Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000097.1 Hibiscus syriacus cultivar Beakdansim tig00000180_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: 40978
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:284 original size:17 final size:17
Alignment explanation
Indices: 246--286 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
236 AAAATGAGAT
246 AAAAAA-TAAGAAATAA
1 AAAAAAGTAAGAAATAA
262 AGAAAAAGTAA-AAATAA
1 A-AAAAAGTAAGAAATAA
279 CAAAAAAG
1 -AAAAAAG
287 AATGAAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.05
17 17 0.77
18 4 0.18
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAAAGTAAGAAATAA
Found at i:387 original size:31 final size:29
Alignment explanation
Indices: 313--387 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 29
303 TAATAATAAT
*
313 AAACAACAATAAAATAATGAGGAAAAATAC
1 AAACAAAAATAAAATAATGA-GAAAAATAC
*
343 AAAGAAAATATAAAATAATGA-AAAAATAC
1 AAACAAAA-ATAAAATAATGAGAAAAATAC
372 AATCACATAAAATAAA
1 AA--ACA-AAAATAAA
388 GAAAAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 10 0.26
30 6 0.16
31 19 0.50
32 3 0.08
ACGTcount: A:0.69, C:0.08, G:0.07, T:0.16
Consensus pattern (29 bp):
AAACAAAAATAAAATAATGAGAAAAATAC
Found at i:499 original size:2 final size:2
Alignment explanation
Indices: 492--519 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
482 TAATACTAGT
492 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
520 ATTTATAAAC
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:565 original size:24 final size:24
Alignment explanation
Indices: 538--597 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
528 ACAAGGTATA
* *
538 AAAATAATAGTAATAATAAATATT
1 AAAATAAAAATAATAATAAATATT
* *
562 AAAATAAAAATACTAATAAATA-A
1 AAAATAAAAATAATAATAAATATT
*
585 AAAACAAAAATAA
1 AAAATAAAAATAA
598 ATGAAATTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (24 bp):
AAAATAAAAATAATAATAAATATT
Found at i:643 original size:2 final size:2
Alignment explanation
Indices: 630--678 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
620 AATCAAAGTA
*
630 AT AT AT -T A- AT AT AT AT CT 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
670 AT AT AT AT A
1 AT AT AT AT A
679 AAGTATAATG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1203 original size:17 final size:17
Alignment explanation
Indices: 1166--1208 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1156 TAACTATTTT
*
1166 TAGAATCCTATTGACAA
1 TAGAATCCTAATGACAA
1183 TAGAATCCTAATG-CAA
1 TAGAATCCTAATGACAA
*
1199 CTAGACTCCT
1 -TAGAATCCT
1209 TGCTCGGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (17 bp):
TAGAATCCTAATGACAA
Found at i:1824 original size:20 final size:20
Alignment explanation
Indices: 1787--1823 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1777 CTCTAAACCC
*
1787 TTTTCAAAATTTCATTTTGT
1 TTTTCAAAATTCCATTTTGT
1807 TTTTCAAAA-TCCATTTT
1 TTTTCAAAATTCCATTTT
1824 TAGCTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.27, C:0.14, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGT
Found at i:2110 original size:21 final size:21
Alignment explanation
Indices: 2084--2160 Score: 75
Period size: 23 Copynumber: 3.6 Consensus size: 21
2074 GGTGTCAAAT
2084 TGCATCCATGCACCCCTGTAG
1 TGCATCCATGCACCCCTGTAG
**
2105 TGCATCCATGCACCTGCCACTAG
1 TGCATCCATGCACC--CCTGTAG
* * **
2128 TGCATCGATACA-CTATGTAG
1 TGCATCCATGCACCCCTGTAG
2148 TGCATCCATGCAC
1 TGCATCCATGCAC
2161 TCCATTTTCG
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
20 13 0.30
21 14 0.33
22 1 0.02
23 15 0.35
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (21 bp):
TGCATCCATGCACCCCTGTAG
Found at i:2132 original size:23 final size:21
Alignment explanation
Indices: 2084--2133 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2074 GGTGTCAAAT
**
2084 TGCATCCATGCACCCCTGTAG
1 TGCATCCATGCACCCCACTAG
2105 TGCATCCATGCACCTGCCACTAG
1 TGCATCCATGCACC--CCACTAG
2128 TGCATC
1 TGCATC
2134 GATACACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 14 0.56
23 11 0.44
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.24
Consensus pattern (21 bp):
TGCATCCATGCACCCCACTAG
Found at i:23434 original size:25 final size:25
Alignment explanation
Indices: 23406--23467 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
23396 TGGCTATAAT
* *
23406 GTAATTTTTTTAACTTTGTATTTTA
1 GTAATTTTTTTAACTTTATATTTGA
** *
23431 GTAATTTTTAAAATTTTATATTTGA
1 GTAATTTTTTTAACTTTATATTTGA
*
23456 GTAATTGTTTTA
1 GTAATTTTTTTA
