Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009450.1 Kokia drynarioides strain JFW-HI SEQ_124157, 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: 21166
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:843 original size:14 final size:14
Alignment explanation
Indices: 802--845 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
792 TTTACGTGTA
* *
802 GATTCATAAATGCG
1 GATTCATAAAGGTG
**
816 GATTCATAGGGGTG
1 GATTCATAAAGGTG
830 GATTCATAAAGGTG
1 GATTCATAAAGGTG
844 GA
1 GA
846 CTTATAGATG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.27
Consensus pattern (14 bp):
GATTCATAAAGGTG
Found at i:3348 original size:36 final size:36
Alignment explanation
Indices: 3301--3399 Score: 164
Period size: 36 Copynumber: 2.8 Consensus size: 36
3291 AAGGTCATGG
*
3301 TTACTCCCTATTAACCCAAAGGTCATGATGCTT-ATT
1 TTACTCCCTATTGACCCAAAGGTCATGATG-TTCATT
3337 TTACTCCCTATTGACCCAAAGGTCATGATGTTCATT
1 TTACTCCCTATTGACCCAAAGGTCATGATGTTCATT
*
3373 TTACTCCCTGTTGACCCAAAGGTCATG
1 TTACTCCCTATTGACCCAAAGGTCATG
3400 CCTGTTACCA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 2 0.03
36 58 0.97
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.34
Consensus pattern (36 bp):
TTACTCCCTATTGACCCAAAGGTCATGATGTTCATT
Found at i:4965 original size:96 final size:96
Alignment explanation
Indices: 4781--4972 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
4771 AATTTACGAA
* * *
4781 AAGGATATTTGATTATCTTGATTTGTAGAAAGATTGCACCTAGTAAATTAAGGCGCAATATTTCA
1 AAGGATATTTGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAATTAAGGCACAATATTTCA
*
4846 AAATCGAAGATAAGGAAACATTGCCTCGATT
66 AAATCGAAGATAAAGAAACATTGCCTCGATT
* * * *
4877 AAGGGTATTTGATTGT-TTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTT
1 AAGGATATTTGATTATCTT-GATTTGAAGAAAAATTGCACCTAGTAAATTAAGGCACAATA-TTT
* *
4940 CGAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
64 C-AAAATCGAAGATAAAGA-AACATTGCCTCGATT
4973 TTTAAAGCTT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 4 0.05
96 70 0.85
97 8 0.10
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (96 bp):
AAGGATATTTGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAATTAAGGCACAATATTTCA
AAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:5661 original size:59 final size:58
Alignment explanation
Indices: 5288--5663 Score: 348
Period size: 59 Copynumber: 6.4 Consensus size: 58
5278 TTAAACATTT
* * * * * *
5288 AGGGGTAAAAAGGGTAATTTT-GAGAGTTTCGAGGTCGAAAATGGAGTTTTTGGACA-TCC
1 AGGGGTAAAAATGGAAATTTTGGA-AGTTTTGGGGTCAAAAATGGA-TTTTTGGA-AGTTC
* * * ** * *
5347 GGGGGT-AAAATGGTAATTTTTGAAAGTTTCAGTGCCAAAAATGGAATTTTTGGAAGTTC
1 AGGGGTAAAAATGG-AAATTTTGGAAGTTTTGGGGTCAAAAATGG-ATTTTTGGAAGTTC
* * * *
5406 AGGGCTAAAAATGGAATTTTTTGAAGTTTTGGGGTC-AAAATGGGATTTTTGGAAGTTT
1 AGGGGTAAAAATGGAAATTTTGGAAGTTTTGGGGTCAAAAAT-GGATTTTTGGAAGTTC
* * * * * *
5464 GGGGGTAAAAAT-GAAATTTTTGGAAGTTTCGAGGTTAAAAATTGATTTTTGAAAGTTC
1 AGGGGTAAAAATGGAAA-TTTTGGAAGTTTTGGGGTCAAAAATGGATTTTTGGAAGTTC
* * * * * *
