Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005962.1 Hibiscus syriacus cultivar Beakdansim tig00014008_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: 61046
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:696 original size:30 final size:30
Alignment explanation
Indices: 662--1167 Score: 392
Period size: 30 Copynumber: 17.1 Consensus size: 30
652 AACTCTCCTC
* * * *
662 CACCTCCTCCTCCTCCTTATGTTTATAAAT
1 CACCTCCTCCTCCTCCATATGTGTACAAGT
* **
692 CACCTCCTCCACCTCCATATAAGTACAAGT
1 CACCTCCTCCTCCTCCATATGTGTACAAGT
* * * * *
722 CATCTCCACCTCCTCCGTAT-TTTACAAAT
1 CACCTCCTCCTCCTCCATATGTGTACAAGT
* * *
751 CACCTCCTCCCCCTCCATACGTCTACAAGT
1 CACCTCCTCCTCCTCCATATGTGTACAAGT
* *
781 CTCCTCCTCCTCCTCCATATGAGTACAAGT
1 CACCTCCTCCTCCTCCATATGTGTACAAGT
811 CACCTCCT-C-CCTCCATATGTGTACAAGT
1 CACCTCCTCCTCCTCCATATGTGTACAAGT
* *
839 CA-TTGCCT-CTACCTCCATACGTGTACAAGTT
1 CACCT-CCTCCT-CCTCCATATGTGTACAAG-T
* *
870 CTCCTCCTCTTCCTCCATATGT-TCACAAGT
1 CACCTCCTCCTCCTCCATATGTGT-ACAAGT
* *
900 CACCTCCT-CTACCACCATATGTCTACAAGT
1 CACCTCCTCCT-CCTCCATATGTGTACAAGT
* * *
930 CACCTCC-AC-CCTCCATACGTCTACAAGT
1 CACCTCCTCCTCCTCCATATGTGTACAAGT
* ** * *
958 CTCCTCCTCCAACTCCATATGAGTATAAGT
1 CACCTCCTCCTCCTCCATATGTGTACAAGT
* * *
988 CACCTCCTCCTCCTCCTTATGTTTATGAA-T
1 CACCTCCTCCTCCTCCATATGTGTA-CAAGT
* ** *
1018 --CCTCCTCCCCCTCCATACATGTACAAAT
1 CACCTCCTCCTCCTCCATATGTGTACAAGT
*
1046 CACCGCCT-CTACCTCCATATGTGTACAAGT
1 CACCTCCTCCT-CCTCCATATGTGTACAAGT
* ** *
1076 CTCCTCCTCCTCC-CCATATAAGTACAAAT
1 CACCTCCTCCTCCTCCATATGTGTACAAGT
* * * *
1105 CACCACCTCCACCACCATATGTCTACAAGT
1 CACCTCCTCCTCCTCCATATGTGTACAAGT
* * * *
1135 CACCTTCTCCACCTCCATATGAGTACAAAT
1 CACCTCCTCCTCCTCCATATGTGTACAAGT
1165 CAC
1 CAC
1168 TACCACATGT
Statistics
Matches: 374, Mismatches: 82, Indels: 40
0.75 0.17 0.08
Matches are distributed among these distances:
27 3 0.01
28 66 0.18
29 48 0.13
30 230 0.61
31 25 0.07
32 2 0.01
ACGTcount: A:0.24, C:0.40, G:0.07, T:0.29
Consensus pattern (30 bp):
CACCTCCTCCTCCTCCATATGTGTACAAGT
Found at i:766 original size:59 final size:61
Alignment explanation
Indices: 664--1167 Score: 346
Period size: 58 Copynumber: 8.5 Consensus size: 61
654 CTCTCCTCCA
* * * **
664 CCTCCTCCTCCTCCTTATGTTTATAAATCACCTCCTCCACCTCCATATAAGTACAAGTCAT
1 CCTCCTCCTCCTCCATATGTTTACAAATCACCTCCTCCCCCTCCATATGTGTACAAGTCAT
* * * *
725 -CTCCACCTCCTCCGTAT-TTTACAAATCACCTCCTCCCCCTCCATACGTCTACAAGTC-T
1 CCTCCTCCTCCTCCATATGTTTACAAATCACCTCCTCCCCCTCCATATGTGTACAAGTCAT
** *
783 CCTCCTCCTCCTCCATATGAGTACAAGTCACCTCCT--CCCTCCATATGTGTACAAGTCAT
1 CCTCCTCCTCCTCCATATGTTTACAAATCACCTCCTCCCCCTCCATATGTGTACAAGTCAT
* * * * **
842 --TGCCT-CTACCTCCATACGTGTACAAGTTCTCCTCCTCTTCCTCCATATGT-TCACAAGTCA-
1 CCT-CCTCCT-CCTCCATATGTTTACAA-ATCACCTCCTCCCCCTCCATATGTGT-ACAAGTCAT
* * * * * *
902 CCTCCT-CTACCACCATATGTCTACAAGTCACCT-C-CACCCTCCATACGTCTACAAGTC-T
