Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000168.1 Hibiscus syriacus cultivar Beakdansim tig00000297_pilon, 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: 84384
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:642 original size:20 final size:20
Alignment explanation
Indices: 617--658 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
607 CTTATATGTT
617 ATGACTTGCTTTGAATATGA
1 ATGACTTGCTTTGAATATGA
*
637 ATGACTTGTTTTGAATATGA
1 ATGACTTGCTTTGAATATGA
657 AT
1 AT
659 TGTGATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (20 bp):
ATGACTTGCTTTGAATATGA
Found at i:700 original size:23 final size:21
Alignment explanation
Indices: 673--715 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
663 ATATAAAAAA
673 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
694 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
715 T
1 T
716 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:4163 original size:12 final size:12
Alignment explanation
Indices: 4138--4230 Score: 73
Period size: 12 Copynumber: 7.8 Consensus size: 12
4128 ACGGAGATAT
* *
4138 CAGAAATCAAAA
1 CAGAATTCAGAA
4150 CAGAATTCAGAA
1 CAGAATTCAGAA
4162 CAGATATT-AGAA
1 CAGA-ATTCAGAA
* * *
4174 CAGAATCCATAT
1 CAGAATTCAGAA
*
4186 CAGAAATCAGAA
1 CAGAATTCAGAA
**
4198 CAGAATTCAGGT
1 CAGAATTCAGAA
*
4210 CATGTA-TCAGAA
1 CA-GAATTCAGAA
4222 CAGAATTCA
1 CAGAATTCA
4231 AGTCGAAAAT
Statistics
Matches: 61, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
11 4 0.07
12 52 0.85
13 5 0.08
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:4165 original size:24 final size:24
Alignment explanation
Indices: 4138--4230 Score: 89
Period size: 24 Copynumber: 3.9 Consensus size: 24
4128 ACGGAGATAT
*
4138 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * * * *
4162 CAGATATTAGAACAGAATCCATAT
1 CAGAAATCAGAACAGAATTCAGAA
**
4186 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAA
*
4210 CATG-TATCAGAACAGAATTCA
1 CA-GAAATCAGAACAGAATTCA
4231 AGTCGAAAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 55 0.98
25 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.19
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:4242 original size:24 final size:24
Alignment explanation
Indices: 4170--4244 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
4160 AACAGATATT
* *
4170 AGAACAGAATCCATA-TCAGAAATC
1 AGAACAGAATTCA-AGTCATAAATC
* **
4194 AGAACAGAATTCAGGTCATGTATC
1 AGAACAGAATTCAAGTCATAAATC
4218 AGAACAGAATTCAAGTCGA-AAATC
1 AGAACAGAATTCAAGTC-ATAAATC
4242 AGA
1 AGA
4245 TAAATAATAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
24 40 0.98
25 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (24 bp):
AGAACAGAATTCAAGTCATAAATC
Found at i:4244 original size:48 final size:48
Alignment explanation
Indices: 4134--4227 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
4124 TTAAACGGAG
* *
4134 ATATCAGAAATCAAAACAGAATTCAGAACAGATATTAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCC
**
4182 ATATCAGAAATCAGAACAGAATTCAGGTCATG-TATCAGAACAGAAT
1 ATATCAGAAATCAGAACAGAATTCAGAACA-GATATCAGAACAGAAT
4228 TCAAGTCGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 40 0.98
49 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.20
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCC
Found at i:5373 original size:18 final size:18
Alignment explanation
Indices: 5352--5387 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5342 TTGTCATCCG
*
5352 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
5370 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
5388 GTCATTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:6707 original size:13 final size:13
Alignment explanation
Indices: 6689--6733 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
6679 CAACAGTCAA
6689 CGGGTCAACGGGT
1 CGGGTCAACGGGT
6702 CGGGTCAACGGGT
1 CGGGTCAACGGGT
* * *
6715 CAGGTAAATGGGT
1 CGGGTCAACGGGT
6728 CGGGTC
1 CGGGTC
6734 GGGTCGGGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.44, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:10383 original size:21 final size:21
Alignment explanation
Indices: 10336--10395 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
10326 ATGAAAATAT
* ***
10336 TGTTAATGTTGGTGATTTTAA
1 TGTTAATGTTGATGATAACAA
*
10357 TATTAATGTTGATGATAACAA
1 TGTTAATGTTGATGATAACAA
*
10378 TGTTAATATTGATGATAA
1 TGTTAATGTTGATGATAA
10396 TGTGCATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.45
Consensus pattern (21 bp):
TGTTAATGTTGATGATAACAA
Found at i:16449 original size:30 final size:30
Alignment explanation
Indices: 16415--16478 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
16405 TAAGATTTTT
*
16415 ACATA-ATACTCTATATTTTAACTTAAATTC
1 ACATATATA-TCTATATTTTAACTTAAAGTC
* * *
16445 ACATATCTATTTTTATTTTAACTTAAAGTC
1 ACATATATATCTATATTTTAACTTAAAGTC
16475 ACAT
1 ACAT
16479 TATTTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.45
Consensus pattern (30 bp):
ACATATATATCTATATTTTAACTTAAAGTC
Found at i:16453 original size:26 final size:27
Alignment explanation
Indices: 16424--16491 Score: 68
Period size: 30 Copynumber: 2.4 Consensus size: 27
16414 TACATAATAC
*
16424 TCTATATTTTAACTTAAATTCACA-TA
1 TCTATATTTTAACTTAAAGTCACATTA
16450 TCTATTTTTATTTTAACTTAAAGTCACATTA
1 TCTA----TATTTTAACTTAAAGTCACATTA
*
16481 T-TTTATTTTAA
1 TCTATATTTTAA
16492 ATTATTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
26 12 0.34
30 20 0.57
31 3 0.09
ACGTcount: A:0.34, C:0.12, G:0.01, T:0.53
Consensus pattern (27 bp):
TCTATATTTTAACTTAAAGTCACATTA
Found at i:16530 original size:29 final size:29
Alignment explanation
Indices: 16503--16640 Score: 177
Period size: 29 Copynumber: 4.7 Consensus size: 29
16493 TTATTAATTT
* *
16503 TATTTTATTTTTATTTTAGCCTAAAATTA
1 TATTTTATTTTTATTTTAACCTAAAAATA
*
16532 TATTTTATTTTTATTTTAACTTAAAAATA
1 TATTTTATTTTTATTTTAACCTAAAAATA
* * *
16561 TATTTTAATCTTATTTTAACTTAAAAATA
1 TATTTTATTTTTATTTTAACCTAAAAATA
* *
16590 TATTTTATTTTTATCTTAGCTTCTAAAAATA
1 TATTTTATTTTTATTTTAAC--CTAAAAATA
*
16621 TATCTTATTTTTATTTTAAC
1 TATTTTATTTTTATTTTAAC
16641 TTATTACATA
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
29 69 0.73
31 25 0.27
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.57