23468 GATTCTTATA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (25 bp):
GTAATTTTTTTAACTTTATATTTGA
Found at i:24984 original size:12 final size:12
Alignment explanation
Indices: 24967--24997 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
24957 TTAATCTTCA
24967 TAGTCAGTTGAC
1 TAGTCAGTTGAC
24979 TAGTCAGTTGAC
1 TAGTCAGTTGAC
*
24991 TCGTCAG
1 TAGTCAG
24998 ATGTTAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (12 bp):
TAGTCAGTTGAC
Found at i:25539 original size:31 final size:31
Alignment explanation
Indices: 25499--25574 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
25489 GGCATGATTG
* *
25499 TATAGCATTGAAAAGTT-ATAATATGAGGTGA
1 TATAACATTGAAAAGTTCA-AATATGAGATGA
*
25530 TATAACATTGAAAAGTTCAGATATGAGATGA
1 TATAACATTGAAAAGTTCAAATATGAGATGA
* *
25561 TATATCACTGAAAA
1 TATAACATTGAAAA
25575 AAATATGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (31 bp):
TATAACATTGAAAAGTTCAAATATGAGATGA
Found at i:26356 original size:21 final size:21
Alignment explanation
Indices: 26314--26356 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
26304 TTTCTGGGCT
* *
26314 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
26335 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
26356 A
1 A
26357 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:26408 original size:20 final size:20
Alignment explanation
Indices: 26383--26420 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
26373 GAATGCTAGA
*
26383 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
26403 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
26421 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:26445 original size:13 final size:13
Alignment explanation
Indices: 26427--26451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26417 CCCATATAAA
26427 AAAAAAGAAGAAG
1 AAAAAAGAAGAAG
26440 AAAAAAGAAGAA
1 AAAAAAGAAGAA
26452 AGAATAAACT
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAGAAG
Found at i:33186 original size:21 final size:21
Alignment explanation
Indices: 33144--33186 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
33134 TTTCTGGGCT
* *
33144 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
33165 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
33186 A
1 A
33187 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:33238 original size:20 final size:20
Alignment explanation
Indices: 33213--33250 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33203 GAATGCTAGA
*
33213 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
33233 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
33251 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:33937 original size:23 final size:23
Alignment explanation
Indices: 33893--33937 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
33883 ATTATTATAT
*
33893 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
33916 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
33938 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:34120 original size:10 final size:10
Alignment explanation
Indices: 34105--34136 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
34095 AAGTATAAGC
*
34105 TTTCATCTCA
1 TTTCATATCA
34115 TTTCATATCA
1 TTTCATATCA
34125 TTTCATATCA
1 TTTCATATCA
34135 TT
1 TT
34137 ATGACATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTCATATCA
Found at i:34638 original size:66 final size:66
Alignment explanation
Indices: 34526--34776 Score: 301
Period size: 66 Copynumber: 3.8 Consensus size: 66
34516 GGGGTGTTAC
* ** *
34526 AAATATGGTCAACAAGTTCATATATGAGGCGATATATAACTGAAAAGAAAAATTGATGTTTTTCA
1 AAATATGGTCAACAAGTTCTTATATGAGATGATATATCACTGAAAAGAAAAA-TGATGTTTTTCA
34591 TT
65 TT
* * * * * * *
34593 AAAT-CGGTCAACAAGTT-TTGATGTGAGCTGATATATCATTGAAAAGAAAAATAACGTTTTCCA
1 AAATATGGTCAACAAGTTCTT-ATATGAGATGATATATCACTGAAAAGAAAAATGATGTTTTTCA
34656 TT
65 TT
* *
34658 AAATATGATCAACAAGTTCTTATATGAGGA-GATATATCACTGAAAAGAAAAATGATATTTTTTC
1 AAATATGGTCAACAAGTTCTTATATGA-GATGATATATCACTGAAAAGAAAAATGAT-GTTTTTC
34722 ATT
64 ATT
* * *
34725 AAATATGGTCAATAAGTTCATATATGAGATGATATATCACTAAAAAGAAAAA
1 AAATATGGTCAACAAGTTCTTATATGAGATGATATATCACTGAAAAGAAAAA
34777 GGACACAAAT
Statistics
Matches: 155, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
65 16 0.10
66 79 0.51
67 60 0.39
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (66 bp):
AAATATGGTCAACAAGTTCTTATATGAGATGATATATCACTGAAAAGAAAAATGATGTTTTTCAT
T
Done.