Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002966.1 Hibiscus syriacus cultivar Beakdansim tig00006135_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: 74684
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:769 original size:24 final size:23
Alignment explanation
Indices: 735--780 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
725 TCTGAAAATC
*
735 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCG-ATATTGACCAAT
*
759 ATCAAAGTCCGATATTGACCAA
1 ATCAAAATCCGATATTGACCAA
781 GACCAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (23 bp):
ATCAAAATCCGATATTGACCAAT
Found at i:1477 original size:20 final size:20
Alignment explanation
Indices: 1449--1697 Score: 259
Period size: 20 Copynumber: 12.5 Consensus size: 20
1439 AAATTTCAGT
* *
1449 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1469 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1489 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1509 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1529 GTTGCGA-TTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1548 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
1568 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1588 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1608 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1628 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
1648 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
1668 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
1688 GTTGCGATTT
1 GTTGCGATTT
1698 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 28, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.09
20 180 0.91
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:1555 original size:79 final size:79
Alignment explanation
Indices: 1454--1658 Score: 272
Period size: 79 Copynumber: 2.6 Consensus size: 79
1444 TCAGTGTTGT
* * *
1454 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTCTCGTTGCGATTT
1 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATACGCGTTGCGATAT
1519 ACGGATTATCG-TTGC
66 ACGGA-TA-CGATTGC
*
1534 GA-TTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATAT
1 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATACGCGTTGCGATAT
1598 ACGGATACGCATTGC
66 ACGGATACG-ATTGC
* * * * *
1613 GATTTACGGATACGCGTTGCGATATACGGA-TACACGTTGCGATTTA
1 GATTTACAGATTCTCGTTGCGATTTACGGATTA-TCGTTGCGATTTA
1659 TGTGTTCGCG
Statistics
Matches: 112, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
77 2 0.02
78 2 0.02
79 71 0.63
80 37 0.33
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (79 bp):
GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATACGCGTTGCGATAT
ACGGATACGATTGC
Found at i:2266 original size:25 final size:25
Alignment explanation
Indices: 2237--2287 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2227 TCTCCCTCAG
2237 ATTCCTTAAGACGGAACAAAAAATA
1 ATTCCTTAAGACGGAACAAAAAATA
2262 ATTCCTTAAGACGGAACAAAAAATA
1 ATTCCTTAAGACGGAACAAAAAATA
2287 A
1 A
2288 GTACAGAAGT
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:0.53, C:0.16, G:0.12, T:0.20
Consensus pattern (25 bp):
ATTCCTTAAGACGGAACAAAAAATA
Found at i:5528 original size:2 final size:2
Alignment explanation
Indices: 5521--5545 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5511 CATTTAAAAT
5521 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5546 TTATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5983 original size:60 final size:59
Alignment explanation
Indices: 5849--6027 Score: 159
Period size: 60 Copynumber: 3.0 Consensus size: 59
5839 TATCCTCAAG
* * * * * **
5849 TATGGCCCTTATTTTAAATTGATTCC-TAAACTTTTAAATATTTTGATTTCATCCCTAAAC
1 TATGACCCTTATTCTAAATTG-GTCCTTAAACTTTTTAACATTTCAATTTCATCCC-AAAC
* ** * *
5909 TACGACTATCATTCTAAATCGGTCCTTAAACTTTTTAACATTTCAATTTCATCTCCAAAC
1 TATGACCCTTATTCTAAATTGGTCCTTAAACTTTTTAACATTTCAATTTCATC-CCAAAC
*
5969 TATGACCCTTATTCTAAATTGGT--TACAAACTTTTTGAACA-TTCTAATTTCATCCCAAAC
1 TATGACCCTTATTCTAAATTGGTCCT-TAAACTTTTT-AACATTTC-AATTTCATCCCAAAC
6028 CATACGTACA
Statistics
Matches: 96, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
58 1 0.01
59 21 0.22
60 72 0.75
61 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (59 bp):
TATGACCCTTATTCTAAATTGGTCCTTAAACTTTTTAACATTTCAATTTCATCCCAAAC
Found at i:6251 original size:60 final size:60
Alignment explanation