5522 AGGGGTAAAAAAGGAAATTTTTGAAGTTTTAGGGTCAAAACTAGAGTTTTTGGAAGTTT
1 AGGGGTAAAAATGGAAATTTTGGAAGTTTTGGGGTCAAAAATGGA-TTTTTGGAAGTTC
* *
5581 AGGGGTAAAAAAGGAATTTTTGGAAGTTTTGGGGTCAAAAATAGGATTTTTGGAAGTTC
1 AGGGGTAAAAATGGAAATTTTGGAAGTTTTGGGGTCAAAAAT-GGATTTTTGGAAGTTC
*
5640 AGAGGTAAAAATGGAAATTTTGGA
1 AGGGGTAAAAATGGAAATTTTGGA
5664 CAGCTGACAC
Statistics
Matches: 256, Mismatches: 50, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
57 3 0.01
58 94 0.37
59 148 0.58
60 11 0.04
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.33
Consensus pattern (58 bp):
AGGGGTAAAAATGGAAATTTTGGAAGTTTTGGGGTCAAAAATGGATTTTTGGAAGTTC
Found at i:5662 original size:29 final size:29
Alignment explanation
Indices: 5348--5663 Score: 291
Period size: 29 Copynumber: 10.8 Consensus size: 29
5338 TGGACATCCG
*
5348 GGGGT-AAAATGGTAATTTTTGAAAGTTTCA
1 GGGGTAAAAATGG-AATTTTTGGAAGTTT-A
* ** *
5378 GTGCCAAAAATGGAATTTTTGGAAGTTCA
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* * *
5407 GGGCTAAAAATGGAATTTTTTGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* * *
5436 GGGGTCAAAATGGGATTTTTGGAAGTTTG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* *
5465 GGGGTAAAAATGAAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* * * *
5494 GAGGTTAAAAATTG-ATTTTTGAAAGTTCA
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTA
*
5523 GGGGTAAAAAAGGAAATTTTT-GAAGTTTTA
1 GGGGTAAAAATGG-AATTTTTGGAAG-TTTA
* * *
5553 -GGGTCAAAACTAGAGTTTTTGGAAGTTTA
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTA
* *
5582 GGGGTAAAAAAGGAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
*
5611 GGGGTCAAAAATAGG-ATTTTTGGAAGTTCA
1 GGGGT-AAAAAT-GGAATTTTTGGAAGTTTA
* *
5641 GAGGTAAAAATGGAAATTTTGGA
1 GGGGTAAAAATGGAATTTTTGGA
5664 CAGCTGACAC
Statistics
Matches: 231, Mismatches: 44, Indels: 23
0.78 0.15 0.08
Matches are distributed among these distances:
28 11 0.05
29 143 0.62
30 68 0.29
31 9 0.04
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTA
Found at i:6707 original size:16 final size:16
Alignment explanation
Indices: 6686--6739 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
6676 ACATTATTTA
6686 TTATTATTAAAAATAT
1 TTATTATTAAAAATAT
*
6702 TTATTATT---ATTA-
1 TTATTATTAAAAATAT
* *
6714 ATATTATTAAAAACAT
1 TTATTATTAAAAATAT
6730 TTATTATTAA
1 TTATTATTAA
6740 TAGTCATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
12 7 0.24
13 3 0.10
15 2 0.07
16 17 0.59
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTATTAAAAATAT
Found at i:6708 original size:22 final size:21
Alignment explanation
Indices: 6665--6714 Score: 86
Period size: 19 Copynumber: 2.5 Consensus size: 21
6655 TTTCCTTTTT
6665 TTATTATTAAAACATTATTTA
1 TTATTATTAAAACATTATTTA
6686 TTATTATTAAAA-A-TATTTA
1 TTATTATTAAAACATTATTTA
6705 TTATTATTAA
1 TTATTATTAA
6715 TATTATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 16 0.55
20 1 0.03
21 12 0.41
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATTATTAAAACATTATTTA
