Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001030.1 Hibiscus syriacus cultivar Beakdansim tig00002051_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: 63739
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:542 original size:12 final size:12
Alignment explanation
Indices: 525--549 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
515 AATTTTTCAG
525 TTTTTAAAAATA
1 TTTTTAAAAATA
537 TTTTTAAAAATA
1 TTTTTAAAAATA
549 T
1 T
550 CAAAATACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTTAAAAATA
Found at i:882 original size:40 final size:40
Alignment explanation
Indices: 815--925 Score: 110
Period size: 40 Copynumber: 2.9 Consensus size: 40
805 TTTCCCTGAA
* *
815 TTCT-GTGTTG-TTCACGTAATTTGTTTTTC-GAAAATGT
1 TTCTCGTGTTGTTTCACGTAATGTGTTTTTCGGAAAATAT
*
852 TT-TCCGTATTTGTTTCACGTAATCGT-TTTTTCGGAAAATAT
1 TTCT-CGT-GTTGTTTCACGTAAT-GTGTTTTTCGGAAAATAT
*
893 TTCTCGTGTTGTTTCACGT-AT-TGGTTTTCGGAA
1 TTCTCGTGTTGTTTCACGTAATGTGTTTTTCGGAA
926 TGTAATTCAT
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
36 1 0.02
37 3 0.05
38 11 0.18
39 5 0.08
40 27 0.44
41 13 0.21
42 1 0.02
ACGTcount: A:0.18, C:0.14, G:0.19, T:0.50
Consensus pattern (40 bp):
TTCTCGTGTTGTTTCACGTAATGTGTTTTTCGGAAAATAT
Found at i:1117 original size:23 final size:22
Alignment explanation
Indices: 1091--1181 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 22
1081 TTTTCATCAA
*
1091 AATATTTATATTATTAAATTTAT
1 AATA-TTATAATATTAAATTTAT
* *
1114 AATA-TATAATATTATATTTTT
1 AATATTATAATATTAAATTTAT
* *
1135 AATATATATAAAATAATCAATTATAT
1 AATAT-TAT--AATATTAAATT-TAT
* *
1161 TATATATATAATATTATATTT
1 AATAT-TATAATATTAAATTT
1182 TATTTTAATA
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
21 18 0.35
23 8 0.15
24 8 0.15
25 8 0.15
26 10 0.19
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTATAATATTAAATTTAT
Found at i:1125 original size:30 final size:28
Alignment explanation
Indices: 1119--1199 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 28
1109 TTTATAATAT
*
1119 ATAATATTATATTTTTAATATATATAAA
1 ATAATATTATATTATTAATATATATAAA
* *
1147 ATAATCAAT-TA-TATT-ATATATATAAT
1 ATAAT-ATTATATTATTAATATATATAAA
* *
1173 ATTATATTTTATT-TTAATAATATATAA
1 ATAATATTATATTATTAAT-ATATATAA
1200 TAAATTTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
25 2 0.05
26 18 0.42
27 6 0.14
28 15 0.35
29 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
ATAATATTATATTATTAATATATATAAA
Found at i:1126 original size:21 final size:21
Alignment explanation
Indices: 1097--1142 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1087 TCAAAATATT
*
1097 TATATTATTAAATTTATAATA
1 TATAATATTAAATTTATAATA
* *
1118 TATAATATTATATTTTTAATA
1 TATAATATTAAATTTATAATA
1139 TATA
1 TATA
1143 TAAAATAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATAATATTAAATTTATAATA
Found at i:1387 original size:27 final size:27
Alignment explanation
Indices: 1347--1404 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
1337 TTTATTTCAC
*
1347 TAAAATATACAAAA-AATATTTTATTAA
1 TAAAATATACAAAATAATA-TTTAATAA
1374 TAAAATTATA-AAAATAATATTTAATAA
1 TAAAA-TATACAAAATAATATTTAATAA
1401 TAAA
1 TAAA
1405 TAAATTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAAATATACAAAATAATATTTAATAA
Found at i:1607 original size:14 final size:14
Alignment explanation
Indices: 1583--1617 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1573 AAATTTAATT
*
1583 CATTTTACGGAAAA
1 CATTTTCCGGAAAA
*
1597 TATTTTCCGGAAAA
1 CATTTTCCGGAAAA
1611 CATTTTC
1 CATTTTC
1618 TAGAAATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:3555 original size:5 final size:5
Alignment explanation
Indices: 3545--3581 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
3535 GGGTGTTGTT
3545 GAAGA GAAGA GAAGA GAAGA G-AGA GAAGA GAAGA GAA
