Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014699.1 Kokia drynarioides strain JFW-HI SEQ_129738, 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: 35948
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:2007 original size:97 final size:95
Alignment explanation
Indices: 1831--2014 Score: 221
Period size: 97 Copynumber: 1.9 Consensus size: 95
1821 AAAAAGATGT
* * *
1831 TCGATTATCTCGATTTGAGGAAAGGTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATTGAAG
1 TCGATTATCTCGATTTGAGAAAAAGTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAG
*
1896 ATAAGGAAACATTGCCTCGATTAAGGGTAC
66 ATAAAGAAACATTGCCTCGATTAAGGGTAC
* * * *
1926 TCGATTATTTCGATTTGAAGAAAAAATTGCACCTAGTAAGTTAATGCGTAAATTTTC-GAAACTC
1 TCGATTATCTCGATTTG-AG-AAAAAGTGCACCTAGTAAGTTAAGGCGCAAATTTTCAG-AA-TC
*
1990 GAA-ATAAA-AGAATATTGCCTCGATT
62 GAAGATAAAGA-AACATTGCCTCGATT
2015 TTAAAGTTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
95 16 0.21
96 4 0.05
97 51 0.68
98 4 0.05
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (95 bp):
TCGATTATCTCGATTTGAGAAAAAGTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAG
ATAAAGAAACATTGCCTCGATTAAGGGTAC
Found at i:2262 original size:29 final size:29
Alignment explanation
Indices: 2228--2292 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
2218 AAATGAGACT
*
2228 TTTTGGATACCTTGGGGGC-AAAATGGTAG
1 TTTTGGAT-CCTTGGGGGCAAAAATGGAAG
** *
2257 TTTTGGATTTTTGGGGGCAAAAATGGAAT
1 TTTTGGATCCTTGGGGGCAAAAATGGAAG
2286 TTTTGGA
1 TTTTGGA
2293 AGTTTTAGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.25, C:0.06, G:0.32, T:0.37
Consensus pattern (29 bp):
TTTTGGATCCTTGGGGGCAAAAATGGAAG
Found at i:2308 original size:29 final size:29
Alignment explanation
Indices: 2275--2467 Score: 228
Period size: 30 Copynumber: 6.6 Consensus size: 29
2265 TTTTGGGGGC
2275 AAAAATGGAATTTTTGGAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGGAAGTTTTAGGG-T
* **
2305 AAAAATGGAATTTATGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTTAGGGT
* *
2334 AAAAATGGATTTTTTGGAAG-TTTGGGGAT
1 AAAAATGGAATTTTTGGAAGTTTTAGGG-T
2363 AAAAATGGAATTTTTGGAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGGAAGTTTTAGGG-T
* **
2393 AAAAATGGAATTTTTGAAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTTAGGGT
* *
2422 GAAAATGTAATTTTTGGAAGTTTT-GTGGT
1 AAAAATGGAATTTTTGGAAGTTTTAG-GGT
*
2451 AAAAAATAGAATTTTTG
1 -AAAAATGGAATTTTTG
2468 AAAGCTCAGG
Statistics
Matches: 139, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
28 7 0.05
29 62 0.45
30 70 0.50
ACGTcount: A:0.35, C:0.01, G:0.27, T:0.37
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTTAGGGT
Found at i:2311 original size:30 final size:30
Alignment explanation
Indices: 2275--2467 Score: 232
Period size: 29 Copynumber: 6.5 Consensus size: 30
2265 TTTTGGGGGC
2275 AAAAATGGAATTTTTGGAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGGAAGTTTTAGGGTT
* * *
2305 AAAAATGGAATTTATGGAAG-TTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTTAGGGTT
* * *
2334 AAAAATGGATTTTTTGGAAG-TTTGGGGAT
1 AAAAATGGAATTTTTGGAAGTTTTAGGGTT
2363 AAAAATGGAATTTTTGGAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGGAAGTTTTAGGGTT
* **
2393 AAAAATGGAATTTTTGAAAGTTCGAGGG-T
1 AAAAATGGAATTTTTGGAAGTTTTAGGGTT
* * *
2422 GAAAATGTAATTTTTGGAAGTTTT-GTGGTA
1 AAAAATGGAATTTTTGGAAGTTTTAG-GGTT
*
2452 AAAAATAGAATTTTTG
1 AAAAATGGAATTTTTG
