Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007716.1 Hibiscus syriacus cultivar Beakdansim tig00109945_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4364108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 17
Found at i:2375696 original size:30 final size:30
Alignment explanation
Indices: 2375662--2375738 Score: 145
Period size: 30 Copynumber: 2.6 Consensus size: 30
2375652 ATATAATTTA
*
2375662 CCCATTAAATCACATTCTTTTTTTTTATTG
1 CCCATCAAATCACATTCTTTTTTTTTATTG
2375692 CCCATCAAATCACATTCTTTTTTTTTATTG
1 CCCATCAAATCACATTCTTTTTTTTTATTG
2375722 CCCATCAAATCACATTC
1 CCCATCAAATCACATTC
2375739 GATAAAATAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (30 bp):
CCCATCAAATCACATTCTTTTTTTTTATTG
Found at i:2377121 original size:26 final size:27
Alignment explanation
Indices: 2377080--2377131 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
2377070 TTGAGTTTTT
2377080 TTAAAATAA-TAATTTTAAATTTTTCG
1 TTAAAATAATTAATTTTAAATTTTTCG
**
2377106 TTAAAATAATTTTTTTTTAAATTTTT
1 TTAAAATAA-TTAATTTTAAATTTTT
2377132 AAACGACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
28 13 0.59
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TTAAAATAATTAATTTTAAATTTTTCG
Found at i:2377505 original size:12 final size:12
Alignment explanation
Indices: 2377488--2377546 Score: 57
Period size: 12 Copynumber: 4.7 Consensus size: 12
2377478 ACGGCTATTA
*
2377488 TTTTTATTATAT
1 TTTTTAATATAT
2377500 TTTTTAATATATT
1 TTTTTAATATA-T
2377513 TTTTTAA-ATAT
1 TTTTTAATATAT
*
2377524 TATTTAAAATATTAT
1 T-TTT-TAATA-TAT
2377539 TTTTTAAT
1 TTTTTAAT
2377547 CGAAAATGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 2 0.05
12 16 0.41
13 13 0.33
14 4 0.10
15 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTTAATATAT
Found at i:2377516 original size:14 final size:15
Alignment explanation
Indices: 2377492--2377528 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2377482 CTATTATTTT
2377492 TATTATATTTTTT-AA
1 TATTAT-TTTTTTAAA
2377507 TA-TATTTTTTTAAA
1 TATTATTTTTTTAAA
2377521 TATTATTT
1 TATTATTT
2377529 AAAATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.30
14 7 0.35
15 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTATTTTTTTAAA
Found at i:2377523 original size:24 final size:25
Alignment explanation
Indices: 2377483--2377542 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
2377473 AATATACGGC
* * *
2377483 TATTATTTTTATTATATTTTTTAATA
1 TATTATTTTTA-AATATTATTTAAAA
2377509 TATT-TTTTTAAATATTATTTAAAA
1 TATTATTTTTAAATATTATTTAAAA
2377533 TATTATTTTT
1 TATTATTTTT
2377543 TAATCGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.50
25 11 0.37
26 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TATTATTTTTAAATATTATTTAAAA
Found at i:2382305 original size:42 final size:40
Alignment explanation
Indices: 2382258--2382734 Score: 273
Period size: 42 Copynumber: 11.2 Consensus size: 40
2382248 TCGAGTATAT
*
2382258 ATTTAATAATAATTATTTCAATTTAATCATTTCAATTTAATG
1 ATTTAATAATAATTATTT-AATTTAATAATTT-AATTTAATG
* * *
2382300 ATTTAATAATAACTATTTAACTTTAATAATTTAATAATAATT
1 ATTTAATAATAATTATTTAA-TTTAATAATTTAAT-TTAATG
* * * * * *
2382342 ATTTAACT-TTAATGATTTAAATTAAATACTTTAATAATAATT
1 ATTTAA-TAATAATTATTT-AATTTAATAATTTAAT-TTAATG
* * * ** * * * *
2382384 ACTTAACT-TTAATGATTTAAAAATAATTACTTCACTTTAATA
1 ATTTAA-TAATAATTATTT-AATTTAA-TAATTTAATTTAATG
* * *
2382426 ATTTAACT-TTAATGATTT-ATTAATAATTATTTAAATTTAATG
1 ATTTAA-TAATAATTATTTAATT--TAATAATTT-AATTTAATG
* * * *
2382468 ATTGAA-ATATAATAATTTAATAATAATTATTTAACTTTAATG
1 ATTTAATA-ATAATTATTTAAT-TTAATAATTTAA-TTTAATG
* *
2382510 ATTTCAATTAAATAATT-TAATAATAATTACTTAATTTAACTTTAATG
1 ATTT-AA-T-AATAATTAT-TTAAT--TTA-ATAATTTAA-TTTAATG
*
2382557 ATTTAATAATAATTACTTTACTTTAATAATTTAACTTTAATG
1 ATTTAATAATAATTA-TTTAATTTAATAATTTAA-TTTAATG
* * * *
2382599 ATTTATTAATAATTATTTAACTTTAATGATTAAAATTTAATA
1 ATTTAATAATAATTATTTAA-TTTAATAATT-TAATTTAATG
* * *
2382641 ATTTAATAATAATTATTTAATTTTAATGATTTCAATTAAATA
1 ATTTAATAATAATTATTTAA-TTTAATAATTT-AATTTAATG
* *
2382683 ATTTAATAATAATTACTTAACTTTAATGATTTAACTTTAATG
1 ATTTAATAATAATTATTTAA-TTTAATAATTTAA-TTTAATG
2382725 ATTTAATAAT
1 ATTTAATAAT
2382735 TTAATAATTA
Statistics
Matches: 358, Mismatches: 51, Indels: 52
0.78 0.11 0.11
Matches are distributed among these distances:
40 1 0.00
41 16 0.04
42 275 0.77
43 19 0.05
44 8 0.02
45 13 0.04
46 7 0.02
47 19 0.05
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (40 bp):
ATTTAATAATAATTATTTAATTTAATAATTTAATTTAATG
Found at i:2382317 original size:28 final size:28
Alignment explanation
Indices: 2382293--2382785 Score: 145
Period size: 28 Copynumber: 17.4 Consensus size: 28
2382283 ATCATTTCAA
2382293 TTTAATGATTTAATAATAACTATTTAAC
1 TTTAATGATTTAATAATAACTATTTAAC
* *
2382321 TTTAATAATTTAATAATAATTATTTAAC
1 TTTAATGATTTAATAATAACTATTTAAC
* *
2382349 TTTAATGATTTAA-ATTAAATACTTTAA-
1 TTTAATGATTTAATAATAACTA-TTTAAC
* * * * *
2382376 TAATAATTACTTAACT-TTAA-TGATTTAAA
1 T-TTAATGATTTAA-TAATAACT-ATTTAAC
** * * * *
2382405 AATAATTACTTCACT-TTAA-TAATTTAAC
1 TTTAATGA-TTTAATAATAACT-ATTTAAC
* * *
2382433 TTTAATGATTTATTAATAATTATTTAAA
1 TTTAATGATTTAATAATAACTATTTAAC
*
2382461 TTTAATGATTGAA-ATATAA-TAATTTAA-
1 TTTAATGATTTAATA-ATAACT-ATTTAAC
* * *
2382488 TAATAATTATTTAACT-TTAA-TGATTTCAA-
1 T-TTAATGATTTAA-TAATAACT-ATTT-AAC
* *
2382517 TTAAATAATTTAATAATAATTACTTAATTTAAC
1 TTTAATGATTTAATAAT-A--AC-T-ATTTAAC
*
2382550 TTTAATGATTTAATAATAATTACTTT-AC
1 TTTAATGATTTAATAATAACTA-TTTAAC
* *
2382578 TTTAATAATTTAACT-TTAA-TGATTT-A-
1 TTTAATGATTTAA-TAATAACT-ATTTAAC
* * * *
2382604 TTAATAATTATTTAACT-TTAA-TGATTAAAA
1 TT--TAATGATTTAA-TAATAACT-ATTTAAC
* * *
2382634 TTTAATAATTTAATAATAATTATTTAAT
1 TTTAATGATTTAATAATAACTATTTAAC
*
2382662 TTTAATGATTTCAAT--TAAATAATTTAA-
1 TTTAATGATTT-AATAATAACT-ATTTAAC
* * * *
2382689 TAATAATTACTTAACT-TTAA-TGATTTAAC
1 T-TTAATGATTTAA-TAATAACT-ATTTAAC
*
2382718 TTTAATGATTTAATAATTTAA-TAATTAAAC
1 TTTAATGATTTAATAA--TAACT-ATTTAAC
* *
2382748 TTTAATGATTTATTAATAATTATTTAAC
1 TTTAATGATTTAATAATAACTATTTAAC
2382776 TTTAATGATT
1 TTTAATGATT
2382786 AAAGTTTAAT
Statistics
Matches: 366, Mismatches: 58, Indels: 82
0.72 0.11 0.16
Matches are distributed among these distances:
26 2 0.01
27 29 0.08
28 256 0.70
29 27 0.07
30 28 0.08
31 1 0.00
32 3 0.01
33 20 0.05
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (28 bp):
TTTAATGATTTAATAATAACTATTTAAC
Found at i:2382339 original size:70 final size:69
Alignment explanation
Indices: 2382258--2382716 Score: 367
Period size: 70 Copynumber: 6.7 Consensus size: 69
2382248 TCGAGTATAT
* *
2382258 ATTTAATAATAATTATTTCAA-TTTAATCATTTCAATTTAATGATTTAATAATAACTATTTAACT
1 ATTTAATAATAATTATTT-AACTTTAATGATTT-AATTTAATGATTTAATAATAATTATTTAACT
*
2382322 TTAATA
64 TTAATG
* *
2382328 ATTTAATAATAATTATTTAACTTTAATGATTTAAATTAAAT-ACTTTAATAATAATTACTTAACT
1 ATTTAATAATAATTATTTAACTTTAATGATTT-AATTTAATGA-TTTAATAATAATTATTTAACT
2382392 TTAATG
64 TTAATG
* * * * * *
2382398 ATTTAAAAATAATTACTTCACTTTAATAATTTAACTTTAATGATTTATTAATAATTATTTAAATT
1 ATTTAATAATAATTATTTAACTTTAATGATTTAA-TTTAATGATTTAATAATAATTATTTAACTT
2382463 TAATG
65 TAATG
* * * * * *
2382468 ATTGAA-ATATAATAATTTAA-TAATAATTATTTAACTTTAATGATTTCAATTA-AATAATTTAA
1 ATTTAATA-ATAATTATTTAACT-TTAATGATTTAA-TTTAATGATTT-AATAATAATTATTTAA
2382530 ---TAAT-
62 CTTTAATG
* * * * * * *
2382534 AATTACT--T-A--ATTTAACTTTAATGATTTAATAATAATTACTTTACT-TTAATAATTTAACT
1 ATTTAATAATAATTATTTAACTTTAATGATTTAAT-TTAATGA-TTTAATAATAATTATTTAACT
2382593 TTAATG
64 TTAATG
* * * *
2382599 ATTTATTAATAATTATTTAACTTTAATGATTAAAATTTAATAATTTAATAATAATTATTTAATTT
1 ATTTAATAATAATTATTTAACTTTAATGATT-TAATTTAATGATTTAATAATAATTATTTAACTT
2382664 TAATG
65 TAATG
* * * * *
2382669 ATTTCAATTA-AATAATTTAA-TAATAATTACTTAACTTTAATGATTTAA
1 ATTT-AATAATAATTATTTAACT-TTAATGATTTAA-TTTAATGATTTAA
2382717 CTTTAATGAT
Statistics
Matches: 314, Mismatches: 49, Indels: 52
0.76 0.12 0.13
Matches are distributed among these distances:
60 1 0.00
61 33 0.11
62 4 0.01
63 1 0.00
64 5 0.02
65 5 0.02
66 3 0.01
67 5 0.02
68 1 0.00
69 15 0.05
70 231 0.74
71 10 0.03
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (69 bp):
ATTTAATAATAATTATTTAACTTTAATGATTTAATTTAATGATTTAATAATAATTATTTAACTTT
AATG
Found at i:2382560 original size:14 final size:14
Alignment explanation
Indices: 2382543--2382802 Score: 160
Period size: 14 Copynumber: 18.4 Consensus size: 14
2382533 TAATTACTTA
2382543 ATTTAACTTTAATG
1 ATTTAACTTTAATG
* *
2382557 ATTTAA-TAATAATT
1 ATTTAACT-TTAATG
*
2382571 ACTTT-ACTTTAATA
1 A-TTTAACTTTAATG
2382585 ATTTAACTTTAATG
1 ATTTAACTTTAATG
*
2382599 ATTT-A-TTAATAATT
1 ATTTAACTT--TAATG
2382613 ATTTAACTTTAATG
1 ATTTAACTTTAATG
* * *
2382627 ATTAAAATTTAATA
1 ATTTAACTTTAATG
* *
2382641 ATTTAA-TAATAATT
1 ATTTAACT-TTAATG
*
2382655 ATTTAATTTTAATG
1 ATTTAACTTTAATG
* *
2382669 ATTTCAA-TTAAATA
1 ATTT-AACTTTAATG
* *
2382683 ATTTAA-TAATAATT
1 ATTTAACT-TTAATG
*
2382697 ACTTAACTTTAATG
1 ATTTAACTTTAATG
2382711 ATTTAACTTTAATG
1 ATTTAACTTTAATG
* *
2382725 ATTTAATAATTTAATA
1 ATTT-A-ACTTTAATG
*
2382741 ATTAAACTTTAATG
1 ATTTAACTTTAATG
*
2382755 ATTT-A-TTAATAATT
1 ATTTAACTT--TAATG
2382769 ATTTAACTTTAATG
1 ATTTAACTTTAATG
* * *
2382783 ATTAAAGTTTAATA
1 ATTTAACTTTAATG
2382797 ATTTAA
1 ATTTAA
2382803 TAATAGTAAT
Statistics
Matches: 191, Mismatches: 36, Indels: 38
0.72 0.14 0.14
Matches are distributed among these distances:
12 4 0.02
13 10 0.05
14 151 0.79
15 12 0.06
16 14 0.07
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (14 bp):
ATTTAACTTTAATG
Found at i:2382638 original size:7 final size:8
Alignment explanation
Indices: 2382628--2382806 Score: 69
Period size: 8 Copynumber: 23.0 Consensus size: 8
2382618 ACTTTAATGA
2382628 TTAA-AAT
1 TTAATAAT
2382635 TTAATAAT
1 TTAATAAT
2382643 TTAATAA-
1 TTAATAAT
*
2382650 -TAATTAT
1 TTAATAAT
2382657 TTAAT--T
1 TTAATAAT
*
2382663 TTAATGAT
1 TTAATAAT
*
2382671 TT--CAAT
1 TTAATAAT
*
2382677 TAAATAAT
1 TTAATAAT
2382685 TTAATAAT
1 TTAATAAT
*
2382693 AATTACTTAACT
1 --TTA-ATAA-T
*
2382705 TTAATGAT
1 TTAATAAT
*
2382713 TT-A-ACT
1 TTAATAAT
*
2382719 TTAATGAT
1 TTAATAAT
2382727 TTAATAAT
1 TTAATAAT
2382735 TTAATAA-
1 TTAATAAT
*
2382742 TTAA-ACT
1 TTAATAAT
*
2382749 TTAATGAT
1 TTAATAAT
*
2382757 TTATTAAT
1 TTAATAAT
*
2382765 AATTATTTAACT
1 --TTA-ATAA-T
*
2382777 TTAATGA-
1 TTAATAAT
*
2382784 TTAA-AGT
1 TTAATAAT
2382791 TTAATAAT
1 TTAATAAT
2382799 TTAATAAT
1 TTAATAAT
2382807 AGTAATGATA
Statistics
Matches: 127, Mismatches: 24, Indels: 41
0.66 0.12 0.21
Matches are distributed among these distances:
6 18 0.14
7 22 0.17
8 62 0.49
9 4 0.03
10 12 0.09
11 7 0.06
12 2 0.02
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (8 bp):
TTAATAAT
Found at i:2385210 original size:173 final size:173
Alignment explanation
Indices: 2384921--2385270 Score: 628
Period size: 173 Copynumber: 2.0 Consensus size: 173
2384911 CATCAAATAT
* *
2384921 AAAATGATCCCTAATTACTATTTAGTTCTCAACATTTTCAAACTTTGTAATTTAATCCCTAAATT
1 AAAATGATCCCTAATTACTATTTAGCTCTCAACATTTTCAAACTTTGCAATTTAATCCCTAAATT
* *
2384986 TATATATTCTTGCAAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATACCAAC
66 TATAAATTCTTGCAAATTTAACCAATTAAGCATACTAATAATAAATTCCAGCATAGTATACCAAC
*
2385051 TTTTTATAATTTACTCTTATTCCTTAAATTCCTCAAATTTTAC
131 TTTTAATAATTTACTCTTATTCCTTAAATTCCTCAAATTTTAC
*
2385094 AAAATGATCCCTAATTACTATTTGGCTCTCAACATTTTCAAACTTTGCAATTTAATCCCTAAATT
1 AAAATGATCCCTAATTACTATTTAGCTCTCAACATTTTCAAACTTTGCAATTTAATCCCTAAATT
* *
2385159 TATAAATTCTTTCAAATTTAACCAATTAAGCATAGTAATAATAAATTCCAGCATAGTATACCAAC
66 TATAAATTCTTGCAAATTTAACCAATTAAGCATACTAATAATAAATTCCAGCATAGTATACCAAC
2385224 TTTTAATAATTTACTCTTATTCCTTAAATTCCTCAAATTTTAC
131 TTTTAATAATTTACTCTTATTCCTTAAATTCCTCAAATTTTAC
2385267 AAAA
1 AAAA
2385271 CAGACCCTAA
Statistics
Matches: 169, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
173 169 1.00
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (173 bp):
AAAATGATCCCTAATTACTATTTAGCTCTCAACATTTTCAAACTTTGCAATTTAATCCCTAAATT
TATAAATTCTTGCAAATTTAACCAATTAAGCATACTAATAATAAATTCCAGCATAGTATACCAAC
