Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022406.1 Corchorus olitorius cultivar O-4 contig22439, 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: 23131
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:1393 original size:7 final size:7
Alignment explanation
Indices: 1381--1405 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1371 ATTGCCGTTC
1381 TATAATA
1 TATAATA
1388 TATAATA
1 TATAATA
1395 TATAATA
1 TATAATA
1402 TATA
1 TATA
1406 TATCTTATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATAATA
Found at i:10312 original size:54 final size:54
Alignment explanation
Indices: 10228--10334 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
10218 CGGATACCAC
10228 GTGGCAAGGATTTGGATATTTCTTTACAATCTAGTAAATGGAAATGTATTTGGT
1 GTGGCAAGGATTTGGATATTTCTTTACAATCTAGTAAATGGAAATGTATTTGGT
*
10282 GTGGCAAGGATTTGGATATTTCTTTGCAATCTAGTAAATGGAAATGTATTTGG
1 GTGGCAAGGATTTGGATATTTCTTTACAATCTAGTAAATGGAAATGTATTTGG
10335 GGTGCTTTGG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.38
Consensus pattern (54 bp):
GTGGCAAGGATTTGGATATTTCTTTACAATCTAGTAAATGGAAATGTATTTGGT
Found at i:11638 original size:331 final size:331
Alignment explanation
Indices: 10874--11854 Score: 1227
Period size: 331 Copynumber: 3.0 Consensus size: 331
10864 CTCTTCAATC
* * ** * * * ** *
10874 TTTTTTGCGAAAAACGCATTTCGGAGCCCCGGCTCAGTTTTGCTTGACTTTTGGCGTTAAAGTTC
1 TTTTTAGCGAATAACGCATTTCGGAGCCCCAACTCAGTTTTGCATGAATCTTGGCGCCAAAGATC
* *
10939 CTTGAAATATCTATATTCATCTACCCAAACCTCAGCTA-AATTGGATTTACGGATATGTTTTTAC
66 CTTGAAATATCTATATTCATCTACCCAAATCTCAGC-ACAATTGGATTTAAGGATATGTTTTTAC
*
11003 GAGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTTGGAAAAAAGATTGGGAAAATGATA
130 GAGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTAGG-AAAAA-ATTGGGAAAATGATA
* * *
11068 TTAGAAAGGTTAGAAGCCCTTCAATCTTTATCGTGTTGAATTATA-AATTTTTATGAGTATTTTG
193 TTAGAAAGGTTAGAAGCCCTTCAATCTTTTTTGTGTTGAATTATATATTTTTTATGAGTATTTTG
* * * * * *
11132 GCCAAAAATAGAGGAAATA-TTTCCGGGTCAGTTTTTTTCAAAA-GTTAGGCGAAATCGTATACT
258 GCCAAAAAT-GAGGAAAAATTTTTCGGGTCAG-TTTTTACAAAATTTTAGTCGAAATCGTGTACT
*
11195 AATCATCACGG
321 AATCATCACGA
* * ** * *
11206 TTTTTGGCGAATAACGCATTTTGGAGCCCCGGCTCAGTTTTGCTTGACTCTTGGCGCCAAAGATC
1 TTTTTAGCGAATAACGCATTTCGGAGCCCCAACTCAGTTTTGCATGAATCTTGGCGCCAAAGATC
*
11271 CTTTAAATAATCTATATTCATCTACCCAAATCTCAGC-CAATGTGGATTTAAGGATATGTTTTTA