2468 AAAGCTCAGG
Statistics
Matches: 139, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
28 1 0.01
29 74 0.53
30 64 0.46
ACGTcount: A:0.35, C:0.01, G:0.27, T:0.37
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTTAGGGTT
Found at i:2427 original size:59 final size:59
Alignment explanation
Indices: 2275--2471 Score: 245
Period size: 59 Copynumber: 3.3 Consensus size: 59
2265 TTTTGGGGGC
* * * * * *
2275 AAAAATGGAATTTTTGGAAGTTTTAGGGTTAAAAATGGAATTTATGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGAAAGTTTGAGGGATAAAAATGGAATTTTTGGAAGTTTTGGGTT
* *
2334 AAAAATGGATTTTTTGGAAGTTTG-GGGATAAAAATGGAATTTTTGGAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGAAAGTTTGAGGGATAAAAATGGAATTTTTGGAAGTTTT-GGGTT
* * * *
2393 AAAAATGGAATTTTTGAAAGTTCGAGGG-TGAAAATGTAATTTTTGGAAGTTTTGTGGTA
1 AAAAATGGAATTTTTGAAAGTTTGAGGGATAAAAATGGAATTTTTGGAAGTTTTG-GGTT
*
2452 AAAAATAGAATTTTTGAAAG
1 AAAAATGGAATTTTTGAAAG
2472 CTCAGGGGTA
Statistics
Matches: 122, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
58 27 0.22
59 92 0.75
60 3 0.02
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.37
Consensus pattern (59 bp):
AAAAATGGAATTTTTGAAAGTTTGAGGGATAAAAATGGAATTTTTGGAAGTTTTGGGTT
Found at i:2487 original size:59 final size:57
Alignment explanation
Indices: 2275--2494 Score: 228
Period size: 59 Copynumber: 3.8 Consensus size: 57
2265 TTTTGGGGGC
* * * * *
2275 AAAAATGGAATTTTTGGAAGTTTTAGGGTTAAAAATGGAATTTATGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGAAAG-TTCAGGGGTAAAAATGGAATTTTTGGAAGTTT-TGGGT
* * *
2334 AAAAATGGATTTTTTGGAAGTT-TGGGGATAAAAATGGAATTTTTGGAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGAAAGTTCAGGGG-TAAAAATGGAATTTTTGGAAGTTTT-GGG-T
* *
2393 AAAAATGGAATTTTTGAAAGTTC-GAGGGTGAAAATGTAATTTTTGGAAGTTTTGTGGT
1 AAAAATGGAATTTTTGAAAGTTCAG-GGGTAAAAATGGAATTTTTGGAAGTTTTG-GGT
* * * *
2451 AAAAAATAGAATTTTTGAAAGCTCAGGGGTAGAAATGTAATTTT
1 -AAAAATGGAATTTTTGAAAGTTCAGGGGTAAAAATGGAATTTT
2495 AGGACAATTT
Statistics
Matches: 140, Mismatches: 13, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
57 3 0.02
58 30 0.21
59 103 0.74
60 4 0.03
ACGTcount: A:0.35, C:0.01, G:0.27, T:0.36
Consensus pattern (57 bp):
AAAAATGGAATTTTTGAAAGTTCAGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGT
Found at i:2487 original size:88 final size:88
Alignment explanation
Indices: 2275--2494 Score: 187
Period size: 88 Copynumber: 2.5 Consensus size: 88
2265 TTTTGGGGGC
* ** * *
2275 AAAAATGGAATTTTTGGAAGTTTTAGGGTTAAAAATGGAATTTATGGAAGTTTGGGGGTAAAAAT
1 AAAAATGGAATTTTTGAAAGTTCGAGGG-TAAAAATGGAATTTTTGGAAGTTTGGGGATAAAAAT
* * *
2340 GGATTTTTTGGAAG-TTTGGGGAT
65 GGAATTTTTGGAAGTTTTAGGGTT
* ** * * *
2363 AAAAATGGAATTTTTGGAAGTTTTAGGGTTAAAAATGGAATTTTTGAAAGTTCGAGGG-TGAAAA
1 AAAAATGGAATTTTTGAAAGTTCGAGGG-TAAAAATGGAATTTTTGGAAGTTTG-GGGATAAAAA
* *
2427 TGTAATTTTTGGAAGTTTT-GTGGTA
64 TGGAATTTTTGGAAGTTTTAG-GGTT
* * * *
2452 AAAAATAGAATTTTTGAAAGCTC-AGGGGTAGAAATGTAATTTT
1 AAAAATGGAATTTTTGAAAGTTCGA-GGGTAAAAATGGAATTTT
2495 AGGACAATTT
Statistics
Matches: 114, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
88 84 0.74
89 30 0.26
ACGTcount: A:0.35, C:0.01, G:0.27, T:0.36
Consensus pattern (88 bp):
AAAAATGGAATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTGGGGATAAAAATG
GAATTTTTGGAAGTTTTAGGGTT
Found at i:2492 original size:29 final size:28
Alignment explanation
Indices: 2329--2494 Score: 84
