Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003844.1 Hibiscus syriacus cultivar Beakdansim tig00008242_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: 412420
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:356439 original size:25 final size:25
Alignment explanation
Indices: 356386--356445 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
356376 CTTTTCTTTG
*
356386 CTTTTTC-TTCTTTTGAGTGCTGGA
1 CTTTTTCTTTCTTTTGAGTGCTGCA
* *
356410 TTTTTTCTTTCTTTTGAGTGCTTCA
1 CTTTTTCTTTCTTTTGAGTGCTGCA
356435 CTTTTT-TTTCT
1 CTTTTTCTTTCT
356446 GATTTTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.07, C:0.17, G:0.13, T:0.63
Consensus pattern (25 bp):
CTTTTTCTTTCTTTTGAGTGCTGCA
Found at i:367580 original size:35 final size:36
Alignment explanation
Indices: 367511--367590 Score: 135
Period size: 35 Copynumber: 2.2 Consensus size: 36
367501 TACTATCTGT
**
367511 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
367547 TCATCACCATAGTCCATCACCA-TATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
367582 TCATCACCA
1 TCATCACCA
367591 AATTCTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 22 0.52
36 20 0.48
ACGTcount: A:0.30, C:0.39, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACGCCTATA
Found at i:369728 original size:21 final size:22
Alignment explanation
Indices: 369678--369729 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
369668 GGAAAGGAGC
369678 CAAAGGATGTGACTCTTCAAGAAT
1 CAAAGGATGTGACTCTTC-A-AAT
* *
369702 CTAAGGCTGTGACTCTTC-AAT
1 CAAAGGATGTGACTCTTCAAAT
369723 CAAAGGA
1 CAAAGGA
369730 CATGATCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 8 0.33
24 16 0.67
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (22 bp):
CAAAGGATGTGACTCTTCAAAT
Found at i:371723 original size:35 final size:36
Alignment explanation
Indices: 371654--371731 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
371644 TACTATCTGT
** *
371654 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACACCTATA
371690 TCATCACCATAGTCCATCACCA-TATCACACCTATA
1 TCATCACCATAGTCCATCACCATTATCACACCTATA
371725 TCATCAC
1 TCATCAC
371732 TAAATTCCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 19 0.49
36 20 0.51
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.28
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACACCTATA
Found at i:371727 original size:11 final size:11
Alignment explanation
Indices: 371654--371731 Score: 61
Period size: 11 Copynumber: 6.6 Consensus size: 11
371644 TACTATCTGT
*
371654 TCATCACCATCT
1 TCATCACCAT-A
371666 TCCATCACCATTA
1 T-CATCACCA-TA
*
371679 TCA-CGCCTATA
1 TCATCACC-ATA
371690 TCATCACCATA
1 TCATCACCATA
371701 GTCCATCACCATA
1 -T-CATCACCATA
371714 TCA-CACCTATA
1 TCATCACC-ATA
371725 TCATCAC
1 TCATCAC
371732 TAAATTCCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
10 4 0.07
11 19 0.35
12 12 0.22
13 19 0.35
14 1 0.02
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.28
Consensus pattern (11 bp):
TCATCACCATA
Found at i:371741 original size:35 final size:36
Alignment explanation
Indices: 371654--371741 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 36
371644 TACTATCTGT
** *
371654 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCAAATTCCATCACCATTATCACACCTATA
* *
371690 TCATCACCATAGTCCATCACCA-TATCACACCTATA
1 TCATCACCAAATTCCATCACCATTATCACACCTATA
*
371725 TCATCACTAAATTCCAT
1 TCATCACCAAATTCCAT
371742 TTCCATTTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 26 0.57
36 20 0.43
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.30
Consensus pattern (36 bp):
TCATCACCAAATTCCATCACCATTATCACACCTATA
Found at i:372987 original size:11 final size:11
Alignment explanation
Indices: 372965--373011 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
372955 TTTGAGGATT
372965 TGGTGATGATA
1 TGGTGATGATA
372976 TAGGTG-TGATA
1 T-GGTGATGATA
372987 TGGTGATGGACTA
1 TGGTGAT-GA-TA
373000 TGGTGATGATA
1 TGGTGATGATA
373011 T
1 T
373012 AGGCGTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 11 0.34
12 8 0.25
13 9 0.28
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:372991 original size:22 final size:24
Alignment explanation
Indices: 372965--373011 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
372955 TTTGAGGATT
372965 TGGTGAT-GA-TATAGGTG-TGATA
