Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003094.1 Hibiscus syriacus cultivar Beakdansim tig00006457_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: 19166
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1077 original size:19 final size:20
Alignment explanation
Indices: 1021--1075 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
1011 ATTCATTTGA
1021 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1041 CTATCGC-ACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1060 TTATCGCAATGCGAAA
1 CTATCGCAACGCGAAA
1076 TGAAAATCGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1128 original size:32 final size:33
Alignment explanation
Indices: 1082--1158 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 33
1072 GAAATGAAAA
* **
1082 TCGCATTGCAATTTTCTCGTTACGAT-TTCATT
1 TCGCATTGCGATTTTCTCGTTACGATAGCCATT
*
1114 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTACGATAGCCATT
*
1147 TCGCGTTGCGAT
1 TCGCATTGCGAT
1159 AGTCTGTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 24 0.62
33 15 0.38
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTACGATAGCCATT
Found at i:3148 original size:20 final size:19
Alignment explanation
Indices: 3113--3164 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
3103 CGAAACTAAA
3113 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
3132 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
*
3152 ATCGCAATGCGAA
1 ATCGCAACGCGAA
3165 TGAAAATCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3215 original size:17 final size:17
Alignment explanation
Indices: 3112--3209 Score: 62
Period size: 20 Copynumber: 5.6 Consensus size: 17
3102 ACGAAACTAA
3112 AATCGCAACGCGAAATG
1 AATCGCAACGCGAAATG
3129 ACTATCGCAACGCGGAAATGG
1 A--ATCGCAACGC-GAAAT-G
* *
3150 CTATCGCAATGCG-AATG
1 -AATCGCAACGCGAAATG
*
3167 AAAATCGTAA--CGACAA--
1 --AATCGCAACGCGA-AATG
3183 AATCGCAACGCGAAATG
1 AATCGCAACGCGAAATG
3200 AATCGCAACG
1 AATCGCAACG
3210 ACAAATCGCA
Statistics
Matches: 63, Mismatches: 6, Indels: 24
0.68 0.06 0.26
Matches are distributed among these distances:
14 7 0.11
15 2 0.03
16 5 0.08
17 12 0.19
18 11 0.17
19 11 0.17
20 14 0.22
21 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.22, T:0.14
Consensus pattern (17 bp):
AATCGCAACGCGAAATG
Found at i:3218 original size:30 final size:32
Alignment explanation
Indices: 3152--3227 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 32
3142 GGAAATGGCT
* *
3152 ATCGCAATGCG-AATGAAAATCGTAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
3184 ATCGCAACGCGAAATG-AATCGCAACGAC-AA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
*
3214 ATCGCAACGGGAAA
1 ATCGCAACGCGAAA
3228 CACAAATCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
30 15 0.38
31 11 0.28
32 10 0.25
33 4 0.10
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:3256 original size:19 final size:18
Alignment explanation
Indices: 3234--3328 Score: 89
Period size: 18 Copynumber: 5.7 Consensus size: 18
3224 GAAACACAAA
3234 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
3253 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
3269 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
3285 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
3301 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
3317 TCGTATTGCGAT
1 TCGCATTGCGAT
3329 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
14 18 0.29
16 16 0.25
18 19 0.30
19 10 0.16
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:3275 original size:14 final size:14
Alignment explanation
Indices: 3256--3312 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
3246 TTTCATTTCG
3256 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3270 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
3286 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
3302 CGTTGCGATTT
1 CGTTGCGATTT
3313 CATTTCGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3286 original size:32 final size:32
Alignment explanation
Indices: 3239--3328 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
3229 ACAAATCGCA
*
3239 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
3272 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
*
3304 TTGCGATTTCATTTCGTATTGCGAT
1 TTGCGATTTCATTTCGCATTGCGAT
3329 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 49 0.89
33 6 0.11
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCATTGCGATTTTGTCG
Found at i:3354 original size:19 final size:20
Alignment explanation
Indices: 3322--3366 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
3312 TCATTTCGTA
3322 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
3342 TTGCG-TAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
3361 TTGCGA
1 TTGCGA
3367 AAGTAAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.13, C:0.22, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:3856 original size:17 final size:18
Alignment explanation
Indices: 3831--3874 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3821 GTCAATCAGA
*
3831 TGATGGCTCTGG-TGAGG
1 TGATGGCTCTGGACGAGG
*
3848 TGATAGCTCTGGACGAGG
1 TGATGGCTCTGGACGAGG
3866 TGATGGCTC
1 TGATGGCTC
3875 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.16, C:0.16, G:0.41, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGACGAGG
Found at i:5182 original size:20 final size:20
Alignment explanation
Indices: 5157--5194 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5147 AATAGTTTCT
5157 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
5177 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
5195 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:5243 original size:19 final size:19
Alignment explanation
Indices: 5221--5271 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
5211 GGAACTAAAA
5221 TCGCGTTGCGATTTGCATT
1 TCGCGTTGCGATTTGCATT
5240 TCGCGTTGCGATTTGCATT
1 TCGCGTTGCGATTTGCATT
5259 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5272 CTTGGTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.10, C:0.22, G:0.27, T:0.41
Consensus pattern (19 bp):
TCGCGTTGCGATTTGCATT
Found at i:5480 original size:22 final size:22
Alignment explanation
Indices: 5455--5498 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5445 GATTTAGATA
5455 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
5477 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
5499 TGAGAGTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:5708 original size:19 final size:20
Alignment explanation
Indices: 5684--5735 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
5674 GATTATGTAT
*
5684 TATCGCGTTGCGAAAGTCA-
1 TATCGCGTTGCGAAAGTAAG
5703 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
5723 TATCTCGTTGCGA
1 TATCGCGTTGCGA
5736 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:5769 original size:20 final size:20
Alignment explanation
Indices: 5664--5777 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
5654 CGCTTTGAAA
*
5664 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
5685 ATCGCGTTGCGAAAGTCA-T
1 ATCGCATTGCGATAGTCAGT
* * *
5704 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
5724 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
5745 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
5765 ATCGCATTGCGAT
1 ATCGCATTGCGAT
5778 TTTCCCAATT
Statistics
Matches: 75, Mismatches: 15, Indels: 7
0.77 0.15 0.07
Matches are distributed among these distances:
19 20 0.27
20 31 0.41
21 24 0.32
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:5795 original size:21 final size:21
Alignment explanation
Indices: 5766--5858 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
5756 ATAGTCAGTA
5766 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
5787 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
5807 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
5828 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
5848 TCGCATTGCGA
1 TCGCATTGCGA
5859 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:5796 original size:41 final size:41
Alignment explanation
Indices: 5705--5839 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
5695 GAAAGTCATA
* * * ** *
5705 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
5745 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
5787 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
5828 TCGCGTTGCGAT
1 TCGCGTTGCGAT
5840 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:5840 original size:41 final size:41
Alignment explanation
Indices: 5766--5858 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
5756 ATAGTCAGTA
5766 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
5807 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
5848 TCGCATTGCGA
1 TCGCATTGCGA
5859 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Done.