66 CTTGAAAT-ATCTATATTCATCTACCCAAATCTCAGCACAAT-TGGATTTAAGGATATGTTTTTA
*
11335 CGAGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTAGGAAAAAATTGGAAAAATGATAT
129 CGAGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTAGGAAAAAATTGGGAAAATGATAT
* * * *
11400 TAGAAAGTTTAGAAGCACTCCAATCTTTTTTGTGTTGAATTATATATTTTTTATCAGTATTTTGG
194 TAGAAAGGTTAGAAGCCCTTCAATCTTTTTTGTGTTGAATTATATATTTTTTATGAGTATTTTGG
11465 CCAAAAATGAGGAAAAATTTTTCGGGTCAGTTTTTACAAAATTTTAGTCGAAATCGTGTACTAA-
259 CCAAAAATGAGGAAAAATTTTTCGGGTCAGTTTTTACAAAATTTTAGTCGAAATCGTGTACTAAT
11529 CAATCACGA
324 C-ATCACGA
* * *
11538 TTTTTAGCTAA-AACCGCGTTTCCGG-GCCCCAACTCAGTTTTGCAT-AATTTTGGGCGCC-AAG
1 TTTTTAGCGAATAA-CGCATTT-CGGAGCCCCAACTCAGTTTTGCATGAATCTT-GGCGCCAAAG
* * *
11599 ACTCCTTGAAATATCCATATTTATCTACCTAAATCTCAGCAACAA-TGGATTTAAGGATATGTTT
63 A-TCCTTGAAATATCTATATTCATCTACCCAAATCTCAGC-ACAATTGGATTTAAGGATATGTTT
* * * **
11663 CTACGAGCATCAGAATCTTGTTTCGATTT-AAT-GAACAATTAATTAGGAAAAAAAAGGGAAAAT
126 TTACGAGCATCTGAATCTAGTTTCGATTTAAATAG-A-AATTAATTAGGAAAAAATTGGGAAAAT
* * *
11726 GATATTAG-AAGCGCTAGAAGCCCTTCAATTTTTTTTGTGTTGAATTATATATCTTTTATGAGTA
189 GATATTAGAAAG-GTTAGAAGCCCTTCAATCTTTTTTGTGTTGAATTATATATTTTTTATGAGTA
* * *
11790 TTTTGGCCAAAAATTGAGGAAAAATTTTT-GAAGTCAGTTTTTGCAAAATTTTAGTTGAAATCGT
253 TTTTGGCCAAAAA-TGAGGAAAAATTTTTCG-GGTCAGTTTTTACAAAATTTTAGTCGAAATCGT
11854 G
316 G
11855 AAAGCAATTC
Statistics
Matches: 576, Mismatches: 55, Indels: 36
0.86 0.08 0.05
Matches are distributed among these distances:
329 1 0.00
330 7 0.01
331 244 0.42
332 228 0.40
333 96 0.17
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (331 bp):
TTTTTAGCGAATAACGCATTTCGGAGCCCCAACTCAGTTTTGCATGAATCTTGGCGCCAAAGATC
CTTGAAATATCTATATTCATCTACCCAAATCTCAGCACAATTGGATTTAAGGATATGTTTTTACG
AGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTAGGAAAAAATTGGGAAAATGATATTA
GAAAGGTTAGAAGCCCTTCAATCTTTTTTGTGTTGAATTATATATTTTTTATGAGTATTTTGGCC
AAAAATGAGGAAAAATTTTTCGGGTCAGTTTTTACAAAATTTTAGTCGAAATCGTGTACTAATCA
TCACGA
Found at i:13207 original size:332 final size:332
Alignment explanation
Indices: 11912--14330 Score: 2751
Period size: 332 Copynumber: 7.2 Consensus size: 332
11902 AAGATTCTCA
* * *
11912 AAATATCTATATTTATGTACCCAAATCTCAGCGAAAGTGGATTTAAGGATATGTTTTTACGAGCA
1 AAATATCTATATTCATCTACCCAAATCTCAGC-AAAATGGATTTAAGGATATGTTTTTACGAGCA
*
11977 TCTGAATCTAGTTTCGATTTAAATAGAAATTAATATGG-AAAAAATTGAAAAAATGATATTAGAA
