Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 56
Found at i:201637 original size:23 final size:24
Alignment explanation
Indices: 201597--201643 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
201587 GAGTAATATT
* *
201597 ATTTATATATTTAATAATATAATA
1 ATTTATATATATAATAATAAAATA
*
201621 ATTTA-ATATATATTAATAAAATA
1 ATTTATATATATAATAATAAAATA
201644 CTAATAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTTATATATATAATAATAAAATA
Found at i:201652 original size:29 final size:24
Alignment explanation
Indices: 201467--201648 Score: 77
Period size: 24 Copynumber: 7.3 Consensus size: 24
201457 AATATAATTT
* *
201467 TAATAA-TTATATTTTTAATTATTA
1 TAATAATTTATATATTTAA-TAATA
* *
201491 TTAATATACTCATATATTATAATAATA
1 -TAATA-ATTTATATATT-TAATAATA
*
201518 T-ATAATATTATAT-TTTAAATAATT
1 TAATAAT-TTATATATTT-AATAATA
* *
201542 TATTATATTTATATTATTTTATAATA
1 TAATA-ATTTATA-TATTTAATAATA
* * * * * *
201568 TTATTAAATTAT-TAATAAAGAGTA
1 -TAATAATTTATATATTTAATAATA
*
201592 -ATATTATTTATATATTTAATAATA
1 TA-ATAATTTATATATTTAATAATA
*
201616 TAATAATTTAATATATATTAATAAAA
1 TAATAATTT-ATATAT-TTAATAATA
*
201642 TACTAAT
1 TAATAAT
201649 AATTAAAATT
Statistics
Matches: 117, Mismatches: 25, Indels: 29
0.68 0.15 0.17
Matches are distributed among these distances:
22 1 0.01
23 7 0.06
24 31 0.26
25 27 0.23
26 29 0.25
27 19 0.16
28 3 0.03
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (24 bp):
TAATAATTTATATATTTAATAATA
Found at i:201655 original size:15 final size:14
Alignment explanation
Indices: 201607--201657 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
201597 ATTTATATAT
201607 TTAATAATATAATAA
1 TTAA-AATATAATAA
* *
201622 TTTAATATATATTAA
1 -TTAAAATATAATAA
201637 -TAAAATACTAATAA
1 TTAAAATA-TAATAA
201651 TTAAAAT
1 TTAAAAT
201658 TAAGGGCGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 6 0.21
14 5 0.17
15 14 0.48
16 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAAATATAATAA
Found at i:201981 original size:29 final size:30
Alignment explanation
Indices: 201905--201981 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
201895 TCCGAAAATA
*
201905 TAATTCATTTTACGTAAAACAGTTTTCATG
1 TAATTCATTTTACGTAAAACAGTTTTCAAG
* *
201935 TCATTCATTTTACATAAAACAGTTTT-AAG
1 TAATTCATTTTACGTAAAACAGTTTTCAAG
*
201964 TAATCCATTTTACGTAAA
1 TAATTCATTTTACGTAAA
201982 TATTTCCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 17 0.41
30 24 0.59
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (30 bp):
TAATTCATTTTACGTAAAACAGTTTTCAAG
Found at i:209494 original size:20 final size:21
Alignment explanation
Indices: 209469--209561 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
209459 TTTTCCCAAT
*
209469 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
209489 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
209510 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
209530 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
209551 TCGCAATGCGA
1 TCGCAATGCGA
209562 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:209515 original size:41 final size:41
Alignment explanation
Indices: 209469--209561 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
209459 TTTTCCCAAT
209469 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
209510 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
209551 TCGCAATGCGA
1 TCGCAATGCGA
209562 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:209574 original size:41 final size:41
Alignment explanation
Indices: 209488--209622 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
209478 GAATAAGTAA
* *
209488 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
209529 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
209570 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
209611 TTCGCAACGCGA
1 ATCGCAACGCGA
209623 TAATACATAA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:209596 original size:21 final size:20
Alignment explanation
Indices: 209547--209644 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 20
209537 GCGAATTGGG
* *
209547 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
209567 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
* * * *
209588 AAAATCGCAACGAGATACTT
1 AAAATCGCAATGCGATAATA
*** *
209608 ACTTTCGCAACGCGATAATA
1 AAAATCGCAATGCGATAATA
*
209628 CATAATCGCAATGCGAT
1 -AAAATCGCAATGCGAT
209645 TTTCAAAGCG
Statistics
Matches: 56, Mismatches: 20, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
20 30 0.54
21 26 0.46
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.22
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:209623 original size:41 final size:41
Alignment explanation
Indices: 209547--209638 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
209537 GCGAATTGGG
* * *
209547 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* * *
209588 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
*
209629 ATAATCGCAA
1 AAAATCGCAA
209639 TGCGATTTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:209862 original size:22 final size:22
Alignment explanation
Indices: 209814--209865 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
209804 CTCACTCTCA
*
209814 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCATC
* *
209836 CCCATCTCCGGCGAAATCTATC
1 CCCATCTCCGACGAAATCCATC
*
209858 TCCATCTC
1 CCCATCTC
209866 TCAGAGTCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.44, G:0.12, T:0.23
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCATC
Found at i:210140 original size:20 final size:20
Alignment explanation
Indices: 210115--210152 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
210105 CGATTCTCTC
210115 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
210135 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
210153 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:211999 original size:20 final size:20
Alignment explanation
Indices: 211974--212019 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
211964 TAGTTTACTT
211974 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
211994 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
212014 TCGCAA
1 TCGCAA
212020 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:212048 original size:14 final size:14
Alignment explanation
Indices: 212029--212086 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
212019 ATGCGAAATA
212029 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
212043 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AC
212061 AAAATCGCAACGAC
1 AAAATCGCAACGAC
212075 AAAATCGCAACG
1 AAAATCGCAACG
212087 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:212070 original size:32 final size:33
Alignment explanation
Indices: 212013--212103 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
212003 GGAAATGGCT
212013 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
212046 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
* *
212078 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATAAAAATCGCAA
212104 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATAAAAATCGCAACGACAAA
Found at i:212139 original size:14 final size:14
Alignment explanation
Indices: 212120--212177 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
212110 TTGTGTTTCG
212120 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
212134 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
212150 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
212166 CGTTGCGATTTT
1 CGTTGCGATTTT
212178 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:212154 original size:32 final size:33
Alignment explanation
Indices: 212115--212193 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
212105 GCGATTTGTG
212115 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
212147 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
212180 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
212194 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:212192 original size:19 final size:19
Alignment explanation
Indices: 212134--212251 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
212124 GCGATTTTGT
212134 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
212152 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
212166 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
212185 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
212205 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
212224 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
212244 TGTTGCGA
1 CGTTGCGA
