Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003293.1 Hibiscus syriacus cultivar Beakdansim tig00006924_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: 65118
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:6832 original size:24 final size:24
Alignment explanation
Indices: 6805--6854 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
6795 ATTTGATATG
*
6805 GTTATCAAGTTAATCATTAAACTA
1 GTTAACAAGTTAATCATTAAACTA
6829 GTTAACAAGTTAATCATTAAACTA
1 GTTAACAAGTTAATCATTAAACTA
6853 GT
1 GT
6855 GTTTGATGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (24 bp):
GTTAACAAGTTAATCATTAAACTA
Found at i:12427 original size:32 final size:33
Alignment explanation
Indices: 12391--12465 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
12381 GTCTTTCGAG
*
12391 ACATATGGACAGGATTACCTATGTTCTAAG-GA
1 ACATATGGACAGGATTACCTAGGTTCTAAGAGA
* * **
12423 ACATATGGATA-GTTTACCTAGGTTCTTCGAGA
1 ACATATGGACAGGATTACCTAGGTTCTAAGAGA
12455 AC-TATGGACAG
1 ACATATGGACAG
12466 TTGTCGAGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 21 0.60
32 14 0.40
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (33 bp):
ACATATGGACAGGATTACCTAGGTTCTAAGAGA
Found at i:16118 original size:2 final size:2
Alignment explanation
Indices: 16111--16137 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16101 GAAGATTGTG
16111 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
16138 AAAGCGTATA
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:18857 original size:15 final size:16
Alignment explanation
Indices: 18837--18877 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
18827 GTTTATCTCA
*
18837 AAATGATT-AAGCGTT
1 AAATGATTCAAACGTT
*
18852 AAATGATTCAAATGTT
1 AAATGATTCAAACGTT
18868 AAATGATTCA
1 AAATGATTCA
18878 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (16 bp):
AAATGATTCAAACGTT
Found at i:19786 original size:18 final size:18
Alignment explanation
Indices: 19763--19803 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
19753 AGAATGTAAG
19763 ATTACCAGTAGG-AATAAA
1 ATTACCAGT-GGAAATAAA
*
19781 ATTACCGGTGGAAATAAA
1 ATTACCAGTGGAAATAAA
19799 ATTAC
1 ATTAC
19804 TGGGAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.24
Consensus pattern (18 bp):
ATTACCAGTGGAAATAAA
Found at i:21265 original size:18 final size:18
Alignment explanation
Indices: 21242--21276 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21232 ATGATGTTCT
21242 AAATAAAATAATTGAAAA
1 AAATAAAATAATTGAAAA
* *
21260 AAATAAAGTTATTGAAA
1 AAATAAAATAATTGAAA
21277 GAGATTGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
AAATAAAATAATTGAAAA
Found at i:21681 original size:157 final size:156
Alignment explanation
Indices: 21435--21747 Score: 599
Period size: 157 Copynumber: 2.0 Consensus size: 156
21425 ATAAAGTTAT
*
21435 TGGTTTTATAAAAAAATGGTATATCGCGGTAATGCTAGGAAATAATAATAATAAATTTGAATTTA
1 TGGTTTTATAAAAAAATGGTATATCACGGTAATGCTAGGAAATAATAATAATAAATTTGAATTTA
21500 ATAAAGATATAATTAAAATAGCAAATTTAAAATAAAATAATAAATATTATAATGTAAAACAAATC
66 ATAAAGATATAATTAAAATAGCAAATTTAAAATAAAATAATAAATATTATAATGTAAAACAAATC
21565 CGAAAAAGCCCAAGCATAAAAATCCA
131 CGAAAAAGCCCAAGCATAAAAATCCA
21591 TGGTTTTATAAAAAAAATGGTATATCACGGTAATGCTAGGAAATAATAATAATAAATTTGAATTT
1 TGGTTTTAT-AAAAAAATGGTATATCACGGTAATGCTAGGAAATAATAATAATAAATTTGAATTT
*
21656 AATAAAGATATAATTAAAATGGCAAATTTAAAATAAAATAATAAATATTATAATGTAAAACAAAT
65 AATAAAGATATAATTAAAATAGCAAATTTAAAATAAAATAATAAATATTATAATGTAAAACAAAT
21721 CCGAAAAAGCCCAAGCATAAAAATCCA
130 CCGAAAAAGCCCAAGCATAAAAATCCA
21748 AACGTGAAAG
Statistics
Matches: 154, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
156 9 0.06
157 145 0.94
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (156 bp):
TGGTTTTATAAAAAAATGGTATATCACGGTAATGCTAGGAAATAATAATAATAAATTTGAATTTA
ATAAAGATATAATTAAAATAGCAAATTTAAAATAAAATAATAAATATTATAATGTAAAACAAATC
CGAAAAAGCCCAAGCATAAAAATCCA
Found at i:23578 original size:2 final size:2
Alignment explanation
Indices: 23571--23598 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23561 AAATCATTTA
23571 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
23599 TAAAAATTAG
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:35223 original size:13 final size:13
Alignment explanation
Indices: 35205--35236 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
35195 TTATCTAAAA
35205 TTATAAATATATT
1 TTATAAATATATT
35218 TTATAAATATATT
1 TTATAAATATATT
35231 TT-TAAA
1 TTATAAA
35237 AGAATGCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATAAATATATT
Found at i:36464 original size:19 final size:20
Alignment explanation
Indices: 36440--36490 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
36430 AATGACCAAT
36440 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
36459 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
36479 AAAATCGCAACG
1 AAAATCGCAACG
36491 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:36484 original size:20 final size:20
