Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007035.1 Hibiscus syriacus cultivar Beakdansim tig00018232_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: 67332
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:10402 original size:22 final size:22
Alignment explanation
Indices: 10322--10404 Score: 103
Period size: 22 Copynumber: 3.8 Consensus size: 22
10312 CCATCATATA
*
10322 ACTAAAGTGCCTTAACACTGAT
1 ACTAAAGTGCCTTAGCACTGAT
* * *
10344 ACTAAAGTGTCTCATCACTGAT
1 ACTAAAGTGCCTTAGCACTGAT
* **
10366 ACGAAAGTGTATTAGCACTGAT
1 ACTAAAGTGCCTTAGCACTGAT
10388 ACTAAAGTGCCTTAGCA
1 ACTAAAGTGCCTTAGCA
10405 TTGGAGGGAA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (22 bp):
ACTAAAGTGCCTTAGCACTGAT
Found at i:12980 original size:2 final size:2
Alignment explanation
Indices: 12973--13000 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12963 CAATTTTTCA
12973 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
13001 TAACATCAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13625 original size:2 final size:2
Alignment explanation
Indices: 13618--13648 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13608 TTTATTTTAT
*
13618 TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13649 TTGCATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27645 original size:21 final size:20
Alignment explanation
Indices: 27578--27652 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
27568 CAGTTTCCAA
* * *
27578 AATCGCAACGCGATTCTTGAC
1 AATCGCAATGCGATT-TTCAT
27599 AATCGCAATGCGATTTTCAT
1 AATCGCAATGCGATTTTCAT
* *
27619 ATTCGCATTGCGATTTTCCAT
1 AATCGCAATGCGATTTT-CAT
*
27640 AATCGCAACGCGA
1 AATCGCAATGCGA
27653 ATATGAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 18 0.40
21 27 0.60
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (20 bp):
AATCGCAATGCGATTTTCAT
Found at i:27734 original size:20 final size:20
Alignment explanation
Indices: 27640--27868 Score: 232
Period size: 20 Copynumber: 11.4 Consensus size: 20
27630 GATTTTCCAT
* ** *
27640 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
27660 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
27680 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
27700 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
27720 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
27740 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
27760 TATCGCAACACGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
27780 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* *
27800 AATCGCAACG-ATAATCTGTA
1 AATCGCAACGCGT-ATCCGTA
*
27820 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
27840 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
27860 AATCACAAC
1 AATCGCAAC
27869 ACTGAAATTT
Statistics
Matches: 183, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
19 2 0.01
20 179 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:28600 original size:24 final size:24
Alignment explanation
Indices: 28561--28607 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28551 AAATTTGGTC
28561 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
28585 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
28608 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:28799 original size:12 final size:12
Alignment explanation
Indices: 28782--28806 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28772 ATATAATCCT
28782 GAAGAAGAAAAA
1 GAAGAAGAAAAA
28794 GAAGAAGAAAAA
1 GAAGAAGAAAAA
28806 G
1 G
28807 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:31173 original size:53 final size:52
Alignment explanation
Indices: 31083--31253 Score: 170
Period size: 53 Copynumber: 3.2 Consensus size: 52
31073 GCAACGAGAG
31083 AATCGCAATGCGAAATGAAAATCCTAACAAGAAAATCGCAATACGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCTAACAAGAAAATCGCAATAC-GAAATGAA
* * *