212252 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:214256 original size:14 final size:14
Alignment explanation
Indices: 214237--214290 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
214227 CGAAATGGTT
214237 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
214251 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
*
214270 ATCGCAACGTGAAA
1 ATCGCAACGAGAAA
214284 ATCGCAA
1 ATCGCAA
214291 TGCAATTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:214263 original size:33 final size:33
Alignment explanation
Indices: 214218--214293 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
214208 AAAACAGGCT
* ***
214218 ATCGCAACGCGAAATGGTTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
214251 ATCGCAATGCGAAATGAAAATCGCAACGTGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
214284 ATCGCAATGC
1 ATCGCAATGC
214294 AATTTCATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:214283 original size:19 final size:19
Alignment explanation
Indices: 214247--214283 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
214237 ATCGCAACGA
*
214247 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGCGAAAT
*
214266 GAAAATCGCAACGTGAAA
1 GAAAATCGCAACGCGAAA
214284 ATCGCAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAACGCGAAAT
Found at i:214370 original size:20 final size:20
Alignment explanation
Indices: 214313--214370 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
214303 TCGCATTGCG
* *
214313 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
214333 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
214353 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
214371 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:214524 original size:14 final size:14
Alignment explanation
Indices: 214505--214558 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
214495 CGAAATGGTT
214505 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
214519 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
214538 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
214552 ATCGCAA
1 ATCGCAA
214559 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:214576 original size:33 final size:33
Alignment explanation
Indices: 214486--214563 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
214476 AAAACAGGCT
* ***
214486 ATCGCAACGCGAAATGGTTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
214519 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
214552 ATCGCAATGCGA
1 ATCGCAATGCGA
214564 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:214639 original size:20 final size:20
Alignment explanation
Indices: 214582--214639 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
214572 TCGCATTGCG
* * *
214582 ATTTTCTCGTTGCGATAACT
1 ATTTTCGCGTTGCGATAGCC
*
214602 ATTTTTGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
214622 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
214640 TCAAATGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:215722 original size:24 final size:24
Alignment explanation
Indices: 215695--215748 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
215685 GTATTCGAAA
* *
215695 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
215719 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
215743 TTTGAT
1 TTTGAT
215749 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:215937 original size:13 final size:13
Alignment explanation
Indices: 215919--215943 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
215909 ATATAATCCT
215919 GAAGAAGAAAAAA
1 GAAGAAGAAAAAA
215932 GAAGAAGAAAAA
1 GAAGAAGAAAAA
215944 GTCACCGAAG
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAAAAA
Found at i:218236 original size:20 final size:19
Alignment explanation
Indices: 218211--218258 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
218201 CTTAATGTAC
**
218211 ATCGCAACGCGGAAATTACT
1 ATCGCAACGC-GAAATTAAA
*
218231 ATCGCAATGCGAAATTAAA
1 ATCGCAACGCGAAATTAAA
218250 ATCGCAACG
1 ATCGCAACG
218259 AGAGAATCGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (19 bp):
ATCGCAACGCGAAATTAAA
Found at i:218253 original size:19 final size:19
Alignment explanation
Indices: 218231--218355 Score: 73
Period size: 19 Copynumber: 7.4 Consensus size: 19
218221 GGAAATTACT
*
218231 ATCGCAATGCGAAATTAAA
1 ATCGCAATGCGAAATGAAA
*
218250 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
218264 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
218283 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
218297 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
218316 ATCGCAA--CG-AGTG--A
1 ATCGCAATGCGAAATGAAA
* *
218330 TTCGCAATCCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
218349 ATCGCAA
1 ATCGCAA
218356 CACAATTTAA
Statistics
Matches: 78, Mismatches: 13, Indels: 30
0.64 0.11 0.25
Matches are distributed among these distances:
14 24 0.31
15 2 0.03
16 9 0.12
17 9 0.12
18 2 0.03
19 32 0.41
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:218273 original size:33 final size:33
Alignment explanation
Indices: 218231--218356 Score: 173
Period size: 33 Copynumber: 3.8 Consensus size: 33
218221 GGAAATTACT
*
218231 ATCGCAATGCGAAATTAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
218264 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
218296 TTTCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
218330 TTCGCAATCCGAAATGAAAATCGCAAC
1 ATCGCAATGCGAAATGAAAATCGCAAC
218357 ACAATTTAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:218343 original size:66 final size:66
Alignment explanation
Indices: 218232--218356 Score: 214
Period size: 66 Copynumber: 1.9 Consensus size: 66
218222 GAAATTACTA
* *
218232 TCGCAATGCGAAATTAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATCCGAAATGAAAATCGCAACGCTAAT
218297 T
66 T
* *
218298 TCGCAATGCGAAATGAAAATCGCAACGAGTGATTCGCAATCCGAAATGAAAATCGCAAC
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATCCGAAATGAAAATCGCAAC
218357 ACAATTTAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.18
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATCCGAAATGAAAATCGCAACGCTAAT
T
Found at i:218410 original size:19 final size:19
Alignment explanation
Indices: 218365--218418 Score: 90
Period size: 20 Copynumber: 2.8 Consensus size: 19
218355 ACACAATTTA
218365 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
218384 ATTTTCGCGTTGCGATTTTC
1 A-TTTCGCGTTGCGATTTTC
*
218404 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
218419 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:218544 original size:14 final size:14
Alignment explanation
Indices: 218525--218561 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
218515 CATCAATTAA
218525 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
218539 ACAAATCACCTTTT
1 ACAAATCAACTTTT
218553 ACAAATCAA
1 ACAAATCAA
218562 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:219984 original size:21 final size:21
Alignment explanation
Indices: 219918--219984 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
219908 GTGAATCGGG
*
219918 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
219938 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
219960 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
219981 CTCT
1 CTCT
219985 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:220003 original size:42 final size:41
Alignment explanation
Indices: 219918--220040 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
219908 GTGAATCGGG
* * * * *
219918 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
219960 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
220002 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
220041 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:221967 original size:20 final size:20
Alignment explanation
Indices: 221930--222062 Score: 113
Period size: 20 Copynumber: 7.0 Consensus size: 20
221920 TTGAAAAGAA
* *
221930 AATCGCAACG-AGATAATGAG
1 AATCGCAACGCGGA-AATGAC
221950 AATCGCAACGCGGAAATGAC
1 AATCGCAACGCGGAAATGAC
*
221970 TATCGCAACGCGGAAATGAC
1 AATCGCAACGCGGAAATGAC
*
221990 TATCGCAACGC-GAAATGAC
1 AATCGCAACGCGGAAATGAC
* *
222009 TATCGCGAC-C----A-GAC
1 AATCGCAACGCGGAAATGAC
* *
222023 AATCGCAACG-AGATAATGAG
1 AATCGCAACGCGGA-AATGAC
222043 AATCGCAACGCGGAAATGAC
1 AATCGCAACGCGGAAATGAC
222063 TTCGCGTTGC
Statistics
Matches: 95, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
18 1 0.01
19 17 0.18
20 62 0.65
21 4 0.04
ACGTcount: A:0.39, C:0.23, G:0.24, T:0.14
Consensus pattern (20 bp):
AATCGCAACGCGGAAATGAC
