Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015300.1 Kokia drynarioides strain JFW-HI SEQ_130345, 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: 72467
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 207 characters in sequence are not A, C, G, or T
Found at i:677 original size:18 final size:20
Alignment explanation
Indices: 640--677 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
630 AATTATATCT
*
640 ATTTATATTTTTCATTTTAA
1 ATTTATATTTTTCATGTTAA
660 ATTTAT-TTTTTCA-GTTAA
1 ATTTATATTTTTCATGTTAA
678 GAATTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 7 0.41
20 6 0.35
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
ATTTATATTTTTCATGTTAA
Found at i:682 original size:20 final size:20
Alignment explanation
Indices: 640--683 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
630 AATTATATCT
* *
640 ATTTATATTTTTCATTTTAA
1 ATTTATATTTTTCAGTTAAA
660 ATTTAT-TTTTTCAGTTAAGA
1 ATTTATATTTTTCAGTTAA-A
680 ATTT
1 ATTT
684 CATAACACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
ATTTATATTTTTCAGTTAAA
Found at i:1464 original size:22 final size:23
Alignment explanation
Indices: 1426--1469 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1416 GTTAATTTTT
1426 ATTTAAATTTTACATTA-AATTA
1 ATTTAAATTTTACATTATAATTA
*
1448 ATTTATATTTTGA-ATTATAATT
1 ATTTAAATTTT-ACATTATAATT
1470 TAAACGTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTAAATTTTACATTATAATTA
Found at i:3316 original size:26 final size:26
Alignment explanation
Indices: 3287--3342 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
3277 GAATTGGGAT
3287 TTTCTTTTTATCATTTCTATAAACTG
1 TTTCTTTTTATCATTTCTATAAACTG
3313 TTTCTTTTTATCATTTCTATAAACTG
1 TTTCTTTTTATCATTTCTATAAACTG
3339 TTTC
1 TTTC
3343 AAACAAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.21, C:0.16, G:0.04, T:0.59
Consensus pattern (26 bp):
TTTCTTTTTATCATTTCTATAAACTG
Found at i:4440 original size:17 final size:17
Alignment explanation
Indices: 4414--4514 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 17
4404 CTTTTTAATT
* *
4414 AATTTTAATTTACAATA
1 AATTTAAATTTAAAATA
4431 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
* * *
4448 AATTTAAACTCAAAAGTG
1 AATTTAAATTTAAAA-TA
* *
4466 AATTTAAATTTAGAACA
1 AATTTAAATTTAAAATA
* * *
4483 AATTCAAACTTAAAGTA
1 AATTTAAATTTAAAATA
* *
4500 AA-ATAAAGTTAAAAT
1 AATTTAAATTTAAAAT
4515 TTGGACTCAG
Statistics
Matches: 64, Mismatches: 19, Indels: 3
0.74 0.22 0.03
Matches are distributed among these distances:
16 9 0.14
17 42 0.66
18 13 0.20
ACGTcount: A:0.54, C:0.06, G:0.05, T:0.35
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:5629 original size:12 final size:12
Alignment explanation
Indices: 5612--5662 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
5602 TTGGAAATTT
*
5612 AGAAAGAGAGTG
1 AGAAAGAGAGAG
*
5624 AGAAAGAGAGAA
1 AGAAAGAGAGAG
* *
5636 AGAGAGAAAGAG
1 AGAAAGAGAGAG
5648 AGAAAGAGAGAG
1 AGAAAGAGAGAG
5660 AGA
1 AGA
5663 GAGATCTTAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (12 bp):
AGAAAGAGAGAG
Found at i:5633 original size:2 final size:2
Alignment explanation
Indices: 5616--5666 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
5606 AAATTTAGAA
* * * * *
