Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011759.1 Corchorus capsularis cultivar CVL-1 contig11780, 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: 37811
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3186 original size:2 final size:2
Alignment explanation
Indices: 3179--3209 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3169 TTTGTCAGCA
3179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3210 ATTCACAACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4494 original size:50 final size:50
Alignment explanation
Indices: 4414--4509 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
4404 CCAGAAAAAA
* *
4414 TAATTTATTTTTGTTTGGGATTGCTCGCATCATATATTGATACGGGCTAT
1 TAATTAATTTTTGTTTGGGATTGCTCGCATCATATATAGATACGGGCTAT
4464 TAATTAATTTTTGTTTGGGATTGCAT-GCATCATATATAGATACGGG
1 TAATTAATTTTTGTTTGGGATTGC-TCGCATCATATATAGATACGGG
4510 GACAATTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
50 42 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (50 bp):
TAATTAATTTTTGTTTGGGATTGCTCGCATCATATATAGATACGGGCTAT
Found at i:7754 original size:2 final size:2
Alignment explanation
Indices: 7747--7781 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7737 TGCCTTTCAA
7747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7782 ATCCAACACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8566 original size:319 final size:319
Alignment explanation
Indices: 8020--8599 Score: 715
Period size: 319 Copynumber: 1.8 Consensus size: 319
8010 TTATAAGTAT
* * * * *
8020 ACGATTTCGGCTAATTTTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAAT
1 ACGATTTCGGCTAAATTTGTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTCTAGCGAAAAT
* * * *
8085 AATCATTAAAAAAATATATAATTCGACAAAAAAAATTGAAGGGCTTTTAACGCTTCTAATATCAT
66 AATCAGT-AAAAAATATATAATTCAACAAAAAAAATTGAAAGGCTTTTAACACTTCTAATATCAT
* * * * *
8150 TTTTTCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAAATGCTCGTGAAAAC
130 TTTTCCAATTTTTTCCAAATTAATTTCCAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAAC
* ** *
8215 AAATCATTAATTCCAATGTGGCCAATATTTGGTTAGATGAATAT-ATATATTTCAAGAAGTCTTG
195 AAATCATTAATACCAATGTAACCAAGATTTGGTTAGATGAATATAATATATTTCAAGAAGTCTTG
8279 GCACCAAAAATCATGCAGAACTGAGCCGGGTTCCGAAACACGTTTTTAGCTGAAAACGTC
260 GCACCAAAAATCATGCAGAACTGAGCCGGGTTCCGAAACACGTTTTTAGCTGAAAACGTC
* *
8339 ACGATTTCGGCTAAAATTTGT-CAAAAATTGACTCGAAATAT-TTTCCTCAATTTCTAGCGAAAA
1 ACGATTTCGGCT-AAATTTGTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTCTAGCGAAAA
* ** * * *
8402 TATTC-GT-AAAAATATATAATTCAACTCCAAAAAATTGAAAGTCTTTTACACACTTTTGATATC
65 TAATCAGTAAAAAATATATAATTCAAC-AAAAAAAATTGAAAGGCTTTTA-ACACTTCTAATATC
* * *
8465 GTTTTTCCTATTTTATTTCCAAATTATTTTCCAATTAAATCGAAACAAGATAT-AAATGCTCGTA
128 ATTTTTCC-AATTT-TTTCCAAATTAATTTCCAATTAAATCGAAACAAGAT-TCAAATGCTCGTA
* * ** * *
8529 AAAACAAATCGTTAA-ACACAATTTAACTGAGATTTGGTTAGATGAATATAGATATATTTTAAGG
190 AAAACAAATCATTAATAC-CAATGTAACCAAGATTTGGTTAGATGAATATA-ATATATTTCAAGA
8593 AGTCTTG
253 AGTCTTG
8600 CTGCTGTCAC
Statistics
Matches: 217, Mismatches: 35, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
315 17 0.08
316 18 0.08
317 18 0.08
318 28 0.13
319 111 0.51
320 7 0.03
321 18 0.08
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (319 bp):
ACGATTTCGGCTAAATTTGTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTCTAGCGAAAAT
AATCAGTAAAAAATATATAATTCAACAAAAAAAATTGAAAGGCTTTTAACACTTCTAATATCATT
TTTCCAATTTTTTCCAAATTAATTTCCAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACA
AATCATTAATACCAATGTAACCAAGATTTGGTTAGATGAATATAATATATTTCAAGAAGTCTTGG
CACCAAAAATCATGCAGAACTGAGCCGGGTTCCGAAACACGTTTTTAGCTGAAAACGTC
Found at i:11767 original size:330 final size:327
Alignment explanation
Indices: 10839--12201 Score: 1282
Period size: 330 Copynumber: 4.1 Consensus size: 327
10829 GTAAAAACAA
* * * * * *
10839 TGGCTGGGATTTGGTTAGATGAATATAGATATTTCAAGGAGT-TTTGGCACCATAAATCATACAA
1 TGGCTGAGATTTGATTAGATGAATATAGATATTTC---GAGTCTTAGGCA-TAAAAATCATGCAA
* * * * * *
10903 AACTGAACTGGGCCC-CGGAACGCGTCTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTC
62 AACTGAGC-GAGCCCTC-AAATGCG--TTTTTAGCCAAAAACTGTGATGGTTATTACACGATTTC
* * * *
10967 GGTTAAAATTTTGCAAAAATTAACCCGAAAGATATTTCCTCATTTTTTAGCCACAATGCTCATAA
123 GGTTAAAATTTTGCAAAAATTAACCCGAAAGATATTTCCTCAATTTTTAGCTAAAATACTCATAA
* * * *
11032 AAAATATATAATTCAACGCCAAAAACACTGAA-GGATTTTCACGATTTTAATATCATTTTTCATA
188 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCATTTTTCATA
* * *
11096 TTTTTTCTGAATTAATTTCTAATTAAATTGAAACAAGATTTAGATACTCGTAAAAACAAATCCTT
253 TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTT
*
11161 AAATGCAATG
318 AAATCCAATG
* * * * * **
11171 TGG-TAAGATTTTATTAGATGAATATAGATATTTTAAGGAGTC-TCGGCGTCAAAAATCATGCGG
1 TGGCTGAGATTTGATTAGATGAATATAGATA-TTT--CGAGTCTTAGGCAT-AAAAATCATGCAA
* * * *
11234 AACTGAGCG-GCCCCCGAAATGCGTTTTTAGCTGAAAAAAAAACTGTGATGGTTAGTACACAAAT
62 AACTGAGCGAGCCCTC-AAATGCGTTTTTAGC-----CAAAAACTGTGATGGTTATTACAC-GAT
* * * * * * * *
11298 TT-GGATAAAATTTTGCAAAAAATAACCC-AAATAATTTTTCCACAATTTTTGGATAAAATATTC
120 TTCGGTTAAAATTTTGCAAAAATTAACCCGAAA-GATATTTCCTCAATTTTTAGCTAAAATACTC
* * ** * * *
11361 ATAAAATATATATAATTTAATACCACAAAGATTGGAGGACTTTTCACGCTTTTAATATCATTTTT
184 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCATTTTT
* * *
11426 CATGTTTTTTCTGAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
249 CATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAAT
* *
11491 TCTTAAATCTAACG
314 TCTTAAATCCAATG
* * * *
11505 TGGCTGAGATTTGATTAGATAAATATGGATATCTCGAGTCTTAGCGCATAAAAAGCATGCAAAAC
1 TGGCTGAGATTTGATTAGATGAATATAGATATTTCGAGTCTTAG-GCATAAAAATCATGCAAAAC
* * *
11570 TGAGCCGATG-CCTCATATTGCTTTTTTAGCCAAAAACTGTGATGGTTATTACACGGTTTCGGTT
65 TGAG-CGA-GCCCTCA-AATGCGTTTTTAGCCAAAAACTGTGATGGTTATTACACGATTTCGGTT
* * * * *
11634 AAAAATTTGTAAATATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAA
127 AAAATTTTGCAAAAATTAACCCGAAAGATATTTCCTCAATTTTTAGCTAAAATACTCATAAAAAA
* * * * *
11699 TATATAATTTAACGCCAAAAAGATTGAAGGGCTTTT-ATCG-TCTCTAATATCGTTTTTCTTACT
192 TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCA-CGCT-TTTAATATCATTTTTCATATT
* *
11762 TTTTCTGAATTAATTTTTAATTAAATCGAAACAAGAAACAAGATTTACATGCTCGTAAAAACAAA
255 TTTTCTGAATTAATTTCTAATTAAAT-----C--GAAACAAGATTTAGATGCTCGTAAAAACAAA
11827 -TCTTTAAATCCAATG
313 TTC-TTAAATCCAATG
* * * *
11842 TGGCTGAGATTTGATTAGATGAATATAGATATTTCAAATAGTCTCAGAGTAAAAAAATTCATGCA
1 TGGCTGAGATTTGATTAGATGAATATAGATATTTC---GAGTCTTAG-GCATAAAAA-TCATGCA
* * * *
11907 AAATTGAGTC-AGGTCCTCGGAATGCGTTTTTAGCCAAAATTCTGTGATGGTTAGTTAGTCCACG
61 AAACTGAG-CGA-GCCCTC-AAATGCGTTTTTAGCCAAAA-ACTGTGATGGTTA-TTA---CACG
* * * * *
11971 ATTTCAGCTAAAATTTTGCAAAAATTGACACGAAAGAT-TTCTCCTCAACTTTTAGCTAAAATAC
118 ATTTCGGTTAAAATTTTGCAAAAATTAACCCGAAAGATATT-TCCTCAATTTTTAGCTAAAATAC
* * * * * *
12035 TCAT-GAAAATATATAATTCAACGCCAAAAATATTGGAGAGTTTTTCACGCTTTTAATATCATAT
182 TCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCATTT
* ** *
12099 TTCTTATTTTTT-AAAATTAATATCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAACA
247 TTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT-AAAAACA
12163 AATTCTTAAATCCAATG
311 AATTCTTAAATCCAATG
* *
12180 TTGCTGAGATTTGGTTAGATGA
1 TGGCTGAGATTTGATTAGATGA
12202 TGTAAAGTAT
Statistics
Matches: 842, Mismatches: 140, Indels: 92
0.78 0.13 0.09
Matches are distributed among these distances:
328 8 0.01
329 9 0.01
330 156 0.19
331 50 0.06
332 14 0.02
333 112 0.13
334 110 0.13
335 39 0.05
336 3 0.00
337 92 0.11
338 41 0.05
339 3 0.00
340 16 0.02
341 35 0.04
342 12 0.01
343 3 0.00
344 17 0.02
345 60 0.07
346 62 0.07
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (327 bp):
TGGCTGAGATTTGATTAGATGAATATAGATATTTCGAGTCTTAGGCATAAAAATCATGCAAAACT
GAGCGAGCCCTCAAATGCGTTTTTAGCCAAAAACTGTGATGGTTATTACACGATTTCGGTTAAAA
TTTTGCAAAAATTAACCCGAAAGATATTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATA
TAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCATTTTTCATATTTTTTCT
GAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTAAATCCAA
TG
Found at i:12902 original size:15 final size:16
Alignment explanation
Indices: 12882--12912 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
12872 CAAAGTTCAT
12882 TATATTATAAT-TAAA
1 TATATTATAATCTAAA
12897 TATATTATAATCTAAA
1 TATATTATAATCTAAA
12913 AATAATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TATATTATAATCTAAA
Found at i:23916 original size:333 final size:330
Alignment explanation
Indices: 23246--26174 Score: 2343
Period size: 333 Copynumber: 8.8 Consensus size: 330
23236 ATTGCTTCAA
* * **
23246 TTTTGCATGATTTTTGGCTCCGAGACTACTTGAAATATCTATATTCATCTAATCAAAATCTCAAT
1 TTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATC-AAATCTCAGC
* *
23311 CACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTCATTATAAATTA
65 CACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * * *
23376 ATTTGGAAAAAATA-GGAAAACGATATTAGAAATG-TTCAAAGA-CCTTCAATCTTTTTGGCGTT
130 A-TT-CAAAAAATATGAAAAACGATATTA-AAA-GCGTGAAAAATCCTTCAATATTTTTGGCGTT
* * * * * *
23438 GAATTATGTAT-TTTCTATGAGTATTTTAGCCAAAAATTGAGCAAATATCTTTCGGGTCA-ATTT
191 GAATTATATATATTT-TATGAGTATTTTAGCCAAAAATTAAGGAAAAATCTTTCAGGTCATTTTT
* * ** * *
23501 TACAAAATTTTAGCCGAAATCGAGTAGGTAAT-ACCATCACAATTTTTAGCTAAAAAAGCG-TTC
255 TGCAAAATTTTAGTCGAAATC--GT--GTAATAACCATCACGGTTTTTGGCTAAAAACGCGTTTC
* * *
23564 TGAGGCCTCAGCTCAG
316 -GGGGCCCCGGCTCAG
* * * * * * *
23580 TTTTGTATGATTTTCGGCGCCAAGACTCCTTGAGATATCCATGTTCTTCTAATCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
** *
23645 ACATTGGATTTAAGAATTTGTTTTTAAAAGCATCTGAATCTTGTTTCGATTTAATTGGAAATTAA
66 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * * *
23710 TTCATAAAAATATGAAAAATGATATTAAAAGCATGAAAAATCCTCCAATATTTTTGGCCTTAAAT
131 TTCA-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAATCCTTCAATATTTTTGGCGTTGAAT
* * * * *
23775 TATTTATATTTAATGAGTAATTTATCCAAAAATTAAGGAAAAATTTTTCAGGTCATTTTTTTTGC
195 TATATATATTTTATGAGTATTTTAGCCAAAAATTAAGGAAAAATCTTTCAGGTCA--TTTTTTGC
* * * * *
23840 AAAATTTTAGTCAAAATCGTGTACTAACCATTACGGTTTATGGCTAAAAGCGCGTTTCGGGGGTC
258 AAAATTTTAGTCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGG-C
*
23905 CGACACAGTTTTGCATGAAG
321 C--C-C-G----GC-T-CAG
* * * * * * *
23925 TTTTGCATGATTTTTGGTGCTGACACT-CTTCGAAATATCTATAGTCATCTAATAAAATCTTAGA
1 TTTTGCATGATTTTTGGCGCCGAGACTCCTT-GAAATATCTATATTCATCTAATCAAATCTCAGC
*
23989 CACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
65 CACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * * *
24054 ATTTGGAAAAAATA-GGAAAACGATATTAGAAA-CGTCCAAAGA-CCTTCAATCTTTTTGGCATT