Found at i:222085 original size:19 final size:19
Alignment explanation
Indices: 222063--222117 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
222053 CGGAAATGAC
222063 TTCGCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTTAT
**
222082 TTCGCGTTGCGATAGTTAT
1 TTCGCGTTGCGATTTTTAT
222101 TTCCGCGTTGCGATTTT
1 TT-CGCGTTGCGATTTT
222118 CATTCTCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTTAT
Found at i:222659 original size:20 final size:20
Alignment explanation
Indices: 222634--222686 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
222624 GCGCTATGTA
222634 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
222654 AATCGCGTTGCAAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
222674 TATCTCGTTGCGA
1 AATCGCGTTGCGA
222687 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:222720 original size:20 final size:20
Alignment explanation
Indices: 222695--222748 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
222685 GATTTTGTAT
222695 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
222715 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
222735 TATCGCATTGCGAT
1 TATCGCATTGCGAT
222749 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:222733 original size:61 final size:61
Alignment explanation
Indices: 222635--222751 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
222625 CGCTATGTAA
* * * * *
222635 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCAAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCAAAAGTCAGTATCGCATTGCGATTTTGTATT
* * * *
222696 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCAAAAGTCAGTATCGCATTGCGATTTT
222752 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCAAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:222767 original size:61 final size:61
Alignment explanation
Indices: 222635--222769 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
222625 CGCTATGTAA
* * * * * ** *
222635 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCAAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCAAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * * *
222696 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCAAAAGTCAGTATCGCATTGCGATTTT-CCAAT
222758 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
222770 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCAAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:222859 original size:21 final size:21
Alignment explanation
Indices: 222819--222859 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
222809 ATTGTATACC
**
222819 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
222840 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
222860 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:227437 original size:2 final size:2
Alignment explanation
Indices: 227430--227464 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
227420 AATATTAATA
227430 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
227465 CATCATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:227447 original size:23 final size:26
Alignment explanation
Indices: 227421--227481 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 26
227411 TCATAATTAA
227421 ATATTAATAATATATATAT-AT-A-T
1 ATATTAATAATATATATATCATCATT
227444 ATATTATATATATATATATATCATCATT
1 ATATTA-ATA-ATATATATATCATCATT
227472 ATATTAATAA
1 ATATTAATAA
227482 AAAAATATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
23 6 0.18
24 3 0.09
25 10 0.30
26 3 0.09
27 4 0.12
28 7 0.21
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
ATATTAATAATATATATATCATCATT
Found at i:227451 original size:15 final size:15
Alignment explanation
Indices: 227433--227462 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
227423 ATTAATAATA
227433 TATATATATATATAT
1 TATATATATATATAT
227448 TATATATATATATAT
1 TATATATATATATAT
227463 ATCATCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:227451 original size:17 final size:17
Alignment explanation
Indices: 227431--227464 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
227421 ATATTAATAA
227431 TATATATATATATATAT
1 TATATATATATATATAT
227448 TATATATATATATATAT
1 TATATATATATATATAT
227465 CATCATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:239563 original size:171 final size:168
Alignment explanation
Indices: 239278--239612 Score: 625
Period size: 171 Copynumber: 2.0 Consensus size: 168
239268 ATTGCCACCC
* *
239278 CTACATATTCATGGGATACTTATCTATACAAAAAGTTTACAAATGCTATCACTCGCCTTCTAAAA
1 CTACATATTCATGGGATACTTATCTACACAAAAAGTTTACAAATGCTATCACCCGCCTTCTAAAA
239343 AAATTATTAGTGCTAATGTTACTTTTGTTGAACATTATTCTTTTTTTCAGTCTATTTATCTTCAG
66 AAATTATTAGTGCTAATGTTACTTTTGTTGAACATTATTCTTTTTTTCAGTCTATTTATCTTCAG
239408 GGGAGACTTTGATTGAAGAAGATAACACTAGGAATACTTAT
131 GGGAGACTTTGATT---GAAGATAACACTAGGAATACTTAT
239449 CTACATATTCATGGGATACTTATCTACACAAAAAGTTTACAAATGCTATCACCCGCCTTCTAAAA
1 CTACATATTCATGGGATACTTATCTACACAAAAAGTTTACAAATGCTATCACCCGCCTTCTAAAA
239514 AAATTATTAGTGCTAATGTTACTTTTGTTGAACATTATTCTTTTTTTCAGTCTATTTATCTTCAG
66 AAATTATTAGTGCTAATGTTACTTTTGTTGAACATTATTCTTTTTTTCAGTCTATTTATCTTCAG
239579 GGGAGACTTTGATTGAAGATAACACTAGGAATAC
131 GGGAGACTTTGATTGAAGATAACACTAGGAATAC
239613 ATCTCTCCTT
Statistics
Matches: 162, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
168 20 0.12
171 142 0.88
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (168 bp):
CTACATATTCATGGGATACTTATCTACACAAAAAGTTTACAAATGCTATCACCCGCCTTCTAAAA
AAATTATTAGTGCTAATGTTACTTTTGTTGAACATTATTCTTTTTTTCAGTCTATTTATCTTCAG
GGGAGACTTTGATTGAAGATAACACTAGGAATACTTAT
Found at i:243668 original size:15 final size:15
Alignment explanation
Indices: 243648--243677 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
243638 CAAATTATAT
243648 CTCTAAATTAGGAAA
1 CTCTAAATTAGGAAA
*
243663 CTCTAAGTTAGGAAA
1 CTCTAAATTAGGAAA
243678 GATACTAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (15 bp):
CTCTAAATTAGGAAA
Found at i:243866 original size:21 final size:21
Alignment explanation
Indices: 243842--243883 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
243832 ATGTTCATTG
*
243842 AGATACTTTCTTGTATTTCAA
1 AGATACTTTCTCGTATTTCAA
243863 AGATACTTTCTCGTATTTCAA
1 AGATACTTTCTCGTATTTCAA
243884 TGGATATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (21 bp):
AGATACTTTCTCGTATTTCAA
Found at i:252625 original size:16 final size:17
Alignment explanation
Indices: 252585--252632 Score: 80
Period size: 18 Copynumber: 2.8 Consensus size: 17
252575 TGTTTATGAG
252585 AGAATTGGAATCTGTGA
1 AGAATTGGAATCTGTGA
252602 AGGAATTGGAATCTGT-A
1 A-GAATTGGAATCTGTGA
252619 AGAATTGGAATCTG
1 AGAATTGGAATCTG
252633 AATCTGAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 13 0.43
17 3 0.10
18 14 0.47
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (17 bp):
AGAATTGGAATCTGTGA
Found at i:253060 original size:43 final size:38
Alignment explanation
Indices: 253000--253222 Score: 149
Period size: 33 Copynumber: 6.2 Consensus size: 38
252990 TGAATTAGAA
253000 ACCCGACCCGAATATCACACTTAAAAAACCAAACTCGACCCG
1 ACCCGACCCGAATATCACACTTAAAAAACCAAA----ACCCG
253042 ACCCGAACCCGAATATCACACTT---AAA--AAAACCCG
1 ACCCG-ACCCGAATATCACACTTAAAAAACCAAAACCCG
253076 ACCCGACCCGAATATCACACTT----AA--AAAACCCG
1 ACCCGACCCGAATATCACACTTAAAAAACCAAAACCCG
* *
253108 A-CCTACCCGAATATCACACTT---AAA--AAAACCTG
1 ACCCGACCCGAATATCACACTTAAAAAACCAAAACCCG
* * ** *
253140 ACCCGACCCGACTATCAAACTTAAAAAAACC-TGATCCG
1 ACCCGACCCGAATATCACACTT-AAAAAACCAAAACCCG
* * ***
253178 ACCCGATCCCGAACATCCCACTTAAAAAACCCCGACCCG
1 ACCCGA-CCCGAATATCACACTTAAAAAACCAAAACCCG
253217 ACCCGA
1 ACCCGA
253223 ACTCGAACCC
Statistics
Matches: 155, Mismatches: 15, Indels: 25
0.79 0.08 0.13
Matches are distributed among these distances:
31 19 0.12
32 21 0.14
33 34 0.22
34 10 0.06
37 3 0.02
38 20 0.13
39 23 0.15
40 3 0.02
42 5 0.03
43 17 0.11
ACGTcount: A:0.40, C:0.38, G:0.09, T:0.13
Consensus pattern (38 bp):
ACCCGACCCGAATATCACACTTAAAAAACCAAAACCCG
Found at i:253116 original size:31 final size:33
Alignment explanation
Indices: 253037--253223 Score: 234
Period size: 33 Copynumber: 5.5 Consensus size: 33
253027 ACCAAACTCG
253037 ACCCGACCCGAACCCGAATATCACACTTAAAAAA
1 ACCCGACCCG-ACCCGAATATCACACTTAAAAAA
253071 ACCCGACCCGACCCGAATATCACACTT-AAAAA
1 ACCCGACCCGACCCGAATATCACACTTAAAAAA
*
253103 ACCCGA-CCTACCCGAATATCACACTTAAAAAA
1 ACCCGACCCGACCCGAATATCACACTTAAAAAA
* * *
253135 ACCTGACCCGACCCGACTATCAAACTTAAAAAA
1 ACCCGACCCGACCCGAATATCACACTTAAAAAA
* *
253168 ACCTGATCCGACCCGATCCCGAACATCCCACTTAAAAAA
1 A-C----CCGACCCGA-CCCGAATATCACACTTAAAAAA
*
