Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007922.1 Hibiscus syriacus cultivar Beakdansim tig00110327_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: 874983
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:842576 original size:66 final size:67
Alignment explanation
Indices: 842438--842587 Score: 234
Period size: 66 Copynumber: 2.3 Consensus size: 67
842428 ATCCATTCAA
842438 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTATAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTATAGGGGAATCGATACCCCCA
842503 GG
66 GG
* *
842505 GGGGAATCGATACCCCCTCAACGAATATGAA-TTCCAGAATGCTAGT-GGGGAATCGATA-CCCC
1 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTA-TAGGGGAATCGATACCCCC
842567 AGGG
65 A-GG
*
842571 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
842588 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
65 5 0.06
66 41 0.53
67 31 0.40
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.17
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTATAGGGGAATCGATACCCCCA
GG
Found at i:843260 original size:149 final size:149
Alignment explanation
Indices: 843069--843372 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
843059 GGGTAGAGGG
843069 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
843134 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
843199 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
843218 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
843283 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
843348 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
843367 TCTACG
1 TCTACG
843373 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:843395 original size:23 final size:23
Alignment explanation
Indices: 843351--843395 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
843341 ATCATTATAT
*
843351 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
843374 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
843396 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:846480 original size:36 final size:36
Alignment explanation
Indices: 846420--846502 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 36
846410 TCCCATTATG
* *
846420 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATCTACCAAACTTTG-AAAACC
*
846456 ATTTTTCAAAGAAACATTTA-CAAACTTTGAAAACC
1 ATTTTTCAAAGAAACATCTACCAAACTTTGAAAACC
846491 ATTTTTTCAAAG
1 A-TTTTTCAAAG
846503 TTGGTTGTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 6 0.14
36 26 0.62
37 10 0.24
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATCTACCAAACTTTGAAAACC
Found at i:846936 original size:19 final size:19
Alignment explanation
Indices: 846912--846949 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
846902 TGAATGAATG
*
846912 TCTAAATAAACGAGTCCAA
1 TCTAAATAAACGAATCCAA
846931 TCTAAATAAACGAATCCAA
1 TCTAAATAAACGAATCCAA
846950 CCACTTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.21, G:0.08, T:0.21
Consensus pattern (19 bp):
TCTAAATAAACGAATCCAA
Found at i:850396 original size:10 final size:9
Alignment explanation
Indices: 850361--850459 Score: 81
Period size: 10 Copynumber: 10.3 Consensus size: 9
850351 GCTGCTGGAA
*
850361 ACCGGTTTA
1 ACCGGTTTG
*
850370 ACCGGTTTTCA
1 ACCGG-TTT-G
850381 ACCGGTTCTG
1 ACCGGTT-TG
850391 ACCGGTTTG
1 ACCGGTTTG
*
850400 ACCGGTTTCA
1 ACCGGTTT-G
*
850410 ACCGGTTCG
1 ACCGGTTTG
*
850419 AACCAGTTTG
1 -ACCGGTTTG
*
850429 ACCGGTCTG
1 ACCGGTTTG
850438 AACCGGTTTG
1 -ACCGGTTTG
*
850448 ACCGGTCTG
1 ACCGGTTTG
850457 ACC
1 ACC
850460 CGACCCGACC
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
9 33 0.45
10 34 0.46
11 7 0.09
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:850405 original size:19 final size:19
Alignment explanation
Indices: 850362--850459 Score: 78
Period size: 19 Copynumber: 5.1 Consensus size: 19
850352 CTGCTGGAAA
* * *
850362 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
850382 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
850401 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
*
850421 CCAGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
850440 CCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
850458 CC
1 CC
850460 CGACCCGACC
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.09
19 39 0.58
20 14 0.21
21 8 0.12
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.29
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:850427 original size:29 final size:28
Alignment explanation
Indices: 850361--850459 Score: 117
Period size: 29 Copynumber: 3.4 Consensus size: 28
850351 GCTGCTGGAA
*
850361 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTT-TG
*
850391 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTTG
* * *
850419 AACCAGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTTG
*
850448 ACCGGTCTGACC
1 ACCGGTTTGACC
850460 CGACCCGACC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 11 0.18
29 36 0.60
30 13 0.22
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.28
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTTG
Found at i:850477 original size:17 final size:17
Alignment explanation
Indices: 850455--850510 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 17
850445 TTGACCGGTC
850455 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
850472 T-----GACCCGACCGT
1 TGACCCGACCCGACCGT
850484 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
850501 TGACCCGACC
1 TGACCCGACC
850511 TGATCCGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 12 0.35
17 22 0.65
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:850489 original size:29 final size:29
Alignment explanation
Indices: 850455--850510 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
850445 TTGACCGGTC
850455 TGACCCGACCCGACCGTTGACCCGACCGT
1 TGACCCGACCCGACCGTTGACCCGACCGT
850484 TGACCCGACCCGACCGTTGACCCGACC
