Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000407.1 Hibiscus syriacus cultivar Beakdansim tig00000749_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: 61972
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:1104 original size:20 final size:21
Alignment explanation
Indices: 1069--1109 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1059 AAAATTTATT
1069 TTTTATTAAATATTTTTAATA
1 TTTTATTAAATATTTTTAATA
*
1090 TTTTATTTAAT-TTTTTAATA
1 TTTTATTAAATATTTTTAATA
1110 ATTATGACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTATTAAATATTTTTAATA
Found at i:10298 original size:17 final size:17
Alignment explanation
Indices: 10278--10327 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
10268 GGAGGTCAAC
10278 GATCAACGGTCGGGTCA
1 GATCAACGGTCGGGTCA
10295 GATCAACGGTCGGGTCA
1 GATCAACGGTCGGGTCA
* *
10312 GGTCAACGGACGGGTC
1 GATCAACGGTCGGGTC
10328 GGTCGGGTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.22, C:0.24, G:0.38, T:0.16
Consensus pattern (17 bp):
GATCAACGGTCGGGTCA
Found at i:10365 original size:19 final size:19
Alignment explanation
Indices: 10343--10387 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
10333 GGTCGGGTCG
10343 GGTCAAACCGGTTCTG-ACC
1 GGTCAAACCGGTTC-GAACC
*
10362 GGTCAAATCGGTTCGAACC
1 GGTCAAACCGGTTCGAACC
10381 GGTCAAA
1 GGTCAAA
10388 ACCGATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (19 bp):
GGTCAAACCGGTTCGAACC
Found at i:18727 original size:13 final size:13
Alignment explanation
Indices: 18711--18746 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
18701 CAATCCCTAA
*
18711 ATTCCTAAATTAT
1 ATTCCAAAATTAT
18724 ATTCCAAAATTAT
1 ATTCCAAAATTAT
18737 ATTCCAAAAT
1 ATTCCAAAAT
18747 CTAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (13 bp):
ATTCCAAAATTAT
Found at i:20219 original size:7 final size:6
Alignment explanation
Indices: 20192--20357 Score: 58
Period size: 7 Copynumber: 25.5 Consensus size: 6
20182 TAATGTGACT
*
20192 ATATGA A-ATGA TATATGA ATATGCA ATACGTGA TATATGTG ATATG-
1 ATATGA ATATGA -ATATGA ATATG-A ATA--TGA -ATATG-A ATATGA
* *
20238 ATATGA A-ATGA CATATGA ATATGTA ATACGTGA TACATGTG ATATG-
1 ATATGA ATATGA -ATATGA ATATG-A ATA--TGA -ATATG-A ATATGA
* *
20284 ATATGA A-ATGA CATATGA ATATGTA ATACGTGA TACATGTG ATATG-
1 ATATGA ATATGA -ATATGA ATATG-A ATA--TGA -ATATG-A ATATGA
20330 ATATGA A-ATGA CATATGA ATATGTA ATA
1 ATATGA ATATGA -ATATGA ATATG-A ATA
20358 CATGATACAT
Statistics
Matches: 126, Mismatches: 7, Indels: 53
0.68 0.04 0.28
Matches are distributed among these distances:
5 31 0.25
6 28 0.22
7 51 0.40
8 3 0.02
9 13 0.10
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (6 bp):
ATATGA
Found at i:20244 original size:46 final size:46
Alignment explanation
Indices: 20192--20388 Score: 351
Period size: 46 Copynumber: 4.3 Consensus size: 46
20182 TAATGTGACT
* * *
20192 ATATGAAATGATATATGAATATGCAATACGTGATATATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
20238 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
20284 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
*
20330 ATATGAAATGACATATGAATATGTAATACATGATACATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
20376 ATATGAAAT-ACAT
1 ATATGAAATGACAT
20389 GGTTACACAT
Statistics
Matches: 147, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
45 4 0.03
46 143 0.97
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
Found at i:20556 original size:21 final size:21
Alignment explanation
Indices: 20532--20595 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
20522 TATCCTATAA
20532 GACATATGATAGGTCCTTCGG
1 GACATATGATAGGTCCTTCGG
* **
20553 GACACA-GATGACATCCTTCGG
1 GACATATGAT-AGGTCCTTCGG
20574 G----ATGATAGGTCCTTCGG
1 GACATATGATAGGTCCTTCGG
20591 GACAT
1 GACAT
20596 TTATACGAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 12
0.65 0.10 0.24
Matches are distributed among these distances:
17 11 0.34
18 3 0.09
20 3 0.09
21 15 0.47
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (21 bp):
GACATATGATAGGTCCTTCGG
Found at i:25853 original size:35 final size:35
Alignment explanation
Indices: 25807--25874 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
25797 TGTGCAGGGC
*
25807 GAACAGATTCCCCCTGGGGGGTTTCGATTCCCCGG
1 GAACAGATTCCCCCTGGGGGGTATCGATTCCCCGG
25842 GAACAGATTCCCCCTGGGGGGTATCGATTCCCC
1 GAACAGATTCCCCCTGGGGGGTATCGATTCCCC
25875 CCTAAATGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.22
Consensus pattern (35 bp):
GAACAGATTCCCCCTGGGGGGTATCGATTCCCCGG
Found at i:25872 original size:20 final size:20
