Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009117.1 Hibiscus syriacus cultivar Beakdansim tig00112604_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: 576650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:508711 original size:8 final size:8
Alignment explanation
Indices: 508695--508726 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
508685 AGTTCTTGTG
508695 TTTCTAGC
1 TTTCTAGC
*
508703 TTGCTAGC
1 TTTCTAGC
508711 TTTCTAGC
1 TTTCTAGC
508719 TTTCTAGC
1 TTTCTAGC
508727 CTTGTCGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (8 bp):
TTTCTAGC
Found at i:511734 original size:21 final size:21
Alignment explanation
Indices: 511708--511747 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
511698 GGGAGCGTCA
*
511708 GTGCATCGATGCATACACAAG
1 GTGCATCGATACATACACAAG
*
511729 GTGCATCGGTACATACACA
1 GTGCATCGATACATACACA
511748 TGGTAAATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.20
Consensus pattern (21 bp):
GTGCATCGATACATACACAAG
Found at i:511757 original size:21 final size:21
Alignment explanation
Indices: 511719--511759 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
511709 TGCATCGATG
**
511719 CATACACAAGGTGCATCGGTA
1 CATACACAAGGTAAATCGGTA
*
511740 CATACACATGGTAAATCGGT
1 CATACACAAGGTAAATCGGT
511760 GCATCAAGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (21 bp):
CATACACAAGGTAAATCGGTA
Found at i:511928 original size:64 final size:65
Alignment explanation
Indices: 511831--511953 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 65
511821 GGTGCACTAA
* *
511831 TTGTGCATCAATACATAAAATGCATTCGATG-TTTCA-AAATAGCCTGAGTGCATCGATGTATGT
1 TTGTGCATCAATACATAAAATACATTCGATGTTTTCATAAA-AACCTGAGTGCATCGATGTATGT
511894 C
65 C
* * * *
511895 TTGTGCATCGATGCATCAAATACATTTGATGTTTTCATAAAAACCTGAGTGCATCGATG
1 TTGTGCATCAATACATAAAATACATTCGATGTTTTCATAAAAACCTGAGTGCATCGATG
511954 CATGGAGAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 26 0.51
65 22 0.43
66 3 0.06
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (65 bp):
TTGTGCATCAATACATAAAATACATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGTATGTC
Found at i:511965 original size:19 final size:19
Alignment explanation
Indices: 511941--511995 Score: 110
Period size: 19 Copynumber: 2.9 Consensus size: 19
511931 ATAAAAACCT
511941 GAGTGCATCGATGCATGGA
1 GAGTGCATCGATGCATGGA
511960 GAGTGCATCGATGCATGGA
1 GAGTGCATCGATGCATGGA
511979 GAGTGCATCGATGCATG
1 GAGTGCATCGATGCATG
511996 AACTACATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.25, C:0.16, G:0.36, T:0.22
Consensus pattern (19 bp):
GAGTGCATCGATGCATGGA
Found at i:511966 original size:65 final size:64
Alignment explanation
Indices: 511833--511975 Score: 162
Period size: 65 Copynumber: 2.2 Consensus size: 64
511823 TGCACTAATT
* * * * * ****
511833 GTGCATCAATACATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGTATGTCTT
1 GTGCATCGATGCATAAAATACATTCGATGTTTCAAAATAACCTGAGTGCATCGATGCATGGAGA
* *
511897 GTGCATCGATGCATCAAATACATTTGATGTTTTCATAAA-AACCTGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATAAAATACATTCGATG-TTTCA-AAATAACCTGAGTGCATCGATGCATGGAG
511961 A
64 A
511962 GTGCATCGATGCAT
1 GTGCATCGATGCAT
511976 GGAGAGTGCA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
64 24 0.36
65 39 0.59
66 3 0.05
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATACATTCGATGTTTCAAAATAACCTGAGTGCATCGATGCATGGAGA
Found at i:512857 original size:45 final size:46
Alignment explanation
Indices: 512805--512912 Score: 148
Period size: 45 Copynumber: 2.4 Consensus size: 46
512795 GGTGCACTAA
* *
512805 GAGTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAGCTT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-ACCCT
* * *
512850 GTGTGCATCCATGCATCAAATGCATTCGATGTTTTCATAAAACCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCT
512896 GAGTGCATCGATGCATA
1 GAGTGCATCGATGCATA
512913 GTATGTGCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
45 28 0.53
46 22 0.42
