Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004429.1 Hibiscus syriacus cultivar Beakdansim tig00009710_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: 132253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:1135 original size:19 final size:20
Alignment explanation
Indices: 1086--1143 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1076 AATAGTTTCT
** *
1086 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1106 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
*
1126 G-AATTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1144 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1689 original size:20 final size:20
Alignment explanation
Indices: 1664--1717 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1654 GATTTTGTAT
*
1664 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAATAAG
*
1684 TATCGCATTGCGATAATCAG
1 TATCGCATTGCGATAATAAG
1704 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1718 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAATAAG
Found at i:5456 original size:20 final size:20
Alignment explanation
Indices: 5413--5767 Score: 210
Period size: 20 Copynumber: 17.4 Consensus size: 20
5403 CAGTTTCCAG
* *
5413 AATCGCAACGCGATTCTGGAA
1 AATCGCAACGCGAATC-CGAA
**
5434 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGAA
**
5454 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATCCGA-A
* ** *
5474 AATCGCAACGCGATTCTTAC
1 AATCGCAACGCGAATCCGAA
* * * *
5494 TATCGCAACGAGTATTCGTAAA
1 AATCGCAACGCGAATCCG--AA
* *
5516 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* *
5536 AATCGCAACGAGAATACGTAA
1 AATCGCAACGCGAATCCG-AA
* *
5557 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* *
5577 AATCGCAACGAGAATACGTAA
1 AATCGCAACGCGAATCCG-AA
* * *
5598 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* *
5618 AATCGCAACGAGAATACGTAA
1 AATCGCAACGCGAATCCG-AA
* * *
5639 AATCGCAACGCGATTCTGAT
1 AATCGCAACGCGAATCCGAA
* * **
5659 TATCGCAAC-CAGAATACGTT
1 AATCGCAACGC-GAATCCGAA
* * *
5679 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGAA
** *
5699 AATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCCGAA
** *
5719 AATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCCGAA
* * *
5739 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGAA
5759 AATCGCAAC
1 AATCGCAAC
5768 ACTTAAATTT
Statistics
Matches: 263, Mismatches: 62, Indels: 19
0.76 0.18 0.06
Matches are distributed among these distances:
19 2 0.01
20 182 0.69
21 63 0.24
22 16 0.06
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGAA
Found at i:5571 original size:41 final size:41
Alignment explanation
Indices: 5432--5767 Score: 341
Period size: 41 Copynumber: 8.3 Consensus size: 41
5422 GCGATTCTGG
* ** * * *
5432 AAAATCGCAACGCGAATATGAAAATCGCAACGCG-A-ACAT
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
* * * * *
5471 ATAAATCGCAACGCG-ATTCTTACTATCGCAACGAGTATTCGT
1 A-AAATCGCAACGCGTATCCGTA-AATCGCAACGAGAATACGT
5513 AAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
1 -AAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
5555 AAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
*
5596 AAAATCGCAATGCGTATCCGTAAATCGCAACGAGAATACGT
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
* * *
5637 AAAATCGCAACGCG-ATTC-TGATTATCGCAACCAGAATACGT
1 AAAATCGCAACGCGTATCCGT-A-AATCGCAACGAGAATACGT
* * * * * *
5678 -TAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
*
5718 -AAATCGCAACG-ATAATCCGTAAATCGCAACGAGAAT-CTGT
1 AAAATCGCAACGCGT-ATCCGTAAATCGCAACGAGAATAC-GT
5758 -AAATCGCAAC
1 AAAATCGCAAC
5768 ACTTAAATTT
Statistics
Matches: 254, Mismatches: 31, Indels: 23
0.82 0.10 0.07
Matches are distributed among these distances:
39 6 0.02
40 95 0.37
41 115 0.45
42 32 0.13
43 6 0.02
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
AAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
Found at i:6450 original size:12 final size:12
Alignment explanation
Indices: 6429--6462 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6419 ACCACATTTC
*
6429 CAATACCAAACA
1 CAATATCAAACA
6441 CAATATCAAACA
1 CAATATCAAACA
*
6453 CAATCTCAAA
1 CAATATCAAA
6463 ACCTACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:6614 original size:24 final size:24
Alignment explanation
Indices: 6587--6640 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
6577 AGTATTCGAA
6587 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
6611 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
6635 TTTGAT
1 TTTGAT
6641 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:9167 original size:33 final size:33
Alignment explanation
Indices: 9111--9388 Score: 367
Period size: 33 Copynumber: 8.2 Consensus size: 33
9101 TCATTTGACT
* * * *
9111 ATCGCAACGCGGAAATTACAATCGCAACAAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
9145 ATCGCAATGCGAAATGAAAATCGCAACGTGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
9178 ATCGCAACGCGAATATGAAAATCGCAACGCGGAAATGA
1 ATCGCAATGCGAA-ATGAAAATCGCAA--C-GAGA-GA
9216 CTATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 --ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
9251 ATCGCAATGCGAAACGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
9284 ATTGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
9317 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
9350 ATCGCAATGCGAAATGAAAATCACAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
9383 ATCGCA
1 ATCGCA
9389 CTCGTTGCGA
Statistics
Matches: 217, Mismatches: 20, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
33 160 0.74
34 22 0.10
35 2 0.01
36 4 0.02
37 3 0.01
38 1 0.00
39 13 0.06
40 12 0.06
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:9178 original size:14 final size:14
Alignment explanation
Indices: 9159--9186 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9149 CAATGCGAAA
9159 TGAAAATCGCAACG
1 TGAAAATCGCAACG
9173 TGAAAATCGCAACG
1 TGAAAATCGCAACG
9187 CGAATATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:9196 original size:20 final size:19
Alignment explanation
Indices: 9144--9377 Score: 131
Period size: 19 Copynumber: 13.5 Consensus size: 19
9134 GCAACAAGAG
*
9144 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
9163 AATCGCAA--CG---TGAA
1 AATCGCAACGCGAAATGAA
9177 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAA-ATGAA
*
9197 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATGAA
* *
9217 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
9236 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
* *
9250 AATCGCAATGCGAAACGAA
1 AATCGCAACGCGAAATGAA
*
9269 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
* *
9283 AATTGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
9302 AATCGTAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
9316 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
9335 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
9349 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
9368 AATCACAACG
1 AATCGCAACG
9378 AGGGAATCGC
Statistics
Matches: 169, Mismatches: 19, Indels: 54
0.70 0.08 0.22
Matches are distributed among these distances:
14 50 0.30
15 4 0.02
16 10 0.06
17 10 0.06
18 4 0.02
19 60 0.36
20 28 0.17
21 3 0.02
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:9255 original size:14 final size:14
Alignment explanation
Indices: 9236--9356 Score: 62
Period size: 14 Copynumber: 7.6 Consensus size: 14
9226 GCGAAATGAA
9236 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
9250 AATCGCAATGCGAAACGAA
1 AATCGCAA--CG--A-GAG
9269 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
9283 AATTGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
9302 AATCGTAACGAGAG
1 AATCGCAACGAGAG
*
9316 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
9335 AATCGCAACGAGAG
1 AATCGCAACGAGAG
9349 AATCGCAA
1 AATCGCAA
9357 TGCGAAATGA
Statistics
Matches: 82, Mismatches: 10, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
14 36 0.44
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 28 0.34
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:9544 original size:14 final size:14
Alignment explanation
Indices: 9525--9561 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
9515 CATCAATTAA
9525 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
9539 ACAAATCATCTTTT
1 ACAAATCAACTTTT
9553 ACAAATCAA
1 ACAAATCAA
9562 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:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:9702 original size:82 final size:84
Alignment explanation
Indices: 9528--9704 Score: 331
Period size: 83 Copynumber: 2.1 Consensus size: 84
9518 CAATTAAACA
9528 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
1 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
9593 ATTTCCTCATCTACTATTG
66 ATTTCCTCATCTACTATTG
*
9612 AATCAACTTTTACAAATCATCTTTTAC-AATGAATTAAACAATCAAAAAATAAGCAATAATTC-T
1 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
9675 ATTTCCTCATCTACTATTG
66 ATTTCCTCATCTACTATTG
9694 AATCAACTTTT
1 AATCAACTTTT
9705 GCAGCCATAC
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
82 31 0.34
83 34 0.37
84 27 0.29
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (84 bp):
AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
ATTTCCTCATCTACTATTG
Found at i:11078 original size:42 final size:41
Alignment explanation
Indices: 10993--11115 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
10983 GTGAATCGGG
* * * * *
10993 CTCTTGAATGGTGGGA-GGGACCTCTTCAATGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
11035 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
11077 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
11116 CGAGTCAGGT
