Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005285.1 Hibiscus syriacus cultivar Beakdansim tig00011957_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: 45995
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:1366 original size:29 final size:30
Alignment explanation
Indices: 1334--1397 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
1324 AATAAATAAT
* *
1334 AAAAACTGTATAACATA-TATTATATTTTC
1 AAAAACTATATAACATATTAATATATTTTC
*
1363 AAAAACTATATAATATATTAATATATTTTC
1 AAAAACTATATAACATATTAATATATTTTC
1393 AAAAA
1 AAAAA
1398 ACGTTTTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAAACTATATAACATATTAATATATTTTC
Found at i:1490 original size:35 final size:35
Alignment explanation
Indices: 1428--1518 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 35
1418 TTAATACTAT
1428 ATTATATAC-ATA-TTTTCAAAACTGTTTTAA-AA
1 ATTATATACTATAGTTTTCAAAACTGTTTTAATAA
1460 ATTATATACTATATGTTTTCAAAA-TCGTTTTAATAA
1 ATTATATACTATA-GTTTTCAAAACT-GTTTTAATAA
* *
1496 A-TATATATTATACGTTTTTAAAA
1 ATTATATACTATA-GTTTTCAAAA
1519 GTAAGTTCCA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
32 9 0.18
33 3 0.06
34 1 0.02
35 35 0.69
36 3 0.06
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (35 bp):
ATTATATACTATAGTTTTCAAAACTGTTTTAATAA
Found at i:2550 original size:16 final size:16
Alignment explanation
Indices: 2529--2560 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2519 GGGTTCCTTC
*
2529 TATTAATTAAGTCATT
1 TATTAATGAAGTCATT
2545 TATTAATGAAGTCATT
1 TATTAATGAAGTCATT
2561 ATAATATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (16 bp):
TATTAATGAAGTCATT
Found at i:4510 original size:15 final size:13
Alignment explanation
Indices: 4490--4527 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
4480 CTTTCTTAGC
4490 ATTATCATATATATT
1 ATTATCAT-TAT-TT
4505 ATTATCATTATTT
1 ATTATCATTATTT
4518 A-TATCATTAT
1 ATTATCATTAT
4528 CATCAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 3 0.13
14 3 0.13
15 8 0.35
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTATCATTATTT
Found at i:4671 original size:2 final size:2
Alignment explanation
Indices: 4664--4690 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4654 CATATCCATC
4664 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
4691 GTATTTGTTA
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:4823 original size:23 final size:23
Alignment explanation
Indices: 4797--4857 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
4787 CTCGTATAAA
* *
4797 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
4820 TGCACCGTATTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
4843 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
4858 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:5571 original size:13 final size:14
Alignment explanation
Indices: 5555--5587 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
5545 ATTACATATT
5555 TATATCAC-ATTCA
1 TATATCACAATTCA
5568 TATATCACTAATTCA
1 TATATCAC-AATTCA
5583 TATAT
1 TATAT
5588 AATTACATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
15 10 0.56
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (14 bp):
TATATCACAATTCA
Found at i:6505 original size:20 final size:20
Alignment explanation
Indices: 6480--6517 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6470 CATTTTCCTT
*
6480 TAGGGGTATCGATACCCTAC
1 TAGGGGTATCAATACCCTAC
6500 TAGGGGTATCAATACCCT
1 TAGGGGTATCAATACCCT
6518 CATGACATTA
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:0.24, T:0.26
Consensus pattern (20 bp):
TAGGGGTATCAATACCCTAC
Found at i:9835 original size:2 final size:2
Alignment explanation
Indices: 9828--9887 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
9818 CATATCCATC
9828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9870 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
9888 TGTTATGGTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10048 original size:23 final size:23
Alignment explanation
Indices: 9991--10049 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
9981 CGTATAAATG
