Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003914.1 Hibiscus syriacus cultivar Beakdansim tig00008465_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: 254784
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
File 1 of 2
Found at i:1900 original size:27 final size:26
Alignment explanation
Indices: 1857--1909 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 26
1847 AACTTATCTG
1857 CTTATGACTCTATCTGTGCTAGTCTT
1 CTTATGACTCTATCTGTGCTAGTCTT
1883 CTTATGACTTCTATCTGTGCTAGTCTT
1 CTTATGAC-TCTATCTGTGCTAGTCTT
1910 ACTTTTCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.47
Consensus pattern (26 bp):
CTTATGACTCTATCTGTGCTAGTCTT
Found at i:7582 original size:15 final size:14
Alignment explanation
Indices: 7563--7609 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
7553 AATAAATATT
7563 TTAAATTTAAAAAA
1 TTAAATTTAAAAAA
7577 TATAAATATTAAAAAA
1 T-TAAAT-TTAAAAAA
* *
7593 TTAAATATAAAATA
1 TTAAATTTAAAAAA
7607 TTA
1 TTA
7610 TTAATTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 10 0.34
15 10 0.34
16 9 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAAATTTAAAAAA
Found at i:7596 original size:24 final size:23
Alignment explanation
Indices: 7554--7609 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
7544 TAATTTATGA
** *
7554 ATAAATATTTTAAATTTAAAAAAT
1 ATAAATATTAAAAAATT-AAAAAT
*
7578 ATAAATATTAAAAAATTAAATAT
1 ATAAATATTAAAAAATTAAAAAT
7601 A-AAATATTA
1 ATAAATATTA
7610 TTAATTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 8 0.29
23 6 0.21
24 14 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATAAATATTAAAAAATTAAAAAT
Found at i:7669 original size:21 final size:19
Alignment explanation
Indices: 7640--7688 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
7630 AAAAAAAATC
7640 AATTA-TATTTAATTTTAAA
1 AATTATTATTT-ATTTTAAA
*
7659 ACATTATTATTTATTTTACA
1 A-ATTATTATTTATTTTAAA
7679 AATT-TTATTT
1 AATTATTATTT
7689 CCAGGCTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 6 0.22
19 4 0.15
20 12 0.44
21 5 0.19
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTATTATTTATTTTAAA
Found at i:18599 original size:32 final size:32
Alignment explanation
Indices: 18526--18730 Score: 182
Period size: 32 Copynumber: 6.2 Consensus size: 32
18516 GATTACAACT
*
18526 TAAAACAAGTTCTAACCTAAAATA---GTATC
1 TAAAACAAGTTCCAACCTAAAATATGGGTATC
* *
18555 CAAAAGCAAGTTCCAACTTAAAATATGGGTATC
1 TAAAA-CAAGTTCCAACCTAAAATATGGGTATC
* * * *
18588 TAAAACAAGTTCTAACCTACAATATGGTTGCAACC
1 TAAAACAAGTTCCAACCTAAAATATGG--G-TATC
*
18623 TAAAATCAAGTTCCAACTTAAAATATGGGTATC
1 TAAAA-CAAGTTCCAACCTAAAATATGGGTATC
* * *
18656 TAAAACAAGTTTCAACCTAAAATATGGTTGCAACC
1 TAAAACAAGTTCCAACCTAAAATATGG--G-TATC
* * *
18691 TAAAAACAAGTTCCAACTTAAAATACGAGTATC
1 T-AAAACAAGTTCCAACCTAAAATATGGGTATC
18724 TAAAACA
1 TAAAACA
18731 TTCACCCTAA
Statistics
Matches: 140, Mismatches: 24, Indels: 21
0.76 0.13 0.11
Matches are distributed among these distances:
29 4 0.03
30 17 0.12
32 45 0.32
33 19 0.14
34 4 0.03
35 10 0.07
36 41 0.29
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (32 bp):
TAAAACAAGTTCCAACCTAAAATATGGGTATC
Found at i:18635 original size:36 final size:35
Alignment explanation
Indices: 18504--18715 Score: 153
Period size: 32 Copynumber: 6.3 Consensus size: 35
18494 TTTGATTTTC
* * * *
18504 AACCTAAAATACGATTACAACTTAAAACAAGTTCT
1 AACCTAAAATATGGTTGCAACCTAAAACAAGTTCT
* *
18539 AACCTAAAATA--G-T--ATCC-AAAAGCAAGTTCC
1 AACCTAAAATATGGTTGCAACCTAAAA-CAAGTTCT
* * *
18569 AACTTAAAATATGG--G-TATCTAAAACAAGTTCT
1 AACCTAAAATATGGTTGCAACCTAAAACAAGTTCT
* *
18601 AACCTACAATATGGTTGCAACCTAAAATCAAGTTCC
1 AACCTAAAATATGGTTGCAACCTAAAA-CAAGTTCT
* * *
18637 AACTTAAAATATGG--G-TATCTAAAACAAGTT-T
1 AACCTAAAATATGGTTGCAACCTAAAACAAGTTCT
*
18668 CAACCTAAAATATGGTTGCAACCTAAAAACAAGTTCC
1 -AACCTAAAATATGGTTGCAACCT-AAAACAAGTTCT
*
18705 AACTTAAAATA
1 AACCTAAAATA
18716 CGAGTATCTA
Statistics
Matches: 138, Mismatches: 24, Indels: 29
0.72 0.13 0.15
Matches are distributed among these distances:
29 4 0.03
30 19 0.14
32 41 0.30
33 11 0.08
34 3 0.02
35 21 0.15
36 39 0.28
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (35 bp):
AACCTAAAATATGGTTGCAACCTAAAACAAGTTCT
Found at i:18639 original size:18 final size:18
Alignment explanation
Indices: 18587--18714 Score: 56
Period size: 18 Copynumber: 7.4 Consensus size: 18
18577 ATATGGGTAT
*
18587 CTAAAA-CAAGTTCTAAC
1 CTAAAATCAAGTTCCAAC
* * *
18604 CTACAAT-ATGGTTGCAAC
1 CTAAAATCA-AGTTCCAAC
18622 CTAAAATCAAGTTCCAAC
1 CTAAAATCAAGTTCCAAC
* * * *
18640 TTAAAAT-ATGGGT---AT
1 CTAAAATCA-AGTTCCAAC
*
18655 CTAAAA-CAAGTTTCAAC
1 CTAAAATCAAGTTCCAAC
* *
18672 CTAAAAT-ATGGTTGCAAC
1 CTAAAATCA-AGTTCCAAC
*
18690 CTAAAAACAAGTTCCAAC
1 CTAAAATCAAGTTCCAAC
*
18708 TTAAAAT
1 CTAAAAT
18715 ACGAGTATCT
Statistics
Matches: 78, Mismatches: 22, Indels: 21
0.64 0.18 0.17
Matches are distributed among these distances:
14 2 0.03
15 7 0.09
17 15 0.19
18 52 0.67
19 2 0.03
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (18 bp):
CTAAAATCAAGTTCCAAC
Found at i:18673 original size:68 final size:68
Alignment explanation
Indices: 18556--18730 Score: 289
Period size: 68 Copynumber: 2.6 Consensus size: 68
18546 AATAGTATCC
* *
18556 AAAAGCAAGTTCCAACTTAAAATATGGGTATCTAAAACAAGTTCTAACCTACAATATGGTTGCAA
1 AAAAACAAGTTCCAACTTAAAATATGGGTATCTAAAACAAGTTCTAACCTAAAATATGGTTGCAA
18621 CCT
66 CCT
*
18624 AAAATCAAGTTCCAACTTAAAATATGGGTATCTAAAACAAGTT-TCAACCTAAAATATGGTTGCA
1 AAAAACAAGTTCCAACTTAAAATATGGGTATCTAAAACAAGTTCT-AACCTAAAATATGGTTGCA
18688 ACCT
65 ACCT
* *
18692 AAAAACAAGTTCCAACTTAAAATACGAGTATCTAAAACA
1 AAAAACAAGTTCCAACTTAAAATATGGGTATCTAAAACA
18731 TTCACCCTAA
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
67 1 0.01
68 100 0.99
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (68 bp):
AAAAACAAGTTCCAACTTAAAATATGGGTATCTAAAACAAGTTCTAACCTAAAATATGGTTGCAA
CCT
Found at i:19460 original size:31 final size:29
Alignment explanation
Indices: 19404--19466 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 29
19394 TTAATTTAAT
* *
19404 TACCAAAAGTATTTTTTGATTAAAATACG
1 TACCAAAAGTATTTTTTGATCAAAATAAG
* *
19433 TACCTAAAATTATATTTTTGGTCAAAATAAG
1 TACC-AAAAGTAT-TTTTTGATCAAAATAAG
19464 TAC
1 TAC
19467 TTAATGTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 4 0.14
30 7 0.25
31 17 0.61
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (29 bp):
TACCAAAAGTATTTTTTGATCAAAATAAG
Found at i:23560 original size:31 final size:31
Alignment explanation
Indices: 23522--23644 Score: 129
Period size: 31 Copynumber: 4.0 Consensus size: 31
23512 ACATGGTCTC
**
23522 TAATGTTATCGATTTGTTCGATTATAGTCCA
1 TAATGTTATCGATCCGTTCGATTATAGTCCA
* * * *
23553 TAATGTTATTGATCTGTTCGATTATAATACA
1 TAATGTTATCGATCCGTTCGATTATAGTCCA
* * *
23584 TAATGTTATCGATCCGTTTGATTATGGTCCT
1 TAATGTTATCGATCCGTTCGATTATAGTCCA
* * * *
23615 TAATATTATCGATTCATTCGATTTTAGTCC
1 TAATGTTATCGATCCGTTCGATTATAGTCC
23645 CTCAGTTGTT
Statistics
Matches: 75, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.46
Consensus pattern (31 bp):
TAATGTTATCGATCCGTTCGATTATAGTCCA
Found at i:25602 original size:10 final size:10
Alignment explanation
Indices: 25570--25596 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
25560 CATTTAGGAC
25570 CATTTAGATG
1 CATTTAGATG
25580 CATTTAGATG
1 CATTTAGATG
25590 CATTTAG
1 CATTTAG
25597 GAGCATATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (10 bp):
CATTTAGATG
Found at i:25602 original size:20 final size:20
Alignment explanation
Indices: 25570--25612 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
25560 CATTTAGGAC
*
25570 CATTTAGATGCATTTAGATG
1 CATTTAGATGCATATAGATG
*
25590 CATTTAGGA-GCATATAGTTG
1 CATTTA-GATGCATATAGATG
25610 CAT
1 CAT
25613 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGATGCATATAGATG
Found at i:26564 original size:112 final size:112
Alignment explanation
Indices: 26367--26590 Score: 439
Period size: 112 Copynumber: 2.0 Consensus size: 112
26357 TTGTAAGGAA
26367 CGAATGAATCTTGCTTTGTGCTTGTTGATTTCGAGCCCCACCATGAACTAATCCTATTTGGTGGG
1 CGAATGAATCTTGCTTTGTGCTTGTTGATTTCGAGCCCCACCATGAACTAATCCTATTTGGTGGG
*
26432 AGTTTGCATGGTTATTTAAGTTGTTATTTTAATGAATGGTTGTTGTT
66 AGTTCGCATGGTTATTTAAGTTGTTATTTTAATGAATGGTTGTTGTT
26479 CGAATGAATCTTGCTTTGTGCTTGTTGATTTCGAGCCCCACCATGAACTAATCCTATTTGGTGGG
1 CGAATGAATCTTGCTTTGTGCTTGTTGATTTCGAGCCCCACCATGAACTAATCCTATTTGGTGGG
26544 AGTTCGCATGGTTATTTAAGTTGTTATTTTAATGAATGGTTGTTGTT
66 AGTTCGCATGGTTATTTAAGTTGTTATTTTAATGAATGGTTGTTGTT
26591 TCATGCTCTA
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (112 bp):
CGAATGAATCTTGCTTTGTGCTTGTTGATTTCGAGCCCCACCATGAACTAATCCTATTTGGTGGG