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:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:11569 original size:14 final size:14
Alignment explanation
Indices: 11550--11606 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
11540 GCGAAATGAA
11550 AATCGCAACGAGAG
1 AATCGCAACGAGAG
11564 AATCGCAACGAGAAATG
1 AATCGCAACGAG--A-G
*
11581 AAAATCGCAACGATAG
1 --AATCGCAACGAGAG
11597 AATCGCAACG
1 AATCGCAACG
11607 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 22 0.59
16 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:11579 original size:33 final size:33
Alignment explanation
Indices: 11532--11625 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
11522 AAAAATGATT
11532 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
11565 ATCGCAACGAGAAATGAAAATCGCAACGATAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
**
11598 ATCGCAACGCGAAACCAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
11626 TGATTATAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:11588 original size:19 final size:19
Alignment explanation
Indices: 11508--11593 Score: 83
Period size: 19 Copynumber: 4.7 Consensus size: 19
11498 CACGAAACTT
*
11508 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAAC--GAGAAATG
** *
11529 ATTATCGCAACGCGAAATG
1 AAAATCGCAACGAGAAATG
11548 AAAATCGCAACGAG--A-G
1 AAAATCGCAACGAGAAATG
11564 --AATCGCAACGAGAAATG
1 AAAATCGCAACGAGAAATG
11581 AAAATCGCAACGA
1 AAAATCGCAACGA
11594 TAGAATCGCA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
14 12 0.23
16 2 0.04
17 2 0.04
19 28 0.53
21 9 0.17
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGAGAAATG
Found at i:11649 original size:19 final size:19
Alignment explanation
Indices: 11627--11778 Score: 95
Period size: 19 Copynumber: 8.1 Consensus size: 19
11617 ATCGCAACGT
*
11627 GATTATAGTTTCGCGTTGC
1 GATTTTAGTTTCGCGTTGC
*
11646 GATTTTGGTTTCGCGTTGC
1 GATTTTAGTTTCGCGTTGC
*
11665 GATTTTCA-TTTCGCATTGC
1 GATTTT-AGTTTCGCGTTGC
*
11684 GATTCTA---T--CGTTGC
1 GATTTTAGTTTCGCGTTGC
* *
11698 GATTTTCA-TTTCTCGTTAC
1 GATTTT-AGTTTCGCGTTGC
11717 GATTTTCA-TTTCGCGTTGC
1 GATTTT-AGTTTCGCGTTGC
* * * *
11736 GATAGTCATTTTTCACGTTGC
1 GAT-TTTA-GTTTCGCGTTGC
*
11757 GATTTTAAGTTTCGTGTTGC
1 GATTTT-AGTTTCGCGTTGC
11777 GA
1 GA
11779 AAGTAAACTA
Statistics
Matches: 105, Mismatches: 18, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
14 10 0.10
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 64 0.61
20 13 0.12
21 14 0.13
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.46
Consensus pattern (19 bp):
GATTTTAGTTTCGCGTTGC
Found at i:11702 original size:52 final size:52
Alignment explanation
Indices: 11640--11738 Score: 153
Period size: 52 Copynumber: 1.9 Consensus size: 52
11630 TATAGTTTCG
** *
11640 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTAT
1 CGTTGCGATTTTCATTTCGCGTTACGATTTTCATTTCGCATTGCGATTCTAT
* *
11692 CGTTGCGATTTTCATTTCTCGTTACGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTACGATTTTCATTTCGCATTGCGAT
11739 AGTCATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.46
Consensus pattern (52 bp):
CGTTGCGATTTTCATTTCGCGTTACGATTTTCATTTCGCATTGCGATTCTAT
Found at i:11745 original size:38 final size:40
Alignment explanation
Indices: 11692--11778 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
11682 GCGATTCTAT
** * *
11692 CGTTGCGATTTTCA-TTTCTCGTTACGATTTTCA-TTTCG
1 CGTTGCGATAGTCATTTTCACGTTACGATTTTAAGTTTCG
*
11730 CGTTGCGATAGTCATTTTTCACGTTGCGATTTTAAGTTTCG
1 CGTTGCGATAGTCA-TTTTCACGTTACGATTTTAAGTTTCG
*
11771 TGTTGCGA
1 CGTTGCGA
11779 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
38 12 0.30
40 16 0.40
41 12 0.30
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTTCACGTTACGATTTTAAGTTTCG
Found at i:12051 original size:94 final size:92
Alignment explanation
Indices: 11887--12080 Score: 316
Period size: 94 Copynumber: 2.1 Consensus size: 92
11877 AAGAATACAC
* * *
11887 AATTTAGTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGAGTTAAAGAATACACAG
1 AATTTACTTCAACCAAAAGACAAAACAAAGACAAATACTACTTCACAGAGTTAAAGAATAAACAG
11952 TTTAGCAGAATGGGCAGCAACCGAATA
66 TTTAGCAGAATGGGCAGCAACCGAATA
*
11979 AATTTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAAC
1 AATTTACTTCAACCAAAAGACAAAAC-AAAGACAAATACT-ACTTCACAGAGTTAAAGAATAAAC
* *
12044 AGTTTAGCAGTATTGGCAGCAACCGAATA
64 AGTTTAGCAGAATGGGCAGCAACCGAATA
12073 AATTTACT
1 AATTTACT
12081 AAGCAATCTA
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
92 25 0.27
93 13 0.14
94 56 0.60
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (92 bp):
AATTTACTTCAACCAAAAGACAAAACAAAGACAAATACTACTTCACAGAGTTAAAGAATAAACAG
TTTAGCAGAATGGGCAGCAACCGAATA
Found at i:14189 original size:22 final size:20
Alignment explanation
Indices: 14110--14226 Score: 103
Period size: 20 Copynumber: 5.7 Consensus size: 20
14100 CTTTAAAAAT
14110 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
14130 CGCGTTGTGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
14150 TGTCATTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
14171 CGCGTTGCGATTTTTACGGATA
1 CGCGTTGCGA--TTTACGGATA
* * * *
14193 CTCGTTGCGATAGTAAGAAT-
1 CGCGTTGCGAT-TTACGGATA
14213 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
14227 TATGTTTGCG
Statistics
Matches: 77, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
19 2 0.03
20 36 0.47
21 20 0.26
22 19 0.25
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:14201 original size:42 final size:42
Alignment explanation
Indices: 14112--14225 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 42
14102 TTAAAAATCG
* * **
14112 CGTTGCGATTTACGGATACGCGTTGTGA-TTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTTACGGATACT
*
14153 CATTGCGATTTACGGATACGCGTTGCGATTTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTTACGGATACT
* * *
14195 CGTTGCGATAGTAAGAAT-CGCGTTGCGATTT
1 CGTTGCGAT-TTACGGATACGCGTTGCGATTT
14226 ATATGTTTGC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 26 0.42
42 31 0.50
43 5 0.08
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (42 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTTACGGATACT
Found at i:14257 original size:20 final size:20
Alignment explanation
Indices: 14212--14261 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
14202 ATAGTAAGAA
*
14212 TCGCGTTGCGATTTATATGT
1 TCGCGTTGCGATTTATATAT
*
14232 TTGCGTTGCGATTT-TCATAT
1 TCGCGTTGCGATTTAT-ATAT
14252 TCGCGTTGCG
1 TCGCGTTGCG
14262 GTTATGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.12, C:0.18, G:0.26, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTATATAT
Found at i:14784 original size:29 final size:29
Alignment explanation
Indices: 14742--14857 Score: 196
Period size: 29 Copynumber: 4.0 Consensus size: 29
14732 GTTCCGGGGG
14742 TAGGTCGCCATGCACGCCCGGCGACCTAC
1 TAGGTCGCCATGCACGCCCGGCGACCTAC
14771 TAGGTCGCCATGCACGCCCGGCGACCTAC
1 TAGGTCGCCATGCACGCCCGGCGACCTAC
**
14800 TAGGTCGCCATGCACGCCCGGCGACCTGG
1 TAGGTCGCCATGCACGCCCGGCGACCTAC
* *
14829 TAGGTCGCCATGCATGCCCTGCGACCTAC
1 TAGGTCGCCATGCACGCCCGGCGACCTAC
14858 CAGCACCTCC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.16, C:0.40, G:0.28, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCGGCGACCTAC
Found at i:14873 original size:10 final size:10
Alignment explanation
Indices: 14866--14984 Score: 102
Period size: 10 Copynumber: 11.3 Consensus size: 10
14856 ACCAGCACCT
14866 CCATGCACGC
1 CCATGCACGC
14876 CCATGCACGC
1 CCATGCACGC
*
14886 CCA-ACGAC-C
1 CCATGC-ACGC
14895 TCCATGCACGC
1 -CCATGCACGC
14906 CCATGCACGACC
1 CCATGCACG--C
14918 TCCATGCACGC
1 -CCATGCACGC
14929 CCAATG-AC-C
1 CC-ATGCACGC
14938 TCCATGCACGC
1 -CCATGCACGC
14949 CCATGCACGACC
1 CCATGCACG--C
14961 TCCATGCACGC
1 -CCATGCACGC
*
14972 CCAGGCACGC
1 CCATGCACGC
14982 CCA
1 CCA
14985 ACGACCTCCA
Statistics
Matches: 92, Mismatches: 3, Indels: 28
0.75 0.02 0.23
Matches are distributed among these distances:
9 6 0.07
10 58 0.63
11 8 0.09
12 2 0.02
13 18 0.20
ACGTcount: A:0.23, C:0.49, G:0.18, T:0.11
Consensus pattern (10 bp):
CCATGCACGC
Found at i:14919 original size:23 final size:22
Alignment explanation
Indices: 14876--14980 Score: 146
Period size: 23 Copynumber: 4.8 Consensus size: 22
14866 CCATGCACGC
14876 CCATGCACGCCCA--ACGACCT
1 CCATGCACGCCCAGCACGACCT
14896 CCATGCACGCCCATGCACGACCT
1 CCATGCACGCCCA-GCACGACCT
*
14919 CCATGCACGCCCA--ATGACCT
1 CCATGCACGCCCAGCACGACCT
14939 CCATGCACGCCCATGCACGACCT
1 CCATGCACGCCCA-GCACGACCT
14962 CCATGCACGCCCAGGCACG
1 CCATGCACGCCCA-GCACG
14981 CCCAACGACC
Statistics
Matches: 76, Mismatches: 3, Indels: 9
0.86 0.03 0.10
Matches are distributed among these distances:
20 32 0.42
23 44 0.58
ACGTcount: A:0.23, C:0.48, G:0.18, T:0.11
Consensus pattern (22 bp):
CCATGCACGCCCAGCACGACCT
Found at i:14925 original size:53 final size:53
Alignment explanation
Indices: 14862--15004 Score: 198
Period size: 43 Copynumber: 2.9 Consensus size: 53
14852 ACCTACCAGC
14862 ACCTCCATGCACGCCCATGCACGCCCAACGACCTCCATGCACGCCCATGCACG
1 ACCTCCATGCACGCCCATGCACGCCCAACGACCTCCATGCACGCCCATGCACG
*
14915 A---CC-T------CCATGCACGCCCAATGACCTCCATGCACGCCCATGCACG
1 ACCTCCATGCACGCCCATGCACGCCCAACGACCTCCATGCACGCCCATGCACG
*
14958 ACCTCCATGCACGCCCAGGCACGCCCAACGACCTCCATGCACGCCCA
1 ACCTCCATGCACGCCCATGCACGCCCAACGACCTCCATGCACGCCCA
15005 GCTCGCCAAA
Statistics
Matches: 77, Mismatches: 3, Indels: 20
0.77 0.03 0.20
Matches are distributed among these distances:
43 39 0.51
46 2 0.03
47 1 0.01
49 1 0.01
50 2 0.03
53 32 0.42
ACGTcount: A:0.23, C:0.49, G:0.17, T:0.11
Consensus pattern (53 bp):
ACCTCCATGCACGCCCATGCACGCCCAACGACCTCCATGCACGCCCATGCACG
Found at i:15666 original size:21 final size:21
Alignment explanation
Indices: 15641--15684 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
15631 AATTTAGTTA
15641 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