Alignment explanation
Indices: 36440--36757 Score: 165
Period size: 20 Copynumber: 15.6 Consensus size: 20
36430 AATGACCAAT
* *
36440 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
36459 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
36479 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
36499 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
36519 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
36540 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
36563 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
36583 TGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
36603 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
36623 AGAATCGCAATGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
36646 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
36666 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
36686 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
36706 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
36726 AGAATTGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
36746 AAAATCGCAACG
1 AAAATCGCAACG
36758 TTAAAAAGAA
Statistics
Matches: 242, Mismatches: 45, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
19 17 0.07
20 180 0.74
21 14 0.06
23 31 0.13
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:36618 original size:40 final size:40
Alignment explanation
Indices: 36565--36755 Score: 238
Period size: 40 Copynumber: 4.7 Consensus size: 40
36555 TTTAGAAGAA
** * *
36565 AATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
*
36605 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAGAAGAA
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGA-TT-G-AGAG
* *
36648 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* *
36688 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* * * *
36728 AATTGCAACGCGATTTAGAAAATCGCAA
1 AATCGCAATGCGATTGAGAGAATCGCAA
36756 CGTTAAAAAG
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 94 0.71
41 3 0.02
42 1 0.01
43 34 0.26
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.23
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
Found at i:36655 original size:83 final size:83
Alignment explanation
Indices: 36544--36722 Score: 277
Period size: 83 Copynumber: 2.2 Consensus size: 83
36534 GCTTCCAAGT
* * ** * * *
36544 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATC
1 TCGCAATGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
36609 GCAATGCGATTGAGAGAA
66 GCAATGCGATTGAGAGAA
36627 TCGCAATGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAATGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
* *
36692 GCAATGCGATTTATAGAA
66 GCAATGCGATTGAGAGAA
36710 TCGCAATGCGATT
1 TCGCAATGCGATT
36723 GAGAGAATTG
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 87 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (83 bp):
TCGCAATGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAATGCGATTGAGAGAA
Found at i:36767 original size:20 final size:20
Alignment explanation
Indices: 36744--36787 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
36734 AACGCGATTT
*
36744 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
36764 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
36784 AGAA
1 AGAA
36788 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:36876 original size:6 final size:6
Alignment explanation
Indices: 36865--36914 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
36855 GACACGTATT
36865 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
36912 ACC
1 ACC
36915 CGAGACGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:37624 original size:6 final size:6
Alignment explanation
Indices: 37598--37687 Score: 159
Period size: 6 Copynumber: 15.5 Consensus size: 6
37588 TCTCGTCTCG
37598 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
37643 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
37688 AATACGTGTC
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.18
6 69 0.82
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:37798 original size:20 final size:20
Alignment explanation
Indices: 37775--38009 Score: 143
Period size: 20 Copynumber: 11.6 Consensus size: 20
37765 TTCTTTTGAC
37775 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
37795 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
37815 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
37835 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
37855 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
37875 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
37898 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
37919 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
37937 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
37959 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
37979 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
37998 CGTTGCGATTTT
1 CGTTGCGATTTT
