Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 37 of 37
Found at i:8262354 original size:33 final size:32
Alignment explanation
Indices: 8262310--8262403 Score: 152
Period size: 33 Copynumber: 2.9 Consensus size: 32
8262300 AACGCGAAAC
**
8262310 CAAATCGCAACGCGAAATGAAAATCGCAACGA
1 CAAATCGCAACGCGAAACCAAAATCGCAACGA
8262342 CAGAATCGCAACGCGAAACCAAAATCGCAACGA
1 CA-AATCGCAACGCGAAACCAAAATCGCAACGA
8262375 CAAGATCGCAACGCGAAACCAAAATCGCA
1 CAA-ATCGCAACGCGAAACCAAAATCGCA
8262404 TTGCGATTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 3 0.05
33 55 0.95
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.07
Consensus pattern (32 bp):
CAAATCGCAACGCGAAACCAAAATCGCAACGA
Found at i:8262421 original size:19 final size:19
Alignment explanation
Indices: 8262399--8262533 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
8262389 GAAACCAAAA
*
8262399 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
8262418 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
8262434 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
8262451 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
8262467 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
8262484 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
8262503 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
8262523 TCGTGTTGCGA
1 TCGCGTTGCGA
8262534 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:8262440 original size:14 final size:14
Alignment explanation
Indices: 8262421--8262477 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
8262411 TTTCATTTCG
8262421 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
8262435 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
8262452 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
8262468 CGTTGCGATT
1 CGTTGCGATT
8262478 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:8262446 original size:33 final size:33
Alignment explanation
Indices: 8262404--8262496 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
8262394 CAAAATCGCA
*
8262404 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
8262437 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
8262470 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
8262497 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:8264398 original size:14 final size:14
Alignment explanation
Indices: 8264379--8264415 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
8264369 TGATTGTTTA
8264379 ATGATTTGTAAAAG
1 ATGATTTGTAAAAG
8264393 ATGATTTGTAAAAG
1 ATGATTTGTAAAAG
*
8264407 TTGATTTGT
1 ATGATTTGT
8264416 GTAATTGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (14 bp):
ATGATTTGTAAAAG
Found at i:8264398 original size:37 final size:38
Alignment explanation
Indices: 8264327--8264398 Score: 128
Period size: 37 Copynumber: 1.9 Consensus size: 38
8264317 TAATTGATTG
*
8264327 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
8264365 TTTTTGATTGTTTAA-TGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
8264399 TGTAAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 18 0.55
38 15 0.45
ACGTcount: A:0.29, C:0.01, G:0.17, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:8264536 original size:19 final size:19
Alignment explanation
Indices: 8264520--8264621 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
8264510 AAAAATGACT
8264520 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
8264539 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
8264558 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
8264572 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
8264591 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
8264611 ATCGCAATGCG
1 ATCGCAATGCG
8264622 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:8264640 original size:19 final size:18
Alignment explanation
Indices: 8264628--8264941 Score: 362
Period size: 19 Copynumber: 18.1 Consensus size: 18
8264618 TGCGTTTATA
8264628 ATTTCGCATTGCGA-TT-
1 ATTTCGCATTGCGATTTC
*
8264644 ATCTCG--TTGCGATTTC
1 ATTTCGCATTGCGATTTC
8264660 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
8264679 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
8264696 -TTTCG--TTGCGATTTC
1 ATTTCGCATTGCGATTTC
8264711 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
8264730 ATTTCGCATTGCGATTTC
1 ATTTCGCATTGCGATTTC
* *
8264748 ATTTCGTATTGCGATTTA
1 ATTTCGCATTGCGATTTC
8264766 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
8264785 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
*
8264802 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
8264818 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
8264837 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
*
8264854 -TCTCG--TTGCGATTTC
1 ATTTCGCATTGCGATTTC
8264869 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
8264888 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
*
8264905 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
8264921 ATTTCCGCATTGCGATTTC
1 ATTT-CGCATTGCGATTTC
8264940 AT
1 AT
8264942 GGGATTTTCA
Statistics
Matches: 259, Mismatches: 12, Indels: 51
0.80 0.04 0.16
Matches are distributed among these distances:
14 30 0.12
15 8 0.03
16 42 0.16
17 18 0.07
18 53 0.20
19 102 0.39
20 6 0.02
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (18 bp):
ATTTCGCATTGCGATTTC
Found at i:8264688 original size:51 final size:51
Alignment explanation
Indices: 8264628--8264938 Score: 523
Period size: 51 Copynumber: 6.0 Consensus size: 51
8264618 TGCGTTTATA
*
8264628 ATTTCGCATTGCGATTATCTCGTTGCGATTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTTC
*
8264679 ATTTCGCATTGCGATTCTTTCGTTGCGATTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTTC
* *