15662 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
15683 AT
1 AT
15685 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:18795 original size:11 final size:11
Alignment explanation
Indices: 18760--19688 Score: 165
Period size: 11 Copynumber: 77.5 Consensus size: 11
18750 ATTTCTATGT
* *
18760 ATTTATTAATC
1 ATTTAATAATG
*
18771 ATTATAAAAATG
1 ATT-TAATAATG
18783 ATTTAATAATG
1 ATTTAATAATG
*
18794 ATTTAAATAAATA
1 ATTT-AAT-AATG
*
18807 ATGATT--TGATG
1 AT--TTAATAATG
*
18818 ATTTAGTAATG
1 ATTTAATAATG
*
18829 ATTTGATAATAATC
1 A-TT--TAATAATG
18843 ATTATAATAATG
1 ATT-TAATAATG
*
18855 ATTTTATAATAATT
1 A--TT-TAATAATG
* * *
18869 ATTTAGTTATT
1 ATTTAATAATG
* *
18880 ATTTAGTAATT
1 ATTTAATAATG
18891 ATTTATAATAATG
1 A-TT-TAATAATG
18904 ATTTAATACTAATG
1 ATTT-A-A-TAATG
18918 ATTTAAT-A--
1 ATTTAATAATG
*
18926 ATTTAGTAATG
1 ATTTAATAATG
18937 ATTTAATACTAATG
1 ATTT-A-A-TAATG
*
18951 ATTTCAT-A--
1 ATTTAATAATG
* *
18959 ATTTAGTGATG
1 ATTTAATAATG
18970 ATTTAATACTAATG
1 ATTT-A-A-TAATG
18984 ATTTAATAATG
1 ATTTAATAATG
*
18995 ATTTGTTACTAATG
1 A--T-TTAATAATG
19009 ATTTAATAATG
1 ATTTAATAATG
19020 ATTT-A-AAT-
1 ATTTAATAATG
19028 ATTTAATGATTTGATG
1 ATTTAAT-A----ATG
*
19044 ATTTAGTAATG
1 ATTTAATAATG
*
19055 ATTTGATAATAAG
1 ATTTAATAAT--G
19068 CATTATAATAATG
1 -ATT-TAATAATG
*
19081 ATTTTATAATAATT
1 A--TT-TAATAATG
* * *
19095 ATTTAGTTATT
1 ATTTAATAATG
* *
19106 ATTTAGTAATT
1 ATTTAATAATG
19117 ATTTATAATAATG
1 A-TT-TAATAATG
19130 ATTTAATACTAATG
1 ATTT-A-A-TAATG
19144 ATTTAAT-A--
1 ATTTAATAATG
*
19152 ATTTAGTAATG
1 ATTTAATAATG
19163 ATTTAATACTAATG
1 ATTT-A-A-TAATG
19177 ATTTAAT-A--
1 ATTTAATAATG
* *
19185 ATTTAGTGATG
1 ATTTAATAATG
19196 ATTTAATACTAATG
1 ATTT-A-A-TAATG
19210 ATTTAATACTAATG
1 ATTT-A-A-TAATG
19224 ATTTAATAATG
1 ATTTAATAATG
19235 ATTT-A-AAT-
1 ATTTAATAATG
19243 ATTTAATGATTTGATG
1 ATTTAAT-A----ATG
*
19259 ATTTAGTAATG
1 ATTTAATAATG
*
19270 ATTTGATAATAATC
1 A-TT--TAATAATG
*
19284 ATTATAGTAATG
1 ATT-TAATAATG
*
19296 ATTTGATAATAATC
1 A-TT--TAATAATG
*
19310 ATTATAGTAATG
1 ATT-TAATAATG
*
19322 ATTTGATAATAATC
1 A-TT--TAATAATG
*
19336 ATTATAAAAATG
1 ATT-TAATAATG
*
19348 ATTTAGTAATAATC
1 A-TT--TAATAATG
*
19362 ATTATAAAAATG
1 ATT-TAATAATG
19374 ATTTAATAATG
1 ATTTAATAATG
19385 ATTT-A-AAT-
1 ATTTAATAATG
19393 ATTTAATGATTTGATG
1 ATTTAAT-A----ATG
*
19409 ATTTAGTAATG
1 ATTTAATAATG
*
19420 ATTTGATAATAATT
1 A-TT--TAATAATG
19434 ATTATAATAATG
1 ATT-TAATAATG
*
19446 ATTTTATAATAATT
1 A--TT-TAATAATG
* * *
19460 ATTTAGTTATT
1 ATTTAATAATG
* *
19471 ATTTAGTAATT
1 ATTTAATAATG
19482 ATTTATAATAATG
1 A-TT-TAATAATG
19495 ATTTAATACTAATG
1 ATTT-A-A-TAATG
*
19509 ATTTGATAATG
1 ATTTAATAATG
19520 ATTT-A-AAT-
1 ATTTAATAATG
*
19528 ATTTAATGAT-
1 ATTTAATAATG
*
19538 -TTGATAATAATT
1 ATT--TAATAATG
19550 ATTATAATAATG
1 ATT-TAATAATG
*
19562 ATTTTATAATAATT
1 A--TT-TAATAATG
* * *
19576 ATTTAGTTATT
1 ATTTAATAATG
* *
19587 ATTTAGTAATT
1 ATTTAATAATG
19598 ATTTATAATAATG
1 A-TT-TAATAATG
19611 ATTTAATACTAATG
1 ATTT-A-A-TAATG
*
19625 ATTTCAT-A--
1 ATTTAATAATG
*
19633 ATTTAGTAATG
1 ATTTAATAATG
19644 ATTTAATACTAATG
1 ATTT-A-A-TAATG
19658 ATTTAATAATAATG
1 A-TT--TAATAATG
19672 ATTTAATAATG
1 ATTTAATAATG
19683 ATTTAA
1 ATTTAA
19689 ATATTTAATG
Statistics
Matches: 713, Mismatches: 85, Indels: 240
0.69 0.08 0.23
Matches are distributed among these distances:
8 44 0.06
9 25 0.04
10 11 0.02
11 209 0.29
12 121 0.17
13 67 0.09
14 196 0.27
15 20 0.03
16 19 0.03
17 1 0.00
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (11 bp):
ATTTAATAATG
Found at i:18841 original size:14 final size:14
Alignment explanation
Indices: 18824--19711 Score: 300
Period size: 14 Copynumber: 64.3 Consensus size: 14
18814 GATGATTTAG
*
18824 TAATGATTTGATAA
1 TAATGATTTAATAA
*
18838 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
18850 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
18864 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
18876 T-ATTATTTAGTAA
1 TAATGATTTAATAA
18889 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
18899 TAATGATTTAATAC
1 TAATGATTTAATAA
18913 TAATGATTTAATAATTTA
1 TAATGATTTAAT-A---A
*
18931 GTAATGATTTAATAC
1 -TAATGATTTAATAA
*
18946 TAATGATTTCATAA
1 TAATGATTTAATAA
*
18960 TTTAGTGATGATTTAATAC
1 --TA---ATGATTTAATAA
18979 TAATGA-TT--TAA
1 TAATGATTTAATAA
** *
18990 TAATGATTTGTTAC
1 TAATGATTTAATAA
19004 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
19015 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
19031 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
19050 TAATGATTTGATAA
1 TAATGATTTAATAA
19064 TAA-GCA-TT-ATAA
1 TAATG-ATTTAATAA
*
19076 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
19090 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
19102 T-ATTATTTAGTAA
1 TAATGATTTAATAA
19115 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
19125 TAATGATTTAATAC
1 TAATGATTTAATAA
19139 TAATGATTTAATAATTTA
1 TAATGATTTAAT-A---A
*
19157 GTAATGATTTAATAC
1 -TAATGATTTAATAA
19172 TAATGATTTAATAA
1 TAATGATTTAATAA
*
19186 TTTAGTGATGATTTAATAC
1 --TA---ATGATTTAATAA
*
19205 TAATGATTTAATAC
1 TAATGATTTAATAA
19219 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
19230 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
19246 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
19265 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
19279 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
19291 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
19305 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
19317 TAATGATTTGATAA
1 TAATGATTTAATAA
*
19331 TAATCA-TT-ATAA
1 TAATGATTTAATAA
* *
19343 AAATGATTTAGTAA
1 TAATGATTTAATAA
*
19357 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
19369 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
19380 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
19396 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
19415 TAATGATTTGATAA
1 TAATGATTTAATAA
*
19429 TAATTA-TT-ATAA
1 TAATGATTTAATAA
*
19441 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
19455 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
19467 T-ATTATTTAGTAA
1 TAATGATTTAATAA
19480 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
19490 TAATGATTTAATAC
1 TAATGATTTAATAA
*
19504 TAATGA-TT--TGA
1 TAATGATTTAATAA
*
19515 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
19531 TAATGATTTGATAA
1 TAATGATTTAATAA
*
19545 TAATTA-TT-ATAA
1 TAATGATTTAATAA
*
19557 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
19571 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
19583 T-ATTATTTAGTAA
1 TAATGATTTAATAA
19596 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
19606 TAATGATTTAATAC
1 TAATGATTTAATAA
*
19620 TAATGATTTCATAATTTAG
1 TAATGA-TT--TAA--TAA
*
19639 TAATGATTTAATAC
1 TAATGATTTAATAA
19653 TAATGATTTAATAA
1 TAATGATTTAATAA
19667 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
19678 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
19694 TAATGATTTAATAC
1 TAATGATTTAATAA
19708 TAAT
1 TAAT
19712 AATAATGATT
Statistics
Matches: 685, Mismatches: 84, Indels: 210
0.70 0.09 0.21
Matches are distributed among these distances:
10 16 0.02
11 104 0.15
12 92 0.13
13 62 0.09
14 233 0.34
15 20 0.03
16 58 0.08
17 7 0.01
18 7 0.01
19 80 0.12
20 6 0.01
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:18937 original size:19 final size:19
Alignment explanation
Indices: 18913--18977 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
18903 GATTTAATAC
18913 TAATGATTTAATAATTTAG
1 TAATGATTTAATAATTTAG
*
18932 TAATGA-TT--TAA--TAC
1 TAATGATTTAATAATTTAG
*
18946 TAATGATTTCATAATTTAG
1 TAATGATTTAATAATTTAG
*
18965 TGATGATTTAATA
1 TAATGATTTAATA
18978 CTAATGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 8 0.22
15 2 0.05
16 3 0.08
17 3 0.08
18 2 0.05
19 19 0.51
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (19 bp):
TAATGATTTAATAATTTAG
Found at i:18949 original size:25 final size:25
Alignment explanation
Indices: 18921--19025 Score: 84
Period size: 25 Copynumber: 3.9 Consensus size: 25
18911 ACTAATGATT
*
18921 TAATAATTTAGTAATGATTTAATAC
1 TAATAATTTAATAATGATTTAATAC
*
18946 TAATGATTTCATAATTTAGTGATGATTTAATAC
1 TAAT-AATT--TAA--TA---ATGATTTAATAC
* **
18979 TAATGATTTAATAATGATTTGTTAC
1 TAATAATTTAATAATGATTTAATAC
*
19004 TAATGATTTAATAATGATTTAA
1 TAATAATTTAATAATGATTTAA
19026 ATATTTAATG
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
25 34 0.53
26 3 0.05
28 4 0.06
30 5 0.08
32 2 0.03
33 16 0.25
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (25 bp):
TAATAATTTAATAATGATTTAATAC
Found at i:19163 original size:19 final size:19
Alignment explanation
Indices: 19139--19203 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
19129 GATTTAATAC
19139 TAATGATTTAATAATTTAG
1 TAATGATTTAATAATTTAG
*
19158 TAATGA-TT--TAA--TAC
1 TAATGATTTAATAATTTAG
19172 TAATGATTTAATAATTTAG
1 TAATGATTTAATAATTTAG
*
19191 TGATGATTTAATA
1 TAATGATTTAATA
19204 CTAATGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 8 0.21
15 2 0.05
16 3 0.08
17 3 0.08
18 2 0.05
19 20 0.53
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.46
Consensus pattern (19 bp):
TAATGATTTAATAATTTAG
Found at i:19173 original size:226 final size:225
Alignment explanation
Indices: 18779--19688 Score: 956
Period size: 226 Copynumber: 4.0 Consensus size: 225
18769 TCATTATAAA
** *
18779 AATGATTTAATAATGATTTAAATAAATAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
1 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAAGCA
*
18844 TTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTTA
66 TTATAATAATGATTTGATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTTA
* *
18909 ATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCATAATTTAGTGATGATTT
131 ATACTAATGATTTAATAATTTAATAATGATTTAATACTAATGATTTCATAATTTAGTAATGATTT
18974 AATACTAATGATTTAATAATGATTTGTTACT
196 AATACTAATGATTTAATAATGATTT-TTACT
19005 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAAGCA
1 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAAGCA
*
19070 TTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTTA
66 TTATAATAATGATTTGATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTTA
* * *
19135 ATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTAATAATTTAGTGATGATTT
131 ATACTAATGATTTAATAATTTAATAATGATTTAATACTAATGATTTCATAATTTAGTAATGATTT
19200 AATACTAATGA-TT--T-A--A----TACT
196 AATACTAATGATTTAATAATGATTTTTACT
*
19220 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
1 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAAGCA
* * * * * *
19285 TTATAGTAATGATTTGATAATAATCATTATAGTAATGATTT-GATAATAATCATTATAAAAATGA
66 TTATAATAATGATTTGATAATAATTATT-TAGTTATTATTTAG-TAATTAT--TTATAATAATGA
* * * * * * *
19349 TTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTA
127 TTTAATACTAATGATT-T---AATAATTTAATAATGATTT-AATA-CTAATGATTTCATAATTTA
* * * *
19414 GTAATGATTTGATAATAATTATTATAATAATGATTTTATAAT
186 GTAATGATTTAATACTAATGATT-TAATAATGATTTT-TACT
* * * * * * *
19456 AATTATTTAGTTATTATTTAGTAATTATTT-AT-A-ATAATGATTTAATACTAATGATTTGATAA
1 AATGATTTAATAATGATTTA--AA-TATTTAATGATTTGATGA-TT--TAGTAATGATTTGATAA
* * *
19518 T--G-ATTTAAATATTTAATGATTTGATAATAATTA-TTA--TA--A--TAATGA-T-TTTATAA
60 TAAGCA-TT--ATA-ATAATGATTTGATAATAATTATTTAGTTATTATTTAGTAATTATTTATAA
* * * * * * *
19571 TAATTATTTAGTTATTATTTA-GTAATTATTTATAATAATGATTTAATACTAATGATTTCATAAT
121 TAATGATTTA-ATACTAATGATTTAA-TAATT-TAATAATGATTTAATACTAATGATTTCATAAT
* * *
19635 TTAGTAATGATTTAATACTAATGATTTAATAATAATGATTTAAT
183 TTAGTAATGATTTAATACTAATGATTTAATAATGAT-TTTTACT
19679 AATGATTTAA
1 AATGATTTAA
19689 ATATTTAATG
Statistics
Matches: 589, Mismatches: 58, Indels: 77
0.81 0.08 0.11
Matches are distributed among these distances:
215 94 0.16
216 16 0.03
218 24 0.04
219 1 0.00
220 1 0.00
222 18 0.03
223 26 0.04
224 73 0.12
225 10 0.02
226 215 0.37
227 1 0.00
228 15 0.03
229 7 0.01
230 1 0.00
231 1 0.00
232 3 0.01
234 1 0.00
236 26 0.04
237 5 0.01
238 6 0.01
239 26 0.04
240 19 0.03
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (225 bp):
AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAAGCA
TTATAATAATGATTTGATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTTA
ATACTAATGATTTAATAATTTAATAATGATTTAATACTAATGATTTCATAATTTAGTAATGATTT
AATACTAATGATTTAATAATGATTTTTACT
Found at i:19291 original size:26 final size:26
Alignment explanation
Indices: 19262--19466 Score: 196
Period size: 26 Copynumber: 8.2 Consensus size: 26
19252 TTTGATGATT
19262 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
19288 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
19314 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
**
19340 TAAAAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
19366 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
19388 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
*
19412 TAGTAATGATTTGATAATAATTATTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
19438 TAATAATGATTTTATAATAATTATT-
1 TAGTAATGATTTGATAATAATCATTA
19463 TAGT
1 TAGT
19467 TATTATTTAG
Statistics
Matches: 157, Mismatches: 12, Indels: 21
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.01
20 5 0.03
22 3 0.02
23 11 0.07
24 9 0.06
25 12 0.08
26 110 0.70
27 6 0.04
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:19322 original size:52 final size:49
Alignment explanation
Indices: 19259--19528 Score: 216
Period size: 52 Copynumber: 5.4 Consensus size: 49
19249 TGATTTGATG
* *
19259 ATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATC
1 ATTTAGTAATGATTT-ATAATAAT-ATTATAATAATGATTTAATAATAATC
* *
19310 ATTATAGTAATGATTTGATAATAATCATTATAAAAATGATTTAGTAATAATC
1 ATT-TAGTAATGATTT-ATAATAAT-ATTATAATAATGATTTAATAATAATC
** * * *
19362 ATTATAAAAATGA-TT-TAATAATGATT-T-A-AAT-ATTTAATGATTTGATG
1 ATT-TAGTAATGATTTATAATAAT-ATTATAATAATGATTTAAT-A-ATAATC
* *
19409 ATTTAGTAATGATTTGATAATAATTATTATAATAATGATTTTATAATAATT
1 ATTTAGTAATGATTT-ATAATAA-TATTATAATAATGATTTAATAATAATC
* * * * *
19460 ATTTAGTTATTATTTAGTAATTAT-TTATAATAATGATTTAATACTAATG
1 ATTTAGTAATGATTTA-TAATAATATTATAATAATGATTTAATAATAATC
19509 ATTT-GATAATGATTTA-AATA
1 ATTTAG-TAATGATTTATAATA
19529 TTTAATGATT
Statistics
Matches: 180, Mismatches: 26, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
45 6 0.03
46 11 0.06
47 12 0.07
48 2 0.01
49 53 0.29
50 4 0.02
51 27 0.15
52 59 0.33
53 6 0.03
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.46
Consensus pattern (49 bp):
ATTTAGTAATGATTTATAATAATATTATAATAATGATTTAATAATAATC
Found at i:19675 original size:47 final size:46
Alignment explanation
Indices: 18844--19186 Score: 159
Period size: 46 Copynumber: 7.5 Consensus size: 46
18834 ATAATAATCA
* * * *
18844 TTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTAT
1 TTATAATAATGATTTAATAATAATGATTTA---ATAATTTAGTAATGAT
*
18893 TTATAATAATGATTTAATACTAATGATTTAATAATTTAGTAATGAT
1 TTATAATAATGATTTAATAATAATGATTTAATAATTTAGTAATGAT
* * * *
18939 TTAATACTAATGATTTCATAATTTAGTGATGATT--TAA--TACTAATGA-
1 TT-ATAATAATGATTTAATAA--TAATGAT--TTAATAATTTAGTAATGAT
** *
18985 TT-TAATAATGATTTGTTACTAATGATTTAATAATGATT--TAAAT-AT
1 TTATAATAATGATTTAATAATAATGATTTAATAAT--TTAGT-AATGAT
* * * *
19030 TTAATGAT-TTGATGATT--TAGTAATGATTTGAT-A---A-TAA-GCA-
1 TT-ATAATAATGAT--TTAATAATAATGATTTAATAATTTAGTAATG-AT
* * * * *
19070 TTATAATAATGATTTTATAATAATTATTTAGTT-ATTATTTAGTAATTAT
1 TTATAATAATGA--TT-TAATAA-TAATGATTTAATAATTTAGTAATGAT
*
19119 TTATAATAATGATTTAATACTAATGATTTAATAATTTAGTAATGAT
1 TTATAATAATGATTTAATAATAATGATTTAATAATTTAGTAATGAT
*
19165 TTAATACTAATGATTTAATAAT
1 TT-ATAATAATGATTTAATAAT
19187 TTAGTGATGA
Statistics
Matches: 224, Mismatches: 34, Indels: 74
0.67 0.10 0.22
Matches are distributed among these distances:
39 4 0.02
40 10 0.04
41 3 0.01
42 10 0.04
43 4 0.02
44 22 0.10
45 12 0.05
46 57 0.25
47 46 0.21
48 6 0.03
49 48 0.21
51 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (46 bp):
TTATAATAATGATTTAATAATAATGATTTAATAATTTAGTAATGAT
Found at i:19697 original size:47 final size:47
Alignment explanation
Indices: 19406--19534 Score: 89
Period size: 49 Copynumber: 2.6 Consensus size: 47
19396 TAATGATTTG
* * * * *
19406 ATGATTTAGTAATGATTTGATAATAATTATTATAATAATGATTTTATAATA
1 ATGATTTAATAATGATTT-A-AAT-ATT-TAATACTAATGATTTAATACTA
* * * * *
19457 ATTATTTAGTTATTATTTAGTAATTATTT-ATAATAATGATTTAATACTA
1 ATGATTTAATAATGATTTA--AA-TATTTAATACTAATGATTTAATACTA
*
19506 ATGATTTGATAATGATTTAAATATTTAAT
1 ATGATTTAATAATGATTTAAATATTTAAT
19535 GATTTGATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
46 5 0.08
47 4 0.06
49 32 0.49
50 2 0.03
51 21 0.32
52 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.50
Consensus pattern (47 bp):
ATGATTTAATAATGATTTAAATATTTAATACTAATGATTTAATACTA
Found at i:19719 original size:20 final size:20
Alignment explanation
Indices: 19675--19730 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
19665 AATAATGATT
19675 TAATAATGATTTAA-A-T-A
1 TAATAATGATTTAATACTAA
*
19692 T-TTAATGATTTAATACTAA
1 TAATAATGATTTAATACTAA
*
19711 TAATAATGATTTGATACTAA
1 TAATAATGATTTAATACTAA
19731 AAATCATTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 11 0.34
17 2 0.06
18 1 0.03
19 2 0.06
20 16 0.50
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (20 bp):
TAATAATGATTTAATACTAA
Found at i:21818 original size:15 final size:14
Alignment explanation
Indices: 21793--21823 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
21783 TTCAACACAA
21793 AACTTTAATATAAT
1 AACTTTAATATAAT
21807 AACTTATAATATAAT
1 AACTT-TAATATAAT
21822 AA
1 AA
21824 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:21831 original size:16 final size:16
Alignment explanation
Indices: 21798--21844 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
21788 CACAAAACTT
*
21798 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
21813 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
21829 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
21845 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:21960 original size:32 final size:34
Alignment explanation
Indices: 21885--21966 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
21875 CCAAACCCTT
* *
21885 AAAC-AACTAATAAAATATTTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTCATATAACTA
21918 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTTCA-TATAACTA
*
21951 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
21967 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
32 11 0.25
33 8 0.18
34 20 0.45
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTTTTTCATATAACTA
Found at i:22095 original size:46 final size:49
Alignment explanation
Indices: 22003--22103 Score: 140
Period size: 45 Copynumber: 2.1 Consensus size: 49
21993 TCAACAAACA
22003 AATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
1 AATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
*
22052 AATATAAC-TAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTTT
1 AATATAACTTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTTT
22097 AACTATA
1 AA-TATA
22104 TAACTATCAA
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
45 15 0.31
46 15 0.31
47 5 0.10
48 6 0.12
49 8 0.16
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.40
Consensus pattern (49 bp):
AATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
Found at i:22230 original size:16 final size:18
Alignment explanation
Indices: 22201--22239 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
22191 ACTAATTAAC
*
22201 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
22219 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
