Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015031.1 Kokia drynarioides strain JFW-HI SEQ_130075, 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: 59192
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Warning! 622 characters in sequence are not A, C, G, or T
Found at i:357 original size:59 final size:59
Alignment explanation
Indices: 177--479 Score: 261
Period size: 58 Copynumber: 5.2 Consensus size: 59
167 TCGAGGGGGC
* * ** * * * *
177 AAAATGGTATTTTTGGATTTTCGAGGGTAAAATGGTAATTTTGGGAAA-ATTC-AGGGT-T
1 AAAATGGAATTTTTAGACATTCGAGGGAAAAATGGTAATTTT-TGAAAGTTTCGA-GGTCA
* * * *
235 AAAATAGAATTTTTAGACATTCGAGGGTAAAAGGGTAA--TTTGAGAGTTTCGAGGTCA
1 AAAATGGAATTTTTAGACATTCGAGGGAAAAATGGTAATTTTTGAAAGTTTCGAGGTCA
* * *
292 AAAATGGAGTTTTTAGACATTTGAGGGCAAAATGGTAATTTTTGAAAGTTTCGAGGTCA
1 AAAATGGAATTTTTAGACATTCGAGGGAAAAATGGTAATTTTTGAAAGTTTCGAGGTCA
* ** *
351 AAAATGGAAATTTTAGAGGTTCG-GGGTAAAAATGG-AATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTAGACATTCGAGGG-AAAAATGGTAATTTTTGAAAGTTTCGAGGTCA
* * * *
409 AAAATGGAA-TTTTGGA-AGTTCGAGAGTAAAAAT-GAAAATTTTGAAAG-TTCGAGGGT-A
1 AAAATGGAATTTTTAGACA-TTCGAG-GGAAAAATGGTAATTTTTGAAAGTTTCGA-GGTCA
466 AAAATGGAATTTTT
1 AAAATGGAATTTTT
480 GGAATTTTTG
Statistics
Matches: 205, Mismatches: 28, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
55 3 0.01
56 8 0.04
57 60 0.29
58 90 0.44
59 44 0.21
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (59 bp):
AAAATGGAATTTTTAGACATTCGAGGGAAAAATGGTAATTTTTGAAAGTTTCGAGGTCA
Found at i:414 original size:30 final size:30
Alignment explanation
Indices: 279--581 Score: 250
Period size: 29 Copynumber: 10.1 Consensus size: 30
269 GTAATTTGAG
* *
279 AGTTTCGAGGTCAAAAATGGAGTTTTTAGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
* *
309 CA-TTT-GAGGGC-AAAATGGTAATTTTTGAA
1 -AGTTTCGAGGTCAAAAATGG-AATTTTTGGA
* *
338 AGTTTCGAGGTCAAAAATGGAAATTTTAG-
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
* *
367 AGGTTCGGGGT-AAAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
396 AGTTTCGAGGTCAAAAATGGAA-TTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
* * *
425 AG-TTCGAGAGT-AAAAATGAAAATTTTGAA
1 AGTTTCGAG-GTCAAAAATGGAATTTTTGGA
*
454 AG-TTCGAGGGTAAAAATGGAATTTTTGGAATTTTTGGA
1 AGTTTCGA-GGT-CAAA---AA----TGGAATTTTTGGA
* * *
492 AGTTTTGGGGTCACAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
* * * *
522 AGTTTAGGGGT-AAAAATTGAATTTTTGAA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
551 AGTTTCGAGGTC-AAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
580 AG
1 AG
582 CTCAGGAGTA
Statistics
Matches: 221, Mismatches: 31, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
28 38 0.17
29 100 0.45
30 48 0.22
31 11 0.05
34 4 0.02
37 2 0.01
38 15 0.07
39 3 0.01
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (30 bp):
AGTTTCGAGGTCAAAAATGGAATTTTTGGA
Found at i:479 original size:29 final size:29
Alignment explanation
Indices: 177--480 Score: 195
Period size: 29 Copynumber: 10.5 Consensus size: 29