Found at i:6721 original size:19 final size:19
Alignment explanation
Indices: 6665--6721 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
6655 TTTCCTTTTT
6665 TTATTATTAAAACATTATTTA
1 TTATTATT-AAA-ATTATTTA
*
6686 TTATTATTAAAAATATTTA
1 TTATTATTAAAATTATTTA
*
6705 TTATTATTAATATTATT
1 TTATTATTAAAATTATT
6722 AAAAACATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 22 0.67
20 3 0.09
21 8 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTATTAAAATTATTTA
Found at i:6725 original size:28 final size:29
Alignment explanation
Indices: 6678--6738 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
6668 TTATTAAAAC
* *
6678 ATTATTTATTATTATTAAAAATATTTATT
1 ATTATTTAATATTATTAAAAACATTTATT
6707 ATTA-TTAATATTATTAAAAACATTTATT
1 ATTATTTAATATTATTAAAAACATTTATT
6735 ATTA
1 ATTA
6739 ATAGTCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (29 bp):
ATTATTTAATATTATTAAAAACATTTATT
Found at i:7367 original size:15 final size:15
Alignment explanation
Indices: 7341--7402 Score: 90
Period size: 15 Copynumber: 4.2 Consensus size: 15
7331 TGGGCTGACT
*
7341 TTGGGCCA-TTGTAC
1 TTGGGCCATTTGTAA
7355 TTGGGCCATTTGTAA
1 TTGGGCCATTTGTAA
* *
7370 TTAGGCCGTTTGTAA
1 TTGGGCCATTTGTAA
7385 TTGGGCCATTTGTAA
1 TTGGGCCATTTGTAA
7400 TTG
1 TTG
7403 TACTTTGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
14 8 0.19
15 34 0.81
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (15 bp):
TTGGGCCATTTGTAA
Found at i:7460 original size:34 final size:33
Alignment explanation
Indices: 7422--7500 Score: 113
Period size: 34 Copynumber: 2.4 Consensus size: 33
7412 TTGGACTTTC
* *
7422 TAAATTTAATTTTATAATAAATTTAAATTTCAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTTC-AA
*
7456 TAAATTTAAATTTAAAATAAACTTAAATTTCAA
1 TAAATTTAATTTTAAAATAAACTTAAATTTCAA
*
7489 TAAATTCAATTT
1 TAAATTTAATTT
7501 CCAATAGGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 12 0.30
34 28 0.70
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (33 bp):
TAAATTTAATTTTAAAATAAACTTAAATTTCAA
Found at i:7506 original size:16 final size:17
Alignment explanation
Indices: 7422--7494 Score: 96
Period size: 17 Copynumber: 4.4 Consensus size: 17
7412 TTGGACTTTC
*
7422 TAAATTT-AATTTTATAA
1 TAAATTTAAATTTCA-AA
7439 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
*
7456 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTCAAA
*
7473 TAAACTTAAATTTC-AA
1 TAAATTTAAATTTCAAA
7489 TAAATT
1 TAAATT
7495 CAATTTCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.14
17 37 0.74
18 6 0.12
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:9420 original size:88 final size:88
Alignment explanation
Indices: 9308--9508 Score: 359
Period size: 88 Copynumber: 2.3 Consensus size: 88
9298 GTTAAAAATA
* *
9308 TAATTTTTGGAT-GCCGAGGGCAAAACGATAATTTTTGGATGCTCGGGGGTAAAACTGTAATTAT
1 TAATTTTTGGATATCCGAGGGCAAAACGATAATTTTTGGATGCTCGAGGGTAAAACTGTAATTAT
9372 CAGACAGTTTGGGATCAAAATGG
66 CAGACAGTTTGGGATCAAAATGG
*
9395 TAATTTTTGGATATCCGAGGGCAAAACGGTAATTTTTGGATGCTCGAGGGTAAAACTGTAATTAT
