Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007494.1 Hibiscus syriacus cultivar Beakdansim tig00020729_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: 265578
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
File 2 of 2
Found at i:215538 original size:25 final size:26
Alignment explanation
Indices: 215510--215559 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
215500 AAAATGAATA
215510 CATAA-TTCTAGCACT-AAACTTATCG
1 CATAATTTC-AGCACTGAAACTTATCG
*
215535 CATAATTTCAGCAGTGAAACTTATC
1 CATAATTTCAGCACTGAAACTTATC
215560 ATTGAGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (26 bp):
CATAATTTCAGCACTGAAACTTATCG
Found at i:220319 original size:3 final size:3
Alignment explanation
Indices: 220311--220378 Score: 93
Period size: 3 Copynumber: 22.3 Consensus size: 3
220301 TTTTTCAACC
*
220311 ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATGA
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
220359 AAT ATT ATT ATT ATTT ATT A
1 ATT ATT ATT ATT A-TT ATT A
220379 GAAACCCAGG
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 52 0.90
4 4 0.07
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:221514 original size:11 final size:11
Alignment explanation
Indices: 221498--221522 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
221488 CCTGTAGTGA
221498 TTATTTTAATT
1 TTATTTTAATT
221509 TTATTTTAATT
1 TTATTTTAATT
221520 TTA
1 TTA
221523 CTAGTTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTTAATT
Found at i:223787 original size:49 final size:49
Alignment explanation
Indices: 223731--223827 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
223721 TTTGTGTCCG
*
223731 TAATTAGCATTCATTATTCTTTGAATTCTTTGAATTAATTTAACTTTAC
1 TAATTAGCATTCATTATTATTTGAATTCTTTGAATTAATTTAACTTTAC
223780 TAATTAGCATTCATTATTATTTGAATTCTTTGAATTAATTTAACTTTA
1 TAATTAGCATTCATTATTATTTGAATTCTTTGAATTAATTTAACTTTA
223828 ATAACTTATC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (49 bp):
TAATTAGCATTCATTATTATTTGAATTCTTTGAATTAATTTAACTTTAC
Found at i:224537 original size:30 final size:30
Alignment explanation
Indices: 224501--224557 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
224491 TCAATTTGCA
*
224501 CTCGCACCAGCCATCCTAGCAAAAACAAAT
1 CTCGCACCAGCCATCATAGCAAAAACAAAT
224531 CTCGCACCAGCCATCATAGCAAAAACA
1 CTCGCACCAGCCATCATAGCAAAAACA
224558 TTCATGTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.37, G:0.11, T:0.12
Consensus pattern (30 bp):
CTCGCACCAGCCATCATAGCAAAAACAAAT
Found at i:225889 original size:13 final size:13
Alignment explanation
Indices: 225871--225897 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
225861 AAAGAGAATT
225871 AAGGGTCGATCCC
1 AAGGGTCGATCCC
225884 AAGGGTCGATCCC
1 AAGGGTCGATCCC
225897 A
1 A
225898 CAGAGACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.15
Consensus pattern (13 bp):
AAGGGTCGATCCC
Found at i:229511 original size:180 final size:180
Alignment explanation
Indices: 229209--229538 Score: 633
Period size: 180 Copynumber: 1.8 Consensus size: 180
229199 AAACCAGACA
* *
229209 TTTATCCCTGAGGATATATCGAAAAATAAGTTAGACCGAATTGTGGGACATATAACTGCAGATAA
1 TTTATCCCTGAGGATATATCAAAAAATAAGCTAGACCGAATTGTGGGACATATAACTGCAGATAA
*
229274 TTACATCACATTCACTGATGATGAGATCCTGGAAGGTGGGATGAGATCCGTCAAAGCTTTAAATA
66 TTACATCACATTCACTGATGATGAGATCCCGGAAGGTGGGATGAGATCCGTCAAAGCTTTAAATA
229339 TCATTACTCACTGCCACGACAACCTCTGCGGTGTAGTCAAAGGCATCACG
131 TCATTACTCACTGCCACGACAACCTCTGCGGTGTAGTCAAAGGCATCACG
229389 TTTATCCCTGAGGATATATCAAAAAATAAGCTAGACCGAATTGTGGGACATATAACTGCAGATAA
1 TTTATCCCTGAGGATATATCAAAAAATAAGCTAGACCGAATTGTGGGACATATAACTGCAGATAA
229454 TTACATCACATTCACTGATGATGAGATCCCGGAAGGTGGGATGAGATCCGTCAAAGCTTTAAATA
66 TTACATCACATTCACTGATGATGAGATCCCGGAAGGTGGGATGAGATCCGTCAAAGCTTTAAATA
