Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011759.1 Kokia drynarioides strain JFW-HI SEQ_126754, 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: 98581
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:9629 original size:22 final size:22
Alignment explanation
Indices: 9574--9630 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
9564 TATTTTTATT
*
9574 TAAATT-TAATTATAAAAAATA
1 TAAATTATAAATATAAAAAATA
* * *
9595 TATAA-TATTAATATAAAAATTG
1 TA-AATTATAAATATAAAAAATA
9617 TAAATTATAAATAT
1 TAAATTATAAATAT
9631 TTTATTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATTATAAATATAAAAAATA
Found at i:15388 original size:60 final size:58
Alignment explanation
Indices: 15295--15423 Score: 186
Period size: 60 Copynumber: 2.2 Consensus size: 58
15285 TTAATATAAC
* * *
15295 ATTTGGCACCTGAATTTGAAACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTGACTCA
1 ATTTGGTACCTGAACTTGAAACTTTTTCCTAATTTGGTACCT-AA-TCTTTTTTGACTCA
* * *
15355 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAATCTTTTTTGACTTA
1 ATTTGGTACCTGAACTTGAAACTTTTTCCTAATTTGGTACCTAATCTTTTTTGACTCA
15413 ATTTGGTACCT
1 ATTTGGTACCT
15424 AATCTTTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 22 0.35
59 2 0.03
60 38 0.61
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (58 bp):
ATTTGGTACCTGAACTTGAAACTTTTTCCTAATTTGGTACCTAATCTTTTTTGACTCA
Found at i:15416 original size:27 final size:28
Alignment explanation
Indices: 15322--15449 Score: 113
Period size: 28 Copynumber: 4.5 Consensus size: 28
15312 GAAACTTTTT
*
15322 CCTAATTTGGTACCTAAACTTTTTTTTGA
1 CCTAATTTGGTACCTAATC-TTTTTTTGA
*
15351 -CTCAATTTGGTACTTGAA-CTTGACACTTTTT--
1 CCT-AATTTGGTACCT-AATCTT-----TTTTTGA
15382 CCTAATTTGGTACCTAATC-TTTTTTGA
1 CCTAATTTGGTACCTAATCTTTTTTTGA
*
15409 CTTAATTTGGTACCTAATCTTTTTTTGA
1 CCTAATTTGGTACCTAATCTTTTTTTGA
*
15437 CCCAATTTGGTAC
1 CCTAATTTGGTAC
15450 TTGAACTTGA
Statistics
Matches: 82, Mismatches: 5, Indels: 25
0.73 0.04 0.22
Matches are distributed among these distances:
25 5 0.06
27 18 0.22
28 23 0.28
29 12 0.15
30 5 0.06
31 12 0.15
32 2 0.02
33 5 0.06
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.47
Consensus pattern (28 bp):
CCTAATTTGGTACCTAATCTTTTTTTGA
Found at i:15493 original size:87 final size:87
Alignment explanation
Indices: 15324--15492 Score: 286
Period size: 86 Copynumber: 2.0 Consensus size: 87
15314 AACTTTTTCC
*
15324 TAATTTGGTACCTAAACTTTTTTTTGACTCAATTTGGTACTTGAACTTGACACTTTTTCCTAATT
1 TAATTTGGTACCTAAACTTTTTTTTGACCCAATTTGGTACTTGAACTTGACACTTTTTCCTAATT
*
15389 TGGTACCTAATCTTTTTTGACT
66 TGGTACCTAAACTTTTTTGACT
* **
15411 TAATTTGGTACCTAATC-TTTTTTTGACCCAATTTGGTACTTGAACTTGACACTTTTTTTTAATT
1 TAATTTGGTACCTAAACTTTTTTTTGACCCAATTTGGTACTTGAACTTGACACTTTTTCCTAATT
15475 TGGTACCTAAACTTTTTT
66 TGGTACCTAAACTTTTTT
15493 TTTTTACCCA
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
86 61 0.79
87 16 0.21
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (87 bp):
TAATTTGGTACCTAAACTTTTTTTTGACCCAATTTGGTACTTGAACTTGACACTTTTTCCTAATT
TGGTACCTAAACTTTTTTGACT
Found at i:15503 original size:62 final size:62
Alignment explanation
Indices: 15409--15556 Score: 178
Period size: 62 Copynumber: 2.4 Consensus size: 62
15399 TCTTTTTTGA
* * * *
15409 CTTAATTTGGTACCT-AA--TCTTTTTTTGACCCAATTTGGTACTTGAACTTGACACTTTTTT
1 CTTAATTTGGTACCTAAACTTTTTTTTTTGACCCAATTTGATACCTAAACTTGACA-TTTTTT
* *
15469 -TTAATTTGGTACCTAAACTTTTTTTTTTTACCCAATTTGATACCTAAACTTGGCATTTTTT
1 CTTAATTTGGTACCTAAACTTTTTTTTTTGACCCAATTTGATACCTAAACTTGACATTTTTT