1 TAATTTTTGGATATCCGAGGGCAAAACGATAATTTTTGGATGCTCGAGGGTAAAACTGTAATTAT
9460 CAGACAGTTTGGGATCAAAATGG
66 CAGACAGTTTGGGATCAAAATGG
*
9483 TAATTTTTGGATATCCGAGGGTAAAA
1 TAATTTTTGGATATCCGAGGGCAAAA
9509 TTGTGATTTT
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
87 12 0.11
88 97 0.89
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (88 bp):
TAATTTTTGGATATCCGAGGGCAAAACGATAATTTTTGGATGCTCGAGGGTAAAACTGTAATTAT
CAGACAGTTTGGGATCAAAATGG
Found at i:9455 original size:29 final size:29
Alignment explanation
Indices: 9308--9457 Score: 112
Period size: 29 Copynumber: 5.2 Consensus size: 29
9298 GTTAAAAATA
*
9308 TAATTTTTGGATGC-CGAGGGCAAAAC-G
1 TAATTTTTGGATGCTCGAGGGTAAAACTG
*
9335 ATAATTTTTGGATGCTCGGGGGTAAAACTG
1 -TAATTTTTGGATGCTCGAGGGTAAAACTG
* ** * * * *
9365 TAATTATCAGACAGTTTG-GGATCAAAA-TGG
1 TAATTTTTGGA-TGCTCGAGGGT-AAAACT-G
* * *
9395 TAATTTTTGGAT-ATCCGAGGGCAAAACGG
1 TAATTTTTGGATGCT-CGAGGGTAAAACTG
9424 TAATTTTTGGATGCTCGAGGGTAAAACTG
1 TAATTTTTGGATGCTCGAGGGTAAAACTG
9453 TAATT
1 TAATT
9458 ATCAGACAGT
Statistics
Matches: 92, Mismatches: 21, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
28 15 0.16
29 57 0.62
30 20 0.22
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (29 bp):
TAATTTTTGGATGCTCGAGGGTAAAACTG
Found at i:9545 original size:88 final size:88
Alignment explanation
Indices: 9308--9537 Score: 329
Period size: 88 Copynumber: 2.6 Consensus size: 88
9298 GTTAAAAATA
* * * * *
9308 TAATTTTTGGAT-GCCGAGGGCAAAACGATAATTTTTGGATGCTCGGGGGTAAAACTGTAATTAT
1 TAATTTTTGGATATCCGAGGGCAAAACGGTAATTTTTGAAAGCTCGAGGGTAAAACTGTAATTAT
9372 CAGACAGTTTGGGATCAAAATGG
66 CAGACAGTTTGGGATCAAAATGG
* *
9395 TAATTTTTGGATATCCGAGGGCAAAACGGTAATTTTTGGATGCTCGAGGGTAAAACTGTAATTAT
1 TAATTTTTGGATATCCGAGGGCAAAACGGTAATTTTTGAAAGCTCGAGGGTAAAACTGTAATTAT
9460 CAGACAGTTTGGGATCAAAATGG
66 CAGACAGTTTGGGATCAAAATGG
* ** * *
9483 TAATTTTTGGATATCCGAGGGTAAAATTGTGATTTTTGAAAAGTTC-AGGGTAAAA
1 TAATTTTTGGATATCCGAGGGCAAAACGGTAATTTTTG-AAAGCTCGAGGGTAAAA
9538 ATCTAATTTT
Statistics
Matches: 131, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
87 12 0.09
88 115 0.88
89 4 0.03
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (88 bp):
TAATTTTTGGATATCCGAGGGCAAAACGGTAATTTTTGAAAGCTCGAGGGTAAAACTGTAATTAT
CAGACAGTTTGGGATCAAAATGG
Found at i:9577 original size:30 final size:30
Alignment explanation
Indices: 9500--9693 Score: 169
Period size: 30 Copynumber: 6.5 Consensus size: 30
9490 TGGATATCCG
* *
9500 AGGG-TAAAATTGTGATTTTTGAAAAG-TTC
1 AGGGTTAAAA-TGTAATTTTTGAAAAGTTTA
* *
9529 AGGGTAAAAATCTAATTTTTGAAAAGTTTA
1 AGGGTTAAAATGTAATTTTTGAAAAGTTTA
* * * *
9559 AGTGTTAAAATGTTATTTTTGGAAAGTTTG
1 AGGGTTAAAATGTAATTTTTGAAAAGTTTA
* *
9589 AGGGTT-AAATATAATTTTTGGAAAGTTTA
1 AGGGTTAAAATGTAATTTTTGAAAAGTTTA
* * *
9618 AGGGTCAAAATGCAATTTTTAAAAAGTTTA
1 AGGGTTAAAATGTAATTTTTGAAAAGTTTA
* * * * * **
9648 GGGGTCAAAATATAATCTTTGGAAAGTTCG
1 AGGGTTAAAATGTAATTTTTGAAAAGTTTA
*
9678 AGGGTCAAAATGTAAT
1 AGGGTTAAAATGTAAT
9694 ATCTAGACAA
