Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002231.1 Hibiscus syriacus cultivar Beakdansim tig00004538_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: 29469
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5775 original size:22 final size:20
Alignment explanation
Indices: 5749--5807 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
5739 ATAGGGCAGA
5749 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTT--AG
* * *
5771 GGGAACCGATTCCCCCATAG
1 GGGAATCGATACCCCCTTAG
5791 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
5808 GGGTTCTGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 16 0.52
22 15 0.48
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.17
Consensus pattern (20 bp):
GGGAATCGATACCCCCTTAG
Found at i:10164 original size:37 final size:37
Alignment explanation
Indices: 10105--10230 Score: 153
Period size: 37 Copynumber: 3.4 Consensus size: 37
10095 TTTGACCTTC
* *
10105 GAAGAAAATCAATCTTAAGCCTTCACGGAAGAGTAGT
1 GAAGCAAATAAATCTTAAGCCTTCACGGAAGAGTAGT
* * *
10142 GAAGCAAGTAAATCTTAAGCCTTTACGGAAAAGTAGT
1 GAAGCAAATAAATCTTAAGCCTTCACGGAAGAGTAGT
* * * * *
10179 GAACCAAATCATTCTTAAGCTTTCATGGAAGAGTAGT
1 GAAGCAAATAAATCTTAAGCCTTCACGGAAGAGTAGT
*
10216 GAAGCAAATCAATCT
1 GAAGCAAATAAATCT
10231 CGAGTCTGAT
Statistics
Matches: 74, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.25
Consensus pattern (37 bp):
GAAGCAAATAAATCTTAAGCCTTCACGGAAGAGTAGT
Found at i:10440 original size:111 final size:110
Alignment explanation
Indices: 10282--10815 Score: 531
Period size: 111 Copynumber: 4.8 Consensus size: 110
10272 TTCTAAAGAA
* * ** *** * * **
10282 TTTTCAAGTCCTATACTCTCTGAAAGAAGATGAAGCATACTTGTCTTCCGAATATTTTTTTAGTC
1 TTTTCAAGTCCTATACTCTCTGAAAGAAGAGGGAGCGGACCCATCTTCTGAAGATTTTTCAAGTC
10347 TTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATTAAGTT
66 TTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATTAAGTT
* * * *
10392 TTTCCCAAGTCCAATACTCTCTGAAAGAAGAGGGAGCGGGCCCATCTTCTGAAGATTTTTCGAGT
1 TTT-TCAAGTCCTATACTCTCTGAAAGAAGAGGGAGCGGACCCATCTTCTGAAGATTTTTCAAGT
* * * * *
10457 TTTATCTCCCTGAAAGAAGAGTGGAGCAAACCCGTCTTATCAAGTAT
65 CTTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATTAAGT-T
* * * * *
10504 TTTTCAAGTTCTATACTC-CTTGAAAGAAGATGGAGCAGACCCATTTTCTGAAGATTTTTTAAGT
1 TTTTCAAGTCCTATACTCTC-TGAAAGAAGAGGGAGCGGACCCATCTTCTGAAGATTTTTCAAGT
* * * *
10568 CCTATACTCCCTGAAAGAAGAG-GGAGC-GAACCCGT-TT-TTCGAAGAT
65 CTTAT-CTCCCTGAAAGAATAGTGGAGCAG-ACCCATCTTATT--AAGTT
* ***
10614 TTTTCAAGTCCTATACTCTCTGAAAGAAGAGGGAACGGACATGTCTTCTGAAGATTTTTCAAGTC
1 TTTTCAAGTCCTATACTCTCTGAAAGAAGAGGGAGCGGACCCATCTTCTGAAGATTTTTCAAGTC
* *
10679 TTATCTCCCTGAAAGAATAGTGGAGCATACCCATCTTATGAAGTT
66 TTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATTAAGTT
* * * * ** * * *
10724 TTTCTCAAGTCCTACACTCCCTAAAAGAAGAGGGAGCGGGCCCGCCTTCCGAAGATATTTCGAGT
1 TTT-TCAAGTCCTATACTCTCTGAAAGAAGAGGGAGCGGACCCATCTTCTGAAGATTTTTCAAGT
