGTTCCAGGAAG
323 CAATTAGATTCTTTAGAGTCCAG-TTCTAAAAGTGAAGTGCCCCACGGTATTAAGTTCCAGGAAG
9491038 AAAA
387 AAAA
9491042 CACTGGTACT
Statistics
Matches: 344, Mismatches: 42, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
413 6 0.02
414 336 0.98
415 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (414 bp):
TGAGGGCACTACTTTGAATATGGTGTCAAAGATGGATGTAGTTCCCGATGTAGAAAAGGTTTCTC
CTCCATTGGCAGCATCTGCCGTTGAAAGTGAAATTACTACTCAATTAGCTTCTTCAGAGTCAGAT
TCTAAAACTGAAGTCCCCCATGGTCTTAAGTCCCAGAAAGAAAATAATGATGCTTCTGAGGGAAA
TGGCGAGAAAATTGGTAAAATTGAGGGCACTACTTTGAATATGGTGTCAAAGATCGATTTAGTTC
CTGATGTAGAAAAGGTTTCTCCTCCAAGGGCAGCTTATGCCGTCGAAAGTGAAATTACTACTCAA
TTAGATTCTTTAGAGTCCAGTTCTAAAAGTGAAGTGCCCCACGGTATTAAGTTCCAGGAAGAAAA
TAGTGGTGCTTCTGAGGGAAATGG
Found at i:9491102 original size:216 final size:216
Alignment explanation
Indices: 9490659--9491124 Score: 557
Period size: 216 Copynumber: 2.2 Consensus size: 216
9490649 TGGTGAGGGC
*
9490659 ACTACTTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATGTAGAAAATGTTTCTCCTCCATT
1 ACTACTTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATGTAGAAAAGGTTTCTCCTCCATT
* * *
9490724 GGCAGTTTCTGCTGTTGAAAGTGAAATTACTACTCAATTAGCTTCTTCAGAGTCCAGTTCTACAA
66 GGCAGCTTATGCTGTCGAAAGTGAAATTACTACTCAATTAGCTTCTTCAGAGTCCAGTTCTACAA
* * * * * *
9490789 TTGAAGTCCCCCATGGTCTTAAGTCCCAGAAAGAAAATAATGGTGCTTCTGAGGGAAATGGTGAG
131 GTGAAGTCCCCCACGGTCTTAAGTCCCAGAAAGAAAACAATGGTACTTCTAAGGGAAATCGTGAG
*
9490854 AATGTTGGTAAATTTGAGGCT
196 AATGTAGGTAAATTTGAGGCT
* *
9490875 ACTATTTTGAATATGGTGTCAAAGATCGATTTAGTTCCTGATGTAGAAAAGGTTTCTCCTCCATT
1 ACTACTTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATGTAGAAAAGGTTTCTCCTCCATT
** * *
9490940 GGCAGCTTATGCTGTCGAAAGTGCTATTAC-ATCTCAATTAGCTTCTTTAGAGT-CTGCTTCTGA
66 GGCAGCTTATGCTGTCGAAAGTGAAATTACTA-CTCAATTAGCTTCTTCAGAGTCCAG-TTCT-A
* * * * * * * *
9491003 -AAGTGAAGTGCCTCACGGTGTTAAGTTCCAGGAAGAAAACACTGGTACTTCTAATGGAAATCTT
128 CAAGTGAAGTCCCCCACGGTCTTAAGTCCCAGAAAGAAAACAATGGTACTTCTAAGGGAAATCGT
* * *
9491067 GA-AA-GTACAGTTAAGA-TTGGGGGT
193 GAGAATGT--AGGTAA-ATTTGAGGCT
** *
9491091 ACTACTTTGAATACAGAGTCAAAGATGGATTTAG
1 ACTACTTTGAATATGGTGTCAAAGATGGATTTAG
9491125 CAATGAAAGA
Statistics
Matches: 211, Mismatches: 33, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
214 2 0.01
215 5 0.02
216 202 0.96
217 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (216 bp):
ACTACTTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATGTAGAAAAGGTTTCTCCTCCATT
GGCAGCTTATGCTGTCGAAAGTGAAATTACTACTCAATTAGCTTCTTCAGAGTCCAGTTCTACAA
GTGAAGTCCCCCACGGTCTTAAGTCCCAGAAAGAAAACAATGGTACTTCTAAGGGAAATCGTGAG
AATGTAGGTAAATTTGAGGCT
Found at i:9542202 original size:22 final size:23
Alignment explanation
Indices: 9542168--9542219 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
9542158 TCATGCAATG
* * *
9542168 TAAAAAGTAAGTCACTCAATACT
1 TAAAAACTAAGTCACGCAATACC
*
9542191 TAAAAACT-AGTCACGCAATGCC
1 TAAAAACTAAGTCACGCAATACC
9542213 TAAAAAC
1 TAAAAAC
9542220 CATTAGAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (23 bp):
TAAAAACTAAGTCACGCAATACC
Found at i:9542381 original size:9 final size:9
Alignment explanation
Indices: 9542367--9542400 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
9542357 AAAAGTCATT
9542367 TTAAAATGC
1 TTAAAATGC
9542376 TTAAAAATGC
1 TT-AAAATGC
*
9542386 TCAAAATGC
1 TTAAAATGC
9542395 TTAAAA
1 TTAAAA
9542401 GTTTTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (9 bp):
TTAAAATGC
Found at i:9564341 original size:23 final size:23
Alignment explanation
Indices: 9564287--9564352 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
9564277 TAAGCAATGC
*
9564287 ATAAATCATACAATGGCTTACTA
1 ATAAATCACACAATGGCTTACTA
*
9564310 ACT-AGTCACACAATGGCTTACTA
1 A-TAAATCACACAATGGCTTACTA
*
9564333 ATAAATCACGCAAT-GCTTAC
1 ATAAATCACACAATGGCTTAC
9564353 CAATTAGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 7 0.19
23 29 0.78
24 1 0.03
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (23 bp):
ATAAATCACACAATGGCTTACTA
Found at i:9564373 original size:22 final size:22
Alignment explanation
Indices: 9564358--9564455 Score: 67
Period size: 21 Copynumber: 4.5 Consensus size: 22
9564348 CTTACCAATT
*
9564358 AGTCATGTAATACTTAAAAATA
1 AGTCATGCAATACTTAAAAATA
** * *
9564380 AGTCATGCAATAC-CCAAAGTC
1 AGTCATGCAATACTTAAAAATA
* * *
9564401 AGTCATGCAAT--GTATAGAGTA
1 AGTCATGCAATACTTA-AAAATA
* *
9564422 AGTCAAGCAATACTTAAAAATT
1 AGTCATGCAATACTTAAAAATA
*
9564444 AGTCACGCAATA
1 AGTCATGCAATA
9564456 TCCAAAAATC
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
21 29 0.51
22 26 0.46
23 2 0.04
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (22 bp):
AGTCATGCAATACTTAAAAATA
Found at i:9564678 original size:60 final size:61
Alignment explanation
Indices: 9564564--9564678 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 61
9564554 TACTTGACAA
* * **
9564564 AAAATGTTCAAAAGTTTCTGTTCATATATCAAAAAGCATTCTAAAATATTTAAAAATACTC
1 AAAATGTTCAAAAGTTTCTCTTCATATATCAAAAAGCACTCTAAAATACCTAAAAATACTC
* *
9564625 AAAATGTTCAAAGGTTT-TCTTCGTATATCAAAAA-CTACTCTAAAATACCTAAAA
1 AAAATGTTCAAAAGTTTCTCTTCATATATCAAAAAGC-ACTCTAAAATACCTAAAA
9564679 TGTTTTAACG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 1 0.02
60 30 0.64
61 16 0.34
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (61 bp):
AAAATGTTCAAAAGTTTCTCTTCATATATCAAAAAGCACTCTAAAATACCTAAAAATACTC
Found at i:9577871 original size:23 final size:24
Alignment explanation
Indices: 9577818--9577871 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
9577808 GGTCCACATT
*
9577818 TTTAATAAAAAAATATATATAATA
1 TTTAAAAAAAAAATATATATAATA
** *
9577842 AGT-AAAAAAAAATTTATATAA-A
1 TTTAAAAAAAAAATATATATAATA
9577864 TTTAAAAA
1 TTTAAAAA
9577872 TTTATTTCAT
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
22 2 0.09
23 20 0.87
24 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
TTTAAAAAAAAAATATATATAATA
Found at i:9582590 original size:32 final size:30
Alignment explanation
Indices: 9582554--9582613 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
9582544 CGTAAATTTT
9582554 TAATTAAAAATAATTTTAATATATAAATATAA
1 TAATTAAAAATAATTTTAA-AT-TAAATATAA
** *
9582586 TAATTTTAATTAATTTTAAATTAAATAT
1 TAATTAAAAATAATTTTAAATTAAATAT
9582614 TTATTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.28
31 2 0.08
32 16 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TAATTAAAAATAATTTTAAATTAAATATAA
Found at i:9584309 original size:30 final size:29
Alignment explanation
Indices: 9584274--9584371 Score: 117
Period size: 30 Copynumber: 3.3 Consensus size: 29
9584264 GTCATAATAG
*
9584274 TTTATTTAACTTAAATTAGAAATATAAAAA
1 TTTATTTAACTTAAA-TAAAAATATAAAAA
* *
9584304 CTTATTTGACTTAAAATAAAAATATAAAAA
1 TTTATTTAACTT-AAATAAAAATATAAAAA
* *
9584334 TTTAATTAAACAT-AATAAAAATATAAAAA
1 TTT-ATTTAACTTAAATAAAAATATAAAAA
9584363 TTTATTTAA
1 TTTATTTAA
9584372 ATTTCTTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 5 0.09
29 19 0.33
30 25 0.43
31 9 0.16
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (29 bp):
TTTATTTAACTTAAATAAAAATATAAAAA
Found at i:9584338 original size:21 final size:22
Alignment explanation
Indices: 9584314--9584361 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
9584304 CTTATTTGAC
9584314 TTAAAATAAAAAT-ATAAAAAT
1 TTAAAATAAAAATAATAAAAAT
* *
9584335 TT-AATTAAACATAATAAAAAT
1 TTAAAATAAAAATAATAAAAAT
*
9584356 ATAAAA
1 TTAAAA
9584362 ATTTATTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
20 8 0.38
21 11 0.52
22 2 0.10
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
TTAAAATAAAAATAATAAAAAT
Found at i:9584382 original size:29 final size:29
Alignment explanation
Indices: 9584293--9584373 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 29
9584283 CTTAAATTAG
* ** *
9584293 AAATATAAAAACTTATTTGACTTAAAATAA
1 AAATATAAAAATTTATTT-AAATATAATAA
* *
9584323 AAATATAAAAATTTAATTAAACATAATAA
1 AAATATAAAAATTTATTTAAATATAATAA
9584352 AAATATAAAAATTTATTTAAAT
1 AAATATAAAAATTTATTTAAAT
9584374 TTCTTAAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 27 0.63
30 16 0.37
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (29 bp):
AAATATAAAAATTTATTTAAATATAATAA
Found at i:9592563 original size:31 final size:31
Alignment explanation
Indices: 9592527--9592588 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
9592517 TGAATGGTGA
*
9592527 TGAATTGGTCTATTTGCATTTGTTGACTATG
1 TGAATTGGTCTATTTGCATGTGTTGACTATG
9592558 TGAATTGGTCTATTTGCATGTGTTGACTATG
1 TGAATTGGTCTATTTGCATGTGTTGACTATG
9592589 GATAGTGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.47
Consensus pattern (31 bp):
TGAATTGGTCTATTTGCATGTGTTGACTATG
Found at i:9592598 original size:31 final size:31
Alignment explanation
Indices: 9592527--9592599 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