1 GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAA
3582 TGATCGATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:4764 original size:28 final size:26
Alignment explanation
Indices: 4705--4768 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 26
4695 TATTTTCGTC
4705 AATAAATTTAAAAATTATAAATACTT
1 AATAAATTTAAAAATTATAAATACTT
*
4731 ATTAAATTAGTAAAAGATTA-AAATTA-TT
1 AATAAATT--TAAAA-ATTATAAA-TACTT
4759 AATAAATTTA
1 AATAAATTTA
4769 TCTAAATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
26 9 0.28
28 17 0.53
29 6 0.19
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (26 bp):
AATAAATTTAAAAATTATAAATACTT
Found at i:10180 original size:2 final size:2
Alignment explanation
Indices: 10173--10205 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10163 AAAATTAATC
10173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10206 CACAACTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14622 original size:14 final size:14
Alignment explanation
Indices: 14603--14632 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
14593 TATTATTTAC
14603 TAAAATATTTATGG
1 TAAAATATTTATGG
14617 TAAAATATTTATGG
1 TAAAATATTTATGG
14631 TA
1 TA
14633 TCTTAATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
TAAAATATTTATGG
Found at i:17508 original size:33 final size:33
Alignment explanation
Indices: 17463--17561 Score: 157
Period size: 33 Copynumber: 3.1 Consensus size: 33
17453 GATTGACAAG
*
17463 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
17496 TTGGAAAATTCATCTTGGTTGGTGGCCAACTCA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
17529 TTGGAAAATTC-T-TTGGTAGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
17560 TT
1 TT
17562 TTTCATATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 19 0.31
32 1 0.02
33 42 0.68
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.37
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:20236 original size:21 final size:21
Alignment explanation
Indices: 20210--20249 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20200 AGACAAGTAG
*
20210 TACTCCACAACAGGTGGAGCA
1 TACTCCAAAACAGGTGGAGCA
20231 TACTCCAAAACAGGTGGAG
1 TACTCCAAAACAGGTGGAG
20250 TTTCAGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGCA
Found at i:22238 original size:33 final size:33
Alignment explanation
Indices: 22201--22299 Score: 157
Period size: 33 Copynumber: 3.1 Consensus size: 33
22191 GATTGGCAAG
*
22201 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
22234 TTGGAAAATTCATCTTGGTTGGTGGCCAACTCA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
22267 TTGGAAAATTC-T-TTGGTAGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
22298 TT
1 TT
22300 TTCATATTGA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 19 0.31
32 1 0.02
33 42 0.68
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.37
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:24325 original size:22 final size:22
Alignment explanation
Indices: 24297--24339 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
24287 CTTTACCCAA
24297 TAACAAAATTAAGATTAGAGTT
1 TAACAAAATTAAGATTAGAGTT
24319 TAACAAAATTAAGATTAGAGT
1 TAACAAAATTAAGATTAGAGT
24340 CTCAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.30
Consensus pattern (22 bp):
TAACAAAATTAAGATTAGAGTT
Found at i:25836 original size:59 final size:59
Alignment explanation
Indices: 25759--25932 Score: 177
Period size: 60 Copynumber: 2.9 Consensus size: 59
25749 CTAAAATATA
* *
25759 ACTCTCATTTTAAATTAGTCACAAACTTTAAAATATTCCAATTTCATCTTCAAACTATG
1 ACTCTCATTTTAAATTAGTCACAAACTTTTAAATATTCCAATTTCATCCTCAAACTATG
* ** * * **
25818 TCTCTCATTTTAAATTAGTCTTTAAATTTTTGAATATTTTAATTTCATCCTCAAACTATG
1 ACTCTCATTTTAAATTAGTC-ACAAACTTTTAAATATTCCAATTTCATCCTCAAACTATG
* * * * * * * *
