Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002153.1 Hibiscus syriacus cultivar Beakdansim tig00004395_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: 70688
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:3531 original size:2 final size:2
Alignment explanation
Indices: 3524--3551 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3514 ATCCTGTCTG
3524 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
3552 AAGTATAATG
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):
TA
Found at i:9218 original size:2 final size:2
Alignment explanation
Indices: 9213--9238 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9203 AATTCAACTA
9213 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
9239 AAATTCCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:11758 original size:13 final size:13
Alignment explanation
Indices: 11740--11764 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11730 TTTGATTCAT
11740 TAAATTTTAATTA
1 TAAATTTTAATTA
11753 TAAATTTTAATT
1 TAAATTTTAATT
11765 TATATATTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATTTTAATTA
Found at i:12945 original size:25 final size:25
Alignment explanation
Indices: 12917--12967 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
12907 AAATTGGAAC
12917 GTTCAAAAGTTCAAGAACCAATTTA
1 GTTCAAAAGTTCAAGAACCAATTTA
*
12942 GTTCAAAAGTTTAAGAACCAATTTA
1 GTTCAAAAGTTCAAGAACCAATTTA
12967 G
1 G
12968 AATGAGAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (25 bp):
GTTCAAAAGTTCAAGAACCAATTTA
Found at i:15631 original size:3 final size:3
Alignment explanation
Indices: 15623--15656 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
15613 AAACATGCAC
*
15623 TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
15657 TACGCAGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:20421 original size:26 final size:26
Alignment explanation
Indices: 20361--20424 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
20351 AAATATATTG
20361 AATTTCAT--AACATTCGTATAGTTT
1 AATTTCATAAAACATTCGTATAGTTT
* * *
20385 -TTTTAATTAAAACATTTGTATAGTTT
1 AATTTCA-TAAAACATTCGTATAGTTT
20411 AATTTCATAAAACA
1 AATTTCATAAAACA
20425 ACATAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 4 0.13
24 1 0.03
26 22 0.71
27 4 0.13
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (26 bp):
AATTTCATAAAACATTCGTATAGTTT
Found at i:20494 original size:12 final size:13
Alignment explanation
Indices: 20477--20516 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
20467 TTAAAATTCA
20477 ATTATT-AATAAT
1 ATTATTAAATAAT
20489 ATTATTAGAATAAT
1 ATTATTA-AATAAT
*
20503 ATTATAAAATAAT
1 ATTATTAAATAAT
20516 A
1 A
20517 AATTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 6 0.24
13 7 0.28
14 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (13 bp):
ATTATTAAATAAT
Found at i:21177 original size:9 final size:9
Alignment explanation
Indices: 21145--21170 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
21135 AAATATTAGA
21145 AAATAAAAG
1 AAATAAAAG
21154 AAATAAAAG
1 AAATAAAAG
21163 AAATAAAA
1 AAATAAAA
21171 ATAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.12
Consensus pattern (9 bp):
AAATAAAAG
Found at i:22473 original size:30 final size:30
Alignment explanation
Indices: 22439--22505 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
22429 TTATCCTGTC
22439 ATTTTTAATTAATCAAATAATTATTTTATA
1 ATTTTTAATTAATCAAATAATTATTTTATA
* * *
22469 ATTTTTTATTAATTAAATGATTATTTTATA
1 ATTTTTAATTAATCAAATAATTATTTTATA
*
22499 TTTTTTA
1 ATTTTTA
22506 TAAAAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (30 bp):
ATTTTTAATTAATCAAATAATTATTTTATA
Found at i:22548 original size:27 final size:27
Alignment explanation
Indices: 22510--22573 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
22500 TTTTTATAAA
22510 AAATATTTTAGAATCTAATGACTATCT
1 AAATATTTTAGAATCTAATGACTATCT
22537 AAATATTTTAGAATCTAATGACTATCT
1 AAATATTTTAGAATCTAATGACTATCT
*
22564 AAATAATTTA
1 AAATATTTTA
22574 TCCTTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (27 bp):
AAATATTTTAGAATCTAATGACTATCT
Found at i:23416 original size:22 final size:23
Alignment explanation
Indices: 23369--23429 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
23359 TAATTATTAA
* *
23369 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
23390 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
23413 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
23430 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:23743 original size:20 final size:20
Alignment explanation