9592517 TGAATGGTGA
* *
9592527 TGAATTGGTCTATTTGCATTTGTTGACTATG
1 TGAAGTGGTCTATTTGCATGTGTTGACTATG
*
9592558 TGAATTGGTCTATTTGCATGTGTTGACTATG
1 TGAAGTGGTCTATTTGCATGTGTTGACTATG
9592589 -GATAGTGGTCT
1 TGA-AGTGGTCT
9592600 CTTTCTTTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 2 0.05
31 37 0.95
ACGTcount: A:0.19, C:0.10, G:0.26, T:0.45
Consensus pattern (31 bp):
TGAAGTGGTCTATTTGCATGTGTTGACTATG
Found at i:9598435 original size:14 final size:14
Alignment explanation
Indices: 9598416--9598443 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9598406 ATATTATGGT
9598416 GTATTGGGTTAGAC
1 GTATTGGGTTAGAC
9598430 GTATTGGGTTAGAC
1 GTATTGGGTTAGAC
9598444 CAAGTTGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.36, T:0.36
Consensus pattern (14 bp):
GTATTGGGTTAGAC
Found at i:9617029 original size:13 final size:14
Alignment explanation
Indices: 9617011--9617044 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
9617001 ATGTGTATTT
9617011 AATTATGGTTAA-G
1 AATTATGGTTAATG
9617024 AATTATGGTTAATG
1 AATTATGGTTAATG
9617038 -ATTATGG
1 AATTATGG
9617045 ATGTCATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 19 0.95
14 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (14 bp):
AATTATGGTTAATG
Found at i:9625013 original size:15 final size:15
Alignment explanation
Indices: 9624993--9625028 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
9624983 GGATAAAATT
9624993 TATAAATATTTATAA
1 TATAAATATTTATAA
*
9625008 TATAAATATTTTTAA
1 TATAAATATTTATAA
9625023 TA-AAAT
1 TATAAAT
9625029 TCATTCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAAATATTTATAA
Found at i:9630503 original size:12 final size:11
Alignment explanation
Indices: 9630483--9630512 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
9630473 ACAACAAAAG
9630483 AAAAAAATAAA
1 AAAAAAATAAA
9630494 AAAAATAATAAA
1 AAAAA-AATAAA
9630506 AAAAAAA
1 AAAAAAA
9630513 ACAGGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:9634831 original size:2 final size:2
Alignment explanation
Indices: 9634819--9634849 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
9634809 AAAAATGCTC
9634819 AT AT AT CAT 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
9634850 GTATGTACGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9638554 original size:36 final size:35
Alignment explanation
Indices: 9638478--9638605 Score: 100
Period size: 36 Copynumber: 3.6 Consensus size: 35
9638468 TGCGCCGTTT
* * * * *
9638478 ATAAACTAACTTAGTTGGTTTCTTTCTGCGCCCTAG-
1 ATAAACTATCTCAGTTGG-TTCTTACTACG-CCAAGC
*
9638514 ATAAACCT-TCTCAGTTGGTTCATTTCTACAG-CAAGC
1 ATAAA-CTATCTCAGTTGGTTC-TTACTAC-GCCAAGC
* **
9638550 ATAAACTATCTGAGTTGGATTCTTACTACGCCGTGC
1 ATAAACTATCTCAGTTGG-TTCTTACTACGCCAAGC
9638586 ATAAACTATCTCAGTTGGTT
1 ATAAACTATCTCAGTTGGTT
9638606 TCAAGCCACT
Statistics
Matches: 76, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
35 11 0.14
36 59 0.78
37 6 0.08
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (35 bp):
ATAAACTATCTCAGTTGGTTCTTACTACGCCAAGC
Found at i:9639760 original size:20 final size:18
Alignment explanation
Indices: 9639728--9639764 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
9639718 TATTCTAAAA
9639728 GAAAAAAAAATAAAGGAG
1 GAAAAAAAAATAAAGGAG
9639746 GAAAATAAAAGATAAAGGA
1 GAAAA-AAAA-ATAAAGGA
9639765 AAAATAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.08
Consensus pattern (18 bp):
GAAAAAAAAATAAAGGAG
Found at i:9639768 original size:18 final size:18
Alignment explanation
Indices: 9639727--9639771 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
9639717 TTATTCTAAA
9639727 AGAAAA-AAAAATAAAGG
1 AGAAAATAAAAATAAAGG
9639744 AGGAAAATAAAAGATAAAGG
1 A-GAAAATAAAA-ATAAAGG
9639764 A-AAAATAA
1 AGAAAATAA
9639772 GAAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 12 0.48
19 4 0.16
20 8 0.32
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (18 bp):
AGAAAATAAAAATAAAGG
Found at i:9639780 original size:20 final size:19
Alignment explanation
Indices: 9639732--9639781 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
9639722 CTAAAAGAAA
9639732 AAAAAATAAAGGAGGAAAAT
1 AAAAAATAAAGGA-GAAAAT
*
9639752 AAAAGATAAAGGA-AAAAT
1 AAAAAATAAAGGAGAAAAT
9639770 AAGAAAAATAAA
1 -A-AAAAATAAA
9639782 AATAAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 1 0.04
20 20 0.77
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAAAATAAAGGAGAAAAT
Found at i:9647287 original size:16 final size:16
Alignment explanation
Indices: 9647266--9647309 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
9647256 TATATTTTTG
*
9647266 TATTTTAATTTTT-TT
1 TATTTTTATTTTTCTT
*
9647281 TACTTTTTCTTTTTCTT
1 TA-TTTTTATTTTTCTT
9647298 TATTTTTATTTT
1 TATTTTTATTTT
9647310 CTAGTTGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 2 0.08
16 18 0.75
17 4 0.17
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.80
Consensus pattern (16 bp):
TATTTTTATTTTTCTT
Found at i:9647302 original size:110 final size:111
Alignment explanation
Indices: 9647071--9647302 Score: 244
Period size: 110 Copynumber: 2.1 Consensus size: 111
9647061 TTAATAATAT
* * * * *
9647071 TTTTTCTTT-TTTAATCTTTTAATTTTATTTTTACTAACATTTTAAAATATTAATAATTTATTAT
1 TTTTTCTTTATTTAATCTTTTAATTTTATTTTCACTAAAAATTTAAAACACTAATAATTTATTAT
*
9647135 TAAATTATTACAATGATTTTTATTTAAATTTCTTTTTATTTTTTCC
66 TAAATTATTACAATGATTTTTATTTAAATTTCTTTTTACTTTTTCC
* * * * * * *
9647181 CTATT-TGTATTTAATTTTTTAATTTCTGTTTTCATTAAAAATTT-AAACACTACTAATTTATTA
1 TTTTTCTTTATTTAATCTTTTAATTT-TATTTTCACTAAAAATTTAAAACACTAATAATTTATTA
* *
9647244 TTAAATTGTTA-ATAT-ATTTTTGTATTTTAATTT-TTTTTACTTTTT-C
65 TTAAATTATTACA-ATGA-TTTT-TATTTAAATTTCTTTTTACTTTTTCC
9647290 TTTTTCTTTATTT
1 TTTTTCTTTATTT
9647303 TTATTTTCTA
Statistics
Matches: 98, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
109 8 0.08
110 67 0.68
111 23 0.23
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.62
Consensus pattern (111 bp):
TTTTTCTTTATTTAATCTTTTAATTTTATTTTCACTAAAAATTTAAAACACTAATAATTTATTAT
TAAATTATTACAATGATTTTTATTTAAATTTCTTTTTACTTTTTCC
Found at i:9656484 original size:33 final size:33
Alignment explanation
Indices: 9656402--9656487 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 33
9656392 ATATCACATG
* *
9656402 ATACTAACATAATATGCTAACATATTATAATTA
1 ATACTAACATAATATGTTAACATATCATAATTA
* ** * *
9656435 ATAATAATGTAGTATGTTGACATATCATAATTA
1 ATACTAACATAATATGTTAACATATCATAATTA
*
9656468 ATGCTAACATAATATGTTAA
1 ATACTAACATAATATGTTAA
9656488 TTTGACATAA
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.37
Consensus pattern (33 bp):
ATACTAACATAATATGTTAACATATCATAATTA
Found at i:9660903 original size:59 final size:60
Alignment explanation
Indices: 9660815--9660935 Score: 149
Period size: 59 Copynumber: 2.0 Consensus size: 60
9660805 TTCATTTTTA
*
9660815 AATATTTCTATTACCAATCAAATAGTCAATTCCTCTTTT-AAGATGGACAAAAAAATCAAC
1 AATATTTCTATTACCAATCAAATAGTCAATT-CTCTTTTCAAGATAGACAAAAAAATCAAC
** * * *
9660875 AATATTT-TATTACCAATCATGT-GATCAATTCTCTTTTCATGGTAGACAAGAAAATCAAC
1 AATATTTCTATTACCAATCAAATAG-TCAATTCTCTTTTCAAGATAGACAAAAAAATCAAC
9660934 AA
1 AA
9660936 CATATCAACT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
58 8 0.15
59 38 0.72
60 7 0.13
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.33
Consensus pattern (60 bp):
AATATTTCTATTACCAATCAAATAGTCAATTCTCTTTTCAAGATAGACAAAAAAATCAAC
Found at i:9662483 original size:23 final size:23
Alignment explanation
Indices: 9662456--9662510 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
9662446 AGTAGTCAAC
9662456 AAATTATTATCTTGTTCGTACAA
1 AAATTATTATCTTGTTCGTACAA
9662479 AAATTATTATCTTGTTCGTACAA
1 AAATTATTATCTTGTTCGTACAA
9662502 AAATTATTA
1 AAATTATTA
9662511 ACTTTTACCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (23 bp):
AAATTATTATCTTGTTCGTACAA
Found at i:9674722 original size:21 final size:21
Alignment explanation
Indices: 9674698--9674737 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9674688 ATTAATAAAA
*
9674698 ATTAATTTGTTAAGATATTTT
1 ATTAATTTGTTAAAATATTTT
* *
9674719 ATTATTTTTTTAAAATATT
1 ATTAATTTGTTAAAATATT
9674738 AAATTTAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
ATTAATTTGTTAAAATATTTT
Found at i:9682168 original size:6 final size:6
Alignment explanation
Indices: 9682157--9682199 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
9682147 CTTTCTTCGT
9682157 GCGGTG GCGGTG GCGGTG GCGGTG GCGGTG GCGGTG GCGGTG G
1 GCGGTG GCGGTG GCGGTG GCGGTG GCGGTG GCGGTG GCGGTG G
9682200 ATGTGGAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.16, G:0.67, T:0.16
Consensus pattern (6 bp):
GCGGTG
Found at i:9682205 original size:18 final size:18
Alignment explanation
Indices: 9682157--9682205 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
9682147 CTTTCTTCGT
*