* * *
15530 CCTAACTTGGTACCTAAGCTTTTTTTT
1 CTTAATTTGGTACCTAAACTTTTTTTT
15557 AGATTTAATT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
59 14 0.19
60 2 0.03
61 6 0.08
62 53 0.71
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.49
Consensus pattern (62 bp):
CTTAATTTGGTACCTAAACTTTTTTTTTTGACCCAATTTGATACCTAAACTTGACATTTTTT
Found at i:15545 original size:31 final size:31
Alignment explanation
Indices: 15317--15546 Score: 128
Period size: 31 Copynumber: 7.7 Consensus size: 31
15307 AATTTGAAAC
15317 TTTTTCCTAATTTGGTACCTAAACTT----T
1 TTTTTCCTAATTTGGTACCTAAACTTGACAT
* * * *
15344 TTTTTGACTCAATTTGGTACTTGAACTTGACAC
1 TTTTT-CCT-AATTTGGTACCTAAACTTGACAT
*
15377 TTTTTCCTAATTTGGTACCTAATCTT----T
1 TTTTTCCTAATTTGGTACCTAAACTTGACAT
** * *
15404 TTTGACTTAATTTGGTACCTAATCTT----T
1 TTTTTCCTAATTTGGTACCTAAACTTGACAT
* * * *
15431 TTTTGACCCAATTTGGTACTTGAACTTGACACT
1 TTTT-TCCTAATTTGGTACCTAAACTTGACA-T
* ***
15464 TTTTT-TTAATTTGGTACCTAAACTT-TTTT
1 TTTTTCCTAATTTGGTACCTAAACTTGACAT
* * *
15493 TTTTTACCCAATTTGATACCTAAACTTGGCAT
1 TTTTT-CCTAATTTGGTACCTAAACTTGACAT
*
15525 TTTTTCCTAACTTGGTACCTAA
1 TTTTTCCTAATTTGGTACCTAA
15547 GCTTTTTTTT
Statistics
Matches: 153, Mismatches: 35, Indels: 26
0.71 0.16 0.12
Matches are distributed among these distances:
27 32 0.21
28 19 0.12
29 22 0.14
31 62 0.41
32 8 0.05
33 10 0.07
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.48
Consensus pattern (31 bp):
TTTTTCCTAATTTGGTACCTAAACTTGACAT
Found at i:15781 original size:59 final size:60
Alignment explanation
Indices: 15717--15864 Score: 158
Period size: 59 Copynumber: 2.5 Consensus size: 60
15707 TTAATATTAA
** ***
15717 AAAAAGATTAGGTACCAAATTGGGAA-AAAGAGTCAAGTTTAGGTACCAAATTGAACCAC
1 AAAAAGATTAAATACCAAATTAAAAATAAAGAGTCAAGTTTAGGTACCAAATTGAACCAC
* * * **
15776 AAAAAGTTTAAATACCAACTTAAAAATAAAGTGTCAAGTTTAGGTACCAAATTGAATAAC
1 AAAAAGATTAAATACCAAATTAAAAATAAAGAGTCAAGTTTAGGTACCAAATTGAACCAC
* **
15836 -AAAAGTTTCGATACCAAATTAAAAA-AAAG
1 AAAAAGATTAAATACCAAATTAAAAATAAAG
15865 TATCAAATTC
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
58 4 0.05
59 41 0.55
60 30 0.40
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (60 bp):
AAAAAGATTAAATACCAAATTAAAAATAAAGAGTCAAGTTTAGGTACCAAATTGAACCAC
Found at i:15814 original size:60 final size:58
Alignment explanation
Indices: 15741--15870 Score: 179
Period size: 60 Copynumber: 2.2 Consensus size: 58
15731 CCAAATTGGG
* * *
15741 AAAAAGAGTCAAGTTTAGGTACCAAATTGAACCACAAAAAGTTTAAATACCAACTTAAA
1 AAAAAGTGTCAAGTTTAGGTACCAAATTGAACAAC-AAAAGTTTAAATACCAAATTAAA
* **
15800 AATAAAGTGTCAAGTTTAGGTACCAAATTGAATAACAAAAGTTTCGATACCAAATTAAA
1 AA-AAAGTGTCAAGTTTAGGTACCAAATTGAACAACAAAAGTTTAAATACCAAATTAAA
*
15859 AAAAAGTATCAA
1 AAAAAGTGTCAA
15871 ATTCAGATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
58 9 0.14
59 24 0.38
60 30 0.48
ACGTcount: A:0.51, C:0.13, G:0.12, T:0.24
Consensus pattern (58 bp):
AAAAAGTGTCAAGTTTAGGTACCAAATTGAACAACAAAAGTTTAAATACCAAATTAAA
Found at i:16892 original size:57 final size:58
Alignment explanation
Indices: 16809--16968 Score: 141
Period size: 57 Copynumber: 2.8 Consensus size: 58
16799 TTAATATAAT
* * * * * **
16809 ATTTGGTACTTGAATTTGATACTTTTT-TAAATTTGGTATCTAATTTTTTTTTACCTA
1 ATTTAGTACTTAAACTTGACACTTTTTCTAAATTTGGTACCTAAACTTTTTTTACCTA
* *
16866 ATTTAGTACTTAAACTTGACACTTTTTCTTAATTTGGTACCTAAACTTTTTTTGGACCCA
1 ATTTAGTACTTAAACTTGACACTTTTTCTAAATTTGGTACCTAAACTTTTTTT--ACCTA
* *
16926 ATTT-GATACCTGAACTT-AGCA-TTTTTCCT-AATTTGGTACCTAA
