Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001418.1 Hibiscus syriacus cultivar Beakdansim tig00002756_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: 51677
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:8800 original size:51 final size:51
Alignment explanation
Indices: 8740--8836 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
8730 ACGGTTGGTA
* * * *
8740 ATTCACTTCTTTTTATTTGGATGGATAATCAGGATCGGTGAGGTAACAATG
1 ATTCACTTCTTTTAACTTGGATAGATAATCAGGACCGGTGAGGTAACAATG
*
8791 ATTCACTTCTTTTAACTTGGATAGATAATCATGACCGGTGAGGTAA
1 ATTCACTTCTTTTAACTTGGATAGATAATCAGGACCGGTGAGGTAA
8837 TAATTATTGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (51 bp):
ATTCACTTCTTTTAACTTGGATAGATAATCAGGACCGGTGAGGTAACAATG
Found at i:11492 original size:23 final size:23
Alignment explanation
Indices: 11466--11517 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
11456 AATAACATAT
* **
11466 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAACGCTTATATAATAAAA
11489 TAGGTAACGCTTATATAATAAAA
1 TAGGTAACGCTTATATAATAAAA
11512 TAGGTA
1 TAGGTA
11518 TTTAACCGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (23 bp):
TAGGTAACGCTTATATAATAAAA
Found at i:11500 original size:87 final size:87
Alignment explanation
Indices: 11353--11571 Score: 384
Period size: 87 Copynumber: 2.5 Consensus size: 87
11343 ATTCAATCGA
* * **
11353 AAATATTATCAAGTACAACAACATATTAAGTAGCGCTTATATAATGTAATAGGTTGCGCTTATAT
1 AAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATAT
11418 AATAAAATAAGTATTTAACCGG
66 AATAAAATAAGTATTTAACCGG
11440 AAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATAT
1 AAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATAT
*
11505 AATAAAATAGGTATTTAACCGG
66 AATAAAATAAGTATTTAACCGG
*
11527 AAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAAT
1 AAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAAT
11572 AAAATAAGTA
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 126 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.32
Consensus pattern (87 bp):
AAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATAT
AATAAAATAAGTATTTAACCGG
Found at i:11562 original size:64 final size:64
Alignment explanation
Indices: 11489--11644 Score: 233
Period size: 64 Copynumber: 2.5 Consensus size: 64
11479 TATAATGTAA
*
11489 TAGGTAACGCTTATATAATAAAATAGGTATTTAACCGGAAATATTATCAAGTACAATAACATAT
1 TAGGTAACGCTTATATAATAAAATAGGTATTTAACCGAAAATATTATCAAGTACAATAACATAT
* * *
11553 TAGGTAACGCTTATATAATAAAATAAGTATTTAATCGAAAATATTATCAAGTACAGTAACATAT
1 TAGGTAACGCTTATATAATAAAATAGGTATTTAACCGAAAATATTATCAAGTACAATAACATAT
* * **
11617 TAGAT-ACGCTTATACAATGTAATAGGTA
1 TAGGTAACGCTTATATAATAAAATAGGTA
11645 ACGCTTATAT
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
63 19 0.23
64 64 0.77
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (64 bp):
TAGGTAACGCTTATATAATAAAATAGGTATTTAACCGAAAATATTATCAAGTACAATAACATAT
Found at i:12284 original size:24 final size:25
Alignment explanation
Indices: 12236--12285 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
12226 TAATAAATAA
* **
12236 TAAATATAATTATAATAATTTTATT
1 TAAATATAAATATAATAATCATATT
12261 TAAATA-AAATATAATAATCATATT
1 TAAATATAAATATAATAATCATATT
12285 T
1 T
12286 TTTTATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TAAATATAAATATAATAATCATATT
Found at i:12317 original size:28 final size:30
Alignment explanation
Indices: 12233--12318 Score: 76
Period size: 30 Copynumber: 2.9 Consensus size: 30
