Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004758.1 Hibiscus syriacus cultivar Beakdansim tig00010737_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: 62154
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4742 original size:21 final size:21
Alignment explanation
Indices: 4716--4758 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
4706 TTCTGGGTTG
4716 TGTGCATCGATGCA-TCTTCAA
1 TGTGCATCGATGCACTC-TCAA
4737 TGTGCATCGATGCACTCTCAA
1 TGTGCATCGATGCACTCTCAA
4758 T
1 T
4759 TAAATGAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTGCATCGATGCACTCTCAA
Found at i:7398 original size:21 final size:21
Alignment explanation
Indices: 7356--7398 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
7346 AAAGTGGGAG
**
7356 AAATTAGGGATTCCTGAGATT
1 AAATTAGGGATTAATGAGATT
7377 AAATTAGGGATTGAATGA-ATT
1 AAATTAGGGATT-AATGAGATT
7398 A
1 A
7399 GTGGGGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (21 bp):
AAATTAGGGATTAATGAGATT
Found at i:8053 original size:21 final size:21
Alignment explanation
Indices: 8024--8069 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
8014 TTAATATCGT
**
8024 GTTCGTGTTTGTTCGTTTAAC
1 GTTCGTGTTCATTCGTTTAAC
* *
8045 GTTCTTGTTCATTCGTTTAGC
1 GTTCGTGTTCATTCGTTTAAC
8066 GTTC
1 GTTC
8070 ATGAACATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.17, G:0.22, T:0.52
Consensus pattern (21 bp):
GTTCGTGTTCATTCGTTTAAC
Found at i:10148 original size:11 final size:11
Alignment explanation
Indices: 10120--10148 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
10110 ATTCGATGAC
10120 TAAATTTATTT
1 TAAATTTATTT
10131 T-AATTTATTT
1 TAAATTTATTT
10141 TAAATTTA
1 TAAATTTA
10149 ATAGATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TAAATTTATTT
Found at i:10440 original size:30 final size:29
Alignment explanation
Indices: 10401--10475 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 29
10391 TAAAATTATC
*
10401 TTTTGTTTTTGTTTTAACTTATTAAATATA
1 TTTTATTTTT-TTTTAACTTATTAAATATA
10431 TTTTATTTTTTTCTTAACTTATTAAATATA
1 TTTTATTTTTTT-TTAACTTATTAAATATA
10461 -TTTATTTTTATTTTA
1 TTTTATTTTT-TTTTA
10476 GTGTAAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 14 0.33
30 28 0.67
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTATTTTTTTTTAACTTATTAAATATA
Found at i:10725 original size:29 final size:29
Alignment explanation
Indices: 10693--10783 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 29
10683 ATATTTTAAT
* * **
10693 ATATTTTTTAAATTTTAGATAATGATAAA
1 ATATTTTTTAAATTTAAAATAAAAATAAA
*
10722 ATATATTTTAAATTTAAAATAAAAATAAA
1 ATATTTTTTAAATTTAAAATAAAAATAAA
* * * *
10751 ATA-TTTTT-AAGTGAAGATAAGAATAAA
1 ATATTTTTTAAATTTAAAATAAAAATAAA
10778 ATATTT
1 ATATTT
10784 AAATATATTT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
27 18 0.35
28 6 0.12
29 27 0.53
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.42
Consensus pattern (29 bp):
ATATTTTTTAAATTTAAAATAAAAATAAA
Found at i:10770 original size:27 final size:28
Alignment explanation
Indices: 10717--10783 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
10707 TTAGATAATG
* *
10717 ATAAAATATATTTTAAATTTAAAATAAAA
1 ATAAAATAT-TTTTAAAGTGAAAATAAAA
* *
10746 ATAAAATATTTTT-AAGTGAAGATAAGA
1 ATAAAATATTTTTAAAGTGAAAATAAAA