5616 AG AG AG TG AG AA AG AG AG AA AG AG AG AA AG AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5658 AG AG AG AG A
1 AG AG AG AG A
5667 TCTTAGGTGA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.57, C:0.00, G:0.41, T:0.02
Consensus pattern (2 bp):
AG
Found at i:5634 original size:8 final size:8
Alignment explanation
Indices: 5623--5666 Score: 79
Period size: 8 Copynumber: 5.5 Consensus size: 8
5613 GAAAGAGAGT
5623 GAGAAAGA
1 GAGAAAGA
5631 GAGAAAGA
1 GAGAAAGA
5639 GAGAAAGA
1 GAGAAAGA
5647 GAGAAAGA
1 GAGAAAGA
*
5655 GAGAGAGA
1 GAGAAAGA
5663 GAGA
1 GAGA
5667 TCTTAGGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (8 bp):
GAGAAAGA
Found at i:6859 original size:21 final size:22
Alignment explanation
Indices: 6835--6878 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6825 AACCTTAATT
6835 TAAATTTAATTAT-AAAACATA
1 TAAATTTAATTATGAAAACATA
* *
6856 TAAATTTTATTATGAAAATATA
1 TAAATTTAATTATGAAAACATA
6878 T
1 T
6879 TTTTAGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATTTAATTATGAAAACATA
Found at i:13509 original size:49 final size:49
Alignment explanation
Indices: 13437--13784 Score: 277
Period size: 49 Copynumber: 7.1 Consensus size: 49
13427 TACAGGTCTC
* *
13437 AGTACCATGAA-ACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCT
1 AGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCT
* * * * * *
13485 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGTGAACCT
1 AGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCT
* * * *
13534 TGTACCTCAGAAG-CATGAAGGGAAATATTTAAGCCGCAACGGTGAATAC-
1 AGTACCAC-GAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAAT-CT
* * * *
13583 AGTACCACGAAGACATGAAGGGAAAGATTTAAGTCGCAATGACGAACCTT
1 AGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC-T
* * *
13633 A-TACCTC-AGAGACATGAATGGAAAGATTTAAACCGCAACGGCGAATAC-
1 AGTACCACGA-AGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAAT-CT
* * * * * * *
13681 AGTACCATGAAGATACGAAGGGAAATG-TTTAAGTCGCAATGGCAAACCTT
1 AGTACCACGAAGACATGAAGGGAAA-GATTTAAGCCGCAACGGCGAATC-T
* * *
13731 A-TACCTTA-GAAG-CATTAAAGGAAA-ATTTAAGCCGCAACGGCGAATTT
1 AGTACC--ACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCT
13778 AGTACCA
1 AGTACCA
13785 TGCGGATTGA
Statistics
Matches: 233, Mismatches: 50, Indels: 36
0.73 0.16 0.11
Matches are distributed among these distances:
46 1 0.00
47 2 0.01
48 38 0.16
49 177 0.76
50 14 0.06
51 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (49 bp):
AGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCT
Found at i:13630 original size:98 final size:97
Alignment explanation
Indices: 13453--13784 Score: 436
Period size: 98 Copynumber: 3.4 Consensus size: 97
13443 ATGAAACATA
*
13453 AAGGGAAAGATTTAAGCCGCAACGGCGAAT-CTAGTACCACGAAGATATGGAGGGAAAGGTTTAA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATAC-AGTACCACGAAGATATGAAGGGAAA-GTTTAA
* * *
13517 GTCGCAACGGTGAACCTTGTACCTCAGAAGCATG
64 GTCGCAATGGCGAACCTTATACCTCAGAAGCATG
* * *
13551 AAGGGAAATATTTAAGCCGCAACGGTGAATACAGTACCACGAAGACATGAAGGGAAAGATTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATACAGTACCACGAAGATATGAAGGGAAAG-TTTAAG
*
13616 TCGCAATGACGAACCTTATACCTCAG-AGACATG
65 TCGCAATGGCGAACCTTATACCTCAGAAG-CATG
* * * *
