Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007346.1 Hibiscus syriacus cultivar Beakdansim tig00019683_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: 32397
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1083 original size:15 final size:16
Alignment explanation
Indices: 1058--1087 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1048 AAAGTTTATG
1058 TTCGTTTATGTTCGTA
1 TTCGTTTATGTTCGTA
1074 TTCG-TTATGTTCGT
1 TTCGTTTATGTTCGT
1088 TTATTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.10, C:0.13, G:0.20, T:0.57
Consensus pattern (16 bp):
TTCGTTTATGTTCGTA
Found at i:3447 original size:37 final size:37
Alignment explanation
Indices: 3406--3476 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
3396 TGTATGAAGT
3406 TTATCTTTAATAACTCAATAAGTGTATGTTTAAAAAC
1 TTATCTTTAATAACTCAATAAGTGTATGTTTAAAAAC
* * *
3443 TTATCTTTAATAATTTAATGAGTGTATGTTTAAA
1 TTATCTTTAATAACTCAATAAGTGTATGTTTAAA
3477 TATTATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (37 bp):
TTATCTTTAATAACTCAATAAGTGTATGTTTAAAAAC
Found at i:3497 original size:37 final size:37
Alignment explanation
Indices: 3426--3497 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
3416 TAACTCAATA
* *
3426 AGTGTATGTTTAAAAACTTATCTTTAATAATTTAATG
1 AGTGTATGTTTAAAAACTTATATTTAACAATTTAATG
* *
3463 AGTGTATGTTTAAATA-TTATATTATAACACTTTAA
1 AGTGTATGTTTAAAAACTTATATT-TAACAATTTAA
3498 AGAAATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 6 0.20
37 24 0.80
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.46
Consensus pattern (37 bp):
AGTGTATGTTTAAAAACTTATATTTAACAATTTAATG
Found at i:9342 original size:24 final size:24
Alignment explanation
Indices: 9310--9357 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
9300 AGAAACTCTC
*
9310 GCTCATACTCTATCACTGAGCGAT
1 GCTCATACTCCATCACTGAGCGAT
9334 GCTCATACTCCATCACTGAGCGAT
1 GCTCATACTCCATCACTGAGCGAT
9358 CTCTCTGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (24 bp):
GCTCATACTCCATCACTGAGCGAT
Found at i:13477 original size:161 final size:161
Alignment explanation
Indices: 13212--13537 Score: 634
Period size: 161 Copynumber: 2.0 Consensus size: 161
13202 ATCACTTAAT
*
13212 AATTTTTTAACTCATCAATAGAACCTGTAGATGCCTAGGTTATTGAGAAAATTTTATGATTTCCC
1 AATTTTTCAACTCATCAATAGAACCTGTAGATGCCTAGGTTATTGAGAAAATTTTATGATTTCCC
13277 ATATATCTACTTGACCTTTAGCAACATTTAGTAATTTTATATTATTGAGCTTTCCTAAAGCTCAT
66 ATATATCTACTTGACCTTTAGCAACATTTAGTAATTTTATATTATTGAGCTTTCCTAAAGCTCAT
13342 TTTATTATTTATTATTTCAGATTAAAAAGGA
131 TTTATTATTTATTATTTCAGATTAAAAAGGA
*
13373 AATTTTTCAACTCATCAATAGAACCTGTAGATGTCTAGGTTATTGAGAAAATTTTATGATTTCCC
1 AATTTTTCAACTCATCAATAGAACCTGTAGATGCCTAGGTTATTGAGAAAATTTTATGATTTCCC
13438 ATATATCTACTTGACCTTTAGCAACATTTAGTAATTTTATATTATTGAGCTTTCCTAAAGCTCAT
66 ATATATCTACTTGACCTTTAGCAACATTTAGTAATTTTATATTATTGAGCTTTCCTAAAGCTCAT
13503 TTTATTATTTATTATTTCAGATTAAAAAGGA
131 TTTATTATTTATTATTTCAGATTAAAAAGGA
13534 AATT
1 AATT
13538 GATTTTGTGC
Statistics
Matches: 163, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 163 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (161 bp):
AATTTTTCAACTCATCAATAGAACCTGTAGATGCCTAGGTTATTGAGAAAATTTTATGATTTCCC
ATATATCTACTTGACCTTTAGCAACATTTAGTAATTTTATATTATTGAGCTTTCCTAAAGCTCAT
TTTATTATTTATTATTTCAGATTAAAAAGGA
Found at i:14504 original size:2 final size:2
Alignment explanation