47 3 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (46 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCT
Found at i:515536 original size:23 final size:22
Alignment explanation
Indices: 515508--515588 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
515498 CATGTCCTTT
515508 TGCATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
* *
515530 GTGCATCGGTGCATC-TTC-ATGA
1 -TGCATCGATGCA-CATTCAAGGA
*
515552 TGTATCGATGCACATTCAAATGGA
1 TGCATCGATGCACATTC-AA-GGA
515576 TGCATCGATGCAC
1 TGCATCGATGCAC
515589 TGTTAAGTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 13 0.28
22 3 0.06
23 15 0.32
24 15 0.32
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:515600 original size:44 final size:44
Alignment explanation
Indices: 515511--515607 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
515501 GTCCTTTTGC
* *
515511 ATCGATGCACATTCAAGGAGTGCATCGGTGCATCTTCATGATGT
1 ATCGATGCACATTCAAGGAGTGCATCGATGCATCTTCAAGATGT
*
515555 ATCGATGCACATTCAAATGGA-TGCATCGATGCA-CTGTTAAG-TGT
1 ATCGATGCACATTC-AA-GGAGTGCATCGATGCATCT-TCAAGATGT
515599 ATCGATGCA
1 ATCGATGCA
515608 TTAAGCACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 28 0.60
45 16 0.34
46 3 0.06
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAGTGCATCGATGCATCTTCAAGATGT
Found at i:521392 original size:65 final size:65
Alignment explanation
Indices: 521259--521418 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 65
521249 TGCACTAAGT
* * ****
521259 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCTGAGTGCATTGATGCATGTCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAACCTGAGTGCATCGATGCATGGAGA
*
521323 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AACCTGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAACCTGAGTGCATCGATGCATGGAG
521387 A
65 A
* *
521388 GTGCATCGATGCATGAACTGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
521419 CAATTTATTT
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
64 28 0.33
65 54 0.64
66 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAACCTGAGTGCATCGATGCATGGAGA
Found at i:525188 original size:38 final size:37
Alignment explanation
Indices: 525098--525191 Score: 100
Period size: 39 Copynumber: 2.5 Consensus size: 37
525088 TATTTCACTC
** *
525098 TAACATTCAAAATTCCTAATTTCTTAAATTTTACCCCCA
1 TAACATTCAAAATTATTAATTTCTTAAATTTT--CCACA
* *
525137 TAACATTCTAAATTATTAATTTCTTAAATTATT-CATA
1 TAACATTCAAAATTATTAATTTCTTAAATT-TTCCACA
525174 TTAACATTCAAAATTATT
1 -TAACATTCAAAATTATT
525192 TTTTAAATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
37 2 0.04
38 16 0.34
39 27 0.57
40 2 0.04
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (37 bp):
TAACATTCAAAATTATTAATTTCTTAAATTTTCCACA
Found at i:525203 original size:34 final size:37
Alignment explanation
Indices: 525137--525212 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 37
525127 TTTACCCCCA
525137 TAACATTCTAAATTATTAATTTCTTAAATTATTCATAT
1 TAACATTCTAAA-TATTAATTTCTTAAATTATTCATAT
* * *
525175 TAACATTC-AAA-ATT-ATTTTTTAAATTATTTATTT
1 TAACATTCTAAATATTAATTTCTTAAATTATTCATAT
525209 TAAC
1 TAAC
525213 TTCGAAACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 21 0.60
35 3 0.09
37 3 0.09
38 8 0.23
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.51
Consensus pattern (37 bp):
TAACATTCTAAATATTAATTTCTTAAATTATTCATAT
Found at i:528543 original size:38 final size:38
Alignment explanation
Indices: 528484--528651 Score: 221
Period size: 38 Copynumber: 4.4 Consensus size: 38
528474 ATCAATTAAT
* * *
528484 CACTTCGGTGAAAATGATGGGCACGACCTTATGTGTAG
1 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAG
*
528522 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAA
1 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAG
** *
528560 CACTTCGACGCATATGGTGGGCACGACCATATGTGTAG
1 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAG
* * *
528598 CACTTTGGTGCATATGGTGGGCATGACCTTATATGTAAG
1 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGT-AG
