Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006679.1 Hibiscus syriacus cultivar Beakdansim tig00016564_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: 65511
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:578 original size:19 final size:19
Alignment explanation
Indices: 556--694 Score: 86
Period size: 19 Copynumber: 7.8 Consensus size: 19
546 CAAAATTGCA
556 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
575 TTGCGATTTTTATTTCACG
1 TTGCGATTTTCATTTCGCG
594 TTGCGA--TTC---T--CG
1 TTGCGATTTTCATTTCGCG
* **
606 TCGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
625 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
639 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* *
659 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
679 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
695 AACCAAAGAC
Statistics
Matches: 92, Mismatches: 14, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
12 7 0.08
14 13 0.14
16 2 0.02
17 5 0.05
19 33 0.36
20 31 0.34
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:664 original size:34 final size:33
Alignment explanation
Indices: 586--669 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
576 TGCGATTTTT
*
586 ATTTCACGTTGCGA-T-TCTCGTCGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
*
617 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
650 ATTTCCGCGTTGCGATTCTC
1 ATTT-CGCGTTGCGATTCTC
670 ATTATCTCGT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
31 13 0.27
32 1 0.02
33 19 0.40
34 15 0.31
ACGTcount: A:0.13, C:0.26, G:0.23, T:0.38
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
Found at i:671 original size:20 final size:20
Alignment explanation
Indices: 637--694 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
627 GCGATTCTCT
**
637 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
657 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
677 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
695 AACCAAAGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:2502 original size:81 final size:78
Alignment explanation
Indices: 2363--2514 Score: 216
Period size: 81 Copynumber: 1.9 Consensus size: 78
2353 TAGATTGCTT
2363 AGTAAATTTATTCGGTTGCTGCCAAAACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAAAACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
2428 GTCTTTTGGTTGA
66 GTCTTTTGGTTGA
* ** * *
2441 AGTAAATTTATTCTG-TGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAAAACTGCTAAA--CTGT-TT-ATTAACACTGTGAAGTTAGT
2505 ATTTGTCTTT
62 ATTTGTCTTT
2515 GTTTGTCTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
77 17 0.26
78 14 0.22
79 3 0.05
80 2 0.03
81 29 0.45
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (78 bp):
AGTAAATTTATTCGGTTGCTGCCAAAACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
GTCTTTTGGTTGA
Found at i:2828 original size:21 final size:21
Alignment explanation
Indices: 2804--2870 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2794 TCATTCCTCG
2804 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2825 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2846 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2867 AGAG
1 AGAG
2871 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2828 original size:42 final size:42
Alignment explanation
Indices: 2752--2870 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
2742 GACTCGCCTG
* * * * * * *
2752 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
2794 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
2836 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
2871 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:4244 original size:14 final size:14
Alignment explanation
Indices: 4225--4258 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
4215 ATTGTTTAAT
4225 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
4239 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
4253 TGATTT
1 TGATTT
4259 ATTTAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:4422 original size:18 final size:18
Alignment explanation
Indices: 4367--4437 Score: 78
Period size: 18 Copynumber: 4.1 Consensus size: 18
4357 AAAAAGTACT
*
4367 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATG-AA
