Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003558.1 Hibiscus syriacus cultivar Beakdansim tig00007510_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: 56346
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:1196 original size:18 final size:20
Alignment explanation
Indices: 1169--1212 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1159 TAATTCTTAC
1169 ATTA-ATTATTTT-T-ATTG
1 ATTATATTATTTTGTGATTG
*
1186 ATTATATTATTTTGTGCTTG
1 ATTATATTATTTTGTGATTG
1206 ATTATAT
1 ATTATAT
1213 GTCCCCTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 1 0.04
20 10 0.43
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.61
Consensus pattern (20 bp):
ATTATATTATTTTGTGATTG
Found at i:3510 original size:16 final size:16
Alignment explanation
Indices: 3491--3524 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3481 TAAAATTTGC
3491 TAGCAAAAAAATATTT
1 TAGCAAAAAAATATTT
* *
3507 TAGCCAAAAATTATTT
1 TAGCAAAAAAATATTT
3523 TA
1 TA
3525 CTAAGGTGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (16 bp):
TAGCAAAAAAATATTT
Found at i:12336 original size:14 final size:14
Alignment explanation
Indices: 12317--12343 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12307 ATATTTTTAA
12317 CTAAAAAATAAATC
1 CTAAAAAATAAATC
12331 CTAAAAAATAAAT
1 CTAAAAAATAAAT
12344 ATAGTTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (14 bp):
CTAAAAAATAAATC
Found at i:15000 original size:24 final size:25
Alignment explanation
Indices: 14968--15016 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
14958 CAAGCTAATC
*
14968 TTGCCCAAAG-AAAAGGGATGCATT
1 TTGCCCAAAGAAAAAAGGATGCATT
14992 TTGCCCAAAGAAAAAAGGATGCATT
1 TTGCCCAAAGAAAAAAGGATGCATT
15017 CGAATCAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20
Consensus pattern (25 bp):
TTGCCCAAAGAAAAAAGGATGCATT
Found at i:17947 original size:54 final size:54
Alignment explanation
Indices: 17845--18094 Score: 360
Period size: 54 Copynumber: 4.6 Consensus size: 54
17835 TAAGAAGTTA
* * *
17845 ATATGATTAATTTCGTGAGTTGCACACACATAGTGTCGAAATGGTTGTTCATCAAC
1 ATATGATGAATTCCGTGAGTTG--CACACATAGTGTCGAAACGGTTGTTCATCAAC
* *
17901 ATATGATGAATTCCATGAGTTGCACACATAGTGTCGAAACGATTGTTCATCAAC
1 ATATGATGAATTCCGTGAGTTGCACACATAGTGTCGAAACGGTTGTTCATCAAC
* * * *
17955 ATACGATGGATTCTGTGAGTTGCACATATAGTG-CTGAAACGGTTGTTCATCAAC
1 ATATGATGAATTCCGTGAGTTGCACACATAGTGTC-GAAACGGTTGTTCATCAAC
18009 ATATGATGAATT-CGATGAGTTGCACACATAGTGTCGAAACGGTTGTTCATCAAC
1 ATATGATGAATTCCG-TGAGTTGCACACATAGTGTCGAAACGGTTGTTCATCAAC
*
18063 ATATGATGAATTCGGTGAGTTGCACACATAGT
1 ATATGATGAATTCCGTGAGTTGCACACATAGT
18095 TCCGTTTGGT
Statistics
Matches: 174, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
53 2 0.01
54 151 0.87
55 2 0.01
56 19 0.11
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (54 bp):
ATATGATGAATTCCGTGAGTTGCACACATAGTGTCGAAACGGTTGTTCATCAAC
Found at i:18078 original size:27 final size:27
Alignment explanation
Indices: 17994--18078 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 27
17984 AGTGCTGAAA
17994 CGGTTGTTCATCAACATATGATGAATT
1 CGGTTGTTCATCAACATATGATGAATT
* * *
18021 CGATGAGTTGCA-C-ACATAGTG-TCGAA-A
1 CGGT-TGTT-CATCAACATA-TGAT-GAATT
18048 CGGTTGTTCATCAACATATGATGAATT
1 CGGTTGTTCATCAACATATGATGAATT
18075 CGGT
1 CGGT
18079 GAGTTGCACA
Statistics
Matches: 44, Mismatches: 6, Indels: 16
0.67 0.09 0.24
Matches are distributed among these distances:
25 2 0.05
26 9 0.20
27 22 0.50
28 9 0.20
29 2 0.05
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (27 bp):
CGGTTGTTCATCAACATATGATGAATT
Found at i:18091 original size:27 final size:27
Alignment explanation
Indices: 18007--18092 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
17997 TTGTTCATCA
*
18007 ACATATGATGAATTCGATGAGTTGCAC
1 ACATATGATGAATTCGGTGAGTTGCAC
* *
18034 ACATAGTG-TCGAA-ACGGT-TGTT-CATC
1 ACATA-TGAT-GAATTCGGTGAGTTGCA-C
18060 AACATATGATGAATTCGGTGAGTTGCAC