TTTTAATAATTTACTCTTATTCCTTAAATTCCTCAAATTTTAC
Found at i:2385797 original size:24 final size:24
Alignment explanation
Indices: 2385734--2385797 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
2385724 TTGCATGATA
2385734 CAGACGTGCA-ACCCCCCCACATG
1 CAGACGTGCAGACCCCCCCACATG
* *
2385757 TAGACGTACAGGA-CCCCCCACATG
1 CAGACGTGCA-GACCCCCCCACATG
2385781 CAGACGTGCAG-CCCCCC
1 CAGACGTGCAGACCCCCC
2385798 TGCTCAACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 14 0.41
24 19 0.56
25 1 0.03
ACGTcount: A:0.25, C:0.45, G:0.20, T:0.09
Consensus pattern (24 bp):
CAGACGTGCAGACCCCCCCACATG
Found at i:2395553 original size:31 final size:32
Alignment explanation
Indices: 2395509--2395568 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
2395499 GTTTTAAAGA
2395509 AAAATTAAAAGTTTAGATACTAAA-ACATATC
1 AAAATTAAAAGTTTAGATACTAAACACATATC
* *
2395540 AAAATTGATAGTTTAGATACTAAACACAT
1 AAAATTAAAAGTTTAGATACTAAACACAT
2395569 TATGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (32 bp):
AAAATTAAAAGTTTAGATACTAAACACATATC
Found at i:2398183 original size:20 final size:20
Alignment explanation
Indices: 2398158--2398205 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2398148 TCTATCTTAC
* *
2398158 AATTTAATTTATTTCAAATT
1 AATTTAATTTACTTCAAACT
2398178 AATTTAATTTACTTCAAACT
1 AATTTAATTTACTTCAAACT
2398198 AATTTAAT
1 AATTTAAT
2398206 CTAATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTAATTTACTTCAAACT
Found at i:2406303 original size:20 final size:22
Alignment explanation
Indices: 2406261--2406306 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
2406251 TGATAGAGAT
2406261 ATAAAATATGTTGTATAAAATC
1 ATAAAATATGTTGTATAAAATC
*
2406283 ATAAAATAT-TT-TATTAAATC
1 ATAAAATATGTTGTATAAAATC
2406303 ATAA
1 ATAA
2406307 TTTATATTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.52
21 2 0.09
22 9 0.39
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (22 bp):
ATAAAATATGTTGTATAAAATC
Found at i:2419232 original size:45 final size:45
Alignment explanation
Indices: 2419163--2419314 Score: 225
Period size: 45 Copynumber: 3.4 Consensus size: 45
2419153 TGGTATATGG
* * *
2419163 TTATGGAAT-AATGGCAAGTGTATTGGTAAAATAAGCCTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
2419207 TTATGGAACAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
2419252 TTATGGTATTAAATGGTAAGTATATTGGTAAAATAAGGTTACGAGC
1 TTATGG-AATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
2419298 TTATGGGATAAATGGTA
1 TTATGGAATAAATGGTA
2419315 GAAGATTTTA
Statistics
Matches: 97, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
44 8 0.08
45 47 0.48
46 42 0.43
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:2426842 original size:45 final size:45
Alignment explanation
Indices: 2426773--2426925 Score: 211
Period size: 45 Copynumber: 3.4 Consensus size: 45
2426763 TGGTATATGG
* * *
2426773 TTATGGAAT-AATGGCAAGTGTATTGGTAAAAAAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
2426817 TTATGGAACAAATGGTAAGTATATTGGTAAAATAAGCTTAC-ATGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGA-GC
* *
2426862 TTATGGTATTAAATGGTAAGTATATTGGTAAAATAAGGTTACGAGC
1 TTATGG-AATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
2426908 TTATGGGATAAATGGTAA
1 TTATGGAATAAATGGTAA
2426926 AAGATTTTAT
Statistics
Matches: 96, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
44 9 0.09
45 46 0.48
46 40 0.42
47 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.31
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:2433587 original size:31 final size:31
Alignment explanation
Indices: 2433544--2433621 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
2433534 GGTAACATCG
2433544 AGTAAC-AGATTTGTTATAAATCGATAACGTT
1 AGTAACTA-ATTTGTTATAAATCGATAACGTT
*
2433575 AGTAACTAATTTGTTATAAATCGATAATGTT
1 AGTAACTAATTTGTTATAAATCGATAACGTT
* *
2433606 AGTGACTAGTTTGTTA
1 AGTAACTAATTTGTTA
2433622 CTTTTGAAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 42 0.98
32 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.40
Consensus pattern (31 bp):
AGTAACTAATTTGTTATAAATCGATAACGTT
Found at i:2441411 original size:24 final size:24
Alignment explanation
Indices: 2441384--2441430 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2441374 ACAATTAAAT
2441384 GAACGTAAACGAACACAAATGAAC
1 GAACGTAAACGAACACAAATGAAC
*
2441408 GAACGTAAACGAACATAAATGAA
1 GAACGTAAACGAACACAAATGAA
2441431 TAAACATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.55, C:0.17, G:0.17, T:0.11
Consensus pattern (24 bp):
GAACGTAAACGAACACAAATGAAC
Found at i:2441440 original size:24 final size:24
Alignment explanation
Indices: 2441389--2441440 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2441379 TAAATGAACG
* *
2441389 TAAACGAACACAAATGAACGAACG
1 TAAACGAACACAAATGAACAAACA
* *
2441413 TAAACGAACATAAATGAATAAACA
1 TAAACGAACACAAATGAACAAACA
2441437 TAAA
1 TAAA
2441441 ATTAATTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.60, C:0.15, G:0.12, T:0.13
Consensus pattern (24 bp):
TAAACGAACACAAATGAACAAACA
Found at i:2446290 original size:92 final size:91
Alignment explanation
Indices: 2446132--2446427 Score: 414
Period size: 92 Copynumber: 3.2 Consensus size: 91
2446122 ATTTCAATCT
* * * * *
2446132 TTCCTCCATTCGAACAAGAACATTTCACCACATACGTATTCATGCAATCTACATGGAAAATGGAT
1 TTCCTCTATTCGAACAAGAACATTTCACCACATATGTATTCATGAAATCTATATGGAAACT-GAT
*
2446197 TAAACAATTCAATAGGTATAACATTCT
65 TAAACAATTCAATAGGTATAACATTCC
2446224 TTCCTCTATTCGAACAAGAACATTTCACCACATATGTATTCATGAAATCTATATGGCAAACTGAT
1 TTCCTCTATTCGAACAAGAACATTTCACCACATATGTATTCATGAAATCTATATGG-AAACTGAT
* *
2446289 TAAACAATTCAACATGTATAACATTCC
65 TAAACAATTCAATAGGTATAACATTCC
* * * *
2446316 TTCATCTATTTGAACAAGACCATTTCACCATATATGTATTCATGAAATCTATATGGAAAACAT-A
1 TTCCTCTATTCGAACAAGAACATTTCACCACATATGTATTCATGAAATCTATATGG-AAAC-TGA
* *
2446380 TCAAACAATTCAATCGGTATAACATTCC
64 TTAAACAATTCAATAGGTATAACATTCC
*
2446408 TTCCTCTATTAGAACAAGAA
1 TTCCTCTATTCGAACAAGAA
2446428 GGAAACACTT
Statistics
Matches: 182, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
92 177 0.97
93 5 0.03
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (91 bp):
TTCCTCTATTCGAACAAGAACATTTCACCACATATGTATTCATGAAATCTATATGGAAACTGATT
AAACAATTCAATAGGTATAACATTCC
Found at i:2446990 original size:34 final size:34
Alignment explanation
Indices: 2446944--2447008 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
2446934 AATTCAATTC
*
2446944 AATCATGACAACATGCAATAGTTCACCATTCGAA
1 AATCATGACAACATGCAATACTTCACCATTCGAA
* *
2446978 AATCATGGCAACATGCAATACTTTACCATTC
1 AATCATGACAACATGCAATACTTCACCATTC
2447009 AACTTGATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (34 bp):
AATCATGACAACATGCAATACTTCACCATTCGAA
Found at i:2447038 original size:41 final size:41
Alignment explanation
Indices: 2446979--2447107 Score: 186
Period size: 41 Copynumber: 3.1 Consensus size: 41
2446969 CCATTCGAAA
* * * * *
2446979 ATCATGGCAACATGCAATACTTTACCATTCAACTTGATTCG
1 ATCATGACAGCATACAATAATTCACCATTCAACTTGATTCG
2447020 ATCATGACAGCATACAATAATTCACCATTCAACTTGATTCG
1 ATCATGACAGCATACAATAATTCACCATTCAACTTGATTCG
** *
2447061 ATCATGATTGAATACAATAATTCACCATTCAACTTGATTCG
1 ATCATGACAGCATACAATAATTCACCATTCAACTTGATTCG
2447102 ATCATG
1 ATCATG
2447108 GTAACATGCA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (41 bp):
ATCATGACAGCATACAATAATTCACCATTCAACTTGATTCG
Found at i:2447147 original size:41 final size:41
Alignment explanation
Indices: 2447102--2447181 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
2447092 ACTTGATTCG
* *
2447102 ATCATGGTAACATGCATTTATTCACAAACCAATTCAATTAT
1 ATCATGATAACATGCATTAATTCACAAACCAATTCAATTAT
* *
2447143 ATCATGATAACATGTATTAATTCACAATCCAATTCAATT
1 ATCATGATAACATGCATTAATTCACAAACCAATTCAATT
2447182 TAAATCAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (41 bp):
ATCATGATAACATGCATTAATTCACAAACCAATTCAATTAT
Found at i:2451391 original size:28 final size:28
Alignment explanation
Indices: 2451360--2451415 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2451350 TAGGCTTTTT
2451360 TTTATCAATTAGGAGAATAAATTATTTC
1 TTTATCAATTAGGAGAATAAATTATTTC
2451388 TTTATCAATTAGGAGAATAAATTATTTC
1 TTTATCAATTAGGAGAATAAATTATTTC
2451416 CCTAATCCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (28 bp):
TTTATCAATTAGGAGAATAAATTATTTC
Found at i:2454250 original size:92 final size:92
Alignment explanation
Indices: 2454088--2454386 Score: 377
Period size: 92 Copynumber: 3.2 Consensus size: 92
2454078 TACATTTCAA
* * *
2454088 TCTTTCCTCCATTCGAACAAGAACATTTCACCACATATGTATTCATGCAATCTACATGGCAAA-T
1 TCTTTCCTCTATTCGAACAAGAACATTTCACCACATATGTATTCATGCAATCTATATGGCAAACA
* * *
2454152 GAATTAATCATTTCAATAGGTGTACCAT
66 G-ATTAAACATTTCAATAGGTATAACAT
* * * * *
2454180 TATTTCCTCTATTCGAACAAGAACATTTCACCACATATGTTTTCATGGAATCTATATGGAAAACC
1 TCTTTCCTCTATTCGAACAAGAACATTTCACCACATATGTATTCATGCAATCTATATGGCAAACA
*
2454245 GATTAAACAATTCAATAGGTATAACAT
66 GATTAAACATTTCAATAGGTATAACAT
* * * * *
2454272 TCCTTACTCTATTTGAACAAAAACATTTCACCACATATGTATTCATGCAATCTTTATGGCAAACA
1 TCTTTCCTCTATTCGAACAAGAACATTTCACCACATATGTATTCATGCAATCTATATGGCAAACA
* * *
2454337 AATTAAACAATTT-AATTGGAATAACAT
66 GATTAAAC-ATTTCAATAGGTATAACAT
*
2454364 TCTTTCCTCTATTCGAACTAGAA
1 TCTTTCCTCTATTCGAACAAGAA
2454387 GGAAACACTC
Statistics
Matches: 175, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
92 171 0.98
93 4 0.02
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.33
Consensus pattern (92 bp):
TCTTTCCTCTATTCGAACAAGAACATTTCACCACATATGTATTCATGCAATCTATATGGCAAACA
GATTAAACATTTCAATAGGTATAACAT
Found at i:2454810 original size:14 final size:17
Alignment explanation
Indices: 2454776--2454811 Score: 51
Period size: 14 Copynumber: 2.3 Consensus size: 17
2454766 AACATAGCCA
2454776 TCAATGATTATTTCAAT
1 TCAATGATTATTTCAAT
2454793 TCAA-GATTA-TTC-AT
1 TCAATGATTATTTCAAT
2454807 TCAAT
1 TCAAT
2454812 TCCAGATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.33
15 3 0.17
16 5 0.28
17 4 0.22
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (17 bp):
TCAATGATTATTTCAAT
Found at i:2454954 original size:34 final size:34
Alignment explanation
Indices: 2454915--2454983 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
2454905 CAATTCAATT
*
2454915 CAATCATGACA-ACATGCAATAGTTCACCATTCAA
1 CAATCATGACAGA-ATGCAATACTTCACCATTCAA
* *
2454949 CAATCATGGCAGAATGCAATACTTCACTATTCAA
1 CAATCATGACAGAATGCAATACTTCACCATTCAA
2454983 C
1 C
2454984 TTGATTCGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 30 0.97
35 1 0.03
ACGTcount: A:0.39, C:0.26, G:0.10, T:0.25
Consensus pattern (34 bp):
CAATCATGACAGAATGCAATACTTCACCATTCAA
Found at i:2456808 original size:32 final size:32
Alignment explanation
Indices: 2456767--2456845 Score: 88
Period size: 35 Copynumber: 2.4 Consensus size: 32
2456757 TTGATTAGTG
* *
2456767 TTAAACATTAATATT-ATAATATAGAGAGTTTA
1 TTAAGCATTAATATTAAAAATATAGAGAG-TTA
2456799 TTAAGCATTAATATTAACAAAATATAGAGAGTTA
1 TTAAGCATTAATATT-A-AAAATATAGAGAGTTA
*
2456833 CTAGAGCATTAAT
1 TTA-AGCATTAAT
2456846 TTTGAAGGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
32 14 0.35
34 5 0.12
35 21 0.52
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.35
Consensus pattern (32 bp):
TTAAGCATTAATATTAAAAATATAGAGAGTTA
Found at i:2457316 original size:14 final size:14
Alignment explanation
Indices: 2457297--2457324 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2457287 CTTTATAGAT
2457297 TTTATCCATGATAA
1 TTTATCCATGATAA
2457311 TTTATCCATGATAA
1 TTTATCCATGATAA
2457325 CTCCATTAAT
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:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TTTATCCATGATAA
Found at i:2457972 original size:19 final size:20
Alignment explanation
Indices: 2457948--2457988 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
2457938 CCAATACGAC
*
2457948 TTGTGTTCTTTT-TGCTTAA
1 TTGTGTTCTTTTGTGCTGAA
2457967 TTGTGTTCTTTTGTGCTGAA
1 TTGTGTTCTTTTGTGCTGAA
2457987 TT
1 TT
2457989 CTTCTTGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.61
Consensus pattern (20 bp):
TTGTGTTCTTTTGTGCTGAA