10773 ATAAAATATTT
1 ATAAAATATTT
10784 AAATATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 21 0.62
28 4 0.12
29 9 0.26
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (28 bp):
ATAAAATATTTTTAAAGTGAAAATAAAA
Found at i:10808 original size:15 final size:16
Alignment explanation
Indices: 10782--10811 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10772 AATAAAATAT
10782 TTAAATATATTTTAAG
1 TTAAATATATTTTAAG
10798 TTAAA-ATATTTTAA
1 TTAAATATATTTTAA
10812 AAAATTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTAAATATATTTTAAG
Found at i:10840 original size:188 final size:188
Alignment explanation
Indices: 10624--11200 Score: 749
Period size: 188 Copynumber: 3.0 Consensus size: 188
10614 TTCTTTTTTT
* * *
10624 AAAATATCTTAACTTAAATTATATTTTATTTTTAAATTGAAATACATTTTGAAGTTAGGATATTT
1 AAAATTTCTTAACTTAAATTAAATTTTATTTTTAAATTAAAATACATTTTGAAGTTAGGATATTT
*
10689 TAATATATTTTTTAAATTTTAGATAATGATAAAATATATTTTAAATTTAAAATAAAAATAAAATA
66 TAATATATTTTTTAAATTTTAGATAATGATAAAATATATTTTTAATTTAAAATAAAAATAAAATA
10754 TTTTTAAGTGAAGATAAGAATAAAATATTTAAATATATTTTAAGTTAAAATATTTTAA
131 TTTTTAAGTGAAGATAAGAATAAAATATTTAAATATATTTTAAGTTAAAATATTTTAA
*
10812 AAAATTTCTTAACTTAAATTAAATTTTATTTTTAAATTAAAATGCATTTTGAAGTTAGGATATTT
1 AAAATTTCTTAACTTAAATTAAATTTTATTTTTAAATTAAAATACATTTTGAAGTTAGGATATTT
* * *
10877 TAATATATTTTTAAAAATTTAGATAATGATAAAATATATTTTTAATTTGAAATAAAAATAAAATA
66 TAATATATTTTTTAAATTTTAGATAATGATAAAATATATTTTTAATTTAAAATAAAAAT-AAA-A
10942 TATTTTTAAGTGAAGATAAGAATAAAATATTTAAATATATTTTAAGTTAAAATATTTTAAAAA
129 TATTTTTAAGTGAAGATAAGAATAAAATATTTAAATATATTTTAAGTTAAAATATTTT---AA
* ** ** *
11005 ACATAATTTTCAGTGATGATAAATATAAAAAAAAACTTATTTTTAAATTAAAAAACATTTTTGAA
1 A-A-AA-TTTC-----T--TAACT-TAAATTAAATTTTATTTTTAAATTAAAATACA-TTTTGAA
* *
11070 GTTAAGATATTTTAATATA-TTTTTAAATATTTATATAATGATAAAAATATATTTTTAATTTAAA
54 GTTAGGATATTTTAATATATTTTTTAAAT-TTTAGATAATGAT-AAAATATATTTTTAATTTAAA
* * *
11134 ATAAAAAT-AAA-A----TAAGTGAAGATAATAA-AAAATATTT-AATATATTTTACGTTAAAAC
117 ATAAAAATAAAATATTTTTAAGTGAAGATAAGAATAAAATATTTAAATATATTTTAAGTTAAAAT
11191 ATTTTAA
182 ATTTTAA
11198 AAA
1 AAA
11201 TATATTTTTA
Statistics
Matches: 347, Mismatches: 23, Indels: 35
0.86 0.06 0.09
Matches are distributed among these distances:
188 116 0.33
189 3 0.01
190 59 0.17
191 1 0.00
192 1 0.00
193 6 0.02
194 1 0.00
195 2 0.01
196 27 0.08
197 9 0.03
198 15 0.04
201 1 0.00
202 1 0.00
203 5 0.01
204 35 0.10
205 37 0.11
206 28 0.08
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (188 bp):
AAAATTTCTTAACTTAAATTAAATTTTATTTTTAAATTAAAATACATTTTGAAGTTAGGATATTT
TAATATATTTTTTAAATTTTAGATAATGATAAAATATATTTTTAATTTAAAATAAAAATAAAATA
TTTTTAAGTGAAGATAAGAATAAAATATTTAAATATATTTTAAGTTAAAATATTTTAA
Found at i:10916 original size:31 final size:31
Alignment explanation
Indices: 10878--10950 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
10868 AGGATATTTT
* **
10878 AATATATTTTTAAAAATTT-AGATAATGATAA
1 AATATATTTTT-AAAATTTGAAATAAAAATAA
10909 AATATATTTTT--AATTTGAAATAAAAATAA
1 AATATATTTTTAAAATTTGAAATAAAAATAA
10938 AATATATTTTTAA
1 AATATATTTTTAA
10951 GTGAAGATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 5 0.14
29 20 0.56
31 11 0.31
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (31 bp):
