Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004671.1 Hibiscus syriacus cultivar Beakdansim tig00010474_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: 103534
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:9966 original size:4 final size:4
Alignment explanation
Indices: 9959--9995 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
9949 GAAAGAAATA
*
9959 ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
9996 ATGAGGAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:13562 original size:20 final size:21
Alignment explanation
Indices: 13539--13582 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
13529 AATATGGTGT
**
13539 AAAAAATTTAAATGCAT-TGC
1 AAAAAATAAAAATGCATATGC
13559 -AAAAATAAAAATGCATATGC
1 AAAAAATAAAAATGCATATGC
13579 AAAA
1 AAAA
13583 TGCAGGGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
19 14 0.70
20 3 0.15
21 3 0.15
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.23
Consensus pattern (21 bp):
AAAAAATAAAAATGCATATGC
Found at i:19989 original size:22 final size:22
Alignment explanation
Indices: 19961--20006 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
19951 TTCTTATTTG
*
19961 TGTCTAAATCGTCCATATGATA
1 TGTCTAAATAGTCCATATGATA
*
19983 TGTCTAAATAGTCCGTATGATA
1 TGTCTAAATAGTCCATATGATA
20005 TG
1 TG
20007 CGTTCTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (22 bp):
TGTCTAAATAGTCCATATGATA
Found at i:20336 original size:91 final size:88
Alignment explanation
Indices: 20184--20359 Score: 307
Period size: 91 Copynumber: 2.0 Consensus size: 88
20174 ACATAGAGAC
* *
20184 TGTAGAAGAATAACACGCAATAAATGCCCATCCTTTAAAAGCTATCCGCTCCGACTTATCGGCCT
1 TGTAGAAGAATAACACACAATAAATGCCCACCCTTTAAAAGCTATCCGCTCCGACTTATCGGCCT
20249 CATCGCCGGTACCTCAGAATGAA
66 CATCGCCGGTACCTCAGAATGAA
20272 TGTAGAAGAATAACACACAATAAATGCCCCCCACCCTTTAAAAGCTATCCGCTCCGACTTATCGG
1 TGTAGAAGAATAACACACAATAAATG---CCCACCCTTTAAAAGCTATCCGCTCCGACTTATCGG
20337 CCTCATCGCCGGTACCTCAGAAT
63 CCTCATCGCCGGTACCTCAGAAT
20360 TCTCTTCCCA
Statistics
Matches: 83, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
88 25 0.30
91 58 0.70
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (88 bp):
TGTAGAAGAATAACACACAATAAATGCCCACCCTTTAAAAGCTATCCGCTCCGACTTATCGGCCT
CATCGCCGGTACCTCAGAATGAA
Found at i:25072 original size:197 final size:197
Alignment explanation
Indices: 24673--25199 Score: 534
Period size: 197 Copynumber: 2.7 Consensus size: 197
24663 TTGGAAATTA
* * * * * * * *
24673 ACAAAATCGGTTTCAATTTGAGAAAACCGGTATAGA-ACTACCGAAATTGTTGAAATTTGTATCA
1 ACAAAACCGATTTCAATTTGAAAAAACCAGTAAAGAGA-TACCGGAA-TGTTGACATTTGTATCG
* * *
24737 ATA-TGTTTATAAGTATATGTACCAAAGTATCGGTACTGTAGGAATTTAACAAAAATGAAAAAAG
64 ATACT-TTTATAAGTATATGTACCAAAGTATAGGTACTTTAGGAATTTAA-AAGAATGAAAAAA-
* * * *
24801 GAAAATGTCTCGAAAGTATCAATACCTTACACACATGTATCGATACATAACAATATAACATGTTG
126 GAAAATGCCTAGAAAGTATCAATACCTTACAAACATCTATCGATACATAACAATATAACATGTTG
*
24866 AAGTTTG
191 AAATTTG
* * *
24873 ACAAAACC-AGTTTTAGTTTGAAAAAACCAGTAAAGAGATACCGGAATGGTTGACATTTGTATTG
1 ACAAAACCGA-TTTCAATTTGAAAAAACCAGTAAAGAGATACCGGAAT-GTTGACATTTGTATCG
* * * * *
24937 ATACTTTTATAAGTATATGCACCAAAGTATAGGTACTTTAGGAATTTAAAAGAATTACAATA-AT
