Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000662.1 Hibiscus syriacus cultivar Beakdansim tig00001291_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: 59711
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:373 original size:9 final size:9
Alignment explanation
Indices: 354--443 Score: 67
Period size: 9 Copynumber: 9.6 Consensus size: 9
344 CATCAAATAT
354 TAATA-TTA
1 TAATATTTA
*
362 AAATATTTAA
1 TAATATTT-A
*
372 AAATATTTA
1 TAATATTTA
381 TTAATATTTA
1 -TAATATTTA
* *
391 TTATATTTT
1 TAATATTTA
400 TAATATTTA
1 TAATATTTA
409 TAATAATATTA
1 TAAT-AT-TTA
*
420 TATTATATTTT
1 TA--ATATTTA
431 TAATA-TTA
1 TAATATTTA
439 TAATA
1 TAATA
444 AAATAATCAA
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
8 11 0.16
9 24 0.36
10 19 0.28
11 9 0.13
12 2 0.03
13 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TAATATTTA
Found at i:391 original size:10 final size:10
Alignment explanation
Indices: 351--437 Score: 78
Period size: 10 Copynumber: 9.0 Consensus size: 10
341 TTTCATCAAA
351 TATTAATA-T
1 TATTAATATT
*
360 TA-AAATATT
1 TATTAATATT
**
369 TAAAAATATT
1 TATTAATATT
379 TATTAATATT
1 TATTAATATT
389 TATT-ATATT
1 TATTAATATT
398 T-TTAATATT
1 TATTAATATT
407 TATAATAATATT
1 TAT--TAATATT
419 ATATT-ATATT
1 -TATTAATATT
429 T-TTAATATT
1 TATTAATATT
438 ATAATAAAAT
Statistics
Matches: 67, Mismatches: 3, Indels: 16
0.78 0.03 0.19
Matches are distributed among these distances:
8 8 0.12
9 23 0.34
10 25 0.37
11 1 0.01
12 7 0.10
13 3 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TATTAATATT
Found at i:428 original size:40 final size:38
Alignment explanation
Indices: 363--437 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 38
353 TTAATATTAA
363 AATATTTAAAAATATTTATTAATATTTATT-ATATTTTT
1 AATATTTAAAAATATTTATTAATATTT-TTAATATTTTT
401 AATATTTATAATAATATTATATT-ATATTTTTAATATT
1 AATATTTA-AA-AATATT-TATTAATATTTTTAATATT
438 ATAATAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
38 8 0.24
39 4 0.12
40 17 0.52
41 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (38 bp):
AATATTTAAAAATATTTATTAATATTTTTAATATTTTT
Found at i:440 original size:19 final size:18
Alignment explanation
Indices: 374--437 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
364 ATATTTAAAA
374 ATATTTATTAATATTTATT
1 ATATTT-TTAATATTTATT
393 ATATTTTTAATATTTA-T
1 ATATTTTTAATATTTATT
410 A-A----TAATATTATATT
1 ATATTTTTAATATT-TATT
424 ATATTTTTAATATT
1 ATATTTTTAATATT
438 ATAATAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
12 7 0.18
13 2 0.05
14 2 0.05
15 1 0.03
16 1 0.03
17 2 0.05
18 10 0.26
19 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTTTAATATTTATT
Found at i:556 original size:26 final size:25
Alignment explanation
Indices: 494--556 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
484 TATTTTAATA
*
494 AATATATAATAAACTTTTTATATTTT
1 AATAT-TAATAAACTTATTATATTTT
*
520 AATAATGAATAATA-TTATTATATATTT
1 AAT-ATTAATAA-ACTTATTATAT-TTT
547 AATATTAATA
1 AATATTAATA
557 TAATAATCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 22 0.71
27 9 0.29
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
AATATTAATAAACTTATTATATTTT
Found at i:596 original size:24 final size:23
Alignment explanation
Indices: 576--621 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
566 AATAATATTT
576 TAATAAAGATATTTTAAAATATAC
1 TAATAAAGAT-TTTTAAAATATAC
* *
600 TAATTAATATTTTTAAAATATA
1 TAATAAAGATTTTTAAAATATA
622 ATACAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TAATAAAGATTTTTAAAATATAC
Found at i:11520 original size:2 final size:2
Alignment explanation
Indices: 11515--11546 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11505 TTTTCGAATA
11515 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
11547 CGAAATTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11927 original size:19 final size:20
Alignment explanation
Indices: 11900--11944 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
11890 AAACAACGGA
*
11900 TAAA-AAAAACAAAAGATTT
1 TAAACAAAACCAAAAGATTT
**
11919 TAAACAAAACCCGAAGATTT
1 TAAACAAAACCAAAAGATTT
11939 TAAACA
1 TAAACA