22235 ATTTA
1 ATTTA
22240 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:22592 original size:29 final size:29
Alignment explanation
Indices: 22550--22641 Score: 148
Period size: 29 Copynumber: 3.2 Consensus size: 29
22540 GTGACGCCGG
*
22550 GGCGACCTACAAGGTCGCTGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
22579 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
** *
22608 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
22637 GGCGA
1 GGCGA
22642 TGTAACCCCC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.24, C:0.30, G:0.32, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:23217 original size:2 final size:2
Alignment explanation
Indices: 23210--23236 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23200 TTTTTAAAAC
23210 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 A
23237 CCCCCATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23428 original size:24 final size:24
Alignment explanation
Indices: 23401--23500 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
23391 GATATCAAAA
*
23401 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
23425 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
23449 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
23473 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
23497 ATCA
1 ATCA
23501 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:23500 original size:48 final size:48
Alignment explanation
Indices: 23394--23502 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
23384 AAACGGAGAT
* * * * *
23394 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
23442 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
23490 ATCAGAAATCAGA
1 ATCAGAAATCAGA
23503 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:24651 original size:18 final size:18
Alignment explanation
Indices: 24630--24665 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24620 CTTCCATCCG
*
24630 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
24648 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
24666 GTCCTTTCGA
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:25970 original size:7 final size:7
Alignment explanation
Indices: 25958--25996 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
25948 GGTCAACGTG
25958 GGTCAAC
1 GGTCAAC
25965 GGTCAAC
1 GGTCAAC
25972 TGGTCAAC
1 -GGTCAAC
25980 GGTCAAC
1 GGTCAAC
25987 GGGTCAAC
1 -GGTCAAC
25995 GG
1 GG
25997 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.15
Consensus pattern (7 bp):
GGTCAAC
Found at i:25978 original size:15 final size:15
Alignment explanation
Indices: 25948--25996 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
25938 GGTCAACAGT
25948 GGTCAACGTGGGTCAAC
1 GGTCAAC-T-GGTCAAC
25965 GGTCAACTGGTCAAC
1 GGTCAACTGGTCAAC
*
25980 GGTCAACGGGTCAAC
1 GGTCAACTGGTCAAC
25995 GG
1 GG
25997 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 23 0.74
16 1 0.03
17 7 0.23
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.16
Consensus pattern (15 bp):
GGTCAACTGGTCAAC
Found at i:26004 original size:13 final size:13
Alignment explanation
Indices: 25986--26061 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
25976 CAACGGTCAA
25986 CGGGTCAACGGGT
1 CGGGTCAACGGGT
25999 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
26017 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
26030 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
26043 CGGGTAAACGGGT
1 CGGGTCAACGGGT
26056 CGGGTC
1 CGGGTC
26062 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.14, C:0.22, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:26010 original size:8 final size:8
Alignment explanation
Indices: 25938--26012 Score: 70
Period size: 8 Copynumber: 9.5 Consensus size: 8
25928 TCAAAGTTTT
25938 GGTCAACAG
1 GGTCAAC-G
25947 TGGTCAACGTG
1 -GGTCAAC--G
25958 GGTCAAC-
1 GGTCAACG
*
25965 GGTCAACT
1 GGTCAACG
25973 GGTCAAC-
1 GGTCAACG
25980 GGTCAACG
1 GGTCAACG
25988 GGTCAACG
1 GGTCAACG
25996 GGT---CG
1 GGTCAACG
26001 GGTCAACG
1 GGTCAACG
26009 GGTC
1 GGTC
26013 GGGTCGGGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
5 5 0.09
7 14 0.24
8 24 0.41
10 14 0.24
11 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.36, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:26017 original size:18 final size:18
Alignment explanation
Indices: 25980--26035 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
25970 ACTGGTCAAC
25980 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
26001 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
26019 GGTCAACTGGTCGGGTC
1 GGTCAACGGGTCGGGTC
26036 AACTGGTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 23 0.68
21 11 0.32
ACGTcount: A:0.14, C:0.23, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:26024 original size:31 final size:31
Alignment explanation
Indices: 25986--26047 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
25976 CAACGGTCAA
25986 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
* *
26017 CGGGTCAACTGGTCGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
26048 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
Found at i:28023 original size:2 final size:2
Alignment explanation
Indices: 28016--28050 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28006 TTTTTAAAAC
28016 AT AT 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 AT AT A
28051 CCCCCATCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28243 original size:24 final size:24
Alignment explanation
Indices: 28216--28315 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
28206 GATATCAAAA
*
28216 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
28240 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
28264 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
28288 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
28312 ATCA
1 ATCA
28316 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:28315 original size:48 final size:48
Alignment explanation
Indices: 28209--28317 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
28199 AAACGGAGAT
* * * * *
28209 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
28257 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
28305 ATCAGAAATCAGA
1 ATCAGAAATCAGA
28318 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:29466 original size:18 final size:18
Alignment explanation
Indices: 29445--29480 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29435 CTTCCATCCG
*
29445 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
29463 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
29481 GTCCTTTCGA
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:30785 original size:7 final size:7
Alignment explanation
Indices: 30773--30811 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
30763 GGTCAACGTG
30773 GGTCAAC
1 GGTCAAC
30780 GGTCAAC
1 GGTCAAC
30787 TGGTCAAC
1 -GGTCAAC
30795 GGTCAAC
1 GGTCAAC
30802 GGGTCAAC
1 -GGTCAAC
30810 GG
1 GG
30812 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.15
Consensus pattern (7 bp):
GGTCAAC
Found at i:30793 original size:15 final size:15
Alignment explanation
Indices: 30763--30811 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
30753 GGTCAACAGT
30763 GGTCAACGTGGGTCAAC
1 GGTCAAC-T-GGTCAAC
30780 GGTCAACTGGTCAAC
1 GGTCAACTGGTCAAC
*
30795 GGTCAACGGGTCAAC
1 GGTCAACTGGTCAAC
30810 GG
1 GG
30812 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 23 0.74
16 1 0.03
17 7 0.23
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.16
Consensus pattern (15 bp):
GGTCAACTGGTCAAC
Found at i:30819 original size:13 final size:13
Alignment explanation
Indices: 30801--30876 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
30791 CAACGGTCAA
30801 CGGGTCAACGGGT
1 CGGGTCAACGGGT
30814 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
30832 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
30845 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
30858 CGGGTAAACGGGT
1 CGGGTCAACGGGT
30871 CGGGTC
1 CGGGTC
30877 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.14, C:0.22, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:30825 original size:8 final size:8
Alignment explanation
Indices: 30753--30827 Score: 70
Period size: 8 Copynumber: 9.5 Consensus size: 8
30743 TCAAAGTTTT
30753 GGTCAACAG
1 GGTCAAC-G
30762 TGGTCAACGTG
1 -GGTCAAC--G
30773 GGTCAAC-
1 GGTCAACG
*
30780 GGTCAACT
1 GGTCAACG
30788 GGTCAAC-
1 GGTCAACG
30795 GGTCAACG
1 GGTCAACG
30803 GGTCAACG
1 GGTCAACG
30811 GGT---CG
1 GGTCAACG
30816 GGTCAACG
1 GGTCAACG
30824 GGTC
1 GGTC
30828 GGGTCGGGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
5 5 0.09
7 14 0.24
8 24 0.41
10 14 0.24
11 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.36, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:30832 original size:18 final size:18
Alignment explanation
Indices: 30795--30850 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
30785 ACTGGTCAAC
30795 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
30816 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
30834 GGTCAACTGGTCGGGTC
1 GGTCAACGGGTCGGGTC
30851 AACTGGTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 23 0.68
21 11 0.32
ACGTcount: A:0.14, C:0.23, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:30839 original size:31 final size:31
Alignment explanation
Indices: 30801--30862 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
30791 CAACGGTCAA
30801 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
* *
30832 CGGGTCAACTGGTCGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
30863 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
Found at i:32840 original size:2 final size:2