8264730 ATTTCGCATTGCGATTTCATTTCGTATTGCGATTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTTCATTTCGCATTGCGATTTTC
8264785 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCGCATTGCGATTTTC
8264837 ATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTTC
8264888 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTT
1 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTT-CGCATTGCGATTT
8264939 CATGGGATTT
Statistics
Matches: 248, Mismatches: 5, Indels: 12
0.94 0.02 0.05
Matches are distributed among these distances:
51 120 0.48
52 61 0.25
53 22 0.09
54 3 0.01
55 42 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (51 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTTC
Found at i:8264899 original size:158 final size:155
Alignment explanation
Indices: 8264628--8264938 Score: 527
Period size: 158 Copynumber: 2.0 Consensus size: 155
8264618 TGCGTTTATA
8264628 ATTTCGCATTGCGATTATCTCGTTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
* *
8264693 TTCTTTCGTTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATTTCGTATT
66 TTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG--TT
8264758 GCGA-TTTAATTT-CGCATTGCGATTTTC
127 GCGATTTTAATTTCCGCATTGCGATTTTC
*
8264785 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
8264850 ATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
65 ATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
*
8264915 ATTTTCATTTCCGCATTGCGATTT
130 ATTTTAATTTCCGCATTGCGATTT
8264939 CATGGGATTT
Statistics
Matches: 147, Mismatches: 4, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
154 6 0.04
155 7 0.05
156 17 0.12
157 30 0.20
158 87 0.59
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (155 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
TTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA
TTTTAATTTCCGCATTGCGATTTTC
Found at i:8267860 original size:20 final size:20
Alignment explanation
Indices: 8267832--8268239 Score: 477
Period size: 20 Copynumber: 20.4 Consensus size: 20
8267822 AAATTTCAGT
* * * *
8267832 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
8267852 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
8267872 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
8267892 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
8267912 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
8267932 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
8267952 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
8267972 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
8267992 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
8268012 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
8268032 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
8268052 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
8268072 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
8268092 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
8268112 GTTGCGATATAC-GATACGC
1 GTTGCGATTTACGGATACGC
* **
8268131 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
8268151 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
8268171 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
8268191 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
8268211 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
8268231 GTTGCGATT
1 GTTGCGATT
8268240 ATGGAAAATC
Statistics
Matches: 342, Mismatches: 35, Indels: 22
0.86 0.09 0.06
Matches are distributed among these distances:
19 23 0.07
20 313 0.92
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:8271195 original size:18 final size:18
Alignment explanation
Indices: 8271174--8271215 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
8271164 ATCTAAAACT
8271174 GGTATCGATACCGGAAGG
1 GGTATCGATACCGGAAGG
*
8271192 GGTATCGGTACCGGAAGG
1 GGTATCGATACCGGAAGG
8271210 GGTATC
1 GGTATC
8271216 AGTACCATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.40, T:0.19
Consensus pattern (18 bp):
GGTATCGATACCGGAAGG
Found at i:8271220 original size:18 final size:18
Alignment explanation
Indices: 8271182--8271221 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
8271172 CTGGTATCGA
*
8271182 TACCGGAAGGGGTATCGG
1 TACCGGAAGGGGTATCAG
8271200 TACCGGAAGGGGTATCAG
1 TACCGGAAGGGGTATCAG
8271218 TACC
1 TACC
8271222 ATAGTATGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.20, G:0.38, T:0.17
Consensus pattern (18 bp):
TACCGGAAGGGGTATCAG
Found at i:8271625 original size:2 final size:2
Alignment explanation
Indices: 8271620--8271680 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
8271610 AAGAGGAAGA
8271620 AT AT AT AT AT A- AT 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 AT AT AT AT AT AT AT
* *
8271661 AT AT AT AC AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT
8271681 TATGTTTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8273015 original size:21 final size:21
Alignment explanation
Indices: 8272990--8273033 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
8272980 AATATAAATT
*
8272990 GTGTATCGATGCACTACTACA
1 GTGTACCGATGCACTACTACA
*
8273011 GTGTACCGATGCACTGCTACA
1 GTGTACCGATGCACTACTACA
8273032 GT
1 GT
8273034 AACTTCAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (21 bp):
GTGTACCGATGCACTACTACA
Found at i:8273587 original size:23 final size:23
Alignment explanation
Indices: 8273561--8273624 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
8273551 AGCTCGTATA
8273561 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
8273584 AATTGCACCGAAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
8273607 AATTGCATCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
8273625 TATAAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Done.