AGTTCGCATGGTTATTTAAGTTGTTATTTTAATGAATGGTTGTTGTT
Found at i:29468 original size:18 final size:18
Alignment explanation
Indices: 29441--29510 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
29431 TTAAGGAGTA
*
29441 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
29459 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
* *
29481 GTCCTTCGGGATATAGTG
1 GTCCTACGGGACATAGTG
29499 GTCCTACGGGAC
1 GTCCTACGGGAC
29511 GAATACTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 25 0.58
20 4 0.09
22 14 0.33
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:35410 original size:17 final size:17
Alignment explanation
Indices: 35388--35421 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35378 CATCTTGCTA
35388 GCGGTGGATTACGTTTC
1 GCGGTGGATTACGTTTC
35405 GCGGTGGATTACGTTTC
1 GCGGTGGATTACGTTTC
35422 AAAGTGGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.18, G:0.35, T:0.35
Consensus pattern (17 bp):
GCGGTGGATTACGTTTC
Found at i:40060 original size:71 final size:70
Alignment explanation
Indices: 39944--40086 Score: 268
Period size: 71 Copynumber: 2.0 Consensus size: 70
39934 GAAGGCATTT
39944 GGCAGTGCACGTCGAAGGCTTTCTCTCCTCCCCTTAGACCTTGCTTTTATATTTTTGTTGTTGGG
1 GGCAGTGCACGTCGAAGGCTTTCTCTCCTCCCCTTAGACCTTGCTTTTATA-TTTTGTTGTTGGG
40009 TTGTAA
65 TTGTAA
*
40015 GGCAGTGCACGTCGAAGGCTTTCTCTCCTCCCCTTAGTCCTTGCTTTTATATTTTGTTGTTGGGT
1 GGCAGTGCACGTCGAAGGCTTTCTCTCCTCCCCTTAGACCTTGCTTTTATATTTTGTTGTTGGGT
40080 TGTAA
66 TGTAA
40085 GG
1 GG
40087 AACGAATGAA
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
70 21 0.30
71 50 0.70
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.41
Consensus pattern (70 bp):
GGCAGTGCACGTCGAAGGCTTTCTCTCCTCCCCTTAGACCTTGCTTTTATATTTTGTTGTTGGGT
TGTAA
Found at i:44051 original size:2 final size:2
Alignment explanation
Indices: 44044--44070 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44034 GCCCACACTC
44044 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
44071 AAGAACCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45143 original size:22 final size:21
Alignment explanation
Indices: 45096--45145 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
45086 GAATATTTGA
*
45096 TAAAATTAAATAAATAGACTT
1 TAAAATTAAATAAATAGAATT
* **
45117 AAAAATATAAATAAATTTAATT
1 TAAAAT-TAAATAAATAGAATT
45139 TAAAATT
1 TAAAATT
45146 GAAGAAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAATTAAATAAATAGAATT
Found at i:49853 original size:37 final size:37
Alignment explanation
Indices: 49779--49853 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
49769 TATTATAATT
**
49779 AATTTATATATTTTCTTTAAAAAATTTAAATTCATAA
1 AATTTATATATTTTCTTTAAAAAATTTAAAAACATAA
* * *
49816 AATTTATATAATTTTTTTTACAAAA-TTAAAAAGATAA
1 AATTTATAT-ATTTTCTTTAAAAAATTTAAAAACATAA
49853 A
1 A
49854 TAGGTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 19 0.59
38 13 0.41
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
AATTTATATATTTTCTTTAAAAAATTTAAAAACATAA
Found at i:50370 original size:2 final size:2
Alignment explanation
Indices: 50363--50388 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50353 TCAGAGGTTT
50363 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
50389 ACTTATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51838 original size:13 final size:13
Alignment explanation
Indices: 51820--51891 Score: 93
Period size: 13 Copynumber: 6.0 Consensus size: 13
51810 ACCGGTCAAC
51820 GGTCAACGGGTCG
1 GGTCAACGGGTCG
51833 GGTCAA-----CG
1 GGTCAACGGGTCG
51841 G-TCAACGGGTCG
1 GGTCAACGGGTCG
51853 GGTCAACGGGTCG
1 GGTCAACGGGTCG
51866 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
51879 GGTAAACGGGTCG
1 GGTCAACGGGTCG
51892 TGACCGGTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
7 4 0.08
8 3 0.06
12 3 0.06
13 42 0.81
ACGTcount: A:0.18, C:0.22, G:0.44, T:0.15
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:51838 original size:20 final size:20
Alignment explanation
Indices: 51813--51861 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
51803 TAATAGCACC
51813 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGTCAACGGGTCG
51833 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGTCAACGGGTCG
51853 GGTCAACGG
1 GGTCAACGG
51862 GTCGGGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.41, T:0.14
Consensus pattern (20 bp):
GGTCAACGGTCAACGGGTCG
Found at i:51908 original size:9 final size:10
Alignment explanation
Indices: 51894--51948 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
51884 ACGGGTCGTG
51894 ACCGGTC-AA
1 ACCGGTCAAA
51903 ACCGGTCAAA
1 ACCGGTCAAA
51913 ACCGGTTCAAA
1 ACCGG-TCAAA
*
51924 ACCGGT-TAA
1 ACCGGTCAAA
*
51933 ACCAGTCAAA
1 ACCGGTCAAA
51943 ACCGGT
1 ACCGGT
51949 TTCCAGCGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
9 14 0.36
10 15 0.38
11 10 0.26
ACGTcount: A:0.36, C:0.29, G:0.20, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:51916 original size:19 final size:20
Alignment explanation
Indices: 51894--51948 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
51884 ACGGGTCGTG
51894 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGTCAAA
*
51913 ACCGGTTCAAAACCGGT-TAA
1 ACCGG-TCAAAACCGGTCAAA
*
51933 ACCAGTCAAAACCGGT
1 ACCGGTCAAAACCGGT
51949 TTCCAGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.50
20 8 0.25
21 8 0.25
ACGTcount: A:0.36, C:0.29, G:0.20, T:0.15
Consensus pattern (20 bp):
ACCGGTCAAAACCGGTCAAA
Found at i:59095 original size:13 final size:13
Alignment explanation
Indices: 59077--59126 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
59067 ACCGGTCAAC
59077 GGTCAACGGGTCG
1 GGTCAACGGGTCG
59090 GGTCAA-----CG
1 GGTCAACGGGTCG
59098 G-TCAACGGGTCG
1 GGTCAACGGGTCG
59110 GGTCAACGGGTCG
1 GGTCAACGGGTCG
59123 GGTC
1 GGTC
59127 GGGTCAACGG
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
7 4 0.13
8 3 0.10
12 3 0.10
13 21 0.68
ACGTcount: A:0.16, C:0.24, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:59095 original size:20 final size:20
Alignment explanation
Indices: 59070--59136 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
59060 TAATAGCACC
59070 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGTCAACGGGTCG
59090 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGTCAACGGGTCG
59110 GGTCAACGGGT---CGGGTCG
1 GGTCAAC-GGTCAACGGGTCG
59128 GGTCAACGG
1 GGTCAACGG
59137 GTCGGGTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.04
18 14 0.30
20 27 0.59
21 3 0.07
ACGTcount: A:0.18, C:0.24, G:0.43, T:0.15
Consensus pattern (20 bp):
GGTCAACGGTCAACGGGTCG
Found at i:59126 original size:18 final size:18
Alignment explanation
Indices: 59083--59143 Score: 88
Period size: 18 Copynumber: 3.3 Consensus size: 18
59073 CAACGGTCAA
59083 CGGGTCGGGTCAAC-GGT
1 CGGGTCGGGTCAACGGGT
59100 CAACGGGTCGGGTCAACGGGT
1 ---CGGGTCGGGTCAACGGGT
59121 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
59139 CGGGT
1 CGGGT
59144 AAACGGGTCG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
18 23 0.57
20 14 0.35
21 3 0.08
ACGTcount: A:0.13, C:0.23, G:0.48, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:59135 original size:31 final size:32
Alignment explanation
Indices: 59077--59153 Score: 120
Period size: 31 Copynumber: 2.4 Consensus size: 32
59067 ACCGGTCAAC
59077 GGTCAACGGGTCGGGTCAACGGTCAACGGGTCG
1 GGTCAACGGGTCGGGTC-ACGGTCAACGGGTCG
*
59110 GGTCAACGGGTCGGGTC-GGGTCAACGGGTCG
1 GGTCAACGGGTCGGGTCACGGTCAACGGGTCG
*
59141 GGTAAACGGGTCG
1 GGTCAACGGGTCG
59154 TGACCGGTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 25 0.60
33 17 0.40
ACGTcount: A:0.17, C:0.22, G:0.45, T:0.16
Consensus pattern (32 bp):
GGTCAACGGGTCGGGTCACGGTCAACGGGTCG
Found at i:59143 original size:13 final size:13
Alignment explanation
Indices: 59097--59126 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
59087 TCGGGTCAAC
59097 GGTCAACGGGTCG
1 GGTCAACGGGTCG
59110 GGTCAACGGGTCG
1 GGTCAACGGGTCG
59123 GGTC
1 GGTC
59127 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:59148 original size:13 final size:13
Alignment explanation
Indices: 59121--59153 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
59111 GTCAACGGGT
*
59121 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
59134 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
59147 CGGGTCG
1 CGGGTCG
59154 TGACCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:59163 original size:31 final size:31
Alignment explanation
Indices: 59081--59164 Score: 105
Period size: 31 Copynumber: 2.6 Consensus size: 31
59071 GTCAACGGTC
* *
59081 AACGGGTCGGGTCAACGGTCAACGGGTCGGGTC
1 AACGGGTCGGG--ACCGGTCAACGGGTCGGGTA