Found at i:2462257 original size:22 final size:22
Alignment explanation
Indices: 2462232--2462301 Score: 140
Period size: 22 Copynumber: 3.2 Consensus size: 22
2462222 TCAAATAACT
2462232 AAAGTGCCTTAGCACTACTATG
1 AAAGTGCCTTAGCACTACTATG
2462254 AAAGTGCCTTAGCACTACTATG
1 AAAGTGCCTTAGCACTACTATG
2462276 AAAGTGCCTTAGCACTACTATG
1 AAAGTGCCTTAGCACTACTATG
2462298 AAAG
1 AAAG
2462302 AAAGTGCCTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (22 bp):
AAAGTGCCTTAGCACTACTATG
Found at i:2463740 original size:12 final size:12
Alignment explanation
Indices: 2463710--2463760 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
2463700 ATTGTGCAAT
*
2463710 TGATATAAAATG
1 TGATATGAAATG
2463722 TGATATGAAATG
1 TGATATGAAATG
*
2463734 TGATATGTAATG
1 TGATATGAAATG
* *
2463746 TTGATGTGATATG
1 -TGATATGAAATG
2463759 TG
1 TG
2463761 CATTATGATG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
12 24 0.73
13 9 0.27
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.39
Consensus pattern (12 bp):
TGATATGAAATG
Found at i:2470304 original size:37 final size:37
Alignment explanation
Indices: 2470251--2470355 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
2470241 CATTTTCGTC
2470251 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
2470288 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
2470325 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
2470356 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:2470610 original size:18 final size:17
Alignment explanation
Indices: 2470579--2470612 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2470569 AATTATTACT
*
2470579 TTACTATTTTTTTTATC
1 TTACTATTTATTTTATC
2470596 TTACTTATTTATTTTAT
1 TTAC-TATTTATTTTAT
2470613 TTTTCCCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (17 bp):
TTACTATTTATTTTATC
Found at i:2476416 original size:183 final size:183
Alignment explanation
Indices: 2476108--2476644 Score: 959
Period size: 183 Copynumber: 2.9 Consensus size: 183
2476098 ATTAAATCCG
* * *
2476108 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGAAAACTCGAAATCCCTGGCTTTATGA
1 TAAAGCTGAGATATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
2476173 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTACTT
2476238 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
2476291 TAAAGCTGAGATATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGATATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
2476356 ATAGATTATGTTCAAACTATGACATTGCTCGGACACTTGGCAATTCGGTGTTTTCTCCACTACTT
66 ATAGATTATGTTCAAACTATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTACTT
* *
2476421 TTGTCAGGCCAAAGAATTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
2476474 TAAAGCTGAGATATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGATATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
**
2476539 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTACT
66 ATAGATTATGTTCAAACT-ATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTACT
*
2476603 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
2476645 TAAACCAGAT
Statistics
Matches: 339, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
182 1 0.00
183 338 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGATATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTACTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:2477865 original size:36 final size:36
Alignment explanation
Indices: 2477825--2477941 Score: 99
Period size: 36 Copynumber: 3.1 Consensus size: 36
2477815 ATACTTTGTC
*
2477825 TCACTTGAGACTATTTTTCTCGAAAGAAGATTTATT
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
** * ** * * *
2477861 TCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTC
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
* *
2477897 TCGCTTGAGACTGTTTTCACTCGAAAGAAGGTATTTCATT
1 TCACTTGAGACTGTTTT-TCTCGAAAGAA-G-ATTT-ATT
2477937 TCACT
1 TCACT
2477942 CAAGGCTGTT
Statistics
Matches: 57, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
36 40 0.70
37 7 0.12
38 1 0.02
39 4 0.07
40 5 0.09
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (36 bp):
TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
Found at i:2477876 original size:72 final size:76
Alignment explanation
Indices: 2477784--2477945 Score: 219
Period size: 72 Copynumber: 2.2 Consensus size: 76
2477774 ATGCAGATGA
* * *
2477784 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTATTTT-TCTC
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACTATTTTCACTC
2477846 GAAAGAA-G-AT
65 GAAAGAAGGTAT
* *
2477856 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACTGTTTTCACTCG
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACTATTTTCACTCG
2477920 AAAGAAGGTAT
66 AAAGAAGGTAT
2477931 TTCATTTCACTCAAG
1 TT-ATTTCACTCAAG
2477946 GCTGTTTTGT
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
71 1 0.01
72 50 0.63
73 11 0.14
74 1 0.01
75 4 0.05
76 12 0.15
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (76 bp):
TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACTATTTTCACTCG
AAAGAAGGTAT
Found at i:2478034 original size:15 final size:14
Alignment explanation
Indices: 2478011--2478050 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
2478001 AAAATTCGTC
2478011 TCCCTTGAAACAGTT
1 TCCCTTGAAACA-TT
*
2478026 TCTCTTGAAAACATT
1 TCCCTTG-AAACATT
2478041 TCCCTTGAAA
1 TCCCTTGAAA
2478051 TTAATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 3 0.14
15 14 0.64
16 5 0.23
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (14 bp):
TCCCTTGAAACATT
Found at i:2478110 original size:39 final size:39
Alignment explanation
Indices: 2478053--2478131 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
2478043 CCTTGAAATT
* *
2478053 AATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACATAA
1 AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACATAA
* *
2478092 AATTTTGTCTC-CCTTGAGACAGTTTCTCTTGAAACATAA
1 AATTTTGTCTCTCC-TGAGACAGTTTCCCTCGAAACATAA
2478131 A
1 A
2478132 CATTGAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.06
39 33 0.94
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (39 bp):
AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACATAA
Found at i:2478204 original size:106 final size:104
Alignment explanation
Indices: 2478030--2478349 Score: 470
Period size: 106 Copynumber: 3.1 Consensus size: 104
2478020 ACAGTTTCTC
* * *
2478030 TTGAAAACATTTCCCTTGAAATTA-ATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACATAAAA
1 TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACA-GAAA
2478094 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
2478134 TTGAAAACATTTCCCTTGAAATGATTTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
1 TTGAAAACATTTCCCTTGAAATGA-TATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
2478199 GTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 -TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
2478240 TTGAAAACATTTCCCTTGAAATGA-ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G-AAT
1 TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAT
* * **
2478302 TTTATCTCCATTGAGACAGTTTCTCTCCAAACATAAA-A
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
2478340 TTTGAAAACA
1 -TTGAAAACA
2478350 ATTTAACGAA
Statistics
Matches: 200, Mismatches: 12, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
100 1 0.00
101 43 0.22
102 2 0.01
103 1 0.00
104 53 0.26
105 3 0.01
106 97 0.49
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:2478296 original size:36 final size:36
Alignment explanation
Indices: 2478249--2478324 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
2478239 ATTGAAAACA
* *
2478249 TTTCCCTTGAAATGAATTTTATCTCGC-TTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTC-CATTGAGACAG
2478285 TTTCCCTTGAAACGAATTTTATCTCCATTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCATTGAGACAG
2478321 TTTC
1 TTTC
2478325 TCTCCAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 1 0.03
36 36 0.97
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCATTGAGACAG
Found at i:2478724 original size:105 final size:105
Alignment explanation
Indices: 2478524--2479259 Score: 1034
Period size: 105 Copynumber: 7.0 Consensus size: 105
2478514 ATATCGTGAC
* * * * * * *
2478524 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTTAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
*
2478589 AATTTCAGAGCCAATTTCAACTTCAGAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2478630 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
2478695 ATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* **
2478735 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCATTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
2478800 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
**
2478840 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCATTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
2478905 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2478945 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGAACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
2479010 ATCTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
2479050 ACTCCAGACAATGCAAGTTCAAC-TCTACGATGAAGGGACCGCTTCTTGTCAACAA-AA-TT-TC
1 ACTCCAGACAACGCAAGTTCAACTTC-ACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCC
* * *
2479111 -A-TTCAAAGTCAATTTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
2479150 ACTCGAGACAACCCAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
** * * * *
2479215 GGTTCCAAAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
2479256 ACTC
1 ACTC
2479260 GGAACAATGC
Statistics
Matches: 577, Mismatches: 45, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
100 74 0.13
101 5 0.01
102 3 0.01
103 4 0.01
104 5 0.01
105 402 0.70
106 84 0.15
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:2479855 original size:37 final size:37
Alignment explanation
Indices: 2479802--2479907 Score: 140
Period size: 37 Copynumber: 2.9 Consensus size: 37
2479792 CATTTTCGTC
2479802 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
2479839 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
2479876 CTACTAAGATTTAAATTCCTAAAGATAGGATA
1 CTACTAGGATTCAAACTCCTAAAAATAGGATA
2479908 CACAAGCACT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:2480106 original size:2 final size:2
Alignment explanation
Indices: 2480099--2480126 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2480089 TAATACTTTG
2480099 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
2480127 TTTTTTCCTT
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:2482049 original size:16 final size:16
Alignment explanation
Indices: 2482028--2482072 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2482018 TTTTGCTTGA
*
2482028 CTCGTTGCTCATTTAG
1 CTCGTTGCTCATTAAG
* *
2482044 CTCGTTACTTATTAAG
1 CTCGTTGCTCATTAAG
*
2482060 CTCGATGCTCATT
1 CTCGTTGCTCATT
2482073 GACCACCTCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (16 bp):
CTCGTTGCTCATTAAG
Found at i:2483331 original size:27 final size:28
Alignment explanation
Indices: 2483279--2483344 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
2483269 TGTTATTTTG
*
2483279 TTAAATATATTTTATTATTAGCTTAAT-
1 TTAAAAATATTTTATTATTAGCTTAATA
* **
2483306 TTAAAAATATTTTATTTTTATTTTAATA
1 TTAAAAATATTTTATTATTAGCTTAATA
*
2483334 ATAAAAATATT
1 TTAAAAATATT
2483345 AAAATATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
27 23 0.70
28 10 0.30
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
TTAAAAATATTTTATTATTAGCTTAATA
Found at i:2483537 original size:27 final size:27
Alignment explanation
Indices: 2483502--2483581 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
2483492 ATATATATTT
2483502 TTAA-AATAAAATATTTTTAAGTTAAG
1 TTAATAATAAAATATTTTTAAGTTAAG
* *
2483528 TTAATAATAAAATATATTTAA--TAAT
1 TTAATAATAAAATATTTTTAAGTTAAG
2483553 TTAAT-ATAAACAATATTTGTTAAAGTTAA
1 TTAATAAT-AA-AATATTT-TT-AAGTTAA
2483582 TATATATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