Period size: 29 Copynumber: 5.7 Consensus size: 28
2319 TGGAAGTTTG
* * * * *
2329 GGGGTAAAAATGGATTTTTTGGAAGTTT
1 GGGGTAGAAATGTAATTTTTGAAAGTTC
* * * *
2357 GGGGATAAAAATGGAATTTTTGGAAGTTTTA
1 GGGG-TAGAAATGTAATTTTTGAAAG--TTC
* * *
2388 GGGTTAAAAATGGAATTTTTGAAAGTTC
1 GGGGTAGAAATGTAATTTTTGAAAGTTC
* *
2416 GAGGGT-GAAAATGTAATTTTTGGAAGTTTT
1 G-GGGTAG-AAATGTAATTTTTGAAAG-TTC
* * *
2446 GTGGTAAAAAATAG-AATTTTTGAAAGCTC
1 GGGGT-AGAAAT-GTAATTTTTGAAAGTTC
2475 AGGGGTAGAAATGTAATTTT
1 -GGGGTAGAAATGTAATTTT
2495 AGGACAATTT
Statistics
Matches: 110, Mismatches: 17, Indels: 21
0.74 0.11 0.14
Matches are distributed among these distances:
28 8 0.07
29 54 0.49
30 42 0.38
31 6 0.05
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (28 bp):
GGGGTAGAAATGTAATTTTTGAAAGTTC
Found at i:3487 original size:13 final size:13
Alignment explanation
Indices: 3469--3493 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3459 TTCATTTCTC
3469 TTTTGCTGGTTTT
1 TTTTGCTGGTTTT
3482 TTTTGCTGGTTT
1 TTTTGCTGGTTT
3494 AGTAAACATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.24, T:0.68
Consensus pattern (13 bp):
TTTTGCTGGTTTT
Found at i:3718 original size:10 final size:10
Alignment explanation
Indices: 3703--3749 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
3693 CTTGTTTATT
3703 ATTATTAATA
1 ATTATTAATA
3713 ATTATTAATA
1 ATTATTAATA
*
3723 A-TATTATTA
1 ATTATTAATA
3732 ATTATTTAATA
1 ATTA-TTAATA
*
3743 AATATTA
1 ATTATTA
3750 TCTTTAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
ATTATTAATA
Found at i:3718 original size:13 final size:12
Alignment explanation
Indices: 3699--3733 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
3689 TCAGCTTGTT
*
3699 TATTATTATTAA
1 TATTATTAATAA
3711 TAATTATTAATAA
1 T-ATTATTAATAA
3724 TATTATTAAT
1 TATTATTAAT
3734 TATTTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATTATTAATAA
Found at i:3719 original size:16 final size:16
Alignment explanation
Indices: 3698--3759 Score: 53
Period size: 16 Copynumber: 4.0 Consensus size: 16
3688 TTCAGCTTGT
3698 TTATTATTATTAATAA
1 TTATTATTATTAATAA
3714 TTATTA--A-TAAT-A
1 TTATTATTATTAATAA
3726 TTATTAATTATTTAATAA
1 TTATT-ATTA-TTAATAA
*
3744 ATATTATCT-TTAATAA
1 TTATTAT-TATTAATAA
3760 AAGCCTTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
12 6 0.16
13 5 0.13
14 1 0.03
15 1 0.03
16 13 0.34
17 6 0.16
18 6 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTATTATTAATAA
Found at i:3757 original size:24 final size:19
Alignment explanation
Indices: 3705--3750 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
3695 TGTTTATTAT
*
3705 TATTAATAATTATTAATAA
1 TATTATTAATTATTAATAA
3724 TATTATTAATTATTTAATAAA
1 TATTATTAATTA-TTAAT-AA
3745 TATTAT
1 TATTAT
3751 CTTTAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 11 0.46
20 5 0.21
21 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTATTAATTATTAATAA
Found at i:4493 original size:13 final size:13
Alignment explanation
Indices: 4475--4499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4465 TTGGACTTGA
4475 TTTGTAATTGGAC
1 TTTGTAATTGGAC
4488 TTTGTAATTGGA
1 TTTGTAATTGGA
4500 TATTATTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (13 bp):
TTTGTAATTGGAC
Found at i:4522 original size:6 final size:6
Alignment explanation
Indices: 4511--4579 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
4501 ATTATTTAGA
* *
