Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009266.1 Hibiscus syriacus cultivar Beakdansim tig00112921_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: 1543912
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:532776 original size:16 final size:16
Alignment explanation
Indices: 532755--532793 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
532745 TTCATATCAG
532755 CTGCTGCCTCTGCCAT
1 CTGCTGCCTCTGCCAT
532771 CTGCTGCCTCTGCCAT
1 CTGCTGCCTCTGCCAT
*
532787 CTACTGC
1 CTGCTGC
532794 TTATGCACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.08, C:0.44, G:0.18, T:0.31
Consensus pattern (16 bp):
CTGCTGCCTCTGCCAT
Found at i:536033 original size:38 final size:38
Alignment explanation
Indices: 535982--536061 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
535972 GTGAGAAATC
535982 CACCCGATCTGAAACCATGCCGAAACTCTGTCCGTAGG
1 CACCCGATCTGAAACCATGCCGAAACTCTGTCCGTAGG
536020 CACCCGATCTGAAACCATGCCGAAACTCTGTCCGTAGG
1 CACCCGATCTGAAACCATGCCGAAACTCTGTCCGTAGG
536058 CACC
1 CACC
536062 TAAATAAGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.26, C:0.36, G:0.20, T:0.17
Consensus pattern (38 bp):
CACCCGATCTGAAACCATGCCGAAACTCTGTCCGTAGG
Found at i:536767 original size:18 final size:18
Alignment explanation
Indices: 536721--536757 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
536711 GAGATGACTC
536721 AACATTGGTGCGACAACA
1 AACATTGGTGCGACAACA
*
536739 AACATTGGTGCGATAACA
1 AACATTGGTGCGACAACA
536757 A
1 A
536758 CCATGAGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (18 bp):
AACATTGGTGCGACAACA
Found at i:538395 original size:27 final size:26
Alignment explanation
Indices: 538365--538425 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
538355 TAAAGTGGCA
*
538365 ATCATTTTATACATTTTTATATTCTCT
1 ATCATTTTATACATTATT-TATTCTCT
* *
538392 ATCATTATTTTACATTATTTATTCTTT
1 ATCATT-TTATACATTATTTATTCTCT
538419 A-CATTTT
1 ATCATTTT
538426 GTATTCTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 2 0.07
26 4 0.13
27 14 0.47
28 10 0.33
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (26 bp):
ATCATTTTATACATTATTTATTCTCT
Found at i:538421 original size:16 final size:16
Alignment explanation
Indices: 538400--538438 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
538390 CTATCATTAT
538400 TTTACATTATT-TATTC
1 TTTACATT-TTGTATTC
538416 TTTACATTTTGTATTC
1 TTTACATTTTGTATTC
538432 TTT-CATT
1 TTTACATT
538439 CATTCCATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.21, C:0.13, G:0.03, T:0.64
Consensus pattern (16 bp):
TTTACATTTTGTATTC
Found at i:540488 original size:24 final size:23
Alignment explanation
Indices: 540455--540499 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
540445 ACACTTGAAG
*
540455 AAAAAAAATGAGAGAAAATAAAA
1 AAAAAAAATGAAAGAAAATAAAA
540478 AAAAGAAAATGAAAGAAAATAA
1 AAAA-AAAATGAAAGAAAATAA
540500 GAAAGTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (23 bp):
AAAAAAAATGAAAGAAAATAAAA
Found at i:540510 original size:24 final size:24
Alignment explanation
Indices: 540458--540530 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
540448 CTTGAAGAAA
* **
540458 AAAAATGAGAGAAAATAA-AAAAA
1 AAAAATGAAAGAAAATAAGAAAGT
540481 AGAAAATGAAAGAAAATAAGAAAGT
1 A-AAAATGAAAGAAAATAAGAAAGT
540506 AAAAA-G-AA-AAAA-AAGAAAGAT
1 AAAAATGAAAGAAAATAAGAAAG-T
540527 AAAA
1 AAAA
540531 TAGAAAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
20 7 0.16
21 9 0.20
22 2 0.05
23 2 0.05
24 20 0.45
25 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (24 bp):
AAAAATGAAAGAAAATAAGAAAGT
Found at i:540542 original size:40 final size:38
Alignment explanation
Indices: 540469--540566 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 38
540459 AAAATGAGAG
* * *
540469 AAAATAAAAAAAAGAAAATGAAAGAAAATAAGAAAGTA
1 AAAAGAAAAAAAAGAAAATAAAAGAAAATAAGAAAGAA
540507 AAAAGAAAAAAAAGAAAGATAAAATAGAAAA-AAGAAAGAA
1 AAAAGAAAAAAAAGAAA-AT-AAA-AGAAAATAAGAAAGAA
540547 AAAAGAAAACAAAAGGAAAA
1 AAAAGAAAA-AAAA-GAAAA
540567 AGGGAAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
38 16 0.31
39 2 0.04
40 19 0.37
41 11 0.21
42 4 0.08
ACGTcount: A:0.79, C:0.01, G:0.14, T:0.06
Consensus pattern (38 bp):
AAAAGAAAAAAAAGAAAATAAAAGAAAATAAGAAAGAA
Found at i:540560 original size:11 final size:10
Alignment explanation
Indices: 540452--540611 Score: 60
Period size: 10 Copynumber: 15.1 Consensus size: 10
540442 AGTACACTTG
540452 AAGAAAAAAA
1 AAGAAAAAAA
540462 ATGAGAGAAAATAA
1 A--AGA-AAAA-AA
540476 AA-AAAAGAAA
1 AAGAAAA-AAA
*
540486 ATGAAAGAAAA
1 AAGAAA-AAAA
*
540497 TAAGAAAGTAAA
1 -AAGAAA-AAAA
540509 AAG-AAAAAA
1 AAGAAAAAAA
*
540518 AAGAAAGATAA
1 AAGAAA-AAAA
* *
540529 AA-TAGAAAA
1 AAGAAAAAAA
540538 AAGAAAGAAAA
1 AAGAAA-AAAA
*
540549 AAGAAAACAA
1 AAGAAAAAAA
*
540559 AAG-GAAAAA
1 AAGAAAAAAA
**
540568 GGGAAAAAATA
1 AAGAAAAAA-A
* *
540579 AA-TAAATAA
1 AAGAAAAAAA
540588 AAGAAAGAGAAGA
1 AAGAAA-A-AA-A
540601 AAGAAAAAAA
1 AAGAAAAAAA
540611 A
1 A
540612 TGAGGGTTCA
Statistics
Matches: 110, Mismatches: 22, Indels: 36
0.65 0.13 0.21
Matches are distributed among these distances:
9 19 0.17
10 31 0.28
11 30 0.27
12 16 0.15
13 11 0.10
14 3 0.03
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.06
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:540574 original size:59 final size:59
Alignment explanation
Indices: 540469--540609 Score: 134
Period size: 59 Copynumber: 2.4 Consensus size: 59
540459 AAAATGAGAG
* ** *
540469 AAAATAAAAAAAAGAAA-ATGAAAGAAAATAAGAAAGTAAAAAGAAAAAA-AAGA-AAGAT
1 AAAATAGAAAAAAGAAAGAAAAAAGAAAATAAGAAAGGAAAAAGAAAAAATAA-ATAA-AT
*
540527 AAAATAGAAAAAAGAAAGAAAAAAGAAAA-CA-AAAGGAAAAAGGGAAAAAATAAATAAAT
1 AAAATAGAAAAAAGAAAGAAAAAAGAAAATAAGAAAGGAAAAA--GAAAAAATAAATAAAT
540586 -AAA-AGAAAGAGAAGAAAGAAAAAA
1 AAAATAGAAA-A-AAGAAAGAAAAAA
540610 AATGAGGGTT
Statistics
Matches: 71, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
57 14 0.20
58 21 0.30
59 32 0.45
60 4 0.06
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.06
Consensus pattern (59 bp):
AAAATAGAAAAAAGAAAGAAAAAAGAAAATAAGAAAGGAAAAAGAAAAAATAAATAAAT
Found at i:540609 original size:20 final size:18
Alignment explanation
Indices: 540457--540609 Score: 96
Period size: 20 Copynumber: 7.9 Consensus size: 18
540447 ACTTGAAGAA
*
540457 AAAAAATGAGAGAAAATAA-
1 AAAAAA-GAAAGAAAA-AAG
**
540476 AAAAAAGAAA-ATGAAAG
1 AAAAAAGAAAGAAAAAAG
*
540493 AAAATAAGAAAGTAAAAAGAA
1 AAAA-AAGAAAG-AAAAA-AG
540514 AAAAAAGAAAGATAAAATAG
1 AAAAAAGAAAGA-AAAA-AG
540534 AAAAAAGAAAGAAAAAAG
1 AAAAAAGAAAGAAAAAAG
* *
540552 AAAACAA-AAGGAAAAAGGG
1 AAAA-AAGAAAGAAAAA-AG
* *
540571 AAAAAATAAATAAATAAAAG
1 AAAAAAGAAA-GAA-AAAAG
540591 AAAGAGAAGAAAGAAAAAA
1 AAA-A-AAGAAAGAAAAAA
540610 AATGAGGGTT
Statistics
Matches: 106, Mismatches: 15, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
16 2 0.02
17 6 0.06
18 25 0.24
19 20 0.19
20 37 0.35
21 11 0.10
22 5 0.05
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (18 bp):
AAAAAAGAAAGAAAAAAG
Found at i:542708 original size:102 final size:102
Alignment explanation
Indices: 542532--542773 Score: 337
Period size: 102 Copynumber: 2.4 Consensus size: 102
542522 CGATTCGACG
* * *
542532 AATTTTATCTAAATTGATATTGTTTTTCTTAAAA-ACAAATTGTCTCCCTTGAGACAATTTCCTC
1 AATTTTATCTCACTTGAGATTGTTTTTCTTAAAACA-AAATTGTCTCCCTTGAGACAATTTCCTC
* * * *
542596 TTGAAACACAAATTTTGAGA-TTGTTTCACTTGAAACAA
65 TTGAAACACAAA-TTTAAAACTAGTTTCACTCGAAACAA
** * *
542634 AATTTTATCTCGTTTGGGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAATTTCC-C
1 AATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAA-TTGTCTCCCTTGAGACAATTTCCTC
542698 TTGAAACACAAATTTAAAACTAGTTTCACTCGAAACAA
65 TTGAAACACAAATTTAAAACTAGTTTCACTCGAAACAA
542736 AATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA
1 AATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA
542774 TTTTATATCA
Statistics
Matches: 124, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
101 5 0.04
102 96 0.77
103 23 0.19
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (102 bp):
AATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTGTCTCCCTTGAGACAATTTCCTCT
TGAAACACAAATTTAAAACTAGTTTCACTCGAAACAA
Found at i:542778 original size:36 final size:37
Alignment explanation
Indices: 542730--542805 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 37
542720 GTTTCACTCG
*
542730 AAACAAAATTTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACAAAATTTTATATCACTTGAGATTGTTTTTCTTA
542767 AAAC-AAATTTTATATCACTTGAGATTGTTTTTCTTA
1 AAACAAAATTTTATATCACTTGAGATTGTTTTTCTTA
542803 AAA
1 AAA
542806 TCCATTTCGT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 34 0.89
37 4 0.11
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.45
Consensus pattern (37 bp):
AAACAAAATTTTATATCACTTGAGATTGTTTTTCTTA
Found at i:542821 original size:138 final size:137
Alignment explanation
Indices: 542610--542892 Score: 318
Period size: 138 Copynumber: 2.1 Consensus size: 137
542600 AACACAAATT
* * ** *
542610 TTGAGATTGTTTCACTTGAAACAAAATTTTATCTCGTTTGGGATTGTTTTTCTTAAAACAAAATT
1 TTGAGATTGTTTCACTTAAAACAAAATTTTATATCACTTGAGATTGTTTTTCTTAAAAC-AAATT
* * *
542675 TGTCTCGCTTGAGACAATTTCCCTTGAAACACAAATTTAAAACTAGTTTCACTCGAAACAAAATT
65 TGTCTCGCTCGAGAAAATTTCCATTGAAACACAAATTTAAAA-TAGTTTCACTCGAAACAAAATT
542740 TTATCTCAC
129 TTATCTCAC
** *
542749 TTGAGATTGTTTTTCTTAAAAC-AAATTTTATATCACTTGAGATTGTTTTTCTTAAAATC-CATT
1 TTGAGATTGTTTCACTTAAAACAAAATTTTATATCACTTGAGATTGTTTTTCTTAAAA-CAAATT
* ****** * * * *
542812 TCGTTTCGCTCGAGAAAATTTCCATTGAAATTTTTTTTTGAAATTGTTTCTCTCGAAACAAATTT
65 T-GTCTCGCTCGAGAAAATTTCCATTGAAACACAAATTTAAAATAGTTTCACTCGAAACAAAATT
542877 TTATCTCAC
129 TTATCTCAC
542886 TTGAGAT
1 TTGAGAT
542893 ATTTTCTCTT
Statistics
Matches: 120, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
137 39 0.32
138 61 0.51
139 20 0.17
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (137 bp):
TTGAGATTGTTTCACTTAAAACAAAATTTTATATCACTTGAGATTGTTTTTCTTAAAACAAATTT
GTCTCGCTCGAGAAAATTTCCATTGAAACACAAATTTAAAATAGTTTCACTCGAAACAAAATTTT
ATCTCAC
Found at i:545459 original size:14 final size:14
Alignment explanation
Indices: 545440--545488 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
545430 ACCCAAACTG
545440 AGTCAACTCGTCCA
1 AGTCAACTCGTCCA
* ***
545454 AGTCAACTCATGTG
1 AGTCAACTCGTCCA
*
545468 AGTCAACTCGTCCC
1 AGTCAACTCGTCCA
545482 AGTCAAC
1 AGTCAAC
545489 CTATTGACTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (14 bp):
AGTCAACTCGTCCA
Found at i:546255 original size:2 final size:2
Alignment explanation
Indices: 546248--546300 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
546238 TTTTCCACTC
546248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
546290 AT AT AT AT AT A
1 AT AT AT AT AT A
546301 AAAAAAAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:549827 original size:13 final size:14
Alignment explanation
Indices: 549809--549896 Score: 51
Period size: 13 Copynumber: 6.2 Consensus size: 14
549799 AGCTCTTGCG
549809 ATACTTTATATA-T
1 ATACTTTATATACT