24 2 0.05
25 10 0.23
26 10 0.23
27 17 0.39
28 2 0.05
30 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.42
Consensus pattern (27 bp):
TTAATAATAAAATATTTTTAAGTTAAG
Found at i:2483588 original size:2 final size:2
Alignment explanation
Indices: 2483581--2483613 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2483571 GTTAAAGTTA
2483581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2483614 TATGAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2488835 original size:34 final size:34
Alignment explanation
Indices: 2488793--2488870 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
2488783 CTAAGAGGAA
*
2488793 GGTATCGATATCATGGACTCCATAATATAGAAAT
1 GGTATCGATATCATGGACTCCATAATACAGAAAT
*
2488827 GGTATCGATATCATGGATTCCATAATACAGAAAT
1 GGTATCGATATCATGGACTCCATAATACAGAAAT
2488861 GGTATCGATA
1 GGTATCGATA
2488871 CCATAATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (34 bp):
GGTATCGATATCATGGACTCCATAATACAGAAAT
Found at i:2488874 original size:25 final size:22
Alignment explanation
Indices: 2488846--2488896 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
2488836 ATCATGGATT
2488846 CCATAATACAGAAATGGTATCGATA
1 CCATAATACAG-AA--GTATCGATA
*
2488871 CCATAATATAGAAGTATCGATA
1 CCATAATACAGAAGTATCGATA
2488893 CCAT
1 CCAT
2488897 GGTAGCGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 13 0.52
24 2 0.08
25 10 0.40
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (22 bp):
CCATAATACAGAAGTATCGATA
Found at i:2489396 original size:55 final size:55
Alignment explanation
Indices: 2489248--2489745 Score: 491
Period size: 55 Copynumber: 9.2 Consensus size: 55
2489238 TATCGGTACC
* * * *
2489248 AAGTGTGCAAAACCCACATAACTT-ATAATATTTTTATGAACGACCGTATCGGCACT
1 AAGTGTGCAAAA-CCACAGAA-TTCATAATGTGTTTATGAACGACCGTATCGACACT
* * * * * *
2489304 AAGTGTG-TAACCCACATAATTCATAATATGTTTATGAATGACCATATCGACACT
1 AAGTGTGCAAAACCACAGAATTCATAATGTGTTTATGAACGACCGTATCGACACT
* * *
2489358 AAGTGTGCAAAACCATAGAATTCACAATGTGTTTATGAATGACCGTATCGACACT
1 AAGTGTGCAAAACCACAGAATTCATAATGTGTTTATGAACGACCGTATCGACACT
* ** *
2489413 AAGTGTGCAAAACCACAAAATTCATAATGTGTTTATGAACGACCACATTGACACT
1 AAGTGTGCAAAACCACAGAATTCATAATGTGTTTATGAACGACCGTATCGACACT
* * *
2489468 AAGTGTGC-AACCCACAGAATTCATAATGTCTTTATGAACGACCGTATCGGCACT
1 AAGTGTGCAAAACCACAGAATTCATAATGTGTTTATGAACGACCGTATCGACACT
* * *
2489522 AAGTG-GCAAAACCAC-GAAATTCTTAATGTCTTTATGAACGACCGTATCGACATT
1 AAGTGTGCAAAACCACAG-AATTCATAATGTGTTTATGAACGACCGTATCGACACT
* * * * * *
2489576 AAGTGTGTAAAACCATAAAATTCATAATGTATTTATGAACAACTGTATCTG-CACT
1 AAGTGTGCAAAACCACAGAATTCATAATGTGTTTATGAACGACCGTATC-GACACT
* * * * *
2489631 AAGTGTGAAAAATCAC-GAGATTCATAATGTGTTTATGAACGATCGTATAGGCACT
1 AAGTGTGCAAAACCACAGA-ATTCATAATGTGTTTATGAACGACCGTATCGACACT
* * * * * *
2489686 AAGTGTAC-AACCCA-AGGAATCCATAA--TG--TATGAACGACCGTATCAATACG
1 AAGTGTGCAAAACCACA-GAATTCATAATGTGTTTATGAACGACCGTATCGACACT
2489736 AAGTGTGCAA
1 AAGTGTGCAA
2489746 TCATAATATG
Statistics
Matches: 370, Mismatches: 60, Indels: 29
0.81 0.13 0.06
Matches are distributed among these distances:
50 23 0.06
51 1 0.00
52 2 0.01
53 5 0.01
54 145 0.39
55 186 0.50
56 8 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (55 bp):
AAGTGTGCAAAACCACAGAATTCATAATGTGTTTATGAACGACCGTATCGACACT
Found at i:2489636 original size:218 final size:217
Alignment explanation
Indices: 2489248--2489729 Score: 575
Period size: 218 Copynumber: 2.2 Consensus size: 217
2489238 TATCGGTACC
* * *
2489248 AAGTGTGCAAAACCCACATAACTT-ATAATATTTTTATGAACGACCGTATCGGCACTAAGTGTGT
1 AAGTGTGC--AACCCACAGAA-TTCATAAT-GTTTTATGAACGACCGTATCGGCACTAAGTGTGA
* * * *
2489312 AACCCACATAATTCATAATATGTTTATGAATGACCATATCGACACTAAGTGTGCAAAACCATAGA
62 AAACCACATAATTCATAATATCTTTATGAACGACCATATCGACACTAAGTGTGCAAAACCATAAA
* ** *
2489377 ATTCACAATGTGTTTATGAATGACCGTATCGACACTAAGTGTGCAAAACCACAAAATTCATAATG
127 ATTCACAATGTATTTATGAACAACCGTATCGACACTAAGTGTGAAAAACCACAAAATTCATAATG
*
2489442 TGTTTATGAACGACCACATTGACACT
192 TGTTTATGAACGACCACATAGACACT
2489468 AAGTGTGCAACCCACAGAATTCATAATGTCTTTATGAACGACCGTATCGGCACTAAGTG-GCAAA
1 AAGTGTGCAACCCACAGAATTCATAATGT-TTTATGAACGACCGTATCGGCACTAAGTGTG-AAA
* * * * *
2489532 ACCACGA-AATTCTTAATGTCTTTATGAACGACCGTATCGACATTAAGTGTGTAAAACCATAAAA
64 ACCAC-ATAATTCATAATATCTTTATGAACGACCATATCGACACTAAGTGTGCAAAACCATAAAA
* * * * *
2489596 TTCATAATGTATTTATGAACAACTGTATCTG-CACTAAGTGTGAAAAATCACGAGATTCATAATG
128 TTCACAATGTATTTATGAACAACCGTATC-GACACTAAGTGTGAAAAACCACAAAATTCATAATG
* ** *
2489660 TGTTTATGAACGATCGTATAGGCACT
192 TGTTTATGAACGACCACATAGACACT
* *
2489686 AAGTGTACAACCCA-AGGAATCCATAATG---TATGAACGACCGTATC
1 AAGTGTGCAACCCACA-GAATTCATAATGTTTTATGAACGACCGTATC
2489730 AATACGAAGT
Statistics
Matches: 228, Mismatches: 28, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
214 16 0.07
217 5 0.02
218 197 0.86
219 2 0.01
220 8 0.04
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (217 bp):
AAGTGTGCAACCCACAGAATTCATAATGTTTTATGAACGACCGTATCGGCACTAAGTGTGAAAAC
CACATAATTCATAATATCTTTATGAACGACCATATCGACACTAAGTGTGCAAAACCATAAAATTC
ACAATGTATTTATGAACAACCGTATCGACACTAAGTGTGAAAAACCACAAAATTCATAATGTGTT
TATGAACGACCACATAGACACT
Found at i:2489716 original size:109 final size:108
Alignment explanation
Indices: 2489280--2489716 Score: 479
Period size: 109 Copynumber: 4.0 Consensus size: 108
2489270 TTATAATATT
* * * *
2489280 TTTATGAACGACCGTATCGGCACTAAGTGTG-TAACCCAC-ATAATTCATAATATGTTTATGAAT
1 TTTATGAACGACCGTATC-GCACTAAGTGTGCAAAACCACGA-AATTCATAATGTGTTTATGAAC
* * *
2489343 GACCATATCGACACTAAGTGTGCAAAACCATAGAATTCACAATGTG
64 GACCATATCGACACTAAGTGTAC-AAACCATAGAATTCATAATGTA
* *
2489389 TTTATGAATGACCGTATCGACACTAAGTGTGCAAAACCACAAAATTCATAATGTGTTTATGAACG
1 TTTATGAACGACCGTATCG-CACTAAGTGTGCAAAACCACGAAATTCATAATGTGTTTATGAACG
* * * * * *
2489454 ACCACATTGACACTAAGTGTGCAACCCACAGAATTCATAATGTC
65 ACCATATCGACACTAAGTGTACAAACCATAGAATTCATAATGTA
* *
2489498 TTTATGAACGACCGTATCGGCACTAAGTG-GCAAAACCACGAAATTCTTAATGTCTTTATGAACG
1 TTTATGAACGACCGTATC-GCACTAAGTGTGCAAAACCACGAAATTCATAATGTGTTTATGAACG
* * *
2489562 ACCGTATCGACATTAAGTGTGTA-AAACCATAAAATTCATAATGTA
65 ACCATATCGACACTAA--GTGTACAAACCATAGAATTCATAATGTA
* * * * *
2489607 TTTATGAACAACTGTATCTGCACTAAGTGTGAAAAATCACGAGATTCATAATGTGTTTATGAACG
1 TTTATGAACGACCGTATC-GCACTAAGTGTGCAAAACCACGAAATTCATAATGTGTTTATGAACG
* * * * * *
2489672 ATCGTATAGGCACTAAGTGTACAACCCA-AGGAATCCATAATGTA
65 ACCATATCGACACTAAGTGTACAAACCATA-GAATTCATAATGTA
2489716 T
1 T
2489717 GAACGACCGT
Statistics
Matches: 280, Mismatches: 39, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
108 51 0.18
109 134 0.48
110 94 0.34
111 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (108 bp):
TTTATGAACGACCGTATCGCACTAAGTGTGCAAAACCACGAAATTCATAATGTGTTTATGAACGA
CCATATCGACACTAAGTGTACAAACCATAGAATTCATAATGTA
Found at i:2491755 original size:30 final size:30
Alignment explanation
Indices: 2491721--2491843 Score: 97
Period size: 30 Copynumber: 4.1 Consensus size: 30
2491711 TTTGTTATTT
2491721 TATTTTAATCAC-TTAAGTTTCTGTTTTTAC
1 TATTTTAATC-CTTTAAGTTTCTGTTTTTAC
** * **
2491751 TATTTTTGTCCTTTAAGTTTCTATTTTCGC
1 TATTTTAATCCTTTAAGTTTCTGTTTTTAC
* * ** * * *
2491781 TGTTTTAGTTTTTTTAACTTTCTGTTTATGC
1 TATTTTA-ATCCTTTAAGTTTCTGTTTTTAC
2491812 TATTTTAATCCTTTAAG-TTCATGTTTTTAC
1 TATTTTAATCCTTTAAGTTTC-TGTTTTTAC
2491842 TA
1 TA
2491844 GATCTCTTAT
Statistics
Matches: 69, Mismatches: 21, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
29 4 0.06
30 43 0.62
31 22 0.32
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.59
Consensus pattern (30 bp):
TATTTTAATCCTTTAAGTTTCTGTTTTTAC
Found at i:2492109 original size:16 final size:16
Alignment explanation
Indices: 2492078--2492115 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
2492068 GCAAACCAAC
2492078 TTTTATCTTAAAAATTG
1 TTTT-TCTTAAAAATTG
2492095 ATTTTTCTT-AAAATTG
1 -TTTTTCTTAAAAATTG
2492111 TTTTT
1 TTTTT
2492116 AAAAGACGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 4 0.20
18 4 0.20
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTTTCTTAAAAATTG
Found at i:2493184 original size:32 final size:32
Alignment explanation
Indices: 2493148--2493209 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2493138 TCTTACATGT
* * *
2493148 ACTAACTAATTTCAGTTCTTTTGTTTGTGTAC
1 ACTAACTAATCTCACTTCTTTTATTTGTGTAC
* *
2493180 ACTAACTTATCTCCCTTCTTTTATTTGTGT
1 ACTAACTAATCTCACTTCTTTTATTTGTGT
2493210 CATTTTTCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (32 bp):
ACTAACTAATCTCACTTCTTTTATTTGTGTAC
Found at i:2497276 original size:200 final size:201
Alignment explanation
Indices: 2496925--2497391 Score: 535
Period size: 200 Copynumber: 2.3 Consensus size: 201
2496915 CTGTTTATAG
* * * * * * * * **
2496925 CATAGCTCAAGGCGAGAAAGGCTATTTGTCAACGAGAACTTTTGAGTTCGATTTCATT-AAGCTC
1 CATAGCTCAAGGCGAGAAGGGTTATCTGACAACAAAAACCTTCGAGTTCGATCCCATTCAA-CTC
* * * ** * * *
2496989 GAGGGCT-TATCAACCGCACAGTAGCAGCAAGGAACTACTTTCCGATTAAAGTTTAAACTAAGGT
65 GA-AGATGTATCAACTGCATGGTAGCAGCAAGGAACTACCTTCCGATTAAAGTTTAAACAAAGCT
**
2497053 CTTTAAGTCAAGAAGAAGACCTAGGTTGACTGCAATTTAGCAAAAAGG-GCTATATCCCAGTCAA
129 CTTTAAGTCAAGAAGAAGACCTAGGTTGACTGCAATTTAGCAAAAAGGAAATATATCCCAGTCAA
2497117 ATTTACAA
194 ATTTACAA
* * * * ** ***
2497125 CATAGTTTAAGGCGAGAAGGGTTATCTGACAATAATAATTTTCGAGTTCGATTTTATTCAACTCG
1 CATAGCTCAAGGCGAGAAGGGTTATCTGACAACAAAAACCTTCGAGTTCGATCCCATTCAACTCG
* * * *
2497190 AAGATGTATCAACTGCATGGTAGCAGCGAGGAACTACCTTCCGGTTGAATTTTAAACAAAGCTCT
66 AAGATGTATCAACTGCATGGTAGCAGCAAGGAACTACCTTCCGATTAAAGTTTAAACAAAGCTCT
** * *
2497255 TTAAGTCAAGAAGAAGACCTAGGTTGGTTGCGATTTAGCAAAAAGGAAATATATCTCAGTCAAAT
131 TTAAGTCAAGAAGAAGACCTAGGTTGACTGCAATTTAGCAAAAAGGAAATATATCCCAGTCAAAT
*
2497320 TTACAG
196 TTACAA
* *
2497326 CATAGCTCAAGGCGAGAAGGGTTATTTGTCAACAAAAACCTTCGAGTTCGATCCCATTCAACTCG
1 CATAGCTCAAGGCGAGAAGGGTTATCTGACAACAAAAACCTTCGAGTTCGATCCCATTCAACTCG
2497391 A
66 A
2497392 GGGAATATCA
Statistics
Matches: 222, Mismatches: 42, Indels: 5
0.83 0.16 0.02
Matches are distributed among these distances:
199 2 0.01
200 143 0.64
201 77 0.35
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (201 bp):
CATAGCTCAAGGCGAGAAGGGTTATCTGACAACAAAAACCTTCGAGTTCGATCCCATTCAACTCG
AAGATGTATCAACTGCATGGTAGCAGCAAGGAACTACCTTCCGATTAAAGTTTAAACAAAGCTCT
TTAAGTCAAGAAGAAGACCTAGGTTGACTGCAATTTAGCAAAAAGGAAATATATCCCAGTCAAAT
TTACAA
Found at i:2497887 original size:65 final size:65
Alignment explanation
Indices: 2497781--2498025 Score: 266
Period size: 65 Copynumber: 3.8 Consensus size: 65
2497771 GAAGCGATGC
* * *
2497781 AACTTACAAAAGATTGGATTTCAAGTTCACAACGAAGGATATCCAACTCAAAGCCAATTCGGTGA
1 AACTTACTAAAGATTGGATTTCAAATTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGA
* * ** *
2497846 AACTTACTCAAGATTCGATTTCAAATTCGTAACGAATGATATCCAACTCAAAGCCAATTTGGTGA
1 AACTTACTAAAGATTGGATTTCAAATTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGA
* * * * *
2497911 AGCAATATTTAAGATTGGATTTCAATTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTG
1 AAC-TTACTAAAGATTGGATTTCAAATTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTG
*
2497976 G
65 A
* * * * * *
2497977 AGC--A--ATA-CTTAGATTTCAACTTCACAATGAAGGATATCCAACTCAAAGC
1 AACTTACTAAAGATTGGATTTCAAATTCACAACGAAGGATATCCAACTCAAAGC
2498026 TCAACTTCAC
Statistics
Matches: 155, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
60 38 0.25
61 1 0.01
63 1 0.01
65 59 0.38
66 56 0.36
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (65 bp):
AACTTACTAAAGATTGGATTTCAAATTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGA
Found at i:2497956 original size:66 final size:66
Alignment explanation
Indices: 2497790--2498025 Score: 297
Period size: 66 Copynumber: 3.7 Consensus size: 66
2497780 CAACTTACAA
* * * *
2497790 AAGATTGGATTTCAAGTTCACAACGAAGGATATCCAACTCAAAGCCAATTCGGTGAAAC-TTACT
1 AAGATTGGATTTCAAATTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCAATACT
*
2497854 C
66 T
* ** * *
2497855 AAGATTCGATTTCAAATTCGTAACGAATGATATCCAACTCAAAGCCAATTTGGTGAAGCAATATT
1 AAGATTGGATTTCAAATTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCAATACT
2497920 T
66 T
* *
2497921 AAGATTGGATTTCAATTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGGAGCAATACT
1 AAGATTGGATTTCAAATTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCAATACT
2497986 T
66 T
* *
2497987 ---A---GATTTCAACTTCACAATGAAGGATATCCAACTCAAAGC
1 AAGATTGGATTTCAAATTCACAACGAAGGATATCCAACTCAAAGC
2498026 TCAACTTCAC
Statistics
Matches: 151, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
60 36 0.24
63 1 0.01
65 52 0.34
66 62 0.41
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (66 bp):
AAGATTGGATTTCAAATTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCAATACT
T
Found at i:2499750 original size:30 final size:29
Alignment explanation
Indices: 2499640--2499750 Score: 80
Period size: 30 Copynumber: 3.7 Consensus size: 29
2499630 TTGACACTTT
* * *
2499640 ACTTTCTGTTATTT-TATTTTAGTCACTTA
1 ACTTTCTATT-TTTCTATTTTAGTTATTTA
* * *
2499669 AGTTTCTATTTTTGCTATTTTTGTTCTTTA
1 ACTTTCTATTTTT-CTATTTTAGTTATTTA
* * * *
2499699 AGTTTCTATTTTCTTTGTTTTAGTTTTTTA
1 ACTTTCTATTTT-TCTATTTTAGTTATTTA
*
2499729 ACTTTCTGTTTATTCTATTTTA
1 ACTTTCTATTT-TTCTATTTTA
2499751 ATCCTTTAAG
Statistics
Matches: 64, Mismatches: 14, Indels: 7
0.75 0.16 0.08
Matches are distributed among these distances:
28 3 0.05
29 8 0.12
30 51 0.80
31 2 0.03
ACGTcount: A:0.16, C:0.11, G:0.08, T:0.65
Consensus pattern (29 bp):
ACTTTCTATTTTTCTATTTTAGTTATTTA
Found at i:2501288 original size:201 final size:200
Alignment explanation
Indices: 2500909--2501275 Score: 432
Period size: 201 Copynumber: 1.8 Consensus size: 200
2500899 GAGCAATGAT
* * * * *
2500909 CTACTTTCCGGTTAAAGTTTAAACTAAGGTCTTTAAATCAAGAAGAATACTTAGGTTGGCTGCAT
1 CTACCTTCCGGTTAAAGTTTAAACAAAGCTCTTTAAATCAAGAAGAAGACCTAGGTTGGCTGCAT
* * *
2500974 TTAGCAACAAGGAACTATATCCCCATCAAATTTACAACATAGTTTAAGGCGAGAAGAGTTATCTG
66 TTAGCAACAAGGAAATATATCCCCATCAAATTTACAACATAGCTCAAGGCGAGAAGAGTTATCTG
* * * *** *
2501039 ACAACAAGAATTTTTGAGTTCAATTTTATTCAGCTCGAAGATATATCAACTGCATGGTAGTAGCG
131 ACAACAAAAACTTCTGAGTTCAATCCCATTCAACTCGAAGATATATCAACTGCATGGTAGTAGCG
2501104 AGGAA
196 AGGAA
* * * * *
2501109 CTACCTTCCGGTTGAATTTTAAACAAAGCTCTTTAAGTCAAGAAGAAGACCTAGGTTTGTTGCAA
1 CTACCTTCCGGTTAAAGTTTAAACAAAGCTCTTTAAATCAAGAAGAAGACCTAGGTTGGCTGC-A
* * * * * *
2501174 TTTAGCAATAAGGAAATATAT-CTCAGTCAAATTTACAGCCTAGCTCAAGGTGAGAAGGGTTATC
65 TTTAGCAACAAGGAAATATATCCCCA-TCAAATTTACAACATAGCTCAAGGCGAGAAGAGTTATC
* **
2501238 TGTCAACAAAAACCTTCT-AGTTTGATCCCATTCAACTC
129 TGACAACAAAAA-CTTCTGAGTTCAATCCCATTCAACTC
2501276 AAGGGAATAT
Statistics
Matches: 135, Mismatches: 29, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
200 56 0.41
201 76 0.56
202 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (200 bp):
CTACCTTCCGGTTAAAGTTTAAACAAAGCTCTTTAAATCAAGAAGAAGACCTAGGTTGGCTGCAT
TTAGCAACAAGGAAATATATCCCCATCAAATTTACAACATAGCTCAAGGCGAGAAGAGTTATCTG
ACAACAAAAACTTCTGAGTTCAATCCCATTCAACTCGAAGATATATCAACTGCATGGTAGTAGCG
AGGAA
Found at i:2501743 original size:65 final size:65
Alignment explanation
Indices: 2501666--2501919 Score: 266
Period size: 65 Copynumber: 3.9 Consensus size: 65
2501656 GAAGCGACGC
* *
2501666 AACTTACACAAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTCAGTGA
1 AACTTACTCAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTCAGTGA
** * **
2501731 AACTTACTCAAGATTGGATTTCAACTTTGCAACGAATGATATCCAACTCAAAGCCAATTTGGTGA
1 AACTTACTCAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTCAGTGA
* * * * * * **
2501796 AGCAATATTCAAGATTGGATTTCAATTTCATAACGAAGGATATCCAACTTAAAGCCAATTTGGTG
1 AAC-TTACTCAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTCAGTG
2501861 A
65 A
* * * * *
2501862 AAC--AAT--A-CTTGGATTTCAACTTCACAATGATGGATATCTAACTCAAAGCTCAACTTCA
1 AACTTACTCAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGC-CAA-TTCA
2501920 CGACGAATGA
Statistics
Matches: 159, Mismatches: 27, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
60 35 0.22
61 4 0.03
62 2 0.01
63 2 0.01
65 60 0.38
66 56 0.35
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (65 bp):
AACTTACTCAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTCAGTGA
Found at i:2501838 original size:66 final size:65
Alignment explanation
Indices: 2501674--2501870 Score: 263
Period size: 66 Copynumber: 3.0 Consensus size: 65
2501664 GCAACTTACA
* * ** *
2501674 CAAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTCAGTGAAAC-TTAC
1 CAAGATTGGATTTCAATTTCA-AACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAATAC
2501738 T
65 T
* *
2501739 CAAGATTGGATTTCAACTTTGC-AACGAATGATATCCAACTCAAAGCCAATTTGGTGAAGCAATA
1 CAAGATTGGATTTCAA-TTT-CAAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAATA
*
2501803 TT
64 CT
*
2501805 CAAGATTGGATTTCAATTTCATAACGAAGGATATCCAACTTAAAGCCAATTTGGTGAAACAATAC
1 CAAGATTGGATTTCAATTTCA-AACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAATAC
2501870 T
65 T
2501871 TGGATTTCAA
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
64 1 0.01
65 52 0.45
66 61 0.53
67 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (65 bp):
CAAGATTGGATTTCAATTTCAAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAATACT
Found at i:2501952 original size:32 final size:32
Alignment explanation
Indices: 2501911--2501993 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
2501901 AACTCAAAGC
*
2501911 TCAACTTCACGACGAATGAGCCA-CCTACAATT
1 TCAACTTCACGACGAAGGAGCCAGCC-ACAATT
* *
2501943 TCAACTTCACTACGAAGGAGCCAGCCACGATT
1 TCAACTTCACGACGAAGGAGCCAGCCACAATT
*
2501975 TCAACTTCACGAAGAAGGA
1 TCAACTTCACGACGAAGGA
2501994 TATCGTGCCC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
32 43 0.96
33 2 0.04
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (32 bp):
TCAACTTCACGACGAAGGAGCCAGCCACAATT
Found at i:2503577 original size:29 final size:27
Alignment explanation
Indices: 2503522--2503613 Score: 78
Period size: 30 Copynumber: 3.2 Consensus size: 27
2503512 CTATTTTATT
* * * *
2503522 TATTTATTATTTTGACACTTTACTTTC
1 TATTTTTTATTTTGTCACTTAAGTTTC
*
2503549 TGTTCTTTTATTTTAGTCACTTAAGTTTC
1 TATT-TTTTATTTT-GTCACTTAAGTTTC
2503578 TATTTTTGCTATTTTTGTC-CTTTAAGTTTC
1 TATTTTT--TA-TTTTGTCAC-TTAAGTTTC
2503608 TATTTT
1 TATTTT
2503614 CACTGTTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
27 3 0.06
28 11 0.21
29 15 0.28
30 20 0.38
31 4 0.08
ACGTcount: A:0.17, C:0.13, G:0.08, T:0.62
Consensus pattern (27 bp):
TATTTTTTATTTTGTCACTTAAGTTTC
Found at i:2507489 original size:25 final size:25
Alignment explanation
Indices: 2507455--2507508 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
2507445 TTGGTATGAA
2507455 TCATTAATGGAAAAATAGTCATTTC
1 TCATTAATGGAAAAATAGTCATTTC
2507480 TCATTAATGGAAAAATAGTCATTTC
1 TCATTAATGGAAAAATAGTCATTTC
2507505 TCAT
1 TCAT
2507509 AAAATGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (25 bp):
TCATTAATGGAAAAATAGTCATTTC
Found at i:2517482 original size:58 final size:56
Alignment explanation
Indices: 2517392--2517556 Score: 188
Period size: 58 Copynumber: 2.9 Consensus size: 56
2517382 ATTATATAAT
* * *
2517392 GGCACTGAGTGTGCGAAATGATAAGAAATTCATAATTTGTTTATGAATTT-CTGTATA
1 GGCAATGAGTGTGCAAAAAGATAAG-AATTCATAATTTGTTTATGAATTTCCT-TATA
* ** *
2517449 GGCACTTTGTGTGCAAAAAAGATAAGAAGTTCATAATTTGTTTATGAATTTCCTTATG
1 GGCAATGAGTGTGC-AAAAAGATAAGAA-TTCATAATTTGTTTATGAATTTCCTTATA
* * *
2517507 GGCAATGAGTGTGCAAAAAGTTATGGAATTCATAATTTGTATATGAATTT
1 GGCAATGAGTGTGCAAAAAGATA-AGAATTCATAATTTGTTTATGAATTT
2517557 ATATATAAGA
Statistics
Matches: 93, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
57 43 0.46
58 48 0.52
59 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (56 bp):
GGCAATGAGTGTGCAAAAAGATAAGAATTCATAATTTGTTTATGAATTTCCTTATA
Found at i:2517838 original size:67 final size:67
Alignment explanation
Indices: 2517766--2518424 Score: 859
Period size: 67 Copynumber: 9.8 Consensus size: 67
2517756 TAAAAGATTA
* *
2517766 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCAT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
2517831 TT
66 TT
* * * * * ** * **
2517833 AAGGCCTAACTGTACATTGACAAAAATGTATCAATTATGCCCTTTAGATGAAATGCTAAGCACCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
2517898 TT
66 TT
* *
2517900 GAGGCCTAATTGTGCATTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
2517965 TT
66 TT
* *
2517967 GAGGCCTAACTGTGCATTGACAGAAATGTGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
2518032 TT
66 TT
* * * * *
2518034 GAGTCCTAATTGTGAATTGATAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
2518099 TT
66 TT
* * * * *
2518101 TAGGCCTAAATGTGTATTGAAAGAAAGGTGTCAATTATGCCAGCTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
2518166 TT
66 TT
* * * *
2518168 GAGACCTAACTGTGCATTGACAGAAAAGTGTTAATTAGGCCAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
2518233 TT
66 TT
* * * * * * * * * *
2518235 CAGTCCTAACTGTGCATTGACAAAAAGGTGTTAATCATTCTAGTTATATGAAAGGATAAATGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
2518300 TT
66 TT
* * * * * *
2518302 TAGGCCTAACTGTGCATTGCCAGAAATGTTTCAATCATGTCAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
2518367 TT
66 TT
* * * *
2518369 GAGACCTAGCTGTGCATTTAACAGAAAGGCGTCAATTATGCCAGTTAGATGAAAGG
1 GAGGCCTAACTGTGCA-TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
2518425 TTAAATACCA
Statistics
Matches: 509, Mismatches: 82, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
67 477 0.94
68 32 0.06
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (67 bp):
GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TT
Found at i:2518509 original size:81 final size:81
Alignment explanation
Indices: 2518374--2518770 Score: 542
Period size: 81 Copynumber: 4.9 Consensus size: 81
2518364 CCTTTGAGAC
* * * * ** *
2518374 CTAGCTGTGCATTTAACAGAAAGGCGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCACTAA
1 CTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGA
*
2518439 GTAAAATACTAATGGA
66 GTAAAATATTAATGGA
* * *
2518455 CTAGCTATGCATTTGACAAAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGA
1 CTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGA
* *
2518520 GTAAAAGATTAATGGC
66 GTAAAATATTAATGGA
**
2518536 CTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCTGGTTAGATGAAAGGTTAAATACCTTTGA
1 CTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGA
*
2518601 GTAAAAGATTAATGGA
66 GTAAAATATTAATGGA
* * * * *
2518617 CTAGTTGTGCATTTGACAAAAAGGTGTCAATCATGCAAGTTGGATTAAAGGTTAAATACTTTTGA
1 CTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGA
* *
2518682 GGAAAATATTAATGGC
66 GTAAAATATTAATGGA
* * * * *
2518698 CTAGTTGTGCATTTGATAAAAAGCTGTCAATCATGCTAGTTAGATGAAAGGTTAAATGCCTTTGA
1 CTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGA
2518763 GTAAAATA
66 GTAAAATA
2518771 CTAGTTGTAT
Statistics
Matches: 282, Mismatches: 34, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 282 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (81 bp):
CTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGA
GTAAAATATTAATGGA
Found at i:2518853 original size:45 final size:45
Alignment explanation
Indices: 2518807--2519247 Score: 630
Period size: 45 Copynumber: 9.8 Consensus size: 45
2518797 GTATAAACGA
* * *
2518807 CATGAAAGAATGCCATAAATGAAATGTATAATAGTGTAATATCGA
1 CATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTATCGG
* *
2518852 CATGAAAGGATGCCATAAATTAAATGTATAATAGTGTATTATTGG
1 CATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTATCGG
* * *
2518897 CATGAAATGATGCCCTAAATGAAATGTATAATAGTGTAATATCGG
1 CATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTATCGG
* * *
2518942 TATGAAAGGATGTCATAAATGAAATGTATAATAGTGTATTATAGG
1 CATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTATCGG
* * * *
2518987 CATGAAATGATACCCTAAATGAAATGTATAATAGTGTAATATCGG
1 CATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTATCGG
* * *
2519032 CATGAAAGGATGTCATAAATAAAATGTATAATAATGTATTATCGG
1 CATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTATCGG
* * * *
2519077 CATGAAAGGATGCCCTAAATGAAATGTACAATAGTGTAATATCAG
1 CATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTATCGG
2519122 CATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTATCGG
1 CATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTATCGG
* *
2519167 CATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTATTATCGA
1 CATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTATCGG
* * * *
2519212 CATGAAATGATGCCATGATTGAAATGCATAATAGTG
1 CATGAAAGGATGCCATAAATGAAATGTATAATAGTG
2519248 CATAATAAGT
Statistics
Matches: 348, Mismatches: 48, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 348 1.00
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (45 bp):
CATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTATCGG
Found at i:2521411 original size:20 final size:21
Alignment explanation
Indices: 2521383--2521436 Score: 56
Period size: 24 Copynumber: 2.5 Consensus size: 21
2521373 CATTCGTTCA
*
2521383 TTTACGTTCGAT-TATGTTTG
1 TTTATGTTCGATCTATGTTTG
*
2521403 TTTATGTTCGTTCGGCTATGTTTG
1 TTTATGTTCGAT---CTATGTTTG
2521427 TTTATGTTCG
1 TTTATGTTCG
2521437 TTCATTTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.36
24 18 0.64
ACGTcount: A:0.11, C:0.11, G:0.22, T:0.56
Consensus pattern (21 bp):
TTTATGTTCGATCTATGTTTG
Found at i:2521446 original size:24 final size:24
Alignment explanation
Indices: 2521394--2521449 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
2521384 TTACGTTCGA
*
2521394 TTATGTTTGTTTATGTTCGTTCGG
1 TTATGTTTGTTTATGTTCGTTCAG
* *
2521418 CTATGTTTGTTTATGTTCGTTCAT
1 TTATGTTTGTTTATGTTCGTTCAG
2521442 TTATGTTT
1 TTATGTTT
2521450 AACCCAATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.61
Consensus pattern (24 bp):
TTATGTTTGTTTATGTTCGTTCAG
Found at i:2524970 original size:57 final size:57
Alignment explanation
Indices: 2524898--2525006 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
2524888 ATTACATAAT
* *
2524898 GGCACTGAGTGTGCAAAAA-TATAAGAAATTCATAATTTGTTTATGAATTTCCTTATG
1 GGCACTAAGTCTGCAAAAAGT-TAAGAAATTCATAATTTGTTTATGAATTTCCTTATG
*
2524955 GGCACTAAGTCTGCAAAAAGTTAAGGAATTCATAATTTGTTTATGAATTTCC
1 GGCACTAAGTCTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCC
2525007 ATATAAGAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
57 47 0.98
58 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (57 bp):
GGCACTAAGTCTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCTTATG
Found at i:2525027 original size:57 final size:57
Alignment explanation
Indices: 2524905--2525040 Score: 161
Period size: 57 Copynumber: 2.4 Consensus size: 57
2524895 AATGGCACTG
* ** *
2524905 AGTGTGCAAAAATATAAGAAATTCATAATTTGTTTATGAATTTCCTTATGGGCACTA
1 AGTGTGCAAAAATATAAGAAATTCATAATTTGTTTATGAATTTCCATATAAGAACTA
* * *
2524962 AGTCTGCAAAAAGT-TAAGGAATTCATAATTTGTTTATGAATTTCCATATAAGAACTTT
1 AGTGTGCAAAAA-TATAAGAAATTCATAATTTGTTTATGAATTTCCATATAAGAAC-TA
*
2525020 A-TGTGCAAAAA-CTAAGAAATT
1 AGTGTGCAAAAATATAAGAAATT
2525041 TTATGAATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
56 8 0.12
57 56 0.84
58 3 0.04
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (57 bp):
AGTGTGCAAAAATATAAGAAATTCATAATTTGTTTATGAATTTCCATATAAGAACTA
Found at i:2525319 original size:67 final size:67
Alignment explanation
Indices: 2525211--2525884 Score: 1017
Period size: 67 Copynumber: 10.0 Consensus size: 67
2525201 TAAAATATTA
* * *
2525211 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTTTGCCAGTTAGATGAAAGGATAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
2525276 TT
66 TT
* *
2525278 GAGGCCTAACTGTGCATTGACAGAAAGGTGGT-AATTATGCCAGTTAGATGAAAGGCTAAGTACC
1 GAGGCCTAACTGTGCATTGACAGAAAGGT-GTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCC
2525342 TTT
65 TTT
* *
2525345 GAGGCCTAGCTGTGCATTGACAGAAAGGTGTTAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
2525410 TT
66 TT
* *
2525412 GAGGCCTAGCTGTGCATTGACAGAAAGGTGTTAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
2525477 TT
66 TT
* *
2525479 GAGGCCTAGCTGTGCATTGACAGAAAGGTGTTAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
2525544 TT
66 TT
* *
2525546 GAGGCCTAACTGTGCATTGATAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGCCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
2525611 TT
66 TT
* * *
2525613 GAGGCCTAACTGTGCATAGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
2525678 TT
66 TT
* * *
2525680 GAGGCCTAACTGTGCATTGATAGAAAGGTGTCAATCATGTTAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
2525745 TT
66 TT
** * * *
2525747 TTGGCCTAACTGTGCATTGACAGAAAGGTGTCAATCATGCCAGTTAGATGATAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
2525812 TT
66 TT
* ** * * * * * * *
2525814 GAGACCTAGTTGTGTATTTGACAGAAAGGTGCCAATTATGTAATTTAGATGAAAGGTTAAATACC
1 GAGGCCTAACTGTGCA-TTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCC
2525879 TTT
65 TTT
2525882 GAG
1 GAG
2525885 TAAAAGATTA
Statistics
Matches: 566, Mismatches: 38, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
66 2 0.00
67 517 0.91
68 47 0.08
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (67 bp):
GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
TT
Found at i:2526235 original size:81 final size:81
Alignment explanation
Indices: 2525818--2526215 Score: 616
Period size: 81 Copynumber: 4.9 Consensus size: 81
2525808 GCCTTTGAGA
* * * * * ** *
2525818 CCTAGTTGTGTATTTGACAGAAAGGTGCCAATTATGTAATTTAGATGAAAGGTTAAATACCTTTG
1 CCTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTG
2525883 AGTAAAAGATTAATGG
66 AGTAAAAGATTAATGG
* * * *
2525899 CCTAGATGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTG
1 CCTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTG
2525964 AGTAAAAGATTAATGG
66 AGTAAAAGATTAATGG
*
2525980 CCTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTT
1 CCTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTG
*
2526045 AGTAAAATATTAATGG
66 AGTAAAAGATTAATGG
* * *
2526061 CCTAGCTGTGCATTTGACAAAAAGATGTCAATCATGCCAGTTAGATGAAAGGGTAAATACTTTTG
1 CCTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTG
*
2526126 AGCAAAAGATTAATGG
66 AGTAAAAGATTAATGG
* *
2526142 CCTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAATGTTAAATGCCTTTG
1 CCTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTG
2526207 AGTAAAAGA
66 AGTAAAAGA
2526216 CTAGATGTAT
Statistics
Matches: 292, Mismatches: 25, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 292 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (81 bp):
CCTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTG
AGTAAAAGATTAATGG
Found at i:2526598 original size:45 final size:45
Alignment explanation
Indices: 2526249--2526580 Score: 436
Period size: 45 Copynumber: 7.4 Consensus size: 45
2526239 GTTGTATAAA
* * * *
2526249 CGACATGAAAGGATTCCATAAATGAAATGTATAGTAAG-GTAATA-
1 CGACATGAAAGGATGCCCTAAATGAAATGTATAAT-AGTGTATTAT
* * * * *
2526293 CTGGCATGAAATGATGACATAAATGAAATGTATAACAGTGTATTAT
1 C-GACATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTATTAT
*
2526339 CTG-CATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTAATAT
1 C-GACATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTATTAT
* * *
2526384 CAACATGAAATGATGCCCTAAATGAAATGTATAATAGTGAATTAT
1 CGACATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTATTAT
* * *
2526429 CGGCATGAAATGATGCCCTAAATGAAATGTATAATAGTGTAATAT
1 CGACATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTATTAT
*
2526474 CGACATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTAT
1 CGACATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTATTAT
* *
2526519 CGTCATGAAAGGATTCCCTAAATGAAATGTATAATAGTGTATTAT
1 CGACATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTATTAT
*
2526564 CAACATGAAAGGATGCC
1 CGACATGAAAGGATGCC
2526581 ATGATTAAAA
Statistics
Matches: 254, Mismatches: 30, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
44 3 0.01
45 248 0.98
46 3 0.01
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (45 bp):
CGACATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTATTAT
Found at i:2526617 original size:90 final size:89
Alignment explanation
Indices: 2526253--2526635 Score: 419
Period size: 90 Copynumber: 4.3 Consensus size: 89
2526243 TATAAACGAC
* * * ** * *
2526253 ATGAAAGGATTCCATAAATGAAATGTATAGTAAG-GTAATA-CTGGCATGAAATGATGACATAAA
1 ATGAAAGGATGCCCTAAATGAAATGTATAAT-AGTGTAATATC-AACATGAAAGGATGCCATAAA
* * * *
2526316 TGAAATGTATAACAGTGTATTATCTGC
64 TGAAATGTATAATAGTGAATTAT-AGT
* *
2526343 ATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTAATATCAACATGAAATGATGCCCTAAATG
1 ATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTAATATCAACATGAAAGGATGCCATAAATG
* *
2526408 AAATGTATAATAGTGAATTATCGGC
66 AAATGTATAATAGTGAATTAT-AGT
* *
2526433 ATGAAATGATGCCCTAAATGAAATGTATAATAGTGTAATATCGACATGAAAGGATGCCATAAATG
1 ATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTAATATCAACATGAAAGGATGCCATAAATG
* *
2526498 AAATGTATAATAGTGTATTATCGT
66 AAATGTATAATAGTGAATTATAGT
* * * *
2526522 CATGAAAGGATTCCCTAAATGAAATGTATAATAGTGTATTATCAACATGAAAGGATGCCATGATT
1 -ATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTAATATCAACATGAAAGGATGCCATAAAT
* * * * *
2526587 AAAATGCATAATGGTGCATAATAAGT
65 GAAATGTATAATAGTGAATTAT-AGT
* * *
2526613 ATGAATGGATGCTCTCAATGAAA
1 ATGAAAGGATGCCCTAAATGAAA
2526636 ATAAAGAATA
Statistics
Matches: 256, Mismatches: 33, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
89 3 0.01
90 250 0.98
91 3 0.01
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (89 bp):
ATGAAAGGATGCCCTAAATGAAATGTATAATAGTGTAATATCAACATGAAAGGATGCCATAAATG
AAATGTATAATAGTGAATTATAGT
Found at i:2532139 original size:21 final size:21
Alignment explanation
Indices: 2532113--2532164 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2532103 TATACGGCAT
2532113 CGATACTACTTAGTGTA-GTAA
1 CGATACTACTTAGT-TAGGTAA
*
2532134 CGATACT-CTTAGTTATGGTAC
1 CGATACTACTTAGTTA-GGTAA
2532155 CGATACTACT
1 CGATACTACT
2532165 CCTTTGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 6 0.22
21 17 0.63
22 2 0.07
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (21 bp):
CGATACTACTTAGTTAGGTAA
Found at i:2532722 original size:33 final size:33
Alignment explanation
Indices: 2532647--2532714 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
2532637 TAATTTTCTC
*
2532647 TTTGAGAGGGTGTCTCAAGAATTTGGTGTATAA
1 TTTGAGAGGGTGTCTCAAGAATTAGGTGTATAA
2532680 TTTGAGAGGGTGTCTCAAGAAATTAGGT-TATAA
1 TTTGAGAGGGTGTCTCAAG-AATTAGGTGTATAA
2532713 TT
1 TT
2532715 CTTGAGGGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
33 26 0.79
34 7 0.21
ACGTcount: A:0.29, C:0.06, G:0.28, T:0.37
Consensus pattern (33 bp):
TTTGAGAGGGTGTCTCAAGAATTAGGTGTATAA
Found at i:2545315 original size:77 final size:77
Alignment explanation
Indices: 2545188--2545353 Score: 323
Period size: 77 Copynumber: 2.2 Consensus size: 77
2545178 TTTTTTCAAT
2545188 ATAATGGGTATGTAAAATTTCTTAATTTTTTTCTTCTTCCATTAATATATTGAACTATATTTAAT
1 ATAATGGGTATGTAAAATTTCTTAATTTTTTTCTTCTTCCATTAATATATTGAACTATATTTAAT
2545253 ATCTAATCTAAA
66 ATCTAATCTAAA
2545265 ATAATGGGTATGTAAAATTTCTTAATTTTTTTCTTCTTCCATTAATATATTGAACTATATTTAAT
1 ATAATGGGTATGTAAAATTTCTTAATTTTTTTCTTCTTCCATTAATATATTGAACTATATTTAAT
2545330 ATCTAATCTAAA
66 ATCTAATCTAAA
*
2545342 ATAATGCGTATG
1 ATAATGGGTATG
2545354 CATTTGACCC
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 88 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (77 bp):
ATAATGGGTATGTAAAATTTCTTAATTTTTTTCTTCTTCCATTAATATATTGAACTATATTTAAT
ATCTAATCTAAA
Found at i:2545586 original size:30 final size:30
Alignment explanation
Indices: 2545461--2545607 Score: 123
Period size: 31 Copynumber: 4.8 Consensus size: 30
2545451 ACTTTGATTG
* * *
2545461 AATTTAGAGATCAAATTGATACTTTATCTAA
1 AATTTA-AGATTAAATTAATATTTTATCTAA
** *
2545492 AGATCAAATATTAAATTAATATTTTATCTAA
1 A-ATTTAAGATTAAATTAATATTTTATCTAA
* * *
2545523 AGTTTAAGAGTGAAATTAATATTTTATTTAA
1 AATTTAAGA-TTAAATTAATATTTTATCTAA
* * *
2545554 AATTTAAGATTAAATTAATATTCTACCGAA
1 AATTTAAGATTAAATTAATATTTTATCTAA
* * *
2545584 AATTTAGAAATCAAATTAAAATTT
1 AATTTA-AGATTAAATTAATATTT
2545608 AATCAATTTT
Statistics
Matches: 91, Mismatches: 22, Indels: 6
0.76 0.18 0.05
Matches are distributed among these distances:
