Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008765.1 Hibiscus syriacus cultivar Beakdansim tig00111861_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: 51336
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1684 original size:24 final size:24
Alignment explanation
Indices: 1650--1703 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1640 CTGAAACATC
* *
1650 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1674 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1698 ATCAAA
1 ATCAAA
1704 TTTCGAATAC
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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:2788 original size:20 final size:20
Alignment explanation
Indices: 2760--2820 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
2750 GACATTCATT
2760 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAAAA
*
2780 TGGCTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAAAA
* *
2800 TGATTATCGCAACGAGAAAA
1 TGACTATCGCAACGCGAAAA
2820 T
1 T
2821 CGCAATGCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACGCGAAAA
Found at i:2863 original size:14 final size:14
Alignment explanation
Indices: 2844--2897 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
2834 GAAAATCGCA
2844 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
2858 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
2875 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
2891 TTGCGAT
1 TTGCGAT
2898 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:2881 original size:33 final size:33
Alignment explanation
Indices: 2839--2916 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
2829 AAAATGAAAA
***
2839 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
2872 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
2905 TCGCGTTGCGAT
1 TCGCATTGCGAT
2917 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:4943 original size:20 final size:19
Alignment explanation
Indices: 4908--4974 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
4898 GAAACTTAAA
4908 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
4927 ATCGCAACGCAGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
4947 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
4966 ATCGCAACG
1 ATCGCAACG
4975 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:4982 original size:14 final size:14
Alignment explanation
Indices: 4963--5020 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4953 ATGCGAAATG
4963 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
4977 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
4993 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
5009 AAAATCGCAACG
1 AAAATCGCAACG
5021 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:5005 original size:32 final size:32
Alignment explanation
Indices: 4905--5025 Score: 143
Period size: 32 Copynumber: 3.5 Consensus size: 32
4895 TACGAAACTT
* *
4905 AAAATCGCAACGCGAAATGACTATCGCAACGCAG
1 AAAATCGCAACGCGAAATGA-AATCGCAACG-AC
*
4939 AAATGGCTATCGCAATGCGAAATGAAAATCGCAACGAC
1 AAA-----ATCGCAACGCGAAATG-AAATCGCAACGAC
4977 AAAATCGCAACGCGAAATGAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAATCGCAACGAC
5009 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
5026 CACAAATCGC
Statistics
Matches: 77, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
32 30 0.39
33 15 0.19
34 3 0.04
38 4 0.05
39 24 0.31
40 1 0.01
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.12
Consensus pattern (32 bp):
AAAATCGCAACGCGAAATGAAATCGCAACGAC
Found at i:5573 original size:18 final size:18
Alignment explanation
Indices: 5547--5591 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5537 GTCGATCAGA
*