* *
59114 AACGGGTCGGGTCGGGTCAACGGGTCGGGTA
1 AACGGGTCGGGACCGGTCAACGGGTCGGGTA
*
59145 AACGGGTCGTGACCGGTCAA
1 AACGGGTCGGGACCGGTCAA
59165 ACCGGTCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 33 0.75
33 11 0.25
ACGTcount: A:0.19, C:0.23, G:0.43, T:0.15
Consensus pattern (31 bp):
AACGGGTCGGGACCGGTCAACGGGTCGGGTA
Found at i:59176 original size:10 final size:10
Alignment explanation
Indices: 59156--59210 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
59146 ACGGGTCGTG
59156 ACCGGTC-AA
1 ACCGGTCAAA
59165 ACCGGTCAAA
1 ACCGGTCAAA
59175 ACCGGTTCAAA
1 ACCGG-TCAAA
*
59186 ACCGGT-TAA
1 ACCGGTCAAA
59195 ACCGGTCAAA
1 ACCGGTCAAA
59205 ACCGGT
1 ACCGGT
59211 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:59211 original size:19 final size:19
Alignment explanation
Indices: 59156--59211 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
59146 ACGGGTCGTG
*
59156 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
59175 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
59195 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
59212 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:69999 original size:19 final size:19
Alignment explanation
Indices: 69975--70014 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
69965 AAAAGTAGTC
69975 AATATCACAATTTACTATA
1 AATATCACAATTTACTATA
*
69994 AATATCACAGTTTACTATA
1 AATATCACAATTTACTATA
70013 AA
1 AA
70015 AATTAAAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (19 bp):
AATATCACAATTTACTATA
Found at i:71314 original size:2 final size:2
Alignment explanation
Indices: 71264--71306 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
71254 ATTTTTGAAG
71264 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
71306 A
1 A
71307 GTTATATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72717 original size:21 final size:21
Alignment explanation
Indices: 72657--72891 Score: 180
Period size: 20 Copynumber: 11.6 Consensus size: 21
72647 TTTCCTAATA
*
72657 CGCAATGCGAA-TACGTAAAC
1 CGCAATGCGAATTACGTAAAT
*
72677 CGCAACGCG-ATTACGTAAAT
1 CGCAATGCGAATTACGTAAAT
* *
72697 CGCAATGCGAATTAGGAAAAT
1 CGCAATGCGAATTACGTAAAT
* *
72718 CGCAATGTG-ATTACGT-ATT
1 CGCAATGCGAATTACGTAAAT
* * * * *
72737 CGCATTGCGATTTTCCTAATT
1 CGCAATGCGAATTACGTAAAT
* * *
72758 CGCATTGCGATTTACGT-ATT
1 CGCAATGCGAATTACGTAAAT
** * * * *
72778 CGCGTTGCGATTTTCCTAATT
1 CGCAATGCGAATTACGTAAAT
*
72799 CGCAAAGCGAA-TACGTAAAT
1 CGCAATGCGAATTACGTAAAT
* *
72819 CGCAACGCG-ATTACCTAAAT
1 CGCAATGCGAATTACGTAAAT
* *
72839 CGCAATGCGAATTAAGAAAAT
1 CGCAATGCGAATTACGTAAAT
72860 CGCAATGCGAA-TACGTAAAT
1 CGCAATGCGAATTACGTAAAT
*
72880 AGCAATGCGAAT
1 CGCAATGCGAAT
72892 CTGACTATCG
Statistics
Matches: 172, Mismatches: 35, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
19 11 0.06
20 97 0.56
21 64 0.37
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (21 bp):
CGCAATGCGAATTACGTAAAT
Found at i:72722 original size:41 final size:40
Alignment explanation
Indices: 72657--72734 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
72647 TTTCCTAATA
*
72657 CGCAATGCGAATACGTAAACCGCAACGCGATTACGTAAAT
1 CGCAATGCGAATACGAAAACCGCAACGCGATTACGTAAAT
* * * *
72697 CGCAATGCGAATTAGGAAAATCGCAATGTGATTACGTA
1 CGCAATGCGAA-TACGAAAACCGCAACGCGATTACGTA
72735 TTCGCATTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
40 11 0.34
41 21 0.66
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (40 bp):
CGCAATGCGAATACGAAAACCGCAACGCGATTACGTAAAT
Found at i:72810 original size:142 final size:143
Alignment explanation
Indices: 72614--72876 Score: 429
Period size: 142 Copynumber: 1.8 Consensus size: 143
72604 ATTCTGACTA
* *
72614 TCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAATACGCAATGCGAATACGTAAACCG
1 TCGCATTGCGATTTCACAAATTCGCGTTGCGATTTTCCTAATACGCAAAGCGAATACGTAAACCG
* * * *
72679 CAACGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGTGATTACGTATTCGCATTG
66 CAACGCGATTACCTAAATCGCAATGCGAATTAAGAAAATCGCAATGCGAATACGTATTCGCATTG
72744 CGATTTTCCTAAT
131 CGATTTTCCTAAT
** * *
72757 TCGCATTGCGATTT-ACGTATTCGCGTTGCGATTTTCCTAATTCGCAAAGCGAATACGTAAATCG
1 TCGCATTGCGATTTCACAAATTCGCGTTGCGATTTTCCTAATACGCAAAGCGAATACGTAAACCG
72821 CAACGCGATTACCTAAATCGCAATGCGAATTAAGAAAATCGCAATGCGAATACGTA
66 CAACGCGATTACCTAAATCGCAATGCGAATTAAGAAAATCGCAATGCGAATACGTA
72877 AATAGCAATG
Statistics
Matches: 110, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
142 96 0.87
143 14 0.13
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (143 bp):
TCGCATTGCGATTTCACAAATTCGCGTTGCGATTTTCCTAATACGCAAAGCGAATACGTAAACCG
CAACGCGATTACCTAAATCGCAATGCGAATTAAGAAAATCGCAATGCGAATACGTATTCGCATTG
CGATTTTCCTAAT
Found at i:72829 original size:41 final size:41
Alignment explanation
Indices: 72677--72869 Score: 140
Period size: 41 Copynumber: 4.7 Consensus size: 41
72667 ATACGTAAAC
* * * **** *
72677 CGCAACGCGATTACGTAAATCGCAATGCGAATTAGGAAAAT
1 CGCAATGCGAATACGTAAATCGCAATGCGATTTTCCTAATT
* * * *
72718 CGCAATGTGATTACGT-ATTCGCATTGCGATTTTCCTAATT
1 CGCAATGCGAATACGTAAATCGCAATGCGATTTTCCTAATT
* * * **
72758 CGCATTGCGATTTACGT-ATTCGCGTTGCGATTTTCCTAATT
1 CGCAATGCGA-ATACGTAAATCGCAATGCGATTTTCCTAATT
* * * *
72799 CGCAAAGCGAATACGTAAATCGCAACGCGA-TTACCTAAAT
1 CGCAATGCGAATACGTAAATCGCAATGCGATTTTCCTAATT
* *
72839 CGCAATGCGAATTAAGAAAATCGCAATGCGA
1 CGCAATGCGAA-TACGTAAATCGCAATGCGA
72870 ATACGTAAAT
Statistics
Matches: 123, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
40 47 0.38
41 76 0.62
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (41 bp):
CGCAATGCGAATACGTAAATCGCAATGCGATTTTCCTAATT
Found at i:72879 original size:41 final size:41
Alignment explanation
Indices: 72792--72891 Score: 121
Period size: 41 Copynumber: 2.5 Consensus size: 41
72782 TTGCGATTTT
* * * * *
72792 CCTAATTCGCAAAGCGAA-TACGTAAATCGCAACGCGATTA
1 CCTAAATCGCAATGCGAATTAAGAAAATCGCAACGCGAATA
*
72832 CCTAAATCGCAATGCGAATTAAGAAAATCGCAATGCGAATA
1 CCTAAATCGCAATGCGAATTAAGAAAATCGCAACGCGAATA
* *
72873 CGTAAATAGCAATGCGAAT
1 CCTAAATCGCAATGCGAAT
72892 CTGACTATCG
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 16 0.31
41 35 0.69
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (41 bp):
CCTAAATCGCAATGCGAATTAAGAAAATCGCAACGCGAATA
Found at i:72903 original size:142 final size:141
Alignment explanation
Indices: 72596--72915 Score: 426
Period size: 142 Copynumber: 2.2 Consensus size: 141
72586 TTCCAGATTC
* * *
72596 GCAACGCGATTCTGACTATCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAATACGCA
1 GCAATGCGAATCTGACTATCGCATTGCGATTT-ACAAATTCGCGTTGCGATTTTCCTAATACGCA
* * * *
72661 ATGCGAATACGTAAACCGCAACGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGT
65 AAGCGAATACGTAAACCGCAACGCGATTACCTAAATCGCAATGCGAATTAAGAAAATCGCAATGC
* * *
72726 GATTACGTATTC
130 GAATACGTAATA
* * ** ** *
72738 GCATTGCG-ATTTTCCTAATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCCTAATTCGC
1 GCAATGCGAATCTGACT-A-TCGCATTGCGATTTACAAATTCGCGTTGCGATTTTCCTAATACGC
*
72802 AAAGCGAATACGTAAATCGCAACGCGATTACCTAAATCGCAATGCGAATTAAGAAAATCGCAATG
64 AAAGCGAATACGTAAACCGCAACGCGATTACCTAAATCGCAATGCGAATTAAGAAAATCGCAATG
72867 CGAATACGTAAATA
129 CGAATACGT-AATA
*
72881 GCAATGCGAATCTGACTATCGCAATGCGATTTACA
1 GCAATGCGAATCTGACTATCGCATTGCGATTTACA
72916 TAGCGCCATT
Statistics
Matches: 150, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
141 4 0.03
142 117 0.78
143 24 0.16
144 5 0.03
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (141 bp):
GCAATGCGAATCTGACTATCGCATTGCGATTTACAAATTCGCGTTGCGATTTTCCTAATACGCAA
AGCGAATACGTAAACCGCAACGCGATTACCTAAATCGCAATGCGAATTAAGAAAATCGCAATGCG
AATACGTAATA
Found at i:73466 original size:20 final size:19
Alignment explanation
Indices: 73441--73512 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
73431 TTCTAAACTT
73441 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
73461 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
** *
73481 ACTATCGCAATGAGAGAAATG
1 AAAATCGCAA-CAGA-AAATG
73502 AAAATCGCAAC
1 AAAATCGCAAC
73513 GAGACAATCG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.51, C:0.18, G:0.17, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:73523 original size:14 final size:14
Alignment explanation
Indices: 73501--73565 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
73491 TGAGAGAAAT
73501 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
73515 GACAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
73533 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
73548 GATAATCGCAACGC
1 GAAAATCGCAACGA
73562 GAAA
1 GAAA
73566 CCAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:73535 original size:33 final size:33
