Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000480.1 Hibiscus syriacus cultivar Beakdansim tig00000910_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: 869251
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:823811 original size:23 final size:23
Alignment explanation
Indices: 823781--823824 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
823771 CGATACCCCC
823781 TTGAAGGGGAACCGATTCCCCTT
1 TTGAAGGGGAACCGATTCCCCTT
*
823804 TTGAAGGGGAATCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
823825 CCTGTAGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (23 bp):
TTGAAGGGGAACCGATTCCCCTT
Found at i:829367 original size:19 final size:19
Alignment explanation
Indices: 829343--829381 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
829333 TTCTCCTTTA
829343 GTGTCTCATCAATCTTATC
1 GTGTCTCATCAATCTTATC
829362 GTGTCTCATCAATCTTATC
1 GTGTCTCATCAATCTTATC
829381 G
1 G
829382 AGGTCTACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.41
Consensus pattern (19 bp):
GTGTCTCATCAATCTTATC
Found at i:830884 original size:65 final size:64
Alignment explanation
Indices: 830811--830991 Score: 187
Period size: 65 Copynumber: 2.8 Consensus size: 64
830801 TTGGACCCTT
*
830811 AGTGCATCGGTGTGCATAAGAGTGCATCGATGCATGACATGCATTCGATGTTTCA-AAATAGC-C
1 AGTGCATCGGTGTGCAT-AGAGTGCATCGATGCATGAAATGCATTCGATGTTTCATAAA-A-CTC
830874 AG
63 AG
* *
830876 AGTGCATCGATGCATGGC-T-G-GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACT
1 AGTGCATCGGTG--T-GCATAGAGTGCATCGATGCATGAAATGCATTCGATG-TTTCATAAAACT
*
830938 CTG
62 CAG
*
830941 AGTGCATC-G-ATGCATAGTATGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGGTGTGCATAG-A-GTGCATCGATGCATGAAATGCATTCGATGTT
830992 CAATTTATTC
Statistics
Matches: 98, Mismatches: 7, Indels: 23
0.77 0.05 0.18
Matches are distributed among these distances:
60 2 0.02
61 2 0.02
62 1 0.01
64 30 0.31
65 56 0.57
66 3 0.03
67 2 0.02
68 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (64 bp):
AGTGCATCGGTGTGCATAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCATAAAACTCAG
Found at i:831039 original size:65 final size:64
Alignment explanation
Indices: 830832--831032 Score: 216
Period size: 65 Copynumber: 3.1 Consensus size: 64
830822 GTGCATAAGA
* * * *
830832 GTGCATCGATGCATGACATGCATTCGATGTTTCAAAATAGCCA-GAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTC-AATTAACCATGAGTGCATCGATGCATGGTTG
* * *
830896 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACTC-TGAGTGCATCGATGCATAGT
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAT-TAAC-CATGAGTGCATCGATGCATGGT
830959 AT-
63 -TG
*
830961 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTA-ACCATGAGTGCATCGATGCATGG-T
831024 TG
63 TG
831026 GTGCATC
1 GTGCATC
831033 AGTGCATCAC
Statistics
Matches: 115, Mismatches: 11, Indels: 21
0.78 0.07 0.14
Matches are distributed among these distances:
63 4 0.03
64 48 0.42
65 62 0.54
66 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAACCATGAGTGCATCGATGCATGGTTG
Found at i:839281 original size:33 final size:33
Alignment explanation
Indices: 839244--839306 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
839234 AAATGAAAAT
*
839244 GGATTTTGAA-AATCAAAATGAAATCTTGAAGAA
1 GGATTTAGAACAATCAAAATGAAAT-TTGAAGAA
**
839277 GGATTTAGAACTCTCAAAATGAAATTTGAA
1 GGATTTAGAACAATCAAAATGAAATTTGAA
839307 AGTATTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 14 0.54
34 12 0.46
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (33 bp):
GGATTTAGAACAATCAAAATGAAATTTGAAGAA
Found at i:843297 original size:8 final size:8
Alignment explanation