1 ATTTAG-TACTTAAACTTGA-CACTTTTT-CTAAATTTGGTACCTAA
16969 GCGTTTTATT
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
57 23 0.27
58 21 0.24
59 21 0.24
60 21 0.24
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (58 bp):
ATTTAGTACTTAAACTTGACACTTTTTCTAAATTTGGTACCTAAACTTTTTTTACCTA
Found at i:23196 original size:21 final size:21
Alignment explanation
Indices: 23158--23200 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
23148 GATTTCTATA
* *
23158 GATACAAGTGATAGTTCTACC
1 GATACAAGTGACACTTCTACC
23179 GATACAAGTGACACTTCTACC
1 GATACAAGTGACACTTCTACC
23200 G
1 G
23201 GCACAAGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (21 bp):
GATACAAGTGACACTTCTACC
Found at i:23206 original size:21 final size:21
Alignment explanation
Indices: 23161--23208 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
23151 TTCTATAGAT
* * *
23161 ACAAGTGATAGTTCTACCGAT
1 ACAAGTGACACTTCTACCGAC
*
23182 ACAAGTGACACTTCTACCGGC
1 ACAAGTGACACTTCTACCGAC
23203 ACAAGT
1 ACAAGT
23209 CATGCTCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (21 bp):
ACAAGTGACACTTCTACCGAC
Found at i:26595 original size:28 final size:28
Alignment explanation
Indices: 26500--26592 Score: 98
Period size: 28 Copynumber: 3.3 Consensus size: 28
26490 GTCTCATCAT
*
26500 AAAGGCGTCCTTTGATAGAGATT-GCCAC
1 AAAGGCTTCCTTTGATAGAG-TTAGCCAC
* * * *
26528 AAAGGCATCCTTTGATAAAGTCAGCCAT
1 AAAGGCTTCCTTTGATAGAGTTAGCCAC
* * *
26556 AAAGACTTCTTTTGACAGAGTTAGCCAC
1 AAAGGCTTCCTTTGATAGAGTTAGCCAC
26584 AAAGGCTTC
1 AAAGGCTTC
26593 TTTCGAGAGG
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
27 1 0.02
28 51 0.98
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (28 bp):
AAAGGCTTCCTTTGATAGAGTTAGCCAC
Found at i:29280 original size:22 final size:22
Alignment explanation
Indices: 29239--29281 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
29229 TTCTTCTTCT
* *
29239 TCTTCTTCTTTTTGTGATAATA
1 TCTTCTTCTTTCTCTGATAATA
*
29261 TCTTCTTCTTTCTCTTATAAT
1 TCTTCTTCTTTCTCTGATAAT
29282 TTGTTAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.05, T:0.60
Consensus pattern (22 bp):
TCTTCTTCTTTCTCTGATAATA
Found at i:32526 original size:6 final size:6
Alignment explanation
Indices: 32515--32558 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
32505 ATCATAAAAT
* *
32515 ATATAA ATATAA ATATCA ATATCA ATATCA ATATCA ATATCA AT
1 ATATCA ATATCA ATATCA ATATCA ATATCA ATATCA ATATCA AT
32559 TTATTTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATCA
Found at i:34306 original size:16 final size:16
Alignment explanation
Indices: 34285--34315 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34275 ACCTTTAAAA
*
34285 ATATTTTGAATTTTCC
1 ATATTTTAAATTTTCC
34301 ATATTTTAAATTTTC
1 ATATTTTAAATTTTC
34316 TAAAGTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.58
Consensus pattern (16 bp):
ATATTTTAAATTTTCC
Found at i:38242 original size:158 final size:158
Alignment explanation
Indices: 37948--38270 Score: 475
Period size: 158 Copynumber: 2.0 Consensus size: 158
37938 ATCTCTGTAT
* * * *
37948 CATGTAGTGCTCACACGAGCTGTGAAATGGGTCTGCTCACACGAGCTGTGGGTCGAGATGTTAGT
1 CATGTAATGCTCACACGAGCTGTGAAATGGGCCTGCTCACACGAGCTGTGGGTCAAGATGTTAGG
* * * ** * *
38013 CTACACGATGCTGCTCACACGAGTTGTGGAGAATTTGTAACATATGCTGGATCTCAGCCATCGGT
66 CTACACAATGCTGCTCACACAAGCTGTGGAGAATCCGCAACAAATGCTGGATCTCAGCCATCGGT
38078 AAGACATCTAAGACCAGCACCCATAGAA
131 AAGACATCTAAGACCAGCACCCATAGAA
*
38106 CATGTAATGCTCACACGAGCTGTGAAGTGGGCCTGCTCACACGAGCTGTGGGTCAAGATGTTAGG