64 ATACTTTTATAAGTATATGTACCAAAGTATAGGTACTTTAGGAATTTAAAAGAATGAAAAAAGAA
* * * * *
25001 AGTGCCTATAAAGTATCGATACCTTAGAAACATCTATCGATACATGACAATATAACATGTTGAAA
129 AATGCCTAGAAAGTATCAATACCTTACAAACATCTATCGATACATAACAATATAACATGTTGAAA
25066 TTTG
194 TTTG
* * * * *
25070 ACAAAACCGATTTCAATATGACAAAACCAGTAAA-ACGCTATC-GATTATGTTGGCA---GTATC
1 ACAAAACCGATTTCAATTTGAAAAAACCAGTAAAGA-GATACCGGA--ATGTTGACATTTGTATC
* * *
25130 GATACTTTTATAAGTATATGTATCATAGTATCA-GTACTTTAGGAATTGAAAAGAAATGAAAAAA
63 GATACTTTTATAAGTATATGTACCAAAGTAT-AGGTACTTTAGGAATTTAAAAG-AATGAAAAAA
25194 TGAAAA
126 -GAAAA
25200 CATCTCGAAA
Statistics
Matches: 269, Mismatches: 46, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
194 51 0.19
195 8 0.03
196 3 0.01
197 100 0.37
198 3 0.01
199 10 0.04
200 92 0.34
201 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.30
Consensus pattern (197 bp):
ACAAAACCGATTTCAATTTGAAAAAACCAGTAAAGAGATACCGGAATGTTGACATTTGTATCGAT
ACTTTTATAAGTATATGTACCAAAGTATAGGTACTTTAGGAATTTAAAAGAATGAAAAAAGAAAA
TGCCTAGAAAGTATCAATACCTTACAAACATCTATCGATACATAACAATATAACATGTTGAAATT
TG
Found at i:28295 original size:2 final size:2
Alignment explanation
Indices: 28288--28329 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
28278 ATGGGGAAGG
28288 AT AT AT AT AT AT 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
28330 CTGAAATCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29114 original size:15 final size:15
Alignment explanation
Indices: 29094--29123 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29084 AGACTACTAG
29094 AACATTGTTATGTAT
1 AACATTGTTATGTAT
*
29109 AACATTGTTTTGTAT
1 AACATTGTTATGTAT
29124 GTTTGGTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (15 bp):
AACATTGTTATGTAT
Found at i:31486 original size:199 final size:199
Alignment explanation
Indices: 31130--31694 Score: 761
Period size: 199 Copynumber: 2.8 Consensus size: 199
31120 AAAGAAAACA
* * * * *
31130 TATCGATACTTTTATTCCAATATGCATCTCAAACAATTTACACGCAAAAAAATATCGATATACAT
1 TATCGATACTTTTATTCCAATATGCTTCTC-AACAATTTGCACGC-ACAAAGTATCGATACACAT
* * * * * * ** *
31195 ATAAAAAATATCGATACTTGTAATTTTGAAACCTATTACTATAAAGCAATACGTAAATTTACAAT
64 GTATAAAGTATCGATACGTGAAATTTTGAAACCTATTACTTTAAAGTTATAGGTAAATTTACAAT
* ** * * *
31260 GTAAACGGTAAAAATCTACCGGTTTAATTATAATAGGCGTAAACATCAAGTATCGATACTTTTTG
129 GTAAACGGTAAAAGTCTACAAGTTTAATGATAATAGGCGTAAACATCAAGTACCGATACGTTTTG
*
31325 TACATG
194 TACAGG
*
31331 TATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACATGT
1 TATCGATACTTTTATTCCAATATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACATGT
* * * *
31396 ATAAAGTATCGATACGTGGAATTTCGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATTT
66 ATAAAGTATCGATACGTGAAATTTTGAAACCTATTACTTTAAAGTTATAGGTAAATTTACAATGT
*
31461 AAACGGTAATAGTCTACAAGTTTAATGATAATAGGCGTAAACATCAAGTACCGATACGTTTTGTA
131 AAACGGTAAAAGTCTACAAGTTTAATGATAATAGGCGTAAACATCAAGTACCGATACGTTTTGTA
*
31526 TAGG
196 CAGG
* * * * *
31530 TATCAATACTTTTATTCCGATATGCTTCTCAACAATTTGCACACACAAAGTATAGATACATATGT
1 TATCGATACTTTTATTCCAATATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACATGT
**
31595 ATAAAGTATCGATACGCAAAATTTTGAAACCTATTACTTTAAAGTTATAGGTAAATTTACAATGT
