Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005143.1 Hibiscus syriacus cultivar Beakdansim tig00011582_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: 63102
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:3809 original size:23 final size:23
Alignment explanation
Indices: 3783--3831 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
3773 TTCTTTGTTT
*
3783 TTTCTTCTTTTGGAGTGCTTGAC
1 TTTCTTCTTTTAGAGTGCTTGAC
*
3806 TTTCTTTTTTTAGAGTGCTTGAC
1 TTTCTTCTTTTAGAGTGCTTGAC
3829 TTT
1 TTT
3832 TTTTTGCTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.10, C:0.14, G:0.18, T:0.57
Consensus pattern (23 bp):
TTTCTTCTTTTAGAGTGCTTGAC
Found at i:3836 original size:23 final size:23
Alignment explanation
Indices: 3781--3836 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
3771 TTTTCTTTGT
*
3781 TTTTTCTTCTTTTGGAGTGCTTGAC
1 TTTTT-TT-TTTTAGAGTGCTTGAC
*
3806 TTTCTTTTTTTAGAGTGCTTGAC
1 TTTTTTTTTTTAGAGTGCTTGAC
3829 TTTTTTTT
1 TTTTTTTT
3837 GCTGATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 22 0.79
24 2 0.07
25 4 0.14
ACGTcount: A:0.09, C:0.12, G:0.16, T:0.62
Consensus pattern (23 bp):
TTTTTTTTTTTAGAGTGCTTGAC
Found at i:9329 original size:93 final size:93
Alignment explanation
Indices: 9214--9382 Score: 302
Period size: 93 Copynumber: 1.8 Consensus size: 93
9204 TTGGAGTGCT
*
9214 TGACTTTTTCTTTGCTGATTTTTTTATTTTCTTTTACTTGCACTTCACTTGCACTTCTTTTTGTA
1 TGACTTTTTCTTTACTGATTTTTTTATTTTCTTTTACTTGCACTTCACTTGCACTTCTTTTTGTA
*
9279 TTTTTCTTTTGTTGTTGTTGCACGTTGC
66 ATTTTCTTTTGTTGTTGTTGCACGTTGC
* *
9307 TGACTTTTTCTTTACTGGTTTTTTTATTTTCTTTTACTTGCACTTCACTTGTACTTCTTTTTGTA
1 TGACTTTTTCTTTACTGATTTTTTTATTTTCTTTTACTTGCACTTCACTTGCACTTCTTTTTGTA
9372 ATTTTCTTTTG
66 ATTTTCTTTTG
9383 GATCGTATCA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.11, C:0.17, G:0.11, T:0.62
Consensus pattern (93 bp):
TGACTTTTTCTTTACTGATTTTTTTATTTTCTTTTACTTGCACTTCACTTGCACTTCTTTTTGTA
ATTTTCTTTTGTTGTTGTTGCACGTTGC
Found at i:11143 original size:5 final size:5
Alignment explanation
Indices: 11133--11179 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
11123 TCTCAAAAAG
* *
11133 AAGAA AAGAA AAGAA AAGAA AAAAA AAAAGA AAG-A AAG-A AAGAA AAG
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGA-A AAGAA AAGAA AAGAA AAG
11180 TTGAAAGCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 8 0.21
5 27 0.71
6 3 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:15408 original size:14 final size:14
Alignment explanation
Indices: 15389--15416 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15379 ATACTATCTA
15389 TTTCCATCACCATC
1 TTTCCATCACCATC
15403 TTTCCATCACCATC
1 TTTCCATCACCATC
15417 CTCTATCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:15814 original size:18 final size:18
Alignment explanation
Indices: 15791--15826 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
15781 ACAAAAAGGG
15791 GAAAAAGA-AAGAAGAAAA
1 GAAAAAGAGAA-AAGAAAA
15809 GAAAAAGAGAAAAGAAAA
1 GAAAAAGAGAAAAGAAAA
15827 AACTCCTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
GAAAAAGAGAAAAGAAAA
Found at i:15828 original size:14 final size:14
Alignment explanation
Indices: 15798--15827 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
15788 GGGGAAAAAG
15798 AAAGAAGAAAAGAA
1 AAAGAAGAAAAGAA
15812 AAAG-AGAAAAGAA
1 AAAGAAGAAAAGAA
15825 AAA
1 AAA
15828 ACTCCTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAGAAGAAAAGAA
Found at i:15879 original size:25 final size:26
Alignment explanation
Indices: 15851--15907 Score: 98
Period size: 25 Copynumber: 2.2 Consensus size: 26
15841 ATTGGAGTGC
*
15851 AAAAGTAAAGAAAAAGAA-GAAAAAG
1 AAAAGAAAAGAAAAAGAAGGAAAAAG
15876 AAAAGAAAAGAAAAAGAAGGAAAAAG
1 AAAAGAAAAGAAAAAGAAGGAAAAAG
15902 AAAAGA
1 AAAAGA
15908 GCTGCAAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 17 0.57
