Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013371.1 Corchorus capsularis cultivar CVL-1 contig13392, 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: 55978
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:11372 original size:29 final size:29
Alignment explanation
Indices: 11329--11399 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
11319 CTGAGTGCGT
* * *
11329 AAAATGTTCCAAAATTGAAATTCCGGGTAC
1 AAAATG-TCCAAAATTGAAATTCAGAGAAC
* *
11359 AAAATGTCCAAAATTGAAGTTCATAGAAC
1 AAAATGTCCAAAATTGAAATTCAGAGAAC
11388 AAAATGTCCAAA
1 AAAATGTCCAAA
11400 CGTTACGAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 30 0.83
30 6 0.17
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.24
Consensus pattern (29 bp):
AAAATGTCCAAAATTGAAATTCAGAGAAC
Found at i:12616 original size:24 final size:26
Alignment explanation
Indices: 12575--12630 Score: 89
Period size: 24 Copynumber: 2.2 Consensus size: 26
12565 TACATGTACC
12575 AAAATATAAGAAATTTTTTGAACAAA
1 AAAATATAAGAAATTTTTTGAACAAA
*
12601 AAAATATAAG-AATTTTTT-ACCAAA
1 AAAATATAAGAAATTTTTTGAACAAA
12625 AAAATA
1 AAAATA
12631 ACAATTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 11 0.38
25 8 0.28
26 10 0.34
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (26 bp):
AAAATATAAGAAATTTTTTGAACAAA
Found at i:12922 original size:3 final size:3
Alignment explanation
Indices: 12914--12946 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
12904 AACTTGCTCC
12914 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
12947 ATATTAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
GTT
Found at i:18576 original size:322 final size:320
Alignment explanation
Indices: 15917--19295 Score: 2963
Period size: 322 Copynumber: 10.5 Consensus size: 320
15907 GAATAATGTT
* * * * * * * *
15917 TTAATTCAG-AAAAAATAGGGAAAACGATATTATAAGCTTGAAAAACCCTTCAATTTTTCTTTTG
1 TTAATTTAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAA--TAT-TTTTA
* ** ** **
15981 GCATTGAATTATATA-TTTTTATGTGTATTGTGTATAAAAATTGAGGAAAAATCTTTCGAATCAA
63 GCGTTGAATTATATATTTTTTATGAATATTGTGGCTAAAAATT-AGGAAAAATCTTTCGGGTCAA
* * * * * *
16045 TTTTTACCGAAAATCGTG---T----T-ACGATTTTTGGCTACAAACGCGTTACAGGGCACTGAC
127 TTTTTGCCG-AAATCGTGTACTAACATCACGATTTTTGGCTAAAAACGCGTTCCGGGGCCCCGAC
* * *
16102 TTAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATGTAACAAAATCTT
191 TTAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCTAACAAAATCTC
* * * *
16167 AGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATTTGAATCATGTTTCGGTTCAATCAGAAA
256 AGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAGAAA
** * * * * * *
16232 TT-ATTTCTAAAAAAATAGGAAAAAGAATATTAGAAGCGTGAAGAGGCCTTCAGT-CTTTTCGAC
1 TTAATTTAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTAG-C
* * * * *
16295 GTTGAATTATATTTTTTTTGTGAATATTGTGGCTAAAAATTTAGGAAAAATCCTTAGGGTCAGTT
65 GTTGAATTATATATTTTTTATGAATATTGTGGCTAAAAA-TTAGGAAAAATCTTTCGGGTCAATT
* * * * * **
16360 TTTGCCAAAATCGTGTA-T-CCATCACCG-TTTTTAGCTAAAAATGTGTTCCATGGCCCCGACTT
129 TTTGCCGAAATCGTGTACTAACATCA-CGATTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTT
* * * * * *
16422 AGTTCTGCATAATTTTTGGCGCCAAGAATTATTGAAATTTCTATATTCATCTAACCAAATCTCAG
193 AGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCTAACAAAATCTCAG
* * *
16487 TCACGA-TGGATTTAAGGATATTTTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAA
258 CCAC-ATTGGATTTAAGGAT-TTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAGAAA
* * * * * * **
16551 TTAATTCAGAATAAAATAGGAAAAACGACATTAGAAGCATGAAAAGCCCTTCAATATTTTTGGTA
1 TTAATTTAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTAGCG
* * * * * * * *
16616 TTGACTCAT-TTTTTTTTATTATTATTGTGGCTAAAATTTGAGGAAAAATCTTTTGCGTCAATTT
66 TTGAATTATATATTTTTTATGAATATTGTGGCTAAAAATT-AGGAAAAATCTTTCGGGTCAATTT
* ** ** *
16680 TTGCCGAAATTGTGTACTAACCATCACGGGTTTTGGCTAAAAACTTGTTCC-GGGCCCCGGCTTA
130 TTGCCGAAATCGTGTACTAA-CATCACGATTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTTA
* * * * * *
16744 GTTTTGCATGATTTTTGACGTCAAGACTCATTGAAATATCTATAATCATCTAAGAAAATATCAGA
194 GTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCTAACAAAATCTCAGC
* * * **
16809 AACATTGAATTTAAGGATTT-TTTTCTATGAGCATCAAAATCATGTTTCGATTTAATCAGAAA
259 CACATTGGATTTAAGGATTTGTTTT-TACGAGCATCTGAATCATGTTTCGATTTAATCAGAAA
** * * * * * * *
16871 TTAATTCGGAAATAAATAGGAAAATCGATATTACAAGCGTGAAAAACCCTTCAATTTTTTTTGCG
1 TTAATTTAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTAGCG
* * * * ** *
16936 TTGAAATATAGATTTTTTATGATTATTGTGTCTAAAAATTGAGGAAAAATCTTTCACGTCATTTT
66 TTGAATTATATATTTTTTATGAATATTGTGGCTAAAAATT-AGGAAAAATCTTTCGGGTCAATTT
* * * * * *
17001 TTGCCGATATCACGGTTATTGTGTCCAAGTGATTTTTTGCCGATATCATGGTTTTTGGTTAAAAA
130 TTGCCG--A--A-----ATCGTGT---ACT-A----------ACATCACGATTTTTGGCTAAAAA
* * ***
17066 CGCGTTCCGGGGCCCCGGACTTAATTTTGCATGATTTTTTGCGCCAAGAAC-CAACCAAATATCT
172 CGCGTTCCGGGGCCCC-GACTTAGTTTTGCATGATTTTTGGCGCCAAG-ACTCATTGAAATATCT
* * * * * ** *
17130 ATATTCAT-TGAATAGAATCTCAGCAACATTGGATGTAAGAATTTGTTTTTATAAGCATTTGAAT
235 ATATTCATCT-AACAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
*
17194 CATGCTTCGATTTAATCAGAAA
299 CATGTTTCGATTTAATCAGAAA
* * * * * *
17216 TTAATTCA-CAAAAAATAGGAAAAACGATATCAGAAGCATGAAAAGCCTTTCAAT-TTTTTCAGC
1 TTAATTTAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTT-AGC
** *
17279 GTTGAATTATATATTTTTTATG---A--GTGATTAAAAATTGAGGAAAAATCTTTCGGGTTAATT
65 GTTGAATTATATATTTTTTATGAATATTGTGGCTAAAAATT-AGGAAAAATCTTTCGGGTCAATT
* * * ** * * *
17339 TTTGCCGAAATCGTATAC-AACA--AGGTTTTTTTTACTAAAAACGCGTCCCGGGGACTCAGA-T
129 TTTGCCGAAATCGTGTACTAACATCACG-ATTTTTGGCTAAAAACGCGTTCCGGGG-CCCCGACT
* ** * *