167 TCGAGGGGGC
* * **
177 AAAATGGTATTTTTGGATTTTCGAGGGT-
1 AAAATGGAATTTTTGAAAGTTCGAGGGTA
* * *
205 AAAATGGTAATTTTGGGAAAATTC-AGGGTT
1 AAAATGG-AATTTT-TGAAAGTTCGAGGGTA
* *
235 AAAATAGAATTTTTAGACA-TTCGAGGGT-
1 AAAATGGAATTTTT-GAAAGTTCGAGGGTA
* *
263 AAAAGGGTAA--TTTGAGAGTTTCGA-GGTCA
1 AAAATGG-AATTTTTGAAAG-TTCGAGGGT-A
* * * *
292 AAAATGGAGTTTTTAGACA-TTTGAGGG-C
1 AAAATGGAATTTTT-GAAAGTTCGAGGGTA
320 AAAATGGTAATTTTTGAAAGTTTCGA-GGTCA
1 AAAATGG-AATTTTTGAAAG-TTCGAGGGT-A
* *
351 AAAATGGAAATTTT-AGAGGTTCG-GGGTA
1 AAAATGGAATTTTTGA-AAGTTCGAGGGTA
*
379 AAAATGGAATTTTTGGAAGTTTCGA-GGTCA
1 AAAATGGAATTTTTGAAAG-TTCGAGGGT-A
* *
409 AAAATGGAA-TTTTGGAAGTTCGAGAGTA
1 AAAATGGAATTTTTGAAAGTTCGAGGGTA
* *
437 AAAATGAAAATTTTGAAAGTTCGAGGGTA
1 AAAATGGAATTTTTGAAAGTTCGAGGGTA
466 AAAATGGAATTTTTG
1 AAAATGGAATTTTTG
481 GAATTTTTGG
Statistics
Matches: 218, Mismatches: 31, Indels: 53
0.72 0.10 0.18
Matches are distributed among these distances:
26 3 0.01
27 6 0.03
28 61 0.28
29 100 0.46
30 38 0.17
31 10 0.05
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGAAAGTTCGAGGGTA
Found at i:484 original size:9 final size:9
Alignment explanation
Indices: 470--499 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
460 AGGGTAAAAA
470 TGGAATTTT
1 TGGAATTTT
479 TGGAATTTT
1 TGGAATTTT
*
488 TGGAAGTTT
1 TGGAATTTT
497 TGG
1 TGG
500 GGTCACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (9 bp):
TGGAATTTT
Found at i:543 original size:29 final size:29
Alignment explanation
Indices: 479--618 Score: 154
Period size: 29 Copynumber: 4.8 Consensus size: 29
469 ATGGAATTTT
* *
479 TGGAATTTTTGGAAGTTTTGGGGTCACAAA
1 TGGAATTTTTGGAAGTTTAGGGGT-AAAAA
509 TGGAATTTTTGGAAGTTTAGGGGTAAAAA
1 TGGAATTTTTGGAAGTTTAGGGGTAAAAA
* * * * *
538 TTGAATTTTTGAAAGTTTCGAGGTCAAAA
1 TGGAATTTTTGGAAGTTTAGGGGTAAAAA
* * *
567 TGGAATTTTTGGAAGCTCAGGAGTAAAAA
1 TGGAATTTTTGGAAGTTTAGGGGTAAAAA
* *
596 TGTAATTTTTAGATAGTTTAGGG
1 TGGAATTTTTGGA-AGTTTAGGG
619 ACCTCCAAGA
Statistics
Matches: 89, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
29 60 0.67
30 29 0.33
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
TGGAATTTTTGGAAGTTTAGGGGTAAAAA
Found at i:573 original size:97 final size:96
Alignment explanation
Indices: 383--580 Score: 276
Period size: 97 Copynumber: 2.1 Consensus size: 96
373 GGGGTAAAAA
*
383 TGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTGGAAGTTCGAGAGTAAAAATGAAAAT
1 TGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTGGAAGTTAGAGAGTAAAAATGAAAAT
448 TTTGAAAGTTCGAGGGTAAAAATGGAATTTT
66 TTTGAAAGTTCGAGGGTAAAAATGGAATTTT
* * * *
479 TGGAATTTTTGGAAGTTTTGGGGTCACAAATGGAATTTTTGGAAGTTTAG-GGGTAAAAATTG-A
1 TGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAA-TTTTGGAAG-TTAGAGAGTAAAAA-TGAA
* *
542 ATTTTTGAAAGTTTCGA-GGTCAAAATGGAATTTT
63 AATTTTGAAAG-TTCGAGGGTAAAAATGGAATTTT
576 TGGAA
1 TGGAA
581 GCTCAGGAGT
Statistics
Matches: 91, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
96 32 0.35
97 49 0.54
98 10 0.11
