Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002314.1 Hibiscus syriacus cultivar Beakdansim tig00004714_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: 58155
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:3741 original size:15 final size:14
Alignment explanation
Indices: 3707--3756 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
3697 TTTAGTTTCA
*
3707 TTTTTTCTCTATTTTC
1 TTTTTTC-CT-TTTTG
*
3723 TTTTTTCTTTTGTTG
1 TTTTTTCCTTT-TTG
3738 TTTTTTCCTTTTTG
1 TTTTTTCCTTTTTG
3752 TTTTT
1 TTTTT
3757 GTTGTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.33
15 13 0.43
16 7 0.23
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.80
Consensus pattern (14 bp):
TTTTTTCCTTTTTG
Found at i:3743 original size:22 final size:22
Alignment explanation
Indices: 3718--3769 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
3708 TTTTTCTCTA
3718 TTTTCTTTTT-TCTTTTGTTGTT
1 TTTTCTTTTTGT-TTTTGTTGTT
3740 TTTTCCTTTTTGTTTTTGTTGTT
1 TTTT-CTTTTTGTTTTTGTTGTT
3763 TTTTCTT
1 TTTTCTT
3770 CTTCACCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.25
23 20 0.71
24 1 0.04
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (22 bp):
TTTTCTTTTTGTTTTTGTTGTT
Found at i:4048 original size:30 final size:30
Alignment explanation
Indices: 3998--4070 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
3988 TTCGACGGGC
* *
3998 GGCGACGTCGAC-AGCTAGGATCTCCGCTCT
1 GGCGACGGCGACGA-CTAGGATCTCCACTCT
*
4028 GGCGGCGGCGACGACTAGGATCTCCACTCT
1 GGCGACGGCGACGACTAGGATCTCCACTCT
*
4058 GGCGACGGTGACG
1 GGCGACGGCGACG
4071 TTTGATGCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 36 0.97
31 1 0.03
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (30 bp):
GGCGACGGCGACGACTAGGATCTCCACTCT
Found at i:10863 original size:42 final size:42
Alignment explanation
Indices: 10788--10893 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 42
10778 TGTTCTGTTA
* * * * * *
10788 TCACTCAAGTAATATCATATATGAGGAATACTTGTTCTACTT
1 TCACTCAAGGAATATCAAATCTGAGGAAGACTTGTTCCACTG
* *
10830 TCACTCAAGGAATATCAGATCT-AGGGAAGACTTGTTCCGCTG
1 TCACTCAAGGAATATCAAATCTGA-GGAAGACTTGTTCCACTG
* *
10872 TCACTCAGGGAAAATCAAATCT
1 TCACTCAAGGAATATCAAATCT
10894 TGAAAAAGAG
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 1 0.02
42 52 0.98
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (42 bp):
TCACTCAAGGAATATCAAATCTGAGGAAGACTTGTTCCACTG
Found at i:11248 original size:42 final size:41
Alignment explanation
Indices: 11172--11252 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 41
11162 AGGTCTTATG
* * * *
11172 GATGGCTCGAAGGACTTATCATCTTTCTCGAAAGACTTACA
1 GATGACTCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
*
11213 GATGACTCGAAGGATTTAAGCATCATGCTCGAAAGACTTA
1 GATGACTCGAAGGACTT-AGCATCATGCTCGAAAGACTTA
11253 TTGATAGCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 15 0.44
42 19 0.56
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (41 bp):
GATGACTCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
Found at i:11341 original size:233 final size:233
Alignment explanation
Indices: 10901--12521 Score: 2095
Period size: 233 Copynumber: 7.0 Consensus size: 233
10891 TCTTGAAAAA
* * * * *
10901 GAGAGACCTGTGAAAACATCATGCCCAAAGTTCTTATGGATGGCCCAAAGGACTTATAATCTTGC
1 GAGAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC
* *
10966 TCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTAATGGCCTA
66 TCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCA
* * * *
11031 AAAGACTTATATAATTTGGAAATAGTTTACTAGGTGAGAAACCTTTCTTACTTTTC-AATAATTT