17400 TAGTTTAGCATGATTTTTAACGCGAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCA
192 TAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCTAACAAAATCTCA
* *
17465 GGCACATTGGATTTAAGGATTT-TTTTTACGAGAATCTGAATCATGTTTCGATTTAATCAGAAA
257 GCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAGAAA
* **
17528 TTAA-TTAGGAAAAAAA-AAGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGC
1 TTAATTTA-GAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTAGC
* * * *
17591 ATTAAATTATATAGCTTTTT-TGAGTATTGTGGCTAAAAATTGAGGAAAAATCTTTCGGGTCAAT
65 GTTGAATTATATA-TTTTTTATGAATATTGTGGCTAAAAATT-AGGAAAAATCTTTCGGGTCAAT
** * * * * * * *
17655 AGTCGCCGAAATCGTG---T-ACATCACGGTTCTTGGGTAAAAACACGTTCCGAGGCCCTGACTT
128 TTTTGCCGAAATCGTGTACTAACATCACGATTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTT
* * * * * *
17716 ATTTTTGAATGATTTTTGGCACCAAAACTCATTGAAATATCTATATTCATCAAACAAAATCTTAG
193 AGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCTAACAAAATCTCAG
* * * * * *
17781 CCACGTTGGATATAAGGATATTTTTTTTTACGAGCATCTAAATTATGTTTCGATTTAATCAAAAA
258 CCACATTGGATTTAAGG--ATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAGAAA
* * * * * * ** *
17846 TTAATTCAGAATAAAATAGGGAAAACGATATTAGAAGCGTGATAAGCCCTTCAGTATTTTCGGCA
1 TTAATTTAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTAGCG
* * *
17911 TTGAATTATATATTTTTTATGAGTATTGTGGCTATAAATTAGGGAAAAATCTTTTGGGTCAATTT
66 TTGAATTATATATTTTTTATGAATATTGTGGCTAAAAATTA-GGAAAAATCTTTCGGGTCAATTT
* * * *
17976 TTGCCG--A-C----A-T--CAT---GGTTTTTGGCTAAAAACGCATTCCTGGACCCC-AGCTTA
130 TTGCCGAAATCGTGTACTAACATCACGATTTTTGGCTAAAAACGCGTTCCGGGGCCCCGA-CTTA
** * * * *
18027 GTTTCACATGATTTTTGACGCCAAGACTCATTGATATATCTATATTCATCTACCAAAATATCAGC
194 GTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCTAACAAAATCTCAGC
* * * * * *
18092 GACATTGGATTTAAGGATTTATTTTTGCGAGCATGTGAATAATGTTTCGGTTTAATCAGAAA
259 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAGAAA
* * *
18154 TTAATTTAGATAAAAACAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTT-GAC
1 TTAATTTAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTAG-C
* * *
18218 GTTGAATTATATGTTTTTTATGAGTATTGTGGCTAAAAATTAAGAATAAATCTTTCGGGTCAATT
65 GTTGAATTATATATTTTTTATGAATATTGTGGCTAAAAATTAGGAA-AAATCTTTCGGGTCAATT
* *
18283 TTTGCCGAAATCGTGTACTAACTATCATGATTTTTGGCTAAAAACGCGTTCCGGAAG-CCCGACT
129 TTTGCCGAAATCGTGTACTAAC-ATCACGATTTTTGGCTAAAAACGCGTTCCGG-GGCCCCGACT
* * * *
18347 TAGTTTTGCATGATTTTTTGCGTCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCACA
192 TAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCTAACAAAATCTCA
* * * * *
18412 ACCACATTGGATTTAAGGATTTGATTTCACGAGCATCTAAATCATGTTTCAGA-TTAATCAGAAT
257 GCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTC-GATTTAATCAGAAA
* * * * *
18476 TTATTTTAGAAAAAAAATAGTAAAAA-AATATTCGAAGCGTGAAAAACCCTTCAATCTTTTTAGC
1 TTAATTTAG-AAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTAGC
* * * *
18540 GTTGAATTATATATTATATATGAATATTATGGCTAAAAATTTAGGAAAAATCCTTCGGGTCAATT
65 GTTGAATTATATATTTTTTATGAATATTGTGGCTAAAAA-TTAGGAAAAATCTTTCGGGTCAATT
* *
18605 TTTGCCGAAATCGTATTTTTGT-CTAAAAAATCACACGATTTTTGGCTAAAAACGCGTTTCGGGG
129 TTTGCCGAAATCG------TGTACT--AACAT--CACGATTTTTGGCTAAAAACGCGTTCCGGGG
** *** * * * *
18669 TACC-AGCTTAGTTTTATTTTATTTTTGGCGCCAAGACTCGTTGAATTATCTATATTCATCTAAA
184 CCCCGA-CTTAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCTAAC
* * *
18733 AAAATCTCTGTCACATTGGATTTAAGGATTTGTTTTTGCGAGCATCTGAATCATGTTTCGATTTA
248 AAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTA
18798 ATCAGAAA
313 ATCAGAAA
* * *
18806 TTAATTTAGGAAAAAAATAGGAAAAACAATATTAGAAGCATGAAAAGCTCTTCAATTTTTTTAGG
1 TTAATTTA-GAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTA-G
* * * * *
18871 TGTTGAATTATATATTATTTATGAGTATTGTAGCTAAAAATCGAGGAAAAATCTTTCGGGTCAAT
64 CGTTGAATTATATATTTTTTATGAATATTGTGGCTAAAAAT-TAGGAAAAATCTTTCGGGTCAAT
* * * * *
18936 TTTTGCAGAAATCGTGTAC-ACCATCAC-AGTTTTTTGCTAAAAACGCATTTCGGGGCCCCAGA-
128 TTTTGCCGAAATCGTGTACTAACATCACGA-TTTTTGGCTAAAAACGCGTTCCGGGGCCCC-GAC
* * * * * *
18998 TTAGTTTAGCATGATTTATATAGCACCATGTA-T-ATAT-ATATATATATATTCATCTAACAAAA
191 TTAGTTTTGCATGATTT-T-TGGCGCCAAG-ACTCAT-TGAAATATCTATATTCATCTAACAAAA
* * * * *
19060 TCTTAGTCACTTTGGATTTAAGGATTTGTTTATACGAACATCTGAATCATGCTTT-GATTTAATC
252 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATG-TTTCGATTTAATC
**
19124 AGAGT
316 AGAAA
* * ** * *
19129 TTAATTCAGAATAAAATAGGAAAAATGATATTAGAAGCGTGAAAAGCCATTAAATA-TTTTAGGC
1 TTAATTTAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTA-GC
* * * * *
19193 ATTGACTTATATATTTTTTATG-ATAATTGTGGCTAAAACTTAGGTAAAACTCTTTTGGGTCAAT
65 GTTGAATTATATATTTTTTATGAAT-ATTGTGGCTAAAAATTAGG-AAAAATCTTTCGGGTCAAT
* *
19257 TTTTGCCGAAATCGTGTACTAATCACCACGGTTTTTGGC
128 TTTTGCCGAAATCGTGTACTAA-CATCACGATTTTTGGC
19296 GAGCATCTGA
Statistics
Matches: 2492, Mismatches: 441, Indels: 254
0.78 0.14 0.08
Matches are distributed among these distances:
307 4 0.00
308 154 0.06
309 1 0.00
310 95 0.04
311 8 0.00
312 110 0.04
313 132 0.05
314 39 0.02
315 132 0.05
316 4 0.00
317 51 0.02
318 157 0.06
319 208 0.08
320 148 0.06
321 213 0.09
322 345 0.14
323 122 0.05
324 16 0.01
325 3 0.00
326 3 0.00
327 4 0.00
328 5 0.00
329 6 0.00
330 172 0.07
331 33 0.01
332 70 0.03
333 2 0.00
334 1 0.00
335 1 0.00
337 1 0.00
339 38 0.02
341 1 0.00
343 29 0.01
344 69 0.03
345 109 0.04
346 6 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (320 bp):
TTAATTTAGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTAGCG
TTGAATTATATATTTTTTATGAATATTGTGGCTAAAAATTAGGAAAAATCTTTCGGGTCAATTTT
TGCCGAAATCGTGTACTAACATCACGATTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTTAGT
TTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCTAACAAAATCTCAGCCA
CATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAGAAA
Found at i:20329 original size:324 final size:315
Alignment explanation
Indices: 19583--20417 Score: 902
Period size: 324 Copynumber: 2.6 Consensus size: 315
19573 CCGCCACGTT
* * *
19583 TGAATTCATGTTTCGGATTAATCAAAAATTAATTTAGAAAAAAAAATAGAAAAACGATATTTGAA
1 TGAA-TCATGTTTCGGTTTAATCAAAAATT-ATTT--CAAAAAAAATAGAAAAA--ATATTAGAA
* *
19648 GCA-TGAAAATCCCTTCAATTTTTT-GGCATTGAATTATATATTATTTATGAGTATTGTGGCTAA
60 G-AGTGAAAAACCCTTCAATTTTTTCGGCATTGAATTATATATTTTTTATGAGTATTGTGGCTAA
* * *
19711 AAATAGAGGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTACTAACCATCACAGTTTTTT
124 AAATTGA-GAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTG
* * * *
19776 GCGAAAAACGCGTTCCGGAGCCCTAGATTAGTGTAGAATGACTTTTAGCGCCAAATCTTTGAAAT
188 GCAAAAAACGCATTCCGGAGCCCCAGATTAGTGTAGAATGACTTTTAGCGCCAAATCATTGAAAT
* * * * *
19841 ATTTATATTCATATAAACAGATCTCAGCTACATTGGATTTAAGTATTTGTTTTTACAAGCATC
253 ATCTATATTCATATAAACAAATCTCAGCCACATTGGATTTAAGGATGTGTTTTTACAAGCATC
* * ** * * * *
19904 TAAATCATGTTCCAATTTAATCAAAAATTAATTCAGAATAAATAAGGAAAAACAATATTAGAAGC
1 TGAATCATGTTTCGGTTTAATCAAAAATTATTTCAAAAAAAAT-A-G-AAAA-AATATTAGAAGA
* * * * * *
19969 GTCAAAAGCCCTTCAATATTTTCGGTATTGAATTATATATTTTTTATGAGTATCGTAGCTAAAAA
62 GTGAAAAACCCTTCAATTTTTTCGGCATTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAA
* * *
20034 TTGCAGAAAAATCTTTCGAGTCAATTTTTTGCCGAAATCATGTACTAATTCATCACGGTTTTTGG
127 TTG-AGAAAAATCTTTCGGGTCAA-TTTTTGCCGAAATCGTGTACTAA-CCATCACGGTTTTTGG
* * * * * * * *
20099 CAAAAAATGCATTCC-GAGGCCCCGGCTTAGTTTTGTATGATTTTTTGCGCCAAGACTCATTGAA
189 CAAAAAACGCATTCCGGA-GCCCCAGATTAGTGTAGAATGACTTTTAGCGCCAA-A-TCATTGAA
* * * * **
20163 ATATCTATATTTATCTAACCAAATCTCCGCCACATTGGATTTAAGGATGTGTTTTTATGAGCATC
251 ATATCTATATTCATATAAACAAATCTCAGCCACATTGGATTTAAGGATGTGTTTTTACAAGCATC
* *
20228 TGAATCATGTTTCGGTTTAATGAGAAATTATTTCATAAAAAAATAGTAAGAAAATATTAGAAGAG
1 TGAATCATGTTTCGGTTTAATCAAAAATTATTTCA-AAAAAAATAG-AA-AAAATATTAGAAGAG
* * * * *
20293 TGAAAAACCCTTTAATCTTTTTCAGCGTTGAATTATATATTTTCTATGAGTATTTTGGCTAAAAA
63 TGAAAAACCCTTCAAT-TTTTTCGGCATTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAA
* * * * *
20358 TTAGGGAAAAATCTTTTGGGTCAATTTTTGCCAAAATCGTATACTAACCATCATGGTTTT
127 TT-GAGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTACTAACCATCACGGTTTT
20418 GACGTGTATC
Statistics
Matches: 421, Mismatches: 77, Indels: 31
0.80 0.15 0.06
Matches are distributed among these distances:
317 7 0.02
318 1 0.00
319 31 0.07
320 83 0.20
321 29 0.07
322 63 0.15
323 49 0.12
324 151 0.36
325 7 0.02
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (315 bp):
TGAATCATGTTTCGGTTTAATCAAAAATTATTTCAAAAAAAATAGAAAAAATATTAGAAGAGTGA
AAAACCCTTCAATTTTTTCGGCATTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGA
GAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAA
CGCATTCCGGAGCCCCAGATTAGTGTAGAATGACTTTTAGCGCCAAATCATTGAAATATCTATAT
TCATATAAACAAATCTCAGCCACATTGGATTTAAGGATGTGTTTTTACAAGCATC
Found at i:21315 original size:2 final size:2
Alignment explanation
Indices: 21308--21333 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21298 ACTCATTGAA
21308 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
21334 TCATCTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21701 original size:181 final size:180
Alignment explanation
Indices: 21402--21739 Score: 475
Period size: 181 Copynumber: 1.9 Consensus size: 180
21392 ATATCATATT
* * * * *
21402 TCGATTTAATCAGAATTTAATTCAGAATATAAAAAGAAAAACGATATTAGAAACGTGAAAATCCA
1 TCGATTTAATCAGAAATTAATTCAAAATAAAAAAAGAAAAACGATATTAGAAACATGAAAAGCCA
* * *
21467 TTAAATATTTTCGGCATTGACTTATATATTTTTTATGAGAATTGTGGCTAAAAATTTG-GGAAAA
66 TTAAATATTTTCGGAATTGAATTATATACTTTTTATGAGAATTGTGGCTAAAAA-TTGAGGAAAA
*
21531 ATCTTTTGGGTCAATTTTTGCCGAAATCATGACGAGCATCTGAATCGTGTA
130 ATCTTTAGGGTCAATTTTTGCCGAAATCATGACGAGCATCTGAATCGTGTA
* *
21582 TCGATTTAATCAGAAATTAATTCAAAATAAAAAAAAGGAAAATGATATTA-AAAGCATGAAAAG-
1 TCGATTTAATCAGAAATTAATTCAAAAT-AAAAAAAGAAAAACGATATTAGAAA-CATGAAAAGC
* * * *
21645 CACTTAAATATTTTTGGAATTGAATTATATACTTTTTATGAGTATTTTGTCTAAAAATTGAGGAA
64 CA-TTAAATATTTTCGGAATTGAATTATATACTTTTTATGAGAATTGTGGCTAAAAATTGAGGAA
*
21710 AAATCTTTAGGGTCAATTTTTGCCTAAATC
128 AAATCTTTAGGGTCAATTTTTGCCGAAATC
21740 GTGCACTAAC
Statistics
Matches: 138, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
180 34 0.25
181 104 0.75
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (180 bp):
TCGATTTAATCAGAAATTAATTCAAAATAAAAAAAGAAAAACGATATTAGAAACATGAAAAGCCA
TTAAATATTTTCGGAATTGAATTATATACTTTTTATGAGAATTGTGGCTAAAAATTGAGGAAAAA
TCTTTAGGGTCAATTTTTGCCGAAATCATGACGAGCATCTGAATCGTGTA
Found at i:22797 original size:320 final size:318
Alignment explanation
Indices: 21562--25018 Score: 3198
Period size: 323 Copynumber: 10.6 Consensus size: 318
21552 CGAAATCATG
* * * * *
21562 ACGAGCATCTGAATCGTGTATCGATTTAATCAGAAATTAATTCAAAATAAAAAAAAGGAAAATGA
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGAAT--AAAATAGGAAAAAGA
* * * * * * * *
21627 TATTAAAAGCATGAAAAGCACTTAAATATTTTTGGAATTGAATTATATACTTTTTATGAGTATTT
64 TATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATATTTTTTATGAGTATTG
* * *
21692 TGTCTAAAAATTGAGGAAAAATCTTTAGGGTCAATTTTTGCCTAAATCGTGCACTAA-CTATCAC
129 TGGCTAAAAATTGAGGAAAAATCTTT-GGGTCAATTTTTGCCGAAATCGTGTACTAATC-ATCAC
* * * * * * * *
21756 GATTTTTTTGCTAAAAACGCATTTCGGGGCACCGGCTGAGTTTTACAAGATTTTTGGCTCCAAGA
192 GA--TTTTGGCTAAAAACGC-TTTCGGAGCCCCGGCTTAGTTTTGCATGATTTTTGACGCCAAGA
* ** ** *
21821 -ATCATTGAATTATCTATATTCATCTAATAAAATCTCAGCCACATTTTATTTAAGGATTTATTTT