Indices: 843284--843308 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
843274 GGCAAGAACA
843284 CCCAAAAC
1 CCCAAAAC
843292 CCCAAAAC
1 CCCAAAAC
843300 CCCAAAAC
1 CCCAAAAC
843308 C
1 C
843309 ATTCCGCCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (8 bp):
CCCAAAAC
Found at i:847909 original size:49 final size:48
Alignment explanation
Indices: 847797--847918 Score: 127
Period size: 49 Copynumber: 2.5 Consensus size: 48
847787 GTTGACGATA
* * *
847797 TTCACTTTCGTTGTGCTTGCCTTCTATGGTTGGTTTGTTTGCCTTCACC
1 TTCA-TTTCCTTGTGCTTGCCTTCTATGGTTGGTTTGTTTGCATTCAAC
* * * * *
847846 TTCACTTCCTTTGTGTTTGTCTTCTATGGTTGGTTTGTTTTCATTCATAT
1 TTCATTTCC-TTGTGCTTGCCTTCTATGGTTGGTTTGTTTGCATTCA-AC
**
847896 TTGTTTTCCTTGTGCTTGCCTTC
1 TTCATTTCCTTGTGCTTGCCTTC
847919 ATTTATCTGA
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
48 3 0.05
49 49 0.84
50 6 0.10
ACGTcount: A:0.07, C:0.21, G:0.18, T:0.54
Consensus pattern (48 bp):
TTCATTTCCTTGTGCTTGCCTTCTATGGTTGGTTTGTTTGCATTCAAC
Found at i:851461 original size:63 final size:63
Alignment explanation
Indices: 851362--851567 Score: 394
Period size: 63 Copynumber: 3.3 Consensus size: 63
851352 CGTATAATTG
* *
851362 ATTGGGTTTATAAACCTTGCTAAAGGGGTTTCGAAACTATAAGTGATTTTTTGAAACTGTCTC
1 ATTGGGTTTCTAAACCCTGCTAAAGGGGTTTCGAAACTATAAGTGATTTTTTGAAACTGTCTC
851425 ATTGGGTTTCTAAACCCTGCTAAAGGGGTTTCGAAACTATAAGTGATTTTTTGAAACTGTCTC
1 ATTGGGTTTCTAAACCCTGCTAAAGGGGTTTCGAAACTATAAGTGATTTTTTGAAACTGTCTC
851488 ATTGGGTTTCTAAACCCTGCTAAAGGGGTTTCGAAACTATAAGTGATTTTTTGAAACTGTCTC
1 ATTGGGTTTCTAAACCCTGCTAAAGGGGTTTCGAAACTATAAGTGATTTTTTGAAACTGTCTC
851551 ATTGGGTTTCTAAACCC
1 ATTGGGTTTCTAAACCC
851568 CCAAAAAACT
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 141 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (63 bp):
ATTGGGTTTCTAAACCCTGCTAAAGGGGTTTCGAAACTATAAGTGATTTTTTGAAACTGTCTC
Found at i:855951 original size:17 final size:18
Alignment explanation
Indices: 855917--855951 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
855907 CTAGTAATCC
* *
855917 TATTTCCTGGTAATTTTT
1 TATTCCCTGATAATTTTT
855935 TATTCCCTGATAATTTT
1 TATTCCCTGATAATTTT
855952 ACATTCCGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.14, G:0.09, T:0.57
Consensus pattern (18 bp):
TATTCCCTGATAATTTTT
Found at i:859564 original size:30 final size:29
Alignment explanation
Indices: 859493--859560 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
859483 TGTATGATTT
*
859493 TGAAAGAAAATAAAGTTTAAGTGATAAAA
1 TGAAACAAAATAAAGTTTAAGTGATAAAA
859522 TGAAACAAAATAAAGTTTAAGTGATAAAA
1 TGAAACAAAATAAAGTTTAAGTGATAAAA
859551 TGAAACAAAA
1 TGAAACAAAA
859561 ATAACAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.60, C:0.03, G:0.15, T:0.22
Consensus pattern (29 bp):
TGAAACAAAATAAAGTTTAAGTGATAAAA
Found at i:862626 original size:15 final size:15
Alignment explanation
Indices: 862608--862638 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
862598 ATGAGCAGAA
862608 CGTAAAGGGGAATTT
1 CGTAAAGGGGAATTT
862623 CGTAAAGGGGAATTT
1 CGTAAAGGGGAATTT
862638 C
1 C
862639 TTTTTCACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.26
Consensus pattern (15 bp):
CGTAAAGGGGAATTT
Found at i:865934 original size:18 final size:18
Alignment explanation
Indices: 865911--865947 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
865901 CAAAGAGTTT
865911 CGGTTGAGATTGTTTTTG
1 CGGTTGAGATTGTTTTTG
865929 CGGTTGAGATTGTTTTTG
1 CGGTTGAGATTGTTTTTG
865947 C
1 C
865948 ATCTAGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.08, G:0.32, T:0.49
Consensus pattern (18 bp):
CGGTTGAGATTGTTTTTG
Done.