Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012092.1 Kokia drynarioides strain JFW-HI SEQ_127091, 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: 300402
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 195 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:262481 original size:29 final size:27
Alignment explanation
Indices: 262444--262525 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 27
262434 GGAAGTTCAA
262444 GGGTAAAATGGTAATTTTGGTAAAATCG
1 GGGTAAAATGGTAATTTTGG-AAAATCG
* * *
262472 GGGTAAAAATGG-AATTTTTGAAAGTTTGG
1 GGGT-AAAATGGTAATTTTGGAAA--ATCG
262501 GGGTAAAATGGTAATTTTTGGAAAA
1 GGGTAAAATGGTAA-TTTTGGAAAA
262526 GTCGAGGTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
27 3 0.07
28 18 0.41
29 15 0.34
30 8 0.18
ACGTcount: A:0.37, C:0.01, G:0.29, T:0.33
Consensus pattern (27 bp):
GGGTAAAATGGTAATTTTGGAAAATCG
Found at i:262536 original size:116 final size:117
Alignment explanation
Indices: 262326--262577 Score: 291
Period size: 116 Copynumber: 2.2 Consensus size: 117
262316 TGGATACTCG
* * * *
262326 AGGGCAAAATGGTAATTTAGGAAAATTTAGGGTCAAAAATGGAATTTTTAGATATTTAGGGGTAA
1 AGGGTAAAATGGTAATTTTGGAAAATTCAGGGTCAAAAATGGAATTTTTAGAAATTTAGGGGTAA
* * *
262391 AATGGTAATTTTTAAAAAAATGGGTGTCAAAAAT-AGAGTTTTTGGAAGTTCA
66 AATGGTAATTTTTAAAAAAATGAGTGTCAAAAATGA-AATTTTTGAAAGTTCA
* *
262443 AGGGTAAAATGGTAATTTTGGTAAAA-TCGGGGT-AAAAATGGAATTTTT-GAAAGTTTGGGGGT
1 AGGGTAAAATGGTAATTTTGG-AAAATTCAGGGTCAAAAATGGAATTTTTAGAAA-TTTAGGGGT
** * *
262505 AAAATGGTAATTTTTGGAAAAGTCGAG-GTCAAAAATGAAATTTTTGAAAGTTCG
64 AAAATGGTAATTTTTAAAAAAAT-GAGTGTCAAAAATGAAATTTTTGAAAGTTCA
*
262559 AGCGTAAAAAT-GTAATTTT
1 AGGGT-AAAATGGTAATTTT
262578 TGGATAGTTT
Statistics
Matches: 116, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
115 3 0.03
116 77 0.66
117 32 0.28
118 4 0.03
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.33
Consensus pattern (117 bp):
AGGGTAAAATGGTAATTTTGGAAAATTCAGGGTCAAAAATGGAATTTTTAGAAATTTAGGGGTAA
AATGGTAATTTTTAAAAAAATGAGTGTCAAAAATGAAATTTTTGAAAGTTCA
Found at i:262554 original size:59 final size:58
Alignment explanation
Indices: 262326--262581 Score: 211
Period size: 59 Copynumber: 4.4 Consensus size: 58
262316 TGGATACTCG
* * ** * * *
262326 AGGGCAAAATGGTAA-TTTAGGAAAATTTAGGGTCAAAAATGGAATTTTTAGATA-TTTA
1 AGGGTAAAATGGTAATTTTTGGAAAATCGA-GGTCAAAAATGAAATTTTT-GAAAGTTCA
* ** * * *
262384 GGGGTAAAATGGTAATTTTTAAAAAAAT-GGGTGTCAAAAAT-AGAGTTTTTGGAAGTTCA
1 AGGGTAAAATGGTAATTTTT-GGAAAATCGAG-GTCAAAAATGA-AATTTTTGAAAGTTCA
* * **
262443 AGGGTAAAATGGTAA-TTTTGGTAAAATCGGGGT-AAAAATGGAATTTTTGAAAGTTTG
1 AGGGTAAAATGGTAATTTTTGG-AAAATCGAGGTCAAAAATGAAATTTTTGAAAGTTCA
* *
262500 GGGGTAAAATGGTAATTTTTGGAAAAGTCGAGGTCAAAAATGAAATTTTTGAAAGTTCG
1 AGGGTAAAATGGTAATTTTTGGAAAA-TCGAGGTCAAAAATGAAATTTTTGAAAGTTCA
*
262559 AGCGTAAAAAT-GTAATTTTTGGA
1 AGGGT-AAAATGGTAATTTTTGGA
262582 TAGTTTAGGG
Statistics
Matches: 160, Mismatches: 26, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
57 36 0.22
58 39 0.24
59 75 0.47
60 10 0.06
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (58 bp):
AGGGTAAAATGGTAATTTTTGGAAAATCGAGGTCAAAAATGAAATTTTTGAAAGTTCA
