Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003042.1 Hibiscus syriacus cultivar Beakdansim tig00006330_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: 82414
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1684 original size:20 final size:20
Alignment explanation
Indices: 1659--1706 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1649 ATGAGAACCT
1659 GAAACCTGATCATGTTTTGA
1 GAAACCTGATCATGTTTTGA
1679 GAAACCTGATCATGTTTTGA
1 GAAACCTGATCATGTTTTGA
*
1699 GGAACCTG
1 GAAACCTG
1707 TTGCTGAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (20 bp):
GAAACCTGATCATGTTTTGA
Found at i:10360 original size:21 final size:21
Alignment explanation
Indices: 10334--10434 Score: 150
Period size: 21 Copynumber: 4.8 Consensus size: 21
10324 ACATAGAATT
*
10334 TGTCCCAAATGACCACATATA
1 TGTCCCAAATGACCACTTATA
*
10355 TGTCCCTAATGACCACTTATA
1 TGTCCCAAATGACCACTTATA
*
10376 TGTCCCAAAGGACCACTTATA
1 TGTCCCAAATGACCACTTATA
10397 TGTCCCGAAA-GACCACTTATA
1 TGTCCC-AAATGACCACTTATA
*
10418 TGTCCCGAATGACCACT
1 TGTCCCAAATGACCACT
10435 CCTTAAGAAC
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
20 2 0.03
21 68 0.93
22 3 0.04
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.26
Consensus pattern (21 bp):
TGTCCCAAATGACCACTTATA
Found at i:10709 original size:26 final size:26
Alignment explanation
Indices: 10680--10732 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
10670 ACATGTTCAC
10680 ATAATCACATAGGCATATTATATCAT
1 ATAATCACATAGGCATATTATATCAT
10706 ATAATCACATAGGCATATTATATCAT
1 ATAATCACATAGGCATATTATATCAT
10732 A
1 A
10733 GCTCATGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (26 bp):
ATAATCACATAGGCATATTATATCAT
Found at i:15342 original size:2 final size:2
Alignment explanation
Indices: 15335--15409 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
15325 TATTTGGATC
15335 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
15377 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
15410 ATTAAGGCAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18283 original size:21 final size:21
Alignment explanation
Indices: 18259--18323 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
18249 AGGGGGAACA
18259 GATTCCCCCTGGGGGGGTATC
1 GATTCCCCCTGGGGGGGTATC
* *
18280 GATT-CCCC-----GGGAATA
1 GATTCCCCCTGGGGGGGTATC
18295 GATTCCCCCTGGGGGGGTATC
1 GATTCCCCCTGGGGGGGTATC
18316 GATTCCCC
1 GATTCCCC
18324 TCTAAATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 9 0.26
16 4 0.12
20 4 0.12
21 17 0.50
ACGTcount: A:0.14, C:0.31, G:0.32, T:0.23
Consensus pattern (21 bp):
GATTCCCCCTGGGGGGGTATC
Found at i:18299 original size:36 final size:36
Alignment explanation
Indices: 18252--18323 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
18242 TATGTGCAGG
18252 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
*
18288 GGGAATAGATTCCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
18324 TCTAAATGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.17, C:0.29, G:0.33, T:0.21
Consensus pattern (36 bp):
GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
Found at i:18797 original size:19 final size:20
Alignment explanation
Indices: 18763--18801 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
18753 ATGAAATGAC
*
18763 ATATGAATATGCAATATATG
1 ATATGAATATGAAATATATG
18783 ATATG-ATATGAAATATATG
1 ATATGAATATGAAATATATG
18802 GTTACACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (20 bp):
ATATGAATATGAAATATATG
Found at i:21250 original size:12 final size:13
Alignment explanation
Indices: 21233--21290 Score: 63
Period size: 12 Copynumber: 4.8 Consensus size: 13
21223 TATGTGCGTG
21233 TATATA-TATTAT
1 TATATATTATTAT
*
21245 TATATA-GATATAT
1 TATATATTAT-TAT
21258 TAT-TATTATTAT
1 TATATATTATTAT
21270 TAT-TATTATTAT
1 TATATATTATTAT
21282 TATAT-TTAT
1 TATATATTAT
21291 ATTTCATTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
12 32 0.78
13 9 0.22
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
TATATATTATTAT
Found at i:21261 original size:3 final size:3
Alignment explanation
Indices: 21255--21284 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
21245 TATATAGATA
21255 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21285 ATTTATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:23352 original size:19 final size:20
Alignment explanation
Indices: 23328--23372 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
23318 AATATACTAT
23328 TTTTTAAATT-AATTTTAAA
1 TTTTTAAATTGAATTTTAAA
*
23347 TTTTT-ATTTGAATTTTAAA
1 TTTTTAAATTGAATTTTAAA
*
23366 TTATTAA
1 TTTTTAA
23373 TAAAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 3 0.14
19 18 0.82
20 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTAAATTGAATTTTAAA
Found at i:34747 original size:38 final size:37
Alignment explanation
Indices: 34670--34747 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
34660 TTTTTATATT
*
34670 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
34707 TTTAATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAA-TTTTGTAAAAAAAATTATATAAATATTAT-CAA
34745 TTT
1 TTT
34748 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 18 0.51
38 17 0.49
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:34929 original size:20 final size:20
Alignment explanation
Indices: 34893--34930 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34883 ATCATATTCC
**
34893 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
34913 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
34931 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:36010 original size:18 final size:18
Alignment explanation
Indices: 35984--36018 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35974 ACTGAATATT
* *
35984 TGTCTCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
36002 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