*
10789 C-TATTTTACCCTGAAAGAATAGTGGAG
65 CTTA-TCT-CCCTGAAAGAATAGTGGAG
10816 TATACTCATC
Statistics
Matches: 349, Mismatches: 60, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
109 16 0.05
110 83 0.24
111 210 0.60
112 40 0.11
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (110 bp):
TTTTCAAGTCCTATACTCTCTGAAAGAAGAGGGAGCGGACCCATCTTCTGAAGATTTTTCAAGTC
TTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATTAAGTT
Found at i:10574 original size:55 final size:55
Alignment explanation
Indices: 10241--10760 Score: 440
Period size: 55 Copynumber: 9.4 Consensus size: 55
10231 CGAGTCTGAT
* * * * * *
10241 CTCCCTTGAAAGAAGAGGGACCAGACTCGTTTTCTAAAGAATTTTCAAGTCCTATA
1 CTCCC-TGAAAGAAGAGGGAGCAGACCCATCTTCTGAAGATTTTTCAAGTCCTATA
* * * * *** * * ** *
10297 CTCTCTGAAAGAAGATGAAGCATACTTGTCTTCCGAATATTTTTTTAGTCTTAT-
1 CTCCCTGAAAGAAGAGGGAGCAGACCCATCTTCTGAAGATTTTTCAAGTCCTATA
* * * *
10351 CTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATTAAG-TTTTTCCCAAGTCCAATA
1 CTCCCTGAAAGAAGAG-GGAGCAGACCCATCTTCTGAAGATTTTT--CAAGTCCTATA
* * * * **
10408 CTCTCTGAAAGAAGAGGGAGCGGGCCCATCTTCTGAAGATTTTTCGAGTTTTAT-
1 CTCCCTGAAAGAAGAGGGAGCAGACCCATCTTCTGAAGATTTTTCAAGTCCTATA
* * * * *
10462 CTCCCTGAAAGAAGAGTGGAGCAAACCCGTCTTATCAAGTATTTTTCAAGTTCTATA
1 CTCCCTGAAAGAAGAG-GGAGCAGACCCATCTTCTGAAG-ATTTTTCAAGTCCTATA
* * * *
10519 CTCCTTGAAAGAAGATGGAGCAGACCCATTTTCTGAAGATTTTTTAAGTCCTATA
1 CTCCCTGAAAGAAGAGGGAGCAGACCCATCTTCTGAAGATTTTTCAAGTCCTATA
* *
10574 CTCCCTGAAAGAAGAGGGAGC-GAACCCGT-TTTTCGAAGATTTTTCAAGTCCTATA
1 CTCCCTGAAAGAAGAGGGAGCAG-ACCCATCTTCT-GAAGATTTTTCAAGTCCTATA
* * * *** *
10629 CTCTCTGAAAGAAGAGGGAACGGACATGTCTTCTGAAGATTTTTCAAGTCTTAT-
1 CTCCCTGAAAGAAGAGGGAGCAGACCCATCTTCTGAAGATTTTTCAAGTCCTATA
* * * * *
10683 CTCCCTGAAAGAATAGTGGAGCATACCCATCTTATGAAGTTTTTCTCAAGTCCTACA
1 CTCCCTGAAAGAAGAG-GGAGCAGACCCATCTTCTGAAGATTTT-TCAAGTCCTATA
*
10740 CTCCCTAAAAGAAGAGGGAGC
1 CTCCCTGAAAGAAGAGGGAGC
10761 GGGCCCGCCT
Statistics
Matches: 366, Mismatches: 83, Indels: 30
0.76 0.17 0.06
Matches are distributed among these distances:
54 51 0.14
55 191 0.52
56 77 0.21
57 47 0.13
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (55 bp):
CTCCCTGAAAGAAGAGGGAGCAGACCCATCTTCTGAAGATTTTTCAAGTCCTATA
Found at i:10803 original size:221 final size:221
Alignment explanation
Indices: 10397--10807 Score: 538
Period size: 221 Copynumber: 1.9 Consensus size: 221
10387 AAGTTTTTCC
* * * * *
10397 CAAGTCCAATACTCTCTGAAAGAAGAGGGAGCGGGCCCATCTTCTGAAGATTTTTCGAGTTTTAT
1 CAAGTCCAATACTCTCTGAAAGAAGAGGGAACGGACACATCTTCTGAAGATTTTTCAAGTCTTAT
* * * * *
10462 CTCCCTGAAAGAAGAGTGGAGCAAACCCGTCTTATCAAGTATTTTTCAAGTTCTATACTCCTTGA
66 CTCCCTGAAAGAAGAGTGGAGCAAACCCATCTTATCAAGTATTTTTCAAGTCCTACACTCCCTAA
* ** * * *
10527 AAGAAGATGGAGCAGACCCATTTTCTGAAGATTTTTTAAGTCCTATACTCCCTGAAAGAAGAGGG
131 AAGAAGAGGGAGCAGACCCACCTTCCGAAGATATTTCAAGTCCTATACTCCCTGAAAGAAGAGGG
10592 AGCGAACCCGTTTTTCGAAGATTTTT