254 CA-CATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
21885 T
318 T
* * * * * * *
21886 GCAAGCATCTGAATCATGTTGT-GA-TTAATTCAGAAATTAATTTATAAAAAAATAGCAAGAACG
1 ACGAGCATCTGAATCATGTT-TCGATTTAA-TCAGAAATTAATTCAGAATAAAATAGGAA-AAAG
* * * * * * *
21949 ATGTTAGAAGCATGAAAAGCCCTTTAATTTTTTTGG-AGTTAAATTATATATTATTTATGAGTAT
63 ATATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCA-TTGAATTATATATTTTTTATGAGTAT
* * * *
22013 TGTGGCTAAAAATTGAGGAAAAATCCTTCGGGTCAATTTTTTCCGAAATCGTGTATTAATCATAA
127 TGTGGCTAAAAATTGAGGAAAAAT-CTTTGGGTCAATTTTTGCCGAAATCGTGTACTAATCATCA
* * * * * * * ** *
22078 CGGTTTTTTGCTAAAAACACGTTCCGAGGCCCCAGATTAGTTTAACATGCTTTTT-AGCGCCAAG
191 C-GATTTTGGCTAAAAACGCTTTCGGA-GCCCCGGCTTAGTTTTGCATGATTTTTGA-CGCCAAG
** * * * *
22142 ACTTATAGAAATATCTATATTCATATAAACAAATCTCAACCACATTGGATTTAAGGATTTGTTTT
253 ACACATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
22207 T
318 T
22208 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGAATAAAATAGGAAAAAACGA
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGAATAAAATAGG-AAAAA-GA
* * ** * *
22273 TATTAGAAGCGTCAAAAGTCCTTCAATATTTTCTTCATTGAATTTTATATTTTTTATGAGTATCG
64 TATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATATTTTTTATGAGTATTG
* * *
22338 TTGCTAAAAATTGAGGAAAAATCTTTCGAGTCAAGTTTTTGCCAAAATCGTGTACTAATCATCAC
129 TGGCTAAAAATTGAGGAAAAATCTTT-GGGTCAA-TTTTTGCCGAAATCGTGTACTAATCATCAC
** * * *
22403 GATTTTTGGCTAAAAATACGTTCTGAGGCCCCAGCTTAGTTTTGCATGATTTTTTG-CGCCAAGA
192 GA-TTTTGGCTAAAAACGCTTTCGGA-GCCCCGGCTTAGTTTTGCATGA-TTTTTGACGCCAAGA
* * * *
22467 CTCATTGAAATATCTATATCCATCTAACCAAATCTCAGCCACATTCGATTTAAGGATGTGTTTTT
254 CACATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* * * * * * *
22532 ACGAGCATCTCAATCATGTTTCGATTTAATAAAAAATTATTTC-GTA-AAAATAGTAAAAAAATA
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGAATAAAATAGGAAAAAGATA
** * * * * * *
22595 TTAGAAAAGTGAAAAACCCTTCAATCTTTTCAGCGTTGAAATATATATTTTTTATGAGTATTGAG
66 TTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATATTTTTTATGAGTATTGTG
* * * *
22660 GAT-AAAATTGAGAAAAAAAAATCCTTTAGGTCAATTTTTGCCGAAATCGTGTACTAATGATCAC
131 GCTAAAAATTGAG---GAAAAAT-CTTTGGGTCAATTTTTGCCGAAATCGTGTACTAATCATCAC
22724 GATTTTGGCTAAAAACGCTTTCTGGAGCCCCGGCTTAGTTTTGCATGATTTTTGACGCCAAGACA
192 GATTTTGGCTAAAAACGCTTTC-GGAGCCCCGGCTTAGTTTTGCATGATTTTTGACGCCAAGACA
* * **
22789 -ACTTGAAATATCTATATTCATCTAACCAAATCTTAGCCACGTTGGATTTAAGGA--AATTTTT
256 CA-TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* * * *
22850 ACGAGCATCTGAATCATGTTTCGATTAAATTAGAAATTAATTCAAAATAAAATAGGAAAACGATA
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGAATAAAATAGGAAAAAGATA
** * *
22915 TTAGAAGTTTGAAAA-CCCTTCAATATTTTCGGCATTGAATTATATATGTTTTCATGAGTAACT-
66 TTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATAT-TTTTTATGAGT-ATTG
* *
22978 TAGCTAAAAATTGAGGAAAAATCTTTCGAGTCAATTTTTTGCCGAAATCGTGTACTAATCATCAC
129 TGGCTAAAAATTGAGGAAAAATCTTT-GGGTCAA-TTTTTGCCGAAATCGTGTACTAATCATCAC
* * * * * * *
23043 GGTTTTTGGATAAAAATG-TGTTCCGAGGCCCCGACTTAGTTTTGCAAGATTTTTTG-TGCCAAG
192 -GATTTTGGCTAAAAACGCT-TTCGGA-GCCCCGGCTTAGTTTTGCATGA-TTTTTGACGCCAAG
* * * * **
23106 ACTA-ATTGAAATATCTTTATTCATCTAACTAAATCTTAGCCACTTTGGATTTAAGAGAAAAAAT
253 AC-ACATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAG-G---ATTT
23170 -TTTTT
313 GTTTTT
* *
23175 ACGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTCAGAATAAAATAGGAAAAACGAT
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGAATAAAATAGGAAAAA-GAT
* * *
23240 TTTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGAATTTAATTATATATTTTTTATGAGTATTGT
65 ATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATATTTTTTATGAGTATTGT
* * * * *
23305 GTCTAAAAATTAAGGAAAAATCTTTGGGGTCAATTTTTACCGAAATCGTGTACTAACCATCATGA
130 GGCTAAAAATTGAGGAAAAATCTTT-GGGTCAATTTTTGCCGAAATCGTGTACTAATCATCACGA
* * ** * * *
23370 TTTTTGGCTAAAAACGCGTTTCAGG-GCACCGCCTTAGTTTTATATGATTTTTGGCGTCAAGACT
194 -TTTTGGCTAAAAACGC-TTTC-GGAGCCCCGGCTTAGTTTTGCATGATTTTTGACGCCAAGACA
* *
23434 CATTGAATTATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
256 CATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* * * * * *
23497 ACGAGCATCTGTATCATGTTTCGGTTTAATCAGAAATTAAATTTGAAAAAAAAAAAGGAAAAACG
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATT-AA-TTCAGAATAAAATAGGAAAAA-G
* * * * * * * * *
23562 ATCTTAGAAGCATGAAAAGTCCTCCAATTTTTTTGGCGTTGAATTATATATTATTTATCAGTATT
63 ATATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATATTTTTTATGAGTATT
* * * *
23627 GTGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTACCGAAAATCGTGTA-T-GTTATCA
128 GTGGCTAAAAATTGAGGAAAAATCTTT-GGGTCAATTTTTGCCG-AAATCGTGTACTAATCATCA
* * * * *
23690 CGATATTTTGCTAAAAACATG-TTAT-GGGGCCCCAGATTAGTTTTGCATGATTTTT-ACTGGCA
191 CGAT-TTTGGCTAAAAAC--GCTT-TCGGAGCCCCGGCTTAGTTTTGCATGATTTTTGAC-GCCA
* * * * * *
23752 ATACTCATTAAAATATCTATATTCATATAAACAAATCTCAGCCACATTGGATGTAAGGATTTGTT
251 AGACACATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
23817 TTT
316 TTT
*
23820 ACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAATAAAATAGGAAAAACGAT
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGAATAAAATAGGAAAAA-GAT
* * * * *
23885 AATAGAAGCGTGAAAAGCCCTTCAATATTTTCGGTATTGAATTTTATTTTTTTTATGAGTATCGT
65 ATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATATTTTTTATGAGTATTGT
** * * *
23950 ATCTAAAAATTGAGGTAAAATCTTTCGAGTCCATTTTTGCCGAAATCGTGTACTAATCATCACGG
130 GGCTAAAAATTGAGGAAAAATCTTT-GGGTCAATTTTTGCCGAAATCGTGTACTAATCATCAC-G
* * * * * *
24015 TTTTTGGTTAAAAACACGTTCCGGGGCCCCTGCGTTATGGGGCCCCATATTAGTTTAGCATGATT
193 ATTTTGGCTAAAAACGC-TTTCGGAG-CCC--C-------GG---C---TTAGTTTTGCATGATT