* * *
9991 CACCAAAGTGCCGCGTAGAATTG
1 CACCATAGTGCCACGTAGAATTA
*
10014 CACCATACTGCCACGTAGAATTA
1 CACCATAGTGCCACGTAGAATTA
*
10037 CACCGTAGTGCCA
1 CACCATAGTGCCA
10050 TATAATAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.19
Consensus pattern (23 bp):
CACCATAGTGCCACGTAGAATTA
Found at i:12799 original size:16 final size:16
Alignment explanation
Indices: 12757--12873 Score: 96
Period size: 16 Copynumber: 7.2 Consensus size: 16
12747 TTTAAACTGT
*
12757 AATAAAAAACAAATAC
1 AATAAAAAACAAATGC
* * *
12773 AATCAATAACAAATTC
1 AATAAAAAACAAATGC
*
12789 AATATAAAACAAATGC
1 AATAAAAAACAAATGC
***
12805 AAGCTAAAACAAA-GTC
1 AATAAAAAACAAATG-C
12821 AATCTAAAAAA-AAATGC
1 AA--TAAAAAACAAATGC
12838 AATAAAAAACAAACT-C
1 AATAAAAAACAAA-TGC
12854 AATAAAAAAACAAATGC
1 AAT-AAAAAACAAATGC
12871 AAT
1 AAT
12874 CAATAAGAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
15 8 0.10
16 47 0.58
17 21 0.26
18 5 0.06
ACGTcount: A:0.65, C:0.15, G:0.04, T:0.16
Consensus pattern (16 bp):
AATAAAAAACAAATGC
Found at i:12847 original size:33 final size:33
Alignment explanation
Indices: 12759--12876 Score: 132
Period size: 32 Copynumber: 3.6 Consensus size: 33
12749 TAAACTGTAA
* * *
12759 TAAAAAACAAATACAATCAATAACAAATTCAA-
1 TAAAAAACAAATGCAATCAAAAACAAACTCAAT
* * * *
12791 TATAAAACAAATGCAAGCTAAAACAAAGTCAAT
1 TAAAAAACAAATGCAATCAAAAACAAACTCAAT
*
12824 CTAAAAAA-AAATGCAATAAAAAACAAACTCAAT
1 -TAAAAAACAAATGCAATCAAAAACAAACTCAAT
*
12857 AAAAAAACAAATGCAATCAA
1 TAAAAAACAAATGCAATCAA
12877 TAAGAAATTC
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
32 32 0.46
33 32 0.46
34 6 0.09
ACGTcount: A:0.64, C:0.15, G:0.04, T:0.16
Consensus pattern (33 bp):
TAAAAAACAAATGCAATCAAAAACAAACTCAAT
Found at i:13627 original size:26 final size:26
Alignment explanation
Indices: 13541--13702 Score: 148
Period size: 26 Copynumber: 6.0 Consensus size: 26
13531 ATATTAACAC
*
13541 AATAACAGTCTGCACT-AACAAGTTATGT
1 AATAACAGTATGCA-TGAACAA--TATGT
* * * *
13569 AATAACAGTATTCAATTATTCCAATATGC
1 AATAACAGTATGC-ATGA--ACAATATGT
*
13598 AATAATAGTATGCATGAACAATATGT
1 AATAACAGTATGCATGAACAATATGT
*
13624 AATAACAGTATGCATGAACAATATGC
1 AATAACAGTATGCATGAACAATATGT
*
13650 AATAACATTATGCA-GTAACAATATGT
1 AATAACAGTATGCATG-AACAATATGT
* * *
13676 AATAACACTATGGATGAAGAATATGT
1 AATAACAGTATGCATGAACAATATGT
13702 A
1 A
13703 TTAGCAAGTT
Statistics
Matches: 112, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
25 1 0.01
26 75 0.67
27 1 0.01
28 15 0.13
29 17 0.15
31 3 0.03
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (26 bp):
AATAACAGTATGCATGAACAATATGT
Found at i:13681 original size:13 final size:13
Alignment explanation
Indices: 13590--13687 Score: 92
Period size: 13 Copynumber: 7.5 Consensus size: 13
13580 TCAATTATTC
13590 CAATATGCAATAA
1 CAATATGCAATAA
* *
13603 TAGTATGC-ATGAA
1 CAATATGCAAT-AA
*
13616 CAATATGTAATAA
1 CAATATGCAATAA
*
13629 CAGTATGC-ATGAA
1 CAATATGCAAT-AA
13642 CAATATGCAATAA
1 CAATATGCAATAA
* *
13655 CATTATGCAGTAA
1 CAATATGCAATAA
*
13668 CAATATGTAATAA
1 CAATATGCAATAA
*
13681 CACTATG
1 CAATATG
13688 GATGAAGAAT
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
12 4 0.06
13 59 0.88
14 4 0.06
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (13 bp):
CAATATGCAATAA
Found at i:15668 original size:15 final size:15
Alignment explanation
Indices: 15650--15747 Score: 67
Period size: 15 Copynumber: 6.5 Consensus size: 15
15640 GCTTAGCTGG
*
15650 TTCTGGTTCATTAAT
1 TTCTGGTTCACTAAT
* **
15665 TTCTGGCTCAGCTGGT
1 TTCTGGTTCA-CTAAT
*
15681 TT-TGGTTCATTAAT
1 TTCTGGTTCACTAAT
* * *
15695 TTTTGGCTCAACT-AG
1 TTCTGGTTC-ACTAAT
*
15710 TTCTGGTTCATTAAT
1 TTCTGGTTCACTAAT
15725 TT-TGGGTTCACTAAT
1 TTCT-GGTTCACTAAT
15740 TTCTGGTT
1 TTCTGGTT
15748 TTGCTTCATC
Statistics
Matches: 61, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
14 7 0.11
15 47 0.77
16 7 0.11
ACGTcount: A:0.16, C:0.15, G:0.19, T:0.49
Consensus pattern (15 bp):
TTCTGGTTCACTAAT
Found at i:15727 original size:30 final size:30
Alignment explanation
Indices: 15594--15726 Score: 212
Period size: 30 Copynumber: 4.4 Consensus size: 30