196 AGCGAACCCGTTTTTCGAAGATTTTT
* **
10618 CAAGTCCTATACTCTCTGAAAGAAGAGGGAACGGACATGTCTTCTGAAGATTTTTCAAGTCTTAT
1 CAAGTCCAATACTCTCTGAAAGAAGAGGGAACGGACACATCTTCTGAAGATTTTTCAAGTCTTAT
* * *
10683 CTCCCTGAAAGAATAGTGGAGCATACCCATCTTATGAAGT-TTTTCTCAAGTCCTACACTCCCTA
66 CTCCCTGAAAGAAGAGTGGAGCAAACCCATCTTATCAAGTATTTT-TCAAGTCCTACACTCCCTA
* * * * **
10747 AAAGAAGAGGGAGCGGGCCCGCCTTCCGAAGATATTTCGAGT-CTATTTTACCCTGAAAGAA
130 AAAGAAGAGGGAGCAGACCCACCTTCCGAAGATATTTCAAGTCCTATACT-CCCTGAAAGAA
10808 TAGTGGAGTA
Statistics
Matches: 160, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
220 9 0.06
221 151 0.94
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (221 bp):
CAAGTCCAATACTCTCTGAAAGAAGAGGGAACGGACACATCTTCTGAAGATTTTTCAAGTCTTAT
CTCCCTGAAAGAAGAGTGGAGCAAACCCATCTTATCAAGTATTTTTCAAGTCCTACACTCCCTAA
AAGAAGAGGGAGCAGACCCACCTTCCGAAGATATTTCAAGTCCTATACTCCCTGAAAGAAGAGGG
AGCGAACCCGTTTTTCGAAGATTTTT
Found at i:12150 original size:2 final size:2
Alignment explanation
Indices: 12143--12253 Score: 213
Period size: 2 Copynumber: 55.5 Consensus size: 2
12133 GATAATCTAC
12143 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
12185 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
*
12227 AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12254 AGTTTATACA
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 107 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12731 original size:23 final size:23
Alignment explanation
Indices: 12700--12765 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
12690 CACCAAAGCT
* *
12700 CGTATAATTGCATCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
12723 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
12746 CGTAGAATTGCACCGTAGTG
1 CGTAGAATTGCACCGAAGTG
12766 TCATATAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:13454 original size:21 final size:21
Alignment explanation
Indices: 13430--13472 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
13420 TCATATTCGT
* *
13430 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
13451 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
13472 T
1 T
13473 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:18339 original size:15 final size:16
Alignment explanation
Indices: 18319--18348 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18309 AATACAATAA
18319 ATAAAA-TTATTTATC
1 ATAAAACTTATTTATC
18334 ATAAAACTTATTTAT
1 ATAAAACTTATTTAT
18349 TACTAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAAACTTATTTATC
Found at i:18363 original size:17 final size:16
Alignment explanation
Indices: 18321--18366 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
18311 TACAATAAAT
*
18321 AAAATTATTTATCATA
1 AAAATTATTTATTATA
*
18337 AAACTTATTTATTACTA
1 AAAATTATTTATTA-TA
*
18354 AAAATAATTTATT
1 AAAATTATTTATT
18367 TATTATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (16 bp):
AAAATTATTTATTATA