9682157 GCGGTGGCGGTGGCGGTG
1 GCGGTGGAGGTGGCGGTG
*
9682175 GCGGTGGCGGTGGCGGTG
1 GCGGTGGAGGTGGCGGTG
*
9682193 GCGGTGGATGTGG
1 GCGGTGGAGGTGG
9682206 AGAAAAGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.02, C:0.14, G:0.65, T:0.18
Consensus pattern (18 bp):
GCGGTGGAGGTGGCGGTG
Found at i:9684972 original size:11 final size:11
Alignment explanation
Indices: 9684956--9684993 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9684946 CAAGAAGTAA
9684956 ATATAAAATAT
1 ATATAAAATAT
* *
9684967 ATATAAATTTT
1 ATATAAAATAT
9684978 ATAT-AAATAT
1 ATATAAAATAT
9684988 ATATAA
1 ATATAA
9684994 TATTGAGTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATAAAATAT
Found at i:9689285 original size:26 final size:26
Alignment explanation
Indices: 9689242--9689309 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
9689232 TGATGCAATA
** * *
9689242 TCGGTTTCAATCGATTTTTTAGAGGG
1 TCGGTTTCGGTCGGTTTTTTAGAGAG
*
9689268 TTGGTTTCGGTCGGTTTTTTAGAGAG
1 TCGGTTTCGGTCGGTTTTTTAGAGAG
9689294 TCGGTTTCGGTCGGTT
1 TCGGTTTCGGTCGGTT
9689310 CGGTCGGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.12, C:0.12, G:0.32, T:0.44
Consensus pattern (26 bp):
TCGGTTTCGGTCGGTTTTTTAGAGAG
Found at i:9693989 original size:21 final size:20
Alignment explanation
Indices: 9693955--9693994 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
9693945 AGTATTTAAT
9693955 AAACCATGCTATTTTAGTTTG
1 AAACCATGCTATTTT-GTTTG
9693976 AAACCATG-TAATTTTGTTT
1 AAACCATGCT-ATTTTGTTT
9693995 AAAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (20 bp):
AAACCATGCTATTTTGTTTG
Found at i:9696291 original size:8 final size:8
Alignment explanation
Indices: 9696278--9696330 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
9696268 ATGTGATTAA
*
9696278 AATTAATT
1 AATTAACT
*
9696286 AATTAACC
1 AATTAACT
9696294 AATTAACT
1 AATTAACT
* *
9696302 AGTTAATT
1 AATTAACT
9696310 AAATTAACT
1 -AATTAACT
*
9696319 AAATAACT
1 AATTAACT
9696327 AATT
1 AATT
9696331 TATTTGTAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
8 29 0.83
9 6 0.17
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (8 bp):
AATTAACT
Found at i:9696325 original size:25 final size:24
Alignment explanation
Indices: 9696280--9696327 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
9696270 GTGATTAAAA
*
9696280 TTAATTAATTAACCAATTAACTAG
1 TTAATTAATTAACCAAATAACTAG
*
9696304 TTAATTAAATTAACTAAATAACTA
1 TTAATT-AATTAACCAAATAACTA
9696328 ATTTATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (24 bp):
TTAATTAATTAACCAAATAACTAG
Found at i:9705418 original size:207 final size:211
Alignment explanation
Indices: 9705056--9705479 Score: 581
Period size: 207 Copynumber: 2.0 Consensus size: 211
9705046 AGAAGAATAA
* * *
9705056 TTCTGTTGATCACCATCTAGAGCCTTGACTGTGAGAATATTATGATTCATTTCTTTCCTTCTCTC
1 TTCTGTTGATCACAATCTAGAGCCTTGACTGTGAG-AGATTATGATTCATTTATTTCCTTCTCTC
*
9705121 TGGAGGACAACAATAATAATATGGAAAATTTTCTGATTTGAATCTTCTTTTGATTCTCTGTGCAT
65 TGGAGGA-AACAATAATAATATGGAAAATTTTCTGATTTGAATCTTCTTTTGATTCACTGTGCAT
* * *
9705186 GGTGAGTGGTGTGAGTGATGTTAGCAAGTTGTTGACATTTTTGAGGCAAACTTCCCTTACTTGTA
129 GATGAGTAGTGTGACTGATGTTAGCAAGTTGTTGACA-TTTTGAGGCAAACTTCCCTTACTTGTA
* *
9705251 AATTGCTTAGTAAATTTGC
193 AATTGCGTAGTAAACTTGC
* * *
9705270 TTCTGTTGATCATAATCTAGAGCCTTGACTTTG-G-GATTATGATTCATTTATTT-TTTCTGC-C
1 TTCTGTTGATCACAATCTAGAGCCTTGACTGTGAGAGATTATGATTCATTTATTTCCTTCT-CTC
* * * * *
9705331 TGGATG-AA-AATATTAATATGGAAAATTTTTTGATTTTAATCTTCTTTTGATTCACTGTGCTTG
65 TGGAGGAAACAATAATAATATGGAAAATTTTCTGATTTGAATCTTCTTTTGATTCACTGTGCATG
** * *
9705394 ATGAGTAGTGTGACTGATGTTAGCAAGTTGTTGACATTTTGAGGTGAACTTCGCTTACTTTTAAA
130 ATGAGTAGTGTGACTGATGTTAGCAAGTTGTTGACATTTTGAGGCAAACTTCCCTTACTTGTAAA
9705459 TTGCGTAGTAAACTTGC
195 TTGCGTAGTAAACTTGC
9705476 TTCT
1 TTCT
9705480 TTATCAGTCA
Statistics
Matches: 188, Mismatches: 21, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
206 44 0.23
207 83 0.44
208 2 0.01
210 10 0.05
211 18 0.10
213 1 0.01
214 30 0.16
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (211 bp):
TTCTGTTGATCACAATCTAGAGCCTTGACTGTGAGAGATTATGATTCATTTATTTCCTTCTCTCT
GGAGGAAACAATAATAATATGGAAAATTTTCTGATTTGAATCTTCTTTTGATTCACTGTGCATGA
TGAGTAGTGTGACTGATGTTAGCAAGTTGTTGACATTTTGAGGCAAACTTCCCTTACTTGTAAAT
TGCGTAGTAAACTTGC
Found at i:9713463 original size:98 final size:98
Alignment explanation
Indices: 9713292--9713474 Score: 251
Period size: 98 Copynumber: 1.9 Consensus size: 98
9713282 CTTTGATACC
* * * **
9713292 TAACTAATAAATTGTATTGAAATTAAAGCCGACATCGCCAATTAATAATACTGCTTTGGTAATAA
1 TAACTAATAAATTGTATTCAAACTAAAACAAACATCGCCAATTAATAATACTGCTTTGGTAATAA
* *
9713357 AAGCAAATTTTATTTTGTAGGGGTGCTTTAGCT
66 AAGAAAATTTTATTTGGTAGGGGTGCTTTAGCT
* * * *
9713390 TAACTAATAAATT-TGATTCAAACTAAAACAAACATCTCCAATTTATAATATTGTTTTGGTAATA
1 TAACTAATAAATTGT-ATTCAAACTAAAACAAACATCGCCAATTAATAATACTGCTTTGGTAATA
9713454 AAAGAAAATTTTATTTGGTAG
65 AAAGAAAATTTTATTTGGTAG
9713475 TAATACTTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
97 1 0.01
98 72 0.99
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (98 bp):
TAACTAATAAATTGTATTCAAACTAAAACAAACATCGCCAATTAATAATACTGCTTTGGTAATAA
AAGAAAATTTTATTTGGTAGGGGTGCTTTAGCT
Found at i:9715007 original size:17 final size:17
Alignment explanation
Indices: 9714967--9715013 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
9714957 AATTTTTAAT
9714967 TAAAATATAAATTAAAAA
1 TAAAA-ATAAATTAAAAA
* *
9714985 TGAAAATAGATTAAAAA
1 TAAAAATAAATTAAAAA
9715002 TAAAAAATAAAT
1 T-AAAAATAAAT
9715014 ACTAATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (17 bp):
TAAAAATAAATTAAAAA
Found at i:9731136 original size:14 final size:13
Alignment explanation
Indices: 9731105--9731142 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
9731095 TTGAGAAGCT
9731105 CTTTAAAAAAAAA
1 CTTTAAAAAAAAA
*
9731118 TTTTAAAACAAAAA
1 CTTTAAAA-AAAAA
9731132 CTTTAAAAAAA
1 CTTTAAAAAAA
9731143 TAGCTTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (13 bp):
CTTTAAAAAAAAA
Found at i:9733693 original size:26 final size:26
Alignment explanation
Indices: 9733663--9733722 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
9733653 TACACACCCC
9733663 AATCAAACAGTGTGCCAGAAAGGAAA
1 AATCAAACAGTGTGCCAGAAAGGAAA
9733689 AATCAAACAGTGTGCCAGAAAGGAAA
1 AATCAAACAGTGTGCCAGAAAGGAAA
9733715 AATCAAAC
1 AATCAAAC
9733723 TTTATTGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.52, C:0.17, G:0.20, T:0.12
Consensus pattern (26 bp):
AATCAAACAGTGTGCCAGAAAGGAAA
Found at i:9753046 original size:22 final size:23
Alignment explanation
Indices: 9753021--9753074 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
9753011 AAACAACCCT
9753021 TAAATTATTTTGA-AA-ATTTAAA
1 TAAATT-TTTTGATAATATTTAAA
* *
9753043 TAAATTTTTTTATAATATTTAAT
1 TAAATTTTTTGATAATATTTAAA
9753066 TAAATTTTT
1 TAAATTTTT
9753075 ATACTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 5 0.18
22 8 0.29
23 15 0.54
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TAAATTTTTTGATAATATTTAAA
Found at i:9776162 original size:3 final size:3
Alignment explanation
Indices: 9776156--9776189 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
9776146 CTCCTCCTCC
*
9776156 TCT TCT TCT TCC TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
9776190 GTCGTTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:9776170 original size:12 final size:12
Alignment explanation
Indices: 9776153--9776189 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
9776143 AACCTCCTCC
9776153 TCCTCTTCTTCT
1 TCCTCTTCTTCT
9776165 TCCTCTTCTTCT
1 TCCTCTTCTTCT
*
9776177 TCTTCTTCTTCT
1 TCCTCTTCTTCT
9776189 T
1 T
9776190 GTCGTTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (12 bp):
TCCTCTTCTTCT
Found at i:9788436 original size:77 final size:77
Alignment explanation
Indices: 9788318--9788465 Score: 215
Period size: 77 Copynumber: 1.9 Consensus size: 77
9788308 TGTGTAAGTC
* *
9788318 AGAGACTAAAATCAAGATATCACTAATTTTTTCTATTAATATAAACAGTATACATATGGATCCAA
1 AGAGACTAAAATCAAGATATCACTAATTTTTTCTATCAATATAAACAATATACATATGGATCCAA
9788383 CATAGACGAGTG
66 CATAGACGAGTG
* * * ** * *
9788395 AGAGACTCAAATCTAGATATCACTAATTTTTTTTATCAATATAAACAATATATGTTTGGATTCAA
1 AGAGACTAAAATCAAGATATCACTAATTTTTTCTATCAATATAAACAATATACATATGGATCCAA
9788460 CATAGA
66 CATAGA
9788466 TGCAAACGGA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
77 62 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (77 bp):
AGAGACTAAAATCAAGATATCACTAATTTTTTCTATCAATATAAACAATATACATATGGATCCAA
CATAGACGAGTG
Found at i:9793887 original size:22 final size:22
Alignment explanation
Indices: 9793848--9793908 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 22
9793838 ACAAGGCATA
*
9793848 ATACGATTAATTCGTTTAAAGG
1 ATACGATTAATTCATTTAAAGG
9793870 ATACGATTAACTT-ATTT-AA--
1 ATACGATTAA-TTCATTTAAAGG
