Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003152.1 Hibiscus syriacus cultivar Beakdansim tig00006627_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: 61540
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3478 original size:2 final size:2
Alignment explanation
Indices: 3467--3500 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3457 TAAATACACG
3467 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3501 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8143 original size:2 final size:2
Alignment explanation
Indices: 8126--8348 Score: 60
Period size: 2 Copynumber: 113.5 Consensus size: 2
8116 TTGAAATAAT
* * *
8126 TA TA -A TA TA T- TA -A TA TA TA TA TA TA TA CA TA TA TG TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
8165 CT- TA TA -A TA -A TA TA -A TA TG TA TA AA CTA TG TA TA AA T- TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
8204 TA TA GTT TA TA TT TA TA TA GTA TG TA TA AA T- TA TA CTA TA TA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA
* * * * * *
8246 TA AA CTA TA TA TG T- TA TA -A AA TA TA AA TA -A TA -A CA TA AA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
8285 CTA TA TA TA TA TA TA TA TA TA CCA TG TA GTT TA TA TT TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
*
8328 CTA TA TA TA AA T- TA TA TA TA T
1 -TA TA TA TA TA TA TA TA TA TA T
8349 TATGTATAAA
Statistics
Matches: 156, Mismatches: 41, Indels: 48
0.64 0.17 0.20
Matches are distributed among these distances:
1 14 0.09
2 130 0.83
3 12 0.08
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:15112 original size:16 final size:17
Alignment explanation
Indices: 15062--15113 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
15052 ATTAAAAATA
15062 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
15079 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
15094 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
15110 AATT
1 AATT
15114 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:16308 original size:2 final size:2
Alignment explanation
Indices: 16301--16340 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
16291 ATCTTACCTC
16301 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16341 ATAAAAGTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16457 original size:29 final size:29
Alignment explanation
Indices: 16403--16470 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
16393 GTGTTTATAA
* *
16403 ATTTTATAACAGATGAATCAATTTTA-TT
1 ATTTTATAATAGATGAACCAATTTTATTT
16431 ATTTTATAATATGCATGAACCAA-TTTATTT
1 ATTTTATAATA-G-ATGAACCAATTTTATTT
16461 ATTTT-TAATA
1 ATTTTATAATA
16471 AGATCACATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 10 0.29
29 10 0.29
30 15 0.43
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (29 bp):
ATTTTATAATAGATGAACCAATTTTATTT
Found at i:20712 original size:21 final size:19
Alignment explanation
Indices: 20686--20733 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
20676 AACACAGAAG
20686 TCAAATTCGCAATACTGAATT
1 TCAAATTCG-AA-ACTGAATT
* *
20707 TCAAATTCGTAACTTAATT
1 TCAAATTCGAAACTGAATT
20726 TCAAATTC
1 TCAAATTC
20734 ACAACTCGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.60
20 1 0.04
21 9 0.36
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (19 bp):
TCAAATTCGAAACTGAATT
Found at i:20739 original size:19 final size:19
Alignment explanation
Indices: 20703--20739 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20693 CGCAATACTG
**
20703 AATTTCAAATTCGTAACTT
1 AATTTCAAATTCACAACTT
20722 AATTTCAAATTCACAACT
1 AATTTCAAATTCACAACT
20740 CGATTTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTTCAAATTCACAACTT
Found at i:20745 original size:19 final size:19
Alignment explanation
Indices: 20703--20745 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
20693 CGCAATACTG
** *
20703 AATTTCAAATTCGTAACTT
1 AATTTCAAATTCACAACTC
