Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006090.1 Hibiscus syriacus cultivar Beakdansim tig00014440_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: 74588
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:1263 original size:17 final size:16
Alignment explanation
Indices: 1241--1356 Score: 62
Period size: 16 Copynumber: 7.2 Consensus size: 16
1231 TAGCAAAAAA
*
1241 TAAATAATTAATTAATT
1 TAAATAAATAA-TAATT
1258 TAAATAAATAATAA-T
1 TAAATAAATAATAATT
* *
1273 TATATAAAT-ATTATT
1 TAAATAAATAATAATT
* *
1288 CT-AATAAAAAATTATT
1 -TAAATAAATAATAATT
* *
1304 TATATAATATATTAA-T
1 TAAATAA-ATAATAATT
*
1320 AAAATATAATAACT-ATT
1 TAAATA-AATAA-TAATT
* *
1337 TAAAAAAATACTAATT
1 TAAATAAATAATAATT
1353 TAAA
1 TAAA
1357 AATAAATTTC
Statistics
Matches: 75, Mismatches: 15, Indels: 19
0.69 0.14 0.17
Matches are distributed among these distances:
14 3 0.04
15 17 0.23
16 34 0.45
17 21 0.28
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAATAAATAATAATT
Found at i:1264 original size:21 final size:19
Alignment explanation
Indices: 1238--1282 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
1228 AATTAGCAAA
*
1238 AAATAAATAATTAATTAATTT
1 AAATAAATAA-TAATT-ATAT
1259 AAATAAATAATAATTATAT
1 AAATAAATAATAATTATAT
1278 AAATA
1 AAATA
1283 TTATTCTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.35
20 5 0.22
21 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATAAATAATAATTATAT
Found at i:1317 original size:16 final size:15
Alignment explanation
Indices: 1255--1317 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
1245 TAATTAATTA
* *
1255 ATTTAAATAAATAAT
1 ATTTATATAAATATT
*
1270 AATTATATAAATATT
1 ATTTATATAAATATT
*
1285 ATTCTA-ATAAAAAATT
1 ATT-TATAT-AAATATT
1301 ATTTATATAATATATT
1 ATTTATATAA-ATATT
1317 A
1 A
1318 ATAAAATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
15 20 0.53
16 18 0.47
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTATATAAATATT
Found at i:1339 original size:21 final size:22
Alignment explanation
Indices: 1307--1351 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1297 AATTATTTAT
*
1307 ATAATATATTAATAAAATA-TA
1 ATAATATATTAAAAAAATACTA
1328 ATAACTAT-TTAAAAAAATACTA
1 ATAA-TATATTAAAAAAATACTA
1350 AT
1 AT
1352 TTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAATATATTAAAAAAATACTA
Found at i:18650 original size:44 final size:45
Alignment explanation
Indices: 18587--18709 Score: 176
Period size: 44 Copynumber: 2.6 Consensus size: 45
18577 ACGGTTACGG
18587 ATTCGGCTTTGAATATAGCATTCTTTATAGAATTTATTCAC-AGA
1 ATTCGGCTTTGAATATAGCATTCTTTATAGAATTTATTCACTAGA
18631 ATTCGGCTTTGAATATAGCATTCTTTATAGAATTTATTCACGTTGATAAGA
1 ATTCGGCTTTGAATATAGCATTCTTTATAGAATTTATTCAC-----T-AGA
*
18682 ATTTGGCTTTGAATATAGCATTCTTTAT
1 ATTCGGCTTTGAATATAGCATTCTTTAT
18710 TTTATGTATT
Statistics
Matches: 71, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
44 41 0.58
51 30 0.42
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (45 bp):
ATTCGGCTTTGAATATAGCATTCTTTATAGAATTTATTCACTAGA
Found at i:18736 original size:51 final size:51
Alignment explanation
Indices: 18628--18728 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
18618 ATTTATTCAC
* *
18628 AGAATTCGGCTTTGAATATAGCATTCTTTATAGAATTTATTCACGTTGATA
1 AGAATTTGGCTTTGAATATAGCATTCTTTATAGAATGTATTCACGTTGATA
***
18679 AGAATTTGGCTTTGAATATAGCATTCTTTATTTTATGTATTCACGTTGAT