130 A-TT-CAAAAAATATGAAAAACGATATTA-AAAGCGT-GAAAAATCCTTCAATATTTTTGGCGTT
* * * * * *
24116 GAATTATGTAT-TTTCTATGAGTATTTTAGCCAAAAATTGAGCAGATATCTTTCAGGTCAGTTTT
191 GAATTATATATATTT-TATGAGTATTTTAGCCAAAAATTAAGGAAAAATCTTTCAGGTCATTTTT
* * * ** ** *
24180 TACAAAATTTTAGCCGAAATCGAATAGGTAATAGCCATCATAGTTTTTAACTAAAAAAGCGTTAT
255 TGCAAAATTTTAGTCGAAATCG--T--GTAATAACCATCACGGTTTTTGGCTAAAAACGCGTT-T
*
24245 -GGGGCCCCGGCTCCG
315 CGGGGCCCCGGCTCAG
* * * * * * *
24260 TTTTGTATGATTTTCGGCGCCAAGACTCCTTGAGATATCCATGTTCTTCTAATCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
* ** *
24325 ACATCGGATTTAAGAATTTGTTTTTAAAAGCATCTGAATCTTGTTTCGATTTAATTGGAAATTAA
66 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * *
24390 TTCATAAAAATATGAAAAAAGATATTAAAAGCGTGAAAAATCCTCCAATATTTTTGGCCTTAAAT
131 TTCA-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAATCCTTCAATATTTTTGGCGTTGAAT
* * * *
24455 TATTTATATTTAATGAGTATTTTATCCAAAAATTGAGGAAAAAT-TTATCAGGTCATTTATTTTG
195 TATATATATTTTATGAGTATTTTAGCCAAAAATTAAGGAAAAATCTT-TCAGGTCA-TT-TTTTG
* * ** * * * *
24519 CGAAATTTCT-GTCAAAATAATGTACTAACCATTATGGTTTTTGGCTAAAAACGCGTTTCGGGGT
257 CAAAATTT-TAGTCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGC
*
24583 TCCGGCTCAG
321 CCCGGCTCAG
* * * * *
24593 TTTTGCATGATTTTTGGCGCTGACACTTCTTGAAATATCTATATTCATCTAATAAAATCTTAGCC
1 TTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
* * * *
24658 ACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTAA
66 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT-A
* * * * * * * *
24723 ATCTGAAAAAAATTATGAAAATCAATATTAAAAGCATGAAAAACCCTTTAATCA-ATTTGGCATT
130 AT-T-CAAAAAA-TATGAAAAACGATATTAAAAGCGTGAAAAATCCTTCAAT-ATTTTTGGCGTT
* * * * * * *
24787 GAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGAA-GAAATATCTTTCTGGTCAATTTT
191 GAATTATATATATTTTATGAGTATTTTAGCCAAAAATT-AAGGAAAAATCTTTCAGGTCATTTTT
* * * * * * * * * * * *
24851 TGTAAAATTTAAGCCGCAACCGTGTAATAATCATCATGTTTTTTTGACTAAAAACAC-ATTCCGG
255 TGCAAAATTTTAGTCGAAATCGTGTAATAACCATCACG-GTTTTTGGCTAAAAACGCGTTTCGGG
* * *
24915 GACCCGGTTCAA
319 GCCCCGGCTCAG
* * * * * * *
24927 TTTTGAATGATTTTTGGTGCAGAAACTCTTTGAAATATCTATATTCGTCTAACCAAA--T----C
1 TTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
** * *
24986 AC-----A--T--CCA-TTGTTTTTACAAGCATCTGAATCATGTTTC-ATTTTAATTAGAAATTA
66 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGA-TTTAATTAGAAATTA
* * * *
25040 ATTTGGAAAAAATAGGAAAAACGATA-TAATTAGGAGCGTG-AAAAGCCGTTCAATCTTTTTGGC
130 A-TT-CAAAAAATATGAAAAACGATATTAA--A--AGCGTGAAAAATCC-TTCAATATTTTTGGC
* * * ** * * * *
25103 GTTGAATTATATAT-TTTTTTGGAGTATTGTGGCC-AAAATGGAGGAAAAATATTCCTGGTCAAT
188 GTTGAATTATATATATTTTAT-GAGTATTTTAGCCAAAAATTAAGGAAAAATCTTTCAGGTCATT
*
25166 TTTTGCAAAATATTAGT-GAAATCGTG---TAA-CATCAC-------GGC-AAACAACGCG-TTC
252 TTTTGCAAAATTTTAGTCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAA-AACGCGTTTC
*
25217 TGGGGCCCCGGGTCAG
316 -GGGGCCCCGGCTCAG
** * * *
25233 TTTTGCATGATTTTTTACGCCGAGACTTCTTGCAATATCTATTTTCATCTAATCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
* * * *
25298 AAATTGGATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAA
66 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * * * * *
25363 TACGGAAAAGTAGGAAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATATTTTTGGCGTTGAA
131 TTC-AAAAAATATG-AAAAACGATATTAAAAGCGTGAAAAATCCTTCAATATTTTTGGCGTTGAA
* * *
25428 TTATATATATTTTTATGTGTATTTTAACCAAAAATTGAA--AAAATATCTTTCCGGTCAATTTTT
194 TTATATATA-TTTTATGAGTATTTTAGCCAAAAATT-AAGGAAAA-ATCTTTCAGGTC-ATTTTT
* ** * * * **
25491 TGTAAAATTTTAG-CTGAAATCGTGTAATAATTATCACGGTTTTTGGCTAAAAACGAGCTCCAAG
255 TGCAAAATTTTAGTC-GAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGG
*
25555 G-CCCGGGTCAG
319 GCCCCGGCTCAG
* ** * * * *
25566 TTTTGCAAT-ATTTTTGGCACTAAGACTCCTTGAGATATCCATAATCATCTAATCAAATCTCATC
1 TTTTGC-ATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGC
* * * * * * *
25630 CACATTGTATTTAAGGATTTGTTTCTACGAGCATCTGAATCTTATTTCAATTGAATTTGAAATTA
65 CACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * * * *
25695 GTTCATATAAAATATGAAAAACGATATGAAAAACGTGAAAAGTCCTCCAATATTTTTGACGTTAA
130 ATTCA-A-AAAATATGAAAAACGATATTAAAAGCGTGAAAAATCCTTCAATATTTTTGGCGTTGA
* * * ** * *
25760 ATTATATATATTTCATGA-TCACTTTAGCCAAAATTTGAA--AAAAAAATTTCTGGCCA---TTT
193 ATTATATATATTTTATGAGT-ATTTTAGCCAAAAATT-AAGGAAAAATCTTTCAGGTCATTTTTT
** ** * * * * * *
25819 AAAAAAAATTAGTAGAAATCGTATACTAACCATCATGGTTTTTTGCTAAAAATGCGTTTCGGGGC
256 GCAAAATTTTAGTCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGC
*
25884 CCCGGTTCAG
321 CCCGGCTCAG
*
25894 TTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
* * * * *
25959 ACATTGCATTTCAGGATTTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAAAAATTAA
66 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* ** * * **
26024 TTTAGAAAAATATGAAAAACGATATTAAAAGCGTGAAATGTCCTCCAATCTTTTTGAAGTTGAAT
131 TTCA-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAATCCTTCAATATTTTTGGCGTTGAAT
* * * * * ** * *
26089 TATATATATTTTATGAGTATGTTAGACAAAAGTTGAGGAAAAATGTTTTTGGTCAATTTTTACAA
195 TATATATATTTTATGAGTATTTTAGCCAAAAATTAAGGAAAAATCTTTCAGGTCATTTTTTGCAA
* *
26154 AATATTAG-CTGAAATAGTGTA
260 AATTTTAGTC-GAAATCGTGTA
26175 CGTTCTGGGG
Statistics
Matches: 2061, Mismatches: 413, Indels: 245
0.76 0.15 0.09
