Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008858.1 Hibiscus syriacus cultivar Beakdansim tig00112081_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: 30824
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:7452 original size:64 final size:65
Alignment explanation
Indices: 7384--7564 Score: 172
Period size: 64 Copynumber: 2.8 Consensus size: 65
7374 TTGGAACACT
*
7384 TGATGCATC-AGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGC
1 TGATGCATCGA-TGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGC
7447 C
65 C
***** **
7448 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTC
1 TGATGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCC
* *** * **
7512 AGAGTGCATCGATGCATGGAGAGTGCATC-AGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCACCAAGTGTGCATCGA-TGCATCAAATGCATTCGATGTT
7565 CAATTAATTC
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
64 52 0.53
65 47 0.47
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (65 bp):
TGATGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCC
Found at i:7536 original size:19 final size:19
Alignment explanation
Indices: 7512--7562 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
7502 GAAAATATTC
7512 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
7531 AGAGTGCATC-AGTGCATGG
1 AGAGTGCATCGA-TGCATGG
7550 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
7563 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:7538 original size:65 final size:65
Alignment explanation
Indices: 7405--7564 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
7395 TGCACCAAGT
* ***
7405 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* **
7469 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
7533 A
65 A
*
7534 GTGCATC-AGTGCATGGAATGCATTCGATGTT
1 GTGCATCGA-TGCATGAAATGCATTCGATGTT
7565 CAATTAATTC
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 38 0.45
65 46 0.55
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:7804 original size:20 final size:21
Alignment explanation
Indices: 7781--7820 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
7771 GAATCGAATA
7781 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
7801 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
7821 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:13403 original size:91 final size:92
Alignment explanation
Indices: 13306--13568 Score: 204
Period size: 95 Copynumber: 2.8 Consensus size: 92
13296 TATTTATATG
13306 ATATAAAATTCATCATTTTTATATACATATATGAATCTAAATAGATGATTGAGATTAAATTATGT
1 ATATAAAATTCATCATTTTTATATACATATATGAATCTAAATAGATGATTGAGATTAAATTATGT
*
13371 ATATTAATATTTTAAT-TATTCATTTA
66 AAATTAATATTTTAATATATTCATTTA
* * * * ** *
13397 TTATAAATAATT--TTATTTTAAT-TTCAATTATTCATGAAAT-TCATTTA-ATGATT-ATATCT
1 ATAT-AA-AATTCATCATTTTTATATAC-A-TA-T-ATG-AATCT-AAATAGATGATTGAGAT-T
*
13456 ---TTATGTAAATTAATAATATCTTTATATATTCATTTA
57 AAATTATGTAAATTAAT-AT-T-TTAATATATTCATTTA
* ** * **
13492 AAATAAAATTCATCAGCTTTATATACATATATGAATCTAAATGGATGACCGAGATTAAATTATGT
1 ATATAAAATTCATCATTTTTATATACATATATGAATCTAAATAGATGATTGAGATTAAATTATGT
*
13557 ACATTAATATTT
66 AAATTAATATTT
13569 CAAAACTCAT
Statistics
Matches: 127, Mismatches: 23, Indels: 43
0.66 0.12 0.22
Matches are distributed among these distances:
90 2 0.02
91 30 0.24
92 16 0.13
93 18 0.14
94 21 0.17
95 38 0.30
96 2 0.02
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (92 bp):
ATATAAAATTCATCATTTTTATATACATATATGAATCTAAATAGATGATTGAGATTAAATTATGT
AAATTAATATTTTAATATATTCATTTA
Found at i:15901 original size:118 final size:118
Alignment explanation
Indices: 15690--15920 Score: 356
Period size: 118 Copynumber: 2.0 Consensus size: 118
15680 TTGGGTCGGA
* * * *
15690 TCGAAACCCATTGAGTTCGAATCCTGTGCCATCCTTACCGATACCCTACTATTTGATCGATGCTA
1 TCGAAACCCATCGAATTCGAATCCTGTGCCATCCTTACCGACACCCTACTATTTGATCGATACTA
*
15755 TCTTTTAGATCAATAGTCATGACCCAATATCAAATATGACATTCATACAAAGG
66 TCTTTTAGATCAATACTCATGACCCAATATCAAATATGACATTCATACAAAGG
* * *
15808 TCGAAACCCATCGAATTCGAGTCTTGTG-CATCCTTACCGACACCTTACTATTTGTATCGATACT
1 TCGAAACCCATCGAATTCGAATCCTGTGCCATCCTTACCGACACCCTACTATTTG-ATCGATACT
* *
15872 ATCTTTTATATCAATACTCATGACTCAATATCAAATATGACATTCATAC
65 ATCTTTTAGATCAATACTCATGACCCAATATCAAATATGACATTCATAC
15921 GATATTAATA
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
117 24 0.24
118 78 0.76
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (118 bp):
TCGAAACCCATCGAATTCGAATCCTGTGCCATCCTTACCGACACCCTACTATTTGATCGATACTA
TCTTTTAGATCAATACTCATGACCCAATATCAAATATGACATTCATACAAAGG
Found at i:24985 original size:20 final size:20
Alignment explanation
Indices: 24960--25001 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
24950 CGACTCCTCT
24960 CAATTCTTACTTTATCCGTA
1 CAATTCTTACTTTATCCGTA
24980 CAATTCTTACTTTATCCGTA
1 CAATTCTTACTTTATCCGTA
25000 CA
1 CA
25002 TCATATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.43
Consensus pattern (20 bp):
CAATTCTTACTTTATCCGTA
Found at i:28739 original size:21 final size:21
Alignment explanation
Indices: 28697--28745 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
28687 TTACCAAAAA
*
28697 TATTATTATTTCTATCGGTTT
1 TATTATTATTTCTATCGATTT
*
28718 TATTATTTTTTCTA-CTGATTT
1 TATTATTATTTCTATC-GATTT
*
28739 TGTTATT
1 TATTATT
28746 GTTGGGCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.65
Consensus pattern (21 bp):
TATTATTATTTCTATCGATTT
Found at i:30315 original size:9 final size:9
Alignment explanation
Indices: 30301--30325 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30291 TAGATTGTAA
30301 AAATAAAAT
1 AAATAAAAT
30310 AAATAAAAT
1 AAATAAAAT
30319 AAATAAA
1 AAATAAA
30326 TATGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:30518 original size:8 final size:9
Alignment explanation
Indices: 30490--30523 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 9
30480 TAAAAAACCA
30490 AAATAAAAT
1 AAATAAAAT
30499 AAAATAAAAT
1 -AAATAAAAT
30509 AAAT-AAAT
1 AAATAAAAT
30517 AAATAAA
1 AAATAAA
30524 GGACCAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 6 0.26
10 9 0.39
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Done.