549822 ATACTTTATATACTT
1 ATACTTTATATAC-T
* *
549837 ATGTTCTTTACATTA-T
1 A--TACTTTATA-TACT
549853 ATAC-TTATATACT
1 ATACTTTATATACT
* *
549866 TTAGTCTTTATA-ATT
1 ATA--CTTTATATACT
549881 ATACTTTATATA-T
1 ATACTTTATATACT
549894 ATA
1 ATA
549897 ATATACTTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
12 2 0.03
13 30 0.52
14 3 0.05
15 7 0.12
16 7 0.12
17 7 0.12
18 2 0.03
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.53
Consensus pattern (14 bp):
ATACTTTATATACT
Found at i:549867 original size:22 final size:22
Alignment explanation
Indices: 549809--549868 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
549799 AGCTCTTGCG
* *
549809 ATACTTTATATA-TATACTTTAT
1 ATAC-TTATATACTTTACATTAT
* *
549831 ATACTTATGTTCTTTACATTAT
1 ATACTTATATACTTTACATTAT
549853 ATACTTATATACTTTA
1 ATACTTATATACTTTA
549869 GTCTTTATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (22 bp):
ATACTTATATACTTTACATTAT
Found at i:549906 original size:24 final size:23
Alignment explanation
Indices: 549874--549924 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
549864 CTTTAGTCTT
549874 TATAATTATACTTTATATATATAA
1 TATAATTATACTTTATAT-TATAA
* * *
549898 TATACTTATGCTTTATATTATTA
1 TATAATTATACTTTATATTATAA
549921 TATA
1 TATA
549925 TGCCTATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (23 bp):
TATAATTATACTTTATATTATAA
Found at i:550014 original size:2 final size:2
Alignment explanation
Indices: 550009--550448 Score: 123
Period size: 2 Copynumber: 223.0 Consensus size: 2
549999 CACACACGTG
* *
550009 TA TA TA TA TA TA TA CTT TA TA T- TA TA TA CT- TA TA CTT TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* *
550050 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CT- TT TA TA CTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA
* * * * *
550093 TT TA AA CTA TA TA AA CTA TA T- TA TT TA TA CA TA GTA TA TA TA
1 TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * * *
550135 -A TT TA TA GTT TA TA T- TA -A TA AA CTA TA TA -A TT TA TA AA CA
1 TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* *
550175 -A TA TA TA TA T- TT TA TA -A T- TA TA TA TA -A TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
550212 -A GT- TG TA TA TA TT TA -A T- TA TA -A T- TCA TA TA TA -A TT TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
* **
550249 TA T- TA -A TA AA CTA TA TA GG T- TA TA TA TA GT- TCA -A TA GT-
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA T-A TA TA -TA
* * * * * *
550287 TCA TA TA TA AA CTC TA TA GTT TA TA CA TGG TA TA TA TA GTT TA TA
1 T-A TA TA TA TA -TA TA TA -TA TA TA TA T-A TA TA TA TA -TA TA TA
* *
550332 CA TA -A TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA
* * * *
550375 -A TA -A TA TA AA TA TA AA CTA TA TA GTT TA TA TA CA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
550416 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
550449 ATTGTTTCAA
Statistics
Matches: 318, Mismatches: 64, Indels: 112
0.64 0.13 0.23
Matches are distributed among these distances:
1 31 0.10
2 263 0.83
3 24 0.08
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:550113 original size:49 final size:48
Alignment explanation
Indices: 550011--550163 Score: 127
Period size: 49 Copynumber: 3.1 Consensus size: 48
550001 CACACGTGTA
* *
550011 TATATATATATACTTTATATTATATAC-TTATACTTTATATATATATATA-
1 TATATATATATA-TATATATTATATACTTTATACTTTA-A-ATATATAAAC
*
550060 TATATATATATATATATACTTTTATACTTTATA-TTTAAACTATATAAAC
1 TATATATATATATATATA-TTATATACTTTATACTTTAAA-TATATAAAC
* * * * *
550109 TATAT-TATTTATACATAGTATATATAATTTATAGTTTATAT-TAATAAAC
1 TATATATATATATATATA-T-TATATACTTTATACTTTAAATAT-ATAAAC
550158 TATATA
1 TATATA
550164 ATTTATAAAC
Statistics
Matches: 87, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
47 1 0.01
48 25 0.29
49 51 0.59
50 10 0.11
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.50
Consensus pattern (48 bp):
TATATATATATATATATATTATATACTTTATACTTTAAATATATAAAC
Found at i:550168 original size:49 final size:49
Alignment explanation
Indices: 550103--550203 Score: 132
Period size: 49 Copynumber: 2.1 Consensus size: 49
550093 TTTAAACTAT
* * * * *
550103 ATAAACTATATTATTTATACATAGTATATATAATTTATAGTT-TATATTA
1 ATAAACTATATAATTTATAAACAATATATATAATTTATAATTATATA-TA
*
550152 ATAAACTATATAATTTATAAACAATATATATATTTTATAATTATATATA
1 ATAAACTATATAATTTATAAACAATATATATAATTTATAATTATATATA
550201 ATA
1 ATA
550204 TATAAATAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 41 0.91
50 4 0.09
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.47
Consensus pattern (49 bp):
ATAAACTATATAATTTATAAACAATATATATAATTTATAATTATATATA
Found at i:550363 original size:91 final size:93
Alignment explanation
Indices: 550260--550448 Score: 228
Period size: 93 Copynumber: 2.1 Consensus size: 93
550250 ATTAATAAAC
* * * **
550260 TATATAGGTTATATATAGT-T-CAATAGT-TCATATATAAACTCTATAG-TT-TATACATGGTAT
1 TATATAGGTTATATATAGTATACAATAATAT-AAATATAAACTATATAGTTTATATACATAATAT
*
550320 ATATAGTTTATACATAATATATATATATATA
65 ATATA-TATATACAT-ATATATATATATATA
* *
550351 TATATAGTTTATATATAGTATATAATAATATAAATATAAACTATATAGTTTATATACATAATATA
1 TATATAGGTTATATATAGTATACAATAATATAAATATAAACTATATAGTTTATATACATAATATA
*
550416 TATATATATATATATATATATATATATA
66 TATATATATACATATATATATATATATA
550444 T-TATA
1 TATATA
550449 ATTGTTTCAA
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
91 18 0.21
92 5 0.06
93 36 0.43
94 10 0.12
95 15 0.18
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (93 bp):
TATATAGGTTATATATAGTATACAATAATATAAATATAAACTATATAGTTTATATACATAATATA
TATATATATACATATATATATATATATA
Found at i:555578 original size:33 final size:33
Alignment explanation
Indices: 555532--555603 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
555522 TCCTTTTCGT
* *
555532 TTTAATTGTTTTTGGATCAAATTATAGATGTGA
1 TTTAATTGATTTTGAATCAAATTATAGATGTGA
555565 TTTAATTGATTTTGAATCAAATTATAGATGTGA
1 TTTAATTGATTTTGAATCAAATTATAGATGTGA
555598 TTTAAT
1 TTTAAT
555604 CATTGGTGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.49
Consensus pattern (33 bp):
TTTAATTGATTTTGAATCAAATTATAGATGTGA
Found at i:559206 original size:24 final size:25
Alignment explanation
Indices: 559157--559208 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
559147 GTGTTATCTG
* **
559157 ATTTATGTTCTGATTTCTGATTTGA
1 ATTTATGTTCTGATATCTGACATGA
559182 ATTT-TGTTCTGATATCTGACATGA
1 ATTTATGTTCTGATATCTGACATGA
559206 ATT
1 ATT
559209 ATATTTGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (25 bp):
ATTTATGTTCTGATATCTGACATGA
Found at i:559580 original size:159 final size:160
Alignment explanation
Indices: 559284--559726 Score: 597
Period size: 159 Copynumber: 2.7 Consensus size: 160
559274 GAAGTATATT
* * *
559284 TGCATGCTCCTTAGCTTTATGCTCAGGGCCTTACTACGTGTGTTGGTGGGTGTATGGCTATGGGG
1 TGCAGGCTCCTT-GCTTTATGCTCAGGGCCTTACTAGGTGTG-TGGTGGGTGTATGGTTATGGGG
* *
559349 AACCTACACATTATGGAGTGTTCGGTTGGAGGGATTATTATGGTTTTTGATAAATGTTTTATGGG
64 AACCTACACATTATGGAGTGTTCGGTTGGAGGGATTAATATGGTTTTTGATAAATGTTTTATAGG
559414 AGGGTGTTGTTGGAGG-A-A-GTTACCGTTAC
129 AGGGTGTTGTTGGAGGAATACGTTACCGTTAC
* * *
559443 TGCAGGCTCCTCTGCTTTATTCTCAGGGCCTTACTAGGTGTGCTGATGGGTGTATGGTTTTGGGG
1 TGCAGGCTCCT-TGCTTTATGCTCAGGGCCTTACTAGGTGTG-TGGTGGGTGTATGGTTATGGGG
* * * *
559508 AACCTACATATTATGGAGTGTTCGGTTGGAGTGATTACTATGGTTTTTGATAAATGTTTTATAGT
64 AACCTACACATTATGGAGTGTTCGGTTGGAGGGATTAATATGGTTTTTGATAAATGTTTTATAGG
*
559573 AGTGTGTTGTTGGAGGAAGTTACCGTTACCGTTAC
129 AGGGTGTTGTTGGAGGAA--TA-CGTTACCGTTAC
* * * * * *
559608 TGTAGGCTCGTTGCTTTGTGCTCAGGGCCTTACTTGGTGTGTAGGTAGGTGTATGGTTCTGGGGA
1 TGCAGGCTCCTTGCTTTATGCTCAGGGCCTTACTAGGTGTGT-GGTGGGTGTATGGTTATGGGGA
559673 ACCTACACATTATGGAGTGTTCGGATT-GAGGGATTAATATGGTTTTTGAATAAA
65 ACCTACACATTATGGAGTGTTCGG-TTGGAGGGATTAATATGGTTTTTG-ATAAA
559727 AATATGTTTT
Statistics
Matches: 250, Mismatches: 24, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
159 131 0.52
160 2 0.01
163 2 0.01
164 88 0.35
165 27 0.11
ACGTcount: A:0.19, C:0.13, G:0.31, T:0.37
Consensus pattern (160 bp):
TGCAGGCTCCTTGCTTTATGCTCAGGGCCTTACTAGGTGTGTGGTGGGTGTATGGTTATGGGGAA
CCTACACATTATGGAGTGTTCGGTTGGAGGGATTAATATGGTTTTTGATAAATGTTTTATAGGAG
GGTGTTGTTGGAGGAATACGTTACCGTTAC
Found at i:568985 original size:135 final size:135
Alignment explanation
Indices: 568754--569002 Score: 340
Period size: 135 Copynumber: 1.8 Consensus size: 135
568744 TTGACTTCCA
* * *
568754 ATTTGGAGACTTTCGGCTTCGAATTTGGCAAAATGGAATGTGGAATCGAATTTAGGACGTCAAAA
1 ATTTGGAGACTTTCGGCTTCGAATTTGGCAAAATGGAATGTGGAATCGAACTCAGGACATCAAAA
* *
568819 AACATAAATTATGTCTTTTCAAAAAAATTGACTTTTTGGTCAAAGTCAAAGACAACGAGTTTGAC
66 AACATAAAATATGACTTTTCAAAAAAATTGACTTTTTGGTCAAAGTCAAAGACAACGAGTTTGAC
568884 TGACG
131 TGACG
* * * * * * *
568889 ATTTTGAGGCTTTCGGGTTCGAATTTGG-AATAATGGACT-TCGGATTCGGACTCAGGACATCGA
1 ATTTGGAGACTTTCGGCTTCGAATTTGGCAA-AATGGAATGT-GGAATCGAACTCAGGACATCAA
* *
568952 AAAACATAAAATATGACTTTTCGAAAAATTTGACTTTTTGGTCAAAGTCAA
64 AAAACATAAAATATGACTTTTCAAAAAAATTGACTTTTTGGTCAAAGTCAA
569003 CGGTTCGGGT
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
134 3 0.03
135 95 0.97
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (135 bp):
ATTTGGAGACTTTCGGCTTCGAATTTGGCAAAATGGAATGTGGAATCGAACTCAGGACATCAAAA
AACATAAAATATGACTTTTCAAAAAAATTGACTTTTTGGTCAAAGTCAAAGACAACGAGTTTGAC
TGACG
Found at i:571688 original size:24 final size:24
Alignment explanation
Indices: 571656--571701 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
571646 AACTCTTATG
571656 GATTGAAGAGGATGTTTCTGGTAA
1 GATTGAAGAGGATGTTTCTGGTAA
*
571680 GATTTAAGAGGATGTTTCTGGT
1 GATTGAAGAGGATGTTTCTGGT
571702 GCATTTGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.04, G:0.33, T:0.37
Consensus pattern (24 bp):
GATTGAAGAGGATGTTTCTGGTAA
Found at i:573582 original size:19 final size:19
Alignment explanation
Indices: 573558--573603 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
573548 TAACTTTTGT
*
573558 TTTATTTTAGTGCTTAAAC
1 TTTATTTTAGTACTTAAAC
573577 TTTATTTTAGTACTTAAAC
1 TTTATTTTAGTACTTAAAC
573596 TTTATTTT
1 TTTATTTT
573604 TTCAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.07, T:0.59
Consensus pattern (19 bp):
TTTATTTTAGTACTTAAAC
Found at i:574156 original size:10 final size:11
Alignment explanation
Indices: 574125--574150 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
574115 TTTTTTAAAA
574125 TTCTCAATTTT
1 TTCTCAATTTT
574136 TTCTCAATTTT
1 TTCTCAATTTT
574147 TTCT
1 TTCT
574151 TATTTTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.65
Consensus pattern (11 bp):
TTCTCAATTTT
Found at i:575965 original size:20 final size:21
Alignment explanation
Indices: 575940--575978 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
575930 CTTCTTCCTC
*
575940 TCTTTTTTTCC-TCTCCCCCT
1 TCTTTTTCTCCATCTCCCCCT
575960 TCTTTTTCTCCATCTCCCC
1 TCTTTTTCTCCATCTCCCC
575979 AAATACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (21 bp):
TCTTTTTCTCCATCTCCCCCT
Found at i:593499 original size:15 final size:15