12223 TTATAATAAA
12233 TAAT-AAATATAAT--TATAATAATTTTATT
1 TAATAAAATATAATAATATAAT-ATTTTATT
* *
12261 TAAATAAAATATAATAATCATATTTTTTTATT
1 T-AATAAAATATAATAAT-ATAATATTTTATT
12293 T-ATAAAAT-T-ATAGATATAATATTTTA
1 TAATAAAATATAATA-ATATAATATTTTA
12319 ATAATAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
28 13 0.27
29 6 0.12
30 16 0.33
32 9 0.19
33 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (30 bp):
TAATAAAATATAATAATATAATATTTTATT
Found at i:12448 original size:17 final size:17
Alignment explanation
Indices: 12423--12466 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
12413 TATTTAATGT
*
12423 TTATAATTATATTGTAA
1 TTATGATTATATTGTAA
12440 TTATGATTATATTGTAA
1 TTATGATTATATTGTAA
12457 TTATGATTAT
1 TTATGATTAT
12467 TTTCATCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
TTATGATTATATTGTAA
Found at i:13134 original size:14 final size:14
Alignment explanation
Indices: 13052--13138 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 14
13042 ATAATTTATA
**
13052 ATTTATAATAATCTT
1 ATTT-TAATAATAAT
13067 ATTTTAATAAT-AT
1 ATTTTAATAATAAT
** *
13080 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
13094 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
13108 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
13122 ATTTTAATAATAAT
1 ATTTTAATAATAAT
13136 ATT
1 ATT
13139 GACATAAATA
Statistics
Matches: 54, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
13 11 0.20
14 38 0.70
15 5 0.09
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:13134 original size:28 final size:28
Alignment explanation
Indices: 13066--13134 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
13056 ATAATAATCT
*
13066 TATTTTAATAAT-ATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
13093 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
13121 TATTTTAATAATAA
1 TATTTTAATAATAA
13135 TATTGACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 9 0.28
28 21 0.66
29 2 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:13620 original size:785 final size:779
Alignment explanation
Indices: 12447--14355 Score: 2917
Period size: 785 Copynumber: 2.4 Consensus size: 779
12437 TAATTATGAT
*
12447 TATATTGTAATTATGATTA-TTTTCATCACTTCATTATGATTATTTTTAAAAATTATATTGTAAT
1 TATATTGTAATTATGATTATTTTTCATCACTTCATTATGATTATTTTTTAAAATTATATTGTAAT
*
12511 TATATATAATTT-TTTTTA--TTATTATTAGAAAGCTAATATCAAAATAGAAAT-ATAGTGTCAT
66 TATATAT--TTTATTTTTATTTTATTATTAGAAAGCTAATATCAAAATAGAAATAATAGTGTCCT
12572 TTTTTTCATTAGTTATATTGTGGCAACTTACAAACTAAAAAATTAAAATTAATTTGTATAATTTG
129 TTTTTTCATTAGTTATATTGT-GCAACTTACAAACTAAAAAATTAAAATTAATTTGTATAATTTG
*
12637 TGTTTACTAATTTTATCATTAAAAAGTCTATTTTACCGGTTTTGTTATTGTTGGGCATAACAAAA
193 TGTTTACTAATTTTATCATTAAAAAATCTATTTTACCGG--TTGTTATTGTTGGGCATAACAAAA
* *
12702 CCTG-TAAAAATTACCTAAAACATTATTATTTCTACCTAAAACATCAATGTTTTTTAACATTTCC
256 CCGGATAAAAATTACCTAAAACATTATTATTTCTACCTAAAACATCAATGTTTTTTAACATTTTC
* *
12766 GATAAAATGCCCAACAATAACAAAACCGGTAAAAAAATAATAAAATCAGTAGCGCTTTACCGATT
321 GATAAAATGCCCAACAATAACAAAATCGGTAAAAAAATAACAAAATCAGTAGCGCTTTACCGATT
*
12831 TTGTTAAAATAATGATGTTTTCGGTAATTTTTACCGGTTTTGTTATTGTTGTATACCGG-T-TAT
386 TTGTTAAAATAATGATGTTTTCGGTAATTTTTACCGATTTTGTTATTGTTGTATACCGGTTATAT
12894 TGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTAACATATGTGTCGATACTTTTAGA
451 TGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTAACATATGTGTCGATACTTTTAGA
*
12959 AAATGTATCGACACATATGTTTAACTATTCTCTCATTATAATATAATTAAT-ATATATTATTTTT