15584 ATCAATTTTA
*
15594 GGTTCATTAATTTCTGGCTTAGCTGGTTCT
1 GGTTCATTAATTTCTGGCTCAGCTGGTTCT
*
15624 GGTTCATTAATTTCTGGCTTAGCTGGTTCT
1 GGTTCATTAATTTCTGGCTCAGCTGGTTCT
*
15654 GGTTCATTAATTTCTGGCTCAGCTGGTTTT
1 GGTTCATTAATTTCTGGCTCAGCTGGTTCT
* * *
15684 GGTTCATTAATTTTTGGCTCAACTAGTTCT
1 GGTTCATTAATTTCTGGCTCAGCTGGTTCT
15714 GGTTCATTAATTT
1 GGTTCATTAATTT
15727 TGGGTTCACT
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 97 1.00
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (30 bp):
GGTTCATTAATTTCTGGCTCAGCTGGTTCT
Found at i:15744 original size:30 final size:31
Alignment explanation
Indices: 15594--15747 Score: 167
Period size: 30 Copynumber: 5.1 Consensus size: 31
15584 ATCAATTTTA
* *
15594 GGTTCATTAATTTCT-GGCTTAGCTGGTTCT
1 GGTTCATTAATTTCTGGGCTCAGCTAGTTCT
* *
15624 GGTTCATTAATTTCT-GGCTTAGCTGGTTCT
1 GGTTCATTAATTTCTGGGCTCAGCTAGTTCT
* *
15654 GGTTCATTAATTTCT-GGCTCAGCTGGTTTT
1 GGTTCATTAATTTCTGGGCTCAGCTAGTTCT
* *
15684 GGTTCATTAATTT-TTGGCTCAACTAGTTCT
1 GGTTCATTAATTTCTGGGCTCAGCTAGTTCT
* *
15714 GGTTCATTAATTT-TGGGTTCA-CTAATTTCT
1 GGTTCATTAATTTCTGGGCTCAGCT-AGTTCT
15744 GGTT
1 GGTT
15748 TTGCTTCATC
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
29 3 0.03
30 111 0.97
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (31 bp):
GGTTCATTAATTTCTGGGCTCAGCTAGTTCT
Found at i:16354 original size:17 final size:17
Alignment explanation
Indices: 16334--16375 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
16324 CACTAAACAT
16334 ATATATTCATGCAGAAC
1 ATATATTCATGCAGAAC
*
16351 ATATA--CATGCAGTAC
1 ATATATTCATGCAGAAC
16366 ATATATTCAT
1 ATATATTCAT
16376 TGATTTCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 14 0.64
17 8 0.36
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (17 bp):
ATATATTCATGCAGAAC
Found at i:16449 original size:19 final size:18
Alignment explanation
Indices: 16425--16532 Score: 63
Period size: 17 Copynumber: 6.4 Consensus size: 18
16415 ATTCTATCAC
16425 AACATATATTATATCAATA
1 AACATATATTATATC-ATA
*
16444 AACATA-AAT-TATC--A
1 AACATATATTATATCATA
*
16458 AA-ATA-AATATATCAT-
1 AACATATATTATATCATA
* *
16473 AACATATATTATATAAAA
1 AACATATATTATATCATA
* * *
16491 AAAAT-TATTCTATCGT-
1 AACATATATTATATCATA
*
16507 AACATATATTCTATCAATA
1 AACATATATTATATC-ATA
16526 AACATAT
1 AACATAT
16533 CATCAATAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
13 6 0.09
14 7 0.10
15 2 0.03
16 7 0.10
17 27 0.39
18 7 0.10
19 13 0.19
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (18 bp):
AACATATATTATATCATA
Found at i:16539 original size:15 final size:15
Alignment explanation
Indices: 16519--16547 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16509 CATATATTCT
16519 ATCAATAAACATATC
1 ATCAATAAACATATC
16534 ATCAATAAACATAT
1 ATCAATAAACATAT
16548 AAATTAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (15 bp):
ATCAATAAACATATC
Found at i:17362 original size:28 final size:29
Alignment explanation
Indices: 17300--17371 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
17290 TTTAACGGAG
* *
17300 AGTGGTCTGATTGAATCAATTAAAAGGTTT
1 AGTGGTCTGATTGAATCAA-TAAAAAGTTC
17330 AGTGGTCTGATTGAGA-CAA-AAAAAGTTC
1 AGTGGTCTGATTGA-ATCAATAAAAAGTTC
*
17358 AGTGGTCAGATTGA
1 AGTGGTCTGATTGA
17372 TTAATGACCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 20 0.53
30 17 0.45
31 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (29 bp):
AGTGGTCTGATTGAATCAATAAAAAGTTC
Found at i:27013 original size:21 final size:21
Alignment explanation
Indices: 26968--27012 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
26958 CGTTTATAAA
* *
26968 TTTTAAAAAATTTAAAATTAT
1 TTTTAAAAAATATAAAATCAT
26989 TTTTAAAAAA-ATAAAATCAT
1 TTTTAAAAAATATAAAATCAT
27009 TTTT
1 TTTT
27013 TTCTAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTTAAAAAATATAAAATCAT
Found at i:28149 original size:14 final size:14
Alignment explanation
Indices: 28130--28156 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28120 AAATTAAACT
28130 TAAATATTAATATG
1 TAAATATTAATATG
28144 TAAATATTAATAT
1 TAAATATTAATAT
28157 TATATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