Consensus pattern (29 bp):
TATTTTATTTTTATTTTAACCTAAAAATA
Found at i:16575 original size:58 final size:60
Alignment explanation
Indices: 16503--16754 Score: 190
Period size: 60 Copynumber: 4.2 Consensus size: 60
16493 TTATTAATTT
* * *
16503 TATTTTATTTTTATTTTAGCCTAAAATTATATTTTATTTTTATTTTAAC-T-TAAAAATA
1 TATTTTATTTTTATTTTAACCTAAAAATATATTTTATTTTTATCTTAACTTCTAAAAATA
* * * *
16561 TATTTTAATCTTATTTTAACTTAAAAATATATTTTATTTTTATCTTAGCTTCTAAAAATA
1 TATTTTATTTTTATTTTAACCTAAAAATATATTTTATTTTTATCTTAACTTCTAAAAATA
* * * * * * * * * * *
16621 TATCTTATTTTTATTTTAACTTATTACATACATTATATTCTTAACTTAAATTAT-TAAATA
1 TATTTTATTTTTATTTTAACCTA-AAAATATATTTTATTTTTATCTTAACTTCTAAAAATA
* ** * * * * *
16681 TAATTTATCCTTATTTTAACATAAAATTGATATTTTATTCTTATTTTTAA-TTC-AAAATTTTA
1 TATTTTATTTTTATTTTAACCTAAAAAT-ATATTTTATTTTTA-TCTTAACTTCTAAAA--ATA
16743 TATTTTATTTTT
1 TATTTTATTTTT
16755 TTTAATTTAA
Statistics
Matches: 148, Mismatches: 38, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
58 42 0.28
59 3 0.02
60 67 0.45
61 25 0.17
62 11 0.07
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.56
Consensus pattern (60 bp):
TATTTTATTTTTATTTTAACCTAAAAATATATTTTATTTTTATCTTAACTTCTAAAAATA
Found at i:16793 original size:35 final size:35
Alignment explanation
Indices: 16711--16829 Score: 132
Period size: 35 Copynumber: 3.4 Consensus size: 35
16701 ATAAAATTGA
* * * *
16711 TATTTTATTCTTATTTTTAATTCAAAATTTTATATTT
1 TATTTTATT-TTA-ATTTAATTTAAAAATGTATATTT
* *
16748 TATTTT-TTTTAATTTAATTTTAAAATGTATATGT
1 TATTTTATTTTAATTTAATTTAAAAATGTATATTT
*
16782 TATTTTATTTTATTTTAATTTAAAAATGTATATTT
1 TATTTTATTTTAATTTAATTTAAAAATGTATATTT
* *
16817 TAATTTAATTTAA
1 TATTTTATTTTAA
16830 AATTTTTATT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 23 0.33
35 38 0.55
36 2 0.03
37 6 0.09
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.62
Consensus pattern (35 bp):
TATTTTATTTTAATTTAATTTAAAAATGTATATTT
Found at i:16823 original size:25 final size:25
Alignment explanation
Indices: 16787--16869 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
16777 TATGTTATTT
*
16787 TATTTTATTTTAATTTAAAAATGTA
1 TATTTTAATTTAATTTAAAAATGTA
* *
16812 TATTTTAATTTAATTTAAAATTTTTA
1 TATTTTAATTTAATTTAAAA-ATGTA
* * *
16838 TTATTTTAATTTTATTT-TAAAGGTA
1 -TATTTTAATTTAATTTAAAAATGTA
16863 TATTTTA
1 TATTTTA
16870 TTTTTATCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
24 7 0.15
25 21 0.44
26 5 0.10
27 15 0.31
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (25 bp):
TATTTTAATTTAATTTAAAAATGTA
Found at i:16954 original size:25 final size:28
Alignment explanation
Indices: 16920--17039 Score: 106
Period size: 29 Copynumber: 4.3 Consensus size: 28
16910 AATATTTAAA
* *
16920 TTAAGGTAATAATAAA-T-AATAT-TTT
1 TTAAGTTAATAAAAAATTAAATATATTT
16945 TTAAGTTAATAAAAAATTAAAATATATTT
1 TTAAGTTAATAAAAAATT-AAATATATTT
* **
16974 TTAAGTTAAAAGAAAAAGGAAATATATTT
1 TTAAGTTAATA-AAAAATTAAATATATTT
* *
17003 TTATGTTAAGAAAAAA--AATATATATTT
1 TTAAGTTAATAAAAAATTAA-ATATATTT
17030 TTAATGTTAA
1 TTAA-GTTAA
17040 GATGTTTAAT
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
25 14 0.17
26 3 0.04
27 11 0.14
28 15 0.19
29 32 0.40
30 5 0.06
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (28 bp):
TTAAGTTAATAAAAAATTAAATATATTT
Found at i:16979 original size:29 final size:26
Alignment explanation
Indices: 16937--17039 Score: 109
Period size: 29 Copynumber: 3.7 Consensus size: 26
16927 AATAATAAAT
16937 AATAT-TTTTTAAGTTAATAAAAAATTAA
1 AATATATTTTTAAGTTAA-AAAAAA--AA
16965 AATATATTTTTAAGTTAAAAGAAAAAGGA
1 AATATATTTTTAAGTTAAAA-AAAAA--A
*
16994 AATATATTTTTATGTTAAGAAAAAAAA
1 AATATATTTTTAAGTTAA-AAAAAAAA
*
17021 TATATATTTTTAATGTTAA
1 AATATATTTTTAA-GTTAA
17040 GATGTTTAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
27 13 0.20
28 12 0.18
29 39 0.59
30 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (26 bp):
AATATATTTTTAAGTTAAAAAAAAAA
Found at i:17085 original size:23 final size:23
Alignment explanation
Indices: 17059--17104 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
17049 TTTAATATGT
* *
17059 GAATTTAATATATATAATGATAA
1 GAATTTAAGATATATAAGGATAA
17082 GAATTTAAGATATATAAGGATAA
1 GAATTTAAGATATATAAGGATAA
17105 TGAGCAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (23 bp):
GAATTTAAGATATATAAGGATAA
Found at i:17469 original size:7 final size:7
Alignment explanation
Indices: 17437--17488 Score: 50
Period size: 7 Copynumber: 6.9 Consensus size: 7
17427 TAGGATTTAA
17437 AAATAAT
1 AAATAAT
17444 GAAAGTAAT
1 -AAA-TAAT
17453 AAAATAAT
1 -AAATAAT
*
17461 AAATGAT
1 AAATAAT
17468 AAATAAT
1 AAATAAT
*
17475 GAGATAAT
1 -AAATAAT
17483 AAATAA
1 AAATAA
17489 AGTAAATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
7 17 0.46
8 13 0.35
9 7 0.19
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (7 bp):
AAATAAT
Found at i:17484 original size:15 final size:15
Alignment explanation
Indices: 17437--17488 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
17427 TAGGATTTAA
17437 AAATAATGAAAGTAAT
1 AAATAATGAAA-TAAT
*
17453 AAAATAAT-AAATGAT
1 -AAATAATGAAATAAT
*
17468 AAATAATGAGATAAT
1 AAATAATGAAATAAT
17483 AAATAA
1 AAATAA
17489 AGTAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 7 0.23
15 14 0.45
16 3 0.10
17 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (15 bp):
AAATAATGAAATAAT
Found at i:18321 original size:63 final size:63
Alignment explanation
Indices: 18239--18434 Score: 169
Period size: 72 Copynumber: 3.0 Consensus size: 63
18229 TTTATTATTT
* * * ** *
18239 GAGAGTTCTAAGTAAATAAAATAATTAATTCCTAAATAAAATAATCATATTAAAAATCCTACTA
1 GAGATTTCTAAATAAATAAAATAAATAATTAATAAATAAAATAATCAAATTAAAAATCCTA-TA
*
18303 GA-ATTTCTAAATAAATAAATAAATAAAATAATTAATAATAATAATAAAATAATCAAACTAAAAA
1 GAGATTTCTAAATAAAT--A-AAAT-AAATAA-T--TAAT-A-AATAAAATAATCAAATTAAAAA
* *
18367 TTCTATT
57 TCCTATA
* * * * *
18374 GAGATTTCTAATTAAATAAAATAACTAATTTATAAATAAAATAATTAAATTAAGAATCCTA
1 GAGATTTCTAAATAAATAAAATAAATAATTAATAAATAAAATAATCAAATTAAAAATCCTA
18435 AATTTTCATT
Statistics
Matches: 106, Mismatches: 16, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
63 35 0.33
64 3 0.03
65 4 0.04
66 4 0.04
67 6 0.06
68 6 0.06
69 4 0.04
70 3 0.03
71 4 0.04
72 37 0.35
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (63 bp):