AATATATTTTTAAAATTTGAAATAAAAATAA
Found at i:10937 original size:29 final size:29
Alignment explanation
Indices: 10905--10971 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
10895 TTAGATAATG
*
10905 ATAAAATATATTTTTAATTTGAA-ATAAAA
1 ATAAAATATATTTTTAA-GTGAAGATAAAA
*
10934 ATAAAATATATTTTTAAGTGAAGATAAGA
1 ATAAAATATATTTTTAAGTGAAGATAAAA
10963 ATAAAATAT
1 ATAAAATAT
10972 TTAAATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 4 0.11
29 31 0.89
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.37
Consensus pattern (29 bp):
ATAAAATATATTTTTAAGTGAAGATAAAA
Found at i:10998 original size:15 final size:16
Alignment explanation
Indices: 10972--11001 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10962 AATAAAATAT
10972 TTAAATATATTTTAAG
1 TTAAATATATTTTAAG
10988 TTAAA-ATATTTTAA
1 TTAAATATATTTTAA
11002 AAAACATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTAAATATATTTTAAG
Found at i:11282 original size:28 final size:28
Alignment explanation
Indices: 11251--11304 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
11241 ACATTAAAAT
11251 AAAAATAAATATATTTAATAAGTTAAGA
1 AAAAATAAATATATTTAATAAGTTAAGA
* *
11279 AAAATTAAATATATTTAATAATTTAA
1 AAAAATAAATATATTTAATAAGTTAA
11305 AACAAAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (28 bp):
AAAAATAAATATATTTAATAAGTTAAGA
Found at i:11405 original size:2 final size:2
Alignment explanation
Indices: 11398--11449 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
11388 CCATAAATTA
*
11398 AT AT AT AT AT AA 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
11440 AT AT AT AT AT
1 AT AT AT AT AT
11450 TTATTATCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11621 original size:5 final size:5
Alignment explanation
Indices: 11611--11666 Score: 53
Period size: 5 Copynumber: 11.6 Consensus size: 5
11601 AAATAAATTT
* * * *
11611 ATTAA ATTAA AATAA ATT-T ATTAA ATTAA AATAA ATT-T ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
*
11659 AATAA ATT
1 ATTAA ATT
11667 TATTCATCCA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
4 6 0.15
5 33 0.85
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAA
Found at i:11624 original size:19 final size:19
Alignment explanation
Indices: 11600--11670 Score: 142
Period size: 19 Copynumber: 3.7 Consensus size: 19
11590 TGTTTGGTGG
11600 AAAATAAATTTATTAAATT
1 AAAATAAATTTATTAAATT
11619 AAAATAAATTTATTAAATT
1 AAAATAAATTTATTAAATT
11638 AAAATAAATTTATTAAATT
1 AAAATAAATTTATTAAATT
11657 AAAATAAATTTATT
1 AAAATAAATTTATT
11671 CATCCAATCG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATAAATTTATTAAATT
Found at i:13189 original size:25 final size:24
Alignment explanation
Indices: 13137--13189 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
13127 TATTATCATT
*
13137 ATTTCTAAAATGTTATAAAATTAT
1 ATTTCTAAAATGTTATAAAATTAC
*
13161 ATTTCTTAAAATTTTAT-AAATTCAC
1 ATTTC-TAAAATGTTATAAAATT-AC
13186 ATTT
1 ATTT
13190 TAATATAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTTCTAAAATGTTATAAAATTAC
Found at i:19191 original size:41 final size:40
Alignment explanation
Indices: 19104--19206 Score: 107
Period size: 41 Copynumber: 2.5 Consensus size: 40
19094 AGTACAAATA
***
19104 TTTAGCGGCGTTTATTAAAAATGTTACTAAAATACGAGCC
