Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019091.1 Corchorus olitorius cultivar O-4 contig19124, 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: 85190
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5312 original size:14 final size:14
Alignment explanation
Indices: 5293--5322 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5283 CTTGATGAAA
5293 ATATATTATTTATC
1 ATATATTATTTATC
*
5307 ATATATTGTTTATC
1 ATATATTATTTATC
5321 AT
1 AT
5323 GTTTAATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (14 bp):
ATATATTATTTATC
Found at i:9602 original size:23 final size:24
Alignment explanation
Indices: 9556--9602 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
9546 CTAATTTTTA
*
9556 ATTTTTAATTTAGTAATAATTGCT
1 ATTTTTAATTTAATAATAATTGCT
9580 ATTTTTAA-TTAATAA-AATGTGCT
1 ATTTTTAATTTAATAATAAT-TGCT
9603 GTCATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 10 0.48
24 8 0.38
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (24 bp):
ATTTTTAATTTAATAATAATTGCT
Found at i:18196 original size:2 final size:2
Alignment explanation
Indices: 18189--18213 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18179 AAAAATTAGC
18189 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 T
18214 TATTATCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20793 original size:13 final size:13
Alignment explanation
Indices: 20775--20799 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20765 ACTTAAAAAC
20775 ATTTATTTATTTT
1 ATTTATTTATTTT
20788 ATTTATTTATTT
1 ATTTATTTATTT
20800 ATCTAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:21697 original size:11 final size:11
Alignment explanation
Indices: 21654--21691 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
21644 TTCCTATATA
*
21654 AAATAAATTAT
1 AAATTAATTAT
21665 CAAA-TAATTAT
1 -AAATTAATTAT
21676 AAATTAATTAT
1 AAATTAATTAT
21687 AAATT
1 AAATT
21692 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:27008 original size:22 final size:22
Alignment explanation
Indices: 26980--27024 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
26970 TTCCTCTCTG
*
26980 TTTCCCCTGTTTTCCTCTGTTT
1 TTTCCCCTGCTTTCCTCTGTTT
*
27002 TTTCCCCTGCTTTGCTCTGTTT
1 TTTCCCCTGCTTTCCTCTGTTT
27024 T
1 T
27025 CACTTTGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.00, C:0.31, G:0.11, T:0.58
Consensus pattern (22 bp):
TTTCCCCTGCTTTCCTCTGTTT
Found at i:31457 original size:82 final size:80
Alignment explanation
Indices: 31337--31488 Score: 277
Period size: 82 Copynumber: 1.9 Consensus size: 80
31327 TAGTATTTTA
31337 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAAATTTT
1 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAAATTTT
31402 AATTTTTTGTATTTG
66 AATTTTTTGTATTTG
*
31417 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAATT
1 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAAATT
31482 TTAATTT
64 TTAATTT
31489 GGGGCTAAAC
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
80 21 0.30
82 48 0.70
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (80 bp):
TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAAATTTT
AATTTTTTGTATTTG
Found at i:40361 original size:30 final size:30
Alignment explanation
Indices: 40325--40383 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
40315 CGAAAATATG
*
40325 AAGCCACCCATTGGGGAATCAGGAAAGAAC
1 AAGCCACCCATTGGGCAATCAGGAAAGAAC
* * *
40355 AAGCCACCGATTGGGCAATCTGGTAAGAA
1 AAGCCACCCATTGGGCAATCAGGAAAGAA
40384 TAGAAAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.14
Consensus pattern (30 bp):
AAGCCACCCATTGGGCAATCAGGAAAGAAC
Found at i:56310 original size:338 final size:331
Alignment explanation
Indices: 55183--58104 Score: 2654
Period size: 338 Copynumber: 8.9 Consensus size: 331
55173 TCCTCTTTTT
* *
55183 TTTTTGGC-AAAACTACTC-ATAAATATATATAATTCAACGCCAAAAGGATT-AGAGGACTTTTC
1 TTTTTGGCTAAAA-TACTCTAAAAATATATATAATTCAACGCCAAAAAGATTGA-AGGACTTTTC
*
55245 ACGCTTTTAATATCGTTTTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCA
64 ACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCA
* * * * * * * *
55310 GATGCACATAAAAACAAATCCTTGAATCCAATGTGCCTGAGATTTTATTTGATGAATAAATATAT
129 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
* * * * *
55375 TTCAAGGAGTCTCGGCGCCAAAAAT-ATGCAAAAC-AGAGCCGTGGTCCTGGAATGCGTTTTTAC
194 TTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTA-AGCCGGGGCCCTGAAACGCGTTTTTAG
* * *
55438 CCAAAAACCGTGA----T-GTACACGATTTCGGTTAAAATTTTGCAAAAATTGATCCGAAAGA-T
258 CCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATT
*
55497 ATTTCCTCAT
323 A-TTCCTCAA
* * ** * * *
