Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007291.1 Hibiscus syriacus cultivar Beakdansim tig00019377_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: 57484
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:5945 original size:18 final size:18
Alignment explanation
Indices: 5902--5946 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5892 ATTATAAATG
*
5902 AATTTTAACATCATATTA
1 AATTTTAATATCATATTA
*
5920 AATATTAATAT-ATATTA
1 AATTTTAATATCATATTA
5937 TAATTTTAAT
1 -AATTTTAAT
5947 TCTAAAATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTTTAATATCATATTA
Found at i:6998 original size:12 final size:12
Alignment explanation
Indices: 6942--7009 Score: 59
Period size: 12 Copynumber: 5.7 Consensus size: 12
6932 GGTTATATTG
6942 AATAAAATTAAA
1 AATAAAATTAAA
* * *
6954 ATTAAGACTAAA
1 AATAAAATTAAA
*
6966 TTAATAAAA-TGAA
1 --AATAAAATTAAA
*
6979 TA-AAAATTAAA
1 AATAAAATTAAA
6990 AATAAAATTAAA
1 AATAAAATTAAA
7002 AATAAAAT
1 AATAAAAT
7010 ATACAATTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
10 4 0.09
11 5 0.12
12 26 0.60
13 3 0.07
14 5 0.12
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26
Consensus pattern (12 bp):
AATAAAATTAAA
Found at i:7001 original size:19 final size:19
Alignment explanation
Indices: 6979--7018 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
6969 ATAAAATGAA
6979 TAAAAATTAAAA-ATAAAAT
1 TAAAAA-TAAAATATAAAAT
*
6998 TAAAAATAAAATATACAAT
1 TAAAAATAAAATATAAAAT
7017 TA
1 TA
7019 TATCGATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAATAAAATATAAAAT
Found at i:7651 original size:16 final size:16
Alignment explanation
Indices: 7630--7660 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7620 TTTAGTCAAA
*
7630 GATTAAATTAATATAT
1 GATTAAAGTAATATAT
7646 GATTAAAGTAATATA
1 GATTAAAGTAATATA
7661 CAACCAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (16 bp):
GATTAAAGTAATATAT
Found at i:7758 original size:2 final size:2
Alignment explanation
Indices: 7753--7798 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
7743 TTTTCTTTGA
7753 AT AT AT AT AT AT 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
7795 AT AT
1 AT AT
7799 GTGTGTGTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12122 original size:2 final size:2
Alignment explanation
Indices: 12112--12141 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12102 TGTGTGTGTC
*
12112 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12142 CAAGAACATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:13079 original size:18 final size:18
Alignment explanation
Indices: 13056--13093 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
13046 ACTCTTGTTG
13056 CCGTCTATTTTTACTTAT
1 CCGTCTATTTTTACTTAT
13074 CCGTCTATTTTTACTTAT
1 CCGTCTATTTTTACTTAT
13092 CC
1 CC
13094 AACAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.26, G:0.05, T:0.53
Consensus pattern (18 bp):
CCGTCTATTTTTACTTAT
Found at i:21912 original size:4 final size:4
Alignment explanation
Indices: 21903--21932 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
21893 GATTTACTGA