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (96 bp):
TGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTGGAAGTTAGAGAGTAAAAATGAAAAT
TTTGAAAGTTCGAGGGTAAAAATGGAATTTT
Found at i:593 original size:58 final size:58
Alignment explanation
Indices: 481--614 Score: 171
Period size: 58 Copynumber: 2.3 Consensus size: 58
471 GGAATTTTTG
* * * * * *
481 GAATTTTTGGAAGTTTTGGGGTCACAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATT
1 GAATTTTTGAAAGTTTCGAGGTCACAAATGGAATTTTTGGAAGCTCAGGAGTAAAAA-T
540 GAATTTTTGAAAGTTTCGAGGTCA-AAATGGAATTTTTGGAAGCTCAGGAGTAAAAAT
1 GAATTTTTGAAAGTTTCGAGGTCACAAATGGAATTTTTGGAAGCTCAGGAGTAAAAAT
*
597 GTAATTTTTAGATAGTTT
1 G-AATTTTT-GAAAGTTT
615 AGGGACCTCC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
57 2 0.03
58 36 0.55
59 28 0.42
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.37
Consensus pattern (58 bp):
GAATTTTTGAAAGTTTCGAGGTCACAAATGGAATTTTTGGAAGCTCAGGAGTAAAAAT
Found at i:2406 original size:30 final size:30
Alignment explanation
Indices: 2370--2660 Score: 250
Period size: 29 Copynumber: 10.0 Consensus size: 30
2360 NNTTTAGACA
*
2370 TTTGAGGG-CAAAATGGTAATTTTTGAAAGT
1 TTTGAGGGTCAAAATGG-AATTTTTGGAAGT
* * *
2400 TTTGA-GGTCAAAATGGAAATTTTAG-AGG
1 TTTGAGGGTCAAAATGGAATTTTTGGAAGT
* * *
2428 TTCG-GGGTAAAAATGGAACTTTTGGAAGT
1 TTTGAGGGTCAAAATGGAATTTTTGGAAGT
*
2457 TTT-AGGGTCGAAAATGAAATTTTTGGAAGT
1 TTTGAGGGTC-AAAATGGAATTTTTGGAAGT
*
2487 TTCG-GGGTCAAAAATGGAA-TTTTGGAAG-
1 TTTGAGGGTC-AAAATGGAATTTTTGGAAGT
* * * * *
2515 TTCGAGAGT-AAAATTGAAAATTTTGAAAG-
1 TTTGAGGGTCAAAA-TGGAATTTTTGGAAGT
* *
2544 TTTGAGGGTAAAAATGGAATTTTTGGAATT
1 TTTGAGGGTCAAAATGGAATTTTTGGAAGT
2574 TTTG-GGGTCACAAATGGAATTTTTGGAAGT
1 TTTGAGGGTCA-AAATGGAATTTTTGGAAGT
* * *
2604 TTAG-GGGT-ACAAATTGAATTTTTGAAAGT
1 TTTGAGGGTCA-AAATGGAATTTTTGGAAGT
*
2633 TTCGA-GGTCAAAATGGAATTTTTGGAAG
1 TTTGAGGGTCAAAATGGAATTTTTGGAAG
2661 CTCAGGAGTA
Statistics
Matches: 214, Mismatches: 33, Indels: 29
0.78 0.12 0.11
Matches are distributed among these distances:
27 4 0.02
28 30 0.14
29 100 0.47
30 80 0.37
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (30 bp):
TTTGAGGGTCAAAATGGAATTTTTGGAAGT
Found at i:2552 original size:88 final size:86
Alignment explanation
Indices: 2370--2660 Score: 322
Period size: 88 Copynumber: 3.3 Consensus size: 86
2360 NNTTTAGACA
* * * *
2370 TTTGAGGG-CAAAATGGTAATTTTTGAAAGTTTTGAGGTC-AAAATGGAAATTTTAGAGGTTCG-
1 TTTGAGGGTCAAAATGG-AATTTTTGGAAGTTTTGGGGTCAAAAATGG-AATTTTGGAAGTTCGA
* * *
2432 GGGTAAAAATGGAACTTTTGGAAG
64 GGGT-AAAATTGAAATTTTGAAAG
* * *
2456 TTTTAGGGTCGAAAATGAAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTGGAAGTTCGAG
1 TTTGAGGGTC-AAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTGGAAGTTCGAG
*
2521 AGTAAAATTGAAAATTTTGAAAG
65 GGTAAAATTG-AAATTTTGAAAG
* * * *
2544 TTTGAGGGTAAAAATGGAATTTTTGGAATTTTTGGGGTCACAAATGGAATTTTTGGAAGTT-TAG
1 TTTGAGGGTCAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAA-TTTTGGAAGTTCGA-
*
2608 GGGTACAAATTGAATTTTTGAAAG