528637 CACTAT-GGTGCATAT
1 CACT-TCGGTGCATAT
528652 ATTTGACTCG
Statistics
Matches: 114, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
38 98 0.86
39 15 0.13
40 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (38 bp):
CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAG
Found at i:531129 original size:19 final size:19
Alignment explanation
Indices: 531099--531147 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
531089 TACTAAAACA
531099 TTCAAC-AAAACGAAGAAC
1 TTCAACAAAAACGAAGAAC
531117 TTCAACAAAAACGAAGAAC
1 TTCAACAAAAACGAAGAAC
531136 TTCAACAAAAAC
1 TTCAACAAAAAC
531148 TAAAATCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.57, C:0.22, G:0.08, T:0.12
Consensus pattern (19 bp):
TTCAACAAAAACGAAGAAC
Found at i:539996 original size:3 final size:3
Alignment explanation
Indices: 539982--540036 Score: 83
Period size: 3 Copynumber: 18.0 Consensus size: 3
539972 TGTAATATTA
* *
539982 AAT AAT ATAT AAT AAT AAT AAT AAT AAT TAT AAT TAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
540028 AAT AAT AAT
1 AAT AAT AAT
540037 TATATAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:540714 original size:113 final size:113
Alignment explanation
Indices: 540271--540685 Score: 615
Period size: 113 Copynumber: 3.7 Consensus size: 113
540261 TAGAGTCATT
* ** * *
540271 CAAAAGGTTGAATAAGCTCTTCTTATTATGAAC-T-TTC-T-CTTCTTCAGATGAATTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*** * * * * **
540332 TTATGAACTCTTTCTGGAAGAGCTAATCCATCAAATGATGAATTCAAG
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* * * *
540380 CAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTTTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
540444 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
540492 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
540557 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
540605 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
540670 TTATGAACTTGAACTG
66 TTATGAACTCGAACTG
540686 ACACTGTTGA
Statistics
Matches: 282, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
108 25 0.09
109 6 0.02
110 3 0.01
111 1 0.00
112 65 0.23
113 182 0.65
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
Found at i:541772 original size:83 final size:83
Alignment explanation
Indices: 541554--542422 Score: 1403
Period size: 83 Copynumber: 10.7 Consensus size: 83
541544 TTGGGGTTCA
541554 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
541619 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
* * * *
541637 TACC--A--A-ATCATATAACTCAAAAAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
* *
541697 AAATTCAATAACTGATTT
66 AAATTCAATGATTGATTT
* *
541715 TACCAAACCAGATCAAATAACTTAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
541780 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
*
541798 TACC--A--A-ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTATTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
541858 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
*
541876 TACCAAA-C---T-AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTATTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
541936 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
* *
541954 TACCAAATCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTATGAGCACATT-C-CTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
542017 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
* * **
542035 TACCAAACCAGATCAGATAACTCAAAGAACATTTCTAGAAGATGCTATGAGCACATTATTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
542100 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
* **
542118 TACCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
542183 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
**
542201 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
542266 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