1 CATGTAATGCTCACACGAGCTGTGAAATGGGCCTGCTCACACGAGCTGTGGGTCAAGATGTTAGG
* * *
38171 CTACACAATGCTTCTCACACAAGCTGTGGAGAATCCGCAACAAATGCTGGATCTCAGCTATTGGT
66 CTACACAATGCTGCTCACACAAGCTGTGGAGAATCCGCAACAAATGCTGGATCTCAGCCATCGGT
* * * *
38236 AGGACATCTAAGACCAGCACTCGTATAA
131 AAGACATCTAAGACCAGCACCCATAGAA
38264 CATGTAA
1 CATGTAA
38271 ATCCCGAAAT
Statistics
Matches: 146, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
158 146 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (158 bp):
CATGTAATGCTCACACGAGCTGTGAAATGGGCCTGCTCACACGAGCTGTGGGTCAAGATGTTAGG
CTACACAATGCTGCTCACACAAGCTGTGGAGAATCCGCAACAAATGCTGGATCTCAGCCATCGGT
AAGACATCTAAGACCAGCACCCATAGAA
Found at i:44314 original size:23 final size:23
Alignment explanation
Indices: 44288--44335 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
44278 TTTGAGCGGA
*
44288 AATTCAGAATGAAGTTGTTGAAC
1 AATTCAGAATGAAGTTGTTCAAC
44311 AATTCAGAATGAAGTTGTTCAAC
1 AATTCAGAATGAAGTTGTTCAAC
44334 AA
1 AA
44336 ACACATCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (23 bp):
AATTCAGAATGAAGTTGTTCAAC
Found at i:47267 original size:23 final size:25
Alignment explanation
Indices: 47228--47288 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
47218 GAAAGAGAGG
*
47228 AAGAAGAAAGAAAGAATT-GAGAGAA
1 AAGAAGAAA-ATAGAATTGGAGAGAA
*
47253 AGGAA-AAAATAGAATTGGAGAGAA
1 AAGAAGAAAATAGAATTGGAGAGAA
47277 AAGAAGAAAATA
1 AAGAAGAAAATA
47289 AACATATTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 7 0.23
24 14 0.45
25 10 0.32
ACGTcount: A:0.64, C:0.00, G:0.26, T:0.10
Consensus pattern (25 bp):
AAGAAGAAAATAGAATTGGAGAGAA
Found at i:53719 original size:23 final size:23
Alignment explanation
Indices: 53693--53749 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
53683 TGACGTCGCA
53693 TCCAATCAGCAGCTTCTAGAAGG
1 TCCAATCAGCAGCTTCTAGAAGG
*
53716 TCCAATCAACAGCTTCTAGAAGG
1 TCCAATCAGCAGCTTCTAGAAGG
*
53739 TCCAGTCAGCA
1 TCCAATCAGCA
53750 ATGATGAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (23 bp):
TCCAATCAGCAGCTTCTAGAAGG
Found at i:55527 original size:29 final size:31
Alignment explanation
Indices: 55472--55725 Score: 140
Period size: 30 Copynumber: 8.5 Consensus size: 31
55462 TGAAAACAGA
*
55472 GTAAATGTGTTATTTTTAGAAAGTTTG-GGG
1 GTAAATATGTTATTTTTAGAAAGTTTGAGGG
55502 GTAAATATGTTATTTTTA-AAAGTTTGAGGG
1 GTAAATATGTTATTTTTAGAAAGTTTGAGGG
* * * *
55532 GCAAAAAAGTTATTTTTTG-AAGTTT-AGGG
1 GTAAATATGTTATTTTTAGAAAGTTTGAGGG
* * * * *
55561 GCAAAAAT-ATAATTTTAGAGAAGTTTGA-AG
1 GTAAATATGTTATTTTTAGA-AAGTTTGAGGG
* * *
55591 GTAAAAATG-TAATTTTAGAGAAGTTCGA-GG
1 GTAAATATGTTATTTTTAGA-AAGTTTGAGGG
* * *
55621 GTAAAAAT-TTAATTTTAGAGAAGTTAT-A-TG
1 GTAAATATGTTATTTTTAGA-AAGTT-TGAGGG
* * * * *
55651 GTAAAAATGTGATTCTT-GAAAGTTCGAAGG
1 GTAAATATGTTATTTTTAGAAAGTTTGAGGG
* * *
55681 GTAAAAAAGTGATTTTT-GAAAGTTTGA-GG
1 GTAAATATGTTATTTTTAGAAAGTTTGAGGG
* *
55710 GTAAAAATGTAATTTT
1 GTAAATATGTTATTTT
55726 GTTAGAGGAG
Statistics
Matches: 188, Mismatches: 25, Indels: 23
0.80 0.11 0.10
Matches are distributed among these distances:
28 7 0.04
29 41 0.22
30 134 0.71
31 6 0.03
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.37
Consensus pattern (31 bp):
GTAAATATGTTATTTTTAGAAAGTTTGAGGG
Found at i:55766 original size:122 final size:118
Alignment explanation
Indices: 55572--55874 Score: 376
Period size: 122 Copynumber: 2.5 Consensus size: 118
55562 CAAAAATATA
* * * *
55572 ATTTTAGAGAAGTTTGAAGGTAAAAATGTAATTTTAGAGAAGTTCGAGGGTAAAAATTTAATTTT
1 ATTTTTGA-AAGTTTGAGGGTAAAAATGTAATTTTAGAGAAGTTCGAGGGTAAAAATGTAATTTC
* *