66 ATAAAGTATCGATACGTGAAATTTTGAAACCTATTACTTTAAAGTTATAGGTAAATTTACAATGT
** * *
31660 AAACGGTAAAAGTCTACTGGTATATTGATAATAGG
131 AAACGGTAAAAGTCTACAAGTTTAATGATAATAGG
31695 TAAAATACAA
Statistics
Matches: 320, Mismatches: 44, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
199 279 0.87
200 13 0.04
201 28 0.09
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (199 bp):
TATCGATACTTTTATTCCAATATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACATGT
ATAAAGTATCGATACGTGAAATTTTGAAACCTATTACTTTAAAGTTATAGGTAAATTTACAATGT
AAACGGTAAAAGTCTACAAGTTTAATGATAATAGGCGTAAACATCAAGTACCGATACGTTTTGTA
CAGG
Found at i:32225 original size:197 final size:194
Alignment explanation
Indices: 31932--32312 Score: 496
Period size: 197 Copynumber: 1.9 Consensus size: 194
31922 AAATATCTCG
* * *
31932 AAAGTATCGATACCTTACACATATGTATCGATACATGACAATATAACAGGTTGAAGTTTGACAAA
1 AAAGTATCGATACCTTACACACATGTATCGATACATGACAATAGAACAGGTTGAAATTTGACAAA
* * * * *
31997 ATCGGTTTCAATTTGATAAAACCGATAAAGAGTTACCGGAATGGTTGACATTTGTATCGATACTT
66 ATCGGTTTCAATTTGACAAAACCGATAAAGAGATACCGGAATGGTTGA-A--AGTATCAATACGT
* *
32062 TTATAAGTATATGCACTAAAGTATCAG-TACTCTAGGAATTTAAAAGAATTGCAATAATAGCGCC
128 TTATAAGTATATGCACCAAAGTAT-AGATACTCTAGGAATTGAAAAGAATTGCAATAATAGCGCC
32126 TAT
192 TAT
* * *
32129 AAAGTATCGATACCTTAGACACATGTATCGATACATGACAATAGAACATGTTGAAATTTGATAAA
1 AAAGTATCGATACCTTACACACATGTATCGATACATGACAATAGAACAGGTTGAAATTTGACAAA
* * * * *
32194 ATTGGTTT-ATATTTGACAAAACTGGTAAAGAGATACTGGAATTGTTGAAAGTATCAATACGTTT
66 ATCGGTTTCA-ATTTGACAAAACCGATAAAGAGATACCGGAATGGTTGAAAGTATCAATACGTTT
** * * *
32258 ATAAGTATATGTTCCATAGTATTGATACTTTAGGAATTGAAAAGAATTGCAATAA
130 ATAAGTATATGCACCAAAGTATAGATACTCTAGGAATTGAAAAGAATTGCAATAA
32313 GAAAACATCT
Statistics
Matches: 159, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
193 1 0.01
194 58 0.36
196 2 0.01
197 98 0.62
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (194 bp):
AAAGTATCGATACCTTACACACATGTATCGATACATGACAATAGAACAGGTTGAAATTTGACAAA
ATCGGTTTCAATTTGACAAAACCGATAAAGAGATACCGGAATGGTTGAAAGTATCAATACGTTTA
TAAGTATATGCACCAAAGTATAGATACTCTAGGAATTGAAAAGAATTGCAATAATAGCGCCTAT
Found at i:34474 original size:57 final size:57
Alignment explanation
Indices: 34386--34496 Score: 195
Period size: 57 Copynumber: 1.9 Consensus size: 57
34376 GCGCACTAGG
* * *
34386 CACATCATAGTGCCAATTATAACTTATCATAATCTACACTCCAATTGCAATCATGCA
1 CACATCACAGTGCCAATTATAACTGATCATAATCTACACTCCAAGTGCAATCATGCA
34443 CACATCACAGTGCCAATTATAACTGATCATAATCTACACTCCAAGTGCAATCAT
1 CACATCACAGTGCCAATTATAACTGATCATAATCTACACTCCAAGTGCAATCAT
34497 AACATGAGCA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.28
Consensus pattern (57 bp):
CACATCACAGTGCCAATTATAACTGATCATAATCTACACTCCAAGTGCAATCATGCA
Found at i:41876 original size:25 final size:25
Alignment explanation
Indices: 41821--41870 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
41811 TGACTCAAAG
41821 AATTCAAGGTAACCACACTTACAAC
1 AATTCAAGGTAACCACACTTACAAC
41846 AATTCAAGGTAACCACACTTACAAC
1 AATTCAAGGTAACCACACTTACAAC
41871 TCTTCATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.20
Consensus pattern (25 bp):
AATTCAAGGTAACCACACTTACAAC