253207 CCCCGACCCGACCCGAA
1 ACCCGACCCGACCCGAA
253224 CTCGAACCCG
Statistics
Matches: 134, Mismatches: 11, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
31 19 0.14
32 21 0.16
33 47 0.35
34 20 0.15
38 9 0.07
39 18 0.13
ACGTcount: A:0.40, C:0.38, G:0.10, T:0.13
Consensus pattern (33 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAA
Found at i:253125 original size:64 final size:68
Alignment explanation
Indices: 253039--253223 Score: 234
Period size: 64 Copynumber: 2.7 Consensus size: 68
253029 CAAACTCGAC
*
253039 CCGACCCGAACCCGAATATCACACTTAAAAAAACCCGACCCGACCCGAATATCACACTT-AAAAA
1 CCGACCCG-ACCCGAATATCACACTTAAAAAAACCCGACCCGACCCGAATATCAAACTTAAAAAA
253103 A-C-
65 ACCT
* * *
253105 CCGA-CCTACCCGAATATCACACTTAAAAAAACCTGACCCGACCCGACTATCAAACTTAAAAAAA
1 CCGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACCCGAATATCAAACTTAAAAAAA
253169 CCTGAT
66 CC---T
* * *
253175 CCGACCCGATCCCGAACATCCCACTTAAAAAACCCCGACCCGACCCGAA
1 CCGACCCGA-CCCGAATATCACACTTAAAAAAACCCGACCCGACCCGAA
253224 CTCGAACCCG
Statistics
Matches: 101, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
64 47 0.47
65 8 0.08
66 5 0.05
70 4 0.04
71 3 0.03
72 34 0.34
ACGTcount: A:0.39, C:0.38, G:0.10, T:0.13
Consensus pattern (68 bp):
CCGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACCCGAATATCAAACTTAAAAAAA
CCT
Found at i:256286 original size:10 final size:10
Alignment explanation
Indices: 256250--256294 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
256240 TTTCCAACTG
*
256250 AATAAGTTAA
1 AATAAATTAA
*
256260 AATAAA-TAT
1 AATAAATTAA
*
256269 ATTAAATTAA
1 AATAAATTAA
256279 AATAAATTAA
1 AATAAATTAA
256289 AATAAA
1 AATAAA
256295 GTTAGTCTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 7 0.24
10 22 0.76
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (10 bp):
AATAAATTAA
Found at i:256512 original size:31 final size:30
Alignment explanation
Indices: 256475--256538 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
256465 TGACCAAATC
256475 TTAATTAAATAAAAACAAAAGTGATCATACA
1 TTAATTAAATAAAAACAAAAGTGA-CATACA
* *
256506 TTAATTAAATAAAAACAAACGTGACATATA
1 TTAATTAAATAAAAACAAAAGTGACATACA
256536 TTA
1 TTA
256539 TGTTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.28
Consensus pattern (30 bp):
TTAATTAAATAAAAACAAAAGTGACATACA
Found at i:257703 original size:20 final size:20
Alignment explanation
Indices: 257680--257729 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
257670 TATCTGACTT
*
257680 GTTTCAAAACCCCCTATTTG
1 GTTTCAAAACCCCCTATTTA
*
257700 GTTT-ATAAA-CCCTTATTTA
1 GTTTCA-AAACCCCCTATTTA
*
257719 GTTTCTAAACC
1 GTTTCAAAACC
257730 ACTCTGCTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (20 bp):
GTTTCAAAACCCCCTATTTA
Found at i:260593 original size:16 final size:16
Alignment explanation
Indices: 260557--260587 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
260547 ACCTGATTCT
*
260557 TCGGTTAGTATATTTG
1 TCGGTTAGTACATTTG
260573 TCGGTTAGTACATTT
1 TCGGTTAGTACATTT
260588 TCCGGTCACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.10, G:0.23, T:0.48
Consensus pattern (16 bp):
TCGGTTAGTACATTTG
Found at i:278286 original size:16 final size:16
Alignment explanation
Indices: 278254--278287 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
278244 GAAGACTTTA
278254 TTATCTCTTCATCTTC
1 TTATCTCTTCATCTTC
278270 TTATCCTCTTCAT-TTC
1 TTAT-CTCTTCATCTTC
278286 TT
1 TT
278288 CTCTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATCTCTTCATCTTC
Found at i:281092 original size:64 final size:68
Alignment explanation
Indices: 280952--281173 Score: 217
Period size: 64 Copynumber: 3.3 Consensus size: 68
280942 GATATTCTTT
* * * * * *
280952 AATTTGAATATTAGTATGATAA-TTAT-TCTTTTAAATATATCAAATTAAAAAGTTATTTATTAT
1 AATTTGAATATTA-AAAGATAATTTATACCTTTTGAATATTTCAAATT-AAAA--TATATATTAT
281015 CTATTTA
62 CTATTTA
*
281022 ACTTTGAATATTAAAAGATAATTATATA-CTTTTGAATATTTCAAATT-AAA-ATA-A-TATCTA
1 AATTTGAATATTAAAAGATAATT-TATACCTTTTGAATATTTCAAATTAAAATATATATTATCTA
281082 TTTA
65 TTTA
* * * * *
281086 AGTTTGAATAGTAAAA-AGAGTTTATACCTTTTGAATATTTCAAATTAAAATATATTATTATCTG
1 AATTTGAATATTAAAAGATAATTTATACCTTTTGAATATTTCAAATTAAAATATA-TATTATCTA
281150 TTTA
65 TTTA
*
281154 AATTTGGATATTAAAAGATA
1 AATTTGAATATTAAAAGATA
281174 TCTTATTAGA
Statistics
Matches: 127, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
62 4 0.03
63 23 0.18
64 27 0.21
65 4 0.03
66 2 0.02
67 1 0.01
68 22 0.17
69 11 0.09
70 13 0.10
71 20 0.16
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.45
Consensus pattern (68 bp):
AATTTGAATATTAAAAGATAATTTATACCTTTTGAATATTTCAAATTAAAATATATATTATCTAT
TTA
Found at i:281951 original size:21 final size:21
Alignment explanation
Indices: 281925--281971 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
281915 CGGTAAAGTG
281925 CTACCTAAAACATTATTTTTC
1 CTACCTAAAACATTATTTTTC
281946 CTACCTAAAACATTATTTTTC
1 CTACCTAAAACATTATTTTTC
*
281967 TTACC
1 CTACC
281972 AGAAATGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.43
Consensus pattern (21 bp):
CTACCTAAAACATTATTTTTC
Found at i:285342 original size:23 final size:24
Alignment explanation
Indices: 285306--285350 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
285296 TTTAATATTA
*
285306 TTATTTATAAAATATTAAAATAAT
1 TTATTTATAAAATACTAAAATAAT
*
285330 TTATTTAT-TAATACTAAAATA
1 TTATTTATAAAATACTAAAATA
285351 TCATTTCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATTTATAAAATACTAAAATAAT
Found at i:285719 original size:19 final size:19
Alignment explanation
Indices: 285674--285722 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 19
285664 TGAGTATTTT
285674 TATACTATTAAAATATAATA
1 TATA-TATTAAAATATAATA
285694 TATATATTAGAAATATTAATA
1 TATATATTA-AAATA-TAATA
*
285715 AATATATT
1 TATATATT
285723 TTAAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 9 0.35
21 12 0.46
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TATATATTAAAATATAATA
Found at i:285719 original size:21 final size:20
Alignment explanation
Indices: 285679--285770 Score: 66
Period size: 21 Copynumber: 4.6 Consensus size: 20
285669 ATTTTTATAC
*
285679 TATTAAAATA-TAATATATA
1 TATTAAAATATTAATAAATA
285698 TATTAGAAATATTAATAAATA
1 TATTA-AAATATTAATAAATA
* *
285719 TATTTTAAATATT--TTAATA
1 TA-TTAAAATATTAATAAATA
* * *
285738 -ATTAATATTTTGATGAAATGA
1 TATTAAAATATTAAT-AAAT-A
285759 TATTAAAATATT
1 TATTAAAATATT
285771 TTATTAATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
17 7 0.12
18 1 0.02
19 11 0.20
20 8 0.14
21 18 0.32
22 11 0.20
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
TATTAAAATATTAATAAATA
Found at i:286180 original size:2 final size:2
Alignment explanation
Indices: 286173--286244 Score: 135
Period size: 2 Copynumber: 35.5 Consensus size: 2
286163 CATCCAAGTA
286173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
286215 AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
286245 GTAGAGAAAT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 67 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:288757 original size:28 final size:29
Alignment explanation
Indices: 288717--288787 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 29
288707 AGCCGAAACA
288717 ATGGAAATTTCATATACAAATCAAC-TTC
1 ATGGAAATTTCATATACAAATCAACTTTC
*
288745 ATGGAAATTTCATATATAAATCAACTTTC
1 ATGGAAATTTCATATACAAATCAACTTTC
*
288774 ATAGAAATTTCATA
1 ATGGAAATTTCATA
288788 ACCGAACTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 24 0.60
29 16 0.40
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (29 bp):
ATGGAAATTTCATATACAAATCAACTTTC
Found at i:288952 original size:30 final size:31
Alignment explanation
Indices: 288884--288941 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
288874 CTTTTAAAAC
*
288884 TTGCAATACAGTTCCCCAACATTTAGTCAGT
1 TTGCAATACAGATCCCCAACATTTAGTCAGT
288915 TTGCAATACA-ATCCCCAACATTTAGTC
1 TTGCAATACAGATCCCCAACATTTAGTC
288942 CATTTTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (31 bp):
TTGCAATACAGATCCCCAACATTTAGTCAGT
Found at i:289480 original size:88 final size:91
Alignment explanation
Indices: 289335--289503 Score: 238
Period size: 88 Copynumber: 1.9 Consensus size: 91
289325 ACCGGCACCG
* *
289335 ATGCACCAATCCATGCATCGATGCACCATGGATTAAATTGAACATCGAATGTATTTTATGCATCG
1 ATGCACCAAACCATGCATCGATGCACCATGGATT-AATTGAACATCGAATGCATTTTATGCATCG
289400 ATGCA-CTTAGTGCATTTGATGCATCT
65 ATGCACCTTAGTGCATTTGATGCATCT
* * *
289426 ATGCA-CAAACCATGCATCGATGCA-CTTGGCTT-TTTGAAACATCGAATGCATTTTATGCATCG
1 ATGCACCAAACCATGCATCGATGCACCATGGATTAATTG-AACATCGAATGCATTTTATGCATCG
289488 ATGCACTCTTAGTGCA