55637 AGAGAAG-TTATATGGTAAAAATGTGATTCTTGAAAGTTCGAAGGGTAAAAAAGTG
65 AAAGAAGTTTA-AGGGTAAAAATGTGATTCTTGAAAGTT-GAAGGGTAAAAAAGTG
*
55692 ATTTTTGAAAGTTTGAGGGTAAAAATGTAATTTTGTTAGAGGAGTTCGAGGGTAAAAATGTAATT
1 ATTTTTGAAAGTTTGAGGGTAAAAATGTAA--TT-TTAGAGAAGTTCGAGGGTAAAAATGTAATT
* * * ***
55757 TCAAAGAAGTTTAAGGGTAAAAATGTGATTTTTGGAAGTTTAAGGGTAAAATTTTG
63 TCAAAGAAGTTTAAGGGTAAAAATGTGATTCTTGAAAGTTGAAGGGTAAAAAAGTG
* * * * *
55813 ATTTTTG-ATGTTTGGGGGCAAAAATGTAATATTAGAGAAGTTCGAGGGTGAAAATGTAATTT
1 ATTTTTGAAAGTTTGAGGGTAAAAATGTAATTTTAGAGAAGTTCGAGGGTAAAAATGTAATTT
55875 TTTTTTTAAA
Statistics
Matches: 160, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
117 29 0.18
118 1 0.01
119 21 0.13
120 26 0.16
121 21 0.13
122 59 0.37
123 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (118 bp):
ATTTTTGAAAGTTTGAGGGTAAAAATGTAATTTTAGAGAAGTTCGAGGGTAAAAATGTAATTTCA
AAGAAGTTTAAGGGTAAAAATGTGATTCTTGAAAGTTGAAGGGTAAAAAAGTG
Found at i:55776 original size:30 final size:30
Alignment explanation
Indices: 55550--55875 Score: 245
Period size: 30 Copynumber: 10.9 Consensus size: 30
55540 GTTATTTTTT
* * *
55550 GAAGTTTAGGGGCAAAAATATAATTTTAGA
1 GAAGTTTAAGGGTAAAAATGTAATTTTAGA
55580 GAAGTTTGAA-GGTAAAAATGTAATTTTAGA
1 GAAGTTT-AAGGGTAAAAATGTAATTTTAGA
** *
55610 GAAGTTCGAGGGTAAAAATTTAATTTTAGA
1 GAAGTTTAAGGGTAAAAATGTAATTTTAGA
* *
55640 GAAG-TTATATGGTAAAAATGTGATTCTT-GA
1 GAAGTTTA-AGGGTAAAAATGTAATT-TTAGA
* * * *
55670 -AAGTTCGAAGGGTAAAAAAGTGATTTTTGA
1 GAAGTT-TAAGGGTAAAAATGTAATTTTAGA
*
55700 -AAGTTTGAGGGTAAAAATGTAATTTTGTTAGA
1 GAAGTTTAAGGGTAAAAATGTAA--TT-TTAGA
* ** * *
55732 GGAGTTCGAGGGTAAAAATGTAATTTCAAA
1 GAAGTTTAAGGGTAAAAATGTAATTTTAGA
* *
55762 GAAGTTTAAGGGTAAAAATGTGATTTTTG-
1 GAAGTTTAAGGGTAAAAATGTAATTTTAGA
* * * *
55791 GAAGTTTAAGGGTAAAATTTTGATTTT--T
1 GAAGTTTAAGGGTAAAAATGTAATTTTAGA
* ** * *
55819 GATGTTTGGGGGCAAAAATGTAATATTAGA
1 GAAGTTTAAGGGTAAAAATGTAATTTTAGA
** *
55849 GAAGTTCGAGGGTGAAAATGTAATTTT
1 GAAGTTTAAGGGTAAAAATGTAATTTT
55876 TTTTTTAAAA
Statistics
Matches: 235, Mismatches: 47, Indels: 28
0.76 0.15 0.09
Matches are distributed among these distances:
28 19 0.08
29 45 0.19
30 139 0.59
31 8 0.03
32 4 0.02
33 20 0.09
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.34
Consensus pattern (30 bp):
GAAGTTTAAGGGTAAAAATGTAATTTTAGA
Found at i:55795 original size:29 final size:29
Alignment explanation
Indices: 55500--55876 Score: 202
Period size: 30 Copynumber: 12.7 Consensus size: 29
55490 GAAAGTTTGG
* * ** *
55500 GGGTAAATATGTTATTTTTAAAAGTTTGAG
1 GGGTAAAAATGTAATTTTTGGAAGTTT-AA
* * * * *
55530 GGGCAAAAAAGTTATTTTTTGAAGTTTAG
1 GGGTAAAAATGTAATTTTTGGAAGTTTAA
* * *
55559 GGGCAAAAATATAATTTTAGAGAAGTTTGAA
1 GGGTAAAAATGTAATTTTTG-GAAGTTT-AA
* **
55590 -GGTAAAAATGTAATTTTAGAGAAGTTCGA
1 GGGTAAAAATGTAATTTTTG-GAAGTTTAA
* *
55619 GGGTAAAAATTTAATTTTAGAGAAG-TTATA
1 GGGTAAAAATGTAATTTTTG-GAAGTTTA-A
* * * * *
55649 TGGTAAAAATGTGATTCTTGAAAGTTCGAA
1 GGGTAAAAATGTAATTTTTGGAAGTT-TAA
* * * *
55679 GGGTAAAAAAGTGATTTTTGAAAGTTTGA
1 GGGTAAAAATGTAATTTTTGGAAGTTTAA
* **
55708 GGGTAAAAATGTAATTTTGTTAGAGGAGTTCGA
1 GGGTAAAAATGTAA-TTT-TT-G-GAAGTTTAA
***
55741 GGGTAAAAATGTAATTTCAAAGAAGTTTAA
1 GGGTAAAAATGTAATTT-TTGGAAGTTTAA
*
55771 GGGTAAAAATGTGATTTTTGGAAGTTTAA
1 GGGTAAAAATGTAATTTTTGGAAGTTTAA
* * * * **
55800 GGGTAAAATTTTGATTTTT-GATGTTTGG
1 GGGTAAAAATGTAATTTTTGGAAGTTTAA
* * * **
55828 GGGCAAAAATGTAATATTAGAGAAGTTCGA
1 GGGTAAAAATGTAATTTTTG-GAAGTTTAA
*
55858 GGGTGAAAATGTAATTTTT
1 GGGTAAAAATGTAATTTTT
55877 TTTTTAAAAC
Statistics