1 AGAATTTGGCTTTGAATATAGCATTCTTTATAGAATGTATTCACGTTGAT
18729 GCGAATTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (51 bp):
AGAATTTGGCTTTGAATATAGCATTCTTTATAGAATGTATTCACGTTGATA
Found at i:23981 original size:18 final size:18
Alignment explanation
Indices: 23958--23992 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
23948 AAGGGTGTGC
23958 GTGCAGGGACGGATCGAG
1 GTGCAGGGACGGATCGAG
*
23976 GTGCAGGGACTGATCGA
1 GTGCAGGGACGGATCGA
23993 ACCCTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.17, G:0.46, T:0.14
Consensus pattern (18 bp):
GTGCAGGGACGGATCGAG
Found at i:41394 original size:21 final size:21
Alignment explanation
Indices: 41370--41419 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
41360 TCGTAATGTG
41370 AATTTGAACTATCGCAACGCA
1 AATTTGAACTATCGCAACGCA
*
41391 AATTT-AGACTATCGCAACGCG
1 AATTTGA-ACTATCGCAACGCA
41412 AATTTGAA
1 AATTTGAA
41420 AACTGAGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (21 bp):
AATTTGAACTATCGCAACGCA
Found at i:42944 original size:167 final size:168
Alignment explanation
Indices: 42650--42981 Score: 612
Period size: 167 Copynumber: 2.0 Consensus size: 168
42640 GTTGAAAATA
42650 TCAGAAATGGTTGTAGGTTAAATGCTAGTACATGCTAAGATTCAATGCTTAGAAATGTCAACAAC
1 TCAGAAATGGTTGTAGGTTAAATGCTAGTACATGCTAAGATTCAATGCTTAGAAATGT--ACAAC
*
42715 AACAAAAATCCATTCACAATTTTCTGTATTTTTGACCCAATCAATTTCATTGTGGCCTTAAGCTA
64 AACAAAAATCCATTCACAACTTTCTGTATTTTTGACCCAATCAATTTCATTGTGGCCTTAAGCTA
42780 ATAGATAACAAACAATTACACATAAAAAGAATGCTAAGAT
129 ATAGATAACAAACAATTACACATAAAAAGAATGCTAAGAT
*
42820 TCAGAAATGGTTGTATGTTAAATGCTAGTACATGCTAAGATTCAATGCTTAGAAATGT-CAACAA
1 TCAGAAATGGTTGTAGGTTAAATGCTAGTACATGCTAAGATTCAATGCTTAGAAATGTACAACAA
42884 CAAAAATCCATTCACAACTTTCTGTATTTTTGACCCAATCAATTTCATTGTGGCCTTAAGCTAAT
66 CAAAAATCCATTCACAACTTTCTGTATTTTTGACCCAATCAATTTCATTGTGGCCTTAAGCTAAT
*
42949 AGATAACAAACAATTACACATAAAATGAATGCT
131 AGATAACAAACAATTACACATAAAAAGAATGCT
42982 GTCAGATTAA
Statistics
Matches: 159, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
167 102 0.64
170 57 0.36
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (168 bp):
TCAGAAATGGTTGTAGGTTAAATGCTAGTACATGCTAAGATTCAATGCTTAGAAATGTACAACAA
CAAAAATCCATTCACAACTTTCTGTATTTTTGACCCAATCAATTTCATTGTGGCCTTAAGCTAAT
AGATAACAAACAATTACACATAAAAAGAATGCTAAGAT
Found at i:47464 original size:31 final size:31
Alignment explanation
Indices: 47429--47491 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
47419 AATTTGGTGA
47429 ATTCAATATGTCATTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACTAGGAACTCCC
47460 ATTCAATATGTCATTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACTAGGAACTCCC
47491 A
1 A
47492 AACTCTTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.32
Consensus pattern (31 bp):
ATTCAATATGTCATTCTCACTAGGAACTCCC
Found at i:50752 original size:22 final size:22
Alignment explanation
Indices: 50721--50763 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
50711 GTTTAAAAAT
50721 ACTAACATTTATATAGCTATTA
1 ACTAACATTTATATAGCTATTA
* *
50743 ACTAATATTTATATAGTTATT
1 ACTAACATTTATATAGCTATT
50764 TAATAAATCG
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:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (22 bp):
ACTAACATTTATATAGCTATTA
Found at i:60898 original size:31 final size:31
Alignment explanation