Found at i:263741 original size:19 final size:16
Alignment explanation
Indices: 263681--263740 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
263671 TTTATTAAAA
*
263681 TATTATT-TT-TTTAT
1 TATTATTATTATTAAT
*
263695 TATCATTATTATTAAT
1 TATTATTATTATTAAT
263711 TATTATTATTATTAA-
1 TATTATTATTATTAAT
*
263726 TGTTATTTATTATTA
1 TATTA-TTATTATTA
263741 TCACCATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
14 6 0.15
15 6 0.15
16 27 0.69
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TATTATTATTATTAAT
Found at i:263752 original size:3 final size:3
Alignment explanation
Indices: 263681--263741 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
263671 TTTATTAAAA
* * *
263681 TAT TAT T-T TTT TAT TAT CAT TAT TAT TAAT TAT TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
*
263726 TGT TATT TAT TAT TAT
1 TAT TA-T TAT TAT TAT
263742 CACCATTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.83
4 6 0.12
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:264471 original size:17 final size:17
Alignment explanation
Indices: 264451--264497 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
264441 TTTAATTAAT
*
264451 TTAAATTTAAATTCAAA
1 TTAAATTTAAACTCAAA
* *
264468 TTAAATTTAAGCTCAAT
1 TTAAATTTAAACTCAAA
264485 TTAAATTTAAACT
1 TTAAATTTAAACT
264498 TAAAAGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAAATTTAAACTCAAA
Found at i:264519 original size:25 final size:25
Alignment explanation
Indices: 264484--264547 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
264474 TTAAGCTCAA
*
264484 TTTAAATTTAAACTTAAAAGAAAAG
1 TTTAAACTTAAACTTAAAAGAAAAG
264509 TTTAAACTTAAACTTAAAAGAAAAG
1 TTTAAACTTAAACTTAAAAGAAAAG
264534 TTTAAACTTAAACT
1 TTTAAACTTAAACT
264548 AAATTTAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (25 bp):
TTTAAACTTAAACTTAAAAGAAAAG
Found at i:265352 original size:50 final size:50
Alignment explanation
Indices: 265270--265547 Score: 196
Period size: 50 Copynumber: 5.6 Consensus size: 50
265260 AGGTATAAGG
* * *
265270 TTCGCCATTACGACTTAAA-CATTTTCCC-TTTGTGCCTTCATGGTACTGGA
1 TTCGCCGTTACGGCTTAAATC--TTTCCCTTTTGTGTCTTCATGGTACTGGA
* * **
265320 TTCGCCGTTGCGGCTTAAATCTTTCCCTTTTGTATCTTTGTGGTACTGGA
1 TTCGCCGTTACGGCTTAAATCTTTCCCTTTTGTGTCTTCATGGTACTGGA
* * * *
265370 TTCGCCCGTTACGGCTTAGATATTT-CCTTTTATGTCTAT-ATGGTATTGGA
1 TTCG-CCGTTACGGCTTAAATCTTTCCCTTTTGTGTCT-TCATGGTACTGGA
** **
265420 TTCGCCGTTATTGCTTAAATCTTTCCC-TTCATG-CTTC-TGAGGTGCAC-GG-
1 TTCGCCGTTACGGCTTAAATCTTTCCCTTTTGTGTCTTCAT--GGT--ACTGGA
** * * * * *
265469 TTCGCCGTTGTGACTTAAACCTTTCCCTTTTGTATCTTCGTGGTATTGGA
1 TTCGCCGTTACGGCTTAAATCTTTCCCTTTTGTGTCTTCATGGTACTGGA
* * *
265519 TCCGTCGTTACGGCTTAGATCTTTCCCTT
1 TTCGCCGTTACGGCTTAAATCTTTCCCTT
265548 CATGTCTCTG
Statistics
Matches: 178, Mismatches: 35, Indels: 30
0.73 0.14 0.12
Matches are distributed among these distances:
47 2 0.01
48 3 0.02
49 55 0.31
50 93 0.52
51 24 0.13
52 1 0.01
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (50 bp):
TTCGCCGTTACGGCTTAAATCTTTCCCTTTTGTGTCTTCATGGTACTGGA
Found at i:265662 original size:100 final size:98