4511 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TAAA-A TAAACT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT
* *
4557 TAATTT TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT
4580 CTATTTGATC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
4 2 0.04
5 10 0.20
6 37 0.73
7 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:4539 original size:17 final size:17
Alignment explanation
Indices: 4517--4579 Score: 99
Period size: 17 Copynumber: 3.7 Consensus size: 17
4507 TAGATAAATT
*
4517 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
4534 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
4551 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
4568 TAAATTTAAATT
1 TAAATTTAAATT
4580 CTATTTGATC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:5732 original size:17 final size:17
Alignment explanation
Indices: 5710--5751 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
5700 TATCTCTGGT
*
5710 GAACTCTTA-TAATCGGC
1 GAACTCTCACTAAT-GGC
5727 GAACTCATCACTAATGGC
1 GAACTC-TCACTAATGGC
5745 GAACTCT
1 GAACTCT
5752 ACGTTATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 11 0.50
19 4 0.18
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (17 bp):
GAACTCTCACTAATGGC
Found at i:6908 original size:20 final size:20
Alignment explanation
Indices: 6896--6934 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6886 AATAATTTTC
6896 AAAAATT-CAAAATATTTAT
1 AAAAATTCCAAAATATTTAT
*
6915 AAAAATTCCAAAATTTTTAT
1 AAAAATTCCAAAATATTTAT
6935 TTTTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATTCCAAAATATTTAT
Found at i:6912 original size:19 final size:19
Alignment explanation
Indices: 6885--6933 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
6875 AAAAAAATTG
6885 AAATAATTTTCAAAAATT-CA
1 AAAT-ATTTT-AAAAATTCCA
6905 AAATATTTATAAAAATTCCA
1 AAATATTT-TAAAAATTCCA
6925 AAAT-TTTTA
1 AAATATTTTA
6934 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.07
19 14 0.52
20 11 0.41
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATATTTTAAAAATTCCA
Found at i:7147 original size:9 final size:9
Alignment explanation
Indices: 7130--7159 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
7120 TGAATTTTAC
*
7130 AATTCGAAT
1 AATTTGAAT
7139 AATTTGAAT
1 AATTTGAAT
7148 AATTTGAAT
1 AATTTGAAT
7157 AAT
1 AAT
7160 AGATTTGTGT
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:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (9 bp):
AATTTGAAT
Found at i:7258 original size:19 final size:19
Alignment explanation
Indices: 7235--7292 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
7225 CAAAAATTAC
7235 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
* *
7254 TAAAATTTAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
7273 AAAAATTCCAAAATTTTTAT
1 AAAAATT-CAAAATATTTAT
7293 TTTTTTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.12
19 18 0.56
20 10 0.31
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:12681 original size:26 final size:24
Alignment explanation
Indices: 12627--12682 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
12617 CACTCAAATT
12627 CATAATAAATAAAATATAAATATA
1 CATAATAAATAAAATATAAATATA
* *
12651 AATAATATAATTAAAATTTTAAATA-A
1 CATAATA-AA-TAAAA-TATAAATATA
12677 CATAAT
1 CATAAT
12683 TCAAGAAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 6 0.23
25 2 0.08
26 11 0.42