*
9793889 ATATGATTAATTCATTTAAA
1 ATACGATTAATTCATTTAAA
9793909 CATGAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 2 0.06
19 13 0.38
20 2 0.06
21 2 0.06
22 13 0.38
23 2 0.06
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (22 bp):
ATACGATTAATTCATTTAAAGG
Found at i:9793898 original size:19 final size:19
Alignment explanation
Indices: 9793874--9793913 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
9793864 TAAAGGATAC
*
9793874 GATTAACTT-ATTTAAATAT
1 GATTAA-TTCATTTAAACAT
9793893 GATTAATTCATTTAAACAT
1 GATTAATTCATTTAAACAT
9793912 GA
1 GA
9793914 AAAATAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (19 bp):
GATTAATTCATTTAAACAT
Found at i:9794552 original size:34 final size:34
Alignment explanation
Indices: 9794492--9794558 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
9794482 NNNNNNNNNN
* *
9794492 TTTATTATAATCTTATATATTTTATTTTTATTTT
1 TTTAATATAATCTTATATATTTTATTTTAATTTT
*
9794526 TTTAATATAAT-TTTTATATTTATATTTTAATTT
1 TTTAATATAATCTTATATATTT-TATTTTAATTT
9794559 CTCTTACTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 9 0.31
34 20 0.69
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (34 bp):
TTTAATATAATCTTATATATTTTATTTTAATTTT
Found at i:9794553 original size:25 final size:25
Alignment explanation
Indices: 9794511--9794637 Score: 68
Period size: 25 Copynumber: 5.0 Consensus size: 25
9794501 ATCTTATATA
* *
9794511 TTTTATTTTTATTTTTTTAATATAAT
1 TTTTATATTTA-TATTTTAATATAAT
**
9794537 TTTTATATTTATATTTTAAT-TTCT
1 TTTTATATTTATATTTTAATATAAT
* *
9794561 CTTACTTATATTATATAAATTT--TA-ATT
1 -TT--TTATATT-TAT-ATTTTAATATAAT
* *
9794588 TTTTATATTT-TATTTTATTTTTAAT
1 TTTTATATTTATATTTTA-ATATAAT
9794613 TTTTATATTT-TATTTTAATTATAAT
1 TTTTATATTTATATTTTAA-TATAAT
9794638 ATTATAAAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
21 4 0.05
22 1 0.01
23 1 0.01
24 10 0.13
25 34 0.44
26 12 0.15
27 9 0.12
28 3 0.04
29 4 0.05
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTATATTTATATTTTAATATAAT
Found at i:9794600 original size:26 final size:25
Alignment explanation
Indices: 9794571--9794625 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
9794561 CTTACTTATA
9794571 TTATATAAATTTTAATTTTTTATATT
1 TTATATAAATTTTAA-TTTTTATATT
* * *
9794597 TTATTTTATTTTTAATTTTTATATT
1 TTATATAAATTTTAATTTTTATATT
9794622 TTAT
1 TTAT
9794626 TTTAATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (25 bp):
TTATATAAATTTTAATTTTTATATT
Found at i:9794639 original size:19 final size:20
Alignment explanation
Indices: 9794598--9794640 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
9794588 TTTTATATTT
* *
9794598 TATTTTATTTTTAATTTTTA
1 TATTTTATTTTTAATTATAA
9794618 TATTTTA-TTTTAATTATAA
1 TATTTTATTTTTAATTATAA
9794637 TATT
1 TATT
9794641 ATAAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTTTATTTTTAATTATAA
Found at i:9798857 original size:19 final size:21
Alignment explanation
Indices: 9798833--9798871 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
9798823 CAAACAATTT
9798833 ATTTTTATT-TAAT-TTTTTA
1 ATTTTTATTCTAATATTTTTA
9798852 ATTTTTATTCTAATATTTTT
1 ATTTTTATTCTAATATTTTT
9798872 CTTGCACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (21 bp):
ATTTTTATTCTAATATTTTTA
Found at i:9800275 original size:21 final size:21
Alignment explanation
Indices: 9800249--9800604 Score: 82
Period size: 21 Copynumber: 16.3 Consensus size: 21
9800239 GTTTAATATA
9800249 TTTATATTTTTATTATTAATT
1 TTTATATTTTTATTATTAATT
*
9800270 TTTATATAATATCTT-TTAAATATATT
1 TTTATAT--T-T-TTATT-ATTA-ATT
* * *
9800296 TTAATATCATATATT-TT-ATT
1 TTTATAT-TTTTATTATTAATT
*
9800316 TTTAT-TTATTA-TA-TAATAT
1 TTTATATTTTTATTATTAAT-T
*
9800335 TTTATATTTATTATTAATATATT
1 TTTATATTT-TTATTATTA-ATT
9800358 TTTAT-TTTTTATTAATT--TT
1 TTTATATTTTTATT-ATTAATT
* * *
9800377 TATATAATATCATTTCTTA-AATATAT
1 T-T-T-ATAT-TTTTATTATTA-AT-T
* *
9800403 TTTATATATATATT-TT-ATT
1 TTTATATTTTTATTATTAATT
*
9800422 TTTAT-TTATTATTA-TAATAT
1 TTTATATTTTTATTATTAAT-T
*
9800442 TTTATA-TTTTATTTTTAATATT
1 TTTATATTTTTATTATT-A-ATT
*
9800464 ATTTATATTTATATTATTAATT
1 -TTTATATTTTTATTATTAATT
* * *
9800486 TTTATATAATATCATTTCTTAAATAT
1 TTTATAT--TTTTA-TTATT-AAT-T
* * * * *
9800512 ATTTTTAATGTCATATATTTATT
1 -TTTATATTTTTAT-TATTAATT
*
9800535 TTTAT-TTATTATTA-TAATAT
1 TTTATATTTTTATTATTAAT-T
*
9800555 TTTATA-TTTTATTTTTAATAT
1 TTTATATTTTTATTATTAAT-T
*
9800576 ATTTATATTTATATTATTAATT
1 -TTTATATTTTTATTATTAATT
9800598 TTTATAT
1 TTTATAT
9800605 AATATCATAT
Statistics
Matches: 245, Mismatches: 43, Indels: 94
0.64 0.11 0.25
Matches are distributed among these distances:
17 2 0.01
18 10 0.04
19 21 0.09
20 38 0.16
21 41 0.17
22 31 0.13
23 39 0.16
24 29 0.12
25 17 0.07
26 12 0.05
27 5 0.02
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTATATTTTTATTATTAATT
Found at i:9800296 original size:26 final size:26
Alignment explanation
Indices: 9800267--9800644 Score: 85
Period size: 26 Copynumber: 14.8 Consensus size: 26
9800257 TTTATTATTA
*
9800267 ATTTTTATATAATATCTTTTAAATAT
1 ATTTTTATATAATATATTTTAAATAT
* * ** *
9800293 ATTTTAATATCATATATTTTATTTTT
1 ATTTTTATATAATATATTTTAAATAT
9800319 ATTTATTATAT-A-ATATTTT--ATAT
1 ATTT-TTATATAATATATTTTAAATAT
*
9800342 -TTATTAT-TAATATATTTT---TAT
1 ATTTTTATATAATATATTTTAAATAT
9800363 -TTTTTAT-TAAT-T-TTTATATAATAT
1 ATTTTTATATAATATATTT-TA-AATAT
* *
9800387 CATTTCT-TA-AATATATTTTATATAT
1 -ATTTTTATATAATATATTTTAAATAT
* * * *
9800412 ATATTTTATTTTTATTTATTATTATA-AT
1 AT-TTTTA-TATAATATATT-TTAAATAT
* *
9800440 A-TTTTATAT--TTTATTTTTAATAT
1 ATTTTTATATAATATATTTTAAATAT
* * *
9800463 -TATTTATAT--T-TATATT-ATTA-
1 ATTTTTATATAATATATTTTAAATAT
9800483 ATTTTTATATAATATCATTTCTTAAATAT
1 ATTTTTATATAATAT-A-TT-TTAAATAT
* * ** *
9800512 ATTTTTAATGTCATATA-TTTATTTTT
1 ATTTTT-ATATAATATATTTTAAATAT
* *
9800538 ATTTATTAT-T-ATAATATTTTATATTTT
1 ATTT-TTATATAAT-ATATTTTA-AATAT
* *
9800565 ATTTTTA-ATATATTTATATTTATATTATT
1 ATTTTTATATA-ATATAT-TTTA-AATA-T
9800594 AATTTTTATATAATATCATATTTTAAATAT
1 -ATTTTTATAT-A-AT-ATATTTTAAATAT
* * *
9800624 ATTTTAATGTCATATATTTTA
1 ATTTTTATATAATATATTTTA
9800645 TTTTTATTTA
Statistics
Matches: 270, Mismatches: 39, Indels: 86
0.68 0.10 0.22
Matches are distributed among these distances:
19 3 0.01
20 3 0.01
21 29 0.11
22 17 0.06
23 19 0.07
24 8 0.03
25 25 0.09
26 65 0.24
27 27 0.10
28 22 0.08
29 21 0.08
30 15 0.06
31 5 0.02
32 8 0.03
33 3 0.01
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (26 bp):
ATTTTTATATAATATATTTTAAATAT
Found at i:9800375 original size:17 final size:18
Alignment explanation
Indices: 9800313--9800379 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 18
9800303 CATATATTTT
*
9800313 ATTTTTATTTATTATATA
1 ATTTTTATTTTTTATATA
9800331 ATATTTTATATTTATTATTAATA
1 AT-TTTTAT-TTT-TTA-T-ATA
9800354 TATTTTTATTTTTTAT-TA
1 -ATTTTTATTTTTTATATA
9800372 ATTTTTAT
1 ATTTTTAT
9800380 ATAATATCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
17 8 0.19
18 4 0.10
19 6 0.14
20 3 0.07
21 6 0.14
22 4 0.10
23 9 0.21
24 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTATTTTTTATATA
Found at i:9800424 original size:6 final size:6
Alignment explanation
Indices: 9800415--9800490 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
9800405 TATATATATA
* * * *
9800415 TTTTAT TTTTAT TTATTAT TATAAT ATTTTAT ATTTTAT TTTTAA TATTAT
1 TTTTAT TTTTAT TT-TTAT TTTTAT -TTTTAT -TTTTAT TTTTAT TTTTAT
* * *
9800466 TTATAT TTATAT TATTAAT TTTTAT
1 TTTTAT TTTTAT T-TTTAT TTTTAT
9800491 ATAATATCAT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
6 35 0.64
7 20 0.36
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAT
Found at i:9800449 original size:15 final size:14
Alignment explanation
Indices: 9800245--9800713 Score: 144
Period size: 15 Copynumber: 34.2 Consensus size: 14
9800235 ATAAGTTTAA
9800245 TATATT-TATATTT
1 TATATTATATATTT
9800258 T-TATTAT-TAATTTT
1 TATATTATAT-A-TTT
* *
9800272 TATATAATATCTTT
1 TATATTATATATTT
9800286 TA-A--ATATATTT
1 TATATTATATATTT
*
9800297 TAATATCATATATTT
1 T-ATATTATATATTT
*
9800312 TAT-TTTTAT-TTAT
1 TATATTATATATT-T
9800325 TATA-TA-ATATTT
1 TATATTATATATTT
*
9800337 TATATT-TATTATTAA
1 TATATTATA-TATT-T
*
9800352 TATATT-TTTATTT
1 TATATTATATATTT
*
9800365 TTTATTA-AT-TTT
1 TATATTATATATTT
*
9800377 TATATAATATCATTT
1 TATATTATAT-ATTT
*
9800392 CT-TA-AATATATTT
1 -TATATTATATATTT
9800405 TATA-TATATATTT
1 TATATTATATATTT
9800418 TAT-TT-T-TA-TT
1 TATATTATATATTT
9800428 TATTATTATAATATTT
1 TA-TATTAT-ATATTT
*
9800444 TATATTTTAT-TTT
1 TATATTATATATTT
*
9800457 TAATATTATTTATATT
1 T-ATATTATATAT-TT
9800473 TATATTAT-TAATTTT
1 TATATTATAT-A-TTT
*
9800488 TATATAATATCATTT
1 TATATTATAT-ATTT
*
9800503 CT-TA-AATATATTT
1 -TATATTATATATTT
9800516 T-TAATGTCATATA-TT
1 TAT-AT-T-ATATATTT
9800531 TAT-TT-T-TA-TT
1 TATATTATATATTT