Alignment explanation
Indices: 73496--73576 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
73486 CGCAATGAGA
73496 GAAATGAAAATCGCAACGAGACAATCGCAACGC
1 GAAATGAAAATCGCAACGAGACAATCGCAACGC
*
73529 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGACAATCGCAACGC
**
73562 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
73577 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGACAATCGCAACGC
Found at i:73594 original size:19 final size:19
Alignment explanation
Indices: 73572--73731 Score: 98
Period size: 19 Copynumber: 9.1 Consensus size: 19
73562 GAAACCAAAA
*
73572 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
73591 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
73605 TCTCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
73624 TCGTGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
73638 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
73657 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
73671 TCTCGTTACGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
73690 TACACGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
73710 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
73730 TC
1 TC
73732 AACCAAAAGA
Statistics
Matches: 107, Mismatches: 17, Indels: 34
0.68 0.11 0.22
Matches are distributed among these distances:
14 27 0.25
16 8 0.07
17 9 0.08
19 31 0.29
20 31 0.29
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:73622 original size:33 final size:33
Alignment explanation
Indices: 73580--73703 Score: 194
Period size: 33 Copynumber: 3.7 Consensus size: 33
73570 AATCGCATTG
73580 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTA
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTA
* *
73613 CGATTTTCATTTCGTGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTA
73646 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTA
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTA
** *
73679 CGATAGTCATTTACACGTTGCGATT
1 CGATTTTCATTT-CGCGTTGCGATT
73704 TTCATTCTCT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 72 0.87
34 11 0.13
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTCTCTCGTTA
Found at i:73647 original size:14 final size:14
Alignment explanation
Indices: 73594--73682 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
73584 TTTCATTTCG
73594 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
73608 CGTTACGATTTTCATTT
1 CGTTGCGA--TTC-TCT
73625 CGTGTTGCGATTCTCT
1 C--GTTGCGATTCTCT
*
73641 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
73660 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
73674 CGTTACGAT
1 CGTTGCGAT
73683 AGTCATTTAC
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 24 0.41
16 9 0.16
17 9 0.16
19 16 0.28
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:73689 original size:66 final size:68
Alignment explanation
Indices: 73577--73731 Score: 215
Period size: 66 Copynumber: 2.2 Consensus size: 68
73567 CAAAATCGCA
** **
73577 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTACGATTTTCATTT-CGTGTTGCG-ATTCTC
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTACGATAGTCATTTACACGTTGCGTATTCTC
73640 TCG
66 TCG
73643 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTACGATAGTCATTTACACGTTGCGATTTTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTACGATAGTCATTTACACGTTGCG----T-A
73708 TTCTCTCG
61 TTCTCTCG
73716 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
73732 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
66 46 0.59
67 7 0.09
73 25 0.32
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (68 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTACGATAGTCATTTACACGTTGCGTATTCTC
TCG
Found at i:73708 original size:20 final size:19
Alignment explanation
Indices: 73577--73732 Score: 81
Period size: 20 Copynumber: 8.9 Consensus size: 19
73567 CAAAATCGCA
*
73577 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCACG
*
73596 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCACG
* **
73610 TTACGATTTTCATTTCGTG
1 TTGCGATTTTCATTTCACG
*
73629 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCACG
*
73643 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCACG
*
73662 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCACG
* **
73676 TTACGATAGTCATTTACACG
1 TTGCGATTTTCATTT-CACG
*
73696 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATT-TCACG
73716 TTGCGATTTTCATTTCA
1 TTGCGATTTTCATTTCA
73733 ACCAAAAGAC
Statistics
Matches: 103, Mismatches: 17, Indels: 34
0.67 0.11 0.22
Matches are distributed among these distances:
14 27 0.26
16 8 0.08
17 9 0.09
19 27 0.26
20 31 0.30
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACG
Found at i:75609 original size:94 final size:93
Alignment explanation
Indices: 75421--75796 Score: 553
Period size: 94 Copynumber: 4.1 Consensus size: 93
75411 TAGATTGCTT
* * *
75421 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTCAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
75482 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
* *
75511 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
75576 ATTTGTCTTTGTTTTATCTTTTGGATGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
75605 AGTAAATTTGTTTGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
75670 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
75699 AGTAAATTTGTTCGTTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
75764 ATTTATCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
75792 AGTAA
1 AGTAA
75797 TGCAATCCAT
Statistics
Matches: 261, Mismatches: 20, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
90 34 0.13
92 3 0.01
93 26 0.10
94 198 0.76
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:75914 original size:20 final size:19
Alignment explanation
Indices: 75887--75963 Score: 109
Period size: 19 Copynumber: 4.0 Consensus size: 19
75877 TCTTTTGGTT
75887 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
75906 GAGAATGAAAATTGCAACGC
1 GA-AATGAAAATCGCAACGA
* *
75926 GAAACGAAAATCGCAACGT
1 GAAATGAAAATCGCAACGA
75945 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
75964 CAAAATCGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
19 33 0.66
20 17 0.34
ACGTcount: A:0.49, C:0.17, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:75935 original size:39 final size:38
Alignment explanation
Indices: 75887--76011 Score: 125
Period size: 39 Copynumber: 3.4 Consensus size: 38
75877 TCTTTTGGTT
* *
75887 GAAATGAAAATCGCAACGAGAGAATGAAAATTGCAACGC
1 GAAACGAAAATCGCAACGAGA-AATGAAAATCGCAACGC
*
75926 GAAACGAAAATCGCAACGTGAAATGAAAATCGCAA--C
1 GAAACGAAAATCGCAACGAGAAATGAAAATCGCAACGC
* **
75962 G--AC-AAAATCGCAACGCGAAACCAAAAATCGCAACGC
1 GAAACGAAAATCGCAACGAGAAA-TGAAAATCGCAACGC
* *
75998 GAAACTATAATCGC
1 GAAACGAAAATCGC
76012 GTTGCGATTT
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
33 16 0.22
34 12 0.16
36 4 0.05
38 15 0.21
39 26 0.36
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (38 bp):
GAAACGAAAATCGCAACGAGAAATGAAAATCGCAACGC
Found at i:75988 original size:20 final size:19
Alignment explanation
Indices: 75887--76002 Score: 116
Period size: 20 Copynumber: 6.3 Consensus size: 19
75877 TCTTTTGGTT
* *
75887 GAAATGAAAATCGCAACGA
1 GAAACGAAAATCGCAACGC
* *
75906 GAGAATGAAAATTGCAACGC
1 GA-AACGAAAATCGCAACGC
*
75926 GAAACGAAAATCGCAACGT
1 GAAACGAAAATCGCAACGC
*
75945 GAAATGAAAATCGCAA--C
1 GAAACGAAAATCGCAACGC
75962 G--AC-AAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
75978 GAAACCAAAAATCGCAACGC
1 GAAA-CGAAAATCGCAACGC
75998 GAAAC
1 GAAAC
76003 TATAATCGCG
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 33 0.40
20 34 0.41
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.09
Consensus pattern (19 bp):
GAAACGAAAATCGCAACGC
Found at i:76030 original size:19 final size:18
Alignment explanation
Indices: 76008--76090 Score: 57
Period size: 19 Copynumber: 4.7 Consensus size: 18
75998 GAAACTATAA
76008 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTT-ATT
* *
76027 TCGCATTGCGA---T-TC
1 TCGCGTTGCGATTTTATT
* *
76041 TCTCGTTGAGATTTTTATT
1 TCGCGTTGCGA-TTTTATT
*
76060 TCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTT-ATT
*
76079 TCACGTTGCGAT
1 TCGCGTTGCGAT
76091 AGTCATTTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
14 9 0.19
16 1 0.02
18 5 0.10
19 33 0.69
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (18 bp):
TCGCGTTGCGATTTTATT
Found at i:77999 original size:14 final size:14
Alignment explanation
Indices: 77980--78015 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
77970 ATTGTTTAAT
