Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006922.1 Hibiscus syriacus cultivar Beakdansim tig00017745_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: 41755
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:2030 original size:22 final size:23
Alignment explanation
Indices: 2004--2055 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 23
1994 AATGAAAGTG
2004 TTTTTCTAAGTTAAAGATTATTT
1 TTTTTCTAAGTTAAAGATTATTT
*
2027 TTTTCTCATAAGTTAGAGATTATTT
1 TTTT-TC-TAAGTTAAAGATTATTT
2052 TTTT
1 TTTT
2056 CTCATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 4 0.15
24 2 0.08
25 20 0.77
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.58
Consensus pattern (23 bp):
TTTTTCTAAGTTAAAGATTATTT
Found at i:2041 original size:25 final size:25
Alignment explanation
Indices: 2010--2062 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
2000 AGTGTTTTTC
2010 TAAGTTAAAGATTATTTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTTCTCA
*
2035 TAAGTTAGAGATTATTTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTTCTCA
2060 TAA
1 TAA
2063 TAAATTAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (25 bp):
TAAGTTAAAGATTATTTTTTTCTCA
Found at i:3072 original size:10 final size:10
Alignment explanation
Indices: 3057--3096 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
3047 TGCGTTGACA
3057 GTTGACCGAC
1 GTTGACCGAC
3067 GTTGACCAGAAC
1 GTTGACC-G-AC
*
3079 TTTGACCGAC
1 GTTGACCGAC
3089 GTTGACCG
1 GTTGACCG
3097 GGCATTGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 16 0.62
11 2 0.08
12 8 0.31
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.23
Consensus pattern (10 bp):
GTTGACCGAC
Found at i:5529 original size:23 final size:23
Alignment explanation
Indices: 5489--5544 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
5479 TGAATTATGT
* *
5489 TATGATACCTGACCTGGATTCTGA
1 TATGATA-TTGACATGGATTCTGA
5513 TATGATATTGACATGGATTCTGA
1 TATGATATTGACATGGATTCTGA
5536 TATGATATT
1 TATGATATT
5545 TGACCTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 23 0.77
24 7 0.23
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (23 bp):
TATGATATTGACATGGATTCTGA
Found at i:6551 original size:2 final size:2
Alignment explanation
Indices: 6544--6589 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
6534 AAAGCTATCG
6544 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
6586 AT AT
1 AT AT
6590 GGGAAAACTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12746 original size:53 final size:53
Alignment explanation
Indices: 12688--12792 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 53
12678 TCTAAAGAGT
* *
12688 AAAAATATGATAACAAAACAATCCTACATGGGTAAGAAACATAGAAGAGCATA
1 AAAAATATGAGAACAAAACAATCCCACATGGGTAAGAAACATAGAAGAGCATA
12741 AAAAATATGAGAACAAAACAATCCCACATGGGTAAGAAACATAGAAGAGCAT
1 AAAAATATGAGAACAAAACAATCCCACATGGGTAAGAAACATAGAAGAGCAT
12793 CCCAACTAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.54, C:0.14, G:0.16, T:0.15
Consensus pattern (53 bp):
AAAAATATGAGAACAAAACAATCCCACATGGGTAAGAAACATAGAAGAGCATA
Found at i:15859 original size:24 final size:24
Alignment explanation
Indices: 15813--15860 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
15803 TATCACATTG
* *
15813 TTAAAAATAATTTGTTTATTAAAT
1 TTAAAAATAATGTGTATATTAAAT
15837 TTAAAAACTAATGTGTATA-TAAAT
1 TTAAAAA-TAATGTGTATATTAAAT
15861 AATTAAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (24 bp):
TTAAAAATAATGTGTATATTAAAT
Found at i:25499 original size:77 final size:75
Alignment explanation
Indices: 25397--25545 Score: 237
Period size: 76 Copynumber: 2.0 Consensus size: 75
25387 TTTTTCTTTG
*
25397 GAGCATTTTAGCTAAAACGTTTCAATTTTTTGTCAAAATAATTTTTTTTTATGAAAATCGTTAGT
1 GAGCATTTTAGCTAAAACGTTTCAATTTTTGGTCAAAATAA-TTTTTTTTATGAAAATCGTTAGT
*
25462 TGACTAACAAA
65 TAACTAACAAA
*
25473 GAGCATTTTAGCCCT-AAACGTTTCAATTTTTGGTCAAAATAATTTTTTTTATGAAGATCGTTAG
1 GAGCATTTTAG--CTAAAACGTTTCAATTTTTGGTCAAAATAATTTTTTTTATGAAAATCGTTAG
25537 TTAACTAAC
64 TTAACTAAC
25546 GATCAACATC
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
76 40 0.59
77 26 0.38
78 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42
Consensus pattern (75 bp):
GAGCATTTTAGCTAAAACGTTTCAATTTTTGGTCAAAATAATTTTTTTTATGAAAATCGTTAGTT
AACTAACAAA
Found at i:27968 original size:21 final size:21
Alignment explanation
Indices: 27925--27969 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
27915 GATTTCTGGG
* *
27925 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
27946 CAAGGGGAACCGATACGCC-TT
1 CAAGGGGAACCGATAC-CCATT
27967 CAA
1 CAA
27970 ACGAACAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:29696 original size:149 final size:149
Alignment explanation
Indices: 29426--29732 Score: 553
Period size: 149 Copynumber: 2.1 Consensus size: 149
29416 GAGTCGAGGG
* * *
29426 TCTACGCGGTCCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAATACACAT
1 TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
29491 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATAA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATAA
29556 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
29575 TCTACGCGGTCCTTC-AGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACA
1 TCTACGCGGTCCTTCGA-GACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACA
*
29639 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
65 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATA
29704 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
29724 TCTACGCGG
1 TCTACGCGG
29733 CACTTCGGTG
Statistics
Matches: 152, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 151 0.99
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATAA
TATGGCACTACGGTGCAAT
Found at i:29741 original size:23 final size:23
Alignment explanation
Indices: 29708--29752 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
29698 ATTATTATAT
*
29708 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
29731 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
29753 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:33066 original size:21 final size:21
Alignment explanation
Indices: 33037--33081 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
33027 GATTTCTGGG
* *
33037 CAAGAGGAATCGGTACCCATT
1 CAAGAGGAACCGATACCCATT
* *
33058 CAAGGGGAACCGATACCCCTT
1 CAAGAGGAACCGATACCCATT
33079 CAA
1 CAA
33082 ACGAACAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGAGGAACCGATACCCATT
Found at i:34853 original size:149 final size:149
Alignment explanation
Indices: 34540--34846 Score: 587
Period size: 149 Copynumber: 2.1 Consensus size: 149
34530 GAGTCGAGGG
* *
34540 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
34605 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
34670 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
34689 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
34754 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
34819 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
34838 TCTACGCGG
1 TCTACGCGG
34847 CACTTCGATG
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 155 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:34858 original size:23 final size:23
Alignment explanation
Indices: 34822--34866 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
34812 ATTATTATAT
* *
34822 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGATGCAATTATACGC
*
34845 GGCACTTCGATGCAATTATACG
1 GGCACTACGATGCAATTATACG
34867 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTACGATGCAATTATACGC
Done.