Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002607.1 Hibiscus syriacus cultivar Beakdansim tig00005270_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: 49424
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3341 original size:13 final size:12
Alignment explanation
Indices: 3320--3369 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 12
3310 ACCCATTTCG
*
3320 TTATATTTTGTTT
1 TTAT-TTTTTTTT
3333 TTATTTTTTTATT
1 TTATTTTTTT-TT
3346 TTCATTTTATTTTT
1 TT-ATTTT-TTTTT
3360 TTATTTTTTT
1 TTATTTTTTT
3370 AGCGAACTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
12 8 0.24
13 13 0.39
14 9 0.27
15 3 0.09
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (12 bp):
TTATTTTTTTTT
Found at i:3343 original size:8 final size:8
Alignment explanation
Indices: 3330--3370 Score: 55
Period size: 8 Copynumber: 4.8 Consensus size: 8
3320 TTATATTTTG
3330 TTTTTATT
1 TTTTTATT
3338 TTTTTATTT
1 TTTTTA-TT
3347 TCATTTTATT
1 T--TTTTATT
3357 TTTTTATT
1 TTTTTATT
3365 TTTTTA
1 TTTTTA
3371 GCGAACTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 19 0.63
9 3 0.10
10 3 0.10
11 5 0.17
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTATT
Found at i:3602 original size:16 final size:16
Alignment explanation
Indices: 3581--3611 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3571 CAAACATAGA
3581 AGTGCAGAAAAAAAAT
1 AGTGCAGAAAAAAAAT
3597 AGTGCAGAAAAAAAA
1 AGTGCAGAAAAAAAA
3612 AACAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.19, T:0.10
Consensus pattern (16 bp):
AGTGCAGAAAAAAAAT
Found at i:5310 original size:76 final size:75
Alignment explanation
Indices: 5219--5383 Score: 242
Period size: 76 Copynumber: 2.2 Consensus size: 75
5209 TTAAACTCAA
*
5219 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
5283 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * *
5295 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
*
5360 TTTAATTAGG
66 TTTAATTAAG
*
5370 ATTTAGAATATTAT
1 ATTTAGGATATTAT
5384 ATTATTTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 37 0.46
76 43 0.54
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:5369 original size:19 final size:19
Alignment explanation
Indices: 5341--5403 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
5331 TGTATTTTAG
*
5341 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
5360 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
5379 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
5400 TTTA
1 TTTA
5404 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:6051 original size:17 final size:18
Alignment explanation
Indices: 6024--6070 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
6014 AATCTCTTTA
6024 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
*
6043 A-TTTTTATTTAATTCTT
1 ATTTTTTATTTAATTATT
6060 ATTTTTTATTT
1 ATTTTTTATTT
6071 TAACCACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 14 0.54
18 11 0.42
19 1 0.04
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:6603 original size:16 final size:15
Alignment explanation
Indices: 6577--6607 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
6567 TATTAAAAAA
6577 TAATATAATAAATAT
1 TAATATAATAAATAT
6592 TAATAGTAATAAATAT
1 TAATA-TAATAAATAT
6608 AAAAGGGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
TAATATAATAAATAT
Found at i:7403 original size:64 final size:69
Alignment explanation
Indices: 7278--7469 Score: 198
Period size: 64 Copynumber: 2.8 Consensus size: 69
7268 TAAAACATCT
* * * * *
7278 TAAATCCTAATTAAAATACTTAAAA-CTATTTAAAATAAAATAC----CTAAAAAAT-TATATAA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATAAAGAATAAAAATAA
*
7337 TATTC
65 TATCC
7342 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAG-----A-ATAAA
7407 AATAATATCC
60 AATAATATCC
* *
7417 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA
1 TAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAA
7470 ATATAATGTT
Statistics
Matches: 107, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
63 5 0.05
64 36 0.34
68 4 0.04
73 1 0.01
74 2 0.02
75 27 0.25
76 32 0.30
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (69 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGAATAAAAATAAT
ATCC
Found at i:7420 original size:75 final size:76
Alignment explanation
Indices: 7333--7497 Score: 244
Period size: 76 Copynumber: 2.2 Consensus size: 76
7323 AAAAAATTAT
*
7333 ATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
7397 AAAAT-ATAAAA
65 AAAATGATAAAA
* *
7408 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
1 ATAATATCCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
* * *
7473 TAATGTTCAAA
66 AAATGATAAAA
*
7484 ATATTATCCTAAAT
1 ATAATATCCTAAAT
7498 TTGAGTTTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 32 0.40
76 48 0.60
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
AAATGATAAAA
Found at i:12701 original size:38 final size:38
Alignment explanation
Indices: 12625--12698 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
12615 ACTTGAAGAT
*
12625 TAAATTATTCTCTCAGTCTCATTAAAAACATATTTTTA
1 TAAATTATTCCCTCAGTCTCATTAAAAACATATTTTTA
*
12663 TAAATTATTCCCT-TGTCTCATTAAAAACATATTTTT
1 TAAATTATTCCCTCAGTCTCATTAAAAACATATTTTT
12699 TATTAACTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 22 0.65
38 12 0.35
ACGTcount: A:0.35, C:0.16, G:0.03, T:0.46
Consensus pattern (38 bp):