Found at i:45057 original size:2 final size:2
Alignment explanation
Indices: 45050--45080 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45040 ATTCTTCAGT
45050 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45081 TAAACATGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45766 original size:54 final size:54
Alignment explanation
Indices: 45689--45814 Score: 157
Period size: 54 Copynumber: 2.3 Consensus size: 54
45679 ATAAGTTCTT
* * * *
45689 TGGGGTGCACACGTAGTGTCGATACGGTCA-TTCATAAGCTCAATATGAATTTCA
1 TGGGGTGCACACATAGTGTCGATACGGT-ATTTCACAAACTCAATATGAATTACA
* * *
45743 TGGGTTGCACACTTAGT-TACGATACGGTATTTCACAAACTCATTATGAATTACA
1 TGGGGTGCACACATAGTGT-CGATACGGTATTTCACAAACTCAATATGAATTACA
45797 TGGGGTGCACACATAGTG
1 TGGGGTGCACACATAGTG
45815 CCAATACGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
53 2 0.03
54 59 0.97
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (54 bp):
TGGGGTGCACACATAGTGTCGATACGGTATTTCACAAACTCAATATGAATTACA
Found at i:45822 original size:54 final size:54
Alignment explanation
Indices: 45718--46195 Score: 542
Period size: 54 Copynumber: 8.8 Consensus size: 54
45708 CGATACGGTC
* * * * * ** * **
45718 ATTCATAAGCTCAATATGAATTTCATGGGTTGCACACTTAGTTACGATACGGTA
1 ATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAA
* * * * * *
45772 TTTCACAAACTCATTATGAATTACATGGGGTGCACACATAGTGCCAATACGAAA
1 ATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAA
* * *
45826 ATTCATAAACTGATTATGAATTTCTTAGGTTGCACACATAATGTCAATACGAAAA
1 ATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACG-AAA
* * *
45881 ATTCATAAACTAATTATGAATTTCTTAGGTTGCACACATAGTGCAAATATGAAA
1 ATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAA
* * * *
45935 ATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACTAAA
1 ATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAA
* * * * * *
45989 ATTTATAAACACATTATGAATTTCTTAAGTTGCACACACAGTGCCAATATGGAA
1 ATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAA
* * *
46043 ATTCATAAACTTATTATGAATGTCTTAAGTTGCACACATAGTGCCAATACGAAA
1 ATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAA
* * * * * * *
46097 ATTCATAAACTTATTATGAATTTCTTAAGTTGCACAAACAATGTCAATACGGAA
1 ATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAA
* * *
46151 ATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCC
1 ATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCC
46196 CATTCAGTAA
Statistics
Matches: 369, Mismatches: 54, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
54 320 0.87
55 49 0.13
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (54 bp):
ATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAA
Found at i:48522 original size:21 final size:21
Alignment explanation
Indices: 48474--48515 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
48464 ACTTAAAATT
*
48474 GAAAATAAGTTGATTTTGAAA
1 GAAAAAAAGTTGATTTTGAAA
48495 GAAAAAAAGTTGATTTTGAAA
1 GAAAAAAAGTTGATTTTGAAA
48516 ATCAAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (21 bp):
GAAAAAAAGTTGATTTTGAAA
Found at i:48571 original size:30 final size:30
Alignment explanation
Indices: 48536--48607 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