Indices: 60860--60921 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
60850 AATCCTGATG
60860 CACCAACAAACAAA-AAACCAAATAATTCAGC
1 CACCAACAAACAAAGAAA-CAAATAATTCAGC
60891 CACCAACAAACAAAGAAACAAATAATTCAGC
1 CACCAACAAACAAAGAAACAAATAATTCAGC
60922 TCTGACTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.58, C:0.27, G:0.05, T:0.10
Consensus pattern (31 bp):
CACCAACAAACAAAGAAACAAATAATTCAGC
Found at i:63797 original size:15 final size:15
Alignment explanation
Indices: 63779--63829 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
63769 TTCCGGAAAA
63779 TGAATTACTGGAATT
1 TGAATTACTGGAATT
* **
63794 TGAATTATTGGAAAA
1 TGAATTACTGGAATT
63809 TGAATTACTGGAATT
1 TGAATTACTGGAATT
63824 TGAATT
1 TGAATT
63830 TTGGAAAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:63843 original size:29 final size:30
Alignment explanation
Indices: 63773--63844 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
63763 TTGGTTTTCC
63773 GGAAAATGAATTACTGGAATTTGAATTATT
1 GGAAAATGAATTACTGGAATTTGAATTATT
63803 GGAAAATGAATTACTGGAATTTGAATT-TT
1 GGAAAATGAATTACTGGAATTTGAATTATT
63832 GGAAAATGAATTA
1 GGAAAATGAATTA
63845 AATTTCTGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 15 0.36
30 27 0.64
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.35
Consensus pattern (30 bp):
GGAAAATGAATTACTGGAATTTGAATTATT
Found at i:63886 original size:14 final size:14
Alignment explanation
Indices: 63854--63887 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
63844 AAATTTCTGG
*
63854 AAAACGTTTTCCGA
1 AAAATGTTTTCCGA
*
63868 AAAATGTTTTCCGT
1 AAAATGTTTTCCGA
63882 AAAATG
1 AAAATG
63888 AATTACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (14 bp):
AAAATGTTTTCCGA
Found at i:64097 original size:29 final size:32
Alignment explanation
Indices: 64065--64129 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 32
64055 ATTTATTATT
*
64065 AATAGT-ATTTT-TATAATTTTA-T-TAATAAA
1 AATAGTAATTTTGTAT-ATTTTAGTGAAATAAA
*
64094 AATATTAATTTTGTATATTTTAGTGAAATAAA
1 AATAGTAATTTTGTATATTTTAGTGAAATAAA
64126 AATA
1 AATA
64130 TTATAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
29 5 0.17
30 11 0.37
31 4 0.13
32 10 0.33
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (32 bp):
AATAGTAATTTTGTATATTTTAGTGAAATAAA
Found at i:64308 original size:26 final size:25
Alignment explanation
Indices: 64265--64356 Score: 75
Period size: 26 Copynumber: 3.7 Consensus size: 25
64255 ATAAATTTTT
*
64265 TATTATATATTAAAATAAAAATATAA
1 TATT-TATATTAATATAAAAATATAA
* * *
64291 TATCTTATATTATTATAATAAT-TGAT
1 TAT-TTATATTAATATAAAAATAT-AA
*
64317 TATTT-TATATAATATTAAAATATAA
1 TATTTATAT-TAATATAAAAATATAA
64342 TA-TTATATT-ATATAA
1 TATTTATATTAATATAA
64357 TATTAATAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
23 5 0.10
24 6 0.12
25 18 0.35
26 22 0.42
27 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
TATTTATATTAATATAAAAATATAA
Found at i:64340 original size:15 final size:15
Alignment explanation
Indices: 64322--64362 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
64312 TTGATTATTT
64322 TATATAATATT-AAA
1 TATATAATATTAAAA
* *
64336 -ATATAATATTATAT
1 TATATAATATTAAAA
64350 TATATAATATTAA
1 TATATAATATTAA
64363 TAAATTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 10 0.45
14 1 0.05
15 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TATATAATATTAAAA
Found at i:64341 original size:13 final size:14