Matches are distributed among these distances:
304 3 0.00
305 9 0.00
306 56 0.03
308 1 0.00
312 2 0.00
313 5 0.00
314 3 0.00
315 3 0.00
316 11 0.01
317 21 0.01
318 87 0.04
319 75 0.04
320 19 0.01
321 31 0.02
322 69 0.03
323 13 0.01
326 4 0.00
327 136 0.07
328 139 0.07
330 1 0.00
331 33 0.02
332 49 0.02
333 482 0.23
334 184 0.09
335 215 0.10
336 113 0.05
337 23 0.01
338 2 0.00
341 1 0.00
342 1 0.00
343 26 0.01
344 7 0.00
345 189 0.09
346 20 0.01
347 27 0.01
348 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (330 bp):
TTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
TTCAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAATCCTTCAATATTTTTGGCGTTGAATT
ATATATATTTTATGAGTATTTTAGCCAAAAATTAAGGAAAAATCTTTCAGGTCATTTTTTGCAAA
ATTTTAGTCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGG
CTCAG
Found at i:24598 original size:680 final size:664
Alignment explanation
Indices: 23246--26168 Score: 2563
Period size: 680 Copynumber: 4.4 Consensus size: 664
23236 ATTGCTTCAA
* * *
23246 TTTTGCATGATTTTTGGCT-CCGAGACTACTTGAAATATCTATATTCATCTAATCAAAATCTCA-
1 TTTTGCATGATTTTTGG-TGCTGACACT-CTTGAAATATCTATATTCATCTAAT-AAAATCTTAG
* *
23309 ATCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTCATTATAAAT
63 A-CACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* *
23374 TAATTTGGAAAAAATAGGAAAACGATATTAGAAATGTTCAAAGACCTTCAATCTTTTTGGCGTTG
127 TAATTTGGAAAAAATAGGAAAACGATATTAGAAACG-TCAAAGACCTTCAATCTTTTTGGCATTG
* *
23439 AATTATGTATTTTCTATGAGTATTTTAGCCAAAAATTGAGCAAATATCTTTCGGGTCAATTTTAC
191 AATTATGTATTTTCTATGAGTATTTTAGCCAAAAATTGAGCAAATATCTTTCAGGTCATTTTTAC
* * *
23504 AAAATTTTAGCCGAAATCGAGTAGGTAATACCATCACAATTTTTAGCTAAAAAAGCGTTCTGAGG
256 AAAATTTTAGCCGAAATCGAATAGGTAATACCATCACAATTTTTAACTAAAAAAGCGTTATGAGG
*
23569 CCTCAGCTCAGTTTTGTATGATTTTCGGCGCCAAGACTCCTTGAGATATCCATGTTCTTCTAATC
321 CCCCAGCTCAGTTTTGTATGATTTTCGGCGCCAAGACTCCTTGAGATATCCATGTTCTTCTAATC
*
23634 AAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTAAAAGCATCTGAATCTTGTTTCGATTTAA
386 AAATCTCAGCCACATCGGATTTAAGAATTTGTTTTTAAAAGCATCTGAATCTTGTTTCGATTTAA
*
23699 TTGGAAATTAATTCATAAAAATATGAAAAATGATATTAAAAGCATGAAAAATCCTCCAATATTTT
451 TTGGAAATTAATTCATAAAAATATGAAAAAAGATATTAAAAGCATGAAAAATCCTCCAATATTTT
*
23764 TGGCCTTAAATTATTTATATTTAATGAGTAATTTATCCAAAAATTAAGGAAAAATTTTTCAGGTC
516 TGGCCTTAAATTATTTATATTTAATGAGTAATTTATCCAAAAATTAAGGAAAAATTTATCAGGTC
* ** *
23829 ATTTTTTTTGCAAAATTTTAGTCAAAATCGTGTACTAACCATTACGGTTTATGGCTAAAAGCGCG
581 ATTTATTTTGCAAAATTTTAGTCAAAATAATGTACTAACCATTACGGTTTATGGCTAAAAACGCG
23894 TTTCGGGGGTCCGACACAGTTTTGCATGAAG
646 TTTCGGGGGTCCG--AC-----T-C----AG
*
23925 TTTTGCATGATTTTTGGTGCTGACACTCTTCGAAATATCTATAGTCATCTAATAAAATCTTAGAC
1 TTTTGCATGATTTTTGGTGCTGACACTCTT-GAAATATCTATATTCATCTAATAAAATCTTAGAC
*
23990 ACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
65 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
24055 TTTGGAAAAAATAGGAAAACGATATTAGAAACGTCCAAAGACCTTCAATCTTTTTGGCATTGAAT
130 TTTGGAAAAAATAGGAAAACGATATTAGAAACGT-CAAAGACCTTCAATCTTTTTGGCATTGAAT
*
24120 TATGTATTTTCTATGAGTATTTTAGCCAAAAATTGAGCAGATATCTTTCAGGTCAGTTTTTACAA
194 TATGTATTTTCTATGAGTATTTTAGCCAAAAATTGAGCAAATATCTTTCAGGTCA-TTTTTACAA
* * *
24185 AATTTTAGCCGAAATCGAATAGGTAATAGCCATCATAGTTTTTAACTAAAAAAGCGTTATGGGGC
258 AATTTTAGCCGAAATCGAATAGGTAATA-CCATCACAATTTTTAACTAAAAAAGCGTTATGAGGC
* *
24250 CCCGGCTCCGTTTTGTATGATTTTCGGCGCCAAGACTCCTTGAGATATCCATGTTCTTCTAATCA
322 CCCAGCTCAGTTTTGTATGATTTTCGGCGCCAAGACTCCTTGAGATATCCATGTTCTTCTAATCA
24315 AATCTCAGCCACATCGGATTTAAGAATTTGTTTTTAAAAGCATCTGAATCTTGTTTCGATTTAAT
387 AATCTCAGCCACATCGGATTTAAGAATTTGTTTTTAAAAGCATCTGAATCTTGTTTCGATTTAAT
*
24380 TGGAAATTAATTCATAAAAATATGAAAAAAGATATTAAAAGCGTGAAAAATCCTCCAATATTTTT
452 TGGAAATTAATTCATAAAAATATGAAAAAAGATATTAAAAGCATGAAAAATCCTCCAATATTTTT
* *
24445 GGCCTTAAATTATTTATATTTAATGAGTATTTTATCCAAAAATTGAGGAAAAATTTATCAGGTCA
517 GGCCTTAAATTATTTATATTTAATGAGTAATTTATCCAAAAATTAAGGAAAAATTTATCAGGTCA
* * *
24510 TTTATTTTGCGAAATTTCT-GTCAAAATAATGTACTAACCATTATGGTTTTTGGCTAAAAACGCG
582 TTTATTTTGCAAAATTT-TAGTCAAAATAATGTACTAACCATTACGGTTTATGGCTAAAAACGCG
* *
24574 TTTCGGGGTTCCGGCTCAG
646 TTTCGGGGGTCCGACTCAG
* *
24593 TTTTGCATGATTTTTGGCGCTGACACTTCTTGAAATATCTATATTCATCTAATAAAATCTTAGCC
1 TTTTGCATGATTTTTGGTGCTGACAC-TCTTGAAATATCTATATTCATCTAATAAAATCTTAGAC
* * * *
24658 ACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTAA
65 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT-A
* * * * * * * * **
24723 ATCTGAAAAAAATTATGAAAATCAATATTA-AAAGCATGAAAAACCCTTTAATCAATTTGGCATT
129 ATTTGGAAAAAA-TAGGAAAA-CGATATTAGAAA-CGTCAAAGA-CCTTCAATCTTTTTGGCATT
* * * * * *
24787 GAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGAAG-AAATATCTTTCTGGTCAATTTT
190 GAATTATGTATTTTCTATGAGTATTTTAGCCAAAAATTG-AGCAAATATCTTTCAGGTC-ATTTT
** * * * * *** * *
24851 TGTAAAATTTAAGCCGCAACCG--T--GTAATAATCATCATGTTTTTTTGACTAAAAACA-CATT
253 TACAAAATTTTAGCCGAAATCGAATAGGTAAT-ACCATCA-CAATTTTTAACTAAAAA-AGCGTT
** * * * * * * * * * * * * *
24911 CCG-GGACCCGGTTCAATTTTGAATGATTTTTGGTG-CAGAAACTCTTTGAAATATCTATATTCG
315 ATGAGGCCCCAGCTCAGTTTTGTATGATTTTCGGCGCCA-AGACTCCTTGAGATATCCATGTTCT
* * * *
24974 TCTAACCAAA--T----CACATC---------CA-TTGTTTTTACAAGCATCTGAATCATGTTTC
379 TCTAATCAAATCTCAGCCACATCGGATTTAAGAATTTGTTTTTAAAAGCATCTGAATCTTGTTTC
* * * * *
