Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004075.1 Hibiscus syriacus cultivar Beakdansim tig00008921_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: 45493
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:1616 original size:19 final size:19
Alignment explanation
Indices: 1592--1628 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1582 GTTTACAGAT
1592 TAATTT-AGAATGATAATTA
1 TAATTTAAGAAT-ATAATTA
1611 TAATTTAAGAATATAATT
1 TAATTTAAGAATATAATT
1629 TGAATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (19 bp):
TAATTTAAGAATATAATTA
Found at i:1746 original size:22 final size:23
Alignment explanation
Indices: 1706--1748 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1696 AACTCTAAAA
*
1706 TAAAATATTAATATCAAAATACT
1 TAAAATATTAAAATCAAAATACT
*
1729 TAAAA-ATTAAAATTAAAATA
1 TAAAATATTAAAATCAAAATA
1749 ACTATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAAATATTAAAATCAAAATACT
Found at i:13553 original size:60 final size:60
Alignment explanation
Indices: 13489--13612 Score: 187
Period size: 60 Copynumber: 2.1 Consensus size: 60
13479 CTTCTAGGGG
* **
13489 CTAATTTAAAATGATATTCATAGTT-TGGGGATGAAATTTGAATGTTTAAAAGTTTAAGGA
1 CTAATTTAAAATGAGATTCATAGTTCT-GGGATGAAATTAAAATGTTTAAAAGTTTAAGGA
**
13549 CTAATTTGGAATGAGATTCATAGTTCTGGGATGAAATTAAAATGTTTAAAAGTTTAAGGA
1 CTAATTTAAAATGAGATTCATAGTTCTGGGATGAAATTAAAATGTTTAAAAGTTTAAGGA
13609 CTAA
1 CTAA
13613 GTTGAAATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (60 bp):
CTAATTTAAAATGAGATTCATAGTTCTGGGATGAAATTAAAATGTTTAAAAGTTTAAGGA
Found at i:13630 original size:60 final size:60
Alignment explanation
Indices: 13497--13639 Score: 173
Period size: 60 Copynumber: 2.4 Consensus size: 60
13487 GGCTAATTTA
* * ** *
13497 AAATGATATTCATAGTTTGGGGATGAAATTTGAATGTTTAAAAGTTTAAGGACTAATTTG
1 AAATGAGACTCATAGTTTGGGGATGAAATTAAAATGTTTAAAAGTTTAAGGACTAAGTTG
* *
13557 GAATGAGATTCATAGTTCT-GGGATGAAATTAAAATGTTTAAAAGTTTAAGGACTAAGTTG
1 AAATGAGACTCATAGTT-TGGGGATGAAATTAAAATGTTTAAAAGTTTAAGGACTAAGTTG
* *
13617 AAAT-ATGGCTCATAATTTGGGGA
1 AAATGA-GACTCATAGTTTGGGGA
13640 CATATGATGC
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.03
60 68 0.96
61 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (60 bp):
AAATGAGACTCATAGTTTGGGGATGAAATTAAAATGTTTAAAAGTTTAAGGACTAAGTTG
Found at i:15979 original size:76 final size:76
Alignment explanation
Indices: 15882--16026 Score: 227
Period size: 76 Copynumber: 1.9 Consensus size: 76
15872 ATAAGGTTGC
* * **
15882 ACCCAAGAATGTTATGGTTCACTAAGAAATAGATTATGATATGAAATGTTAATATTTTTATTAAT
1 ACCCAAAAATGTCATGGTTCACTAAGAAATAGATTACAATATGAAATGTTAATATTTTTATTAAT
15947 AAAATGGGTTT
66 AAAATGGGTTT
* * *
15958 ACCCAAAAATGTCATGTTTCACTAAGAAATATATTGCAATATGAAATGTTAATATTTTTATTAAT
1 ACCCAAAAATGTCATGGTTCACTAAGAAATAGATTACAATATGAAATGTTAATATTTTTATTAAT