Alignment explanation
Indices: 32833--32865 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32823 TTTTTAAAAC
32833 AT 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 AT A
32866 CCCCCATCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33058 original size:24 final size:24
Alignment explanation
Indices: 33031--33130 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
33021 GATATCAAAA
*
33031 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
33055 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
33079 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
33103 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
33127 ATCA
1 ATCA
33131 GATAAATATT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:33130 original size:48 final size:48
Alignment explanation
Indices: 33024--33132 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
33014 AAACGGAGAT
* * * * *
33024 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
33072 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
33120 ATCAGAAATCAGA
1 ATCAGAAATCAGA
33133 TAAATATTCA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:34275 original size:18 final size:18
Alignment explanation
Indices: 34254--34289 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
34244 CTTCCATCCG
*
34254 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
34272 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
34290 GTCCTTTCGA
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:35593 original size:7 final size:7
Alignment explanation
Indices: 35581--35619 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
35571 GGTCAACGTG
35581 GGTCAAC
1 GGTCAAC
35588 GGTCAAC
1 GGTCAAC
35595 TGGTCAAC
1 -GGTCAAC
35603 GGTCAAC
1 GGTCAAC
35610 GGGTCAAC
1 -GGTCAAC
35618 GG
1 GG
35620 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.15
Consensus pattern (7 bp):
GGTCAAC
Found at i:35601 original size:15 final size:15
Alignment explanation
Indices: 35571--35619 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
35561 GGTCAACAGT
35571 GGTCAACGTGGGTCAAC
1 GGTCAAC-T-GGTCAAC
35588 GGTCAACTGGTCAAC
1 GGTCAACTGGTCAAC
*
35603 GGTCAACGGGTCAAC
1 GGTCAACTGGTCAAC
35618 GG
1 GG
35620 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 23 0.74
16 1 0.03
17 7 0.23
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.16
Consensus pattern (15 bp):
GGTCAACTGGTCAAC
Found at i:35627 original size:13 final size:13
Alignment explanation
Indices: 35609--35684 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
35599 CAACGGTCAA
35609 CGGGTCAACGGGT
1 CGGGTCAACGGGT
35622 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
35640 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
35653 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
35666 CGGGTAAACGGGT
1 CGGGTCAACGGGT
35679 CGGGTC
1 CGGGTC
35685 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.14, C:0.22, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:35633 original size:8 final size:8
Alignment explanation
Indices: 35561--35635 Score: 70
Period size: 8 Copynumber: 9.5 Consensus size: 8
35551 TCAAAGTTTT
35561 GGTCAACAG
1 GGTCAAC-G
35570 TGGTCAACGTG
1 -GGTCAAC--G
35581 GGTCAAC-
1 GGTCAACG
*
35588 GGTCAACT
1 GGTCAACG
35596 GGTCAAC-
1 GGTCAACG
35603 GGTCAACG
1 GGTCAACG
35611 GGTCAACG
1 GGTCAACG
35619 GGT---CG
1 GGTCAACG
35624 GGTCAACG
1 GGTCAACG
35632 GGTC
1 GGTC
35636 GGGTCGGGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
5 5 0.09
7 14 0.24
8 24 0.41
10 14 0.24
11 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.36, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:35640 original size:18 final size:18
Alignment explanation
Indices: 35603--35658 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
35593 ACTGGTCAAC
35603 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
35624 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
35642 GGTCAACTGGTCGGGTC
1 GGTCAACGGGTCGGGTC
35659 AACTGGTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 23 0.68
21 11 0.32
ACGTcount: A:0.14, C:0.23, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:35647 original size:31 final size:31
Alignment explanation
Indices: 35609--35670 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
35599 CAACGGTCAA
35609 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
* *
35640 CGGGTCAACTGGTCGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
35671 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
Found at i:37651 original size:2 final size:2
Alignment explanation
Indices: 37644--37674 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
37634 TTTTTAAAAC
37644 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
37675 CCCCCATCCC
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:37866 original size:24 final size:24
Alignment explanation
Indices: 37839--37938 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
37829 GATATCAAAA
*
37839 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
37863 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
37887 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
37911 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
37935 ATCA
1 ATCA
37939 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:37938 original size:48 final size:48
Alignment explanation
Indices: 37832--37940 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
37822 AAACGGAGAT
* * * * *
37832 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
37880 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
37928 ATCAGAAATCAGA
1 ATCAGAAATCAGA
37941 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:39087 original size:17 final size:18
Alignment explanation
Indices: 39065--39099 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39055 CTTCCATCCG
39065 ATCTTAT-ATTTAATTCA
1 ATCTTATCATTTAATTCA
*
39082 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
39100 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.51
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:40405 original size:7 final size:7
Alignment explanation
Indices: 40393--40431 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
40383 GGTCAACGTG
40393 GGTCAAC
1 GGTCAAC
40400 GGTCAAC
1 GGTCAAC
40407 TGGTCAAC
1 -GGTCAAC
40415 GGTCAAC
1 GGTCAAC
40422 GGGTCAAC
1 -GGTCAAC
40430 GG
1 GG
40432 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.15
Consensus pattern (7 bp):
GGTCAAC
Found at i:40413 original size:15 final size:15
Alignment explanation
Indices: 40383--40431 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
40373 GGTCAACAGT
40383 GGTCAACGTGGGTCAAC
1 GGTCAAC-T-GGTCAAC
40400 GGTCAACTGGTCAAC
1 GGTCAACTGGTCAAC
*
40415 GGTCAACGGGTCAAC
1 GGTCAACTGGTCAAC
40430 GG
1 GG
40432 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 23 0.74
16 1 0.03
17 7 0.23
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.16
Consensus pattern (15 bp):
GGTCAACTGGTCAAC
Found at i:40439 original size:13 final size:13
Alignment explanation
Indices: 40421--40496 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
40411 CAACGGTCAA
40421 CGGGTCAACGGGT
1 CGGGTCAACGGGT
40434 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
40452 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
40465 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
40478 CGGGTAAACGGGT
1 CGGGTCAACGGGT
40491 CGGGTC
1 CGGGTC
40497 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.14, C:0.22, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:40445 original size:8 final size:8
Alignment explanation
Indices: 40373--40447 Score: 70
Period size: 8 Copynumber: 9.5 Consensus size: 8
40363 TCAAAGTTTT
40373 GGTCAACAG
1 GGTCAAC-G
40382 TGGTCAACGTG
1 -GGTCAAC--G
40393 GGTCAAC-
1 GGTCAACG
*
40400 GGTCAACT
1 GGTCAACG
40408 GGTCAAC-
1 GGTCAACG
40415 GGTCAACG
1 GGTCAACG
40423 GGTCAACG
1 GGTCAACG
40431 GGT---CG
1 GGTCAACG
40436 GGTCAACG
1 GGTCAACG
40444 GGTC
1 GGTC
40448 GGGTCGGGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
5 5 0.09
7 14 0.24
8 24 0.41
10 14 0.24
11 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.36, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:40452 original size:18 final size:18
Alignment explanation
Indices: 40415--40470 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
40405 ACTGGTCAAC
40415 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
40436 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
40454 GGTCAACTGGTCGGGTC
1 GGTCAACGGGTCGGGTC
40471 AACTGGTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 23 0.68
21 11 0.32
ACGTcount: A:0.14, C:0.23, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:40459 original size:31 final size:31
Alignment explanation
Indices: 40421--40482 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
40411 CAACGGTCAA
40421 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
* *
40452 CGGGTCAACTGGTCGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
40483 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
Found at i:41311 original size:32 final size:32
Alignment explanation
Indices: 41270--41345 Score: 152
Period size: 32 Copynumber: 2.4 Consensus size: 32
41260 GGGTGTTACA
41270 GGCGACCTCTCCATTGGCTGGCTCGTCTGCAT
1 GGCGACCTCTCCATTGGCTGGCTCGTCTGCAT
41302 GGCGACCTCTCCATTGGCTGGCTCGTCTGCAT
1 GGCGACCTCTCCATTGGCTGGCTCGTCTGCAT
41334 GGCGACCTCTCC
1 GGCGACCTCTCC
41346 TCGTATAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.09, C:0.37, G:0.28, T:0.26
Consensus pattern (32 bp):
GGCGACCTCTCCATTGGCTGGCTCGTCTGCAT
Found at i:41472 original size:29 final size:29
Alignment explanation
Indices: 41430--41489 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