Alignment explanation
Indices: 265432--265742 Score: 315
Period size: 99 Copynumber: 3.1 Consensus size: 98
265422 CGCCGTTATT
* * * *
265432 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTGCACGGTTCGCCGTTGTGACTTAAACCTTTCCCT
1 GCTTAGATCTTTCCCTTCATGCTTCTGAGGTACACGGTTCACCGTTGCGACTTAAACCTTTCCCT
* * * * *
265497 TTTGTATCTTCGTGGTATTGGATCCGTCGTTACG
66 TGTGTCT-TTAGTGGTACTGGATCCGTCATTACG
* * *
265531 GCTTAGATCTTTCCCTTCATG-TCTCTGAGGTACAAGGTTCATCGTTGCGACTTAAACCCTTCCC
1 GCTTAGATCTTTCCCTTCATGCT-TCTGAGGTACACGGTTCACCGTTGCGACTTAAACCTTTCCC
* *
265595 TTGTGTCTTTATTACGGTACTGGAT-C-TACTATTGCG
65 TTGTGTCTTTAGT--GGTACTGGATCCGT-C-ATTACG
* * *
265631 GCTTAGATCTTTCCCTTCATGCTTCTAAGGTACACGATTCACCGTTACGACTTAAACCTTTCCCT
1 GCTTAGATCTTTCCCTTCATGCTTCTGAGGTACACGGTTCACCGTTGCGACTTAAACCTTTCCC-
* ** * *
265696 TTGTATCTTT-GCAGTACTGGATCCGCCATTGCG
65 TTGTGTCTTTAGTGGTACTGGATCCGTCATTACG
*
265729 ATCTTAGATCTTTC
1 -GCTTAGATCTTTC
265743 TCGTCATGTT
Statistics
Matches: 176, Mismatches: 26, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
98 20 0.11
99 77 0.44
100 69 0.39
101 10 0.06
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.38
Consensus pattern (98 bp):
GCTTAGATCTTTCCCTTCATGCTTCTGAGGTACACGGTTCACCGTTGCGACTTAAACCTTTCCCT
TGTGTCTTTAGTGGTACTGGATCCGTCATTACG
Found at i:277381 original size:58 final size:58
Alignment explanation
Indices: 277311--277613 Score: 289
Period size: 58 Copynumber: 5.2 Consensus size: 58
277301 ACCCGGGGGC
* * * *
277311 AAAATGGAAATTTTGGAAAAGTTAGGGGTCAAAAATGGAATTTT-TAAACATTCGAGGT
1 AAAATGGTAATTTTGGAAAAATTAGGGGTCAAAAATGGAATTTTGGAAA-GTTCGAGGT
* * * * *
277369 AAAATGATAATTTT-AAAAAATTGGGGGTCAAAAATGGAGTTTTTGG-AAGTTCAGGGGT
1 AAAATGGTAATTTTGGAAAAATTAGGGGTCAAAAATGGA-ATTTTGGAAAGTTC-GAGGT
** * *
277427 AAAATGGTAATTTTTGGAAAAACCA--GGTCAAAAATGGAATTTTGGAAAGTTTGGGGT
1 AAAATGGTAA-TTTTGGAAAAATTAGGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGT
* * *
277484 AAAATGGTGATTTTTGGAAAAA-TCGGGGTC-AAAATGGAATTTTGGAAAGTTCAAGGGT
1 AAAATGGT-AATTTTGGAAAAATTAGGGGTCAAAAATGGAATTTTGGAAAGTTCGA-GGT
* * * * *
277542 AAAATGGTAATTTTGGAAAAGTCA-AGGTAAAAAATGGAATTTTGGAAAGTTCTAGGCT
1 AAAATGGTAATTTTGGAAAAATTAGGGGTCAAAAATGGAATTTTGGAAAGTTCGAGG-T
*
277600 AAAATTGTAATTTT
1 AAAATGGTAATTTT
277614 TTGGATAGTT
Statistics
Matches: 202, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
57 91 0.45
58 102 0.50
59 4 0.02
60 5 0.02
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (58 bp):
AAAATGGTAATTTTGGAAAAATTAGGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGT
Found at i:277440 original size:28 final size:29
Alignment explanation
Indices: 277306--277613 Score: 160
Period size: 29 Copynumber: 10.7 Consensus size: 29
277296 TTGATACCCG
* *
277306 GGGGCAAAATGGAAATTTTGGAAAAGTT-A
1 GGGGTAAAATGGTAATTTTGG-AAAGTTCA
* *
277335 GGGGTCAAAAATGG-AATTTT-TAAACATTC-
1 GGGGT--AAAATGGTAATTTTGGAAA-GTTCA
* * ** * *
277364 GAGGTAAAATGATAATTTTAAAAAATT-G
1 GGGGTAAAATGGTAATTTTGGAAAGTTCA
*
277392 GGGGTCAAAAATGG-AGTTTTTGG-AAGTTCA
1 GGGGT--AAAATGGTA-ATTTTGGAAAGTTCA
***
277422 GGGGTAAAATGGTAATTTTTGGAAAAACCA
1 GGGGTAAAATGGTAA-TTTTGGAAAGTTCA
