Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000193.1 Hibiscus syriacus cultivar Beakdansim tig00000343_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: 84302
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2331 original size:19 final size:17
Alignment explanation
Indices: 2294--2336 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
2284 GTTGTTTTTA
*
2294 AAATAAAAATAAAAATT
1 AAATAAAAAAAAAAATT
2311 AAATAAAAGAAAAATAATT
1 AAATAAAA-AAAAA-AATT
2330 AAATAAA
1 AAATAAA
2337 CATATTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.35
18 4 0.17
19 11 0.48
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
AAATAAAAAAAAAAATT
Found at i:2667 original size:42 final size:42
Alignment explanation
Indices: 2588--2667 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
2578 AGATCAATCC
* * *
2588 TTTTCATCTAGGGATCGATTCTTTTAGTGAAGTGATCGGTCA
1 TTTTCATCGAGGGATCGATTCTTTTAGTAAAGGGATCGGTCA
* *
2630 TTTTCCTCGAGGGATCGA-TCTTTTTGTAAAAGGGATCG
1 TTTTCATCGAGGGATCGATTCTTTTAGT-AAAGGGATCG
2668 ATCCAAAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 8 0.25
42 24 0.75
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (42 bp):
TTTTCATCGAGGGATCGATTCTTTTAGTAAAGGGATCGGTCA
Found at i:2709 original size:18 final size:19
Alignment explanation
Indices: 2688--2742 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
2678 CAATGGAATC
*
2688 CAAGGGATCAATCCTTTT-
1 CAAGGGATCGATCCTTTTG
2706 CAAGGGGATCGATCCTTTTG
1 CAA-GGGATCGATCCTTTTG
2726 CTAA-GGATCGATCCTTT
1 C-AAGGGATCGATCCTTT
2743 GAGCCAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 3 0.09
19 27 0.82
20 1 0.03
21 2 0.06
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (19 bp):
CAAGGGATCGATCCTTTTG
Found at i:5193 original size:54 final size:54
Alignment explanation
Indices: 5088--5437 Score: 465
Period size: 54 Copynumber: 6.5 Consensus size: 54
5078 CTATGTGGTT
* * *
5088 TTGCACACATAATGACC-ATACTGTAATTCAC--ACTCATTATGAATTACATGGG
1 TTGCACACATAGTG-CCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* * **
5140 CTGCACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTATATGGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGT-GGG
* *
5195 TT-CATACATAGTGCCGATACGGTAATTCATAAACTCATTATGAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* * * *
5248 TTTCACACATAGTGTCGATATGGTAATTCACAAACTCATTATGAATTACTTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* *
5302 TTGCATACATAGTGGCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* * * *
5356 TTGCACTCATAGTGCCGATACGATAATTCATAAACTCGTTATGAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* *
5410 TTGCACACATAGTGCTGATACGATAATT
1 TTGCACACATAGTGCCGATACGGTAATT
5438 ACGGCATATA
Statistics
Matches: 264, Mismatches: 29, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
51 1 0.00
52 25 0.09
53 5 0.02
54 229 0.87
55 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (54 bp):
TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
Found at i:9487 original size:30 final size:30
Alignment explanation
Indices: 9443--9549 Score: 160
Period size: 30 Copynumber: 3.5 Consensus size: 30
9433 GAAGGAGGAA
* *
9443 GGAATAAGGAAGAAGAAAGAAATGAATTAT
1 GGAAGAAGAAAGAAGAAAGAAATGAATTAT
*
9473 GGAAGAATAAAGAAGAAAGAAATGAATTAT
1 GGAAGAAGAAAGAAGAAAGAAATGAATTAT
*
9503 GGAAGAAGGAAGAAGAAAGAAATGAATTAT
1 GGAAGAAGAAAGAAGAAAGAAATGAATTAT
9533 GGAAGAAAGAAGAGAAG
1 GGAAG-AAGAA-AGAAG
9550 TATTTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
30 60 0.87
31 4 0.06
32 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.29, T:0.13
