Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008291.1 Hibiscus syriacus cultivar Beakdansim tig00110955_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: 34525
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:937 original size:22 final size:22
Alignment explanation
Indices: 911--952 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
901 TATGTATGTC
911 TTTGT-GATACATTTATCTCTCT
1 TTTGTGGA-ACATTTATCTCTCT
933 TTTGTGGAACATTTATCTCT
1 TTTGTGGAACATTTATCTCT
953 ACCTTTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (22 bp):
TTTGTGGAACATTTATCTCTCT
Found at i:1602 original size:19 final size:20
Alignment explanation
Indices: 1577--1627 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 20
1567 TATAGTAAAT
1577 TAAATAAATAATATATTTTA
1 TAAATAAATAATATATTTTA
1597 -AAAT-AA-AATATATTTTA
1 TAAATAAATAATATATTTTA
*
1614 TTTAATAAATAATA
1 -TAAATAAATAATA
1628 CTAATATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.42
18 2 0.08
19 7 0.27
20 2 0.08
21 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATAAATAATATATTTTA
Found at i:7016 original size:2 final size:2
Alignment explanation
Indices: 7009--7033 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6999 TAGTTTACCC
7009 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 T
7034 TTGAAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7276 original size:21 final size:20
Alignment explanation
Indices: 7252--7291 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
7242 CATCATAAAC
*
7252 TAATTTATTACAAATTAATAA
1 TAATTTATTA-AAACTAATAA
*
7273 TAATTTTTTAAAACTAATA
1 TAATTTATTAAAACTAATA
7292 CAATCACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATTTATTAAAACTAATAA
Found at i:8561 original size:18 final size:19
Alignment explanation
Indices: 8535--8574 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
8525 AATGCTCAAA
8535 ACTAACCTTG-GTATCGAT
1 ACTAACCTTGAGTATCGAT
*
8553 ACTAGCCTTGAAGTATCGAT
1 ACTAACCTTG-AGTATCGAT
8573 AC
1 AC
8575 CCTACCCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (19 bp):
ACTAACCTTGAGTATCGAT
Found at i:8723 original size:20 final size:20
Alignment explanation
Indices: 8672--8727 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
8662 ATTATGAAAT
8672 CTCAGTCTCGATACCAAGCC
1 CTCAGTCTCGATACCAAGCC
8692 CTTCAGTCTCGATACCGAA-CC
1 C-TCAGTCTCGATACC-AAGCC
*
8713 CTCAGTATCGATACC
1 CTCAGTCTCGATACC
8728 CCTTAAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 14 0.42
21 17 0.52
22 2 0.06
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (20 bp):
CTCAGTCTCGATACCAAGCC
Found at i:10468 original size:25 final size:24
Alignment explanation
Indices: 10423--10482 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
10413 TAATAAATTA
10423 AAATTTAAAAAATGATAAAAAAAAT
1 AAATTTAAAAAATGAT-AAAAAAAT
* *
10448 AAATTTAAAAAGTTAGT-AAAAAAT
1 AAATTTAAAAAATGA-TAAAAAAAT
*
10472 AAAGTTAAAAA
1 AAATTTAAAAA
10483 TTTAATTTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.55
25 13 0.42
26 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (24 bp):
AAATTTAAAAAATGATAAAAAAAT
Found at i:12640 original size:3 final size:3
Alignment explanation
Indices: 12623--12667 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
12613 GGGTCTTTTA
*
12623 TAT TAT TTT TA- TAT TAT TAAT TAT TAT TAAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT T-AT TAT TAT TAT TAT TA
12668 ATTTTACATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:12647 original size:10 final size:10
Alignment explanation
Indices: 12634--12667 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
12624 ATTATTTTTA
12634 TATTATTAAT
1 TATTATTAAT
12644 TATTATTAAT
1 TATTATTAAT
12654 TATTATT-AT
1 TATTATTAAT
12663 TATTA
1 TATTA
12668 ATTTTACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTAAT
Found at i:12658 original size:13 final size:13
Alignment explanation
Indices: 12634--12670 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
12624 ATTATTTTTA
12634 TATTATTAATTAT
1 TATTATTAATTAT
12647 TATTAATT-ATTAT
1 TATT-ATTAATTAT
12660 TATTATTAATT
1 TATTATTAATT
12671 TTACATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.14
13 16 0.73
14 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATTAATTAT
Found at i:12679 original size:16 final size:16
Alignment explanation
Indices: 12635--12680 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
12625 TTATTTTTAT
12635 ATTATTAATTATTATTA
1 ATTATTAA-TATTATTA
*
12652 ATTATTATTATTATTA
1 ATTATTAATATTATTA
12668 ATT-TTACATATTA
1 ATTATTA-ATATTA
12681 CATTTTTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 3 0.12
16 16 0.62
17 7 0.27
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTAATATTATTA
Found at i:26049 original size:15 final size:15
Alignment explanation
Indices: 26029--26071 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
26019 CACTTAAAAA
*
26029 AAAAAAAAGGAAATG
1 AAAAAAAAGAAAATG
*
26044 AAAAAAATGAAAATG
1 AAAAAAAAGAAAATG
*
26059 AAAAAGAAGAAAA
1 AAAAAAAAGAAAA
26072 AATAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (15 bp):
AAAAAAAAGAAAATG
Found at i:27224 original size:140 final size:141
Alignment explanation
Indices: 27007--27276 Score: 402
Period size: 140 Copynumber: 1.9 Consensus size: 141
26997 AACATCAACT
27007 GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
1 GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
* ** *
27072 GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATC
66 GGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
27137 TACCCTTAGAC
131 TACCCTTAGAC
* * *
27148 GACCAGA-CTTCCTCATCACGTA-GAGCCGTGTCAACCTTA-GATAATCAGCCGTCCTCATCACG
1 GACCAGATC-TCCTCATCACGTAGGAG-AGTGTCAACATTAGGATAACCAGCCGTCCTCATCACG
* * * *
27210 TAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTATGAGCCGTGTCA
64 TAGGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCA
27275 TC
129 TC
27277 CCTTGACCAG
Statistics
Matches: 116, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
140 85 0.73
141 31 0.27
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (141 bp):
GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
TACCCTTAGAC
Found at i:27523 original size:3 final size:3
Alignment explanation
Indices: 27509--27550 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
27499 GTCTTTTTAT
*
27509 TTA TTT TTA TTA TTAA TTA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
27551 ATTTTACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27534 original size:16 final size:17
Alignment explanation
Indices: 27505--27550 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
27495 CCGGGTCTTT
*
27505 TTAT-TTATTTTTATTA
1 TTATATTATTATTATTA
27521 TTA-ATTATTATTATTA
1 TTATATTATTATTATTA
27537 TTATATTATTATTA
1 TTATATTATTATTA
27551 ATTTTACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATTATTATTATTA
Done.