9800541 TATTATTATAATATTT
1 TA-TATTAT-ATATTT
*
9800557 TATATTTTAT-TTT
1 TATATTATATATTT
*
9800570 TA-ATATATTTATATT
1 TATAT-TATATAT-TT
9800585 TATATTAT-TAATTTT
1 TATATTATAT-A-TTT
9800600 TATATAATATCATATTT
1 TATAT--TAT-ATATTT
9800617 TA-A--ATATATTT
1 TATATTATATATTT
9800628 TA-ATGTCATATATTT
1 TATAT-T-ATATATTT
9800643 TAT-TT-T-TA-TT
1 TATATTATATATTT
9800653 TATTATTATA-ATTT
1 TA-TATTATATATTT
* *
9800667 TATATTTTTTTCATTT
1 TATA-TTATAT-ATTT
* *
9800683 CTTTAATATAT-TTT
1 -TATATTATATATTT
*
9800697 TATATTTTATATTT
1 TATATTATATATTT
9800711 TAT
1 TAT
9800714 TTTAATTTGT
Statistics
Matches: 352, Mismatches: 32, Indels: 143
0.67 0.06 0.27
Matches are distributed among these distances:
10 14 0.04
11 25 0.07
12 38 0.11
13 75 0.21
14 61 0.17
15 92 0.26
16 34 0.10
17 11 0.03
18 1 0.00
19 1 0.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
TATATTATATATTT
Found at i:9800620 original size:112 final size:112
Alignment explanation
Indices: 9800240--9800674 Score: 707
Period size: 112 Copynumber: 4.0 Consensus size: 112
9800230 AAAATATAAG
*
9800240 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATC--TT-TTAAATATATTTTAATA
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTAATA
9800302 TCATATATTTTATTTTTATTTATTA-TATAATATTTTATA-TTTATT
66 TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
* *
9800347 ATTAATATATTTTTATTT-T-TTATTAATTTTTATATAATATCATTTCTTAAATATATTTT-ATA
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTAATA
9800409 T-ATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
66 TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
9800455 TTTAATATTATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATA-TATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATA-TTTTAA
*
9800520 TGTCATATA-TTTATTTTTATTTATTATTATAATATTTTATATTTTATT
64 TATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
9800568 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTAAT
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTAAT
*
9800632 GTCATATATTTTATTTTTATTTATTATTAT-A-ATTTTATATTTT
65 ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTT
9800675 TTTCATTTCT
Statistics
Matches: 310, Mismatches: 5, Indels: 23
0.92 0.01 0.07
Matches are distributed among these distances:
105 22 0.07
106 24 0.08
107 36 0.12
108 25 0.08
109 10 0.03
110 13 0.04
111 52 0.17
112 72 0.23
113 51 0.16
114 5 0.02
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (112 bp):
TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTAATA
TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
Found at i:9800718 original size:30 final size:29
Alignment explanation
Indices: 9800283--9800728 Score: 132
Period size: 29 Copynumber: 15.6 Consensus size: 29
9800273 ATATAATATC
**
9800283 TTTTAAATATATTTTAATATCATATATTTTA
1 TTTT-AATATATTTT-ATATTTTATATTTTA
* *
9800314 TTTTTATTTATTATATAATATTTTATA-TTTA
1 TTTTAATATATT-T-T-ATATTTTATATTTTA
* *
9800345 TTATTAATATATTTT-TATTTTTTA-TTAA
1 TT-TTAATATATTTTATATTTTATATTTTA
* * * * *
9800373 TTTTTATATAATATCAT-TTCTTA-AATATA
1 TTTTAATAT-ATTTTATATT-TTATATTTTA
9800402 TTTT-ATATA---TATATTTTAT-TTTTA
1 TTTTAATATATTTTATATTTTATATTTTA
*
9800426 -TTT-AT-TATTATAATATTTTATATTTTA
1 TTTTAATATATT-TTATATTTTATATTTTA
9800453 TTTTTAATAT-TATTTATA-TTTATATTATTAA
1 -TTTTAATATAT-TTTATATTTTATATT-TT-A
* * * * *
9800484 TTTTTATATAATATCAT-TTCTTA-AATATA
1 TTTTAATAT-ATTTTATATT-TTATATTTTA
* *
9800513 TTTT--TA-ATGTCATATATTTAT-TTTTA
1 TTTTAATATATTTTATAT-TTTATATTTTA
* * *
9800539 -TTTATTAT-TATAATATTTTATATTTTA
1 TTTTAATATATTTTATATTTTATATTTTA
9800566 TTTTTAATATA-TTTATA-TTTATATTATTAA
1 -TTTTAATATATTTTATATTTTATATT-TT-A
* * * * *
9800596 TTTTTATATAATATCATATTTTA-AATATA
1 TTTTAATAT-ATTTTATATTTTATATTTTA
9800625 TTTTAATGTCATATATTT-TATTTT-TA-TTTA
1 TTTTAA--T-ATAT-TTTATATTTTATATTTTA
9800655 TTATT-ATA-ATTTTATATTTT-T-TTCATT-
1 TT-TTAATATATTTTATATTTTATATT--TTA
9800682 TCTTTAATATATTTTTATATTTTATATTTTA
1 T-TTTAATATA-TTTTATATTTTATATTTTA
* *
9800713 TTTTAATTTGTTTTAT
1 TTTTAATATATTTTAT
9800729 CTATATTATA
Statistics
Matches: 315, Mismatches: 43, Indels: 116
0.66 0.09 0.24
Matches are distributed among these distances:
22 2 0.01
23 5 0.02
24 8 0.03
25 14 0.04
26 31 0.10
27 32 0.10
28 38 0.12
29 59 0.19
30 54 0.17
31 41 0.13
32 31 0.10
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (29 bp):
TTTTAATATATTTTATATTTTATATTTTA
Found at i:9805501 original size:23 final size:23
Alignment explanation
Indices: 9805474--9805522 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
9805464 TAGTATAGAC
9805474 ATTACTAAAGTTCTAATTTTTGG
1 ATTACTAAAGTTCTAATTTTTGG
9805497 ATTACTAAAGTTCTAATTTTTGG
1 ATTACTAAAGTTCTAATTTTTGG
9805520 ATT
1 ATT
9805523 CAAATACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49
Consensus pattern (23 bp):
ATTACTAAAGTTCTAATTTTTGG
Found at i:9817871 original size:2 final size:2
Alignment explanation
Indices: 9817864--9817889 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9817854 TTTGAGATAC
9817864 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
9817890 GTATGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9819743 original size:2 final size:2
Alignment explanation
Indices: 9819730--9819777 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
9819720 TATATAATCA
9819730 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9819770 AT AT AT AT
1 AT AT AT AT
9819778 TGAGAGAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9829255 original size:36 final size:36
Alignment explanation
Indices: 9829208--9829286 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
9829198 AACAGTATAA
*
9829208 TATGATTTGAACTTTTAGATAGAATTAAATTAAGAT
1 TATGATTTGAACTCTTAGATAGAATTAAATTAAGAT
*
9829244 TATGATTTGAACTCTTAGATAGAATTAGATTAAGAT
1 TATGATTTGAACTCTTAGATAGAATTAAATTAAGAT
9829280 TATGATT
1 TATGATT
9829287 CGAGAGATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.42
Consensus pattern (36 bp):
TATGATTTGAACTCTTAGATAGAATTAAATTAAGAT
Found at i:9833338 original size:31 final size:29
Alignment explanation
Indices: 9833303--9833371 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
9833293 AATTAAAATA
* *
9833303 TTAAATAAGTCTTTGAACTTTTTATATT-TTT
1 TTAAATAAAT-TTT-AA-TTTTTAAATTATTT
*
9833334 TTAAATAAATTTTTATTTTTAAATTATTT
1 TTAAATAAATTTTAATTTTTAAATTATTT
9833363 TTAAATAAA
1 TTAAATAAA
9833372 CTCGTATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.26
29 13 0.38
30 3 0.09
31 9 0.26
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (29 bp):
TTAAATAAATTTTAATTTTTAAATTATTT
Found at i:9837534 original size:29 final size:30
Alignment explanation
Indices: 9837489--9837557 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
9837479 AAATTTAAAA
* *
9837489 TAAA-TTTTATTTTTTTATTATATG-T-AAT
1 TAAATTTTTATATATTTATT-TATGATCAAT
*
9837517 TAAATTTTTATATATTTATTTTTGATCAAT
1 TAAATTTTTATATATTTATTTATGATCAAT
9837547 TAAATTTTTAT
1 TAAATTTTTAT
9837558 CATTAATGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.20
29 14 0.40
30 14 0.40
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (30 bp):
TAAATTTTTATATATTTATTTATGATCAAT
Found at i:9837554 original size:15 final size:15
Alignment explanation
Indices: 9837514--9837563 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
9837504 TATTATATGT
9837514 AATTAAATTTTTAT-
1 AATTAAATTTTTATC
*
9837528 ATATT-TATTTTTGATC
1 A-ATTAAATTTTT-ATC
9837544 AATTAAATTTTTATC
1 AATTAAATTTTTATC
9837559 -ATTAA
1 AATTAA
9837564 TGGTTGACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 12 0.40
15 11 0.37
16 7 0.23
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (15 bp):
AATTAAATTTTTATC
Found at i:9837576 original size:29 final size:29
Alignment explanation
Indices: 9837513--9837587 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
9837503 TTATTATATG
* * **
9837513 TAATTAAATTTTTATATATTTATTTTTGA
1 TAATTAAATTTTTATACATTAATGGTTGA
9837542 TCAATTAAATTTTTAT-CATTAATGGTTGA
1 T-AATTAAATTTTTATACATTAATGGTTGA
9837571 CTAATTATTAATTTTTA
1 -TAATTA--AATTTTTA
9837588 AAATATCAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
29 15 0.39
30 15 0.39
31 8 0.21
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (29 bp):
TAATTAAATTTTTATACATTAATGGTTGA
Found at i:9837908 original size:22 final size:22
Alignment explanation
Indices: 9837866--9837909 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
9837856 GATCTTATTT
**
9837866 AAATTTTTTAACATAGTTTATA
1 AAATTTTTTAACATAAATTATA
9837888 AAATTTTTTAA-AGTAAATTATA
1 AAATTTTTTAACA-TAAATTATA
9837910 TTTAGTCTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (22 bp):
AAATTTTTTAACATAAATTATA
Found at i:9838816 original size:3 final size:3
Alignment explanation
Indices: 9838808--9838842 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
9838798 AAAAGCAAAC
*