GAGATTTCTAAATAAATAAAATAAATAATTAATAAATAAAATAATCAAATTAAAAATCCTATA
Found at i:18365 original size:72 final size:71
Alignment explanation
Indices: 18251--18393 Score: 182
Period size: 72 Copynumber: 2.0 Consensus size: 71
18241 GAGTTCTAAG
** * *
18251 TAAATAAAATAATTAATTCCTAAATAAAATAATCATATTAAAAATCCTACTAGA-ATTTCTAAAT
1 TAAATAAAATAATTAATTAATAAATAAAATAATCAAACTAAAAATCCTA-TAGAGATTTCTAAAT
18315 AAATAAA
65 AAATAAA
* * *
18322 TAAATAAAATAATTAA-TAATAATAATAAAATAATCAAACTAAAAATTCTATTGAGATTTCTAAT
1 TAAATAAAATAATTAATTAAT-A-AATAAAATAATCAAACTAAAAATCCTATAGAGATTTCTAAA
18386 TAAATAAA
64 TAAATAAA
18394 ATAACTAATT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
70 2 0.03
71 20 0.32
72 40 0.65
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (71 bp):
TAAATAAAATAATTAATTAATAAATAAAATAATCAAACTAAAAATCCTATAGAGATTTCTAAATA
AATAAA
Found at i:18412 original size:72 final size:71
Alignment explanation
Indices: 18273--18423 Score: 171
Period size: 72 Copynumber: 2.1 Consensus size: 71
18263 TTAATTCCTA
* * *
18273 AATAAAATAATCATATTAAAAATCCTACTAGAATTTCTAAATAAATAAATAAATAAAATAATTAA
1 AATAAAATAATCAAACTAAAAATCCTACTAGAATTTCTAAATAAATAAATAAATAAAATAATAAA
18338 TAATAAT
66 TAA-AAT
* * * * * *
18345 AATAAAATAATCAAACTAAAAATTCTA-TTGAGATTTCTAATTAAATAAAATAACT-AATTTATA
1 AATAAAATAATCAAACTAAAAATCCTACTAGA-ATTTCTAAATAAAT-AAATAAATAAAATAATA
18408 AATAAAAT
64 AATAAAAT
*
18416 AATTAAAT
1 AATAAAAT
18424 TAAGAATCCT
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
71 13 0.19
72 47 0.70
73 7 0.10
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (71 bp):
AATAAAATAATCAAACTAAAAATCCTACTAGAATTTCTAAATAAATAAATAAATAAAATAATAAA
TAAAAT
Found at i:21944 original size:64 final size:64
Alignment explanation
Indices: 21884--22004 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
21874 TAAAATCGGA
* *
21884 TACAGGTCA-AGTCAGGTAAATTTGACACCAGATTCAGATCGGGTTCAGGTCAGGTCAAATCAG
1 TACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCAGGTTCAGGTCAGGTCAAATCAG
* * * ** **
21947 TTCGGGTTATTTTCAGGTTGATTTGACACCAGATCCAGATCAGGTTCAGGTCAGGTCA
1 TACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCAGGTTCAGGTCAGGTCA
22005 TTTTCAGTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
63 6 0.12
64 42 0.88
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (64 bp):
TACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCAGGTTCAGGTCAGGTCAAATCAG
Found at i:22588 original size:219 final size:224
Alignment explanation
Indices: 22324--22820 Score: 778
Period size: 217 Copynumber: 2.2 Consensus size: 224
22314 ATTTAAGAAT
*
22324 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACACATTGATG
1 TAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAAACAACACACACATTGATG
22389 AGAGATCAAATCGAAATAATTTTAAATAT-TGAGGTTGAAATTAATACAAAAAAGTACTAAATTA
66 AGAGATCAAATCGAAATAATTTTAAAT-TGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTA
* * *
22453 TACCCATTTAAAAAGTTATGAGCCAA-TT-AAA-A-AAAT-AG-AATTAGGTAATAAGTATGGAT
130 TACACATTTAAAAAGATATGAGCCAATTTAAAATAGAAATAAGTAA-TAAGTAATAAGTATGGAT
* *
22512 CATTTTCATATGCAAATAAAATTTGGAGGAC
194 CAATTTCAGATGCAAATAAAATTTGGAGGAC
*
22543 TCAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAAAC-A-ACACACATTGATG
1 TAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAAACAACACACACATTGATG
* *
22606 AGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTAT
66 AGAGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTAT
* *
22671 ACACATTTAAAAAGATATGGGCCAATTTTAAAATAGAAATAAGTAATAAGTAATAAGTATGGGTC
131 ACACATTTAAAAAGATATGAGCCAA-TTTAAAATAGAAATAAGTAATAAGTAATAAGTATGGATC
*
22736 AATTTCAGGTGCAAATAAAATTTGGAGGAC
195 AATTTCAGATGCAAATAAAATTTGGAGGAC
* *
22766 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATATATTAAACAACACA
1 TAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAAACAACACA
22821 AAAGGGATCA
Statistics
Matches: 253, Mismatches: 15, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
216 1 0.00
217 96 0.38
218 1 0.00
219 49 0.19
220 3 0.01
221 1 0.00
222 4 0.02
223 92 0.36
224 3 0.01
225 3 0.01
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (224 bp):
TAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAAACAACACACACATTGATG
AGAGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTAT
ACACATTTAAAAAGATATGAGCCAATTTAAAATAGAAATAAGTAATAAGTAATAAGTATGGATCA
ATTTCAGATGCAAATAAAATTTGGAGGAC
Found at i:23002 original size:27 final size:28
Alignment explanation
Indices: 22972--23032 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
22962 ATATAGTTTA
** *
22972 TATATATATTATGTATAAAGTATAA-AC
1 TATATATACCATGTATAAACTATAATAC
22999 TATATATACCATGTATAAACTATAATAC
1 TATATATACCATGTATAAACTATAATAC
23027 TATATA
1 TATATA
23033 GTTTATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (28 bp):
TATATATACCATGTATAAACTATAATAC
Found at i:23088 original size:11 final size:11
Alignment explanation
Indices: 23074--23111 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
23064 ACTACATAGT
23074 TTATATATAAA
1 TTATATATAAA
*
23085 TTATATATGAA
1 TTATATATAAA
23096 TTATATATAAA
1 TTATATATAAA
*
23107 CTATA
1 TTATA
23112 CAATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:23119 original size:20 final size:20
Alignment explanation
Indices: 23019--23121 Score: 75
Period size: 20 Copynumber: 5.0 Consensus size: 20
23009 ATGTATAAAC
*
23019 TATAATACTATATAGTTTATA
1 TATAA-ACTATATAATTTATA
* *
23040 TATGAACTAT-TGAA-CTATA
1 TATAAACTATAT-AATTTATA
* * *
23059 TAGAAACTACATAGTTTATA
1 TATAAACTATATAATTTATA
* *
23079 TATAAATTATATATGAATTATA
1 TATAAACTATATA--ATTTATA
*
23101 TATAAACTATACAATTTATA
1 TATAAACTATATAATTTATA
23121 T
1 T
23122 TTATATATTA
Statistics
Matches: 61, Mismatches: 16, Indels: 11
0.69 0.18 0.12
Matches are distributed among these distances:
19 13 0.21
20 28 0.46
21 4 0.07
22 16 0.26
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.42
Consensus pattern (20 bp):
TATAAACTATATAATTTATA
Found at i:23186 original size:22 final size:20
Alignment explanation
Indices: 23161--23221 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 20
23151 TATATTGTAC
23161 AAATTATATAGTTTATTAATAT
1 AAATTATATAGTTTA-T-ATAT
23183 AAATTATATAGTTTATATAT
1 AAATTATATAGTTTATATAT
* *
23203 ATATATATATAGTATATAT
1 AAAT-TATATAGTTTATAT
23222 GGTTTAGGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 7 0.19