55507 TTTTTGGCTAAAATACTAATAAAAA-ATATATAATTCGACATCAAAAAGATTAAAGGGCTTTTAA
1 TTTTTGGCTAAAATACT-CTAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCA
* * ** * * * *
55571 CACTTCTAATATTTTTTTTTCCAATTTTTTTCCGAATTAGTTTCCAATTAAATCGAAACAAGATT
65 CGCTTTTAATA-TCGTTTTT-C-ATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT
* * * * * *
55636 CAAATGCTCGAAAAAACAAATCCTTAAATCTAATGTGTCTAAGATTTGGTTAGATGAATATAGAT
127 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGAT
* * * * *
55701 ATTTCAAGGA-T-T--GCACCAAAAATCATGCAATACTGAGTCGGGTCCC-GAAACGCGTTTTTA
192 ATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCTGAAACGCGTTTTTA
* * * *
55761 GCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGGAAAAATTGATCCGAAAGAT
257 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAAT
* *
55826 TTTTCCTCGA
322 TATTCCTCAA
* ** * * * * *
55836 TTTCT-AATGAAAATACTCATAAAAA-ACATATAATTCAATGCCAAAAAAATTGAAAGCCTTTTT
1 TTTTTGGCT-AAAATACTC-TAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGAC-TTTT
* * *
55899 CACGCTTTTAATATCG-TTTTCATATTTTTCAGAATTAATTTCTTATTAAATCGAAACAAAATTC
63 CACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * *
55963 AGATGCTCGTAAAAACAAATTCTTCAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATA
128 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATA
* **
56028 TTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAAGTTGGGGCCCTGAAACGCGTTTTTAG
193 TTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCTGAAACGCGTTTTTAG
* * * **
56093 CAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACAAGAAAAATT
258 CCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATT
56158 ATTCCGTCAA
323 ATTCC-TCAA
* * *
56168 TTTTTGGCTAAAATACTCATAATATATATATATATATAATTCACCGCCAAAAATATTGGAGGACT
1 TTTTTGGCTAAAATACTC-T-A-A-A-A-ATATATATAATTCAACGCCAAAAAGATTGAAGGACT
* * * *
56233 TTTCAAGCTTTTAATATTGTTTTTAATATTTTTCTGAATTAATTTTTAATTAAATCGAAGA-AAG
60 TTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAA-ACAAG
* * * ** * * *
56297 ATTCAGGTGCTCGTAAAAACAAATTCTTAAATCCAATTTAACTGAGATTTGGTTAAATGAATATG
124 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA
* * * * * *
56362 GATATCTCAAAGAGTCTTGGCGCCAAAAATCATGTAAAACTTAA-CCGGGGCCCTGGAATGCGTT
189 GATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAAC-TAAGCCGGGGCCCTGAAACGCGTT
* * * * * *
56426 TTTAGCCAAAAACTGTGATGATTATTACACGATTTTGATCGACTAGAATTTTGCAAAAATTGACT
253 TTTAGCCAAAAACCGTGATGGTTAGTACACGA--TT--TCGGCTAAAATTTTGCAAAAATTGACC
*
56491 CG-AAAGTTACTTCCTCAA
314 CGAAAAATTA-TTCCTCAA
** * * * * * * *
56509 TTTTTATCCACAATACTC-ATAAA-A-AT-T-A-T--ACGCCAAAAAGTTTGCAGGTCTTTTCAT
1 TTTTTGGCTAAAATACTCTAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCAC
* * * * *
56566 GCTTCTAATATCATTTTTCCTATTATTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCA
66 GCTTTTAATATCGTTTTTCATA-T-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCA
* *** * * * *
56631 GATGCTTGT-TTTACAAATCCTTAAATCCAATTTGGCTGAAATTTGGTTAGATGAATGTAGATAT
129 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
* * * ** * * *
56695 TT-AAGGAGTCTCGGCGCAAAAAAATCATGCAACATTGAA-CTTGGGCCCAGGAACGGGTTTTTA
194 TTCAAGGAGTCTCGGCGC-CAAAAATCATGCAAAACT-AAGCCGGGGCCCTGAAACGCGTTTTTA
* * * * **
56758 GCCAAAAACCGTGATTTCGACTAACGTACACGATATCGGCTAATATTTTGCAAAAATTGACTAGA
257 GCCAAAAACCGTGA--T-G-GTTA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGA
* * *
56823 AATATTTTTTTCTCAA
317 AA-AATTATTCCTCAA
* * * *
56839 TTTTTGTCTAAAATACT-TATAAAATATATATAATTCAACTCAAAAAAGATTGGAGGACTTTTCA
1 TTTTTGGCTAAAATACTCTA-AAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCA
**
56903 CAATTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAG
65 CGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAG
* * * * * * *
56968 ATGCACGTAAAAACAAATCCTTAAATGCAATCTGGATGATACTTGATTAGATGAATATAGATAAT
130 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATT
** * * *
57033 TCAAGGAGTCTCGATGCCAAAAATCATGTAAAATTGAA-CCGGGG-CCTCGAAACGCTTTTTTAG
195 TCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACT-AAGCCGGGGCCCT-GAAACGCGTTTTTAG
* * * *
57096 CAAAGAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAATGACCAGAAAAA
258 C-CA-AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAA
**
57161 TT-TTCCTTGA
321 TTATTCCTCAA
* * * * *
57171 TTTTTAGCCACAAT-CTCATAAAAA-ATATATAATTCAACGCTAAAAAGATTGAAGGGCTTTTCA
1 TTTTTGGCTAAAATACTC-TAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCA
* * * * *
57234 CGCTTCTAATATCGTTTTTCCTATTTTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATT
65 CGCTTTTAATATCGTTTTT-C-A-TATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT
* * *
57299 CAGATG-TCTGT-------AA-----AAA--CAAT-T-GCTGGGATTTGGTTAGATGAACATAGA