**
542284 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
542349 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
*
542367 TACCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
542423 GGCATTTGTT
Statistics
Matches: 745, Mismatches: 26, Indels: 30
0.93 0.03 0.04
Matches are distributed among these distances:
78 219 0.29
79 4 0.01
80 2 0.00
81 79 0.11
82 3 0.00
83 438 0.59
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.28
Consensus pattern (83 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
AAATTCAATGATTGATTT
Found at i:543583 original size:13 final size:12
Alignment explanation
Indices: 543564--543632 Score: 66
Period size: 13 Copynumber: 5.2 Consensus size: 12
543554 CTTGACACCC
*
543564 CTTTTTCTTTTT
1 CTTTTTTTTTTT
543576 CTTTTTTCTTTTCT
1 CTTTTTT-TTTT-T
543590 CTCTTTTTTTTTT
1 CT-TTTTTTTTTT
*
543603 CTTTCTTTTTTCT
1 CTTT-TTTTTTTT
543616 CTTTTTCTTCTTTT
1 CTTTTT-TT-TTTT
543630 CTT
1 CTT
543633 CAAGCATAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
12 10 0.21
13 20 0.42
14 13 0.27
15 5 0.10
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
CTTTTTTTTTTT
Found at i:543602 original size:15 final size:16
Alignment explanation
Indices: 543575--543632 Score: 68
Period size: 15 Copynumber: 3.7 Consensus size: 16
543565 TTTTTCTTTT
543575 TCTTTTTTCTTTTCTC
1 TCTTTTTTCTTTTCTC
*
543591 TCTTTTTT-TTTTCTT
1 TCTTTTTTCTTTTCTC
543606 TCTTTTTTCTCTTT-T-
1 TCTTTTTTCT-TTTCTC
543621 TCTTCTTTTCTT
1 TCTT-TTTTCTT
543633 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
15 19 0.50
16 16 0.42
17 3 0.08
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TCTTTTTTCTTTTCTC
Found at i:543602 original size:20 final size:19
Alignment explanation
Indices: 543564--543624 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
543554 CTTGACACCC
543564 CTTTTTCTTTTTCTTTTTT
1 CTTTTTCTTTTTCTTTTTT
543583 CTTTTCTCTCTTTT-TTTTTT
1 CTTTT-TCT-TTTTCTTTTTT
*
543603 CTTTCT-TTTTTCTCTTTTT
1 CTTTTTCTTTTTCT-TTTTT
543622 CTT
1 CTT
543625 CTTTTCTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
17 4 0.11
18 2 0.05
19 14 0.38
20 13 0.35
21 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
CTTTTTCTTTTTCTTTTTT
Found at i:543602 original size:27 final size:26
Alignment explanation
Indices: 543564--543632 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 26
543554 CTTGACACCC
*
543564 CTTTTTCTTTTTCTTTTTTCTTTTCTCT
1 CTTTTT-TTTTTCTTTCTT-TTTTCTCT
543592 CTTTTTTTTTTCTTTCTTTTTTCTCT
1 CTTTTTTTTTTCTTTCTTTTTTCTCT
543618 -TTTTCTTCTTTTCTT
1 CTTTT-TT-TTTTCTT
543633 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
25 4 0.11
26 10 0.26
27 18 0.47
28 6 0.16
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (26 bp):
CTTTTTTTTTTCTTTCTTTTTTCTCT
Found at i:543607 original size:24 final size:23
Alignment explanation
Indices: 543571--543632 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
543561 CCCCTTTTTC
543571 TTTTTCTTTTTTCTTTTCTCTCT
1 TTTTTCTTTTTTCTTTTCTCTCT
* *
543594 TTTTTTTTTCTTTCTTTTTTCTC-
1 TTTTTCTTT-TTTCTTTTCTCTCT
543617 TTTTTCTTCTTTTCTT
1 TTTTTCTT-TTTTCTT
543633 CAAGCATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 21 0.62
24 13 0.38
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTCTTTTTTCTTTTCTCTCT
Found at i:543619 original size:33 final size:33
Alignment explanation
Indices: 543565--543629 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
543555 TTGACACCCC
*
543565 TTTTTCTTTTTCTTTTTTC-TTTTCTCTCTTTTT
1 TTTTTCTTTTTCTTTTCTCTTTTTCT-TCTTTTT
543598 TTTTTCTTTCTT-TTTTCTCTTTTTCTTCTTTT
1 TTTTTCTTT-TTCTTTTCTCTTTTTCTTCTTTT
543630 CTTCAAGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (33 bp):
TTTTTCTTTTTCTTTTCTCTTTTTCTTCTTTTT
Found at i:554280 original size:19 final size:19
Alignment explanation
Indices: 554252--554302 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
554242 AAATAAAATG
* *
554252 AAATATTATAATAATATAT
1 AAATACTATAAAAATATAT
554271 AAATACTATAAAAATATAT
1 AAATACTATAAAAATATAT