16023 AAAA
66 AAAA
16027 GAGTTAATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.37
Consensus pattern (76 bp):
ACCCAAAAATGTCATGGTTCACTAAGAAATAGATTACAATATGAAATGTTAATATTTTTATTAAT
AAAATGGGTTT
Found at i:16200 original size:41 final size:41
Alignment explanation
Indices: 16155--16285 Score: 101
Period size: 41 Copynumber: 3.1 Consensus size: 41
16145 TATTTAGATG
16155 AATTTGGGGATAAAATTGGAAGATATAAACTTCTAGGGACT
1 AATTTGGGGATAAAATTGGAAGATATAAACTTCTAGGGACT
* * * * * *
16196 AATTT-AGGTTAAATTATGGTTGAA-ATGTATTACATATTTA--GA-T
1 AATTTGGGGATAAA--AT--TGGAAGATATA-AAC-T-TCTAGGGACT
16239 GAATTTGGGGATAAAATTGGAAGATATAAACTTCTAGGGACT
1 -AATTTGGGGATAAAATTGGAAGATATAAACTTCTAGGGACT
16281 AATTT
1 AATTT
16286 AAAATGATAT
Statistics
Matches: 65, Mismatches: 12, Indels: 26
0.63 0.12 0.25
Matches are distributed among these distances:
39 3 0.05
40 7 0.11
41 18 0.28
42 7 0.11
43 7 0.11
44 13 0.20
45 7 0.11
46 3 0.05
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.35
Consensus pattern (41 bp):
AATTTGGGGATAAAATTGGAAGATATAAACTTCTAGGGACT
Found at i:16206 original size:85 final size:85
Alignment explanation
Indices: 16111--16286 Score: 352
Period size: 85 Copynumber: 2.1 Consensus size: 85
16101 AAACAAATTA
16111 AATTTAGGTTAAATTATGGTTGAAATGTATTACATATTTAGATGAATTTGGGGATAAAATTGGAA
1 AATTTAGGTTAAATTATGGTTGAAATGTATTACATATTTAGATGAATTTGGGGATAAAATTGGAA
16176 GATATAAACTTCTAGGGACT
66 GATATAAACTTCTAGGGACT
16196 AATTTAGGTTAAATTATGGTTGAAATGTATTACATATTTAGATGAATTTGGGGATAAAATTGGAA
1 AATTTAGGTTAAATTATGGTTGAAATGTATTACATATTTAGATGAATTTGGGGATAAAATTGGAA
16261 GATATAAACTTCTAGGGACT
66 GATATAAACTTCTAGGGACT
16281 AATTTA
1 AATTTA
16287 AAATGATATT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 91 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.37
Consensus pattern (85 bp):
AATTTAGGTTAAATTATGGTTGAAATGTATTACATATTTAGATGAATTTGGGGATAAAATTGGAA
GATATAAACTTCTAGGGACT
Found at i:16340 original size:60 final size:60
Alignment explanation
Indices: 16276--16429 Score: 202
Period size: 60 Copynumber: 2.6 Consensus size: 60
16266 AAACTTCTAG
* **
16276 GGACTAATTTAAAATGATATTCATAGTTTGGGGATGAAATTTGAATGTTCAAAAGTTTAA
1 GGACTAATTTGAAATGATATTCATAGTTTGGGGATGAAATTAAAATGTTCAAAAGTTTAA
* * *
16336 GGACTAATTTGGAATGATATTAATAGTTCT-GGGATGAAATTAAAATGTTTAAAAGTTTAA
1 GGACTAATTTGAAATGATATTCATAGTT-TGGGGATGAAATTAAAATGTTCAAAAGTTTAA
* ** *
16396 GGACTAATTTGAAATTATGGTCATAATTTGGGGA
1 GGACTAATTTGAAATGATATTCATAGTTTGGGGA
16430 CATACGATGC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
59 1 0.01
60 78 0.98
61 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (60 bp):
GGACTAATTTGAAATGATATTCATAGTTTGGGGATGAAATTAAAATGTTCAAAAGTTTAA
Found at i:16410 original size:29 final size:29
Alignment explanation
Indices: 16313--16410 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