77980 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
77994 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
78008 TGATTTGT
1 TGATTTGT
78016 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:78196 original size:19 final size:19
Alignment explanation
Indices: 78174--78310 Score: 87
Period size: 19 Copynumber: 7.7 Consensus size: 19
78164 CGAAACTAAA
78174 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
78193 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
78208 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
78226 TTCGAATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
78241 -TCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
*
78259 TTCGCATTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * **
78278 TTCTCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
78297 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
78311 AGACATTAAG
Statistics
Matches: 87, Mismatches: 20, Indels: 21
0.68 0.16 0.16
Matches are distributed among these distances:
14 16 0.18
16 5 0.06
17 6 0.07
19 51 0.59
20 9 0.10
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:78220 original size:33 final size:33
Alignment explanation
Indices: 78178--78272 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
78168 ACTAAATTCG
*
78178 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
78211 CGTTGCGATTTTCATTTCGAATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
78244 CGTTGCGATTTTTATTTCGCATTGCGATT
1 CGTTGCGATTTTCATTTCGCATTGCGATT
78273 TTCATTTCTC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:80859 original size:24 final size:24
Alignment explanation
Indices: 80825--80878 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
80815 CTGAAAAATC
*
80825 ATCAAAATCCGAGTATTGTCCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
80849 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
80873 ATCAAA
1 ATCAAA
80879 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:81823 original size:61 final size:61
Alignment explanation
Indices: 81755--81928 Score: 201
Period size: 61 Copynumber: 2.9 Consensus size: 61
81745 ATTTACTAAT
* * *
81755 TCGCAATGCGAATACATAAATCGCAATGCG-ATTATGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTATGAAAATCGCAATGCGAATTACG-AAA
* * * *
81816 TCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATTTACGTAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTATGAAAATCGCAATGCGAATTACGAAA
* * * *
81877 TCGCATTGCGAATTA-GTAAATCGCAACGAGAATT-TGGGAAATCGCAATGCGA
1 TCGCAATGCGAA-TACGTAAATCGCAATGCGAATTAT-GAAAATCGCAATGCGA
81929 TAGTCAGAAT
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
61 72 0.74
62 25 0.26
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (61 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATTATGAAAATCGCAATGCGAATTACGAAA
Found at i:81825 original size:41 final size:40
Alignment explanation
Indices: 81747--81902 Score: 210
Period size: 41 Copynumber: 3.9 Consensus size: 40
81737 TCGTTGTGAT
* *
81747 TTAC-TAATTCGCAATGCGAA-TACATAAATCGCAATGCGA
1 TTACGTAAATCGCAATGCGAATTAGA-AAATCGCAATGCGA
*
81786 TTATGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGA
1 TTACGTAAATCGCAATGCGAATTA-GAAAATCGCAATGCGA
81827 TTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGA
1 TTACGTAAATCGCAATGCGAATTA-GAAAATCGCAATGCGA
* *
81868 TTTACGT-AATCGCATTGCGAATTAGTAAATCGCAA
1 -TTACGTAAATCGCAATGCGAATTAGAAAATCGCAA
81903 CGAGAATTTG
Statistics
Matches: 107, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
39 3 0.03
40 25 0.23
41 72 0.67
42 7 0.07
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (40 bp):
TTACGTAAATCGCAATGCGAATTAGAAAATCGCAATGCGA
Found at i:81909 original size:20 final size:21
Alignment explanation
Indices: 81747--81928 Score: 196
Period size: 20 Copynumber: 9.0 Consensus size: 21
81737 TCGTTGTGAT
*
81747 TTAC-TAATTCGCAATGCGAA
1 TTACGTAAATCGCAATGCGAA
*
81767 -TACATAAATCGCAATGCG-A
1 TTACGTAAATCGCAATGCGAA
*
81786 TTATGTAAATCGCAATGCGAA
1 TTACGTAAATCGCAATGCGAA
* *
81807 TTAGGAAAATCGCAATGCG-A
1 TTACGTAAATCGCAATGCGAA
81827 TTACGTAAATCGCAATGCGAA
1 TTACGTAAATCGCAATGCGAA
* * *
81848 TTAGGAAAATCGCAATGCGAT
1 TTACGTAAATCGCAATGCGAA
*
81869 TTACGT-AATCGCATTGCGAA
1 TTACGTAAATCGCAATGCGAA
* *
81889 TTA-GTAAATCGCAACGAGAA
1 TTACGTAAATCGCAATGCGAA
** *
81909 TTTGGGAAATCGCAATGCGA
1 TTACGTAAATCGCAATGCGA
81929 TAGTCAGAAT
Statistics
Matches: 135, Mismatches: 21, Indels: 11
0.81 0.13 0.07
Matches are distributed among these distances:
19 6 0.04
20 75 0.56
21 54 0.40
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (21 bp):
TTACGTAAATCGCAATGCGAA
Found at i:81920 original size:41 final size:41
Alignment explanation
Indices: 81755--81928 Score: 187
Period size: 41 Copynumber: 4.3 Consensus size: 41
81745 ATTTACTAAT
* *
81755 TCGCAATGCGAA-TA-CATAAATCGCAATGCGA-TTATGTAAA
1 TCGCAATGCGAATTAGGA-AAATCGCAATGCGATTTA-GGAAA
*
81795 TCGCAATGCGAATTAGGAAAATCGCAATGCGA-TTACGTAAA
1 TCGCAATGCGAATTAGGAAAATCGCAATGCGATTTA-GGAAA
* *
81836 TCGCAATGCGAATTAGGAAAATCGCAATGCGATTTACGTAA
1 TCGCAATGCGAATTAGGAAAATCGCAATGCGATTTAGGAAA
* * * * *
81877 TCGCATTGCGAATTA-GTAAATCGCAACGAGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAATCGCAATGCG-ATTTAGGAAA
81918 TCGCAATGCGA
1 TCGCAATGCGA
81929 TAGTCAGAAT
Statistics
Matches: 117, Mismatches: 13, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
40 24 0.21
41 89 0.76
42 4 0.03
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (41 bp):
TCGCAATGCGAATTAGGAAAATCGCAATGCGATTTAGGAAA
Found at i:89382 original size:16 final size:16
Alignment explanation
Indices: 89361--89395 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
89351 CTTATTCAGG
*
89361 AAAAATGATATAATTT
1 AAAAATAATATAATTT
89377 AAAAATAATATAATTT
1 AAAAATAATATAATTT
89393 AAA
1 AAA
89396 TACTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
AAAAATAATATAATTT
Found at i:92729 original size:23 final size:23
Alignment explanation
Indices: 92697--92761 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
92687 TATATTTTTG
*
92697 TGACATGTTTATCTCTGTCATTA
1 TGACACGTTTATCTCTGTCATTA
* * *
92720 TGACACGTTTATTTATGTCTTTA
1 TGACACGTTTATCTCTGTCATTA
* *
92743 TGAGACGTTTTTCTCTGTC
1 TGACACGTTTATCTCTGTC
92762 TTTTGGTAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.17, G:0.15, T:0.49
Consensus pattern (23 bp):
TGACACGTTTATCTCTGTCATTA
Found at i:94018 original size:16 final size:17
Alignment explanation
Indices: 93999--94030 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
93989 TACTACCATA
93999 ATATTAT-TTTTATATT
1 ATATTATATTTTATATT
94015 ATATTATATTTTATAT
1 ATATTATATTTTATAT
94031 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:94889 original size:2 final size:2
Alignment explanation
Indices: 94884--94946 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
94874 TTAAGAAGAG
94884 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
94926 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
94947 GAGGCGGTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:95980 original size:20 final size:20
Alignment explanation
Indices: 95944--95981 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
95934 ATCATATTCC
**
95944 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
95964 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
95982 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:97053 original size:57 final size:57
Alignment explanation
Indices: 96974--97086 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
96964 ATAGTCCCCC
96974 AATCATAGGGTGTTATTCTATTAAGTCTCTCGACTATTAAAAGTTATGAAATAGTCG
1 AATCATAGGGTGTTATTCTATTAAGTCTCTCGACTATTAAAAGTTATGAAATAGTCG
*
97031 AATCATGGGGTGTTATTCTATTAAGTCTCTCGACTATTAAAAGTTATGAAATAGTC
1 AATCATAGGGTGTTATTCTATTAAGTCTCTCGACTATTAAAAGTTATGAAATAGTC
97087 ATTCGATTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (57 bp):
AATCATAGGGTGTTATTCTATTAAGTCTCTCGACTATTAAAAGTTATGAAATAGTCG
Found at i:97540 original size:17 final size:16
Alignment explanation
Indices: 97506--97536 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
97496 TCACACCTTA
97506 ATAAATTTTTATAAAT
1 ATAAATTTTTATAAAT
97522 ATAAATTTTTATAAA
1 ATAAATTTTTATAAA
97537 ATATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAAATTTTTATAAAT
Found at i:104739 original size:18 final size:18
Alignment explanation
Indices: 104716--104763 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
104706 AGTCACTAAT
*
104716 TGATCCTAGTTT-GCAACC
1 TGATCCTA-TTTCACAACC
104734 TGATCCTATTTCACAACC
1 TGATCCTATTTCACAACC
104752 TGA-CCTTATTTC
1 TGATCC-TATTTC