9838808 ACT ACT ACT AGT ACT ACT ACT ACT ACT ACT ACT AC
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT AC
9838843 ATATAGTTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.31
Consensus pattern (3 bp):
ACT
Found at i:9855104 original size:27 final size:27
Alignment explanation
Indices: 9855074--9855248 Score: 174
Period size: 27 Copynumber: 6.4 Consensus size: 27
9855064 AAAAATTACA
9855074 TTAAAAATATAATTATTATATATCATG
1 TTAAAAATATAATTATTATATATCATG
*
9855101 TTAAAAATTTAATTATTATATATCATG
1 TTAAAAATATAATTATTATATATCATG
* *
9855128 TTGAAAAATAT-ATT-TGTACATATTATG
1 TT-AAAAATATAATTAT-TATATATCATG
* * * *
9855155 TTAAAAATTTAATTATTACATATTATA
1 TTAAAAATATAATTATTATATATCATG
* *
9855182 TTAAAAAATATAATTGTTATACATCATG
1 TT-AAAAATATAATTATTATATATCATG
* * * * *
9855210 TTAAAGATTTAGTTATTATATATTATT
1 TTAAAAATATAATTATTATATATCATG
9855237 TTAAAAAATATA
1 TT-AAAAATATA
9855249 GATATAATTA
Statistics
Matches: 121, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
26 8 0.07
27 77 0.64
28 36 0.30
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (27 bp):
TTAAAAATATAATTATTATATATCATG
Found at i:9855116 original size:54 final size:54
Alignment explanation
Indices: 9855058--9855248 Score: 206
Period size: 54 Copynumber: 3.5 Consensus size: 54
9855048 TAAAACTTGT
* * *
9855058 ATTATAAAAAATTACATT-AAAAATATAATTATTATATATCATGTTAAAAATTTA
1 ATTATTAAATATTATATTAAAAAATATAATT-TTATATATCATGTTAAAAATTTA
* * * * * *
9855112 ATTATTATATATCATGTTGAAAAATAT-ATTTGTACATATTATGTTAAAAATTTA
1 ATTATTAAATATTATATTAAAAAATATAATTT-TATATATCATGTTAAAAATTTA
* * *
9855166 ATTATTACATATTATATTAAAAAATATAATTGTTATACATCATGTTAAAGATTTA
1 ATTATTAAATATTATATTAAAAAATATAATT-TTATATATCATGTTAAAAATTTA
* * *
9855221 GTTATTATATATTATTTTAAAAAATATA
1 ATTATTAAATATTATATTAAAAAATATA
9855249 GATATAATTA
Statistics
Matches: 114, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
53 1 0.01
54 58 0.51
55 54 0.47
56 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (54 bp):
ATTATTAAATATTATATTAAAAAATATAATTTTATATATCATGTTAAAAATTTA
Found at i:9855275 original size:61 final size:54
Alignment explanation
Indices: 9855068--9855302 Score: 163
Period size: 54 Copynumber: 4.2 Consensus size: 54
9855058 ATTATAAAAA
* * * * *
9855068 ATTACATT-AAAAATATAATTATTATATATCATGTTAAAAATTTAATTATTATAT
1 ATTATATTAAAAAATATAATTATTATACAACATATT-AAAATTTAATTATTACAT
* * * * * *
9855122 ATCATGTTGAAAAATAT-A-T-TTGTACATATTATGTTAAAAATTTAATTATTACAT
1 ATTATATTAAAAAATATAATTATTATACA-A-CATATT-AAAATTTAATTATTACAT
* * * * *
9855176 ATTATATTAAAAAATATAATTGTTATACATCATGTTAAAGATTTAGTTATTATAT
1 ATTATATTAAAAAATATAATTATTATACAACATATTAAA-ATTTAATTATTACAT
* *
9855231 ATTATTTTAAAAAATATAGATATAATTATCACACAACATATTAAAATTTTAATTATTACAC
1 ATTATATTAAAAAATATA-AT-T-ATTAT---ACAACATATTAAAA-TTTAATTATTACAT
*
9855292 GTTATATTAAA
1 ATTATATTAAA
9855303 TTGAATCCAA
Statistics
Matches: 142, Mismatches: 25, Indels: 21
0.76 0.13 0.11
Matches are distributed among these distances:
52 5 0.04
53 1 0.01
54 46 0.32
55 44 0.31
56 3 0.02
57 7 0.05
58 4 0.03
60 1 0.01
61 31 0.22
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.44
Consensus pattern (54 bp):
ATTATATTAAAAAATATAATTATTATACAACATATTAAAATTTAATTATTACAT
Found at i:9857622 original size:17 final size:18
Alignment explanation
Indices: 9857600--9857633 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9857590 TCTCATTATT
9857600 AATA-TTTTATTTAATTC
1 AATATTTTTATTTAATTC
9857617 AATATTTTTATTTAATT
1 AATATTTTTATTTAATT
9857634 TTTTGAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
AATATTTTTATTTAATTC
Found at i:9858470 original size:28 final size:29
Alignment explanation
Indices: 9858434--9858488 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
9858424 ATTGAAGAAA
** *
9858434 ATTTAAATAAGTTTTTATTTTTTTATTAT
1 ATTTAAATAAAATTTTATATTTTTATTAT
9858463 ATTT-AATAAAATTTTATATTTTTATT
1 ATTTAAATAAAATTTTATATTTTTATT
9858489 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (29 bp):
ATTTAAATAAAATTTTATATTTTTATTAT
Found at i:9872453 original size:350 final size:341
Alignment explanation
Indices: 9871821--9872471 Score: 878
Period size: 350 Copynumber: 1.9 Consensus size: 341
9871811 NNNNNNNNNN
* * * *
9871821 CTAAGAAAATAAAAGAATAAGAAAAATATAATAGAACCTAAGAACTGTAATTTTGATCTTTTTGA
1 CTAAGAAAATAAAAGAATAAGAAAAAGATAATAGAACCTAAGAACTATAATCTTGATCTTCTTGA
* * * * * *
9871886 ATCCTTCAAATTCTTCTCAACTTTAATGACTTTATTACTTGATTTTTAGTTCTCAATTTGGTGTT
66 ATCCTTCAAATTCTTATCAACTTCAATGACTTTATGACTTGATTTTCAGTTCTCAATCTAGTGTT
* * *
9871951 TCATTCTTTTCTAAAAGTCCTCAAAAAGATTGCCTTTATAGGACAATGGCTTTGTGGCTTGATTT
131 TCATTCTCTTCTAAAAGTCCTCAAAAAGATTACCTTTATAGGACAATGACTTTGTGGCTTGATTT
** *
9872016 TTAACTCTTAATCTTGTGTTTCGTTCTTCTCTAAAAGTCATCCAAAAAGTTATTTTTATAAGACT
196 CCAACTCTTAATCTGGTGTTTCGTTCTTCTCTAAAAGTCATCCAAAAAGTTATTTTTATAAGACT
9872081 TTGAAGTTATGCTAAGTTAGATGAAGAAAGAATTCAATTCCCCATCAAGTTACGCATCATCATTA
261 TTGAAGTTATGCTAAGTTAGATGAAGAAAGAATTCAATTCCCCATCAAGTTACGCATCATCATTA
9872146 AATTAAATTTAAACAA
326 AATTAAATTTAAACAA
*
9872162 NNNNNNNNNNCTAAGAAAATAAAAGAATAAGAAAAAGATAATAGAACCTAAGAATTATAATCTTG
1 ----------CTAAGAAAATAAAAGAATAAGAAAAAGATAATAGAACCTAAGAACTATAATCTTG
* * * *
9872227 ATCTTCTTGAATCTTTCAAATTCTTATCAGCTTCAATGACTTTATGGCTTGA-TTTCAGTTCTTA
56 ATCTTCTTGAATCCTTCAAATTCTTATCAACTTCAATGACTTTATGACTTGATTTTCAGTTCTCA
* * * * *
9872291 ATCTAGTGTTTCGTTCCTCTT-TAAAAGTCCTTAGAAAGATTACTTTTATAGGATAATGACTTTG
121 ATCTAGTGTTTCATT-CTCTTCTAAAAGTCCTCAAAAAGATTACCTTTATAGGACAATGACTTTG
* * * * *
9872355 TGGTTTGATTTCCAACTCTTAATCTGGTGTTTCGTTCCTT-TTTAAAAGTCTTTCAAAAAGTTGT
185 TGGCTTGATTTCCAACTCTTAATCTGGTGTTTCGTT-CTTCTCTAAAAGTCATCCAAAAAGTTAT
9872419 TTTTATAAGACTTTGAAGTTATG-TCAAGTTAGATGAAGAAAGAATTCAATTCC
249 TTTTATAAGACTTTGAAGTTATGCT-AAGTTAGATGAAGAAAGAATTCAATTCC
9872472 AATTAGGGTT
Statistics
Matches: 266, Mismatches: 31, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
349 1 0.00
350 162 0.61
351 103 0.39
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.38
Consensus pattern (341 bp):
CTAAGAAAATAAAAGAATAAGAAAAAGATAATAGAACCTAAGAACTATAATCTTGATCTTCTTGA
ATCCTTCAAATTCTTATCAACTTCAATGACTTTATGACTTGATTTTCAGTTCTCAATCTAGTGTT
TCATTCTCTTCTAAAAGTCCTCAAAAAGATTACCTTTATAGGACAATGACTTTGTGGCTTGATTT
CCAACTCTTAATCTGGTGTTTCGTTCTTCTCTAAAAGTCATCCAAAAAGTTATTTTTATAAGACT
TTGAAGTTATGCTAAGTTAGATGAAGAAAGAATTCAATTCCCCATCAAGTTACGCATCATCATTA
AATTAAATTTAAACAA
Found at i:9876029 original size:7 final size:7
Alignment explanation
Indices: 9876012--9876041 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
9876002 ATCGCTTAAA
9876012 CATTAGAC
1 CATT-GAC
9876020 CATTGAC
1 CATTGAC
9876027 CATTGAC
1 CATTGAC
9876034 CATTGAC
1 CATTGAC
9876041 C
1 C
9876042 CCACTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (7 bp):
CATTGAC
Found at i:9879016 original size:2 final size:2
Alignment explanation
Indices: 9879009--9879042 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
9878999 ATACTCCTTT
* *
9879009 CA CA CA CA CC CA CC CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
9879043 TATATATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:9892824 original size:15 final size:15
Alignment explanation
Indices: 9892800--9892860 Score: 86
Period size: 15 Copynumber: 4.1 Consensus size: 15
9892790 ACATTACAAT
9892800 GTAATGTGATTACAG
1 GTAATGTGATTACAG
*
9892815 GTAATATGATTACAG
1 GTAATGTGATTACAG
* *
9892830 GTAATGTGATTGCAA
1 GTAATGTGATTACAG
*
9892845 GTAATGTGATTGCAG
1 GTAATGTGATTACAG
9892860 G
1 G
9892861 GAAAATAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.33
Consensus pattern (15 bp):
GTAATGTGATTACAG
Found at i:9893069 original size:60 final size:58
Alignment explanation
Indices: 9892996--9893179 Score: 186
Period size: 56 Copynumber: 3.2 Consensus size: 58
9892986 CTAATTATTA
**
9892996 AAATATAAGTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTT
1 AAATATATTTTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATTT-TT
*
9893056 AAATATATTTTTAATATCA--TATA-TTTTATT-TTTATTTATTAGTATAATAT--TTTATT
1 AAATATATTTTTAATAT-ATTTATATTTTTATTATTAATTT-TTA-TATAATATCATTT-TT
* * * *
9893112 --TTTTATTTTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTA
1 AAATATATTTTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTTT
9893169 AAATATATTTT
1 AAATATATTTT
9893180 AATGTCATAT
Statistics
Matches: 101, Mismatches: 11, Indels: 25
0.74 0.08 0.18
Matches are distributed among these distances:
53 1 0.01
54 13 0.13
55 12 0.12
56 20 0.20
57 18 0.18
58 10 0.10
59 11 0.11
60 15 0.15
61 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (58 bp):
AAATATATTTTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTTT
Found at i:9893124 original size:21 final size:22
Alignment explanation
Indices: 9893082--9893155 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