Indices: 6152--6275 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
6142 GGATGAGTTT
* *
6152 GGGATGAAATTAGAATATTCAAATGTTTAGGGACTAATTT-AGAAAGAGGGTCATAGTATG
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAG-AAGAGGGTCATAGTATG
* * * * *
6212 GGGATGAAATTAGAATGTTTAAAAGTTTAAGGA-TCAATTTAAGACGAGGGTTATAGTTTG
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACT-AATTTAAGAAGAGGGTCATAGTATG
6272 GGGA
1 GGGA
6276 CAGTTAACCG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 1 0.02
60 52 0.95
61 2 0.04
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (60 bp):
GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAGAAGAGGGTCATAGTATG
Found at i:20058 original size:34 final size:34
Alignment explanation
Indices: 20015--20083 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
20005 ACATATGTAA
20015 TAATTGGCCAAACCGAGGAAAGATCTAAACTCAC
1 TAATTGGCCAAACCGAGGAAAGATCTAAACTCAC
*
20049 TAATTGGCCAAACCGAGGAAAGATCTAAGCTCAC
1 TAATTGGCCAAACCGAGGAAAGATCTAAACTCAC
20083 T
1 T
20084 TCAGTGAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (34 bp):
TAATTGGCCAAACCGAGGAAAGATCTAAACTCAC
Found at i:26198 original size:85 final size:85
Alignment explanation
Indices: 26055--26228 Score: 285
Period size: 85 Copynumber: 2.0 Consensus size: 85
26045 CAAGAAATAA
** * * *
26055 CAAGTGCTCGGTATCGCAACAAGGCAAGTCAAATGACATGAGTCCTCATAATGATGGTCTGTCTC
1 CAAGTGCTCGGTATAACAACAAGGCAAGGCAAACGACATGAGTCCTCATAATGATGGTCCGTCTC
26120 GTCGAATATCTCCTCCTGGC
66 GTCGAATATCTCCTCCTGGC
* *
26140 CAAGTGCTCGGTATAACAACAAGGCAAGGCAAACGTCATGAGTCCTCGTAATGATGGTCCGTCTC
1 CAAGTGCTCGGTATAACAACAAGGCAAGGCAAACGACATGAGTCCTCATAATGATGGTCCGTCTC
26205 GTCGAATATCTCCTCCTGGC
66 GTCGAATATCTCCTCCTGGC
26225 CAAG
1 CAAG
26229 GTCACATAAG
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24
Consensus pattern (85 bp):
CAAGTGCTCGGTATAACAACAAGGCAAGGCAAACGACATGAGTCCTCATAATGATGGTCCGTCTC
GTCGAATATCTCCTCCTGGC
Found at i:31152 original size:18 final size:19
Alignment explanation
Indices: 31117--31155 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
31107 AATAAGAAGT
31117 ATAATTTGATTAAAAGTAG
1 ATAATTTGATTAAAAGTAG
*
31136 ATAATTTTATT-AAAGTAG
1 ATAATTTGATTAAAAGTAG
31154 AT
1 AT
31156 TTCTACCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (19 bp):
ATAATTTGATTAAAAGTAG
Found at i:47332 original size:2 final size:2
Alignment explanation
Indices: 47325--47364 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
47315 AACGGTTTCT
47325 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
47365 ATTTGTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:54035 original size:6 final size:6
Alignment explanation
Indices: 54024--54083 Score: 120
Period size: 6 Copynumber: 10.0 Consensus size: 6
54014 TGTATTAACC
54024 ACCCTG ACCCTG ACCCTG ACCCTG ACCCTG ACCCTG ACCCTG ACCCTG
1 ACCCTG ACCCTG ACCCTG ACCCTG ACCCTG ACCCTG ACCCTG ACCCTG
54072 ACCCTG ACCCTG
1 ACCCTG ACCCTG
54084 CTCAAGATAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.17
Consensus pattern (6 bp):
ACCCTG
Found at i:74298 original size:167 final size:168
Alignment explanation
Indices: 74013--74347 Score: 577
Period size: 167 Copynumber: 2.0 Consensus size: 168
74003 AATACATTAT
74013 CAATGTAATTCATCATTATTTTAAAACTTTGGCATGTAAATGTGATATCCGATGCATCACAGCAA
1 CAATGTAATTCATCATTATTTTAAAACTTTGGCATGTAAATGTGATATCCGATGCATCACAGCAA
*
74078 TTAAAGATGAATGAAAACCTAATCTCGTTTGCAATAAAAACCATGGCTGTAGCCTGTACTGATTC
66 TTAAAGATGAATGAAAACCTAATCTCATTTGCAATAAAAACCATGGCTGTAGCCTGTACTGATTC
* *
74143 TAACATTGGGTCCGAA-AGCCAAGTTTCA-CATGAAGAAC
131 CAACATTGGGTCC-AAGAGCCAAG-TTCAGAATGAAGAAC
*
74181 CAATGTAATTCATCATTA-TTTAAAACTTTGGCATGTAAATGTGATATCTGATGCATCACAGCAA
1 CAATGTAATTCATCATTATTTTAAAACTTTGGCATGTAAATGTGATATCCGATGCATCACAGCAA
* *
74245 TTAAAGATGAATGAAAACCTAATCTCATTTGCAATAAAACCCATGGTTGTAGCCTGTACTGATTC
66 TTAAAGATGAATGAAAACCTAATCTCATTTGCAATAAAAACCATGGCTGTAGCCTGTACTGATTC
74310 CAACATTGGGTCCAAGAGCCAAGTTCAGAATGAAGAAC
131 CAACATTGGGTCCAAGAGCCAAGTTCAGAATGAAGAAC
74348 TGCTATCTAT
Statistics
Matches: 159, Mismatches: 6, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
166 6 0.04
167 135 0.85
168 18 0.11
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (168 bp):
CAATGTAATTCATCATTATTTTAAAACTTTGGCATGTAAATGTGATATCCGATGCATCACAGCAA
TTAAAGATGAATGAAAACCTAATCTCATTTGCAATAAAAACCATGGCTGTAGCCTGTACTGATTC
CAACATTGGGTCCAAGAGCCAAGTTCAGAATGAAGAAC
Done.