11945 GATCCACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (20 bp):
TAAACAAAACCAAAAGATTT
Found at i:13593 original size:18 final size:20
Alignment explanation
Indices: 13570--13606 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13560 TCAAAAGATC
13570 CTCATT-AA-GTTGTTTGAT
1 CTCATTCAACGTTGTTTGAT
13588 CTCATTCAACGTTGTTTGA
1 CTCATTCAACGTTGTTTGA
13607 GGTTAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (20 bp):
CTCATTCAACGTTGTTTGAT
Found at i:21692 original size:23 final size:22
Alignment explanation
Indices: 21661--21729 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
21651 CACCACAGCT
*
21661 CGTATAATTGCACCTAAGTGCCA
1 CGTAGAATTGCACCT-AGTGCCA
* * * *
21684 CTTAGAATTGCACCGGAGTGTCG
1 CGTAGAATTGCACC-TAGTGCCA
21707 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACC-TAGTGCCA
21730 TATAATAATG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
CGTAGAATTGCACCTAGTGCCA
Found at i:22470 original size:19 final size:20
Alignment explanation
Indices: 22433--22470 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22423 TTTTTTATTA
*
22433 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
22453 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
22471 TCTAGCGTTC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:22522 original size:21 final size:21
Alignment explanation
Indices: 22498--22540 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
22488 TCATATTCGT
*
22498 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
22519 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
22540 T
1 T
22541 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:28607 original size:23 final size:22
Alignment explanation
Indices: 28576--28644 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
28566 CACCACAGCT
* *
28576 CGTATAATTACACCTAAGTGCCA
1 CGTAGAATTGCACCT-AGTGCCA
* * *
28599 CTTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACC-TAGTGCCA
28622 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACC-TAGTGCCA
28645 TAGAATAATG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (22 bp):
CGTAGAATTGCACCTAGTGCCA
Found at i:28831 original size:103 final size:103
Alignment explanation
Indices: 28660--28877 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
28650 TAATGTCCAT
* *
28660 AAGGACCACATATCATTCCTTAAGAATCATATATATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
28725 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
28763 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
28828 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
28866 AAGGACCACATA
1 AAGGACCACATA
28878 GACCCTATAC
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:29441 original size:21 final size:21
Alignment explanation
Indices: 29417--29458 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29407 TTCATATTCG
*
29417 TTTGAGGGGGTATCGATTCCC
1 TTTGAAGGGGTATCGATTCCC
*
29438 TTTGAATGGGTATCGATTCCC
1 TTTGAAGGGGTATCGATTCCC
29459 CTAGCCCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.36
Consensus pattern (21 bp):
TTTGAAGGGGTATCGATTCCC
Found at i:34630 original size:14 final size:15
Alignment explanation
Indices: 34604--34633 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
34594 ATTTATCTGG
34604 TTTAATATTAAAAAA
1 TTTAATATTAAAAAA
34619 TTTAAT-TTAAAAAA
1 TTTAATATTAAAAAA
34633 T
1 T
34634 ATAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTAATATTAAAAAA
Found at i:44092 original size:60 final size:60
Alignment explanation
Indices: 44014--44128 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
44004 AGAGTCCAAT
* *
44014 GATTATTTTGTAACTTTTAATAATCGAATG-ACTCAACAAAACAACATCATATAGTTGGAA
1 GATTATTTTATAACTTTTAATAAT-GAATGAACTCAACAAAACAACACCATATAGTTGGAA
* * * * *
44074 GATTATTTTATAATTTTTAATAGTTAATGAACTTAACAAAACAACACCCTATAGT
1 GATTATTTTATAACTTTTAATAATGAATGAACTCAACAAAACAACACCATATAGT
44129 CGAGGGACTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
59 4 0.09
60 43 0.91
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.36
Consensus pattern (60 bp):
GATTATTTTATAACTTTTAATAATGAATGAACTCAACAAAACAACACCATATAGTTGGAA
Done.