30 26 0.29
31 62 0.68
32 3 0.03
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.40
Consensus pattern (30 bp):
AATTTAAGATTAAATTAATATTTTATCTAA
Found at i:2545600 original size:61 final size:62
Alignment explanation
Indices: 2545461--2545607 Score: 145
Period size: 61 Copynumber: 2.4 Consensus size: 62
2545451 ACTTTGATTG
* * * * * * *
2545461 AATTTAGAGATCAAATTGATACTTTATCTAAAGATCAAATATTAAATTAATATTTTATCTAA
1 AATTTAGAAATCAAATTAATATTTTATCTAAAGATCAAAGATTAAATTAATATTCTACCGAA
* * * * **
2545523 AGTTTA-AGAGTGAAATTAATATTTTATTTAAA-ATTTAAGATTAAATTAATATTCTACCGAA
1 AATTTAGA-AATCAAATTAATATTTTATCTAAAGATCAAAGATTAAATTAATATTCTACCGAA
*
2545584 AATTTAGAAATCAAATTAAAATTT
1 AATTTAGAAATCAAATTAATATTT
2545608 AATCAATTTT
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
61 42 0.64
62 24 0.36
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.40
Consensus pattern (62 bp):
AATTTAGAAATCAAATTAATATTTTATCTAAAGATCAAAGATTAAATTAATATTCTACCGAA
Found at i:2545703 original size:22 final size:23
Alignment explanation
Indices: 2545648--2545705 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
2545638 AACTAACAAA
2545648 AATAA-ATAAATAAATAAAGTCT
1 AATAACATAAATAAATAAAGTCT
*
2545670 AATAACCA-AAATATAATGAA-TC-
1 AATAA-CATAAATA-AATAAAGTCT
2545692 AATAACATAAATAA
1 AATAACATAAATAA
2545706 TCAAATCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
21 3 0.10
22 15 0.48
23 7 0.23
24 6 0.19
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.24
Consensus pattern (23 bp):
AATAACATAAATAAATAAAGTCT
Found at i:2549711 original size:64 final size:64
Alignment explanation
Indices: 2549589--2549711 Score: 140
Period size: 64 Copynumber: 1.9 Consensus size: 64
2549579 TTATTAAGAC
* * * ** * * *
2549589 TTGATACTCTTGTGTGGTATTTTATTTTGAATATCTTGTGTTGATTTGATTGTGTTGTTGAGAT
1 TTGATACTCTTGTGTGGTATTTTAATATGAACATCTTGTGAAGATTCGATTCTATTGTTGAGAT
* *
2549653 TTGATACTCTTGTGTGTTAATTTTAATATGAACATCTTGTGAAGA-TCGGTTCTATTGTT
1 TTGATACTCTTGTGTGGT-ATTTTAATATGAACATCTTGTGAAGATTCGATTCTATTGTT
2549712 TTTATGTTCC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
64 27 0.56
65 21 0.44
ACGTcount: A:0.20, C:0.07, G:0.21, T:0.51
Consensus pattern (64 bp):
TTGATACTCTTGTGTGGTATTTTAATATGAACATCTTGTGAAGATTCGATTCTATTGTTGAGAT
Found at i:2562166 original size:16 final size:16
Alignment explanation
Indices: 2562141--2562200 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
2562131 TAATAAATAA
2562141 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
* *
2562157 ACGAAAATAAACAAAT
1 ACGAACATAAACAAAC
2562173 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
2562189 ACGAACATAAAC
1 ACGAACATAAAC
2562201 GTTGGAGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.63, C:0.22, G:0.07, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:2562442 original size:11 final size:11
Alignment explanation
Indices: 2562426--2562497 Score: 90
Period size: 11 Copynumber: 6.4 Consensus size: 11
2562416 TCAAGAATCG
*
2562426 AGCTCGATTGA
1 AGCTCGATTCA
2562437 AGCTCGATTCTA
1 AGCTCGATTC-A
*
2562449 AGATCGATTCA
1 AGCTCGATTCA
*
2562460 AGCTCGATTCTG
1 AGCTCGATTC-A
2562472 AGCTCGATTCA
1 AGCTCGATTCA
*
2562483 AGCTCAATTCA
1 AGCTCGATTCA
2562494 AGCT
1 AGCT
2562498 AGACATTTCC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
11 33 0.62
12 20 0.38
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:2562462 original size:23 final size:23
Alignment explanation
Indices: 2562429--2562492 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2562419 AGAATCGAGC
*
2562429 TCGATTGAAGCTCGATTCTAAGA
1 TCGATTCAAGCTCGATTCTAAGA
* *
2562452 TCGATTCAAGCTCGATTCTGAGC
1 TCGATTCAAGCTCGATTCTAAGA
*
2562475 TCGATTCAAGCTCAATTC
1 TCGATTCAAGCTCGATTC
2562493 AAGCTAGACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (23 bp):
TCGATTCAAGCTCGATTCTAAGA
Found at i:2563050 original size:14 final size:14
Alignment explanation
Indices: 2563018--2563044 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2563008 GAATGAACAT
2563018 AAACGAACATAACC
1 AAACGAACATAACC
2563032 AAACGAACATAAC
1 AAACGAACATAAC
2563045 TGAACGTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.26, G:0.07, T:0.07
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:2564049 original size:18 final size:17
Alignment explanation
Indices: 2563995--2564043 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2563985 TTGGACCCTT
* *
2563995 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
2564013 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
2564031 AGTGCATTCGATG
1 AGTGCA-TCGATG
2564044 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:2564083 original size:64 final size:64
Alignment explanation
Indices: 2564015--2564224 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 64
2564005 TGCACTAAGA
* *
2564015 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTTG
* * ** * * *
2564079 GTGCATCGATGCATCAAATACATTCGATGTTTTTATAAA-ATCCTTAGTTCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGTT
*
2564143 A
64 G
* * ** * *
2564144 GTGCATCGATGCATGAAATGCATTCAATG-TTCAATTTAATTCATG-GTGCATTGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG-T
2564207 TG
63 TG
2564209 GTGCATCGATGCATCA
1 GTGCATCGATGCATCA
2564225 CTCTGAAAAA
Statistics
Matches: 115, Mismatches: 25, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 43 0.37
65 65 0.57
66 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTTG
Found at i:2564592 original size:19 final size:19
Alignment explanation
Indices: 2564570--2564610 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
2564560 CTATAACACT
2564570 TTTCCCTTAAAACATAACA
1 TTTCCCTTAAAACATAACA
2564589 TTT-CCTTAAAACATAACA
1 TTTCCCTTAAAACATAACA
2564607 TTTC
1 TTTC
2564611 TCCCCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (19 bp):
TTTCCCTTAAAACATAACA
Found at i:2564686 original size:2 final size:2
Alignment explanation
Indices: 2564681--2564710 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2564671 TAGCCAATTG
2564681 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2564711 GTTTAAGCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2564700 original size:13 final size:13
Alignment explanation
Indices: 2564682--2564707 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2564672 AGCCAATTGA
2564682 TATATATATATAT
1 TATATATATATAT
2564695 TATATATATATAT
1 TATATATATATAT
2564708 ATAGTTTAAG
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:2564701 original size:15 final size:15
Alignment explanation
Indices: 2564681--2564709 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2564671 TAGCCAATTG
2564681 ATATATATATATATT
1 ATATATATATATATT
2564696 ATATATATATATAT
1 ATATATATATATAT
2564710 AGTTTAAGCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:2567971 original size:178 final size:178
Alignment explanation
Indices: 2567672--2568028 Score: 714
Period size: 178 Copynumber: 2.0 Consensus size: 178
2567662 TATGATACCA
2567672 AAGTCCTAAACTAGGAGTGTCCTTAAGGTATCTAAAGATTCTCTTAACAGCTAGTAAATGTGATT
1 AAGTCCTAAACTAGGAGTGTCCTTAAGGTATCTAAAGATTCTCTTAACAGCTAGTAAATGTGATT
2567737 CCTTAGGACATGATTGAAATCTAGCACATAAGCAAACACTAAACATAATGTCTGGTCTACTTACA
66 CCTTAGGACATGATTGAAATCTAGCACATAAGCAAACACTAAACATAATGTCTGGTCTACTTACA
2567802 GTTAGATAAAGTAAAGAGCCAATCATTGACCTATATAATTTAACATCT
131 GTTAGATAAAGTAAAGAGCCAATCATTGACCTATATAATTTAACATCT
2567850 AAGTCCTAAACTAGGAGTGTCCTTAAGGTATCTAAAGATTCTCTTAACAGCTAGTAAATGTGATT
1 AAGTCCTAAACTAGGAGTGTCCTTAAGGTATCTAAAGATTCTCTTAACAGCTAGTAAATGTGATT
2567915 CCTTAGGACATGATTGAAATCTAGCACATAAGCAAACACTAAACATAATGTCTGGTCTACTTACA
66 CCTTAGGACATGATTGAAATCTAGCACATAAGCAAACACTAAACATAATGTCTGGTCTACTTACA
2567980 GTTAGATAAAGTAAAGAGCCAATCATTGACCTATATAATTTAACATCT
131 GTTAGATAAAGTAAAGAGCCAATCATTGACCTATATAATTTAACATCT
2568028 A
1 A
2568029 CATATTTACC
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
178 179 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (178 bp):
AAGTCCTAAACTAGGAGTGTCCTTAAGGTATCTAAAGATTCTCTTAACAGCTAGTAAATGTGATT
CCTTAGGACATGATTGAAATCTAGCACATAAGCAAACACTAAACATAATGTCTGGTCTACTTACA
GTTAGATAAAGTAAAGAGCCAATCATTGACCTATATAATTTAACATCT
Found at i:2572550 original size:43 final size:42
Alignment explanation
Indices: 2572484--2572569 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 42
2572474 AAAAATAGGC
2572484 TTGAAATGCTCAACTTGAGGTTTGATGCTTTCTCTTTGATTG
1 TTGAAATGCTCAACTTGAGGTTTGATGCTTTCTCTTTGATTG
2572526 TTGAAATGCTCAAACTTGAGGTTTGATGCTTTCTCTTTGATTG
1 TTGAAATGCTC-AACTTGAGGTTTGATGCTTTCTCTTTGATTG
2572569 T
1 T
2572570 CTCTTGATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 11 0.26
43 32 0.74
ACGTcount: A:0.20, C:0.14, G:0.21, T:0.45
Consensus pattern (42 bp):
TTGAAATGCTCAACTTGAGGTTTGATGCTTTCTCTTTGATTG
Found at i:2572908 original size:46 final size:45
Alignment explanation
Indices: 2572812--2572908 Score: 124
Period size: 46 Copynumber: 2.1 Consensus size: 45
2572802 TGCACTAAAA
*
2572812 GTGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCG
1 GTGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCG
* * **
2572857 ATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTTAGTGCATCG
1 GTGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAGAGTGCATCG
2572903 GTGCAT
1 GTGCAT
2572909 GGTAAGTGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
45 19 0.43
46 22 0.50
47 3 0.07
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (45 bp):
GTGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCG
Found at i:2572983 original size:65 final size:64
Alignment explanation
Indices: 2572848--2572993 Score: 168
Period size: 65 Copynumber: 2.2 Consensus size: 64
2572838 AAATAGCCAG
* *
2572848 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGGTGCATGGTA
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCATAGTGCATCGATGCATGGTA
* ** * *
2572913 AGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGAT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCCATAGTGCATCGATGCATGG-T
*
2572977 T
64 A
* *
2572978 GGTGCATCGGTGCATC
1 AGTGCATCGATGCATC
2572994 TCTCTGAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
63 3 0.04
64 22 0.32
65 43 0.63
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (64 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCATAGTGCATCGATGCATGGTA
Found at i:2577264 original size:139 final size:138
Alignment explanation
Indices: 2576982--2577382 Score: 470
Period size: 139 Copynumber: 2.9 Consensus size: 138
2576972 AACTTAAAAG
* *
2576982 ATTAAACCTAAAATGTAGGATCTAA-TATTAA-CCTTATCAATTTTAGCAATTTATTGGATCGAA
1 ATTAAA-CTAAAAT-TAGGATCTAATTATTAATCCTAATCAATTTTAACAATTTATTGGATCGAA
* ** *
2577045 TAATTAAAATGGAACAACGGGCATAAA--TGAGGACCAAATAAAAAATCCACCTAAATTAAAGGA
64 TAATTAATATGGAACTTCGAGCATAAATGTGAGGACCAAATAAAAAATCCACCTAAATTAAAGGA
2577108 CTAAAGTGAA
129 CTAAAGTGAA
* * * **
2577118 ATTAAACTAAAATTCAGGATCTAATTATTAATGCTAATCAATTTTAACAAATTATCGGATCTTAT
1 ATTAAACTAAAATT-AGGATCTAATTATTAATCCTAATCAATTTTAACAATTTATTGGATCGAAT
* ** *
2577183 AATTAATATGGAACTTCGAGCATAAATGTGAGGACCAAATAAAATATTTACCTGAATTAAAGGAC
65 AATTAATATGGAACTTCGAGCATAAATGTGAGGACCAAATAAAAAATCCACCTAAATTAAAGGAC
2577248 TAAAGTGAA
130 TAAAGTGAA
* ** * * *
2577257 ATTAAACTAAAATGGAGTCTCTAATTATTTATCCTAACCAATTTTATCAATTTATTGGATCGAAT
1 ATTAAACTAAAAT-TAGGATCTAATTATTAATCCTAATCAATTTTAACAATTTATTGGATCGAAT
* * * ** * *
2577322 AATTAATATGAAACCTT-GTGTATAAATGCAAGGACCAAATAAAAAATTCATCTAAATTAAA
65 AATTAATATGGAA-CTTCGAGCATAAATGTGAGGACCAAATAAAAAATCCACCTAAATTAAA
2577383 AAGATTAGGG
Statistics
Matches: 223, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
134 1 0.00
135 16 0.07
136 12 0.05
137 48 0.22
139 143 0.64
140 3 0.01
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (138 bp):
ATTAAACTAAAATTAGGATCTAATTATTAATCCTAATCAATTTTAACAATTTATTGGATCGAATA
ATTAATATGGAACTTCGAGCATAAATGTGAGGACCAAATAAAAAATCCACCTAAATTAAAGGACT
AAAGTGAA
Found at i:2577570 original size:28 final size:30
Alignment explanation
Indices: 2577496--2577571 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