25023 -ATTTTAATTAGAAATTAATTTGGA-AAAAATAGGAAAAACGATA-TAATTAGGAGCGTG-AAAA
444 GA-TTTAATTGGAAATTAA-TT-CATAAAAATATGAAAAAAGATATTAA--A--AGCATGAAAAA
* * * * * * ** ** **
25084 GCCGTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTTTGGAGT-ATTGTGGCC-AAAATGGAG
502 TCC-TCCAATATTTTTGGCCTTAAATTATTTATATTTAAT-GAGTAATT-TATCCAAAAATTAAG
* * * * * * *
25146 GAAAAATATT-CCTGGTCA-AT-TTTTGCAAAATATTAGT-GAAAT--CGT-GTAA-CA-T-C--
564 GAAAAAT-TTATCAGGTCATTTATTTTGCAAAATTTTAGTCAAAATAATGTACTAACCATTACGG
* ** **
25199 ---ACGGC-AAACAACGCG-TTCTGGGGCCCCGGGTCAG
628 TTTATGGCTAAA-AACGCGTTTC-GGGGGTCCGACTCAG
*** * * * * * * *
25233 TTTTGCATGATTTTTTACGCCGAGACTTCTTGCAATATCTATTTTCATCTAATCAAATCTCAGCC
1 TTTTGCATGATTTTTGGTGCTGACAC-TCTTGAAATATCTATATTCATCTAATAAAATCTTAGAC
* * * *
25298 AAATTGGATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAA
65 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
** * * * * * *
25363 TACGG-AAAAGTAGGAAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATATTTTTGGCGTTGA
130 TTTGGAAAAAATAGG--AAAACGATATTAGAAACGTCAAAGA-CCTTCAATCTTTTTGGCATTGA
* * * * ** *
25427 ATTATATATATTTTTATGTGTATTTTAACCAAAAATTGAAAAAATATCTTTCCGGTCAATTTTTT
192 ATTATGTAT-TTTCTATGAGTATTTTAGCCAAAAATTGAGCAAATATCTTTCAGGTC-A-TTTTT
** * ** ** ** * * * ***
25492 GTAAAATTTTAGCTGAAATCG--T--GTAATAATTATCACGGTTTTTGGCTAAAAACGAGCTCCA
254 ACAAAATTTTAGCCGAAATCGAATAGGTAAT-ACCATCACAATTTTTAACTAAAAAAGCGTTATG
* * * * * * ** *
25553 AGG-CCCGGGTCAGTTTTGCAAT-ATTTTTGGCACTAAGACTCCTTGAGATATCCATAATCATCT
318 AGGCCCCAGCTCAGTTTTG-TATGATTTTCGGCGCCAAGACTCCTTGAGATATCCATGTTCTTCT
* * * * * ** * *
25616 AATCAAATCTCATCCACATTGTATTTAAGGATTTGTTTCTACGAGCATCTGAATCTTATTTCAAT
382 AATCAAATCTCAGCCACATCGGATTTAAGAATTTGTTTTTAAAAGCATCTGAATCTTGTTTCGAT
* * * * * * * *
25681 TGAATTTGAAATTAGTTCATATAAAATATGAAAAACGATATGAAAAACGTGAAAAGTCCTCCAAT
447 TTAATTGGAAATTAATTCATA-AAAATATGAAAAAAGATATTAAAAGCATGAAAAATCCTCCAAT
* * * * * * * * *
25746 ATTTTTGACGTTAAATTATATATATTTCATGA-TCACTTTAGCCAAAATTTGAA-AAAAAAATT-
511 ATTTTTGGCCTTAAATTATTTATATTTAATGAGT-AATTTATCCAAAAATT-AAGGAAAAATTTA
* * * ** ** * * * * *
25808 TCTGGCCATTTA-----AAAAAAATTAGT-AGAAATCGTATACTAACCATCATGGTTTTTTGCTA
574 TCAGGTCATTTATTTTGCAAAATTTTAGTCA-AAATAATGTACTAACCATTACGGTTTATGGCTA
* ** **
25867 AAAATGCGTTTCGGGGCCCCGGTTCAG
638 AAAACGCGTTTCGGGGGTCCGACTCAG
* * * * *
25894 TTTTGCATGATTTTTGGCG-TCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGC
1 TTTTGCATGATTTTTGGTGCT-GACACT-CTTGAAATATCTATATTCATCTAATAAAATCTTAGA
* * * * *
25958 CACATTGCATTTCAGGATTTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAAAAATTA
64 CACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * * *
26023 ATTTAG-AAAAATATGAAAAACGATATTA-AAAGCGTGAAATGTCCTCCAATCTTTTT-GAAGTT
129 ATTTGGAAAAAATA-GGAAAACGATATTAGAAA-CGTCAAA-GACCTTCAATCTTTTTGGCA-TT
* * * * * * * **
26085 GAATTATATATATTT-TATGAGTATGTTAGACAAAAGTTGAGGAAAAATGTTTTTGGTCAATTTT
190 GAATTATGTAT-TTTCTATGAGTATTTTAGCCAAAAATTGAGCAAATATCTTTCAGGTC-ATTTT
* *
26149 TACAAAATATTAGCTGAAAT
253 TACAAAATTTTAGCCGAAAT
26169 AGTGTACGTT
Statistics
Matches: 1890, Mismatches: 263, Indels: 203
0.80 0.11 0.09
Matches are distributed among these distances:
637 3 0.00
638 46 0.02
639 121 0.06
640 178 0.09
641 1 0.00
645 5 0.00
646 1 0.00
647 2 0.00
648 3 0.00
649 12 0.01
650 5 0.00
651 52 0.03
652 78 0.04
653 28 0.01
654 41 0.02
655 95 0.05
656 3 0.00
658 21 0.01
659 37 0.02
660 48 0.03
661 150 0.08
662 7 0.00
665 1 0.00
666 2 0.00
667 63 0.03
668 135 0.07
669 17 0.01
670 14 0.01
671 95 0.05
672 4 0.00
673 1 0.00
677 1 0.00
678 190 0.10
679 80 0.04
680 349 0.18
681 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (664 bp):
TTTTGCATGATTTTTGGTGCTGACACTCTTGAAATATCTATATTCATCTAATAAAATCTTAGACA
CATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAAT
TTGGAAAAAATAGGAAAACGATATTAGAAACGTCAAAGACCTTCAATCTTTTTGGCATTGAATTA
TGTATTTTCTATGAGTATTTTAGCCAAAAATTGAGCAAATATCTTTCAGGTCATTTTTACAAAAT
TTTAGCCGAAATCGAATAGGTAATACCATCACAATTTTTAACTAAAAAAGCGTTATGAGGCCCCA
GCTCAGTTTTGTATGATTTTCGGCGCCAAGACTCCTTGAGATATCCATGTTCTTCTAATCAAATC
TCAGCCACATCGGATTTAAGAATTTGTTTTTAAAAGCATCTGAATCTTGTTTCGATTTAATTGGA
AATTAATTCATAAAAATATGAAAAAAGATATTAAAAGCATGAAAAATCCTCCAATATTTTTGGCC
TTAAATTATTTATATTTAATGAGTAATTTATCCAAAAATTAAGGAAAAATTTATCAGGTCATTTA
TTTTGCAAAATTTTAGTCAAAATAATGTACTAACCATTACGGTTTATGGCTAAAAACGCGTTTCG
GGGGTCCGACTCAG
Found at i:26375 original size:963 final size:962
Alignment explanation
Indices: 25212--27131 Score: 2350
Period size: 963 Copynumber: 2.0 Consensus size: 962
25202 GCAAACAACG
** * * *
25212 CGTTCTGGGGCCCCGGGTCAGTTTTGCATGATTTTTTACGCCGAGACTTCTTGCAATATCTATTT
1 CGTTCTGGGGCCCCGGGTCAGCGTTGCATGAATTTTGACGCCGAGACTTCTTGAAATATCTATTT
* * * *** * *
25277 TCATCTAATCAAATCTCAGCCAAATTGGATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGT
66 TCATCGAACCAAATCTCAGCCAAATTGGATTTAAGGATTTAGTAAGACAAGCATCTAAATCATGT
* *
25342 TTCGATTTAATTAGAAATTAATACGGAAAAGTAGGAAAAAACGATATTAGAAGCGTAAAAAACCC
131 TTCGATTTAATTAGAAATTAATACGGAAAAATAGGAAAAAACGATATTAGAAGCATAAAAAACCC
* * * *
25407 TTCAATATTTTTGGCGTTGAATTATATATATTTTTATGTGTATTTTAACCAAAAATTGAAAAAAT
196 TTCAATATTTTTGGCATTGAATTATATA-ACTTTTATGAGTATTGTAACCAAAAATTGAAAAAAT
* * * * * *
25472 ATCTTTCCG-GTCAATTTTTTGTAAAATTTTAGCTGAAATCGTGTAATAATTATCAC-GGTTTTT