65 ATGCAC-CTTAGTGCA
289504 CCGATGCACT
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
87 3 0.04
88 29 0.41
89 6 0.09
90 27 0.39
91 5 0.07
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (91 bp):
ATGCACCAAACCATGCATCGATGCACCATGGATTAATTGAACATCGAATGCATTTTATGCATCGA
TGCACCTTAGTGCATTTGATGCATCT
Found at i:295257 original size:21 final size:20
Alignment explanation
Indices: 295195--295263 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
295185 TGCTTAATGA
295195 ATCGATACACCT-AACAGTGC
1 ATCGATACACCTGAA-AGTGC
* *
295215 ATCGATGCATCCTTGAATGTGC
1 ATCGATACA-CC-TGAAAGTGC
*
295237 ATCGATACACCATGAAGGTGC
1 ATCGATACACC-TGAAAGTGC
*
295258 ACCGAT
1 ATCGAT
295264 GCATGTCTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 8 0.20
21 17 0.43
22 13 0.32
23 2 0.05
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGATACACCTGAAAGTGC
Found at i:295280 original size:23 final size:22
Alignment explanation
Indices: 295211--295289 Score: 97
Period size: 21 Copynumber: 3.6 Consensus size: 22
295201 ACACCTAACA
295211 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
* * *
295233 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
* *
295254 GTGCACCGATGCATGTCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
295277 GTGCATCGATGCA
1 GTGCATCGATGCA
295290 CAAGGCCATG
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 17 0.37
22 12 0.26
23 17 0.37
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:295282 original size:44 final size:42
Alignment explanation
Indices: 295195--295286 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 42
295185 TGCTTAATGA
*
295195 ATCGATACACCTAACAGTGCATCGATGCATCCTTGAATGTGC
1 ATCGATACACCTAACAGTGCACCGATGCATCCTTGAATGTGC
* *
295237 ATCGATACACCATGAA-GGTGCACCGATGCATGTCTTGAATGTGC
1 ATCGATACACC-T-AACAGTGCACCGATGCAT-CCTTGAATGTGC
295281 ATCGAT
1 ATCGAT
295287 GCACAAGGCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
42 11 0.25
43 14 0.32
44 19 0.43
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (42 bp):
ATCGATACACCTAACAGTGCACCGATGCATCCTTGAATGTGC
Found at i:295307 original size:43 final size:42
Alignment explanation
Indices: 295210--295312 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 42
295200 TACACCTAAC
* *
295210 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGA
1 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACAAGGA
* * * *
295252 AGGTGCACCGATGCATGTCTTGAATGTGCATCGATGCACAAGGCC
1 A-GTGCATCGATGCAT-CCTTGAATGTGCATCGATACACAAGG-A
295297 A-TGCATCGATGCATCC
1 AGTGCATCGATGCATCC
295313 ATCGGGTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
42 2 0.04
43 25 0.50
44 22 0.44
45 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.24
Consensus pattern (42 bp):
AGTGCATCGATGCATCCTTGAATGTGCATCGATACACAAGGA
Found at i:297089 original size:24 final size:24
Alignment explanation
Indices: 297062--297111 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
297052 ATAAAGAACC
297062 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
297086 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
297110 AA
1 AA
297112 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:302585 original size:23 final size:23
Alignment explanation
Indices: 302559--302607 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
302549 ATAAAGAACC
302559 AAAATAAA-CTTAAACATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
302582 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
302605 AAA
1 AAA
302608 CCACCACCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:304273 original size:14 final size:15
Alignment explanation
Indices: 304248--304276 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
304238 TTGATTTTGA
304248 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
304263 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
304277 AAATGTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:305030 original size:45 final size:45
Alignment explanation
Indices: 304981--305066 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
304971 ACATCGAATG
* *
304981 CATTTTATGCATCGATGCACATACCATGCATCAATGCACTCAGTA
1 CATTTGATGCATCGATGCACAAACCATGCATCAATGCACTCAGTA
305026 CATTTGATGCATCGATGCACAAACCATGCATCAATGCACTC
1 CATTTGATGCATCGATGCACAAACCATGCATCAATGCACTC
305067 TGGCTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (45 bp):
CATTTGATGCATCGATGCACAAACCATGCATCAATGCACTCAGTA
Found at i:308222 original size:2 final size:2
Alignment explanation
Indices: 308215--308245 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
308205 GAATTAAATA
308215 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
308246 ACTCAGCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:308316 original size:18 final size:18
Alignment explanation
Indices: 308293--308329 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
308283 TAGCCCACTG
308293 CCCATTTAAATTTTAAAA
1 CCCATTTAAATTTTAAAA
308311 CCCATTTAAATTTTAAAA
1 CCCATTTAAATTTTAAAA
308329 C
1 C
308330 TAAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (18 bp):
CCCATTTAAATTTTAAAA
Found at i:310348 original size:15 final size:16
Alignment explanation
Indices: 310317--310349 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
310307 ACTGTTTTTT
310317 AATTAAAAAAATATTA
1 AATTAAAAAAATATTA
*
310333 AATTCAAAAAAT-TTA
1 AATTAAAAAAATATTA
310348 AA
1 AA
310350 AAAATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AATTAAAAAAATATTA
Found at i:319479 original size:81 final size:81
Alignment explanation
Indices: 319344--319582 Score: 469
Period size: 81 Copynumber: 3.0 Consensus size: 81
319334 ATTATGGATA
319344 TATGCCTTAACAATATTTTTATGGGTTTTAATGTTTGTGTTTAGGGTAATGTTGTGTGGTTGATA
1 TATGCCTTAACAATATTTTTATGGGTTTTAATGTTTGTGTTTAGGGTAATGTTGTGTGGTTGATA
319409 TTGTAATTGAAGTATT
66 TTGTAATTGAAGTATT
*
319425 TATGCCTTAACCATATTTTTATGGGTTTTAATGTTTGTGTTTAGGGTAATGTTGTGTGGTTGATA
1 TATGCCTTAACAATATTTTTATGGGTTTTAATGTTTGTGTTTAGGGTAATGTTGTGTGGTTGATA
319490 TTGTAATTGAAGTATT
66 TTGTAATTGAAGTATT
319506 TATGCCTTAACAATATTTTTATGGGTTTTAATGTTTGTGTTTAGGGTAATGTTGTGTGGTTGATA
1 TATGCCTTAACAATATTTTTATGGGTTTTAATGTTTGTGTTTAGGGTAATGTTGTGTGGTTGATA
319571 TTGTAATTGAAG
66 TTGTAATTGAAG
319583 AATTAATGTA
Statistics
Matches: 156, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 156 1.00
ACGTcount: A:0.23, C:0.04, G:0.24, T:0.49
Consensus pattern (81 bp):
TATGCCTTAACAATATTTTTATGGGTTTTAATGTTTGTGTTTAGGGTAATGTTGTGTGGTTGATA
TTGTAATTGAAGTATT
Found at i:319597 original size:34 final size:35
Alignment explanation
Indices: 319552--319628 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 35
319542 GTGTTTAGGG
*
319552 TAATGTTGTGTGGTTG-ATATTGTAATTGAAGAAT
1 TAATGTAGTGTGGTTGTATATTGTAATTGAAGAAT
* **
319586 TAATGTAGTGTGGTTGTTATGTTGTAATTGAAGTGT
1 TAATGTAGTGTGGTTG-TATATTGTAATTGAAGAAT
319622 TAATGTA
1 TAATGTA
319629 ATGATGTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 15 0.41
36 22 0.59
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (35 bp):
TAATGTAGTGTGGTTGTATATTGTAATTGAAGAAT
Found at i:320437 original size:42 final size:42
Alignment explanation
Indices: 320186--320536 Score: 317
Period size: 43 Copynumber: 8.2 Consensus size: 42
320176 TGAGAACAAA
* * *
320186 AAACGCCGCAATAGGTTAAGATCTATCGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAAC
* * * *
320229 AAACGCTGCAAAATGTCAATATCTATAGCGACGTTTTTGGAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
* * * *
320272 AAACGCCGCAAAAGTTTGATATCTATAGCGGCGTTTTAGGATAC
1 AAACGCCGCAAAAG-GTCAGATCTATAGCGGCGTTTTTGGA-AC
* * * * * *
320316 AAATGCCGCAAAAGGTAAAATCTATAGCTGTGTTTTTTGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
*** * * **
320358 AAACGCTATAAAAGGTTGATATCTATAGCGGCG-TTTTGGAGT
1 AAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAAC
* * *
320400 AAACGTCGTAAAAGGTCAGATCTATAGCGGCGTTTTTGTAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
*
320442 AAACGCCGCAAAAGGTCAGATCTATGGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
* ** * * *
320485 AAAAGCCGCAAAATATCAGATCTATAGTGGCATTTTTTGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
*
320528 AAATGCCGC
1 AAACGCCGC
320537 TAATTACCTT
Statistics
Matches: 250, Mismatches: 52, Indels: 12
0.80 0.17 0.04
Matches are distributed among these distances:
41 15 0.06
42 74 0.30
43 145 0.58
44 16 0.06
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:324264 original size:42 final size:41
Alignment explanation
Indices: 324218--324532 Score: 349
Period size: 42 Copynumber: 7.6 Consensus size: 41
324208 TATGACAATT