5547 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
5565 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
5583 TGATGGCTC
1 TGATGGCTC
5592 CCGAAATGGA
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:7237 original size:22 final size:22
Alignment explanation
Indices: 7212--7255 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
7202 GATTTAGATA
7212 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
7234 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
7256 TGAGAGAGTG
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:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:7468 original size:20 final size:20
Alignment explanation
Indices: 7443--7536 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
7433 GATTATGTAT
7443 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
7463 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
7483 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
7504 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
7524 TATCGCATTGCGA
1 TATCGCGTTGCGA
7537 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:7537 original size:20 final size:20
Alignment explanation
Indices: 7423--7537 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
7413 CGCTTTGAAA
*
7423 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
7444 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
7464 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
7484 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
7505 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
7525 ATCGCATTGCGAT
1 ATCGCATTGCGAT
7538 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:7555 original size:21 final size:21
Alignment explanation
Indices: 7526--7618 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
7516 ATAGTCAGTA
7526 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
7547 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
7567 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
7588 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
7608 TCGCATTGCGA
1 TCGCATTGCGA
7619 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:7556 original size:41 final size:41
Alignment explanation
Indices: 7465--7599 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
7455 AAAGTCAGTA
* * * ** *
7465 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
7505 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
7547 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
7588 TCGCGTTGCGAT
1 TCGCGTTGCGAT
7600 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:7600 original size:41 final size:41
Alignment explanation
Indices: 7526--7618 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
7516 ATAGTCAGTA
7526 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
7567 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
7608 TCGCATTGCGA
1 TCGCATTGCGA
7619 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:9706 original size:118 final size:118
Alignment explanation
Indices: 9498--9737 Score: 471
Period size: 118 Copynumber: 2.0 Consensus size: 118
9488 CTTTATTCAC
9498 AATATTTAATTATTATAATATTAATTTTGCAAATGTAAAATAAAACATATACATTTCTAATAAAT
1 AATATTTAATTATTATAATATTAATTTTGCAAATGTAAAATAAAACATATACATTTCTAATAAAT
*
9563 ATCAAGATAAAAAACATAAATAAAATATTCATAAATAATATTACGAAAATATA
66 ATCAAGATAAAAAACATAAATAAAATATTCATAAATAACATTACGAAAATATA
9616 AATATTTAATTATTATAATATTAATTTTGCAAATGTAAAATAAAACATATACATTTCTAATAAAT
1 AATATTTAATTATTATAATATTAATTTTGCAAATGTAAAATAAAACATATACATTTCTAATAAAT
9681 ATCAAGATAAAAAACATAAATAAAATATTCATAAATAACATTACGAAAATATA
66 ATCAAGATAAAAAACATAAATAAAATATTCATAAATAACATTACGAAAATATA
9734 AATA
1 AATA
9738 AATAAGAAAA