TAAATATTAATATG
Found at i:33338 original size:3 final size:3
Alignment explanation
Indices: 33332--33356 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
33322 TTCACTACCA
33332 TCC TCC TCC TCC TCC TCC TCC TCC T
1 TCC TCC TCC TCC TCC TCC TCC TCC T
33357 TATCGTCGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (3 bp):
TCC
Found at i:34965 original size:22 final size:22
Alignment explanation
Indices: 34928--34971 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
34918 ACATCCATCC
*
34928 CCATCTCCGACGAAATCAGTCT
1 CCATCTCCGACAAAATCAGTCT
* *
34950 CCATCTCCGGCAAAATCCGTCT
1 CCATCTCCGACAAAATCAGTCT
34972 ATCTCCATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACAAAATCAGTCT
Found at i:35252 original size:17 final size:17
Alignment explanation
Indices: 35230--35266 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
35220 ACCCTGTGAA
35230 TTTAGTATTTGTCTTTG
1 TTTAGTATTTGTCTTTG
35247 TTTAGTATTTGTCTTTG
1 TTTAGTATTTGTCTTTG
35264 TTT
1 TTT
35267 TGTCTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.05, G:0.16, T:0.68
Consensus pattern (17 bp):
TTTAGTATTTGTCTTTG
Found at i:35503 original size:20 final size:20
Alignment explanation
Indices: 35474--35605 Score: 221
Period size: 20 Copynumber: 6.6 Consensus size: 20
35464 TTTTCCGACT
35474 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
35494 ATCACAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
35514 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
35534 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
35554 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
35574 ATCGCAATGCGATTATG-ACT
1 ATCGCAATGCGAATATGTA-A
35594 ATCGCAATGCGA
1 ATCGCAATGCGA
35606 TTCGGACTAT
Statistics
Matches: 107, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
19 1 0.01
20 106 0.99
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:35606 original size:20 final size:20
Alignment explanation
Indices: 35470--35680 Score: 153
Period size: 20 Copynumber: 10.6 Consensus size: 20
35460 GCGATTTTCC
35470 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATAT
* *
35490 GTA-AATCACAATGCGAATAT
1 G-ACTATCGCAATGCGAATAT
*
35510 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGAATAT
*
35530 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGAATAT
*
35550 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGAATAT
* *
35570 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGAATAT
* **
35590 GACTATCGCAATGCGATTCG
1 GACTATCGCAATGCGAATAT
* * *
35610 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGAATAT
* * * *
35630 GACTGTCGCAACGCGATTCT
1 GACTATCGCAATGCGAATAT
* * * *
35650 GACTGTCGCAACGCGATTCT
1 GACTATCGCAATGCGAATAT
35670 GACTATCGCAA
1 GACTATCGCAA
35681 CACTGAATTT
Statistics
Matches: 178, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
19 1 0.01
20 176 0.99
21 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (20 bp):
GACTATCGCAATGCGAATAT
Found at i:35618 original size:60 final size:60
Alignment explanation
Indices: 35498--35680 Score: 176
Period size: 60 Copynumber: 3.0 Consensus size: 60
35488 ATGTAAATCA
* * * *
35498 CAATGCGAATATGTAAATCGCAATGCGAATATGTA-AATCGCAATGCGAATAT-GTA-AATCG
1 CAATGCGAATATGTAAATCGCAATGCGATTATG-ACTATCGCAATGCG-AT-TCGGACTATCG
35558 CAATGCGAATATGTAAATCGCAATGCGATTATGACTATCGCAATGCGATTCGGACTATCG
1 CAATGCGAATATGTAAATCGCAATGCGATTATGACTATCGCAATGCGATTCGGACTATCG
* * * ** * * * * *
35618 CAACGCGATTCTG-ACTGTCGCAACGCGATTCTGACTGTCGCAACGCGATTCTGACTATCG
1 CAATGCGAATATGTA-AATCGCAATGCGATTATGACTATCGCAATGCGATTCGGACTATCG
35678 CAA
1 CAA
35681 CACTGAATTT
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
58 1 0.01
59 6 0.06
60 98 0.93
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (60 bp):
CAATGCGAATATGTAAATCGCAATGCGATTATGACTATCGCAATGCGATTCGGACTATCG
Found at i:35681 original size:20 final size:20
Alignment explanation
Indices: 35574--35681 Score: 162
Period size: 20 Copynumber: 5.4 Consensus size: 20
35564 GAATATGTAA
* *
35574 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
