Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005856.1 Hibiscus syriacus cultivar Beakdansim tig00013752_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: 64758
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2582 original size:21 final size:21
Alignment explanation
Indices: 2556--2604 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2546 ATTTATAAGT
*
2556 TGGTGATAATAGGGCGTGAT-A
1 TGGTGATAATA-AGCGTGATAA
*
2577 TGGTGATGATAAGCGTGATAA
1 TGGTGATAATAAGCGTGATAA
2598 TGGTGAT
1 TGGTGAT
2605 GACTATGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.29, C:0.04, G:0.37, T:0.31
Consensus pattern (21 bp):
TGGTGATAATAAGCGTGATAA
Found at i:2595 original size:33 final size:35
Alignment explanation
Indices: 2575--2640 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
2565 TAGGGCGTGA
2575 TATGGTGATGATA-A-GCGTGATAATGGTGATGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGAC
2608 TATGGTGATGATATAGGCGTGATAATGGTGATG
1 TATGGTGATGATATAGGCGTGATAATGGTGATG
2641 GACAGATTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 13 0.42
34 1 0.03
35 17 0.55
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.32
Consensus pattern (35 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGAC
Found at i:4475 original size:27 final size:28
Alignment explanation
Indices: 4445--4506 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
4435 TTTTTCTTTG
* *
4445 CTTTTCTTCTTTTTGAATGC-TGAATTT
1 CTTTTCTTCTTTTGGAATGCTTCAATTT
*
4472 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAATGCTTCAATTT
4500 CTTTTCT
1 CTTTTCT
4507 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 8 0.28
29 4 0.14
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.60
Consensus pattern (28 bp):
CTTTTCTTCTTTTGGAATGCTTCAATTT
Found at i:16670 original size:30 final size:31
Alignment explanation
Indices: 16617--16676 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
16607 CTTAGCTTTA
***
16617 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCACTTAGATATCATT
*
16647 TATTATGTTTGCATATCACTTAGATATCAT
1 TATTATGTTTACATATCACTTAGATATCAT
16677 GGCATCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (31 bp):
TATTATGTTTACATATCACTTAGATATCATT
Found at i:18682 original size:24 final size:21
Alignment explanation
Indices: 18647--18689 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
18637 GGCTCATTCT
*
18647 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
18670 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
18690 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:19862 original size:15 final size:16
Alignment explanation
Indices: 19836--19871 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
19826 GTGCTTCAAC
19836 TTCTTT-CTTTT-CTT
1 TTCTTTGCTTTTCCTT
19850 TTCTTTGCTTTTCCTT
1 TTCTTTGCTTTTCCTT
19866 TT-TTTG
1 TTCTTTG
19872 AGTGATGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 6 0.30
15 9 0.45
16 5 0.25
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.75
Consensus pattern (16 bp):
TTCTTTGCTTTTCCTT
Found at i:26677 original size:11 final size:11
Alignment explanation
Indices: 26663--26735 Score: 51
Period size: 11 Copynumber: 6.3 Consensus size: 11
26653 TAATATAGGC
26663 ATGATATGGTG
1 ATGATATGGTG
*
26674 ATGATATATGTG
1 ATGATAT-GGTG
*
26686 -TGATAATGTTG
1 ATGAT-ATGGTG
26697 ATGGACTATGGTG
1 AT-GA-TATGGTG
*
26710 ATGATATAGGCG
1 ATGATAT-GGTG
26722 -TGATAATGGTG
1 ATGAT-ATGGTG
26733 ATG
1 ATG
26736 GACAGATTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
11 23 0.48
12 15 0.31
13 9 0.19
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.36
Consensus pattern (11 bp):
ATGATATGGTG
Found at i:26690 original size:36 final size:36
Alignment explanation
Indices: 26649--26728 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
26639 TTATAAGTTG
* *
26649 GTGATAATATAGGCAT-GA-TATGGTGATGATATATGT
1 GTGATAATAT-GG-ATGGACTATGGTGATGATATAGGC
* *
26685 GTGATAATGTTGATGGACTATGGTGATGATATAGGC
1 GTGATAATATGGATGGACTATGGTGATGATATAGGC
26721 GTGATAAT
1 GTGATAAT
26729 GGTGATGGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
34 2 0.05
35 3 0.08
36 33 0.87
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (36 bp):
GTGATAATATGGATGGACTATGGTGATGATATAGGC
Found at i:26729 original size:36 final size:36
Alignment explanation
Indices: 26667--26738 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
26657 ATAGGCATGA
* * *
26667 TATGGTGATGATATATGTGTGATAATGTTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
26703 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
26739 AGATTGTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.04, G:0.33, T:0.35
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:30611 original size:13 final size:12
Alignment explanation
Indices: 30592--30677 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
30582 ATATAGACGT
30592 GATATGGTGATG
1 GATATGGTGATG
30604 GAATATGGTGAT-
1 G-ATATGGTGATG
*
30616 GATATAGGCG-T-
1 GATAT-GGTGATG
30627 GATAATGGTGATG
1 GAT-ATGGTGATG
30640 GACTATGGTGAT-
1 GA-TATGGTGATG
*
30652 GATATAGGCG-T-
1 GATAT-GGTGATG
30663 GATAATGGTGATG
1 GAT-ATGGTGATG
30676 GA
1 GA
30678 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:30647 original size:36 final size:36
Alignment explanation
Indices: 30574--30678 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
30564 ATTTATAAGT
* * *
30574 TGGTGATAATATAGACGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
30609 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
30645 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
30679 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:33828 original size:16 final size:16
Alignment explanation
Indices: 33807--33839 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
33797 TTCTTCCACC
