Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001183.1 Hibiscus syriacus cultivar Beakdansim tig00002350_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: 80293
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:3461 original size:51 final size:51
Alignment explanation
Indices: 3406--3530 Score: 211
Period size: 49 Copynumber: 2.5 Consensus size: 51
3396 TATCTAATTA
3406 AATTAGATAGAATCAGTTTTTATTCTATTAGTTATTAGATAGGATCA-TTTT
1 AATTAGATAGAATCAG-TTTTATTCTATTAGTTATTAGATAGGATCATTTTT
*
3457 AATTAGATAGAATCAGTTTT-TTATATTAGTTATTAGATAGGATCATTTTT
1 AATTAGATAGAATCAGTTTTATTCTATTAGTTATTAGATAGGATCATTTTT
3507 AATTAGATAGAATCA-TTTTATTCT
1 AATTAGATAGAATCAGTTTTATTCT
3531 GTTGCTAATT
Statistics
Matches: 70, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
49 28 0.40
50 26 0.37
51 16 0.23
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (51 bp):
AATTAGATAGAATCAGTTTTATTCTATTAGTTATTAGATAGGATCATTTTT
Found at i:3484 original size:23 final size:20
Alignment explanation
Indices: 3438--3527 Score: 58
Period size: 19 Copynumber: 4.0 Consensus size: 20
3428 TTCTATTAGT
*
3438 TATTAGATAGGATCATTTTA
1 TATTAGATAGAATCATTTTA
3458 -ATTAGATAGAATCAGTTTTTTA
1 TATTAGATAGAATCA---TTTTA
3480 TATTAGTTATTAGATAGGATCATTTT-
1 TATTAG--A-TAG--A--ATCATTTTA
3506 TAATTAGATAGAATCATTTTA
1 T-ATTAGATAGAATCATTTTA
3527 T
1 T
3528 TCTGTTGCTA
Statistics
Matches: 56, Mismatches: 1, Indels: 25
0.68 0.01 0.30
Matches are distributed among these distances:
19 13 0.23
20 8 0.14
21 1 0.02
22 6 0.11
23 5 0.09
24 3 0.05
25 2 0.04
26 4 0.07
27 9 0.16
28 1 0.02
30 4 0.07
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (20 bp):
TATTAGATAGAATCATTTTA
Found at i:3512 original size:27 final size:29
Alignment explanation
Indices: 3458--3512 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
3448 GATCATTTTA
3458 ATTAGATAGAATCAGTTTTTTATATTAGTT
1 ATTAGATAGAATCAG-TTTTTATATTAGTT
*
3488 ATTAGATAGGATCA-TTTTTA-ATTAG
1 ATTAGATAGAATCAGTTTTTATATTAG
3513 ATAGAATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 6 0.25
30 13 0.54
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.47
Consensus pattern (29 bp):
ATTAGATAGAATCAGTTTTTATATTAGTT
Found at i:3513 original size:20 final size:20
Alignment explanation
Indices: 3488--3525 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3478 TATATTAGTT
*
3488 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
3508 ATTAGATAGAATCATTTT
1 ATTAGATAGAATCATTTT
3526 ATTCTGTTGC
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:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:10463 original size:20 final size:21
Alignment explanation
Indices: 10438--10477 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
10428 TCTATTAATT
*
10438 ATTAGATAGGATCA-TTTTTA
1 ATTAGATAGAATCAGTTTTTA
10458 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTT
10478 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (21 bp):
ATTAGATAGAATCAGTTTTTA
Found at i:19942 original size:80 final size:80
Alignment explanation
Indices: 19809--19969 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
19799 ATTATTGTTC
*
19809 AACTATGGTTGACATCAGACACTCCATATAGTTTAGGTAAACTAACCTTGAAATTAAAACGAGCA
1 AACTATGGTTAACATCAGACACTCCATATAGTTTAGGTAAACTAACCTTGAAATTAAAACGAGCA
19874 AGAGTCTGCAAAGCA
66 AGAGTCTGCAAAGCA
*
19889 AACTATGGTTAACATCAGACACTCCATATAGTTTCGGTAAACTAACCTTGAAATTAAAACGAGCA
1 AACTATGGTTAACATCAGACACTCCATATAGTTTAGGTAAACTAACCTTGAAATTAAAACGAGCA
19954 AGAGTCTGCAAAGCA
66 AGAGTCTGCAAAGCA
19969 A
1 A
19970 GCTGAACAAG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (80 bp):
AACTATGGTTAACATCAGACACTCCATATAGTTTAGGTAAACTAACCTTGAAATTAAAACGAGCA
AGAGTCTGCAAAGCA
Found at i:27962 original size:21 final size:21
Alignment explanation
Indices: 27936--27979 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
27926 ATTCTGGGCT
*
27936 AGGGGAATCGATACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
27957 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
27978 AG
1 AG
27980 CGAATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:29641 original size:103 final size:103
Alignment explanation
Indices: 29416--29633 Score: 427
Period size: 103 Copynumber: 2.1 Consensus size: 103
29406 GTCGAGGGTC
29416 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
29481 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
29519 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
29584 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
29622 TATGTGGTCCTT
1 TATGTGGTCCTT