Matches: 271, Mismatches: 64, Indels: 24
0.75 0.18 0.07
Matches are distributed among these distances:
28 19 0.07
29 61 0.23
30 163 0.60
31 4 0.01
32 4 0.01
33 20 0.07
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTAA
Found at i:56183 original size:30 final size:30
Alignment explanation
Indices: 56123--56181 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
56113 TTCAAAAAGG
56123 TTAATGGACTAAATTGAAAATGAAATAAAA
1 TTAATGGACTAAATTGAAAATGAAATAAAA
* *
56153 TTAATGG-GTAAATTTAAAAT-AAATTAAAA
1 TTAATGGACTAAATTGAAAATGAAA-TAAAA
56182 ATATGTTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 16 0.62
30 7 0.27
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.31
Consensus pattern (30 bp):
TTAATGGACTAAATTGAAAATGAAATAAAA
Found at i:61878 original size:24 final size:24
Alignment explanation
Indices: 61844--61903 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
61834 ACATCATCGA
*
61844 CATTTGTTCCTGCAACTGCTCTTG
1 CATTTGATCCTGCAACTGCTCTTG
*
61868 CATTTGATCCTGCAATTGCTCTTG
1 CATTTGATCCTGCAACTGCTCTTG
61892 CATTTGATCCTG
1 CATTTGATCCTG
61904 TATCTCTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.15, C:0.27, G:0.17, T:0.42
Consensus pattern (24 bp):
CATTTGATCCTGCAACTGCTCTTG
Found at i:65700 original size:29 final size:29
Alignment explanation
Indices: 65668--65854 Score: 98
Period size: 29 Copynumber: 6.4 Consensus size: 29
65658 TTTGAGGTTG
*
65668 AAAATGTGATTTTTGGAAATTTGAGGGCA
1 AAAATGTAATTTTTGGAAATTTGAGGGCA
** * *
65697 AAAATGATAA-TTTTGGATGTTCGAAGGC-
1 AAAATG-TAATTTTTGGAAATTTGAGGGCA
*
65725 AAAATGGTAATTTTT-G-AATGTTCAAGGGCA
1 AAAAT-GTAATTTTTGGAAAT-TT-GAGGGCA
* * *
65755 AAAATGTGATTTTT-GAAAGTTCGAGGGTA
1 AAAATGTAATTTTTGGAAA-TTTGAGGGCA
* * * * *
65784 AAAATGTGAGTATTGGAAGTTTAAGGG-A
1 AAAATGTAATTTTTGGAAATTTGAGGGCA
** ** * *
65812 AATTTGTAATTTTAAAGAAGTTTGAGGGTA
1 AAAATGTAATTTT-TGGAAATTTGAGGGCA
65842 AAAATGTAATTTT
1 AAAATGTAATTTT
65855 AAATAAGTTA
Statistics
Matches: 118, Mismatches: 29, Indels: 21
0.70 0.17 0.12
Matches are distributed among these distances:
27 1 0.01
28 19 0.16
29 72 0.61
30 25 0.21
31 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAATTTGAGGGCA
Found at i:66029 original size:29 final size:29
Alignment explanation
Indices: 65725--66079 Score: 191
Period size: 30 Copynumber: 12.1 Consensus size: 29
65715 GTTCGAAGGC
* * *
65725 AAAATGGTAATTTTTGAATGTTCAAGGGCA
1 AAAAT-GTAATTTTTGAAAGTTTAAGGGTA
* **
65755 AAAATGTGATTTTTGAAAGTTCGAGGGTA
1 AAAATGTAATTTTTGAAAGTTTAAGGGTA
* * * *
65784 AAAATGTGAGTATTGGAAGTTTAAGGG-A
1 AAAATGTAATTTTTGAAAGTTTAAGGGTA
** ** *
65812 AATTTGTAATTTTAAAGAAGTTTGAGGGTA
1 AAAATGTAATTTTTGA-AAGTTTAAGGGTA
**
65842 AAAATGTAATTTTAAATAAG-TTAAGGGGTA
1 AAAATGTAATTTTTGA-AAGTTTAA-GGGTA
** * *
65872 AAAATGTGGTTTTTGGAAGTTCAAGGGGTA
1 AAAATGTAATTTTTGAAAGTTTAA-GGGTA
* * * *
65902 AAATTGTGATTTTTGAAAGTTT-AGAAGCA
1 AAAATGTAATTTTTGAAAGTTTAAG-GGTA
* *
65931 AAAATGTAATTTTGGAAAAGTTTAAGCGTA
1 AAAATGTAATTTTTG-AAAGTTTAAGGGTA
* * ** *
65961 AAATTGTAA--TTTCAAAGAAATACGGGTA
1 AAAATGTAATTTTTGAAAG-TTTAAGGGTA
* * * * *
65989 AAAATATGATTTTTGAAAGTTTGAGCGCA
1 AAAATGTAATTTTTGAAAGTTTAAGGGTA
* * *
66018 AAAATGTAA-TTTTGAAGAAATTCAAGGGTG
1 AAAATGTAATTTTTG-A-AAGTTTAAGGGTA
* * *
66048 AAAATGTAATTTTTGATAGTTCAAGGTTA
1 AAAATGTAATTTTTGAAAGTTTAAGGGTA
66077 AAA
1 AAA
66080 CGTTATGTTT
Statistics
Matches: 244, Mismatches: 68, Indels: 27
0.72 0.20 0.08
Matches are distributed among these distances:
27 4 0.02
28 29 0.12
29 97 0.40
30 107 0.44
31 7 0.03