**
554290 GTATA-TATAAAAA
1 AAATACTATAAAAA
554303 AGAATTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATACTATAAAAATATAT
Found at i:556408 original size:3 final size:3
Alignment explanation
Indices: 556390--556438 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
556380 TGTAATATTA
* * *
556390 AAT AAT ATAT ATT AAT AAT AAT AAT AAT TAT AAT TAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
556436 AAT
1 AAT
556439 TATTATATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:558769 original size:20 final size:23
Alignment explanation
Indices: 558722--558770 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 23
558712 AAAATGAGAT
*
558722 AAAAAATAAGAAAATAAAAGAAG
1 AAAAAATAAGAAAATAAAACAAG
*
558745 TAAAAAT-A-AAAAT-AAACAAG
1 AAAAAATAAGAAAATAAAACAAG
558765 AAAAAA
1 AAAAAA
558771 AGAATAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 11 0.48
21 5 0.22
22 1 0.04
23 6 0.26
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.10
Consensus pattern (23 bp):
AAAAAATAAGAAAATAAAACAAG
Found at i:559073 original size:21 final size:20
Alignment explanation
Indices: 559035--559077 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
559025 ATAAGTATTA
559035 AAATAAAAATAATAATAACAG
1 AAATAAAAATAATAATAA-AG
*
559056 AAATAAAAGA-AATTATAAAG
1 AAATAAAA-ATAATAATAAAG
559076 AA
1 AA
559078 TATGAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 15 0.75
22 1 0.05
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (20 bp):
AAATAAAAATAATAATAAAG
Found at i:561118 original size:14 final size:14
Alignment explanation
Indices: 561099--561125 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
561089 AATATGCATG
561099 TCTGGAATCTTGAC
1 TCTGGAATCTTGAC
561113 TCTGGAATCTTGA
1 TCTGGAATCTTGA
561126 AGTTATGATC
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:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (14 bp):
TCTGGAATCTTGAC
Found at i:561236 original size:200 final size:200
Alignment explanation
Indices: 560893--561293 Score: 694
Period size: 200 Copynumber: 2.0 Consensus size: 200
560883 GATCTCCGAT
* * * * *
560893 TGCATGTTTGGAATCTTGAGTATGAAATTTTGAAGTTTTGATCTCTGATCTCGAATTCTTCAAAT
1 TGCATGTCTGGAATCTTGACTATGAAATCTTGAAGTTATGATCCCTGATCTCGAATTCTTCAAAT
* *
560958 ATTCAAATCTGATGTGTACATTCTATTTGTTTCTTGATTTGGGAAATGCTTCTCAACCAATCTCA
66 ATTCAAATATGATGTGCACATTCTATTTGTTTCTTGATTTGGGAAATGCTTCTCAACCAATCTCA
*
561023 AGTATGAGCCTTGATCGGCTTCCGAGTACATGTACTTTTCAATGAATCTTTGTACAGTAATCTGC
131 AGTATGAGCCTTGATCGGCTTCCGAGTACATGTACTTTTCAATGAATCTTTATACAGTAATCTGC
561088 GAATA
196 GAATA
* *
561093 TGCATGTCTGGAATCTTGACTCTGGAATCTTGAAGTTATGATCCCTGATCTCGAATTCTTCAAAT
1 TGCATGTCTGGAATCTTGACTATGAAATCTTGAAGTTATGATCCCTGATCTCGAATTCTTCAAAT
561158 ATTCAAATATGATGTGCACATTCTATTTGTTTCTTGATTTGGGAAATGCTTCTCAACCAATCTCA
66 ATTCAAATATGATGTGCACATTCTATTTGTTTCTTGATTTGGGAAATGCTTCTCAACCAATCTCA
* *
561223 AGTATGAGCCTTGATCGGCTTCCGAGTACCTGTACTTTTCAATGAATCTTTATACAGTAATCTGT
131 AGTATGAGCCTTGATCGGCTTCCGAGTACATGTACTTTTCAATGAATCTTTATACAGTAATCTGC
561288 GAATA
196 GAATA
561293 T
1 T
561294 CTTTTGCATA
Statistics
Matches: 189, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
200 189 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (200 bp):
TGCATGTCTGGAATCTTGACTATGAAATCTTGAAGTTATGATCCCTGATCTCGAATTCTTCAAAT
ATTCAAATATGATGTGCACATTCTATTTGTTTCTTGATTTGGGAAATGCTTCTCAACCAATCTCA
AGTATGAGCCTTGATCGGCTTCCGAGTACATGTACTTTTCAATGAATCTTTATACAGTAATCTGC
GAATA
Found at i:572408 original size:11 final size:12
Alignment explanation
Indices: 572395--572460 Score: 71
Period size: 13 Copynumber: 5.2 Consensus size: 12
572385 TAATACAAAA
572395 ATAATAATATA-
1 ATAATAATATAT
*
572406 ATAATACTATTGAT
1 ATAATAATA-T-AT
572420 ATAATAATATAT
1 ATAATAATATAT
572432 ATAATATATATAT
1 ATAATA-ATATAT
*
572445 ATATATATTATAT
1 ATA-ATAATATAT
572458 ATA
1 ATA
572461 TAACTTATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
11 8 0.17
12 9 0.19
13 19 0.40
14 11 0.23