21903 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
21933 TTCATGTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:34521 original size:3 final size:3
Alignment explanation
Indices: 34513--34637 Score: 180
Period size: 3 Copynumber: 41.7 Consensus size: 3
34503 TTTATCCATT
* *
34513 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA GTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
34561 GCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
34608 TTA ATA TTA TATA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TT
34638 TAATAAATAA
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
2 2 0.02
3 105 0.95
4 3 0.03
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:35042 original size:16 final size:16
Alignment explanation
Indices: 35021--35062 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
35011 ACAGAGACAG
35021 AAACAGAACAAAAAAA
1 AAACAGAACAAAAAAA
* *
35037 AAACAG-AGAAAAGAA
1 AAACAGAACAAAAAAA
35052 AAACA-AACAAA
1 AAACAGAACAAA
35063 CGATCTCAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.79, C:0.12, G:0.10, T:0.00
Consensus pattern (16 bp):
AAACAGAACAAAAAAA
Found at i:35899 original size:19 final size:19
Alignment explanation
Indices: 35860--35895 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35850 CAATTTAGTC
35860 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
35879 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
35896 TAATATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:35904 original size:19 final size:19
Alignment explanation
Indices: 35863--35904 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
35853 TTTAGTCATT
*
35863 TATTTTATATGTTTTAATT
1 TATTTTATATGTTTTAATA
35882 TATTTTAT-TGTTTTTAATA
1 TATTTTATATG-TTTTAATA
35901 TATT
1 TATT
35905 ATTTTAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TATTTTATATGTTTTAATA
Found at i:41133 original size:414 final size:414
Alignment explanation
Indices: 40363--41190 Score: 1640
Period size: 414 Copynumber: 2.0 Consensus size: 414
40353 AATGCTCGTA
40363 CATCTGCATTACAAGAAGCTAAACCACATGAAGATCAACAAGTGGATCCAGCATCTTCAAGCAAA
1 CATCTGCATTACAAGAAGCTAAACCACATGAAGATCAACAAGTGGATCCAGCATCTTCAAGCAAA
40428 AATCCGCTTATATCAGATATGAAAGTAGGGGATCTTAATACTGATCAGTTAATCCAGATTTAAAT
66 AATCCGCTTATATCAGATATGAAAGTAGGGGATCTTAATACTGATCAGTTAATCCAGATTTAAAT
40493 GAGCTGAATGAGAAACAAAAAGTAAATGAAGAGCTGACCAGACAGATCAAGAGCTTAGAAGAACG
131 GAGCTGAATGAGAAACAAAAAGTAAATGAAGAGCTGACCAGACAGATCAAGAGCTTAGAAGAACG
40558 AATGAAATCCGTGGAAATAACTGAATCATTCTATGGATTTGATGCTAGTGAGTTAAGTTTGGTTC
196 AATGAAATCCGTGGAAATAACTGAATCATTCTATGGATTTGATGCTAGTGAGTTAAGTTTGGTTC
40623 CAGACCTAATCCTCCCTATCAAGTTCAAAGCTCCCGAATTTGATAAATATAACGGTACTACATGC
261 CAGACCTAATCCTCCCTATCAAGTTCAAAGCTCCCGAATTTGATAAATATAACGGTACTACATGC
40688 CCTTCATCCCACATTACTATGTTTTGTCGAAGAATGGCAGGATATGTGAAGGACGAGAAATTGTT
326 CCTTCATCCCACATTACTATGTTTTGTCGAAGAATGGCAGGATATGTGAAGGACGAGAAATTGTT
40753 AATTCACTGCTTCCAGGATAGTTT
391 AATTCACTGCTTCCAGGATAGTTT
40777 CATCTGCATTACAAGAAGCTAAACCACATGAAGATCAACAAGTGGATCCAGCATCTTCAAGCAAA
1 CATCTGCATTACAAGAAGCTAAACCACATGAAGATCAACAAGTGGATCCAGCATCTTCAAGCAAA