31136 AATCGCAATGCGAAATGAAAATCGC-AACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATC-CTAACAAGAAAATCGCAATACGAAATGAA
* * * * * *
31188 AATCGTAACGAGAGAATCG-CAATGC-AGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCTA-ACAA-GAAAATCGCAATACGAAATGAA
*
31241 AATCGCATTGCGA
1 AATCGCAATGCGA
31254 TTCTCTCGTT
Statistics
Matches: 99, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
52 21 0.21
53 76 0.77
54 2 0.02
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCCTAACAAGAAAATCGCAATACGAAATGAA
Found at i:31178 original size:33 final size:33
Alignment explanation
Indices: 31136--31229 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
31126 CGGAAATGAA
31136 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
31169 AATCGCAATGCGAAATGAAAATCGTAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
31202 AATCGCAATGCAGAAATGAAAATCGCAA
1 AATCGCAATGC-GAAATGAAAATCGCAA
31230 TGCGAAATGA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 43 0.74
34 15 0.26
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:31267 original size:86 final size:86
Alignment explanation
Indices: 31069--31247 Score: 313
Period size: 86 Copynumber: 2.1 Consensus size: 86
31059 CGGAAATTAC
*
31069 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCTAACAAGAAAATCGCAATACGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCTAACAAGAAAATCGCAATACAGAAATG
31134 AAAATCGCAATGCGAAATGAA
66 AAAATCGCAATGCGAAATGAA
* * * *
31155 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGTAACGAGAGAATCGCAATGCAGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCTAACAAGAAAATCGCAATACAGAAATG
31220 AAAATCGCAATGCGAAATGAA
66 AAAATCGCAATGCGAAATGAA
31241 AATCGCA
1 AATCGCA
31248 TTGCGATTCT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (86 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCTAACAAGAAAATCGCAATACAGAAATG
AAAATCGCAATGCGAAATGAA
Found at i:31287 original size:53 final size:52
Alignment explanation
Indices: 31224--31339 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
31214 GAAATGAAAA
*
31224 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
31276 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
31329 TCGCATTGCGA
1 TCGCATTGCGA
31340 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:31302 original size:19 final size:19
Alignment explanation
Indices: 31262--31349 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
31252 GATTCTCTCG
31262 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
31282 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
31301 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
31315 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
31334 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
31350 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:31459 original size:14 final size:14
Alignment explanation
Indices: 31440--31476 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
31430 CATCAATTAC
31440 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
31454 ACAAATCATCTTTT
1 ACAAATCAACTTTT
31468 ACAAATCAA
1 ACAAATCAA
31477 TTAAACAATA
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:33446 original size:19 final size:19
Alignment explanation
Indices: 33404--33540 Score: 149
Period size: 19 Copynumber: 7.4 Consensus size: 19
33394 TATTTTACTT
* *
33404 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
** *
33424 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAACCAAAA
*
33443 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
33462 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
33481 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
33500 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
33514 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
33533 TCGCAACG
1 TCGCAACG
33541 AGAGAATCGT
Statistics
Matches: 98, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 71 0.72