26 13 0.43
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (26 bp):
AAAAGAAAAGAAAAAGAAGGAAAAAG
Found at i:15905 original size:16 final size:16
Alignment explanation
Indices: 15857--15893 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
15847 GTGCAAAAGT
*
15857 AAAGAAAA-AGAAGAA
1 AAAGAAAAGAAAAGAA
15872 AAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAGAA
15888 AAAGAA
1 AAAGAA
15894 GGAAAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:15906 original size:15 final size:14
Alignment explanation
Indices: 15857--15907 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
15847 GTGCAAAAGT
15857 AAAGAAAAAGAAGAA
1 AAAG-AAAAGAAGAA
15872 AAAGAAAAG-A-AA
1 AAAGAAAAGAAGAA
*
15884 AGA-AAAAGAAGGAA
1 AAAGAAAAGAA-GAA
15898 AAAGAAAAGA
1 AAAGAAAAGA
15908 GCTGCAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
11 5 0.17
12 5 0.17
13 1 0.03
14 9 0.30
15 10 0.33
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:20197 original size:14 final size:14
Alignment explanation
Indices: 20165--20196 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
20155 GTGCTGCAAC
20165 AAAAAGATGAAAAG
1 AAAAAGATGAAAAG
20179 AAAAAGA-GAAAAG
1 AAAAAGATGAAAAG
20192 AAAAA
1 AAAAA
20197 AACTCCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (14 bp):
AAAAAGATGAAAAG
Found at i:20241 original size:10 final size:11
Alignment explanation
Indices: 20221--20255 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
20211 ATTGGAGTGC
20221 AAAAGAAAAGA
1 AAAAGAAAAGA
*
20232 AAAA-AGAAGA
1 AAAAGAAAAGA
20242 AAAAGAAAAGA
1 AAAAGAAAAGA
20253 AAA
1 AAA
20256 GCAAGTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:35095 original size:14 final size:14
Alignment explanation
Indices: 35076--35103 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35066 ATACTATCTA
35076 TTTCCATCACCATC
1 TTTCCATCACCATC
35090 TTTCCATCACCATC
1 TTTCCATCACCATC
35104 CTCCATCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:35745 original size:16 final size:16
Alignment explanation
Indices: 35724--35762 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
35714 GTAAGTTATC
*
35724 TTCATTTTCTTACTAT
1 TTCATTTCCTTACTAT
* *
35740 TTCATTTCCTTATTCT
1 TTCATTTCCTTACTAT
35756 TTCATTT
1 TTCATTT
35763 ATTCTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (16 bp):
TTCATTTCCTTACTAT
Found at i:42516 original size:18 final size:18
Alignment explanation
Indices: 42495--42529 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42485 CAAAAAGTGA
42495 AAAAGA-AAGAAGAAAAAC
1 AAAAGAGAA-AAGAAAAAC
42513 AAAAGAGAAAAGAAAAA
1 AAAAGAGAAAAGAAAAA
42530 AAACTCCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAGAGAAAAGAAAAAC
Found at i:47955 original size:14 final size:14
Alignment explanation
Indices: 47938--47965 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47928 GTTAAGGATT
47938 GATGGTGATGGAAA
1 GATGGTGATGGAAA
47952 GATGGTGATGGAAA
1 GATGGTGATGGAAA
47966 TAGTATCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GATGGTGATGGAAA
Found at i:48352 original size:19 final size:20
Alignment explanation
Indices: 48305--48355 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
48295 GAAACCCCTT
**
48305 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
48325 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
48344 TGAAGATACATG
1 TGAAAATACATG
48356 CTCTTGGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:51152 original size:15 final size:16
Alignment explanation
Indices: 51132--51189 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
51122 AGGATAAGGT
51132 AATGAAATAAGAAAG-
1 AATGAAATAAGAAAGA
* *
51147 AATGAAAGAATAAAGA
1 AATGAAATAAGAAAGA
*
51163 AATGAAAT-AGTAAGA
1 AATGAAATAAGAAAGA
51178 AAGTGAAGATAA
1 AA-TGAA-ATAA