13649 AATGGAAAGATTTAAACCGCAACGGCGAATACAGTACCATGAAGATACGAAGGGAAATGTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATACAGTACCACGAAGATATGAAGGGAAA-GTTTAAG
* * *
13714 TCGCAATGGCAAACCTTATACCTTAGAAGCATT
65 TCGCAATGGCGAACCTTATACCTCAGAAGCATG
* **
13747 AAAGGAAA-ATTTAAGCCGCAACGGCGAATTTAGTACCA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATACAGTACCA
13785 TGCGGATTGA
Statistics
Matches: 206, Mismatches: 23, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
97 30 0.15
98 172 0.83
99 4 0.02
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (97 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAATACAGTACCACGAAGATATGAAGGGAAAGTTTAAGT
CGCAATGGCGAACCTTATACCTCAGAAGCATG
Found at i:14225 original size:17 final size:17
Alignment explanation
Indices: 14197--14255 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
14187 CAACAGAGTC
*
14197 TAAATCTATTTTAAAAT
1 TAAATTTATTTTAAAAT
* *
14214 TAAGTTTATTTTAAATT
1 TAAATTTATTTTAAAAT
** *
14231 TAAATTTATTGGAAATT
1 TAAATTTATTTTAAAAT
14248 TAAATTTA
1 TAAATTTA
14256 AATTTATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (17 bp):
TAAATTTATTTTAAAAT
Found at i:14967 original size:3 final size:3
Alignment explanation
Indices: 14959--14997 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
14949 CATTAATTTT
* *
14959 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14998 GTAAAAAGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:16183 original size:30 final size:29
Alignment explanation
Indices: 16149--16318 Score: 154
Period size: 29 Copynumber: 5.9 Consensus size: 29
16139 AACCTCGAAT
*
16149 TTTCCAAAAAGTACATTTTTACCACTAAAC
1 TTTCCAAAAATTACATTTTTACC-CTAAAC
* * *
16179 TTTCC-AAAATTCCATTTTAACCCTAAAT
1 TTTCCAAAAATTACATTTTTACCCTAAAC
*
16207 TTTACAATAAA-TACA-TTTTACCCATAAAC
1 TTTCCAA-AAATTACATTTTTACCC-TAAAC
*
16236 TTTCAAAAAATTACATTTTTGACCCTAAAC
1 TTTCCAAAAATTACATTTTT-ACCCTAAAC
* *
16266 TTTCTAAAAAATACA-TTTTACCCCTAAA-
1 TTTCCAAAAATTACATTTTTA-CCCTAAAC
* *
16294 TTTTCAAAATTTACCA-TTTTACCCT
1 TTTCCAAAAATTA-CATTTTTACCCT
16319 CGAGTGTCTG
Statistics
Matches: 116, Mismatches: 16, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
28 33 0.28
29 49 0.42
30 30 0.26
31 4 0.03
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.38
Consensus pattern (29 bp):
TTTCCAAAAATTACATTTTTACCCTAAAC
Found at i:16189 original size:58 final size:55
Alignment explanation
Indices: 16118--16318 Score: 192
Period size: 58 Copynumber: 3.5 Consensus size: 55
16108 GAGGTCCCCG
* *
16118 AACTTTTCAAAATTCCATTTTAA-CCTCGAATTTTCCAAAAAGTACATTTTTACCACTA
1 AACTTTCCAAAATTCCATTTTAACCCT-AAATTTTCCAAAAA-TACA-TTTTACC-CTA
*
16176 AACTTTCCAAAATTCCATTTTAACCCTAAATTTTACAATAAATACATTTTACCCATA
1 AACTTTCCAAAATTCCATTTTAACCCTAAATTTTCCAA-AAATACATTTTACCC-TA
* * * * *
16233 AACTTTCAAAAAATTACATTTTTGACCCTAAACTTTCTAAAAAATACATTTTACCCCTA
1 AACTTTC-CAAAATTCCA-TTTTAACCCTAAATTTTC-CAAAAATACATTTTA-CCCTA
*
16292 AA-TTTTCAAAATTTACCATTTT-ACCCT
1 AACTTTCCAAAA-TT-CCATTTTAACCCT
16319 CGAGTGTCTG
Statistics
Matches: 122, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
56 1 0.01
57 25 0.20
58 52 0.43
59 39 0.32
60 5 0.04
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.38
Consensus pattern (55 bp):