38010 ATTGGTCATT
Statistics
Matches: 175, Mismatches: 32, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.10
20 125 0.71
21 13 0.07
22 4 0.02
23 14 0.08
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:37821 original size:40 final size:40
Alignment explanation
Indices: 37777--37884 Score: 162
Period size: 40 Copynumber: 2.7 Consensus size: 40
37767 CTTTTGACCG
* *
37777 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* *
37817 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* *
37857 TTGCGATTCTCTCAGTCGCATTGCGATT
1 TTGCGATTCTCTAAATCGCATTGCGATT
37885 TTCTTCTAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:37999 original size:19 final size:20
Alignment explanation
Indices: 37959--38009 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
37949 TTCTTTTTAA
*
37959 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
37979 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
37998 CGTTGCGATTTT
1 CGTTGCGATTTT
38010 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:38353 original size:25 final size:26
Alignment explanation
Indices: 38264--38354 Score: 114
Period size: 26 Copynumber: 3.5 Consensus size: 26
38254 ACCGAAGTGC
*
38264 TAATACACAT-AAGATCGTTCCCACCA
1 TAATACACATAAAG-TCGTGCCCACCA
* * *
38290 TAATTCACATAAGGTCATGCCCACCA
1 TAATACACATAAAGTCGTGCCCACCA
38316 TAATACACATAAAGTCGTGCCCACCA
1 TAATACACATAAAGTCGTGCCCACCA
*
38342 T-ATACACTTAAAG
1 TAATACACATAAAG
38355 GCCTTACACA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
25 11 0.20
26 43 0.77
27 2 0.04
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.23
Consensus pattern (26 bp):
TAATACACATAAAGTCGTGCCCACCA
Found at i:41324 original size:2 final size:2
Alignment explanation
Indices: 41317--41368 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
41307 CTATCATGCA
41317 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
41359 AT AT AT AT AT
1 AT AT AT AT AT
41369 GAAACACATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42583 original size:34 final size:36
Alignment explanation
Indices: 42538--42627 Score: 148
Period size: 34 Copynumber: 2.6 Consensus size: 36
42528 AATTCAAAGA
*
42538 TTTTGTGTTTCAAGAGAAACATTTTCAAAGG-TT-T
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
*
42572 TTTTATGTTTCAAGAGAAACAATTTCAAAGGTTTCT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
42608 TTTTGTGTTTCAAGAGAAAC
1 TTTTGTGTTTCAAGAGAAAC
42628 TGTCTTAAGG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
34 29 0.57
35 2 0.04
36 20 0.39
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (36 bp):
TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
Found at i:42840 original size:65 final size:65
Alignment explanation
Indices: 42755--42911 Score: 183
Period size: 65 Copynumber: 2.4 Consensus size: 65
42745 AACTTCCAAA
* ** ** *
42755 AGAAACTGTCTCAAGGGAGACGGAATTTGTTT-AATGTAAAACATATTCAAAGATTT-TGTTTCA
1 AGAAACTATCTCAAGGGAGACAAAATTCATTTCAA-GGAAAACATATTCAAAG-TTTATGTTTCA
42818 AG
64 AG
* * * * *
42820 AGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATATTTTCAATGTTTATGTTTCAAG
1 AGAAACTATCTCAAGGGAGACAAAATTCATTTCAAGGAAAACATATTCAAAGTTTATGTTTCAAG
42885 AGAAACTATCTCAAGGGAGACAAAATT
1 AGAAACTATCTCAAGGGAGACAAAATT
42912 TTGTTTCAAG
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 3 0.04
65 73 0.94
66 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (65 bp):
AGAAACTATCTCAAGGGAGACAAAATTCATTTCAAGGAAAACATATTCAAAGTTTATGTTTCAAG
Found at i:42931 original size:37 final size:37
Alignment explanation
Indices: 42876--42962 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 37
42866 TCAATGTTTA
* * *
42876 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTT
*
42913 TGTTTCAAGGGAACCTATCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTT
**
42950 CATTTCAAGGGAA
1 TGTTTCAAGGGAA
42963 TTTTTTTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTT
Found at i:42988 original size:103 final size:102
Alignment explanation
Indices: 42802--43060 Score: 340
Period size: 103 Copynumber: 2.5 Consensus size: 102
42792 AAAACATATT
42802 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATATTTT
1 CAAA-ATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATATTTT
*
42867 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGA
65 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGA
* * * *
42905 CAAAATTTTGTTTCAAGGGAACCTATCTCAAGAGAGACAAAACTTCATTTCAAGGGAATTTTTTT
1 CAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTCATTTCAAGGGAAATATTTT
* * *
42970 TAATGTTTATGTTTCAAGAGAAATTGTCTCAAGAGAGA
65 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGA
* * * * * * * *
43008 CAAAACTTAG-TTCTAAAAGAAAATGTCTCAAGGGAGACGAAATTTATTTCAAG
1 CAAAATTTTGTTTC-AAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAG
43061 AGAGACGAGA
Statistics
Matches: 136, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
102 49 0.36
103 87 0.64