324218 GCGGCGTTTGGTATTAAAACGCCACAAACGTATGTGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCACAAA-GTATGTGTCTATA
* **
324260 GCGGCGTTTGTGTA--AAAATGCCACTAAAGTATGAATCTATA
1 GCGGCGTTTG-GTATTAAAACGCCAC-AAAGTATGTGTCTATA
324301 GCGGCGTTTGGTATTAAAACGCCACAAAAGTATGTGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCAC-AAAGTATGTGTCTATA
* *
324343 GCGGCGTTTAGTATTAAAACGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCAC-AAAGTATGTGTCTATA
* * *
324385 GCGGCGTTTGTGTA--AAAATGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTG-GTATTAAAACGCCAC-AAAGTATGTGTCTATA
* *
324426 GCGGCGTTTGGTATTAAAATGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCAC-AAAGTATGTGTCTATA
* *
324468 GCGGCGTTT-GTATAAAAACGCCACTAAAATACTAGT-T-TATA
1 GCGGCGTTTGGTATTAAAACGCCAC-AAAGTA-T-GTGTCTATA
* *
324509 GCGGCATTT-GTATAAAAACGCCAC
1 GCGGCGTTTGGTATTAAAACGCCAC
324533 TACATTACGA
Statistics
Matches: 243, Mismatches: 21, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
40 6 0.02
41 109 0.45
42 120 0.49
43 8 0.03
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTGGTATTAAAACGCCACAAAGTATGTGTCTATA
Found at i:324292 original size:41 final size:41
Alignment explanation
Indices: 324218--324581 Score: 355
Period size: 41 Copynumber: 8.8 Consensus size: 41
324208 TATGACAATT
324218 GCGGCGTTTG-GTATTAAAACGCCAC-AAACGTATGTGTCTATA
1 GCGGCGTTTGTGTA--AAAACGCCACTAAA-GTATGTGTCTATA
* **
324260 GCGGCGTTTGTGTAAAAATGCCACTAAAGTATGAATCTATA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTATGTGTCTATA
*
324301 GCGGCGTTTG-GTATTAAAACGCCACAAAAGTATGTGTCTATA
1 GCGGCGTTTGTGTA--AAAACGCCACTAAAGTATGTGTCTATA
* * * *
324343 GCGGCGTTTAGTATTAAAACGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTT-GTGTAAAAACGCCACTAAAGTATGTGTCTATA
* * *
324385 GCGGCGTTTGTGTAAAAATGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTATGTGTCTATA
* * *
324426 GCGGCGTTTG-GTATTAAAATGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTTGTGTA--AAAACGCCACTAAAGTATGTGTCTATA
* *
324468 GCGGCGTTTGTATAAAAACGCCACTAAAATACTAGT-T-TATA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTA-T-GTGTCTATA
* * * * * *
324509 GCGGCATTTGTATAAAAACGCCACTACATTACGAT-TCTTTA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTATG-TGTCTATA
* * *
324550 GCGGCGTTTTTATACAAACGCCACTAAAGTAT
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTAT
324582 AGTATTTTGC
Statistics
Matches: 276, Mismatches: 33, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.00
40 8 0.03
41 142 0.51
42 116 0.42
43 8 0.03
44 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTGTAAAAACGCCACTAAAGTATGTGTCTATA
Found at i:324327 original size:83 final size:83
Alignment explanation
Indices: 324218--324581 Score: 402
Period size: 83 Copynumber: 4.4 Consensus size: 83
324208 TATGACAATT
* *
324218 GCGGCGTTTGGTATTAAAACGCCAC-AAACGTATGTGTCTATAGCGGCGTTTGTGTAAAAATGCC
1 GCGGCGTTTGGTATTAAAACGCCACTAAA-GTATGTGTCTATAGCGGCGTTTGTATAAAAACGCC
* * *
324282 ACTAAAGTATGAATCTATA
65 ACAAAAGTACGAGTCTATA
* *
324301 GCGGCGTTTGGTATTAAAACGCCACAAAAGTATGTGTCTATAGCGGCGTTTAGTATTAAAACGCC
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTATGTGTCTATAGCGGCGTTT-GTATAAAAACGCC
*
324366 ACAAAAGTACGTGTCTATA
65 ACAAAAGTACGAGTCTATA
* * * * *
324385 GCGGCGTTTGTGTA--AAAATGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAATGC
1 GCGGCGTTTG-GTATTAAAACGCCACTAAAGTATGTGTCTATAGCGGCGTTT-GTATAAAAACGC
*
324448 CACAAAAGTACGTGTCTATA
64 CACAAAAGTACGAGTCTATA
* * *
324468 GCGGCGTTT-GTATAAAAACGCCACTAAAATACTAGT-T-TATAGCGGCATTTGTATAAAAACGC
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTA-T-GTGTCTATAGCGGCGTTTGTATAAAAACGC
* * * * *
324530 CACTACATTACGATTCTTTA
64 CACAAAAGTACGAGTCTATA
*
324550 GCGGCGTTT-TTA-TACAAACGCCACTAAAGTAT
1 GCGGCGTTTGGTATTA-AAACGCCACTAAAGTAT
324582 AGTATTTTGC
Statistics
Matches: 244, Mismatches: 29, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
81 5 0.02
82 50 0.20
83 146 0.60
84 39 0.16
85 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (83 bp):
GCGGCGTTTGGTATTAAAACGCCACTAAAGTATGTGTCTATAGCGGCGTTTGTATAAAAACGCCA
CAAAAGTACGAGTCTATA
Found at i:324414 original size:125 final size:124
Alignment explanation
Indices: 324218--324581 Score: 502
Period size: 125 Copynumber: 2.9 Consensus size: 124
324208 TATGACAATT
* *
324218 GCGGCGTTTGGTATTAAAACGCCACAAACGTATGTGTCTATAGCGGCGTTTGTGTAAAAATGCCA
1 GCGGCGTTT-GTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAATGCCA
*
324283 CTAAAGTATGAATCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTATGTGTCTATA
65 CTAAAGTACGAATCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTATGTGTCTATA
324343 GCGGCGTTTAGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAATGCCA
1 GCGGCGTTT-GTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAATGCCA
* * *
324408 CTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAATGCCACAAAAGTACGTGTCTATA
65 CTAAAGTACGAATCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTATGTGTCTATA
* * * * *
324468 GCGGCGTTTGTATAAAAACGCCACTAAAA-TAC-TAGTTTATAGCGGCATTTGTATAAAAACGCC
1 GCGGCGTTTGTATTAAAACGCCAC-AAAAGTACGT-GTCTATAGCGGCGTTTGTGTAAAAATGCC
* * * * * *
324531 ACTACATTACGATTCTTTAGCGGCGTTT-TTA-TACAAACGCCACTAAAGTAT
64 ACTAAAGTACGAATCTATAGCGGCGTTTGGTATTA-AAACGCCACAAAAGTAT
324582 AGTATTTTGC
Statistics
Matches: 216, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
122 2 0.01
123 17 0.08
124 66 0.31
125 131 0.61
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (124 bp):
GCGGCGTTTGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAATGCCAC
TAAAGTACGAATCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTATGTGTCTATA
Found at i:325037 original size:34 final size:33
Alignment explanation
Indices: 324998--325106 Score: 148
Period size: 34 Copynumber: 3.2 Consensus size: 33
324988 GCTATAAGCT
* *
324998 AATAATTAGACCATTAATCAAATCAAGTGCACCA
1 AATAATCAGACCAATAATCAAA-CAAGTGCACCA
*
325032 AATAATCAGACCAACAATCAAACTAAGTGCACCA
1 AATAATCAGACCAATAATCAAAC-AAGTGCACCA
*
325066 AATAATCAAACCAATAATCAAACCAAGTGCACC-
1 AATAATCAGACCAATAATCAAA-CAAGTGCACCA
325099 AATAATCA
1 AATAATCA
325107 AAATAATGGT
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
33 9 0.13
34 58 0.85
35 1 0.01
ACGTcount: A:0.50, C:0.24, G:0.07, T:0.18
Consensus pattern (33 bp):
AATAATCAGACCAATAATCAAACAAGTGCACCA
Found at i:325083 original size:12 final size:12
Alignment explanation
Indices: 325066--325091 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
325056 AAGTGCACCA
325066 AATAATCAAACC
1 AATAATCAAACC
325078 AATAATCAAACC
1 AATAATCAAACC
325090 AA
1 AA
325092 GTGCACCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (12 bp):
AATAATCAAACC
Found at i:325202 original size:46 final size:46
Alignment explanation
Indices: 325096--325204 Score: 173
Period size: 46 Copynumber: 2.4 Consensus size: 46
325086 AACCAAGTGC
* *
325096 ACCAATAATCAAAATAATGGTAAGCTAATATGTCTAAAATATCCAT
1 ACCAATAATCAGACTAATGGTAAGCTAATATGTCTAAAATATCCAT
* * *
325142 ACCAATAATAAGACTAATGGTAAGCTAATATGTGTAAAATATCTAT
1 ACCAATAATCAGACTAATGGTAAGCTAATATGTCTAAAATATCCAT
325188 ACCAATAATCAGACTAA
1 ACCAATAATCAGACTAA
325205 AATATATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.28
Consensus pattern (46 bp):
ACCAATAATCAGACTAATGGTAAGCTAATATGTCTAAAATATCCAT
Found at i:327138 original size:18 final size:19
Alignment explanation
Indices: 327096--327138 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
327086 TCTACCTTAA
* *
327096 CCTTAGCCTCAGATGGTTT
1 CCTTAACCTCAGATGGATT
327115 CC-TAACCTCAGAT-GATT
1 CCTTAACCTCAGATGGATT
327132 CCTTAAC
1 CCTTAAC
327139 ATTGTCATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 14 0.67
19 2 0.10
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (19 bp):
CCTTAACCTCAGATGGATT
Found at i:327820 original size:11 final size:13
Alignment explanation
Indices: 327787--327818 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
327777 CAACAAAAAA
*
327787 ATATTATCAACAT
1 ATATTATAAACAT
327800 ATATTATAAACAT
1 ATATTATAAACAT
327813 ATATTA
1 ATATTA
327819 AAAGCACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATTATAAACAT
Found at i:329969 original size:42 final size:42
Alignment explanation
Indices: 329890--329969 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 42
329880 GAACTCGAAC
* * *
329890 ATTTTTGCCTTAGCAGCTTTAATTTACTTATTCTTGCAATTA
1 ATTTTTGCCTTAGCAACTTTAATTTACTTACTATTGCAATTA
* * **
329932 ATTTTTGCCTTAGCAATTTTTATTTGTTTACTATTGCA
1 ATTTTTGCCTTAGCAACTTTAATTTACTTACTATTGCA
329970 TATTTTTCTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.53
Consensus pattern (42 bp):
ATTTTTGCCTTAGCAACTTTAATTTACTTACTATTGCAATTA