229519 TCATTACTCACTGCCACGAC
131 TCATTACTCACTGCCACGAC
229539 CATGTTCTGC
Statistics
Matches: 147, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
180 147 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (180 bp):
TTTATCCCTGAGGATATATCAAAAAATAAGCTAGACCGAATTGTGGGACATATAACTGCAGATAA
TTACATCACATTCACTGATGATGAGATCCCGGAAGGTGGGATGAGATCCGTCAAAGCTTTAAATA
TCATTACTCACTGCCACGACAACCTCTGCGGTGTAGTCAAAGGCATCACG
Found at i:238762 original size:21 final size:21
Alignment explanation
Indices: 238736--238784 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
238726 CCACCCGTAC
238736 CAGAAGAAGGCCAAGGCGATA
1 CAGAAGAAGGCCAAGGCGATA
238757 CAGAAGAAGGCCAAGGCGATA
1 CAGAAGAAGGCCAAGGCGATA
238778 CAGAAGA
1 CAGAAGA
238785 TTTCACGCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.45, C:0.18, G:0.33, T:0.04
Consensus pattern (21 bp):
CAGAAGAAGGCCAAGGCGATA
Found at i:243153 original size:28 final size:26
Alignment explanation
Indices: 243113--243179 Score: 62
Period size: 27 Copynumber: 2.4 Consensus size: 26
243103 ATGCATGATT
*
243113 AAATATTAGGGGGTAAATTTCAATTTATA
1 AAAT-TTA-GGGGT-AAGTTCAATTTATA
* *
243142 AAATTTCAGGGGTGAGTTGAATTTATA
1 AAATTT-AGGGGTAAGTTCAATTTATA
*
243169 ACATTTAGGGG
1 AAATTTAGGGG
243180 GCGAAAACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 5 0.15
27 16 0.48
28 7 0.21
29 5 0.15
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (26 bp):
AAATTTAGGGGTAAGTTCAATTTATA
Found at i:244439 original size:2 final size:2
Alignment explanation
Indices: 244432--244460 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
244422 TCACATATGG
244432 AT 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 AT A
244461 AATCAGAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:246798 original size:24 final size:24
Alignment explanation
Indices: 246771--246830 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
246761 TATTTCTTTG
*
246771 TTTTATATTTTTATTTGA-TTATAT
1 TTTTATATTTTTATCT-ATTTATAT
**
246795 TTTTAT-TTACCTATCTATTTATAT
1 TTTTATATT-TTTATCTATTTATAT
246819 TTTTATATTTTT
1 TTTTATATTTTT
246831 TTTCTTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
23 3 0.11
24 23 0.82
25 2 0.07
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTATATTTTTATCTATTTATAT
Found at i:250739 original size:21 final size:21
Alignment explanation
Indices: 250693--250749 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
250683 ACTTTGATGA
*
250693 AGAAGATAAAGCTAAAAAGAT
1 AGAAGATAAAGATAAAAAGAT
* *
250714 GGAAGA-AAAGATAAAAATATT
1 AGAAGATAAAGATAAAAAGA-T
*
250735 AGAAGATCAA-ATAAA
1 AGAAGATAAAGATAAA
250750 GATGGTCCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 11 0.38
21 16 0.55
22 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.18, T:0.16
Consensus pattern (21 bp):
AGAAGATAAAGATAAAAAGAT
Found at i:257332 original size:11 final size:11
Alignment explanation
Indices: 257316--257351 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
257306 GTCCTAAGTT
257316 GAAAAAAAAAA
1 GAAAAAAAAAA
257327 GAAAAAAAAAA
1 GAAAAAAAAAA
257338 -AAAAGAAAAAA
1 GAAAA-AAAAAA
257349 GAA
1 GAA
257352 GAGAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.17
11 17 0.74
12 2 0.09
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:257333 original size:8 final size:8
Alignment explanation
Indices: 257320--257348 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
257310 TAAGTTGAAA
257320 AAAAAAAG
1 AAAAAAAG
257328 AAAAAAA-
1 AAAAAAAG
257335 AAAAAAAG
1 AAAAAAAG
257343 AAAAAA
1 AAAAAA
257349 GAAGAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:257334 original size:12 final size:12
Alignment explanation
Indices: 257317--257358 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
257307 TCCTAAGTTG
