Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006879.1 Hibiscus syriacus cultivar Beakdansim tig00017525_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: 97812
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:603 original size:2 final size:2
Alignment explanation
Indices: 598--634 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
588 ACACACACAC
598 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
635 TAGAATTAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11345 original size:2 final size:2
Alignment explanation
Indices: 11338--11362 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11328 TTCACCACAA
11338 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11363 AACAATAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11561 original size:31 final size:31
Alignment explanation
Indices: 11495--11561 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
11485 TTAGCGATTG
** **
11495 AGGGACTAAAATCAAATAGATTGATAATGTC
1 AGGGACTAAAATCAAATAGATCAATAACATC
*
11526 AGGGACTAAAATCAAATAGATCAATAACATT
1 AGGGACTAAAATCAAATAGATCAATAACATC
11557 AGGGA
1 AGGGA
11562 TCATTCTCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.22
Consensus pattern (31 bp):
AGGGACTAAAATCAAATAGATCAATAACATC
Found at i:14141 original size:21 final size:21
Alignment explanation
Indices: 14103--14146 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
14093 AAACTATAAG
* *
14103 TTAGGGTTTAGAGGTTATTGT
1 TTAGGGTTTAGAAGTTATGGT
* *
14124 TTAGGGTTTATAATTTATGGT
1 TTAGGGTTTAGAAGTTATGGT
14145 TT
1 TT
14147 TAAGTTAGGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.52
Consensus pattern (21 bp):
TTAGGGTTTAGAAGTTATGGT
Found at i:17624 original size:60 final size:60
Alignment explanation
Indices: 17511--17628 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
17501 AATAGTCATG
* * * *
17511 TGACCATTTTGTAACTTTTAATAGTTGAAGGACTCAACAAATCAACACTCTATAGTCGAA
1 TGACCATTTTATAACTTTTAATAGTCGAAGGACTCAAAAAATCAACACCCTATAGTCGAA
* * * *
17571 TGACCATTTTATAAGTTTTAATAGTCGAGGGACTTAATAAAAT-AGCACCCTATAGTCG
1 TGACCATTTTATAACTTTTAATAGTCGAAGGACTCAA-AAAATCAACACCCTATAGTCG
17629 GGATCATTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 45 0.92
61 4 0.08
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (60 bp):
TGACCATTTTATAACTTTTAATAGTCGAAGGACTCAAAAAATCAACACCCTATAGTCGAA
Found at i:19685 original size:27 final size:27
Alignment explanation
Indices: 19645--19696 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
19635 TTGATGTTAC
*
19645 TTTTAAATCTGATTCGAGAATTATTAA
1 TTTTAAATCCGATTCGAGAATTATTAA
* *
19672 TTTTAGATCCGATTCGAGTATTATT
1 TTTTAAATCCGATTCGAGAATTATT
19697 TATACTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (27 bp):
TTTTAAATCCGATTCGAGAATTATTAA
Found at i:21521 original size:15 final size:15
Alignment explanation
Indices: 21501--21532 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
21491 AGAAAGCACA
21501 AATAAATCCTCAAGC
1 AATAAATCCTCAAGC
21516 AATAAATCCTCAAGC
1 AATAAATCCTCAAGC
21531 AA
1 AA
21533 GGTGAGTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (15 bp):
AATAAATCCTCAAGC
Found at i:43365 original size:30 final size:30
Alignment explanation
Indices: 43331--43389 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
43321 ATTTAAATTT
43331 TCTTCGATTAATTATTTATTTTATAGATGG
1 TCTTCGATTAATTATTTATTTTATAGATGG
43361 TCTTCGATTAATTATTTATTTTATAGATG
1 TCTTCGATTAATTATTTATTTTATAGATG
43390 ATGTTCATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.07, G:0.12, T:0.54
Consensus pattern (30 bp):
TCTTCGATTAATTATTTATTTTATAGATGG