AACTTTCCAAAATTCCATTTTAACCCTAAATTTTCCAAAAATACATTTTACCCTA
Found at i:16311 original size:29 final size:27
Alignment explanation
Indices: 16121--16317 Score: 128
Period size: 29 Copynumber: 6.8 Consensus size: 27
16111 GTCCCCGAAC
* * *
16121 TTTTCAAAATTCCATTTTA-ACCTCGAA
1 TTTTCAAAATTACATTTTACCCCT-AAA
* *
16148 TTTTCCAAAAAGTACATTTTTACCACTAAA
1 TTTT-C-AAAATTACA-TTTTACCCCTAAA
* * *
16178 CTTTCCAAAATTCCATTTTAACCCTAAA
1 -TTTTCAAAATTACATTTTACCCCTAAA
* *
16206 TTTTACAATAAATACATTTTACCCATAAA
1 TTTT-CAA-AATTACATTTTACCCCTAAA
*
16235 CTTTCAAAAAATTACATTTTTGA-CCCTAAA
1 TTTTC--AAAATTACA-TTTT-ACCCCTAAA
* *
16265 CTTTCTAAAAAATACATTTTACCCCTAAA
1 -TTT-TCAAAATTACATTTTACCCCTAAA
16294 TTTTCAAAATTTACCATTTTACCC
1 TTTTCAAAA-TTA-CATTTTACCC
16318 TCGAGTGTCT
Statistics
Matches: 131, Mismatches: 23, Indels: 30
0.71 0.12 0.16
Matches are distributed among these distances:
27 12 0.09
28 22 0.17
29 60 0.46
30 28 0.21
31 8 0.06
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (27 bp):
TTTTCAAAATTACATTTTACCCCTAAA
Found at i:16428 original size:28 final size:29
Alignment explanation
Indices: 16353--16436 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 29
16343 TTCCTCGGAT
16353 GTCTAAAAATT-CCATTTTTGACCTCGAAAA
1 GTCTAAAAATTACCA-TTTT-ACCTCGAAAA
*
16383 TTCTAAAAATTACCATTTTACCTCGAAAA
1 GTCTAAAAATTACCATTTTACCTCGAAAA
* * *
16412 GTC-CAAAATTACTATTTTCCCTCGA
1 GTCTAAAAATTACCATTTTACCTCGA
16437 GCATCCAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 19 0.40
29 12 0.25
30 14 0.29
31 3 0.06
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.35
Consensus pattern (29 bp):
GTCTAAAAATTACCATTTTACCTCGAAAA
Found at i:22638 original size:13 final size:13
Alignment explanation
Indices: 22620--22647 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
22610 AGGCCCTTGA
22620 GCTCTTAGAAGGG
1 GCTCTTAGAAGGG
22633 GCTCTTAGAAGGG
1 GCTCTTAGAAGGG
22646 GC
1 GC
22648 CACACTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.21
Consensus pattern (13 bp):
GCTCTTAGAAGGG
Found at i:37840 original size:22 final size:20
Alignment explanation
Indices: 37815--37859 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 20
37805 TGGATTTGTA
37815 GTTTAAGGTTTATGATTTTGAG
1 GTTTAAGGTTTATG--TTTGAG
37837 GTTTAAGGTTTATGTTTGAG
1 GTTTAAGGTTTATGTTTGAG
37857 GTT
1 GTT
37860 ACGGGTACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 9 0.39
22 14 0.61
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (20 bp):
GTTTAAGGTTTATGTTTGAG
Found at i:38705 original size:8 final size:8
Alignment explanation
Indices: 38692--38716 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
38682 TACTTTTATT
38692 AATTTTAA
1 AATTTTAA
38700 AATTTTAA
1 AATTTTAA
38708 AATTTTAA
1 AATTTTAA
38716 A
1 A
38717 GGGTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:41448 original size:16 final size:16
Alignment explanation
Indices: 41422--41472 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
41412 AAAAATTAAA
41422 TTATATATTTTTATATT
1 TTAT-TATTTTTATATT
* *
41439 TTATTATTTTAATAGT
1 TTATTATTTTTATATT
*
41455 TTA-TATCTTTATAATT
1 TTATTATTTTTAT-ATT
41471 TT
1 TT
41473 TATAATATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 7 0.25
16 17 0.61