Found at i:330367 original size:18 final size:19
Alignment explanation
Indices: 330344--330383 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
330334 CCAAACTTTG
*
330344 GTATCGATGCCCTAG-TTA
1 GTATCGATACCCTAGTTTA
*
330362 GTATCGGTACCCTAGTTTA
1 GTATCGATACCCTAGTTTA
330381 GTA
1 GTA
330384 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (19 bp):
GTATCGATACCCTAGTTTA
Found at i:330496 original size:20 final size:20
Alignment explanation
Indices: 330473--330511 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
330463 AGGAAGTATC
330473 GATACTAAAGGATCAATATT
1 GATACTAAAGGATCAATATT
* *
330493 GATACTGAGGGATCAATAT
1 GATACTAAAGGATCAATAT
330512 CGGTACCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (20 bp):
GATACTAAAGGATCAATATT
Found at i:332303 original size:3 final size:3
Alignment explanation
Indices: 332295--332340 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
332285 ATTCGACCCA
332295 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
332341 TATATATCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:332344 original size:6 final size:7
Alignment explanation
Indices: 332295--332347 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 7
332285 ATTCGACCCA
332295 ATTAT-T
1 ATTATAT
332301 ATTAT-T
1 ATTATAT
332307 ATTAT-T
1 ATTATAT
332313 ATTAT-T
1 ATTATAT
332319 ATTAT-T
1 ATTATAT
332325 ATTAT-T
1 ATTATAT
332331 ATTATAT
1 ATTATAT
332338 ATTTATAT
1 A-TTATAT
332346 AT
1 AT
332348 CTAGTGATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
6 35 0.78
7 3 0.07
8 7 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
ATTATAT
Found at i:334416 original size:26 final size:26
Alignment explanation
Indices: 334381--334435 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
334371 AAATATTCTA
*
334381 ATAAATAAATA-TAAAAAACACTAAAT
1 ATAAAAAAATATTAAAAAA-ACTAAAT
* *
334407 ATAAAAAAATATTACAAAAATTAAAT
1 ATAAAAAAATATTAAAAAAACTAAAT
334433 ATA
1 ATA
334436 CATATTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.25
Consensus pattern (26 bp):
ATAAAAAAATATTAAAAAAACTAAAT
Found at i:337550 original size:8 final size:8
Alignment explanation
Indices: 337534--337569 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
337524 AACTATATAA
337534 TATATATG
1 TATATATG
*
337542 TATAGATG
1 TATATATG
*
337550 TATATATA
1 TATATATG
337558 TATATATG
1 TATATATG
337566 TATA
1 TATA
337570 AAGTAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (8 bp):
TATATATG
Found at i:338108 original size:24 final size:22
Alignment explanation
Indices: 338068--338164 Score: 63
Period size: 24 Copynumber: 4.3 Consensus size: 22
338058 AATATTTTTT
* *
338068 AAATATAAAAATCTTAAATTTG
1 AAATATAAAAATCTTAAATATA
*
338090 AAATATAAAAGTATTTTAAATATA
1 AAATATAAAA--ATCTTAAATATA
* ** *
338114 AAATAT-ATAAT-TTAGTTTTA
1 AAATATAAAAATCTTAAATATA
* *
338134 AAATATAAAAAATATTTAAATTTA
1 AAATAT-AAAAAT-CTTAAATATA
338158 AAATATA
1 AAATATA
338165 TAATAAAATA
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
20 12 0.20
21 2 0.03
22 14 0.24
23 3 0.05
24 28 0.47
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (22 bp):
AAATATAAAAATCTTAAATATA
Found at i:338162 original size:68 final size:66
Alignment explanation
Indices: 338035--338164 Score: 163
Period size: 68 Copynumber: 1.9 Consensus size: 66
338025 TTTAATTTTA
* * * * *
338035 ATTTTAAATATATATATATATTTAATATTTTTTAAATATAAAAATCTTAAATTTGAAATATAAAA
1 ATTTTAAATATAAATATATAATT-ATAGTTTTAAAATATAAAAATCTTAAATTTAAAATATAAAA
338100 GT
65 GT
*
338102 ATTTTAAATATAAAATATATAATT-TAGTTTTAAAATATAAAAAATATTTAAATTTAAAATATA
1 ATTTTAAATAT-AAATATATAATTATAGTTTTAAAATAT-AAAAAT-CTTAAATTTAAAATATA
338165 TAATAAAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
66 12 0.22
67 17 0.31
68 25 0.46
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (66 bp):
ATTTTAAATATAAATATATAATTATAGTTTTAAAATATAAAAATCTTAAATTTAAAATATAAAAG
T
Found at i:338224 original size:2 final size:2
Alignment explanation
Indices: 338217--338252 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
338207 TTATTTTGCA
338217 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
338253 GTATGTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:340788 original size:13 final size:13
Alignment explanation
Indices: 340770--340794 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
340760 TCTCGGTGTA
340770 TTTTCTGTCTCTC
1 TTTTCTGTCTCTC
340783 TTTTCTGTCTCT
1 TTTTCTGTCTCT
340795 GTCCCTCTTC
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:0.28, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTTCTGTCTCTC
Found at i:340795 original size:19 final size:21
Alignment explanation
Indices: 340773--340814 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
340763 CGGTGTATTT
*
340773 TCTGTCTCTCTT-T-TCTGTC
1 TCTGTCCCTCTTCTCTCTGTC
340792 TCTGTCCCTCTTCTCTCTGTC
1 TCTGTCCCTCTTCTCTCTGTC
340813 TC
1 TC
340815 CTCTCTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 1 0.05
21 8 0.40
ACGTcount: A:0.00, C:0.38, G:0.10, T:0.52
Consensus pattern (21 bp):
TCTGTCCCTCTTCTCTCTGTC
Found at i:341030 original size:16 final size:16
Alignment explanation
Indices: 340998--341050 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
340988 TGACGTGACA
*
340998 GCGG-TGGAGGCATAG
1 GCGGCTGGAGGCAGAG
*
341013 GCGGCTGGAGACAGAG
1 GCGGCTGGAGGCAGAG
341029 GCGGCTGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
*
341045 GTGGCT
1 GCGGCT
341051 AGGGATTAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
15 4 0.12
16 29 0.88
ACGTcount: A:0.19, C:0.17, G:0.53, T:0.11
Consensus pattern (16 bp):
GCGGCTGGAGGCAGAG
Found at i:341169 original size:9 final size:10
Alignment explanation
Indices: 341136--341174 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
341126 TGGGCTTGTA
341136 ATTTAATATT
1 ATTTAATATT
341146 ATTTATATATGT
1 ATTTA-ATAT-T
341158 ATTTAATA-T
1 ATTTAATATT
341167 ATTTAATA
1 ATTTAATA
341175 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.33
10 5 0.19
11 7 0.26
12 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:341178 original size:3 final size:3
Alignment explanation
Indices: 341170--341249 Score: 115
Period size: 3 Copynumber: 26.7 Consensus size: 3
341160 TTAATATATT
* * * *
341170 TAA TAA TAA TAA TAA TAA TGA TAA TTA TAA TAA TAA TAA TAA TTA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
341218 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
341250 TTTATAATAT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:341258 original size:18 final size:18
Alignment explanation
Indices: 341170--341248 Score: 131
Period size: 18 Copynumber: 4.4 Consensus size: 18
341160 TTAATATATT
*
341170 TAATAATAATAATAATAA
1 TAATAATTATAATAATAA
*
341188 TGATAATTATAATAATAA
1 TAATAATTATAATAATAA
*
341206 TAATAATTATAGTAATAA
1 TAATAATTATAATAATAA
341224 TAATAATTATAATAATAA
1 TAATAATTATAATAATAA
341242 TAATAAT
1 TAATAAT
341249 ATTTATAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TAATAATTATAATAATAA
Found at i:341259 original size:9 final size:9
Alignment explanation
Indices: 341161--341248 Score: 97
Period size: 9 Copynumber: 9.8 Consensus size: 9
341151 TATATGTATT
341161 TAATATATT-
1 TAATA-ATTA
*
341170 TAATAATAA
1 TAATAATTA
*
341179 TAATAATAA
1 TAATAATTA
*
341188 TGATAATTA
1 TAATAATTA
*
341197 TAATAATAA
1 TAATAATTA
341206 TAATAATTA
1 TAATAATTA
* *
341215 TAGTAATAA
1 TAATAATTA
341224 TAATAATTA
1 TAATAATTA
*
341233 TAATAATAA
1 TAATAATTA
341242 TAATAAT
1 TAATAAT
341249 ATTTATAATA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
8 2 0.03
9 65 0.97
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
TAATAATTA
Found at i:341946 original size:113 final size:113
Alignment explanation
Indices: 341578--342479 Score: 1458
Period size: 113 Copynumber: 8.0 Consensus size: 113
341568 ATAGAATTAT
* * * *
341578 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
341643 ATTATGAA-TTTCTCTGGAAAAGATAATCCATCAATTGAT-GAATTCA
66 ATTATGAACCTTCTCTGGCAAAGATAATCCATCAAGTGATGGATTTGA
*
341689 GGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 -GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
341754 CATTATGAA-CTTCTCTGGAAAAGATAATCCATCAAGTGATGGATTTGA
65 CATTATGAACCTTCTCTGGCAAAGATAATCCATCAAGTGATGGATTTGA
*
341802 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
341867 ATTATGAACCTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACCTTCTCTGGCAAAGATAATCCATCAAGTGATGGATTTGA
*
341915 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
341980 ATTATGAACCTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACCTTCTCTGGCAAAGATAATCCATCAAGTGATGGATTTGA