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 121 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.34
Consensus pattern (118 bp):
AATATTTAATTATTATAATATTAATTTTGCAAATGTAAAATAAAACATATACATTTCTAATAAAT
ATCAAGATAAAAAACATAAATAAAATATTCATAAATAACATTACGAAAATATA
Found at i:9978 original size:25 final size:24
Alignment explanation
Indices: 9924--10009 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 24
9914 AAATTACAAT
*
9924 AAAAAAATATAAAAGATAGAATAAGAA
1 AAAAAAATATAACA-A-AGAA-AAGAA
*
9951 AAAAATAATATAACAAAGAAAAGGA
1 AAAAA-AATATAACAAAGAAAAGAA
*
9976 AAAGAAA-ATAACAAA-AGAAAGTAA
1 AAAAAAATATAACAAAGA-AAAG-AA
10000 AAAAATAATA
1 AAAAA-AATA
10010 AAAAAAAACC
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 1 0.02
23 12 0.24
24 7 0.14
25 10 0.20
26 5 0.10
27 6 0.12
28 8 0.16
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.13
Consensus pattern (24 bp):
AAAAAAATATAACAAAGAAAAGAA
Found at i:9996 original size:23 final size:25
Alignment explanation
Indices: 9924--10037 Score: 75
Period size: 22 Copynumber: 4.7 Consensus size: 25
9914 AAATTACAAT
9924 AAAAAAAT-ATAA-AAGATAGAATAA-G
1 AAAAAAATAATAACAA-A-AGAA-AAGG
9949 AAAAAAATAATATA-ACAAAGAAAAGG
1 AAAAAAATAATA-ACA-AAAGAAAAGG
* *
9975 AAAAGAA-AATAACAAAAG-AAAGT
1 AAAAAAATAATAACAAAAGAAAAGG
**
9998 AAAAAAATAAT-A-AAAA-AAAACC
1 AAAAAAATAATAACAAAAGAAAAGG
*
10020 AAAAAAATAATAAAAAAA
1 AAAAAAATAATAACAAAA
10038 TAATATGTAG
Statistics
Matches: 75, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
22 18 0.24
23 12 0.16
24 12 0.16
25 15 0.20
26 14 0.19
27 3 0.04
28 1 0.01
ACGTcount: A:0.77, C:0.04, G:0.08, T:0.11
Consensus pattern (25 bp):
AAAAAAATAATAACAAAAGAAAAGG
Found at i:10011 original size:11 final size:11
Alignment explanation
Indices: 9997--10042 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
9987 CAAAAGAAAG
9997 TAAAAAAATAA
1 TAAAAAAATAA
10008 TAAAAAAA-AA
1 TAAAAAAATAA
*
10018 CCAAAAAAATAA
1 -TAAAAAAATAA
10030 TAAAAAAATAA
1 TAAAAAAATAA
10041 TA
1 TA
10043 TGTAGCGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 2 0.06
11 27 0.87
12 2 0.06
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.15
Consensus pattern (11 bp):
TAAAAAAATAA
Found at i:14502 original size:20 final size:20
Alignment explanation
Indices: 14479--14520 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
14469 TTTATTTTAA
14479 TTCTATTCAATTTAGTCGTG
1 TTCTATTCAATTTAGTCGTG
14499 TTCTATTCAATTTAGTCGTG
1 TTCTATTCAATTTAGTCGTG
14519 TT
1 TT
14521 GCGGCTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.52
Consensus pattern (20 bp):
TTCTATTCAATTTAGTCGTG
Found at i:20935 original size:21 final size:20
Alignment explanation
Indices: 20890--20938 Score: 89
Period size: 20 Copynumber: 2.4 Consensus size: 20
20880 TATTTAAGTC
20890 GAATTTTTTACAAAATAAAT
1 GAATTTTTTACAAAATAAAT
20910 GAATTTTTTACAAAATAAAT
1 GAATTTTTTACAAAATAAAT
20930 GAAATTTTT
1 G-AATTTTT
20939 GAAGTATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (20 bp):
GAATTTTTTACAAAATAAAT
Found at i:21238 original size:45 final size:45
Alignment explanation
Indices: 21187--21276 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
21177 ACTGGTTTGC
* * *
21187 GTCTTTCTGCTTATTCAACTTCTCTAGATTCACCTGCATGCATAA
1 GTCTTTCTGCCTATACAACTTCTCTAGATCCACCTGCATGCATAA
* * *
21232 GTCTTTCTTCCTATACAACTTCTCTTGGTCCACCTGCATGCATAA
1 GTCTTTCTGCCTATACAACTTCTCTAGATCCACCTGCATGCATAA
21277 TTTCTTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.39
Consensus pattern (45 bp):
GTCTTTCTGCCTATACAACTTCTCTAGATCCACCTGCATGCATAA
Found at i:23343 original size:240 final size:238
Alignment explanation
Indices: 22896--23349 Score: 615
Period size: 240 Copynumber: 1.9 Consensus size: 238
22886 CCAGTAGTGA
* * ** *