20 12 0.12
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:33521 original size:33 final size:33
Alignment explanation
Indices: 33479--33571 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
33469 GCGAAACCAA
33479 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
** *
33512 AATCGCAACGCGAAACCAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
*
33545 AATCGTAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
33572 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:33538 original size:52 final size:55
Alignment explanation
Indices: 33404--33540 Score: 190
Period size: 52 Copynumber: 2.5 Consensus size: 55
33394 TATTTTACTT
* * *
33404 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGCGAAATGAAAATCGCAAC-AG-AACCAAAA
*
33462 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAAC-G-A-CAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAA
33514 TCGCAACGCGAAACCAAAATCGCAACG
1 TCGCAACGCGAAACCAAAATCGCAACG
33541 AGAGAATCGT
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
52 31 0.41
53 1 0.01
55 1 0.01
57 29 0.39
58 13 0.17
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (55 bp):
TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAA
Found at i:33568 original size:52 final size:52
Alignment explanation
Indices: 33438--33576 Score: 156
Period size: 52 Copynumber: 2.7 Consensus size: 52
33428 AACGCGAAAT
* * * *
33438 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGAAACGCGAAACGAAAATCGCAACGCGAAACCAAAATCGCAACGA
** *
33490 GA-AAT-GAAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGA
1 GAGAATCGAAACGCGAAACGA-A-AATCGCAACGCGAAACCAAAATCGCAACGA
* * *
33542 GAGAATCGTAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGAAACGCGAAACGAAAATCGCAACGCGA
33577 TTTTGGTTTC
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
50 8 0.11
51 4 0.06
52 45 0.64
53 4 0.06
54 9 0.13
ACGTcount: A:0.46, C:0.24, G:0.21, T:0.09
Consensus pattern (52 bp):
GAGAATCGAAACGCGAAACGAAAATCGCAACGCGAAACCAAAATCGCAACGA
Found at i:33576 original size:19 final size:19
Alignment explanation
Indices: 33404--33576 Score: 141
Period size: 19 Copynumber: 9.6 Consensus size: 19
33394 TATTTTACTT
* *
33404 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-GAAAA
* *
33424 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAACGAAAA
* *
33443 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAACGAAAA
*
33462 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACGAAAA
*
33481 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACGAAAA
*
33500 TCGCAA--CG--AC-AGAA
1 TCGCAACGCGAAACGAAAA
*
33514 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACGAAAA
*
33533 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAACGAAAA
* *
33547 TCGTAACGCGAAATGAAAA
1 TCGCAACGCGAAACGAAAA
*
33566 TCGCAATGCGA
1 TCGCAACGCGA
33577 TTTTGGTTTC
Statistics
Matches: 123, Mismatches: 20, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
14 17 0.14
15 2 0.02
16 4 0.03
17 4 0.03
18 3 0.02
19 81 0.66
20 12 0.10
ACGTcount: A:0.46, C:0.25, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACGAAAA
Found at i:33607 original size:14 final size:14
Alignment explanation
Indices: 33588--33646 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
33578 TTTGGTTTCG
33588 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
33602 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
33619 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
33635 CGTTGCGATTTT
1 CGTTGCGATTTT
33647 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:33614 original size:33 final size:33
Alignment explanation
Indices: 33572--33695 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
33562 AAAATCGCAA
*
33572 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
33605 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
33638 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