Alignment explanation
Indices: 593479--593523 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
593469 ATTATAGTAG
*
593479 TGACTAAAATATTAA
1 TGACTAAAATATAAA
593494 TGACTAAAATATAAA
1 TGACTAAAATATAAA
593509 TGACTAAAATATAAA
1 TGACTAAAATATAAA
593524 CCAAATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.29
Consensus pattern (15 bp):
TGACTAAAATATAAA
Found at i:594974 original size:130 final size:129
Alignment explanation
Indices: 594708--595339 Score: 457
Period size: 130 Copynumber: 4.9 Consensus size: 129
594698 AGAGATTTTT
* * * *
594708 GAAGAT-AAATC-TG-AAAAGAGATCTGCTCCGCTGCTCTTCAGGGTAGATTAGATCTAGAAACG
1 GAAGATCAAATCATGAAAAAGGGATCTGCTCCACTG-TCTTCAGGGTAGATCAGATCTGGAAACG
* * * * * ** * * *
594770 TTGATTCACTTCATTGCTCTTTAAG-GAAGATTGAATTGAGG-AAGATTT-ATTCCAATACTCCT
65 TTGATTCACTCCACTG-TTTTTCAGAGAAGATTGAATCG-GGTTTGATTTGCTT-CACTGCTCCT
594832 AAGG
127 AA-G
* *
594836 GTAA-ATCAAATCAT-AAAAAGGGATCTGCTCCACTGTGCTTCAGGGTATATCAGATTTGGAAAC
1 G-AAGATCAAATCATGAAAAAGGGATCTGCTCCACTGT-CTTCAGGGTAGATCAGATCTGGAAAC
* * *
594899 GTTGATTCACTCCAATGTTTTTCAGAGAAGATTGAATCGGGTTTGATTTGCTTCAATGCTCTTAA
64 GTTGATTCACTCCACTGTTTTTCAGAGAAGATTGAATCGGGTTTGATTTGCTTCACTGCTCCT-A
594964 AG
128 AG
* * * * ** * *
594966 AAAGATCAAATC-CGAGAAAGGGGATCTTCTCTGCTACTCTTCAGGGTAGATCAGATCT-GAAAT
1 GAAGATCAAATCATGA-AAAAGGGATCTGCTCCACT-GTCTTCAGGGTAGATCAGATCTGGAAAC
* * * * *
595029 GTTGATTCACTTCACTGCTCTTT-AGAAAAGATTGAATCGGGTTTGATTTGGTTTACTGCTCCTC
64 GTTGATTCACTCCACTG-TTTTTCAGAGAAGATTGAATCGGGTTTGATTTGCTTCACTGCTCCT-
*
595093 AGG
127 AAG
* * ** * * * * *
595096 GAAGATCAAATC-TGAAAAGGGGATCTTCTCCGTTGCTCTTTAGGATAGATCATATTTGGAAACA
1 GAAGATCAAATCATGAAAAAGGGATCTGCTCCACTG-TCTTCAGGGTAGATCAGATCTGGAAACG
** * * * * *
595160 TTGATTCACTTTATTGTTCTTTAAG-GAAGATTGAATCGGGTTTAATTTGCTTCACTACTCCTCA
65 TTGATTCACTCCACTGTT-TTTCAGAGAAGATTGAATCGGGTTTGATTTGCTTCACTGCTCCTAA
595224 G
129 G
* * * * ***
595225 TGAAGATCAAAT-ATGAAAAAAGGGGATTTGCT-CACTATATTTCAGGGTTGATCAGATCCATAA
1 -GAAGATCAAATCATG-AAAAA-GGGATCTGCTCCACTGT-CTTCAGGGTAGATCAGATCTGGAA
* * * *
595288 ACTTTGATTCACTCCACTGCTCTTCAAAGAAGATTGAATCGGGTTTGATTTG
62 ACGTTGATTCACTCCACTGTTTTTCAGAGAAGATTGAATCGGGTTTGATTTG
595340 TTTCTCTTCT
Statistics
Matches: 399, Mismatches: 81, Indels: 45
0.76 0.15 0.09
Matches are distributed among these distances:
128 3 0.01
129 54 0.14
130 230 0.58
131 103 0.26
132 9 0.02
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (129 bp):
GAAGATCAAATCATGAAAAAGGGATCTGCTCCACTGTCTTCAGGGTAGATCAGATCTGGAAACGT
TGATTCACTCCACTGTTTTTCAGAGAAGATTGAATCGGGTTTGATTTGCTTCACTGCTCCTAAG
Found at i:595233 original size:260 final size:259
Alignment explanation
Indices: 594707--595339 Score: 621
Period size: 260 Copynumber: 2.4 Consensus size: 259
594697 GAGAGATTTT
* * * * *
594707 TGAAGAT-AAATCTGAAAA-GAGATCTGCTCCGCTGCTCTTCAGGGTAGATTAGATCTAGAAACG
1 TGAAGATCAAATCTGAAAAGGGGATCTTCT-CGCTACTCTTCAGGGTAGATCAGATCT-GAAATG
* * * **
594770 TTGATTCACTTCATTGCTCTTTAAGGAAGATTGAATTGAGG-AAGATTT-ATTCCAATACTCCTA
64 TTGATTCACTTCACTGCTCTTTAA-AAAGATTGAATCG-GGTTTGATTTGATTCCAATACTCCTA
* *
594833 AGGGTAAATCAAATCATAAAAAGGGATCTGCTCCACTGTGCTTCAGGGTATATCAGATTTGGAAA
127 AGGGTAAATCAAATCATAAAAAGGGATCTGCTCCACTGTGCTTCAGGATAGATCAGATTTGGAAA
* * * * *
594898 CGTTGATTCACTCCAATGTTTTTCAGAGAAGATTGAATCGGGTTTGATTTGCTTCAATGCTCTTA
192 CATTGATTCACTCCAATGTTTTTAAGAGAAGATTGAATCGGGTTTAATTTGCTTCAATACTCCTA
594963 AAG
257 AAG
* *
594966 -AAAGATCAAATCCGAGAAAGGGGATCTTCTCTGCTACTCTTCAGGGTAGATCAGATCTGAAATG
1 TGAAGATCAAATCTGA-AAAGGGGATCTTCTC-GCTACTCTTCAGGGTAGATCAGATCTGAAATG
* * * * *
595030 TTGATTCACTTCACTGCTCTTTAGAAAAGATTGAATCGGGTTTGATTTGGTT-TACTGCTCCTCA
64 TTGATTCACTTCACTGCTCTTTA-AAAAGATTGAATCGGGTTTGATTTGATTCCAATACTCCTAA
* * ** * *
595094 GGG-AAGATCAAATC-TGAAAAGGGGATCTTCTCCGTTGCT-CTTTAGGATAGATCATATTTGGA
128 GGGTAA-ATCAAATCAT-AAAAAGGGATCTGCTCCACTG-TGCTTCAGGATAGATCAGATTTGGA
** * *
595156 AACATTGATTCACTTTATTGTTCTTTAAG-GAAGATTGAATCGGGTTTAATTTGCTTCACTACTC
190 AACATTGATTCACTCCAATGTT-TTTAAGAGAAGATTGAATCGGGTTTAATTTGCTTCAATACTC
*
595220 CT-CAG
254 CTAAAG
* * * *
595225 TGAAGATCAAATATGAAAAAAGGGGAT-TTGCTCACTA-TATTTCAGGGTTGATCAGATCCAT-A
1 TGAAGATCAAATCTG--AAAAGGGGATCTT-CTCGCTACT-CTTCAGGGTAGATCAGAT-C-TGA
* *
595287 AACT-TTGATTCACTCCACTGCTCTTCAAAGAAGATTGAATCGGGTTTGATTTG
60 AA-TGTTGATTCACTTCACTGCTCTTTAAA-AAGATTGAATCGGGTTTGATTTG
595340 TTTCTCTTCT
Statistics
Matches: 311, Mismatches: 43, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
258 5 0.02
259 15 0.05
260 187 0.60
261 101 0.32
262 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (259 bp):
TGAAGATCAAATCTGAAAAGGGGATCTTCTCGCTACTCTTCAGGGTAGATCAGATCTGAAATGTT
GATTCACTTCACTGCTCTTTAAAAAGATTGAATCGGGTTTGATTTGATTCCAATACTCCTAAGGG
TAAATCAAATCATAAAAAGGGATCTGCTCCACTGTGCTTCAGGATAGATCAGATTTGGAAACATT
GATTCACTCCAATGTTTTTAAGAGAAGATTGAATCGGGTTTAATTTGCTTCAATACTCCTAAAG
Found at i:606553 original size:35 final size:35
Alignment explanation
Indices: 606509--606613 Score: 113
Period size: 35 Copynumber: 3.0 Consensus size: 35
606499 ACAGCTTAAT
606509 CGGTCTGAACCTATATAAGGAATTACCAATTTGAC
1 CGGTCTGAACCTATATAAGGAATTACCAATTTGAC
** * * * *
606544 CGAGT-TGAACCTACCGTAAGGAATTATCAGTTCGAT
1 CG-GTCTGAACCTA-TATAAGGAATTACCAATTTGAC
* *
606580 CGGTCTGAACCAATATAAGAAATTACCAATTTGA
1 CGGTCTGAACCTATATAAGGAATTACCAATTTGA
606614 TCGAACTGAA
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
35 27 0.50
36 27 0.50
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (35 bp):
CGGTCTGAACCTATATAAGGAATTACCAATTTGAC
Found at i:606616 original size:35 final size:35
Alignment explanation
Indices: 606489--606616 Score: 105
Period size: 35 Copynumber: 3.6 Consensus size: 35
606479 ATTAGATCCG
* ** * *
606489 TAAGAAATTAACAGCTTAATCGGTCTGAACCTATA
1 TAAGAAATTACCAATTTGATCGGTCTGAACCAATA
* * ***
606524 TAAGGAATTACCAATTTGACCGAGT-TGAACCTACCG
1 TAAGAAATTACCAATTTGATCG-GTCTGAACC-AATA
* * * *
606560 TAAGGAATTATCAGTTCGATCGGTCTGAACCAATA
1 TAAGAAATTACCAATTTGATCGGTCTGAACCAATA
606595 TAAGAAATTACCAATTTGATCG
1 TAAGAAATTACCAATTTGATCG
606617 AACTGAACAT
Statistics
Matches: 69, Mismatches: 21, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
35 43 0.62
36 26 0.38
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (35 bp):
TAAGAAATTACCAATTTGATCGGTCTGAACCAATA
Found at i:607733 original size:27 final size:27
Alignment explanation
Indices: 607703--607762 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
607693 ATTCTTGTCT
* *
607703 TTTTACAATATAAGGGTATTTTCGTAA
1 TTTTACAACATAAGGGTATTTTCATAA
** *
607730 TTTTACCCCATAATGGTATTTTCATAA
1 TTTTACAACATAAGGGTATTTTCATAA
607757 TTTTAC
1 TTTTAC
607763 CTAACCGAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (27 bp):
TTTTACAACATAAGGGTATTTTCATAA
Found at i:607763 original size:27 final size:27
Alignment explanation
Indices: 607712--607763 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
607702 TTTTTACAAT
*
607712 ATAAGGGTATTTTCGTAATTTTACCCC
1 ATAAGGGTATTTTCATAATTTTACCCC
*
607739 ATAATGGTATTTTCATAATTTTACC
1 ATAAGGGTATTTTCATAATTTTACC
607764 TAACCGAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (27 bp):
ATAAGGGTATTTTCATAATTTTACCCC
Found at i:608755 original size:20 final size:19
Alignment explanation
Indices: 608732--608782 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
608722 TATTAATCAA
608732 TATCGATACCATTG-AGGCAG
1 TATCGATACCATTGAAGG--G
608752 TATCGATACCATTGTAAGGG
1 TATCGATACCATTG-AAGGG
608772 TATCGATACCA
1 TATCGATACCA
608783 AGAAAACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 26 0.90
22 3 0.10
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (19 bp):
TATCGATACCATTGAAGGG
Found at i:608902 original size:95 final size:96
Alignment explanation
Indices: 608750--608935 Score: 268
Period size: 95 Copynumber: 1.9 Consensus size: 96
608740 CCATTGAGGC
* * *
608750 AGTATCGATACCATTGTAAGGGTATCGATACCAAGAAAACATCGAATCTAATTTTGGTATCGATA
1 AGTATCGATACCATGGTAAGGGTATCAATAACAAGAAAACATCGAATCTAATTTTGGTATCGATA
**
608815 -CCGTAAGGGGGTATCGGTACCATAGTATGGT
66 CCCG-AAGGAAGTATCGGTACCATAGTATGGT
** *
608846 AGTATCGATACCATGGTAAGGGTATCAATAAC-AGGCAACATCGAATTTAATTTTGGTATCGATA
1 AGTATCGATACCATGGTAAGGGTATCAATAACAAGAAAACATCGAATCTAATTTTGGTATCGATA
*
608910 CCCGGAGGAAGTATCGGTACCATAGT
66 CCCGAAGGAAGTATCGGTACCATAGT
608936 GTTGAAGTTG
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
95 48 0.60
96 32 0.40
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (96 bp):
AGTATCGATACCATGGTAAGGGTATCAATAACAAGAAAACATCGAATCTAATTTTGGTATCGATA
CCCGAAGGAAGTATCGGTACCATAGTATGGT
Found at i:609441 original size:45 final size:45
Alignment explanation
Indices: 609379--609950 Score: 810
Period size: 45 Copynumber: 12.8 Consensus size: 45
609369 ATGAAAATAA
* * * *
609379 AAATGCATATGGGTGCATTATCAACAGAAAAGGATGCCATAGTTA
1 AAATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTATAGTTG
* * * *
609424 AAATACATATGGGTGCATTGTCAACAGAAAAGGATGCCATAGCTG
1 AAATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTATAGTTG
*
609469 AAATGCATATGAGTGCATTGT-AACA-AAAAGTATGCTATAGTTG
1 AAATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTATAGTTG
*
609512 AAATGCATATGGGTGCATTGTCAACAAAAAAGTATGCTATAGTTG
1 AAATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTATAGTTG
* *
609557 AAATGCATATGGGTGCATTGTCAACAGAAAAGTATGTTATAGTTA
1 AAATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTATAGTTG
* * *
609602 AAATGTATATGGGTGCATTGTCAATAGAAAAGTATGCTATATTTG
1 AAATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTATAGTTG
* * * * *
609647 AAATGCATATAGGTGTATTGTTAACAAAAAAGTATGTTATAGTTG
1 AAATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTATAGTTG
* * * *
609692 AAATGTATATGGGTGCATTGTCAAGAGAGAAGTATGTTATAGTTG
1 AAATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTATAGTTG
**
609737 AAATGCATATGGGTGCATTGTCAACAGCGAAGTATGCTATAGTTG
1 AAATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTATAGTTG
*
609782 AAATGCATATAGGTGCATTGTCAACA-AAGAAGTATGCTATAGTTG
1 AAATGCATATGGGTGCATTGTCAACAGAA-AAGTATGCTATAGTTG
*
609827 AAATGCATAAGGGTGCATTGTCAACAGAAAAGTATGCTATAGTTG
1 AAATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTATAGTTG
* * *
609872 AAATGCATATAGGTACATTGTCAACAG-AAAGATATGCTATAATTG
1 AAATGCATATGGGTGCATTGTCAACAGAAAAG-TATGCTATAGTTG
*
609917 AAATGCATATGGGTGCATTATCAACAGAAAAGTA
1 AAATGCATATGGGTGCATTGTCAACAGAAAAGTA
609951 ATGTTGTAGT
Statistics
Matches: 472, Mismatches: 49, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
43 35 0.07
44 12 0.03
45 419 0.89
46 6 0.01
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (45 bp):
AAATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTATAGTTG
Found at i:610780 original size:22 final size:23
Alignment explanation
Indices: 610738--610795 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
610728 AAAGTCAATG
610738 GTCAACGGTCAGAACAATCAA-A
1 GTCAACGGTCAGAACAATCAACA
*
610760 GTCAACGGTCAG-ACTAGTCAACA
1 GTCAACGGTCAGAAC-AATCAACA
*
610783 GTTAACGGGTCAG
1 GTCAAC-GGTCAG