22896 AATATTATGAATTTCATCATTCGTGCATAAATCTGTACTGGGTAAATTGTCCGGATCAGAAAATT
1 AATATTATGAATTTCATCAGTCGTGCAGAAATCTGTACCAGGTAAATTGTCAGGATCAGAAAATT
* * * * *
22961 TCCCCGAGAACTGCATCATCTGTTTACTGGAAAAATTCTGAGGGAGATAGTTCAGGAAAACTCGT
66 TCCCCGAGAACTGCAACATCAGTTCAATGGAAAAATTCTGAGGGAGATAGGTCAGGAAAACTCGT
* * * **
23026 GGAGATCCCAATGCCTGAAATGATATTGGATGAGGCAGAGGATTCAATTATTAATGGATGATGGT
131 GGAGATCCCAATGCCTGAAATGATATTCGATGAGGCAGAGGATTCAACTATTAATAGATGATGAA
*
23091 CTGCATTATCATCTGTAACCGCAGGCAACATCTGTACTGGGTG
196 CTACATTATCATCTGTAACCGCAGGCAACATCTGTACTGGGTG
*
23134 AATATTATGAATTTCATCAGTCGTGCAGAAATCTGTACCAGGTAAATTGTCAGGATCAGAAGATT
1 AATATTATGAATTTCATCAGTCGTGCAGAAATCTGTACCAGGTAAATTGTCAGGATCAGAAAATT
** * * ** * *
23199 TCCCCGAGAGTTGCAACATCAGTTCAATGGGAAGATTCAGTGAGGGATCTGGGTCAGGTAAACTC
66 TCCCCGAGAACTGCAACATCAGTTCAATGGAAAAATTC--TGAGGGAGATAGGTCAGGAAAACTC
* *
23264 GTGGAGATTCCATTG-CTAGAAATGATATTCGATGAGGCAGAGGATTCAACTA-TATATAGATGA
129 GTGGAGATCCCAATGCCT-GAAATGATATTCGATGAGGCAGAGGATTCAACTATTA-ATAGATGA
23327 TGAACTACATTATCATCTGTAAC
192 TGAACTACATTATCATCTGTAAC
23350 TGCGGGCATT
Statistics
Matches: 185, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
238 89 0.48
239 4 0.02
240 92 0.50
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (238 bp):
AATATTATGAATTTCATCAGTCGTGCAGAAATCTGTACCAGGTAAATTGTCAGGATCAGAAAATT
TCCCCGAGAACTGCAACATCAGTTCAATGGAAAAATTCTGAGGGAGATAGGTCAGGAAAACTCGT
GGAGATCCCAATGCCTGAAATGATATTCGATGAGGCAGAGGATTCAACTATTAATAGATGATGAA
CTACATTATCATCTGTAACCGCAGGCAACATCTGTACTGGGTG
Found at i:27334 original size:12 final size:13
Alignment explanation
Indices: 27311--27343 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
27301 TATATTTTTA
*
27311 TTATAATTATATT
1 TTATATTTATATT
27324 TT-TATTTATATT
1 TTATATTTATATT
27336 TTATATTT
1 TTATATTT
27344 TTTTTGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATATTTATATT
Found at i:27354 original size:18 final size:21
Alignment explanation
Indices: 27301--27364 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 21
27291 TTATATAAAA
27301 TATATTTTTA-TTATA---AT
1 TATATTTTTATTTATATTTAT
27318 TATATTTTTATTTATA-TT-T
1 TATATTTTTATTTATATTTAT
27337 TATATTTTT-TTTGA-ATTTAT
1 TATATTTTTATTT-ATATTTAT
27357 TATATTTT
1 TATATTTT
27365 AAATTGATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
17 10 0.24
18 9 0.22
19 13 0.32
20 9 0.22
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TATATTTTTATTTATATTTAT
Found at i:27598 original size:3 final size:3
Alignment explanation
Indices: 27590--27614 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
27580 CTTTCCATTC
27590 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
27615 TTCATATAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28620 original size:24 final size:24
Alignment explanation
Indices: 28593--28643 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
28583 TATTAAAATT
*
28593 GTATTACTTCATTACTGGCACTTG
1 GTATTACTTCATTACTAGCACTTG
*
28617 GTATTACTTCATTCCTAGCACTTG
1 GTATTACTTCATTACTAGCACTTG
28641 GTA
1 GTA
28644 ATATGGCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (24 bp):
GTATTACTTCATTACTAGCACTTG
Found at i:29668 original size:21 final size:20
Alignment explanation
Indices: 29638--29679 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
29628 TTTTTTATTC
29638 GAATTATTTTTTTCATTTTTT
1 GAATTA-TTTTTTCATTTTTT
* *
29659 GAATTGTTTTTTCTTTTTTT
1 GAATTATTTTTTCATTTTTT
29679 G
1 G
29680 GAACATGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.14, C:0.05, G:0.10, T:0.71
Consensus pattern (20 bp):
GAATTATTTTTTCATTTTTT
Found at i:29845 original size:25 final size:25
Alignment explanation
Indices: 29813--29868 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