TAAATTATTCCCTCAGTCTCATTAAAAACATATTTTTA
Found at i:15834 original size:14 final size:14
Alignment explanation
Indices: 15815--15849 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
15805 TGAAACCCAA
15815 GGTAAAAGCCTTTT
1 GGTAAAAGCCTTTT
15829 GGTAAAAGCCTTTT
1 GGTAAAAGCCTTTT
15843 GGTAAAA
1 GGTAAAA
15850 AGGGTTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31
Consensus pattern (14 bp):
GGTAAAAGCCTTTT
Found at i:17936 original size:17 final size:18
Alignment explanation
Indices: 17914--17947 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17904 TAACCACGAT
17914 AAACGC-AACGCAATCAA
1 AAACGCGAACGCAATCAA
*
17931 AAACGCGACCGCAATCA
1 AAACGCGAACGCAATCA
17948 GGATAAACGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.32, G:0.15, T:0.06
Consensus pattern (18 bp):
AAACGCGAACGCAATCAA
Found at i:33583 original size:14 final size:14
Alignment explanation
Indices: 33531--33583 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
33521 TTGAATGTTA
*
33531 TTAATAATT-TAAT
1 TTAAAAATTATAAT
*
33544 TTAAAAATTAAAAT
1 TTAAAAATTATAAT
* *
33558 TTAACATATTATATT
1 TTAA-AAATTATAAT
33573 TTAAAAATTAT
1 TTAAAAATTAT
33584 TCATGAACTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
13 8 0.25
14 13 0.41
15 11 0.34
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAAAAATTATAAT
Found at i:41378 original size:52 final size:52
Alignment explanation
Indices: 41303--41417 Score: 171
Period size: 52 Copynumber: 2.2 Consensus size: 52
41293 TAAAATTAGC
* * * *
41303 AACATAAT-AAAATTGATTCTATCTAATTAAAACAGATCTTATCTAATAACT
1 AACAGAATAAAAACTGATTATATCTAATTAAAACAGATCATATCTAATAACT
*
41354 AACAGAATAAAAACTGATTATATCTAATTAAAACTGATCATATCTAATAACT
1 AACAGAATAAAAACTGATTATATCTAATTAAAACAGATCATATCTAATAACT
41406 AACAGAA-AAAAA
1 AACAGAATAAAAA
41418 TATCTAGTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 12 0.21
52 46 0.79
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.30
Consensus pattern (52 bp):
AACAGAATAAAAACTGATTATATCTAATTAAAACAGATCATATCTAATAACT
Found at i:41388 original size:20 final size:20
Alignment explanation
Indices: 41363--41401 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41353 TAACAGAATA
*
41363 AAAACTGATTATATCTAATT
1 AAAACTGATCATATCTAATT
41383 AAAACTGATCATATCTAAT
1 AAAACTGATCATATCTAAT
41402 AACTAACAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCATATCTAATT
Found at i:44090 original size:20 final size:20
Alignment explanation
Indices: 44065--44104 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
44055 AACAACAGAA
*
44065 TAAAACTGATTCTATCTAAT
1 TAAAACTGATCCTATCTAAT
44085 TAAAACTGATCCTATCTAAT
1 TAAAACTGATCCTATCTAAT
44105 AACTAACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAACTGATCCTATCTAAT
Found at i:44133 original size:52 final size:52
Alignment explanation
Indices: 44054--44172 Score: 206
Period size: 52 Copynumber: 2.3 Consensus size: 52
44044 TGCATAAAAT
* *
44054 TAAC-AACAGAAT-AAAACTGATTCTATCTAATTAAAACTGATCCTATCTAA
1 TAACTAACAGAATAAAAACTGATTATATCTAATTAAAACTGATCATATCTAA
44104 TAACTAACAGAATAAAAACTGATTATATCTAATTAAAACTGATCATATCTAA
1 TAACTAACAGAATAAAAACTGATTATATCTAATTAAAACTGATCATATCTAA
44156 TAACTAACAGAATAAAA
1 TAACTAACAGAATAAAA
44173 TATCTAATTA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
50 4 0.06
51 8 0.12
52 53 0.82
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (52 bp):
TAACTAACAGAATAAAAACTGATTATATCTAATTAAAACTGATCATATCTAA
Found at i:44143 original size:20 final size:20
Alignment explanation
Indices: 44118--44156 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
44108 TAACAGAATA
*
44118 AAAACTGATTATATCTAATT
1 AAAACTGATCATATCTAATT
44138 AAAACTGATCATATCTAAT
1 AAAACTGATCATATCTAAT
44157 AACTAACAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCATATCTAATT
Found at i:45340 original size:12 final size:12
Alignment explanation
Indices: 45325--45398 Score: 59
Period size: 12 Copynumber: 6.4 Consensus size: 12
45315 CAGTTTGTTT
45325 TTATTAAAATTA
1 TTATTAAAATTA
45337 TTATT---ATTA
1 TTATTAAAATTA
45346 TTATTATAAA-TA
1 TTATTA-AAATTA
**
45358 TTATTATCATTA
1 TTATTAAAATTA
45370 TTATTATAAA-TA
1 TTATTA-AAATTA
**
45382 TTATTATTATTA
1 TTATTAAAATTA
45394 TTATT
1 TTATT
45399 TACAAGCCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
9 9 0.18
11 2 0.04
12 36 0.73
13 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATTAAAATTA
Found at i:45341 original size:3 final size:3
Alignment explanation
Indices: 45333--45398 Score: 87
Period size: 3 Copynumber: 22.0 Consensus size: 3
45323 TTTTATTAAA
* * * * *
45333 ATT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATC ATT ATT ATT ATA AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
45381 ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
45399 TACAAGCCCA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:45352 original size:24 final size:24
Alignment explanation
Indices: 45329--45398 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
45319 TTGTTTTTAT
45329 TAAA-ATTATTATTATTATTATTA
1 TAAATATTATTATTATTATTATTA
*
45352 TAAATATTATTATCATTATTATTA
1 TAAATATTATTATTATTATTATTA
45376 TAAATATTATTATTATTATTATT
1 TAAATATTATTATTATTATTATT
45399 TACAAGCCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
23 4 0.09
24 40 0.91
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
TAAATATTATTATTATTATTATTA
Done.