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (102 bp):
CAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATATTTTC
AATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGA
Found at i:43063 original size:19 final size:21
Alignment explanation
Indices: 43035--43084 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
43025 AGAAAATGTC
*
43035 TCAAGGGAGACGAAATTTATT
1 TCAAGAGAGACGAAATTTATT
* *
43056 TCAAGAGAGACGAGATTTGTT
1 TCAAGAGAGACGAAATTTATT
43077 TCAAGAGA
1 TCAAGAGA
43085 AACTATCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACGAAATTTATT
Found at i:44790 original size:183 final size:183
Alignment explanation
Indices: 44482--44835 Score: 611
Period size: 183 Copynumber: 1.9 Consensus size: 183
44472 ATCAGGTTTA
* *
44482 ACTGAAGGGTTCGTCTCATCACAAAGTCTTCAGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCGTCTCATCACAAAGTCTTCAGACTGAAAAAAGCAGTGGAGCAAACACCGAATT
* *
44547 GCCAAGTTTTCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
44612 TCCTCTATAACCAATTGCCTTAGTGAAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGAAATAGCTCAGCTTTAGAGGGACAAATC
*
44665 ACTGAAGGGTTCGTCTCATCACAAAGTCTT-TGAACTGAAAAAAGCAGTGGAGCAAACACCGAAT
1 ACTGAAGGGTTCGTCTCATCACAAAGTCTTCAG-ACTGAAAAAAGCAGTGGAGCAAACACCGAAT
*
44729 TGCCAAGTGTCCGAGCAGTGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
65 TGCCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
* * *
44794 TTTCTCTATAACCAATTGCTTTAGTGGAATAGCTCAGCTTTA
130 TTCCTCTATAACCAATTGCCTTAGTGAAATAGCTCAGCTTTA
44836 CGGATTTAAT
Statistics
Matches: 161, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
182 1 0.01
183 160 0.99
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCGTCTCATCACAAAGTCTTCAGACTGAAAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGAAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:50032 original size:21 final size:21
Alignment explanation
Indices: 49997--50036 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
49987 AATTTCAATT
49997 ATTAAATTAATTAATATTTTA
1 ATTAAATTAATTAATATTTTA
50018 ATTATAATTAA-TAATATTT
1 ATTA-AATTAATTAATATTT
50037 CAACCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTAAATTAATTAATATTTTA
Found at i:50325 original size:78 final size:79
Alignment explanation
Indices: 50237--50392 Score: 210
Period size: 79 Copynumber: 2.0 Consensus size: 79
50227 GTTAATATGT
** *
50237 TTTAACATTTTCGGTAAAGTATTACCTAAAACATT-TTTTTTCTACC-GCAAATATTAATAT-TG
1 TTTAACATTTTCGGTAAAACACTACCTAAAACATTATTTTTTCTACCAG-AAATATTAATATATG
*
50299 AGCGCTACCTAAAATA
65 -GCGATACCTAAAATA
* *
50315 TTTAACATTTTCGGTAAAACACTACCTAAAATATTATTTTTTCTACCAGAAATGTTAATATATGG
1 TTTAACATTTTCGGTAAAACACTACCTAAAACATTATTTTTTCTACCAGAAATATTAATATATGG
*
50380 TGATACCTAAAAT
66 CGATACCTAAAAT
50393 GTTATTTATT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
78 31 0.46
79 34 0.50
80 3 0.04
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (79 bp):
TTTAACATTTTCGGTAAAACACTACCTAAAACATTATTTTTTCTACCAGAAATATTAATATATGG
CGATACCTAAAATA
Found at i:51289 original size:36 final size:36
Alignment explanation
Indices: 51232--51583 Score: 560
Period size: 36 Copynumber: 9.8 Consensus size: 36
51222 ATGCACTACA
* *
51232 TCCTTCCGTTCGACTTAAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* * *
51268 TTCTTCTGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
51304 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* **
51340 TCATTCCGTTCCTCTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
**
51376 TCCTTCCGTTCCTCTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
51412 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* **
51448 TCATTCCGTTCCTCTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
*
51484 TCTTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
*
51520 TCCTTCCGTTCGACTTGAATTGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
*
51556 TCCTTCCGTTCGACTTGAATTGGAAGTG
1 TCCTTCCGTTCGACTTGAATCGGAAGTG
51584 TAGATGAAAT
Statistics
Matches: 296, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 296 1.00
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.31
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
Found at i:53173 original size:15 final size:15
Alignment explanation
Indices: 53153--53181 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53143 TGATAAAAAA
53153 GAGAAAACAACTCTC
1 GAGAAAACAACTCTC
53168 GAGAAAACAACTCT
1 GAGAAAACAACTCT
53182 TAAGAAAACT
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:0.48, C:0.24, G:0.14, T:0.14
Consensus pattern (15 bp):
GAGAAAACAACTCTC
Found at i:53187 original size:15 final size:15
Alignment explanation
Indices: 53154--53190 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
53144 GATAAAAAAG
*
53154 AGAAAACAACTCTCG
1 AGAAAACAACTCTCA
*
53169 AGAAAACAACTCTTA
1 AGAAAACAACTCTCA
53184 AGAAAAC
1 AGAAAAC
53191 TCTCTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.22, G:0.11, T:0.14
Consensus pattern (15 bp):
AGAAAACAACTCTCA
Done.