260 AACTTT-CGAGTCAA-TTTTTGCAAAATTCTAACCGAAATCGTGTAATAATCATCACAGGTTTTT
* * * * * *
25535 GGCTAAAAACGAGCTCCAAGGCC-CGGGTCAGTTTTGCAAT-ATTTTTGGCACTAAGACTC-CTT
323 GGCTAAAAACGAGCTCCAAGACCTCGGCTAAATTTTGC-ATGATTTTTGGCACCAAAACTCTC-T
* * *
25597 GAGATATCCATAATCATCTAATCAAATCTCATCCACATTGTATTTAAGGATTTGTTTCTACGAGC
386 GAGATATCCATAATCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTCTACGAGC
* * * *
25662 ATCTGAATCTTATTTCAATTGAATTTGAAATTAGTTCATATAAAATATGAAAAACGATATGAAAA
451 ATCCGAATCTTATTTCAATTGAATTAGAAATTAATTCAGA-AAAATATGAAAAACGATATGAAAA
*
25727 ACGTGAAAAGTCC-TCCAATATTTTTGACGTTAAATTATATATATTTCATGA-TCACTTTAGCCA
515 ACGTGAAAAGTCCGT-CAAT-TTTTTGACGTTAAATTATATAAATTTCATGAGT--CTTTAGCCA
* *
25790 AAATTTGAAAAAAAAATTTCT-GG-CCAT-TTAAAAAAAATT-AGTAGAAATCGTATACTAACCA
576 AAAATTGAAAAAAAAATTTCTCGGTCCATATTAAAAAAAATTCAGCAGAAATCGTATAC-AACCA
* * * * * *
25851 TCATGG-TTTTTTGCTAAAAATGCGTTTCGGGGCCCCGGTTCAGTTTTGCATGATTTTTGGCGTC
640 TCACGGCTTTTTGGCTAAAAACGCGTTTCAGGGCCACGGTTCAGTTTTGCATGATTTTTGGAGTC
* *
25915 GAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTCAGGATTTGT
705 GAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAACCACATTG-A-TTAAGGATTTGT
* * *
25980 TTTTACGATCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTAGAAAAATATGAAAAACG
768 TTTTACGAGCATCTGAATCTTATTTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAACG
* *
26045 ATATTAAAAGCGTGAA-ATGTCCTCCAATCTTTTT-GAAGTTGAATTATATATATTTTATGAGTA
833 ATATTAAAAGCATGAAGAT-TCCTCCAATCTTTTTCG-AGTTGAATTATATATACTTTATGAGTA
* * *** * *
26108 T-GTTAGAC-AAAAGTTGAGGAAAAATGTTTTTGGTCAATTTTTACAAAATATTAGCTGAAATAG
896 TCG-T-GACTAAAAATTGAGGAAAAATATTTCACGTCAATTCTTACAAAATATTAGCCGAAATAG
26171 TGTA
959 TGTA
* * *
26175 CGTTCTGGGGCTCCGGTTCAGCGTTGCATGAATTTTGGCGCCGAGAC-TCGTTGAAATATCT-TT
1 CGTTCTGGGGCCCCGGGTCAGCGTTGCATGAATTTTGACGCCGAGACTTC-TTGAAATATCTATT
* * *
26238 ATTCATCGAACCAAATCTCAGCTACATTGGATTTAAGGATTT-GTAAGACAAGCATCTGAATCAT
65 -TTCATCGAACCAAATCTCAGCCAAATTGGATTTAAGGATTTAGTAAGACAAGCATCTAAATCAT
** *
26302 GTTTCGATTTAATTAGAAATTAATTTGGAAAATAATAGG-AAAAACGATATTAGAAGCATGAAAA
129 GTTTCGATTTAATTAGAAATTAATACGG-AAA-AATAGGAAAAAACGATATTAGAAGCATAAAAA
* * * * **
26366 GCCCTTCAATCTTTTTGGCATTGAATTATATAACTTTTATGAGTATTGTAGCTAAAAATTGAGGA
192 ACCCTTCAATATTTTTGGCATTGAATTATATAACTTTTATGAGTATTGTAACCAAAAATTGAAAA
* * **
26431 ATTAACTTTCGAGTCAATTTTTGCAAAATTCTAACCGAAATCGTGTGATAATCATCACAATTTTT
257 AATAACTTTCGAGTCAATTTTTGCAAAATTCTAACCGAAATCGTGTAATAATCATCAC-AGGTTT
* * ** *
26496 TTGGCTAAAAACGCGTTCTGAGACCTCGTCTAAATTTTGCATGATTTTTGGCACCAAAACTCTCT
321 TTGGCTAAAAACGAGCTCCAAGACCTCGGCTAAATTTTGCATGATTTTTGGCACCAAAACTCTCT
* * * *
26561 GAGATATCCATATTCATCTAATCAAATCTCGGCTACATTGGATTTAAGAATTTGTTTTTACGAGC
386 GAGATATCCATAATCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTCTACGAGC
* * * ** * * *
26626 ATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAATTATATTATAAG
451 ATCCGAATCTTATTTCAATTGAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATGAAAAA
* * * * * **
26691 CGTGAAAAGTCCGTCAATTTTTTGGCTTTGAATTATATAAATTTTATGAGTTTTTAGTTAAAAAT
516 CGTGAAAAGTCCGTCAATTTTTTGACGTTAAATTATATAAATTTCATGAGTCTTTAGCCAAAAAT
*** * * * * * * * * *
26756 TGACGGAAAAATTTTTCGGTTCATATTTACAAAATTTCAGCCGAAATCGTGTACCACCATCCCGG
581 TGAAAAAAAAATTTCTCGGTCCATATTAAAAAAAATTCAGCAGAAATCGTATACAACCATCACGG
* *
26821 CTTTTTGGCTAAAAACGCGTTTCAGGGCCACTGTTTAGTTTTGCATGATTTTTGGAGTCGAGACT
646 CTTTTTGGCTAAAAACGCGTTTCAGGGCCACGGTTCAGTTTTGCATGATTTTTGGAGTCGAGACT
*
26886 CCTTGAAATATCTATATTCATCTAATTAAATCTCAACCACATTGATTAAGGATTTGTTTTTACGA
711 CCTTGAAATATCTATATTCATCTAATCAAATCTCAACCACATTGATTAAGGATTTGTTTTTACGA
* * * * * *
26951 GCATTTGAATTTTATTTCGATTTAATTAGAAATTAATTCAGAAAAGTATTAAAAATGATATTAAA
776 GCATCTGAATCTTATTTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAACGATATTAAA
* *
27016 AGCATGAAGATTCCTCCAATCTTTTTCGCGTTGAATTATATATACTTTATGAGTATCGTGGCTAA
841 AGCATGAAGATTCCTCCAATCTTTTTCGAGTTGAATTATATATACTTTATGAGTATCGTGACTAA
*
27081 AAATTGAGGAAAAATATTTCACGTCAATTCTTACAAAATTTTAGCCGAAAT
906 AAATTGAGGAAAAATATTTCACGTCAATTCTTACAAAATATTAGCCGAAAT
27132 CATATACCAA
Statistics
Matches: 808, Mismatches: 128, Indels: 42
0.83 0.13 0.04
Matches are distributed among these distances:
961 59 0.07
962 113 0.14
963 376 0.47
964 147 0.18
965 113 0.14
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (962 bp):
CGTTCTGGGGCCCCGGGTCAGCGTTGCATGAATTTTGACGCCGAGACTTCTTGAAATATCTATTT
TCATCGAACCAAATCTCAGCCAAATTGGATTTAAGGATTTAGTAAGACAAGCATCTAAATCATGT
TTCGATTTAATTAGAAATTAATACGGAAAAATAGGAAAAAACGATATTAGAAGCATAAAAAACCC
TTCAATATTTTTGGCATTGAATTATATAACTTTTATGAGTATTGTAACCAAAAATTGAAAAAATA
ACTTTCGAGTCAATTTTTGCAAAATTCTAACCGAAATCGTGTAATAATCATCACAGGTTTTTGGC
TAAAAACGAGCTCCAAGACCTCGGCTAAATTTTGCATGATTTTTGGCACCAAAACTCTCTGAGAT
ATCCATAATCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTCTACGAGCATCCG
AATCTTATTTCAATTGAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATGAAAAACGTGA
AAAGTCCGTCAATTTTTTGACGTTAAATTATATAAATTTCATGAGTCTTTAGCCAAAAATTGAAA
AAAAAATTTCTCGGTCCATATTAAAAAAAATTCAGCAGAAATCGTATACAACCATCACGGCTTTT
TGGCTAAAAACGCGTTTCAGGGCCACGGTTCAGTTTTGCATGATTTTTGGAGTCGAGACTCCTTG
AAATATCTATATTCATCTAATCAAATCTCAACCACATTGATTAAGGATTTGTTTTTACGAGCATC
TGAATCTTATTTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCAT
GAAGATTCCTCCAATCTTTTTCGAGTTGAATTATATATACTTTATGAGTATCGTGACTAAAAATT