1 TTTAGCGGCGTTTATTAAAAATACCACTAAAATACGAGCC
* * **
19144 TATAGCGGCGTTTACTTAAAAATACCACTAAAATATGAGTT
1 TTTAGCGGCGTTTA-TTAAAAATACCACTAAAATACGAGCC
* *
19185 TTTAGCGACGTTTGTTTAAAAA
1 TTTAGCGGCGTTT-ATTAAAAA
19207 CGCCGTTAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
40 13 0.25
41 38 0.75
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (40 bp):
TTTAGCGGCGTTTATTAAAAATACCACTAAAATACGAGCC
Found at i:34205 original size:41 final size:41
Alignment explanation
Indices: 34160--34415 Score: 237
Period size: 41 Copynumber: 6.2 Consensus size: 41
34150 TAACAGAGAA
* * * *
34160 GTACTTTAGCGACGTTTTTATACAAACGCCGCTAAAGACTC
1 GTACTTTAGCGGCATTTTTATACAAACGCCGCTATAGACTT
* *
34201 GTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTT
1 GTACTTTAGCGGCATTTTTATACAAACGCCGCTATAGACTT
* ** * * *
34242 GAACTTTAGTTGCATTTTTATAAAAACGCCGCT-TACAATT
1 GTACTTTAGCGGCATTTTTATACAAACGCCGCTATAGACTT
* * * * * *
34282 GTACTTTAGTGGCGTTTGTGTTTATAAACGCCGCTAAAGACTA
1 GTACTTTAGCGGCATTT-T-TATACAAACGCCGCTATAGACTT
* * * *
34325 GTACATTAGCGGCATTTATATACAACCGCCGCTATACACTT
1 GTACTTTAGCGGCATTTTTATACAAACGCCGCTATAGACTT
* * * *
34366 GTA-TGTTAGCGACATTTTTATACGAACGCCACTATAGACTC
1 GTACT-TTAGCGGCATTTTTATACAAACGCCGCTATAGACTT
34407 GTACTTTAG
1 GTACTTTAG
34416 TGGCGTTTGA
Statistics
Matches: 173, Mismatches: 37, Indels: 10
0.79 0.17 0.05
Matches are distributed among these distances:
40 19 0.11
41 123 0.71
42 14 0.08
43 17 0.10
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (41 bp):
GTACTTTAGCGGCATTTTTATACAAACGCCGCTATAGACTT
Found at i:34340 original size:83 final size:81
Alignment explanation
Indices: 34124--34415 Score: 239
Period size: 83 Copynumber: 3.5 Consensus size: 81
34114 GGTTCATCTA
* ** ** * *
34124 TAGTGGCGTTTTTTTAACAAACATCG-TAACAGAGAAGTACTTTAGCGACGTTTTTATACAAACG
1 TAGTGGCGTTTTTAT-ACAAACGCCGCTAA-AGACTAGTACTTTAGCGGCATTTTTATACAAACG
* *
34188 CCGC-TAAAGACTCGTACTT
64 CCGCTTACA-A-TTGTACTT
* * * ** *
34207 TAGTGGCGTTTTTATACAAACGCCGCTATAGACTTGAACTTTAGTTGCATTTTTATAAAAACGCC
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTAGTACTTTAGCGGCATTTTTATACAAACGCC
34272 GCTTACAATTGTACTT
66 GCTTACAATTGTACTT
* * * * *
34288 TAGTGGCGTTTGTGTTTATAAACGCCGCTAAAGACTAGTACATTAGCGGCATTTATATACAACCG
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTAGTACTTTAGCGGCATTTTTATACAAACG
*
34353 CCGCTATACACTTGTA-TGT
64 CCGCT-TACAATTGTACT-T
* * * * * * *
34372 TAGCGACATTTTTATACGAACGCCACTATAGACTCGTACTTTAG
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTAGTACTTTAG
34416 TGGCGTTTGA
Statistics
Matches: 166, Mismatches: 37, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
81 18 0.11
82 64 0.39
83 66 0.40
84 18 0.11
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (81 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTAGTACTTTAGCGGCATTTTTATACAAACGCC
GCTTACAATTGTACTT
Found at i:34347 original size:124 final size:125
Alignment explanation
Indices: 34180--34440 Score: 330
Period size: 124 Copynumber: 2.1 Consensus size: 125
34170 GACGTTTTTA
* * * * * *
34180 TACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTTGAA
1 TACAAACGCCGCTAAAGACTAGTACATTAGCGGCATTTATATACAAACGCCGCTATACACTTGAA
* * * *
34245 CT-TTAGTTG-CATTTTTATAAAAACGCCGCT-TACAATTGTACTTTAGTGGCGTTTGTGTT
