Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008231.1 Hibiscus syriacus cultivar Beakdansim tig00110868_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: 67858
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:5397 original size:56 final size:56
Alignment explanation
Indices: 5311--5428 Score: 236
Period size: 56 Copynumber: 2.1 Consensus size: 56
5301 GGAGAGGTGG
5311 AGAGGTGGAGATGAAGGAGACAAGTTGTAATCTCGATTCTATACTGGTCGGACAGT
1 AGAGGTGGAGATGAAGGAGACAAGTTGTAATCTCGATTCTATACTGGTCGGACAGT
5367 AGAGGTGGAGATGAAGGAGACAAGTTGTAATCTCGATTCTATACTGGTCGGACAGT
1 AGAGGTGGAGATGAAGGAGACAAGTTGTAATCTCGATTCTATACTGGTCGGACAGT
5423 AGAGGT
1 AGAGGT
5429 TATAGATCAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.31, C:0.12, G:0.33, T:0.25
Consensus pattern (56 bp):
AGAGGTGGAGATGAAGGAGACAAGTTGTAATCTCGATTCTATACTGGTCGGACAGT
Found at i:9987 original size:66 final size:67
Alignment explanation
Indices: 9915--10040 Score: 191
Period size: 68 Copynumber: 1.9 Consensus size: 67
9905 TTTTTTAGAG
* * *
9915 TAAACTACTTATTTGGTCAC-ATATATTATTTAATTTATGTTTTAATCATTCGATTATTATTTAG
1 TAAACTACTTATTTAGTCACTATATATTATCTAATTTATGTTTTAATCACTCGATTATTATTTAG
9979 GA
66 GA
* *
9981 TAAACTACTTATTTAGTCACTTATATGTTATCTAATTTATGTTTTGATCACTCGATTATT
1 TAAACTACTTATTTAGTCAC-TATATATTATCTAATTTATGTTTTAATCACTCGATTATT
10041 TTTTTTTTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
66 19 0.36
68 34 0.64
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (67 bp):
TAAACTACTTATTTAGTCACTATATATTATCTAATTTATGTTTTAATCACTCGATTATTATTTAG
GA
Found at i:10098 original size:21 final size:22
Alignment explanation
Indices: 10067--10111 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
10057 TATCTGACAT
10067 TTTTTTCAATTATGTTTAGATG
1 TTTTTTCAATTATGTTTAGATG
*
10089 TTTTTT-AATTATGTTTGGATG
1 TTTTTTCAATTATGTTTAGATG
10110 TT
1 TT
10112 GAAATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.62
Consensus pattern (22 bp):
TTTTTTCAATTATGTTTAGATG
Found at i:20218 original size:10 final size:10
Alignment explanation
Indices: 20203--20237 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
20193 ATTATTCATG
20203 ATATTATCAA
1 ATATTATCAA
*
20213 ATATTATTAA
1 ATATTATCAA
20223 A-ATTATCAA
1 ATATTATCAA
20232 ATATTA
1 ATATTA
20238 CTATTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATTATCAA
Found at i:20227 original size:19 final size:19
Alignment explanation
Indices: 20175--20237 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
20165 GAATTATTTT
*
20175 TATTATTAAATTTATCAAA
1 TATTATTAAAATTATCAAA
* *
20194 TTATTCA-TGATATTATCAAA
1 -TATT-ATTAAAATTATCAAA
20214 TATTATTAAAATTATCAAA
1 TATTATTAAAATTATCAAA
20233 TATTA
1 TATTA
20238 CTATTATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.03
19 20 0.56
20 14 0.39
21 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (19 bp):
TATTATTAAAATTATCAAA
Found at i:20246 original size:19 final size:19
Alignment explanation
Indices: 20203--20247 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
20193 ATTATTCATG
*
20203 ATATTATCAAATATTATTA
1 ATATTATCAAATATTACTA
*
20222 AAATTATCAAATATTACTA
1 ATATTATCAAATATTACTA
*
20241 TTATTAT
1 ATATTAT
20248 TGTAATATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATTATCAAATATTACTA
Found at i:22050 original size:32 final size:32
Alignment explanation
Indices: 22014--22077 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
22004 TTATAATAGG
22014 TGTAAAAGTATGATAAATTTTAATGATTATTT
1 TGTAAAAGTATGATAAATTTTAATGATTATTT
22046 TGTAAAAGTATGATAAATTTTAATGATTATTT
1 TGTAAAAGTATGATAAATTTTAATGATTATTT
22078 ACTATTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (32 bp):
TGTAAAAGTATGATAAATTTTAATGATTATTT
Found at i:28335 original size:31 final size:31
Alignment explanation
Indices: 28299--28395 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 31
28289 ATATTATTCA
28299 TAATAATTTGATAAATTTAATAATCATTTTG
1 TAATAATTTGATAAATTTAATAATCATTTTG
* * * * *
28330 TAATAATTTAATAATTTTTTATGATCATTTTC
1 TAATAATTTGATAA-ATTTAATAATCATTTTG
* * *
28362 TAATCATTTGA-AAAGTTTACTAATTATTTTG
1 TAATAATTTGATAAA-TTTAATAATCATTTTG
28393 TAA
1 TAA
28396 CATTTAAAAA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
31 29 0.57
32 22 0.43
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.51
Consensus pattern (31 bp):
TAATAATTTGATAAATTTAATAATCATTTTG
Found at i:37570 original size:43 final size:44
Alignment explanation
Indices: 37497--37579 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 44
37487 TACAATTTCC
***
37497 AGTGGAAAACTAAAATGGTAAACGTTAAGGGAGTATTTTTTTTT
1 AGTGGAAAACTAAAATGGTAAACAACAAGGGAGTATTTTTTTTT
*
37541 AGTGGAAAA-TAAAATGGTAAACAACAAGGGATTATTTTT
1 AGTGGAAAACTAAAATGGTAAACAACAAGGGAGTATTTTT
37580 GTTTCTTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
43 26 0.74
44 9 0.26
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.33
Consensus pattern (44 bp):
AGTGGAAAACTAAAATGGTAAACAACAAGGGAGTATTTTTTTTT
Found at i:45799 original size:2 final size:2
Alignment explanation
Indices: 45792--45834 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
45782 TCAATGAATT
45792 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45833 TA
1 TA
45835 CGAAGATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:46119 original size:19 final size:19
Alignment explanation
Indices: 46095--46132 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
46085 AGATATTACG
46095 TTAATAAGTACATAAATAA
1 TTAATAAGTACATAAATAA
46114 TTAATAAGTACATAAATAA
1 TTAATAAGTACATAAATAA
46133 CTCAGTCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (19 bp):
TTAATAAGTACATAAATAA
Found at i:57123 original size:21 final size:22
Alignment explanation
Indices: 57099--57140 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
57089 AGAAATAATC
* *
57099 CAAATTCT-AAAATATCAAAAT
1 CAAATACTAAAAATACCAAAAT
57120 CAAATACTAAAAATACCAAAA
1 CAAATACTAAAAATACCAAAA
57141 AAAATAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (22 bp):
CAAATACTAAAAATACCAAAAT
Found at i:57154 original size:22 final size:23
Alignment explanation
Indices: 57106--57154 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
57096 ATCCAAATTC
* * *
57106 TAAAATATCAAAATCAAATACTA
1 TAAAATACCAAAATAAAATAATA
57129 -AAAATACCAAAA-AAAATAATA
1 TAAAATACCAAAATAAAATAATA
57150 TAAAA
1 TAAAA
57155 AAAGACCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.20
Consensus pattern (23 bp):
TAAAATACCAAAATAAAATAATA
Done.