29634 ATGGACATTA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:29745 original size:23 final size:23
Alignment explanation
Indices: 29645--29763 Score: 125
Period size: 23 Copynumber: 5.3 Consensus size: 23
29635 TGGACATTAT
* *
29645 TATATGGCACTACAGTGCAACTC
1 TATATGGCACTACGGTGCAATTC
****
29668 TGCGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
29691 TATATGGCACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAATTC
***
29714 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
29737 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
29758 TATATG
1 TATATG
29764 AGCTGTGGTG
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
21 6 0.08
22 3 0.04
23 68 0.88
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:29753 original size:46 final size:46
Alignment explanation
Indices: 29645--29755 Score: 195
Period size: 46 Copynumber: 2.4 Consensus size: 46
29635 TGGACATTAT
* *
29645 TATATGGCACTACAGTGCAACTCTGCGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
29691 TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
*
29737 TATATGGCACTTCGGTGCA
1 TATATGGCACTACGGTGCA
29756 TTTATATGAG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.25
Consensus pattern (46 bp):
TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
Found at i:33525 original size:21 final size:21
Alignment explanation
Indices: 33499--33542 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
33489 ATTCTGGGCT
* *
33499 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
33520 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
33541 AG
1 AG
33543 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:35203 original size:101 final size:102
Alignment explanation
Indices: 34980--35195 Score: 416
Period size: 101 Copynumber: 2.1 Consensus size: 102
34970 GTCGAGGGTC
34980 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGAGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAT-AGTGAAGTCTGGTGAGACACATAC
35045 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
65 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
35083 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAT-GTGAAGTCTGGTGAGACACATACT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATAGTGAAGTCTGGTGAGACACATACT
35147 TGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
35184 TATGTGGTCCTT
1 TATGTGGTCCTT
35196 ATGGACATTA
Statistics
Matches: 113, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
101 73 0.65
103 40 0.35
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATAGTGAAGTCTGGTGAGACACATACT
TGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:35259 original size:46 final size:46
Alignment explanation
Indices: 35207--35314 Score: 198
Period size: 46 Copynumber: 2.3 Consensus size: 46
35197 TGGACATTAT
35207 TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
*
35253 TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTTCAATTC
1 TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
*
35299 TATATGGCACTTCGGT
1 TATATGGCACTACGGT
35315 ACATTTATAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (46 bp):
TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
Found at i:35307 original size:23 final size:23
Alignment explanation
Indices: 35207--35314 Score: 126
Period size: 23 Copynumber: 4.7 Consensus size: 23
35197 TGGACATTAT
35207 TATATGGCACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAACTC
*** *
35230 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAACTC
35253 TATATGGCACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAACTC
*** * *
35276 TACGCGGCACTACGGTTCAATTC
1 TATATGGCACTACGGTGCAACTC
*
35299 TATATGGCACTTCGGT
1 TATATGGCACTACGGT
35315 ACATTTATAT
Statistics
Matches: 68, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAACTC
Found at i:41989 original size:6 final size:6
Alignment explanation
Indices: 41978--42002 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41968 ACGACTTCAA
41978 TAAAAT TAAAAT TAAAAT TAAAAT T
1 TAAAAT TAAAAT TAAAAT TAAAAT T
42003 TTGTTAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TAAAAT
Found at i:46074 original size:17 final size:19
Alignment explanation
Indices: 46030--46089 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
46020 CAAATATTAT
*
46030 TTTATAATAATTTGATAAA
1 TTTATAATAATTTTATAAA
*
46049 TTTAAAATAATTTTA-AAA
1 TTTATAATAATTTTATAAA
46067 TTT-TAATAATATTTATAATA
1 TTTATAATAAT-TTTATAA-A
46087 TTT
1 TTT
46090 GGTTCGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 6 0.17
18 10 0.29
19 15 0.43
20 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTATAATAATTTTATAAA
Done.