Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000334.1 Hibiscus syriacus cultivar Beakdansim tig00000619_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: 62642
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3278 original size:2 final size:2
Alignment explanation
Indices: 3271--3297 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3261 AGATTTAATA
3271 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
3298 CAGTTTAAAA
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:8856 original size:47 final size:47
Alignment explanation
Indices: 8782--8878 Score: 167
Period size: 47 Copynumber: 2.1 Consensus size: 47
8772 TTTTTTTACC
* *
8782 AATAGATGGATTCGGATGGAGATGATAATTAGAACTTAACATATAAA
1 AATAAATGGATTCGGATGGAGATGATAATTAAAACTTAACATATAAA
*
8829 AATAAATGGATTCGGATGGAGGTGATAATTAAAACTTAACATATAAA
1 AATAAATGGATTCGGATGGAGATGATAATTAAAACTTAACATATAAA
8876 AAT
1 AAT
8879 TGGAAAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (47 bp):
AATAAATGGATTCGGATGGAGATGATAATTAAAACTTAACATATAAA
Found at i:9197 original size:2 final size:2
Alignment explanation
Indices: 9184--9258 Score: 134
Period size: 2 Copynumber: 38.0 Consensus size: 2
9174 TGTGTTTACT
*
9184 TA TA TT TA TA 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 TA TA TA TA TA
9226 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9259 GGTTTAGGAT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12233 original size:14 final size:14
Alignment explanation
Indices: 12214--12258 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
12204 TGATAATATA
12214 TTTGTTCATTTATG
1 TTTGTTCATTTATG
* *
12228 TTTGTTCGTCTATG
1 TTTGTTCATTTATG
*
12242 TTCGTTCATTTATG
1 TTTGTTCATTTATG
12256 TTT
1 TTT
12259 AACTCAATCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.11, C:0.11, G:0.16, T:0.62
Consensus pattern (14 bp):
TTTGTTCATTTATG
Found at i:12406 original size:33 final size:33
Alignment explanation
Indices: 12363--12465 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 33
12353 TGTTGTTGTG
* *
12363 GTTTATGTTCATTTGTTTTGTTCATTTATGTTC
1 GTTTACGTTCATTTATTTTGTTCATTTATGTTC
* * * *
12396 GTTTACGTTCATTTCTTGTGCTCTTTTATGTTC
1 GTTTACGTTCATTTATTTTGTTCATTTATGTTC
* * * *
12429 GTTTACGTTCGTTCATTTGCGTTCGTTTATGTTC
1 GTTTACGTTCATTTATTT-TGTTCATTTATGTTC
12463 GTT
1 GTT
12466 CATCATTTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
33 42 0.74
34 15 0.26
ACGTcount: A:0.10, C:0.15, G:0.17, T:0.58
Consensus pattern (33 bp):
GTTTACGTTCATTTATTTTGTTCATTTATGTTC
Found at i:19553 original size:2 final size:2
Alignment explanation
Indices: 19546--19581 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19536 GTCCTGAAAA
19546 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19582 GTATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:21491 original size:2 final size:2
Alignment explanation
Indices: 21484--21540 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
21474 TTGAATGAAG
21484 TA TA TA TA TA 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 TA TA TA TA TA
*
21526 TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA T
21541 TCATGATGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28496 original size:15 final size:16
Alignment explanation
Indices: 28478--28511 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28468 TTTATTTTCA
*
28478 TATAAAT-TATTAGAT
1 TATAAATCTATAAGAT
28493 TATAAATCTATAAGAT
1 TATAAATCTATAAGAT
28509 TAT
1 TAT
28512 CTCTATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (16 bp):
TATAAATCTATAAGAT
Found at i:28556 original size:45 final size:45
Alignment explanation
Indices: 28477--28572 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
28467 TTTTATTTTC
** *
28477 ATATAAATTATTAGATTATAAATCTATAAGATTATCTCTAT-AATT
1 ATATAAATTATTAGATTATAAAGATATAAGATTAT-TATATAAATT
* * *
28522 ATATAAATTATTAGATTATAAGGATATGATATTATTATATAAATT
1 ATATAAATTATTAGATTATAAAGATATAAGATTATTATATAAATT
28567 AT-TAAA
1 ATATAAA
28573 ATATAAATTC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
44 8 0.18
45 36 0.82
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (45 bp):
ATATAAATTATTAGATTATAAAGATATAAGATTATTATATAAATT
Found at i:31558 original size:21 final size:19
Alignment explanation
Indices: 31534--31901 Score: 187
Period size: 19 Copynumber: 19.0 Consensus size: 19
31524 CAACGCGATT
31534 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
** *
31555 TTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCG
** *
31574 TTGCGATTTTCCAA-AT--
1 TTGCGATAGTCCAAGTTCG
* * *
31590 TTACGTTAGTCCAAATTCG
1 TTGCGATAGTCCAAGTTCG
31609 TTGCGATAGTCCAAGTTCACG