610796 GTCAAGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 2 0.06
22 17 0.55
23 6 0.19
24 6 0.19
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.17
Consensus pattern (23 bp):
GTCAACGGTCAGAACAATCAACA
Found at i:612856 original size:35 final size:35
Alignment explanation
Indices: 612740--612867 Score: 123
Period size: 35 Copynumber: 3.6 Consensus size: 35
612730 CTTAGATCCG
* *
612740 TAAGGAATTACTAGCTCGATCGGTCTAAACCTATA
1 TAAGGAATTACCAGTTCGATCGGTCTAAACCTATA
* * ** * * **
612775 TAAAGAATTACCAATTTTACCAAGT-TAAACCTGCCA
1 TAAGGAATTACCAGTTCGATC-GGTCTAAACCT-ATA
*
612811 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
1 TAAGGAATTACCAGTTCGATCGGTCTAAACCTATA
*
612846 TAAGGAATTACCAGTTTGATCG
1 TAAGGAATTACCAGTTCGATCG
612868 AACTGAACCT
Statistics
Matches: 70, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
35 45 0.64
36 25 0.36
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (35 bp):
TAAGGAATTACCAGTTCGATCGGTCTAAACCTATA
Found at i:612874 original size:35 final size:35
Alignment explanation
Indices: 612810--612878 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
612800 TAAACCTGCC
**
612810 ATAAGGAATTACCAGTTCGATCGGTCTGAACCTAT
1 ATAAGGAATTACCAGTTCGATCGAACTGAACCTAT
*
612845 ATAAGGAATTACCAGTTTGATCGAACTGAACCTA
1 ATAAGGAATTACCAGTTCGATCGAACTGAACCTA
612879 CAAAGACTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTCGATCGAACTGAACCTAT
Found at i:613979 original size:26 final size:27
Alignment explanation
Indices: 613949--614007 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
613939 ATTCTTATCT
*
613949 TTTTACAACATAA-TGTATTTTCGTAA
1 TTTTACAACATAAGGGTATTTTCGTAA
** *
613975 TTTTACCCCTTAAGGGTATTTTCGTAA
1 TTTTACAACATAAGGGTATTTTCGTAA
614002 TTTTAC
1 TTTTAC
614008 CTAACCAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.47
Consensus pattern (27 bp):
TTTTACAACATAAGGGTATTTTCGTAA
Found at i:616621 original size:35 final size:35
Alignment explanation
Indices: 616557--616695 Score: 147
Period size: 35 Copynumber: 3.9 Consensus size: 35
616547 GCTTAGATCC
* * *
616557 ATAAGGAATTACTAGGTCGATC-AGTCTGAACCTAT
1 ATAAGGAATTACCAGTTTGATCGAG-CTGAACCTAT
* * * * *
616592 GTAAAGAATTACCAATTTGACCGAGCTGAACCTACC
1 ATAAGGAATTACCAGTTTGATCGAGCTGAACCTA-T
*
616628 ATAAGGAATTACCAGTTCGATCG-GTCTGAACCTAT
1 ATAAGGAATTACCAGTTTGATCGAG-CTGAACCTAT
*
616663 ATAAGGAATTACCAGTTTGATCGAACTGAACCT
1 ATAAGGAATTACCAGTTTGATCGAGCTGAACCT
616696 GCAAAGACTT
Statistics
Matches: 84, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
35 55 0.65
36 29 0.35
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTTGATCGAGCTGAACCTAT
Found at i:616672 original size:71 final size:71
Alignment explanation
Indices: 616555--616695 Score: 210
Period size: 71 Copynumber: 2.0 Consensus size: 71
616545 CAGCTTAGAT
* * *
616555 CCATAAGGAATTACTAGGTCGATCAGTCTGAACCTATGTAAAGAATTACCAATTTGACCGAGCTG
1 CCATAAGGAATTACCAGGTCGATCAGTCTGAACCTATATAAAGAATTACCAATTTGACCGAACTG
616620 AACCTA
66 AACCTA
* * * * *
616626 CCATAAGGAATTACCAGTTCGATCGGTCTGAACCTATATAAGGAATTACCAGTTTGATCGAACTG
1 CCATAAGGAATTACCAGGTCGATCAGTCTGAACCTATATAAAGAATTACCAATTTGACCGAACTG
616691 AACCT
66 AACCT
616696 GCAAAGACTT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (71 bp):
CCATAAGGAATTACCAGGTCGATCAGTCTGAACCTATATAAAGAATTACCAATTTGACCGAACTG
AACCTA
Found at i:617780 original size:27 final size:27
Alignment explanation
Indices: 617749--617808 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
617739 ATTCTTGTCT
* *
617749 TTTTACAACATAATGGTATTTTCGTAA
1 TTTTACAACATAAGGGTATTTACGTAA
** *
617776 TTTTACCCCTTAAGGGTATTTACGTAA
1 TTTTACAACATAAGGGTATTTACGTAA
617803 TTTTAC
1 TTTTAC
617809 CTAACCAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (27 bp):
TTTTACAACATAAGGGTATTTACGTAA
Found at i:618234 original size:17 final size:18
Alignment explanation
Indices: 618214--618252 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
618204 GATACATAGC
618214 AAAC-GAATTTACATT-AG
1 AAACTGAATTTA-ATTGAG
618231 AAACTGAATTTAATTGAG
1 AAACTGAATTTAATTGAG
618249 AAAC
1 AAAC
618253 CAAATTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (18 bp):
AAACTGAATTTAATTGAG
Found at i:619484 original size:27 final size:27
Alignment explanation
Indices: 619423--619484 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
619413 CAAGCTAAGT
* *
619423 CTTCTCTTCTTCTTTTTTTAATGTTCT
1 CTTCTCTTCTTCTTTTTTTAATGCTCC
* *
619450 CTTTTCTTTTTCCTTTTTTTAAT-CTCC
1 CTTCTCTTCTT-CTTTTTTTAATGCTCC
619477 CTTCTCTT
1 CTTCTCTT
619485 AGGGTTTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.66
Consensus pattern (27 bp):
CTTCTCTTCTTCTTTTTTTAATGCTCC
Found at i:620399 original size:20 final size:22
Alignment explanation
Indices: 620374--620413 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
620364 AGTCGTATAT
620374 AGCCG-TTGGGGA-TGTTTTGG
1 AGCCGTTTGGGGATTGTTTTGG
620394 AGCCGTTTGGGGATTGTTTT
1 AGCCGTTTGGGGATTGTTTT
620414 TTTTTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.10, C:0.10, G:0.40, T:0.40
Consensus pattern (22 bp):
AGCCGTTTGGGGATTGTTTTGG
Found at i:628307 original size:3 final size:3
Alignment explanation
Indices: 628299--628345 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
628289 TCTGCAAATG
* * * *
628299 TAA TAA TAA TAA TAT TAA TAA TAG TAA TAG TAA TAG TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
628346 TTATTATTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:628319 original size:12 final size:12
Alignment explanation
Indices: 628298--628345 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
628288 GTCTGCAAAT
628298 GTAATAATAATA
1 GTAATAATAATA
* *
628310 ATATTAATAATA
1 GTAATAATAATA
*
628322 GTAATAGTAATA
1 GTAATAATAATA
628334 GTAATAATAATA
1 GTAATAATAATA
628346 TTATTATTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (12 bp):
GTAATAATAATA
Found at i:631512 original size:17 final size:17
Alignment explanation
Indices: 631492--631538 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
631482 AAAAGGTATT
631492 TAATATACAATACAAAA
1 TAATATACAATACAAAA
* **
631509 TAATATATAATGTGAAAA
1 TAATATACAAT-ACAAAA
631527 TAATAT-CAATAC
1 TAATATACAATAC
631539 GACACAAAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (17 bp):
TAATATACAATACAAAA
Found at i:635491 original size:20 final size:20
Alignment explanation
Indices: 635466--635559 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
635456 AATTGGGAAA
*
635466 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
635486 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
635507 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
635527 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
635547 TTCGCAACGCGAT
1 ATCGCAACGCGAT
635560 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:636162 original size:19 final size:19
Alignment explanation
Indices: 636115--636156 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
636105 ACGAGATAAT
*
636115 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
636134 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
636153 CGCA
1 CGCA
636157 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:636229 original size:39 final size:38
Alignment explanation
Indices: 636152--636322 Score: 172
Period size: 39 Copynumber: 4.6 Consensus size: 38
636142 GAAACAAAAA
*
636152 TCGCATTGCGATTTTTATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
636190 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGC-GTTGCGATTTTCATT
* * * **
636229 TCGCGTTGCGA---TTGTCT-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
** * *
636262 TCGCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTTATTT-CGCGTTGCGATTTTCATT
* *
636301 ATCTCGTTGCGATTTTCATTTC
1 -TCGCGTTGCGATTTTTATTTC
636323 AACCAAAAGA
Statistics
Matches: 110, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
33 23 0.21
35 1 0.01
36 7 0.06
38 23 0.21
39 39 0.35
40 17 0.15
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
Found at i:636299 original size:20 final size:19
Alignment explanation
Indices: 636152--636322 Score: 181
Period size: 19 Copynumber: 9.1 Consensus size: 19
636142 GAAACAAAAA
* *
636152 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
636171 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
636190 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
636209 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
636229 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
636245 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
636262 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
636281 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
636301 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
636321 TC
1 TC
636323 AACCAAAAGA
Statistics
Matches: 132, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
14 10 0.08
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 67 0.51
20 50 0.38
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:636683 original size:33 final size:32
Alignment explanation
Indices: 636641--636767 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
636631 AGACCATGAC
*
636641 CGTTACGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
636674 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
636707 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
636740 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
636768 AGTAATTTCA
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:636728 original size:66 final size:66
Alignment explanation
Indices: 636641--636766 Score: 234
Period size: 66 Copynumber: 1.9 Consensus size: 66
636631 AGACCATGAC
636641 CGTTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTA
1 CGTTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTA
636706 G
66 G
* *
636707 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
1 CGTTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGA
636767 TAGTAATTTC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (66 bp):
CGTTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTA
G
Found at i:637819 original size:20 final size:20
Alignment explanation
Indices: 637794--637846 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
637784 GTGCTATGTA
637794 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
637814 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
637834 TATCTCGTTGCGA
1 AATCGCGTTGCGA
637847 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:637880 original size:20 final size:20
Alignment explanation
Indices: 637855--637908 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
637845 GATTTTGTAT
637855 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
637875 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
637895 TATCGCATTGCGAT
1 TATCGCATTGCGAT
637909 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:637893 original size:61 final size:61
Alignment explanation
Indices: 637795--637911 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
637785 TGCTATGTAA