* *
35594 ATCGCAATGCGATTCGGACT
1 ATCGCAACGCGATTCTGACT
35614 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
35634 GTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
35654 GTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
35674 ATCGCAAC
1 ATCGCAAC
35682 ACTGAATTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:36280 original size:14 final size:14
Alignment explanation
Indices: 36261--36287 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36251 CGGGTAGTAA
36261 TCAACCCCAGTTTT
1 TCAACCCCAGTTTT
36275 TCAACCCCAGTTT
1 TCAACCCCAGTTT
36288 ATGGTGCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.37, G:0.07, T:0.33
Consensus pattern (14 bp):
TCAACCCCAGTTTT
Found at i:36535 original size:24 final size:24
Alignment explanation
Indices: 36503--36556 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
36493 GTATTCGAAA
36503 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
36527 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
36551 TTTGAT
1 TTTGAT
36557 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:38814 original size:18 final size:18
Alignment explanation
Indices: 38791--38825 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
38781 AGAAAAAGGC
*
38791 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
38809 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
38826 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:39147 original size:139 final size:140
Alignment explanation
Indices: 38885--39153 Score: 504
Period size: 139 Copynumber: 1.9 Consensus size: 140
38875 AAACATTGTA
38885 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
38950 TGATTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
39015 TATGTGTATT
131 TATGTGTATT
*
39025 TTATGTGT-AACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGTTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
39089 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
39154 CGCAACGCGA
Statistics
Matches: 126, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
139 118 0.94
140 8 0.06
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
TATGTGTATT
Found at i:39149 original size:20 final size:20
Alignment explanation
Indices: 39124--39386 Score: 243
Period size: 20 Copynumber: 13.8 Consensus size: 20
39114 TTACACATTC
*
39124 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
39144 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
39164 A-TTGATTATCGCAACTC--
1 ATTTGACTATCGCAACGCGA
*
39181 A---GA-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
39197 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* *
39217 ATATGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
39237 ATTTGCCTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
*
39257 ATTTGCCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
39277 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
39297 ATTTGATTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
* *
39317 ATTTGACTATTGCAACGAGA
1 ATTTGACTATCGCAACGCGA
39337 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
39351 ATTTTATTATCGCAACAG-GT
1 ATTTGACTATCGCAAC-GCGA
39371 A-TTGACTATCGCAACG
1 ATTTGACTATCGCAACG
39387 AGAAAATTGC
Statistics
Matches: 204, Mismatches: 24, Indels: 32
0.78 0.09 0.12
Matches are distributed among these distances:
14 20 0.10
15 2 0.01
16 2 0.01
17 1 0.00
18 2 0.01
19 29 0.14
20 146 0.72
21 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:39415 original size:53 final size:52
Alignment explanation
Indices: 39285--39436 Score: 160
Period size: 53 Copynumber: 2.8 Consensus size: 52
39275 GAATTTGACT
* * * *
39285 ATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATTGCAACGAGAAA
1 ATCGCAAAGCGAATTAGACTATCGCAACGG-TA-TTGACTATCGCAACGAGAAA
* ** *
39339 ATCGCAACGCGAATTTTATTATCGCAACAGGTATTGACTATCGCAACGAGAAA
1 ATCGCAAAGCGAATTAGACTATCGCAAC-GGTATTGACTATCGCAACGAGAAA
* * * *
39392 ATTGCAAAGCGTATTAGACTATCGCAACGCGAATTGACTTTCGCA
1 ATCGCAAAGCGAATTAGACTATCGCAACG-GTATTGACTATCGCA
39437 TTGCGATTTT
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