17 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (16 bp):
TTATTATTTTTATATT
Found at i:47684 original size:24 final size:23
Alignment explanation
Indices: 47635--47684 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
47625 TAAAGTAGGT
* *
47635 TATATATTATTTTTCTAATATTA
1 TATATATGATTTTTCTAATATCA
47658 TATATTATGATTTTTACTAAT-TCA
1 TATA-TATGATTTTT-CTAATATCA
47682 TAT
1 TAT
47685 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (23 bp):
TATATATGATTTTTCTAATATCA
Found at i:47741 original size:52 final size:54
Alignment explanation
Indices: 47658--47818 Score: 161
Period size: 58 Copynumber: 2.9 Consensus size: 54
47648 TCTAATATTA
* *
47658 TATATTATGATTTTTACT-AATTCATATTTTAATAATAATTATATTAAT-ATTAAAT
1 TATA-TATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAATAATTAAAT
* * *
47713 TATATATTA-TTTTATTAAATTGTATTTAATAATAAATATGTTAAAATATAATTAAAT
1 TATATATTATTTTTATTAAATTATATTTAATAATAATTATATT---A-ATAATTAAAT
*
47770 TATTTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAA-AATT
1 TATATATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAATAATT
47819 TAATAACAAT
Statistics
Matches: 89, Mismatches: 9, Indels: 18
0.77 0.08 0.16
Matches are distributed among these distances:
52 16 0.18
53 12 0.13
54 9 0.10
55 6 0.07
56 2 0.02
57 15 0.17
58 28 0.31
59 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (54 bp):
TATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAATAATTAAAT
Found at i:47815 original size:58 final size:57
Alignment explanation
Indices: 47706--47822 Score: 164
Period size: 58 Copynumber: 2.0 Consensus size: 57
47696 TTATATTAAT
* *
47706 ATTAAATTATATATTATTTTATTAAATTGTATTTAATAATAAATATGTTAAAATATA
1 ATTAAATTATATATTATTTTATTAAATTATATTTAATAATAAATATATTAAAATATA
* * *
47763 ATTAAATTATTTATTATTTTTATTAAATTATATTTAATAAT-AATCTTATTAAAATTTA
1 ATTAAATTATATATTA-TTTTATTAAATTATATTTAATAATAAAT-ATATTAAAATATA
47821 AT
1 AT
47823 AACAATAATC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 18 0.34
58 35 0.66
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (57 bp):
ATTAAATTATATATTATTTTATTAAATTATATTTAATAATAAATATATTAAAATATA
Found at i:47998 original size:16 final size:15
Alignment explanation
Indices: 47977--48030 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 15
47967 TGAATTATTG
47977 ATTACAGTCTTATTCC
1 ATTACAG-CTTATTCC
*
47993 ATTACAGCTCTATTCT
1 ATTACAGCT-TATTCC
*
48009 ATTACAACTTTATTCC
1 ATTACAGC-TTATTCC
48025 ATTACA
1 ATTACA
48031 ACGAATCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 2 0.06
16 30 0.91
17 1 0.03
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.43
Consensus pattern (15 bp):
ATTACAGCTTATTCC
Found at i:48031 original size:16 final size:16
Alignment explanation
Indices: 47986--48032 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
47976 GATTACAGTC
*
47986 TTATTCCATTACAGCT
1 TTATTCCATTACAACT
* *
48002 CTATTCTATTACAACT
1 TTATTCCATTACAACT
48018 TTATTCCATTACAAC
1 TTATTCCATTACAAC
48033 GAATCAAACG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.02, T:0.43
Consensus pattern (16 bp):
TTATTCCATTACAACT
Found at i:52297 original size:24 final size:24
Alignment explanation
Indices: 52270--52316 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