64 GGGTA-AAATTGAAATTTTGAAAG
2632 TTTCGA-GGTCAAAATGGAATTTTTGGAAG
1 TTT-GAGGGTCAAAATGGAATTTTTGGAAG
2661 CTCAGGAGTA
Statistics
Matches: 174, Mismatches: 22, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
86 7 0.04
87 75 0.43
88 84 0.48
89 8 0.05
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (86 bp):
TTTGAGGGTCAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTGGAAGTTCGAGG
GTAAAATTGAAATTTTGAAAG
Found at i:2656 original size:117 final size:118
Alignment explanation
Indices: 2379--2697 Score: 350
Period size: 117 Copynumber: 2.7 Consensus size: 118
2369 ATTTGAGGGC
* * *
2379 AAAATGGTAATTTTTGAAAGTTTTGAGGTCAAAATGGAAATTTT-AGAGGTTCG-GGGTAAAAAT
1 AAAATGG-AATTTTTGAAAGTTTCGAGGTCAAAATGGAAATTTTGA-AAGTTTGAGGGTAAAAAT
* *
2442 GGAACTTTTGGAAGTTTTAGGGTCGAAAATGAAATTTTTGGAAGTTTCGGGGTCA
64 GGAATTTTTGGAAGTTTTAGGGTCGAAAATGAAATTTTTGGAAGTTTAGGGGTCA
* *
2497 AAAATGGAA-TTTTGGAAG-TTCGAGAGT-AAAATTGAAAATTTTGAAAGTTTGAGGGTAAAAAT
1 AAAATGGAATTTTTGAAAGTTTCGAG-GTCAAAA-TGGAAATTTTGAAAGTTTGAGGGTAAAAAT
* * *
2559 GGAATTTTTGGAATTTTTGGGGTC-ACAAATGGAATTTTTGGAAGTTTAGGGGT-A
64 GGAATTTTTGGAAGTTTTAGGGTCGA-AAATGAAATTTTTGGAAGTTTAGGGGTCA
* * * * * *
2613 CAAATTGAATTTTTGAAAGTTTCGAGGTCAAAATGGAATTTTTGGAAG-CTCAGGAGTAAAAATG
1 AAAATGGAATTTTTGAAAGTTTCGAGGTCAAAATGGAAATTTTGAAAGTTTGAGG-GTAAAAATG
* *
2677 TAATTTTTAGACAG-TTTAGGG
65 GAATTTTTGGA-AGTTTTAGGG
2698 ACCTCCAAGA
Statistics
Matches: 169, Mismatches: 22, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
115 9 0.05
116 37 0.22
117 105 0.62
118 18 0.11
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (118 bp):
AAAATGGAATTTTTGAAAGTTTCGAGGTCAAAATGGAAATTTTGAAAGTTTGAGGGTAAAAATGG
AATTTTTGGAAGTTTTAGGGTCGAAAATGAAATTTTTGGAAGTTTAGGGGTCA
Found at i:2674 original size:29 final size:30
Alignment explanation
Indices: 2379--2693 Score: 192
Period size: 29 Copynumber: 10.7 Consensus size: 30
2369 ATTTGAGGGC
* * *
2379 AAAATGGTAATTTTTGAAAGTTT--TGAGGTC
1 AAAATGG-AATTTTTGGAAGTTTCAGGA-GTA
* * * *
2409 AAAATGGAAATTTTAG-AGGTTC-GGGGTA
1 AAAATGGAATTTTTGGAAGTTTCAGGAGTA
* * *
2437 AAAATGGAACTTTTGGAAGTTTTAGG-GTCG
1 AAAATGGAATTTTTGGAAGTTTCAGGAGT-A
* *
2467 AAAATGAAATTTTTGGAAGTTTC-GGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCAGGAGT-A
2497 AAAATGGAA-TTTTGGAAG-TTC-GAGAGTA
1 AAAATGGAATTTTTGGAAGTTTCAG-GAGTA
* * * * *
2525 AAATTGAAAATTTTGAAAGTTTGAGG-GTA
1 AAAATGGAATTTTTGGAAGTTTCAGGAGTA
** *
2554 AAAATGGAATTTTTGGAA-TTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCAGGAGT-A
* *
2584 CAAATGGAATTTTTGGAAGTTT-AGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCAGGAGTA
* * * *
2613 CAAATTGAATTTTTGAAAGTTTC--GAGGTC
1 AAAATGGAATTTTTGGAAGTTTCAGGA-GTA
*
2642 AAAATGGAATTTTTGGAAG-CTCAGGAGTA
1 AAAATGGAATTTTTGGAAGTTTCAGGAGTA
* *
2671 AAAATGTAATTTTTAGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
2694 AGGGACCTCC
Statistics
Matches: 225, Mismatches: 42, Indels: 35
0.75 0.14 0.12
Matches are distributed among these distances:
28 40 0.18
29 110 0.49