127 CAGATGCTC-GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGA
* * * * * * *
57347 TATTTCAAGGAGTCTCCGCTCCAAAAATCATTCAAAATTGAA-TC-GGGCCCCGAAACGTGTTTT
191 TATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACT-AAGCCGGGGCCCTGAAACGCGTTTT
* * * * * * *
57410 TAGCCAAAAACCCTAATGATTATTATACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAG
255 TAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAA
57475 A-TATATCCTCAA
320 ATTAT-TCCTCAA
* * * * *
57487 TTTTAGAC-ATAATACT-TATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGA-TTTTC
1 TTTTTGGCTAAAATACTCTA-AAAATATATATAATTCAACGCCAAAAAGATTGAA-GGACTTTTC
* * * *
57549 ACGCTTGTAATATTGTTTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTT
64 ACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * * * * * *
57614 AGATGCTCGTAAACACAAATCCTTAAATGCAATGTAGCTAAGATTTTATCAAATGAATATAGATA
128 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATA
* * * * * *
57679 TTTCAAGGAGTGTCGACGCCAAAAACCATGCAAAACTAAGCCGGGACCCCGAAACACGTTTTTAG
193 TTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCTGAAACGCGTTTTTAG
* * ***
57744 CCAAAAAAACCGTGAT-GTAAGTACACGATTTTGGCTAAAATTTTGCACAAAAAAAAACCCGAAA
258 CC--AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTG--CAAAAATTGACCCGAAA
* *
57808 AATTTTTCCCCAA
319 AATTATTCCTCAA
* ** * *
57821 TTTTTGGATAAAATACT-TATAAAATATATATAATTTGACGCCAAGAATATTGGAGAGG-CTTTT
1 TTTTTGGCTAAAATACTCTA-AAAATATATATAATTCAACGCCAAAAAGATT-GA-AGGACTTTT
*
57884 CACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTT
63 CACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * *
57949 AGATGCTTGTAAAAACAAAT-CTTAAATCCAATGTGGCTAAGATTTGATTAGACGAATAT-GCAT
128 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAG-AT
* * * ** * * *
58012 ATCTCAAGGAGTCTTGGTGTAAAAAATCATGCAAAACTGAGTCGGGGCCC-CAGAACGC-TTTTA
192 ATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCTGA-AACGCGTTTT-
* *
58075 TAGCCAAAAACTGTGATGGTTATTACACGA
255 TAGCCAAAAACCGTGATGGTTAGTACACGA
58105 AAGATATTTT
Statistics
Matches: 2112, Mismatches: 375, Indels: 213
0.78 0.14 0.08
Matches are distributed among these distances:
313 1 0.00
314 46 0.02
315 62 0.03
316 63 0.03
317 19 0.01
318 59 0.03
319 1 0.00
320 4 0.00
321 2 0.00
322 3 0.00
324 46 0.02
325 59 0.03
326 117 0.06
327 59 0.03
328 205 0.10
329 162 0.08
330 123 0.06
331 158 0.07
332 78 0.04
333 45 0.02
334 193 0.09
335 99 0.05
336 82 0.04
337 103 0.05
338 255 0.12
339 14 0.01
340 2 0.00
341 24 0.01
342 28 0.01
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (331 bp):
TTTTTGGCTAAAATACTCTAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCAC
GCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTT
CAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCTGAAACGCGTTTTTAGCCA
AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTATT
CCTCAA
Found at i:56930 original size:665 final size:654
Alignment explanation
Indices: 55196--58104 Score: 2474
Period size: 665 Copynumber: 4.4 Consensus size: 654
55186 TTGGCAAAAC
* * * * *
55196 TACTCATAAATATATATAATTCAACGCCAAAAGGATT-AGAGGACTTTTCACGCTTTTAATATCG
1 TACTCATAAAAACATATAATT-AACGCCAAAAAGATTGA-AGGCCTTTTCACGCTTCTAATATC-
* * * ****
55260 TTTTTCATATTTTTT-TGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACATAAAAA
63 TTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATG--C-TTGTTA
* * * ** * * *
55324 CAAATCCTTGAATCCAATGTGCCTGAGATTTTATTTGATGAATAAATATATTTCAAGGAGTCTCG
125 CAAAT-CTTAAAT-CAATTTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCG
** *** * * * * *
55389 GCGCCAAAAAT-ATGCAAAACAGAGCCGTGGTCCTGGAATGCGTTTTTACCCAAAAACC--G-TG
188 GCGCCAAAAATCATGCAAAATTGAATTG-GGCCCAGAAACGCGTTTTTAGCCAAAAACCGTGATG
* * *
55450 A-T-GTACACGATTTCGGTTAAAATTTTGCAAAAATTGA-TCCGAAAGATATTTCCTCATTTTTT
252 ATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACT-AGAAAGATATTTCCTCAATTTTT
* * * * *
55512 GGCTAAAATACTAATAAAAAATATATAATTCGACAT-CAAAAAGATTAAAGGGCTTTTAACACTT
316 GGCTAAAATACTTATAAAAAATATATAATTCAAC-TCCAAAAAGATTGAAGGACTTTTCACACTT
* * * * * * *
55576 CTAATATTTTTTTTTCCAATTTTTTTCCGAATTAGTTTCCAATTAAATCGAAACAAGATTCAAAT
380 TTAATA-TTGTTTTT-C-ATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT
* * ** * *
55641 GCTCGAAAAAACAAATCCTTAAATCTAATGTGTCTAAGATTTGGTTAGATGAATATAGATATTTC
442 GCTCGTAAAAACAAATCCTTAAATCCAATGTAACTAAGATTTGATTAAATGAATATAGATATTTC
* * * * ** * *
55706 AAGGA-T-T-G-CACCAAAAATCATGCAATACTGAGTCGGGTCCC-GAAACGCGTTTTTAGCCGA
507 AAAGAGTCTCGACGCCAAAAATCATGCAAAACTTAACCGGGGCCCTGAAACGCGTTTTTAGCCAA
*
55766 AAACCGTGATGGTTAGTACACGA-TT--TCGGCTAAAATTTTGGAAAAATTGA-TCCGAAAGATT