27 7 0.27
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (24 bp):
CATAATAAATAAAATATAAATATA
Found at i:13766 original size:42 final size:42
Alignment explanation
Indices: 13718--13798 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
13708 ATTGCTATTG
13718 TTTGGGATTTAGGGTTATTTAAAATTTTGTTTGATTTGTTAT
1 TTTGGGATTTAGGGTTATTTAAAATTTTGTTTGATTTGTTAT
*
13760 TTTGGGATTTAGGGTTATTTAAATTTTTGTTTGATTTGT
1 TTTGGGATTTAGGGTTATTTAAAATTTTGTTTGATTTGT
13799 AATTCAGATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.58
Consensus pattern (42 bp):
TTTGGGATTTAGGGTTATTTAAAATTTTGTTTGATTTGTTAT
Found at i:13817 original size:41 final size:42
Alignment explanation
Indices: 13723--13811 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
13713 TATTGTTTGG
* ** *
13723 GATTTAGGGTTATTTAAAATTTTGTTTGATTTGTTATTTTGG
1 GATTTAGGGTTATTTAAAATTTTGTTTGATTTGTAATTCAGA
*
13765 GATTTAGGGTTATTTAAATTTTTGTTTGATTTGTAATTCAGA
1 GATTTAGGGTTATTTAAAATTTTGTTTGATTTGTAATTCAGA
*
13807 TATTT
1 GATTT
13812 TGGTTAACGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.01, G:0.19, T:0.56
Consensus pattern (42 bp):
GATTTAGGGTTATTTAAAATTTTGTTTGATTTGTAATTCAGA
Found at i:23324 original size:24 final size:21
Alignment explanation
Indices: 23283--23336 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 21
23273 ATTTTCGATT
*
23283 AATAAAATAAATAATTAAATA
1 AATAAAATAAATAATTAAACA
23304 AATAAAACTAAAAGTAATTAAACA
1 AATAAAA-T-AAA-TAATTAAACA
*
23328 TATAAAATA
1 AATAAAATA
23337 CAAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 7 0.25
22 2 0.07
23 4 0.14
24 15 0.54
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.26
Consensus pattern (21 bp):
AATAAAATAAATAATTAAACA
Found at i:29573 original size:97 final size:96
Alignment explanation
Indices: 29387--29579 Score: 232
Period size: 97 Copynumber: 2.0 Consensus size: 96
29377 TTTTTGGGAA
** *
29387 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
* *
29452 GAATCGAAGATAAGGAAACCTTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* * * *
29483 AAGGGTATTCGATTATTTCGATTTGAGGAAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTT
1 AAGGATATTCGATTATCTCGATTTGAAG-AAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTT
29547 C-GAAACTCGAA-ATAACAGAAA-ATTGCCTCGATT
64 CAG-AA-TCGAAGATAA-AGAAACATTGCCTCGATT
29580 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
96 27 0.33
97 47 0.57
98 9 0.11
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:29847 original size:30 final size:28
Alignment explanation
Indices: 29808--29873 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
29798 GGATCCCCGA
29808 GGGTAAAATGGTAATTTTGGGAAAATTCGG
1 GGGTAAAATGG-AATTTTGGG-AAATTCGG
* * * *
29838 GGTTAAAATGGGATTTTTGGAAGTTCGG
1 GGGTAAAATGGAATTTTGGGAAATTCGG
29866 GGGTAAAA
1 GGGTAAAA
29874 ATAGAATCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 14 0.45
29 7 0.23
30 10 0.32
ACGTcount: A:0.32, C:0.03, G:0.35, T:0.30
Consensus pattern (28 bp):
GGGTAAAATGGAATTTTGGGAAATTCGG
Found at i:29875 original size:59 final size:59
Alignment explanation
Indices: 29808--30364 Score: 606
Period size: 59 Copynumber: 9.5 Consensus size: 59
29798 GGATCCCCGA
* ** *
29808 GGGT-AAAATGGTAATTTTGGGAAAATTCGGGGT-TAAAATGGGATTTTTGGAAGTTCGG
1 GGGTAAAAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
* * * * *