104764 TCAATCTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.23, C:0.29, G:0.10, T:0.38
Consensus pattern (18 bp):
TGATCCTATTTCACAACC
Found at i:108906 original size:65 final size:63
Alignment explanation
Indices: 108837--108996 Score: 178
Period size: 65 Copynumber: 2.5 Consensus size: 63
108827 GAATAAATTG
* * * **
108837 AACATCGAATGCATTTTATACATCGATGCACATACCATGCACCGATGCACTTAGGGT-TTTATGA
1 AACATCGAATGCATTTTATGCATCGATGCACA-ACCATGCACCGATGCAATCAGACTATTT-T-A
108901 A
63 A
* * * * *
108902 AACATCGAATACACTTGATGCATCGATGCACCAGCCATGCATCGATGCAATCAGACTATTTTAA
1 AACATCGAATGCATTTTATGCATCGATGCA-CAACCATGCACCGATGCAATCAGACTATTTTAA
*
108966 AACATCGAATGCATTATATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
108997 TCTTAGTGTA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 1 0.01
64 28 0.35
65 45 0.57
66 5 0.06
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTTATGCATCGATGCACAACCATGCACCGATGCAATCAGACTATTTTAA
Found at i:110382 original size:2 final size:2
Alignment explanation
Indices: 110375--110402 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
110365 GTATAATACT
110375 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
110403 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:110407 original size:2 final size:2
Alignment explanation
Indices: 110402--110439 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
110392 ATATATATAT
*
110402 AG AG AG AG AG AG AG AG AG AG CG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
110440 GGATAATTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:115879 original size:24 final size:24
Alignment explanation
Indices: 115852--115924 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 24
115842 ATTTCTATAT
115852 GGTCATTCGGGACAAATTCTACGC
1 GGTCATTCGGGACAAATTCTACGC
* * *
115876 GGTCCTTCGAGACAAATTCCTACGT
1 GGTCATTCGGGACAAATT-CTACGC
115901 GGT-ACTTCGGTG-CAAAATTCTACG
1 GGTCA-TTCGG-GAC-AAATTCTACG
115925 TGGCACTACG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
24 16 0.40
25 18 0.45
26 6 0.15
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (24 bp):
GGTCATTCGGGACAAATTCTACGC
Found at i:115908 original size:25 final size:24
Alignment explanation
Indices: 115857--115909 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
115847 TATATGGTCA
* *
115857 TTCGGGACAAATTCTACGCGGTCC
1 TTCGAGACAAATTCTACGCGGTAC
*
115881 TTCGAGACAAATTCCTACGTGGTAC
1 TTCGAGACAAATT-CTACGCGGTAC
115906 TTCG
1 TTCG
115910 GTGCAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (24 bp):
TTCGAGACAAATTCTACGCGGTAC
Found at i:115916 original size:25 final size:24
Alignment explanation
Indices: 115888--115940 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
115878 TCCTTCGAGA
* *
115888 CAAATTCCTACGTGGTACTTCGGTG
1 CAAATT-CTACGTGGCACTACGGTG
115913 CAAAATTCTACGTGGCACTACGGTG
1 C-AAATTCTACGTGGCACTACGGTG
115938 CAA
1 CAA
115941 TTTATACGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.08
25 18 0.72
26 5 0.20
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (24 bp):
CAAATTCTACGTGGCACTACGGTG
Found at i:130763 original size:3 final size:3
Alignment explanation
Indices: 130755--130800 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
130745 CATCTTAACG
130755 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
130801 TTTTATTTGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:131070 original size:19 final size:18
Alignment explanation
Indices: 131048--131096 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
131038 TTTTATTTTG
131048 TTTATAATAATTTAATATA
1 TTTATAAT-ATTTAATATA
* *
131067 TTTATAATTTTTATTATA
1 TTTATAATATTTAATATA
131085 TTT-TAATGATTT
1 TTTATAAT-ATTT
131097 TTTGGATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 14 0.54
19 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTATAATATTTAATATA
Found at i:139291 original size:2 final size:2
Alignment explanation
Indices: 139284--139357 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
139274 CTTGTACGTG
139284 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
139326 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
139358 CTCTCCCTCA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:141653 original size:15 final size:16
Alignment explanation
Indices: 141624--141656 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
141614 ATGGAGGCAG
141624 TAAAAAAAATGAAAAA
1 TAAAAAAAATGAAAAA
*
141640 TAAAAGAAAT-AAAAA
1 TAAAAAAAATGAAAAA
141655 TA
1 TA
141657 TCTGAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (16 bp):
TAAAAAAAATGAAAAA
Found at i:144546 original size:2 final size:2
Alignment explanation
Indices: 144539--144566 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
144529 GCGGGGTAGT
144539 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
144567 ATTAGAGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:145832 original size:29 final size:29
Alignment explanation
Indices: 145789--145871 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
145779 CTCACCTAAC
145789 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
145819 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
145848 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
145872 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:150601 original size:29 final size:29
Alignment explanation
Indices: 150558--150640 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
150548 CTCACCTAAC
150558 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
150588 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
150617 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
150641 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:151510 original size:2 final size:2
Alignment explanation
Indices: 151505--151545 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
151495 TGTGTGTGAA
151505 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
151546 GTTTCCTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:154746 original size:29 final size:29
Alignment explanation
Indices: 154704--154804 Score: 130
Period size: 29 Copynumber: 3.5 Consensus size: 29
154694 AACCCAACCA
* * **
154704 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACGCCCGGCGACCAAC
*
154733 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACGCCCGGCGACCAAC
* *
154762 GAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACGCCCGGCGACCAAC
*
154791 GAGGTCGCCATGCA
1 TAGGTCGCCATGCA
154805 GGCGACCAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.20, C:0.39, G:0.30, T:0.12
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCGGCGACCAAC
Found at i:154813 original size:24 final size:25
Alignment explanation
Indices: 154751--154816 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 25
154741 CATGCACGCC
154751 CGGCGACCAAGGAGGTCGCCATGCA
1 CGGCGACCAAGGAGGTCGCCATGCA
154776 CGCCCGGCGACCAAGGAGGTCGCCATGCA
1 ----CGGCGACCAAGGAGGTCGCCATGCA
154805 -GGCGACCAAGGA
1 CGGCGACCAAGGA
154817 TTCATGCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
24 12 0.32
29 25 0.68
ACGTcount: A:0.24, C:0.33, G:0.36, T:0.06
Consensus pattern (25 bp):
CGGCGACCAAGGAGGTCGCCATGCA
Found at i:155064 original size:29 final size:29
Alignment explanation
Indices: 155031--155115 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
155021 AGCAGGGGAT
* * **
155031 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* *
155060 GTCGCCGGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
155089 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGCCGGGAGTGCATGGCGACCTACG
155116 GCTACTGTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.18
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:163013 original size:13 final size:13
Alignment explanation
Indices: 162995--163019 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
162985 ATGACAGATT
162995 AAAGAAATTTTTG
1 AAAGAAATTTTTG
163008 AAAGAAATTTTT
1 AAAGAAATTTTT
163020 TTAAAGGCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
AAAGAAATTTTTG
Found at i:164167 original size:13 final size:13
Alignment explanation
Indices: 164149--164173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
164139 ATTGTTACTT
164149 TTTTATTTGAGAG
1 TTTTATTTGAGAG
164162 TTTTATTTGAGA
1 TTTTATTTGAGA
164174 TCCTTAAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (13 bp):
TTTTATTTGAGAG
Found at i:165060 original size:21 final size:21
Alignment explanation
Indices: 165034--165076 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
165024 ATTCTGGGTT
* *
165034 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
165055 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