1 CCTCCTCCT-CCTCCATATGTTTACAAATCACCTCCTCCCCCTCCATATGTGTACAAGTCAT
** ** * * * * * * *
960 CCTCCTCCAACTCCATATGAGTATAAGTCACCTCCTCCTCCTCCTTATGT-T-TATG-AAT
1 CCTCCTCCTCCTCCATATGTTTACAAATCACCTCCTCCCCCTCCATATGTGTACAAGTCAT
* ** * * **
1018 CCTCCTCCCCCTCCATACATGTACAAATCACCGCCTCTACCTCCATATGTGTACAAGTC-T
1 CCTCCTCCTCCTCCATATGTTTACAAATCACCTCCTCCCCCTCCATATGTGTACAAGTCAT
*** * * * *
1078 CCTCCTCCTCC-CCATATAAGTACAAATCACCACCTCCACCACCATATGTCTACAAGTCA-
1 CCTCCTCCTCCTCCATATGTTTACAAATCACCTCCTCCCCCTCCATATGTGTACAAGTCAT
* * **
1137 CCTTCTCCACCTCCATATGAGTACAAATCAC
1 CCTCCTCCTCCTCCATATGTTTACAAATCAC
1168 TACCACATGT
Statistics
Matches: 356, Mismatches: 65, Indels: 45
0.76 0.14 0.10
Matches are distributed among these distances:
57 3 0.01
58 123 0.35
59 114 0.32
60 76 0.21
61 39 0.11
62 1 0.00
ACGTcount: A:0.24, C:0.40, G:0.07, T:0.29
Consensus pattern (61 bp):
CCTCCTCCTCCTCCATATGTTTACAAATCACCTCCTCCCCCTCCATATGTGTACAAGTCAT
Found at i:806 original size:89 final size:89
Alignment explanation
Indices: 596--1167 Score: 453
Period size: 89 Copynumber: 6.4 Consensus size: 89
586 TACGTATAGC
* * * * * *
596 TCTCCTCCTCCGCCTCCATATGA-TACAAGTCTCCACCACCTCCTCCGTACGTGTACAACTCTCC
1 TCTCCTCCTCCACCTCCATATGAGTACAAGTCACCTCC-CCTCCTCCATATGTGTACAA-----A
* * * * * *
660 TCCACCTCCTCCTCCTCCTTATGTTTATAAA
60 T-CACCTCCTCCCCCTCCATACGTCTACAAG
* * * * *
691 TCACCTCCTCCACCTCCATATAAGTACAAGTCATCTCCACCTCCTCCGTAT-TTTACAAATCACC
1 TCTCCTCCTCCACCTCCATATGAGTACAAGTCACCTCC-CCTCCTCCATATGTGTACAAATCACC
755 TCCTCCCCCTCCATACGTCTACAAG
65 TCCTCCCCCTCCATACGTCTACAAG
* * * *
780 TCTCCTCCTCCTCCTCCATATGAGTACAAGTCACCTCCTC-CCTCCATATGTGTACAAGTCA-TT
1 TCTCCTCCTCCACCTCCATATGAGTACAAGTCACCTCCCCTCCTCCATATGTGTACAAATCACCT
** *
843 GCCTCTACCTCCATACGTGTACAAG
66 -CCTCCCCCTCCATACGTCTACAAG
** * * * * *
868 TTCTCCTCCTCTTCCTCCATATG-TTCACAAGTCACCTCCTCTACCACCATATGTCTACAAGTCA
1 -TCTCCTCCTCCACCTCCATATGAGT-ACAAGTCACCTCCCCT-CCTCCATATGTGTACAAATCA
*
932 CCT-C-CACCCTCCATACGTCTACAAG
63 CCTCCTCCCCCTCCATACGTCTACAAG
* * * * **
957 TCTCCTCCTCCAACTCCATATGAGTATAAGTCACCTCCTCCTCCTCCTTATGTTTATGAAT--CC
1 TCTCCTCCTCCACCTCCATATGAGTACAAGTCACCTCC-CCTCCTCCATATGTGTACAAATCACC
* * *
1020 TCCTCCCCCTCCATACATGTACAAA
65 TCCTCCCCCTCCATACGTCTACAAG
* * * * * **
1045 TCACCGCCTCTACCTCCATATGTGTACAAGTCTCCTCCTCCTCC-CCATATAAGTACAAATCACC
1 TCTCCTCCTCCACCTCCATATGAGTACAAGTCACCTCC-CCTCCTCCATATGTGTACAAATCACC
* * * *
1109 ACCTCCACCACCATATGTCTACAAG
65 TCCTCCCCCTCCATACGTCTACAAG
* * *
1134 TCACCTTCTCCACCTCCATATGAGTACAAATCAC
1 TCTCCTCCTCCACCTCCATATGAGTACAAGTCAC
1168 TACCACATGT
Statistics
Matches: 386, Mismatches: 77, Indels: 34
0.78 0.15 0.07
Matches are distributed among these distances:
86 3 0.01
87 20 0.05
88 130 0.34
89 162 0.42
90 2 0.01
91 19 0.05
92 1 0.00
95 26 0.07
96 23 0.06
ACGTcount: A:0.23, C:0.41, G:0.08, T:0.29