29803 GTTAACTAAT
29813 GGGAAATAATAGGATAGACATTTTG
1 GGGAAATAATAGGATAGACATTTTG
29838 GGGAAATAATAGGATAGACATTTTG
1 GGGAAATAATAGGATAGACATTTTG
*
29863 AGGAAA
1 GGGAAA
29869 AATGTAGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.29, T:0.25
Consensus pattern (25 bp):
GGGAAATAATAGGATAGACATTTTG
Found at i:32076 original size:3 final size:3
Alignment explanation
Indices: 32060--32130 Score: 106
Period size: 3 Copynumber: 23.7 Consensus size: 3
32050 TTTTTACCCA
* * *
32060 TAT TAT AAT AAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
32108 TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
32131 AATATATATT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:32086 original size:21 final size:21
Alignment explanation
Indices: 32060--32130 Score: 124
Period size: 21 Copynumber: 3.4 Consensus size: 21
32050 TTTTTACCCA
* *
32060 TATTATAATAATTATTATTAT
1 TATTATTATCATTATTATTAT
32081 TATTATTATCATTATTATTAT
1 TATTATTATCATTATTATTAT
32102 TATTATTATCATTATTATTAT
1 TATTATTATCATTATTATTAT
32123 TATTATTA
1 TATTATTA
32131 AATATATATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTATTATCATTATTATTAT
Found at i:32153 original size:14 final size:15
Alignment explanation
Indices: 32129--32158 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
32119 TTATTATTAT
32129 TAAATATATATTAAA
1 TAAATATATATTAAA
32144 TAAATA-ATATTAAA
1 TAAATATATATTAAA
32158 T
1 T
32159 TACAAAGCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:33533 original size:13 final size:13
Alignment explanation
Indices: 33517--33556 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
33507 ATATAATAAA
33517 TAAATATTTATTT
1 TAAATATTTATTT
*
33530 TAAATAAATTATTT
1 TAAAT-ATTTATTT
33544 T-AATATTTATTT
1 TAAATATTTATTT
33556 T
1 T
33557 TCAATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:34784 original size:77 final size:76
Alignment explanation
Indices: 34686--34842 Score: 219
Period size: 77 Copynumber: 2.1 Consensus size: 76
34676 TTTAAATAAG
* **
34686 TTTAGGATATATTTTTTATA-TTTTATCT-TTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGT
1 TTTAGAATATATTTTAAATATTTTTAT-TATT-TTTTAGGTATTTTAGTTTAAATAGGTTTTAGT
*
34749 ATTTTAATTAGTA
64 ATTTTAATTAGGA
* *
34762 TTTAGAATATTATTTTAAATATTTTTATTATTTTTTAGGTATTTTAGTTTAAATAGTTTTTAGTG
1 TTTAGAATA-TATTTTAAATATTTTTATTATTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTA
34827 TTTTAATTAGGA
65 TTTTAATTAGGA
34839 TTTA
1 TTTA
34843 AGATGTTTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
76 8 0.11
77 56 0.78
78 8 0.11
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.59
Consensus pattern (76 bp):
TTTAGAATATATTTTAAATATTTTTATTATTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAGGA
Found at i:34799 original size:33 final size:34
Alignment explanation
Indices: 34748--34823 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 34
34738 TAGGTTTTAG
* *
34748 TATTTTAATTAGTATTTA-GAATATTATTTTAAA
1 TATTTTTATTAGTATTTAGGAATATTAGTTTAAA
* * * *
34781 TATTTTTATTATTTTTTAGGTATTTTAGTTTAAA
1 TATTTTTATTAGTATTTAGGAATATTAGTTTAAA
34815 TAGTTTTTA
1 TA-TTTTTA
34824 GTGTTTTAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 15 0.43
34 14 0.40
35 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (34 bp):
TATTTTTATTAGTATTTAGGAATATTAGTTTAAA
Found at i:40112 original size:64 final size:64
Alignment explanation
Indices: 40029--40238 Score: 259
Period size: 65 Copynumber: 3.2 Consensus size: 64
40019 GTCACTAAGA
*
40029 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTTG
* *
40093 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATGCATAGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGC-CAGAGTGCATCGATGCATGGT
40156 AT-
63 -TG
* **
