Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008845.1 Hibiscus syriacus cultivar Beakdansim tig00112052_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: 591764
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 3 of 3
Found at i:522292 original size:47 final size:47
Alignment explanation
Indices: 522187--522296 Score: 134
Period size: 49 Copynumber: 2.3 Consensus size: 47
522177 TATATTTACT
*
522187 TTTTTTATTTTTTTATTTTATATATATATTATTTTTACTTTTTTATTA
1 TTTTTTATTTATTTATTTTATATATATATTATTTTTACTTTTTT-TTA
* * *
522235 TTATTTTATTTATTTGTTTTATTTCTATATT-TTTTT-CTTTTTCTTTA
1 TT-TTTTATTTATTTATTTTATATATATATTATTTTTACTTTTT-TTTA
522282 TTTTTATATTTATTT
1 TTTTT-TATTTATTT
522297 TACTTACTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
46 3 0.05
47 20 0.36
48 8 0.15
49 24 0.44
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (47 bp):
TTTTTTATTTATTTATTTTATATATATATTATTTTTACTTTTTTTTA
Found at i:522403 original size:15 final size:15
Alignment explanation
Indices: 522385--522414 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
522375 TATTTATTTC
522385 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
522400 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
522415 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:527843 original size:31 final size:32
Alignment explanation
Indices: 527784--527846 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
527774 AATATTCTTC
*
527784 CACAATAAAAAATTGTAACAAAATTATTTAGT
1 CACAATAAAAAATTATAACAAAATTATTTAGT
*
527816 CACAGTAAAAAAGTTATAA-AAAA-TATTTAGT
1 CACAATAAAAAA-TTATAACAAAATTATTTAGT
527847 GTCGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 8 0.29
32 15 0.54
33 5 0.18
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (32 bp):
CACAATAAAAAATTATAACAAAATTATTTAGT
Found at i:538545 original size:13 final size:13
Alignment explanation
Indices: 538527--538571 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
538517 CATTGCCATT
*
538527 TCATCATCATCCA
1 TCATCAACATCCA
*
538540 TCATCAACATCCT
1 TCATCAACATCCA
*
538553 TCATCAAGA-CCA
1 TCATCAACATCCA
538565 TCATCAA
1 TCATCAA
538572 TTCCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (13 bp):
TCATCAACATCCA
Found at i:538914 original size:19 final size:20
Alignment explanation
Indices: 538892--538935 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
538882 AATTGGAGTG
*
538892 CAAAAAGAA-AAGAAAAAGA
1 CAAAAAGAATAAAAAAAAGA
538911 CAAAAAGAATAAAAAAAAGA
1 CAAAAAGAATAAAAAAAAGA
*
538931 GAAAA
1 CAAAA
538936 CAAATTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.02
Consensus pattern (20 bp):
CAAAAAGAATAAAAAAAAGA
Found at i:544091 original size:13 final size:13
Alignment explanation
Indices: 544073--544117 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
544063 CATTGCCATT
*
544073 TCATCATCATCCA
1 TCATCAACATCCA
*
544086 TCATCAACATCCT
1 TCATCAACATCCA
*
544099 TCATCAAGA-CCA
1 TCATCAACATCCA
544111 TCATCAA
1 TCATCAA
544118 TTCCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (13 bp):
TCATCAACATCCA
Found at i:547439 original size:19 final size:19
Alignment explanation
Indices: 547415--547459 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
547405 ACCCCTTTTA
547415 TTTTTTTTTACTTTTAACT
1 TTTTTTTTTACTTTTAACT
* * **
547434 TTTTTTCTTATTTTTTTCT
1 TTTTTTTTTACTTTTAACT
547453 TTTTTTT
1 TTTTTTT
547460 CTTTCAGACA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTTTACTTTTAACT
Found at i:554565 original size:19 final size:19
Alignment explanation
Indices: 554533--554582 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
554523 AATACGAATG
* *
554533 AATATAATGTAATGCGAAA
1 AATAAAATGCAATGCGAAA
** *
554552 GGTAAAATGCAATGTGAAA
1 AATAAAATGCAATGCGAAA
554571 AATAAAATGCAA
1 AATAAAATGCAA
554583 GGTGCTTATT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.18, T:0.22
Consensus pattern (19 bp):
AATAAAATGCAATGCGAAA
Found at i:558859 original size:22 final size:22
Alignment explanation
Indices: 558835--558882 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
558825 CCAGTTCCAA
*
558835 CCCGACCCGACCCGTTGA-CCGA
1 CCCGACCC-AACCGTTGACCCGA
558857 CCCGACCCAACCGTTGACCCGA
1 CCCGACCCAACCGTTGACCCGA
558879 CCCG
1 CCCG
558883 TTTACCTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.19, C:0.52, G:0.21, T:0.08
Consensus pattern (22 bp):
CCCGACCCAACCGTTGACCCGA
Found at i:558896 original size:22 final size:22
Alignment explanation
Indices: 558871--558912 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