Consensus pattern (89 bp):
TCTCCTCCTCCACCTCCATATGAGTACAAGTCACCTCCCCTCCTCCATATGTGTACAAATCACCT
CCTCCCCCTCCATACGTCTACAAG
Found at i:876 original size:119 final size:116
Alignment explanation
Indices: 662--1167 Score: 393
Period size: 119 Copynumber: 4.3 Consensus size: 116
652 AACTCTCCTC
* ** * **
662 CACCTCCTCCTCCTCCTTATGTTTATAAATCACCTCCTCCACCTCCATATAAGTACAAGTCATCT
1 CACCTCCTCCTCCTCCATATGAGTACAAATCACCTCCT-C-CCTCCATATGTGTACAAGTC-T-T
* * ** * * *
727 CCACCT-CCTCCGTAT-TTTACAAATCACCTCCTCCCCCTCCATACGTCTACAAGT
62 CC-TCTACCTCCATATGAGTACAAGTCACCTCCTCCTCCTCCATATGTCTACAAGT
* *
781 CTCCTCCTCCTCCTCCATATGAGTACAAGTCACCTCCTCCCTCCATATGTGTACAAGTCATTGCC
1 CACCTCCTCCTCCTCCATATGAGTACAAATCACCTCCTCCCTCCATATGTGTACAAGTC-TT-CC
* * * *
846 TCTACCTCCATACGTGTACAAGTTCTCCTCCTCTTCCTCCATATGT-TCACAAGT
64 TCTACCTCCATATGAGTACAAG-TCACCTCCTCCTCCTCCATATGTCT-ACAAGT
* ** * * * *
900 CACCTCCT-CTACCACCATATGTCTACAAGTCACCTCCACCCTCCATACGTCTACAAGTCTCCTC
1 CACCTCCTCCT-CCTCCATATGAGTACAAATCACCTCCTCCCTCCATATGTGTACAAGTCT--TC
* * * * * *
964 CTCCAACTCCATATGAGTATAAGTCACCTCCTCCTCCTCCTTATGTTTATGAA-T
63 CTCTACCTCCATATGAGTACAAGTCACCTCCTCCTCCTCCATATGTCTA-CAAGT
* * *
1018 --CCTCCTCCCCCTCCATA-CATGTACAAATCACCGCCTCTACCTCCATATGTGTACAAGTC-TC
1 CACCTCCTCCTCCTCCATATGA-GTACAAATCACCTCCTC--CCTCCATATGTGTACAAGTCTTC
* * * * *
1079 CTCCT-CCTCCCCATATAAGTACAAATCACCACCTCCACCACCATATGTCTACAAGT
63 CT-CTACCT--CCATATGAGTACAAGTCACCTCCTCCTCCTCCATATGTCTACAAGT
* *
1135 CACCTTCTCCACCTCCATATGAGTACAAATCAC
1 CACCTCCTCCTCCTCCATATGAGTACAAATCAC
1168 TACCACATGT
Statistics
Matches: 309, Mismatches: 57, Indels: 42
0.76 0.14 0.10
Matches are distributed among these distances:
115 6 0.02
116 32 0.10
117 64 0.21
118 51 0.17
119 154 0.50
120 2 0.01
ACGTcount: A:0.24, C:0.40, G:0.07, T:0.29
Consensus pattern (116 bp):
CACCTCCTCCTCCTCCATATGAGTACAAATCACCTCCTCCCTCCATATGTGTACAAGTCTTCCTC
TACCTCCATATGAGTACAAGTCACCTCCTCCTCCTCCATATGTCTACAAGT
Found at i:966 original size:177 final size:176
Alignment explanation
Indices: 688--1167 Score: 483
Period size: 177 Copynumber: 2.7 Consensus size: 176
678 TTATGTTTAT
* * ** * * * **
688 AAATCACCTCCTCCACCTCCATATAAGTACAAGTCATCTCCACCTCCTCCGTAT-TTTACAAAT-
1 AAATCACCGCCTCTACCTCCATATGTGTACAAGTCACCTCCTCCTCC-CCATATAACTACAAATC
* *
751 CACCTCCTCCCCCTCCATACGTCTACAAGTCTCCTCCTCCTCCTCCATATGAGTACAAGTCACCT
65 CACCT-C-CACCCTCCATACGTCTACAAGTCTCCTCCTCCACCTCCATATGAGTACAAGTCACCT
* * *
816 CCT-C-CCTCCATATGTGTA-CAAGTCATTGCCTCTACCTCCATACGTGTAC
128 CCTCCTCCTCCATATGTGTATCAA-TC-CT-CCTCCACCTCCATACATGTAC
* * * * **
865 AAGTTCTCCTCCTCTTCCTCCATATGT-TCACAAGTCACCTCCT-CTACCACCATATGTCTACAA
1 AA-ATCACCGCCTCTACCTCCATATGTGT-ACAAGTCACCTCCTCCT-CC-CCATATAACTACAA
* * *
928 GT-CACCTCCACCCTCCATACGTCTACAAGTCTCCTCCTCCAACTCCATATGAGTATAAGTCACC
62 ATCCACCTCCACCCTCCATACGTCTACAAGTCTCCTCCTCCACCTCCATATGAGTACAAGTCACC