48526 AATTTTGAAT
48536 AATGATTTAGAATTTTCAAAAGTCAAAATC
1 AATGATTTAGAATTTTCAAAAGTCAAAATC
48566 AATGATTTAGAATTTTCAAAAGTCAAAATC
1 AATGATTTAGAATTTTCAAAAGTCAAAATC
*
48596 ATTGATTTAGAA
1 AATGATTTAGAA
48608 AAAGAAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (30 bp):
AATGATTTAGAATTTTCAAAAGTCAAAATC
Found at i:49530 original size:23 final size:23
Alignment explanation
Indices: 49504--49576 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
49494 ACCCTATGAA
49504 GGACTACCGATACTTCCTATTCT
1 GGACTACCGATACTTCCTATTCT
49527 GGACTACCGATACTTCCTATTCT
1 GGACTACCGATACTTCCTATTCT
* *
49550 AGACTACTGATACTTCCTATTCT
1 GGACTACCGATACTTCCTATTCT
49573 GGAC
1 GGAC
49577 AGACTTATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (23 bp):
GGACTACCGATACTTCCTATTCT
Found at i:49916 original size:34 final size:34
Alignment explanation
Indices: 49853--49917 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
49843 AAGGGGTTTT
* *
49853 GGTTCTAGTTAAGCCTGCTGAAAGATAGGGAAAA
1 GGTTCTAGTTAAGCCCGCTGAAAAATAGGGAAAA
*
49887 GGTTCTAGTTTAGCCCG-TGAAAAACTAGGGA
1 GGTTCTAGTTAAGCCCGCTGAAAAA-TAGGGA
49918 GTTTGTAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 6 0.22
34 21 0.78
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (34 bp):
GGTTCTAGTTAAGCCCGCTGAAAAATAGGGAAAA
Found at i:52367 original size:32 final size:32
Alignment explanation
Indices: 52313--52392 Score: 74
Period size: 32 Copynumber: 2.5 Consensus size: 32
52303 CAAATTTTAG
*
52313 AGATGCAAGTGCAAATGAAAATG-TAAATGCAA
1 AGATGCAAGTGCAAACGAAAATGCT-AATGCAA
** * *
52345 AGATGCAAGTGCATGCGTAAATGCTAATGCGA
1 AGATGCAAGTGCAAACGAAAATGCTAATGCAA
52377 A-ATGCAAAGATGCAAA
1 AGATGC-AAG-TGCAAA
52393 TGCAAGAAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
31 4 0.11
32 29 0.76
33 5 0.13
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.19
Consensus pattern (32 bp):
AGATGCAAGTGCAAACGAAAATGCTAATGCAA
Found at i:57193 original size:64 final size:63
Alignment explanation
Indices: 57019--57174 Score: 235
Period size: 64 Copynumber: 2.5 Consensus size: 63
57009 CACTCACCAT
* * *
57019 ATCGAATGTATTTTATGCATCAATGCACTACCATGCATCGATGCACTCATGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACTACCATGCATCGATGCACTCAGGTTTTATGAAAAC
*
57082 AACGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTGTT-TG-AAA
1 ATCGAATGCATTTTATGCATCGATGCAC-TACCATGCATCGATGCACTCAGG-TT-TTATGAAAA
57145 C
63 C
57146 ATCGAATGCATTTTATGCATCGATGCACT
1 ATCGAATGCATTTTATGCATCGATGCACT
57175 GTTAGTGCAC
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
63 26 0.31
64 53 0.62
65 4 0.05
66 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCGATGCACTACCATGCATCGATGCACTCAGGTTTTATGAAAAC
Found at i:65736 original size:64 final size:63
Alignment explanation
Indices: 65595--65750 Score: 190
Period size: 64 Copynumber: 2.5 Consensus size: 63
65585 CACTCCCCAT
* * **
65595 ATCAAATGCATTTTATGCATTGATGCACTGCCATTCATCAATGCACTAAGGTTTTATGAAAAC
1 ATCAAATGCATTTTATGCATCGATGCACTACCATGAATCAATGCACTAAGGTTTTATGAAAAC
* *
65658 ATCAAATGCATTTTATGCATCGATGCACATACCATGAATCGATGCACTCAGGCTTGTT-TG-AAA
1 ATCAAATGCATTTTATGCATCGATGCAC-TACCATGAATCAATGCACTAAGG-TT-TTATGAAAA