* * * * *
637795 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
637856 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
637912 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:637927 original size:61 final size:61
Alignment explanation
Indices: 637795--637929 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
637785 TGCTATGTAA
* * * * * ** *
637795 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
637856 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
637918 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
637930 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:649636 original size:3 final size:3
Alignment explanation
Indices: 649628--649659 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
649618 ACCCCTATGG
*
649628 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
649660 ATCAAAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:650790 original size:14 final size:14
Alignment explanation
Indices: 650771--650797 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
650761 AAATACTTTT
650771 AAAATAATTTTAAG
1 AAAATAATTTTAAG
650785 AAAATAATTTTAA
1 AAAATAATTTTAA
650798 AAGAAAAAAT
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:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
AAAATAATTTTAAG
Found at i:651247 original size:15 final size:15
Alignment explanation
Indices: 651223--651253 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
651213 TAAATAAACC
*
651223 AATAATAATATTAAA
1 AATAAAAATATTAAA
651238 AATAAAAATATTAAA
1 AATAAAAATATTAAA
651253 A
1 A
651254 TTTGGGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAAAAATATTAAA
Found at i:652514 original size:3 final size:3
Alignment explanation
Indices: 652506--652553 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
652496 AAATTTAAAT
*
652506 TAA TAA TAA TAA TAA TAA TAA TAC TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
652553 T
1 T
652554 GATATAAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:652964 original size:102 final size:102
Alignment explanation
Indices: 652779--653156 Score: 540
Period size: 102 Copynumber: 3.7 Consensus size: 102
652769 TCTTTTATTC
* *
652779 TTTCAGGGGAGATAAGATCCAAGGGAAGATGAATCTTCTCCACTCTTGTTTCAGGGAGATAAGAC
1 TTTCA-GGGAGATAAGATCCAAGGGAAGAAGAATCTGCTCCACTCTTGTTTCAGGGAGATAAGAC
* * * * *
652844 TCGAGAAATCTTTGTAAAATAGATCTACTCCATTATTG
65 TCGAGAAATCTTTGTAAAACAGATATGCTCCACTCTTG
* * * *
652882 TTTTAGGGAGATAAGATCCAAGGCAAGAAAAATCTGCTCCACTATTGTTTCAGGGAGATAAGACT
1 TTTCAGGGAGATAAGATCCAAGGGAAGAAGAATCTGCTCCACTCTTGTTTCAGGGAGATAAGACT
* * *
652947 CGAAAAATCTTTCTAAAACGGATATGCTCCACTCTTG
66 CGAGAAATCTTTGTAAAACAGATATGCTCCACTCTTG
** * * * *
652984 TTTCAGGGAGATAAGATTGAAGGGAAGATGAATCTGGTACACTCTTGTTTTAGGGAGATAAGACT
1 TTTCAGGGAGATAAGATCCAAGGGAAGAAGAATCTGCTCCACTCTTGTTTCAGGGAGATAAGACT
*
653049 CGAGAAATCTTTGTAAAACAGATATGTTCCACTCTTG
66 CGAGAAATCTTTGTAAAACAGATATGCTCCACTCTTG
* *
653086 TTTCAGGGAGATAAGATCCAAGGGAAGAAGAATCTGATCTACTCTTGTTTCAGGGAGATAAGACT
1 TTTCAGGGAGATAAGATCCAAGGGAAGAAGAATCTGCTCCACTCTTGTTTCAGGGAGATAAGACT
653151 CGAGAA
66 CGAGAA
653157 TTATTTGGAT
Statistics
Matches: 240, Mismatches: 35, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
102 236 0.98
103 4 0.02
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (102 bp):
TTTCAGGGAGATAAGATCCAAGGGAAGAAGAATCTGCTCCACTCTTGTTTCAGGGAGATAAGACT
CGAGAAATCTTTGTAAAACAGATATGCTCCACTCTTG
Found at i:653369 original size:137 final size:137
Alignment explanation
Indices: 653182--653864 Score: 963
Period size: 137 Copynumber: 5.0 Consensus size: 137
653172 CTTTTTAGGG
* ** * * * * *
653182 ATAATGGAGATAACATGGTTTTTACGCAATGAGGAAGTCTGACTATCTAAGAATGAAACGACTCC
1 ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGAAACGGCTCC
* * *
653247 TACATGATGAGGAGATCTGGTCGGTAGATGACATTTTTCCTTCGTGATGAGGATGTCTGGCCATC
66 TACGTGATGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATC
653312 TTTTTTT
131 TTTTTTT
* *
653319 ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGACATGGCTCC
1 ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGAAACGGCTCC
* * * *
653384 TACATGATGAGGAGATCTGGTCAGTAGATGACATTGTTCCTTCGTGATGAGGATGTCTGACCATC
66 TACGTGATGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATC
653449 TTTTTTT
131 TTTTTTT
* * * * ** *
653456 ATAATGGAGATAACATGGTTCCTACACGATGAGGAATTTTGCCTATCTAAGGATGATGCGACTCC
1 ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGAAACGGCTCC
* * * * *
653521 TACGTGATGAGGAGATCTGGTCAGTAGATGAGATTGTTTCTTCATGATGAGGACGTTTGGCCATC
66 TACGTGATGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATC
653586 TTTTTTTT
131 -TTTTTTT
* * *
653594 ATAATGGAGATAACACGATTCCTACGCGATGAGGAATTCTGGCTATCTAAGAAT-AAAGTGGCTC
1 ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGAAA-CGGCTC
* * *
653658 CTACGTGAGGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGAACGTCTAGCCAT
65 CTACGTGATGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCAT
653723 CTTTTTTTT
130 C-TTTTTTT
** * *
653732 ATAATGGAGATAACACGGTTCCTACAAGAAGAGGAATTCTGGCTATCTAAGGATGACACGGCTCC
1 ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGAAACGGCTCC
* *
653797 TACGTGATGAGGAGATCTGGTCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGACCATC
66 TACGTGATGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATC
653862 TTT
131 TTT
653865 AGGGATAATT
Statistics
Matches: 485, Mismatches: 58, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
137 243 0.50
138 240 0.49
139 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (137 bp):
ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGAAACGGCTCC
TACGTGATGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATC
TTTTTTT
Found at i:653660 original size:138 final size:138
Alignment explanation
Indices: 653182--653864 Score: 967
Period size: 138 Copynumber: 5.0 Consensus size: 138
653172 CTTTTTAGGG
* ** * * * * *
653182 ATAATGGAGATAACATGGTTTTTACGCAATGAGGAAGTCTGACTATCTAAGAATGAAACGACTCC
1 ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGAAACGGCTCC
* * *
653247 TACATGATGAGGAGATCTGGTCGGTAGATGACATTTTTCCTTCGTGATGAGGATGTCTGGCCATC
66 TACGTGATGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATC
653312 -TTTTTTT
131 TTTTTTTT
* *
653319 ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGACATGGCTCC
1 ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGAAACGGCTCC
* * * *
653384 TACATGATGAGGAGATCTGGTCAGTAGATGACATTGTTCCTTCGTGATGAGGATGTCTGACCATC
66 TACGTGATGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATC
653449 -TTTTTTT
131 TTTTTTTT
* * * * ** *
653456 ATAATGGAGATAACATGGTTCCTACACGATGAGGAATTTTGCCTATCTAAGGATGATGCGACTCC
1 ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGAAACGGCTCC
* * * * *
653521 TACGTGATGAGGAGATCTGGTCAGTAGATGAGATTGTTTCTTCATGATGAGGACGTTTGGCCATC
66 TACGTGATGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATC
653586 TTTTTTTT
131 TTTTTTTT
* * *
653594 ATAATGGAGATAACACGATTCCTACGCGATGAGGAATTCTGGCTATCTAAGAAT-AAAGTGGCTC
1 ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGAAA-CGGCTC
* * *
653658 CTACGTGAGGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGAACGTCTAGCCAT
65 CTACGTGATGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCAT
653723 CTTTTTTTT
130 CTTTTTTTT
** * *
653732 ATAATGGAGATAACACGGTTCCTACAAGAAGAGGAATTCTGGCTATCTAAGGATGACACGGCTCC
1 ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGAAACGGCTCC
* *
653797 TACGTGATGAGGAGATCTGGTCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGACCATC
66 TACGTGATGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATC
653862 TTT
131 TTT
653865 AGGGATAATT
Statistics
Matches: 485, Mismatches: 58, Indels: 5
0.89 0.11 0.01
Matches are distributed among these distances:
137 240 0.49
138 243 0.50
139 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (138 bp):
ATAATGGAGATAACACGGTTCCTACGCGATGAGGAATTCTGGCTATCTAAGGATGAAACGGCTCC
TACGTGATGAGGAGATCTGGTCGGTAGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATC
TTTTTTTT
Found at i:654066 original size:62 final size:61
Alignment explanation
Indices: 653967--654198 Score: 207
Period size: 62 Copynumber: 3.8 Consensus size: 61
653957 ATCAGGAAGT
* *
653967 CCTGAATAAAAAAAGTTGAC-TTCCTTCACGAGAAAGTCAAGGATTGACTCTACTGGGGAGC
1 CCTGAAT-AAAAAAGTTGACTTTTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGC
* * * **
654028 CCTGAATAAAAAATGTTAACTTTTCTTCATGAGGAAGTCAAGGATTGACTATACTGGGGAAT
1 CCTGAATAAAAAA-GTTGACTTTTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGC
** * * * * *
654090 CAGGGATAATAAAGATTGA-TTTCTCTTTACGAGGAAGTCAAGGATTGAATCTACTGGGGAGT
1 CCTGAATAAAAAAG-TTGACTTT-TCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGC
*** * * * * *
654152 TAGGGATAATAAAGATTGACTTCTCTTCATGAGGAAGTCAATGATTG
1 CCTGAATAAAAAAG-TTGACTTTTCTTCACGAGGAAGTCAAGGATTG
654199 CAAAGATTGA
Statistics
Matches: 144, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
60 6 0.04
61 16 0.11
62 120 0.83
63 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (61 bp):
CCTGAATAAAAAAGTTGACTTTTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGC
Found at i:654183 original size:124 final size:128
Alignment explanation
Indices: 653907--654198 Score: 326
Period size: 124 Copynumber: 2.3 Consensus size: 128
653897 ATCAAATCAG
* * * *
653907 AAAGATTGATTTCTCTTCACGAGGAAGTCAAGGATTGACTATACTATGGAATCAGGAAGTCCTGA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTATACTAGGGAATCAGG-AG-CATGA
* **
653972 ATAAAAAAAGTTGACTTCCTTCACGAGAAAGTCAAGGATTGACTCTACTGGGGAGCCCTGAATAA
64 AT-AAAAAAGTTGACTTCCTTCACGAGAAAGTCAAGGATTGAATCTACTGGGGAGCCAGGAATAA
654037 A
128 A
* * *
654038 AAATG-TTAACTTTTCTTCATGAGGAAGTCAAGGATTGACTATACTGGGGAATCAGG-G-AT-AA
1 AAA-GATTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTATACTAGGGAATCAGGAGCATGAA
* * * * ** * *
654099 T-AAAGA-TTGATTTCTCTTTACGAGGAAGTCAAGGATTGAATCTACTGGGGAGTTAGGGATAAT
65 TAAAAAAGTTGACTTC-CTTCACGAGAAAGTCAAGGATTGAATCTACTGGGGAGCCAGGAATAAA
*
654162 AAAGATTGACTTCTCTTCATGAGGAAGTCAATGATTG
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTG
654199 CAAAGATTGA
Statistics
Matches: 137, Mismatches: 21, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
123 8 0.06
124 75 0.55
126 3 0.02
127 1 0.01
129 1 0.01
131 48 0.35
132 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (128 bp):
AAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTATACTAGGGAATCAGGAGCATGAAT
AAAAAAGTTGACTTCCTTCACGAGAAAGTCAAGGATTGAATCTACTGGGGAGCCAGGAATAAA
Found at i:654319 original size:29 final size:29
Alignment explanation
Indices: 654286--654344 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
654276 ACAAAATTTC
654286 TCAAAATATATACAT-TAT-TATGAGAATGA
1 TCAAAATATAT-CATGTATGTATG-GAATGA
*
654315 TCAAAATTTATCATGTATGTATGGAATGA
1 TCAAAATATATCATGTATGTATGGAATGA
654344 T
1 T
654345 GTATGATGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 3 0.11
29 20 0.74
30 4 0.15
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (29 bp):
TCAAAATATATCATGTATGTATGGAATGA
