Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004963.1 Hibiscus syriacus cultivar Beakdansim tig00011155_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: 58386
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1339 original size:2 final size:2
Alignment explanation
Indices: 1332--1363 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1322 AATTAATAGA
1332 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
1364 GGTTTAAACG
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:1797 original size:2 final size:2
Alignment explanation
Indices: 1790--1843 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1780 ATTGTTACGA
1790 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
1832 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
1844 AACCGGGCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3926 original size:21 final size:22
Alignment explanation
Indices: 3891--3932 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3881 TTTTGATTAA
* *
3891 GTTATAAATATATTATGTGTAT
1 GTTATAAAAATATTAGGTGTAT
3913 GTTA-AAAAATATTAGGTGTA
1 GTTATAAAAATATTAGGTGTA
3933 ATGATAAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (22 bp):
GTTATAAAAATATTAGGTGTAT
Found at i:8349 original size:23 final size:23
Alignment explanation
Indices: 8323--8367 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
8313 ACCACAACTT
8323 GTAGAATTGCACCGAAGAGCCAC
1 GTAGAATTGCACCGAAGAGCCAC
* *
8346 GTAGAATTGTACCGAAGTGCCA
1 GTAGAATTGCACCGAAGAGCCA
8368 TATAAGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (23 bp):
GTAGAATTGCACCGAAGAGCCAC
Found at i:15023 original size:23 final size:23
Alignment explanation
Indices: 14997--15080 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
14987 CTCGTATAAA
*
14997 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
15020 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
15043 TGCACCGAAGTGCCGCGTAGAAC
1 TGCACCGAAGTGCCACGTAGAAT
15066 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
15081 TATAAGATGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:16996 original size:31 final size:32
Alignment explanation
Indices: 16892--17032 Score: 142
Period size: 32 Copynumber: 4.4 Consensus size: 32
16882 CTAAGGTGAC
* * * *
16892 CCTTGGGTAGGCTCTTAGGCCCCGAGATATTC
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTATTA
* * *
16924 CCTTGGGTAGGCTTTCAGGCCCCATGGTACTT-
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTA-TTA
* * *
16956 CATTGGGTAGGCTATGAGGCCCCAAGGTATT-
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTATTA
*
16987 CCTTGGGTAGGCTCTAAGGCCCCAAGGCATTA
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTATTA
* *
17019 CCTTAGGTTGGCTC
1 CCTTGGGTAGGCTC
17033 CTAGGACCAA
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
31 29 0.32
32 61 0.66
33 2 0.02
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGGTATTA
Found at i:20355 original size:15 final size:15
Alignment explanation
Indices: 20337--20392 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
20327 TAACCGGTTT
20337 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
20352 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
20369 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
20384 CGATTTTAA
1 CGGTTTTAA
20393 TATTATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:20365 original size:17 final size:17
Alignment explanation
Indices: 20340--20390 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
20330 CCGGTTTCGG
20340 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
20357 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
20372 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
20389 TT
1 TT
20391 AATATTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:20534 original size:32 final size:33
Alignment explanation
Indices: 20434--20536 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 33
20424 ACAAAGTTTA
* *
20434 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
20466 TGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
20499 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
20531 CGATAA
1 CGATAA
20537 TTGAAACAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
32 15 0.23
33 51 0.77
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:20555 original size:21 final size:21
Alignment explanation
Indices: 20531--20572 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20521 ACTTCAAGTT
20531 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
20552 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
20573 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:22890 original size:14 final size:15
Alignment explanation
Indices: 22871--22903 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22861 TAAAAACCGG
*
22871 TTTTTT-AACTGGTT
1 TTTTTTAAACCGGTT
22885 TTTTTTAAACCGGTT
1 TTTTTTAAACCGGTT
22900 TTTT
1 TTTT
22904 ATCCGGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.15, C:0.09, G:0.12, T:0.64
Consensus pattern (15 bp):
TTTTTTAAACCGGTT
Found at i:23986 original size:34 final size:32
Alignment explanation
Indices: 23878--23989 Score: 82
Period size: 34 Copynumber: 3.3 Consensus size: 32
23868 TGTTTGTGTT
* *
23878 CGTTCGTTTAACGTTCGTG-GACATTTTCATTTAA
1 CGTTCGTTTAACGTT--TGCGACA-TTTCTTTTAG
* * * *
23912 TGTTCGTTTAAATGTTTGCGAACATGTCTGGTTAG
1 CGTTCGTTT-AACGTTTGCG-ACATTTCT-TTTAG
*
23947 TGTTCGTTTAACGTTTGCGATCATATTCTTTTAG
1 CGTTCGTTTAACGTTTGCGA-CAT-TTCTTTTAG
23981 CGTTCGTTT
1 CGTTCGTTT
23990 GTATAATATC
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
33 3 0.05
34 36 0.58
35 23 0.37
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.46
Consensus pattern (32 bp):
CGTTCGTTTAACGTTTGCGACATTTCTTTTAG
Found at i:37778 original size:21 final size:22
Alignment explanation
Indices: 37750--37802 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
37740 AACTGAATAA
37750 TTATATATAA-AAATTTAAG-T
1 TTATATATAATAAATTTAAGAT
*
37770 TTGATATATAATTAAATTTTAGAT
1 TT-ATATATAA-TAAATTTAAGAT
37794 TTATATATA
1 TTATATATA
37803 CCAACGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 8 0.29
23 15 0.54
24 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (22 bp):
TTATATATAATAAATTTAAGAT
Found at i:45133 original size:19 final size:19
Alignment explanation
Indices: 45086--45133 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
45076 GTTTGCTTTT
* *
45086 TTTGGCTTTTTTCTCTCTC
1 TTTGCCTTTTCTCTCTCTC
***
45105 TTTTTTTTTTCTCTCTCTC
1 TTTGCCTTTTCTCTCTCTC
45124 TTTGCCTTTT
1 TTTGCCTTTT
45134 GATGATTAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.00, C:0.25, G:0.06, T:0.69
Consensus pattern (19 bp):
TTTGCCTTTTCTCTCTCTC
Found at i:52612 original size:32 final size:32
Alignment explanation
Indices: 52571--52635 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
52561 TTCGGCCAAG
52571 TCCCTTCAAAAACTATAAATAGGCTTTCCTAT
1 TCCCTTCAAAAACTATAAATAGGCTTTCCTAT
52603 TCCCTTCAAAAACTATAAATAGGCTTTCCTAT
1 TCCCTTCAAAAACTATAAATAGGCTTTCCTAT
52635 T
1 T
52636 TCATTTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (32 bp):
TCCCTTCAAAAACTATAAATAGGCTTTCCTAT
Found at i:58344 original size:21 final size:20
Alignment explanation
Indices: 58297--58345 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
58287 AACTGAATAA
*
58297 TTATATATACAAATTTAAGT
1 TTATATATACAAATTTAAAT
**
58317 TTGATATATATTAATTTAACAT
1 TT-ATATATACAAATTTAA-AT
58339 TTATATA
1 TTATATA
58346 CACCAACGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.79
22 3 0.12
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (20 bp):
TTATATATACAAATTTAAAT
Done.