558861 ACCCAACCGT
*
558871 TGACCCGACCCGTTTACCTACC
1 TGACCCGACCCGTTAACCTACC
558893 TGACCCGACCCGTTAACCTA
1 TGACCCGACCCGTTAACCTA
558913 ACTGTTGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.43, G:0.14, T:0.21
Consensus pattern (22 bp):
TGACCCGACCCGTTAACCTACC
Found at i:558967 original size:29 final size:29
Alignment explanation
Indices: 558923--558997 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
558913 ACTGTTGACC
558923 GGGTGCTATTTTAGTAATTAATTTAAAATA
1 GGGTGCTATTTTAGTAATTAATTTAAAA-A
*
558953 -TGTGCTATTTTAGTAATTAATTTAAAAA
1 GGGTGCTATTTTAGTAATTAATTTAAAAA
*
558981 GGGTGCTATTTTTGTAA
1 GGGTGCTATTTTAGTAA
558998 AATGGTTGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 1 0.02
29 40 0.98
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.45
Consensus pattern (29 bp):
GGGTGCTATTTTAGTAATTAATTTAAAAA
Found at i:559759 original size:15 final size:14
Alignment explanation
Indices: 559729--559771 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
559719 ACATGATACA
559729 TGATACTTGA-TTCC
1 TGATA-TTGATTTCC
559743 TGAATATTGATTTCC
1 TG-ATATTGATTTCC
559758 TGATATATGATTTC
1 TGATAT-TGATTTC
559772 TGTATTTCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (14 bp):
TGATATTGATTTCC
Found at i:565653 original size:9 final size:8
Alignment explanation
Indices: 565645--565725 Score: 64
Period size: 9 Copynumber: 9.9 Consensus size: 8
565635 TTAATGTTAT
565645 TTATATTA
1 TTATATTA
565653 TTATTATTA
1 TTA-TATTA
565662 TTATA--A
1 TTATATTA
565668 TTATTATTA
1 TTA-TATTA
565677 TTATA--A
1 TTATATTA
565683 TTATAATTA
1 TTAT-ATTA
565692 TTATTATTA
1 TTA-TATTA
565701 TTATTATTA
1 TTA-TATTA
565710 TTAATATATA
1 TT-ATAT-TA
565720 TT-TATT
1 TTATATT
565726 TAATATTACA
Statistics
Matches: 63, Mismatches: 0, Indels: 21
0.75 0.00 0.25
Matches are distributed among these distances:
6 9 0.14
7 4 0.06
8 10 0.16
9 34 0.54
10 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTATATTA
Found at i:565656 original size:3 final size:3
Alignment explanation
Indices: 565648--565712 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
565638 ATGTTATTTA
* * *
565648 TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
565696 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
565713 ATATATATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:566209 original size:11 final size:10
Alignment explanation
Indices: 566193--566231 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
566183 TCAACGCAGC
566193 AAAGAAACAGA
1 AAAGAAA-AGA
*
566204 AAAGAAAAAA
1 AAAGAAAAGA
566214 AAAGAAAAGAA
1 AAAGAAAAG-A
566225 AAAGAAA
1 AAAGAAA
566232 GAAGAGAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:566211 original size:5 final size:5
Alignment explanation
Indices: 566193--566231 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
566183 TCAACGCAGC
*
566193 AAAGA AACAGA AAAGA AAAAA AAAGA AAAGAA AAAGA AA
1 AAAGA AA-AGA AAAGA AAAGA AAAGA AAAG-A AAAGA AA
566232 GAAGAGAAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 20 0.67
6 10 0.33
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:566221 original size:15 final size:15
Alignment explanation
Indices: 566201--566239 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
566191 GCAAAGAAAC
566201 AGAAAAGAAAAAAAA
1 AGAAAAGAAAAAAAA
*
566216 AGAAAAGAAAAAGAA
1 AGAAAAGAAAAAAAA
*
566231 AGAAGAGAA
1 AGAAAAGAA
566240 GCTTACCGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAAAAAA
Found at i:571186 original size:15 final size:15
Alignment explanation
Indices: 571166--571197 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
571156 ATCAATACCT
571166 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
571181 TTTTGCATACATTCA
1 TTTTGCATACATGCA
571196 TT
1 TT
571198 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:578539 original size:14 final size:14
Alignment explanation
Indices: 578522--578566 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
578512 AAAATAATAA
578522 AAAAAAGAGAAAAG
1 AAAAAAGAGAAAAG
578536 AAAAGAA-AGAAAA-
1 AAAA-AAGAGAAAAG
*
578549 AAAAAGGA-AAAAG
1 AAAAAAGAGAAAAG
578562 AAAAA
1 AAAAA
578567 GAGGGGTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
12 5 0.19
13 10 0.37
14 10 0.37
15 2 0.07
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAAGAGAAAAG
Found at i:579858 original size:83 final size:83
Alignment explanation
Indices: 579713--580018 Score: 504