Indices: 14499--14532 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
14489 GTTTTTTTTT
14499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14533 ATTATTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14943 original size:2 final size:2
Alignment explanation
Indices: 14936--14997 Score: 74
Period size: 2 Copynumber: 32.0 Consensus size: 2
14926 TTTAAATTAA
* *
14936 AT AT AT AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT TT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
14976 TT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
14998 CGGTCCGATA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:17037 original size:32 final size:32
Alignment explanation
Indices: 17001--17067 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
16991 GGATTGATTG
* *
17001 TTTTTGGATTGGGTCAATATCGAATCAGTCGA
1 TTTTTGCATTGGGTCAATATCAAATCAGTCGA
* * * *
17033 TTTTTTCTTTGGGTTAATATCAAATTAGTCGA
1 TTTTTGCATTGGGTCAATATCAAATCAGTCGA
17065 TTT
1 TTT
17068 CTAGATCGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.46
Consensus pattern (32 bp):
TTTTTGCATTGGGTCAATATCAAATCAGTCGA
Found at i:19933 original size:18 final size:19
Alignment explanation
Indices: 19910--19949 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
19900 CAGCAGCTCA
* *
19910 TAACTGCTC-TTAACAAGC
1 TAACTGATCTTTAACAAAC
19928 TAACTGATCTTTAACAAAC
1 TAACTGATCTTTAACAAAC
19947 TAA
1 TAA
19950 TAGTTCCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (19 bp):
TAACTGATCTTTAACAAAC
Found at i:21944 original size:63 final size:63
Alignment explanation
Indices: 21845--21966 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
21835 AACCATCTCG
* * * ***
21845 ACTTCATTATGGATTTCTGCATTACCAACTTCTTCATGCACGGTGGTGGTATTTGGTAACTCT
1 ACTTCATTATAGATTTATGCATCACCAACTTCTTCATGCACGACAGTGGTATTTGGTAACTCT
* * *
21908 ACTTCATTATATATTTATGCATCACCATCTTCTTCATGTACGACAGTGGTATTTGGTAA
1 ACTTCATTATAGATTTATGCATCACCAACTTCTTCATGCACGACAGTGGTATTTGGTAA
21967 GTGACTTGGT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 50 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (63 bp):
ACTTCATTATAGATTTATGCATCACCAACTTCTTCATGCACGACAGTGGTATTTGGTAACTCT
Found at i:28927 original size:5 final size:5
Alignment explanation
Indices: 28917--28942 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28907 TATGATTATT
28917 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
28943 TTCTAAGTCA
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:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:30371 original size:15 final size:15
Alignment explanation
Indices: 30351--30390 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
30341 CAAATCCTCC
30351 TCCTATTCCTGAAAT
1 TCCTATTCCTGAAAT
30366 TCCTATTCCTGAAAT
1 TCCTATTCCTGAAAT
*
30381 TCCAATTCCT
1 TCCTATTCCT
30391 AATCCTAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.40
Consensus pattern (15 bp):
TCCTATTCCTGAAAT
Found at i:31962 original size:25 final size:25
Alignment explanation
Indices: 31928--31978 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
31918 AGTGTTAAAG
31928 TAAGGGGGAGTAATTTCAAACTTGA
1 TAAGGGGGAGTAATTTCAAACTTGA
31953 TAAGGGGGAGTAATTTCAAACTTGA
1 TAAGGGGGAGTAATTTCAAACTTGA
31978 T
1 T
31979 TTCAAAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.29
Consensus pattern (25 bp):
TAAGGGGGAGTAATTTCAAACTTGA
Done.