2577486 ATTAGAACAC
*
2577496 TAAAAGGAC-TAAATTGAAGCAATTCAAAA
1 TAAAAGGACTTAAATTGAAACAATTCAAAA
*
2577525 TAAAAGG-CTGAAATTGAAACACA-TC-AAA
1 TAAAAGGACTTAAATTGAAACA-ATTCAAAA
2577553 TAAAAGGACTTAAA-TGAAA
1 TAAAAGGACTTAAATTGAAA
2577572 GAAATAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 16 0.39
29 24 0.59
30 1 0.02
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (30 bp):
TAAAAGGACTTAAATTGAAACAATTCAAAA
Found at i:2577646 original size:29 final size:29
Alignment explanation
Indices: 2577614--2577698 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
2577604 ACTAAAAAAT
* *
2577614 AAATACTAGAATTTAAGGGACTAAAATGA
1 AAATACTAGAAATTAAAGGACTAAAATGA
* * *
2577643 AAATGCTGGAAATTAAAGGA-TAAAATTA
1 AAATACTAGAAATTAAAGGACTAAAATGA
* * *
2577671 AAAGTAATATAAATTAATGGACTAAAAT
1 AAA-TACTAGAAATTAAAGGACTAAAAT
2577699 TTAAAATAGC
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
28 10 0.23
29 28 0.64
30 6 0.14
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.26
Consensus pattern (29 bp):
AAATACTAGAAATTAAAGGACTAAAATGA
Found at i:2590033 original size:16 final size:17
Alignment explanation
Indices: 2589997--2590033 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2589987 AAACTATTCA
2589997 TTTATATTATTATTATG
1 TTTATATTATTATTATG
*
2590014 -TTATATT-TTTTTATG
1 TTTATATTATTATTATG
2590029 TTTAT
1 TTTAT
2590034 GATATTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (17 bp):
TTTATATTATTATTATG
Found at i:2590765 original size:31 final size:31
Alignment explanation
Indices: 2590727--2590805 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
2590717 TATATATTTA
2590727 GTCACTCAACTACTCTTGCAGTTATGTTTTG
1 GTCACTCAACTACTCTTGCAGTTATGTTTTG
* *
2590758 GTCACTCAACTACTCTTGTAGTTATTTTTTG
1 GTCACTCAACTACTCTTGCAGTTATGTTTTG
*
2590789 GTCACTTAACTACTCTT
1 GTCACTCAACTACTCTT
2590806 TTTTTAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (31 bp):
GTCACTCAACTACTCTTGCAGTTATGTTTTG
Found at i:2598997 original size:22 final size:23
Alignment explanation
Indices: 2598946--2598998 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 23
2598936 ACTATCTAAG
**
2598946 GTGGTGGTGCTGTCGAGCGACGT
1 GTGGTGGTGCTACCGAGCGACGT
2598969 GGATGGTGGTGCTACCGAGCGACGT
1 -G-TGGTGGTGCTACCGAGCGACGT
2598994 -TGGTG
1 GTGGTG
2598999 CTTGTGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 5 0.19
24 1 0.04
25 20 0.77
ACGTcount: A:0.11, C:0.17, G:0.47, T:0.25
Consensus pattern (23 bp):
GTGGTGGTGCTACCGAGCGACGT
Found at i:2606186 original size:22 final size:21
Alignment explanation
Indices: 2606150--2606193 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
2606140 AAAGAAAAGG
*
2606150 AAAATAACAAGTAAAACTAAA
1 AAAATAAAAAGTAAAACTAAA
2606171 AAAATGAAAAAGTAAAACTAAA
1 AAAAT-AAAAAGTAAAACTAAA
2606193 A
1 A
2606194 TGCTTTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.14
Consensus pattern (21 bp):
AAAATAAAAAGTAAAACTAAA
Found at i:2608011 original size:20 final size:20
Alignment explanation
Indices: 2607986--2608023 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2607976 CCACATACAA
*
2607986 CTATATGCTCCTAAATGAAT
1 CTATATGATCCTAAATGAAT
*
2608006 CTATATGATCCTATATGA
1 CTATATGATCCTAAATGA
2608024 GCTCTTAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (20 bp):
CTATATGATCCTAAATGAAT
Found at i:2610614 original size:34 final size:34
Alignment explanation
Indices: 2610565--2610643 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 34
2610555 CAATAAGCAA
**
2610565 TCCAGGTGCTTTCATCA-GAAACAGAAATAT-ACAC
1 TCCAGGTGCAATCATCATG-AACAGAAATATGA-AC
*
2610599 TCCAGGTGCAATCATCATGTACAGAAATATGAAC
1 TCCAGGTGCAATCATCATGAACAGAAATATGAAC
2610633 TCCAGGTGCAA
1 TCCAGGTGCAA
2610644 ATAAGATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
34 38 0.95
35 2 0.05
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (34 bp):
TCCAGGTGCAATCATCATGAACAGAAATATGAAC
Found at i:2619169 original size:23 final size:23
Alignment explanation
Indices: 2619118--2619169 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
2619108 TAGTTTTATT
2619118 TTATTTATGAAATATTTTTATAA
1 TTATTTATGAAATATTTTTATAA
**
2619141 AGATTTCA-GAAATATTTTT-TGAA
1 TTATTT-ATGAAATATTTTTAT-AA
2619164 TTATTT
1 TTATTT
2619170 TAGGGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
22 1 0.04
23 21 0.91
24 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (23 bp):
TTATTTATGAAATATTTTTATAA
Found at i:2619407 original size:34 final size:34
Alignment explanation
Indices: 2619369--2619456 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 34
2619359 ACGTTATCTT
*
2619369 ATTGCACATGGAGTGCATATTTTTGTATCTAATG
1 ATTGCACATGGAGTGCATATTTCTGTATCTAATG
* * *
2619403 ATTGCACCTGGAGTGCATA-TTCTGTTTCTGATG
1 ATTGCACATGGAGTGCATATTTCTGTATCTAATG
* * *
2619436 ATAGCACATTGAGTGCTTATT
1 ATTGCACATGGAGTGCATATT
2619457 GAGAACGCTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
33 26 0.58
34 19 0.42
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (34 bp):
ATTGCACATGGAGTGCATATTTCTGTATCTAATG
Found at i:2640422 original size:103 final size:103
Alignment explanation
Indices: 2640265--2640460 Score: 234
Period size: 103 Copynumber: 1.9 Consensus size: 103
2640255 TTGTGCCATC
* * * *
2640265 AGTATCGATACTATCCCCTTGGGTATCGATACTCACCCTAGTATCGATAAAAATTTAACTTCAAT
1 AGTATCGATACTATACCCTTGGGTATCGACACTCACCATAGTATCAATAAAAATTTAACTTCAAT
2640330 GTTCTAAAAAATACCTTGGTATCAATACCCCTATGAGG
66 GTTCTAAAAAATACCTTGGTATCAATACCCCTATGAGG
* * * ** *
2640368 AGTATTGATACTCTACCC-TGGGTATCGACACTC-CCATGAGTATCAATACCAAATTTGGCTTCG
1 AGTATCGATACTATACCCTTGGGTATCGACACTCACCAT-AGTATCAATA-AAAATTTAACTTCA
* * * *
2640431 ATGTTTTAAAAAATGCCTTTGTATCGATAC
64 ATGTTCTAAAAAATACCTTGGTATCAATAC
2640461 TGATTCTCTA
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
101 3 0.04
102 23 0.30
103 51 0.66
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (103 bp):
AGTATCGATACTATACCCTTGGGTATCGACACTCACCATAGTATCAATAAAAATTTAACTTCAAT
GTTCTAAAAAATACCTTGGTATCAATACCCCTATGAGG
Found at i:2657832 original size:40 final size:42
Alignment explanation
Indices: 2657761--2657851 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
2657751 TTAATGGTAC
* * * *
2657761 GGCGTTTTTTGATAAACGCCGCAATATTATT-G-TATCTAGT
1 GGCGTTTTATGACAAACGCCGCAATATTATTGGACATATAGT
*
2657801 GGCGTTTTATGTACAAACGCTGCAATA-TATTGGACATATAGT
1 GGCGTTTTATG-ACAAACGCCGCAATATTATTGGACATATAGT
2657843 GGCGTTTTA
1 GGCGTTTTA
2657852 ACAAAAAACG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
40 14 0.33
41 14 0.33
42 15 0.35
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (42 bp):
GGCGTTTTATGACAAACGCCGCAATATTATTGGACATATAGT
Found at i:2659130 original size:28 final size:28
Alignment explanation
Indices: 2659099--2659152 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
2659089 AATACAAATA
* *
2659099 TTAATATTTTGGAGACTCAATAAACCGT
1 TTAATAGTTTAGAGACTCAATAAACCGT
* *
2659127 TTAATGGTTTAGAGGCTCAATAAACC
1 TTAATAGTTTAGAGACTCAATAAACC
2659153 ATAATAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (28 bp):
TTAATAGTTTAGAGACTCAATAAACCGT
Found at i:2667112 original size:21 final size:21
Alignment explanation
Indices: 2667038--2667135 Score: 81
Period size: 21 Copynumber: 4.7 Consensus size: 21
2667028 AAGCAAGGGA
* * *
2667038 AGCAGAGAGAGCAGCAGCGGA
1 AGCACAGAGAGAAGCAGCGGC
* * * *
2667059 AGCAGC-TAGAGTAGCAGCAGA
1 AGCA-CAGAGAGAAGCAGCGGC
* *
2667080 AGCAGAGAGAGAAGCAGTGGC
1 AGCACAGAGAGAAGCAGCGGC
*
2667101 AGCACAGAGAGAGGCAGCGGC
1 AGCACAGAGAGAAGCAGCGGC
*
2667122 AGAACAGAGAGAAG
1 AGCACAGAGAGAAG
2667136 TAATATATCA
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.40, C:0.17, G:0.40, T:0.03
Consensus pattern (21 bp):
AGCACAGAGAGAAGCAGCGGC
Found at i:2667523 original size:43 final size:43
Alignment explanation
Indices: 2667476--2667595 Score: 136
Period size: 43 Copynumber: 2.8 Consensus size: 43
2667466 TACATTTAGC
** * *
2667476 GGCGTTTGTGATAAAAACGCCGCGAAATCTCAAGACATATTGT
1 GGCGTTTGTGACGAAAACGCCGCTAAATCTCAAGACATATTCT
*
2667519 GGCGTTT-TCGACGAAAATGCCGCTAAATCTCAAGACATATTCT
1 GGCGTTTGT-GACGAAAACGCCGCTAAATCTCAAGACATATTCT
* *
2667562 GCGACGTTTGT-AGGAAAACGCCGCTAAATATCAA
1 G-G-CGTTTGTGACGAAAACGCCGCTAAATCTCAA
2667596 CATCTTCTGC
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
42 1 0.02
43 37 0.57
44 21 0.32
45 5 0.08
46 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (43 bp):
GGCGTTTGTGACGAAAACGCCGCTAAATCTCAAGACATATTCT
Found at i:2667693 original size:43 final size:42
Alignment explanation
Indices: 2667561--2667767 Score: 164
Period size: 43 Copynumber: 4.8 Consensus size: 42
2667551 AGACATATTC
* *
2667561 TGCGACGTTTGTAGGAAAACGCCGCTAAATATCAACATCT-T
1 TGCGGCGTTTGTAGGAAAACGCCGCTAAAAATCAACATCTAT
* * *
2667602 CTGCGGCGTTTGTAGGAAAAACGCCGGTAAAAATAAACATCTAC
1 -TGCGGCGTTTGTAGG-AAAACGCCGCTAAAAATCAACATCTAT
* * * **
2667646 TGCGGCGTTTGTGAAGAAAACGTCGCTAAACATCAACGCCTAT
1 TGCGGCGTTTGT-AGGAAAACGCCGCTAAAAATCAACATCTAT
* ** * * * *
2667689 TGCGGCGTTTGTCTGCCAAAGGCCGTTAAATATCAACACCTAT
1 TGCGGCGTTTGT-AGGAAAACGCCGCTAAAAATCAACATCTAT
* * * * *
2667732 TGCGGCATTTTTCTGCAAAACGCCGCTAAATATCAA
1 TGCGGCGTTTGT-AGGAAAACGCCGCTAAAAATCAA
2667768 TACCTTTTGC
Statistics
Matches: 134, Mismatches: 28, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
42 14 0.10
43 118 0.88
44 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (42 bp):
TGCGGCGTTTGTAGGAAAACGCCGCTAAAAATCAACATCTAT
Found at i:2667736 original size:86 final size:85
Alignment explanation
Indices: 2667560--2667773 Score: 196
Period size: 86 Copynumber: 2.5 Consensus size: 85
2667550 AAGACATATT
* * * *
2667560 CTGCGACGTTTGTAGGAAAACGCCGCTAAATATCAACATCTTCTGCGGCGTTTGTAGGAAAAACG
1 CTGCGGCGTTTGTAAGAAAACGCCGCTAAACATCAACACCTTCTGCGGCGTTTGTAGGAAAAACG
*
2667625 CCGGTAAAAATAAACATCTA
66 CCGGTAAAAATAAACACCTA
* * ** **
2667645 CTGCGGCGTTTGTGAAGAAAACGTCGCTAAACATCAACGCCTAT-TGCGGCGTTTGTCTGCCAAA
1 CTGCGGCGTTTGT-AAGAAAACGCCGCTAAACATCAACACCT-TCTGCGGCGTTTGTAGGAAAAA
* * * *
2667709 GGCCGTTAAATATCAACACCTA
64 CGCCGGTAAAAATAAACACCTA
* * * ** * *
2667731 TTGCGGCATTTTTCTGCAAAACGCCGCTAAATATCAATACCTT
1 CTGCGGCGTTTGTAAG-AAAACGCCGCTAAACATCAACACCTT
2667774 TTGCAACAAA
Statistics
Matches: 102, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
85 14 0.14
86 87 0.85
87 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (85 bp):
CTGCGGCGTTTGTAAGAAAACGCCGCTAAACATCAACACCTTCTGCGGCGTTTGTAGGAAAAACG
CCGGTAAAAATAAACACCTA
Found at i:2669675 original size:17 final size:17
Alignment explanation
Indices: 2669648--2669704 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
2669638 AAGGATGTTG
2669648 ATAACTGTTTTTATTCT-
1 ATAA-TGTTTTTATTCTA
*
2669665 ATATATG-TTTTATTTTA
1 ATA-ATGTTTTTATTCTA
*
2669682 ATAATGTTTTTATAC-A
1 ATAATGTTTTTATTCTA
2669698 ATAATGT
1 ATAATGT
2669705 CTATTTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 19 0.56
17 14 0.41
18 1 0.03
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (17 bp):
ATAATGTTTTTATTCTA
Found at i:2679122 original size:37 final size:36
Alignment explanation
Indices: 2678983--2679220 Score: 259
Period size: 35 Copynumber: 6.6 Consensus size: 36
2678973 CAAATATAGT
* * *
2678983 TTTTGAAAATATATAAAATATAGTTTTTGAAAACTTA-
1 TTTTGAAAACATATAATATATAGTTTTTTAAAAC--AG
* *
2679020 TTTTCAAAAACATATAATATATAGTTTTTTAAAATAG
1 TTTT-GAAAACATATAATATATAGTTTTTTAAAACAG
* *
2679057 TTTTGAAAACGTATAATATATAG-TTTTTAAAACGG
1 TTTTGAAAACATATAATATATAGTTTTTTAAAACAG
* * *
2679092 TTTTTAAAACATATAGTATATAGTTTTTTTAAAATAG
1 TTTTGAAAACATATAATATATAG-TTTTTTAAAACAG
*
2679129 TTTTGAAAACGTATAATATATAGTTTTTTAAAA-AG
1 TTTTGAAAACATATAATATATAGTTTTTTAAAACAG
** *
2679164 TTTTGAAAATGTATAATATATA-TTTTTTAAAAACAAT
1 TTTTGAAAACATATAATATATAGTTTTTT-AAAAC-AG
*
2679201 TTTTGAAAGCATATAATATA
1 TTTTGAAAACATATAATATA
2679221 ATATTATATA
Statistics
Matches: 172, Mismatches: 22, Indels: 14
0.83 0.11 0.07
Matches are distributed among these distances:
34 6 0.03
35 57 0.33
36 28 0.16
37 56 0.33
38 25 0.15
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (36 bp):
TTTTGAAAACATATAATATATAGTTTTTTAAAACAG
Done.