33671 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
33696 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:33626 original size:19 final size:18
Alignment explanation
Indices: 33572--33663 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
33562 AAAATCGCAA
33572 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
33591 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
33605 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
33624 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
33638 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
33657 TGCGATT
1 TGCGATT
33664 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:33673 original size:14 final size:14
Alignment explanation
Indices: 33621--33677 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
33611 TTTGGTTTCG
*
33621 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
33635 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
33654 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
33668 CGTTGCGATT
1 CGTTGCGATT
33678 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:33859 original size:83 final size:87
Alignment explanation
Indices: 33743--34015 Score: 324
Period size: 93 Copynumber: 3.1 Consensus size: 87
33733 ATGGATTGCA
* * **
33743 TTAC-TTCAACCAATAGATAAAACAAAGACAAATACTGACTT-CAG-G-G-TA-TTAGTTTAGCA
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACT-ACTTACAGTGAGATACACAGTTTAGCA
33802 GAATTGGCAGCAACCGAACAAAT
65 GAATTGGCAGCAACCGAACAAAT
*
33825 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----AG-ATACACAGTT
33890 TAGCAGAATTGGCAGCAACCGAACAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
*
33918 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----AG-ATACACAGTT
*
33983 TAGCAGAATTGGCAGCAACCGAATAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
34011 TTACT
1 TTACT
34016 AAGCAATCTA
Statistics
Matches: 173, Mismatches: 6, Indels: 13
0.90 0.03 0.07
Matches are distributed among these distances:
82 7 0.04
83 30 0.17
84 3 0.02
85 1 0.01
90 1 0.01
92 2 0.01
93 129 0.75
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.23
Consensus pattern (87 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTTACAGTGAGATACACAGTTTAGCAG
AATTGGCAGCAACCGAACAAAT
Found at i:33952 original size:93 final size:93
Alignment explanation
Indices: 33793--34015 Score: 437
Period size: 93 Copynumber: 2.4 Consensus size: 93
33783 TCAGGGTATT
33793 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
33858 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
33886 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
33951 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
33979 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
34016 AAGCAATCTA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 129 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:35740 original size:20 final size:20
Alignment explanation
Indices: 35709--35805 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
35699 TTTTGGTTGA
35709 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
35729 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
35749 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
35768 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
35783 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
35803 AAT
1 AAT
35806 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:35761 original size:21 final size:21
Alignment explanation
Indices: 35707--35771 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
35697 TCTTTTGGTT
35707 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
35728 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
35748 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
35769 GAA
1 GAA
35772 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:35775 original size:14 final size:14