131 AAGGACTTATA-ATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAAATTT
* ** *
11095 CAAATCACAGATTTGAATGAGAAACCTTTCTCATTTTTT
195 CAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTT
* * *
11134 GAGAGACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTTC
1 GAGAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC
* * *
11199 TCGAAAGACTTACAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATAGCCCA
66 TCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCA
* * * * * * *
11264 AAGGATTTATAATTTTTGAAATAGTTTAGTAGGTAAGAAACTTTTCTCACCTTTCAAAAAATTTT
131 AAGGACTTATAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAAATTTC
** * *
11329 AATTTTCAGATTTAAATGAGAAACAATTCTCATATTTC
196 AATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTT
* * * * * * * * *
11367 GATAGATATGTAAAAATATCTTGTCCAAAGGTCTTATGCATGGCTCGAATGACTTATCATCTTGC
1 GAGAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC
* *
11432 TCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACGTACTGATGGCCCA
66 TCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCA
* *
11497 AAGGACTTATAAATTTTGGAAAAAGTTTACTAGGTAAGAAACCTTTCTTACTTCT-AAAAAATTT
131 AAGGACTTAT-AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAAATTT
* * * *
11561 CAATTTTCAAATTTTAACGAGAAAACTTTCTCATTTTTT
195 CAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTT
* * *
11600 GAGAGACATGTGAAAACATCCTTCCCAAATGTCTTATGGATGGCCCAAAGGACTTATCATCTTGC
1 GAGAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC
* * * * * * **
11665 TCGAAAGACATACAGATAACCCCAAGGATTTAAGCATCTTGCTCGAAAGACTTATTGATGGTCTG
66 TCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCA
*
11730 AAGGACTTATATATTTTGGAAATAATTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAAA-TT
131 AAGGACTTATA-ATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAAATTT
** *
11794 CAAATCAT-AGATTTGAATGAGAAACCTTTCTCATTTTTT
195 C-AATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTT
* *
11833 GAGAGACATGTGAAAACATCCTACCCAAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGC
1 GAGAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC
* * *
11898 TCGAAAGACTTACAGATGACCTGAAGGATTTAAGCATCATGCTCGGAAGACTTACTGATGGCCCG
66 TCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCA
* *
11963 AATGACTTATAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTT-AAAAAATTTC
131 AAGGACTTATAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAAATTTC
* ** * *
12027 AATTTTCAGATTTAAACGAGAAATATTTCTCATATTTC
196 AATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTT
* * * ** *
12065 GATAGACATGTGAAAACATCTTGCCC----G---AATGGATGGCCTAAATGACTTATCATCTTGC
1 GAGAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC
* * * * *
12123 TTGAAAGACTTACAGATGACCCGAATGATTTAAGCATCTTGCTCGAAATACTTACTGATGGCCCG
66 TCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCA
*
12188 AAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAGCCTTTCTTACTTTTC-AAAAATTT
131 AAGGACTTAT-AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAAATTT
*
12252 CAATTTTCAAATTTAAATGAGAAACCTTTCTCATTTTTTTT
195 CAATTTTCAGATTTAAATGAGAAACCTTTCTCA--TTTTTT
* * * ** *
12293 AAGAGA-ATGTGAAAACATCCCGCCCGAAGAACTTATGGATGGCCCGAAGTACTTATCATCTTGC
1 GAGAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC
* * * *
12357 TCGAAAGACTTACATATGACCTGAAGGATTTAAGCATCATGCTTGAAAGACTTACTAATGGCCCG
66 TCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCC-
* * * *
12422 AAA-GACTTATAAATTTTAGAAATAGTGTACTAGTTAAGAAACCTTTCTCACTTTTC-AAAAATT
