Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008975.1 Hibiscus syriacus cultivar Beakdansim tig00112323_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: 112054
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7017 original size:12 final size:12
Alignment explanation
Indices: 6997--7035 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
6987 TATCTCTATC
*
6997 AATTCAAAAAAT
1 AATTTAAAAAAT
7009 AATTTAAAAAAAT
1 AATTT-AAAAAAT
7022 AATTTAAAAAAT
1 AATTTAAAAAAT
7034 AA
1 AA
7036 AAACTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.52
13 12 0.48
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (12 bp):
AATTTAAAAAAT
Found at i:7018 original size:13 final size:13
Alignment explanation
Indices: 7002--7032 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
6992 CTATCAATTC
7002 AAAAAATAATTTA
1 AAAAAATAATTTA
7015 AAAAAATAATTTA
1 AAAAAATAATTTA
7028 AAAAA
1 AAAAA
7033 TAAAAACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAATAATTTA
Found at i:25596 original size:18 final size:18
Alignment explanation
Indices: 25537--25598 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
25527 TCAATATTCA
*
25537 TCCCGTAGGACCACTATG
1 TCCCATAGGACCACTATG
*
25555 TCTCGA-AGGACCACTGTATATG
1 TC-CCATAGGACCAC----TATG
25577 TCCCATAGGACCACTATG
1 TCCCATAGGACCACTATG
25595 TCCC
1 TCCC
25599 GAACGACTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
18 18 0.51
19 1 0.03
21 2 0.06
22 14 0.40
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (18 bp):
TCCCATAGGACCACTATG
Found at i:27232 original size:64 final size:63
Alignment explanation
Indices: 27099--27240 Score: 155
Period size: 64 Copynumber: 2.2 Consensus size: 63
27089 TAATGAAGGT
** * * *
27099 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTATAGGG
1 ATGCATCGATGCA-TACTGATGCATCAATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
27163 ATGCATCGATGCATGACTTATGCATCAATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTGATGCATCAATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
27225 G
63 G
27226 AGTGCATCGATGCAT
1 A-TGCATCGATGCAT
27241 TACCAATGCA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 57 0.85
65 7 0.10
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCATACTGATGCATCAATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:32157 original size:64 final size:63
Alignment explanation
Indices: 32052--32212 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 63
32042 TAATGAAGGT
* * * **
32052 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGCATTCGATG-TTGTATTATTATAGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCACTAAAATGCATTCGATGTTTCTATT-TTA-AAA
32115 G
63 G
* *
32116 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCAT-ACTAATGCATCGATGCACTAAAATGCATTCGATGTTTCTATTTTAAAAG
*
32179 AGTGCATCGATGCATTACCAATGCATCGATGCAC
1 A-TGCATCGATGCA-TACTAATGCATCGATGCAC
32213 CTTCAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
63 4 0.05
64 72 0.86
65 8 0.10
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCACTAAAATGCATTCGATGTTTCTATTTTAAAAG
Found at i:42512 original size:2 final size:2
Alignment explanation
Indices: 42505--42532 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42495 ACCTGCACAA
42505 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42533 GTTCTGAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43176 original size:31 final size:31
Alignment explanation
Indices: 43119--43177 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
43109 CAATTTAGTC
* * *
43119 ATATTTTTAAATAAATTTTAACATAAAACAT
1 ATATTTTTAAATAAATATAAAAATAAAACAT
43150 ATATTTTTAAATGAAA-ATAAAAATAAAA
1 ATATTTTTAAAT-AAATATAAAAATAAAA
43178 TGCTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (31 bp):
ATATTTTTAAATAAATATAAAAATAAAACAT
Found at i:44345 original size:29 final size:30
Alignment explanation
Indices: 44289--44345 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
44279 GTAAGTTTAG
* *
44289 TTTTTATTTCATTTTAGTGTTTGCCGTTAA
1 TTTTTATTTCATTTTAGTGATTCCCGTTAA
44319 TTTTTATTTCATTTTAGT-ATTCCCGTT
1 TTTTTATTTCATTTTAGTGATTCCCGTT