21 14 0.39
22 15 0.42
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
AAATTATATAGTTTATATAT
Found at i:23289 original size:20 final size:20
Alignment explanation
Indices: 23264--23336 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 20
23254 TGTAAACTGC
*
23264 ATACTATAATTTATATGTAT
1 ATACTATAATTTATATTTAT
*
23284 ATACTATATTTTATACTATTTAT
1 ATACTATA-ATT-TA-TATTTAT
*
23307 ATAAACTATAGTTTATATTTAT
1 AT--ACTATAATTTATATTTAT
23329 ATACTATA
1 ATACTATA
23337 TATATGAACT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 14 0.31
21 2 0.04
22 11 0.24
23 10 0.22
24 2 0.04
25 6 0.13
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.51
Consensus pattern (20 bp):
ATACTATAATTTATATTTAT
Found at i:23335 original size:33 final size:32
Alignment explanation
Indices: 23288--23379 Score: 116
Period size: 33 Copynumber: 2.9 Consensus size: 32
23278 ATGTATATAC
*
23288 TATATTTTATACTATTTATATAAACTATAGTT
1 TATATTTTATACTATATATATAAACTATAGTT
*
23320 TATATTTATATACTATATATATGAACTATAGTT
1 TATATTT-TATACTATATATATAAACTATAGTT
* * *
23353 TACATATGA-ACTATATATATAAA-TATA
1 TATATTTTATACTATATATATAAACTATA
23380 TATATACTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.08
31 13 0.25
32 8 0.15
33 28 0.53
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (32 bp):
TATATTTTATACTATATATATAAACTATAGTT
Found at i:23419 original size:18 final size:18
Alignment explanation
Indices: 23398--23527 Score: 90
Period size: 18 Copynumber: 6.9 Consensus size: 18
23388 AAGGTTGATA
*
23398 TTTATATATGAACTATAG
1 TTTACATATGAACTATAG
*
23416 TTTACATATAAACTATAGTTG
1 TTTACATATGAACTATA---G
23437 ATATTTACATATGAACTATAG
1 ---TTTACATATGAACTATAG
*
23458 TTTACACATGAACTATA-
1 TTTACATATGAACTATAG
*
23475 --T--ATATAAACTATATAG
1 TTTACATATGAAC--TATAG
*
23491 TTTACATATAAACTATATAG
1 TTTACATATGAAC--TATAG
23511 TTTACATATGAACTATA
1 TTTACATATGAACTATA
23528 TACACTATTA
Statistics
Matches: 92, Mismatches: 7, Indels: 26
0.74 0.06 0.21
Matches are distributed among these distances:
13 6 0.07
15 5 0.05
18 36 0.39
20 27 0.29
21 2 0.02
24 16 0.17
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (18 bp):
TTTACATATGAACTATAG
Found at i:23437 original size:42 final size:42
Alignment explanation
Indices: 23391--23474 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
23381 ATATACTAAG
* *
23391 GTTGATATTTATATATGAACTATAGTTTACATATAAACTATA
1 GTTGATATTTACATATGAACTATAGTTTACACATAAACTATA
*
23433 GTTGATATTTACATATGAACTATAGTTTACACATGAACTATA
1 GTTGATATTTACATATGAACTATAGTTTACACATAAACTATA
23475 TATATAAACT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (42 bp):
GTTGATATTTACATATGAACTATAGTTTACACATAAACTATA
Found at i:23476 original size:20 final size:20
Alignment explanation
Indices: 23398--23529 Score: 106
Period size: 20 Copynumber: 7.0 Consensus size: 20
23388 AAGGTTGATA
*
23398 TTTATATATGAAC--TATAG
1 TTTACATATGAACTATATAG
* *
23416 TTTACATATAAACTATAGTTGATA
1 TTTACATATGAACTATA--T-A-G
23440 TTTACATATGAAC--TATAG
1 TTTACATATGAACTATATAG
*
23458 TTTACACATGAACTATATA-
1 TTTACATATGAACTATATAG
23477 --T--ATA--AACTATATAG
1 TTTACATATGAACTATATAG
*
23491 TTTACATATAAACTATATAG
1 TTTACATATGAACTATATAG
23511 TTTACATATGAACTATATA
1 TTTACATATGAACTATATA
23530 CACTATTATA
Statistics
Matches: 91, Mismatches: 8, Indels: 28
0.72 0.06 0.22
Matches are distributed among these distances:
13 9 0.10
15 2 0.02
16 1 0.01
17 1 0.01
18 26 0.29
19 1 0.01
20 35 0.38
22 3 0.03
23 1 0.01
24 12 0.13
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (20 bp):
TTTACATATGAACTATATAG
Found at i:23485 original size:31 final size:32
Alignment explanation
Indices: 23445--23509 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
23435 TGATATTTAC
* *
23445 ATATGAAC-TATAGTTTACACATGAACTATAT
1 ATATAAACATATAGTTTACACATAAACTATAT
*
23476 ATATAAACTATATAGTTTACATATAAACTATAT
1 ATATAAAC-ATATAGTTTACACATAAACTATAT
23509 A
1 A
23510 GTTTACATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.24
33 22 0.76
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (32 bp):
ATATAAACATATAGTTTACACATAAACTATAT
Found at i:23559 original size:18 final size:18
Alignment explanation
Indices: 23526--23685 Score: 133
Period size: 18 Copynumber: 9.2 Consensus size: 18
23516 ATATGAACTA
*
23526 TATACACTAT-TATATAG
1 TATATACTATATATATAG
23543 TATATACTATATATATAG
1 TATATACTATATATATAG
23561 TATATACTATATATATAG
1 TATATACTATATATATAG
23579 TATATACTATATATATA-
1 TATATACTATATATATAG
* * *
23596 AACTATAGT-T-TATAT-T
1 TA-TATACTATATATATAG
*
23612 TATATACTACATACTATAG
1 TATATACTATATA-TATAG
* *
23631 T-T-TA-TATTTATATAC
1 TATATACTATATATATAG
*
23646 TATATATTATATATATA-
1 TATATACTATATATATAG
*
23663 AACTATA-TATACTATATAG
1 TA-TATACTATA-TATATAG
23682 TATA
1 TATA
23686 ATTTACATAT
Statistics
Matches: 117, Mismatches: 13, Indels: 25
0.75 0.08 0.16
Matches are distributed among these distances:
15 10 0.09
16 11 0.09
17 22 0.19
18 72 0.62
19 2 0.02
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (18 bp):
TATATACTATATATATAG
Found at i:23566 original size:20 final size:19
Alignment explanation
Indices: 23524--23685 Score: 127
Period size: 20 Copynumber: 8.4 Consensus size: 19
23514 ACATATGAAC
*
23524 TATATACACTAT-TATATA
1 TATATATACTATATATATA
*
23542 -GTATATACTATATATATA
1 TATATATACTATATATATA
*
23560 -GTATATACTATATATATA
1 TATATATACTATATATATA
*
23578 -GTATATACTATATATATA
1 TATATATACTATATATATA
* * *
23596 AACTATAGT-TTATATTTATA
1 TA-TATA-TACTATATATATA
* *
23616 TACTACATACTATAGTTTATA
1 TA-TATATACTATA-TATATA
*
23637 TTTATATACTATATATTATA
1 TATATATACTATATA-TATA
*
23657 TATATAAACTATATATACTA
1 TATATATACTATATATA-TA
23677 TATAGTATA
1 TATA-TATA
23686 ATTTACATAT
Statistics
Matches: 121, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
17 9 0.07
18 42 0.35
19 4 0.03
20 55 0.45
21 11 0.09
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (19 bp):
TATATATACTATATATATA
Found at i:23574 original size:27 final size:27
Alignment explanation
Indices: 23536--23595 Score: 61
Period size: 29 Copynumber: 2.1 Consensus size: 27
23526 TATACACTAT
23536 TATATAGTATATACTATATA-TATAGTATA
1 TATATA-TATATACTATATACTATAG--TA
*
23565 TACTATATATATAGTATATACTATA-TA
1 TA-TATATATATACTATATACTATAGTA
23592 TATA
1 TATA