** * *
24080 TTT-A-GCAGCAAGACTTATTGAAATATCTATATTCATTTAACCAAATCTCAGCCACATTCGATT
241 TTTGACGC--CAAGACACATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATT
* * *
24143 TCAGGATGTGTTTTA
304 TAAGGATTTGTTTTT
* * *
24158 ACGAGCATCTGAATCATGTTTCGGTTTAATCAGAAATTATTTCGTAAAAAATAGTAAAAAAATAT
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTC---------AG--AATAAA-A-
* * * ** *
24223 TTTTTTTCAAGGTAAAAAAATATTAGAAGCGTGAAAAAACCCTTCAATCTTTTCAACGTTGAATT
53 ------T--AGG-AAAAAGATATTAGAAGCGTG-AAAAGCCCTTCAATATTTTCGGCATTGAATT
* *
24288 ATATATTTTTTATAAGTATTGTTGCTAAAAATTGAGG-AAAATCCTTTGGGTCAATTTTTGCCGA
108 ATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAAT-CTTTGGGTCAATTTTTGCCGA
* * * * * *
24352 AATCGTGTACCAAAT-ATCA-GTGTTTTGACTAAAACACG-TTCCGAAGCCCCGTCTTAGTTTTG
172 AATCGTGTA-CTAATCATCACG-ATTTTGGCTAAAA-ACGCTTTCGGAGCCCCGGCTTAGTTTTG
** * * * * * *
24414 CATGATTTTTGGTGTCAAGGCAAATTGAAATATCTAAATACATCTAACCAAATCTCAGCCACGTT
234 CATGATTTTTGACGCCAAGACACATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATT
*
24479 GGATTTAAAGATTT-TTTTT
299 GGATTTAAGGATTTGTTTTT
* *
24498 ACGAGCATCTGAATCATGTTTCGATTTAATCATAAATTAATTCATAATAAAATAGGAAAAACGAT
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGAATAAAATAGGAAAAA-GAT
* * * *
24563 ATTAGAACCGTGAAAAGCCCTTCAATATTTTCGACATTTAATTATATATCTTTTATGAGTATTGT
65 ATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATATTTTTTATGAGTATTGT
* *
24628 GGATAAAAATT-AGGGAAAAATCTTTCCGGG-CAATTTTTGCCGAAATCGTGTACT-ATCA-C-G
130 GGCTAAAAATTGA-GGAAAAATCTTT--GGGTCAATTTTTGCCGAAATCGTGTACTAATCATCAC
* * * * * *
24688 GTTTTTTGGCTAAAAACGCATTCCGAGGCCCCGACTTAGGTTTGTATGATTTTTGGA-GCCAAGA
192 G-ATTTTGGCTAAAAACGCTTTCGGA-GCCCCGGCTTAGTTTTGCATGATTTTT-GACGCCAAGA
* * * * * * **
24752 CTCATTGCAATATCTATCTTCATCTAACAAAATCTTAGCCACATTGGAGTTAAAAATATT-TTTT
254 CACATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGAT-TTGTTTT
*
24816 A
318 T
** * *
24817 AAAAGCATCTGAATCATGTTTTGATTTAATCAGAAATTAATTCAGAATAAAATAGAAAAAACGAT
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGAATAAAATAGGAAAAA-GAT
* * ** *
24882 ATTAGAAGCGTGAAAAGTCCTTCAATAATTTC-GCATTGAATTATATATAATTTATGAGTATTAT
65 ATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATATTTTTTATGAGTATTGT
* * *
24946 GGCTAAAAATT-AGGGGAAAATCTTTTGGGTCAGTTTTTGCCGAAATCGTGTACTAACCATCACA
130 GGCTAAAAATTGA-GGAAAAATC-TTTGGGTCAATTTTTGCCGAAATCGTGTACTAATCATCAC-
*
25010 GTTTTTGGC
192 GATTTTGGC
25019 GAGCATCTAA
Statistics
Matches: 2596, Mismatches: 403, Indels: 271
0.79 0.12 0.08
Matches are distributed among these distances:
316 3 0.00
317 27 0.01
318 267 0.10
319 221 0.09
320 295 0.11
321 181 0.07
322 239 0.09
323 352 0.14
324 333 0.13
325 192 0.07
326 58 0.02
327 32 0.01
328 1 0.00
329 5 0.00
331 1 0.00
332 1 0.00
336 1 0.00
338 119 0.05
340 44 0.02
341 71 0.03
343 1 0.00
344 1 0.00
347 3 0.00
349 5 0.00
350 1 0.00
354 1 0.00
356 3 0.00
357 8 0.00
358 10 0.00
359 51 0.02
360 69 0.03
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (318 bp):
ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGAATAAAATAGGAAAAAGATA
TTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATATTTTTTATGAGTATTGTG
GCTAAAAATTGAGGAAAAATCTTTGGGTCAATTTTTGCCGAAATCGTGTACTAATCATCACGATT
TTGGCTAAAAACGCTTTCGGAGCCCCGGCTTAGTTTTGCATGATTTTTGACGCCAAGACACATTG
AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
Found at i:23821 original size:645 final size:640
Alignment explanation
Indices: 21562--25001 Score: 3396
Period size: 645 Copynumber: 5.3 Consensus size: 640
21552 CGAAATCATG
* * *
21562 ACGAGCATCTGAATCGTGTATCGATTTAATCAGAAATTAATTCAAAATAAAAAAAAGG-AAAATG
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTC-AAA-AAAAAAAAGGAAAAACG
* * * * *
21626 ATATTAAAAGCATGAAAAG-CACTTAAATATTTTTGGAATTGAATTATATACTTTTTATGAGTAT
64 ATATTAGAAGCGTGAAAAGTC-CTTCAATTTTTTTGGCATTGAATTATATA-TTTTTATGAGTAT
* * * *
21690 T-TTGTCTAAAAATTGAGGAAAAATCTTTAGGGTCAATTTTTGCCTAAATCGTGCACTAACTATC
127 TGTTG-CTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTACTAATTATC
* * * * *
21754 ACGATTTTTTTGCTAAAAACGCAT-TT-CGGGGCACCGGCTGAGTTTTACAAGATTTTTGGCT-C
191 ACGA--TTTTTGCTAAAAA--CATGTTCCGAGGC-CCCGCTTAGTTTTGCATGATTTTT-GCTGC
* * **
21816 CAAGAATCATTGAATTATCTATATTCATCTAATA-AAATCTCAGCCACATTTTATTTAAGGATTT
250 CAAGACTCATTGAAATATCTATATTCATCTAA-ACAAATCTCAGCCACATTGGATTTAAGGATTT
* * * * * *
21880 ATTTTTGCAAGCATCTGAATCATGTTGT-GA-TTAATTCAGAAATTAATTTATAAAAAAATAGCA
314 -TTTTTACGAGCATCTGAATCATGTT-TCGATTTAATT-AGAAATTAATTCAGAATAAAATAGGA
* * * * * * * * *
21943 AGAACGATGTTAGAAGCATGAAAAGCCCTTTAATTTTTTTGGAGTTAAATTATATATTATTTATG
376 AAAACGATATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGAATTGAATTATATATTTTTTATG
* * * *
22008 AGTATTGTGGCTAAAAATTGAGGAAAAATCCTTCGGGTCAATTTTTTCCGAAATCGTGTATTAAT
441 AGTATTGTGGCTAAAAATTAAGGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTACTAAT
* * * * * * * *
22073 CATAACGGTTTTTTGCTAAAAACACG-TTCCGAGGCCCCAG-ATTAGTTTAACATGCTTTTTAGC
506 CATCACGATTTTTGGCTAAAAACGCGTTTCCG-GGCCCC-GCCTTAGTTTTACATGATTTTTGGC
* * * *
22136 GCCAAGACTTATAGAAATATCTATATTCATATAA-ACAAATCTCAACCACATTGGATTTAAGGAT
569 GCCAAGACTCATTGAAATATCTATATTCATCTAACA-AAATCTCAGCCACATTGGATTTAAGGAT
22200 TTGTTTTT
633 TTGTTTTT
* * *
22208 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGAATAAAATAGGAAAAAACGA
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAAAAAAAAAAAGG-AAAAACGA
* *
22273 TATTAGAAGCGTCAAAAGTCCTTCAATATTTTCTT--CATTGAATTTTATATTTTTTATGAGTAT
65 TATTAGAAGCGTGAAAAGTCCTTCAAT-TTTT-TTGGCATTGAATTATATA-TTTTTATGAGTAT
* * * *
22336 CGTTGCTAAAAATTGAGGAAAAATCTTTCGAGTCAAGTTTTTGCCAAAATCGTGTACTAATCATC
127 TGTTGCTAAAAATTGAGGAAAAATCTTTCGGGTCAA-TTTTTGCCGAAATCGTGTACTAATTATC
