Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005749.1 Hibiscus syriacus cultivar Beakdansim tig00013446_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: 235396
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:212311 original size:18 final size:18
Alignment explanation
Indices: 212288--212327 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
212278 GTGTACATGT
212288 GGGTGTAAGGTCCTTACC
1 GGGTGTAAGGTCCTTACC
* *
212306 GGGTGTAGGGTCCTTACT
1 GGGTGTAAGGTCCTTACC
212324 GGGT
1 GGGT
212328 CCTACACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.17, G:0.40, T:0.30
Consensus pattern (18 bp):
GGGTGTAAGGTCCTTACC
Found at i:215713 original size:22 final size:23
Alignment explanation
Indices: 215663--215723 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
215653 AATAACTTTA
*
215663 TCTTTATGACACGTTTTCCTCTAT
1 TCTTT-TGACATGTTTTCCTCTAT
215687 T-TTTTGACATGTTTT-CT-TAT
1 TCTTTTGACATGTTTTCCTCTAT
215707 GTCTTTTAGA-ATGTTTT
1 -TCTTTT-GACATGTTTT
215724 GGTCTTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 3 0.09
21 3 0.09
22 21 0.64
23 5 0.15
24 1 0.03
ACGTcount: A:0.16, C:0.15, G:0.11, T:0.57
Consensus pattern (23 bp):
TCTTTTGACATGTTTTCCTCTAT
Found at i:219889 original size:64 final size:61
Alignment explanation
Indices: 219819--219998 Score: 177
Period size: 65 Copynumber: 2.8 Consensus size: 61
219809 TTGGACCCTT
* *
219819 AGTGCATCTGTGCACTAAGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAACCAG
1 AGTGCATC-GTGCACT--GAGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-AACCAC
* *
219883 AGTGCATCGATGCATGGCTG-GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCT
1 AGTGCATCG-TGCA---CTGAGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAACCA
219947 C
61 C
*
219948 AGTGCATCGGTGCA-TGGTAAGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATC-GTGCACT-G--AGTGCATCGATGCATCAAATGCATTCGATGTT
219999 CAATTTAATT
Statistics
Matches: 100, Mismatches: 5, Indels: 22
0.79 0.04 0.17
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 1 0.01
64 42 0.42
65 49 0.49
66 4 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (61 bp):
AGTGCATCGTGCACTGAGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAACCAC
Found at i:219972 original size:65 final size:65
Alignment explanation
Indices: 219838--219998 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 65
219828 GTGCACTAAG
* *
219838 AGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAACCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAACCACAGTGCATCGATGCATGGCT
* * * *
219902 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAACCACAGTGCATCGATGCATGGC
219965 T
65 T
*
219966 AAGTGCATCGATGCATGAAATGCATTCGATGTT
1 -AGTGCATCGATGCATCAAATGCATTCGATGTT
219999 CAATTTAATT
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 29 0.34
65 54 0.63
66 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAACCACAGTGCATCGATGCATGGCT
Found at i:220509 original size:2 final size:2
Alignment explanation
Indices: 220502--220574 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
220492 TAGCCAATTG
220502 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
220544 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 A
220575 GCTTAAGCTG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:229532 original size:2 final size:2
Alignment explanation
Indices: 229527--229787 Score: 161
Period size: 2 Copynumber: 141.5 Consensus size: 2
229517 CTAAAAAATA
* *
229527 AT AT AT AT AA AT -T A- AT AT AT A- AG A- AT AT A- AT AT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
*
229565 AT A- AT A- AT ACT AT A- AT AT A- AT A- AT ACT AT AT AA AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
229604 AT A- AT A- AT AT A- AT AT A- AT AT AT A- AT AT A- 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
*
229640 CT AT AT A- AT AT AT AT AT A- AT AT A- AT AT AT AT A- 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
229678 AT AT AT A- ACT A- AT AT AT A- AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
229717 AT ACT AT AT A- AT AT ACC AT GCT AT AT A- AT AT AT AGT AT AT A-
1 AT A-T AT AT AT AT AT A-T AT -AT AT AT AT AT AT AT A-T AT AT AT
*
229758 AA AT A- AT AT AT A- AT AT AGT AT A- AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A
229788 AAAAGAAATC
Statistics
Matches: 208, Mismatches: 11, Indels: 80
0.70 0.04 0.27
Matches are distributed among these distances:
1 31 0.15
2 162 0.78
3 15 0.07
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:229588 original size:31 final size:30
Alignment explanation