65 TCTGAATCTAGTTTCGATTTAAATAGAAATTAATATGGAAAAAAATTG-GAAAATGATATTAGAA
* * * * *
12041 AGTTTAGAAGCCCTTCAATCTTTTTTGCGTTGAATTTTATTTTTTATTTTATCAATATTTTGGCC
129 AGGTTAGAAGCCCTTCAATCTTTTTTGCGTTGAA--TTATATATT-TTTTATGAGTATTTTGGCC
* * **
12106 AAAAAATGAGGAAAAATTTTTCGGGTCAGTTTTTTTTTTTTAAAAAAAAGTTTTAGTCGAAATCG
191 AAAAATTGAGGAAAAATTTTTCGGATCAG-------TTTTT--GCAAAA-TTTTAGTCGAAATCG
* * * * * * *
12171 TCTACTAACCATCACGGATTTTAGCTAAAACCGTGTTTCCAGGCCCCGACTCAGTTTTGCATAAT
246 TGTACTAACCATCACGGTTTTTAGCTAAAACCGCGTTTTCGGGCCCCGGCTCAGTTTTGCATAAA
*
12236 TTTTGGCGCCAA-GACTCCTTG
311 CTTTGGCGCCAAGGACTCCTTG
* * * * *
12257 AAATATCCATA-TCAATCTACCCAAATCTCAACAACAATGTATTTAAGAATATGTTTCTACGAGC
1 AAATATCTATATTC-ATCTACCCAAATCTCAGCAA-AATGGATTTAAGGATATGTTTTTACGAGC
* * * * *
12321 ATCAGAATATTGTTTCGATTT-ACTGAAAAATTAAT-TAGG-AAAAAATTGGAAAAATGATATTA
64 ATCTGAATCTAGTTTCGATTTAAAT-AGAAATTAATAT-GGAAAAAAATTGG-AAAATGATATTA
* *
12383 G-AAGCGTCAGAAGCCCTTCAATCTTTTTTGCGTTGTATTATATATTTTTTATGAGTATTTTGGG
126 GAAAG-GTTAGAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTTT-GG
** *
12447 TAAAAAATTTTGCGGAAAAATTTTTC-GAGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTAC
189 CCAAAAA--TTGAGGAAAAATTTTTCGGA-TCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTAC
* * ** ** ** **
12511 TAACCATCACGGTTTTTGGCGAAAAAAGC-AATTCGGAATCCCGGCTCAGTTTTGC-TTGACTTT
251 TAACCATCACGGTTTTTAGCTAAAACCGCGTTTTCGG-GCCCCGGCTCAGTTTTGCATAAAC-TT
* *
12574 TGGCGCCAAAGA-TCTTTG
314 TGGCGCCAAGGACTCCTTG
* * * *
12592 AAATATCTATATTCATCCACCCAAATCTCAGCCAAAGTGGATTTAAGGATACGTTTTTATGAGCA
1 AAATATCTATATTCATCTACCCAAATCTCAG-CAAAATGGATTTAAGGATATGTTTTTACGAGCA
* * ** *
12657 TTTGAATCTAGTTTCGATTTATATAGATTTTAAT-TAGAAAAAAATTGGAAAAATGATATTAGAA
65 TCTGAATCTAGTTTCGATTTAAATAGAAATTAATATGGAAAAAAATTGG-AAAATGATATTAGAA
* * * *
12721 AGGTTAGAAGCCCTTCAATTTTTTTTGCATTGAATTATATATATTTTTTATCAGTATTTTAGCCA
129 AGGTTAGAAGCCCTTCAATCTTTTTTGCGTTGAA-T-TATATATTTTTTATGAGTATTTTGGCCA
* * *
12786 AAAATTGAGGAAATATTTTTCGGATAAGTTTTTGCAAAATTTTAGTCGAAATCGTATACTAACCA
192 AAAATTGAGGAAAAATTTTTCGGATCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCA
* * * *
12851 TCACGGTTTTTAGCTAAAACCGCGTTTTCGGGTCTCGGCTCAGTTTTGCATAAACTGTGGC-ACA
257 TCACGGTTTTTAGCTAAAACCGCGTTTTCGGGCCCCGGCTCAGTTTTGCATAAACTTTGGCGCCA
*
12915 AGGACTCCTTC
322 AGGACTCCTTG
* * **
12926 AAATATCTATATTCATCTACCCAAATCTAAGCTAAAACGGATTTAAGGATATGTTTTTACGATTA