20722 AATTTCAAATTCACAACTC
1 AATTTCAAATTCACAACTC
*
20741 GATTT
1 AATTT
20746 TTGAATTTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (19 bp):
AATTTCAAATTCACAACTC
Found at i:21583 original size:12 final size:12
Alignment explanation
Indices: 21562--21595 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
21552 ACCACATTTC
*
21562 CAATACCAAACA
1 CAATATCAAACA
21574 CAATATCAAACA
1 CAATATCAAACA
*
21586 CAATCTCAAA
1 CAATATCAAA
21596 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:24353 original size:34 final size:34
Alignment explanation
Indices: 24308--24375 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
24298 GTTGCGATTA
* *
24308 TTGCGAAAGTCAAATTTG-AATTGCGATTTTCGCG
1 TTGCGAAAGTCAAATTCGCAA-CGCGATTTTCGCG
*
24342 TTGCGATAGTCAAATTCGCAACGCGATTTTCGCG
1 TTGCGAAAGTCAAATTCGCAACGCGATTTTCGCG
24376 ATACAATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (34 bp):
TTGCGAAAGTCAAATTCGCAACGCGATTTTCGCG
Found at i:24593 original size:64 final size:64
Alignment explanation
Indices: 24514--24671 Score: 280
Period size: 64 Copynumber: 2.5 Consensus size: 64
24504 TGAATTTAAC
24514 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
* * *
24578 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTTTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
24642 AACAAATCAACTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
24672 ATTCAATTAA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 86 0.96
65 4 0.04
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
Found at i:26048 original size:21 final size:21
Alignment explanation
Indices: 26022--26139 Score: 125
Period size: 21 Copynumber: 5.6 Consensus size: 21
26012 ATGAATCGGG
* *
26022 CTCTTGAACGGTGGAAGGGAC
1 CTCTTGAACGATGGAAGGGGC
*
26043 CTCTTGAATGAT-GACAGGGGC
1 CTCTTGAACGATGGA-AGGGGC
* *
26064 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGGAAGGGGC
26085 CTCTTGAACGAT-GAGAGGGGC
1 CTCTTGAACGATGGA-AGGGGC
**
26106 CTCTTGAACGATAGG-AGGCAC
1 CTCTTGAACGAT-GGAAGGGGC
26127 CTCTTGAACGATG
1 CTCTTGAACGATG
26140 ACAGGTGAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 11
0.80 0.10 0.11
Matches are distributed among these distances:
20 4 0.05
21 76 0.93
22 1 0.01
23 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGGAAGGGGC
Found at i:26088 original size:42 final size:42
Alignment explanation
Indices: 26022--26144 Score: 183
Period size: 42 Copynumber: 2.9 Consensus size: 42
26012 ATGAATCGGG
* *
26022 CTCTTGAACGGTGGAAGGGACCTCTTGAATGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
* *
26064 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
* * *
26106 CTCTTGAACGATAGGAGGCACCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGG
26145 TGAATCGGGC
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:26314 original size:4 final size:4
Alignment explanation
Indices: 26284--26325 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
26274 AGGCCACTGA
* *
26284 AAAT AAA- ATAAT ACAT AAAT CAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
26326 TGCCGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 1 0.03
4 30 0.94
5 1 0.03
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:28753 original size:22 final size:22
Alignment explanation
Indices: 28726--28767 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
28716 GAGATAGACG
28726 GATTTCGCCGGAGATGGGGACA
1 GATTTCGCCGGAGATGGGGACA
*
28748 GATTTCGTCGGAGATGGGGA
1 GATTTCGCCGGAGATGGGGA
28768 TGGATGTCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.14, G:0.43, T:0.21
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACA
Found at i:28952 original size:20 final size:20
Alignment explanation
Indices: 28927--28972 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
28917 TAAACGCGCT
28927 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
28947 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
28967 TTGCGA
1 TTGCGA