40842 AATCCGCTTATATCAGATATGAAAGTAGGGGATCTTAATACTGATCAGTTAATCCCAGATTTAAA
66 AATCCGCTTATATCAGATATGAAAGTAGGGGATCTTAATACTGATCAGTTAAT-CCAGATTTAAA
40907 TGAGCTGAATGAGAAAC-AAAAGTAAATGAAGAGCTGACCAGACAGATCAAGAGCTTAGAAGAAC
130 TGAGCTGAATGAGAAACAAAAAGTAAATGAAGAGCTGACCAGACAGATCAAGAGCTTAGAAGAAC
40971 GAATGAAATCCGTGGAAATAACTGAATCATTCTATGGATTTGATGCTAGTGAGTTAAGTTTGGTT
195 GAATGAAATCCGTGGAAATAACTGAATCATTCTATGGATTTGATGCTAGTGAGTTAAGTTTGGTT
41036 CCAGACCTAATCCTCCCTATCAAGTTCAAAGCTCCCGAATTTGATAAATATAACGGTACTACATG
260 CCAGACCTAATCCTCCCTATCAAGTTCAAAGCTCCCGAATTTGATAAATATAACGGTACTACATG
41101 CCCTTCATCCCACATTACTATGTTTTGTCGAAGAATGGCAGGATATGTGAAGGACGAGAAATTGT
325 CCCTTCATCCCACATTACTATGTTTTGTCGAAGAATGGCAGGATATGTGAAGGACGAGAAATTGT
41166 TAATTCACTGCTTCCAGGATAGTTT
390 TAATTCACTGCTTCCAGGATAGTTT
41191 GACAGGACCG
Statistics
Matches: 413, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
414 385 0.93
415 28 0.07
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (414 bp):
CATCTGCATTACAAGAAGCTAAACCACATGAAGATCAACAAGTGGATCCAGCATCTTCAAGCAAA
AATCCGCTTATATCAGATATGAAAGTAGGGGATCTTAATACTGATCAGTTAATCCAGATTTAAAT
GAGCTGAATGAGAAACAAAAAGTAAATGAAGAGCTGACCAGACAGATCAAGAGCTTAGAAGAACG
AATGAAATCCGTGGAAATAACTGAATCATTCTATGGATTTGATGCTAGTGAGTTAAGTTTGGTTC
CAGACCTAATCCTCCCTATCAAGTTCAAAGCTCCCGAATTTGATAAATATAACGGTACTACATGC
CCTTCATCCCACATTACTATGTTTTGTCGAAGAATGGCAGGATATGTGAAGGACGAGAAATTGTT
AATTCACTGCTTCCAGGATAGTTT
Found at i:44185 original size:29 final size:28
Alignment explanation
Indices: 44134--44195 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
44124 CACCTGCGAG
* *
44134 ACAAAAAAAAGACAGAGACAG-AAACAGA
1 ACAAAAAAAAAACAGAGAAAGAAAACA-A
44162 ACAAAAAAAAAACAGAGAAAAGAAAACAA
1 ACAAAAAAAAAACAGAG-AAAGAAAACAA
44191 ACAAA
1 ACAAA
44196 CTACCAACGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 16 0.53
29 9 0.30
30 5 0.17
ACGTcount: A:0.74, C:0.13, G:0.13, T:0.00
Consensus pattern (28 bp):
ACAAAAAAAAAACAGAGAAAGAAAACAA
Found at i:45024 original size:19 final size:20
Alignment explanation
Indices: 45000--45048 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
44990 CAATTTAGTC
45000 ATTTATTTTATATG-TTTT-A
1 ATTTATTTTAT-TGTTTTTAA
45019 ATTTA-TTTATTGTTTTTAA
1 ATTTATTTTATTGTTTTTAA
45038 ATATTATTTTA
1 AT-TTATTTTA
45049 ATAGAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.08
18 9 0.35
19 8 0.31
20 3 0.12
21 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
ATTTATTTTATTGTTTTTAA
Found at i:47294 original size:15 final size:16
Alignment explanation
Indices: 47265--47297 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47255 ATACGTTAGT
*
47265 TTTTTATAATTTTAAA
1 TTTTTATAATATTAAA
47281 TTTTTATAA-ATTAAA
1 TTTTTATAATATTAAA
47296 TT
1 TT
47298 AATGGTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTATAATATTAAA
Found at i:52885 original size:395 final size:395
Alignment explanation
Indices: 52159--52885 Score: 892
Period size: 395 Copynumber: 1.8 Consensus size: 395
52149 GTTTTGATCC
* * * *
52159 GTTTTAGTACTTAAGCTTTCAATTTTTTTTCAAAGCCATACCTAACGTTTGGTTTTCATTTCATT