*** *
277452 GGTCAAAAATGG-AATTTTGGAAAGTT-T
1 GGGGTAAAATGGTAATTTTGGAAAGTTCA
* **
277479 GGGGTAAAATGGTGATTTTTGGAAAAATC-
1 GGGGTAAAATGGT-AATTTTGGAAAGTTCA
277508 GGGGTCAAAATGG-AATTTTGGAAAGTTCA
1 GGGGT-AAAATGGTAATTTTGGAAAGTTCA
*
277537 AGGGTAAAATGGTAATTTTGGAAAAG-TCA
1 GGGGTAAAATGGTAATTTTGG-AAAGTTCA
*
277566 -AGGTAAAAAATGG-AATTTTGGAAAGTTCTA
1 GGGGT--AAAATGGTAATTTTGGAAAGTTC-A
* *
277596 -GGCTAAAATTGTAATTTT
1 GGGGTAAAATGGTAATTTT
277614 TTGGATAGTT
Statistics
Matches: 215, Mismatches: 38, Indels: 52
0.70 0.12 0.17
Matches are distributed among these distances:
27 15 0.07
28 64 0.30
29 74 0.34
30 55 0.26
31 7 0.03
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTGGAAAGTTCA
Found at i:277485 original size:115 final size:115
Alignment explanation
Indices: 277311--277604 Score: 328
Period size: 115 Copynumber: 2.5 Consensus size: 115
277301 ACCCGGGGGC
* ** * * *
277311 AAAATGGAAATTTTGGAAAAGTTAGGGGTCAAAAATGGAATTTT-TAAACATTCGAGGTAAAATG
1 AAAATGGTAATTTTGGAAAAGACA-AGGTCAAAAATGGAATTTTGGAAA-GTTCGAGGTAAAATG
* * *
277375 AT-AATTTT-AAAAAATTGGGGGTCAAAAATGGAGTTTTTGG-AAGTTCAGGGGT
64 ATGAATTTTGAAAAAA-TCGGGGTC-AAAATGGA-ATTTTGGAAAGTTCAAGGGT
* * * *
277427 AAAATGGTAATTTTTGGAAAA-ACCAGGTCAAAAATGGAATTTTGGAAAGTTTGGGGTAAAATGG
1 AAAATGGTAA-TTTTGGAAAAGACAAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGTAAAATGA
* *
277491 TGATTTTTGGAAAAATCGGGGTCAAAATGGAATTTTGGAAAGTTCAAGGGT
65 TGAATTTTGAAAAAATCGGGGTCAAAATGGAATTTTGGAAAGTTCAAGGGT
* * *
277542 AAAATGGTAATTTTGGAAAAGTCAAGGTAAAAAATGGAATTTTGGAAAGTTCTAGGCTAAAAT
1 AAAATGGTAATTTTGGAAAAGACAAGGTCAAAAATGGAATTTTGGAAAGTTCGAGG-TAAAAT
277605 TGTAATTTTT
Statistics
Matches: 150, Mismatches: 21, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
114 16 0.11
115 89 0.59
116 30 0.20
117 15 0.10
ACGTcount: A:0.40, C:0.05, G:0.26, T:0.30
Consensus pattern (115 bp):
AAAATGGTAATTTTGGAAAAGACAAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGTAAAATGAT
GAATTTTGAAAAAATCGGGGTCAAAATGGAATTTTGGAAAGTTCAAGGGT
Found at i:277497 original size:57 final size:57
Alignment explanation
Indices: 277394--277593 Score: 253
Period size: 57 Copynumber: 3.5 Consensus size: 57
277384 AAAAATTGGG
* *
277394 GGTCAAAAATGGAGTTTTTGG-AAGTTCAGGGGTAAAATGGTAATTTTTGGAAAAACCA
1 GGTCAAAAATGGA-ATTTTGGAAAGTTCAGGGGTAAAATGGT-ATTTTTGGAAAAACAA
* **
277452 GGTCAAAAATGGAATTTTGGAAAGTT-TGGGGTAAAATGGTGATTTTTGGAAAAATCGG
1 GGTCAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGT-ATTTTTGGAAAAA-CAA
* * *
277510 GGTC-AAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGGTAATTTTGGAAAAGTCAA
1 GGTCAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTATTTTTGGAAAA-ACAA
*
277567 GGTAAAAAATGGAATTTTGGAAAGTTC
1 GGTCAAAAATGGAATTTTGGAAAGTTC
277594 TAGGCTAAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
57 68 0.54
58 57 0.46
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.29
Consensus pattern (57 bp):
GGTCAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTATTTTTGGAAAAACAA
Found at i:278744 original size:19 final size:19
Alignment explanation
Indices: 278722--278770 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
278712 TTATTTGTTT