30 70 0.31
31 5 0.02
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCAGGAGTA
Found at i:2693 original size:88 final size:89
Alignment explanation
Indices: 2409--2697 Score: 245
Period size: 88 Copynumber: 3.3 Consensus size: 89
2399 TTTTGAGGTC
* * * * * * * * *
2409 AAAATGGAAATTTTAG-AGGTTCGGGGTA-AAAATGGAACTTTTGGAAGTTTTAGGGTCGAAAAT
1 AAAATGGAATTTTTAGAAGTTTAGGGGTACAAATTGAAAATTTTGAAAGTTTGAGGGT-AAAAAT
* * *
2472 GAAATTTTTGGAAGTTTC-GGGGTCA
65 GGAATTTTTGGAAG-CTCAGGAGTCA
* * *
2497 AAAATGGAA-TTTTGGAAG-TTCGAGAGTA-AAATTGAAAATTTTGAAAGTTTGAGGGTAAAAAT
1 AAAATGGAATTTTTAGAAGTTTAG-GGGTACAAATTGAAAATTTTGAAAGTTTGAGGGTAAAAAT
** ** *
2559 GGAATTTTTGGAATTTTTGGGGTCA
65 GGAATTTTTGGAAGCTCAGGAGTCA
* * * *
2584 CAAATGGAATTTTTGGAAGTTTAGGGGTACAAATTG-AATTTTTGAAAGTTTCGA-GGTCAAAAT
1 AAAATGGAATTTTTAGAAGTTTAGGGGTACAAATTGAAAATTTTGAAAGTTT-GAGGGTAAAAAT
2647 GGAATTTTTGGAAGCTCAGGAGT-A
65 GGAATTTTTGGAAGCTCAGGAGTCA
*
2671 AAAATGTAATTTTTAGACAGTTTAGGG
1 AAAATGGAATTTTTAGA-AGTTTAGGG
2698 ACCTCCAAGA
Statistics
Matches: 169, Mismatches: 24, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
86 2 0.01
87 56 0.33
88 100 0.59
89 11 0.07
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.34
Consensus pattern (89 bp):
AAAATGGAATTTTTAGAAGTTTAGGGGTACAAATTGAAAATTTTGAAAGTTTGAGGGTAAAAATG
GAATTTTTGGAAGCTCAGGAGTCA
Found at i:4329 original size:17 final size:17
Alignment explanation
Indices: 4299--4382 Score: 77
Period size: 17 Copynumber: 4.9 Consensus size: 17
4289 ATTGATTTTA
*
4299 AATTTAAGTTTAAAACT
1 AATTTAAATTTAAAACT
4316 -ATTTCAAATTT-AAACT
1 AATTT-AAATTTAAAACT
4332 AAATTTAAATTTAAAA-T
1 -AATTTAAATTTAAAACT
*
4349 GAATTTAAATTTAAAAAAT
1 -AATTTAAATTT-AAAACT
4368 GAATTTAAA-TTAAAA
1 -AATTTAAATTTAAAA
4383 TTAAAAGTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
16 9 0.15
17 27 0.46
18 13 0.22
19 10 0.17
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (17 bp):
AATTTAAATTTAAAACT
Found at i:4335 original size:34 final size:33
Alignment explanation
Indices: 4297--4363 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
4287 TAATTGATTT
*
4297 TAAATTTAAGTTTAAAACT-ATTTCAAATTTAAAC
1 TAAATTTAAATTTAAAA-TAATTT-AAATTTAAAC
4331 TAAATTTAAATTTAAAATGAATTTAAATTTAAA
1 TAAATTTAAATTTAAAAT-AATTTAAATTTAAA
4364 AAATGAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 1 0.03
34 25 0.83
35 4 0.13
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (33 bp):
TAAATTTAAATTTAAAATAATTTAAATTTAAAC
Found at i:4368 original size:19 final size:19
Alignment explanation
Indices: 4333--4382 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
4323 ATTTAAACTA
4333 AATTTAAATTT--AAAATG
1 AATTTAAATTTAAAAAATG
4350 AATTTAAATTTAAAAAATG
1 AATTTAAATTTAAAAAATG
4369 AATTTAAA-TTAAAA
1 AATTTAAATTTAAAA
4383 TTAAAAGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.35
18 6 0.19
19 14 0.45
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
AATTTAAATTTAAAAAATG
Found at i:4388 original size:41 final size:42
Alignment explanation