1 GTTTTAGTACCTAAACTTTCAA-TTTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATT
*
52224 TTAATACACCATCGTTAAAAACTTAACGCGTTTAGTAACTAAACCATCAGTTTGATCCGTATGAA
65 TTAATACACCATCGTTAAAAACTTAAAGCGTTTAGTAACTAAACCATCAGTTTGATCCGTATGAA
* * * * *
52289 TACCTAATCTATCAATTTTTTTTCAAAATTTAACTTTAAATTTTGAATGGGTACTAAAATGAAAC
130 TACCTAAACTATCAA-TTTTTTCCAAAACTTAACGTTAAATTTTGAAAGGGTACTAAAATGAAAC
* * ** *
52354 AAAAACTCAAATTTTTAAGGCGGGGTACTAAAATGAAACAAAAACTAAACTTTAAGTATGATTTT
194 AAAAACTAAAATTTTTAAGGCAGAATACTAAAATGAAACAAAAACTAAACTTTAAGGATGATTTT
* *** * * * * * *
52419 GAAAAAAAAAAATTTAAAGTTTAGGTACTAAAATGGATCAAGATTGATTGTTTAGGTAATAATGC
259 GAAAAAAAAAAATTAAAAGTTTAGGTACTAAAACAAAACAAGACTAATAGTTTAGATAATAATGA
52484 ATAATTTATCCTAAATAATATGATAAAAAAGGTAAACTATGTATTTAGTACCTAAACTATCAATT
324 ATAATTTATCCTAAATAATATGATAAAAAAGGTAAACTATGTATTTAGTACCTAAACTATCAATT
52549 TTAGTCT
389 TTAGTCT
* * *
52556 GTTTTAGTACCTAAACTTTTAA-TTTTTTCAAAACCATACTTAATGTTTAGTTTTCATTTCATTT
1 GTTTTAGTACCTAAACTTTCAATTTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTT
* * ** ** * * * *
52620 TAGTACTCTGTCGTTAAAAACTTAAAGCGTTTAGTATGTAAACTATCAATTTTGTTCTGTTAT-A
66 TAATACACCATCGTTAAAAACTTAAAGCGTTTAGTAACTAAACCATC-AGTTTGATCCG-TATGA
*
52684 GTACCTAAACT-TCCAA-TTTTTCCAAAACTTAACGTTAAATTTTGAACAAGGGTACTAAAATGA
129 ATACCTAAACTAT-CAATTTTTTCCAAAACTTAACGTTAAATTTTG-A-AAGGGTACTAAAATGA
** * * * * * *
52747 AATGAAAACTAAAATTTTTAATGGCATAATACTAAAATGAAACAATAACTAAATTTTAGGGGTGG
191 AACAAAAACTAAAATTTTTAA-GGCAGAATACTAAAATGAAACAAAAACTAAACTTTAAGGATGA
*
52812 TTTTG-AAAAAAAAAA-TAAAAGTTTAGGTACTAAAACAAAACAA-ACTAATAGTTTAGATACTA
255 TTTTGAAAAAAAAAAATTAAAAGTTTAGGTACTAAAACAAAACAAGACTAATAGTTTAGATAAT-
52874 AATGAATAATTT
319 AATGAATAATTT
52886 GCCAAAAACA
Statistics
Matches: 275, Mismatches: 48, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
394 38 0.14
395 113 0.41
396 64 0.23
397 60 0.22
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (395 bp):
GTTTTAGTACCTAAACTTTCAATTTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTT
TAATACACCATCGTTAAAAACTTAAAGCGTTTAGTAACTAAACCATCAGTTTGATCCGTATGAAT
ACCTAAACTATCAATTTTTTCCAAAACTTAACGTTAAATTTTGAAAGGGTACTAAAATGAAACAA
AAACTAAAATTTTTAAGGCAGAATACTAAAATGAAACAAAAACTAAACTTTAAGGATGATTTTGA
AAAAAAAAAATTAAAAGTTTAGGTACTAAAACAAAACAAGACTAATAGTTTAGATAATAATGAAT
AATTTATCCTAAATAATATGATAAAAAAGGTAAACTATGTATTTAGTACCTAAACTATCAATTTT
AGTCT
Found at i:56944 original size:16 final size:15
Alignment explanation
Indices: 56922--56953 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
56912 TCGTGCATTC
56922 TTATA-AAAGTAAAA
1 TTATATAAAGTAAAA
56936 TTATATAAAGTAAAA
1 TTATATAAAGTAAAA
56951 TTA
1 TTA
56954 AATTTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (15 bp):
TTATATAAAGTAAAA
Found at i:56963 original size:20 final size:21
Alignment explanation
Indices: 56925--56965 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
56915 TGCATTCTTA
56925 TAAAAGTAAAATTATATAAAG
1 TAAAAGTAAAATTATATAAAG
* *
56946 TAAAATTAAATTTA-ATAAAG
1 TAAAAGTAAAATTATATAAAG
56966 AACATCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (21 bp):
TAAAAGTAAAATTATATAAAG
Done.