Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003480.1 Hibiscus syriacus cultivar Beakdansim tig00007354_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: 55398
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3023 original size:26 final size:27
Alignment explanation
Indices: 2989--3057 Score: 97
Period size: 26 Copynumber: 2.6 Consensus size: 27
2979 ATATTAATAT
* *
2989 TTAAAGTTTTATTTTTAAAATAT-TAC
1 TTAACGTTTAATTTTTAAAATATATAC
3015 TTAACGTTTAATTTTTAAAATATATAC
1 TTAACGTTTAATTTTTAAAATATATAC
*
3042 TT-ACGCTTAATTTTTA
1 TTAACGTTTAATTTTTA
3058 TTTTTATTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
26 34 0.87
27 5 0.13
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.52
Consensus pattern (27 bp):
TTAACGTTTAATTTTTAAAATATATAC
Found at i:15737 original size:26 final size:27
Alignment explanation
Indices: 15704--15755 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
15694 TTAATTAAAA
**
15704 ATATAAAATTACTAATAATAA-AAATG
1 ATATAAAATTAAAAATAATAATAAATG
15730 ATATAAAATTAAAAATAATAATAAAT
1 ATATAAAATTAAAAATAATAATAAAT
15756 ACCACATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (27 bp):
ATATAAAATTAAAAATAATAATAAATG
Found at i:18232 original size:55 final size:55
Alignment explanation
Indices: 18164--18273 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 55
18154 TTATAACTTA
*
18164 AAACGTCACGAAAAGAATAAAGAACAAATAATATTTGTAC-AAAAATC-AGGATAAT
1 AAACGTCACGAAAAAAATAAAGAAC-AA-AATATTTGTACAAAAAATCAAGGATAAT
*
18219 AAACGTCACGAAAAAAATAAAGGACAAAATATTTGTACAAAAAATCAAGGATAAT
1 AAACGTCACGAAAAAAATAAAGAACAAAATATTTGTACAAAAAATCAAGGATAAT
18274 TTTGTTATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
53 11 0.22
54 9 0.18
55 31 0.61
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.19
Consensus pattern (55 bp):
AAACGTCACGAAAAAAATAAAGAACAAAATATTTGTACAAAAAATCAAGGATAAT
Found at i:27959 original size:354 final size:356
Alignment explanation
Indices: 27075--29534 Score: 4769
Period size: 354 Copynumber: 7.0 Consensus size: 356
27065 AGAAATGTGG
27075 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
1 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
27140 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
66 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
27205 TGAATCAAGTCAACCT-AAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
131 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
27269 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAAGAAGAAT-GGGTTAACTTGATGG
196 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGGTTAACTTGATGG
27333 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
261 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
27398 TGAACCTTGCAAAAACAAGAAA--TGGAAGT
326 TGAACCTTGCAAAAACAAGAAATGTGGAAGT
27427 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
1 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
27492 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATA-TTTACTTGATTGGCTGCCAAGAAAAT
66 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
27556 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTT-TTGCTATTTTTCAGGCTACAA
131 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
27620 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGGTTAACTTGATGG
196 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGGTTAACTTGATGG
27685 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
261 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
27750 TGAACCTTGCAAAAACAAGAAATGTGGAAGT
326 TGAACCTTGCAAAAACAAGAAATGTGGAAGT
27781 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
1 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
27846 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
66 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
27911 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATA-TGA-TTTGTTGCTATTTTTCAGGCTACAA
131 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
27974 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAA-AAGAATGGGGTTAACTTGATGG
196 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGGTTAACTTGATGG
28038 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
261 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
28103 TGAACCTTGCAAAAACAAGAAATGTGGAAGT
326 TGAACCTTGCAAAAACAAGAAATGTGGAAGT
28134 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
1 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
28199 TGAGAAAAGTTAAAAGATTA-GGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
66 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
28263 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
131 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
28328 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGGTTAACTTGATGG
196 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGGTTAACTTGATGG
28393 TGTTTATCAGAGGGAGCTAATAAAT-AACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
261 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
28457 TGAACCTTGC-AAAACAAGAAATGTGGAAGT
326 TGAACCTTGCAAAAACAAGAAATGTGGAAGT
28487 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
1 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
28552 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