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAGTTTAAGGGTA
Found at i:66056 original size:87 final size:87
Alignment explanation
Indices: 65897--66059 Score: 224
Period size: 87 Copynumber: 1.9 Consensus size: 87
65887 GAAGTTCAAG
* * * *
65897 GGGTAAAATTGTGATTTTTGAAAGTTTAGAAGCAAAAATGTAATTTTGGAAAAGTTTAAGCGTAA
1 GGGTAAAAATATGATTTTTGAAAGTTTAGAAGCAAAAATGTAATTTTGGAAAAATTCAAGCGTAA
65962 AATTGTAATTTCAAAGAAATAC
66 AATTGTAATTTCAAAGAAATAC
* *
65984 GGGTAAAAATATGATTTTTGAAAGTTT-GAGCGCAAAAATGTAATTTT-GAAGAAATTCAAGGGT
1 GGGTAAAAATATGATTTTTGAAAGTTTAGA-AGCAAAAATGTAATTTTGGAA-AAATTCAAGCGT
66047 GAAAA-TGTAATTT
64 -AAAATTGTAATTT
66060 TTGATAGTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
86 5 0.07
87 58 0.87
88 4 0.06
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (87 bp):
GGGTAAAAATATGATTTTTGAAAGTTTAGAAGCAAAAATGTAATTTTGGAAAAATTCAAGCGTAA
AATTGTAATTTCAAAGAAATAC
Found at i:67786 original size:35 final size:34
Alignment explanation
Indices: 67745--67825 Score: 126
Period size: 35 Copynumber: 2.4 Consensus size: 34
67735 AATTAAACTT
67745 TAAATTTAAATTCAAAATAAATTTAAATTTTAAAA
1 TAAATTTAAATTCAAAATAAATTTAAA-TTTAAAA
* *
67780 TAAATTTAAACTCAGAATAAATTTAAATTTAAAA
1 TAAATTTAAATTCAAAATAAATTTAAATTTAAAA
*
67814 TAAATTAAAATT
1 TAAATTTAAATT
67826 TGAAATTGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 17 0.40
35 25 0.60
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (34 bp):
TAAATTTAAATTCAAAATAAATTTAAATTTAAAA
Found at i:67822 original size:5 final size:6
Alignment explanation
Indices: 67724--67832 Score: 59
Period size: 6 Copynumber: 18.3 Consensus size: 6
67714 AACTTGTAAT
* * *
67724 TTTAAA TTTTTAA -TTAAA CTTTAAA TTTAAA TTCAAA -ATAAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
67772 TTTTAAA -ATAAA TTTAAA CTCAGAA --TAAA TTTAAA TTTAAA -ATAAA
1 -TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA
*
67818 TTAAAA TTTGAAA TT
1 TTTAAA TTT-AAA TT
67833 GATTTCAATT
Statistics
Matches: 77, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
4 2 0.03
5 16 0.21
6 36 0.47
7 23 0.30
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:67826 original size:17 final size:17
Alignment explanation
Indices: 67745--67831 Score: 111
Period size: 17 Copynumber: 5.1 Consensus size: 17
67735 AATTAAACTT
*
67745 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
67762 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
* * *
67780 TAAATTTAAACTCAGAA
1 TAAATTTAAATTTAAAA
67797 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
67814 TAAATTAAAATTTGAAA
1 TAAATTTAAATTTAAAA
67831 T
1 T
67832 TGATTTCAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
17 44 0.73
18 16 0.27
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:68724 original size:29 final size:30
Alignment explanation
Indices: 68687--68746 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
68677 AAAATTTTAA
68687 TTTATCAAG-TATAAATAATCAATAAAATAT
1 TTTATCAAGATATAAATAA-CAATAAAATAT
* *
68717 TTTA-CAAGATATGAATTACAATAAAATAT
1 TTTATCAAGATATAAATAACAATAAAATAT
68746 T
1 T
68747 AGTGTGATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.37
Consensus pattern (30 bp):
TTTATCAAGATATAAATAACAATAAAATAT
Found at i:69209 original size:155 final size:155
Alignment explanation
Indices: 68927--69236 Score: 575
Period size: 155 Copynumber: 2.0 Consensus size: 155
68917 GAAATTAGAT
68927 AAATATAAGTAATCAATTAATTTTATAATAATTGAGTAATTGTTATGTAAATTTCGAAAAATTAA
1 AAATATAAGTAATCAATTAATTTTATAATAATTGAGTAATTGTTATGTAAATTTCGAAAAATTAA
* *