* *
278722 ATTATCATTATTATTATTA
1 ATTATTATTATTAATATTA
278741 ATTATTATTATTAATATTA
1 ATTATTATTATTAATATTA
*
278760 TTTATTATTAT
1 ATTATTATTAT
278771 CACCATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTATTATTATTAATATTA
Found at i:278745 original size:22 final size:22
Alignment explanation
Indices: 278720--278781 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
278710 TATTATTTGT
278720 TTATTATCATTATTATTATTAA
1 TTATTATCATTATTATTATTAA
* * *
278742 TTATTATTATTAATATTATTTA
1 TTATTATCATTATTATTATTAA
**
278764 TTATTATCACCATTATTA
1 TTATTATCATTATTATTA
278782 ATGTCATTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATTATCATTATTATTATTAA
Found at i:278746 original size:13 final size:13
Alignment explanation
Indices: 278728--278770 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
278718 GTTTATTATC
278728 ATTATTATTATTA
1 ATTATTATTATTA
278741 ATTATTATTATTA
1 ATTATTATTATTA
278754 A-TATTATTTATT-
1 ATTATTA-TTATTA
278766 ATTAT
1 ATTAT
278771 CACCATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.21
13 22 0.79
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:278778 original size:19 final size:19
Alignment explanation
Indices: 278737--278780 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
278727 CATTATTATT
* * *
278737 ATTAATTATTATTATTAAT
1 ATTATTTATTATTATCAAC
*
278756 ATTATTTATTATTATCACC
1 ATTATTTATTATTATCAAC
278775 ATTATT
1 ATTATT
278781 AATGTCATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTATTTATTATTATCAAC
Found at i:278781 original size:3 final size:3
Alignment explanation
Indices: 278720--278770 Score: 66
Period size: 3 Copynumber: 16.3 Consensus size: 3
278710 TATTATTTGT
* *
278720 TTA TTA TCA TTA TTA TTA TTAA TTA TTA TTA TTA ATA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA -TTA TTA
278767 TTA T
1 TTA T
278771 CACCATTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:279476 original size:6 final size:6
Alignment explanation
Indices: 279465--279512 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
279455 CTTTTTAATT
* *
279465 AATTTA AATTTA AATTCA AA-TTA AATTTA AACTT- AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
279511 AA
1 AA
279513 CTCAAAAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 8 0.22
6 28 0.78
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:279488 original size:11 final size:12
Alignment explanation
Indices: 279465--279512 Score: 64
Period size: 11 Copynumber: 4.2 Consensus size: 12
279455 CTTTTTAATT
279465 AATTTAAATTTA
1 AATTTAAATTTA
*
279477 AATTCAAA-TTA
1 AATTTAAATTTA
*
279488 AATTTAAACTT-
1 AATTTAAATTTA
279499 AATTTAAATTTA
1 AATTTAAATTTA
279511 AA
1 AA
279513 CTCAAAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTTAAATTTA
Found at i:279548 original size:17 final size:17
Alignment explanation
Indices: 279463--279549 Score: 86
Period size: 17 Copynumber: 5.0 Consensus size: 17
279453 GACTTTTTAA
*
279463 TTAATTTAAATTTAAA-
1 TTAAATTAAATTTAAAC
279479 TTCAAATTAAATTTAAAC
1 TT-AAATTAAATTTAAAC
*
279497 TTAATTTAAATTTAAAC
1 TTAAATTAAATTTAAAC
* **
279514 TCAAAAGAAAAGTTTAAAC
1 T-TAAATTAAA-TTTAAAC
*