257317 AAAAAAAAAAGA
1 AAAAAAAAAAGA
257329 AAAAAAAAAA-A
1 AAAAAAAAAAGA
257340 AAGAAAAAAGAAGA
1 AA-AAAAAA-AAGA
257354 GAAAA
1 -AAAA
257359 TAAGGTGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 3 0.12
12 16 0.62
13 2 0.08
14 3 0.12
15 2 0.08
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:257337 original size:15 final size:15
Alignment explanation
Indices: 257317--257348 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
257307 TCCTAAGTTG
257317 AAAAAAAAAAGAAAA
1 AAAAAAAAAAGAAAA
257332 AAAAAAAAAAGAAAA
1 AAAAAAAAAAGAAAA
257347 AA
1 AA
257349 GAAGAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAAAA
Found at i:258859 original size:105 final size:105
Alignment explanation
Indices: 258077--258851 Score: 1433
Period size: 105 Copynumber: 7.4 Consensus size: 105
258067 AGGTTTTACC
*
258077 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
258142 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
258182 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
258247 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
258287 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
258352 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
258392 CAGAGCCAATTTCAACTTTACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
258457 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
258497 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
258562 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
258602 CAGAGCCAATTTCAACTTTACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
258667 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
258707 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
258772 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
258812 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
258852 GAAACAACAC
Statistics
Matches: 647, Mismatches: 23, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 647 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:260179 original size:31 final size:29
Alignment explanation
Indices: 260135--260246 Score: 73
Period size: 30 Copynumber: 3.6 Consensus size: 29
260125 TAAAAGGGGT
*
260135 AAACTTCATTTTGGCTCCCTCTGTTTTGAA
1 AAACTTCAATTTGG-TCCCTCTGTTTTGAA
* * **
260165 AAACATTCAATTTGGTCCC-CAAATCGGTTGGGT
1 AAAC-TTCAATTTGGTCCCTC---T-GTTTTGAA
* *
260198 AAACTTCATTTTGGCTCCCTCTGTTTTAAA
1 AAACTTCAATTTGG-TCCCTCTGTTTTGAA
*
260228 AAACATTTAATTTGGTCCC
1 AAAC-TTCAATTTGGTCCC
260247 CAAATCGGTT
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
29 1 0.02
30 19 0.31
31 18 0.30
32 10 0.16
33 12 0.20
34 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.38
Consensus pattern (29 bp):
AAACTTCAATTTGGTCCCTCTGTTTTGAA
Found at i:260230 original size:63 final size:63
Alignment explanation
Indices: 260131--260256 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
260121 TTGCTAAAAG
*
260131 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTGAAAAACATTCAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTCAATTTGGTCCCCAAATCGGTT
*
260194 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTCAATTTGGTCCCCAAATCGGTT
260257 TAATTCCCTT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (63 bp):
GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTCAATTTGGTCCCCAAATCGGTT
Found at i:261632 original size:31 final size:32
Alignment explanation
Indices: 261589--261650 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
261579 ATATGAGCCA
*
261589 CATTATACAGTTCAA-TTCGGTTCGGATTTTT
1 CATTATACAGTTCAATTTCGGTTCGAATTTTT
*
261620 CATTTTACAGTTCAATTTCGGTTCGAATTTT
1 CATTATACAGTTCAATTTCGGTTCGAATTTT
261651 CATACAGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.47
Consensus pattern (32 bp):
CATTATACAGTTCAATTTCGGTTCGAATTTTT
Done.