66 -TGTTAG-CGACATTTTTATAAAAACGCCACTATACAATCGTACTTTAGTGGCGTTTGAGTT
* * *
34304 TATAAACGCCGCTAAAGACTAGTACATTAGCGGCATTTATATACAACCGCCGCTATACACTTGTA
1 TACAAACGCCGCTAAAGACTAGTACATTAGCGGCATTTATATACAAACGCCGCTATACACTTGAA
** * *
34369 TGTTAGCGACATTTTTATACGAACGCCACTATAGACTCGTACTTTAGTGGCGTTTGAGTT
66 TGTTAGCGACATTTTTATAAAAACGCCACTATACAATCGTACTTTAGTGGCGTTTGAGTT
34429 TACAAACGCCGC
1 TACAAACGCCGC
34441 AATTTTATAA
Statistics
Matches: 116, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
123 2 0.02
124 78 0.67
125 36 0.31
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (125 bp):
TACAAACGCCGCTAAAGACTAGTACATTAGCGGCATTTATATACAAACGCCGCTATACACTTGAA
TGTTAGCGACATTTTTATAAAAACGCCACTATACAATCGTACTTTAGTGGCGTTTGAGTT
Found at i:34698 original size:33 final size:33
Alignment explanation
Indices: 34654--34726 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
34644 TTTTGATTTT
*
34654 GATTTTAATTTCGTGGCTTTGGGTTCTGCTTTG
1 GATTTTGATTTCGTGGCTTTGGGTTCTGCTTTG
34687 GATTTTGATTTCGTGGCTTTGGGTTCTGCTTTG
1 GATTTTGATTTCGTGGCTTTGGGTTCTGCTTTG
34720 GATTTTG
1 GATTTTG
34727 TATAGTGGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.08, C:0.11, G:0.29, T:0.52
Consensus pattern (33 bp):
GATTTTGATTTCGTGGCTTTGGGTTCTGCTTTG
Found at i:38212 original size:42 final size:43
Alignment explanation
Indices: 38152--38503 Score: 331
Period size: 43 Copynumber: 8.2 Consensus size: 43
38142 AAGGTAATTA
* **
38152 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGCCTGA-CTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTATGACCTTTT
* ** * *
38194 GCGGCGTTTGTGTTCAAAAATACCGTTATAAGTATGACCTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTATGACCTTTT
*
38237 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTATGACCTTTT
* * *
38280 GCGGCGTTTGT-TCTAAAAACGCCAG-TATAGGTCT-TCTCTTTT
1 GCGGCGTTTGTGTCCAAAAACGCC-GCTATAGGTATGAC-CTTTT
* * *
38322 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATTTGACCTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTATGACCTTTT
** * * * * ** * *
38365 GCGATGTTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGT-ATGACCTTTT
* *
38409 GCGGCGTTTAT-TCCAAAAACGCCGCTATAGATATCGACCTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTAT-GACCTTTT
* * *
38452 GCGGCGTTTGT-TCAAAAAACGCCG-TAATAGATATTGACCTATT
1 GCGGCGTTTGTGTCCAAAAACGCCGCT-ATAGGTA-TGACCTTTT
38495 GCGGCGTTT
1 GCGGCGTTT
38504 TTTGTTCTCA
Statistics
Matches: 259, Mismatches: 41, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.00
42 69 0.27
43 172 0.66
44 17 0.07
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (43 bp):
GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTATGACCTTTT
Found at i:38497 original size:86 final size:85
Alignment explanation
Indices: 38152--38503 Score: 369
Period size: 85 Copynumber: 4.1 Consensus size: 85
38142 AAGGTAATTA
**
38152 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGCCTGA-CTTTTGCGGCGTTTGTGTTCAAAAATA
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTT-TGTTCAAAAA-A
38216 --CCGTTATA-AGTATGACCTTTT
64 CGCCG-TATAGA-TATGACCTTTT
* * *
38237 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCG-TTTGTTCTAAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTTGTTCAAAAAACG
* * *
38301 CCAGTATAGGTCT-TCTCTTTT