65721 C
63 C
** *
65722 ATTGAATGCATTTTATACATCGATGCACT
1 ATCAAATGCATTTTATGCATCGATGCACT
65751 CTTAGTGCAC
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
63 28 0.35
64 47 0.58
65 4 0.05
66 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (63 bp):
ATCAAATGCATTTTATGCATCGATGCACTACCATGAATCAATGCACTAAGGTTTTATGAAAAC
Found at i:66601 original size:81 final size:81
Alignment explanation
Indices: 66462--66768 Score: 395
Period size: 81 Copynumber: 3.8 Consensus size: 81
66452 TAACTCAACA
* * * *
66462 CTTTCATCTAACTTGCATGATTGACACATTTCTGCCAAATGCATAGCTAGG-CATTTAATCTTTA
1 CTTTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCA-TTAATCTTTT
* * *
66526 ACTCAAAGCCAATTAGC
65 ACTCAAAGGCATTTAAC
* * *
66543 CTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAATCTTTTA
* * *
66608 CTAAAAGGTATTTAAA
66 CTCAAAGGCATTTAAC
* * *
66624 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGCTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAATCTTTTA
*
66689 CTCATAGGCATTTAAC
66 CTCAAAGGCATTTAAC
* *
66705 CTTTCATCTAA-TTGGCATAATTTACACATTTTTGTCAAATGCACAGCT-GGACCATTAATCTTT
1 CTTTCATCTAACTT-GCATAATTGACACATTTCTGTCAAATGCACAGCTAGG-CCATTAATCTTT
66768 T
64 T
66769 TATTTAAAAT
Statistics
Matches: 199, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
80 3 0.02
81 194 0.97
82 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (81 bp):
CTTTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAATCTTTTA
CTCAAAGGCATTTAAC
Found at i:68682 original size:19 final size:20
Alignment explanation
Indices: 68639--68684 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
68629 TACTATGCTA
* **
68639 GAAATTTATGTTAGAGTGTT
1 GAAATTGATGTTAGAAAGTT
68659 GAAATTGATGTTAGAAAG-T
1 GAAATTGATGTTAGAAAGTT
68678 GAAATTG
1 GAAATTG
68685 GGTCACTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (20 bp):
GAAATTGATGTTAGAAAGTT
Found at i:73487 original size:2 final size:2
Alignment explanation
Indices: 73480--73512 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
73470 CTGGTGATAA
73480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73513 TCACATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:75400 original size:34 final size:34
Alignment explanation
Indices: 75352--75443 Score: 139
Period size: 34 Copynumber: 2.7 Consensus size: 34
75342 CAGTGCGTGC
* *
75352 AATAAGCACTCCAGGTGCTATCATCAGAAACATA
1 AATATGCACTCCAGGTGCAATCATCAGAAACATA
* *
75386 AATATGCACTCCAGGTGCAATAATCAGATACATA
1 AATATGCACTCCAGGTGCAATCATCAGAAACATA
*
75420 AATATGCACTCCTGGTGCAATCAT
1 AATATGCACTCCAGGTGCAATCAT
75444 ATAATGTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (34 bp):
AATATGCACTCCAGGTGCAATCATCAGAAACATA
Found at i:80513 original size:57 final size:56
Alignment explanation
Indices: 80405--80514 Score: 193
Period size: 57 Copynumber: 1.9 Consensus size: 56
80395 GCGCACTAGG
*
80405 CACATCACAGTGACAATTATAACTTACATAATCTACACTCCAATTGCAATCATGCA
1 CACATCACAGTGACAATTATAACTTACATAATCTACACTCCAAGTGCAATCATGCA
*
80461 CACATCACAGTGCCAATTATAACTTATCATAATCTACACTCCAAGTGCAATCAT
1 CACATCACAGTGACAATTATAACTTA-CATAATCTACACTCCAAGTGCAATCAT
80515 AACATGAGCA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