1 -ACATATGATGAATTCGGTGAGTTGCAC
18088 ACATA
1 ACATA
18093 GTTCCGTTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
25 2 0.04
26 9 0.20
27 24 0.52
28 9 0.20
29 2 0.04
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (27 bp):
ACATATGATGAATTCGGTGAGTTGCAC
Found at i:22099 original size:22 final size:22
Alignment explanation
Indices: 22072--22125 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
22062 AAGTTAACAA
22072 CCGGTCAACGACAGTCAACAGT
1 CCGGTCAACGACAGTCAACAGT
* **
22094 CTGGTCAACGACAGTCAATGGT
1 CCGGTCAACGACAGTCAACAGT
22116 CCGGTCAACG
1 CCGGTCAACG
22126 GTAATCAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.17
Consensus pattern (22 bp):
CCGGTCAACGACAGTCAACAGT
Found at i:24780 original size:97 final size:97
Alignment explanation
Indices: 24581--24799 Score: 266
Period size: 97 Copynumber: 2.3 Consensus size: 97
24571 GAAAATAGAA
*
24581 AACCATAGTTCATAAACCAGTAAATTCTATGATTCCATAAATCAGGAACAATTCATGTTTTCCAT
1 AACCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCAGGAACAATTCATGTTTTCCAT
**
24646 AGAAAACAGGAAACCCGATAATACATTTCAGG
66 AGAAAACAGGAAACCCGATAATACATACCAGG
* * * *
24678 AACCATAATTCATAAACCATTAAATTCCATGATTCCATAAATCATGAACAATTCATAGTTTTCGA
1 AACCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCAGGAACAATTCAT-GTTTTCCA
* * *
24743 T-GAAAAC-TGAAA-TC-ATATATCACATACCATGT
65 TAGAAAACAGGAAACCCGATA-AT-ACATACCA-GG
* *
24775 TACCATGGTTCATAAACCAGTAAAT
1 AACCATAGTTCATAAACCAGTAAAT
24800 CAATACTTTC
Statistics
Matches: 104, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
94 3 0.03
95 3 0.03
96 10 0.10
97 80 0.77
98 8 0.08
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.29
Consensus pattern (97 bp):
AACCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCAGGAACAATTCATGTTTTCCAT
AGAAAACAGGAAACCCGATAATACATACCAGG
Found at i:28283 original size:29 final size:29
Alignment explanation
Indices: 28249--28307 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
28239 CCTAAATTAA
28249 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
28278 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
28307 T
1 T
28308 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:32966 original size:29 final size:29
Alignment explanation
Indices: 32932--32990 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
32922 CCTAAATTAA
32932 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
32961 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
32990 T
1 T
32991 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:41244 original size:24 final size:24
Alignment explanation
Indices: 41212--41277 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
41202 AAAGTGCCAT
*
41212 GTATAATTTGTCCTGAAGAACCAC
1 GTATAATTTGTCCCGAAGAACCAC
*
41236 GTATAATTTGTCCCGAAGGACCAC
1 GTATAATTTGTCCCGAAGAACCAC
*
41260 GTAGAAATTTGTCCCGAA
1 GTA-TAATTTGTCCCGAA
41278 AGACCGTGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
24 25 0.66
25 13 0.34
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (24 bp):
GTATAATTTGTCCCGAAGAACCAC
Found at i:41290 original size:25 final size:25
Alignment explanation
Indices: 41216--41282 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
41206 TGCCATGTAT
* *
41216 AATTTGTCCTG-AAGAACCACGTA-T
1 AATTTGTCCCGAAAG-ACCACGTAGA
*
41240 AATTTGTCCCGAAGGACCACGTAGA
1 AATTTGTCCCGAAAGACCACGTAGA
41265 AATTTGTCCCGAAAGACC
1 AATTTGTCCCGAAAGACC
41283 GTGTAGAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 18 0.49
25 19 0.51
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (25 bp):
AATTTGTCCCGAAAGACCACGTAGA
Found at i:41442 original size:15 final size:15
Alignment explanation
Indices: 41424--41496 Score: 83
Period size: 15 Copynumber: 4.9 Consensus size: 15
41414 ATAGGGTATC
*
41424 TTCACGTAGAACATT
1 TTCACATAGAACATT
* *
41439 TTCACTTAGCACATT
1 TTCACATAGAACATT
* * *
41454 TTCATATAAAACATA