33807 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
33823 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
33839 T
1 T
33840 GAGCTAACTA
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:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:41478 original size:19 final size:19
Alignment explanation
Indices: 41454--41497 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
41444 TAATGAATAT
41454 AAATGATGAAAGAAAAAAG
1 AAATGATGAAAGAAAAAAG
*
41473 AAATGATGAAAGAAAAAGG
1 AAATGATGAAAGAAAAAAG
41492 AAATGA
1 AAATGA
41498 AGATAACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (19 bp):
AAATGATGAAAGAAAAAAG
Found at i:44720 original size:16 final size:16
Alignment explanation
Indices: 44699--44731 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
44689 TTCTTCCACC
44699 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
44715 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
44731 T
1 T
44732 GAGCTAACTA
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:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:48257 original size:16 final size:16
Alignment explanation
Indices: 48236--48268 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
48226 TTCTTCCACC
48236 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
48252 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
48268 T
1 T
48269 GAGCTAACTA
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:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:49401 original size:33 final size:35
Alignment explanation
Indices: 49363--49491 Score: 156
Period size: 36 Copynumber: 3.7 Consensus size: 35
49353 ATGGTGATAA
* * *
49363 AATGGTAATGGA-A-GGATGATGTTATTGGCGTGAT
1 AATGGTGATGGATATGG-TGATGATATAGGCGTGAT
49397 -ATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGG-ATATGGTGATGATATAGGCGTGAT
*
49432 AATGGTGATGGACTATGGTGATGATATAGGAGTGAT
1 AATGGTGATGGA-TATGGTGATGATATAGGCGTGAT
*
49468 AATGGAGATGGATTATGGTGATGA
1 AATGGTGATGGA-TATGGTGATGA
49492 AAATAGTATC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
33 9 0.11
34 1 0.01
35 18 0.21
36 56 0.67
ACGTcount: A:0.30, C:0.02, G:0.36, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGATATGGTGATGATATAGGCGTGAT
Found at i:49413 original size:13 final size:12
Alignment explanation
Indices: 49394--49490 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
49384 TTATTGGCGT
49394 GATATGGTGATG
1 GATATGGTGATG
49406 GAATATGGTGAT-
1 G-ATATGGTGATG
*
49418 GATATAGGCG-T-
1 GATAT-GGTGATG
49429 GATAATGGTGATG
1 GAT-ATGGTGATG
49442 GACTATGGTGAT-
1 GA-TATGGTGATG
*
49454 GATATAG-GA-G
1 GATATGGTGATG
*
49464 TGATAATGGAGATG
1 -GAT-ATGGTGATG
49478 GATTATGGTGATG
1 GA-TATGGTGATG
49491 AAAATAGTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
10 2 0.03
11 18 0.26
12 13 0.19
13 32 0.47
14 3 0.04
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:49449 original size:36 final size:36
Alignment explanation
Indices: 49379--49491 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
49369 AATGGAAGGA
* *
49379 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
49414 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
49450 TGATGATATAGGAGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
49486 TGATGA
1 TGATGA
49492 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.28, C:0.03, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:50989 original size:33 final size:33
Alignment explanation
Indices: 50947--51015 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
50937 GTTGATGAAT
50947 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGTG-TGAAATGGTAATG
* * *
50980 GAAGGATGATGTTATTGGTGTGATATGGTGATG
1 GAAGGATGATGTTAATGGTGTGAAATGGTAATG
51013 GAA
1 GAA
51016 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGTGTGAAATGGTAATG
Found at i:58047 original size:17 final size:18
Alignment explanation
Indices: 58025--58063 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
58015 TGTAGGAGTC
58025 TTTTCTT-TTCTCTT-TTG
1 TTTTCTTCTT-TCTTGTTG
58042 TTTTCTTCTTTCTTGTTG
1 TTTTCTTCTTTCTTGTTG
58060 TTTT
1 TTTT
58064 TTGTTGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (18 bp):
TTTTCTTCTTTCTTGTTG
Found at i:58450 original size:33 final size:33
Alignment explanation
Indices: 58408--58476 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
58398 GTTGATGAAT
*
58408 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
58441 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
58474 GAA
1 GAA
58477 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:58481 original size:13 final size:12
Alignment explanation
Indices: 58462--58558 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
58452 TTATTGGCGT
58462 GATATGGTGATG
1 GATATGGTGATG
58474 GAATATGGTGAT-
1 G-ATATGGTGATG
*
58486 GATATAGGCG-T-
1 GATAT-GGTGATG
58497 GATAATGGTGATG
1 GAT-ATGGTGATG
58510 GACTATGGTGAT-
1 GA-TATGGTGATG
*
58522 GATATAGGCG-T-
1 GATAT-GGTGATG
*
58533 GATAATGGAGATG
1 GAT-ATGGTGATG
58546 GATTATGGTGATG
1 GA-TATGGTGATG
58559 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:58517 original size:36 final size:36
Alignment explanation
Indices: 58447--58559 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
58437 AATGGAAGGA
* *
58447 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
58482 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
58518 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
58554 TGATGA
1 TGATGA
58560 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:64580 original size:4 final size:5
Alignment explanation
Indices: 64552--64577 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
64542 CACTCAAAAG
64552 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
64578 GAAGTTGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Done.