40158 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAGTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAG-CCA-GAGTGCATCGATGCATGG-T
40221 TG
63 TG
*
40223 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
40239 CTCTGAAAAA
Statistics
Matches: 126, Mismatches: 10, Indels: 19
0.81 0.06 0.12
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 46 0.37
65 70 0.56
66 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTTG
Found at i:42912 original size:23 final size:22
Alignment explanation
Indices: 42876--42957 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
42866 GCATGGCCTT
*
42876 GTGCATCGACGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
42898 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
42920 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
*
42943 GATGTATCGATGCAC
1 G-TGCATCGATGCAC
42958 TGTTAAGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 18 0.38
24 13 0.27
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:42932 original size:21 final size:23
Alignment explanation
Indices: 42880--42957 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 23
42870 GGCCTTGTGC
* *
42880 ATCGACGCACATTCAAGGCG-TGC
1 ATCGATGCACATTCAAGG-GATGT
* * *
42903 ATCGGTGCACCTTC-ATGG-TGT
1 ATCGATGCACATTCAAGGGATGT
42924 ATCGATGCACATTCAAAGGGATGT
1 ATCGATGCACATTC-AAGGGATGT
42948 ATCGATGCAC
1 ATCGATGCAC
42958 TGTTAAGTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
21 15 0.34
22 2 0.05
23 14 0.32
24 13 0.30
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (23 bp):
ATCGATGCACATTCAAGGGATGT
Found at i:49680 original size:77 final size:75
Alignment explanation
Indices: 49492--49707 Score: 292
Period size: 76 Copynumber: 2.8 Consensus size: 75
49482 TTTAAACATT
* * *
49492 ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAAGTTTTAGTATTTTAATTAAGTTTTAGG
1 ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAAT-AGTTTTAGTATTTTAATTAGGATTTAGA
* *
49557 ATATTATTTTT
65 ATATCATTTTA
49568 ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGA
1 ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAGGATTTAGA
49633 ATATCATTTTAA
65 ATATCATTTT-A
* * *
49645 ATATTTTTAT-TATT-TTTTAAGTATTTTAGTTTAAATAGTTTTAAATGTTTTAATTAGGATTTA
1 ATA-TTTTATCT-TTGTTTTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAGGATTTA
49708 AGTTGTTTTA
Statistics
Matches: 127, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
75 1 0.01
76 74 0.58
77 44 0.35
78 8 0.06
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.57
Consensus pattern (75 bp):
ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTTAGAA
TATCATTTTA
Found at i:50386 original size:15 final size:15
Alignment explanation
Indices: 50368--50420 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
50358 ATTTTACTGC
50368 TATTATTTTTTATTT
1 TATTATTTTTTATTT
**
50383 TATTATTTTTCCTTT
1 TATTATTTTTTATTT
50398 TATTTATTATTATCTATTT
1 TA-TTATT-TT-T-TATTT
50417 TATT
1 TATT
50421 TTATTAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 15 0.50
16 5 0.17
17 2 0.07
18 3 0.10
19 5 0.17
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTATTTTTTATTT
Found at i:50400 original size:20 final size:20
Alignment explanation
Indices: 50354--50426 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 20
50344 AAATCCAATT
50354 TTTTATTTTACTGCTATTAT-T-
1 TTTTATTTTA-T--TATTATCTA
* *
50375 TTTTATTTTATTATT-TTTCC
1 TTTTATTTTATTATTATCT-A
50395 TTTTA-TTTATTATTATCTA
1 TTTTATTTTATTATTATCTA
50414 TTTTATTTTATTA
1 TTTTATTTTATTA
50427 AATATTTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
17 1 0.02
18 5 0.11
19 14 0.31
20 15 0.33
21 10 0.22
ACGTcount: A:0.21, C:0.07, G:0.01, T:0.71
Consensus pattern (20 bp):
TTTTATTTTATTATTATCTA
Done.