*
4386 ATCGCAA--CGAGA-G-A
1 ATCGCAACGCGAAATGAA
4400 ATCGCAACGCGAAATGAA
1 ATCGCAACGCGAAATGAA
*
4418 ATCGCAACGCGAAATTAA
1 ATCGCAACGCGAAATGAA
4436 AT
1 AT
4438 TCGCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
14 8 0.18
16 5 0.11
17 5 0.11
18 20 0.44
19 7 0.16
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (18 bp):
ATCGCAACGCGAAATGAA
Found at i:4483 original size:33 final size:32
Alignment explanation
Indices: 4441--4567 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
4431 ATTAAATTCG
4441 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
4474 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
4507 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
4540 CGTTGTGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
4568 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:4514 original size:66 final size:66
Alignment explanation
Indices: 4434--4566 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
4424 ACGCGAAATT
*
4434 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
4499 G
66 G
* *
4500 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGTGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
4565 G
66 G
4566 A
1 A
4567 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:6874 original size:12 final size:12
Alignment explanation
Indices: 6857--6881 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6847 TCTTCGGGGA
6857 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6869 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6881 C
1 C
6882 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:7090 original size:24 final size:24
Alignment explanation
Indices: 7056--7109 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
7046 CTTAAACATC
*
7056 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
7080 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
7104 ATCAAA
1 ATCAAA
7110 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:7879 original size:20 final size:20
Alignment explanation
Indices: 7854--7904 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
7844 TGTATTATCT
7854 CGTTGCGAAAGTAAGAATAG
1 CGTTGCGAAAGTAAGAATAG
* *
7874 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTAAGAATAG
*
7894 TGTTGCGAAAG
1 CGTTGCGAAAG
7905 GTAATCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (20 bp):
CGTTGCGAAAGTAAGAATAG
Found at i:8175 original size:19 final size:20
Alignment explanation
Indices: 8119--8186 Score: 129
Period size: 20 Copynumber: 3.5 Consensus size: 20
8109 TCATTTGACA
8119 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
8139 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
8159 ATCGCAACGCG-AAATGGCT
1 ATCGCAACGCGAAAATGGCT
8178 ATCGCAACG
1 ATCGCAACG
8187 ACAAAATCGC
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 17 0.35
20 31 0.65
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:8236 original size:14 final size:14
Alignment explanation
Indices: 8217--8270 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
8207 GAAAATCGCA
8217 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
8231 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
8248 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
8264 TTGCGAT
1 TTGCGAT
8271 AGTCAGTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:8236 original size:33 final size:33
Alignment explanation
Indices: 8199--8269 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
8189 AAAATCGCAA
*
8199 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
8232 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
8265 TGCGA
1 TGCGA
8270 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:8403 original size:14 final size:14
Alignment explanation
Indices: 8384--8420 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
8374 CATCAATTAA
8384 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
8398 ACAAATCATCTTTT
1 ACAAATCAACATTT
8412 ACAAATCAA
1 ACAAATCAA
8421 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:10318 original size:20 final size:18
Alignment explanation
Indices: 10295--10337 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 18
10285 CTCAACGTAA
10295 AAATGACTATCGCAACGCAG