52260 AAGTCACATT
52270 TAAATTT-TATATATATA-TTTTTTA
1 TAAATTTCT-TATATA-ACTTTTTTA
52294 TAAATTTCTTATATAACTTTTTT
1 TAAATTTCTTATATAACTTTTTT
52317 CCACCCACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.05
24 19 0.90
25 1 0.05
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (24 bp):
TAAATTTCTTATATAACTTTTTTA
Found at i:53085 original size:98 final size:98
Alignment explanation
Indices: 52920--53117 Score: 387
Period size: 98 Copynumber: 2.0 Consensus size: 98
52910 GGGATTCAAA
52920 CCCCACCAAGGTCAAATGCTCACATTTTTTTAGTGGGTAAGGCGCTCTCTAAACTTCGTGAACTT
1 CCCCACCAAGGTCAAATGCTCACATTTTTTTAGTGGGTAAGGCGCTCTCTAAACTTCGTGAACTT
*
52985 GATTGGGCTATCCTCGGGCTCAAGAGATAAAAC
66 GATCGGGCTATCCTCGGGCTCAAGAGATAAAAC
53018 CCCCACCAAGGTCAAATGCTCACATTTTTTTAGTGGGTAAGGCGCTCTCTAAACTTCGTGAACTT
1 CCCCACCAAGGTCAAATGCTCACATTTTTTTAGTGGGTAAGGCGCTCTCTAAACTTCGTGAACTT
53083 GATCGGGCTATCCTCGGGCTCAAGAGATAAAAC
66 GATCGGGCTATCCTCGGGCTCAAGAGATAAAAC
53116 CC
1 CC
53118 AACATAGACA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (98 bp):
CCCCACCAAGGTCAAATGCTCACATTTTTTTAGTGGGTAAGGCGCTCTCTAAACTTCGTGAACTT
GATCGGGCTATCCTCGGGCTCAAGAGATAAAAC
Found at i:55863 original size:22 final size:21
Alignment explanation
Indices: 55817--55857 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
55807 TGAAATTAAT
55817 ATTTTCTATTAATTATACATA
1 ATTTTCTATTAATTATACATA
55838 ATTTT-TATTAA-TATA-ATA
1 ATTTTCTATTAATTATACATA
55856 AT
1 AT
55858 AAATTTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 4 0.20
20 6 0.30
21 5 0.25
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTCTATTAATTATACATA
Found at i:56092 original size:24 final size:24
Alignment explanation
Indices: 56046--56092 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
56036 CACGGAAAAT
**
56046 ATTTACTTTACAAATAATTATATA
1 ATTTACTTTACAAATAAAAATATA
56070 ATTTACTTTACAAATAAAAATAT
1 ATTTACTTTACAAATAAAAATAT
56093 TTTTAGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTTACTTTACAAATAAAAATATA
Found at i:57456 original size:81 final size:81
Alignment explanation
Indices: 57321--57484 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
57311 ATTCAATTAT
57321 TAAAATTTATGAATTATTTAATTAGCAAATTGTTATATTTTTATAAAATATTTGTCAACTTGTAA
1 TAAAATTTATGAATTATTTAATTAGCAAATTGTTATATTTTTATAAAATATTTGTCAACTTGTAA
57386 AGTTTAAAAATTTCAC
66 AGTTTAAAAATTTCAC
57402 TAAAATTTATGAATTATTTAATTAGCAAATTGTTATATTTTTATAAAATATTTGTCAACTTGTAA
1 TAAAATTTATGAATTATTTAATTAGCAAATTGTTATATTTTTATAAAATATTTGTCAACTTGTAA
57467 AGTTTAAAAATTTCAC
66 AGTTTAAAAATTTCAC
57483 TA
1 TA
57485 TCTAATATTT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (81 bp):
TAAAATTTATGAATTATTTAATTAGCAAATTGTTATATTTTTATAAAATATTTGTCAACTTGTAA
AGTTTAAAAATTTCAC
Found at i:57523 original size:5 final size:5
Alignment explanation
Indices: 57508--57559 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
57498 ATATACAATG
* * *
57508 TAATA TGATA TAATA TAATA TAA-A CT-ATA TGATA TGATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA -TAATA TAATA TAATA TAATA TAATA
57557 TAA
1 TAA
57560 GAATCTCCGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 3 0.07
5 38 0.93
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:58568 original size:14 final size:15