Alignment explanation
Indices: 35756--35812 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
35746 GAGAAATGAA
35756 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
35770 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
35789 AATCGCAACGAGAG
1 AATCGCAACGAGAG
35803 AATCGCAACG
1 AATCGCAACG
35813 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:35788 original size:33 final size:33
Alignment explanation
Indices: 35707--35829 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
35697 TCTTTTGGTT
*
35707 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
35748 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
35781 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
35814 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
35830 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:35882 original size:21 final size:21
Alignment explanation
Indices: 35857--35930 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
35847 GTTGCGATTC
35857 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
35878 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
35899 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
35920 TCTCGTTGCGA
1 TCTCGTTGCGA
35931 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:36052 original size:33 final size:33
Alignment explanation
Indices: 36010--36080 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
36000 AATACTAACT
36010 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* * *
36043 TGAAAATCGCAACGAGATAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
36076 TGAAA
1 TGAAA
36081 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:36485 original size:20 final size:20
Alignment explanation
Indices: 36460--36592 Score: 205
Period size: 20 Copynumber: 6.7 Consensus size: 20
36450 CTTTAAAAAT
36460 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
36480 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
36500 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
36520 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
36540 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
36560 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
36580 CGCGTTGCGATTT
1 CGCGTTGCGATTT
36593 TCATATTCAC
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 103 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:36611 original size:60 final size:60
Alignment explanation
Indices: 36459--36611 Score: 209
Period size: 60 Copynumber: 2.5 Consensus size: 60
36449 GCTTTAAAAA
* *
36459 TCGCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCATTGCGATTTACGGAT
* * *
36519 ACGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
1 TCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCATTGCGATTTACG-GAT
* ** *
36579 TCGCGTTGCGATTTTCATATTCACGTTGCGATT
1 TCGCGTTGCGATTTACGGATACACGTTGCGATT
36612 ATGGAAAATC
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 81 0.99
61 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCATTGCGATTTACGGAT
Found at i:36640 original size:20 final size:21
Alignment explanation
Indices: 36605--36650 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
36595 ATATTCACGT
*
36605 TGCGATTATGGAAAATCGCAA
1 TGCGAATATGGAAAATCGCAA
*
36626 TGCGAATAT-GAAAATCGCAT
1 TGCGAATATGGAAAATCGCAA
36646 TGCGA
1 TGCGA
36651 TTGTCAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCGAATATGGAAAATCGCAA
Found at i:43314 original size:107 final size:106
Alignment explanation
Indices: 43117--43330 Score: 349
Period size: 107 Copynumber: 2.0 Consensus size: 106
43107 CCTTTACTAA
* *
43117 TATATTGATTTACCCCATCAACCCCACTCCTTACCCTCATGATCCAATCCCTAAACCCTAGTAGC
1 TATATTGATTTACCCCATCAAACCCACTCCTGACCCTCATGATCCAATCCCTAAACCCTAGTAGC
***
43182 TTTGATTTTTTTGGGGAAAAAGGAAAGAACCACACCTGATTT
66 TTTGA-TTTTTTGAAAAAAAAGGAAAGAACCACACCTGATTT
43224 TATATTGATTTACCCCATCAAACCCACTCCTGACCCTCATGATCCAATCCCTAAACCCTAGTAGC