572 AAACCGTGATGGTTAGTACACGATTTGATC-GCTAAAATTTTGCAAAAATTGACT-CGAAAG--T
* * *
55827 TTTCCTCGATTTCTAAT-GAAAA
633 TTTCCTCGATTT-TTATCCACAA
* * * *
55849 TACTCATAAAAAACATATAATTCAATGCCAAAAAAATTGAAAGCCTTTTTCACGCTTTTAATATC
1 TACTCAT-AAAAACATATAATT-AACGCCAAAAAGATTGAAGGCC-TTTTCACGCTTCTAATATC
* * * * ** * *
55914 GTTTTCATA-TTTTTCAGAATTAATTTCTTATTAAATCGAAACAAAATTCAGATGCTCGTAAAAA
63 TTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGT---TA
* * * *
55978 CAAATTCTTCAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTG
125 CAAA-TCTT-AAATCAATTTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCG
* * * *
56043 GCGCCAAAAATCATGCAAAACT-AAGTTGGGGCCCTGAAACGCGTTTTTAGCAAAAAACTGTGAT
188 GCGCCAAAAATCATGCAAAATTGAA-TT-GGGCCCAGAAACGCGTTTTTAGCCAAAAACCGTGAT
* * * *
56107 GGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACAAGAAAAAT-TATTCCGTCAATTT
251 GATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTAGAAAGATAT-TTCC-TCAATTT
* * * * *
56171 TTGGCTAAAATACTCATAATATATATATATATATAATTCACCGCCAAAAATATTGGAGGACTTTT
314 TTGGCTAAAATACT--T-ATA-A-A-AAATATATAATTCAACTCCAAAAAGATTGAAGGACTTTT
* *
56236 CA-AGCTTTTAATATTGTTTTTAATATTTTTCTGAATTAATTTTTAATTAAATCGAAGA-AAGAT
373 CACA-CTTTTAATATTGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAA-ACAAGAT
* * * * * *
56299 TCAGGTGCTCGTAAAAACAAATTCTTAAATCCAATTTAACTGAGATTTGGTTAAATGAATATGGA
436 TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAACTAAGATTTGATTAAATGAATATAGA
* * * * * *
56364 TATCTCAAAGAGTCTTGGCGCCAAAAATCATGTAAAACTTAACCGGGGCCCTGGAATGCGTTTTT
501 TATTTCAAAGAGTCTCGACGCCAAAAATCATGCAAAACTTAACCGGGGCCCTGAAACGCGTTTTT
* * * *
56429 AGCCAAAAACTGTGATGATTATTACACGATTTTGATCGACTAGAATTTTGCAAAAATTGACTCGA
566 AGCCAAAAACCGTGATGGTTAGTACACGA-TTTGATCG-CTAAAATTTTGCAAAAATTGACTCGA
*
56494 AAGTTACTTCCTCAATTTTTATCCACAA
629 AAGTT--TTCCTCGATTTTTATCCACAA
* * * *
56522 TACTCAT-AAAA-AT-T-A-T-ACGCCAAAAAGTTTGCAGGTCTTTTCATGCTTCTAATATCATT
1 TACTCATAAAAACATATAATTAACGCCAAAAAGATTGAAGGCCTTTTCACGCTTCTAATATC-TT
56581 TTTCCTATTATTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGTTTTACA
65 TTTCCTATT-TTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTG--TTACA
* *
56646 AATCCTTAAATCCAATTTGGCTGAAATTTGGTTAGATGAATGTAGATATTT-AAGGAGTCTCGGC
127 AAT-CTTAAAT-CAATTTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGC
* * * *
56710 GCAAAAAAATCATGCAACATTGAACTTGGGCCCAGGAACGGGTTTTTAGCCAAAAACCGTGATTT
190 GC-CAAAAATCATGCAAAATTGAA-TTGGGCCCAGAAACGCGTTTTTAGCCAAAAACCGTGA--T
* * * * * *
56775 CGACTAACGTACACGATATCGGCTAATATTTTGCAAAAATTGACTAGAAATATTTTTTTCTCAAT
251 -GA-TTA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTAGAAAGA-TATTTCCTCAAT
* * * *
56840 TTTTGTCTAAAATACTTATAAAATATATATAATTCAACTCAAAAAAGATTGGAGGACTTTTCACA
312 TTTTGGCTAAAATACTTATAAAAAATATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACA
* *
56905 ATTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT
377 CTTTTAATATTGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT
* * * * * * * * *
56970 GCACGTAAAAACAAATCCTTAAATGCAATCTGGA-TGATACTTGATTAGATGAATATAGATAATT
442 GCTCGTAAAAACAAATCCTTAAATCCAATGT-AACTAAGATTTGATTAAATGAATATAGATATTT
* * * *
57034 CAAGGAGTCTCGATGCCAAAAATCATGTAAAA-TTGAACCGGGG-CCTCGAAACGCTTTTTTAGC
506 CAAAGAGTCTCGACGCCAAAAATCATGCAAAACTT-AACCGGGGCCCT-GAAACGCGTTTTTAGC
* * *
57097 AAAGAAAACCGTGATGGTTAGTACACGATTTCA--GCTAAAATTTTGCAAAAAATGAC-CAGAAA
569 -CA-AAAACCGTGATGGTTAGTACACGATTTGATCGCTAAAATTTTGCAAAAATTGACTC-G-AA
* * *
57159 AATTTTCCTTGATTTTTAGCCACAA
630 AGTTTTCCTCGATTTTTATCCACAA
* * *
57184 T-CTCATAAAAAATATATAATTCAACGCTAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCG
1 TACTCAT-AAAAACATATAATT-AACGCCAAAAAGATTGAAGGCCTTTTCACGCTTCTAATATC-
*
57248 TTTTTCCTATTTTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTCAGATG-TCTG-T-
63 TTTTTCCTA--TTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCT-TGTTA
* * *
57310 --AA----AAA-CAA-TT-GCTGGGATTTGGTTAGATGAACATAGATATTTCAAGGAGTCTCCGC
125 CAAATCTTAAATCAATTTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGC
* * * * * * *
57366 TCCAAAAATCATTCAAAATTGAATCGGGCCCCGAAACGTGTTTTTAGCCAAAAACCCTAATGATT
190 GCCAAAAATCATGCAAAATTGAATTGGGCCCAGAAACGCGTTTTTAGCCAAAAACCGTGATGATT
* * * ** * * *
57431 ATTATACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGATATATCCTCAATTTTAGAC-
255 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTAGAAAGATATTTCCTCAATTTTTGGCT
* * *
57495 ATAATACTTATAAAAAATATATAATTCAA-TGCCAAAAAGATTGAAGGGA-TTTTCACGCTTGTA
320 AAAATACTTATAAAAAATATATAATTCAACT-CCAAAAAGATTGAA-GGACTTTTCACACTTTTA
* *
57558 ATATTGTTTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCG
383 ATATTGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * * * * *
57623 TAAACACAAATCCTTAAATGCAATGTAGCTAAGATTTTATCAAATGAATATAGATATTTCAAGGA
447 TAAAAACAAATCCTTAAATCCAATGTAACTAAGATTTGATTAAATGAATATAGATATTTCAAAGA
* * * * *
57688 GTGTCGACGCCAAAAACCATGCAAAAC-TAAGCCGGGACCCCGAAACACGTTTTTAGCCAAAAAA
512 GTCTCGACGCCAAAAATCATGCAAAACTTAA-CCGGGGCCCTGAAACGCGTTTTTAGCC--AAAA
* * *** * *
57752 ACCGTGAT-GTAAGTACACGATTT--TGGCTAAAATTTTGCACAAAAAAAAACCCGAAAAATTTT
574 ACCGTGATGGTTAGTACACGATTTGATCGCTAAAATTTTG--CAAAAATTGACTCG--AAAGTTT
* * *
57814 TCCCCAATTTTTGGAT--AAAA
635 TCCTCGATTTTT--ATCCACAA
* * * * * *
57834 TACTTATAAAATATATATAATTTGACGCCAAGAATATTGGAGAGG-CTTTTCACGCTTTTAATAT
1 TACTCATAAAA-ACATATAA-TTAACGCCAAAAAGATT-GA-AGGCCTTTTCACGCTTCTAATAT
* * * *
57898 CGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAA
62 C-TTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGT---
* * * * * *
57962 AACAAATCTTAAATCCAATGTGGCTAAGATTTGATTAGACGAATAT-GCATATCTCAAGGAGTCT
123 TACAAATCTTAAAT-CAATTTGGCTGAGATTTGGTTAGATGAATATAG-ATATTTCAAGGAGTCT
* * ** * * * *
58026 TGGTGTAAAAAATCATGCAAAACTGAGTCGGGGCCCCAG-AACGC-TTTTATAGCCAAAAACTGT
186 CGGCGCCAAAAATCATGCAAAATTGAAT-TGGG-CCCAGAAACGCGTTTT-TAGCCAAAAACCGT
* *
58089 GATGGTTATTACACGA
248 GATGATTAGTACACGA
58105 AAGATATTTT
Statistics
Matches: 1854, Mismatches: 280, Indels: 232
0.78 0.12 0.10
Matches are distributed among these distances:
646 1 0.00
647 92 0.05
648 169 0.09
649 92 0.05
650 28 0.02
651 26 0.01
652 35 0.02
653 15 0.01
654 169 0.09
655 102 0.06
656 18 0.01
657 4 0.00
658 2 0.00
659 5 0.00
660 46 0.02
661 25 0.01
662 23 0.01
663 27 0.01
664 190 0.10
665 270 0.15
666 112 0.06
667 112 0.06
668 31 0.02
669 85 0.05
670 49 0.03
671 69 0.04
672 8 0.00
673 48 0.03
674 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (654 bp):
TACTCATAAAAACATATAATTAACGCCAAAAAGATTGAAGGCCTTTTCACGCTTCTAATATCTTT
TTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGTTACAAATC
TTAAATCAATTTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAA
AATCATGCAAAATTGAATTGGGCCCAGAAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACA
CGATTTCGGCTAAAATTTTGCAAAAATTGACTAGAAAGATATTTCCTCAATTTTTGGCTAAAATA
CTTATAAAAAATATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACACTTTTAATATTGTT
TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
ATCCTTAAATCCAATGTAACTAAGATTTGATTAAATGAATATAGATATTTCAAAGAGTCTCGACG
CCAAAAATCATGCAAAACTTAACCGGGGCCCTGAAACGCGTTTTTAGCCAAAAACCGTGATGGTT
AGTACACGATTTGATCGCTAAAATTTTGCAAAAATTGACTCGAAAGTTTTCCTCGATTTTTATCC
ACAA
Found at i:58260 original size:634 final size:629
Alignment explanation
Indices: 57469--58634 Score: 1542
Period size: 634 Copynumber: 1.8 Consensus size: 629
57459 AAAATTGACC
* * **
57469 CGAAAGATATATCCTCAATTTTAGACATAATACTTATAAAAAATATATAATTCAATGCCAAAAAG
1 CGAAAGATATATCCTCAATTTTAGACAAAATACTCATAAAAAATATATAATTCAACACCAAAAAG
* ** *
57534 ATTGAAGGGATTTTCACGCTTGTAATATTGTTTTTCATATTTTTTCTAAATTAATTTCTAATTAA
66 ATTGAAGGGATTTTCACGCTTCTAATATCATTTTTCATATTTTTTCCAAATTAATTTCTAATTAA
* * * *
57599 ATCGAAACAAGATTTAGATGCTCGTAAACACAAATCCTTAAATGCAATGTAGCTAAGATTTTATC
131 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCTAAGATTTGATC
*
57664 AAATGAATATAGATATTTCAAGGAGTGTC-GACGCCAAAAACCATGCAAAACTAAGCCGGGACCC
196 AAATGAATATAGATATTTCAAGGAGTCTCGGA-GCCAAAAACCATGCAAAACTAAGCCGGGACCC
*
57728 C-GAA-ACACGTTTTTAGCCAAAAAAACCGTGA-TGTAAGTACACGATTTTGGCTAAAATTTTGC
260 CAGAATACA--TTTTTAG--AAAAAAACCGTGATTGTAAGTACACGATTTCGGCTAAAATTTTGC
* * *
57790 ACAAAA-AAAAACCCGAAAA-ATTTTTCCCCAATTTTTGGATAAAATACTTATAAAATATATATA
321 A-AAAACAAAAA--C-AAAAGATTTCTCCCCAATTTTTAGATAAAATACTCATAAAA-ATATATA
** * * * * *
57853 ATTTGACGCCAAGAATATTGGAGAGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCT-G
381 ATTCAACGCCAAAAAGATTGGAG-GGCTTTTCACGCTTTTAATATCATATTTCATATTTTT-TAA
* * *
57917 AATTAATTTCTA-ATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACAAA-TCTTAAATCCAA
444 AATTAATTTC-ACAGTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAA
57980 TGTGGCTAAGATTTGATTAGACGAATATGCATATCTCAAGGAGTCTTGGTGTAAAAAATCATGCA
508 TGTGGCTAAGATTTGATTAGACGAATATGCATATCTCAAGGAGTCTTGGTGTAAAAAATCATGCA
58045 AAACTGAGTCGGGGCCCCAGAACGCTTTTATAGCCAAAAACTGTGATGGTTATTACA
573 AAACTGAGTCGGGGCCCCAGAACGCTTTTATAGCCAAAAACTGTGATGGTTATTACA
* * *
58102 CGAAAGATATTTTCTCAATTTTTG-CTAAAATACTCATAAAAACATATATAATTCAACACCAAAA
1 CGAAAGATATATCCTCAATTTTAGAC-AAAATACTCATAAAAA-ATATATAATTCAACACCAAAA
* * * *
58166 AGATTGAAGGGCTTTTGACGTTTCTAATATCATTTTTCCTATTTTTTCCAAATTAATTTCTAATT
64 AGATTGAAGGGATTTTCACGCTTCTAATATCATTTTTCATATTTTTTCCAAATTAATTTCTAATT
* * *
58231 AAATCGAAACAAGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGA
129 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCTAAGATTTGA
* * * * * * * *
58296 TTAGATGAATATAGATATTTCAAGTAGTCTCGGAGCCAAAAATCATGCAAAATTGAGTCGGGTCC
194 TCAAATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAACCATGCAAAACTAAGCCGGGACC
* * * *
58361 CCAGAATGCATTTTTAGATAAAAACCGTGATGGTTTGTTAGTACACGATTTCGGTTAAAATTTTG
259 CCAGAATACATTTTTAGAAAAAAACCGTGA----TTGTAAGTACACGATTTCGGCTAAAATTTTG
** * * *
58426 CAAAAACTGATACAAAAGATTTCTCCTCAATTTTTAGTTAAAATACTCATAAAAATATATAATTC
320 CAAAAACAAAAACAAAAGATTTCTCCCCAATTTTTAGATAAAATACTCATAAAAATATATAATTC
* * *
58491 AACGCCAAAAAGATTGGAGGGCTTTTTACTCTTTTAATATCATATTTCTTATTTTTTAAAATTAA
385 AACGCCAAAAAGATTGGAGGGCTTTTCACGCTTTTAATATCATATTTCATATTTTTTAAAATTAA
* *
58556 TTTCACAGTAAATCGAAACAAGATTCAGATGCTCGTAAAAGCAAATTCTTAAATCCAATGTTGCT
450 TTTCACAGTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCT
* *
58621 GAGATTTGCTTAGA
515 AAGATTTGATTAGA
58635 TGATGTAAAG
Statistics
Matches: 457, Mismatches: 61, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
632 15 0.03
633 112 0.25
634 256 0.56
635 37 0.08
636 6 0.01
637 31 0.07
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (629 bp):
CGAAAGATATATCCTCAATTTTAGACAAAATACTCATAAAAAATATATAATTCAACACCAAAAAG
ATTGAAGGGATTTTCACGCTTCTAATATCATTTTTCATATTTTTTCCAAATTAATTTCTAATTAA
ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCTAAGATTTGATC
AAATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAACCATGCAAAACTAAGCCGGGACCCC
AGAATACATTTTTAGAAAAAAACCGTGATTGTAAGTACACGATTTCGGCTAAAATTTTGCAAAAA
CAAAAACAAAAGATTTCTCCCCAATTTTTAGATAAAATACTCATAAAAATATATAATTCAACGCC
AAAAAGATTGGAGGGCTTTTCACGCTTTTAATATCATATTTCATATTTTTTAAAATTAATTTCAC
AGTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTAAGATT
TGATTAGACGAATATGCATATCTCAAGGAGTCTTGGTGTAAAAAATCATGCAAAACTGAGTCGGG
GCCCCAGAACGCTTTTATAGCCAAAAACTGTGATGGTTATTACA
Found at i:58393 original size:300 final size:299
Alignment explanation
Indices: 57818--58395 Score: 788
Period size: 300 Copynumber: 1.9 Consensus size: 299
57808 AATTTTTCCC
* * ** * * * *
57818 CAATTTTTGGATAAAATACTTATAAAATATATATAATTTGACGCCAAGAATATTGGAGAGGCTTT
1 CAATTTTTGGATAAAATACTCATAAAACATATATAATTCAACACCAAAAAGATTGAAGAGGCTTT
* **
57883 TCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT
66 TCACGCTTTTAATATCATTTTTCATATTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATT
* *
57948 TAGATGCTTGTAAAAACAAATCTTAAATCCAATGTGGCTAAGATTTGATTAGACGAATATGCATA
131 CAGATGCTCGTAAAAACAAATCTTAAATCCAATGTGGCTAAGATTTGATTAGACGAATATGCATA
* * *
58013 TCTCAAGGAGTCTTGGTGTAAAAAATCATGCAAAACTGAGTCGGGGCCCCAGAACGCTTTTATAG
196 TCTCAAGGAGTCTCGGAGCAAAAAATCATGCAAAACTGAGTCGGGGCCCCAGAACGCTTTTATAG
* *
58078 CCAAAAACTGTGATGGTTATTACACGAAAGATATTTTCT
261 ACAAAAACCGTGATGGTTATTACACGAAAGATATTTTCT
*
58117 CAATTTTT-GCTAAAATACTCATAAAAACATATATAATTCAACACCAAAAAGATTGAAG-GGCTT
1 CAATTTTTGGATAAAATACTCAT-AAAACATATATAATTCAACACCAAAAAGATTGAAGAGGCTT
* *
58180 TTGACG-TTTCTAATATCATTTTTCCTATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAG
65 TTCACGCTTT-TAATATCATTTTTCATA-TTTTTCCAAATTAATTTCTAATTAAATCGAAACAAG
* * *
58244 ATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA
128 ATTCAGATGCTCGTAAAAACAAAT-CTTAAATCCAATGTGGCTAAGATTTGATTAGACGAATAT-
* * * * * *
58309 G-ATATTTCAAGTAGTCTCGGAGCCAAAAATCATGCAAAATTGAGTCGGGTCCCCAGAATGCATT
191 GCATATCTCAAGGAGTCTCGGAGCAAAAAATCATGCAAAACTGAGTCGGGGCCCCAGAACGC-TT
*
58373 TT-TAGATAAAAACCGTGATGGTT
255 TTATAGACAAAAACCGTGATGGTT
58396 TGTTAGTACA
Statistics
Matches: 242, Mismatches: 31, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
297 3 0.01
298 37 0.15
299 91 0.38
300 106 0.44
301 5 0.02
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (299 bp):
CAATTTTTGGATAAAATACTCATAAAACATATATAATTCAACACCAAAAAGATTGAAGAGGCTTT
TCACGCTTTTAATATCATTTTTCATATTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATT
CAGATGCTCGTAAAAACAAATCTTAAATCCAATGTGGCTAAGATTTGATTAGACGAATATGCATA
TCTCAAGGAGTCTCGGAGCAAAAAATCATGCAAAACTGAGTCGGGGCCCCAGAACGCTTTTATAG
ACAAAAACCGTGATGGTTATTACACGAAAGATATTTTCT
Found at i:58991 original size:15 final size:16
Alignment explanation
Indices: 58973--59002 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
58963 ATAAATAATA
58973 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
58988 ATATTATAATCTAAA
1 ATATTATAATCTAAA
59003 AATAATTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:59819 original size:69 final size:69
Alignment explanation
Indices: 59708--59846 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
59698 ATCTGCGTCA
*
59708 CGCACCTGGTTTTGGTAGGTGAGTCTACCAATGAGGGCAATTACGTACGCAAGGTCTCGAACCTG
1 CGCACCTGGTTTTGGTAGGTGAGTCTACCAATGAGGGCAATTACGTACGCAAGATCTCGAACCTG