130 AAAGGACTTAT-AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAAATT
** *
12485 TTGATTTTCAAATTTAAATGAGAAACCTTTCTCATTT
194 TCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTT
12522 CATTTTTTTA
Statistics
Matches: 1202, Mismatches: 167, Indels: 39
0.85 0.12 0.03
Matches are distributed among these distances:
225 94 0.08
226 79 0.07
227 17 0.01
228 9 0.01
231 10 0.01
232 134 0.11
233 641 0.53
234 216 0.18
235 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (233 bp):
GAGAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC
TCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCA
AAGGACTTATAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAAATTTC
AATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTT
Found at i:12497 original size:699 final size:695
Alignment explanation
Indices: 10902--12521 Score: 2332
Period size: 699 Copynumber: 2.3 Consensus size: 695
10892 CTTGAAAAAG
* * *
10902 AGAGACCTGTGAAAACATCATGCCCAAAGTTCTTATGGATGGCCCAAAGGACTTATAATCTTGCT
1 AGAGACATGTGAAAACATCCTGCCCAAAG-TCTTATGGATGGCCCAAAGGACTTATCATCTTGCT
*
10967 CGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTAATGGCCTAA
65 CGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTAATGGCCTGA
* *
11032 AAGACTTATATAA-TTTGGAAATAGTTTACTAGGTGAGAAACCTTTCTTACTTTTC-AATA-ATT
130 AAGACTTATA-AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATATT
*
11094 TCAAATCACAGATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTGCC
194 TCAAATCACAGATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTACC
* *
11159 CGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTTCTCGAAAGACTTACAGATGACTCGAA
259 CAAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACTCGAA
* * *
11224 GGATTTAAGCATCATGCTCGAAAGACTTATTGATAGCCCAAAGGATTTATAATTTTTGAAATAGT
324 GGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCAAAGGACTTATAATTTTGGAAATAGT
* * * *
11289 TTAGTAGGTAAGAAACTTTTCTCACCTTTCAAAAAATTTTAATTTTCAGATTTAAATGAGAAACA
389 TTACTAGGTAAGAAACCTTTCTCACCTTTCAAAAAATTTCAATTTTCAGATTTAAACGAGAAACA
* * * * *
11354 ATTCTCATATTTCGATAGATATGTAAAAATATCTTGTCCAAAGGTCTTATGCATGGCTCGAATGA
454 ATTCTCATATTTCGATAGACATGTAAAAACATCTTGCCCAAAGG---TATG-A-GCCTCAAATGA
11419 CTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACG
514 CTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACG
11484 TACTGATGGCCCAAAGGACTTATAAATTTTGGAAAAAGTTTACTAGGTAAGAAACCTTTCTTACT
579 TACTGATGGCCCAAAGGACTTATAAATTTTGGAAAAAGTTTACTAGGTAAGAAACCTTTCTTACT
* *
11549 TCTAAAAAATTTCAATTTTCAAATTTTAACGAGAAAACTTTCTCATTTTTTG
644 TCTAAAAAATTTCAATTTTCAAATTTAAACGAGAAAACTTTCTCATTTTTTA
*
11601 AGAGACATGTGAAAACATCCTTCCCAAATGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCT
1 AGAGACATGTGAAAACATCCTGCCCAAA-GTCTTATGGATGGCCCAAAGGACTTATCATCTTGCT
* * * * * * *
11666 CGAAAGACATACAGATAACCCCAAGGATTTAAGCATCTTGCTCGAAAGACTTATTGATGGTCTGA
65 CGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTAATGGCCTGA
* * *
11731 AGGACTTATATATTTTGGAAATAATTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAA-A-TT
130 AAGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATATTT
*
11794 CAAATCATAGATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTACCC
195 CAAATCACAGATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTACCC
11859 AAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGAC-CTGAA
260 AAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACTC-GAA
* * * * *
11923 GGATTTAAGCATCATGCTCGGAAGACTTACTGATGGCCCGAATGACTTATAATTTTGGAAATATT