1 TATATTGATTTACCCCATCAAACCCACTCCTGACCCTCATGATCCAATCCCTAAACCCTAGTAGC
43289 TTTGA-TTTTTGAAAAAAAATGGGAAAGAACCACACCTGATTT
66 TTTGATTTTTTGAAAAAAAA--GGAAAGAACCACACCTGATTT
43331 GTTAGGTTCT
Statistics
Matches: 100, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
105 11 0.11
107 89 0.89
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.29
Consensus pattern (106 bp):
TATATTGATTTACCCCATCAAACCCACTCCTGACCCTCATGATCCAATCCCTAAACCCTAGTAGC
TTTGATTTTTTGAAAAAAAAGGAAAGAACCACACCTGATTT
Found at i:45478 original size:59 final size:60
Alignment explanation
Indices: 45374--45546 Score: 178
Period size: 60 Copynumber: 2.9 Consensus size: 60
45364 TATTTGGATG
* * * *
45374 AATTTGGCGATGAAATTCG-AA-GATCTAAAAGTTT-AGAGACCAATTTGAAATGAGATTCAT
1 AATTTGGGGATGAAATT-GAAATG-TTTAAAAGTTTAAG-GATCAATTTGAAATGAGATACAT
* *
45434 AATTTTGGGATG-AATT-AGAATGTTTAAAAGTTTAAGGATTAATTT-AAAGTGAGATACAT
1 AATTTGGGGATGAAATTGA-AATGTTTAAAAGTTTAAGGATCAATTTGAAA-TGAGATACAT
* * *
45493 AGTTTGGGGATGAAATTGAAATTTTTAAGAGTTTAAGGATCAATTTGAAATGAG
1 AATTTGGGGATGAAATTGAAATGTTTAAAAGTTTAAGGATCAATTTGAAATGAG
45547 GGTCATAGTC
Statistics
Matches: 94, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
58 3 0.03
59 42 0.45
60 45 0.48
61 4 0.04
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (60 bp):
AATTTGGGGATGAAATTGAAATGTTTAAAAGTTTAAGGATCAATTTGAAATGAGATACAT
Found at i:45538 original size:60 final size:59
Alignment explanation
Indices: 45399--45546 Score: 176
Period size: 59 Copynumber: 2.5 Consensus size: 59
45389 TTCGAAGATC
* * *
45399 TAAAAGTTT-AGAGACCAATTTGAAATGAGATTCATAATTTTGGGATGAATTAGAATGTT
1 TAAAAGTTTAAG-GATCAATTTGAAATGAGATACATAATTTGGGGATGAATTAGAATGTT
* * *
45458 TAAAAGTTTAAGGATTAATTT-AAAGTGAGATACATAGTTTGGGGATGAAATT-GAAATTTT
1 TAAAAGTTTAAGGATCAATTTGAAA-TGAGATACATAATTTGGGGATG-AATTAG-AATGTT
*
45518 TAAGAGTTTAAGGATCAATTTGAAATGAG
1 TAAAAGTTTAAGGATCAATTTGAAATGAG
45547 GGTCATAGTC
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
58 3 0.04
59 36 0.47
60 34 0.45
61 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (59 bp):
TAAAAGTTTAAGGATCAATTTGAAATGAGATACATAATTTGGGGATGAATTAGAATGTT
Found at i:54085 original size:161 final size:161
Alignment explanation
Indices: 53728--54122 Score: 645
Period size: 160 Copynumber: 2.5 Consensus size: 161
53718 AACATTTTTA
*
53728 GTAAAAAAGTAGAAATTGAAGTTACATA-ATATTCTATTGTGGTATATGAGCATGTGGTTCATAT
1 GTAAAAAAG-AGGAATTGAAGTTACATAGATATTCTATTGTGGTATATGAGCATGTGGTTCATAT
* * *
53792 TT-G-AAAAAAAAGCGTACTTACAATAAATGATGAATTGAAGAAATAAGGAAATTATGAAAAATT
65 TTGGTAAAAAAAAGCATACTTAAAATAAATGATGAATTGAAGAAATAAGGAAATTATGAAAAAAT
*
53855 GAGGGCCTAAATTGAAAAATTAAAAAATTATT
130 GAGGGCCTAAATTGAAAAATAAAAAAATTATT
* *
53887 GTAAAAAAGAGGAATTGAAGTTACATAGATATTCTATTGTGGTATATGAGCATGTGATTCAGATT
1 GTAAAAAAGAGGAATTGAAGTTACATAGATATTCTATTGTGGTATATGAGCATGTGGTTCATATT
*
53952 TGGTAAAAAAAA-CATACTTAAAATAAATGATGAATTGAATAAATAAGGAAATTATGAAAAAATG
66 TGGTAAAAAAAAGCATACTTAAAATAAATGATGAATTGAAGAAATAAGGAAATTATGAAAAAATG
54016 AGGGCCTAAATTGAAAAATAAAAAAATTATT
131 AGGGCCTAAATTGAAAAATAAAAAAATTATT
* * *
54047 GTCAAAAAAGAGGAATTGAAGTTACATAGGTATTCTATTATGGTATACGAGCATGTGGTTCATAT
1 GT-AAAAAAGAGGAATTGAAGTTACATAGATATTCTATTGTGGTATATGAGCATGTGGTTCATAT
54112 TTGGTAAAAAA
65 TTGGTAAAAAA
54123 TGATGAATTG
Statistics
Matches: 219, Mismatches: 13, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
158 17 0.08
159 45 0.21
160 81 0.37
161 76 0.35
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (161 bp):
GTAAAAAAGAGGAATTGAAGTTACATAGATATTCTATTGTGGTATATGAGCATGTGGTTCATATT
TGGTAAAAAAAAGCATACTTAAAATAAATGATGAATTGAAGAAATAAGGAAATTATGAAAAAATG
AGGGCCTAAATTGAAAAATAAAAAAATTATT
Found at i:54213 original size:140 final size:141
Alignment explanation
Indices: 53976--54261 Score: 373
Period size: 140 Copynumber: 2.0 Consensus size: 141
53966 TACTTAAAAT
* * *
53976 AAATGATGAATTGAATAAATAAGGAAATTATGAAAAAATGAGGGCCTAAATTGAAAAATAAAAAA