23596 AACTATAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
26 2 0.07
27 4 0.14
29 14 0.50
30 8 0.29
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (27 bp):
TATATATATATACTATATACTATAGTA
Found at i:23609 original size:27 final size:28
Alignment explanation
Indices: 23536--23690 Score: 123
Period size: 27 Copynumber: 5.8 Consensus size: 28
23526 TATACACTAT
* *
23536 TATATAGTATATACTATA---TATATAG
1 TATATACTATATACTATAGTTTATATAC
23561 TATATACTATATA-TATAG--TATATAC
1 TATATACTATATACTATAGTTTATATAC
* *
23586 TATATA-TATAAACTATAGTTTATAT-T
1 TATATACTATATACTATAGTTTATATAC
* *
23612 TATATACTACATACTATAGTTTATAT-T
1 TATATACTATATACTATAGTTTATATAC
* * *
23639 TATATACTATATATTATA-TATATAAAC
1 TATATACTATATACTATAGTTTATATAC
* *
23666 TATATATACTATATAGTATAATTTA
1 --TATATACTATATACTATAGTTTA
23691 CATATGAACT
Statistics
Matches: 108, Mismatches: 13, Indels: 13
0.81 0.10 0.10
Matches are distributed among these distances:
24 9 0.08
25 29 0.27
26 11 0.10
27 39 0.36
29 17 0.16
30 3 0.03
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (28 bp):
TATATACTATATACTATAGTTTATATAC
Found at i:23702 original size:34 final size:36
Alignment explanation
Indices: 23471--23707 Score: 113
Period size: 36 Copynumber: 6.6 Consensus size: 36
23461 ACACATGAAC
* *
23471 TATATATATAAACTATATAGTTTACATATAAACTATATAGT
1 TATACATATAAACTATATA---TAC-TATATACTATATA-T
* *
23512 T-TACATATGAACTATATACACTAT-TA-TATAGTA-
1 TATACATATAAACTATATATACTATATACTATA-TAT
*
23545 TATACTATATATA-TAGTATATACTATATA-TATAGTA-
1 TATAC-ATATAAACTA-TATATACTATATACTATA-TAT
* * * * *
23581 TATACTATATATA-TAAACTATAGTTTATA-TTTATA-
1 TATAC-ATATAAACTATA-TATACTATATACTATATAT
* * * *
23616 TACTACATACTATAGTTTATAT-TTATATACTATATAT
1 TA-TACATA-TAAACTATATATACTATATACTATATAT
* *
23653 TATATATATAAACTATATATACTATATAGTATA-AT
1 TATACATATAAACTATATATACTATATACTATATAT
*
23688 T-TACATATGAACTATATATA
1 TATACATATAAACTATATATA
23708 AAAATCCTAA
Statistics
Matches: 160, Mismatches: 24, Indels: 31
0.74 0.11 0.14
Matches are distributed among these distances:
33 1 0.01
34 26 0.16
35 42 0.26
36 69 0.43
37 6 0.04
40 15 0.09
41 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (36 bp):
TATACATATAAACTATATATACTATATACTATATAT
Found at i:23739 original size:13 final size:14
Alignment explanation
Indices: 23715--23747 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
23705 ATAAAAATCC
23715 TAAACTCTAAACCA
1 TAAACTCTAAACCA
*
23729 TAAAC-CTAAACCC
1 TAAACTCTAAACCA
23742 TAAACT
1 TAAACT
23748 ATACATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACTCTAAACCA
Found at i:23783 original size:9 final size:9
Alignment explanation
Indices: 23769--23977 Score: 51
Period size: 9 Copynumber: 22.4 Consensus size: 9
23759 AGTTTATTAG
23769 TATATATAA
1 TATATATAA
* *
23778 TCTATATGA
1 TATATATAA
23787 TATATATAGA
1 TATATATA-A
* **
23797 -CTATATGG
1 TATATATAA
23805 TATATATAA
1 TATATATAA
* *
23814 -ACTATACAT
1 TA-TATATAA
23823 TATATATAA
1 TATATATAA
*
23832 T-TCAT-TAG
1 TAT-ATATAA
23840 TATATATAA
1 TATATATAA
*
23849 -ACTATATAC
1 TA-TATATAA
23858 TATATAGTTCAA
1 TATATA--T-AA
23870 TAGTATATATA
1 TA-TATATA-A
* *
23881 AACTATATAT
1 TA-TATATAA
*
23891 TATTATATAG
1 TA-TATATAA
*
23901 T-TCAT-TAG
1 TAT-ATATAA
23909 TATATATAA
1 TATATATAA
*
23918 -ACTATATAG
1 TA-TATATAA
23927 TATATATAA
1 TATATATAA
*
23936 -ACTATATAG
1 TA-TATATAA
23945 TATATATAAA
1 TATATAT-AA
23955 CTATATATTAA
1 -TATATA-TAA
*
23966 TTTAT-TAA
1 TATATATAA
23974 TATA
1 TATA
23978 AACATACATA
Statistics
Matches: 145, Mismatches: 31, Indels: 49
0.64 0.14 0.22
Matches are distributed among these distances:
8 23 0.16
9 77 0.53
10 19 0.13
11 18 0.12
12 4 0.03
13 4 0.03
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.43
Consensus pattern (9 bp):
TATATATAA
Found at i:23792 original size:18 final size:18
Alignment explanation
Indices: 23766--23961 Score: 185
Period size: 18 Copynumber: 11.1 Consensus size: 18
23756 TATAGTTTAT
*
23766 TAGTATATATAATCTATA
1 TAGTATATATAAACTATA
*
23784 T-GATATATATAGACTATA
1 TAG-TATATATAAACTATA
*
23802 TGGTATATATAAACTATA
1 TAGTATATATAAACTATA
* * *
23820 CATTATATAT-AATTCAT-
1 TAGTATATATAAACT-ATA
23837 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
* *
23855 TACTATATAGT--TC-A-A
1 TAGTATATA-TAAACTATA
23870 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
* * *
23888 TATTAT-TATATAGT-TCA
1 TAGTATATATAAACTAT-A
23905 TTAGTATATATAAACTATA
1 -TAGTATATATAAACTATA
23924 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
23942 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
23960 TA
1 TA
23962 TTAATTTATT
Statistics
Matches: 144, Mismatches: 20, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.01
15 9 0.06
16 3 0.02
17 23 0.16
18 98 0.68
19 9 0.06
20 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:23815 original size:69 final size:68
Alignment explanation
Indices: 23742--23964 Score: 265
Period size: 69 Copynumber: 3.2 Consensus size: 68
23732 ACCTAAACCC
* *
23742 TAAACTATACATTATATAGTTTATTAGTATATATAATCTATATGATATATATAGACTATATGGTA
1 TAAACTATACATTATATAGTTTATTAGTATATATAAACTATAT-ATATATATAGACTATATAGTA
23807 TATA
65 TATA
* *
23811 TAAACTATACATTATATA-TAATTCATTAGTATATATAAACTATATA-CTATATAG-TTCA-ATA
1 TAAACTATACATTATATAGT--TT-ATTAGTATATATAAACTATATATATATATAGACT-ATATA
23872 GTATATA
62 GTATATA
* * *
23879 TAAACTATATATTATTATATAGTTCATTAGTATATATAAACTATATAGTATATATAAACTATATA
1 TAAAC--TATA-CATTATATAGTTTATTAGTATATATAAACTATATA-TATATATAGACTATATA
23944 GTATATA
62 GTATATA
*
23951 TAAACTATATATTA
1 TAAACTATACATTA
23965 ATTTATTAAT
Statistics
Matches: 133, Mismatches: 9, Indels: 24
0.80 0.05 0.14
Matches are distributed among these distances:
68 16 0.12
69 53 0.40
70 12 0.09
71 35 0.26
72 17 0.13
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.43
Consensus pattern (68 bp):
TAAACTATACATTATATAGTTTATTAGTATATATAAACTATATATATATATAGACTATATAGTAT
ATA
Found at i:23819 original size:36 final size:37
Alignment explanation
Indices: 23742--23964 Score: 233
Period size: 36 Copynumber: 6.4 Consensus size: 37
23732 ACCTAAACCC
* *
23742 TAAACTATACA-T-TATATAG-TTTAT-TAGTATATA
1 TAAACTATATATTATATATAGATTCATATAGTATATA
* * *
23775 TAATCTATATGA-TATATATAGACT-ATATGGTATATA
1 TAAACTATAT-ATTATATATAGATTCATATAGTATATA
*
23811 TAAACTATACATTATATATA-ATTCAT-TAGTATATA