9893072 TCATATATTT
*
9893082 TATTTT-TATTTATTAGTA-TAA
1 TATTTTATATTTA-TATTATTAA
* *
9893103 TATTTTAT-TTTTTATTTTTAA
1 TATTTTATATTTATATTATTAA
9893124 TATATTTATATTTATATTATTAA
1 TAT-TTTATATTTATATTATTAA
9893147 T-TTTTATAT
1 TATTTTATAT
9893156 AATATCATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.07
21 22 0.50
22 7 0.16
23 12 0.27
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (22 bp):
TATTTTATATTTATATTATTAA
Found at i:9893128 original size:23 final size:25
Alignment explanation
Indices: 9893074--9893136 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 25
9893064 TTTTAATATC
9893074 ATATATTTTA-TTTTTATTTATTAG
1 ATATATTTTATTTTTTATTTATTAG
9893098 TATAATATTTTATTTTTTATTT-TTA-
1 -AT-ATATTTTATTTTTTATTTATTAG
9893123 ATATATTTATATTT
1 ATATATTT-TATTT
9893137 ATATTATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.17
24 7 0.20
25 2 0.06
26 11 0.31
27 9 0.26
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (25 bp):
ATATATTTTATTTTTTATTTATTAG
Found at i:9893167 original size:48 final size:45
Alignment explanation
Indices: 9893115--9893237 Score: 113
Period size: 48 Copynumber: 2.6 Consensus size: 45
9893105 TTTTATTTTT
9893115 TATTTTTAATATATTTATATTTATATTATTAATTTTTATATAATATCA
1 TATTTTTAATATATTT-TATTTATATT-TT-ATTTTTATATAATATCA
** * * *
9893163 TATTTAAAATATATTTTAATGTCATATATTTTATTTTTATTTATTATTA
1 TATTTTTAATATATTTT-AT-T--TATATTTTATTTTTATATAATATCA
* *
9893212 TAATTTT-ATATATTTTATTTTTATTT
1 TATTTTTAATATATTTTATTTATATTT
9893238 CTTTAATATT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
44 6 0.10
46 1 0.02
47 3 0.05
48 25 0.40
49 19 0.31
50 2 0.03
51 6 0.10
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (45 bp):
TATTTTTAATATATTTTATTTATATTTTATTTTTATATAATATCA
Found at i:9893208 original size:112 final size:114
Alignment explanation
Indices: 9893005--9893234 Score: 369
Period size: 112 Copynumber: 2.0 Consensus size: 114
9892995 AAAATATAAG
* *
9893005 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTATATTATTAATTTTTATATAATATCATTTCTAAAATATATTTTTAA
*
9893070 TATCATATATTTTATTTTTATTTATTAGTATAATATTT-TATTTTTTATT
66 TATCATATATTTTATTTTTATTTATTAGTATAAT-TTTATATATTTTATT
9893119 TTTAATATATTTATA-TTTATATTATTAATTTTTATATAATATCATATT-TAAAATATA-TTTTA
1 TTTAATATATTTATATTTTATATTATTAATTTTTATATAATATCAT-TTCTAAAATATATTTTTA
* *
9893181 ATGTCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
65 ATATCATATATTTTATTTTTATTTATTAGTATAATTTTATATATTTTATT
9893231 TTTA
1 TTTA
9893235 TTTCTTTAAT
Statistics
Matches: 109, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
111 3 0.03
112 52 0.48
113 37 0.34
114 17 0.16
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (114 bp):
TTTAATATATTTATATTTTATATTATTAATTTTTATATAATATCATTTCTAAAATATATTTTTAA
TATCATATATTTTATTTTTATTTATTAGTATAATTTTATATATTTTATT
Found at i:9893265 original size:34 final size:33
Alignment explanation
Indices: 9893186--9893270 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
9893176 TTTTAATGTC
*
9893186 ATATATTTTATTTTTATTTATTATTATAATTTT
1 ATATATTTTATTTTTATTTATTATAATAATTTT
* *
9893219 ATATATTTTATTTTTATTTCTT-TAATATTTTT
1 ATATATTTTATTTTTATTTATTATAATAATTTT
* *
9893251 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
9893271 TAATTTGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 17 0.37
33 29 0.63
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTATTATAATAATTTT
Found at i:9893318 original size:7 final size:7
Alignment explanation
Indices: 9893306--9893374 Score: 54
Period size: 7 Copynumber: 9.7 Consensus size: 7
9893296 AATGTTAATT
9893306 TTTTATA
1 TTTTATA
9893313 TTTTATTTTA
1 TTTTA---TA
9893323 TTTTA-A
1 TTTTATA
9893329 TTTT-TA
1 TTTTATA
9893335 TTCTTATA
1 TT-TTATA
*
9893343 TTATATA
1 TTTTATA
9893350 TTTTAT-
1 TTTTATA
*
9893356 TTTAATA
1 TTTTATA
*
9893363 TTTTTTA
1 TTTTATA
9893370 TTTTA
1 TTTTA
9893375 ATTATAATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
6 13 0.27
7 25 0.51
8 4 0.08
10 7 0.14
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTATA
Found at i:9893341 original size:6 final size:5
Alignment explanation
Indices: 9893311--9893374 Score: 51
Period size: 5 Copynumber: 12.4 Consensus size: 5
9893301 TAATTTTTTA
* *
9893311 TATTT TATTT TATTT TAATTTT TATTCT TATAT TA-TA TATTT TATTT
1 TATTT TATTT TATTT T-A-TTT TATT-T TATTT TATTT TATTT TATTT
*
9893358 TAATAT T-TTT TATTT TA
1 T-ATTT TATTT TATTT TA
9893375 ATTATAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
4 5 0.11
5 28 0.60
6 10 0.21
7 4 0.09
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:9893541 original size:42 final size:42
Alignment explanation
Indices: 9893482--9893580 Score: 175
Period size: 42 Copynumber: 2.4 Consensus size: 42
9893472 GGGTTTGGAC
*
9893482 TGCAATC--ACATTACATCCATTGGCTGTAATGTGATTGCAT
1 TGCAATCTTACATTGCATCCATTGGCTGTAATGTGATTGCAT
9893522 TGCAATCTTACATTGCATCCATTGGCTGTAATGTGATTGCAT
1 TGCAATCTTACATTGCATCCATTGGCTGTAATGTGATTGCAT
9893564 TGCAATCTTACATTGCA
1 TGCAATCTTACATTGCA
9893581 GTGGTCTGTT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
40 7 0.12
42 49 0.88
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (42 bp):
TGCAATCTTACATTGCATCCATTGGCTGTAATGTGATTGCAT
Found at i:9914373 original size:87 final size:87
Alignment explanation
Indices: 9914227--9914386 Score: 257
Period size: 87 Copynumber: 1.8 Consensus size: 87
9914217 ATGGTAGAAG
* * *
9914227 ACTCATGCTTATATACTTAAAAACCCACATCTCTTATTGATATGAGCTCCATAACATTCTACCTC
1 ACTCATGCTTATATACCTAAAAACCCACATCTATTATTGATATGAGATCCATAACATTCTACCTC
9914292 ACCTAATTGTACAACGTAAAAA
66 ACCTAATTGTACAACGTAAAAA
* * *
9914314 ACTCATGCTTATATACCTAAAAACCCACATCTATTATTGATATGAGATCCGTGACATTCTATCTC
1 ACTCATGCTTATATACCTAAAAACCCACATCTATTATTGATATGAGATCCATAACATTCTACCTC
*
9914379 ATCTAATT
66 ACCTAATT
9914387 ATGTAACGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 66 1.00
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.33
Consensus pattern (87 bp):
ACTCATGCTTATATACCTAAAAACCCACATCTATTATTGATATGAGATCCATAACATTCTACCTC
ACCTAATTGTACAACGTAAAAA
Found at i:9915160 original size:19 final size:20
Alignment explanation
Indices: 9915128--9915166 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
9915118 ATAATGTTCA
9915128 AAAAAAACTCTTAAATTAATT
1 AAAAAAACTCTTAAA-TAATT
9915149 AAAAAAA-T-TTAAATAATT
1 AAAAAAACTCTTAAATAATT
9915167 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 1 0.06
21 7 0.39
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAAACTCTTAAATAATT
Found at i:9915200 original size:21 final size:21
Alignment explanation
Indices: 9915174--9915216 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
9915164 ATTTTTTATT
9915174 TTTTTATTATATTTA-ATTAAA
1 TTTTTA-TATATTTATATTAAA
*
9915195 TTTTTATATTTTTATATTAAA
1 TTTTTATATATTTATATTAAA
9915216 T
1 T
9915217 CATATAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTATATATTTATATTAAA
Found at i:9919735 original size:16 final size:16
Alignment explanation
Indices: 9919716--9919758 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
9919706 TTTACCTTTG
9919716 ATTAATTTTTAAAATT
1 ATTAATTTTTAAAATT
* *
9919732 ATT-ATTATATAAATTT
1 ATTAATT-TTTAAAATT
9919748 ATTAATTTTTA
1 ATTAATTTTTA
9919759 TATTAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
15 3 0.14
16 16 0.73
17 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTAATTTTTAAAATT
Found at i:9938319 original size:13 final size:13
Alignment explanation
Indices: 9938301--9938325 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9938291 TTTTGATCGA
9938301 GATAAGGGATAAG
1 GATAAGGGATAAG
9938314 GATAAGGGATAA
1 GATAAGGGATAA
9938326 TTTCCTTTTT
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:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (13 bp):
GATAAGGGATAAG
Found at i:9957319 original size:34 final size:33
Alignment explanation
Indices: 9957249--9957329 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
9957239 TTTTAATGTC
* * *
9957249 ATATTTTATTTTTATTTTTTATTATAATTTTAT
1 ATATTTTATTTTCATTCTTTAATATAATTTTAT
9957282 ATATTTTATTTTCATCTCTTTAATATAAATTTT-T
1 ATATTTTATTTTCAT-TCTTTAATAT-AATTTTAT
9957316 ATATTATATATTTT
1 ATATT-T-TATTTT
9957330 GTTTTAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 14 0.34
34 14 0.34
35 7 0.17
36 6 0.15
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (33 bp):
ATATTTTATTTTCATTCTTTAATATAATTTTAT
Found at i:9957384 original size:5 final size:5
Alignment explanation
Indices: 9957374--9957428 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
9957364 TAACTTCTTA
* * *
9957374 TATTT TATTT TATTT TATTT TA-TT T-TTT GATTTT TATAT TA-TA TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT TATTT TATTT
9957422 TATTT TA
1 TATTT TA
9957429 ATATNNNNNN
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
4 7 0.17
5 29 0.73