52 1 0.01
53 54 0.63
54 29 0.34
55 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (52 bp):
ATCGCAAAGCGAATTAGACTATCGCAACGGTATTGACTATCGCAACGAGAAA
Found at i:39454 original size:20 final size:20
Alignment explanation
Indices: 39429--39467 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
39419 CGCGAATTGA
39429 CTTTCGCATTGCGATTTTGT
1 CTTTCGCATTGCGATTTTGT
39449 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
39468 AGTTTAGCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.49
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGT
Found at i:39480 original size:20 final size:20
Alignment explanation
Indices: 39425--39482 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
39415 GCAACGCGAA
*
39425 TTGACTTTCGCATTGCGATT
1 TTGACTTTAGCATTGCGATT
* *
39445 TTGTCTTTCGCATTGCGATT
1 TTGACTTTAGCATTGCGATT
* *
39465 TTGAGTTTAGCGTTGCGA
1 TTGACTTTAGCATTGCGA
39483 AAGTATACCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (20 bp):
TTGACTTTAGCATTGCGATT
Found at i:39610 original size:14 final size:13
Alignment explanation
Indices: 39586--39641 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 13
39576 ATAAGAATTA
*
39586 TTTACACATCAAT
1 TTTACAAATCAAT
*
39599 ATTAACAAATCAACT
1 -TTTACAAATCAA-T
39614 TTTACAAATCAATT
1 TTTACAAATCAA-T
*
39628 TTTATAAATCAAT
1 TTTACAAATCAAT
39641 T
1 T
39642 AAACAAGCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
13 2 0.06
14 33 0.92
15 1 0.03
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (13 bp):
TTTACAAATCAAT
Found at i:41137 original size:42 final size:42
Alignment explanation
Indices: 41030--41141 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
41020 TCTAGAATGT
* * *
41030 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** * *
41072 TGGGAGGGGACTCTTGAGGGATGATAGGGGTCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
41114 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
41142 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:41669 original size:20 final size:20
Alignment explanation
Indices: 41638--41713 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
41628 TCGCAACACG
41638 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
* *
41658 AATTATTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
41678 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
41698 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
41714 AGAGAATCGC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:41815 original size:19 final size:20
Alignment explanation
Indices: 41756--41822 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
41746 GCGATTCTTT
*
41756 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
41776 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
41796 CGTTGCGATAGTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
41815 CGTTGCGA
1 CGTTGCGA
41823 AAGTAAACTA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 13 0.28
20 33 0.72
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:41992 original size:18 final size:18
Alignment explanation
Indices: 41969--42018 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
41959 TTTACTAAGC
41969 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
41987 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
42005 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
42019 TATGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:43746 original size:20 final size:20
Alignment explanation
Indices: 43723--43810 Score: 79
Period size: 20 Copynumber: 4.5 Consensus size: 20
43713 TTTGAAACTT
43723 AAAATCGCAACACGAAAATA
1 AAAATCGCAACACGAAAATA
*
43743 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATA
** * **
43763 ACTATCGCAACGCGAATTTA
1 AAAATCGCAACACGAAAATA
** * *
43783 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATA
43802 AAAATCGCA
1 AAAATCGCA
43811 TTGCGATGCT
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
19 7 0.12
20 50 0.88
ACGTcount: A:0.48, C:0.24, G:0.14, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATA
Done.