Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005669.1 Hibiscus syriacus cultivar Beakdansim tig00013258_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: 42103
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2593 original size:30 final size:30
Alignment explanation
Indices: 2536--2665 Score: 203
Period size: 30 Copynumber: 4.4 Consensus size: 30
2526 CCCGAAGGAC
*
2536 CTATCCAGAGGTCA-CAAGA-CC-CGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
2563 CTATCCAGAGGTCATAAAAATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
2593 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
2623 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
2653 CTGTCCATAGGTC
1 CTATCCAGAGGTC
2666 CCGAAGAACC
Statistics
Matches: 95, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
27 14 0.15
28 3 0.03
29 2 0.02
30 76 0.80
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:2682 original size:60 final size:60
Alignment explanation
Indices: 2536--2682 Score: 192
Period size: 60 Copynumber: 2.5 Consensus size: 60
2526 CCCGAAGGAC
*
2536 CTATCCAGAGGTCAC-AAG-ACC-CGGTAACTATCCAGAGGTCATAAAAATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAAATCCTCGGTAA
* * * *
2593 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAAATCCTCGGTAA
* * * *
2653 CTGTCCATAGGTCCCGAAGAACCTAGGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAA
2683 ACCCTCGACT
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
57 14 0.18
58 3 0.04
59 2 0.03
60 58 0.75
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.21
Consensus pattern (60 bp):
CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAAATCCTCGGTAA
Found at i:3691 original size:61 final size:60
Alignment explanation
Indices: 3587--3702 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 60
3577 TAATGAAGGT
*
3587 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATTCATTCGATGTTGTATTACTGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCAT-AAATTCATTCGATGTTGTATTACTGGG
* * *
3648 ATGCATCGATGCACTCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTTATT
1 ATGCATCGATGCACTACTGATGCATCGATGCA-TAAATT-CATTCGATGTTGTATT
3703 TTAAAAGAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 4 0.08
61 44 0.90
62 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (60 bp):
ATGCATCGATGCACTACTGATGCATCGATGCATAAATTCATTCGATGTTGTATTACTGGG
Found at i:5823 original size:85 final size:85
Alignment explanation
Indices: 5712--5871 Score: 284
Period size: 85 Copynumber: 1.9 Consensus size: 85
5702 AAATATTTAT
* *
5712 TTAGTTCCTAAATTTGCCAGGGTGGGTGCATTTGCTTTCTCATCGACCATTCTGATAATTGGTTG
1 TTAGTTCCTAAATTTACCAGGATGGGTGCATTTGCTTTCTCATCGACCATTCTGATAATTGGTTG
5777 CTTATCGGCACTCAAAACAG
66 CTTATCGGCACTCAAAACAG
*
5797 TTAGTTCCTAAATTTATCAGGATGGGTGCATTTGCTTTCTCATCGACCATTCTGATAATTGGTTG
1 TTAGTTCCTAAATTTACCAGGATGGGTGCATTTGCTTTCTCATCGACCATTCTGATAATTGGTTG
*
5862 CTTATTGGCA
66 CTTATCGGCA
5872 TTAAAACTGT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (85 bp):
TTAGTTCCTAAATTTACCAGGATGGGTGCATTTGCTTTCTCATCGACCATTCTGATAATTGGTTG
CTTATCGGCACTCAAAACAG
Found at i:6378 original size:30 final size:30
Alignment explanation
Indices: 6334--6395 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
6324 GACTTGGAAC
6334 TTCGACATGAACCCGTCAAAGAACCAAGAG
1 TTCGACATGAACCCGTCAAAGAACCAAGAG
* * *
6364 TTCGAGATGCACCCGTCATAGAACCAAGAG
1 TTCGACATGAACCCGTCAAAGAACCAAGAG
6394 TT
1 TT
6396 ACATTTGATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (30 bp):
TTCGACATGAACCCGTCAAAGAACCAAGAG
Found at i:11622 original size:21 final size:21
Alignment explanation
Indices: 11596--11635 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11586 TTTAATTGAT
11596 AAAATTTAAAAATGAATAATC
1 AAAATTTAAAAATGAATAATC
* *
11617 AAAATTTAAAGATGGATAA
1 AAAATTTAAAAATGAATAA
11636 AAAATAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.28