16303 TTGGGGATGA
*
16313 AATTTG-AATGTTCAAAAGTTTAAGGACT
1 AATTTGAAATGTTTAAAAGTTTAAGGACT
* * *
16341 AATTTGGAATGATATTAATAGTTCT-GGGA-T
1 AATTTGAAATG-T-TTAAAAGTT-TAAGGACT
* *
16371 GAAATTAAAATGTTTAAAAGTTTAAGGACT
1 -AATTTGAAATGTTTAAAAGTTTAAGGACT
16401 AATTTGAAAT
1 AATTTGAAAT
16411 TATGGTCATA
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
28 7 0.13
29 23 0.43
30 4 0.08
31 18 0.34
32 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (29 bp):
AATTTGAAATGTTTAAAAGTTTAAGGACT
Found at i:16794 original size:72 final size:71
Alignment explanation
Indices: 16671--16804 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 71
16661 AGTTAAAATA
* * *
16671 TCATTTTTCATTTTTTTTAAAGTTCGAAAGTATCAATACATTTGGAAAAGTATCGATACTTTACA
1 TCATTTTTCATTTTTTTTAAAGTTCAAAAGTATCAATACATTTGAAAAAGTATCAATACTTTACA
16736 ACCTTC
66 ACCTTC
*
16742 TCATTTTTCATATTTTTTTTAAA-TTCAAAAGTATCGATAC-TTGTGAAAAAGTATCAATACTTT
1 TCATTTTTC--ATTTTTTTTAAAGTTCAAAAGTATCAATACATT-TGAAAAAGTATCAATACTTT
16805 TAATTTTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
71 11 0.20
72 33 0.59
73 12 0.21
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (71 bp):
TCATTTTTCATTTTTTTTAAAGTTCAAAAGTATCAATACATTTGAAAAAGTATCAATACTTTACA
ACCTTC
Found at i:17198 original size:77 final size:77
Alignment explanation
Indices: 17047--17351 Score: 348
Period size: 77 Copynumber: 4.0 Consensus size: 77
17037 GAATATTTCA
* * * ** *
17047 TAATAAAAATATTAACATTTCAGATCGCAACCTATTTCTTAGTGA-TTATTGACATTCTTGGGTG
1 TAATAAAAATATTAACATTCCAGATTGTAACCTATTTCTTAGTGAGCCA-TGACATTCTTGGGCG
17111 CAA-CTCATTTTAT
65 CAACCT-ATTTTAT
* * * * * *
17124 TAATAAAAATATTAATATTCCTGATTGTAACCTATTTCTTAGTGAGCCATGATATTATTAGGCAC
1 TAATAAAAATATTAACATTCCAGATTGTAACCTATTTCTTAGTGAGCCATGACATTCTTGGGCGC
17189 AACCTATTTTAT
66 AACCTATTTTAT
*
17201 TAATAAAAATATTAACGTTCCAGATTGTAACCTATTTCTTAGTGAGCCATGACATTCTTGGGCGC
1 TAATAAAAATATTAACATTCCAGATTGTAACCTATTTCTTAGTGAGCCATGACATTCTTGGGCGC
*
17266 AACCCATTTTAT
66 AACCTATTTTAT
* * * * * * * *
17278 TAATAAAAATATTAACATTCCA-TTTCGCAAACTATTTCATACTTAACCATGATATTCTT-GGCG
1 TAATAAAAATATTAACATTCCAGATT-GTAACCTATTTCTTAGTGAGCCATGACATTCTTGGGCG
17341 CAACCGTATTT
65 CAACC-TATTT
17352 CTTATATATA
Statistics
Matches: 194, Mismatches: 30, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
76 11 0.06
77 180 0.93
78 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.38
Consensus pattern (77 bp):
TAATAAAAATATTAACATTCCAGATTGTAACCTATTTCTTAGTGAGCCATGACATTCTTGGGCGC
AACCTATTTTAT
Found at i:17328 original size:154 final size:153
Alignment explanation
Indices: 17047--17351 Score: 391
Period size: 154 Copynumber: 2.0 Consensus size: 153
17037 GAATATTTCA
* ** *
17047 TAATAAAAATATTAACATTTCAGATCGCAACCTATTTCTTAGTGATTATTGACATTCTTGGGTGC
