Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014719.1 Kokia drynarioides strain JFW-HI SEQ_129758, 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: 175347
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:3653 original size:18 final size:17
Alignment explanation
Indices: 3630--3667 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
3620 GCACAAGCGA
3630 ACCAGATGCGATCACATG
1 ACCAGATGCGATCAC-TG
*
3648 ACCAGATGTGATCACTG
1 ACCAGATGCGATCACTG
3665 ACC
1 ACC
3668 CAAATGCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (17 bp):
ACCAGATGCGATCACTG
Found at i:3710 original size:18 final size:18
Alignment explanation
Indices: 3689--3728 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3679 ATACAATCAG
3689 ATGCAACCACAAGTTCGA
1 ATGCAACCACAAGTTCGA
* *
3707 ATGCAGCTACAAGTTCGA
1 ATGCAACCACAAGTTCGA
3725 ATGC
1 ATGC
3729 TGCTACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (18 bp):
ATGCAACCACAAGTTCGA
Found at i:3733 original size:18 final size:18
Alignment explanation
Indices: 3697--3736 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3687 AGATGCAACC
3697 ACAAGTTCGAATGCAGCT
1 ACAAGTTCGAATGCAGCT
*
3715 ACAAGTTCGAATGCTGCT
1 ACAAGTTCGAATGCAGCT
3733 ACAA
1 ACAA
3737 CAGAATGCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (18 bp):
ACAAGTTCGAATGCAGCT
Found at i:12503 original size:27 final size:27
Alignment explanation
Indices: 12473--12544 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
12463 CAATAAATTT
* *
12473 CCACAAAGGCTTCCTTTTCATAGGTTG
1 CCACAAAAGCTTCCTTTCCATAGGTTG
*
12500 CCACAAATGCTTCCTTTCCATAGGTTG
1 CCACAAAAGCTTCCTTTCCATAGGTTG
12527 CCACAAAAGCTTCCTTTC
1 CCACAAAAGCTTCCTTTC
12545 ATTCAAAACT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.32
Consensus pattern (27 bp):
CCACAAAAGCTTCCTTTCCATAGGTTG
Found at i:18029 original size:37 final size:37
Alignment explanation
Indices: 17977--18050 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
17967 CGGTGACCAG
* * *
17977 ACACTGACTTACTTTA-AAGACTCTTCATGCATTGACA
1 ACACAGACTCACTTTATAA-ACTATTCATGCATTGACA
*
18014 ACACAGACTCACTTTATAAACTATTCATGTATTGACA
1 ACACAGACTCACTTTATAAACTATTCATGCATTGACA
18051 CAATCTAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 30 0.94
38 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.32
Consensus pattern (37 bp):
ACACAGACTCACTTTATAAACTATTCATGCATTGACA
Found at i:22952 original size:24 final size:26
Alignment explanation
Indices: 22916--22963 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
22906 AGAGAAATGT
22916 AAATGTGATATATGA-A-ATTATGAG
1 AAATGTGATATATGAGAGATTATGAG
22940 AAATGATGA-ATATGAGAGATTATG
1 AAATG-TGATATATGAGAGATTATG
22964 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGTGATATATGAGAGATTATGAG
Found at i:23064 original size:23 final size:22
Alignment explanation
Indices: 23038--23172 Score: 96
Period size: 23 Copynumber: 6.0 Consensus size: 22
23028 TTACTATTCA
23038 GCACTGTGTGTGCTTACTGTTT
1 GCACTGTGTGTGCTTACTGTTT
*
23060 CGCACT-TCGTGTGCTTACTATTT
1 -GCACTGT-GTGTGCTTACTGTTT
23083 CGCACCTCGTGTGT-C-TACTGATTT
1 -GCA-CT-GTGTGTGCTTACTG-TTT
* * ** * *
23107 GCGCTATGTGCACCTACTGATT
1 GCACTGTGTGTGCTTACTGTTT
* * *
23129 ACACTGTGTGTGCCTACTGGATT
1 GCACTGTGTGTGCTTACT-GTTT
23152 GCACTGTGTGTGCTTACTGTT
1 GCACTGTGTGTGCTTACTGTT
23173 AAGTACTTCG
Statistics
Matches: 90, Mismatches: 14, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
21 4 0.04
22 21 0.23
23 54 0.60
24 6 0.07
25 4 0.04
26 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.39
Consensus pattern (22 bp):
GCACTGTGTGTGCTTACTGTTT
Found at i:32360 original size:54 final size:55
Alignment explanation
Indices: 32282--32397 Score: 218
Period size: 54 Copynumber: 2.1 Consensus size: 55
32272 ATAAATACAT
32282 TTTA-AAATTTTAAAAAAATAATATGGTGGACCTAAAATGGGTTCGAGTTAGCCA
1 TTTACAAATTTTAAAAAAATAATATGGTGGACCTAAAATGGGTTCGAGTTAGCCA
32336 TTTACAAA-TTTAAAAAAATAATATGGTGGACCTAAAATGGGTTCGAGTTAGCCA
1 TTTACAAATTTTAAAAAAATAATATGGTGGACCTAAAATGGGTTCGAGTTAGCCA
32390 TTTACAAA
1 TTTACAAA
32398 ATATGAGTTG
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
54 58 0.95
55 3 0.05
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (55 bp):
TTTACAAATTTTAAAAAAATAATATGGTGGACCTAAAATGGGTTCGAGTTAGCCA
Found at i:40619 original size:12 final size:12
Alignment explanation
Indices: 40602--40626 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40592 GTTTGGACCT
40602 AAAGTCGTACCC
1 AAAGTCGTACCC
40614 AAAGTCGTACCC
1 AAAGTCGTACCC
40626 A
1 A
40627 TACTCACAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (12 bp):
AAAGTCGTACCC
Found at i:44820 original size:33 final size:33
Alignment explanation
Indices: 44783--44853 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
44773 ATAGTTTTCA
44783 ATTATTTCTTTGTGGTTTTCAATTGCAATCAAG
1 ATTATTTCTTTGTGGTTTTCAATTGCAATCAAG
44816 ATTATTTCTTTGTGGTTTTCAATTGCAATCAAG
1 ATTATTTCTTTGTGGTTTTCAATTGCAATCAAG