279533 TTAAACTAAATTTAAAC
1 TTAAATTAAATTTAAAC
279550 CCAAAATGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
16 2 0.03
17 35 0.60
18 13 0.22
19 8 0.14
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (17 bp):
TTAAATTAAATTTAAAC
Found at i:281248 original size:13 final size:13
Alignment explanation
Indices: 281230--281257 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
281220 AATGTTTGGT
281230 TACTAGAATAATA
1 TACTAGAATAATA
281243 TACTAGAATAATA
1 TACTAGAATAATA
281256 TA
1 TA
281258 TCACTTACAA
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:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (13 bp):
TACTAGAATAATA
Found at i:294574 original size:31 final size:31
Alignment explanation
Indices: 294529--294601 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
294519 TTAAGGTGTG
* *
294529 TGGGCCACACGAGCTGGGCCAGGTAGGATGTA
1 TGGG-CACATGAGCTGGACCAGGTAGGATGTA
* * *
294561 TGGGCACATGAGCTGGACTAGGTAGGCTGTG
1 TGGGCACATGAGCTGGACCAGGTAGGATGTA
294592 TGGGCACATG
1 TGGGCACATG
294602 GGCGTGTGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 32 0.89
32 4 0.11
ACGTcount: A:0.21, C:0.19, G:0.41, T:0.19
Consensus pattern (31 bp):
TGGGCACATGAGCTGGACCAGGTAGGATGTA
Found at i:296154 original size:56 final size:59
Alignment explanation
Indices: 296093--296201 Score: 143
Period size: 56 Copynumber: 1.9 Consensus size: 59
296083 AGTGATTATC
* * * *
296093 TTAATATTAAATTTAATAT-TTATTT-TGTAGATAA-TATTCTATTAATTTAATAAAAT
1 TTAATAGTAAATTTAATATAATATTTATCTAGATAAGTATTATATTAATTTAATAAAAT
* *
296149 TTAATAGTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAA
1 TTAATAGTAAATTTAATATAATATTTATCTAGATAAGTATTATATTAATTTAA
296202 GGCATAATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
56 17 0.39
57 5 0.11
58 7 0.16
59 15 0.34
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (59 bp):
TTAATAGTAAATTTAATATAATATTTATCTAGATAAGTATTATATTAATTTAATAAAAT
Found at i:297285 original size:15 final size:15
Alignment explanation
Indices: 297258--297296 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
297248 AAATCTATCC
*
297258 AGAA-AAGGCAAATA
1 AGAAGAAGGAAAATA
*
297272 AGATGAAGGAAAATA
1 AGAAGAAGGAAAATA
297287 AGAAGAAGGA
1 AGAAGAAGGA
297297 GAAGGAGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.62, C:0.03, G:0.28, T:0.08
Consensus pattern (15 bp):
AGAAGAAGGAAAATA
Found at i:297453 original size:10 final size:11
Alignment explanation
Indices: 297423--297462 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
297413 TTATATTTAA
297423 AAAATAATTTT
1 AAAATAATTTT
*
297434 AAATTAATTTT
1 AAAATAATTTT
297445 AAAAT-ATTTT
1 AAAATAATTTT
297455 AAAA-AATT
1 AAAATAATT
297463 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 12 0.46
11 14 0.54
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:297468 original size:15 final size:15
Alignment explanation
Indices: 297448--297476 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
297438 TAATTTTAAA
297448 ATATTTTAAAAAATT
1 ATATTTTAAAAAATT
297463 ATATTTTAAAAAAT
1 ATATTTTAAAAAAT
297477 AATTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATTTTAAAAAATT
Done.