1 TGACCCGACCCGACCGTTGACCCGACC
850511 TGATCCGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.12
Consensus pattern (29 bp):
TGACCCGACCCGACCGTTGACCCGACCGT
Found at i:850498 original size:22 final size:22
Alignment explanation
Indices: 850485--850527 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
850475 CCCGACCGTT
850485 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
* *
850507 GACCTGATCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
850528 GTTGACCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.44, G:0.23, T:0.14
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:850510 original size:12 final size:12
Alignment explanation
Indices: 850461--850493 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
850451 GGTCTGACCC
850461 GACCCGACCGTT
1 GACCCGACCGTT
850473 GACCCGACCGTT
1 GACCCGACCGTT
850485 GACCCGACC
1 GACCCGACC
850494 CGACCGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.12
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:850527 original size:29 final size:28
Alignment explanation
Indices: 850455--850534 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 28
850445 TTGACCGGTC
850455 TGACCCGACCCGACCGTTGACCCGACCG
1 TGACCCGACCCGACCGTTGACCCGACCG
850483 TTGACCCGACCCGACCGTTGACCCGACC-
1 -TGACCCGACCCGACCGTTGACCCGACCG
* *
850511 TGATCCGACCGTTGACCGTTGACC
1 TGACCCGACC--CGACCGTTGACC
850535 GTTGACTTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
27 9 0.19
29 38 0.81
ACGTcount: A:0.17, C:0.42, G:0.24, T:0.16
Consensus pattern (28 bp):
TGACCCGACCCGACCGTTGACCCGACCG
Found at i:857756 original size:9 final size:9
Alignment explanation
Indices: 857734--857802 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
857724 TCGGTTTACA
857734 ACCGGTTCTG
1 ACCGGTT-TG
857744 ACCGGTTTG
1 ACCGGTTTG
*
857753 ACCGGTTTCA
1 ACCGGTTT-G
*
857763 ACCGGTTCG
1 ACCGGTTTG
*
857772 AACCAGTTTG
1 -ACCGGTTTG
857782 ACCGGTTTG
1 ACCGGTTTG
*
857791 ACCGGTCTG
1 ACCGGTTTG
857800 ACC
1 ACC
857803 CGACCCGACC
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
9 29 0.58
10 21 0.42
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:857758 original size:19 final size:18
Alignment explanation
Indices: 857734--857802 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
857724 TCGGTTTACA
857734 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTTTG
* *
857753 ACCGGTTTCAACCGGTTCG
1 ACCGGTTT-GACCGGTTTG
*
857772 AACCAGTTTGACCGGTTTG
1 -ACCGGTTTGACCGGTTTG
*
857791 ACCGGTCTGACC
1 ACCGGTTTGACC
857803 CGACCCGACC
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
18 11 0.27
19 23 0.56
20 7 0.17
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.28
Consensus pattern (18 bp):
ACCGGTTTGACCGGTTTG
Found at i:857780 original size:29 final size:30
Alignment explanation
Indices: 857725--857789 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
857715 CCGGTTTAAT
*
857725 CGGTTTACAACCGGTTCTGACCGGTTTGAC
1 CGGTTTACAACCGGTTCTGACCAGTTTGAC
857755 CGGTTT-CAACCGGTTC-GAACCAGTTTGAC
1 CGGTTTACAACCGGTTCTG-ACCAGTTTGAC
857784 CGGTTT
1 CGGTTT
857790 GACCGGTCTG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 1 0.03
29 26 0.79
30 6 0.18
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (30 bp):
CGGTTTACAACCGGTTCTGACCAGTTTGAC
Found at i:857863 original size:22 final size:22
Alignment explanation
Indices: 857799--857863 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
857789 TGACCGGTCT
*
857799 GACCCGACCCGACCGTTGACAC
1 GACCCGACCCGACCGTTGACCC
*
857821 GACCCGACCCAACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
* *
857843 GACCCGATCTGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
857864 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.22, C:0.45, G:0.22, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:857864 original size:7 final size:7
Alignment explanation
Indices: 857852--857876 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
857842 CGACCCGATC
857852 TGACCGT
1 TGACCGT
857859 TGACCGT
1 TGACCGT
857866 TGACCGT
1 TGACCGT
857873 TGAC
1 TGAC
857877 TTTCTTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (7 bp):
TGACCGT
Found at i:864606 original size:26 final size:26
Alignment explanation
Indices: 864577--864627 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
864567 TCACAGATAT
*
864577 ATCATAT-CATGCACATCATATCACAA
1 ATCATATACATACACAT-ATATCACAA
*
864603 ATCATATACATATACATATATCACA
1 ATCATATACATACACATATATCACA
864628 TACATTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (26 bp):
ATCATATACATACACATATATCACAA
Found at i:864630 original size:19 final size:19
Alignment explanation
Indices: 864573--864632 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
864563 CCTATCACAG
864573 ATATATCATATCATGCACAT-C
1 ATATA-CATAT-AT-CACATAC
*
864594 ATATCACA-A-ATCATATAC
1 ATAT-ACATATATCACATAC
864612 ATATACATATATCACATAC
1 ATATACATATATCACATAC
864631 AT
1 AT
864633 TGTTCTCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
17 7 0.21
18 8 0.24
19 10 0.30
20 1 0.03
21 6 0.18
22 1 0.03
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.32
Consensus pattern (19 bp):
ATATACATATATCACATAC
Found at i:864809 original size:23 final size:23
Alignment explanation
Indices: 864783--864827 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
864773 CACCACAGCT
*
864783 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
864806 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
864828 ATATATGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:866668 original size:21 final size:21
Alignment explanation
Indices: 866644--866686 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
866634 TGTTGTTCGT
* *
866644 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
866665 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
866686 T
1 T
866687 GGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Done.