1 TTGCGATAGTCCAAGTT--CG
*
31630 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
** *
31651 TTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCG
*
31670 TAGCGATAGTCCAAGTTC-
1 TTGCGATAGTCCAAGTTCG
* *
31688 --AC-AT--TCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
** *
31704 TTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCG
*
31723 TTACGATAGTCCAAGTTCACG
1 TTGCGATAGTCCAAGTT--CG
* ** *
31744 TTACGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCG
*
31763 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
** * *
31784 TTGCGATTTTCCAAATTCA
1 TTGCGATAGTCCAAGTTCG
*
31803 TTGCGATAATCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
** *
31824 TTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCG
*
31843 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
** *
31864 TTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCG
*
31883 TTGCGATAGTCGAAGTTCG
1 TTGCGATAGTCCAAGTTCG
31902 CGTAAAATCA
Statistics
Matches: 263, Mismatches: 63, Indels: 44
0.71 0.17 0.12
Matches are distributed among these distances:
13 7 0.03
15 3 0.01
16 11 0.04
17 1 0.00
18 2 0.01
19 124 0.47
21 115 0.44
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:31578 original size:40 final size:40
Alignment explanation
Indices: 31534--31904 Score: 381
Period size: 40 Copynumber: 9.6 Consensus size: 40
31524 CAACGCGATT
31534 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
** * ** *
31574 TTGCGATTTTCCAAATTTACGTT---A--GTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
* ** * *
31609 TTGCGATAGTCCAAGTTCACGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT--CG
** * * **
31651 TTGCGATTTTCCAAATT--CGTAGCGATAGTCC-AA---G
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
* * *
31685 TT-C-ACATTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
* * *
31723 TTACGATAGTCCAAGTTCACGTTACGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
* *
31763 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCA
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
*
31803 TTGCGATAATCCAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
*
31843 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
*
31883 TTGCGATAGTCGAAGTTCGCGT
1 TTGCGATAGTCCAAGTTCGCGT
31905 AAAATCACAA
Statistics
Matches: 276, Mismatches: 40, Indels: 30
0.80 0.12 0.09
Matches are distributed among these distances:
32 8 0.03
33 1 0.00
34 14 0.05
35 31 0.11
37 1 0.00
38 4 0.01
39 2 0.01
40 199 0.72
42 16 0.06
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (40 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
Found at i:31622 original size:35 final size:35
Alignment explanation
Indices: 31564--31631 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
31554 GTTGCGATTT
** *
31564 TCCAAATTCGTTGCGATTTTCCAAATTTACGTTAG
1 TCCAAATTCGTTGCGATAGTCCAAATTCACGTTAG
*
31599 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTT
1 TCCAAATTCGTTGCGATAGTCCAAATTCACGTT
31632 GCGATAGTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (35 bp):
TCCAAATTCGTTGCGATAGTCCAAATTCACGTTAG
Found at i:31719 original size:53 final size:53
Alignment explanation
Indices: 31639--31742 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 53
31629 GTTGCGATAG
31639 TCGAAGTTCGCGTTGCGATTTTCCAAATTCG-TAGCGATAGTCCAAGTTCACAT
1 TCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTA-CGATAGTCCAAGTTCACAT
31692 TCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTACGATAGTCCAAGTTCAC
1 TCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTACGATAGTCCAAGTTCAC
31743 GTTACGATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
53 48 0.96
54 2 0.04
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (53 bp):
TCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTACGATAGTCCAAGTTCACAT
Found at i:32368 original size:19 final size:19
Alignment explanation
Indices: 32341--32378 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
32331 ACGTTTTTCA
* *
32341 AACTCTCGCAATACATTTT
1 AACTATCGCAACACATTTT
32360 AACTATCGCAACACATTTT
1 AACTATCGCAACACATTTT
32379 TCAAAATCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (19 bp):
AACTATCGCAACACATTTT
Found at i:44915 original size:6 final size:6
Alignment explanation
Indices: 44896--44956 Score: 104
Period size: 6 Copynumber: 10.2 Consensus size: 6
44886 TTTTTTGACA
* *
44896 AATCTT AATTCT AATCCT AATCCT AATCCT AATCCT AATCCT AATCCT
1 AATCCT AATCCT AATCCT AATCCT AATCCT AATCCT AATCCT AATCCT
44944 AATCCT AATCCT A
1 AATCCT AATCCT A
44957 CTTAGAGGAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (6 bp):
AATCCT
Done.