44849 ATTAT
1 ATTAT
44854 CTTTGCAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.49
Consensus pattern (33 bp):
ATTATTTCTTTGTGGTTTTCAATTGCAATCAAG
Found at i:50162 original size:89 final size:88
Alignment explanation
Indices: 50068--50674 Score: 446
Period size: 89 Copynumber: 6.9 Consensus size: 88
50058 CATCTGGAGG
* * *
50068 TAAAATTGGTAATTTTTTAAAGTTTTGGGGTCAAAAATGAGA-TTTTGGGAGTTCAAGGGTAAAA
1 TAAAAATGG-AATTTTTTAAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAA
50132 TGGTAATTTTTGGAAGTTTCGGGT
65 TGGTAATTTTTGGAAGTTTCGGGT
* ** ** *
50156 TAAAAATGGGATTTTTGGAAGTTCGGGGGGT--AAAATG-GTAATTTTTGGAAGTTTCGAGGTTA
1 TAAAAATGGAATTTTTTAAAGTT-TTGGGGTCAAAAATGAG--ATTTTTGGAAG-TTCGAGGGT-
* * *
50218 AAAATGG-GATTTTTAGAAGTTTAAGGG-
61 AAAATGGTAATTTTTGGAAGTTT-CGGGT
* ** *
50245 T-AAATTGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTAGAGGGTAAAA
1 TAAAAATGG-AATTTTTTAAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAA
*
50309 TGGTAATTTTTGGAAGTTTTGGGGT
65 TGGTAATTTTTGGAAG-TTTCGGGT
* * * * * *
50334 TTAAAAT-GAGA-TTTTTAGAAGTTTAGGGGTTAAAAATGGGATTTTTAGAAGTTCGAGAGTAAA
1 TAAAAATGGA-ATTTTTTA-AAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAA
* * *
50397 ATGGTAATTTTTAGAATTTTTGGGGT
64 ATGGTAATTTTTGGAA-GTTTCGGGT
* * * * * *
50423 TAAAAATGGGA-TTTTTAGAAG-TTCGAGGGTTAGAAATGGGATTTTTAGAAGTTCGAGGGTAAA
1 TAAAAATGGAATTTTTTA-AAGTTTTG-GGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAA
50486 ATGGTAATTTTTGGAAGTTTCGAGGT
64 ATGGTAATTTTTGGAAGTTTCG-GGT
* ** * *
50512 AAAAAAT-GAGATTTTTGGAAGTTTAGGGGT--AAAATG-GTATTTTTTGGAAGTTTTG-GGGTT
1 TAAAAATGGA-ATTTTTTAAAGTTTTGGGGTCAAAAATGAG-A-TTTTTGGAAG-TTCGAGGG--
* *
50572 TAAAATGG-GATTTTTAGAAG-TTCATGGG-
60 TAAAATGGTAATTTTTGGAAGTTTC--GGGT
* * * * * *
50600 T-AAAATGTAATTTTTTGAAGTTTTGAGGTCAAAAATGGGATTTTTTGAAGTTTG-GGTGTAAAA
1 TAAAAATGGAATTTTTTAAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGG-GTAAAA
50663 TGGTAATTTTTG
65 TGGTAATTTTTG
50675 AACAATTTAG
Statistics
Matches: 424, Mismatches: 58, Indels: 75
0.76 0.10 0.13
Matches are distributed among these distances:
85 1 0.00
86 15 0.04
87 59 0.14
88 91 0.21
89 219 0.52
90 38 0.09
91 1 0.00
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (88 bp):
TAAAAATGGAATTTTTTAAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAT
GGTAATTTTTGGAAGTTTCGGGT
Found at i:50164 original size:30 final size:28
Alignment explanation
Indices: 50127--50674 Score: 312
Period size: 30 Copynumber: 18.6 Consensus size: 28
50117 AGTTCAAGGG
50127 TAAAATGGTAATTTTTGGAAGTTTCGGGT
1 TAAAATGG-AATTTTTGGAAGTTTCGGGT
* *
50156 TAAAAATGGGATTTTTGGAAG-TTCGGGGGG
1 T-AAAATGGAATTTTTGGAAGTTTC--GGGT
50186 TAAAATGGTAATTTTTGGAAGTTTCGAGGT
1 TAAAATGG-AATTTTTGGAAGTTTCG-GGT
* * *
50216 TAAAAATGGGATTTTTAGAAGTTTAAGGG-
1 T-AAAATGGAATTTTTGGAAGTTT-CGGGT
* *
50245 TAAATTGGTAATTTTTGGAAGTTTTGGGGT
1 TAAAATGG-AATTTTTGGAAG-TTTCGGGT
* * *
50275 CAAAAAT-GAGATTTTTGGAAG-TTAGAGGG
1 -TAAAATGGA-ATTTTTGGAAGTTTCG-GGT
*
50304 TAAAATGGTAATTTTTGGAAGTTTTGGGGTT
1 TAAAATGG-AATTTTTGGAAG-TTTCGGG-T
* *
50335 TAAAAT-GAGATTTTTAGAAGTTTAGGGGT
1 TAAAATGGA-ATTTTTGGAAGTTT-CGGGT
* *
50364 TAAAAATGGGATTTTTAGAAG-TTCGAGAG-
1 T-AAAATGGAATTTTTGGAAGTTTCG-G-GT
* * *
50393 TAAAATGGTAATTTTTAGAATTTTTGGGGT
1 TAAAATGG-AATTTTTGGAA-GTTTCGGGT
* *
50423 TAAAAATGGGATTTTTAGAAG-TTCGAGGGT
1 T-AAAATGGAATTTTTGGAAGTTTC--GGGT
* * *
50453 TAGAAATGGGATTTTTAGAAG-TTCGAGGG
1 TA-AAATGGAATTTTTGGAAGTTTCG-GGT
50482 TAAAATGGTAATTTTTGGAAGTTTCGAGGT
1 TAAAATGG-AATTTTTGGAAGTTTCG-GGT
* * *
50512 AAAAAAT-GAGATTTTTGGAAGTTTAGGGG
1 -TAAAATGGA-ATTTTTGGAAGTTTCGGGT
* *
50541 TAAAATGGTATTTTTTGGAAGTTTTGGGGTT
1 TAAAATGG-AATTTTTGGAAG-TTTCGGG-T
* *
50572 TAAAATGGGATTTTTAGAAG-TTCATGGG-
1 TAAAATGGAATTTTTGGAAGTTTC--GGGT
* * *
50600 TAAAATGTAATTTTTTGAAGTTTTGAGGT
1 TAAAATGGAATTTTTGGAAGTTTCG-GGT
* * *
50629 CAAAAATGGGATTTTTTGAAGTTT-GGGT
1 -TAAAATGGAATTTTTGGAAGTTTCGGGT
50657 GTAAAATGGTAATTTTTG
1 -TAAAATGG-AATTTTTG
50675 AACAATTTAG
Statistics
Matches: 417, Mismatches: 53, Indels: 98
0.73 0.09 0.17
Matches are distributed among these distances:
27 1 0.00
28 70 0.17
29 108 0.26
30 190 0.46
31 48 0.12
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.39
Consensus pattern (28 bp):
TAAAATGGAATTTTTGGAAGTTTCGGGT
Found at i:50200 original size:59 final size:58
Alignment explanation
Indices: 50066--50674 Score: 550
Period size: 59 Copynumber: 10.3 Consensus size: 58
50056 GACATCTGGA
** * * * * * ***
50066 GGTAAAATTGGTAATTTTTTAAAGTTTTGGGGTCAAAAATGAGA-TTTTGGGAGTTCAAG
1 GGTAAAA-TGGTAATTTTTGGAAG-TTTCGGGTTAAAAATGGGATTTTTAGAAGTTTGGG
* *
50125 GGTAAAATGGTAATTTTTGGAAGTTTCGGGTTAAAAATGGGATTTTTGGAAGTTCGGGG
1 GGTAAAATGGTAATTTTTGGAAGTTTCGGGTTAAAAATGGGATTTTTAGAAGTT-TGGG
**
50184 GGTAAAATGGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTAGAAGTTTAAG
1 GGTAAAATGGTAATTTTTGGAAGTTTCG-GGTTAAAAATGGGATTTTTAGAAGTTTGGG
* * * * * * *