GAGGAAAAATATTTCACGTCAATTCTTACAAAATATTAGCCGAAATAGTGTA
Found at i:27132 original size:329 final size:328
Alignment explanation
Indices: 26198--27132 Score: 996
Period size: 329 Copynumber: 2.8 Consensus size: 328
26188 CGGTTCAGCG
* * * * * *
26198 TTGCATGAATTTTGGCGCCGAGACTCGTTGAAATATCTTTATTCATCGAACCAAATCTCAGCTAC
1 TTGCATGATTTTTGGAGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCTAC
*** * *
26263 ATTGGATTTAAGGATTTG-TAAGACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATT
66 ATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
** * * *
26327 TGGAAAATAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCTTCAATCTTTTTGGCATTGAAT
131 CAGAAAAT-AT--GAAAAATGATATTAAAAGCATGAAAAGTCC-TCAATCTTTTTGGCATTGAAT
* * *
26392 TATATAACTTTTATGAGTATTGTAGCTAAAAATTGAGGAATTAA-CTTTCGAGTCAATTTTTGCA
192 TATATAAC-TTTATGAGTATTGTAGCTAAAAATTGAGGAA-AAATATTTC-AGTCAA-TTTTACA
* * * * ** *
26456 AAATTCTAACCGAAATCGTGTGATAATCATCACAATTTTTTTGGCTAAAAACGCGTTCTGAGACC
253 AAATTTTAGCCGAAATCGTGTGACAACCATCACAAGCTTTTTGGCTAAAAACGCGTTCAGAGACC
26521 TCGTCTAAATT
318 TCGTCTAAATT
* * * * *
26532 TTGCATGATTTTTGGCA-CCAAAACT-CTCTGAGATATCCATATTCATCTAATCAAATCTCGGCT
1 TTGCATGATTTTTGG-AGCCGAGACTCCT-TGAAATATCTATATTCATCTAATCAAATCTCAGCT
* *
26595 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAA
64 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * *
26660 TTCAGAAAAATATGAAAAATTATATTATAAGCGTGAAAAGTCCGTCAAT-TTTTTGGCTTTGAAT
129 TTCAG-AAAATATGAAAAATGATATTAAAAGCATGAAAAGTCC-TCAATCTTTTTGGCATTGAAT
* * * * *
26724 TATATAAATTTTATGAGT-TTTTAGTTAAAAATTGACGGAAAAATTTTTCGGTTC-ATATTTACA
192 TATAT-AACTTTATGAGTATTGTAGCTAAAAATTGA-GGAAAAATATTTCAG-TCAAT-TTTACA
* * ** *
26787 AAATTTCAGCCGAAATCGTGT-ACCACCATC-CCGGCTTTTTGGCTAAAAACGCGTTTCAG-GGC
253 AAATTTTAGCCGAAATCGTGTGACAACCATCACAAGCTTTTTGGCTAAAAACGCG-TTCAGAGAC
* * *
26849 CACTGT-TTAGTT
317 CTC-GTCTAAATT
* * * *
26861 TTGCATGATTTTTGGAGTCGAGACTCCTTGAAATATCTATATTCATCTAATTAAATCTCAACCAC
1 TTGCATGATTTTTGGAGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCTAC
* * *
26926 ATT-GA-TTAAGGATTTGTTTTTACGAGCATTTGAATTTTATTTCGATTTAATTAGAAATTAATT
66 ATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
* * * * *
26989 CAGAAAAGTATTAAAAATGATATTAAAAGCATGAAGATTCCTCCAATCTTTTTCGCGTTGAATTA
131 CAGAAAA-TATGAAAAATGATATTAAAAGCATGAAAAGTCCT-CAATCTTTTTGGCATTGAATTA
* *
27054 TATATACTTTATGAGTATCGTGGCTAAAAATTGAGGAAAAATATTTCACGTCAATTCTTACAAAA
194 TATA-ACTTTATGAGTATTGTAGCTAAAAATTGAGGAAAAATATTTCA-GTCAATT-TTACAAAA
27119 TTTTAGCCGAAATC
256 TTTTAGCCGAAATC
27133 ATATACCAAT
Statistics
Matches: 501, Mismatches: 79, Indels: 47
0.80 0.13 0.07
Matches are distributed among these distances:
326 5 0.01
327 88 0.18
328 46 0.09
329 118 0.24
330 15 0.03
331 42 0.08
332 38 0.08
333 33 0.07
334 68 0.14
335 43 0.09
336 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (328 bp):
TTGCATGATTTTTGGAGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCTAC
ATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
CAGAAAATATGAAAAATGATATTAAAAGCATGAAAAGTCCTCAATCTTTTTGGCATTGAATTATA
TAACTTTATGAGTATTGTAGCTAAAAATTGAGGAAAAATATTTCAGTCAATTTTACAAAATTTTA
GCCGAAATCGTGTGACAACCATCACAAGCTTTTTGGCTAAAAACGCGTTCAGAGACCTCGTCTAA
ATT
Found at i:27415 original size:259 final size:256
Alignment explanation
Indices: 26922--27413 Score: 622
Period size: 259 Copynumber: 1.9 Consensus size: 256
26912 TAAATCTCAA
* **
26922 CCACATTGATTAAGGATTTGTTTTTACGAGCATTTGAATTTTATTTCGATTTAATTAGAAATTAA
1 CCACATTGATTAAGGATTTATTTTTACGAGCATTTGAATCATATTTCGATTTAATTAGAAATTAA
* ** ** *
26987 TTCAGAAAAGTATTAAAAATGATATTAAAAGCATGAAGATTCCTCCAATCTTTTTCGCGTTGAAT
66 TTCAGAAAAATAGGAAAAATGATATTAAAAGCATGAAGAGCCCTCCAATCTTTTTCGCGCTGAAT
27052 TATATATACTTTATGAGTATCGTGGCTAAAAATTGAGGAAAAATATTTCACGTCAATTCTTACAA
131 TATATATA-TTTATGAGTATCGTGGCTAAAAATTGAGGAAAAATATTTCACGTCAATTCTTACAA
27117 AATTTTAGCCGAAATCATATACCAATCACGGTTTTTTTTTCGGCTAAAAACGCGTTCCGAAG
195 AATTTTAGCCGAAATCATATACCAATCACGGTTTTTTTTTCGGCTAAAAACGCGTTCCGAAG
* *
27179 CCACATTGGATTTAAGGATTTATTTTTATGAGCATTTGAATCATGTTTCGATTTAATTA-AATAT
1 CCACATT-GA-TTAAGGATTTATTTTTACGAGCATTTGAATCATATTTCGATTTAATTAGAA-AT
* * * * * *
27243 TAATT-TGAAAAAATAGGGAAAATGATATTAGAAGCGTG-AGAAGCCCTTCAATCTTTTTGGCGC
63 TAATTCAG-AAAAATAGGAAAAATGATATTAAAAGCATGAAG-AGCCCTCCAATCTTTTTCGCGC
* *
27306 TGAATTATATAT-TTTAATGAGTATTGTGGCTAAAAATTGA-GAAAAATATTTCGA-GTCACTT-
126 TGAATTATATATATTT-ATGAGTATCGTGGCTAAAAATTGAGGAAAAATATTTC-ACGTCAATTC
* * * * *
27367 TCTGCAAAATTTTAGCTGAAATCTTGTACC-ATCATGGTATTTTTTTT
189 T-TACAAAATTTTAGCCGAAATCATATACCAATCACGGT-TTTTTTTT
27414 TTTTTTTGCT
Statistics
Matches: 202, Mismatches: 24, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
256 8 0.04
257 60 0.30
258 31 0.15
259 103 0.51
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Consensus pattern (256 bp):
CCACATTGATTAAGGATTTATTTTTACGAGCATTTGAATCATATTTCGATTTAATTAGAAATTAA
TTCAGAAAAATAGGAAAAATGATATTAAAAGCATGAAGAGCCCTCCAATCTTTTTCGCGCTGAAT
TATATATATTTATGAGTATCGTGGCTAAAAATTGAGGAAAAATATTTCACGTCAATTCTTACAAA
ATTTTAGCCGAAATCATATACCAATCACGGTTTTTTTTTCGGCTAAAAACGCGTTCCGAAG
Found at i:28066 original size:331 final size:328
Alignment explanation
Indices: 27451--28282 Score: 843
Period size: 330 Copynumber: 2.5 Consensus size: 328
27441 CCCTATGTCA
* * * * *