324 GGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCAAAGGACTTATAATTTTGGAAATAGT
* * *
11988 TTACTAGGTAAGAAACCTTTCTTA-CTTTTAAAAAATTTCAATTTTCAGATTTAAACGAGAAATA
389 TTACTAGGTAAGAAACCTTTCTCACCTTTCAAAAAATTTCAATTTTCAGATTTAAACGAGAAACA
* * *
12052 TTTCTCATATTTCGATAGACATGTGAAAACATCTTGCCCGAATGG-ATG-GCCT-AAATGACTTA
454 ATTCTCATATTTCGATAGACATGTAAAAACATCTTGCCC-AAAGGTATGAGCCTCAAATGACTTA
* * * * * *
12114 TCATCTTGCTTGAAAGACTTACAGATGACCCGAATGATTTAAGCATCTTGCTCGAAATACTTACT
518 TCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACGTACT
* * * * *
12179 GATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAGCCTTTCTTACTTTTC
583 GATGGCCCAAAGGACTTATAAATTTTGGAAAAAGTTTACTAGGTAAGAAACCTTTCTTACTTCTA
* *
12244 AAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATTTTTTTTA
648 AAAAATTTCAATTTTCAAATTTAAACGAGAAAACTTTCTCA--TTTTTTA
* * * * *
12294 AGAGA-ATGTGAAAACATCCCGCCCGAAGAACTTATGGATGGCCCGAAGTACTTATCATCTTGCT
1 AGAGACATGTGAAAACATCCTGCCCAAAG-TCTTATGGATGGCCCAAAGGACTTATCATCTTGCT
* * * *
12358 CGAAAGACTTACATATGACCTGAAGGATTTAAGCATCATGCTTGAAAGACTTACTAATGGCCCGA
65 CGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTAATGGCCTGA
* * * *
12423 AAGACTTATAAATTTTAGAAATAGTGTACTAGTTAAGAAACCTTTCTCACTTTTCAAAAAT-TTT
130 AAGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATATTT
* ** *
12487 GATTTTCA-A-ATTTAAATGAGAAACCTTTCTCATTT
195 CA-AATCACAGATTTGAATGAGAAACCTTTCTCATTT
12522 CATTTTTTTA
Statistics
Matches: 823, Mismatches: 87, Indels: 29
0.88 0.09 0.03
Matches are distributed among these distances:
691 167 0.20
692 186 0.23
693 15 0.02
694 3 0.00
695 3 0.00
698 72 0.09
699 372 0.45
700 5 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (695 bp):
AGAGACATGTGAAAACATCCTGCCCAAAGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTC
GAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTAATGGCCTGAA
AGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATATTTC
AAATCACAGATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTACCCA
AAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACTCGAAGG
ATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCAAAGGACTTATAATTTTGGAAATAGTTT
ACTAGGTAAGAAACCTTTCTCACCTTTCAAAAAATTTCAATTTTCAGATTTAAACGAGAAACAAT
TCTCATATTTCGATAGACATGTAAAAACATCTTGCCCAAAGGTATGAGCCTCAAATGACTTATCA
TCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACGTACTGAT
GGCCCAAAGGACTTATAAATTTTGGAAAAAGTTTACTAGGTAAGAAACCTTTCTTACTTCTAAAA
AATTTCAATTTTCAAATTTAAACGAGAAAACTTTCTCATTTTTTA
Found at i:16118 original size:17 final size:17
Alignment explanation
Indices: 16083--16121 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
16073 AATTTTTGTA
*
16083 AATTCTATTTTTCTTTT
1 AATTCTATTTTTATTTT
16100 AATTC-ATTTTTATTATT
1 AATTCTATTTTTATT-TT
16117 AATTC
1 AATTC
16122 CTAAGTCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTCTATTTTTATTTT
Found at i:17839 original size:20 final size:21
Alignment explanation
Indices: 17792--17844 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
17782 TGCATGTGTT
17792 GCATGTTTTCATATGCCTTTATG
1 GCATGTTTT--TATGCCTTTATG
* *
17815 ACATGTTTTTATG-CTTTTTG
1 GCATGTTTTTATGCCTTTATG
17835 GCATGTTTTT
1 GCATGTTTTT
17845 CGGTTCTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 15 0.56
21 4 0.15
23 8 0.30
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.55
Consensus pattern (21 bp):
GCATGTTTTTATGCCTTTATG
Found at i:21790 original size:54 final size:54
Alignment explanation
Indices: 21702--22019 Score: 415
Period size: 54 Copynumber: 5.9 Consensus size: 54
21692 CTATGTCTAC
* * * *