516 AAATGTATCGACACATATGTTTAACTATTCTCTCATTATAATATAATTAATGA-ATATTATTATT
*
13023 ATTATAATAAATAATAAATATAATTTATAATTTATAATAATCTTATTTTAATAATATATAATAAT
580 ATTATAATAAATAATAAATATAATTTAT-A---ATAAT--T-TTATTTTAATAAAATATAATAAT
13088 CATAATTTTTTATTTATAAAATTATAGATATAATATTTTAATAATAATATTGACATAAATAATAT
638 CATAATTTTTTATTTATAAAATTATAGATATAATATTTTAATAATAATATTGACATAAATAATAT
*
13153 TAAATAAATTATTCTAATATTTGAAAAATAATATTATTATTTTGTTAATAAATAATATTATTTTA
703 TAAATAAATTATTCTAATATTTAAAAAATAATATTATTATTTTGTTAATAAATAATATTATTTTA
13218 TTGTATTTAATG
768 TTGTATTTAATG
*
13230 -ATATTGTAATTATGATTATTTTTCATCATTTCATTATGATT-TTTTTTAAAATTATATTGTAAT
1 TATATTGTAATTATGATTATTTTTCATCACTTCATTATGATTATTTTTTAAAATTATATTGTAAT
* *
13293 TATATATTTTTTTTTTATTTCTTATTTTATTATTAGAAAGCTAATATCGATATAGAAATAAT-GT
66 TATATA------TTTTATTT-TTATTTTATTATTAGAAAGCTAATATCAAAATAGAAATAATAGT
*
13357 GTCCTTTTTTTCATTAGTTATATTGTGCAACTTAC-AAGTAAAAAATTAAAATTAATTTGTATAA
124 GTCCTTTTTTTCATTAGTTATATTGTGCAACTTACAAACTAAAAAATTAAAATTAATTTGTATAA
*
13421 TTTGTGTTTACTAATTTTATCATTAAAAAATCTATTGTTACCGG-T-TTATTTTTGGGCATAACA
189 TTTGTGTTTACTAATTTTATCATTAAAAAATCTATT-TTACCGGTTGTTATTGTTGGGCATAACA
* * * *
13484 AAACC-GATAAAAATCAGCTAAAACATTATTATTTCTACCTAATACATCAATGTTTTTTAATATT
253 AAACCGGATAAAAATTACCTAAAACATTATTATTTCTACCTAAAACATCAATGTTTTTTAACATT
* * * *
13548 TTCGGTAAAATGTCCAACAATAACAAAATCGGTAAAAAAATAACAAAATCGGTAGCGCTTTGCCG
318 TTCGATAAAATGCCCAACAATAACAAAATCGGTAAAAAAATAACAAAATCAGTAGCGCTTTACCG
* *
13613 GTTTTGTTAAAATAATGATGTTTTTGGTAATTTTTACCGATTTTGTTATTGTTGTATACCGGTTA
383 ATTTTGTTAAAATAATGATGTTTTCGGTAATTTTTACCGATTTTGTTATTGTTGTATACCGGTTA
13678 TATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTAACATATGTGTCGATACTTTT
448 TATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTAACATATGTGTCGATACTTTT
* * *
13743 AGAAAATGTATCGACGCATGTGTTTAACTATTCTCTCATTATAATACAATTAATGAA-A-TATTA
513 AGAAAATGTATCGACACATATGTTTAACTATTCTCTCATTATAATATAATTAATGAATATTATTA
*
13806 TTCTTATAATAAATAATAAATATAATTTATAATAATTTTATTTTAATAAAATATAATAATCATAA
578 TTATTATAATAAATAATAAATATAATTTATAATAATTTTATTTTAATAAAATATAATAATCATAA
13871 TTTTTTTATTTATAAAATTATAGATATAATATTTTAATAATAATATTGACATAAATAATATTAAA
643 -TTTTTTATTTATAAAATTATAGATATAATATTTTAATAATAATATTGACATAAATAATATTAAA
* * * *
13936 TAAATTATTCTAATATTTTAAAAATAATAATATTATTTTTTTAATAAATAATATTATTTTATTAT
707 TAAATTATTCTAATATTTAAAAAATAATATTATTATTTTGTTAATAAATAATATTATTTTATTGT
14001 ATTTGATGTTTATAG
772 ATTT-A-----AT-G
* *
14016 TTATATTATAATTATGATTATTTTTCATCACTTCATTAGGATTATTTTTTAAAATTATATTGTAA
1 -TATATTGTAATTATGATTATTTTTCATCACTTCATTATGATTATTTTTTAAAATTATATTGTAA
* * *
14081 TTATATA---TA-ATTT-TTTT-TTATT--AAAGCTAATATCTAAATAGAAA-AATCGTGTCCTT
65 TTATATATTTTATTTTTATTTTATTATTAGAAAGCTAATATCAAAATAGAAATAATAGTGTCCTT
*
14137 TTTTTCATTAGTTATATTGTGACAATTTACAAACTAAAAAATT-AAATTAATTTGTATAATTTGT
130 TTTTTCATTAGTTATATTGTG-CAACTTACAAACTAAAAAATTAAAATTAATTTGTATAATTTGT
* *
14201 GTTTACTAATTTTATCATT-AAATAT-TATTTTTACCGGTTTTGTTATTGTTGGGCATAATAAAA
194 GTTTACTAATTTTATCATTAAAAAATCTA-TTTTACCGG--TTGTTATTGTTGGGCATAACAAAA
14264 CCGGA-AAAAATTACCTAAAACATTATTATTTCTACCTAAAACATCAATGTTTTTTAACATTTTC
256 CCGGATAAAAATTACCTAAAACATTATTATTTCTACCTAAAACATCAATGTTTTTTAACATTTTC
14328 GATAAAATGCCCAACAATAACAAAATCG
321 GATAAAATGCCCAACAATAACAAAATCG
14356 ATAGCGTTTT
Statistics
Matches: 1040, Mismatches: 49, Indels: 80
0.89 0.04 0.07
Matches are distributed among these distances:
773 12 0.01
774 56 0.05
775 47 0.05
776 17 0.02