Consensus pattern (30 bp):
GGAAGAAGAAAGAAGAAAGAAATGAATTAT
Found at i:10086 original size:17 final size:17
Alignment explanation
Indices: 10064--10100 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
10054 GATTATCTTT
*
10064 CTTCAAAAAAATCCGCA
1 CTTCAAAAAAATCCACA
10081 CTTCAAAAAAATCCACA
1 CTTCAAAAAAATCCACA
10098 CTT
1 CTT
10101 TTTTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.30, G:0.03, T:0.22
Consensus pattern (17 bp):
CTTCAAAAAAATCCACA
Found at i:15481 original size:18 final size:18
Alignment explanation
Indices: 15458--15492 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
15448 AAGAAATTAC
15458 TAAGAGTCCTAGCTAAGG
1 TAAGAGTCCTAGCTAAGG
*
15476 TAAGAGTTCTAGCTAAG
1 TAAGAGTCCTAGCTAAG
15493 TTAAAAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (18 bp):
TAAGAGTCCTAGCTAAGG
Found at i:15501 original size:18 final size:18
Alignment explanation
Indices: 15466--15501 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
15456 ACTAAGAGTC
*
15466 CTAGCTAAGGTAAGAGTT
1 CTAGCTAAGGTAAAAGTT
*
15484 CTAGCTAAGTTAAAAGTT
1 CTAGCTAAGGTAAAAGTT
15502 ATCTTTATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (18 bp):
CTAGCTAAGGTAAAAGTT
Found at i:19243 original size:18 final size:18
Alignment explanation
Indices: 19220--19254 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19210 AAGAAATTAC
19220 TAAGAGTCCTAGCTAAGG
1 TAAGAGTCCTAGCTAAGG
*
19238 TAAGAGTTCTAGCTAAG
1 TAAGAGTCCTAGCTAAG
19255 TTAAAAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (18 bp):
TAAGAGTCCTAGCTAAGG
Found at i:19263 original size:18 final size:18
Alignment explanation
Indices: 19228--19263 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19218 ACTAAGAGTC
*
19228 CTAGCTAAGGTAAGAGTT
1 CTAGCTAAGGTAAAAGTT
*
19246 CTAGCTAAGTTAAAAGTT
1 CTAGCTAAGGTAAAAGTT
19264 ATCTTATCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (18 bp):
CTAGCTAAGGTAAAAGTT
Found at i:24354 original size:200 final size:200
Alignment explanation
Indices: 24011--24411 Score: 766
Period size: 200 Copynumber: 2.0 Consensus size: 200
24001 CACAACATTG
*
24011 AGCTATTCAGAGCTTTCATCCATCAAGACAATCTTGTTAATTTACTATTGATTGTGGGTCGTTTC
1 AGCTATTCAGAGCTTTCATCCACCAAGACAATCTTGTTAATTTACTATTGATTGTGGGTCGTTTC
24076 ACCTGGTGGAATAACAGAGAAAGTCCTTTTATAAGGCTTGATCGTTTTCTGGGGGATGCTAGATT
66 ACCTGGTGGAATAACAGAGAAAGTCCTTTTATAAGGCTTGATCGTTTTCTGGGGGATGCTAGATT
24141 CTTGGCGGCTTTCCCAAATATTTCGCAAAAGCTACTTCTGAAGTCTCTTTCAAATCGTAACACAA
131 CTTGGCGGCTTTCCCAAATATTTCGCAAAAGCTACTTCTGAAGTCTCTTTCAAATCGTAACACAA
24206 TTGAA
196 TTGAA
24211 AGCTATTCAGAGCTTTCATCCACCAAGACAATCTTGTTAATTTACTATTGATTGTGGGTCGTTTC
1 AGCTATTCAGAGCTTTCATCCACCAAGACAATCTTGTTAATTTACTATTGATTGTGGGTCGTTTC
24276 ACCTGGTGGAATAACAGAGAAAGTCCTTTTATAAGGCTTGATCGTTTTCTGGGGGATGCTAGATT
66 ACCTGGTGGAATAACAGAGAAAGTCCTTTTATAAGGCTTGATCGTTTTCTGGGGGATGCTAGATT
* **
24341 CTTGGTGGCTTTCCCAAATATTTCGCAAAAGCTACTTCTGAAGTCTCTTTCAGTTCGTAACACAA
131 CTTGGCGGCTTTCCCAAATATTTCGCAAAAGCTACTTCTGAAGTCTCTTTCAAATCGTAACACAA
24406 TTGAA
196 TTGAA
24411 A
1 A
24412 TCGTAAACGA
Statistics
Matches: 197, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 197 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (200 bp):
AGCTATTCAGAGCTTTCATCCACCAAGACAATCTTGTTAATTTACTATTGATTGTGGGTCGTTTC
ACCTGGTGGAATAACAGAGAAAGTCCTTTTATAAGGCTTGATCGTTTTCTGGGGGATGCTAGATT
CTTGGCGGCTTTCCCAAATATTTCGCAAAAGCTACTTCTGAAGTCTCTTTCAAATCGTAACACAA
TTGAA
Found at i:41390 original size:30 final size:31
Alignment explanation
Indices: 41325--41397 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
