Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008018.1 Hibiscus syriacus cultivar Beakdansim tig00110485_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: 927418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:884238 original size:31 final size:31
Alignment explanation
Indices: 884200--884415 Score: 389
Period size: 31 Copynumber: 7.0 Consensus size: 31
884190 GGGTCGAGGG
884200 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
884231 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
884262 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
884293 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
884324 TTACCTATGTTCTTCGGGACATATGGAATGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
884355 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
884386 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
884416 GTCCTTCGGG
Statistics
Matches: 180, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
31 179 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:888086 original size:16 final size:16
Alignment explanation
Indices: 888047--888113 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 16
888037 GACTGATACA
* *
888047 AATTTGAACAAAAAAT
1 AATTTGAACCAAAAGT
** *
888063 AACATGAAGCAAAAGT
1 AATTTGAACCAAAAGT
*
888079 AATTTGAACCGAAAGT
1 AATTTGAACCAAAAGT
* *
888095 AACTTGAATCAAAAGT
1 AATTTGAACCAAAAGT
888111 AAT
1 AAT
888114 ATGTTGAGTT
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.22
Consensus pattern (16 bp):
AATTTGAACCAAAAGT
Found at i:888108 original size:32 final size:32
Alignment explanation
Indices: 888047--888113 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
888037 GACTGATACA
888047 AATTTGAACAAAAAATAACATGAAGCAAAAGT
1 AATTTGAACAAAAAATAACATGAAGCAAAAGT
** * * *
888079 AATTTGAACCGAAAGTAACTTGAATCAAAAGT
1 AATTTGAACAAAAAATAACATGAAGCAAAAGT
888111 AAT
1 AAT
888114 ATGTTGAGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.22
Consensus pattern (32 bp):
AATTTGAACAAAAAATAACATGAAGCAAAAGT
Found at i:890434 original size:24 final size:24
Alignment explanation
Indices: 890390--890439 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
890380 ATAAAGAACC
*
890390 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
890414 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
890438 AA
1 AA
890440 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:897151 original size:21 final size:21
Alignment explanation
Indices: 897121--897164 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
897111 AGACGAGCTA
* *
897121 TGGCTTTGAAGTAAGGCGCCT
1 TGGCTATGAAGTAAAGCGCCT
*
897142 TGGCTATGAAGTAAAGCTCCT
1 TGGCTATGAAGTAAAGCGCCT
897163 TG
1 TG
897165 ATTCTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (21 bp):
TGGCTATGAAGTAAAGCGCCT
Found at i:899493 original size:24 final size:24
Alignment explanation
Indices: 899449--899498 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
899439 ATAAAGAACC
*
899449 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
899473 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
899497 AA
1 AA
899499 TCAACCATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:902327 original size:19 final size:19
Alignment explanation
Indices: 902303--902344 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
902293 AAAACCAGAA
*
902303 CCCTAGGGGGTATCGATTC
1 CCCTAGGGGGAATCGATTC
*
902322 CCCTAGGGGGAATCGGTTC
1 CCCTAGGGGGAATCGATTC
902341 CCCT
1 CCCT
902345 TTAAAGGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.24
Consensus pattern (19 bp):
CCCTAGGGGGAATCGATTC
Found at i:902356 original size:23 final size:22
Alignment explanation
Indices: 902326--902387 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
902316 CGATTCCCCT
902326 AGGGGGAATCGGTTCCCCTTTAA
1 AGGGGGAATCGGTTCCCCTTT-A
* *
902349 AGGGGGAATCAGTTCACCTTTA
1 AGGGGGAATCGGTTCCCCTTTA
* *
902371 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
902388 TCTGCCCTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.26
