Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000978.1 Hibiscus syriacus cultivar Beakdansim tig00001955_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: 60269
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:15251 original size:14 final size:16
Alignment explanation
Indices: 15232--15268 Score: 60
Period size: 14 Copynumber: 2.4 Consensus size: 16
15222 CATTCATTCC
15232 CTCTCTCT-ATCTCT-
1 CTCTCTCTAATCTCTG
15246 CTCTCTCTAATCTCTG
1 CTCTCTCTAATCTCTG
15262 CTCTCTC
1 CTCTCTC
15269 GATTCAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 6 0.29
16 7 0.33
ACGTcount: A:0.08, C:0.43, G:0.03, T:0.46
Consensus pattern (16 bp):
CTCTCTCTAATCTCTG
Found at i:21531 original size:7 final size:7
Alignment explanation
Indices: 21519--21633 Score: 108
Period size: 7 Copynumber: 16.7 Consensus size: 7
21509 AATCGGATTA
21519 AGGGTTT
1 AGGGTTT
21526 AGGGTTT
1 AGGGTTT
21533 AGGGTTT
1 AGGGTTT
*
21540 AAGGTTT
1 AGGGTTT
*
21547 AGGATTT
1 AGGGTTT
*
21554 AGTGTTT
1 AGGGTTT
*
21561 AGGGCTT
1 AGGGTTT
*
21568 AGGGCTT
1 AGGGTTT
21575 AGGGTTT
1 AGGGTTT
*
21582 ATGGTTT
1 AGGGTTT
**
21589 AAAGTTT
1 AGGGTTT
*
21596 AGAGTTT
1 AGGGTTT
*
21603 AGAGTTT
1 AGGGTTT
21610 A-GGTTT
1 AGGGTTT
*
21616 AAGGTTT
1 AGGGTTT
*
21623 A-AGTTT
1 AGGGTTT
21629 AGGGT
1 AGGGT
21634 GTAATCTAAC
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
6 10 0.11
7 81 0.89
ACGTcount: A:0.22, C:0.02, G:0.34, T:0.43
Consensus pattern (7 bp):
AGGGTTT
Found at i:26574 original size:20 final size:20
Alignment explanation
Indices: 26549--26764 Score: 200
Period size: 20 Copynumber: 10.7 Consensus size: 20
26539 CTATCGCAAA
*
26549 TTCGCGTTGCGATTTTTCAT
1 TTCGCGTTGCGATTTTCCAT
*
26569 TTCGCGTTGCGATTTTCCAG
1 TTCGCGTTGCGATTTTCCAT
* ** *
26589 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
* *
26610 ATCGCGTTGCGATTTTTC-T
1 TTCGCGTTGCGATTTTCCAT
26629 GTTCGCGTTGCGATTTTCCAT
1 -TTCGCGTTGCGATTTTCCAT
* * ** *
26650 TTTGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
* * *
26671 ATCGTGTTGCGATTTTCCAG
1 TTCGCGTTGCGATTTTCCAT
* ** *
26691 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
*
26712 ATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
26732 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
26752 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
26765 AGTCTACAGT
Statistics
Matches: 154, Mismatches: 37, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
20 110 0.71
21 44 0.29
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.41
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:26645 original size:61 final size:61
Alignment explanation
Indices: 26550--26703 Score: 247
Period size: 61 Copynumber: 2.5 Consensus size: 61
26540 TATCGCAAAT
26550 TCGCGTTGCGATTTTTCAT-TTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTTC-TGTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
* *
26611 TCGCGTTGCGATTTTTCTGTTCGCGTTGCGATTTTCCATTTTGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTTCTGTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
* * *
26672 TCGTGTTGCGATTTTCCAGTTCGCGTTGCGAT
1 TCGCGTTGCGATTTTTCTGTTCGCGTTGCGAT
26704 AGTTGAAAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
60 1 0.01
61 86 0.99
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.41
Consensus pattern (61 bp):
TCGCGTTGCGATTTTTCTGTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
Found at i:26680 original size:41 final size:41
Alignment explanation
Indices: 26631--26744 Score: 201
Period size: 41 Copynumber: 2.8 Consensus size: 41
26621 ATTTTTCTGT
*
26631 TCGCGTTGCGATTTTCCATTTTGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
* *
26672 TCGTGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
26713 TCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