27451 GTTTTGCATGATTTCTGGCACCAAGACTCCTTAAAATATATTTATATTCATCTAACCAAATCTCA
1 GTTTTGAATGATTTTTAGCGCCAAGACTCCTT-GAATATATTTATATTCATCTAACCAAATCTCA
* ** * * * *
27516 GCCACATTGTATTTAAGGATTTGTTTTTACGAGTTTCTAAATTTTGTTTTGATTTAATCAGAAAT
65 GCCACATTG-ATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * * * *
27581 TAATTTGGAAATAAAATAGGAAAAACAATATTAGAAGCCTGAAAAAAAAACTTTCAATTTTTTGG
129 TAATTCGG-AA-AAAATATGAAAAACAATATTAGAA-AC-GTAAAAAAAACTTTCAATTTTTTGA
* * * * * * * **
27646 TGTTGAATTATATATTTGTTATGATTATTTTTGCTCGAAATCGAGGAAAAATATTTTAGGTCAAT
190 TGTCGAATTATATATTTGTTATAAGTATTATAGCTCGAAATCGAGGAAAAATATCTCAGACCAAT
*
27711 TTTTGCAAAATTTTAGCCGAAATCGTATACTAATCATCACAGTTTTCGGCTAAATACGCGTTATG
255 TTTTGCAAAATTTTAGCCGAAATCGTATA-T-AT-ATCACAGTTTTCGGCTAAAAACGCG-T-TG
27776 C-GGCC-C-TGCTCAT
315 CAGGCCACGT-CTC-T
* *
27789 -TTTTGAATGATTTTTAGTGCCAAGACTCCTTGAA-ATATCTATATTCATCTAACCAAATCTCAG
1 GTTTTGAATGATTTTTAGCGCCAAGACTCCTTGAATATATTTATATTCATCTAACCAAATCTCAG
* * * *
27852 CTACATTAGATTCAAAGATTTGTTTTTACGAGCATCTGAATCTTGTCTCGATTTAATTAGAAGTT
66 CCACATT-GATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * **
27917 AATCCGGAAAAAATATGAAAAACAATATTAGAAACGTTAAAATCAC-TTCAATCTTTTTGATGTC
130 AATTCGGAAAAAATATGAAAAACAATATTAGAAACGTAAAAAAAACTTTCAAT-TTTTTGATGTC
* * * *
27981 GAATTATATATTTTTTATAAGTATTATAGC-CATAAATTGAGGAAATATATCTCAGACCAATTTT
194 GAATTATATATTTGTTATAAGTATTATAGCTC-GAAATCGAGGAAAAATATCTCAGACCAATTTT
* * * **** * * *
28045 TGCAAAATTTTAGCCGAAATCGTGTATGTTTCGGTTTTTTTGGTTAAAAATGCGTTGCAGGGCCA
258 TGCAAAATTTTAGCCGAAATCGTATATATATCACAGTTTTCGGCTAAAAACGCGTTGCA-GGCCA
*
28110 CGTTTCT
322 CGTCTCT
* * * * * * *
28117 GTTTTGCATGATTTTTAGCGCCAAGACTCCTTGAATTTTTTTTTATTTATCTAATCAAATCTTAG
1 GTTTTGAATGATTTTTAGCGCCAAGACTCCTTGAATATATTTATATTCATCTAACCAAATCTCAG
* * * *
28182 CCACATTGGATTTAAAGATTTCTTTTTATGTGCATCTGAATCTTGTTTCGATTTAACTAGAAATT
66 CCACATT-GATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* ** *
28247 AATTCAG-AAAAATATGAAAAATGATATTAAAAACGT
130 AATTCGGAAAAAATATGAAAAACAATATTAGAAACGT
28283 GAAATTAAAA
Statistics
Matches: 410, Mismatches: 75, Indels: 27
0.80 0.15 0.05
Matches are distributed among these distances:
326 3 0.01
327 1 0.00
328 21 0.05
329 62 0.15
330 92 0.22
331 91 0.22
332 1 0.00
333 23 0.06
334 2 0.00
335 85 0.21
336 3 0.01
337 26 0.06
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (328 bp):
GTTTTGAATGATTTTTAGCGCCAAGACTCCTTGAATATATTTATATTCATCTAACCAAATCTCAG
CCACATTGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
ATTCGGAAAAAATATGAAAAACAATATTAGAAACGTAAAAAAAACTTTCAATTTTTTGATGTCGA
ATTATATATTTGTTATAAGTATTATAGCTCGAAATCGAGGAAAAATATCTCAGACCAATTTTTGC
AAAATTTTAGCCGAAATCGTATATATATCACAGTTTTCGGCTAAAAACGCGTTGCAGGCCACGTC
TCT
Found at i:37323 original size:2 final size:2
Alignment explanation
Indices: 37316--37401 Score: 93
Period size: 2 Copynumber: 42.5 Consensus size: 2
37306 TATTATTATG
* * * *
37316 AT AT AT AT AT AT AT AT AT AT AT AT AT CT TT A- AT CT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
37357 AT AT CT AT AT AT CT AT ACT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT
37401 A
1 A
37402 AAAGTACAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
1 1 0.01
2 65 0.93
3 4 0.06
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37359 original size:19 final size:20
Alignment explanation
Indices: 37317--37398 Score: 89
Period size: 19 Copynumber: 4.2 Consensus size: 20
37307 ATTATTATGA
* * *
37317 TATATATATATATATATATA
1 TATATCTATATATCTATATC
*
37337 TATATCTTTA-ATCTATATC
1 TATATCTATATATCTATATC
37356 TATATCTATATATCTATA-C
1 TATATCTATATATCTATATC
* *
37375 TATATATATATATATATA-C
1 TATATCTATATATCTATATC
37394 TATAT
1 TATAT
37399 ATAAAAGTAC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 39 0.72
20 15 0.28
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATCTATATATCTATATC
Found at i:37489 original size:30 final size:31
Alignment explanation
Indices: 37430--37494 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
37420 AATTTTATGT
* *
37430 TTTCCGATTGTACCCTTATTTTTAAAATATA
1 TTTCCAATTGTACCCTTATTTTAAAAATATA
37461 TTTCCAATTGTACCCTT-TTTTAAAAATATA
1 TTTCCAATTGTACCCTTATTTTAAAAATATA
37491 TTTC
1 TTTC
37495 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTAAAAATATA
Found at i:37501 original size:31 final size:31
Alignment explanation
Indices: 37436--37501 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
37426 ATGTTTTCCG
* *
37436 ATTGTACCCTTATTTTTAAAATATATTTCCA
1 ATTGTACCCTTATTTTAAAAATATATTTCAA
37467 ATTGTACCCTT-TTTTAAAAATATATTTCTAA
1 ATTGTACCCTTATTTTAAAAATATATTTC-AA
37498 ATTG
1 ATTG
37502 CCATTACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (31 bp):
ATTGTACCCTTATTTTAAAAATATATTTCAA
Found at i:37568 original size:15 final size:15
Alignment explanation
Indices: 37520--37581 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
37510 AAATAATATT
*
37520 TTAATTATTCCATTA
1 TTAATTATTCAATTA
*
37535 TT--TT-TT-AATCA
1 TTAATTATTCAATTA
*
37546 TAAATTATTCAATTA
1 TTAATTATTCAATTA
*
37561 TTAATTATTAAATTA
1 TTAATTATTCAATTA
37576 TATAAT
1 T-TAAT
37582 ACGTATATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
11 4 0.11
12 2 0.06
13 4 0.11
14 2 0.06
15 20 0.56
16 4 0.11
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATTATTCAATTA
Done.