50243 GGTAAATTGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTAGAG
1 GGTAAAATGGTAATTTTTGGAAG-TTTCGGGTTAAAAATGGGATTTTTAGAAGTTTGGG
* * *
50302 GGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTTAAAATGAGATTTTTAGAAGTTTAGGG
1 GGTAAAATGGTAATTTTTGGAAG-TTTCGGGTTAAAAATGGGATTTTTAGAAGTTT-GGG
* * * * *
50362 GTTAAAAATGG-GATTTTTAGAAG-TTCGAGAG-T-AAAATGGTAATTTTTAGAATTTTTGGG
1 GGT-AAAATGGTAATTTTTGGAAGTTTCG-G-GTTAAAAATGG-GATTTTTAGAA-GTTTGGG
* * * * * *
50421 GTTAAAAATGG-GATTTTTAGAAG-TTCGAGGGTTAGAAATGGGATTTTTAGAAGTTCGAG
1 GGT-AAAATGGTAATTTTTGGAAGTTTC--GGGTTAAAAATGGGATTTTTAGAAGTTTGGG
* * * *
50480 GGTAAAATGGTAATTTTTGGAAGTTTCGAGGTAAAAAATGAGATTTTTGGAAGTTTAGG
1 GGTAAAATGGTAATTTTTGGAAGTTTCG-GGTTAAAAATGGGATTTTTAGAAGTTTGGG
* * * ***
50539 GGTAAAATGGTATTTTTTGGAAGTTTTGGGGTTTAAAATGGGATTTTTAGAAGTTCATG
1 GGTAAAATGGTAATTTTTGGAAG-TTTCGGGTTAAAAATGGGATTTTTAGAAGTTTGGG
* * * *
50598 GGTAAAAT-GTAATTTTTTGAAGTTTTGAGGTCAAAAATGGGATTTTTTGAAGTTTGGG
1 GGTAAAATGGTAATTTTTGGAAGTTTCG-GGTTAAAAATGGGATTTTTAGAAGTTTGGG
*
50656 TGTAAAATGGTAATTTTTG
1 GGTAAAATGGTAATTTTTG
50675 AACAATTTAG
Statistics
Matches: 463, Mismatches: 67, Indels: 40
0.81 0.12 0.07
Matches are distributed among these distances:
57 20 0.04
58 84 0.18
59 279 0.60
60 66 0.14
61 14 0.03
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (58 bp):
GGTAAAATGGTAATTTTTGGAAGTTTCGGGTTAAAAATGGGATTTTTAGAAGTTTGGG
Found at i:76378 original size:30 final size:29
Alignment explanation
Indices: 76327--76796 Score: 386
Period size: 30 Copynumber: 15.9 Consensus size: 29
76317 CGAACATCTA
*
76327 GGGGTAAAAATGGTAATTTTTGGAAGTTTT
1 GGGGTAAAAATGG-GATTTTTGGAAGTTTT
* * *
76357 GGAGTCAAAAATGGGATTTTTGGGAG-TTC
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTT
* *
76386 GAGGGT-AAAATGGTAATTTTGGAAGTTTT
1 G-GGGTAAAAATGGGATTTTTGGAAGTTTT
* *
76415 AGGGTTAAAAATGGGATTTTTGGAAGTTTG
1 -GGGGTAAAAATGGGATTTTTGGAAGTTTT
*
76445 GGGGT-AAAATGGTAATTTTTGGAAGTTTT
1 GGGGTAAAAATGG-GATTTTTGGAAGTTTT
* **
76474 GGGGTTAAAAATGGGATTTTTAGAAG-TCA
1 GGGG-TAAAAATGGGATTTTTGGAAGTTTT
* *
76503 GAGGGTTAAAAATGAGATTTTTGGAAG-TTC
1 G-GGG-TAAAAATGGGATTTTTGGAAGTTTT
* * *
76533 GAGGGT--AAATGGTAATTTTTTGAAGTTTC
1 G-GGGTAAAAATGG-GATTTTTGGAAGTTTT
* ** *
76562 GAGGTTAAAAATGGGATTTTTAAAAGTTTAA
1 G-GGGTAAAAATGGGATTTTTGGAAGTTT-T
* *
76593 GGGTTAAAAATGGGATTTTTAGAAGTTTT
1 GGGGTAAAAATGGGATTTTTGGAAGTTTT
*
76622 GGGGT-AAAATGGTAATTTTTGGAAGTTTT
1 GGGGTAAAAATGG-GATTTTTGGAAGTTTT
*
76651 GGGGTCAAAAATGGGATTTTTTGAAG-TTT
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTT
*
76680 GAGGGT-AAAATGGTAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGG-GATTTTTGGAAGTTTT
* * * *
76710 GGGTTTTAAAAATGAGATTTTTAGAAGTTTA
1 GGG--GTAAAAATGGGATTTTTGGAAGTTTT
* *
76741 GGGGT-AAAATGGTAATTTTGGAAGTTTT
1 GGGGTAAAAATGGGATTTTTGGAAGTTTT
* *
76769 GGGGTCAAAAATGAGATTTTAGGAAGTT
1 GGGGT-AAAAATGGGATTTTTGGAAGTT
76797 CGAGGGTAAA
Statistics
Matches: 359, Mismatches: 56, Indels: 50
0.77 0.12 0.11
Matches are distributed among these distances:
27 5 0.01
28 70 0.19
29 81 0.23
30 151 0.42
31 46 0.13
32 6 0.02
ACGTcount: A:0.31, C:0.01, G:0.30, T:0.37
Consensus pattern (29 bp):
GGGGTAAAAATGGGATTTTTGGAAGTTTT
Found at i:76494 original size:59 final size:59
Alignment explanation
Indices: 76327--76827 Score: 527
Period size: 59 Copynumber: 8.5 Consensus size: 59
76317 CGAACATCTA
* * * * *
76327 GGGGTAAAAATGGTAATTTTTGGAAGTTTTGGAGTCAAAAATGGGATTTTTGGGAGTTCG
1 GGGGT-AAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTTG
* * *
76387 AGGGTAAAATGGTAA-TTTTGGAAGTTTTAGGGTTAAAAATGGGATTTTTGGAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTTG
**
76445 GGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTCAG
1 GGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTTG
* * * *
76504 AGGGTTAAAAAT-G-AGATTTTTGGAAG-TTCGAGGG-T--AAATGGTAATTTTTTGAAGTTTCG
1 -GGGGT-AAAATGGTA-ATTTTTGGAAGTTTTG-GGGTTAAAAATGG-GATTTTTAGAAGTTT-G
* * * ** ** *
76563 AGGTTAAAAATGG-GATTTTTAAAAGTTTAAGGGTTAAAAATGGGATTTTTAGAAGTTTT
1 GGGGT-AAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTTG
* *
76622 GGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTTGAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTTG
* * * *
76681 AGGGTAAAATGGTAATTTTTGGAAGTTTTGGGTTTTAAAAATGAGATTTTTAGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGAAGTTTTGGG-GTTAAAAATGGGATTTTTAGAAGTTTG
* * *
76741 GGGGTAAAATGGTAA-TTTTGGAAGTTTTGGGGTCAAAAATGAGA-TTTTAGGAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTA-GAAGTTTG
* * *
76799 AGGGTAAAATGGTAAATTTCGGATAGTTT
1 GGGGTAAAATGGTAATTTTTGGA-AGTTT
76828 AGGGATCTTC
Statistics
Matches: 375, Mismatches: 49, Indels: 34
0.82 0.11 0.07
Matches are distributed among these distances:
57 11 0.03
58 123 0.33
59 153 0.41
60 77 0.21
61 11 0.03
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.37
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTTG
Found at i:78614 original size:6 final size:6