165076 A
1 A
165077 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:165192 original size:67 final size:66
Alignment explanation
Indices: 165034--165205 Score: 195
Period size: 66 Copynumber: 2.6 Consensus size: 66
165024 ATTCTGGGTT
* * *
165034 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCTTCAACGAATATGATTTCCAGAATGC
1 AGGGGAATCGGTACCCA-T-AGGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGC
165098 TAG
64 TAG
** * * *
165101 A-GGGAATCGGTACCCCCAGGGGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGC
1 AGGGGAATCGGTACCCATA-GGGGGGAACCGATACCCCCTCAACGAATATG-AATTCCAGAATGC
*
165165 TTG
64 TAG
* *
165168 AGGGGAATCGATACCCATAGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCATAGGGGGGAACCGATACCCCC
165206 ATGAGAAAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
64 1 0.01
66 40 0.45
67 33 0.38
68 14 0.16
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.19
Consensus pattern (66 bp):
AGGGGAATCGGTACCCATAGGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTA
G
Found at i:165571 original size:27 final size:28
Alignment explanation
Indices: 165508--165577 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
165498 CATATTATGA
** *
165508 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATT-AACGTAT
165537 TACATGACATGAATTCATATT-ACGTAT
1 TACATGACATGAATTCATATTAACGTAT
165564 TACATGACATGAAT
1 TACATGACATGAAT
165578 ATGCAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 19 0.50
29 19 0.50
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (28 bp):
TACATGACATGAATTCATATTAACGTAT
Found at i:165634 original size:30 final size:29
Alignment explanation
Indices: 165591--165668 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
165581 CAGAAAAAGT
*
165591 TATATGCACTATGTGATAAAGGTATGTAAA
1 TATATGC-CTATGTGATAAAGGTATGGAAA
* *
165621 TGATATGCCTATGTGTTAAAGTTATGGAAA
1 T-ATATGCCTATGTGATAAAGGTATGGAAA
* *
165651 TACTATGTCTACGTGATA
1 TA-TATGCCTATGTGATA
165669 TGAACTACGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36
Consensus pattern (29 bp):
TATATGCCTATGTGATAAAGGTATGGAAA
Found at i:165945 original size:22 final size:22
Alignment explanation
Indices: 165871--165937 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
165861 TTATGGACAT
165871 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
165893 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
165915 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
165937 A
1 A
165938 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:171569 original size:21 final size:21
Alignment explanation
Indices: 171545--171585 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
171535 TTCTGGGTTA
* *
171545 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
171566 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
171586 CGAATATGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:171660 original size:67 final size:68
Alignment explanation
Indices: 171565--171716 Score: 207
Period size: 68 Copynumber: 2.2 Consensus size: 68
171555 ACCCATTCAA
* * * *
171565 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
171629 GGG
66 GGG
* * * * *
171632 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCATA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
171697 GGG
66 GGG
*
171700 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
171717 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
67 26 0.35
68 48 0.65
ACGTcount: A:0.27, C:0.26, G:0.28, T:0.19
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
GGG
Found at i:172053 original size:29 final size:29
Alignment explanation
Indices: 172019--172090 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
172009 CATATTATGA
** *
172019 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAACGTAT
*
172048 TACATGACATGAATTCATATTATACGTAT
1 TACATGACATGAATTCATATTAAACGTAT
172077 TACATGACATGAAT
1 TACATGACATGAAT
172091 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAACGTAT
Found at i:172147 original size:30 final size:29
Alignment explanation
Indices: 172104--172181 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
172094 CAGAAAAAGT
*
172104 TATATGCACTATGTGATAAAGGTATGTAAA
1 TATATGC-CTATGTGATAAAGGTATGGAAA
* *
172134 TGATATGCCTATGTGTTAAAGTTATGGAAA
1 T-ATATGCCTATGTGATAAAGGTATGGAAA
* *
172164 TACTATGTCTACGTGATA
1 TA-TATGCCTATGTGATA
172182 TGAACTACGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36
Consensus pattern (29 bp):
TATATGCCTATGTGATAAAGGTATGGAAA
Found at i:172456 original size:22 final size:22
Alignment explanation
Indices: 172382--172448 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
172372 TTATGGACAT
172382 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
172404 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
172426 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
172448 A
1 A
172449 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:173714 original size:20 final size:20
Alignment explanation
Indices: 173689--173736 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
173679 TAGAAGAAAA
173689 AAAAAGATCAATCCCTTGAC
1 AAAAAGATCAATCCCTTGAC
* **
173709 AAAAAGGATCGATCCCTTTTC
1 AAAAA-GATCAATCCCTTGAC
173730 AAAAAGA
1 AAAAAGA
173737 ATAAAGATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.21
Consensus pattern (20 bp):
AAAAAGATCAATCCCTTGAC
Found at i:176152 original size:13 final size:13
Alignment explanation
Indices: 176130--176163 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
176120 TCCCACATAG
176130 TATT-GGAAACAC
1 TATTGGGAAACAC
176142 TATTGGGAAACAC
1 TATTGGGAAACAC
176155 TATTGGGAA
1 TATTGGGAA
176164 TGGTATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (13 bp):
TATTGGGAAACAC
Found at i:176282 original size:6 final size:6
Alignment explanation
Indices: 176273--177188 Score: 1804
Period size: 6 Copynumber: 153.3 Consensus size: 6
176263 GTCGTGGTCG
176273 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176321 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176369 TAGT-A -A-TAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176414 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176462 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176510 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176558 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176606 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176654 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176702 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176750 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176798 TAGTAA TAGTAA TAGTAA TAGT-A TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176845 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176893 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176941 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
176989 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
177037 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
177085 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
177133 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA
177181 TAGTAA TA
1 TAGTAA TA
177189 CGTGTCTTCG
Statistics
Matches: 906, Mismatches: 0, Indels: 8
0.99 0.00 0.01
Matches are distributed among these distances:
3 1 0.00
4 2 0.00
5 7 0.01
6 896 0.99
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
TAGTAA
Found at i:177308 original size:21 final size:21
Alignment explanation
Indices: 177283--177356 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
177273 TTTGGAATAA
177283 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
177304 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
177323 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
177344 ATCGCAACGCGAA
1 ATCGCAACGCGAA
177357 TATGTAAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 15 0.35
21 28 0.65
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:177331 original size:40 final size:42
Alignment explanation
Indices: 177269--177352 Score: 154
Period size: 40 Copynumber: 2.0 Consensus size: 42
177259 CCAGTCGTTG
177269 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
177311 CGAATTTGG-A-AAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
177351 CG
1 CG
177353 CGAATATGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 32 0.76
41 1 0.02
42 9 0.21
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (42 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
Found at i:182277 original size:2 final size:2
Alignment explanation