1 TGGTGATGGACTAT-GGTGATGATA
372987 TGGTGATGGACTATGGTGATGATA
1 TGGTGATGGACTATGGTGATGATA
373011 T
1 T
373012 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (24 bp):
TGGTGATGGACTATGGTGATGATA
Found at i:373004 original size:35 final size:37
Alignment explanation
Indices: 372965--373044 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
372955 TTTGAGGATT
* *
372965 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
373000 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
373037 TGGTGATG
1 TGGTGATG
373045 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:376870 original size:11 final size:11
Alignment explanation
Indices: 376848--376894 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
376838 TTTGAGAATT
376848 TGGTGATGATA
1 TGGTGATGATA
376859 TAGGTG-TGATA
1 T-GGTGATGATA
376870 TGGTGATGGACTA
1 TGGTGAT-GA-TA
*
376883 TGGTAATGATA
1 TGGTGATGATA
376894 T
1 T
376895 AGGCGTGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
10 4 0.13
11 11 0.35
12 8 0.26
13 8 0.26
ACGTcount: A:0.28, C:0.02, G:0.34, T:0.36
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:376903 original size:35 final size:37
Alignment explanation
Indices: 376848--376923 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 37
376838 TTTGAGAATT
* * *
376848 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTAATGATATAGGCGTGATAATGGAAGATGGACTA
*
376883 TGGTAATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTAATGATATAGGCGTGATAATGGAAGATGGACTA
376920 TGGT
1 TGGT
376924 GATGGAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 19 0.54
36 4 0.11
37 12 0.34
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTAATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:380933 original size:17 final size:18
Alignment explanation
Indices: 380911--380949 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
380901 TTGTTGGAAA
*
380911 TTTCTTTCTTTTTG-GCT
1 TTTCTTTCTTATTGTGCT
380928 TTTC-TTCTTATTGTGCT
1 TTTCTTTCTTATTGTGCT
380945 TTTCT
1 TTTCT
380950 CTTTTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.03, C:0.18, G:0.10, T:0.69
Consensus pattern (18 bp):
TTTCTTTCTTATTGTGCT
Found at i:380952 original size:16 final size:16
Alignment explanation
Indices: 380911--380956 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
380901 TTGTTGGAAA
380911 TTTCTTTCTTTT-TGGCT
1 TTTC-TTCTTTTGT-GCT
380928 TTTCTTCTTATTGTGCT
1 TTTCTTCTT-TTGTGCT
380945 TTTC-TCTTTTGT
1 TTTCTTCTTTTGT
380957 TTTGAACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.15
16 9 0.33
17 13 0.48
18 1 0.04
ACGTcount: A:0.02, C:0.17, G:0.11, T:0.70
Consensus pattern (16 bp):
TTTCTTCTTTTGTGCT
Found at i:381490 original size:28 final size:25
Alignment explanation
Indices: 381429--381488 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
381419 TAGTCCACAT
381429 CTTTATAATATGCACATTATTATTA
1 CTTTATAATATGCACATTATTATTA
381454 CTTTATAATATGCACATTATTATTA
1 CTTTATAATATGCACATTATTATTA
381479 CTTTATAATA
1 CTTTATAATA
381489 ATTCCTATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.48
Consensus pattern (25 bp):
CTTTATAATATGCACATTATTATTA
Found at i:383103 original size:20 final size:22
Alignment explanation
Indices: 383078--383122 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
383068 GTGATTCGGC
*
383078 AAGTACATAAT-TTTTAA-TGA
1 AAGTACATAATGCTTTAATTGA
383098 AAGTACATAATGCTTTAATTGA
1 AAGTACATAATGCTTTAATTGA
383120 AAG
1 AAG
383123 AATGAGTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 5 0.23
22 6 0.27
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (22 bp):
AAGTACATAATGCTTTAATTGA
Found at i:391238 original size:23 final size:23
Alignment explanation
Indices: 391212--391262 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
391202 TTTCAGATTG
391212 CACTCCACTCACACTCGTGTTTA
1 CACTCCACTCACACTCGTGTTTA
*
391235 CACTCCACTCACACTCGTGTTTG
1 CACTCCACTCACACTCGTGTTTA
391258 CACTC
1 CACTC
391263 GGGGATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.20, C:0.41, G:0.10, T:0.29
Consensus pattern (23 bp):
CACTCCACTCACACTCGTGTTTA
Found at i:391747 original size:13 final size:13
Alignment explanation
Indices: 391722--391764 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
391712 TGTAGGAGTC
391722 TTTTCTCTTTTTTG
1 TTTT-TCTTTTTTG