41420 GTATGGTATG
41430 TCGCCTGGATTGCATGGCGTCCTACAAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
*
41459 TCGCCTGGATTGCATGGCGTCCTACGAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
41488 TC
1 TC
41490 ACTGTAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.25
Consensus pattern (29 bp):
TCGCCTGGATTGCATGGCGTCCTACAAGA
Found at i:42932 original size:29 final size:28
Alignment explanation
Indices: 42870--42932 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
42860 ATTATTTTTT
*
42870 AATA-TTTTTAATAAAAAATTATTTAAA
1 AATATTTTTTAATAAAAAATTATATAAA
*
42897 AATTATTTTTTACTAAAAATATTA-ATATAA
1 AA-TATTTTTTAATAAAAA-ATTATATA-AA
42927 AATATT
1 AATATT
42933 AAAAATATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
27 2 0.07
28 2 0.07
29 18 0.60
30 8 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
AATATTTTTTAATAAAAAATTATATAAA
Found at i:50011 original size:18 final size:18
Alignment explanation
Indices: 49988--50035 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
49978 TACAACATTC
**
49988 CCGGTAATCTTATTCATG
1 CCGGTAATCTTATTCACA
* *
50006 CCGGTAATCATATTCCCA
1 CCGGTAATCTTATTCACA
50024 CCGGTAATCTTA
1 CCGGTAATCTTA
50036 CATTTCGTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (18 bp):
CCGGTAATCTTATTCACA
Found at i:55163 original size:16 final size:16
Alignment explanation
Indices: 55142--55174 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55132 TTACACGACT
*
55142 TGTTATCAACCTGACC
1 TGTTATAAACCTGACC
55158 TGTTATAAACCTGACC
1 TGTTATAAACCTGACC
55174 T
1 T
55175 ATAGTTGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (16 bp):
TGTTATAAACCTGACC
Found at i:57068 original size:24 final size:20
Alignment explanation
Indices: 57042--57093 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 20
57032 TATGTATGAT
57042 ATGTATGTAT-TTTCGATCTA
1 ATGTATGTATGTTT-GATCTA
57062 ATGTATGTATGTTTGATCTA
1 ATGTATGTATGTTTGATCTA
57082 ATGTATGATATG
1 ATGTATG-TATG
57094 CACCATGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48
Consensus pattern (20 bp):
ATGTATGTATGTTTGATCTA
Found at i:57258 original size:39 final size:40
Alignment explanation
Indices: 57182--57439 Score: 119
Period size: 38 Copynumber: 6.8 Consensus size: 40
57172 TGTATGAATG
57182 ATATTTATGTATGTATAATTTATTAATGCATGTATGTATATAT
1 ATATTTATGTATGTATAATTTATTAATGC---TATGTATATAT
*
57225 ATATTTATGTATGTATAATTTGTTAATGC-ATG-------
1 ATATTTATGTATGTATAATTTATTAATGCTATGTATATAT
*
57257 -TA--TATGTATGTATAATTTATTAATGC-ATGTAT-CAT
1 ATATTTATGTATGTATAATTTATTAATGCTATGTATATAT
* * *
57292 ATATGTATGTATG--T-ATGTATGT-ATG-TATGTATGTAT
1 ATATTTATGTATGTATAATTTAT-TAATGCTATGTATATAT
* * * * ** ** *
57328 GTATGTATGTATATATGCATGCATGCATG-TATGTTTGATAT
1 ATATTTATGTATGTAT-AATTTATTAATGCTATGTAT-ATAT
* * * * *
57369 GTGTATATATATGTATAATTTATTAATG-TATGTAT-CAT
1 ATATTTATGTATGTATAATTTATTAATGCTATGTATATAT
**
57407 ATACGTATGTATGTATAATTTATTAATGC-ATGT
1 ATATTTATGTATGTATAATTTATTAATGCTATGT
57440 CTTATAACTC
Statistics
Matches: 170, Mismatches: 26, Indels: 43
0.71 0.11 0.18
Matches are distributed among these distances:
29 26 0.15
31 2 0.01
35 14 0.08
36 17 0.10
38 38 0.22
39 3 0.02
40 27 0.16
41 15 0.09
43 28 0.16
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (40 bp):
ATATTTATGTATGTATAATTTATTAATGCTATGTATATAT
Found at i:57272 original size:29 final size:29
Alignment explanation
Indices: 57230--57299 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
57220 TATATATATT
*
57230 TATGTATGTATAATTTGTTAATGCATGTA
1 TATGTATGTATAATTTATTAATGCATGTA
57259 TATGTATGTATAATTTATTAATGCATGTA
1 TATGTATGTATAATTTATTAATGCATGTA
*
57288 TCATATATGTAT
1 T-ATGTATGTAT
57300 GTATGTATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 29 0.76
30 9 0.24
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (29 bp):
TATGTATGTATAATTTATTAATGCATGTA
Found at i:57302 original size:4 final size:4
Alignment explanation
Indices: 57293--57422 Score: 104
Period size: 4 Copynumber: 32.8 Consensus size: 4
57283 ATGTATCATA
*
57293 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * * * *
57341 TATG CATG CATG CATG TATG TTTG ATATG TGTA TATA TATG TAT- AATT
1 TATG TATG TATG TATG TATG TATG -TATG TATG TATG TATG TATG TATG
* * *
57389 TAT- TAATG TATG TAT- CATA TACG TATG TATG TAT
1 TATG T-ATG TATG TATG TATG TATG TATG TATG TAT
57423 AATTTATTAA
Statistics
Matches: 104, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
3 5 0.05
4 95 0.91
5 4 0.04
ACGTcount: A:0.29, C:0.04, G:0.19, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:57374 original size:115 final size:114
Alignment explanation
Indices: 57097--57422 Score: 312
Period size: 115 Copynumber: 2.8 Consensus size: 114
57087 TGATATGCAC
* *
57097 CATGTATGTATATATGCA-CAATGCA-GTATGTATGTGTCTATGTATATT-TGTATAATTTATTA
1 CATGTATGTATATATGCATC-ATGCATGTATGT-T-TGTATGTGTATATTATGTATAATTTATTA
* * *
57159 A--CA--TATGCATATATGTATGAATGATATTTATGTATGTATAATTTATTAATG
63 ATGCATGTAT-CATATATGTATGTATG-TATGTATGTATG-ATAATGTATTAATG
** * * *
57210 CATGTATGTATATATATATTTATGTATGTATAATTTGTTAATGCATGTATATGTATGTATAATTT
1 CATGTATGTATATATGCA-TCATGCATGTAT-GTTTG-T-ATG--TGTATAT-TATGTATAATTT
57275 ATTAATGCATGTATCATATATGTATGTATGTATGTATGTATG-T-ATGTATGT-ATG
59 ATTAATGCATGTATCATATATGTATGTATGTATGTATGTATGATAATGTAT-TAATG
*
57329 TATGTATGTATATATGCATGCATGCATGTATGTTTGATATGTGTATATATATGTATAATTTATTA
1 CATGTATGTATATATGCAT-CATGCATGTATGTTTG-TATGTGTATAT-TATGTATAATTTATTA
* *
57394 ATGTATGTATCATATACGTATGTATGTAT
63 ATGCATGTATCATATATGTATGTATGTAT
57423 AATTTATTAA
Statistics
Matches: 177, Mismatches: 20, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
113 16 0.09
114 6 0.03
115 56 0.32
116 2 0.01
117 3 0.02
118 13 0.07
119 33 0.19
120 17 0.10
122 13 0.07
123 15 0.08
124 3 0.02
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (114 bp):
CATGTATGTATATATGCATCATGCATGTATGTTTGTATGTGTATATTATGTATAATTTATTAATG
CATGTATCATATATGTATGTATGTATGTATGTATGATAATGTATTAATG
Found at i:57439 original size:19 final size:19
Alignment explanation
Indices: 57378--57439 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
57368 TGTGTATATA
57378 TATGTATAATTTATTAATG
1 TATGTATAATTTATTAATG
* * *
57397 TATGTATCATATACGT-ATG
1 TATGTATAATTTA-TTAATG
57416 TATGTATAATTTATTAATG
1 TATGTATAATTTATTAATG
*
57435 CATGT
1 TATGT
57440 CTTATAACTC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
18 1 0.03
19 32 0.94
20 1 0.03
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (19 bp):
TATGTATAATTTATTAATG
Found at i:59753 original size:18 final size:18
Alignment explanation
Indices: 59730--59766 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
59720 AGGCATTTGA
*
59730 TCCTCTGGTCGTGCTTGT
1 TCCTCTGGTCGAGCTTGT
*
59748 TCCTCTGGTGGAGCTTGT
1 TCCTCTGGTCGAGCTTGT
59766 T
1 T
59767 TCTCGTGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.24, G:0.30, T:0.43
Consensus pattern (18 bp):
TCCTCTGGTCGAGCTTGT
Found at i:64097 original size:19 final size:19
Alignment explanation
Indices: 64073--64118 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
64063 TTCTTGAGTA
64073 TAGCCTTGAGCAACAAGTC
1 TAGCCTTGAGCAACAAGTC
64092 TAGCCTTGAGCAACAAGTC
1 TAGCCTTGAGCAACAAGTC
64111 TAGCCTTG
1 TAGCCTTG
64119 TTTCTCACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (19 bp):
TAGCCTTGAGCAACAAGTC
Found at i:67927 original size:26 final size:26
Alignment explanation
Indices: 67898--67949 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
67888 ACTCAAGAAT
67898 AATACAATTGAGCACAATAAGTGTTC
1 AATACAATTGAGCACAATAAGTGTTC
67924 AATACAATTGAGCACAATAAGTGTTC
1 AATACAATTGAGCACAATAAGTGTTC
67950 TTGAAAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (26 bp):
AATACAATTGAGCACAATAAGTGTTC
Found at i:69957 original size:32 final size:31
Alignment explanation
Indices: 69915--69990 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 31
69905 AAGAGTCGAG
*
69915 GGTTACCTATGTCTTTCGAGACATATGGACA
1 GGTTACCTATGTCCTTCGAGACATATGGACA
*
69946 GTGTTACCTATGTCCTTCGGGACATATGGACA
1 G-GTTACCTATGTCCTTCGAGACATATGGACA
69978 GGATTACCTATGT
1 GG-TTACCTATGT
69991 TCTAAGGAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
31 2 0.05
32 39 0.95
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (31 bp):
GGTTACCTATGTCCTTCGAGACATATGGACA
Found at i:70037 original size:31 final size:31
Alignment explanation
Indices: 69917--70056 Score: 113
Period size: 32 Copynumber: 4.5 Consensus size: 31
69907 GAGTCGAGGG
* *
69917 TTACCTATG-TCTTTCGAGACATATGGACAGT
1 TTACCTAGGTTCTTT-GGGACATATGGACAGT
* * * *
69948 GTTACCTATGTCCTTCGGGACATATGGACAGGA
1 -TTACCTAGGTTCTTTGGGACATATGGACA-GT
* ** * *
69981 TTACCTATGTTCTAAGGAACATATGGATAGT
1 TTACCTAGGTTCTTTGGGACATATGGACAGT
*
70012 TTACCTAGGTTCTTTGGGACCTATGGACA-T
1 TTACCTAGGTTCTTTGGGACATATGGACAGT
* *
70042 TTGCCGAGGTTCTTT
1 TTACCTAGGTTCTTT
70057 ATGACCTTTG
Statistics
Matches: 88, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
30 14 0.16
31 24 0.27
32 46 0.52
33 4 0.05
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (31 bp):
TTACCTAGGTTCTTTGGGACATATGGACAGT
Found at i:71507 original size:288 final size:286
Alignment explanation
Indices: 71153--71692 Score: 785
Period size: 288 Copynumber: 1.9 Consensus size: 286
71143 CAAACCATAA
* * *
71153 AAATTATATCATAATCTCTGAACTCTATAAACTTTTGTTCACCAAATTTTCAAATGAATGCAATT
1 AAATTATATCATAATCTCTGAACCCTATAAACTTTTCTTCACCAAATTTTAAAATGAATGCAATT
* * * **
71218 TAGTCCATTTTAATATTAATTTTAGCTTTACATTTTACAATTGTTTCAATTTGGTCCCTACATAT
66 TAGTCCAATTTAATATTAATTTCAACTTTACATTTTACAATTGTTTCAATTTAATCCCTACATAT
* *
71283 TCTTTAATTTATTTAAATTTCACTTTGTAATTTCATGTTTGTTTAATTTAATCCTTAAAAGTATA
131 TATTTAATTTATTTAAATTTCACTTTCTAATTTCATGTTTGTTTAA-TTAATCCTTAAAAGTATA
* * * *
71348 TTTTTATCCGAAATTAGCCCATAATTATTTCTATTTTTTGTATTTTACTCCAAACCCTAAAAATC