1 AAATG-CTATCGCAACGC-G
10315 AAATTGCTATCGCAACGCG
1 AAA-TGCTATCGCAACGCG
10334 AAAT
1 AAAT
10338 TAAAATCGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.05
19 4 0.18
20 15 0.68
21 2 0.09
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (18 bp):
AAATGCTATCGCAACGCG
Found at i:10338 original size:19 final size:20
Alignment explanation
Indices: 10301--10338 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10291 GTAAAAATGA
10301 CTATCGCAACGCAGAAATTG
1 CTATCGCAACGCAGAAATTG
10321 CTATCGCAACGC-GAAATT
1 CTATCGCAACGCAGAAATT
10339 AAAATCGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (20 bp):
CTATCGCAACGCAGAAATTG
Found at i:10345 original size:19 final size:20
Alignment explanation
Indices: 10303--10350 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
10293 AAAAATGACT
***
10303 ATCGCAACGCAGAAATTGCT
1 ATCGCAACGCAGAAATTAAA
10323 ATCGCAACGC-GAAATTAAA
1 ATCGCAACGCAGAAATTAAA
*
10342 ATCGTAACG
1 ATCGCAACG
10351 ACAAAATCGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCAGAAATTAAA
Found at i:10358 original size:14 final size:14
Alignment explanation
Indices: 10339--10396 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
10329 ACGCGAAATT
*
10339 AAAATCGTAACGAC
1 AAAATCGCAACGAC
*
10353 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
10369 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
10385 AAAATCGTAACG
1 AAAATCGCAACG
10397 TGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:10368 original size:33 final size:32
Alignment explanation
Indices: 10323--10412 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
10313 AGAAATTGCT
*
10323 ATCGCAACGCGAAATTAAAATCGTAACGACAAA
1 ATCGCAACGCGAAA-TAAAATCGCAACGACAAA
* *
10356 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATAAAATCGCAACGACAAA
* * *
10388 ATCGTAACGTGAAACACAAATCGCA
1 ATCGCAACGCGAAATA-AAATCGCA
10413 TTGCGATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 27 0.56
33 21 0.44
ACGTcount: A:0.47, C:0.22, G:0.17, T:0.14
Consensus pattern (32 bp):
ATCGCAACGCGAAATAAAATCGCAACGACAAA
Found at i:10508 original size:20 final size:19
Alignment explanation
Indices: 10408--10528 Score: 101
Period size: 19 Copynumber: 6.6 Consensus size: 19
10398 GAAACACAAA
* *
10408 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATATTCATT
*
10427 TCGCGTTGCGAT-TT--TG
1 TCGCGTTGCGATATTCATT
10443 T--CGTTGCGAT-TTCATT
1 TCGCGTTGCGATATTCATT
* *
10459 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATATTCATT
* *
10478 TCGCATTGCGATATCCATT
1 TCGCGTTGCGATATTCATT
*
10497 TCCGCGTTGCGATAGTCATTT
1 T-CGCGTTGCGATATTCA-TT
*
10518 TCGTGTTGCGA
1 TCGCGTTGCGA
10529 AAGTAAACTA
Statistics
Matches: 85, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
14 11 0.13
16 4 0.05
18 10 0.12
19 35 0.41
20 22 0.26
21 3 0.04
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATATTCATT
Found at i:11023 original size:18 final size:18
Alignment explanation
Indices: 10997--11041 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
10987 GTCGTTCAGA
*
10997 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
11015 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
11033 TGATGGCTC
1 TGATGGCTC
11042 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:12385 original size:20 final size:20
Alignment explanation
Indices: 12360--12433 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
12350 AATAGTTTCT
*
12360 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
12380 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
12400 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
12420 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
12434 GTTGCGATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:12674 original size:22 final size:22
Alignment explanation
Indices: 12647--12690 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12637 AGATGGAGAT
12647 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
*
12669 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
12691 GTGAGAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:12746 original size:17 final size:17
Alignment explanation
Indices: 12724--12760 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
12714 GGGGCTGAGT
12724 TGTGATTTTAGGTTTTA