777 106 0.10
778 31 0.03
779 131 0.13
780 3 0.00
781 5 0.00
782 45 0.04
783 21 0.02
784 2 0.00
785 227 0.22
786 7 0.01
787 120 0.12
788 106 0.10
789 44 0.04
790 58 0.06
791 2 0.00
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (779 bp):
TATATTGTAATTATGATTATTTTTCATCACTTCATTATGATTATTTTTTAAAATTATATTGTAAT
TATATATTTTATTTTTATTTTATTATTAGAAAGCTAATATCAAAATAGAAATAATAGTGTCCTTT
TTTTCATTAGTTATATTGTGCAACTTACAAACTAAAAAATTAAAATTAATTTGTATAATTTGTGT
TTACTAATTTTATCATTAAAAAATCTATTTTACCGGTTGTTATTGTTGGGCATAACAAAACCGGA
TAAAAATTACCTAAAACATTATTATTTCTACCTAAAACATCAATGTTTTTTAACATTTTCGATAA
AATGCCCAACAATAACAAAATCGGTAAAAAAATAACAAAATCAGTAGCGCTTTACCGATTTTGTT
AAAATAATGATGTTTTCGGTAATTTTTACCGATTTTGTTATTGTTGTATACCGGTTATATTGTAA
ATTTACCTATTACATTATAATTATCGGTTTCGATGTAACATATGTGTCGATACTTTTAGAAAATG
TATCGACACATATGTTTAACTATTCTCTCATTATAATATAATTAATGAATATTATTATTATTATA
ATAAATAATAAATATAATTTATAATAATTTTATTTTAATAAAATATAATAATCATAATTTTTTAT
TTATAAAATTATAGATATAATATTTTAATAATAATATTGACATAAATAATATTAAATAAATTATT
CTAATATTTAAAAAATAATATTATTATTTTGTTAATAAATAATATTATTTTATTGTATTTAATG
Found at i:13837 original size:23 final size:27
Alignment explanation
Indices: 13781--13840 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 27
13771 TATTCTCTCA
*
13781 TTATAATACAATTAATGAAATATTATTC
1 TTATAATA-AATTAATGAAATATTAATC
13809 TTATAATAAA-TAAT-AAATA-TAAT-
1 TTATAATAAATTAATGAAATATTAATC
13832 TTATAATAA
1 TTATAATAA
13841 TTTTATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 9 0.29
24 3 0.10
25 5 0.16
26 4 0.13
27 2 0.06
28 8 0.26
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (27 bp):
TTATAATAAATTAATGAAATATTAATC
Found at i:13860 original size:31 final size:31
Alignment explanation
Indices: 13819--13915 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
13809 TTATAATAAA
*
13819 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTTATTAT
* *
13849 TAATAAAATATAATAATCATAATTTTTTTAT
1 TAATAAAATATAATAATAATAATTTTATTAT
* * *
13880 TTATAAAATTATAGAT-ATAAT-ATTTTAATAA
1 TAATAAAA-TATA-ATAATAATAATTTTATTAT
13911 TAATA
1 TAATA
13916 TTGACATAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
30 17 0.31
31 27 0.50
32 8 0.15
33 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (31 bp):
TAATAAAATATAATAATAATAATTTTATTAT
Found at i:13871 original size:30 final size:32
Alignment explanation
Indices: 13819--13888 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
13809 TTATAATAAA
*
13819 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAATTAATAATAATTTTATTAT
* *
13849 TAATAAAATATAA-TAATCATAATTTTTTTAT
1 TAATAAAATATAATTAATAATAATTTTATTAT
*
13880 TTATAAAAT
1 TAATAAAAT
13889 TATAGATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.50
31 17 0.50
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (32 bp):
TAATAAAATATAATTAATAATAATTTTATTAT
Found at i:13905 original size:29 final size:32
Alignment explanation
Indices: 13819--13905 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 32
13809 TTATAATAAA
* *
13819 TAAT-AAATATAAT-TTATAATAATTTTATTT
1 TAATAAAATATAATAATATAATATTTTTATTT
*
13849 TAATAAAATATAATAATCATAATTTTTTTA-TT
1 TAATAAAATATAATAAT-ATAATATTTTTATTT
13881 T-ATAAAAT-T-ATAGATATAATATTTT
1 TAATAAAATATAATA-ATATAATATTTT
13906 AATAATAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
29 12 0.24
30 7 0.14
31 16 0.33
32 4 0.08
33 10 0.20
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (32 bp):
TAATAAAATATAATAATATAATATTTTTATTT
Found at i:18307 original size:27 final size:25