Found at i:18534 original size:23 final size:23
Alignment explanation
Indices: 18485--18547 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
18475 GTGTTATATT
* **
18485 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
18508 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
18531 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
18548 AAATAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:18639 original size:17 final size:17
Alignment explanation
Indices: 18604--18669 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
18594 AAAATAAAAA
*
18604 TATAATATCTTATATTAT
1 TATAATATATTA-ATTAT
*
18622 TATAATATATTCATTAT
1 TATAATATATTAATTAT
* *
18639 TTTATATAATATTAAATAT
1 TATA-AT-ATATTAATTAT
*
18658 TATATTATATTA
1 TATAATATATTA
18670 TAAATATTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 14 0.36
18 13 0.33
19 12 0.31
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TATAATATATTAATTAT
Found at i:18644 original size:14 final size:13
Alignment explanation
Indices: 18613--18670 Score: 52
Period size: 12 Copynumber: 4.7 Consensus size: 13
18603 ATATAATATC
18613 TTATATTATTATA
1 TTATATTATTATA
*
18626 ATATATTCATTAT-
1 TTATATT-ATTATA
*
18639 TT-TA-TATAATA
1 TTATATTATTATA
*
18650 TTA-AATATTATA
1 TTATATTATTATA
18662 TTATATTAT
1 TTATATTAT
18671 AAATATTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
10 4 0.11
11 4 0.11
12 11 0.31
13 11 0.31
14 5 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATATTATTATA
Found at i:18932 original size:42 final size:42
Alignment explanation
Indices: 18870--18989 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
18860 ATGAATTACG
* *
18870 TTCCGGAAAACCAATTACGTGAAACAAACACTGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
18912 TTTCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
18954 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
18990 TTCGGGGAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:19545 original size:22 final size:22
Alignment explanation
Indices: 19517--19569 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
19507 GAGTCGAGGG
*
19517 TATTCATAGGTCCTTCGGGACA
1 TATTCATAGGTCCTTAGGGACA
19539 TATTCATAGGTCCTTAGGGACA
1 TATTCATAGGTCCTTAGGGACA
*
19561 AATTTCATA
1 TA-TTCATA
19570 TGCCACTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (22 bp):
TATTCATAGGTCCTTAGGGACA
Found at i:22282 original size:31 final size:31
Alignment explanation
Indices: 22247--22320 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
22237 GTAATTTTTA
*
22247 ATAGTCGGAGAACTCAACAAAATAGTATCAT
1 ATAGTCGGAGAACTCAACAAAATAATATCAT
* * * *
22278 ATAGTCAGAAAACTTAACAAAATAATATCTT
1 ATAGTCGGAGAACTCAACAAAATAATATCAT
22309 ATAGTCGG-GAAC
1 ATAGTCGGAGAAC
22321 CATTTGTGCA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 3 0.08
31 33 0.92
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (31 bp):
ATAGTCGGAGAACTCAACAAAATAATATCAT
Done.