195 TTTCTAT-CAAAATTAACCCATAATTATTTCTATTTTTTGTAATTTACTCCAAACCCTAAAAATC
71413 ACATCATAAACTTCATTCCAAATCCTAT
259 ACATCATAAACTTCATTCCAAATCCTAT
* *
71441 AAATTATATCATAATC-CTTGAACCCTATAAACTTTTCTTCACCAACTTTTAAAATTAATGCAAT
1 AAATTATATCATAATCTC-TGAACCCTATAAACTTTTCTTCACCAAATTTTAAAATGAATGCAAT
* * * * *
71505 TTAGTCCAATTTGATATTAATTTCAACTTTACATTTTACACTTGTTTCAATTTAATCTCTGCATG
65 TTAGTCCAATTTAATATTAATTTCAACTTTACATTTTACAATTGTTTCAATTTAATCCCTACATA
* * * *
71570 TTATTTAATTTATTTAAATTTTAGTTTCTAATTTCATGTTTGTTTAATTAGTCCTTAAAATTATA
130 TTATTTAATTTATTTAAATTTCACTTTCTAATTTCATGTTTGTTTAATTAATCCTTAAAAGTATA
* * * *
71635 TTTCTATCAAAATTAACCCATAATTGTTTTTATTTTTTGTAATTTACTCTAAATCCTA
195 TTTCTATCAAAATTAACCCATAATTATTTCTATTTTTTGTAATTTACTCCAAACCCTA
71693 TACAATTATA
Statistics
Matches: 222, Mismatches: 29, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
286 44 0.20
287 23 0.10
288 155 0.70
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (286 bp):
AAATTATATCATAATCTCTGAACCCTATAAACTTTTCTTCACCAAATTTTAAAATGAATGCAATT
TAGTCCAATTTAATATTAATTTCAACTTTACATTTTACAATTGTTTCAATTTAATCCCTACATAT
TATTTAATTTATTTAAATTTCACTTTCTAATTTCATGTTTGTTTAATTAATCCTTAAAAGTATAT
TTCTATCAAAATTAACCCATAATTATTTCTATTTTTTGTAATTTACTCCAAACCCTAAAAATCAC
ATCATAAACTTCATTCCAAATCCTAT
Found at i:73548 original size:46 final size:46
Alignment explanation
Indices: 73481--73570 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
73471 CAGAAAAGGC
*
73481 AGAGGAATTTGACCCTCGTGCGAGATCAGGCGCCAATTGAACGAGT
1 AGAGGAATTTGACCCTCGTGCGAGATCAAGCGCCAATTGAACGAGT
* *
73527 AGAGGAATTTGACCCTCGTGCGAGATTAAGTGCCAATTGAACGA
1 AGAGGAATTTGACCCTCGTGCGAGATCAAGCGCCAATTGAACGA
73571 CTACTTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (46 bp):
AGAGGAATTTGACCCTCGTGCGAGATCAAGCGCCAATTGAACGAGT
Found at i:75203 original size:25 final size:25
Alignment explanation
Indices: 75169--75219 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
75159 TGATGGAAGA
75169 ACACTAATCAAATCAGGCCATGTAG
1 ACACTAATCAAATCAGGCCATGTAG
75194 ACACTAATCAAATCAGGCCATGTAG
1 ACACTAATCAAATCAGGCCATGTAG
75219 A
1 A
75220 AGTCAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.20
Consensus pattern (25 bp):
ACACTAATCAAATCAGGCCATGTAG
Found at i:83965 original size:36 final size:36
Alignment explanation
Indices: 83899--84001 Score: 145
Period size: 36 Copynumber: 2.9 Consensus size: 36
83889 TGAGGAGGAG
83899 GTTGAAACTGCTGCA-ATCAAATGCAACAACACACA
1 GTTGAAACTGCTGCAGATCAAATGCAACAACACACA
* *
83934 GTTGAAACTGCTGCAGATCAAATGCAGCAACATACA
1 GTTGAAACTGCTGCAGATCAAATGCAACAACACACA
* * * *
83970 GTTGTAACTACTGCAGATCAAGTTCAACAACA
1 GTTGAAACTGCTGCAGATCAAATGCAACAACA
84002 AGCGCCGCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 15 0.25
36 45 0.75
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (36 bp):
GTTGAAACTGCTGCAGATCAAATGCAACAACACACA
Found at i:87424 original size:15 final size:15
Alignment explanation
Indices: 87398--87430 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
87388 AATTAGAATA
87398 ATTTATTTAATAT-T
1 ATTTATTTAATATAT
87412 ATTTATGTTAATATAT
1 ATTTAT-TTAATATAT
87428 ATT
1 ATT
87431 AAATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 7 0.41
16 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTTATTTAATATAT
Found at i:89327 original size:48 final size:49
Alignment explanation
Indices: 89256--89351 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 49
89246 ATGCCTGTTG
89256 TTGTTTCATACCTGAAAGTAATTCAACAATGAATCTAT-CTACTCGAAA
1 TTGTTTCATACCTGAAAGTAATTCAACAATGAATCTATACTACTCGAAA
*
89304 TTGTTTCATACCTGAAAGTAATTCAACAATGAATCTATATTACTCGAA
1 TTGTTTCATACCTGAAAGTAATTCAACAATGAATCTATACTACTCGAA
89352 TAAGGTGAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 38 0.83
49 8 0.17
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (49 bp):
TTGTTTCATACCTGAAAGTAATTCAACAATGAATCTATACTACTCGAAA
Found at i:92516 original size:23 final size:23
Alignment explanation
Indices: 92490--92539 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
92480 ATTTGTTACA
*
92490 ATTTATTATTGTGAAAGAATATT
1 ATTTATCATTGTGAAAGAATATT
*
92513 ATTTGTCATTGTGAAAGAATATT
1 ATTTATCATTGTGAAAGAATATT
92536 ATTT
1 ATTT
92540 GTCACAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (23 bp):
ATTTATCATTGTGAAAGAATATT
Found at i:92540 original size:23 final size:23
Alignment explanation
Indices: 92497--92543 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
92487 ACAATTTATT
92497 ATTGTGAAAGAATATTATTTGTC
1 ATTGTGAAAGAATATTATTTGTC
92520 ATTGTGAAAGAATATTATTTGTC
1 ATTGTGAAAGAATATTATTTGTC
92543 A
1 A
92544 CAAATACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (23 bp):
ATTGTGAAAGAATATTATTTGTC
Found at i:95034 original size:19 final size:19
Alignment explanation
Indices: 95012--95053 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
95002 ATATTTTGTT
*
95012 ACTATATAACATTTTTGAC
1 ACTATATAACATTTTTAAC
95031 ACTATATAACATTTTTAAC
1 ACTATATAACATTTTTAAC
95050 ACTA
1 ACTA
95054 AAAATAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (19 bp):
ACTATATAACATTTTTAAC
Found at i:96460 original size:19 final size:19
Alignment explanation
Indices: 96426--96479 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
96416 TTTTGCAAAG
*
96426 AACCGGTTGGGAACCGACAA
1 AACCGG-TGTGAACCGACAA
* *
96446 AACCGGTGTGAACCGGCCA
1 AACCGGTGTGAACCGACAA
96465 AACCGGTGTGAACCG
1 AACCGGTGTGAACCG
96480 CAAGTTCAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 25 0.81
20 6 0.19
ACGTcount: A:0.30, C:0.28, G:0.31, T:0.11
Consensus pattern (19 bp):
AACCGGTGTGAACCGACAA
Found at i:96725 original size:27 final size:27
Alignment explanation
Indices: 96687--96802 Score: 160
Period size: 27 Copynumber: 4.3 Consensus size: 27
96677 ATGAATATTT
*
96687 TGATGTTGTGGACTTTCAAGTTCAAAG
1 TGATGATGTGGACTTTCAAGTTCAAAG
*
96714 TGATGATGTGGACTTTTAAGTTCAAAG
1 TGATGATGTGGACTTTCAAGTTCAAAG
*
96741 TGATGTTGTGGACTTTCAAGTTCAAAG
1 TGATGATGTGGACTTTCAAGTTCAAAG
* * * *
96768 TGATGCTATGAAATTTCAAGTTCAAAG
1 TGATGATGTGGACTTTCAAGTTCAAAG
*
96795 TGGTGATG
1 TGATGATG
96803 GCGGTAGTAG
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 78 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.36
Consensus pattern (27 bp):
TGATGATGTGGACTTTCAAGTTCAAAG
Found at i:97166 original size:21 final size:21
Alignment explanation
Indices: 97142--97183 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
97132 AAAAATTATT
97142 TTATATAAATTGGTTCAACCG
1 TTATATAAATTGGTTCAACCG
97163 TTATATAAATTGGTTCAACCG
1 TTATATAAATTGGTTCAACCG
97184 CGGTTTAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (21 bp):
TTATATAAATTGGTTCAACCG
Found at i:113277 original size:26 final size:26
Alignment explanation
Indices: 113248--113305 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
113238 TTAATTTAGT
113248 ATATTTTATTCTTATCTTACTTCAAA
1 ATATTTTATTCTTATCTTACTTCAAA
113274 ATATTTTATTCTTATCTTACTTCAAA
1 ATATTTTATTCTTATCTTACTTCAAA
113300 ATATTT
1 ATATTT
113306 AACATAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (26 bp):
ATATTTTATTCTTATCTTACTTCAAA
Found at i:115711 original size:26 final size:25
Alignment explanation
Indices: 115668--115725 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
115658 GTGTGTGATA
*
115668 AGAAA-AAAAAGAATAAAAGTGAAG
1 AGAAAGAAAAAGAAGAAAAGTGAAG
115692 AGAAAGAAAGAAGAAGAAAAGTGAAG
1 AGAAAGAAA-AAGAAGAAAAGTGAAG
*
115718 AAAAAGAA
1 AGAAAGAA
115726 TATGGGGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 5 0.17
25 3 0.10
26 22 0.73
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (25 bp):
AGAAAGAAAAAGAAGAAAAGTGAAG
Found at i:116178 original size:21 final size:21
Alignment explanation
Indices: 116152--116201 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
116142 ACCCGACCCG
116152 ACTCGACCAAAATAA-AGTTTC
1 ACTCGACCAAAATAATA-TTTC
116173 ACTCGACCAAAATAATATTTC
1 ACTCGACCAAAATAATATTTC
*
116194 ACCCGACC
1 ACTCGACC
116202 CGACCCGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.40, C:0.30, G:0.08, T:0.22
Consensus pattern (21 bp):
ACTCGACCAAAATAATATTTC
Found at i:116840 original size:31 final size:32
Alignment explanation
Indices: 116805--116889 Score: 84
Period size: 30 Copynumber: 2.7 Consensus size: 32
116795 TATCGATTCG
**
116805 TTCAATTTTAGTCTCTCAGTTATTAACT-TTA
1 TTCAATTTTAGTCTCTCAGCCATTAACTCTTA
* * *
116836 TTCAA-TTTAGTCTTTCAGCCGTTAACTCTTG
1 TTCAATTTTAGTCTCTCAGCCATTAACTCTTA
* * *
116867 TTCAGTTTTAGTCTTTCAACCAT
1 TTCAATTTTAGTCTCTCAGCCAT
116890 GTTAGATACT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
30 18 0.41
31 11 0.25
32 15 0.34
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.48
Consensus pattern (32 bp):
TTCAATTTTAGTCTCTCAGCCATTAACTCTTA
Found at i:117232 original size:23 final size:21
Alignment explanation
Indices: 117206--117248 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
117196 TAAATTTAAC
117206 ATAAAAATAATTTTTAAAATAAA
1 ATAAAAAT-A-TTTTAAAATAAA
*
117229 ATAAACATATTTTAAAATAA
1 ATAAAAATATTTTAAAATAA
117249 TATTAGCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAAAATATTTTAAAATAAA
Found at i:120526 original size:6 final size:6
Alignment explanation
Indices: 120515--120542 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
120505 GTAGGATTGT
120515 ATATCC ATATCC ATATCC ATATCC ATAT
1 ATATCC ATATCC ATATCC ATATCC ATAT
120543 GCATTCTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATCC
Found at i:122356 original size:14 final size:14
Alignment explanation
Indices: 122309--122359 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
122299 ATTCTAGAAA
*
122309 CTGAGACAACTCG-
1 CTGAGTCAACTCGT
* *
122322 ATGAGTCAACTCAT
1 CTGAGTCAACTCGT
**
122336 CCAAGTCAACTCGT
1 CTGAGTCAACTCGT
122350 CTGAGTCAAC
1 CTGAGTCAAC
122360 CCATTGACTT
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (14 bp):
CTGAGTCAACTCGT
Done.