56 25 0.49
57 26 0.51
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.27
Consensus pattern (56 bp):
CACATCACAGTGACAATTATAACTTACATAATCTACACTCCAAGTGCAATCATGCA
Found at i:87731 original size:25 final size:25
Alignment explanation
Indices: 87697--87746 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
87687 TGACTCAAAG
87697 AATTCAAGGTAACCACACTTACAAC
1 AATTCAAGGTAACCACACTTACAAC
87722 AATTCAAGGTAACCACACTTACAAC
1 AATTCAAGGTAACCACACTTACAAC
87747 TCTTTATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.20
Consensus pattern (25 bp):
AATTCAAGGTAACCACACTTACAAC
Found at i:91343 original size:2 final size:2
Alignment explanation
Indices: 91336--91369 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
91326 ATTCTTCAAT
91336 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
91370 AACATGTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:92040 original size:54 final size:54
Alignment explanation
Indices: 91976--92531 Score: 574
Period size: 54 Copynumber: 10.3 Consensus size: 54
91966 TATAAGTTAT
* * * *** * *
91976 TTAGGGTGCACACGTAGTGTCGATACGGTTATTCATAAGCTCATTATGAATTTC
1 TTAGGTTGCACACATAGTGTCAATACGAAAATTCATAAACTAATTATGAATTTC
* * * * * ** * * * *
92030 ATGGGTTGCACGCTTAGT-TCCGATACGGTATTTCACAAACTCATTATGAATTAC
1 TTAGGTTGCACACATAGTGT-CAATACGAAAATTCATAAACTAATTATGAATTTC
* * * * *
92084 ATGGGGTGCACACATAGTGCCAATACGAAAATTCATAAACTGATTATGAATTTC
1 TTAGGTTGCACACATAGTGTCAATACGAAAATTCATAAACTAATTATGAATTTC
*
92138 TTAGGTTGCACACATAGTGCCAATACGAAAAATTCATAAACTAATTATGAATTTC
1 TTAGGTTGCACACATAGTGTCAATACG-AAAATTCATAAACTAATTATGAATTTC
* * *
92193 TTAGGTTGTACACATAATGTCAATACAAAAAATTCATAAACTAATTATGAATTTC
1 TTAGGTTGCACACATAGTGTCAATAC-GAAAATTCATAAACTAATTATGAATTTC
*
92248 TTAGGTTGCACACATAGTGTCAATACGAAAATTCATAAACTTATTATGAATTTC
1 TTAGGTTGCACACATAGTGTCAATACGAAAATTCATAAACTAATTATGAATTTC
* * * * * *
92302 TTAAGTTGCACACACAGTGCCAATACTAAAATTTATAAACTCATTATGAATTTC
1 TTAGGTTGCACACATAGTGTCAATACGAAAATTCATAAACTAATTATGAATTTC
* * * ** * * * *
92356 TTAAGTTGCACACACAGTGCCAATGTGGAAATTTATAAACTTATTATGAATGTC
1 TTAGGTTGCACACATAGTGTCAATACGAAAATTCATAAACTAATTATGAATTTC
* * **
92410 TTAAGTTGCACACATAGTGCCAATACGAAAATTCATAAACTTGTTATGAATTTC
1 TTAGGTTGCACACATAGTGTCAATACGAAAATTCATAAACTAATTATGAATTTC
* * * * * *
92464 TTAAGTTGCACAAACAGTGTTAATACGGAAATTCATAAACTTATTATGAATTTC
1 TTAGGTTGCACACATAGTGTCAATACGAAAATTCATAAACTAATTATGAATTTC
* *
92518 TTAAGTTACACACA
1 TTAGGTTGCACACA
92532 CAATGCCCAT
Statistics
Matches: 438, Mismatches: 60, Indels: 8
0.87 0.12 0.02
Matches are distributed among these distances:
53 1 0.00
54 337 0.77
55 100 0.23
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (54 bp):
TTAGGTTGCACACATAGTGTCAATACGAAAATTCATAAACTAATTATGAATTTC
Found at i:94963 original size:19 final size:19
Alignment explanation
Indices: 94939--94991 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
94929 AATTGAAAAT
94939 AAGTTGATTTTGAAAGAAA
1 AAGTTGATTTTGAAAGAAA
94958 AAGTTGATTTTGAAAGAAA
1 AAGTTGATTTTGAAAGAAA
94977 AAGTTGATTTTGAAA
1 AAGTTGATTTTGAAA
94992 ATCAAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (19 bp):
AAGTTGATTTTGAAAGAAA
Done.