44346 TAAAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.16, C:0.12, G:0.11, T:0.61
Consensus pattern (30 bp):
TTTTTATTTCATTTTAGTGATTCCCGTTAA
Found at i:59919 original size:17 final size:17
Alignment explanation
Indices: 59897--59931 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
59887 TTTCGGTTTG
*
59897 AAAAAAACAGGTTTTTA
1 AAAAAAACAGATTTTTA
*
59914 AAAAAAACCGATTTTTA
1 AAAAAAACAGATTTTTA
59931 A
1 A
59932 TCCGGTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.29
Consensus pattern (17 bp):
AAAAAAACAGATTTTTA
Found at i:60002 original size:20 final size:20
Alignment explanation
Indices: 59958--60002 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
59948 GTCATCCAAT
* * *
59958 TTTTTAAACCTCAGATCAGA
1 TTTTTAAACCCCAAACCAGA
*
59978 CTTTTAAACCCCAAACCAGA
1 TTTTTAAACCCCAAACCAGA
59998 TTTTT
1 TTTTT
60003 TTCCAGATAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (20 bp):
TTTTTAAACCCCAAACCAGA
Found at i:83031 original size:15 final size:15
Alignment explanation
Indices: 83011--83040 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
83001 AATTAAAATC
83011 AAATTGAACTTAATA
1 AAATTGAACTTAATA
*
83026 AAATTGAATTTAATA
1 AAATTGAACTTAATA
83041 TTATGAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (15 bp):
AAATTGAACTTAATA
Found at i:96450 original size:29 final size:26
Alignment explanation
Indices: 96400--96452 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
96390 CAATTTAGTC
*
96400 ATATTTTTAATAAATTAAAATAAATT
1 ATATTTTTAATAAATAAAAATAAATT
96426 ATATTTTTAAATGAAAATAAAAATAAA
1 ATATTTTT-AAT--AAATAAAAATAAA
96453 AAAATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 8 0.35
27 3 0.13
29 12 0.52
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
ATATTTTTAATAAATAAAAATAAATT
Found at i:96487 original size:23 final size:23
Alignment explanation
Indices: 96448--96508 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
96438 GAAAATAAAA
*
96448 ATAAAA-AAATTAATAAGTT-AT
1 ATAAAATAATTTAATAAGTTAAT
96469 AGTAAAATAATTTAATAAGTTAAT
1 A-TAAAATAATTTAATAAGTTAAT
*
96493 ATAAAAATATTTTAAT
1 AT-AAAATAATTTAAT
96509 TTAATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 1 0.03
22 5 0.15
23 13 0.38
24 15 0.44
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (23 bp):
ATAAAATAATTTAATAAGTTAAT
Found at i:96524 original size:14 final size:16
Alignment explanation
Indices: 96505--96539 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
96495 AAAAATATTT
96505 TAATTTA-A-TATATA
1 TAATTTATATTATATA
96519 TAATTTATATTATATA
1 TAATTTATATTATATA
96535 TAATT
1 TAATT
96540 AGGGCCACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 1 0.05
16 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATTTATATTATATA
Found at i:96797 original size:39 final size:39
Alignment explanation
Indices: 96754--96837 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 39
96744 AAAAATTAAC
96754 TTAGAAAGTTAAT-GTG-AAATAATTTAAGAAATTAAGAAT
1 TTAGAAAGTT-ATGGTGTAAA-AATTTAAGAAATTAAGAAT
* * * *
96793 TTAGAATGTTATGGTGTCAAAATTTAAGAAATTAGGATT
1 TTAGAAAGTTATGGTGTAAAAATTTAAGAAATTAAGAAT
96832 TTAGAA
1 TTAGAA
96838 TGCTAGAGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 2 0.05
39 35 0.90
40 2 0.05
ACGTcount: A:0.45, C:0.01, G:0.18, T:0.36
Consensus pattern (39 bp):
TTAGAAAGTTATGGTGTAAAAATTTAAGAAATTAAGAAT
Found at i:103397 original size:56 final size:59
Alignment explanation
Indices: 103263--103398 Score: 154
Period size: 56 Copynumber: 2.3 Consensus size: 59
103253 GAATTTGGGG
* * * * *
103263 ATGAAATTGGAATATTCAAAAGTTTGGAGACTAATTGAGACAACGAGTCGTAGTTTAGGG
1 ATGAAATTGGAATATTTAAAAGTTTAGAGACTAATTGAGA-AACGAGTCATAGTTTAAGA
* * *
103323 ATGAAATTAGAATGTTTAAAAGTTTA-AGGACT-ATT-AG-AATGAGTCATAGTTTAAGA
1 ATGAAATTGGAATATTTAAAAGTTTAGA-GACTAATTGAGAAACGAGTCATAGTTTAAGA
103379 ATGAAATTGGAATATTTAAA
1 ATGAAATTGGAATATTTAAA
103399 GTGAAAGTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
56 33 0.51
58 2 0.03
59 4 0.06
60 26 0.40
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (59 bp):
ATGAAATTGGAATATTTAAAAGTTTAGAGACTAATTGAGAAACGAGTCATAGTTTAAGA
Done.