26745 TTTCCATTTC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:26689 original size:102 final size:102
Alignment explanation
Indices: 26574--26767 Score: 354
Period size: 102 Copynumber: 1.9 Consensus size: 102
26564 TTCATTTCGC
*
26574 GTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTC-TGTTCGCGTT
1 GTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT-TTCGCGTT
*
26638 GCGATTTTCCATTTTGCGTTGCGATAGTTGAAAATCGT
65 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGT
26676 GTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG
1 GTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG
26741 CGATTTTCCATTTCGCGTTGCGATAGT
66 CGATTTTCCATTTCGCGTTGCGATAGT
26768 CTACAGTTGT
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
102 88 0.99
103 1 0.01
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (102 bp):
GTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG
CGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGT
Found at i:26801 original size:61 final size:60
Alignment explanation
Indices: 26676--26803 Score: 161
Period size: 61 Copynumber: 2.1 Consensus size: 60
26666 TGAAAATCGT
*
26676 GTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC-C
* * * *
26737 GTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT-C
1 GTTGCGATTTTCCAGTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTCC
26798 GTTGCG
1 GTTGCG
26804 GAAATTCGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
61 41 0.69
62 15 0.25
63 3 0.05
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (60 bp):
GTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCC
Found at i:26803 original size:102 final size:102
Alignment explanation
Indices: 26573--26792 Score: 338
Period size: 102 Copynumber: 2.1 Consensus size: 102
26563 TTTCATTTCG
*
26573 CGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCTGTTCGCGTT
1 CGTTGCGATTTTCCAGTTC-CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCTGTTCGCGTT
*
26638 GCGATTTTCCATTTTGCGTTGCGATAGTTGAAAATCGT
65 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGT
26676 -GTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT-TTCGCGT
1 CGTTGCGATTTTCCAGTTC-CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC-TGTTCGCGT
* * *
26739 TGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGTTGT
64 TGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCGT
26778 CGTTGCGATTTTCCA
1 CGTTGCGATTTTCCA
26793 AATTCGTTGC
Statistics
Matches: 109, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
102 93 0.85
103 16 0.15
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.40
Consensus pattern (102 bp):
CGTTGCGATTTTCCAGTTCCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCTGTTCGCGTTG
CGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGT
Found at i:26916 original size:5 final size:5
Alignment explanation
Indices: 26906--26938 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
26896 CGACCACGAT
*
26906 CGACC CGACC CGACC CGACC CGACC CAACC CGA
1 CGACC CGACC CGACC CGACC CGACC CGACC CGA
26939 GACGGACGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.24, C:0.58, G:0.18, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:27600 original size:22 final size:22
Alignment explanation
Indices: 27572--27624 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
27562 AATTTGGAAA
27572 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
27594 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
27616 ATCGCAACG
1 ATCGCAACG
27625 CGAAATGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:38592 original size:4 final size:4
Alignment explanation
Indices: 38583--38613 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
38573 CAATGCATGT
38583 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
38614 CATAGTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:40142 original size:2 final size:2
Alignment explanation
