Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005762.1 Hibiscus syriacus cultivar Beakdansim tig00013489_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: 53393
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:21506 original size:120 final size:120
Alignment explanation
Indices: 21293--21535 Score: 477
Period size: 120 Copynumber: 2.0 Consensus size: 120
21283 CTCACTTTTC
21293 AGGACCAATCACGTAAAAGGTCACTTCCAAAAGGGATATCCTTAGATAAAGATCATTCCCAAAAG
1 AGGACCAATCACGTAAAAGGTCACTTCCAAAAGGGATATCCTTAGATAAAGATCATTCCCAAAAG
21358 GTATCTGTTGGTAAATCATATTCAAAAGAAAGACCTAAAAGGAAATCTTACGAAA
66 GTATCTGTTGGTAAATCATATTCAAAAGAAAGACCTAAAAGGAAATCTTACGAAA
21413 AGGACCAATCACGTAAAAGGTCACTTCCAAAAGGGATATCCTTAGATAAAGATCATTCCCAAAAG
1 AGGACCAATCACGTAAAAGGTCACTTCCAAAAGGGATATCCTTAGATAAAGATCATTCCCAAAAG
*
21478 GTATCTGTTGGTAAATCATATTCCAAAGAAAGACCTAAAAGGAAATCTTACGAAA
66 GTATCTGTTGGTAAATCATATTCAAAAGAAAGACCTAAAAGGAAATCTTACGAAA
21533 AGG
1 AGG
21536 TACCTAATGG
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 122 1.00
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (120 bp):
AGGACCAATCACGTAAAAGGTCACTTCCAAAAGGGATATCCTTAGATAAAGATCATTCCCAAAAG
GTATCTGTTGGTAAATCATATTCAAAAGAAAGACCTAAAAGGAAATCTTACGAAA
Found at i:24670 original size:10 final size:10
Alignment explanation
Indices: 24641--24709 Score: 72
Period size: 10 Copynumber: 7.1 Consensus size: 10
24631 GCTGCTGGAA
24641 AACCGGTTTG
1 AACCGGTTTG
*
24651 -ACCAGTTTTG
1 AACC-GGTTTG
24661 AACCGGTTTG
1 AACCGGTTTG
*
24671 -ACCGGTCTG
1 AACCGGTTTG
24680 AACCGGTTTG
1 AACCGGTTTG
*
24690 -ACCGGTCTG
1 AACCGGTTTG
*
24699 AACCGGGTTG
1 AACCGGTTTG
24709 A
1 A
24710 CCCGACCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 19 0.40
10 26 0.54
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:24683 original size:19 final size:19
Alignment explanation
Indices: 24641--24711 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
24631 GCTGCTGGAA
* *
24641 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
24661 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
24680 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
24699 AACCGGGTTGACC
1 AACCGGTTTGACC
24712 CGACCCGACT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 35 0.73
20 13 0.27
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:24727 original size:17 final size:17
Alignment explanation
Indices: 24705--24745 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
24695 TCTGAACCGG
*
24705 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
24722 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
24739 GTTGACC
1 GTTGACC
24746 GTTGACCGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:24747 original size:7 final size:7
Alignment explanation
Indices: 24735--24772 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
24725 GACCCGACCC
24735 GACCGTT
1 GACCGTT
24742 GACCGTT
1 GACCGTT
24749 GACCGTT
1 GACCGTT
* *
24756 AACTGTT
1 GACCGTT
24763 GACCGTT
1 GACCGTT
24770 GAC
1 GAC
24773 TTCCTTTGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:27738 original size:20 final size:19
Alignment explanation
Indices: 27702--27740 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
27692 AGTAAAGATG
* *
27702 TGAAAACATATATTATGCA
1 TGAAAACATAAAGTATGCA
27721 TGAAAATCATAAAGTATGCA
1 TGAAAA-CATAAAGTATGCA
27741 AGTGAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (19 bp):
TGAAAACATAAAGTATGCA
Found at i:35911 original size:19 final size:18
Alignment explanation
Indices: 35884--35950 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
35874 CCTTGGCTTG
*
35884 CTTTCTCTTTTTGAATTTT
1 CTTTTTCTTTTTG-ATTTT
35903 CTTTTTCTTTTTTGATTTT
1 CTTTTTC-TTTTTGATTTT
*
35922 C--TTTCTTTTTG-TCTT
1 CTTTTTCTTTTTGATTTT
35937 CTCTTTTCTTTTTG
1 CT-TTTTCTTTTTG
35951 CACTCCAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 4 0.10
16 6 0.14
17 4 0.10
18 10 0.24
19 12 0.29
20 6 0.14
ACGTcount: A:0.04, C:0.16, G:0.06, T:0.73
Consensus pattern (18 bp):
CTTTTTCTTTTTGATTTT
Found at i:42311 original size:23 final size:25
Alignment explanation
Indices: 42284--42347 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 25
42274 GAAAAATCAG
42284 CAAAGAAAATAAAAGCACTC-AAAA
1 CAAAGAAAATAAAAGCACTCGAAAA
* *
42308 -AAAGAAATTGAAAGCACTCGAAAA
1 CAAAGAAAATAAAAGCACTCGAAAA
*
42332 CAAGAGAAAAAAAAAG
1 CAA-AGAAAATAAAAG
42348 AAAGAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
23 17 0.53
24 4 0.12
25 2 0.06
26 9 0.28
ACGTcount: A:0.66, C:0.12, G:0.14, T:0.08
Consensus pattern (25 bp):
CAAAGAAAATAAAAGCACTCGAAAA
Found at i:44495 original size:19 final size:19
Alignment explanation
Indices: 44471--44508 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
44461 AACATGATGG
44471 TTCAATTCTGGAAAATGAA
1 TTCAATTCTGGAAAATGAA
44490 TTCAATTCTGGAAAATGAA
1 TTCAATTCTGGAAAATGAA
44509 GGGTCTCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (19 bp):
TTCAATTCTGGAAAATGAA
Done.