1 TAATAAAAATATTAACATTCCAGATCGCAACCTATTTCTTAGTGACCATTGACATTCTTGGGCGC
* * * * * * *
17112 AACTCATTTTATTAATAAAAATATTAATATTCCTGATTGTAACCTATTTCTTAGTGAGCCATGAT
66 AACCCATTTTATTAATAAAAATATTAACATTCCT-ATTGCAAACTATTTCATACTGAACCATGAT
17177 ATTATTAGGCACAACC-TATTTTAT
130 ATTATT-GGCACAACCGTATTTTAT
* * *
17201 TAATAAAAATATTAACGTTCCAGATTGTAACCTATTTCTTAGTGAGCCA-TGACATTCTTGGGCG
1 TAATAAAAATATTAACATTCCAGATCGCAACCTATTTCTTAGTGA-CCATTGACATTCTTGGGCG
*
17265 CAACCCATTTTATTAATAAAAATATTAACATTCC-ATTTCGCAAACTATTTCATACTTAACCATG
65 CAACCCATTTTATTAATAAAAATATTAACATTCCTA-TT-GCAAACTATTTCATACTGAACCATG
* *
17329 ATATTCTTGGCGCAACCGTATTT
128 ATATTATTGGCACAACCGTATTT
17352 CTTATATATA
Statistics
Matches: 130, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
152 1 0.01
153 10 0.08
154 118 0.91
155 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.38
Consensus pattern (153 bp):
TAATAAAAATATTAACATTCCAGATCGCAACCTATTTCTTAGTGACCATTGACATTCTTGGGCGC
AACCCATTTTATTAATAAAAATATTAACATTCCTATTGCAAACTATTTCATACTGAACCATGATA
TTATTGGCACAACCGTATTTTAT
Found at i:31437 original size:24 final size:24
Alignment explanation
Indices: 31405--31458 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
31395 AAATTGGTGC
*
31405 TGCTTAATATGGAAGGTTGTATTT
1 TGCTTAATATAGAAGGTTGTATTT
31429 TGCTTAATATAGAAGGTTGTATTT
1 TGCTTAATATAGAAGGTTGTATTT
31453 TGCTTA
1 TGCTTA
31459 TGACGTGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (24 bp):
TGCTTAATATAGAAGGTTGTATTT
Found at i:31539 original size:29 final size:29
Alignment explanation
Indices: 31497--31554 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
31487 TTTATAAAAG
*
31497 ATACCAACTGTCCAGTTTACAAGTGATCC
1 ATACCAACTGTCCAGTTCACAAGTGATCC
31526 ATACCAACTGTCCAGTTCACAAGTGATCC
1 ATACCAACTGTCCAGTTCACAAGTGATCC
31555 TTTCTGCCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (29 bp):
ATACCAACTGTCCAGTTCACAAGTGATCC
Found at i:32194 original size:42 final size:42
Alignment explanation
Indices: 32135--32218 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
32125 AGAGTAGCCA
*
32135 TTTTCTAAGTTTGATGCGTAATATTTGAGAGACTTAGGTGAG
1 TTTTCTAAGTTTGATGCGTAATATTCGAGAGACTTAGGTGAG
*
32177 TTTTCTAAGTTTTATGCGTAATATTCGAGAGACTTAGGTGAG
1 TTTTCTAAGTTTGATGCGTAATATTCGAGAGACTTAGGTGAG
32219 ATCAACTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.40
Consensus pattern (42 bp):
TTTTCTAAGTTTGATGCGTAATATTCGAGAGACTTAGGTGAG
Found at i:44442 original size:31 final size:32
Alignment explanation
Indices: 44383--44443 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
44373 AAATATTATA
* *
44383 TATTTTCTTTAAAAATTTAAATTCATAAAATT
1 TATTTTCTTTAAAAATTAAAAATCATAAAATT
44415 TATTTT-TTTACAAAATTAAAAAT-ATAAAA
1 TATTTTCTTTA-AAAATTAAAAATCATAAAA
44444 AAGGTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (32 bp):
TATTTTCTTTAAAAATTAAAAATCATAAAATT
Done.