Statistics
Matches: 133, Mismatches: 29, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
29 43 0.32
30 90 0.68
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.37
Consensus pattern (30 bp):
AGGGTTAAAATGTAATTTTTGAAAAGTTTA
Found at i:9577 original size:59 final size:58
Alignment explanation
Indices: 9500--9693 Score: 192
Period size: 59 Copynumber: 3.3 Consensus size: 58
9490 TGGATATCCG
* * *
9500 AGGG-TAAAATTGTGATTTTTGAAAAGTTCAGGGTAAAAATCTAATTTTTGAAAAGTTTA
1 AGGGTTAAAA-TGTAATTTTTGAAAAGTTCAGGGT-AAAATATAATTTTTGGAAAGTTTA
* * * * *
9559 AGTGTTAAAATGTTATTTTTGGAAAGTTTGAGGGTTAAATATAATTTTTGGAAAGTTTA
1 AGGGTTAAAATGTAATTTTTGAAAAG-TTCAGGGTAAAATATAATTTTTGGAAAGTTTA
* * * * * **
9618 AGGGTCAAAATGCAATTTTTAAAAAGTTTAGGGGTCAAAATATAATCTTTGGAAAGTTCG
1 AGGGTTAAAATGTAATTTTTGAAAAGTTCA-GGGT-AAAATATAATTTTTGGAAAGTTTA
*
9678 AGGGTCAAAATGTAAT
1 AGGGTTAAAATGTAAT
9694 ATCTAGACAA
Statistics
Matches: 112, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
58 3 0.03
59 62 0.55
60 47 0.42
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.37
Consensus pattern (58 bp):
AGGGTTAAAATGTAATTTTTGAAAAGTTCAGGGTAAAATATAATTTTTGGAAAGTTTA
Found at i:10834 original size:3 final size:3
Alignment explanation
Indices: 10828--10906 Score: 133
Period size: 3 Copynumber: 26.3 Consensus size: 3
10818 CTTTTATTTC
10828 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
10876 ATT ATT ATT ATT ATT A-T ATTT ATT ACT ATT A
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT A
10907 AATATTGCAA
Statistics
Matches: 72, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.03
3 68 0.94
4 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:11573 original size:6 final size:6
Alignment explanation
Indices: 11551--11596 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
11541 CTTTTATTCT
*
11551 TTTAAA TTTAGAA --TAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
11597 ATAAACTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
4 2 0.06
5 7 0.20
6 24 0.69
7 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:11573 original size:17 final size:17
Alignment explanation
Indices: 11551--11624 Score: 96
Period size: 17 Copynumber: 4.4 Consensus size: 17
11541 CTTTTATTCT
*
11551 TTTAAATTTAGAATAAA
1 TTTAAATTTAAAATAAA
* *
11568 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
11585 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
11602 CTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
11619 TTTAAA
1 TTTAAA
11625 ATTGGATTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
16 3 0.06
17 43 0.90
18 2 0.04
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:11583 original size:11 final size:12
Alignment explanation
Indices: 11552--11596 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
11542 TTTTATTCTT
11552 TTAAATTTAGAA-
1 TTAAATTTA-AAC
11564 -TAAATTTAAAC
1 TTAAATTTAAAC
*
11575 TTAAA-TTAAAT
1 TTAAATTTAAAC
11586 TTAAATTTAAA
1 TTAAATTTAAA