* * * *
992 TCCTCCTCCTCCTTATGTTTATGAATCCTCCTCCCCCTCCATACATGTAC
127 TCCTCCTCCTCCATATGTGTATCAATCCTCCTCCACCTCCATACATGTAC
* *
1042 AAATCACCGCCTCTACCTCCATATGTGTACAAGTCTCCTCCTCCTCCCCATATAAGTACAAATCA
1 AAATCACCGCCTCTACCTCCATATGTGTACAAGTCACCTCCTCCTCCCCATATAACTACAAAT--
* * * * *
1107 CCACCTCCA-CCACCATATGTCTACAAGTCACCTTCTCCACCTCCATATGAGTACAAATCAC
64 CCACCTCCACCCTCCATACGTCTACAAGTCTCCTCCTCCACCTCCATATGAGTACAAGTCAC
1168 TACCACATGT
Statistics
Matches: 252, Mismatches: 39, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
175 12 0.05
176 35 0.14
177 129 0.51
178 48 0.19
179 26 0.10
180 2 0.01
ACGTcount: A:0.25, C:0.40, G:0.07, T:0.28
Consensus pattern (176 bp):
AAATCACCGCCTCTACCTCCATATGTGTACAAGTCACCTCCTCCTCCCCATATAACTACAAATCC
ACCTCCACCCTCCATACGTCTACAAGTCTCCTCCTCCACCTCCATATGAGTACAAGTCACCTCCT
CCTCCTCCATATGTGTATCAATCCTCCTCCACCTCCATACATGTAC
Found at i:7723 original size:22 final size:21
Alignment explanation
Indices: 7689--7731 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
7679 GGACTTCAGC
7689 GATGGCAACGGTGAGACGAAAA
1 GATGGCAACGGTG-GACGAAAA
** *
7711 GATGGCAGGGGTGGCCGAAAA
1 GATGGCAACGGTGGACGAAAA
7732 TCGATGTGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.35, C:0.14, G:0.42, T:0.09
Consensus pattern (21 bp):
GATGGCAACGGTGGACGAAAA
Found at i:18463 original size:59 final size:60
Alignment explanation
Indices: 18390--18526 Score: 136
Period size: 59 Copynumber: 2.3 Consensus size: 60
18380 AGATTTAGGA
* * *
18390 TAAAGTATAC-AAATGGTCCCT-CGACTATATAGTATTGCTTTATTAAGCCCCTTGACTAT
1 TAAAGT-TACAAAATGGTCCCTCCGACTATAGAATATTGCTTTATTAAGCCCCTCGACTAT
* * * * * * * *
18449 TAAAGTTACAAAATGAT-CCTCCGATTATAGAATGTTGTTTTGTTGAGTCCCTCGTCTAT
1 TAAAGTTACAAAATGGTCCCTCCGACTATAGAATATTGCTTTATTAAGCCCCTCGACTAT
18508 TAAAAGTTACAAAATGGTC
1 T-AAAGTTACAAAATGGTC
18527 ACCCAACTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
58 6 0.10
59 41 0.66
60 15 0.24
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (60 bp):
TAAAGTTACAAAATGGTCCCTCCGACTATAGAATATTGCTTTATTAAGCCCCTCGACTAT
Found at i:20524 original size:126 final size:126
Alignment explanation
Indices: 20292--20526 Score: 287
Period size: 126 Copynumber: 1.9 Consensus size: 126
20282 TTTAACGACC
* * * * * *
20292 TATCCAAATGCGTCGAAGGACCCTCGAAAGCATTCACCACGTGAGCAGCGTCCAATGTCACTACT
1 TATCCAAAGGCGTCGAAGGACCCTCAAAAGCATTAACCACGTGAGCAGCCTCCAAAGCCACTACT
* * * * *
20357 GAACCCTCATGCATATTATTAATTTCCTGCACCATGATTGTATTTCCCTTGATAACCAACT
66 GAACCCGCATGCATAATATTAATTTCATCCACCATCATTGTATTTCCCTTGATAACCAACT
* *
20418 TATCCAAAGGCGT-GAAAGGTCCCTCAAAAGCATTAACCTCGTGAGCAGCCTCCAAAGCCACTAC
1 TATCCAAAGGCGTCG-AAGGACCCTCAAAAGCATTAACCACGTGAGCAGCCTCCAAAGCCACTAC
* *
20482 TGAGCCCGCATGTATAATATTTAA-TTCATCCACCA-CATTTGTATT
65 TGAACCCGCATGCATAATA-TTAATTTCATCCACCATCA-TTGTATT
20527 ACCGCTCCTC