Alignment explanation
Indices: 64323--64365 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
64313 TGATTATTTT
64323 ATATAATATTAA-A
1 ATATAATATTAATA
*
64336 ATATAATATTATATT
1 ATATAATATTA-ATA
64351 ATATAATATTAATA
1 ATATAATATTAATA
64365 A
1 A
64366 ATTAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATAATATTAATA
Found at i:64344 original size:18 final size:19
Alignment explanation
Indices: 64323--64380 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
64313 TGATTATTTT
64323 ATATAATATTAA-AATATA
1 ATATAATATTAATAATATA
* *
64341 ATATTATATTATATAATATT
1 ATATAATATTA-ATAATATA
64361 A-ATAA-ATTAATAA-ATA
1 ATATAATATTAATAATATA
64377 ATAT
1 ATAT
64381 TTTGATGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 3 0.09
17 6 0.18
18 14 0.42
19 4 0.12
20 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATAATATTAATAATATA
Found at i:64605 original size:42 final size:42
Alignment explanation
Indices: 64546--64649 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
64536 ATTACATTCA
* * *
64546 GGAAAACCAATTACGTGAAACAAACATTG-GAAAATATTTTCC
1 GGAAAACGAATTACGTGAAACAAACA-CGAGAAAACATTTTCC
64588 GGAAAACGAATTACGTGAAACAAACACGAGAAAACATTTTCC
1 GGAAAACGAATTACGTGAAACAAACACGAGAAAACATTTTCC
*
64630 GAAAAACGAATTACGTGAAA
1 GGAAAACGAATTACGTGAAA
64650 ACAGGGAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
41 1 0.02
42 56 0.98
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.19
Consensus pattern (42 bp):
GGAAAACGAATTACGTGAAACAAACACGAGAAAACATTTTCC
Found at i:65004 original size:16 final size:13
Alignment explanation
Indices: 64969--65003 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
64959 AATGACCAAT
64969 CCACCACCAGCGG
1 CCACCACCAGCGG
64982 CCACCACCAGCGG
1 CCACCACCAGCGG
64995 CCACCACCA
1 CCACCACCA
65004 CGAGCTGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.57, G:0.17, T:0.00
Consensus pattern (13 bp):
CCACCACCAGCGG
Found at i:65579 original size:86 final size:86
Alignment explanation
Indices: 65407--65579 Score: 328
Period size: 86 Copynumber: 2.0 Consensus size: 86
65397 CATGTTATCA
65407 TTAAAAATTATCACGTTAACAGTTATGTTAATTTTTTAACAATGAGTGATCGAAATAAACTAAAA
1 TTAAAAATTATCACGTTAACAGTTATGTTAATTTTTTAACAATGAGTGATCGAAATAAACTAAAA
*
65472 TGTAACTTTAGATATGTTTTT
66 TGTAACGTTAGATATGTTTTT
65493 TTAAAAATTATCACGTTAACAGTTATGTTAATTTTTTAACAATGAGTGATCGAAATAAAACTAAA
1 TTAAAAATTATCACGTTAACAGTTATGTTAATTTTTTAACAATGAGTGATCGAAAT-AAACTAAA
65558 ATGTAACGTTAGATATGTTTTT
65 ATGTAACGTTAGATATGTTTTT
65580 GAAAAAAATC
Statistics
Matches: 85, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 56 0.66
87 29 0.34
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (86 bp):
TTAAAAATTATCACGTTAACAGTTATGTTAATTTTTTAACAATGAGTGATCGAAATAAACTAAAA
TGTAACGTTAGATATGTTTTT
Found at i:68975 original size:31 final size:31
Alignment explanation
Indices: 68906--68979 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
68896 AACTCGGGGT
* * *
68906 GACCACATCTTAATTAAATAAAAATGTAAAT
1 GACCATATCTTAATTAAATAAAAATGAAAAC
68937 GACCATATCTTAATTAAATAAAAAT-AAAAGC
1 GACCATATCTTAATTAAATAAAAATGAAAA-C
*
68968 GATCATATCTTA
1 GACCATATCTTA
68980 TATTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 3 0.08
31 35 0.92
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.30
Consensus pattern (31 bp):
GACCATATCTTAATTAAATAAAAATGAAAAC
Done.