Found at i:658967 original size:15 final size:16
Alignment explanation
Indices: 658943--658976 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
658933 GAATGTAAAG
*
658943 ATGCAGAAATGCA-AA
1 ATGCAAAAATGCAGAA
658958 ATGCAAAAATGCAGAA
1 ATGCAAAAATGCAGAA
658974 ATG
1 ATG
658977 AGAATGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.53, C:0.12, G:0.21, T:0.15
Consensus pattern (16 bp):
ATGCAAAAATGCAGAA
Found at i:658993 original size:23 final size:23
Alignment explanation
Indices: 658934--658986 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
658924 TATAGATGTG
* *
658934 AATGTAAAGATGCAGAAATGCAA
1 AATGCAAAAATGCAGAAATGCAA
*
658957 AATGCAAAAATGCAGAAATG-AG
1 AATGCAAAAATGCAGAAATGCAA
658979 AATGCAAA
1 AATGCAAA
658987 CTGTGCAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.55, C:0.09, G:0.21, T:0.15
Consensus pattern (23 bp):
AATGCAAAAATGCAGAAATGCAA
Found at i:660178 original size:18 final size:17
Alignment explanation
Indices: 660151--660184 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
660141 GGACATTTGC
660151 CCTTTATCTCTTGTATCT
1 CCTTTATCTCTT-TATCT
*
660169 CCTTTTTCTCTTTATC
1 CCTTTATCTCTTTATC
660185 GGACATACAA
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:0.09, C:0.29, G:0.03, T:0.59
Consensus pattern (17 bp):
CCTTTATCTCTTTATCT
Found at i:663887 original size:20 final size:20
Alignment explanation
Indices: 663847--663885 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
663837 CATTGCAGGA
*
663847 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCCACAAAAG
663867 ATTTCATGGCCTCCACAAA
1 ATTT-ATGGCCTCCACAAA
663886 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCCACAAAAG
Found at i:673754 original size:16 final size:16
Alignment explanation
Indices: 673729--673760 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
673719 TAAATAAACC
*
673729 AATAATAATATTAAAA
1 AATAAAAATATTAAAA
673745 AATAAAAATATTAAAA
1 AATAAAAATATTAAAA
673761 TTCAGGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATAAAAATATTAAAA
Found at i:675020 original size:3 final size:3
Alignment explanation
Indices: 675014--675086 Score: 83
Period size: 3 Copynumber: 24.0 Consensus size: 3
675004 TTTAAATTAT
* * * * * *
675014 TAA TAA TAA TAA TAG TAG TAG TAG TAG TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
675062 TAA TAA TAA TAA TAA TATA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA
675087 GGATATAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 64 0.96
4 3 0.04
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:676151 original size:3 final size:3
Alignment explanation
Indices: 676145--676248 Score: 138
Period size: 3 Copynumber: 35.0 Consensus size: 3
676135 TTTAAATTAT
* * * * * * *
676145 TAA TAA TAA TAA TAG TAG TAG TAG TAG TAG TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
676193 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
676241 T-A TAA TAA
1 TAA TAA TAA
676249 GGATATAAAA
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
2 2 0.02
3 94 0.98
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:677314 original size:3 final size:3
Alignment explanation
Indices: 677308--677408 Score: 141
Period size: 3 Copynumber: 34.0 Consensus size: 3
677298 TTTAAATTAT
* * * * * *
677308 TAA TAA TAA TAA TAG TAG TAG TAG TAG TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
677356 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
677403 TAA TAA
1 TAA TAA
677409 GGATATAAAA
Statistics
Matches: 95, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 93 0.98
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:678475 original size:3 final size:3
Alignment explanation
Indices: 678467--678558 Score: 96
Period size: 3 Copynumber: 31.0 Consensus size: 3
678457 AAATTTAAAT
* * * * * * * * *
678467 TAA TAA TAA TAA TAA TAG TAG TAG TAG TAG TAG TAG TAG TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
678515 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
678559 GGATATAAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
2 2 0.02
3 82 0.98
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:679615 original size:3 final size:3
Alignment explanation
Indices: 679609--679688 Score: 99
Period size: 3 Copynumber: 27.0 Consensus size: 3
679599 TTTAAATTAT
* * * * * *
679609 TAA TAA TAA TAA TAG TAG TAG TAG TAG TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
679657 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
679689 GGATATAAAA
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 72 0.97
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:680790 original size:3 final size:3
Alignment explanation
Indices: 680780--680851 Score: 107
Period size: 3 Copynumber: 25.0 Consensus size: 3
680770 GTAGTAGTAG
680780 TAA T-A TAA TAA TAA TAA TAA -AA TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
680825 T-A TAA TAA TAA TAA TAA TATA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA
680852 GGATATAAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
2 8 0.12
3 53 0.83
4 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:680803 original size:14 final size:14
Alignment explanation
Indices: 680780--680851 Score: 117
Period size: 14 Copynumber: 5.0 Consensus size: 14
680770 GTAGTAGTAG
680780 TAATATAATAATAA
1 TAATATAATAATAA
*
680794 TAATAAAATAATAA
1 TAATATAATAATAA
680808 TAATATAATAATAA
1 TAATATAATAATAA
680822 TAATATAATAATAA
1 TAATATAATAATAA
680836 TAATAATATATAATAA
1 TAAT-ATA-ATAATAA
680852 GGATATAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
14 44 0.81
15 3 0.06
16 7 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATATAATAATAA
Found at i:680806 original size:17 final size:18
Alignment explanation
Indices: 680780--680851 Score: 107
Period size: 17 Copynumber: 4.2 Consensus size: 18
680770 GTAGTAGTAG
680780 TAAT-ATAATAATAATAA
1 TAATAATAATAATAATAA
680797 TAA-AATAATAATAAT-A
1 TAATAATAATAATAATAA
680813 TAATAATAATAAT-ATAA
1 TAATAATAATAATAATAA
680830 TAATAATAATAATATATAA
1 TAATAATAATAATA-ATAA
680849 TAA
1 TAA
680852 GGATATAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.12
17 37 0.74
19 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATAATAATAATAATAA
Found at i:681916 original size:3 final size:3
Alignment explanation
Indices: 681908--681991 Score: 80
Period size: 3 Copynumber: 28.0 Consensus size: 3
681898 AAATTTAAAT
* * * * * * * *
681908 TAA TAA TAA TAA TAA TAG TAG TAG TAG TAG TAG TAG TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
681956 TAAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
681992 GGATATAAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.03
3 70 0.93
4 3 0.04
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:683056 original size:3 final size:3
Alignment explanation
Indices: 683050--683123 Score: 94
Period size: 3 Copynumber: 24.7 Consensus size: 3
683040 TTTAAATTAT
* * * * * *
683050 TAA TAA TAA TAA TAG TAG TAG TAG TAG TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
683098 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
683124 TAAGGATATA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:684194 original size:3 final size:3
Alignment explanation
Indices: 684188--684270 Score: 105
Period size: 3 Copynumber: 28.0 Consensus size: 3
684178 TTTAAATTAT
* * * * * *
684188 TAA TAA TAA TAA TAG TAG TAG TAG TAG TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
684236 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
684271 GGATATAAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 2 0.03
3 75 0.97
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:686099 original size:3 final size:3
Alignment explanation
Indices: 686091--686122 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
686081 AAAATACTAT
686091 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
686123 TACATGTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:688375 original size:18 final size:18
Alignment explanation
Indices: 688352--688404 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
688342 CACTTAGAAT
*
688352 TGTCCCTAATGACCACTA
1 TGTCCCGAATGACCACTA
688370 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
688388 TGTCTCGAATGACCACT
1 TGTCCCGAATGACCACT
688405 CCGTAATAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.26
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:688728 original size:20 final size:19
Alignment explanation
Indices: 688684--688728 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
688674 TAATTCACAT
* *
688684 ATCTCATGTTCATATGATC
1 ATCTTATGTTCATATCATC
688703 -TCTTATGTTCATATCATC
1 ATCTTATGTTCATATCATC
688721 GATCTTAT
1 -ATCTTAT
688729 AACAAATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 16 0.73
20 6 0.27
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.47
Consensus pattern (19 bp):
ATCTTATGTTCATATCATC
Found at i:688812 original size:7 final size:7
Alignment explanation
Indices: 688796--688830 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
688786 TGTATTCACT
*
688796 TATATCA
1 TATAACA
*
688803 TATAATA
1 TATAACA
688810 TATAACA
1 TATAACA
688817 TATAACA
1 TATAACA
688824 TATAACA
1 TATAACA
688831 CATACAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (7 bp):
TATAACA
Found at i:694186 original size:13 final size:14
Alignment explanation
Indices: 694168--694264 Score: 66
Period size: 13 Copynumber: 7.1 Consensus size: 14
694158 AGATCAAATC
*
694168 AAAGCAACG-GAAA
1 AAAGCAAAGAGAAA
694181 AAAGCAAAGAGAAA
1 AAAGCAAAGAGAAA
694195 AAAG-AAA-A-AAA
1 AAAGCAAAGAGAAA
*
694206 AAAGAAAAAAGCATAGAAA
1 AAAG--CAAAG---AGAAA
694225 AAA-CAAAGAGAAA
1 AAAGCAAAGAGAAA
*
694238 AAAACAAA-AG-AA
1 AAAGCAAAGAGAAA
694250 AAAGCAAAGA-AAA
1 AAAGCAAAGAGAAA
694263 AA
1 AA
694265 GACAAGAAGC
Statistics
Matches: 69, Mismatches: 3, Indels: 24
0.72 0.03 0.25
Matches are distributed among these distances:
11 7 0.10
12 10 0.14
13 26 0.38
14 15 0.22
16 4 0.06
18 1 0.01
19 6 0.09
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.01
Consensus pattern (14 bp):
AAAGCAAAGAGAAA
Found at i:694208 original size:11 final size:11
Alignment explanation
Indices: 694178--694264 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
694168 AAAGCAACGG
694178 AAAAAAGCAAAGA
1 AAAAAAG-AAA-A
694191 GAAAAAAGAAAA
1 -AAAAAAGAAAA
694203 AAAAAAGAAAA
1 AAAAAAGAAAA
* *
694214 AAGCATAGAAAA
1 AA-AAAAGAAAA
694226 AACAAAGAGAAAAA
1 AA-AAA-AG-AAAA
694240 AACAAAAGAAAA
1 AA-AAAAGAAAA
**
694252 AGCAAAGAAAA
1 AAAAAAGAAAA
694263 AA
1 AA
694265 GACAAGAAGC
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
11 22 0.35
12 16 0.26
13 7 0.11
14 17 0.27
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:694271 original size:12 final size:12
Alignment explanation
Indices: 694196--694272 Score: 54
Period size: 12 Copynumber: 6.4 Consensus size: 12
694186 AAAGAGAAAA
*
694196 AAGAAAAAA-AA
1 AAGAAAAAAGAC
694207 AAGAAAAAAG-C
1 AAGAAAAAAGAC