1 TGTGATTTTAGGTTTTA
*
12741 TGTGATTTTTGGTTTTA
1 TGTGATTTTAGGTTTTA
12758 TGT
1 TGT
12761 TTGGAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.24, T:0.62
Consensus pattern (17 bp):
TGTGATTTTAGGTTTTA
Found at i:12842 original size:21 final size:21
Alignment explanation
Indices: 12812--12907 Score: 74
Period size: 20 Copynumber: 4.7 Consensus size: 21
12802 CGCTTTGAAA
12812 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGATTATGTATT
* * *
12833 ATCGCGTTGCGA--AAGTCAGT
1 ATCGCATTGCGATTATGT-ATT
* * *
12853 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTATT
*
12874 ATCGCATTGCGA-TA-GTCAGT
1 ATCGCATTGCGATTATGT-ATT
*
12894 ATCGTATTGCGATT
1 ATCGCATTGCGATT
12908 TTCCCAATTC
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
19 5 0.09
20 27 0.47
21 24 0.41
22 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (21 bp):
ATCGCATTGCGATTATGTATT
Found at i:12875 original size:41 final size:41
Alignment explanation
Indices: 12812--12909 Score: 135
Period size: 41 Copynumber: 2.4 Consensus size: 41
12802 CGCTTTGAAA
* * *
12812 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
1 ATCGTATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGT
* *
12853 ATC-TCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGT-ATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGT
12894 ATCGTATTGCGATTTT
1 ATCGTATTGCGATTTT
12910 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
41 48 0.98
42 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (41 bp):
ATCGTATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGT
Found at i:12925 original size:41 final size:41
Alignment explanation
Indices: 12832--12927 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
12822 GATTATGTAT
* ** *
12832 TATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGAAAGTCAGTATCTCATTGCGATTTTCCAA
* *
12873 TATCGCATTGCGATAGTCAGTATCGT-ATTGCGATTTTCCCAA
1 TATCGCGTTGCGAAAGTCAGTATC-TCATTGCGATTTT-CCAA
12915 T-TCGCGTTGCGAA
1 TATCGCGTTGCGAA
12928 TTAGCGATCG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
41 42 0.93
42 3 0.07
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGAAAGTCAGTATCTCATTGCGATTTTCCAA
Found at i:20474 original size:20 final size:20
Alignment explanation
Indices: 20449--20491 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
20439 TCTAAGATCT
* *
20449 CATTTAGGACCATGTAGATG
1 CATTTAGGAACATATAGATG
*
20469 CATTTAGGAACATATAGTTG
1 CATTTAGGAACATATAGATG
20489 CAT
1 CAT
20492 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGAACATATAGATG
Found at i:20761 original size:10 final size:10
Alignment explanation
Indices: 20746--20784 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
20736 ACTGCACAGG
20746 CCATGCTGCA
1 CCATGCTGCA
*
20756 CCATGCCGC-
1 CCATGCTGCA
*
20765 CCATGCTGGA
1 CCATGCTGCA
20775 CCATGCTGCA
1 CCATGCTGCA
20785 GATGTCAGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.18, C:0.41, G:0.23, T:0.18
Consensus pattern (10 bp):
CCATGCTGCA
Found at i:20855 original size:18 final size:18
Alignment explanation
Indices: 20832--20883 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
20822 TTTCTAGATG
20832 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
*
20850 CCCATGTTGGACCACTGC
1 CCCATGCTGGACCACTGC
*
20868 CCCATGCTGGATCACT
1 CCCATGCTGGACCACT
20884 ACCCAATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.17, C:0.40, G:0.21, T:0.21
Consensus pattern (18 bp):
CCCATGCTGGACCACTGC
Found at i:22044 original size:22 final size:20
Alignment explanation
Indices: 22003--22045 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
21993 ACACTACCAC
*
22003 CATTCCATTTTCACATCATT
1 CATTCCATTTTCACAACATT
22023 CATTCCATTTTGCCACAACATT
1 CATTCCATTTT--CACAACATT
22045 C
1 C
22046 TCATTTGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
22 9 0.45
ACGTcount: A:0.26, C:0.33, G:0.02, T:0.40
Consensus pattern (20 bp):
CATTCCATTTTCACAACATT
Found at i:26301 original size:22 final size:20
Alignment explanation
Indices: 26274--26314 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
26264 TTTTTAAAGA
26274 AATAATAAAAATATTATATTTG
1 AATAAT-AAAAT-TTATATTTG
*
26296 AATAATACAATTTATATTT
1 AATAATAAAATTTATATTT
26315 AAAGTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