1 TTCACATAGAACATT
*
41469 TTCACATATAACATT
1 TTCACATAGAACATT
41484 TTCACATAGAACA
1 TTCACATAGAACA
41497 CATTCACATG
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (15 bp):
TTCACATAGAACATT
Found at i:41467 original size:30 final size:30
Alignment explanation
Indices: 41424--41505 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
41414 ATAGGGTATC
* * * * *
41424 TTCACGTAGAACATTTTCACTTAGCACATT
1 TTCACATAAAACATATTCACATAGAACATT
* *
41454 TTCATATAAAACATATTCACATATAACATT
1 TTCACATAAAACATATTCACATAGAACATT
* *
41484 TTCACATAGAACACATTCACAT
1 TTCACATAAAACATATTCACAT
41506 GTTAATAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (30 bp):
TTCACATAAAACATATTCACATAGAACATT
Found at i:41502 original size:15 final size:15
Alignment explanation
Indices: 41424--41505 Score: 74
Period size: 15 Copynumber: 5.5 Consensus size: 15
41414 ATAGGGTATC
* *
41424 TTCACGTAGAACATT
1 TTCACATAGAACATA
* * *
41439 TTCACTTAGCACATT
1 TTCACATAGAACATA
* *
41454 TTCATATAAAACATA
1 TTCACATAGAACATA
* *
41469 TTCACATATAACATT
1 TTCACATAGAACATA
*
41484 TTCACATAGAACACA
1 TTCACATAGAACATA
41499 TTCACAT
1 TTCACAT
41506 GTTAATAAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 54 1.00
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (15 bp):
TTCACATAGAACATA
Found at i:48733 original size:2 final size:2
Alignment explanation
Indices: 48726--48783 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
48716 TAGAATGCTG
48726 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48768 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
48784 GATGTGTAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49388 original size:22 final size:22
Alignment explanation
Indices: 49258--49378 Score: 215
Period size: 22 Copynumber: 5.5 Consensus size: 22
49248 GGTTACATAG
* *
49258 GTCCTTAGGGACATATACACAG
1 GTCCTTCGGGACATATACACAT
49280 GTCCTTCGGGACATATACACAT
1 GTCCTTCGGGACATATACACAT
49302 GTCCTTCGGGACATATACACAT
1 GTCCTTCGGGACATATACACAT
49324 GTCCTTCGGGACATATACACAT
1 GTCCTTCGGGACATATACACAT
*
49346 GTCCTTCGGGACATATACATAT
1 GTCCTTCGGGACATATACACAT
49368 GTCCTTCGGGA
1 GTCCTTCGGGA
49379 TACATGCATA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 96 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (22 bp):
GTCCTTCGGGACATATACACAT
Found at i:49393 original size:22 final size:22
Alignment explanation
Indices: 49251--49402 Score: 126
Period size: 22 Copynumber: 6.9 Consensus size: 22
49241 GGTCGAGGGT
* * *
49251 TACATAGGTCCTTAGGGACATA
1 TACATAAGTCCTTCGGGACACA
* * *
49273 TACACAGGTCCTTCGGGACATA
1 TACATAAGTCCTTCGGGACACA
* * *
49295 TACACATGTCCTTCGGGACATA
1 TACATAAGTCCTTCGGGACACA
* * *
49317 TACACATGTCCTTCGGGACATA
1 TACATAAGTCCTTCGGGACACA
* * *
49339 TACACATGTCCTTCGGGACATA
1 TACATAAGTCCTTCGGGACACA
* *
49361 TACATATGTCCTTCGGGATACA
1 TACATAAGTCCTTCGGGACACA
*
49383 TGCATAAGTCC-TCTGGGACA
1 TACATAAGTCCTTC-GGGACA
49403 TATTTCACAT
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
21 2 0.02
22 118 0.98
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (22 bp):
TACATAAGTCCTTCGGGACACA
Found at i:49394 original size:66 final size:66
Alignment explanation
Indices: 49251--49405 Score: 213
Period size: 66 Copynumber: 2.3 Consensus size: 66
49241 GGTCGAGGGT
* * *
49251 TACATAGGTCCTTAGGGACATATACACAGGTCCTTCGGGACATATACACATGTCCTTCGGGACAT
1 TACATAAGTCCTTCGGGACATATACACAGGTCCTTCGGGACATATACACATGTCCTTCGGGACAC
49316 A
66 A
* * * * *
49317 TACACATGTCCTTCGGGACATATACACATGTCCTTCGGGACATATACATATGTCCTTCGGGATAC
1 TACATAAGTCCTTCGGGACATATACACAGGTCCTTCGGGACATATACACATGTCCTTCGGGACAC
49382 A
66 A
*
49383 TGCATAAGTCC-TCTGGGACATAT
1 TACATAAGTCCTTC-GGGACATAT
49406 TTCACATGCC
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
65 2 0.03
66 76 0.97
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (66 bp):
TACATAAGTCCTTCGGGACATATACACAGGTCCTTCGGGACATATACACATGTCCTTCGGGACAC
A
Done.