1 TAAACTATATATTATATATAGATTCATATAGTATATA
*
23846 TAAACTATATA--CTATATAG-TTCA-ATAGTATATA
1 TAAACTATATATTATATATAGATTCATATAGTATATA
23879 TAAACTATATATTATTATATAG-TTCAT-TAGTATATA
1 TAAACTATATATTA-TATATAGATTCATATAGTATATA
* * *
23915 TAAACTATATAGTATATATAAACT-ATATAGTATATA
1 TAAACTATATATTATATATAGATTCATATAGTATATA
23951 TAAACTATATATTA
1 TAAACTATATATTA
23965 ATTTATTAAT
Statistics
Matches: 161, Mismatches: 15, Indels: 25
0.80 0.07 0.12
Matches are distributed among these distances:
33 38 0.24
34 2 0.01
35 38 0.24
36 83 0.52
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.43
Consensus pattern (37 bp):
TAAACTATATATTATATATAGATTCATATAGTATATA
Found at i:24086 original size:61 final size:61
Alignment explanation
Indices: 24021--24158 Score: 170
Period size: 62 Copynumber: 2.2 Consensus size: 61
24011 TATAATGATC
* * * * * *
24021 AAATTGAACAAATTTTAAATATGAAGCTTTAATTAATAAATTGTAA-CATTAAATTTGGATT
1 AAATTGAAAAAATTTGAAATATGAAGCTTAAATTAATAAATT-AAATCATTAAATTTAGACT
* *
24082 AAATTGAAAAAAAGTTGAAATATGAAGCTTAAATTAATATATTAAATCATTAAATTTAGACT
1 AAATTG-AAAAAATTTGAAATATGAAGCTTAAATTAATAAATTAAATCATTAAATTTAGACT
*
24144 AAATTGAATAAATTT
1 AAATTGAAAAAATTT
24159 AAAACTAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
61 15 0.23
62 50 0.77
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.37
Consensus pattern (61 bp):
AAATTGAAAAAATTTGAAATATGAAGCTTAAATTAATAAATTAAATCATTAAATTTAGACT
Found at i:24967 original size:9 final size:9
Alignment explanation
Indices: 24955--24988 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
24945 TAATATTTTG
24955 TATTTAATT
1 TATTTAATT
*
24964 TATTTAA-G
1 TATTTAATT
24972 TATTTAATT
1 TATTTAATT
24981 TATTTAAT
1 TATTTAAT
24989 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:24994 original size:17 final size:17
Alignment explanation
Indices: 24954--24992 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
24944 TTAATATTTT
24954 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
24971 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
24988 -TATTT
1 GTATTT
24993 TACTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:27268 original size:13 final size:13
Alignment explanation
Indices: 27227--27270 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
27217 TATTTAGTAC
*
27227 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
27240 TGTTTATTGGACT
1 TTTTTATTGTAAT
27253 TTTTTATTGTAAT
1 TTTTTATTGTAAT
27266 TTTTT
1 TTTTT
27271 TATTTATCAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:27375 original size:34 final size:33
Alignment explanation
Indices: 27309--27379 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 33
27299 CGTTAATATG
*
27309 GTTGGATTTATTTTAATTTATTTTTTTAAATTT
1 GTTGGATTTATTTTAATTTATTTTCTTAAATTT
*
27342 GTTGGACTTT-TTGTTAATTTATTTTCCTTAATTTT
1 GTTGGA-TTTATT-TTAATTTATTTT-CTTAAATTT
27377 GTT
1 GTT
27380 TATTACCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 8 0.24
34 15 0.45
35 10 0.30
ACGTcount: A:0.20, C:0.04, G:0.11, T:0.65
Consensus pattern (33 bp):
GTTGGATTTATTTTAATTTATTTTCTTAAATTT
Found at i:33040 original size:26 final size:26
Alignment explanation
Indices: 33004--33057 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
32994 GATGATCATG
33004 TTTAATTCATTCTTATATTAACCGAC
1 TTTAATTCATTCTTATATTAACCGAC
33030 TTTAATTCATTCTTATATTAACCGAC
1 TTTAATTCATTCTTATATTAACCGAC
33056 TT
1 TT
33058 ATACTGCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.48
Consensus pattern (26 bp):
TTTAATTCATTCTTATATTAACCGAC
Found at i:34255 original size:51 final size:52
Alignment explanation
Indices: 34185--34282 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 52
34175 ATATAAAACT
*
34185 AAATTTCAAAAAAGTAATCATATTAATTTGATTATCATAATAATTTATCATA
1 AAATTTCAAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATCATA
34237 AAATTTC-AAAAAGTAATCATATTAATTTAATTATCATAATAATTTA
1 AAATTTCAAAAAAGTAATCATATTAATTTAATTATCATAATAATTTA
34283 ATTATCATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 38 0.84
52 7 0.16
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (52 bp):
AAATTTCAAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATCATA
Found at i:34274 original size:17 final size:17
Alignment explanation
Indices: 34252--34292 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
34242 TCAAAAAGTA
*
34252 ATCATATTAATTTAATT
1 ATCATAATAATTTAATT
34269 ATCATAATAATTTAATT
1 ATCATAATAATTTAATT
34286 ATCATAA
1 ATCATAA
34293 GTTTATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (17 bp):
ATCATAATAATTTAATT
Found at i:39840 original size:16 final size:17
Alignment explanation
Indices: 39813--39848 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
39803 GATATGAGAA
39813 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
39830 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
39846 AAA
1 AAA
39849 ATAACGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:41760 original size:40 final size:40
Alignment explanation
Indices: 41649--41896 Score: 123
Period size: 40 Copynumber: 6.2 Consensus size: 40
41639 TTGATTCTTC
* * * *
41649 CTTGTAATTAGATGTGTATCCCGTACAATATATCACCACTTT
1 CTTGTAATTGGGTGTGTATCCCATACAATACATCA-C-CTTT
* * * * * * * *
41691 C--ATATTTAGGTGTATATTCCGTACGATACATCGCCTTT
1 CTTGTAATTGGGTGTGTATCCCATACAATACATCACCTTT
*
41729 CTTGTAATTGGGTGCGTATCCCATACAATACATCACCACTTT
1 CTTGTAATTGGGTGTGTATCCCATACAATACATCA-C-CTTT
* * * * * * * *
41771 C--ATATTTAGGTGTGTA-CACGTACGATACATAACCTTG
1 CTTGTAATTGGGTGTGTATCCCATACAATACATCACCTTT
*
41808 CTTGTAATTGGATGTGTATCCCATACAATACATCACCACTTT
1 CTTGTAATTGGGTGTGTATCCCATACAATACATCA-C-CTTT
* * * * * * * *
41850 C--ATATTTAGGTGTGTAGCTCATACGATACATCTCCTTG
1 CTTGTAATTGGGTGTGTATCCCATACAATACATCACCTTT
41888 CTTGTAATT
1 CTTGTAATT
41897 TAAAAAACTG
Statistics
Matches: 149, Mismatches: 46, Indels: 24
0.68 0.21 0.11
Matches are distributed among these distances:
37 4 0.03
38 10 0.07
39 25 0.17
40 98 0.66
41 2 0.01
42 10 0.07
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (40 bp):
CTTGTAATTGGGTGTGTATCCCATACAATACATCACCTTT
Found at i:41782 original size:80 final size:79
Alignment explanation
Indices: 41649--41896 Score: 354
Period size: 80 Copynumber: 3.1 Consensus size: 79
41639 TTGATTCTTC
* * * *