Indices: 4330--4417 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 42
4320 CAAATTTAAA
* *
4330 CTAAATTTAAATTTAAAA-TGAATTTAAATTTAAAAAATGAAT
1 CTAAATTTAAAATTAAAAGTAAATTT-AATTTAAAAAATGAAT
* * *
4372 TTAAA-TTAAAATTAAAAGTAAATTTAATTTTAGAAATGAAT
1 CTAAATTTAAAATTAAAAGTAAATTTAATTTAAAAAATGAAT
4413 CTAAA
1 CTAAA
4418 ACCCATCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
41 29 0.74
42 10 0.26
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (42 bp):
CTAAATTTAAAATTAAAAGTAAATTTAATTTAAAAAATGAAT
Found at i:16577 original size:3 final size:3
Alignment explanation
Indices: 16534--16559 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16524 AATTTTTGAC
16534 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
16560 ACAAGCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:17965 original size:48 final size:48
Alignment explanation
Indices: 17910--18005 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
17900 TTGTATTGAC
* *
17910 AATAATACTAATGCCAATCATATTAAGACTAGATCAAAATATTTGAAA
1 AATAATACTAATGCCAATCAAATTAAGACTAGATAAAAATATTTGAAA
* * *
17958 AATAATACTAATGCCATTCAAATTAAGATTCGATAAAAATATTTGAAA
1 AATAATACTAATGCCAATCAAATTAAGACTAGATAAAAATATTTGAAA
18006 TTGTTATGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.30
Consensus pattern (48 bp):
AATAATACTAATGCCAATCAAATTAAGACTAGATAAAAATATTTGAAA
Found at i:22515 original size:31 final size:30
Alignment explanation
Indices: 22479--22543 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
22469 TAATTTTAAA
22479 TAAAAAATATT-TTTATTGCTTTCTAAACAG
1 TAAAAAATATTCTTTATT-CTTTCTAAACAG
*
22509 TAAAAAATATTCTTTATTTTTTCTAAACAG
1 TAAAAAATATTCTTTATTCTTTCTAAACAG
22539 TAAAA
1 TAAAA
22544 TGAGTTTCAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 27 0.82
31 6 0.18
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (30 bp):
TAAAAAATATTCTTTATTCTTTCTAAACAG
Found at i:31123 original size:23 final size:22
Alignment explanation
Indices: 31093--31217 Score: 108
Period size: 23 Copynumber: 5.5 Consensus size: 22
31083 ACGCTAGCGC
*
31093 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTT-GCACTATGTGT
*
31116 GCTTACTGTTTCGTACT-TCGTGT
1 GCTTACTGTTT-GCACTAT-GTGT
* *
31139 GCTTACTGATTTGCGCTATGTGC
1 GCTTACTG-TTTGCACTATGTGT
* * * *
31162 GCCTACTGATTGTACTGTGTGT
1 GCTTACTGTTTGCACTATGTGT
* *
31184 GCCTACTGGATTGCACTATGTGT
1 GCTTACT-GTTTGCACTATGTGT
31207 GCTTACTGTTT
1 GCTTACTGTTT
31218 CCCTAGCACT
Statistics
Matches: 84, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
22 20 0.24
23 60 0.71
24 4 0.05
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.43
Consensus pattern (22 bp):
GCTTACTGTTTGCACTATGTGT
Found at i:35838 original size:33 final size:36
Alignment explanation
Indices: 35796--35862 Score: 104
Period size: 33 Copynumber: 1.9 Consensus size: 36
35786 TGTTTATGTG
*
35796 AAATTGAAGAG-AAAGAGAAGAG-AG-GCAAAGATC
1 AAATTGAAGAGAAAAGAAAAGAGAAGAGCAAAGATC
35829 AAATTGAAGAGAAAAGAAAAGAGAAGAGCAAAGA
1 AAATTGAAGAGAAAAGAAAAGAGAAGAGCAAAGA