Alignment explanation
Indices: 78605--78661 Score: 82
Period size: 6 Copynumber: 9.8 Consensus size: 6
78595 AATTTTGAAG
*
78605 TTAAAT TTAAA- TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTTAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
78651 TCAAAT TTAAA
1 TTAAAT TTAAA
78662 ATAAATTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
5 8 0.18
6 37 0.82
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:78619 original size:23 final size:22
Alignment explanation
Indices: 78592--78661 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 22
78582 TTTTGGACTT
78592 TTTAATTTTGAAGTTAAATTTAAA
1 TTTAATTTT-AA-TTAAATTTAAA
* *
78616 TTAAATTTAAATTTAAATTTAAA
1 TTTAATTTTAA-TTAAATTTAAA
*
78639 TTTAAATTTTAATCAAATTTAAA
1 TTT-AATTTTAATTAAATTTAAA
78662 ATAAATTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
23 25 0.64
24 14 0.36
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (22 bp):
TTTAATTTTAATTAAATTTAAA
Found at i:78633 original size:12 final size:11
Alignment explanation
Indices: 78605--78668 Score: 83
Period size: 11 Copynumber: 5.6 Consensus size: 11
78595 AATTTTGAAG
78605 TTAAATTTAAA
1 TTAAATTTAAA
78616 TTAAATTTAAA
1 TTAAATTTAAA
78627 TTTAAATTTAAA
1 -TTAAATTTAAA
*
78639 TTTAAATTTTAA
1 -TTAAATTTAAA
*
78651 TCAAATTTAAA
1 TTAAATTTAAA
*
78662 ATAAATT
1 TTAAATT
78669 AAAAAGGGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 25 0.53
12 22 0.47
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:78663 original size:18 final size:17
Alignment explanation
Indices: 78605--78671 Score: 91
Period size: 17 Copynumber: 3.9 Consensus size: 17
78595 AATTTTGAAG
78605 TTAAATTTAAATTAAAT
1 TTAAATTTAAATTAAAT
78622 TTAAATTTAAATTTAAAT
1 TTAAATTTAAA-TTAAAT
* *
78640 TTAAATTTTAATCAAAT
1 TTAAATTTAAATTAAAT
*
78657 TTAAA-ATAAATTAAA
1 TTAAATTTAAATTAAA
78672 AAGGGCCCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
16 7 0.16
17 21 0.48
18 16 0.36
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAATTTAAATTAAAT
Found at i:82176 original size:24 final size:24
Alignment explanation
Indices: 82132--82178 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
82122 TGGATGTTCA
* *
82132 ACCTTTCATCTTTCTTGACCTTTG
1 ACCTTCCATCTTTCTTAACCTTTG
82156 ACCTTCCATC-TTCTTTAACCTTT
1 ACCTTCCATCTTTC-TTAACCTTT
82179 CATATTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.15, C:0.32, G:0.04, T:0.49
Consensus pattern (24 bp):
ACCTTCCATCTTTCTTAACCTTTG
Found at i:82484 original size:14 final size:14
Alignment explanation
Indices: 82465--82492 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
82455 ATATTTTAGG
82465 GATATAATTAGAAT
1 GATATAATTAGAAT
82479 GATATAATTAGAAT
1 GATATAATTAGAAT
82493 ATTTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (14 bp):
GATATAATTAGAAT
Found at i:85826 original size:18 final size:18
Alignment explanation
Indices: 85803--85845 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
85793 ATTTCAGTTG
85803 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
85821 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
85839 TAATTAA
1 TAATTAA
85846 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:88256 original size:13 final size:12
Alignment explanation
Indices: 88231--88284 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 12
88221 AGCGTTATAA
*
88231 AATATAAATAAT
1 AATATAAAAAAT
88243 AATATTAAAAAAT
1 AATA-TAAAAAAT
*
88256 AAT-TAAAACAT
1 AATATAAAAAAT
*
88267 GATA-AAAAAAT
1 AATATAAAAAAT
88278 -ATATAAA
1 AATATAAA
88285 TATAATACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 3 0.09
11 18 0.51
12 4 0.11
13 10 0.29
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (12 bp):
AATATAAAAAAT
Found at i:90954 original size:23 final size:23
Alignment explanation
Indices: 90924--91090 Score: 194
Period size: 23 Copynumber: 7.3 Consensus size: 23
90914 TATCTCTATG
*
90924 CTTAAATATTAATGTAATTTGTA
1 CTTAAATATTAATGTGATTTGTA
*
90947 CTTAAATATTAATATGATTTGTA
1 CTTAAATATTAATGTGATTTGTA
*
90970 CTTAAATATTAATATGATTTG-A
1 CTTAAATATTAATGTGATTTGTA
* * *
90992 GCTCAAATATTAATGTGATTTATG
1 -CTTAAATATTAATGTGATTTGTA
* *
91016 CTTAAATATTATTGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTA
*
91039 CTTAAATATTAATATGATTTAG-A
1 CTTAAATATTAATGTGATTT-GTA
* * *
91062 ATTAATTATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTA
91085 CTTAAA
1 CTTAAA
91091 AAATTAAGAT
Statistics
Matches: 122, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
22 2 0.02
23 119 0.98
24 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.47
Consensus pattern (23 bp):
CTTAAATATTAATGTGATTTGTA
Found at i:91020 original size:69 final size:69
Alignment explanation
Indices: 90927--91090 Score: 231
Period size: 69 Copynumber: 2.4 Consensus size: 69
90917 CTCTATGCTT
* *
90927 AAATATTAATGTAATTTGTACTTAAATATTAATATGATTTGTACTTAAATATTAATATGATTT-G
1 AAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTACTTAAATATTAATATGATTTAG
*
90991 AGCTC
66 A-ATC
* * * *
90996 AAATATTAATGTGATTTATGCTTAAATATTATTGTGATTTGTGCTTAAATATTAATATGATTTAG
1 AAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTACTTAAATATTAATATGATTTAG
*
91061 AATT
66 AATC
*
91065 AATTATTAATGTGATTTGTGCTTAAA
1 AAATATTAATGTGATTTGTGCTTAAA
91091 AAATTAAGAT
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
69 82 0.98
70 2 0.02
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.46
Consensus pattern (69 bp):
AAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTACTTAAATATTAATATGATTTAG
AATC
Found at i:91214 original size:36 final size:36
Alignment explanation
Indices: 91160--91273 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
91150 TGATGGCTGT
* * *
91160 TGTGAAAGTAAATGTGTGGGTATGTTCTTCATGCCA
1 TGTGATAGAAAATATGTGGGTATGTTCTTCATGCCA
*
91196 TGTGATAGAAAATATGTGGGTATGTTCTTCATACCA
1 TGTGATAGAAAATATGTGGGTATGTTCTTCATGCCA
* * * *
91232 TATGATAGAGAATATGTAGGTATGTTCTTCATGTCA
1 TGTGATAGAAAATATGTGGGTATGTTCTTCATGCCA
91268 TGTGAT
1 TGTGAT
91274 TAATTATAGT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.38
Consensus pattern (36 bp):
TGTGATAGAAAATATGTGGGTATGTTCTTCATGCCA
Found at i:94382 original size:6 final size:6
Alignment explanation
Indices: 94371--94409 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
94361 TGATCAAAAT
* * *
94371 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
94410 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:100903 original size:187 final size:188
Alignment explanation
Indices: 100671--101012 Score: 442
Period size: 187 Copynumber: 1.8 Consensus size: 188
100661 TAACGATGCT
* *
100671 ACTCACACGAGCTATCGAGAATATACATTCAAGCATAAATCCCAACCATCGTAGGGCTTGTAATC
1 ACTCACACGAGCTATCGAGAATATACATTCAAGCATAAATCCCAACCATCATAGGGCCTGTAATC
* *
100736 CATT-TTAGGATTTCATATCTC-T-TTTTTGACTCACGATATTGCTCACACGAGCTATCAAGGAC
66 CATTCTTA--AATTCATATCTCATCTTTTTGACTCACGATACTGCTCACACGAGCTATCAAGGAC
*
100798 TTGCAACAAATGCGGTACCTC-AGCCATTGATATTATTTTTGTGCATATAACTGTCCCTTA
129 TCGCAACAAATGCGGTACC-CAAGCCATTGATATTATTTTTGTGCATATAACTGTCCCTTA
* * * *
100858 ACTCACACGAGCTGTCGAGAGTATGCACTT-ATGCATAAATCCCAACCATCATAGGGCCTGTAAT
1 ACTCACACGAGCTATCGAGAATATACA-TTCAAGCATAAATCCCAACCATCATAGGGCCTGTAAT
* * * * * * * **
100922 TCATTCTTAAATTCATTTCTCATCTTTTTGATTCACGATACTGCTTATACGAGTTGTTGAGGACT
65 CCATTCTTAAATTCATATCTCATCTTTTTGACTCACGATACTGCTCACACGAGCTATCAAGGACT
*
100987 CGCAACATATGCGGTACCCAAGCCAT
130 CGCAACAAATGCGGTACCCAAGCCAT
101013 CGCGTCGATT
Statistics
Matches: 131, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
186 10 0.08
187 61 0.47
188 60 0.46
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (188 bp):
ACTCACACGAGCTATCGAGAATATACATTCAAGCATAAATCCCAACCATCATAGGGCCTGTAATC
CATTCTTAAATTCATATCTCATCTTTTTGACTCACGATACTGCTCACACGAGCTATCAAGGACTC
GCAACAAATGCGGTACCCAAGCCATTGATATTATTTTTGTGCATATAACTGTCCCTTA
Found at i:110956 original size:22 final size:22
Alignment explanation
Indices: 110930--110971 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
110920 TTTCTAATTT
110930 TTTTTTTAA-TTTATAAAAATA
1 TTTTTTTAATTTTATAAAAATA
*
110951 TTTTTTTAATTTTTTAAAAAT
1 TTTTTTTAATTTTATAAAAAT
110972 TAATTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTTTAATTTTATAAAAATA
Found at i:112364 original size:19 final size:19
Alignment explanation
Indices: 112340--112383 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
112330 ATTTTTCTCA
112340 TAAAAATCA-TTAAAAATT
1 TAAAAATCATTTAAAAATT
*
112358 GTAAAAATTATTTTAAAAATT
1 -TAAAAATCA-TTTAAAAATT
112379 TAAAA
1 TAAAA
112384 CTTTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 5 0.23
21 9 0.41
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
TAAAAATCATTTAAAAATT
Found at i:113202 original size:16 final size:16
Alignment explanation
Indices: 113181--113221 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
113171 TCATAACTTT
113181 TGATAAAAAATATTAA
1 TGATAAAAAATATTAA
113197 TGATAATAAAAATATTAA
1 TGAT-A-AAAAATATTAA
113215 TGGATAA
1 T-GATAA
113222 TTTAATTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 2 0.09
18 13 0.59
19 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (16 bp):
TGATAAAAAATATTAA
Found at i:113209 original size:18 final size:19
Alignment explanation
Indices: 113186--113222 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
113176 ACTTTTGATA
113186 AAAAATATTAAT-GATAAT
1 AAAAATATTAATGGATAAT
113204 AAAAATATTAATGGATAAT
1 AAAAATATTAATGGATAAT
113223 TTAATTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (19 bp):
AAAAATATTAATGGATAAT
Found at i:113461 original size:29 final size:30
Alignment explanation
Indices: 113409--113471 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
113399 TTTAATGTAT
* * * *
113409 AATTATATACATGTATTTTGATTTT-ATGC
1 AATTATATACATGAAATTTCATTTTGATCC
*
113438 AATTTTATACATGAAATTTCATTTTGATCC
1 AATTATATACATGAAATTTCATTTTGATCC
113468 AATT