66 CC-GTATAGATATGAC-CTTTT
* ** * * *
38322 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATTTGACCTTTTGCGATGTTTTTTTCTAGAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTTGTTCAAAAAACG
* * *
38387 CCGCTATATATCATAACTTTTT
66 CCG-TATAGAT-ATGACCTTTT
* *
38409 GCGGCGTTTAT-TCCAAAAACGCCGCTATAGATATCGACCTTTTGCGGCG-TTTGTTCAAAAAAC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTTGTTCAAAAAAC
*
38472 GCCGTAATAGATATTGACCTATT
65 GCCGT-ATAGATA-TGACCTTTT
38495 GCGGCGTTT
1 GCGGCGTTT
38504 TTTGTTCTCA
Statistics
Matches: 225, Mismatches: 29, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
83 1 0.00
84 10 0.04
85 97 0.43
86 89 0.40
87 27 0.12
88 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (85 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTTGTTCAAAAAACG
CCGTATAGATATGACCTTTT
Found at i:56345 original size:15 final size:15
Alignment explanation
Indices: 56325--56355 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
56315 GGTTACCTAC
56325 GTTCTTCGGGACATG
1 GTTCTTCGGGACATG
56340 GTTCTTCGGGACATG
1 GTTCTTCGGGACATG
56355 G
1 G
56356 ACTGTTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.35, T:0.32
Consensus pattern (15 bp):
GTTCTTCGGGACATG
Found at i:56401 original size:31 final size:31
Alignment explanation
Indices: 56340--56495 Score: 205
Period size: 31 Copynumber: 5.2 Consensus size: 31
56330 TCGGGACATG
*
56340 GTTCTTCGGGAC--ATGGACTGTTTACTTAT
1 GTTCTTCGGGACATATGGACTGTTTACCTAT
*
56369 GTTCTTCGGGATATATGG-CATGTTTACCTAT
1 GTTCTTCGGGACATATGGAC-TGTTTACCTAT
*
56400 GTTCTTCGGGACATATGGACTATTTACCTAT
1 GTTCTTCGGGACATATGGACTGTTTACCTAT
*
56431 GTTCTTCGGGACATATGGACTGATTACCTAT
1 GTTCTTCGGGACATATGGACTGTTTACCTAT
* * *
56462 GTGCTTCGGG--ATATGGACTGATTACCTAG
1 GTTCTTCGGGACATATGGACTGTTTACCTAT
56491 GTTCT
1 GTTCT
56496 GATAGATCTA
Statistics
Matches: 114, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
29 33 0.29
30 1 0.01
31 79 0.69
32 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTCTTCGGGACATATGGACTGTTTACCTAT
Found at i:57051 original size:21 final size:21
Alignment explanation
Indices: 57025--57081 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
57015 GGTCGAAATT
*
57025 ACTGTAGTAGGGTATTGGTAC
1 ACTGTAGCAGGGTATTGGTAC
57046 ACTGTAGCAGGGTATTGGTAC
1 ACTGTAGCAGGGTATTGGTAC
57067 ACTGTAGCAGGGTAT
1 ACTGTAGCAGGGTAT
57082 CGATACTCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.30
Consensus pattern (21 bp):
ACTGTAGCAGGGTATTGGTAC
Found at i:57166 original size:20 final size:20
Alignment explanation
Indices: 57143--57181 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
57133 CTGTTCACAT
*
57143 AGTATCGATACTTTTTGCAG
1 AGTATCGATACTATTTGCAG
*
57163 AGTATCGGTACTATTTGCA
1 AGTATCGATACTATTTGCA
57182 CATTGTCGGT
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (20 bp):
AGTATCGATACTATTTGCAG
Found at i:57621 original size:20 final size:20
Alignment explanation
Indices: 57580--57622 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
57570 AAGATTTTTT
*
57580 TATATATTCTTTACTAATAA
1 TATATATTCTATACTAATAA
*
57600 TATATATTCATATATTAA-AA
1 TATATATTC-TATACTAATAA
57620 TAT
1 TAT
57623 CATAAATCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
TATATATTCTATACTAATAA
Done.