66 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
28617 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
131 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
*
28682 GGTTCCATGAGAAGAAAG-AACAAGCTTGCAGAAGAAAAGAAG-AGAAT-GGG-TAACTTGATGG
196 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGGTTAACTTGATGG
28743 TGTTTATCAGAGGGAGCTAATAAAT-AACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
261 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
28807 TGAACCTTGCAAAAACAAGAAATGTGGAAGT
326 TGAACCTTGCAAAAACAAGAAATGTGGAAGT
28838 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
1 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
28903 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
66 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
*
28968 TTAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
131 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
29033 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGGTTAACTTGATGG
196 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGGTTAACTTGATGG
29098 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
261 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
29163 TGAACCTTGCAAAAACAAGAAATGTGGAAGT
326 TGAACCTTGCAAAAACAAGAAATGTGGAAGT
29194 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
1 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
29259 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
66 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
29324 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
131 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
29389 GGTTCCATGAGAAG-AAG-AACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGGTTAACTTGATGG
196 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGGTTAACTTGATGG
29452 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
261 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
29517 TGAACCTTGCAAAAACAA
326 TGAACCTTGCAAAAACAA
29535 CTGTTTATGT
Statistics
Matches: 2088, Mismatches: 4, Indels: 30
0.98 0.00 0.01
Matches are distributed among these distances:
350 85 0.04
351 347 0.17
352 338 0.16
353 342 0.16
354 551 0.26
355 147 0.07
356 278 0.13
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (356 bp):
AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGGTTAACTTGATGG
TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
TGAACCTTGCAAAAACAAGAAATGTGGAAGT
Found at i:28534 original size:706 final size:710
Alignment explanation
Indices: 27075--29534 Score: 4761
Period size: 707 Copynumber: 3.5 Consensus size: 710
27065 AGAAATGTGG
27075 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
1 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
27140 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
66 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
27205 TGAATCAAGTCAACCT-AAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
131 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
27269 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGTTAACTTGATGGT
196 GGTTCCATGAGAAGAAAG-AACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGTTAACTTGATGGT
27334 GTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAATT
260 GTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAATT
27399 GAACCTTGCAAAAACAAGAAA--TGGAAGTAAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTT
325 GAACCTTGCAAAAACAAGAAATGTGGAAGTAAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTT
27462 GGATACAAATCAAAACTATGGGATCTCACTTGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCA
390 GGATACAAATCAAAACTATGGGATCTCACTTGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCA
27527 ATA-TTTACTTGATTGGCTGCCAAGAAAATTGAATCAAGTCAACCTAAAACAAGGTTAAGAAATA
455 ATATTTTACTTGATTGGCTGCCAAGAAAATTGAATCAAGTCAACCTAAAACAAGGTTAAGAAATA
27591 TTGATTTT-TTGCTATTTTTCAGGCTACAAGGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAG
520 TTGATTTTGTTGCTATTTTTCAGGCTACAAGGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAG
27655 AAGAGAAGAAGAATGGGGTTAACTTGATGGTGTTTATCAGAGGGAGCTAATAAATAAACAAGTAT
585 AAGAGAAGAAGAATGGGGTTAACTTGATGGTGTTTATCAGAGGGAGCTAATAAATAAACAAGTAT
27720 TGCATTTGCTTCTGCATGGTCATTACTAATTGAACCTTGCAAAAACAAGAAATGTGGAAGT
650 TGCATTTGCTTCTGCATGGTCATTACTAATTGAACCTTGCAAAAACAAGAAATGTGGAAGT
27781 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
1 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
27846 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
66 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
27911 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATA-TGA-TTTGTTGCTATTTTTCAGGCTACAA
131 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
27974 GGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGAAGAGAA-AAGAATGGGGTTAACTTGATGG
196 GGTTCCATGAGAAGAAAG-AACAAGCTTGCAGAAGAAGAGAAGAAGAAT-GGGTTAACTTGATGG
28038 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
259 TGTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAAT
28103 TGAACCTTGCAAAAACAAGAAATGTGGAAGTAAGTAGCCCTCTTCTTTTAATATAAGGACTTGTT
324 TGAACCTTGCAAAAACAAGAAATGTGGAAGTAAGTAGCCCTCTTCTTTTAATATAAGGACTTGTT
28168 TGGATACAAATCAAAACTATGGGATCTCACTTGAGAAAAGTTAAAAGATTA-GGGGCTTTGTAGC
389 TGGATACAAATCAAAACTATGGGATCTCACTTGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGC
28232 AATATTTTACTTGATTGGCTGCCAAGAAAATTGAATCAAGTCAACCTAAAACAAGGTTAAGAAAT
454 AATATTTTACTTGATTGGCTGCCAAGAAAATTGAATCAAGTCAACCTAAAACAAGGTTAAGAAAT
28297 ATTGATTTTGTTGCTATTTTTCAGGCTACAAGGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAA
519 ATTGATTTTGTTGCTATTTTTCAGGCTACAAGGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAA
28362 GAAGAGAAGAAGAATGGGGTTAACTTGATGGTGTTTATCAGAGGGAGCTAATAAAT-AACAAGTA
584 GAAGAGAAGAAGAATGGGGTTAACTTGATGGTGTTTATCAGAGGGAGCTAATAAATAAACAAGTA
28426 TTGCATTTGCTTCTGCATGGTCATTACTAATTGAACCTTGC-AAAACAAGAAATGTGGAAGT
649 TTGCATTTGCTTCTGCATGGTCATTACTAATTGAACCTTGCAAAAACAAGAAATGTGGAAGT
28487 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
1 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
28552 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
66 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
28617 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
131 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
*
28682 GGTTCCATGAGAAGAAAGAACAAGCTTGCAGAAGAAAAGAAG-AGAATGGG-TAACTTGATGGTG
196 GGTTCCATGAGAAGAAAGAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGTTAACTTGATGGTG
28745 TTTATCAGAGGGAGCTAATAAAT-AACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAATTG
261 TTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAATTG
28809 AACCTTGCAAAAACAAGAAATGTGGAAGTAAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTG
326 AACCTTGCAAAAACAAGAAATGTGGAAGTAAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTG
28874 GATACAAATCAAAACTATGGGATCTCACTTGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAA
391 GATACAAATCAAAACTATGGGATCTCACTTGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAA
*
28939 TATTTTACTTGATTGGCTGCCAAGAAAATTTAATCAAGTCAACCTAAAACAAGGTTAAGAAATAT
456 TATTTTACTTGATTGGCTGCCAAGAAAATTGAATCAAGTCAACCTAAAACAAGGTTAAGAAATAT
29004 TGATTTTGTTGCTATTTTTCAGGCTACAAGGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGA
521 TGATTTTGTTGCTATTTTTCAGGCTACAAGGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGA
29069 AGAGAAGAAGAATGGGGTTAACTTGATGGTGTTTATCAGAGGGAGCTAATAAATAAACAAGTATT
586 AGAGAAGAAGAATGGGGTTAACTTGATGGTGTTTATCAGAGGGAGCTAATAAATAAACAAGTATT
29134 GCATTTGCTTCTGCATGGTCATTACTAATTGAACCTTGCAAAAACAAGAAATGTGGAAGT
651 GCATTTGCTTCTGCATGGTCATTACTAATTGAACCTTGCAAAAACAAGAAATGTGGAAGT
29194 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
1 AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
29259 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
66 TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
29324 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
131 TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
29389 GGTTCCATGAGAAG-AAGAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGGTTAACTTGATGGT
196 GGTTCCATGAGAAGAAAGAACAAGCTTGCAGAAGAAGAGAAGAAGAAT-GGGTTAACTTGATGGT
29453 GTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAATT
260 GTTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAATT
29518 GAACCTTGCAAAAACAA
325 GAACCTTGCAAAAACAA
29535 CTGTTTATGT
Statistics
Matches: 1735, Mismatches: 3, Indels: 28
0.98 0.00 0.02
Matches are distributed among these distances:
704 161 0.09
705 403 0.23
706 429 0.25
707 492 0.28
708 157 0.09
709 36 0.02
710 57 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (710 bp):
AAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTGGATACAAATCAAAACTATGGGATCTCACT
TGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAATATTTTACTTGATTGGCTGCCAAGAAAAT
TGAATCAAGTCAACCTAAAACAAGGTTAAGAAATATTGATTTTGTTGCTATTTTTCAGGCTACAA
GGTTCCATGAGAAGAAAGAACAAGCTTGCAGAAGAAGAGAAGAAGAATGGGTTAACTTGATGGTG
TTTATCAGAGGGAGCTAATAAATAAACAAGTATTGCATTTGCTTCTGCATGGTCATTACTAATTG
AACCTTGCAAAAACAAGAAATGTGGAAGTAAGTAGCCCTCTTCTTTTAATATAAGGACTTGTTTG
GATACAAATCAAAACTATGGGATCTCACTTGAGAAAAGTTAAAAGATTAGGGGGCTTTGTAGCAA
TATTTTACTTGATTGGCTGCCAAGAAAATTGAATCAAGTCAACCTAAAACAAGGTTAAGAAATAT
TGATTTTGTTGCTATTTTTCAGGCTACAAGGTTCCATGAGAAGAAAGAAACAAGCTTGCAGAAGA
AGAGAAGAAGAATGGGGTTAACTTGATGGTGTTTATCAGAGGGAGCTAATAAATAAACAAGTATT
GCATTTGCTTCTGCATGGTCATTACTAATTGAACCTTGCAAAAACAAGAAATGTGGAAGT
Found at i:50372 original size:20 final size:20
Alignment explanation
Indices: 50344--50403 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
50334 TGGTTCACGG
*
50344 AATGGAAGATTACCAGTGGA
1 AATGTAAGATTACCAGTGGA
50364 AATGTAAGATTACCAGT-GA
1 AATGTAAGATTACCAGTGGA
50383 GAATGTAAGATTACCAG-GGA
1 -AATGTAAGATTACCAGTGGA
50403 A
1 A
50404 TAGGATTACT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 3 0.08
20 34 0.92
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.22
Consensus pattern (20 bp):
AATGTAAGATTACCAGTGGA
Found at i:50625 original size:36 final size:36
Alignment explanation
Indices: 50554--50626 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
50544 GTTGGAAAAT
* *
50554 ATTTATATATTTTCTTTTAAAAAATAAATTCATAAA
1 ATTTATATAATTTCTTTTAAAAAATAAAATCATAAA
*
50590 ATTTATATAATTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATATAATTTCTTTTA-AAAAAT-AAAATCATAAA
50626 A
1 A
50627 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 5 0.16
36 23 0.72
37 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (36 bp):
ATTTATATAATTTCTTTTAAAAAATAAAATCATAAA
Done.