35863 GTGAAAAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 11 0.37
34 10 0.33
35 2 0.07
36 7 0.23
ACGTcount: A:0.60, C:0.04, G:0.28, T:0.07
Consensus pattern (36 bp):
AAATTGAAGAGAAAAGAAAAGAGAAGAGCAAAGATC
Found at i:36750 original size:23 final size:23
Alignment explanation
Indices: 36720--36848 Score: 111
Period size: 23 Copynumber: 5.5 Consensus size: 23
36710 GAACGCTAGC
36720 GTGCTTACTGTTTCGCACTTTGT
1 GTGCTTACTGTTTCGCACTTTGT
*
36743 GTGCTTACTGTTTCGCACTTCGT
1 GTGCTTACTGTTTCGCACTTTGT
* *
36766 GTGCTTACTGATTT-GCGCTATGT
1 GTGCTTACTG-TTTCGCACTTTGT
* * * * *
36789 GCGCCTACTGATT-GAACTGTGT
1 GTGCTTACTGTTTCGCACTTTGT
*
36811 GTGCTTATTGTTTCCCCAGCAC-TTGT
1 GTGCTTACTGTTT---C-GCACTTTGT
36837 GTGCTTACTGTT
1 GTGCTTACTGTT
36849 AAGTACTTCG
Statistics
Matches: 83, Mismatches: 17, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
22 17 0.20
23 46 0.55
24 3 0.04
26 14 0.17
27 3 0.04
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (23 bp):
GTGCTTACTGTTTCGCACTTTGT
Found at i:41489 original size:25 final size:25
Alignment explanation
Indices: 41461--41548 Score: 70
Period size: 25 Copynumber: 3.3 Consensus size: 25
41451 GAGATTAGTT
41461 TTTAATAGTATAAATTGATCGAATA
1 TTTAATAGTATAAATTGATCGAATA
* * * *
41486 TTTAATAGAAGAGATATATAGAGATC-AGTG
1 TTTAATAGTATA-A-AT-T---GATCGAATA
*
41516 TTTAATAGTATAAATTGATCGAATT
1 TTTAATAGTATAAATTGATCGAATA
41541 TTTAATAG
1 TTTAATAG
41549 AAGAAGTCAG
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
24 4 0.08
25 20 0.42
26 1 0.02
27 3 0.06
28 3 0.06
29 1 0.02
30 12 0.25
31 4 0.08
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (25 bp):
TTTAATAGTATAAATTGATCGAATA
Found at i:41527 original size:55 final size:55
Alignment explanation
Indices: 41443--41552 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
41433 ACATCGTGTT
* *
41443 GATATATAGAGATTAGTTTTTAATAGTATAAATTGATCGAATATTTAATAGAAGA
1 GATATATAGAGATCAGTGTTTAATAGTATAAATTGATCGAATATTTAATAGAAGA
*
41498 GATATATAGAGATCAGTGTTTAATAGTATAAATTGATCGAATTTTTAATAGAAGA
1 GATATATAGAGATCAGTGTTTAATAGTATAAATTGATCGAATATTTAATAGAAGA
41553 AGTCAGTTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.37
Consensus pattern (55 bp):
GATATATAGAGATCAGTGTTTAATAGTATAAATTGATCGAATATTTAATAGAAGA
Found at i:41833 original size:15 final size:17
Alignment explanation
Indices: 41810--41846 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
41800 TTGATTTAAT
41810 TTATAAAAAT-AT-AAA
1 TTATAAAAATAATAAAA
*
41825 TTATTAAAATAATAAAA
1 TTATAAAAATAATAAAA
41842 TTATA
1 TTATA
41847 TTTTTACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.50
16 2 0.11
17 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTATAAAAATAATAAAA
Found at i:45241 original size:2 final size:2
Alignment explanation
Indices: 45234--45270 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
45224 GTACTTGATC
45234 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45271 AAAGGCCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.