*
342028 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
342093 ATTATGAACCTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACCTTCTCTGGCAAAGATAATCCATCAAGTGATGGATTTGA
*
342141 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
342206 ATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGAT-GAATTCA
66 ATTATGAACCTTCTCTGGCAAAGATAATCCATCAAGTGATGGATTTGA
*
342253 GACAAATGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 G-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
342318 CATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGAT-GAATTCA
65 CATTATGAACCTTCTCTGGCAAAGATAATCCATCAAGTGATGGATTTGA
342366 GACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 G-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
342431 CATTATGAACTTTCTCTGG-AAATG-TCAATCCATCAAATGATAGATTTGA
65 CATTATGAACCTTCTCTGGCAAA-GAT-AATCCATCAAGTGATGGATTTGA
342480 ATCTTTGCTA
Statistics
Matches: 759, Mismatches: 25, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
112 178 0.23
113 576 0.76
114 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACCTTCTCTGGCAAAGATAATCCATCAAGTGATGGATTTGA
Found at i:343388 original size:83 final size:83
Alignment explanation
Indices: 343208--343839 Score: 1006
Period size: 83 Copynumber: 7.6 Consensus size: 83
343198 GTAGTTCTTA
*** *
343208 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTCATCCTCC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CAAATTCATCTTCC
343273 AAATTCAATGATTGGTTCTG
64 AAATTCAATGATTGGTTCTG
* *
343293 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCCA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCA
343357 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
* *
343376 TCC-AACCAGATCAGATAACTCAAAGAAAACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCA
*
343440 AATTCAATGATTGGTTCTAT
65 AATTCAATGATTGGTTCT-G
* * *
343460 CC-AACCAGATCAGATAACTCATAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
*
343524 ATTCAATAATTGGTTCTG
66 ATTCAATGATTGGTTCTG
343542 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATCG-GCAAATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT-GAGCAAATTCATCTTCCA
343606 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
*
343625 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATCG-GCAAATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT-GAGCAAATTCATCTTCCA
343689 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
*
343708 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATCG-GCAAATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT-GAGCAAATTCATCTTCCA
343772 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
*
343791 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGGTATGAG
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
343840 TACATTGCAT
Statistics
Matches: 524, Mismatches: 18, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
82 3 0.01
83 473 0.90
84 4 0.01
85 42 0.08
86 2 0.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:344895 original size:1 final size:1
Alignment explanation
Indices: 344891--344956 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
344881 TGACCCCCCC
* * * ** * * * *
344891 TTTTTCTTTTTTCTTTTTTTTTCTTTTCCTTTTTTCTTTTCTTTTTTTTTCTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
344956 T
1 T
344957 ATTCAAGCAT
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:344912 original size:10 final size:10
Alignment explanation
Indices: 344897--344956 Score: 72
Period size: 10 Copynumber: 6.3 Consensus size: 10
344887 CCCCTTTTTC
344897 TTTTTTCTTT
1 TTTTTTCTTT
344907 TTTTTTC-TT
1 TTTTTTCTTT
**
344916 TTCCTT-TTT
1 TTTTTTCTTT
*
344925 TCTTTTCTTT
1 TTTTTTCTTT
344935 TTTTTTC-TT
1 TTTTTTCTTT
344944 TTTTTTCTTT
1 TTTTTTCTTT
344954 TTT
1 TTT
344957 ATTCAAGCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
9 20 0.49
10 21 0.51
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:344916 original size:23 final size:23
Alignment explanation
Indices: 344890--344956 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
344880 TTGACCCCCC
344890 CTTTTTCTTTTTTCTTTTTTTTT
1 CTTTTTCTTTTTTCTTTTTTTTT
* *
344913 CTTTTCCTTTTTTCTTTTCTTTT
1 CTTTTTCTTTTTTCTTTTTTTTT
*
344936 -TTTTTCTTTTTT-TTCTTTTTT
1 CTTTTTCTTTTTTCTTTTTTTTT
344957 ATTCAAGCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.18
22 11 0.28
23 21 0.54
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (23 bp):
CTTTTTCTTTTTTCTTTTTTTTT
Found at i:344932 original size:28 final size:29
Alignment explanation
Indices: 344889--344945 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
344879 CTTGACCCCC
*
344889 CCTTTTTCTTTTTTCTTTTTTTTTCTTTT
1 CCTTTTTCTCTTTTCTTTTTTTTTCTTTT
344918 CCTTTTT-TCTTTTCTTTTTTTTTCTTTT
1 CCTTTTTCTCTTTTCTTTTTTTTTCTTTT
344946 TTTTCTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (29 bp):
CCTTTTTCTCTTTTCTTTTTTTTTCTTTT
Found at i:344956 original size:7 final size:7
Alignment explanation
Indices: 344891--344947 Score: 69
Period size: 7 Copynumber: 7.7 Consensus size: 7
344881 TGACCCCCCC
344891 TTTTTCT
1 TTTTTCT
344898 TTTTTCT
1 TTTTTCT
*
344905 TTTTTTT
1 TTTTTCT
344912 TCTTTTCCT
1 T-TTTT-CT
344921 TTTTTCT
1 TTTTTCT
*
344928 TTTCTTTT
1 TTT-TTCT
344936 TTTTTCT
1 TTTTTCT
344943 TTTTT
1 TTTTT
344948 TTCTTTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
7 27 0.63
8 14 0.33
9 2 0.05
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:352305 original size:16 final size:17
Alignment explanation
Indices: 352281--352318 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
352271 TGATGTATGC
* *
352281 AAAATGTATT-ATGCCA
1 AAAAGGTATTGATCCCA
352297 AAAAGGTATTGATCCCA
1 AAAAGGTATTGATCCCA
352314 AAAAG
1 AAAAG
352319 TTAACTGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (17 bp):
AAAAGGTATTGATCCCA
Found at i:356046 original size:21 final size:17
Alignment explanation
Indices: 356019--356062 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
356009 TACAACGCCC
356019 AAAATTGGTACTTTTTAATT
1 AAAATT-GT-CTTTTT-ATT
356039 ATAAATTGTCTTTTTATT
1 A-AAATTGTCTTTTTATT
356057 AAAATT
1 AAAATT
356063 TAAAAATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 6 0.26
20 3 0.13
21 5 0.22
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (17 bp):
AAAATTGTCTTTTTATT
Found at i:357267 original size:13 final size:13
Alignment explanation
Indices: 357249--357273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
357239 TCTCTGTGTA
357249 TTTTCTGTCTCTC
1 TTTTCTGTCTCTC
357262 TTTTCTGTCTCT
1 TTTTCTGTCTCT
357274 GTCCCTCTTC
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:0.28, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTTCTGTCTCTC
Found at i:357274 original size:19 final size:21
Alignment explanation
Indices: 357252--357293 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
357242 CTGTGTATTT
*
357252 TCTGTCTCTCTT-T-TCTGTC
1 TCTGTCCCTCTTCTCTCTGTC
357271 TCTGTCCCTCTTCTCTCTGTC
1 TCTGTCCCTCTTCTCTCTGTC
357292 TC
1 TC
357294 CTCTCTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 1 0.05
21 8 0.40
ACGTcount: A:0.00, C:0.38, G:0.10, T:0.52
Consensus pattern (21 bp):
TCTGTCCCTCTTCTCTCTGTC
Found at i:357501 original size:16 final size:16
Alignment explanation
Indices: 357476--357512 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
357466 TGACGTGGCA
357476 GCGG-TGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
357491 GCGGCTGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
357507 GCGGCT
1 GCGGCT
357513 AGGGATTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.16, C:0.19, G:0.57, T:0.08
Consensus pattern (16 bp):
GCGGCTGGAGGCAGAG
Found at i:357636 original size:3 final size:3
Alignment explanation
Indices: 357628--357710 Score: 132
Period size: 3 Copynumber: 27.7 Consensus size: 3
357618 TTAATATATT
*
357628 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
357676 TATA TAG TAA TAA TAA TAA T-A TAA TAA TAA TAA TA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
357711 TTTATAATAT
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.03
3 69 0.93
4 3 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:357834 original size:25 final size:25
Alignment explanation
Indices: 357806--357854 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
357796 ACAAGTTTCG
*
357806 ACTACTCTAAATTTTGTAAGTCTCA
1 ACTAATCTAAATTTTGTAAGTCTCA
* *
357831 ACTAATTTAAATTTTGTAGGTCTC
1 ACTAATCTAAATTTTGTAAGTCTC
357855 GATTAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (25 bp):
ACTAATCTAAATTTTGTAAGTCTCA
Done.