41315 AATCTCTAAA
41325 CTGGTTCAACATTGAACTTGTGCGGTTTAAC
1 CTGGTTCAACATTGAACTTGTGCGGTTTAAC
41356 CTGGTTCAACATTGAACTTGTGCGGTTT-AC
1 CTGGTTCAACATTGAACTTGTGCGGTTTAAC
41386 CTGGTTCAACAT
1 CTGGTTCAACAT
41398 GTAAATACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 14 0.33
31 28 0.67
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
CTGGTTCAACATTGAACTTGTGCGGTTTAAC
Found at i:67942 original size:44 final size:45
Alignment explanation
Indices: 67852--67946 Score: 147
Period size: 44 Copynumber: 2.1 Consensus size: 45
67842 TTTTCTATTC
* * * *
67852 TACTGTGAAGGTTTTTATGGCAGGGGGGTGTTTTTAAGTTTTATG
1 TACTGTAAAGGCTTTTATGCCAGGGGGATGTTTTTAAGTTTTATG
67897 TACTGTAAAGGCTTTTATGCCA-GGGGATGTTTTTAAGTTTTATG
1 TACTGTAAAGGCTTTTATGCCAGGGGGATGTTTTTAAGTTTTATG
67941 TACTGT
1 TACTGT
67947 TATTGGTGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 27 0.59
45 19 0.41
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.44
Consensus pattern (45 bp):
TACTGTAAAGGCTTTTATGCCAGGGGGATGTTTTTAAGTTTTATG
Found at i:68522 original size:16 final size:16
Alignment explanation
Indices: 68501--68533 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
68491 TAATAAATAG
68501 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
68517 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
68533 A
1 A
68534 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:68614 original size:10 final size:10
Alignment explanation
Indices: 68599--68673 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
68589 CATTTAATAA
68599 ATAAACGAAC
1 ATAAACGAAC
68609 ATAAACGAAC
1 ATAAACGAAC
68619 ----ACGAAC
1 ATAAACGAAC
68625 ATAAACGAAC
1 ATAAACGAAC
** *
68635 ACGAAC-ATAA
1 ATAAACGA-AC
68645 ATGAACACGAAC
1 AT-AA-ACGAAC
68657 ATAAACGAAC
1 ATAAACGAAC
68667 ATAAACG
1 ATAAACG
68674 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:68624 original size:16 final size:16
Alignment explanation
Indices: 68603--68667 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
68593 TAATAAATAA
68603 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
68619 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
68635 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
68651 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
68667 A
1 A
68668 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:69439 original size:14 final size:14
Alignment explanation
Indices: 69422--69477 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
69412 AATGAACATA
*
69422 AACGAACATAATCG
1 AACGAACATAACCG
69436 AACGAACAT-A---
1 AACGAACATAACCG
69446 AACGAACATAACCG
1 AACGAACATAACCG
69460 AACGAACATAACCG
1 AACGAACATAACCG
69474 AACG
1 AACG
69478 TTCACGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:69442 original size:24 final size:24
Alignment explanation
Indices: 69402--69476 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
69392 GATTGGGTTA
*
69402 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
69426 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* *
69450 AACATAACCGAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
69474 AAC
1 AAC
69477 GTTCACGAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:69476 original size:10 final size:10
Alignment explanation
Indices: 69415--69462 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
69405 ATAAATGAAT
69415 GAACATAAAC
1 GAACATAAAC
69425 GAACATAATCGAAC
1 GAACAT-A---AAC
69439 GAACATAAAC
1 GAACATAAAC
*
69449 GAACATAACC
1 GAACATAAAC
69459 GAAC
1 GAAC
69463 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Done.