21702 TATCGACACTAAGTATGCAACCCACGGAATTCATAATGAGTTTATGAACGACTG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAACGACCG
* * *
21756 TATTGGCACTAAGTGTGCAATCCACGAAATTCATAATGAGTTTATGAACGACCA
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAACGACCG
* * *
21810 TATCGACACTAAGTGTGCAGCCCA-TAGAATTCATAATGAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACGA-AATTCATAATGAGTTTATGAACGACCG
* * *
21864 TATCAGCACTAAGTGTGCAACCCAC-AGAATTTATAATGAGTTTATGAAAGACCG
1 TATCGGCACTAAGTGTGCAACCCACGA-AATTCATAATGAGTTTATGAACGACCG
* * *
21918 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATAAATGATCG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAACGACCG
* * * * *
21972 TATCGGTATTAAGTGTACAAACCACAAAATTCATAATGAGTTTATGAA
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAA
22020 TGATTATATT
Statistics
Matches: 232, Mismatches: 29, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
53 1 0.00
54 230 0.99
55 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAACGACCG
Found at i:22062 original size:108 final size:106
Alignment explanation
Indices: 21702--22063 Score: 386
Period size: 108 Copynumber: 3.3 Consensus size: 106
21692 CTATGTCTAC
* * ** *
21702 TATCGACACTAAGTATGCAACCCACGGAATTCATAATGAGTTTATGAACGACTGTATTGGCACTA
1 TATCGGCACTAAGTGTGC-ACCCAAAGAATTCATAATGAGTTTATGAACGAC-GTATCGGCACTA
* * *
21767 AGTGTGCAATCCACGAAATTCATAATGAGTTTATGAACGACCA
64 AGTGTGCAAACCACAAAATTCATAATGAGTTTATGAAAGACCA
* * *
21810 TATCGACACTAAGTGTGCAGCCCATAGAATTCATAATGAGTTTATGAACGACCGTATCAGCACTA
1 TATCGGCACTAAGTGTGCA-CCCAAAGAATTCATAATGAGTTTATGAACGA-CGTATCGGCACTA
* * * *
21875 AGTGTGCAACCCACAGAATTTATAATGAGTTTATGAAAGACCG
64 AGTGTGCAAACCACAAAATTCATAATGAGTTTATGAAAGACCA
* * * * *
21918 TATCGGCACTAAGTGTGCAACCC-ACGAAATTCATAATGAGTTTATAAATGATCGTATCGGTATT
1 TATCGGCACTAAGTGTGC-ACCCAAAG-AATTCATAATGAGTTTATGAACGA-CGTATCGGCACT
* * **
21982 AAGTGTACAAACCACAAAATTCATAATGAGTTTATGAATGATTA
63 AAGTGTGCAAACCACAAAATTCATAATGAGTTTATGAAAGACCA
* * *
22026 TATTGGGACTATGTGTGCACCTCAAAGAACTT-ATAATG
1 TATCGGCACTAAGTGTGCACC-CAAAGAA-TTCATAATG
22064 TTATGGAAAT
Statistics
Matches: 215, Mismatches: 32, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
107 5 0.02
108 204 0.95
109 6 0.03
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (106 bp):
TATCGGCACTAAGTGTGCACCCAAAGAATTCATAATGAGTTTATGAACGACGTATCGGCACTAAG
TGTGCAAACCACAAAATTCATAATGAGTTTATGAAAGACCA
Found at i:22062 original size:162 final size:162
Alignment explanation
Indices: 21708--22063 Score: 419
Period size: 162 Copynumber: 2.2 Consensus size: 162
21698 CTACTATCGA
* ** * * *
21708 CACTAAGTATGCAACCCACGGAA-TTCATAATGAGTTTATGAACGACTGTATTGGCACTAAGTGT
1 CACTAAGTGTGCAACCCAAAGAACTT-ATAATGAGTTTATGAAAGACCGTATCGGCACTAAGTGT
* * * ** * *
21772 GCAATCCACGAAATTCATAATGAGTTTATGAACGACCATATCGACACTAAGTGTGCAGCCCATAG
65 GCAACCCACGAAATTCATAATGAGTTTATAAACGACCATATCGACACTAAGTGTACAAACCACAA
*
21837 AATTCATAATGAGTTTATGAACGACCGTATCAG
130 AATTCATAATGAGTTTATGAACGACCATATCAG
* *
21870 CACTAAGTGTGCAACCCACAGAATTTATAATGAGTTTATGAAAGACCGTATCGGCACTAAGTGTG
1 CACTAAGTGTGCAACCCAAAGAACTTATAATGAGTTTATGAAAGACCGTATCGGCACTAAGTGTG
* * * ** *
21935 CAACCCACGAAATTCATAATGAGTTTATAAATGATCGTATCGGTATTAAGTGTACAAACCACAAA
66 CAACCCACGAAATTCATAATGAGTTTATAAACGACCATATCGACACTAAGTGTACAAACCACAAA
* ** **
22000 ATTCATAATGAGTTTATGAATGATTATATTGG
131 ATTCATAATGAGTTTATGAACGACCATATCAG
* *
22032 GACTATGTGTGC-ACCTCAAAGAACTTATAATG
1 CACTAAGTGTGCAACC-CAAAGAACTTATAATG
22064 TTATGGAAAT
Statistics
Matches: 164, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