6 4 0.10
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:9958922 original size:103 final size:103
Alignment explanation
Indices: 9958710--9958915 Score: 367
Period size: 103 Copynumber: 2.0 Consensus size: 103
9958700 GGTGTTGGCG
* *
9958710 CAAATGGGATTTAGATGAAATTTAAATAATCGGCAAAATTGACTTCAAGATAAATCTTTCAATAA
1 CAAATGAGATTTAAATGAAATTTAAATAATCGGCAAAATTGACTTCAAGATAAATCTTTCAATAA
9958775 ACGTTATCTTAAAACTTATTTCATTTTCATCACTCGGT
66 ACGTTATCTTAAAACTTATTTCATTTTCATCACTCGGT
*
9958813 CAAATGAGATTTAAATGAAATTTAAATAATCGGTAAAATTGACTTCAAGATAAATCTTTCAATAA
1 CAAATGAGATTTAAATGAAATTTAAATAATCGGCAAAATTGACTTCAAGATAAATCTTTCAATAA
* *
9958878 ACGTTATCTTGAAACTTATTTTATTTTCATCACTCGGT
66 ACGTTATCTTAAAACTTATTTCATTTTCATCACTCGGT
9958916 ATAATGAATG
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (103 bp):
CAAATGAGATTTAAATGAAATTTAAATAATCGGCAAAATTGACTTCAAGATAAATCTTTCAATAA
ACGTTATCTTAAAACTTATTTCATTTTCATCACTCGGT
Found at i:9963180 original size:21 final size:21
Alignment explanation
Indices: 9963156--9963197 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9963146 CCTGGACTTG
*
9963156 CAAGGGATTAGAGCAAAACAT
1 CAAGGGATTAGAACAAAACAT
9963177 CAAGGGATTAGAACAAAACAT
1 CAAGGGATTAGAACAAAACAT
9963198 GGTCAATCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (21 bp):
CAAGGGATTAGAACAAAACAT
Found at i:9965029 original size:15 final size:16
Alignment explanation
Indices: 9965004--9965040 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
9964994 GTTTAATACT
*
9965004 TTATAATATAATGTGA
1 TTATAATATAATATGA
9965020 TTATAA-ATAATATGA
1 TTATAATATAATATGA
9965035 TTATAA
1 TTATAA
9965041 GGAAGATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (16 bp):
TTATAATATAATATGA
Found at i:9965312 original size:21 final size:20
Alignment explanation
Indices: 9965258--9965313 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
9965248 TAATGCCATA
9965258 TATAATATTTTA-TTTTTATT
1 TATAA-ATTTTATTTTTTATT
* * * *
9965278 TCTTAATATAATTTTTTATAT
1 TATAAATTTTATTTTTTAT-T
9965299 TATAAATTTTATTTT
1 TATAAATTTTATTTT
9965314 AATTTATTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
19 4 0.15
20 10 0.38
21 12 0.46
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TATAAATTTTATTTTTTATT
Found at i:9971266 original size:51 final size:51
Alignment explanation
Indices: 9971179--9971379 Score: 233
Period size: 51 Copynumber: 3.9 Consensus size: 51
9971169 AATGGCATTG
* * * * * * ** *
9971179 TTCTTCCAACAATACCAAGTTCTTTTCTTGAATCAGCTCCCTGCTCCAAAG
1 TTCTCCCAACTATTCCAACTTCTTTTCTAGATTCAGCAGCCTGCTCCAAAC
* * *
9971230 TTTTCCCAACTATTCCAGCTTCTTTTCTAGATTCAGCAGCCGGCTCCAAAC
1 TTCTCCCAACTATTCCAACTTCTTTTCTAGATTCAGCAGCCTGCTCCAAAC
* **
9971281 TTCTCCCAGCTATTCCAACTTCCCTTCTAGATTCAGCAGCCTGCTCCAAAC
1 TTCTCCCAACTATTCCAACTTCTTTTCTAGATTCAGCAGCCTGCTCCAAAC
* *
9971332 TTCTCCCGGA-TATTCCAACTTCTTTTCTTGATTCAGCAGCCTGCTCCA
1 TTCTCCC-AACTATTCCAACTTCTTTTCTAGATTCAGCAGCCTGCTCCA
9971380 GCCTTGTATC
Statistics
Matches: 126, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
51 126 1.00
ACGTcount: A:0.21, C:0.34, G:0.11, T:0.33
Consensus pattern (51 bp):
TTCTCCCAACTATTCCAACTTCTTTTCTAGATTCAGCAGCCTGCTCCAAAC
Found at i:9972903 original size:31 final size:31
Alignment explanation
Indices: 9972868--9972927 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
9972858 TAAAAACAGG
*
9972868 AACATAAAAGATCTTATGATCTCAATATAGA
1 AACATAAAACATCTTATGATCTCAATATAGA
* *
9972899 AACATAAAACATTTTCTGATCTCAATATA
1 AACATAAAACATCTTATGATCTCAATATA
9972928 AATCTCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.32
Consensus pattern (31 bp):
AACATAAAACATCTTATGATCTCAATATAGA
Found at i:9983925 original size:63 final size:63
Alignment explanation
Indices: 9983847--9983973 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
9983837 GGCTTAAACC
9983847 TAACAATCAGACTTAAAACCAAGCATCACCCTAATGACAATAATTGTTAATTATAAAAATCTA
1 TAACAATCAGACTTAAAACCAAGCATCACCCTAATGACAATAATTGTTAATTATAAAAATCTA
*
9983910 TAACAATCAGACTTAAAACCAAGCATCACCCTAATGACAATAATTGTTAATTATAAAGATCTA
1 TAACAATCAGACTTAAAACCAAGCATCACCCTAATGACAATAATTGTTAATTATAAAAATCTA
9983973 T
1 T
9983974 GCCAGCCTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (63 bp):
TAACAATCAGACTTAAAACCAAGCATCACCCTAATGACAATAATTGTTAATTATAAAAATCTA
Found at i:10001269 original size:15 final size:15
Alignment explanation
Indices: 10001249--10001277 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10001239 AGTAAACAAA
10001249 CGTTGACATCTTAAT
1 CGTTGACATCTTAAT
10001264 CGTTGACATCTTAA
1 CGTTGACATCTTAA
10001278 ACTATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (15 bp):
CGTTGACATCTTAAT
Found at i:10023088 original size:22 final size:23
Alignment explanation
Indices: 10023052--10023114 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 23
10023042 TTATTAATTT
*
10023052 TATTT-ATTTATAATAAAAATG-
1 TATTTAATTTAAAATAAAAATGA
*
10023073 TATTTAATTTAAAATATAAATGTAAA
1 TATTTAATTTAAAATAAAAATG---A
10023099 TATTTAATTTAAAATA
1 TATTTAATTTAAAATA
10023115 TAATAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 5 0.14
22 14 0.40
26 16 0.46
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (23 bp):
TATTTAATTTAAAATAAAAATGA
Found at i:10023115 original size:14 final size:14
Alignment explanation
Indices: 10023073--10023115 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
10023063 AATAAAAATG
10023073 TATTTAATTTAAAA
1 TATTTAATTTAAAA
* *
10023087 TA-TAAATGT-AAA
1 TATTTAATTTAAAA
10023099 TATTTAATTTAAAA
1 TATTTAATTTAAAA
10023113 TAT
1 TAT
10023116 AATAAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 5 0.22
13 10 0.43
14 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
TATTTAATTTAAAA
Found at i:10031948 original size:44 final size:44
Alignment explanation
Indices: 10031885--10031973 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
10031875 CTTTATATAT
* * *
10031885 AGAGAGAGGAGAAAATCATAATCTTAATTCTAAACGAATTAAGA
1 AGAGAGAAGAGAAAATCATAATCCTAATTATAAACGAATTAAGA
10031929 AGAGAGAAGAGAAAATCATAATCCTAATTATAAACGAATTAAGA
1 AGAGAGAAGAGAAAATCATAATCCTAATTATAAACGAATTAAGA
10031973 A
1 A
10031974 TTGGAAGGGC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (44 bp):
AGAGAGAAGAGAAAATCATAATCCTAATTATAAACGAATTAAGA
Found at i:10034948 original size:18 final size:18
Alignment explanation
Indices: 10034925--10034969 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
10034915 ATTATGAATT
10034925 AATATTTTTAA-TCAAAAA
1 AATATTTTTAAGT-AAAAA
*
10034943 AATATTTATTAAGTTAAAA
1 AATATTT-TTAAGTAAAAA
10034962 AATATTTT
1 AATATTTT
10034970 ATTTATAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 15 0.62
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AATATTTTTAAGTAAAAA
Found at i:10036185 original size:1 final size:1
Alignment explanation
Indices: 10036181--10036208 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
10036171 TTTTTTTTTT
10036181 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
10036209 TGGGTTGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:10042593 original size:31 final size:28
Alignment explanation
Indices: 10042548--10042609 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 28
10042538 AATTTTCAAG
10042548 TTTTTTTATTTTTTTAATTTATATTATTA
1 TTTTTTTATTTTTTTAATTTATATTA-TA
* *
10042577 TTTTTATTAATTTTTTTTATTTCTATTATA
1 TTTTT-TT-ATTTTTTTAATTTATATTATA
10042607 TTT
1 TTT
10042610 ACACATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.17
30 7 0.24
31 17 0.59
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTTTTTATTTTTTTAATTTATATTATA
Found at i:10042753 original size:21 final size:22
Alignment explanation
Indices: 10042723--10042764 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
10042713 TTGTTCTTCT
10042723 TTTTTCTATTATATGAATTTTA
1 TTTTTCTATTATATGAATTTTA
* *
10042745 TTTTT-TATTATTTTAATTTT
1 TTTTTCTATTATATGAATTTT
10042765 TACAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTTCTATTATATGAATTTTA
Found at i:10043312 original size:13 final size:12
Alignment explanation
Indices: 10043285--10043335 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 12
10043275 ATTAATTTTT
10043285 TAAAAAATAATAA
1 TAAAAAATAA-AA
10043298 TAAATAAATAAAA
1 TAAA-AAATAAAA
10043311 TAAAAAATAAATA
1 TAAAAAATAAA-A
10043324 TAAAAAGATAAA
1 TAAAAA-ATAAA
10043336 GATATGTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.20
13 17 0.49
14 11 0.31
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:10043318 original size:16 final size:16
Alignment explanation
Indices: 10043293--10043323 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10043283 TTTAAAAAAT
*
10043293 AATAATAAATAAATAA
1 AATAAAAAATAAATAA
10043309 AATAAAAAATAAATA
1 AATAAAAAATAAATA
10043324 TAAAAAGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AATAAAAAATAAATAA
Done.