* *
391736 TTTTTGTTTTTTC
1 TTTTTCTTTTTTG
391749 TTTTTCTCTTTTTG
1 TTTTTCT-TTTTTG
391763 TT
1 TT
391765 GCTTTTGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (13 bp):
TTTTTCTTTTTTG
Found at i:392414 original size:35 final size:36
Alignment explanation
Indices: 392368--392479 Score: 190
Period size: 36 Copynumber: 3.1 Consensus size: 36
392358 GAAATGGAAA
392368 ATGGAATTTGGTGATGATATAGGCGTGAT-ATGGTG
1 ATGGAATTTGGTGATGATATAGGCGTGATAATGGTG
*
392403 ATGGACTTTGGTGATGATATAGGCGTGATAATGGTG
1 ATGGAATTTGGTGATGATATAGGCGTGATAATGGTG
**
392439 ATGGAAGATGGTGATGATATAGGCGTGATAATGGTG
1 ATGGAATTTGGTGATGATATAGGCGTGATAATGGTG
392475 ATGGA
1 ATGGA
392480 CAGATTGTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 28 0.39
36 44 0.61
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (36 bp):
ATGGAATTTGGTGATGATATAGGCGTGATAATGGTG
Found at i:396164 original size:15 final size:15
Alignment explanation
Indices: 396114--396165 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
396104 AAAATATGGT
* *
396114 AATGAAATAAGAAAA
1 AATGAAATGATAAAA
*
396129 GATGAAA-GAATAAAGA
1 AATGAAATG-ATAAA-A
396145 AATGAAATGATAAAA
1 AATGAAATGATAAAA
396160 AATGAA
1 AATGAA
396166 GATAACTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 17 0.57
16 12 0.40
17 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (15 bp):
AATGAAATGATAAAA
Found at i:396856 original size:35 final size:36
Alignment explanation
Indices: 396817--396921 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
396807 AAATGGAATT
*
396817 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
*
396852 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
396888 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
396922 AGTTTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.28, C:0.05, G:0.38, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
Found at i:399782 original size:22 final size:22
Alignment explanation
Indices: 399757--399827 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
399747 ATCTTCTATG
* *
399757 ACCATTTCACACCGATTTTATC
1 ACCATTTCACACCGATATCATC
** *
399779 ACCATTTCATGCCTATATCATC
1 ACCATTTCACACCGATATCATC
* *
399801 ACCATTTCACGCCTATATCATC
1 ACCATTTCACACCGATATCATC
399823 ACCAT
1 ACCAT
399828 CTTCCATCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.28, C:0.34, G:0.04, T:0.34
Consensus pattern (22 bp):
ACCATTTCACACCGATATCATC
Found at i:399843 original size:35 final size:35
Alignment explanation
Indices: 399797--399863 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
399787 ATGCCTATAT
399797 CATCACCATTTCACGCCTATATCATCACCATCTTC
1 CATCACCATTTCACGCCTATATCATCACCATCTTC
399832 CATCACCATTTCACGCCTATATCATCACCATC
1 CATCACCATTTCACGCCTATATCATCACCATC
399864 CCTTAACCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.27, C:0.40, G:0.03, T:0.30
Consensus pattern (35 bp):
CATCACCATTTCACGCCTATATCATCACCATCTTC
Found at i:400036 original size:17 final size:16
Alignment explanation
Indices: 399990--400037 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
399980 TCTTTGATAA
*
399990 CAATTCTATCCATTT-
1 CAATTCTTTCCATTTC
400005 CAATTCTTTCCATTTC
1 CAATTCTTTCCATTTC
*
400021 CAATTCCTTTCTATTTC
1 CAATT-CTTTCCATTTC
400038 TTAATTATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 14 0.48
16 5 0.17
17 10 0.34
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (16 bp):
CAATTCTTTCCATTTC
Found at i:401918 original size:15 final size:15
Alignment explanation
Indices: 401898--401947 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
401888 GAACTATATC
401898 AAAAAGAAAGAAAAG
1 AAAAAGAAAGAAAAG
401913 AAAAAG-AAGAAAA-
1 AAAAAGAAAGAAAAG
*
401926 ATTCAAAGAAA-AAAAG
1 A--AAAAGAAAGAAAAG
401942 AAAAAG
1 AAAAAG
401948 TGAAGAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 1 0.03
14 11 0.38
15 14 0.48
16 3 0.10
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (15 bp):
AAAAAGAAAGAAAAG
Found at i:409588 original size:12 final size:12
Alignment explanation
Indices: 409571--409601 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
409561 TGGCCAAAGA
*
409571 TGAAAAGGTATT
1 TGAAAAGGTATG
409583 TGAAAAGGTATG
1 TGAAAAGGTATG
409595 TGAAAAG
1 TGAAAAG
409602 TGTTTAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (12 bp):
TGAAAAGGTATG
Done.