Indices: 182272--182296 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
182262 TATCCATCCT
182272 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
182297 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:182376 original size:4 final size:4
Alignment explanation
Indices: 182367--182391 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
182357 GACCATGATG
182367 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
182392 AGTGGGTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:186202 original size:14 final size:14
Alignment explanation
Indices: 186183--186219 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
186173 CCCGGCATAG
186183 TGAGTTGAAATCTA
1 TGAGTTGAAATCTA
186197 TGAGTTGAAATCTA
1 TGAGTTGAAATCTA
186211 TGAGTTGAA
1 TGAGTTGAA
186220 GGTAGTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.35
Consensus pattern (14 bp):
TGAGTTGAAATCTA
Found at i:216308 original size:37 final size:38
Alignment explanation
Indices: 216224--216310 Score: 142
Period size: 38 Copynumber: 2.3 Consensus size: 38
216214 CCTAAACCCG
216224 AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
*
216262 AACCCGACCCGA-CTCGACCCGAATATTACACTT-AAAA
1 AACCCGACCCGACCT-GACCCGAATATCACACTTAAAAA
216299 AACCCGACCCGA
1 AACCCGACCCGA
216311 ACAAAATAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
37 18 0.38
38 29 0.62
ACGTcount: A:0.38, C:0.38, G:0.11, T:0.13
Consensus pattern (38 bp):
AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
Found at i:216556 original size:37 final size:38
Alignment explanation
Indices: 216470--216559 Score: 146
Period size: 38 Copynumber: 2.4 Consensus size: 38
216460 TTTTCACCCT
216470 AAACCCGAACCCGACACGACCCGAATATCAAACTTAAAA
1 AAACCCG-ACCCGACACGACCCGAATATCAAACTTAAAA
* *
216509 AAACCCGACCCGACTCGACCCGAATATCATACTTAAAA
1 AAACCCGACCCGACACGACCCGAATATCAAACTTAAAA
216547 AAA-CCGACCCGAC
1 AAACCCGACCCGAC
216560 CCGAACAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 10 0.20
38 32 0.65
39 7 0.14
ACGTcount: A:0.42, C:0.36, G:0.11, T:0.11
Consensus pattern (38 bp):
AAACCCGACCCGACACGACCCGAATATCAAACTTAAAA
Found at i:217061 original size:2 final size:2
Alignment explanation
Indices: 217054--217100 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
217044 CCAAAGCCTT
217054 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
217096 TA TA T
1 TA TA T
217101 CACTTCAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:218932 original size:16 final size:16
Alignment explanation
Indices: 218911--218944 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
218901 CTTAAAAAAA
218911 AATTAATTT-TTTTCTT
1 AATTAATTTATTTT-TT
218927 AATTAATTTATTTTTT
1 AATTAATTTATTTTTT
218943 AA
1 AA
218945 ATTTTTAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTAATTTATTTTTT
Found at i:223695 original size:201 final size:199
Alignment explanation
Indices: 223317--223718 Score: 736
Period size: 201 Copynumber: 2.0 Consensus size: 199
223307 ATGTAGACTT
*
223317 TGCAGAAAGTTCCGCTTTTAGCCACTTTCCCACTTCGTGCTCTTAGTGCAGTAGATGCTTCAAAG
1 TGCAGAAAGTTCCGCTTTTAGCCACTTTCCCACTTCATGCTCTTAGTGCAGTAGATGCTTCAAAG
223382 AAGTCGACACCCCGTCCGATTATCCCGAATTGCAGCGCAGCATGCGGGGTTATGCTATCTCGGTG
66 AAGTCGACACCCCGTCCGATTATCCCGAATTGCAGCGCAGCATGCGGGGTTATGCTATCTCGGTG
223447 ACTTAACAATGCCTGCTCTGTGCTCTGAATTTGACGAACGCTTTGATGGGAATCCCACAGTGTAT
131 ACTTAACAATGCC-GCTCTGTGCTCTGAATTTGACGAACGCTTTGATGGGAATCCCACAGTGTAT
223512 GATTG
195 GATTG
223517 TGCAGAAAGTTCCGCTTTTAGCCACTTTCCCACTTCATGCTCTTAGTGCAGTAGATTGCTTCAAA
1 TGCAGAAAGTTCCGCTTTTAGCCACTTTCCCACTTCATGCTCTTAGTGCAGTAGA-TGCTTCAAA
223582 GAAGTCGACACCCATC-TCCGATTATCCCGAATTGCAGCGCAGCATGCGGGGTTATGCTATCTCG
65 GAAGTCGACACCC--CGTCCGATTATCCCGAATTGCAGCGCAGCATGCGGGGTTATGCTATCTC-
223646 GGTGACTTAACAATGCC-CTCTGTGCTCTGAATTTGACGAACGCTTTGATGGGAATCCCACAGTG
127 GGTGACTTAACAATGCCGCTCTGTGCTCTGAATTTGACGAACGCTTTGATGGGAATCCCACAGTG
223710 TATGATTG
192 TATGATTG
223718 T
1 T
223719 AACGCCTTGT
Statistics
Matches: 197, Mismatches: 1, Indels: 7
0.96 0.00 0.03
Matches are distributed among these distances:
200 54 0.27
201 78 0.40
202 47 0.24
203 18 0.09
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.29
Consensus pattern (199 bp):
TGCAGAAAGTTCCGCTTTTAGCCACTTTCCCACTTCATGCTCTTAGTGCAGTAGATGCTTCAAAG
AAGTCGACACCCCGTCCGATTATCCCGAATTGCAGCGCAGCATGCGGGGTTATGCTATCTCGGTG
ACTTAACAATGCCGCTCTGTGCTCTGAATTTGACGAACGCTTTGATGGGAATCCCACAGTGTATG
ATTG
Found at i:224726 original size:18 final size:17
Alignment explanation
Indices: 224691--224741 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
224681 TTATGGTTGT
224691 TATATTTTTTTGTAGTA
1 TATATTTTTTTGTAGTA
224708 TATATTATTATTT-TAGTA
1 TATATT-TT-TTTGTAGTA
*
224726 TAGTTGTTTTTTTGTA
1 TA--TATTTTTTTGTA
224742 CTATTATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
17 6 0.21
18 12 0.43
19 7 0.25
20 3 0.11
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (17 bp):
TATATTTTTTTGTAGTA
Found at i:231169 original size:3 final size:3
Alignment explanation
Indices: 231154--231287 Score: 133
Period size: 3 Copynumber: 44.7 Consensus size: 3
231144 ATCCCTTCTT
* * * * *
231154 TGC TGC AGC TGC TGC TGC GGC TGC TGC TGC TGC TGT TGT TGT TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
* * * * *
231202 TGC TGC TGC TGT TGT TGC TGT TGC TGC TGC TGT TGC TGC TGC TGC TGT
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
* * * * *
231250 TGT TGT TGC TGC TGC TGC TGA TGT TGT TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
231288 AGCATGCCTC
Statistics
Matches: 114, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 114 1.00
ACGTcount: A:0.01, C:0.23, G:0.34, T:0.41
Consensus pattern (3 bp):
TGC
Found at i:231179 original size:21 final size:21
Alignment explanation
Indices: 231154--231287 Score: 169
Period size: 21 Copynumber: 6.4 Consensus size: 21
231144 ATCCCTTCTT
* **
231154 TGCTGCAGCTGCTGCTGCGGC
1 TGCTGCTGCTGCTGCTGTTGC
* *
231175 TGCTGCTGCTGCTGTTGTTGT
1 TGCTGCTGCTGCTGCTGTTGC
*
231196 TGCTGCTGCTGCTGCTGTTGT
1 TGCTGCTGCTGCTGCTGTTGC
*
231217 TGCTGTTGCTGCTGCTGTTGC
1 TGCTGCTGCTGCTGCTGTTGC
* *
231238 TGCTGCTGCTGTTGTTGTTGC
1 TGCTGCTGCTGCTGCTGTTGC
* *
231259 TGCTGCTGCTGATGTTGTTGC
1 TGCTGCTGCTGCTGCTGTTGC
231280 TGCTGCTG
1 TGCTGCTG
231288 AGCATGCCTC
Statistics
Matches: 101, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 101 1.00
ACGTcount: A:0.01, C:0.23, G:0.34, T:0.41
Consensus pattern (21 bp):
TGCTGCTGCTGCTGCTGTTGC
Found at i:239205 original size:20 final size:17
Alignment explanation
Indices: 239180--239220 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 17
239170 AGTTAGGTTT
239180 TTTTTATAAACATAATAACA
1 TTTTTATAAA-A-AATAA-A
239200 TTTTTATAAAAAATAAA
1 TTTTTATAAAAAATAAA
239217 TTTT
1 TTTT
239221 AAAATTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 5 0.24
19 1 0.05
20 10 0.48
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTTTATAAAAAATAAA
Found at i:244177 original size:2 final size:2
Alignment explanation
Indices: 244157--244207 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
244147 TCAATTGGTA
* *
244157 AT AT AT A- AT AA AT AA 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
244198 AT AT AT AT AT
1 AT AT AT AT AT
244208 TGAATAGTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:246877 original size:2 final size:2
Alignment explanation
Indices: 246872--246905 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
246862 ATTTTTTAAA
246872 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
246906 TAATAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:247613 original size:20 final size:20
Alignment explanation
Indices: 247588--247651 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
247578 TACAAAATTG
*
247588 AAAAGATAAATAGATTTAAT
1 AAAAGATAAATAGGTTTAAT
247608 AAAAGAT-AATAGGTTTAAT
1 AAAAGATAAATAGGTTTAAT
*
247627 AAAAGATATATAGGTTTAAT
1 AAAAGATAAATAGGTTTAAT
247647 AAAAG
1 AAAAG
247652 GGTAAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 18 0.44
20 23 0.56
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAAGATAAATAGGTTTAAT
Found at i:251007 original size:19 final size:19
Alignment explanation
Indices: 250983--251044 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
250973 AACACGGAAA
250983 TCGGTTTTTTCGGTTCGGT
1 TCGGTTTTTTCGGTTCGGT
*
251002 TCGGTTTTTT---TAACGGT
1 TCGGTTTTTTCGGT-TCGGT
*
251019 TCGGGTTTTTCGGTTCGGT
1 TCGGTTTTTTCGGTTCGGT
251038 TCGGTTT
1 TCGGTTT
251045 ATCGGTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.37
19 20 0.57
20 1 0.03
ACGTcount: A:0.03, C:0.15, G:0.31, T:0.52
Consensus pattern (19 bp):
TCGGTTTTTTCGGTTCGGT
Done.