36019 GATAATCCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:36619 original size:19 final size:19
Alignment explanation
Indices: 36595--36661 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
36585 CCTTAATATG
36595 TGCATCGATACACTATCTA
1 TGCATCGATACACTATCTA
** *
36614 TGCATCCCTTA-A-TA--TG
1 TGCAT-CGATACACTATCTA
36630 TGCATCGATACACTATCTA
1 TGCATCGATACACTATCTA
*
36649 TGCATCGGTACAC
1 TGCATCGATACAC
36662 AAATCGCATT
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
15 3 0.08
16 7 0.19
17 2 0.06
18 2 0.06
19 19 0.53
20 3 0.08
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (19 bp):
TGCATCGATACACTATCTA
Found at i:36624 original size:35 final size:35
Alignment explanation
Indices: 36573--36654 Score: 155
Period size: 35 Copynumber: 2.3 Consensus size: 35
36563 CTCTATAGTG
*
36573 TATCGATGCATCCCTTAATATGTGCATCGATACAC
1 TATCTATGCATCCCTTAATATGTGCATCGATACAC
36608 TATCTATGCATCCCTTAATATGTGCATCGATACAC
1 TATCTATGCATCCCTTAATATGTGCATCGATACAC
36643 TATCTATGCATC
1 TATCTATGCATC
36655 GGTACACAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (35 bp):
TATCTATGCATCCCTTAATATGTGCATCGATACAC
Found at i:38511 original size:16 final size:18
Alignment explanation
Indices: 38492--38531 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
38482 TTAATAATTA
38492 TATAATTT-TAAATA-AT
1 TATAATTTCTAAATATAT
*
38508 TAT-ATTTCTAAATATTT
1 TATAATTTCTAAATATAT
38525 TATAATT
1 TATAATT
38532 AGAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 4 0.20
16 9 0.45
17 4 0.20
18 3 0.15
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
TATAATTTCTAAATATAT
Found at i:48670 original size:24 final size:24
Alignment explanation
Indices: 48643--48715 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
48633 CGTTCATTTA
48643 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
48667 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
48691 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
48715 C
1 C
48716 ATTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:48672 original size:14 final size:14
Alignment explanation
Indices: 48653--48708 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
48643 CGTTCGTGAA
48653 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
48667 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
48681 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
48691 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
48705 CGTT
1 CGTT
48709 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:48725 original size:24 final size:23
Alignment explanation
Indices: 48654--48728 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
48644 GTTCGTGAAC
* *
48654 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
48678 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
48702 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
48726 GTT
1 GTT
48729 TAATCCAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:49471 original size:10 final size:10
Alignment explanation
Indices: 49456--49530 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
49446 GGGTCTCCAA
49456 CGTTTATGTT
1 CGTTTATGTT
49466 CGTTTATGTT
1 CGTTTATGTT
49476 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
49487 ATGTTCGTGTT
1 -CGTTTATGTT
49498 CGTTTATGTT
1 CGTTTATGTT
49508 CG----TGTT
1 CGTTTATGTT
49514 CGTTTATGTT
1 CGTTTATGTT
49524 CGTTTAT
1 CGTTTAT
49531 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:49487 original size:16 final size:16
Alignment explanation
Indices: 49462--49526 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
49452 CCAACGTTTA
49462 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
49478 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
49494 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
49510 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
49526 T
1 T
49527 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:49612 original size:16 final size:16
Alignment explanation
Indices: 49591--49623 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
49581 AAAAAAATTT
49591 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
49607 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
49623 T
1 T
49624 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:76119 original size:2 final size:2
Alignment explanation
Indices: 76112--76138 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
76102 TATATTATTT
76112 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
76139 TTAATTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:76323 original size:19 final size:18
Alignment explanation
Indices: 76282--76325 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
76272 AATTAATAAA
76282 AAATAAAT-ATATTATTT
1 AAATAAATAATATTATTT
76299 -AA-AAATAATATTATTT
1 AAATAAATAATATTATTT
76315 CAAATAAATAA
1 -AAATAAATAA
76326 ATGATAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.17
16 11 0.48
18 2 0.09
19 6 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATAAATAATATTATTT
Found at i:77927 original size:2 final size:2
Alignment explanation
Indices: 77910--77978 Score: 115
Period size: 2 Copynumber: 35.0 Consensus size: 2
77900 AATTACAATA
77910 AT AT GAT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77951 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
77979 GCACACACAA
Statistics
Matches: 64, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.03
2 60 0.94
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:79063 original size:16 final size:18
Alignment explanation
Indices: 79032--79066 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
79022 TACTTATAGT
79032 TAATTTATTCATTTGTTA
1 TAATTTATTCATTTGTTA
79050 TAATTTATT-A-TTGTTA
1 TAATTTATTCATTTGTTA
79066 T
1 T
79067 TTTTGCAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 1 0.06
18 9 0.53
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (18 bp):
TAATTTATTCATTTGTTA
Done.