Alignment explanation
Indices: 58542--58570 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
58532 TTAAAATATT
58542 TTATTATATTATTAA
1 TTATTATATTATTAA
58557 TTATTA-ATTATTAA
1 TTATTATATTATTAA
58571 AAGTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTATATTATTAA
Found at i:59326 original size:17 final size:16
Alignment explanation
Indices: 59306--59394 Score: 65
Period size: 17 Copynumber: 5.2 Consensus size: 16
59296 TGTTTATACC
59306 AAAAAAATATTTTTGTA
1 AAAAAAATATTTTTG-A
** *
59323 AAAAAACGATTCTTGA
1 AAAAAAATATTTTTGA
*
59339 AAATTAAAATAATTTT-A
1 AAA--AAAATATTTTTGA
59356 CAAAAAAAT-TTATTTGA
1 -AAAAAAATATT-TTTGA
59373 ACAAAAAATATTTTTTGA
1 A-AAAAAATA-TTTTTGA
59391 AAAA
1 AAAA
59395 TAAAAAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
15 1 0.02
16 13 0.23
17 24 0.43
18 16 0.29
19 2 0.04
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (16 bp):
AAAAAAATATTTTTGA
Found at i:59378 original size:18 final size:18
Alignment explanation
Indices: 59355--59391 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
59345 AAATAATTTT
59355 ACAAAAAA-ATTTATTTGA
1 ACAAAAAATATTT-TTTGA
59373 ACAAAAAATATTTTTTGA
1 ACAAAAAATATTTTTTGA
59391 A
1 A
59392 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (18 bp):
ACAAAAAATATTTTTTGA
Found at i:59379 original size:19 final size:17
Alignment explanation
Indices: 59357--59400 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
59347 ATAATTTTAC
59357 AAAAAAATTTATTTGAACA
1 AAAAAAATTT-TTTGAA-A
*
59376 AAAAATATTTTTTGAAA
1 AAAAAAATTTTTTGAAA
59393 AATAAAAA
1 AA-AAAAA
59401 AAATCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 10 0.45
19 9 0.41
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAAAAATTTTTTGAAA
Found at i:59908 original size:16 final size:17
Alignment explanation
Indices: 59877--59910 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
59867 TATATTTTAA
*
59877 TTAATCATGTTTTAATT
1 TTAATCAAGTTTTAATT
59894 TTAATCAAG-TTTAATT
1 TTAATCAAGTTTTAATT
59910 T
1 T
59911 ACTTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
TTAATCAAGTTTTAATT
Found at i:59911 original size:15 final size:16
Alignment explanation
Indices: 59871--59911 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
59861 CTTATTTATA
*
59871 TTTTAA-TTAATCATG
1 TTTTAATTTAATCAAG
59886 TTTTAATTTTAATCAAG
1 TTTTAA-TTTAATCAAG
59903 -TTTAATTTA
1 TTTTAATTTA
59912 CTTAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 5 0.22
17 8 0.35
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (16 bp):
TTTTAATTTAATCAAG
Found at i:62132 original size:14 final size:15
Alignment explanation
Indices: 62108--62137 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
62098 TTAAAATTTT
62108 AAATTAGTAAAAATA
1 AAATTAGTAAAAATA
62123 AAATTA-TAAAAATA
1 AAATTAGTAAAAATA
62137 A
1 A
62138 TAAAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AAATTAGTAAAAATA
Found at i:66897 original size:4 final size:4
Alignment explanation
Indices: 66884--66927 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
66874 AGAGAAGAAT
* *
66884 AAAG AGAAG AAAG AAAG AAAG AAAG AAGG ATAGG AAAG AAAG AA
1 AAAG A-AAG AAAG AAAG AAAG AAAG AAAG A-AAG AAAG AAAG AA
66928 GAAGTAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