AATAATAAAATTTATATTTG
Found at i:28634 original size:23 final size:23
Alignment explanation
Indices: 28616--28676 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
28606 CTCGTATAAA
*
28616 TGCACCGAACTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* **
28639 TTCACCGAAGTGCTGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
28662 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
28677 TATAAAATGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:29353 original size:21 final size:22
Alignment explanation
Indices: 29329--29390 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
29319 TATATTCCTT
*
29329 ATAACCTTT-TCATATAGCTCC
1 ATAACCTTTAGCATATAGCTCC
*
29350 ATAAATCTTTAGCATATAGCTCC
1 AT-AACCTTTAGCATATAGCTCC
*
29373 ATAAATCTTTAGCATATA
1 AT-AACCTTTAGCATATA
29391 ACTTATCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 2 0.05
22 6 0.16
23 29 0.78
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.37
Consensus pattern (22 bp):
ATAACCTTTAGCATATAGCTCC
Found at i:29366 original size:23 final size:23
Alignment explanation
Indices: 29339--29390 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
29329 ATAACCTTTT
29339 CATATAGCTCCATAAATCTTTAG
1 CATATAGCTCCATAAATCTTTAG
29362 CATATAGCTCCATAAATCTTTAG
1 CATATAGCTCCATAAATCTTTAG
29385 CATATA
1 CATATA
29391 ACTTATCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.35
Consensus pattern (23 bp):
CATATAGCTCCATAAATCTTTAG
Found at i:30227 original size:20 final size:20
Alignment explanation
Indices: 30202--30239 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30192 TCCCCTTTGA
30202 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
30222 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
30240 TTAACATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:40102 original size:98 final size:98
Alignment explanation
Indices: 39933--40128 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
39923 TATTACCTGC
39933 GTTCACTAATTCTGATATTTTGAAGTTCTCTTGATCAATTTGATTTTCATCTCTAAAATTAGGAA
1 GTTCACTAATTCTGATATTTTGAAGTTCTCTTGATCAATTTGATTTTCATCTCTAAAATTAGGAA
39998 AATGGAACTTACTAAAAAAATAAAATCACATTT
66 AATGGAACTTACTAAAAAAATAAAATCACATTT
40031 GTTCACTAATTCTGATATTTTGAAGTTCTCTTGATCAATTTGATTTTCATCTCTAAAATTAGGAA
1 GTTCACTAATTCTGATATTTTGAAGTTCTCTTGATCAATTTGATTTTCATCTCTAAAATTAGGAA
40096 AATGGAACTTACTAAAAAAATAAAATCACATTT
66 AATGGAACTTACTAAAAAAATAAAATCACATTT
40129 ACGCCGTCAA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (98 bp):
GTTCACTAATTCTGATATTTTGAAGTTCTCTTGATCAATTTGATTTTCATCTCTAAAATTAGGAA
AATGGAACTTACTAAAAAAATAAAATCACATTT
Found at i:46276 original size:2 final size:2
Alignment explanation
Indices: 46269--46302 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
46259 TAAAATTCAG
46269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46303 TTCAGTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48187 original size:7 final size:7
Alignment explanation
Indices: 48172--48203 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
48162 TATTCCCTTC
*
48172 AGCATTA
1 AGCAATA
48179 AGCAATA
1 AGCAATA
48186 AGCAATA
1 AGCAATA
48193 AGCAATA
1 AGCAATA
48200 AGCA
1 AGCA
48204 TTAATCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (7 bp):
AGCAATA
Found at i:51346 original size:20 final size:20
Alignment explanation
Indices: 51276--51337 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
51266 TTTTCTAGAT
* *
51276 AATAAT-AATAATAATGAAG
1 AATAATAAATAATAATAAAA
* *
51295 TATATATAAAATAATATTAAAA
1 AATA-AT-AAATAATAATAAAA
51317 AATAATAAATAATAATAAAA
1 AATAATAAATAATAATAAAA
51337 A
1 A
51338 TGATTAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.09
20 16 0.47
21 2 0.06
22 13 0.38
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (20 bp):
AATAATAAATAATAATAAAA
Found at i:54967 original size:20 final size:21
Alignment explanation
Indices: 54942--54984 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
54932 GTGCATTTAT
54942 ATTTTATTATT-TAA-TAAAAC
1 ATTTTATT-TTATAATTAAAAC
54962 ATTTTATTTTATAATTAAAAC
1 ATTTTATTTTATAATTAAAAC
54983 AT
1 AT
54985 ATAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.10
20 11 0.52
21 8 0.38
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTATTTTATAATTAAAAC
Done.