* * *
22401 ACGATTTTTGGCTAAAAATACGTTCTGAGGCCCCAGCTTAGTTTTGCATGATTTTTTGC-GCCAA
191 ACGATTTTT-GCTAAAAACATGTTCCGAGGCCCC-GCTTAGTTTTGCATGA-TTTTTGCTGCCAA
* * * *
22465 GACTCATTGAAATATCTATATCCATCTAACCAAATCTCAGCCACATTCGATTTAAGGATGTGTTT
253 GACTCATTGAAATATCTATATTCATCTAAACAAATCTCAGCCACATTGGATTTAAGGAT-TTTTT
* * * * * * *
22530 TTACGAGCATCTCAATCATGTTTCGATTTAATAAAAAATTATTTC-GTA-AAAATAGTAAAAA-A
317 TTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAATAAAATAGGAAAAACG
** * * * ** *
22592 ATATTAGAAAAGTGAAAAACCCTTCAATCTTTTCAGCGTTGAAATATATATTTTTTATGAGTATT
382 ATATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGAATTGAATTATATATTTTTTATGAGTATT
* * ** * *
22657 GAGGAT-AAAATTGAGAAAAAAAAATCCTTT-AGGTCAATTTTTGCCGAAATCGTGTACTAATGA
447 GTGGCTAAAAATT---AAGGAAAAAT-CTTTCGGGTCAATTTTTGCCGAAATCGTGTACTAATCA
* * * *
22720 TCACGA-TTTTGGCTAAAAACGC-TTTCTGGAGCCCCGGCTTAGTTTTGCATGATTTTTGACGCC
508 TCACGATTTTTGGCTAAAAACGCGTTTCCGG-GCCCCGCCTTAGTTTTACATGATTTTTGGCGCC
* * * * **
22783 AAGAC-AACTTGAAATATCTATATTCATCTAACCAAATCTTAGCCACGTTGGATTTAAGGA--AA
572 AAGACTCA-TTGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTTG
22845 TTTTT
636 TTTTT
* * * *
22850 ACGAGCATCTGAATCATGTTTCGATTAAATTAGAAATTAATTCAAAATAAAATAGG-AAAACGAT
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAAAAAAAAAAAGGAAAAACGAT
** * * * *
22914 ATTAGAAGTTTGAAAA-CCCTTCAATATTTTCGGCATTGAATTATATATGTTTTCATGAGTAACT
66 ATTAGAAGCGTGAAAAGTCCTTCAATTTTTTTGGCATTGAATTATATAT-TTTT-ATGAGT-ATT
* * *
22978 -TAGCTAAAAATTGAGGAAAAATCTTTCGAGTCAATTTTTTGCCGAAATCGTGTACTAATCATCA
128 GTTGCTAAAAATTGAGGAAAAATCTTTCGGGTCAA-TTTTTGCCGAAATCGTGTACTAATTATCA
* * ** *
23042 CGGTTTTTGGATAAAAATGTGTTCCGAGGCCCCGACTTAGTTTTGCAAGATTTTTTG-TGCCAAG
192 CGATTTTT-GCTAAAAACATGTTCCGAGGCCCCG-CTTAGTTTTGCATGA-TTTTTGCTGCCAAG
* * * * **
23106 ACTAATTGAAATATCTTTATTCATCT-AACTAAATCTTAGCCACTTTGGATTTAAGAGAAAAAAT
254 ACTCATTGAAATATCTATATTCATCTAAAC-AAATCTCAGCCACATTGGATTTAAG-G---ATTT
*
23170 TTTTTACGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTCAGAATAAAATAGGAAAA
314 TTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAATAAAATAGGAAAA
* *
23235 ACGATTTTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGAATTTAATTATATATTTTTTATGAGT
379 ACGATATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGAATTGAATTATATATTTTTTATGAGT
* * * *
23300 ATTGTGTCTAAAAATTAAGGAAAAATCTTTGGGGTCAATTTTTACCGAAATCGTGTACTAACCAT
444 ATTGTGGCTAAAAATTAAGGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTACTAATCAT
* * * * *
23365 CATGATTTTTGGCTAAAAACGCGTTTCAGGGCACCGCCTTAGTTTTATATGATTTTTGGCGTCAA
509 CACGATTTTTGGCTAAAAACGCGTTTCCGGGCCCCGCCTTAGTTTTACATGATTTTTGGCGCCAA
*
23430 GACTCATTGAATTATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
574 GACTCATTGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
23495 TT
639 TT
* * *
23497 ACGAGCATCTGTATCATGTTTCGGTTTAATCAGAAATTAAATTTGAAAAAAAAAAAGGAAAAACG
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATT-AA-TTCAAAAAAAAAAAGGAAAAACG
* * * * *
23562 ATCTTAGAAGCATGAAAAGTCCTCCAATTTTTTTGGCGTTGAATTATATATTATTTATCAGTATT
64 ATATTAGAAGCGTGAAAAGTCCTTCAATTTTTTTGGCATTGAATTATATATT-TTTATGAGTATT
* * * *
23627 GTGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTACCGAAAATCGTGTA-T-GTTATCA
128 GTTGCTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCCG-AAATCGTGTACTAATTATCA
** * * * * *
23690 CGATATTTTGCTAAAAACATGTTATGGGGCCCCAGATTAGTTTTGCATGATTTTTACTGGCAATA
192 CGAT-TTTTGCTAAAAACATGTTCCGAGGCCCC-GCTTAGTTTTGCATGATTTTTGCTGCCAAGA
* * *
23755 CTCATTAAAATATCTATATTCATATAAACAAATCTCAGCCACATTGGATGTAAGGATTTGTTTTT
255 CTCATTGAAATATCTATATTCATCTAAACAAATCTCAGCCACATTGGATTTAAGGATTT-TTTTT
23820 ACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAATAAAATAGGAAAAACGAT
319 ACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAATAAAATAGGAAAAACGAT
* * * * *
23885 AATAGAAGCGTGAAAAGCCCTTCAATATTTTCGGTATTGAATTTTATTTTTTTTATGAGTATCGT
384 ATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGAATTGAATTATATATTTTTTATGAGTATTGT
** * * * * *
23950 ATCTAAAAATTGAGGTAAAATCTTTCGAGTCCATTTTTGCCGAAATCGTGTACTAATCATCACGG
449 GGCTAAAAATTAAGGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTACTAATCATCACGA
* * *
24015 TTTTTGGTTAAAAACACG-TTCCGGGGCCCCTGCGTTATGGGGCCCCATATTAGTTTAGCATGAT
514 TTTTTGGCTAAAAACGCGTTTCC-GGGCCCC-GCCTTA----G--------T--TTTA-CATGAT
* * * * *
24079 TTTTAGCAG-CAAGACTTATTGAAATATCTATATTCATTTAACCAAATCTCAGCCACATTCGATT
562 TTTTGGC-GCCAAGACTCATTGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATT
* * *
24143 TCAGGATGTGTTTTA
626 TAAGGATTTGTTTTT
* *
24158 ACGAGCATCTGAATCATGTTTCGGTTTAATCAGAAATTATTTCGTAAAAAATAGTAAAAAAATAT
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTC---------A--AAAAAAA-A-
* ** * *** *
24223 TTTTTTTCAAGGTAAAAA-AATATTAGAAGCGTGAAAAAACCCTTCAATCTTTTCAACGTTGAAT
53 --------AAGG-AAAAACGATATTAGAAGCGTG-AAAAGTCCTTCAATTTTTTTGGCATTGAAT
*
24287 TATATATTTTTTATAAGTATTGTTGCTAAAAATTGAGG-AAAATCCTTT-GGGTCAATTTTTGCC
108 TATATA-TTTTTATGAGTATTGTTGCTAAAAATTGAGGAAAAAT-CTTTCGGGTCAATTTTTGCC
* * * *
24350 GAAATCGTGTACCAAATATCA-G-TGTTTTGACT-AAAACACGTTCCGAAGCCCCGTCTTAGTTT
171 GAAATCGTGTACTAATTATCACGAT-TTTTG-CTAAAAACATGTTCCGAGGCCCCG-CTTAGTTT
* * * ** * * * *
24412 TGCATGATTTTTGGTGTCAAGGCAAATTGAAATATCTAAATACATCTAACCAAATCTCAGCCACG
233 TGCATGATTTTTGCTGCCAAGACTCATTGAAATATCTATATTCATCTAAACAAATCTCAGCCACA
* * *
24477 TTGGATTTAAAGATTTTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCATAAATTAATTCA
298 TTGGATTTAAGGATTTTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCA
* * *
24542 TAATAAAATAGGAAAAACGATATTAGAACCGTGAAAAGCCCTTCAATATTTTC-GACATTTAATT
363 GAATAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGA-ATTGAATT