25878 ACCCTAATTCTAAATTGGCCCCTAAACTTTTAAATCTTCCAATTTCATACTCAAA
1 ACTCTCATTTTAAATTAGTCAC-AAACTTTTAAATATTCCAATTTCATCCTCAAA
25933 TTCATCCAAA
Statistics
Matches: 90, Mismatches: 23, Indels: 3
0.78 0.20 0.03
Matches are distributed among these distances:
59 19 0.21
60 71 0.79
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (59 bp):
ACTCTCATTTTAAATTAGTCACAAACTTTTAAATATTCCAATTTCATCCTCAAACTATG
Found at i:32349 original size:8 final size:7
Alignment explanation
Indices: 32324--32357 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
32314 TTTAAAAACA
32324 TTTTAAT
1 TTTTAAT
32331 TTTTAAT
1 TTTTAAT
32338 TTTTAAT
1 TTTTAAT
*
32345 ATTTTAAG
1 -TTTTAAT
32353 TTTTA
1 TTTTA
32358 GTTAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (7 bp):
TTTTAAT
Found at i:32351 original size:15 final size:14
Alignment explanation
Indices: 32324--32357 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
32314 TTTAAAAACA
*
32324 TTTTAATTTTTAAT
1 TTTTAATTTTTAAG
32338 TTTTAATATTTTAAG
1 TTTTAAT-TTTTAAG
32353 TTTTA
1 TTTTA
32358 GTTAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
TTTTAATTTTTAAG
Found at i:32613 original size:32 final size:32
Alignment explanation
Indices: 32547--32617 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
32537 TCACAATATA
* ** *
32547 ATGATGTGATACATATCATATTATTTAAAGTG
1 ATGATGTGATACATATCATATCATAAAAAATG
* *
32579 ATGATGTGATATATATCATGTCATAAAAAATG
1 ATGATGTGATACATATCATATCATAAAAAATG
32611 ATGATGT
1 ATGATGT
32618 AACATGTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (32 bp):
ATGATGTGATACATATCATATCATAAAAAATG
Found at i:33306 original size:36 final size:35
Alignment explanation
Indices: 33259--33333 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 35
33249 ATATATGTTA
* *
33259 ATTTAAAATTTTTAGAGATACAATTGTTTTTTATCC
1 ATTTAAAATTTTTAGAGAGACAATTG-TTTCTATCC
33295 ATTTAAAATTTTTAGAGAGACAATTGTTTCTATCC
1 ATTTAAAATTTTTAGAGAGACAATTGTTTCTATCC
33330 ATTT
1 ATTT
33334 CTTCGATCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
35 12 0.32
36 25 0.68
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (35 bp):
ATTTAAAATTTTTAGAGAGACAATTGTTTCTATCC
Found at i:33940 original size:25 final size:25
Alignment explanation
Indices: 33904--33964 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
33894 GTAATTTGAC
33904 ATAAAATA-TTAATTTTTACAATTA
1 ATAAAATAGTTAATTTTTACAATTA
* *
33928 ATAAGATAGTTAATTTTTATAATTA
1 ATAAAATAGTTAATTTTTACAATTA
33953 ATAAAATAGTTA
1 ATAAAATAGTTA
33965 CAAATTATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 7 0.21
25 26 0.79
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (25 bp):
ATAAAATAGTTAATTTTTACAATTA
Found at i:37018 original size:39 final size:39
Alignment explanation
Indices: 36964--37041 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
36954 CCAAGGTTAA
*
36964 TACAATCTATTCCGTAAACTCGAAGTGAAGAAGTAGAAT
1 TACAATCTATTCCGTAAACTCAAAGTGAAGAAGTAGAAT
37003 TACAATCTATTCCGTAAACTCAAAGTGAAGAAGTAGAAT
1 TACAATCTATTCCGTAAACTCAAAGTGAAGAAGTAGAAT
37042 CAGCTTGATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (39 bp):
TACAATCTATTCCGTAAACTCAAAGTGAAGAAGTAGAAT
Found at i:43214 original size:12 final size:13
Alignment explanation
Indices: 43191--43219 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
43181 TTGAATACGA
43191 AAAAAGATAAAAG
1 AAAAAGATAAAAG
43204 AAAAAGA-AAAAG
1 AAAAAGATAAAAG
43216 AAAA
1 AAAA
43220 TTTGGGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAAAGATAAAAG
Found at i:58686 original size:5 final size:6
Alignment explanation
Indices: 58672--58696 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58662 CATTATTCTC
58672 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
58697 TTGGAAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Done.