28973 TTTACATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:29009 original size:20 final size:20
Alignment explanation
Indices: 28943--29013 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
28933 ATTTGACTTC
**
28943 TGTGTTGCGAATTT-GACTT
1 TGTGTTGCGAATTTAGAAAT
* *
28962 CTGTGTTGCG-ATTTACATAT
1 -TGTGTTGCGAATTTAGAAAT
*
28982 TCGCGTTGCGAATTTAGAAAT
1 T-GTGTTGCGAATTTAGAAAT
29003 TGTGTTGCGAA
1 TGTGTTGCGAA
29014 AATGGAGTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.12
20 27 0.66
21 9 0.22
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.41
Consensus pattern (20 bp):
TGTGTTGCGAATTTAGAAAT
Found at i:32543 original size:5 final size:5
Alignment explanation
Indices: 32533--32739 Score: 336
Period size: 5 Copynumber: 41.8 Consensus size: 5
32523 TACTCTTGGT
32533 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
32583 TATAA TATAA TATAA TATAA TATAA TATAATA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TAT-A-A TATAA TATAA TATAA TATAA
32635 TATAA TAT-A TAATAA TAT-A TATAA TATAA TAT-A TAT-A TATAA TATAA
1 TATAA TATAA T-ATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
32682 TAT-A TATAA TATAA TAT-A TATATA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATA-A TATAA TATAA TATAA TATAA TATAA
32731 TATAA TATA
1 TATAA TATA
32740 TACACACACA
Statistics
Matches: 193, Mismatches: 0, Indels: 18
0.91 0.00 0.09
Matches are distributed among these distances:
4 22 0.11
5 158 0.82
6 9 0.05
7 4 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:32829 original size:5 final size:5
Alignment explanation
Indices: 32814--32857 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
32804 TTCACATAAC
*
32814 TAATAA TAATA TAATA TAATA TAATA TATATA CTTATA TAATA T
1 TAAT-A TAATA TAATA TAATA TAATA TA-ATA -TAATA TAATA T
32858 GCACCCTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 23 0.68
6 10 0.29
7 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (5 bp):
TAATA
Found at i:34235 original size:33 final size:33
Alignment explanation
Indices: 34198--34296 Score: 129
Period size: 33 Copynumber: 3.2 Consensus size: 33
34188 ACTAAAATGA
34198 AAATAATATGAAGTTTCAAGAAAACAAGGATAC
1 AAATAATATGAAGTTTCAAGAAAACAAGGATAC
* *
34231 AAATAA-A-G-GGATT--A-AAAACAAGGATAC
1 AAATAATATGAAGTTTCAAGAAAACAAGGATAC
*
34258 AAATAATATGAAGTTTCAAGAAGACAAGGATAC
1 AAATAATATGAAGTTTCAAGAAAACAAGGATAC
34291 AAATAA
1 AAATAA
34297 AGGGATATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
27 19 0.35
28 2 0.04
29 1 0.02
30 6 0.11
31 1 0.02
32 2 0.04
33 24 0.44
ACGTcount: A:0.57, C:0.08, G:0.16, T:0.19
Consensus pattern (33 bp):
AAATAATATGAAGTTTCAAGAAAACAAGGATAC
Found at i:34255 original size:27 final size:27
Alignment explanation
Indices: 34218--34307 Score: 99
Period size: 27 Copynumber: 3.1 Consensus size: 27
34208 AAGTTTCAAG
34218 AAAACAAGGATACAAATAAAGGGATTA
1 AAAACAAGGATACAAATAAAGGGATTA
* *
34245 AAAACAAGGATACAAATAATATGAAGTTTCA
1 AAAACAAGGATACAAATAA-A-G-GGATT-A
34276 AGAAGACAAGGATACAAATAAAGGGATATA
1 A-AA-ACAAGGATACAAATAAAGGGAT-TA
34306 AA
1 AA
34308 TAAAGCACGG
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
27 19 0.37
28 1 0.02
29 2 0.04
30 7 0.13
31 4 0.08
32 3 0.06
33 16 0.31
ACGTcount: A:0.58, C:0.08, G:0.18, T:0.17
Consensus pattern (27 bp):
AAAACAAGGATACAAATAAAGGGATTA
Found at i:39217 original size:6 final size:6
Alignment explanation
Indices: 39206--39233 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39196 TTTATGCTAA
39206 ACGGGG ACGGGG ACGGGG ACGGGG ACGG
1 ACGGGG ACGGGG ACGGGG ACGGGG ACGG
39234 TAATCCCCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:43867 original size:2 final size:2
Alignment explanation
Indices: 43860--43886 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43850 AGGTGGCTAC
43860 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
43887 TAATTTTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.