Alignment explanation
Indices: 25812--25875 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
25802 AGGGCGAACA
*
25812 GATTCCCCCTGGGGGGTTTC
1 GATTCCCCCTGGGGGGTATC
*
25832 GATT-CCCC----GGG-AAC
1 GATTCCCCCTGGGGGGTATC
25846 AGATTCCCCCTGGGGGGTATC
1 -GATTCCCCCTGGGGGGTATC
25867 GATTCCCCC
1 GATTCCCCC
25876 CTAAATGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
14 1 0.03
15 7 0.21
16 4 0.12
19 4 0.12
20 16 0.47
21 2 0.06
ACGTcount: A:0.12, C:0.34, G:0.30, T:0.23
Consensus pattern (20 bp):
GATTCCCCCTGGGGGGTATC
Found at i:26333 original size:46 final size:46
Alignment explanation
Indices: 26282--26478 Score: 369
Period size: 46 Copynumber: 4.3 Consensus size: 46
26272 CTATGTGACT
* *
26282 ATATGAAATGATATATGAATATGCAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
26328 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
26374 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
26420 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
26466 ATATGAAAT-ACAT
1 ATATGAAATGACAT
26479 GGTTACACAT
Statistics
Matches: 149, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
45 4 0.03
46 145 0.97
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
Found at i:34681 original size:23 final size:23
Alignment explanation
Indices: 34663--34723 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
34653 CTCGTATAAA
34663 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
34686 TGCACCGAAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
34709 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
34724 TATAATATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:36689 original size:3 final size:3
Alignment explanation
Indices: 36681--36710 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
36671 TCCAGATTTC
36681 TCT TCT TCT TCT TCT TCTT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TC-T TCT TCT TCT TC
36711 CCCGTGAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:36704 original size:16 final size:17
Alignment explanation
Indices: 36678--36710 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
36668 GTTTCCAGAT
36678 TTCTCTTCTTCTTCTTC
1 TTCTCTTCTTCTTCTTC
36695 TTCT-TTCTTCTTCTTC
1 TTCTCTTCTTCTTCTTC
36711 CCCGTGAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
TTCTCTTCTTCTTCTTC
Found at i:37722 original size:29 final size:25
Alignment explanation
Indices: 37616--37702 Score: 122
Period size: 25 Copynumber: 3.4 Consensus size: 25
37606 ATAAGTCTAG
* *
37616 ATTCAATATTTTGATACATGATCGT-A
1 ATTC-ATATTATGATACATGA-CATGA
*
37642 TTTCATATTATGATACATGACATGA
1 ATTCATATTATGATACATGACATGA
37667 ATTCATATTATGATACATGACATGA
1 ATTCATATTATGATACATGACATGA
37692 ATTCATATTAT
1 ATTCATATTAT
37703 ATGCATTAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
24 2 0.04
25 51 0.91
26 3 0.05
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.41
Consensus pattern (25 bp):
ATTCATATTATGATACATGACATGA
Found at i:37805 original size:30 final size:31
Alignment explanation
Indices: 37744--37808 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
37734 GTTATATAAG
37744 CTATGTGATAAAGTGATAGAACATGATATGT
1 CTATGTGATAAAGTGATAGAACATGATATGT
* *
37775 CTATGTGATAAAG-GTATGGAA-ATTATATGT
1 CTATGTGATAAAGTG-ATAGAACATGATATGT
37805 CTAT
1 CTAT
37809 ACAATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (31 bp):
CTATGTGATAAAGTGATAGAACATGATATGT
Found at i:38095 original size:23 final size:23
Alignment explanation
Indices: 38027--38087 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
38017 CAATATTATA
*
38027 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
38050 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
38073 TGGCACTTCGTTGCA
1 TGGCACTTCGGTGCA
38088 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:45443 original size:2 final size:2
Alignment explanation
Indices: 45431--45510 Score: 151
Period size: 2 Copynumber: 40.0 Consensus size: 2
45421 TCAAATAACC
*
45431 AT AT AT GT 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
45473 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
45511 GATCCAATTA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45625 original size:19 final size:20
Alignment explanation
Indices: 45596--45635 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
45586 AATATGATCG
45596 ATTTAAAAAATA-ATCAAATA
1 ATTTAAAAAATATA-CAAATA
45616 ATTT-AAAAATATACAAATA
1 ATTTAAAAAATATACAAATA
45635 A
1 A
45636 ATAGCATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
ATTTAAAAAATATACAAATA
Done.