*
694218 ATAGAAAAAACA-
1 A-AGAAAAAAGAC
*
694230 AAGAGAAAAAAAC
1 AAGA-AAAAAGAC
*
694243 AAAAGAAAAAG-C
1 AAGA-AAAAAGAC
694255 AAAGAAAAAAGAC
1 -AAGAAAAAAGAC
694268 AAGAA
1 AAGAA
694273 GCACATTCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
11 13 0.25
12 27 0.51
13 13 0.25
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.01
Consensus pattern (12 bp):
AAGAAAAAAGAC
Found at i:695675 original size:38 final size:39
Alignment explanation
Indices: 695622--695739 Score: 138
Period size: 38 Copynumber: 3.2 Consensus size: 39
695612 TTAAAACCAT
* *
695622 ATTTTATCTCGCTTGAGATAGTTTTACTTGAAA-AAAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAG
* * *
695660 ATTTTATCTCACTTGAGATAGTTTCACTCGAAACATACG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAG
*
695699 A-TTTATCTCGCTTGAGATA---TCCCTCGAAACAAAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAG
*
695734 AGTTTA
1 ATTTTA
695740 AGAAACTAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 14 0.20
36 4 0.06
38 47 0.68
39 4 0.06
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (39 bp):
ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAG
Found at i:696105 original size:194 final size:194
Alignment explanation
Indices: 695738--696146 Score: 547
Period size: 194 Copynumber: 2.1 Consensus size: 194
695728 CAAAAGAGTT
* * *
695738 TAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAGATTTTCAAGGAAATTTTAAAAGGAA
1 TAAGAAACTAAGCCTGATTTTCAGGGATTACTCGATGAAGATTTTCAAGGAAATTTTAAAAGGAA
* * * * * *
695803 GCTAAGCCTAATTTTTAGGGGTTTCTTTACAATTAAGAAACTAAGCCTGGTTTTCAAGGGTTTCT
66 ACTAAGCCTAATATTTAGGGGTTCCTTGACAACTAAGAAACTAAGCCTGATTTTCAAGGGTTTCT
* *
695868 TAATGAAGATTTTCCATGAATTTTAAAGAAAGCTAAGCCTAATTTTTAGGGGTTCATTGACAAC
131 TAATGAAGATTTTCAATGAATTTAAAAGAAAGCTAAGCCTAATTTTTAGGGGTTCATTGACAAC
* * * *
695932 TAAGAAAC-AAGCCTGATTTTCAGGGATTACTCGATGATGATTTTCAATGAATTTTTTTAAAGGA
1 TAAGAAACTAAGCCTGATTTTCAGGGATTACTCGATGAAGATTTTCAAGGAA-ATTTTAAAAGGA
* *
695996 AACTAAGCCTAATATTTAGGGGTTCCTTGA-ATACTAAGAAACTAAGCTTGATTTTCAGGGGTTT
65 AACTAAGCCTAATATTTAGGGGTTCCTTGACA-ACTAAGAAACTAAGCCTGATTTTCAAGGGTTT
* * * * *
696060 CTTGATGATTG-TTTTCAATGAGTTTGAAAAGGAAGCTAA-CCTAATTTTTAGGGGTTCCTTGAC
129 CTTAATGA-AGATTTTCAATGAATTT-AAAAGAAAGCTAAGCCTAATTTTTAGGGGTTCATTGAC
696123 AAC
192 AAC
*
696126 TAAGAAACTAAGCTTGATTTT
1 TAAGAAACTAAGCCTGATTTT
696147 TAAGGGTTTC
Statistics
Matches: 187, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
193 39 0.21
194 125 0.67
195 23 0.12
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (194 bp):
TAAGAAACTAAGCCTGATTTTCAGGGATTACTCGATGAAGATTTTCAAGGAAATTTTAAAAGGAA
ACTAAGCCTAATATTTAGGGGTTCCTTGACAACTAAGAAACTAAGCCTGATTTTCAAGGGTTTCT
TAATGAAGATTTTCAATGAATTTAAAAGAAAGCTAAGCCTAATTTTTAGGGGTTCATTGACAAC
Found at i:696119 original size:96 final size:98
Alignment explanation
Indices: 695738--696163 Score: 551
Period size: 96 Copynumber: 4.4 Consensus size: 98
695728 CAAAAGAGTT
*
695738 TAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAGATTTTCAAGGAAATTTTAAAAGGAA
1 TAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAGATTTTCAATGAAATTTTAAAAGGAA
* * *
695803 GCTAAGCCTAATTTTTAGGGGTTTCTTTACAAT
66 GCTAAGCCTAATTTTTAGGGGTTCCTTGACAAC
* * * * *
695836 TAAGAAACTAAGCCTGGTTTTCAAGGGTTTCTTAATGAAGATTTTCCATG-AATTTT-AAAGAAA
1 TAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAGATTTTCAATGAAATTTTAAAAGGAA
*
695899 GCTAAGCCTAATTTTTAGGGGTTCATTGACAAC
66 GCTAAGCCTAATTTTTAGGGGTTCCTTGACAAC
* * * * * *
695932 TAAGAAAC-AAGCCTGATTTTCAGGGATTACTCGATGATGATTTTCAATGAATTTTTTTAAAGGA
1 TAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAGATTTTCAATGAA-ATTTTAAAAGGA
* *
695996 AACTAAGCCTAATATTTAGGGGTTCCTTGA-ATAC
65 AGCTAAGCCTAATTTTTAGGGGTTCCTTGACA-AC
* * * *
696030 TAAGAAACTAAGCTTGATTTTCAGGGGTTTCTTGATGATTG-TTTTCAATG-AGTTTGAAAAGGA
1 TAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGA-AGATTTTCAATGAAATTTTAAAAGGA
696093 AGCTAA-CCTAATTTTTAGGGGTTCCTTGACAAC
65 AGCTAAGCCTAATTTTTAGGGGTTCCTTGACAAC
* * *
696126 TAAGAAACTAAGCTTGATTTTTAAGGGTTTCTTGATGA
1 TAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGA
696164 GTAAGTCATT
Statistics
Matches: 287, Mismatches: 34, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
95 33 0.11
96 104 0.36
97 26 0.09
98 88 0.31
99 34 0.12
100 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (98 bp):
TAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAGATTTTCAATGAAATTTTAAAAGGAA
GCTAAGCCTAATTTTTAGGGGTTCCTTGACAAC
Found at i:696997 original size:65 final size:67
Alignment explanation
Indices: 696843--697011 Score: 236
Period size: 65 Copynumber: 2.6 Consensus size: 67
696833 TCAAAACAAG
* * * *
696843 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAGCAAATATCTTTGAATATGTTTCCCTTTAAGCAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATATCTTTGAAAATGTTTCCCTTGAAACAA
696908 AA
66 AA
* *
696910 TTTTGTCTCCCTTGAGGCAGTTTCTCTTGAAACATAA-A-CTTTGAAAATGTTTCCCTTGAAAC-
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AATATCTTTGAAAATGTTTCCCTTGAAACA
*
696972 GAA
65 AAA
*
696975 TTTTATCTCTCTTGAGACAGTTTCTCTTGAAACAAAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAT
697012 TTCGTCTCCC
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
64 2 0.02
65 33 0.37
66 21 0.23
67 32 0.36
68 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (67 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATATCTTTGAAAATGTTTCCCTTGAAACAA
AA
Found at i:697005 original size:36 final size:36
Alignment explanation
Indices: 696958--697185 Score: 240
Period size: 36 Copynumber: 6.3 Consensus size: 36
696948 CTTTGAAAAT
* * *
696958 GTTTCCCTTGAAACGAATTTTATCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCATCTCCCTTGAGACA
* *
696994 GTTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCATCTCCCTTGAGACA
* * * ** * *
697030 GTATCGCTAGAAACAAATTTTGTATCCCTTGAGATA
1 GTTTCCCTTGAAACAAATTTCATCTCCCTTGAGACA
* *
697066 GTTTCTCTTAAAACAAATTTCATCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCATCTCCCTTGAGACA
* * * *
697102 GTTTCCCTGGAGATAAATTTCATCTCCCTTGAAACA
1 GTTTCCCTTGAAACAAATTTCATCTCCCTTGAGACA
* * * **
697138 ATTTCCTTTGAAAAAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCATCTCCCTTGAGACA
*
697174 GTTTCCTTTGAA
1 GTTTCCCTTGAA
697186 GCACCAACCA
Statistics
Matches: 158, Mismatches: 34, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 158 1.00
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTCATCTCCCTTGAGACA
Found at i:697101 original size:108 final size:108
Alignment explanation
Indices: 696958--697179 Score: 275
Period size: 108 Copynumber: 2.1 Consensus size: 108
696948 CTTTGAAAAT
* * * * * * *
696958 GTTTCCCTTGAAACGAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCCCT
1 GTTTCCCTTAAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTGGAAACAAATTTCATCTCCCT
* * * *
697023 TGAGACAGTATCGC-TAGAAACAAATTTTGTATCCCTTGAGATA
66 TGAAACAATATC-CTTAGAAAAAAATTTTGTATCCCTTGAGACA
* * *
697066 GTTTCTCTTAAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTGGAGATAAATTTCATCTCCCT
1 GTTTCCCTTAAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTGGAAACAAATTTCATCTCCCT
* * *
697131 TGAAACAATTTCCTTTGAAAAAAATTTTGTCTCCCTTGAGACA
66 TGAAACAATATCCTTAGAAAAAAATTTTGTATCCCTTGAGACA
697174 GTTTCC
1 GTTTCC
697180 TTTGAAGCAC
Statistics
Matches: 95, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
107 1 0.01
108 94 0.99
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (108 bp):
GTTTCCCTTAAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTGGAAACAAATTTCATCTCCCT
TGAAACAATATCCTTAGAAAAAAATTTTGTATCCCTTGAGACA
Found at i:703349 original size:41 final size:41
Alignment explanation
Indices: 703257--703370 Score: 115
Period size: 41 Copynumber: 2.8 Consensus size: 41
703247 AGTTGATATA
* * * **
703257 TAGCGGCGTTTTTACAACAAACACCGTAATAGGGTGGTTTAT
1 TAGCGGCGTTTTT-TAACAAACACCGCAATAGAGTGGTAAAT
* *
703299 T-GCGTCGTTTTTTAACAAACACCGCAATATAGTGGTAAAT
1 TAGCGGCGTTTTTTAACAAACACCGCAATAGAGTGGTAAAT
* *
703339 TAGCGGCG-TTTATACACAAACGCCGCAATAGA
1 TAGCGGCGTTTTTTA-ACAAACACCGCAATAGA
703371 TTAACATATA
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
40 28 0.47
41 30 0.51
42 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (41 bp):
TAGCGGCGTTTTTTAACAAACACCGCAATAGAGTGGTAAAT
Found at i:703408 original size:40 final size:41
Alignment explanation
Indices: 703346--703496 Score: 145
Period size: 42 Copynumber: 3.7 Consensus size: 41
703336 AATTAGCGGC
703346 GTTTATA-CACAAACGCCGCAATAGATTAACATATAGTGGT
1 GTTTATACCACAAACGCCGCAATAGATTAACATATAGTGGT
* * *
703386 GTTT-TAGCCA-AAACGCCACAATAGATCGTGAA-AT-TAGCGGC
1 GTTTATA-CCACAAACGCCGCAATAGAT--T-AACATATAGTGGT
703427 GTTTATACCACAAACGCCGCAATAGATTACACATATAGTGGT
1 GTTTATACCACAAACGCCGCAATAGATTA-ACATATAGTGGT
* * *
703469 ATTTATTCTTA-AAACGCCGCAATA-ATTA
1 GTTTATAC-CACAAACGCCGCAATAGATTA
703497 TAATAAATAG
Statistics
Matches: 91, Mismatches: 9, Indels: 21
0.75 0.07 0.17
Matches are distributed among these distances:
39 3 0.03
40 21 0.23
41 20 0.22
42 44 0.48
43 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (41 bp):
GTTTATACCACAAACGCCGCAATAGATTAACATATAGTGGT
Found at i:703547 original size:41 final size:40
Alignment explanation
Indices: 703480--703639 Score: 162
Period size: 41 Copynumber: 3.9 Consensus size: 40
703470 TTTATTCTTA
* * * *
703480 AAACGCCGCAATAAT-TATAATAAATAGTGGCGTTTTTAGGC
1 AAACGCCACAATAGTGT-TAATCAATAGTGGCGTTTTTA-AC
*
703521 AAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTATAA
1 AAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTA-AC
* * * *
703562 AAATGCCGCAATAGTTTTAATCAATAGTGGCATTTTTTTAAC
1 AAACGCCACAATAGTGTTAATCAATAGTGGC--GTTTTTAAC
* *
703604 AAACGCCACAATAGTG-TAATTAATAGTGGCATTTTT
1 AAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTT
703640 TTGTATAAAC
Statistics
Matches: 100, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
39 5 0.05
41 74 0.74
42 15 0.15
43 6 0.06
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (40 bp):
AAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTAAC
Found at i:703598 original size:82 final size:81
Alignment explanation
Indices: 703436--703639 Score: 216
Period size: 82 Copynumber: 2.5 Consensus size: 81
703426 CGTTTATACC
* * * *
703436 ACAAACGCCGCAATAGAT-TACA-CATATAGTGGTATTTATTCTTAAAACGCCGCAATAATTATA
1 ACAAACGCCACAATAG-TGTA-ATCA-ATAGTGGCATTT-TTATAAAAACGCCGCAATAATTATA
*
703499 ATAAATAGTGGC-GTTTTTA
62 ATAAATAGTGGCATTTTTTA
* * * * *
703518 GGCAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTATAAAAATGCCGCAATAGTTTTAAT
1 -ACAAACGCCACAATAGTG-TAATCAATAGTGGCATTTTTATAAAAACGCCGCAATAATTATAAT
*
703583 CAATAGTGGCATTTTTTTA
64 AAATAGTGGCA-TTTTTTA
*
703602 ACAAACGCCACAATAGTGTAATTAATAGTGGCATTTTT
1 ACAAACGCCACAATAGTGTAATCAATAGTGGCATTTTT
703640 TTGTATAAAC
Statistics
Matches: 102, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
82 50 0.49
83 42 0.41
84 10 0.10
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (81 bp):