* * *
24606 ATATATCTTTTATGAGTATTGTGGATAAAAATTAGGGAAAAATCTTTCCGGG-CAATTTTTGCCG
427 ATATATTTTTTATGAGTATTGTGGCTAAAAATTAAGGAAAAATCTTT-CGGGTCAATTTTTGCCG
* * * * *
24670 AAATCGTGTACT-ATCA-C-GGTTTTTTGGCTAAAAACGC-ATTCCGAGGCCCCGACTTAGGTTT
491 AAATCGTGTACTAATCATCACGATTTTTGGCTAAAAACGCGTTTCCG-GGCCCCGCCTTAGTTTT
** * * * *
24731 GTATGATTTTTGGAGCCAAGACTCATTGCAATATCTATCTTCATCTAACAAAATCTTAGCCACAT
555 ACATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCTAACAAAATCTCAGCCACAT
* ** *
24796 TGGAGTTAAAAATATT-TTTTA
620 TGGATTTAAGGAT-TTGTTTTT
** * * * * *
24817 AAAAGCATCTGAATCATGTTTTGATTTAATCAGAAATTAATTCAGAATAAAATAGAAAAAACGAT
1 ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAAAAAAAAAAAGGAAAAACGAT
** * * *
24882 ATTAGAAGCGTGAAAAGTCCTTCAA-TAATTTCGCATTGAATTATATATAATTTATGAGTATTAT
66 ATTAGAAGCGTGAAAAGTCCTTCAATTTTTTTGGCATTGAATTATATAT-TTTTATGAGTATTGT
* * * *
24946 GGCTAAAAATT-AGGGGAAAATCTTTTGGGTCAGTTTTTGCCGAAATCGTGTACTAA
130 TGCTAAAAATTGA-GGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTACTAA
25002 CCATCACAGT
Statistics
Matches: 2326, Mismatches: 350, Indels: 245
0.80 0.12 0.08
Matches are distributed among these distances:
635 2 0.00
636 43 0.02
637 50 0.02
638 20 0.01
639 28 0.01
640 188 0.08
641 2 0.00
642 64 0.03
643 106 0.05
644 163 0.07
645 365 0.16
646 311 0.13
647 98 0.04
648 97 0.04
649 32 0.01
650 70 0.03
651 30 0.01
658 2 0.00
659 106 0.05
660 9 0.00
661 110 0.05
662 1 0.00
668 1 0.00
670 8 0.00
671 1 0.00
674 5 0.00
675 26 0.01
676 1 0.00
677 5 0.00
678 165 0.07
679 107 0.05
680 39 0.02
681 69 0.03
682 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (640 bp):
ACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAAAAAAAAAAAGGAAAAACGAT
ATTAGAAGCGTGAAAAGTCCTTCAATTTTTTTGGCATTGAATTATATATTTTTATGAGTATTGTT
GCTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTACTAATTATCACGAT
TTTTGCTAAAAACATGTTCCGAGGCCCCGCTTAGTTTTGCATGATTTTTGCTGCCAAGACTCATT
GAAATATCTATATTCATCTAAACAAATCTCAGCCACATTGGATTTAAGGATTTTTTTTACGAGCA
TCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAATAAAATAGGAAAAACGATATTAGAA
GCGTGAAAAGCCCTTCAATATTTTCGGAATTGAATTATATATTTTTTATGAGTATTGTGGCTAAA
AATTAAGGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTACTAATCATCACGATTTTTGG
CTAAAAACGCGTTTCCGGGCCCCGCCTTAGTTTTACATGATTTTTGGCGCCAAGACTCATTGAAA
TATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
Found at i:25679 original size:323 final size:318
Alignment explanation
Indices: 25018--26141 Score: 1222
Period size: 322 Copynumber: 3.5 Consensus size: 318
25008 CAGTTTTTGG
* * * * * * **
25018 CGAGCATCTAAATCATGTATCGATTTAATCAAAAACTAATTCAGAATAAAATATTAAAAACGATA
1 CGAGCATCTGAATCATGT-TTGGTTTAATCAGAAATTAATTCAGAAAAAAATAGGAAAAACGATA
* ** * *
25083 TTAGAAGCGTGAAAAGTCCTTCAATATTTTCGTAATTGAATTATATATATTTTATGAGTATTGTG
65 TTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATATTTTTTATAAGTATTGTG
* * * * * * *
25148 TCTAAAAATTGAGGAAAAATCTCTGGGGTCAATTTTGGCCCAAATCGTGTACTAATCATCACGGT
130 GCTAAAAATTGAGGAAAAATCTTTCGGGTAAATTTT-GCCGAAATCGTGTACTAACCATCACGAT
* * * * *
25213 TTTTGGCTAAAAACGCGTTTCGGGGCACCGGCC-TAGTTTTACATGATTTTTGGCGCCAAGACTC
194 TTTTGGCTAAAAACACGTTCCGAGG--CCGGCCTTAGTTTTGCATGATTTTT-ACGCCAAGACTC
* *
25277 GTTGAATTATCTATATTCATCT-AACAAAATCTCAGTC-CTATTGGATTTAAGGATTTGTTTTTG
256 ATTGAATTATCTATATTCATCTAAAC-AAATCTCAGTCAC-ATTGGATTTAAGGATTTGTTTTTA
* *
25340 CGAGCATCTGAATCATGCTTTGGTTTAATCAGAAATTAATTTAGAAAAAAAATAGGAAAAATGAT
1 CGAGCATCTGAATCATG-TTTGGTTTAATCAGAAATTAATTCAG-AAAAAAATAGGAAAAACGAT
* * * *
25405 ATTAGAAGCATGAAAAACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTATAAGTATTGT
64 ATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATATTTTTTATAAGTATTGT
* * ** ** *
25470 GGCTAAAAACTGAGGATAAATCTTTCGGGTAAAGTTTTGTTGAAATTATGTACTAACCATCACAA
129 GGCTAAAAATTGAGGAAAAATCTTTCGGGTAAA-TTTTGCCGAAATCGTGTACTAACCATCACGA
* * * * * * * *
25535 TTTTTTGCTAAAAACACATTCCGAGTCTCTGCCTTAGTTTTGCAAGATATTTATGACAAGACTCA
193 TTTTTGGCTAAAAACACGTTCCGAGGC-CGGCCTTAGTTTTGCATGATTTTTACGCCAAGACTCA
* * * *
25600 TTAAAATATCTATATCCATATAAACAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTA
257 TTGAATTATCTATATTCATCTAAACAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTA
* ** * *
25662 CGATCATCTGAAATCATGTTTCAATTTAATCAGAAATTAATTCAGAATAAAATCGGAAAAACGAT
1 CGAGCATCTG-AATCATGTTT-GGTTTAATCAGAAATTAATTCAGAAAAAAATAGGAAAAACGAT
* *
25727 ATTGGAAGCGTGAAAAGCCCTTCAATATTTTCGGCACTGAATT-TATATTTTTTATGAA-TATTG
64 ATTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATATTTTTTAT-AAGTATTG
* * *
25790 TGTCTGAAAATTGAGGAAAAATCTTTCGGGTAAATTTTTGCCGAAATCGTGTACTAACTATCACG
128 TGGCTAAAAATTGAGGAAAAATCTTTCGGGTAAA-TTTTGCCGAAATCGTGTACTAACCATCAC-
* ** ** *
25855 GA-TTTTGGCTAAAAACACGTTCC-ATGGCAGGAGGTTAGTTCCGCATGATTTTTAGCGCCAAGG
191 GATTTTTGGCTAAAAACACGTTCCGA-GGCCGG-CCTTAGTTTTGCATGATTTTTA-CGCCAAGA
* * * *
25918 CTCATTGAATTATCTATATTCATCTAACCTAATCTCAGCCACATTGGATTTAA-AATTTGTTTTT
253 CTCATTGAATTATCTATATTCATCTAAACAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTT
25982 A
318 A
* * * * * *
25983 CAAGCATCTGAATCATGTTTTGGTTTAATCAGAAATGAATTTAG-AACAAATATGAAAGACGATA
1 CGAGCATCTGAATCATG-TTTGGTTTAATCAGAAATTAATTCAGAAAAAAATAGGAAAAACGATA
* * * * * *
26047 TTAGAAGCGTGAAAAGCTCTTCAATCTTTTTGTCGTTGAATTATATAATTTTTTATGAGTATTGT
65 TTAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATAT-ATTTTTTATAAGTATTGT
* *
26112 GGCTAAAAATTGAGGGAAAATCTTTTGGGT
129 GGCTAAAAATTGAGGAAAAATCTTTCGGGT
26142 CAACCAAGTG
Statistics
Matches: 663, Mismatches: 121, Indels: 37
0.81 0.15 0.05
Matches are distributed among these distances:
319 50 0.08
320 32 0.05
321 172 0.26
322 220 0.33