68992 TTAAGGATAGAAATGTTTAAATTTATACATGATCCCTTCCTAATTATTACACCAATAACAATCCC
66 TTAAAGATAGAAATGTTTAAATTTATACATAATCCCTTCCTAATTATTACACCAATAACAATCCC
69057 AATTCACTAAACAACTATTAATAAA
131 AATTCACTAAACAACTATTAATAAA
*
69082 AAATATAAGTAATCAATTAATTTTATAATAATTGAGTAATTGTTATGTAAATTTCGGAAAATTAA
1 AAATATAAGTAATCAATTAATTTTATAATAATTGAGTAATTGTTATGTAAATTTCGAAAAATTAA
*
69147 TTAAAGATAGAAATGTTTAAATTTATACATAATCCCTTCCTAATTATTACGCCAATAACAATCCC
66 TTAAAGATAGAAATGTTTAAATTTATACATAATCCCTTCCTAATTATTACACCAATAACAATCCC
*
69212 AATTCACTCAACAACTATTAATAAA
131 AATTCACTAAACAACTATTAATAAA
69237 CGTAATTATT
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
155 150 1.00
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (155 bp):
AAATATAAGTAATCAATTAATTTTATAATAATTGAGTAATTGTTATGTAAATTTCGAAAAATTAA
TTAAAGATAGAAATGTTTAAATTTATACATAATCCCTTCCTAATTATTACACCAATAACAATCCC
AATTCACTAAACAACTATTAATAAA
Found at i:71282 original size:24 final size:24
Alignment explanation
Indices: 71255--71359 Score: 174
Period size: 24 Copynumber: 4.4 Consensus size: 24
71245 TTTAGACAAC
71255 ACGAGCCCAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
*
71279 ACGAGCCTAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
*
71303 ACGAGCCTAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
* *
71327 ACGAGACCAGAATGATTAGCTTTT
1 ACGAGCCCAGAATGATTAGCTCTT
71351 ACGAGCCCA
1 ACGAGCCCA
71360 AACAGAGTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (24 bp):
ACGAGCCCAGAATGATTAGCTCTT
Found at i:72535 original size:16 final size:16
Alignment explanation
Indices: 72516--72546 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
72506 TTTAGCCTTA
*
72516 ATTAATTTTACTCATG
1 ATTAATTTAACTCATG
72532 ATTAATTTAACTCAT
1 ATTAATTTAACTCAT
72547 AATAACCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.48
Consensus pattern (16 bp):
ATTAATTTAACTCATG
Found at i:75815 original size:24 final size:24
Alignment explanation
Indices: 75748--75827 Score: 124
Period size: 24 Copynumber: 3.3 Consensus size: 24
75738 AGCCAACACG
* *
75748 AGCCTAGAATGATTAGCTCTTACG
1 AGCCCAGAATGATTAGCTCTTACA
* *
75772 AGCCTAGAATGTTTAGCTCTTACA
1 AGCCCAGAATGATTAGCTCTTACA
75796 AGCCCAGAATGATTAGCTCTTACA
1 AGCCCAGAATGATTAGCTCTTACA
75820 AGCCCAGA
1 AGCCCAGA
75828 CAGACACAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (24 bp):
AGCCCAGAATGATTAGCTCTTACA
Found at i:80178 original size:2 final size:2
Alignment explanation
Indices: 80171--80197 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
80161 TTCGCTCTTT
80171 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
80198 TTATGTGTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:86505 original size:41 final size:41
Alignment explanation
Indices: 86458--86536 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 41
86448 CTTATTGTAT
86458 TTTTAATTTGTTTGTTATTTT-ATGAATTGTTTTAATATCGG
1 TTTTAATTTGTTTGTTATTTTAAT-AATTGTTTTAATATCGG
* *
86499 TTTTAATTTGTTTGTTGTTTTAATATTTGTTTTAATAT
1 TTTTAATTTGTTTGTTATTTTAATAATTGTTTTAATAT
86537 TTTTAAGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 33 0.94
42 2 0.06
ACGTcount: A:0.22, C:0.01, G:0.13, T:0.65
Consensus pattern (41 bp):
TTTTAATTTGTTTGTTATTTTAATAATTGTTTTAATATCGG
Found at i:86530 original size:12 final size:12
Alignment explanation
Indices: 86513--86538 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
86503 AATTTGTTTG
86513 TTGTTTTAATAT
1 TTGTTTTAATAT
86525 TTGTTTTAATAT
1 TTGTTTTAATAT
86537 TT
1 TT
86539 TTAAGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Done.