29866 GGGTAAAAATAGAATCTTTGGAAGTTTCGAGGTC-AAAATGGGATTTTTGGAGGTT-TG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
* ** * * *
29923 GGGTAAAAATAGAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTAGAAAGTTTGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
* * * * * *
29982 GGGTAAAAATGGAAGTTTTGGAAGTTTTGAGGTCAAAAATGAGATTTTTGAAAGTTTGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
* * * * *
30041 GGGTAAAAATGTG-ATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTTTCGAAAGTTTGA
1 GGGTAAAAATG-GAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
* ** * *
30100 GGGTAAAAATGAAATTTTTGGAAGTTTCAAGGTCAAAAATGGGATTTTCGAAAGTTCGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
*
30159 GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
* * * * * * *
30218 GGGTAAAAACGAAATTTTTGAAAGTTTCGAGGTTAAAAATGGGA-TTTTAGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
* * ** * *
30276 GGGT-AAAATGGTAATTTTTTGAAGTTTCGGAGTCAAAAATGGGATTTTCAGTAGTTCGA
1 GGGTAAAAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
***
30335 GGGTAAAAACAAAATTTTTGGAAGTTTCGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGG
30365 TACCTCCGGG
Statistics
Matches: 428, Mismatches: 62, Indels: 17
0.84 0.12 0.03
Matches are distributed among these distances:
57 36 0.08
58 101 0.24
59 286 0.67
60 5 0.01
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (59 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
Found at i:30360 original size:29 final size:29
Alignment explanation
Indices: 29805--30343 Score: 398
Period size: 29 Copynumber: 18.4 Consensus size: 29
29795 TTCGGATCCC
* * *
29805 CGAGGGT-AAAATGGTAATTTTGGGAAAATT
1 CGAGGGTAAAAATGG-GATTTTTGG-AAGTT
*
29835 CG-GGGTTAAAATGGGATTTTTGGAAGTT
1 CGAGGGTAAAAATGGGATTTTTGGAAGTT
* * * *
29863 CGGGGGTAAAAATAGAATCTTTGGAAGTTT
1 CGAGGGTAAAAATGGGATTTTTGGAAG-TT
* *
29893 CGA-GGTCAAAATGGGATTTTTGGAGGTT
1 CGAGGGTAAAAATGGGATTTTTGGAAGTT
* * *
29921 TG-GGGTAAAAATAGAATTTTTGGAAGTT
1 CGAGGGTAAAAATGGGATTTTTGGAAGTT
** * *
29949 TTAGGGTCAAAAATGGGATTTTAGAAAGTT
1 CGAGGGT-AAAAATGGGATTTTTGGAAGTT
* * * *
29979 TGGGGGTAAAAATGGAAGTTTTGGAAGTTT
1 CGAGGGTAAAAATGGGATTTTTGGAAG-TT
* * *
30009 TGA-GGTCAAAAATGAGATTTTTGAAAGTT
1 CGAGGGT-AAAAATGGGATTTTTGGAAGTT
* * *
30038 TGGGGGTAAAAATGTGATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGGATTTTTGGAAG-TT
* *
30068 CG-GGGTAAAAAATGGGATTTTCGAAAGTT
1 CGAGGGT-AAAAATGGGATTTTTGGAAGTT
* **
30097 TGAGGGTAAAAATGAAATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGGATTTTTGGAAG-TT
* * *
30127 C-AAGGTCAAAAATGGGATTTTCGAAAGTT
1 CGAGGGT-AAAAATGGGATTTTTGGAAGTT
* *
30156 CGGGGGTAAAAATGGAATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGGATTTTTGGAAG-TT
*
30186 TG-GGGTCAAAAATGGGATTTTTGGAAGTT
1 CGAGGGT-AAAAATGGGATTTTTGGAAGTT
* * ** *
30215 CGGGGGTAAAAACGAAATTTTTGAAAGTTT
1 CGAGGGTAAAAATGGGATTTTTGGAAG-TT
* *
30245 CGAGGTTAAAAATGGGA-TTTTAGAAGTT
1 CGAGGGTAAAAATGGGATTTTTGGAAGTT
* *
30273 CGAGGGT-AAAATGGTAATTTTTTGAAGTTT
1 CGAGGGTAAAAATGG-GATTTTTGGAAG-TT
* ** *
30303 CG-GAGTCAAAAATGGGATTTTCAGTAGTT
1 CGAGGGT-AAAAATGGGATTTTTGGAAGTT
30332 CGAGGGTAAAAA
1 CGAGGGTAAAAA
30344 CAAAATTTTT
Statistics
Matches: 404, Mismatches: 80, Indels: 51
0.76 0.15 0.10
Matches are distributed among these distances:
27 7 0.02
28 40 0.10
29 191 0.47
30 159 0.39
31 7 0.02
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (29 bp):
CGAGGGTAAAAATGGGATTTTTGGAAGTT
Done.