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
125 2 0.02
126 85 0.93
127 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (126 bp):
TATCCAAAGGCGTCGAAGGACCCTCAAAAGCATTAACCACGTGAGCAGCCTCCAAAGCCACTACT
GAACCCGCATGCATAATATTAATTTCATCCACCATCATTGTATTTCCCTTGATAACCAACT
Found at i:27343 original size:15 final size:16
Alignment explanation
Indices: 27318--27347 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27308 AAGTTAATCT
27318 TATTGTTATAAAATTA
1 TATTGTTATAAAATTA
27334 TATT-TTATAAAATT
1 TATTGTTATAAAATT
27348 TTAAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TATTGTTATAAAATTA
Found at i:33079 original size:9 final size:9
Alignment explanation
Indices: 33067--33116 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
33057 GCTGTCATTA
33067 TCGTCATCG
1 TCGTCATCG
* *
33076 TCGTCACCA
1 TCGTCATCG
33085 TCGTCATCG
1 TCGTCATCG
33094 TCGTCATCG
1 TCGTCATCG
*
33103 TCGTCGTCG
1 TCGTCATCG
33112 TCGTC
1 TCGTC
33117 CTGAGCAGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.10, C:0.36, G:0.22, T:0.32
Consensus pattern (9 bp):
TCGTCATCG
Found at i:33477 original size:27 final size:27
Alignment explanation
Indices: 33416--33478 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
33406 AAACTAGGTG
* *
33416 AAGGCGACGGCGGCATATGGTAATTGA
1 AAGGCGATGGCGGCATATGGTAATGGA
*
33443 AAGGCGATGGCGGCATCTGGTAATGGA
1 AAGGCGATGGCGGCATATGGTAATGGA
33470 AAGGCGATG
1 AAGGCGATG
33479 ATGACATCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.29, C:0.14, G:0.40, T:0.17
Consensus pattern (27 bp):
AAGGCGATGGCGGCATATGGTAATGGA
Found at i:33486 original size:27 final size:27
Alignment explanation
Indices: 33433--33486 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
33423 CGGCGGCATA
* * *
33433 TGGTAATTGAAAGGCGATGGCGGCATC
1 TGGTAATGGAAAGGCGATGACGACATC
*
33460 TGGTAATGGAAAGGCGATGATGACATC
1 TGGTAATGGAAAGGCGATGACGACATC
33487 ATATATGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.35, T:0.22
Consensus pattern (27 bp):
TGGTAATGGAAAGGCGATGACGACATC
Found at i:35169 original size:111 final size:111
Alignment explanation
Indices: 35027--35248 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
35017 ATTACAAAAA
*
35027 TTAACTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTACTACTAATAATTTAAATTA
1 TTAACTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATACTACTAATAATTTAAATTA
* *
35092 GATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
* *
35138 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAACTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATACTACTAATAATTTAAATTA
35203 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
35249 ATGATTTTCA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.35
Consensus pattern (111 bp):
TTAACTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATACTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:35589 original size:50 final size:50
Alignment explanation
Indices: 35535--35642 Score: 164
Period size: 50 Copynumber: 2.2 Consensus size: 50
35525 AGATACCCAG
* *
35535 GTATAGCGC-GGATCAGGGGGCTCGCTATACCCACGTGGCGCCATATCACC
1 GTATAGCGCGGGA-CAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
* *
35585 GTATATCGCGGGACAGGGGGCACGCTATACCCACGTGGCGCCAAATCAGC
1 GTATAGCGCGGGACAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
35635 GTATAGCG
1 GTATAGCG
35643 TGATTCAGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
50 49 0.94
51 3 0.06
ACGTcount: A:0.22, C:0.30, G:0.31, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGGACAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
Found at i:35652 original size:50 final size:50
Alignment explanation
Indices: 35535--35660 Score: 159
Period size: 50 Copynumber: 2.5 Consensus size: 50
35525 AGATACCCAG
* *
35535 GTATA-GCGCGGATCAGGGGGCTCGCTATACCCACGTGGCGCCATATCACC
1 GTATACGCG-GGATCAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
*
35585 GTATATCGCGGGA-CAGGGGGCACGCTATACCCACGTGGCGCCAAATCAGC
1 GTATA-CGCGGGATCAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
* *
35635 GTATA-GCGTGATTCAGGGGACACGCT
1 GTATACGCGGGA-TCAGGGGGCACGCT
35661 TTACTGCTAC
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
48 5 0.07
50 56 0.84
51 3 0.04
52 3 0.04
ACGTcount: A:0.22, C:0.29, G:0.32, T:0.17
Consensus pattern (50 bp):
GTATACGCGGGATCAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
Found at i:41463 original size:269 final size:261
Alignment explanation
Indices: 41045--41525 Score: 698
Period size: 269 Copynumber: 1.8 Consensus size: 261
41035 ATAAAATTTC
* * * *
41045 ACCCGACCCGACCCGAAATAGCAAAAGAATATTTTTATTCAATAAAAACAGTTACTTAATCGGAA
1 ACCCGACCCGACCCAAAATAACAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATCGGAA
* *
41110 AAAATATATATAGGGGTATTATTGTAATTATTTCTAAATATATAAAGTAAAATTATATACTTTTT
66 AAAATATATATAGGGGTATTATTGTAATTATTCCTAAATATATAAAGTAAAATTATATAATTTTT
* * *
41175 GGGTCGGGTTGGATATTTTTCACCCTAAACCCGAACTCGGCCCGACCTGAATATCAAATTTAAAA
131 GGGTC-GG-TGGATATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCAAACTT-AAA
*
41240 AAAACCGACCCTACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATTAATTAGAAA
193 AAAACCGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATTAATTAGAAA
41305 TCCG
258 TCCG
* *
41309 ACCCGACCCGACCCAAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGGA
1 ACCCGACCCGACCCAAAATAACAAAAAAA-TATTTTTATTCAATAAAAACAGTGACTTAATCGG-
41374 AAAAAATTATATATAGAGGAGTATTATTGTAATTATTCCTAAATATATATAAGGTAAAATTATAT
64 AAAAAA-TATATATAG-GG-GTATTATTGTAATTATTCCTAAATATATA-AA-GTAAAA-T-TAT
*
41439 ATATATTTTTGGGTC-G-GG-TATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCAC
122 ATA-ATTTTTGGGTCGGTGGATATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCAA
*
41501 ACTTAAAAAACCCGACCCGACCCGA
186 ACTTAAAAAAACCGACCCGACCCGA
41526 ATATATGAAT
Statistics
Matches: 193, Mismatches: 14, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
264 25 0.13
265 32 0.17
266 6 0.03
267 9 0.05
268 21 0.11
269 72 0.37
270 4 0.02
271 6 0.03
272 2 0.01
273 6 0.03
274 10 0.05
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (261 bp):
ACCCGACCCGACCCAAAATAACAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATCGGAA
AAAATATATATAGGGGTATTATTGTAATTATTCCTAAATATATAAAGTAAAATTATATAATTTTT
GGGTCGGTGGATATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCAAACTTAAAAAA
ACCGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATTAATTAGAAATCC
G
Found at i:41546 original size:31 final size:32
Alignment explanation
Indices: 41481--41551 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
41471 AACCCGAACT
*
41481 CGACCCGACCCGAATATCACACTTAAAAAACC
1 CGACCCGACCCGAATATCACACATAAAAAACC
* *
41513 CGACCCGACCCGAATAT-ATGA-ATAAGAAACC
1 CGACCCGACCCGAATATCA-CACATAAAAAACC
41544 CGACCCGA
1 CGACCCGA
41552 AATAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 17 0.49
32 18 0.51
ACGTcount: A:0.39, C:0.35, G:0.14, T:0.11
Consensus pattern (32 bp):
CGACCCGACCCGAATATCACACATAAAAAACC
Found at i:42308 original size:13 final size:13
Alignment explanation
Indices: 42287--42316 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42277 CTGTTAACCT
*
42287 TTGACTTTGACCA
1 TTGAATTTGACCA
42300 TTGAATTTGACCA
1 TTGAATTTGACCA
42313 TTGA
1 TTGA
42317 CTTTTTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (13 bp):
TTGAATTTGACCA
Found at i:42876 original size:30 final size:28
Alignment explanation
Indices: 42820--42892 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 28
42810 GACTTCGTTC
*
42820 CCCGTTCTGACATCTGTATATGATAAATTT
1 CCCGTTCTGACATC-GTACATGATAAA-TT
42850 CCCGTTCTGACATC-TACATGGAATAAATT
1 CCCGTTCTGACATCGTACAT-G-ATAAATT
42879 CCTCGTTCTGACAT
1 CC-CGTTCTGACAT
42893 ATGCATGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
28 4 0.10
29 5 0.13
30 30 0.77
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.36
Consensus pattern (28 bp):
CCCGTTCTGACATCGTACATGATAAATT
Found at i:45273 original size:21 final size:21
Alignment explanation
Indices: 45179--45274 Score: 75
Period size: 21 Copynumber: 4.6 Consensus size: 21
45169 TCGAGGGTTC
* * *
45179 TATGTGGTCCTTCGGGATATA
1 TATGTGGTCCTTTGGAACATA
** *
45200 TATGTAATCATTTGGAACATA
1 TATGTGGTCCTTTGGAACATA
* * * *
45221 TATGCGGTTCTTTGGGACACA
1 TATGTGGTCCTTTGGAACATA
* *
45242 TATTTGGTCCTTTGGAATATA
1 TATGTGGTCCTTTGGAACATA
*
45263 TATGTGATCCTT
1 TATGTGGTCCTT
45275 AAGGAGTGGT
Statistics
Matches: 54, Mismatches: 21, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (21 bp):
TATGTGGTCCTTTGGAACATA