Indices: 23718--23785 Score: 127
Period size: 20 Copynumber: 3.4 Consensus size: 20
23708 TTTCCAGATG
23718 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
23738 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
23758 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
23778 TTTTCCAG
1 TTTTCCAG
23786 TAATTCAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:23790 original size:15 final size:15
Alignment explanation
Indices: 23770--23822 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
23760 TTACAGAAAT
**
23770 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
23785 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
*
23800 GTAATTTAAATTCCA
1 GTAATTCAAATTCCA
23815 GTAATTCA
1 GTAATTCA
23823 TTTTCTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.40
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:27100 original size:15 final size:15
Alignment explanation
Indices: 27080--27113 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
27070 AGGCAATGGC
27080 ATATAT-TAATAT-T
1 ATATATATAATATGT
27093 ATATATATAATATGT
1 ATATATATAATATGT
27108 ATATAT
1 ATATAT
27114 GCATGCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 6 0.32
15 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
ATATATATAATATGT
Found at i:41316 original size:21 final size:22
Alignment explanation
Indices: 41292--41333 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41282 AAAAGTAATA
*
41292 TAATA-TAATGTAATTTTATAT
1 TAATATTAATATAATTTTATAT
*
41313 TAATATTAATATATTTTTATA
1 TAATATTAATATAATTTTATA
41334 ATCAAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TAATATTAATATAATTTTATAT
Found at i:58398 original size:11 final size:11
Alignment explanation
Indices: 58382--58411 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
58372 AATGATTTCC
58382 GTGAAATTATA
1 GTGAAATTATA
58393 GTGAAATTATA
1 GTGAAATTATA
*
58404 GTAAAATT
1 GTGAAATT
58412 TATAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.37
Consensus pattern (11 bp):
GTGAAATTATA
Found at i:60550 original size:36 final size:35
Alignment explanation
Indices: 60505--60629 Score: 137
Period size: 36 Copynumber: 3.6 Consensus size: 35
60495 AGCCGGGGGT
*
60505 GGTTCAGATTGTTTAGCTTTGTTCTGAGCTGCTGGC
1 GGTTGAGATTGTTTAGCTTTGTTCTGAGCTGC-GGC
* * *
60541 GGTTGAGATTGTTTAGGTTTTTTCTGAGCTGCCGGA
1 GGTTGAGATTGTTTAGCTTTGTTCTGAGCTG-CGGC
* * * *
60577 GGTCGAGCTTGTTGAGGTTTGTTCTGAGC--CGGC
1 GGTTGAGATTGTTTAGCTTTGTTCTGAGCTGCGGC
*
60610 GGTTGAGCTTGTTTAGCTTT
1 GGTTGAGATTGTTTAGCTTT
60630 TCCCAAAACG
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
33 20 0.26
36 55 0.72
37 1 0.01
ACGTcount: A:0.11, C:0.14, G:0.34, T:0.41
Consensus pattern (35 bp):
GGTTGAGATTGTTTAGCTTTGTTCTGAGCTGCGGC
Found at i:61717 original size:3 final size:3
Alignment explanation
Indices: 61709--61766 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
61699 TTAAATATGG
61709 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
61757 AAT AAT AAT A
1 AAT AAT AAT A
61767 GAAGACATGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:65298 original size:2 final size:2
Alignment explanation
Indices: 65291--65368 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
65281 GGTTACATGA
65291 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
65333 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
65369 GAAATAATAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65601 original size:31 final size:30
Alignment explanation
Indices: 65562--65653 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 30
65552 ATAGTCGAGG
65562 GTTACCTATGTCTTTCAAGACATATGGATA
1 GTTACCTATGTCTTTCAAGACATATGGATA
* ** *
65592 GTTTACCTATGCCCTTT-GGGACATATGGACA
1 G-TTACCTATG-TCTTTCAAGACATATGGATA
*
65623 GTTACATATGT-TCTTCGAA-ACATATGGATA
1 GTTACCTATGTCT-TTC-AAGACATATGGATA
65653 G
1 G
65654 GTCATTCGGG
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
28 1 0.02
29 2 0.04
30 20 0.42
31 21 0.44
32 4 0.08
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (30 bp):
GTTACCTATGTCTTTCAAGACATATGGATA
Found at i:67750 original size:37 final size:37
Alignment explanation
Indices: 67677--67751 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
67667 GTTGGAAAAT
* *
67677 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
67714 ATTTATATATATATT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATAT-T-TTCTTTAAAAAATTGAAAATCATAAA
67751 A
1 A
67752 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 16 0.48
38 15 0.45
39 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Done.