1 AATT
113472 CTTGTAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (30 bp):
AATTATATACATGAAATTTCATTTTGATCC
Found at i:118228 original size:21 final size:22
Alignment explanation
Indices: 118188--118229 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
118178 TTTAAAGTTT
118188 TAAAATTCATAAAAATTATAAG
1 TAAAATTCATAAAAATTATAAG
118210 TAAAACTT-ATAAAAA-TATAA
1 TAAAA-TTCATAAAAATTATAA
118230 TTTTCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 12 0.63
23 2 0.11
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATTCATAAAAATTATAAG
Found at i:118258 original size:20 final size:21
Alignment explanation
Indices: 118216--118269 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
118206 TAAGTAAAAC
*
118216 TTATAAAAATATAATTTTCTT
1 TTATTAAAATATAATTTTCTT
118237 TT-TTAAAATGATAATTTT-TT
1 TTATTAAAAT-ATAATTTTCTT
118257 TTATTAAAA-ATAA
1 TTATTAAAATATAA
118270 CATAATACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.13
20 10 0.33
21 16 0.53
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTATTAAAATATAATTTTCTT
Found at i:120069 original size:16 final size:17
Alignment explanation
Indices: 120030--120069 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
120020 AATAAAAATG
120030 TAATTTTATCATTTTAA
1 TAATTTTATCATTTTAA
*
120047 TAA-TTTAT-ATTTTTA
1 TAATTTTATCATTTTAA
120062 TAATTTTA
1 TAATTTTA
120070 AAGAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 9 0.43
16 9 0.43
17 3 0.14
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATTTTATCATTTTAA
Found at i:121949 original size:2 final size:2
Alignment explanation
Indices: 121937--121983 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
121927 ATTATTCAAA
*
121937 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
121980 AT AT
1 AT AT
121984 TTATTTATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:134474 original size:16 final size:16
Alignment explanation
Indices: 134453--134483 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
134443 CTGAATATAT
134453 TTATTTTTTATTTTTA
1 TTATTTTTTATTTTTA
134469 TTATTTTTTATTTTT
1 TTATTTTTTATTTTT
134484 TCCATAATTT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTATTTTTTATTTTTA
Found at i:134648 original size:15 final size:16
Alignment explanation
Indices: 134628--134666 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
134618 CATCAGAGGA
*
134628 TTTTTTTC-CTTTTTT
1 TTTTTTTCTCTTTTCT
134643 TTTTTTTCTCTTTTCT
1 TTTTTTTCTCTTTTCT
*
134659 TGTTTTTC
1 TTTTTTTC
134667 AGACAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTTTTCTCTTTTCT
Found at i:138803 original size:13 final size:13
Alignment explanation
Indices: 138785--138810 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
138775 TTCAATCACT
138785 CCATTATTTATAG
1 CCATTATTTATAG
138798 CCATTATTTATAG
1 CCATTATTTATAG
138811 TACATATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
CCATTATTTATAG
Found at i:138903 original size:231 final size:222
Alignment explanation
Indices: 138472--138927 Score: 714
Period size: 231 Copynumber: 2.0 Consensus size: 222
138462 GGAAGAACAC
*
138472 AAGATAATAAAAATAGAGCTTTTTATTGAACTAGGGTTTTTAAGAGATGGAGGATTTTTTCAATG
1 AAGATAATAAAAATAAAGCTTTTTATTGAACTAGGGTTTTTAAGAGATGGAGGATTTTTTCAATG
* * * *
138537 ATTTGAAAGTCGATAATTCAATCTCTCCATCCCCTATTTATAGTACATATAATTTCTTAGTTGAA
66 ATTTGAAAGTCAATAATTCAATCACTCCATCCACTATTTATAGTACATATAAATTCTTAGTTGAA
* * *
138602 TCCAATCTAAATTCTAAAATATAATTAGAATTTAAATCTAAACATTAATTCTCTAATTGAATCTA
131 TCCAATCTAAATTCTAAAAGATAATTAGAATTTAAATCTAAACATTAATTCCCTAATTGAATCCA
*
138667 CTTTAAACTTTAAAAGATAAATCTAAA
196 CTTTAAACTCTAAAAGATAAATCTAAA
138694 AAGATAATAAAAATAAAGCTTTTTATTGAACTAGGGTTTTTAAGAGATGGAGGATTTTTTCAATG
1 AAGATAATAAAAATAAAGCTTTTTATTGAACTAGGGTTTTTAAGAGATGGAGGATTTTTTCAATG
*
138759 ATTTGAAAGTCAATAATTCAATCACTCCATTATTTATAGCCATTATTTATAGTACATATAAATTC
66 ATTTGAAAGTCAATAATTCAATCACTCC-------AT--CCACTATTTATAGTACATATAAATTC
* *
138824 TTAGTTGAATCCGATCTAAATTCTAAAAGATAATTATAATTTAAATCTAAACATTAATTCCCTAA
122 TTAGTTGAATCCAATCTAAATTCTAAAAGATAATTAGAATTTAAATCTAAACATTAATTCCCTAA
*
138889 TTGGATCCACTTTAAACTCTAAAAGATAAATCTAAA
187 TTGAATCCACTTTAAACTCTAAAAGATAAATCTAAA
138925 AAG
1 AAG
138928 GTAAATACAA
Statistics
Matches: 212, Mismatches: 13, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
222 90 0.42
229 2 0.01
231 120 0.57
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (222 bp):
AAGATAATAAAAATAAAGCTTTTTATTGAACTAGGGTTTTTAAGAGATGGAGGATTTTTTCAATG
ATTTGAAAGTCAATAATTCAATCACTCCATCCACTATTTATAGTACATATAAATTCTTAGTTGAA
TCCAATCTAAATTCTAAAAGATAATTAGAATTTAAATCTAAACATTAATTCCCTAATTGAATCCA
CTTTAAACTCTAAAAGATAAATCTAAA
Found at i:141784 original size:6 final size:6
Alignment explanation
Indices: 141759--141797 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
141749 TACAATAATA
* * *
141759 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