59773 GAAC
66 GAAC
*
59777 CGCACCTGGTTTTGGTAGGTGAGTCTACCAATTAGGGCAATTACGTACGCAAGATCTCGAACCTG
1 CGCACCTGGTTTTGGTAGGTGAGTCTACCAATGAGGGCAATTACGTACGCAAGATCTCGAACCTG
59842 GAAC
66 GAAC
59846 C
1 C
59847 TGCTTAAACT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (69 bp):
CGCACCTGGTTTTGGTAGGTGAGTCTACCAATGAGGGCAATTACGTACGCAAGATCTCGAACCTG
GAAC
Found at i:60971 original size:28 final size:31
Alignment explanation
Indices: 60914--60974 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
60904 CAATATTTAT
* *
60914 TTTTTTGTGTATTATTAGTATGTAACATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
60945 TTTTTTGTGTATTA-TAATA-ATAA-ATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
60973 TT
1 TT
60975 ATAGTTTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 3 0.11
30 4 0.14
31 14 0.50
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (31 bp):
TTTTTTGTGTATTATTAATATATAACATTAA
Found at i:61142 original size:11 final size:12
Alignment explanation
Indices: 61100--61140 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
61090 AAAACAATTC
61100 TATAAAATTAAT
1 TATAAAATTAAT
* *
61112 TATCAAA-TACT
1 TATAAAATTAAT
61123 TATAAAATTAAT
1 TATAAAATTAAT
61135 TATAAA
1 TATAAA
61141 TTTCATTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (12 bp):
TATAAAATTAAT
Found at i:62368 original size:31 final size:31
Alignment explanation
Indices: 62329--62499 Score: 227
Period size: 31 Copynumber: 5.5 Consensus size: 31
62319 TCCTTTTGTG
**
62329 CACGTGGCATGCCACGTGTCACTTTTTGAAA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* *
62360 CACATGGCATGCCACGTGTCACCTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
62391 CACGTGGCGTGCCACGTGTCAC-TTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * * *
62421 CATGTGGCGTGCCACATGTCGCTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * *
62452 CACGTGGCGTGCCACATGTCGCTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
62483 CACGTGGCATGCCACGT
1 CACGTGGCATGCCACGT
62500 CGGACACCGT
Statistics
Matches: 127, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
30 27 0.21
31 100 0.79
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:62452 original size:61 final size:62
Alignment explanation
Indices: 62320--62497 Score: 234
Period size: 61 Copynumber: 2.9 Consensus size: 62
62310 GGACACGTAT
* * ** * *
62320 CCTTTT-GTGCACGTGGCATGCCACGTGTCACTTTTTGAAACACATGGCATGCCACGTGTCA
1 CCTTTTGGTACACGTGGCGTGCCACGTGTCACTTTTTGGTACACGTGGCATGCCACATGTCA
* * *
62381 CCTTTTGGTACACGTGGCGTGCCACGTGTCAC-TTTTGGTACATGTGGCGTGCCACATGTCG
1 CCTTTTGGTACACGTGGCGTGCCACGTGTCACTTTTTGGTACACGTGGCATGCCACATGTCA
* * *
62442 CTTTTTGGTACACGTGGCGTGCCACATGTCGCTTTTTGGTACACGTGGCATGCCAC
1 CCTTTTGGTACACGTGGCGTGCCACGTGTCACTTTTTGGTACACGTGGCATGCCAC
62498 GTCGGACACC
Statistics
Matches: 101, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
61 57 0.56
62 44 0.44
ACGTcount: A:0.16, C:0.27, G:0.26, T:0.31
Consensus pattern (62 bp):
CCTTTTGGTACACGTGGCGTGCCACGTGTCACTTTTTGGTACACGTGGCATGCCACATGTCA
Found at i:62479 original size:92 final size:92
Alignment explanation
Indices: 62332--62499 Score: 237
Period size: 92 Copynumber: 1.8 Consensus size: 92
62322 TTTTGTGCAC
* *
62332 GTGGCATGCCACGTGTCACTTTTTGAAACACATGGCATGCCACGTGTCACCTTTTGGTACACGTG
1 GTGGCATGCCACATGTCACTTTTTGAAACACATGGCATGCCACATGTCACCTTTTGGTACACGTG
*
62397 GCGTGCCACGTGTCACTTTTGGTACAT
66 GCATGCCACGTGTCACTTTTGGTACAT
* * ** * * * *
62424 GTGGCGTGCCACATGTCGCTTTTTGGTACACGTGGCGTGCCACATGTCGCTTTTTGGTACACGTG
1 GTGGCATGCCACATGTCACTTTTTGAAACACATGGCATGCCACATGTCACCTTTTGGTACACGTG
62489 GCATGCCACGT
66 GCATGCCACGT
62500 CGGACACCGT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
92 65 1.00
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.30
Consensus pattern (92 bp):
GTGGCATGCCACATGTCACTTTTTGAAACACATGGCATGCCACATGTCACCTTTTGGTACACGTG
GCATGCCACGTGTCACTTTTGGTACAT
Found at i:64807 original size:37 final size:40
Alignment explanation
Indices: 64766--64885 Score: 129
Period size: 41 Copynumber: 3.0 Consensus size: 40
64756 AACTCAGTCT
* *
64766 TGTTCG-CGAACATTTT-GT-TTTGTTCAAGCTCGGCTCG
1 TGTTCGTCAAACATTTTGGTGTTCGTTCAAGCTCGGCTCG
* * *
64803 TGTTCGTTTAAATATTTTGGTGTTCGTTCGAGCTCGGCTCG
1 TGTTCG-TCAAACATTTTGGTGTTCGTTCAAGCTCGGCTCG
* * *
64844 TGTTCGTTTAAATATTTTGGTGTTCGTTCGAGCTCGGCTCG
1 TGTTCG-TCAAACATTTTGGTGTTCGTTCAAGCTCGGCTCG
64885 T
1 T
64886 TTAAAATTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
37 6 0.08
39 7 0.09
40 2 0.03
41 59 0.80
ACGTcount: A:0.12, C:0.18, G:0.26, T:0.43
Consensus pattern (40 bp):
TGTTCGTCAAACATTTTGGTGTTCGTTCAAGCTCGGCTCG
Found at i:64827 original size:20 final size:20