Alignment explanation
Indices: 18261--18322 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
18251 GGGCTTTATC
*
18261 TTTCTTTTTC-TTTTTGTTTTATAG
1 TTTCTTTTTCTTTTTTATTTTATAG
*
18285 TTTCTTTTTCTTCTTTTCATTTTCTAG
1 TTTCTTTTTCTT-TTTT-ATTTTATAG
* *
18312 TTCCTTCTTCT
1 TTTCTTTTTCT
18323 ACATTAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 10 0.32
25 1 0.03
26 4 0.13
27 16 0.52
ACGTcount: A:0.06, C:0.18, G:0.05, T:0.71
Consensus pattern (25 bp):
TTTCTTTTTCTTTTTTATTTTATAG
Found at i:28809 original size:28 final size:28
Alignment explanation
Indices: 28748--28809 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
28738 TCAAGCAAAG
* *
28748 AGAATACAACAAAGATTCACGAGACAGT
1 AGAATTCAACAAAGATTCACGAGACAAT
* * * *
28776 AAAATTCAGCAAAGATTCATGAGGCAAT
1 AGAATTCAACAAAGATTCACGAGACAAT
28804 AGAATT
1 AGAATT
28810 TGCAATACCA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (28 bp):
AGAATTCAACAAAGATTCACGAGACAAT
Found at i:29468 original size:44 final size:43
Alignment explanation
Indices: 29412--29505 Score: 134
Period size: 44 Copynumber: 2.2 Consensus size: 43
29402 TGTTCGATCA
*
29412 CATCACATAAGGAGTTAGACCAACATCACCATTTTGCTCGATTC
1 CATCACATAAGGAGTTAGACCAACATCAACATTTTGCTC-ATTC
* ** *
29456 CATCACATAAGGAGTTGGATTAGCATCAACATTTTGCTCATTC
1 CATCACATAAGGAGTTAGACCAACATCAACATTTTGCTCATTC
29499 CATCACA
1 CATCACA
29506 AAATGAAGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 11 0.24
44 34 0.76
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (43 bp):
CATCACATAAGGAGTTAGACCAACATCAACATTTTGCTCATTC
Found at i:29518 original size:43 final size:44
Alignment explanation
Indices: 29435--29518 Score: 118
Period size: 43 Copynumber: 1.9 Consensus size: 44
29425 GTTAGACCAA
* * *
29435 CATCACCATTTTGCTCGATTCCATCACATAAGGAGTTGGATTAG
1 CATCAACATTTTGCTCGATTCCATCACAAAAGAAGTTGGATTAG
29479 CATCAACATTTTGCTC-ATTCCATCACAAAATGAAG-TGGAT
1 CATCAACATTTTGCTCGATTCCATCACAAAA-GAAGTTGGAT
29519 CGACATTTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 18 0.50
44 18 0.50
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (44 bp):
CATCAACATTTTGCTCGATTCCATCACAAAAGAAGTTGGATTAG
Found at i:39989 original size:15 final size:15
Alignment explanation
Indices: 39969--39998 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39959 TCCCCTCCCA
39969 GCCATATTGGTTTCT
1 GCCATATTGGTTTCT
39984 GCCATATTGGTTTCT
1 GCCATATTGGTTTCT
39999 AATATTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (15 bp):
GCCATATTGGTTTCT
Found at i:45341 original size:16 final size:17
Alignment explanation
Indices: 45322--45357 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
45312 TATTCTATGA
45322 TTTG-GTCTTTAATTTT
1 TTTGTGTCTTTAATTTT
*
45338 TTTGTTTCTTTAATTTT
1 TTTGTGTCTTTAATTTT
45355 TTT
1 TTT
45358 TAATTTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.11, C:0.06, G:0.08, T:0.75
Consensus pattern (17 bp):
TTTGTGTCTTTAATTTT
Found at i:49887 original size:42 final size:42
Alignment explanation
Indices: 49828--49988 Score: 254
Period size: 42 Copynumber: 3.9 Consensus size: 42
49818 TTTCCCCGAA
49828 TTCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTT
49870 TTCCCGTGTTTGTTTCACGTAATTCATTTTCC-GAAAATG-T
1 TTCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTT
* * *
49910 TTCCCGTGTTTGTTTCACGTACTTTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTA-ATTCATTTTCCGGAAAATGTT
* *
49953 TTCCTGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAA
49989 TGTAATTTTT
Statistics
Matches: 111, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
40 22 0.20
41 16 0.14
42 52 0.47
43 21 0.19
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTT
Found at i:49963 original size:83 final size:82
Alignment explanation
Indices: 49828--49985 Score: 262
Period size: 83 Copynumber: 1.9 Consensus size: 82
49818 TTTCCCCGAA
*
49828 TTCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTTCCCGTGTTTGTTTCACGTAAT
1 TTCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAACGTTTTCCCGTGTTTGTTTCACGTAAT
49893 TCATTTTCCGAAAATGT
66 TCATTTTCCGAAAATGT
* * *
49910 TTCCCGTGTTTGTTTCACGTACTTTCGTTTTCCGGAAAACGTTTTCCTGTGTTTGTTTCACGTAA
1 TTCCCGTGTTTGTTTCACGTA-ATTCATTTTCCGGAAAACGTTTTCCCGTGTTTGTTTCACGTAA
*
49975 TTCGTTTTCCG
65 TTCATTTTCCG
49986 GAATGTAATT
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 21 0.30
83 49 0.70
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.46
Consensus pattern (82 bp):
TTCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAACGTTTTCCCGTGTTTGTTTCACGTAAT
TCATTTTCCGAAAATGT
Found at i:50192 original size:21 final size:21
Alignment explanation
Indices: 50147--50212 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 21
50137 CATTTCATCA
50147 AATATA-TTATTAAAATATTTA-
1 AATATATTTATT--AATATTTAT
50168 AATATATTTATTAATATTTAT
1 AATATATTTATTAATATTTAT
*
50189 AATA-ATATAATT-ATATTT-T
1 AATATAT-TTATTAATATTTAT
50208 AATAT
1 AATAT
50213 TATATAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 5 0.12
20 16 0.40
21 14 0.35
22 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATATATTTATTAATATTTAT
Found at i:50565 original size:20 final size:20
Alignment explanation
Indices: 50487--50556 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
50477 TTCCCAGATG
50487 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
50507 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
50527 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
50547 TTTTCCAGAA
1 TTTTCCAGAA
50557 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:50565 original size:40 final size:40
Alignment explanation
Indices: 50487--50565 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
50477 TTCCCAGATG
* **
50487 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
50527 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
50566 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:50575 original size:15 final size:15
Alignment explanation
Indices: 50539--50605 Score: 91
Period size: 15 Copynumber: 4.5 Consensus size: 15
50529 TTACAGAAAT
**
50539 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
50554 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
50568 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
50583 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
50598 GTAATTCA
1 GTAATTCA
50606 TTTCTGGGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.27
15 33 0.73
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:50581 original size:29 final size:30
Alignment explanation
Indices: 50539--50608 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
50529 TTACAGAAAT
50539 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
50568 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
50598 GTAATTCATTT
1 GTAATTCATTT
50609 CTGGGAAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.40
30 24 0.60
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Done.