Period size: 83 Copynumber: 3.7 Consensus size: 83
579703 GAACAAATGC
* *
579713 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCCGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
579778 CATTGAATTTGGAAGATG
66 CATTGAATTTGAAAGATG
* * * *
579796 AATATGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
579861 CATTGAAATTGAAAGATG
66 CATTGAATTTGAAAGATG
* * *
579879 AATGCGCTCATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
579944 TATTGAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
579962 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
580019 TGAACCCCAA
Statistics
Matches: 204, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 204 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
CATTGAATTTGAAAGATG
Found at i:582352 original size:45 final size:45
Alignment explanation
Indices: 582302--582594 Score: 381
Period size: 45 Copynumber: 6.5 Consensus size: 45
582292 TTATTCCATT
* ** * *
582302 CCAATAATGCACCCATATGCATTTCAATTACGAAATCATTTCTTG
1 CCAATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATG
* * * * *
582347 TCAATATTACACCCATATGCATTTCAATTATAGCATCATTTCATG
1 CCAATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATG
** *
582392 CCAATAATTTACCCATATGCATTTTAATTATGGCATCCTTTCATG
1 CCAATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATG
* * * *
582437 TCAA-AAGTGCACCCATATACATTTCCACTATGGCATCCTTTCATG
1 CCAATAA-TGCACCCATATGCATTTCAATTATGGCATCCTTTCATG
* *
582482 CCAATAATGCACCCATATGAATTTCAATTATGGCATTCTTTCATG
1 CCAATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATG
*
582527 CCAATAATGCACCCATATGCATTTTAATTATGGCATCCTTTCATG
1 CCAATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATG
*
582572 CCAATAATGTACCCATATGCATT
1 CCAATAATGCACCCATATGCATT
582595 ATTTAGTTCA
Statistics
Matches: 214, Mismatches: 32, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
44 2 0.01
45 210 0.98
46 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (45 bp):
CCAATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATG
Found at i:589355 original size:45 final size:45
Alignment explanation
Indices: 589265--589595 Score: 382
Period size: 45 Copynumber: 7.4 Consensus size: 45
589255 TCATGCTTAT
** *
589265 ATGCA-CCATTATGCATTTC-ATTATAACATCCTTTCATGCCAATA
1 ATGCACCCA-TATGCATTTCAATTATGGCATCATTTCATGCCAATA
*
589309 ATGCACCCATATGCATTTCAATTATGGCATCATTTC-TTCTCAATA
1 ATGCACCCATATGCATTTCAATTATGGCATCATTTCATGC-CAATA
* * * * *
589354 ATGAACCCATGTGCATTTCAATTATAGCATCCTCTCATGCCAATA
1 ATGCACCCATATGCATTTCAATTATGGCATCATTTCATGCCAATA
* * * **
589399 ATGCACCCATATGCAGTTCAGTTATGGCATCCTTTTGTG-CAATTA
1 ATGCACCCATATGCATTTCAATTATGGCATCATTTCATGCCAA-TA
* * **
589444 ATGCACCCATATGCATTTCAACTGTGGCATCATTTCATGATAATA
1 ATGCACCCATATGCATTTCAATTATGGCATCATTTCATGCCAATA
*** * * * *
589489 GCACACCCATATCCATTTCAATTATGGCATCCTTTTATTCCAATA
1 ATGCACCCATATGCATTTCAATTATGGCATCATTTCATGCCAATA
589534 ATGCACCCATATGCATTTCAATTATGGCATCATTTCATGCCAATA
1 ATGCACCCATATGCATTTCAATTATGGCATCATTTCATGCCAATA
589579 ATGCACCCATATGCATT
1 ATGCACCCATATGCATT
589596 ATTTAATTCA
Statistics
Matches: 237, Mismatches: 44, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
44 20 0.08
45 213 0.90
46 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (45 bp):
ATGCACCCATATGCATTTCAATTATGGCATCATTTCATGCCAATA
Found at i:589707 original size:17 final size:17
Alignment explanation
Indices: 589655--589709 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
589645 ATATCCTTTC
* *
589655 CATACATGAAATGAAAA
1 CATACATTAAATTAAAA
589672 CAT--ATTACTAATGTAAAA
1 CATACATTA--AAT-TAAAA
589690 CATACATTAAATTAAAA
1 CATACATTAAATTAAAA
589707 CAT
1 CAT
589710 TCTAACTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
15 3 0.10
17 14 0.45
18 10 0.32
20 4 0.13
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (17 bp):
CATACATTAAATTAAAA
Found at i:591652 original size:45 final size:44
Alignment explanation
Indices: 591568--591670 Score: 152
Period size: 45 Copynumber: 2.3 Consensus size: 44
591558 CCATTCATCA
* * * * *
591568 CACCCATATCCATTTCAATATGGCATCCTTTTATTCCAATATTG
1 CACCCATATGCATTTCAATATGGCATCATTTCATGCCAATAATG
591612 CACCCATATGCATTTCAATTATGGCATCATTTCATGCCAATAATG
1 CACCCATATGCATTTCAA-TATGGCATCATTTCATGCCAATAATG
591657 CACCCATATGCATT
1 CACCCATATGCATT
591671 ATTTAATTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 17 0.32
45 36 0.68
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.35
Consensus pattern (44 bp):
CACCCATATGCATTTCAATATGGCATCATTTCATGCCAATAATG
Done.