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:572433 original size:2 final size:2
Alignment explanation
Indices: 572418--572462 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
572408 AATACTATTG
572418 AT AT A- AT A- AT AT AT AT A- AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
572456 AT AT AT A
1 AT AT AT A
572463 ACTTATAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.10
2 35 0.90
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:572438 original size:17 final size:18
Alignment explanation
Indices: 572398--572463 Score: 75
Period size: 17 Copynumber: 3.7 Consensus size: 18
572388 TACAAAAATA
572398 ATAATATA-ATAATACTAT
1 ATAATATATATAATA-TAT
*
572416 -TGATATA-ATAATATAT
1 ATAATATATATAATATAT
572432 ATAATATATATATATATAT
1 ATAATATATATA-ATATAT
*
572451 ATTATATATATAA
1 ATAATATATATAA
572464 CTTATAAACA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
16 3 0.07
17 18 0.43
18 4 0.10
19 17 0.40
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
ATAATATATATAATATAT
Found at i:572468 original size:13 final size:12
Alignment explanation
Indices: 572418--572469 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 12
572408 AATACTATTG
*
572418 ATATAATAATAT
1 ATATAATTATAT
572430 ATATAATATATATAT
1 ATAT-A-AT-TATAT
572445 ATATATATTATAT
1 ATATA-ATTATAT
572458 ATATAACTTATA
1 ATATAA-TTATA
572470 AACAATGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
12 5 0.14
13 16 0.46
14 6 0.17
15 8 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
ATATAATTATAT
Found at i:572575 original size:24 final size:22
Alignment explanation
Indices: 572550--572621 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
572540 ATGAAAATTA
572550 AAGTAATATATAAATAAAAAAAT
1 AAGTAATA-ATAAATAAAAAAAT
572573 AAAGT-ATAATGAAA-ATAAAAAAT
1 -AAGTAATAAT-AAATA-AAAAAAT
*
572596 AA-TAATAAT-AATAAAAATAT
1 AAGTAATAATAAATAAAAAAAT
572616 AAGTAA
1 AAGTAA
572622 ACATATATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
20 10 0.24
21 5 0.12
22 10 0.24
23 13 0.31
24 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (22 bp):
AAGTAATAATAAATAAAAAAAT
Found at i:576157 original size:3 final size:3
Alignment explanation
Indices: 576149--576179 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
576139 AGATAAAAAT
*
576149 ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
576180 ATATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:576534 original size:13 final size:13
Alignment explanation
Indices: 576513--576650 Score: 169
Period size: 13 Copynumber: 11.0 Consensus size: 13
576503 ACTTTGTGAA
576513 TTGTGTCTCAAAG
1 TTGTGTCTCAAAG
*
576526 TTGTCTCTCAAAG
1 TTGTGTCTCAAAG
* *
576539 TTATTTCTCAAAG
1 TTGTGTCTCAAAG
*
576552 TTGTCTCTCAAAG
1 TTGTGTCTCAAAG
*
576565 TTGTTTCTCAAAG
1 TTGTGTCTCAAAG
576578 TTGTGTCTCAAAG
1 TTGTGTCTCAAAG
* *
576591 -T-TCTCTCTAAG
1 TTGTGTCTCAAAG
576602 TTGTGTCT-AAAG
1 TTGTGTCTCAAAG
576614 TTGTGTCTCAAAG
1 TTGTGTCTCAAAG
*
576627 -T-TCTCTCAAAG
1 TTGTGTCTCAAAG
576638 TTGTGTCTCAAAG
1 TTGTGTCTCAAAG
Statistics
Matches: 107, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
11 17 0.16
12 15 0.14
13 75 0.70
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTGTCTCAAAG
Found at i:576568 original size:39 final size:37
Alignment explanation
Indices: 576518--576650 Score: 196
Period size: 36 Copynumber: 3.6 Consensus size: 37
576508 GTGAATTGTG
* * *
576518 TCTCAAAGTTGTCTCTCAAAGTTATTTCTCAAAGTTGTC
1 TCTCAAAGTTGTGTCTCAAAGTTGTGTCTCAAAG-T-TC
*
576557 TCTCAAAGTTGTTTCTCAAAGTTGTGTCTCAAAGTTC
1 TCTCAAAGTTGTGTCTCAAAGTTGTGTCTCAAAGTTC
*
576594 TCTCTAAGTTGTGTCT-AAAGTTGTGTCTCAAAGTTC
1 TCTCAAAGTTGTGTCTCAAAGTTGTGTCTCAAAGTTC
576630 TCTCAAAGTTGTGTCTCAAAG
1 TCTCAAAGTTGTGTCTCAAAG
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
36 35 0.40
37 20 0.23
38 1 0.01
39 31 0.36
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.40
Consensus pattern (37 bp):
TCTCAAAGTTGTGTCTCAAAGTTGTGTCTCAAAGTTC
Done.