41649 CTTGTAATTAGATGTGTATCCCGTACAATATATCACCACTTTCATATTTAGGTGTATATTC-CGT
1 CTTGTAATTGGATGTGTATCCCATACAATACATCACCACTTTCATATTTAGGTGTGTA--CACGT
* *
41713 ACGATACATCGCCTTT
64 ACGATACATCACCTTG
* *
41729 CTTGTAATTGGGTGCGTATCCCATACAATACATCACCACTTTCATATTTAGGTGTGTACACGTAC
1 CTTGTAATTGGATGTGTATCCCATACAATACATCACCACTTTCATATTTAGGTGTGTACACGTAC
*
41794 GATACATAACCTTG
66 GATACATCACCTTG
* *
41808 CTTGTAATTGGATGTGTATCCCATACAATACATCACCACTTTCATATTTAGGTGTGTAGCTCATA
1 CTTGTAATTGGATGTGTATCCCATACAATACATCACCACTTTCATATTTAGGTGTGTA-CACGTA
*
41873 CGATACATCTCCTTG
65 CGATACATCACCTTG
41888 CTTGTAATT
1 CTTGTAATT
41897 TAAAAAACTG
Statistics
Matches: 151, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
78 1 0.01
79 72 0.48
80 78 0.52
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (79 bp):
CTTGTAATTGGATGTGTATCCCATACAATACATCACCACTTTCATATTTAGGTGTGTACACGTAC
GATACATCACCTTG
Found at i:41935 original size:19 final size:19
Alignment explanation
Indices: 41899--42038 Score: 104
Period size: 19 Copynumber: 7.2 Consensus size: 19
41889 TTGTAATTTA
* *
41899 AAAAACTGGTTTTGCAACCT
1 AAAATCTGGCTTT-CAACCT
*
41919 AAAATCTGGCTTTCAACTTT
1 AAAATCTGGCTTTCAAC-CT
* * *
41939 AAAATTTAGCTTACAACCT
1 AAAATCTGGCTTTCAACCT
* * *
41958 AAAATTTGGATTCCAACCTT
1 AAAATCTGGCTTTCAACC-T
*
41978 AAAATCTGGCTTACAACCT
1 AAAATCTGGCTTTCAACCT
*
41997 AAACTCTGG-TTTGCAACCT
1 AAAATCTGGCTTT-CAACCT
* *
42016 AAAATTCAGG-TTCCAACCT
1 AAAA-TCTGGCTTTCAACCT
42035 AAAA
1 AAAA
42039 ATTCAAGTTC
Statistics
Matches: 98, Mismatches: 18, Indels: 9
0.78 0.14 0.07
Matches are distributed among these distances:
18 2 0.02
19 48 0.49
20 48 0.49
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (19 bp):
AAAATCTGGCTTTCAACCT
Found at i:41958 original size:39 final size:37
Alignment explanation
Indices: 41913--42038 Score: 126
Period size: 39 Copynumber: 3.3 Consensus size: 37
41903 ACTGGTTTTG
41913 CAACCTAAAATCTGGCTTTCAACTTTAAAATTTAGCTTA
1 CAACCTAAAATCTGG-TTTCAAC-TTAAAATTTAGCTTA
* * * *
41952 CAACCTAAAATTTGGATTCCAACCTTAAAATCTGGCTTA
1 CAACCTAAAATCTGG-TTTCAA-CTTAAAATTTAGCTTA
* * * * *
41991 CAACCTAAACTCTGGTTTGCAACCTAAAATTCAGGTTC
1 CAACCTAAAATCTGGTTT-CAACTTAAAATTTAGCTTA
42029 CAACCTAAAA
1 CAACCTAAAA
42039 ATTCAAGTTC
Statistics
Matches: 70, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
38 21 0.30
39 48 0.69
40 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.30
Consensus pattern (37 bp):
CAACCTAAAATCTGGTTTCAACTTAAAATTTAGCTTA
Found at i:42039 original size:20 final size:20
Alignment explanation
Indices: 42010--42056 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
42000 CTCTGGTTTG
*
42010 CAACCT-AAAATTCAGGTTC
1 CAACCTAAAAATTCAAGTTC
42029 CAACCTAAAAATTCAAGTTC
1 CAACCTAAAAATTCAAGTTC
*
42049 CAATCTAA
1 CAACCTAA
42057 TTTCAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.26
Consensus pattern (20 bp):
CAACCTAAAAATTCAAGTTC
Found at i:43149 original size:21 final size:19
Alignment explanation
Indices: 43118--43157 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
43108 ATAGATTTTG
*
43118 GGTTAGTAGTATCGGTACT
1 GGTTAGTAGTATCGATACT
43137 GGTTGAGTGAGTATCGATACT
1 GGTT-AGT-AGTATCGATACT
43158 ACAAGGCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 3 0.17
21 11 0.61
ACGTcount: A:0.23, C:0.10, G:0.33, T:0.35
Consensus pattern (19 bp):
GGTTAGTAGTATCGATACT
Found at i:47438 original size:27 final size:25
Alignment explanation
Indices: 47408--47458 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
47398 TTAATTAATT
47408 AATCGAACATCGATAATTATATTAAAA
1 AATCGAACATC-ATAA-TATATTAAAA
* *
47435 AATCGTACATCATTATATATTAAA
1 AATCGAACATCATAATATATTAAA
47459 TTGAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
26 3 0.14
27 10 0.45
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (25 bp):
AATCGAACATCATAATATATTAAAA
Found at i:49132 original size:36 final size:36
Alignment explanation
Indices: 48998--49135 Score: 170
Period size: 36 Copynumber: 3.9 Consensus size: 36
48988 AGAATGAAAA
* *
48998 CATCAGCACTTTCGATTCAAGT-GAAAGGAAGGAAG
1 CATCGGCACTTTCGATTCAAGTCGAACGGAAGGAAG
* *
49033 CATCGGCACTTTCGATTCAAGACGAACAGAAGGAAG
1 CATCGGCACTTTCGATTCAAGTCGAACGGAAGGAAG
* *
49069 CATCGGCACTTTCAATTCGAGTCGAACGGAAGGAAG
1 CATCGGCACTTTCGATTCAAGTCGAACGGAAGGAAG
* * * * *
49105 CATAGACATTTTCGATTCAATTTGAACGGAA
1 CATCGGCACTTTCGATTCAAGTCGAACGGAA
49136 CACTTTCGAT
Statistics
Matches: 87, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
35 20 0.23
36 67 0.77
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (36 bp):
CATCGGCACTTTCGATTCAAGTCGAACGGAAGGAAG
Found at i:57027 original size:31 final size:32
Alignment explanation
Indices: 56964--57027 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 32
56954 TGCGCATTAA
*
56964 TATTTAATTCTTCAACATGATTATGCGCACCAT
1 TATTTAATTCTTCAACAT-ATTATGCGAACCAT
** *
56997 TATTTAATTCTTGTACAT-TTATGGGAACCAT
1 TATTTAATTCTTCAACATATTATGCGAACCAT
57028 GACATGCGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 11 0.41
33 16 0.59
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (32 bp):
TATTTAATTCTTCAACATATTATGCGAACCAT
Found at i:57040 original size:39 final size:39
Alignment explanation
Indices: 56997--57117 Score: 215
Period size: 39 Copynumber: 3.1 Consensus size: 39
56987 TGCGCACCAT
* *
56997 TATTTAATTCTTGTACATTTATGGGAACCATGACATGCG
1 TATTTAATTCTTGTACATTTGTGGGAACCATGCCATGCG
*
57036 TATTTAATTCTTGTACATTTGTGGGAACCATGCCATGCT
1 TATTTAATTCTTGTACATTTGTGGGAACCATGCCATGCG
57075 TATTTAATTCTTGTACATTTGTGGGAACCATGCCATGCG
1 TATTTAATTCTTGTACATTTGTGGGAACCATGCCATGCG
57114 TATT
1 TATT
57118 ACCTCTAATT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (39 bp):
TATTTAATTCTTGTACATTTGTGGGAACCATGCCATGCG
Found at i:62370 original size:23 final size:23
Alignment explanation
Indices: 62310--62372 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 23
62300 TTAAATACAA
* *
62310 TAAATACTATTATTTATCATAAAAT
1 TAAATATTATTATTT-T-TTAAAAT
*
62335 TGAATATTATTATTTTTTAAATAT
1 TAAATATTATTATTTTTTAAA-AT
62359 TAAATATT-TTATTT
1 TAAATATTATTATTT
62373 ATTATTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 10 0.30
24 10 0.30
25 13 0.39
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (23 bp):
TAAATATTATTATTTTTTAAAAT
Found at i:62380 original size:19 final size:17