Found at i:43653 original size:16 final size:16
Alignment explanation
Indices: 43634--43666 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
43624 GAAATGAATC
*
43634 AAAAGTGAAACAAAAA
1 AAAAATGAAACAAAAA
43650 AAAAATGAAACAAAAA
1 AAAAATGAAACAAAAA
43666 A
1 A
43667 CTAAAGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.06, G:0.09, T:0.06
Consensus pattern (16 bp):
AAAAATGAAACAAAAA
Found at i:44016 original size:17 final size:19
Alignment explanation
Indices: 43976--44015 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
43966 TTTTCAATGG
43976 AAAATACATAGAAAATTTT
1 AAAATACATAGAAAATTTT
*
43995 AAAATATATA-AAAATTTT
1 AAAATACATAGAAAATTTT
44013 AAA
1 AAA
44016 TTAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAATACATAGAAAATTTT
Found at i:44025 original size:18 final size:18
Alignment explanation
Indices: 43987--44026 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
43977 AAATACATAG
* *
43987 AAAATTTTAAAATATATA
1 AAAATTTTAAAATAAAAA
*
44005 AAAATTTTAAATTAAAAA
1 AAAATTTTAAAATAAAAA
44023 AAAA
1 AAAA
44027 CAACTGTCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTTTAAAATAAAAA
Found at i:45506 original size:136 final size:136
Alignment explanation
Indices: 45262--45533 Score: 544
Period size: 136 Copynumber: 2.0 Consensus size: 136
45252 TCCATGGACT
45262 ATTTGTGTACTTTACCATAGTTGTTATGTAGTAAAATGGTTACTTTCACCAAATTTTCTCACCTA
1 ATTTGTGTACTTTACCATAGTTGTTATGTAGTAAAATGGTTACTTTCACCAAATTTTCTCACCTA
45327 TCAACTATTCAAAATATTCTTAATATCATCGACAATATTAAATAATGTACAATTATAACTCTTCG
66 TCAACTATTCAAAATATTCTTAATATCATCGACAATATTAAATAATGTACAATTATAACTCTTCG
45392 CATATC
131 CATATC
45398 ATTTGTGTACTTTACCATAGTTGTTATGTAGTAAAATGGTTACTTTCACCAAATTTTCTCACCTA
1 ATTTGTGTACTTTACCATAGTTGTTATGTAGTAAAATGGTTACTTTCACCAAATTTTCTCACCTA
45463 TCAACTATTCAAAATATTCTTAATATCATCGACAATATTAAATAATGTACAATTATAACTCTTCG
66 TCAACTATTCAAAATATTCTTAATATCATCGACAATATTAAATAATGTACAATTATAACTCTTCG
45528 CATATC
131 CATATC
45534 TATATGAACA
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 136 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.40
Consensus pattern (136 bp):
ATTTGTGTACTTTACCATAGTTGTTATGTAGTAAAATGGTTACTTTCACCAAATTTTCTCACCTA
TCAACTATTCAAAATATTCTTAATATCATCGACAATATTAAATAATGTACAATTATAACTCTTCG
CATATC
Found at i:50280 original size:18 final size:19
Alignment explanation
Indices: 50251--50286 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
50241 AGATGGATGT
50251 TAATATGTTGTTTGAGATA
1 TAATATGTTGTTTGAGATA
50270 TAATA-GTTGTTTGAGAT
1 TAATATGTTGTTTGAGAT
50287 TCTAAGATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (19 bp):
TAATATGTTGTTTGAGATA
Found at i:65322 original size:122 final size:122
Alignment explanation
Indices: 65105--65351 Score: 476
Period size: 122 Copynumber: 2.0 Consensus size: 122
65095 ACACAGAGGG
65105 AAGTACAATGACAATTGCCCTTGTTGTGTCCCTTAACAAAGATGTAGGTGCAAGCGTTTCATACG
1 AAGTACAATGACAATTGCCCTTGTTGTGTCCCTTAACAAAGATGTAGGTGCAAGCGTTTCATACG
*
65170 CTGACGAGGCATCTAGGAACGATAAACAACAGCCTCAACCGACCAACAAGCAATTCT
66 CTAACGAGGCATCTAGGAACGATAAACAACAGCCTCAACCGACCAACAAGCAATTCT
*
65227 AAGTACAATGGCAATTGCCCTTGTTGTGTCCCTTAACAAAGATGTAGGTGCAAGCGTTTCATACG
1 AAGTACAATGACAATTGCCCTTGTTGTGTCCCTTAACAAAGATGTAGGTGCAAGCGTTTCATACG
65292 CTAACGAGGCATCTAGGAACGATAAACAACAGCCTCAACCGACCAACAAGCAATTCT
66 CTAACGAGGCATCTAGGAACGATAAACAACAGCCTCAACCGACCAACAAGCAATTCT
65349 AAG
1 AAG
65352 GGAAAATGCG
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 123 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (122 bp):
AAGTACAATGACAATTGCCCTTGTTGTGTCCCTTAACAAAGATGTAGGTGCAAGCGTTTCATACG
