Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006533.1 Hibiscus syriacus cultivar Beakdansim tig00015931_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: 58691
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2670 original size:35 final size:35
Alignment explanation
Indices: 2624--2694 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
2614 TGTTATCTGT
2624 TCATCACCATCTTCCATCACCATTGCACGCCTATA
1 TCATCACCATCTTCCATCACCATTGCACGCCTATA
* * *
2659 TCATCACCATCTTCTATCACCATTTCACGTCTATA
1 TCATCACCATCTTCCATCACCATTGCACGCCTATA
2694 T
1 T
2695 TAACCACCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.25, C:0.37, G:0.04, T:0.34
Consensus pattern (35 bp):
TCATCACCATCTTCCATCACCATTGCACGCCTATA
Found at i:8476 original size:19 final size:18
Alignment explanation
Indices: 8438--8489 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
8428 TTTCCTTGGC
* *
8438 TTTCTTTCTCTTTTATAA
1 TTTCTTTTTCTTTTTTAA
8456 TTTCTTTTTCTTTTTTGAA
1 TTTCTTTTTCTTTTTT-AA
8475 TTT-TTTCTTCTTTTT
1 TTTCTTT-TTCTTTTT
8490 GTCTTTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.10, C:0.13, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTCTTTTTCTTTTTTAA
Found at i:16222 original size:19 final size:20
Alignment explanation
Indices: 16184--16226 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
16174 TGAAACCCTT
*
16184 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
16204 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
16223 TGAA
1 TGAA
16227 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:22081 original size:14 final size:14
Alignment explanation
Indices: 22062--22089 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22052 ATACTATCTA
22062 TTTCCATCACCATC
1 TTTCCATCACCATC
22076 TTTCCATCACCATC
1 TTTCCATCACCATC
22090 CTCCATCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:24064 original size:14 final size:13
Alignment explanation
Indices: 24047--24096 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
24037 GTGCAAAAAG
24047 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
24061 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
24074 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
24085 AAAGAAAAAGAA
1 AAAGAAAAAGAA
24097 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:24093 original size:19 final size:18
Alignment explanation
Indices: 24041--24096 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
24031 ATTGGAGTGC
24041 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
24058 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
24077 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
24096 A
1 A
24097 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:24094 original size:11 final size:11
Alignment explanation
Indices: 24041--24096 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
24031 ATTGGAGTGC
24041 AAAAAG-AAAG
1 AAAAAGAAAAG
24051 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
24065 AAGAAGAAAAG
1 AAAAAGAAAAG
24076 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
24089 AAAAAGAA
1 AAAAAGAA
24097 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:28651 original size:14 final size:13
Alignment explanation
Indices: 28632--28681 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
28622 AGTGCAAAAG
28632 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
28646 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
28659 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
28670 AAAGAAAAAGAA
1 AAAGAAAAAGAA
28682 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:28678 original size:19 final size:18
Alignment explanation
Indices: 28627--28681 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 18
28617 ATTGGAGTGC
28627 AAAAG-AAAGAAAAAGACA
1 AAAAGAAAAGAAAAAGA-A
28645 AAAAGAAGAAG-AAAAGAA
1 AAAAGAA-AAGAAAAAGAA
28663 GAAAAGAAAAGAAAAAGAA
1 -AAAAGAAAAGAAAAAGAA
28682 TTCAAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
18 9 0.27
19 21 0.64
20 3 0.09
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAGAA
Found at i:43598 original size:27 final size:27
Alignment explanation
Indices: 43568--43623 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 27
43558 CTTGCATAGG
43568 GAACATACATTGTATCTACTTAAGGAT
1 GAACATACATTGTATCTACTTAAGGAT
43595 G---A-ACATTGTATCTACTTAAGGAT
1 GAACATACATTGTATCTACTTAAGGAT
43618 GAACAT
1 GAACAT
43624 TCATCCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
23 22 0.88
24 1 0.04
26 1 0.04
27 1 0.04
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (27 bp):
GAACATACATTGTATCTACTTAAGGAT
Found at i:43604 original size:23 final size:23
Alignment explanation
Indices: 43574--43624 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
43564 TAGGGAACAT
43574 ACATTGTATCTACTTAAGGATGA
1 ACATTGTATCTACTTAAGGATGA
43597 ACATTGTATCTACTTAAGGATGA
1 ACATTGTATCTACTTAAGGATGA
43620 ACATT
1 ACATT
43625 CATCCATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (23 bp):
ACATTGTATCTACTTAAGGATGA
Found at i:45919 original size:24 final size:24
Alignment explanation
Indices: 45892--45947 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
45882 TCCATTGAAG
45892 TTCCAAAGGTTGGAACATTTGGTA
1 TTCCAAAGGTTGGAACATTTGGTA
45916 TTCCAAAGGTTGGAACATTTGGTA
1 TTCCAAAGGTTGGAACATTTGGTA
45940 TTCCAAAG
1 TTCCAAAG
45948 AATGTGCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.32
Consensus pattern (24 bp):
TTCCAAAGGTTGGAACATTTGGTA
Found at i:51427 original size:32 final size:34
Alignment explanation
Indices: 51390--51468 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 34
51380 AACATTGACT
*
51390 TCACCATC-C-ATCACCATTGT-ACGCCTATATCA
1 TCACCATCACTATCACCATT-TCACGCCTATATAA
51422 TCACCATCTACTATCACCATTTCACGCCTATATAA
1 TCACCATC-ACTATCACCATTTCACGCCTATATAA
*
51457 CCACCATTCACT
1 TCACCA-TCACT
51469 TACCATCTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 8 0.20
34 2 0.05
35 28 0.70
36 2 0.05
ACGTcount: A:0.29, C:0.38, G:0.04, T:0.29
Consensus pattern (34 bp):
TCACCATCACTATCACCATTTCACGCCTATATAA
Found at i:57135 original size:17 final size:16
Alignment explanation
Indices: 57101--57140 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
57091 AACATTTTTA
57101 TCCATTT-CAATTCTT
1 TCCATTTCCAATTCTT
*
57116 TCCATTTCCATTTCCTT
1 TCCATTTCCAATT-CTT
57133 TCCATTTC
1 TCCATTTC
57141 TTAATTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.32
16 4 0.18
17 11 0.50
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.53
Consensus pattern (16 bp):
TCCATTTCCAATTCTT
Found at i:58459 original size:25 final size:25
Alignment explanation
Indices: 58431--58482 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
58421 AGAATATGAA
58431 CAGCCCTTGGTTTGAATGATTAAAT
1 CAGCCCTTGGTTTGAATGATTAAAT
*
58456 CAGCCCTTGGTTTGGATGATTAAAT
1 CAGCCCTTGGTTTGAATGATTAAAT
58481 CA
1 CA
58483 TCCTTGAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (25 bp):
CAGCCCTTGGTTTGAATGATTAAAT
Done.