11597 ATAAACTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 18 0.62
12 9 0.31
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (12 bp):
TTAAATTTAAAC
Found at i:11589 original size:34 final size:34
Alignment explanation
Indices: 11551--11624 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 34
11541 CTTTTATTCT
* * *
11551 TTTAAATTTAGAATAAATTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAACTTAAACTTAAAATAAA
*
11585 TTTAAATTTAAAATAAACTTAATCTTAAAATAAA
1 TTTAAATTTAAAATAAACTTAAACTTAAAATAAA
11619 TTTAAA
1 TTTAAA
11625 ATTGGATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (34 bp):
TTTAAATTTAAAATAAACTTAAACTTAAAATAAA
Found at i:17411 original size:50 final size:49
Alignment explanation
Indices: 17328--17422 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 49
17318 TGCATGACTT
*
17328 GATTTAATGATGCATTTAACTAACATGGGAGTTACATAATGCATGATAG
1 GATTTAATGATGCATTTAACTAACATGGAAGTTACATAATGCATGATAG
* *
17377 GATTT-ATGATGCATATTTAACTAACATGTAAGTTACTTAATGCATG
1 GATTTAATGATGC--ATTTAACTAACATGGAAGTTACATAATGCATG
17423 TCATTATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
48 7 0.17
49 5 0.12
50 29 0.71
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (49 bp):
GATTTAATGATGCATTTAACTAACATGGAAGTTACATAATGCATGATAG
Found at i:17432 original size:50 final size:49
Alignment explanation
Indices: 17310--17455 Score: 136
Period size: 50 Copynumber: 2.9 Consensus size: 49
17300 AACTAATGGA
* * *
17310 TTACTAAATGCATGAC-TTGATTTAATGATGC-ATTTAACTAACATGGGAG
1 TTACTTAATGCATGTCATT-ATTT-ATGATGCAATTTAACTAACATGGAAG
* ** *
17359 TTACATAATGCATGAT-AGGATTTATGATGCATATTTAACTAACATGTAAG
1 TTACTTAATGCATG-TCATTATTTATGATGCA-ATTTAACTAACATGGAAG
* *
17409 TTACTTAATGCATGTCATTATTTATGCTGCAAACTTAACTAATCATG
1 TTACTTAATGCATGTCATTATTTATGATGC-AATTTAACTAA-CATG
17456 AGAGTTAATG
Statistics
Matches: 78, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
48 7 0.09
49 17 0.22
50 49 0.63
51 5 0.06
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (49 bp):
TTACTTAATGCATGTCATTATTTATGATGCAATTTAACTAACATGGAAG
Found at i:17677 original size:17 final size:17
Alignment explanation
Indices: 17657--17689 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17647 CAAATACTTA
17657 TTAAATTAAAA-TAAAAC
1 TTAAA-TAAAATTAAAAC
17674 TTAAATAAAATTAAAA
1 TTAAATAAAATTAAAA
17690 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TTAAATAAAATTAAAAC
Found at i:20223 original size:28 final size:28
Alignment explanation
Indices: 20148--20228 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
20138 TCTTCTTTAA
* *
20148 TTAGAATTTTTTCTTCTTTTTTACAAACT
1 TTAG-ATTTTTTCTTTTTTTTTTCAAACT
*
20177 TT-GA-ATTTTCTTTGATTTTTTTCAATA-T
1 TTAGATTTTTTCTTT--TTTTTTTCAA-ACT
20205 TTAGATTTTTTCTTTTTTTTTTCA
1 TTAGATTTTTTCTTTTTTTTTTCA
20229 CTTTTTCTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
26 7 0.16
27 1 0.02
28 22 0.51
29 5 0.12
30 8 0.19
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.65
Consensus pattern (28 bp):
TTAGATTTTTTCTTTTTTTTTTCAAACT
Done.