Indices: 229524--229731 Score: 206
Period size: 31 Copynumber: 7.0 Consensus size: 30
229514 GACCTAAAAA
*
229524 ATAATATATATA-AATTAATATATAAGA-AT
1 ATAATATATATATAA-TAATATATAATATAT
229553 ATAATATATGATATAATAATACTATAATATA-
1 ATAATATAT-ATATAATAATA-TATAATATAT
229584 ATAATACTATATA-AAT-ATATATAATA-AT
1 ATAATA-TATATATAATAATATATAATATAT
*
229612 ATAATATAATATATAAT-ATAATATATATCTAT
1 ATAATAT-ATATATAATAAT-ATATA-ATATAT
229644 ATAATATATATATAAT-ATA-AT-ATATAT
1 ATAATATATATATAATAATATATAATATAT
229671 A-ATATATATATATAACTAATATATAATATAT
1 ATA-ATATATATATAA-TAATATATAATATAT
*
229702 AT-ATATATATTATATATACTATATAATATA
1 ATAATATATA-TATA-ATAATATATAATATA
229732 CCATGCTATA
Statistics
Matches: 156, Mismatches: 4, Indels: 36
0.80 0.02 0.18
Matches are distributed among these distances:
26 1 0.01
27 20 0.13
28 19 0.12
29 22 0.14
30 26 0.17
31 54 0.35
32 14 0.09
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (30 bp):
ATAATATATATATAATAATATATAATATAT
Found at i:229624 original size:57 final size:54
Alignment explanation
Indices: 229523--229788 Score: 227
Period size: 55 Copynumber: 4.9 Consensus size: 54
229513 GGACCTAAAA
*
229523 AATAATATATATAAATTAATATATAAGAATATAATATATGATATAATAATACTATAATAT
1 AATAATATATATAAA-T-ATATATAATAATATAATATA--ATATAAT-ATA-TATAATAT
229583 AATAATACTATATAAATATATATAATAATATAATATAATAT-ATA-ATATAATAT
1 AATAATA-TATATAAATATATATAATAATATAATATAATATAATATATATAATAT
*
229636 -AT-ATCTATAT-AATATATAT-ATAATATAATAT-ATATAATATATAT-ATAT
1 AATAATATATATAAATATATATAATAATATAATATAATATAATATATATAATAT
* * * **
229684 AACTAATATATA-ATATATATATATATATTAT-ATATACTATATAATATACCATGCTAT
1 AA-TAATATATATAAATATATATA-ATAATATAATATA--ATATAATATA-TATAATAT
* * *
229741 -ATAATATATAGTATATA-AAATAAT-ATATAATATAGTATAAT-TATATAA
1 AATAATATATA-TAAATATATATAATAATATAATATAATATAATATATATAA
229789 AAAGAAATCC
Statistics
Matches: 176, Mismatches: 13, Indels: 43
0.76 0.06 0.19
Matches are distributed among these distances:
47 4 0.02
48 19 0.11
49 14 0.08
50 6 0.03
51 18 0.10
52 8 0.05
53 20 0.11
54 4 0.02
55 27 0.15
56 9 0.05
57 12 0.07
59 19 0.11
60 8 0.05
61 8 0.05
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (54 bp):
AATAATATATATAAATATATATAATAATATAATATAATATAATATATATAATAT
Found at i:229678 original size:64 final size:64
Alignment explanation
Indices: 229550--229787 Score: 215
Period size: 64 Copynumber: 3.7 Consensus size: 64
229540 AATATATAAG
* *
229550 AATATAATATATGATATAATAATACTAT-AATATAATA-ATACTATATA-AATATATA-TAATAA
1 AATATAATATATAATATAAT-ATA-TATCTATATAATATATA-TATATATAATATATACTAAT-A
229611 TAT
62 TAT
229614 AATATAATATATAATATAATATATATCTATATAATATATATATAATATAATATATA-TAATATAT
1 AATATAATATATAATATAATATATATCTATATAATATATATAT-ATATAATATATACTAATATAT
* * * **
229678 ATATATAACTA-AT-ATATAATATATATATATATATTATATATACTATATAATATA-CCATGCTA
1 A-ATATAA-TATATAATATAATATATATCTATATAATATATATA-TATATAATATATAC-TAATA
229740 TAT
62 TAT
* *
229743 AATATATAGTATATAAAATAATATATAATATAGTATAAT-TATATA
1 AATATA-A-TATATAATATAATATAT-ATCTA-TATAATATATATA
229788 AAAAGAAATC
Statistics
Matches: 150, Mismatches: 10, Indels: 24
0.82 0.05 0.13
Matches are distributed among these distances:
62 3 0.02
63 14 0.09
64 72 0.48
65 31 0.21
66 4 0.03
67 10 0.07
68 11 0.07
69 5 0.03
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (64 bp):
AATATAATATATAATATAATATATATCTATATAATATATATATATATAATATATACTAATATAT
Found at i:229774 original size:31 final size:29
Alignment explanation
Indices: 229522--229788 Score: 158
Period size: 31 Copynumber: 9.4 Consensus size: 29
229512 TGGACCTAAA
*
229522 AAATAATATAT-ATA-AAT-TAATATATAAG
1 AAATAATATATAATATAATAT-ATATAT-AT
*
229550 AATATAATATATGATATAATA-ATACTATA-
1 AA-ATAATATATAATATAATATATA-TATAT
* * *
229579 ATATAATA-ATACTAT-ATAAATATATAT
1 AAATAATATATAATATAATATATATATAT
229606 -AAT-A-ATATAATATAATATATA-ATAT
1 AAATAATATATAATATAATATATATATAT
*
229631 -AATATATATCT-ATATAATATATATATA-
1 AAATA-ATATATAATATAATATATATATAT
*
229658 ATAT-A-ATAT-ATATAATATATATATAT
1 AAATAATATATAATATAATATATATATAT
*
229684 AACTAATATATAATATATATATATATATTAT
1 AAATAATATATAATATA-ATATATATA-TAT
* * *
229715 ATATACTATATAATATACCATGCTATATA-AT
1 AAATAATATATAATATA--AT-ATATATATAT
* * *
229746 ATATAGTATATAAAATAATATATA-ATAT
1 AAATAATATATAATATAATATATATATAT
*
229774 AGTATAATTATATAA
1 A-AATAA-TATATAA
229789 AAAGAAATCC
Statistics
Matches: 194, Mismatches: 20, Indels: 48
0.74 0.08 0.18
Matches are distributed among these distances:
24 1 0.01
25 33 0.17
26 18 0.09
27 23 0.12
28 27 0.14
29 21 0.11
30 23 0.12
31 40 0.21
32 2 0.01
33 6 0.03
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (29 bp):
AAATAATATATAATATAATATATATATAT
Done.