ACAAACGCCACAATAGTGTAATCAATAGTGGCATTTTTATAAAAACGCCGCAATAATTATAATAA
ATAGTGGCATTTTTTA
Found at i:703640 original size:41 final size:41
Alignment explanation
Indices: 703520--703641 Score: 165
Period size: 41 Copynumber: 3.0 Consensus size: 41
703510 CGTTTTTAGG
* *
703520 CAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTATAA
1 CAAACGCCACAATAGTG-TAATCAATAGTGGCATTTTTTTAA
* * *
703562 -AAATGCCGCAATAGTTTTAATCAATAGTGGCATTTTTTTAA
1 CAAACGCCACAATAG-TGTAATCAATAGTGGCATTTTTTTAA
*
703603 CAAACGCCACAATAGTGTAATTAATAGTGGCATTTTTTT
1 CAAACGCCACAATAGTGTAATCAATAGTGGCATTTTTTT
703642 GTATAAACGC
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
41 56 0.81
42 13 0.19
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (41 bp):
CAAACGCCACAATAGTGTAATCAATAGTGGCATTTTTTTAA
Found at i:705032 original size:42 final size:41
Alignment explanation
Indices: 704882--705348 Score: 478
Period size: 42 Copynumber: 11.2 Consensus size: 41
704872 TTGTATCTAG
* *
704882 AAACGCCGCTATAGA-TC-TGACATTTTGTGGCGTTTGT-ATCCAA
1 AAACGCCGCTATAGACTCGT-AC-TTTAGTGGCGTTT-TAAT--AC
* * * *
704925 AAACACCGCTATATACTAGTACTTTAGTGGCATTTCT-ATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTT-TAATAC
* * * *
704966 AAATGCCGCTATATACTCATACTTTAGTGGCGTTTTAAATCC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTT-AATAC
* * *
705008 AAACGCTGCTATAAACTCGTACTTTAGTGGCGTTTTGAATGC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTT-AATAC
* * *
705050 AAACGCCGCTAAAGACTCGTACTTTAGTAGCGTTTTTATA-
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTAATAC
* * * * *
705090 TAACGTCGCTATAGACTAGTACTTTAGTGGTGTTTTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTAATAC
* * * *
705131 AAACGTCGCTATAGACTCGTACTTTAGTGGTGTTTTTATAT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTAATAC
* * * *
705172 AAACGTCGCTATAGACTAGTACTTTAGTGGCATTTTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTAATAC
* *
705213 AAACGCCGCTATAGACTTGTACTTTAGTGGCGTTTTGAATGC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTT-AATAC
705255 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTAAATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTT-AATAC
* *
705297 AAACACCGCTA-ATGACTCGTACTTTAGTGGCGTTTGTATTTAC
1 AAACGCCGCTATA-GACTCGTACTTTAGTGGCGTTT-TA-ATAC
705340 AAACGCCGC
1 AAACGCCGC
705349 AATTTTACAG
Statistics
Matches: 366, Mismatches: 49, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
40 35 0.10
41 142 0.39
42 146 0.40
43 39 0.11
44 3 0.01
45 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (41 bp):
AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTAATAC
Found at i:707200 original size:35 final size:35
Alignment explanation
Indices: 707149--707223 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
707139 CGTCATGAAC
* * *
707149 AGTAAGGCCCTAAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTAAGCACAAAGCCGAAGAACCTCCA
*
707184 AGTAAGGCCCTGAGCACAAAGCCGAAGAACCTCCA
1 AGTAAGGCCCTAAGCACAAAGCCGAAGAACCTCCA
707219 AGTAA
1 AGTAA
707224 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.28, G:0.25, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTAAGCACAAAGCCGAAGAACCTCCA
Found at i:707328 original size:24 final size:24
Alignment explanation
Indices: 707301--707380 Score: 117
Period size: 24 Copynumber: 3.4 Consensus size: 24
707291 CATAATTCAA
*
707301 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
707325 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
707349 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
*
707372 GTCAGGTAT
1 GTCAAGTAT
707381 AATAACATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
23 21 0.43
24 28 0.57
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:719355 original size:21 final size:21
Alignment explanation
Indices: 719308--719358 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
719298 ATGAAGCAAG
**
719308 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGCCAGAGCAGCAGC
** *
719329 AAAAGCAGCCAGAGCAGCAGT
1 GGAAGCAGCCAGAGCAGCAGC
719350 GGAAGCAGC
1 GGAAGCAGC
719359 GACAGCCAGA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.37, T:0.02
Consensus pattern (21 bp):
GGAAGCAGCCAGAGCAGCAGC
Found at i:719838 original size:43 final size:42
Alignment explanation
Indices: 719735--719871 Score: 107
Period size: 43 Copynumber: 3.2 Consensus size: 42
719725 ATACCTATAC
* * *
719735 CGGCGCTTTTAGCAGAAATGCCGCAAAACATCAATACCTACTG
1 CGGCG-TTTTAGCAAAAATGCCACAAAACATCAACACCTACTG
* * * *
719778 TGGC-ATTTATGAAAAAAATGCCACAAGACATCAACACCTACTG
1 CGGCGTTTTA-G-CAAAAATGCCACAAAACATCAACACCTACTG
* * * * *
719821 CGGCGTTTTAGCGAAAAACGTCGCTAAACATCATA-ACCTATTG
1 CGGCGTTTTAGC-AAAAATGCCACAAAACATCA-ACACCTACTG
719864 CGGCGTTT
1 CGGCGTTT
719872 GTCTAAAAAC
Statistics
Matches: 73, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
41 4 0.05
42 1 0.01
43 63 0.86
44 5 0.07
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (42 bp):
CGGCGTTTTAGCAAAAATGCCACAAAACATCAACACCTACTG
Found at i:719908 original size:85 final size:86
Alignment explanation
Indices: 719807--720101 Score: 364
Period size: 86 Copynumber: 3.4 Consensus size: 86
719797 GCCACAAGAC
* * * *
719807 ATCAACACCTACTGCGGCG-TTTTAGCGAAAAACGTCGCTAAACATCATA-ACCTATTGCGGCGT
1 ATCAACACCTATTGCGGCGTTTTTA-TGAAAAACGCCGCTAAATATCA-ACACCTATTGCGGCGT
719870 TTGTCT-AAAAACGCTGCTAAAT
64 TTGTCTGAAAAACGCTGCTAAAT
* * * *
719892 ATTAACACCTATTGCGGCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTACGGCATTT
1 ATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
719957 GTCTGAAAAACGCTGCTAAAT
66 GTCTGAAAAACGCTGCTAAAT
719978 ATCAACACCTATTGCGGCGTTTTTATGACAAAA-GCCGCTAAATATCAACACCTATTGCGGCGTT
1 ATCAACACCTATTGCGGCGTTTTTATGA-AAAACGCCGCTAAATATCAACACCTATTGCGGCGTT
* *
720042 TGTCACACATGACAAACGCCGCTAAAT
65 TGT----C-TGAAAAACGCTGCTAAAT
* * *
720069 ATCAATACCTATTGCGGCATTTTTTGTGAAAAA
1 ATCAACACCTATTGCGGC-GTTTTTATGAAAAA
720102 ACGTCGCGAA
Statistics
Matches: 183, Mismatches: 17, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
84 1 0.01
85 53 0.29
86 80 0.44
87 3 0.02
90 1 0.01
91 37 0.20
92 8 0.04
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (86 bp):
ATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
GTCTGAAAAACGCTGCTAAAT
Found at i:719942 original size:43 final size:43
Alignment explanation
Indices: 719807--720101 Score: 310
Period size: 43 Copynumber: 6.7 Consensus size: 43
719797 GCCACAAGAC
* * * *
719807 ATCAACACCTACTGCGGCG-TTTTAGCGAAAAACGTCGCTAAAC
1 ATCAACACCTATTGCGGCGTTTTTA-TGAAAAACGCCGCTAAAT
* * *
719850 ATCATA-ACCTATTGCGGCGTTTGTCT-AAAAACGCTGCTAAAT
1 ATCA-ACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAAAT
* *
719892 ATTAACACCTATTGCGGCGTTTTTATGACAAACGCCGCTAAAT
1 ATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAAAT
* * * * *
719935 ATCAACACCTATTACGGCATTTGTCTGAAAAACGCTGCTAAAT
1 ATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAAAT
719978 ATCAACACCTATTGCGGCGTTTTTATGACAAAA-GCCGCTAAAT
1 ATCAACACCTATTGCGGCGTTTTTATGA-AAAACGCCGCTAAAT
* *
720021 ATCAACACCTATTGCGGCGTTTGTCACACATGACAAACGCCGCTAAAT
1 ATCAACACCTATTGCGGCGTTT-T----TATGAAAAACGCCGCTAAAT
* * *
720069 ATCAATACCTATTGCGGCATTTTTTGTGAAAAA
1 ATCAACACCTATTGCGGC-GTTTTTATGAAAAA
720102 ACGTCGCGAA
Statistics
Matches: 209, Mismatches: 31, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
41 1 0.00
42 34 0.16
43 121 0.58
44 15 0.07
47 3 0.01
48 32 0.15
49 3 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (43 bp):
ATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAAAT
Found at i:720080 original size:134 final size:128
Alignment explanation
Indices: 719833--720108 Score: 342
Period size: 128 Copynumber: 2.1 Consensus size: 128
719823 GCGTTTTAGC
* * *
719833 GAAAAACGTCGCTAAACATCATAACCTATTGCGGCGTTTGTCTAAAAACGCTGCTAAATATTAAC
1 GAAAAACGTCGCTAAACATCATAACCTATTGCGGCGTTTGTATAAAAACGCCGCTAAATATCAAC
*
719898 ACCTATTGCGGCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTACGGCATTTGTCT
66 ACCTATTGCGGCGTTTTCATGACAAACGCCGCTAAATATCAACACCTATTACGGCATTTGTCT
* *
719961 GAAAAACG-CTGCTAAATATCA-ACACCTATTGCGGCGTTTTTATGACAAAA-GCCGCTAAATAT
1 GAAAAACGTC-GCTAAACATCATA-ACCTATTGCGGCGTTTGTAT-A-AAAACGCCGCTAAATAT
* *
720023 CAACACCTATTGCGGCGTTTGTCACACATGACAAACGCCGCTAAATATCAATACCTATTGCGGCA
62 CAACACCTATTGCGGCGTTT-T----CATGACAAACGCCGCTAAATATCAACACCTATTACGGCA
* *
720088 TTTTTTGT
122 -TTTGTCT
720096 GAAAAAACGTCGC
1 G-AAAAACGTCGC
720109 GAACTTTAAC
Statistics
Matches: 126, Mismatches: 10, Indels: 16
0.83 0.07 0.11
Matches are distributed among these distances:
127 2 0.02
128 36 0.29
129 31 0.25
130 5 0.04
134 36 0.29
135 6 0.05
136 9 0.07
137 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (128 bp):
GAAAAACGTCGCTAAACATCATAACCTATTGCGGCGTTTGTATAAAAACGCCGCTAAATATCAAC
ACCTATTGCGGCGTTTTCATGACAAACGCCGCTAAATATCAACACCTATTACGGCATTTGTCT
Found at i:721388 original size:23 final size:24
Alignment explanation
Indices: 721362--721409 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
721352 CGGGTAAGAA
* *
721362 GGTTAA-AGTTAACGGGCCGAGTT
1 GGTTAACAGTGAACAGGCCGAGTT
*
721385 GGTTAACAGTGAACAGGTCGAGTT
1 GGTTAACAGTGAACAGGCCGAGTT
721409 G
1 G
721410 ACGGATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.25
Consensus pattern (24 bp):
GGTTAACAGTGAACAGGCCGAGTT
Found at i:721844 original size:24 final size:24
Alignment explanation
Indices: 721815--721863 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
721805 AACTCGACTC
721815 AAAATTTAAACTCAAATAGAAGAT
1 AAAATTTAAACTCAAATAGAAGAT
721839 AAAATTTAAACTCAAATAGAAGAT
1 AAAATTTAAACTCAAATAGAAGAT
721863 A
1 A
721864 TCACATTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.24
Consensus pattern (24 bp):
AAAATTTAAACTCAAATAGAAGAT
Found at i:722112 original size:18 final size:18
Alignment explanation
Indices: 722087--722135 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
722077 CCCAACCTTT
*
722087 TATTTAATTATTAGTATTA
1 TATTTAATTATTA-AATTA
*
722106 T-TTTAATTTTTAAATTA
1 TATTTAATTATTAAATTA
722123 TATTTATATTATT
1 TATTTA-ATTATT
722136 TTTCCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 5 0.20
18 14 0.56
19 6 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TATTTAATTATTAAATTA
Found at i:730335 original size:8 final size:8
Alignment explanation
Indices: 730322--730421 Score: 58
Period size: 8 Copynumber: 13.0 Consensus size: 8
730312 GAGAAAAGAT
730322 AGAAGAAA
1 AGAAGAAA
730330 AGAAGAAA
1 AGAAGAAA
730338 AGAAGAAA
1 AGAAGAAA
730346 AGGGAA-AAA
1 A--GAAGAAA
730355 TAGAA-AAA
1 -AGAAGAAA
730363 ATG-AGAATA
1 A-GAAGAA-A
*
730372 AAAAG-AA
1 AGAAGAAA
730379 A-AAGAAA
1 AGAAGAAA
730386 A-AA-AAA
1 AGAAGAAA
*
730392 AGAAGAGA
1 AGAAGAAA
730400 A-AAGATAA
1 AGAAGA-AA
730408 AG-AGAAA
1 AGAAGAAA
730415 AG-AGAAA
1 AGAAGAAA
730422 GAAAATAAAT
Statistics
Matches: 77, Mismatches: 3, Indels: 25
0.73 0.03 0.24
Matches are distributed among these distances:
6 7 0.09
7 24 0.31
8 35 0.45
9 7 0.09
10 4 0.05
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (8 bp):
AGAAGAAA
Done.