Indices: 40137--40164 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40127 ATATCCATCC
40137 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
40165 TAAAAAAATA
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:40511 original size:17 final size:17
Alignment explanation
Indices: 40462--40511 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
40452 TTGTTCATGT
40462 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
40479 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
40493 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
40510 TT
1 TT
40512 ATAAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:43353 original size:25 final size:26
Alignment explanation
Indices: 43325--43374 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
43315 TACGGGTTGG
43325 GTCGAGTC-AAACCGGGTCAAACTGA
1 GTCGAGTCAAAACCGGGTCAAACTGA
* *
43350 GTCGAGTCAAAACTGGGTTAAACTG
1 GTCGAGTCAAAACCGGGTCAAACTG
43375 CCCCAATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (26 bp):
GTCGAGTCAAAACCGGGTCAAACTGA
Found at i:51375 original size:42 final size:41
Alignment explanation
Indices: 51324--51459 Score: 155
Period size: 42 Copynumber: 3.2 Consensus size: 41
51314 TATCACAATA
51324 AACTTAAAATAAATCATAACGCGATATTTAACTATCGCAACG
1 AACTTAAAATAAATCATAACGCGA-ATTTAACTATCGCAACG
* * *
51366 AACTTAAAATAAATCATAACACGAATTTCAACTATCACAACA
1 AACTTAAAATAAATCATAACGCGAATTT-AACTATCGCAACG
* ** **
51408 AATTTAAAATAAATCGCAACGCGAACTTCGACTATCGCAACGCG
1 AACTTAAAATAAATCATAACGCGAA-TTTAACTATCGCAA--CG
51452 AACTTAAA
1 AACTTAAA
51460 CTATCGCAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
41 4 0.05
42 64 0.82
43 2 0.03
44 8 0.10
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.24
Consensus pattern (41 bp):
AACTTAAAATAAATCATAACGCGAATTTAACTATCGCAACG
Found at i:51474 original size:21 final size:21
Alignment explanation
Indices: 51420--51468 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
51410 TTTAAAATAA
**
51420 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTAAACT
51441 ATCGCAACGCGAACTTAAACT
1 ATCGCAACGCGAACTTAAACT
51462 ATCGCAA
1 ATCGCAA
51469 TACGAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.31, G:0.16, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTAAACT
Found at i:55641 original size:2 final size:2
Alignment explanation
Indices: 55634--55665 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
55624 TAAAATACAT
55634 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55666 ATGGCAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58273 original size:31 final size:30
Alignment explanation
Indices: 58190--58274 Score: 86
Period size: 28 Copynumber: 2.9 Consensus size: 30
58180 AAATTATGTT
*
58190 TCTCATTCTAAATTGATCTCTAAACTTTGA
1 TCTCATTCTAAATTGATCTCTAAACTATGA
* * *
58220 -AT-ATT-TAAATTTCATCCCTAAACTATGA
1 TCTCATTCTAAA-TTGATCTCTAAACTATGA
*
58248 CTCTCATTCTAAATTGGTCTCTAAACT
1 -TCTCATTCTAAATTGATCTCTAAACT
58275 TTTAACATTC
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
27 4 0.10
28 18 0.43
29 1 0.02
30 1 0.02
31 14 0.33
32 4 0.10
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (30 bp):
TCTCATTCTAAATTGATCTCTAAACTATGA
Found at i:58296 original size:59 final size:57
Alignment explanation
Indices: 58190--58304 Score: 151
Period size: 59 Copynumber: 2.0 Consensus size: 57
58180 AAATTATGTT
* *
58190 TCTCATTCTAAATTGATCTCTAAACTTTGAATATTTAAATTTCATCCCTAAACTATGAC
1 TCTCATTCTAAATTGATCTCTAAACTTTGAACATTCAAA-TTCATCCC-AAACTATGAC
* *
58249 TCTCATTCTAAATTGGTCTCTAAACTTTTAACATTCCAAA-TCAATCCCAAACTATG
1 TCTCATTCTAAATTGATCTCTAAACTTTGAACATT-CAAATTC-ATCCCAAACTATG
58305 GTCCTCATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
58 10 0.20
59 37 0.74
60 3 0.06
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (57 bp):
TCTCATTCTAAATTGATCTCTAAACTTTGAACATTCAAATTCATCCCAAACTATGAC
Done.