1 AAATGATGAATTGAAGAAATAAAGAAATTATGAAAAAATGA--G-CAAAATTGAAAAATAAAAAA
* * * *
54041 ATTATTGTCAAAAAAGAGGAATTGAAGTTACATAGGTATTCTATTATGGTATACGAGCATGTGGT
63 ATAATTATCAAAAAAGAGGAATTGAAGTTACATAGGTATTCTATGATGATATACGAGCATGTGGT
* *
54106 TCATATTTGGTAAA
128 TAAAATTTGGTAAA
54120 AAATGATGAATTGAAGAAA-AAAGAAATTATGAAAATTAATGA-CAAAATTGAAAAATAAAAAAA
1 AAATGATGAATTGAAGAAATAAAGAAATTATGAAAA--AATGAGCAAAATTGAAAAATAAAAAAA
* * * *
54183 TAATTATC-ACAAAGAGGAATTGAAAG-TACATATGTATTCTATGATGATTTATGAGCATGTGGT
64 TAATTATCAAAAAAGAGGAATTG-AAGTTACATAGGTATTCTATGATGATATACGAGCATGTGGT
54246 TAAAATTTGGTAAA
128 TAAAATTTGGTAAA
54260 AA
1 AA
54262 TGGACTTAAA
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
140 59 0.47
141 29 0.23
143 15 0.12
144 18 0.14
145 5 0.04
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.29
Consensus pattern (141 bp):
AAATGATGAATTGAAGAAATAAAGAAATTATGAAAAAATGAGCAAAATTGAAAAATAAAAAAATA
ATTATCAAAAAAGAGGAATTGAAGTTACATAGGTATTCTATGATGATATACGAGCATGTGGTTAA
AATTTGGTAAA
Found at i:55027 original size:20 final size:21
Alignment explanation
Indices: 55002--55044 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
54992 TGGCCATGGG
* *
55002 TCGGGTTGGGTTGGGT-TTTT
1 TCGGGTCGGGTCGGGTATTTT
55022 TCGGGTCGGGTCGGGTATTTT
1 TCGGGTCGGGTCGGGTATTTT
55043 TC
1 TC
55045 ACCCTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.02, C:0.12, G:0.42, T:0.44
Consensus pattern (21 bp):
TCGGGTCGGGTCGGGTATTTT
Found at i:55177 original size:28 final size:28
Alignment explanation
Indices: 55063--55187 Score: 142
Period size: 28 Copynumber: 4.2 Consensus size: 28
55053 ATCGAACTCA
* *
55063 ACCCAAATATCACACTTTAAAAAAACTGACCCA
1 ACCCGAATATCACAC-TT-AAAAAA---ACCCG
*
55096 ACCCGAATATCACACTTAAAAAAACACG
1 ACCCGAATATCACACTTAAAAAAACCCG
*
55124 ACCCAAATATCACACTTAAAAAAACCCG
1 ACCCGAATATCACACTTAAAAAAACCCG
* *
55152 ACTCGAATATCAAACTTAAAAAAACCCCG
1 ACCCGAATATCACACTTAAAAAAA-CCCG
55181 ACCCGAA
1 ACCCGAA
55188 CCCAAATTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
28 50 0.61
29 10 0.12
31 6 0.07
32 2 0.02
33 14 0.17
ACGTcount: A:0.49, C:0.30, G:0.06, T:0.15
Consensus pattern (28 bp):
ACCCGAATATCACACTTAAAAAAACCCG
Found at i:58841 original size:34 final size:34
Alignment explanation
Indices: 58803--58869 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
58793 GAAATATATA
* * *
58803 TTATGAGTATATTCATTTTTTATAGTTTAAAATT
1 TTATGAGTAAATTCATATTTTATAATTTAAAATT
* * *
58837 TTATGTGTAAATTTATATTTTGTAATTTAAAAT
1 TTATGAGTAAATTCATATTTTATAATTTAAAAT
58870 AGTGTATTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.34, C:0.01, G:0.09, T:0.55
Consensus pattern (34 bp):
TTATGAGTAAATTCATATTTTATAATTTAAAATT
Found at i:60399 original size:2 final size:2
Alignment explanation
Indices: 60394--60421 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
60384 AATTTTTTTA
60394 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
60422 TACTAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60947 original size:20 final size:20
Alignment explanation
Indices: 60922--60966 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
60912 ATATTGCCAT
* *
60922 TTTTTGACAGAACGTATGAA
1 TTTTTGACAGAACATATAAA
*
60942 TTTTTGACATAACATATAAA
1 TTTTTGACAGAACATATAAA
60962 TTTTT
1 TTTTT
60967 ATTTTTGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (20 bp):
TTTTTGACAGAACATATAAA
Found at i:62444 original size:22 final size:24
Alignment explanation
Indices: 62413--62471 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 24
62403 TACCCTTATA
* *
62413 TATTTTTTAAATTTTTTAA-ATTT
1 TATTTTTTAAATTTTTTAATACTG
*
62436 TA-TTTTTAAAATTTTTAATACTG
1 TATTTTTTAAATTTTTTAATACTG
62459 TATTTTTTAAATT
1 TATTTTTTAAATT
62472 CGTATCTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 15 0.50
23 6 0.20
24 9 0.30
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
TATTTTTTAAATTTTTTAATACTG
Done.