Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000818.1 Hibiscus syriacus cultivar Beakdansim tig00001584_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: 52268
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2326 original size:31 final size:30
Alignment explanation
Indices: 2284--2368 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 30
2274 ACCTATAGCA
*
2284 TTTTCGGTCAAAATAAGTACATAAAATTAT
1 TTTTTGGTCAAAATAAGTACATAAAATTAT
*
2314 CTTTTTGGTCAAAAT-A-TATC-TTAAA-TAT
1 -TTTTTGGTCAAAATAAGTA-CATAAAATTAT
* *
2342 TTTTTAGTCAAAATAAGCACATAAAAT
1 TTTTTGGTCAAAATAAGTACATAAAAT
2369 ATTCGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
27 13 0.30
28 5 0.11
29 11 0.25
30 2 0.05
31 13 0.30
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (30 bp):
TTTTTGGTCAAAATAAGTACATAAAATTAT
Found at i:2489 original size:28 final size:27
Alignment explanation
Indices: 2453--2512 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
2443 AAAACGTTTG
* *
2453 AATAGTTTA-GTACCTATTTTGACATAAA
1 AATATTTTAGGTACATA-TTTGA-ATAAA
*
2481 AATATTTTAGGTACATATTTGATTAAA
1 AATATTTTAGGTACATATTTGAATAAA
2508 AATAT
1 AATAT
2513 AATTTTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.32
28 13 0.46
29 6 0.21
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.42
Consensus pattern (27 bp):
AATATTTTAGGTACATATTTGAATAAA
Found at i:4014 original size:43 final size:43
Alignment explanation
Indices: 3953--4086 Score: 268
Period size: 43 Copynumber: 3.1 Consensus size: 43
3943 CTTTTTTAAA
3953 AATCACATAGAAAATACATAAAGTTTAAAAGCTCATAATACAT
1 AATCACATAGAAAATACATAAAGTTTAAAAGCTCATAATACAT
3996 AATCACATAGAAAATACATAAAGTTTAAAAGCTCATAATACAT
1 AATCACATAGAAAATACATAAAGTTTAAAAGCTCATAATACAT
4039 AATCACATAGAAAATACATAAAGTTTAAAAGCTCATAATACAT
1 AATCACATAGAAAATACATAAAGTTTAAAAGCTCATAATACAT
4082 AATCA
1 AATCA
4087 TACACAAAAA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (43 bp):
AATCACATAGAAAATACATAAAGTTTAAAAGCTCATAATACAT
Found at i:5385 original size:2 final size:2
Alignment explanation
Indices: 5378--5415 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5368 TTCTTCCCCC
5378 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
5416 GGGATGTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22720 original size:2 final size:2
Alignment explanation
Indices: 22713--22742 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22703 GGGTAATTTG
22713 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
22743 CAGAGGCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25377 original size:17 final size:18
Alignment explanation
Indices: 25355--25402 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
25345 ATACAATTAA
*
25355 TATATAAAAATAATATGTT
1 TATATATAAATAATAT-TT
25374 TATATTATAAATAATATTT
1 TATA-TATAAATAATATTT
*
25393 TATTTATAAA
1 TATATATAAA
25403 ATTATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 6 0.23
19 9 0.35
20 11 0.42
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TATATATAAATAATATTT
Found at i:25401 original size:18 final size:20
Alignment explanation
Indices: 25362--25402 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
25352 TAATATATAA
25362 AAATAATATGTTTATATTAT
1 AAATAATATGTTTATATTAT
25382 AAATAATAT-TTTAT-TTAT
1 AAATAATATGTTTATATTAT
25400 AAA
1 AAA
25403 ATTATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.33
19 5 0.24
20 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AAATAATATGTTTATATTAT
Found at i:42476 original size:21 final size:22
Alignment explanation
Indices: 42447--42497 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
42437 GTGGAACCAC
42447 AAAGAAGATTTAATCTGATACA
1 AAAGAAGATTTAATCTGATACA
42469 AAAG-AGATTTAATCTGATAC-
1 AAAGAAGATTTAATCTGATACA
*
42489 GAAGAAGAT
1 AAAGAAGAT
42498 GGCGATGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.11
21 20 0.74
22 4 0.15
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25
Consensus pattern (22 bp):
AAAGAAGATTTAATCTGATACA
Found at i:49677 original size:26 final size:28
Alignment explanation
Indices: 49648--49702 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 28
49638 ACCGAATCAA
*
49648 AAAAAT-GAAGCC-TTTAAA-TCGAACCG
1 AAAAATAGAA-CCGTTTAAAGTCAAACCG
49674 -AAAATAGAACCGTTTAAAGTCAAACCG
1 AAAAATAGAACCGTTTAAAGTCAAACCG
49701 AA
1 AA
49703 CCGAACTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
25 7 0.29
26 9 0.38
27 7 0.29
28 1 0.04
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (28 bp):
AAAAATAGAACCGTTTAAAGTCAAACCG
Found at i:51076 original size:30 final size:30
Alignment explanation
Indices: 51038--51196 Score: 203
Period size: 30 Copynumber: 5.3 Consensus size: 30
51028 GATAAACATT
* *
51038 AACTTAAAGAACTAAAATAGCAAAAATAGA
1 AACTTAAAGGACTAAAATAGCAAAAATAAA
* * *
51068 AATTTAAAGGACCAAAATAGC-AAAACAAA
1 AACTTAAAGGACTAAAATAGCAAAAATAAA
* * * * *
51097 AACGTAAAGGATTGAAATAGTAAAAATAGA
1 AACTTAAAGGACTAAAATAGCAAAAATAAA
* *
51127 AAGTTAAAGGACTAAAATAGCAAAGATAAA
1 AACTTAAAGGACTAAAATAGCAAAAATAAA
51157 AACTTAAAGGACTAAAATAGCAAAAATAAA
1 AACTTAAAGGACTAAAATAGCAAAAATAAA
51187 AACTTAAAGG
1 AACTTAAAGG
51197 GCTGAACTAT
Statistics
Matches: 106, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
29 21 0.20
30 85 0.80
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (30 bp):
AACTTAAAGGACTAAAATAGCAAAAATAAA
Found at i:51087 original size:59 final size:59
Alignment explanation
Indices: 51011--51196 Score: 223
Period size: 59 Copynumber: 3.2 Consensus size: 59
51001 TCACTCAGTG
* ** *
51011 ATTTAAGGGACC-AAATAG-ATAAACATTAACTTAAAGAACTAAAATAGCAAAAATAGAA
1 ATTTAAAGGACCAAAATAGCA-AAACAAAAACTTAAAGGACTAAAATAGCAAAAATAGAA
* * * *
51069 ATTTAAAGGACCAAAATAGCAAAACAAAAACGTAAAGGATTGAAATAGTAAAAATAGAA
1 ATTTAAAGGACCAAAATAGCAAAACAAAAACTTAAAGGACTAAAATAGCAAAAATAGAA
* * * *
51128 AGTTAAAGGACTAAAATAGCAAAGATAAAAACTTAAAGGACTAAAATAGCAAAAATAAAA
1 ATTTAAAGGACCAAAATAGCAAA-ACAAAAACTTAAAGGACTAAAATAGCAAAAATAGAA
*
51188 ACTTAAAGG
1 ATTTAAAGG
51197 GCTGAACTAT
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
58 11 0.10
59 58 0.54
60 39 0.36
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.18
Consensus pattern (59 bp):
ATTTAAAGGACCAAAATAGCAAAACAAAAACTTAAAGGACTAAAATAGCAAAAATAGAA
Done.