CTAACGAGGCATCTAGGAACGATAAACAACAGCCTCAACCGACCAACAAGCAATTCT
Found at i:66730 original size:32 final size:33
Alignment explanation
Indices: 66668--66731 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
66658 GCATTAAAAT
*
66668 AGAAATTAAACGAAAATATGGAAAACTAAAGAA
1 AGAAACTAAACGAAAATATGGAAAACTAAAGAA
* *
66701 AGAAACTAAACGTAAA-ATGGAAAAGTAAAGA
1 AGAAACTAAACGAAAATATGGAAAACTAAAGA
66732 GAGATAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.62, C:0.06, G:0.17, T:0.14
Consensus pattern (33 bp):
AGAAACTAAACGAAAATATGGAAAACTAAAGAA
Found at i:74892 original size:14 final size:16
Alignment explanation
Indices: 74853--74890 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
74843 TCGTTGACAG
74853 AATTTATTCATATATTT
1 AATTT-TTCATATATTT
74870 AATTTTTCATA-ATTT
1 AATTTTTCATATATTT
74885 AATTTT
1 AATTTT
74891 CAATTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.48
16 6 0.29
17 5 0.24
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTTTCATATATTT
Found at i:74966 original size:2 final size:2
Alignment explanation
Indices: 74959--74997 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
74949 AAATATTGAC
74959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
74998 AAAAAAACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:79926 original size:20 final size:20
Alignment explanation
Indices: 79889--79927 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
79879 CTCTAAATCA
* *
79889 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
79909 TTTTTCAAAATCTAATTTT
1 TTTTTCAAAATCTAATTTT
79928 ACTTTCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:84495 original size:20 final size:20
Alignment explanation
Indices: 84472--84509 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
84462 AAAGTTTAAG
84472 TACTTAAT-TGATAGTTTATA
1 TACTTAATGTG-TAGTTTATA
*
84492 TACTTTATGTGTAGTTTA
1 TACTTAATGTGTAGTTTA
84510 CCCTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (20 bp):
TACTTAATGTGTAGTTTATA
Found at i:84674 original size:51 final size:50
Alignment explanation
Indices: 84585--84689 Score: 131
Period size: 51 Copynumber: 2.1 Consensus size: 50
84575 ATGAAAGGTG
*
84585 AACTAATCACTAGGGTGATGAATTTCAAGATAAAATA-TTTTTTTATTAA
1 AACTAATCACTAGGGTGATGAATTTCAAAATAAAATATTTTTTTTATTAA
* * * * *
84634 AACTCATCACGTAGGAGTGATGAGTTTTAAAATGATATATTTTTTTTATTAA
1 AACTAATCAC-TAGG-GTGATGAATTTCAAAATAAAATATTTTTTTTATTAA
84686 AACT
1 AACT
84690 TGTCATGCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 9 0.19
50 4 0.09
51 18 0.38
52 16 0.34
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (50 bp):
AACTAATCACTAGGGTGATGAATTTCAAAATAAAATATTTTTTTTATTAA
Found at i:85014 original size:30 final size:30
Alignment explanation
Indices: 84968--85024 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
84958 TTTCATTTAT
*
84968 GTACCTAAAATATA-TTTTGGTCAAAATAA
1 GTACCTAAAATATATTTTTGGCCAAAATAA
84997 GTACCTAAAATTATATTTTTGGCCAAAA
1 GTACCTAAAA-TATATTTTTGGCCAAAA
85025 ATTGGTACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 10 0.40
30 4 0.16
31 11 0.44
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (30 bp):
GTACCTAAAATATATTTTTGGCCAAAATAA
Found at i:94899 original size:19 final size:19
Alignment explanation
Indices: 94875--94917 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
94865 CCTATGATGG
94875 AAATAACATGAACAAATAA
1 AAATAACATGAACAAATAA
*
94894 AAATAACATGAACAGATAA
1 AAATAACATGAACAAATAA
94913 AAATA
1 AAATA
94918 TATTCTGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.67, C:0.09, G:0.07, T:0.16
Consensus pattern (19 bp):
AAATAACATGAACAAATAA
Done.