Consensus pattern (21 bp):
AAAATTTAAAAATGAATAATC
Found at i:14448 original size:16 final size:16
Alignment explanation
Indices: 14427--14481 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
14417 CGATTATATA
14427 TATATATATAATATTT
1 TATATATATAATATTT
* *
14443 TATATATTTTATATTAAT
1 TATATATATAATATT--T
*
14461 TATATATATAATTTTT
1 TATATATATAATATTT
14477 TATAT
1 TATAT
14482 TAATTATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 19 0.59
18 13 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATATATAATATTT
Found at i:14465 original size:25 final size:26
Alignment explanation
Indices: 14437--14490 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
14427 TATATATATA
*
14437 ATATTTTAT-ATATTTTATATTAATT
1 ATATTATATAATATTTTATATTAATT
*
14462 ATA-TATATAATTTTTTATATTAATT
1 ATATTATATAATATTTTATATTAATT
14487 ATAT
1 ATAT
14491 AATACAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
ATATTATATAATATTTTATATTAATT
Found at i:14772 original size:18 final size:18
Alignment explanation
Indices: 14751--14785 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
14741 ATTATTTAGA
14751 ATTG-AGTTTGAATTTGTG
1 ATTGTAGTTTG-ATTTGTG
14769 ATTGTAGTTTGATTTGT
1 ATTGTAGTTTGATTTGT
14786 AAATCATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (18 bp):
ATTGTAGTTTGATTTGTG
Found at i:16580 original size:3 final size:3
Alignment explanation
Indices: 16572--16599 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
16562 CATCGACCCT
16572 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
16600 CCTCATCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:27332 original size:39 final size:38
Alignment explanation
Indices: 27275--27354 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 38
27265 TGAAAGCTCA
*
27275 ATGCAATCCTGAAGTCTTTAG-TTTTCCCAATACTAAAG
1 ATGCAATCCTGAAATCTTTAGCTTTT-CCAATACTAAAG
27313 ATGCATATCCTGAAATCTTTAGCTTTTCCAATACTAAAG
1 ATGCA-ATCCTGAAATCTTTAGCTTTTCCAATACTAAAG
27352 ATG
1 ATG
27355 TATAGTAATC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
38 5 0.13
39 30 0.77
40 4 0.10
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (38 bp):
ATGCAATCCTGAAATCTTTAGCTTTTCCAATACTAAAG
Found at i:28014 original size:2 final size:2
Alignment explanation
Indices: 28007--28034 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27997 TTCTATAGCC
28007 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
28035 GGATAGAATC
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:41618 original size:32 final size:32
Alignment explanation
Indices: 41555--41692 Score: 185
Period size: 32 Copynumber: 4.4 Consensus size: 32
41545 AGATAAAAAA
*
41555 TTAAAGTTAAGATAA-G-TCAAAA-ATATTTT
1 TTAAAGTTAAGATAATGATAAAAATATATTTT
41584 TTAAAGTTAAGATAATGATAAAAATATATTTT
1 TTAAAGTTAAGATAATGATAAAAATATATTTT
** * *
41616 TTAAAGTTAAGA-AAAAATTAAAAAAAAAATTTT
1 TTAAAGTTAAGATAATGA-T-AAAAATATATTTT
41649 TTAAAGTTAAGATAATGATAAAAATATATTTT
1 TTAAAGTTAAGATAATGATAAAAATATATTTT
41681 TTAAAGTTAAGA
1 TTAAAGTTAAGA
41693 AAAAAAATTT
Statistics
Matches: 94, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
29 15 0.16
30 1 0.01
31 8 0.09
32 43 0.46
33 24 0.26
34 3 0.03
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (32 bp):
TTAAAGTTAAGATAATGATAAAAATATATTTT
Found at i:41655 original size:65 final size:65
Alignment explanation
Indices: 41573--41697 Score: 241
Period size: 65 Copynumber: 1.9 Consensus size: 65
41563 AAGATAAGTC
*
41573 AAAAATATTTTTTAAAGTTAAGATAATGATAAAAATATATTTTTTAAAGTTAAGAAAAAATTAAA
1 AAAAAAATTTTTTAAAGTTAAGATAATGATAAAAATATATTTTTTAAAGTTAAGAAAAAATTAAA
41638 AAAAAAATTTTTTAAAGTTAAGATAATGATAAAAATATATTTTTTAAAGTTAAGAAAAAA
1 AAAAAAATTTTTTAAAGTTAAGATAATGATAAAAATATATTTTTTAAAGTTAAGAAAAAA
41698 AATTTAAAGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (65 bp):
AAAAAAATTTTTTAAAGTTAAGATAATGATAAAAATATATTTTTTAAAGTTAAGAAAAAATTAAA
Done.