Alignment explanation
Indices: 64802--64871 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
64792 AGCTCGGCTC
64802 GTGTTCGTTTAAATATTTTG
1 GTGTTCGTTTAAATATTTTG
* ** **** *
64822 GTGTTCGTTCGAGCTCGGCTC
1 GTGTTCGTT-TAAATATTTTG
64843 GTGTTCGTTTAAATATTTTG
1 GTGTTCGTTTAAATATTTTG
64863 GTGTTCGTT
1 GTGTTCGTT
64872 CGAGCTCGGC
Statistics
Matches: 33, Mismatches: 16, Indels: 2
0.65 0.31 0.04
Matches are distributed among these distances:
20 21 0.64
21 12 0.36
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.49
Consensus pattern (20 bp):
GTGTTCGTTTAAATATTTTG
Found at i:64843 original size:41 final size:41
Alignment explanation
Indices: 64787--64885 Score: 189
Period size: 41 Copynumber: 2.4 Consensus size: 41
64777 ATTTTGTTTT
*
64787 GTTCAAGCTCGGCTCGTGTTCGTTTAAATATTTTGGTGTTC
1 GTTCGAGCTCGGCTCGTGTTCGTTTAAATATTTTGGTGTTC
64828 GTTCGAGCTCGGCTCGTGTTCGTTTAAATATTTTGGTGTTC
1 GTTCGAGCTCGGCTCGTGTTCGTTTAAATATTTTGGTGTTC
64869 GTTCGAGCTCGGCTCGT
1 GTTCGAGCTCGGCTCGT
64886 TTAAAATTTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.12, C:0.19, G:0.27, T:0.41
Consensus pattern (41 bp):
GTTCGAGCTCGGCTCGTGTTCGTTTAAATATTTTGGTGTTC
Found at i:64886 original size:35 final size:37
Alignment explanation
Indices: 64806--64904 Score: 123
Period size: 41 Copynumber: 2.6 Consensus size: 37
64796 CGGCTCGTGT
64806 TCGTTTAAATATTTTGGTGTTCGTTCGAGCTCGGCTCGTG
1 TCGTTTAAATATTTTGGTGTTCGTTCGAGCTCGGC-C--G
64846 TTCGTTTAAATATTTTGGTGTTCGTTCGAGCTCGG-C-
1 -TCGTTTAAATATTTTGGTGTTCGTTCGAGCTCGGCCG
*
64882 TCGTTTAAA-ATTTAGAGTGTTCG
1 TCGTTTAAATATTTTG-GTGTTCG
64905 AAACTCGTTC
Statistics
Matches: 56, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
34 5 0.09
35 16 0.29
39 1 0.02
41 34 0.61
ACGTcount: A:0.16, C:0.15, G:0.25, T:0.43
Consensus pattern (37 bp):
TCGTTTAAATATTTTGGTGTTCGTTCGAGCTCGGCCG
Found at i:65021 original size:18 final size:18
Alignment explanation
Indices: 64998--65032 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
64988 ACAAAAATTG
64998 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
65016 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
65033 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:65276 original size:35 final size:35
Alignment explanation
Indices: 65237--65311 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
65227 TTATATAAAC
*
65237 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGGCTGTTCGT
65272 GAACACTTAAATGAACAATAAACGAGGCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGGCTGTTCGT
65307 GAACA
1 GAACA
65312 TAAACGAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGGCTGTTCGT
Found at i:70970 original size:14 final size:14
Alignment explanation
Indices: 70951--70981 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
70941 ATCTAAACGA
*
70951 GACAGATAATTTGG
1 GACAGATAATATGG
70965 GACAGATAATATGG
1 GACAGATAATATGG
70979 GAC
1 GAC
70982 GGAGGGAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.29, T:0.23
Consensus pattern (14 bp):
GACAGATAATATGG
Found at i:78502 original size:3 final size:3
Alignment explanation
Indices: 78496--78574 Score: 149
Period size: 3 Copynumber: 26.3 Consensus size: 3
78486 AAAGAATGAT
78496 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
78544 TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
78575 ACACTCTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:80522 original size:52 final size:52
Alignment explanation
Indices: 80444--80547 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
80434 GTTCGTTGCG
*
80444 TTAAATGTGAGTTTAGTTAACCTGTTTGTTTATTTGGTAGATAGTAATTTAT
1 TTAAATGTGAGTTTAGTTAACCTGTTTGTTTATTTAGTAGATAGTAATTTAT
*
80496 TTAAATGTGAGTTTAGTTAACCTGTTTGTTTATTTAGTAGATAGTAGTTTAT
1 TTAAATGTGAGTTTAGTTAACCTGTTTGTTTATTTAGTAGATAGTAATTTAT
80548 ATAAGATAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.27, C:0.04, G:0.19, T:0.50
Consensus pattern (52 bp):
TTAAATGTGAGTTTAGTTAACCTGTTTGTTTATTTAGTAGATAGTAATTTAT
Found at i:83549 original size:35 final size:35
Alignment explanation
Indices: 83498--83604 Score: 155
Period size: 35 Copynumber: 3.1 Consensus size: 35
83488 TCAAGGCAAT
* **
83498 GCAAAGTTCTTCTCCATCAAGCAAAGCAA-ATCTGCA
1 GCAAAGTTCTTCTCCATCAA-CAAAGCAACAAC-AAA
83534 GCAAAGTT-TTCTCCATCAACAAAGCAACAACAAA
1 GCAAAGTTCTTCTCCATCAACAAAGCAACAACAAA
83568 GCAAAGTTCTTCTCCATCAACAAAGCAACAACAAA
1 GCAAAGTTCTTCTCCATCAACAAAGCAACAACAAA
83603 GC
1 GC
83605 CTACGAAAGT
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
34 17 0.26
35 41 0.62
36 8 0.12
ACGTcount: A:0.42, C:0.28, G:0.11, T:0.19
Consensus pattern (35 bp):
GCAAAGTTCTTCTCCATCAACAAAGCAACAACAAA
Done.