323 185 0.28
324 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (318 bp):
CGAGCATCTGAATCATGTTTGGTTTAATCAGAAATTAATTCAGAAAAAAATAGGAAAAACGATAT
TAGAAGCGTGAAAAGCCCTTCAATATTTTCGGCATTGAATTATATATTTTTTATAAGTATTGTGG
CTAAAAATTGAGGAAAAATCTTTCGGGTAAATTTTGCCGAAATCGTGTACTAACCATCACGATTT
TTGGCTAAAAACACGTTCCGAGGCCGGCCTTAGTTTTGCATGATTTTTACGCCAAGACTCATTGA
ATTATCTATATTCATCTAAACAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTA
Found at i:27048 original size:321 final size:319
Alignment explanation
Indices: 26443--27917 Score: 1487
Period size: 321 Copynumber: 4.6 Consensus size: 319
26433 CTTCGAAATA
* * * *
26443 TGAAAAGCCCTTCAATTTTTT-TGCATTGAATTATATATTTTTGATGAGTATTGTGTATAAAAAT
1 TGAAAAGCCTTTCAATTTTTTCGGCATTGAATTATATATTTTTTATGAGTATTGTGGATAAAAAT
* * * * **
26507 TAAGGAAAAATCTTTTGGGTCAATTTTTGCCAAAATCATGTACT-AACCATCACGGTTTTTTTGC
66 TGAGGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTA-TGTTCCATCACGG-TTTTTTGC
* * * **
26571 TAAAAATGCGTTCCGGGGCCCCGGCTTACTTTTGCATGATTTTTTATGCCAAGACTCATTGAAAT
129 TAAAAACGCGTTCC-GGG-CCCAGCTTAGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAAT
* * * * * * *
26636 ATCTATGTTTATCTAACCACATCTCAGCCACATTAGATTGAAGGATTTGTTTTTACGAGCATCTA
192 ACCTATATTCATCTAACCAAATCTCAGCCACATTAGATTGAAGGATTTGCTTTTATGAGCATCTG
* * * *
26701 AATCATGTTTCGATTTGATCAGAAATTAATTTTGAAAAAAAAATGAAAACAATATTAGAAGTG
257 AATCATGTTTCGATTTAATCAGAAATTAATTTAGAAAAAAAAATGAAAATAATATTAGAAGCG
** * * * *
26764 TGAAAAGCCTTTCAAACTTTTCGGCATTGAATTTATATATTTTTTATTAGTATTATGGCTCAAAA
1 TGAAAAGCCTTTCAATTTTTTCGGCATTGAA-TTATATATTTTTTATGAGTATTGTGGATAAAAA
* *
26829 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTATGTTCCATCATGGTTTTTGGCT
65 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTATGTTCCATCACGGTTTTTTGCT
* * * *
26894 AAAAACGTGTTCCGGACCTTAGCTTAGTTTTGCATGATTTTTTGCGTCAAGACTCATTGAAATAC
130 AAAAACGCGTTCCGGGCC-CAGCTTAGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATAC
*
26959 CTATATTCATCTAACAAAATCTCAGCCACATTAGATTGAAGGATTTGCTTTTATGAGCATCTGAA
194 CTATATTCATCTAACCAAATCTCAGCCACATTAGATTGAAGGATTTGCTTTTATGAGCATCTGAA
* * * ** * * *
27024 TCATTTTTCAATTTAATGAGAAATTAATTTAGAAAAAAATTTGAAAAATGATATTAGAAACC
259 TCATGTTTCGATTTAATCAGAAATTAATTTAGAAAAAAAAATG-AAAATAATATTAGAAGCG
* * *
27086 TGAAAAGACC-TTCAATTTTTTTTGGCTTTGAGTTATATATTTTTTATGAGTATTGTGG-TCAAA
1 TGAAAAG-CCTTTCAA-TTTTTTCGGCATTGAATTATATATTTTTTATGAGTATTGTGGAT-AAA
* * * ** * *
27149 AGTTGAGAAAAAATCTTTCAAGGTCAATTTTTATCGAAATC--ATATGCTAACCATCACGGTTTT
63 AATTGAGGAAAAATCTTTC-GGGTCAATTTTTGCCGAAATCGTGTATG-T-TCCATCACGGTTTT
* * *
27212 TTGCTAAAATCGCGATCCTGGGCCCCAGCTTAGTTTTGCATGA-TTTTTGACGCCATGACTCATT
125 TTGCTAAAAACGCGTTCC-GGG-CCCAGCTTAGTTTTGCATGATTTTTTG-CGCCAAGACTCATT
* *
27276 GAAATATCC-ATATTCATCTAACCAAATCTCAGCCACATTAGATTGAAGAATTT-CTTTTTATCA
187 GAAATA-CCTATATTCATCTAACCAAATCTCAGCCACATTAGATTGAAGGATTTGC-TTTTATGA
* * * *
27339 GCATCTGAATCATGTTTC-A--TAATCAGAAATTAATTCAG-AAAAAATATGAAAAATAACATTG
250 GCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTTAGAAAAAAAAATG-AAAATAATATTA
*
27400 GAAGCA
314 GAAGCG
* ** * * * *
27406 TGAAAAACCCTTT-AATTTTTTCAACGTTAAATTATATA-TTTTTATGTGTATTGTGGCTAAAAA
1 TG-AAAAGCCTTTCAATTTTTTCGGCATTGAATTATATATTTTTTATGAGTATTGTGGATAAAAA
* * *** *** *
27469 TTAAGG-AAAATCTTTTGGGTC-ATCTTTAAACGAAATCGTGTACAAAT-CATCACGGTTTTTGG
65 TTGAGGAAAAATCTTTCGGGTCAAT-TTTTGCCGAAATCGTGTA-TGTTCCATCACGGTTTTTTG
* * * ** **
27531 CTAAAAACGTGTTTCGGGGCCCCGCCTTAGTTTTGCATGA-TTTTTGTCATCAAGACGAATTGAA
128 CTAAAAACGCG-TTCCGGGCCCAG-CTTAGTTTTGCATGATTTTTTG-CGCCAAGACTCATTGAA
* * * * * * * *
27595 ATATCTATATTCATCTAACCAAATCTTAGTCGCATTGGATTTAAGGATTTGTTTTTATGAGTATC
190 ATACCTATATTCATCTAACCAAATCTCAGCCACATTAGATTGAAGGATTTGCTTTTATGAGCATC
* * * * ** *
27660 TGAATCATGTTTTGATTTAATTAAAAATTAATTTAGAAAAAATACGGAAAATGATATTAGAAGCG
255 TGAATCATGTTTCGATTTAATCAGAAATTAATTTAGAAAAAAAAATGAAAATAATATTAGAAGCG
* * *
27725 TGAAAAGCCTTTCAATCTTTTCGGCATTGAATTATATAATTTTTTCTGAGTATTATGGATAAAAA
1 TGAAAAGCCTTTCAATTTTTTCGGCATTGAATTATAT-ATTTTTTATGAGTATTGTGGATAAAAA
* * * * * *
27790 TAGAGGAAAAACCTTTCGGGTCAATTTTCGCCGAAATTGTGTACGTAT-CATCACGCTTTTTTGC
65 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTATGT-TCCATCACGGTTTTTTGC
* * * *
27854 TAAAAACACGTTCCCGAGTCCCGGCTTAATTTTGCATGATTTTTTGCGCCAAGACTCATTGAAA
129 TAAAAACGCGTT-CCG-GGCCCAGCTTAGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAA
27918 GACTTTTTAA
Statistics
Matches: 944, Mismatches: 170, Indels: 79
0.79 0.14 0.07
Matches are distributed among these distances:
315 7 0.01
316 138 0.15
317 12 0.01
318 36 0.04
319 69 0.07
320 38 0.04
321 208 0.22
322 177 0.19
323 152 0.16
324 103 0.11
325 4 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (319 bp):
TGAAAAGCCTTTCAATTTTTTCGGCATTGAATTATATATTTTTTATGAGTATTGTGGATAAAAAT
TGAGGAAAAATCTTTCGGGTCAATTTTTGCCGAAATCGTGTATGTTCCATCACGGTTTTTTGCTA
AAAACGCGTTCCGGGCCCAGCTTAGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATACCT
ATATTCATCTAACCAAATCTCAGCCACATTAGATTGAAGGATTTGCTTTTATGAGCATCTGAATC
ATGTTTCGATTTAATCAGAAATTAATTTAGAAAAAAAAATGAAAATAATATTAGAAGCG
Found at i:28557 original size:41 final size:40
Alignment explanation
Indices: 28498--28578 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 40
28488 TTTATAACTA
*
28498 GGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATTAG
1 GGGGCTAAACCTGAATTTAATTTATTACCTTAATTATTAG
* *
28538 GGGGCCTAAACCT-AGATTTAATTTATTTCCTTAGTTATTAG
1 GGGG-CTAAACCTGA-ATTTAATTTATTACCTTAATTATTAG
28579 AAGAGTCAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 5 0.14
41 31 0.86
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (40 bp):
GGGGCTAAACCTGAATTTAATTTATTACCTTAATTATTAG
Done.