Found at i:45334 original size:23 final size:21
Alignment explanation
Indices: 45280--45339 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 21
45270 TCCTTAAGGA
* *
45280 GTGGTCTTTCGGGACATATAT
1 GTGGTCATTCGGGACATATAC
*
45301 GTGGTCATTCGGGACATTTCTAC
1 GTGGTCATTCGGGACA--TATAC
*
45324 GTGGTCCTTCGGGACA
1 GTGGTCATTCGGGACA
45340 ATCTTATATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 15 0.45
23 18 0.55
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (21 bp):
GTGGTCATTCGGGACATATAC
Found at i:49430 original size:29 final size:29
Alignment explanation
Indices: 49398--49568 Score: 144
Period size: 30 Copynumber: 5.8 Consensus size: 29
49388 GCATAATCCT
* *
49398 CGTCCTGATTCTGTATGGGATTTATTCTC
1 CGTCCTGAATCTGTATGGGATTTATTCCC
* * *
49427 CGTCCTGATTCTGCATGGGATTTATTCTC
1 CGTCCTGAATCTGTATGGGATTTATTCCC
* * * *
49456 CGTCCTGATTCTGCATGGGACCTCATTCCC
1 CGTCCTGAATCTGTATGGGA-TTTATTCCC
* ** *
49486 CGTTCTGACATCTGTATGGGATAAACTCCC
1 CGTCCTGA-ATCTGTATGGGATTTATTCCC
* **
49516 CGTTCTGACATCTGTATGGGATAAATTCCC
1 CGTCCTGA-ATCTGTATGGGATTTATTCCC
* *
49546 CGTTCTGACATCTGTATGAGATT
1 CGTCCTGA-ATCTGTATGGGATT
49569 ATATCTCCGT
Statistics
Matches: 126, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
29 48 0.38
30 68 0.54
31 10 0.08
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (29 bp):
CGTCCTGAATCTGTATGGGATTTATTCCC
Found at i:49517 original size:30 final size:30
Alignment explanation
Indices: 49482--49563 Score: 155
Period size: 30 Copynumber: 2.7 Consensus size: 30
49472 GGGACCTCAT
49482 TCCCCGTTCTGACATCTGTATGGGATAAAC
1 TCCCCGTTCTGACATCTGTATGGGATAAAC
*
49512 TCCCCGTTCTGACATCTGTATGGGATAAAT
1 TCCCCGTTCTGACATCTGTATGGGATAAAC
49542 TCCCCGTTCTGACATCTGTATG
1 TCCCCGTTCTGACATCTGTATG
49564 AGATTATATC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.33
Consensus pattern (30 bp):
TCCCCGTTCTGACATCTGTATGGGATAAAC
Found at i:51957 original size:13 final size:13
Alignment explanation
Indices: 51921--51963 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
51911 ATCGAAAACA
*
51921 TTTCTTCCTTGTT
1 TTTCTTCTTTGTT
*
51934 CTTTGTTCTTTGTT
1 -TTTCTTCTTTGTT
*
51948 TTTCTTCTTTCTT
1 TTTCTTCTTTGTT
51961 TTT
1 TTT
51964 ATAAAATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.00, C:0.19, G:0.07, T:0.74
Consensus pattern (13 bp):
TTTCTTCTTTGTT
Found at i:55124 original size:21 final size:19
Alignment explanation
Indices: 55095--55138 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
55085 ATTTATTTTA
55095 TTTTTATTTTAGGAAT-TATC
1 TTTTTATTTTA--AATGTATC
55115 TTTTTAATTTTAAATGTATC
1 TTTTT-ATTTTAAATGTATC
55135 TTTT
1 TTTT
55139 AGGATTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.14
20 13 0.59
21 6 0.27
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.64
Consensus pattern (19 bp):
TTTTTATTTTAAATGTATC
Done.