141798 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:153382 original size:35 final size:34
Alignment explanation
Indices: 153343--153452 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 34
153333 CCAAACTCAT
**
153343 TTTAAATTTATTTTAAGA-TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTAATTT-AAA
*
153378 TTTAAATTTATTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
* *
153412 TTTAACTTTATTTTCAAATTTAAAATT-ATTATAAA
1 TTTAAATTTATTTT-AAATTTAAATTTAATT-TAAA
153447 TTTAAA
1 TTTAAA
153453 ATAAATAAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
34 19 0.29
35 46 0.71
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
Found at i:153386 original size:6 final size:6
Alignment explanation
Indices: 153375--153452 Score: 58
Period size: 6 Copynumber: 13.5 Consensus size: 6
153365 ATTTGTTTTA
* * *
153375 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AACTTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
153421 -ATTTT CAAATTT AAAATT --ATTAT AAATTT AAA
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAA
153453 ATAAATAAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
4 2 0.04
5 14 0.25
6 34 0.60
7 7 0.12
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:153392 original size:11 final size:11
Alignment explanation
Indices: 153378--153433 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
153368 TGTTTTAAAA
153378 TTTAAATTTAT
1 TTTAAATTTAT
*
153389 TTTAAATTTAAA
1 TTTAAATTT-AT
*
153401 TTT-AATTTAAG
1 TTTAAATTT-AT
*
153412 TTTAACTTTAT
1 TTTAAATTTAT
153423 TTTCAAATTTA
1 TTT-AAATTTA
153434 AAATTATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 23 0.62
12 14 0.38
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:153410 original size:52 final size:52
Alignment explanation
Indices: 153343--153452 Score: 157
Period size: 52 Copynumber: 2.1 Consensus size: 52
153333 CCAAACTCAT
* * * *
153343 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAATTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
* * *
153395 TTTAAATTTAATTTAAGTTTAACTTTATTTTCAAATTTAAAATTATTATAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
153447 TTTAAA
1 TTTAAA
153453 ATAAATAAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (52 bp):
TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
Found at i:153454 original size:17 final size:17
Alignment explanation
Indices: 153343--153452 Score: 132
Period size: 17 Copynumber: 6.4 Consensus size: 17
153333 CCAAACTCAT
153343 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
153361 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
153378 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
153395 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
153412 TTTAACTTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
153430 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
153447 TTTAAA
1 TTTAAA
153453 ATAAATAAAG
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
17 52 0.66
18 27 0.34
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:154099 original size:30 final size:29
Alignment explanation
Indices: 154030--154346 Score: 288
Period size: 29 Copynumber: 10.8 Consensus size: 29
154020 GGCGTCCCTA
*
154030 AACTGTCCAAAAATCCCATTTTTACCCTTG
1 AACT-TCCAAAAATCCCATTTTTACCCTCG
* * **
154060 AACTACCAAAAATCTCATTTTTAACCCTAA
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG
* * * *
154090 AACTTCCAAAAATCTCATTTTCACCCCCA
1 AACTTCCAAAAATCCCATTTTTACCCTCG
* *
154119 AACTTCAAAAAATCCTATTTTTGACCCTCG
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG
*
154149 AATTTCCAAAAATCCCATTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
*
154178 AACTTCCAAAAATCCCATTTTTGA-AC-CG
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG
*
154206 AACTTCCAAAAATTCCATTTTTGACCC-CG
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG
** *
154235 AACTTTTAAAAATCCCATTTTTAACCC-CAA
1 AACTTCCAAAAATCCCATTTTT-ACCCTC-G
* *
154265 AACTTCCAAAACTTCCATTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
*
154294 AAAC-TCTCAAAATTACCC-TTTTTACCCTCG
1 -AACTTC-CAAAAAT-CCCATTTTTACCCTCG
* *
154324 AA-TGTCTAAAAATTCCATTTTTA
1 AACT-TCCAAAAATCCCATTTTTA
154347 AACCTTGAAT
Statistics
Matches: 239, Mismatches: 36, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
28 27 0.11
29 114 0.48
30 96 0.40
31 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCTCG
Found at i:154130 original size:59 final size:58
Alignment explanation
Indices: 154025--154295 Score: 278
Period size: 59 Copynumber: 4.6 Consensus size: 58
154015 CCCTAGGCGT
** * *
154025 CCCTAAACTGTCCAAAAATCCCATTTTTACCCTTGAACTACCAAAAATCTCATTTTTAA
1 CCCTAAACT-TCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAA
* * * * * *
154084 CCCTAAAACTTCCAAAAATCTCATTTTCACCCCCAAACTTCAAAAAATCCTATTTTTGA
1 CCCT-AAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAA
* * *
154143 CCCTCGAATTTCCAAAAATCCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAA
1 CCCT-AAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTT-AA
* * **
154203 -CC-GAACTTCCAAAAATTCCATTTTTGA-CCCCGAACTTTTAAAAATCCCATTTTTAA
1 CCCTAAACTTCCAAAAATCCCATTTTT-ACCCCCGAACTTCCAAAAATCCCATTTTTAA
* * * *
154259 CCCCAAAACTTCCAAAACTTCCATTTTTACCCTCGAA
1 -CCCTAAACTTCCAAAAATCCCATTTTTACCCCCGAA
154296 ACTCTCAAAA
Statistics
Matches: 177, Mismatches: 28, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
56 2 0.01
57 45 0.25
58 4 0.02
59 120 0.68
60 6 0.03
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (58 bp):
CCCTAAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAA
Found at i:154306 original size:59 final size:57
Alignment explanation
Indices: 154029--154346 Score: 272
Period size: 59 Copynumber: 5.4 Consensus size: 57
154019 AGGCGTCCCT
* * * * *
154029 AAACTGTCCAAAAATCCCATTTTTACCCTTGAACTACCAAAAATCTCATTTTTAACCCTA
1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACT-TCAAAAATCCCATTTTTAACCC-C
* * * * *
154089 AAACTTCCAAAAA-TCTCATTTTCACCCCCAAACTTCAAAAAATCCTATTTTTGACCCTC
1 AAACTTCCAAAAATTC-CATTTTTACCCTCGAACTTC-AAAAATCCCATTTTTAACCC-C
* * *
154148 GAATTTCCAAAAATCCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAA--CC
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTT-CAAAAATCCCATTTTT-AACCCC
* *
154205 GAACTTCCAAAAATTCCATTTTTGACCC-CGAACTTTTAAAAATCCCATTTTTAACCCC
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCGAAC-TTCAAAAATCCCATTTTTAACCCC
* *
154263 AAAACTTCCAAAACTTCCATTTTTACCCTCGAAACTCTCAAAATTACCC-TTTTT-ACCCTC
1 -AAACTTCCAAAAATTCCATTTTTACCCTCG-AACT-TCAAAAAT-CCCATTTTTAACCC-C
* *
154323 GAA-TGTCTAAAAATTCCATTTTTA
1 AAACT-TCCAAAAATTCCATTTTTA
154347 AACCTTGAAT
Statistics
Matches: 214, Mismatches: 28, Indels: 33
0.78 0.10 0.12
Matches are distributed among these distances:
56 2 0.01
57 42 0.20
58 16 0.07
59 128 0.60
60 23 0.11
61 3 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (57 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCAAAAATCCCATTTTTAACCCC
Found at i:158257 original size:25 final size:25
Alignment explanation
Indices: 158209--158267 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
158199 AGGCTTTGAA
*
158209 ATTTTTAATTTCCATATTTATTGTT
1 ATTTTTAATTTCAATATTTATTGTT
* *
158234 GTTTTTAATTTTAAT-TTTATTTGTT
1 ATTTTTAATTTCAATATTTA-TTGTT
*
158259 ATGTTTAAT
1 ATTTTTAAT
158268 AAAGGGGGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.24, C:0.03, G:0.07, T:0.66
Consensus pattern (25 bp):
ATTTTTAATTTCAATATTTATTGTT
Found at i:167897 original size:25 final size:25
Alignment explanation
Indices: 167863--167911 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
167853 AGGGTTCGCA
* *
167863 TACATCAAAAGTTCGCACAACAAAG
1 TACAACAAAAGTTAGCACAACAAAG
*
167888 TACAACAAAAGTTAGCACTACAAA
1 TACAACAAAAGTTAGCACAACAAA
167912 ATAAAATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.22, G:0.10, T:0.16
Consensus pattern (25 bp):
TACAACAAAAGTTAGCACAACAAAG
Found at i:169213 original size:13 final size:13
Alignment explanation
Indices: 169195--169233 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
169185 GGAGCACACA
*
169195 TAAAACATATCTT
1 TAAAACATAACTT
169208 TAAAACATAACTT
1 TAAAACATAACTT
* *
169221 GAAAACATCACTT
1 TAAAACATAACTT
169234 GAAAGTGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.31
Consensus pattern (13 bp):
TAAAACATAACTT
Found at i:172030 original size:91 final size:91
Alignment explanation
Indices: 171864--172070 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 91
171854 TCTTATCAAT
**
171864 ATGAATGAAATGATTTTCTTATTAACTACTAACATATTTGCATGAATTAATATGTACTCCTTAAA
1 ATGAATGAAATGATTTTCTTATTAACTACTAACATATTTGCATGAATTAATATGTAAGCCTTAAA
*
171929 CTTGAATTTATATTATTGTATAAGAA
66 CTTGAATTTATACTATTGTATAAGAA
*
171955 ATTAATGAAATGATTTTCTTATTAACTACTAACATATTTGCATGAATTAATATGTAAGCCTTGAA
1 ATGAATGAAATGATTTTCTTATTAACTACTAACATATTTGCATGAATTAATATGTAAGCCTT-AA
* *
172020 A-TTGATTTTATACTCTTGTATAAGAA
65 ACTTGAATTTATACTATTGTATAAGAA
* *
172046 ATGAATGAAATGGTTTTCATATTAA
1 ATGAATGAAATGATTTTCTTATTAA
172071 GGCTCCATTT
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
91 103 0.97
92 3 0.03
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (91 bp):
ATGAATGAAATGATTTTCTTATTAACTACTAACATATTTGCATGAATTAATATGTAAGCCTTAAA
CTTGAATTTATACTATTGTATAAGAA
Found at i:172583 original size:45 final size:46
Alignment explanation
Indices: 172491--172585 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 46
172481 AAATTAGTAG
** * * * * *
172491 TACACCACATGATAACTACAATATTTTCTAAGTGCTTGACTAGTAT
1 TACACCACATGATAACTACAATATCGTCCAAATGCATAACTAATAT
*
172537 TACA-CACATGATAACTACTATATCGTCCAAATGCATAACTAATAT
1 TACACCACATGATAACTACAATATCGTCCAAATGCATAACTAATAT
172582 TACA
1 TACA
172586 AAATAGTAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
45 37 0.90
46 4 0.10
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (46 bp):
TACACCACATGATAACTACAATATCGTCCAAATGCATAACTAATAT
Done.