4 28 0.78
5 8 0.22
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:66909 original size:21 final size:21
Alignment explanation
Indices: 66885--66927 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
66875 GAGAAGAATA
66885 AAGAGAAGA-AAGAAAGAAAGA
1 AAGA-AAGATAAGAAAGAAAGA
* *
66906 AAGAAGGATAGGAAAGAAAGA
1 AAGAAAGATAAGAAAGAAAGA
66927 A
1 A
66928 GAAGTAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (21 bp):
AAGAAAGATAAGAAAGAAAGA
Found at i:67047 original size:29 final size:31
Alignment explanation
Indices: 66991--67048 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
66981 AATTATTTAA
66991 TTTGTTAGTTAGTAGTAATAATTTGTTATTT
1 TTTGTTAGTTAGTAGTAATAATTTGTTATTT
* *
67022 TTTGTTAGTTTG-A-TATTAATTTGTTAT
1 TTTGTTAGTTAGTAGTAATAATTTGTTAT
67049 AAATTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.52
30 1 0.04
31 11 0.44
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (31 bp):
TTTGTTAGTTAGTAGTAATAATTTGTTATTT
Found at i:67490 original size:24 final size:24
Alignment explanation
Indices: 67456--67504 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
67446 TGATGTGGAA
*
67456 CCAGTACAAAATGAAGATCCAACT
1 CCAGTACAAAATAAAGATCCAACT
* *
67480 CCAGTAGAAAATAAAGATCGAACT
1 CCAGTACAAAATAAAGATCCAACT
67504 C
1 C
67505 TGTGTATGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.22, G:0.14, T:0.16
Consensus pattern (24 bp):
CCAGTACAAAATAAAGATCCAACT
Found at i:70461 original size:43 final size:43
Alignment explanation
Indices: 70393--70498 Score: 153
Period size: 43 Copynumber: 2.5 Consensus size: 43
70383 TGGGTCACTG
* * *
70393 TATAA-TTAATAACATGTCAAGATATTAATAAGAGTCAAGTAA
1 TATAATTTAATAACATGTCAACATATTAACAAGAATCAAGTAA
*
70435 TATAATTTAATAACATG-CAACCATATTAACACGAATCAAGTAA
1 TATAATTTAATAACATGTCAA-CATATTAACAAGAATCAAGTAA
70478 TATAATTTAATAACATGTCAA
1 TATAATTTAATAACATGTCAA
70499 TGAATAATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
42 8 0.14
43 46 0.81
44 3 0.05
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.31
Consensus pattern (43 bp):
TATAATTTAATAACATGTCAACATATTAACAAGAATCAAGTAA
Found at i:71700 original size:47 final size:48
Alignment explanation
Indices: 71646--71782 Score: 181
Period size: 47 Copynumber: 2.9 Consensus size: 48
71636 TTTATGATTT
* * *
71646 TTTACCAATATAATACAAAAAT-AATAATTAAATATCAAAATGGGTTA
1 TTTACCAAAATAATACAAAAATAAATATTTATATATCAAAATGGGTTA
* * *
71693 TTTACCAAAATGATA-AAAAATAAATATTTATTTATCAAAATGAGTTA
1 TTTACCAAAATAATACAAAAATAAATATTTATATATCAAAATGGGTTA
* *
71740 TTTACCAAAATAGTAC-AAAATAAATATTTATATACCAAAATGG
1 TTTACCAAAATAATACAAAAATAAATATTTATATATCAAAATGG
71783 TATCCACACT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
46 6 0.08
47 71 0.92
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (48 bp):
TTTACCAAAATAATACAAAAATAAATATTTATATATCAAAATGGGTTA
Found at i:72039 original size:12 final size:12
Alignment explanation
Indices: 72022--72061 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
72012 TTTACTCAAC
72022 TAAATAAAAAAT
1 TAAATAAAAAAT
*
72034 TAAATAACAAA-
1 TAAATAAAAAAT
*
72045 TCAATAAAAAAT
1 TAAATAAAAAAT
72057 TAAAT
1 TAAAT
72062 TTAACAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (12 bp):
TAAATAAAAAAT
Done.