161 3 0.02
162 159 0.97
163 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (162 bp):
CACTAAGTGTGCAACCCAAAGAACTTATAATGAGTTTATGAAAGACCGTATCGGCACTAAGTGTG
CAACCCACGAAATTCATAATGAGTTTATAAACGACCATATCGACACTAAGTGTACAAACCACAAA
ATTCATAATGAGTTTATGAACGACCATATCAG
Found at i:33088 original size:31 final size:31
Alignment explanation
Indices: 33052--33122 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
33042 TTAAAAAACA
33052 TAAGTTTTGGTCACTTACATTATC-ATTTTAT
1 TAAGTTTTGGTCACTTACATTA-CGATTTTAT
** *
33083 TAAGTTTTGGTCACTTATGTTACGGTTTTAT
1 TAAGTTTTGGTCACTTACATTACGATTTTAT
33114 TAAGTTTTG
1 TAAGTTTTG
33123 ATCATTTGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACATTACGATTTTAT
Found at i:37126 original size:24 final size:24
Alignment explanation
Indices: 37074--37128 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
37064 CATATAGTTC
*
37074 CAGGAGTACACGAATGTACTAACA
1 CAGGAGTACACAAATGTACTAACA
* * **
37098 TAGGAGTACCCAAATGTACTAGTA
1 CAGGAGTACACAAATGTACTAACA
37122 CAGGAGT
1 CAGGAGT
37129 GCTCGTATGC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (24 bp):
CAGGAGTACACAAATGTACTAACA
Found at i:40045 original size:29 final size:31
Alignment explanation
Indices: 39975--40048 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 31
39965 AAAATTCAAC
* *
39975 TTTGGTCCCTAAACTTTTCTAAACTTTATAT
1 TTTGGTCACTAAACTTTTCTAAAATTTATAT
* *
40006 TTTGG-CTACTAGAC-TTT-TAAAATTTATGT
1 TTTGGTC-ACTAAACTTTTCTAAAATTTATAT
40035 TTTGGTCACTAAAC
1 TTTGGTCACTAAAC
40049 AAAATTTGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
29 21 0.58
30 5 0.14
31 10 0.28
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (31 bp):
TTTGGTCACTAAACTTTTCTAAAATTTATAT
Found at i:42437 original size:23 final size:23
Alignment explanation
Indices: 42404--42455 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
42394 ATTACCATCA
*
42404 CTACTCTCTTATTCTTGAACCTC
1 CTACTCGCTTATTCTTGAACCTC
42427 CTACTCGCTTATTCTTGAACCTC
1 CTACTCGCTTATTCTTGAACCTC
42450 CTACTC
1 CTACTC
42456 ATCTACTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.17, C:0.37, G:0.06, T:0.40
Consensus pattern (23 bp):
CTACTCGCTTATTCTTGAACCTC
Found at i:43398 original size:25 final size:24
Alignment explanation
Indices: 43364--43423 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 24
43354 AATATTCAAC
* *
43364 AATGTACTAAAACAGGAGGGCAATA
1 AATGCACTAAAACAGGAGGGC-ACA
* * *
43389 AATGCACTAATACTGGAGTGCACA
1 AATGCACTAAAACAGGAGGGCACA
43413 AATGCACTAAA
1 AATGCACTAAA
43424 CATGATCGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (24 bp):
AATGCACTAAAACAGGAGGGCACA
Found at i:43444 original size:24 final size:24
Alignment explanation
Indices: 43417--43464 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
43407 TGCACAAATG
*
43417 CACTAAACATGATCGATCGATAAA
1 CACTAAACATGATCAATCGATAAA
*
43441 CACTAAACATGGTCAATCGATAAA
1 CACTAAACATGATCAATCGATAAA
43465 AACTCTACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.21
Consensus pattern (24 bp):
CACTAAACATGATCAATCGATAAA
Found at i:58008 original size:18 final size:20
Alignment explanation
Indices: 57967--58013 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
57957 TGTGCTGCCA
57967 GTATCGATACTAACCTTGTG
1 GTATCGATACTAACCTTGTG
57987 GTATCGATACTAACC-T-TG
1 GTATCGATACTAACCTTGTG
58005 GTATCGATA
1 GTATCGATA
58014 TTGTCCCCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 11 0.41
19 1 0.04
20 15 0.56
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (20 bp):
GTATCGATACTAACCTTGTG
Done.