51190 CTTACAACTC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 20 0.59
16 11 0.32
17 2 0.06
18 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.16
Consensus pattern (16 bp):
AATGAAATAAGAAAGA
Found at i:51426 original size:21 final size:21
Alignment explanation
Indices: 51393--51432 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
51383 AGTAGTCTTT
*
51393 TTCTTTCTCTTTCTCTTTTTC
1 TTCTTCCTCTTTCTCTTTTTC
*
51414 TTCTTCCTTTTTCTCTTTT
1 TTCTTCCTCTTTCTCTTTT
51433 GTTGCAGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (21 bp):
TTCTTCCTCTTTCTCTTTTTC
Found at i:51639 original size:20 final size:21
Alignment explanation
Indices: 51616--51661 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
51606 ATTAAGTAAT
*
51616 TTGATAAT-TAAGAAATGAAA
1 TTGATAATGGAAGAAATGAAA
51636 TTGA-AATGGAAGAAATGAAA
1 TTGATAATGGAAGAAATGAAA
*
51656 GTGATA
1 TTGATA
51662 GAAATGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 3 0.14
20 18 0.82
21 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (21 bp):
TTGATAATGGAAGAAATGAAA
Found at i:61188 original size:344 final size:343
Alignment explanation
Indices: 60551--61239 Score: 1172
Period size: 344 Copynumber: 2.0 Consensus size: 343
60541 AACTCCACCC
* *
60551 ACCAATGTAAAGGCATACGTAATTTCCTTGGGCATGCATGCTTCTACCAGCGGTTCATAAAAGAT
1 ACCAATGTAAAGGCATACGTAATTTCCTTGGGCATGCAGGCTTCTACCAGCAGTTCATAAAAGAT
60616 TTTTCTCAAATCTCAAAACTTTTGTGTTTTTGCTCCAAAATTAACCATTTATATTTAACGATGAT
66 TTTTCTCAAATCTCAAAACTTTTGTGTTTTTGCTCCAAAATTAACCATTTATATTTAACGATGAT
* *
60681 TTTTAAATGTTTTTACAGATTTGAAGAAAAATCATTCATGAGCACCAATCGTTGTTGTACCAGAC
131 TTTTAAATGTTTTTACAGATTTGAAGAAAAAACATTCATGAGCACCAATCGTTGTTCTACCAGAC
*
60746 TGGAATGAACCTTTCGAGCTCATATACGATACTAGTGATTACGCAGTTGGGGCAGTGCTAGGGCA
196 TGGAATGAACCTTTCGAACTCATATACGATACTAGTGATTACGCAGTTGGGGCAGTGCTAGGGCA
* *
60811 ACGAAAAAAAACTCTTTCATGTTATCTACTATGCTAGTCGTACTCTTAACGATGCACAAGTAAAC
261 ACGAAAAAAAACTCTTTCATGTTATCCACTATGCTAGCCGTAC-CTTAACGATGCACAAGTAAAC
60876 TATACCACAACTAAAAACGA
325 TATA-CACAACTAAAAACGA
* *
60896 ACCAATGTGAAAGGCATACGTAATTTCCTTGGGCATGCAGGTTTCTACCAGCAGTTCATAGAAGA
1 ACCAATGT-AAAGGCATACGTAATTTCCTTGGGCATGCAGGCTTCTACCAGCAGTTCATAAAAGA
60961 TTTTTCTCAAATCTCAAAACTTGTT-T-TTTTT-CTCCAAAATTAACCATTTATATTTAACGATG
65 TTTTTCTCAAATCTCAAAACTT-TTGTGTTTTTGCTCCAAAATTAACCATTTATATTTAACGATG
*
61023 ATTTTTAAATGTTTTTACAGATTTGATGAAAAAACATTCATGAGCACCAATCGTTG-TCTACCAG
129 ATTTTTAAATGTTTTTACAGATTTGAAGAAAAAACATTCATGAGCACCAATCGTTGTTCTACCAG
*
61087 ACTGGAATGAACCTTTCGAACTCATATACGATGCTAGTGATTACGCAGTT-GGGCAGTGCTAGGG
194 ACTGGAATGAACCTTTCGAACTCATATACGATACTAGTGATTACGCAGTTGGGGCAGTGCTAGGG
*
61151 CAACGAAAAAGTAAACTCTTTCATGTTATCCACTATGCTAGCCGTACCTTAATGATGCACAAGTA
259 CAACGAAAAA--AAACTCTTTCATGTTATCCACTATGCTAGCCGTACCTTAACGATGCACAAGTA
*
61216 AACTGTACACAACTAAAAACGA
322 AACTATACACAACTAAAAACGA
61238 AC
1 AC
61240 TTCTTGCAAT
Statistics
Matches: 327, Mismatches: 13, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
342 41 0.13
343 78 0.24
344 118 0.36
345 13 0.04
346 75 0.23
347 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (343 bp):
ACCAATGTAAAGGCATACGTAATTTCCTTGGGCATGCAGGCTTCTACCAGCAGTTCATAAAAGAT
TTTTCTCAAATCTCAAAACTTTTGTGTTTTTGCTCCAAAATTAACCATTTATATTTAACGATGAT
TTTTAAATGTTTTTACAGATTTGAAGAAAAAACATTCATGAGCACCAATCGTTGTTCTACCAGAC
TGGAATGAACCTTTCGAACTCATATACGATACTAGTGATTACGCAGTTGGGGCAGTGCTAGGGCA
ACGAAAAAAAACTCTTTCATGTTATCCACTATGCTAGCCGTACCTTAACGATGCACAAGTAAACT
ATACACAACTAAAAACGA
Found at i:62984 original size:12 final size:12
Alignment explanation
Indices: 62967--63007 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
62957 GTAGGAGTTA
62967 TTTTCTTTTCTT
1 TTTTCTTTTCTT
*
62979 TTTTCTTTTATT
1 TTTTCTTTTCTT
*
62991 CTTTCTTTTTCTT
1 TTTTC-TTTTCTT
63004 TTTT
1 TTTT
63008 GTAGCACTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTCTT
Done.