Alignment explanation
Indices: 62356--62394 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
62346 ATTTTTTAAA
*
62356 TATTAAATATTTTATTTAT
1 TATTAAA-ATATTATTT-T
62375 TATTAAAATATTATTTT
1 TATTAAAATATTATTTT
62392 TAT
1 TAT
62395 AATTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 8 0.42
19 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTAAAATATTATTTT
Found at i:62393 original size:20 final size:19
Alignment explanation
Indices: 62342--62394 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 19
62332 AATTGAATAT
*
62342 TATTATTTTTTAAATATTAAA
1 TATTA-TTTTT-ATTATTAAA
62363 TATT-TTATTTATTATTAAAA
1 TATTATT-TTTATTATT-AAA
62383 TATTATTTTTAT
1 TATTATTTTTAT
62395 AATTTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 7 0.25
20 15 0.54
21 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATTTTTATTATTAAA
Found at i:62459 original size:31 final size:29
Alignment explanation
Indices: 62370--62460 Score: 71
Period size: 31 Copynumber: 3.0 Consensus size: 29
62360 AAATATTTTA
* **
62370 TTTATT-ATTAAAATATT-ATTTTTATAAT
1 TTTATTAATAAAAATATTCATAATTAT-AT
*
62398 TTTATTAATAAAAATATTCATATTGGTATAT
1 TTTATTAATAAAAATATTCATAAT--TATAT
62429 TTTATTGAAATAAAAATATT-ATAAATTATAT
1 TTTATT--AATAAAAATATTCAT-AATTATAT
62460 T
1 T
62461 AATTATTTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
28 6 0.11
29 10 0.19
30 4 0.08
31 14 0.26
32 5 0.09
33 14 0.26
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (29 bp):
TTTATTAATAAAAATATTCATAATTATAT
Found at i:62560 original size:21 final size:22
Alignment explanation
Indices: 62529--62600 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
62519 TAAATATCAT
* *
62529 TATTAAAATATTAT-TATATTAA
1 TATT-AAATATTATAAATAATAA
*
62551 TATTAAATA-TATAAATAATAT
1 TATTAAATATTATAAATAATAA
*
62572 TATTAAATATTAATAATTTAATAA
1 TATTAAATATT-ATAA-ATAATAA
62596 TATTA
1 TATTA
62601 TTTCTATGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
20 3 0.07
21 19 0.46
22 5 0.12
23 4 0.10
24 10 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTAAATATTATAAATAATAA
Found at i:62586 original size:27 final size:28
Alignment explanation
Indices: 62534--62602 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
62524 ATCATTATTA
* *
62534 AAATATTATTATATTAATATTAAAT-ATAT
1 AAATAATATTAT-TAAATATTAAATAAT-T
62563 AAATAATATTATTAAATATT-AATAATT
1 AAATAATATTATTAAATATTAAATAATT
*
62590 TAATAATATTATT
1 AAATAATATTATT
62603 TCTATGAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 16 0.44
28 9 0.25
29 11 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
AAATAATATTATTAAATATTAAATAATT
Found at i:62748 original size:26 final size:24
Alignment explanation
Indices: 62719--62781 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
62709 TATGAAAAGT
62719 ATAATATTATATTATTAGAA-ATATTA
1 ATAATA-TATATT-TTA-AATATATTA
*
62745 ATAA-ATATATTTTAAATATTTTA
1 ATAATATATATTTTAAATATATTA
62768 ATAAT-TAATATTTT
1 ATAATAT-ATATTTT
62782 GATTAAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 13 0.39
24 13 0.39
25 1 0.03
26 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATAATATATATTTTAAATATATTA
Found at i:69649 original size:15 final size:15
Alignment explanation
Indices: 69629--69662 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
69619 AGATAAAACT
* *
69629 CTAACTTGTTAATTG
1 CTAACTTGCTAATTA
69644 CTAACTTGCTAATTA
1 CTAACTTGCTAATTA
69659 CTAA
1 CTAA
69663 ACTTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (15 bp):
CTAACTTGCTAATTA
Found at i:69849 original size:105 final size:105
Alignment explanation
Indices: 69644--69851 Score: 258
Period size: 105 Copynumber: 2.0 Consensus size: 105
69634 TTGTTAATTG
*
69644 CTAACTTGCTAATTACTAAACTTTTAAAATATTTCGAATTAATTTACGAACATGTGGACACCCGT
1 CTAACTTGCTAATTACTAAACTTTTAAAATATTTCAAATTAATTTACGAACATGTGGACACCCGT
* * * *
69709 TCCAGGGCATGACCCGCATTATTGTGGTCTCGATAAAACT
66 TCCAGAGCATGACCCACATTATTATGATCTCGATAAAACT
* * * * * *
69749 CTAACTTGCTAATTACTAACCTTTTAGAATATTTCAAATTAATTTACGACCTTGTAGTA-ACTCG
1 CTAACTTGCTAATTACTAAACTTTTAAAATATTTCAAATTAATTTACGAACATGT-GGACACCCG
* * *
69813 TTCTAGAGTATGACCCATATTATTATGAT-TCAGATAAAA
65 TTCCAGAGCATGACCCACATTATTATGATCTC-GATAAAA
69852 TTATTAAATA
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
104 2 0.02
105 83 0.95
106 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (105 bp):
CTAACTTGCTAATTACTAAACTTTTAAAATATTTCAAATTAATTTACGAACATGTGGACACCCGT
TCCAGAGCATGACCCACATTATTATGATCTCGATAAAACT
Found at i:70259 original size:249 final size:251
Alignment explanation
Indices: 69811--70301 Score: 749
Period size: 249 Copynumber: 2.0 Consensus size: 251
69801 TGTAGTAACT
* *
69811 CGTTCTAGAGTATGACCCATATTATTATGATTCAGATAAAATTATTAAATATTAACAATTAACTT
1 CGTTCTAGAGTATGACCCACATTATTATGATTCAGATAAAATTATTAAATATTAACAACTAACTT
* * *
69876 TTATTTTTATTTGATTGGTCATTTTTTATTTAAGTTTCTACCCCTTTAATTTTATGTAATTTTAA
66 TTAATTTTATTTGATTGGTCATTTTTTATTTAAGGTTCTACCCCTTTAATTTTATGCAATTTTAA
* * *
69941 TTTCAGCCATCAAATTTCCAACATTTATATTTCAGCCCTTAAGTTCTAGCTTTTTTAGTTTTCTT
131 TTTCAGCCATCAAATTTCCAACACTTATATTTCAGCCCTTAAATTCTAGCTTTTTTAGTTTTATT
* *
70006 TATTTTCT-TAATTAGCTTTA-TTTCT-ACTTTCTTTATTTTGGCCCTTGTGATGACC
196 TATTTT-TAAAATTAGATTTACTTT-TGACTTTCTTTATTTTGGCCCTTGTGATGACC
*
70061 CGTTCTAG-GATATGACCCACATTATTATGATTCATATAAAATTATTAAATATTAACAACTAACT
1 CGTTCTAGAG-TATGACCCACATTATTATGATTCAGATAAAATTATTAAATATTAACAACTAACT
* *
70125 TTTAATTTTATTTGATT-GTCATTTTTTATTTATGGTTCTACCCCTTTAATTTTATGCACTTTTA
65 TTTAATTTTATTTGATTGGTCATTTTTTATTTAAGGTTCTACCCCTTTAATTTTATGCAATTTTA
* * * * *
70189 ATTTCATCCATTAAATTTCCAGCACTTATATTTCAGCCCTTAAATTGTAGCTTTTTTATTTTTAT
130 ATTTCAGCCATCAAATTTCCAACACTTATATTTCAGCCCTTAAATTCTAGCTTTTTTAGTTTTAT
*
70254 TTATTTTTAAAATTAGATTTACTTTTGACTTTCTTTATTTTGGTCCTT
195 TTATTTTTAAAATTAGATTTACTTTTGACTTTCTTTATTTTGGCCCTT
70302 TATTTGATGA
Statistics
Matches: 218, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
248 1 0.00
249 119 0.55
250 98 0.45
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (251 bp):
CGTTCTAGAGTATGACCCACATTATTATGATTCAGATAAAATTATTAAATATTAACAACTAACTT
TTAATTTTATTTGATTGGTCATTTTTTATTTAAGGTTCTACCCCTTTAATTTTATGCAATTTTAA
TTTCAGCCATCAAATTTCCAACACTTATATTTCAGCCCTTAAATTCTAGCTTTTTTAGTTTTATT
TATTTTTAAAATTAGATTTACTTTTGACTTTCTTTATTTTGGCCCTTGTGATGACC
Done.