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCTTTA
Found at i:906238 original size:22 final size:21
Alignment explanation
Indices: 906196--906235 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
906186 AAGTTTATTT
*
906196 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
906217 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
906236 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:917780 original size:77 final size:77
Alignment explanation
Indices: 917665--917817 Score: 220
Period size: 77 Copynumber: 2.0 Consensus size: 77
917655 ATATAGTAAG
* *
917665 TAAACATTAAAAGAATAATTCTGATTACAACTCTTTTAATTGATATTTAATTTGGAA-TAATTAA
1 TAAACATTAAAAGAATAATTCGGATTACAACTCTTTTAATGGATATTTAATTT-GAATTAATTAA
917729 ATAAGAGTTTAAA
65 ATAAGAGTTTAAA
** * *
917742 TAAACATTAAAGAGCGTAATTCGGATTATAAGTC-TTTAATGGATATTTAATTTGAATTAATTAA
1 TAAACATTAAA-AGAATAATTCGGATTACAACTCTTTTAATGGATATTTAATTTGAATTAATTAA
917806 ATAAGAGTTTAA
65 ATAAGAGTTTAA
917818 TTAATTCGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
76 3 0.04
77 48 0.71
78 17 0.25
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.39
Consensus pattern (77 bp):
TAAACATTAAAAGAATAATTCGGATTACAACTCTTTTAATGGATATTTAATTTGAATTAATTAAA
TAAGAGTTTAAA
Found at i:918476 original size:16 final size:16
Alignment explanation
Indices: 918437--918503 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 16
918427 GACTGATACA
*
918437 AATTTGAACCAAAAAT
1 AATTTGAACCAAAAGT
** *
918453 AACATGAAGCAAAAGT
1 AATTTGAACCAAAAGT
*
918469 AATTTGAACCGAAAGT
1 AATTTGAACCAAAAGT
* **
918485 AACTTGAATAAAAAGT
1 AATTTGAACCAAAAGT
918501 AAT
1 AAT
918504 CTAAATCGAA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.22
Consensus pattern (16 bp):
AATTTGAACCAAAAGT
Found at i:918478 original size:32 final size:32
Alignment explanation
Indices: 918437--918503 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
918427 GACTGATACA
*
918437 AATTTGAACCAAAAATAACATGAAGCAAAAGT
1 AATTTGAACCAAAAATAACATGAAGAAAAAGT
* * * *
918469 AATTTGAACCGAAAGTAACTTGAATAAAAAGT
1 AATTTGAACCAAAAATAACATGAAGAAAAAGT
918501 AAT
1 AAT
918504 CTAAATCGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.22
Consensus pattern (32 bp):
AATTTGAACCAAAAATAACATGAAGAAAAAGT
Found at i:918514 original size:32 final size:32
Alignment explanation
Indices: 918463--918534 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
918453 AACATGAAGC
* * * *
918463 AAAAGTAATTTGAACCGAAAGTAACTTGAATA
1 AAAAGTAATCTAAACCGAAAGTAACCTGAACA
*
918495 AAAAGTAATCTAAATCGAAAGTAACCTGAACA
1 AAAAGTAATCTAAACCGAAAGTAACCTGAACA
918527 AAAAGTAA
1 AAAAGTAA
918535 CCTGACACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.21
Consensus pattern (32 bp):
AAAAGTAATCTAAACCGAAAGTAACCTGAACA
Found at i:918531 original size:16 final size:17
Alignment explanation
Indices: 918441--918539 Score: 57
Period size: 16 Copynumber: 6.2 Consensus size: 17
918431 GATACAAATT
*
918441 TGAACCAAAAA-TAACA
1 TGAACCAAAAAGTAACC
* **
918457 TGAAGC-AAAAGTAATT
1 TGAACCAAAAAGTAACC
* *
918473 TGAACC-GAAAGTAACT
1 TGAACCAAAAAGTAACC
* *
918489 TGAA-TAAAAAGTAATC
1 TGAACCAAAAAGTAACC
* * *
918505 TAAATC-GAAAGTAACC
1 TGAACCAAAAAGTAACC
918521 TGAA-CAAAAAGTAACC
1 TGAACCAAAAAGTAACC
918537 TGA
1 TGA
918540 CACATGTCAA
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
15 5 0.08
16 58 0.92
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.19
Consensus pattern (17 bp):
TGAACCAAAAAGTAACC
Found at i:924877 original size:34 final size:35
Alignment explanation
Indices: 924807--924881 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
924797 TATAGCTAAA
*
924807 AAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
924842 AAAATCGTATTTATTCGAATTTTGCC-AAAATAGC
1 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
924876 AAAATC
1 AAAATC
924882 CCGAAAATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 14 0.36
35 25 0.64
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (35 bp):
AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Done.