1 AAATATCTATATTCATCTACCCAAATCTCAGC-AAAATGGATTTAAGGATATGTTTTTACGAGCA
*
12991 TCTGAATCTAGTTTCGATTTAAATTGAAATTAATATGGAAAAAAATTGGAAAATGATATTAGAAA
65 TCTGAATCTAGTTTCGATTTAAATAGAAATTAATATGGAAAAAAATTGGAAAATGATATTAGAAA
* * * *
13056 GTTTAGAATCCCTTCAATC-TTTTTGCGTTGAATTATATATTTTTTTATCAGTATTTTAGCCAAA
130 GGTTAGAAGCCCTTCAATCTTTTTTGCGTTGAATTATATA-TTTTTTATGAGTATTTTGGCCAAA
* * * *
13120 AATTGAGGAAATATTTTTCGGATCAGTTTTTGCAAAATTTTAGTCGAAATCGTATACTGACCGTC
194 AATTGAGGAAAAATTTTTCGGATCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATC
* * * *
13185 ACGGTTTTTAGCTAAAACCGCGTTTTCGGGTCTCGGCTCAGTTTTGCATAAACTGTGGC-ACAAG
259 ACGGTTTTTAGCTAAAACCGCGTTTTCGGGCCCCGGCTCAGTTTTGCATAAACTTTGGCGCCAAG
* *
13249 GACTTCTTC
324 GACTCCTTG
* * **
13258 AAATATCTATATTCATCTACCGAAATCTCAGCTAAAACGGATTTAAGGATATGTTTTTACGATTA
1 AAATATCTATATTCATCTACCCAAATCTCAGC-AAAATGGATTTAAGGATATGTTTTTACGAGCA
*
13323 TCTGAATCTAGTTTCGATTTAAATTGAAATTAATATGGAAAAAAATTGGAAAATGATATTAGAAA
65 TCTGAATCTAGTTTCGATTTAAATAGAAATTAATATGGAAAAAAATTGGAAAATGATATTAGAAA
* * * * *
13388 -GTGTAGAATCCCTTCAATCTTTTTTTCATTGAATTTTGTATTTTTTATGAGTATTTTGGCCAAA
130 GGT-TAGAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAA
* * * *
13452 AAATGAGGAAAAATTTTTCGGGTCAGGTTTTGCAAAATTTTAGTCGAAATCGTGTATTAACCATC
194 AATTGAGGAAAAATTTTTCGGATCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATC
* * * * **
13517 ACGATTTTTAGCTAAAACTGAGTTTCCGGGCCCCGGCTCAGTTTTGCATAATTTTTGGCGCCAA-
259 ACGGTTTTTAGCTAAAACCGCGTTTTCGGGCCCCGGCTCAGTTTTGCATAAACTTTGGCGCCAAG
13581 GACTCCTTG
324 GACTCCTTG
* * * *
13590 AAATATCCATATTCATCTACCCAATTTTCAGCAACAATGGATTTAAGGAT-TTTTTTTACGAGCA
1 AAATATCTATATTCATCTACCCAAATCTCAGCAA-AATGGATTTAAGGATATGTTTTTACGAGCA
* ** *
13654 TCAGAATCTTTTTTCGATTT-AATCAAAAATTAAT-TAGGAAAAAAAATTGGAAAATGATATTAG
65 TCTGAATCTAGTTTCGATTTAAAT-AGAAATTAATAT-GG-AAAAAAATTGGAAAATGATATTAG
* * * *
13717 -AAGCGTTAGAAGTCCTTCAATATTTTTTGCGTAGAATTATATATTTTTTATGAGTATTTCGGCC
127 AAAG-GTTAGAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCC
* * *
13781 AAAAATTGTGGAAAAATTTTTC-GAGTC--TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAT
191 AAAAATTGAGGAAAAATTTTTCGGA-TCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAAC
* * ** ** **
13843 CATCACGG-TTTTCGGTGAAAAAAGC-AATTCGGAGCCCCGTG-TCAGTTTTGC-TTGACTTTTG
255 CATCACGGTTTTTAGCT-AAAACCGCGTTTTCGG-GCCCCG-GCTCAGTTTTGCATAAAC-TTTG
*
13904 GCGCCAAAGA-TCCTTG
316 GCGCCAAGGACTCCTTG
* * *
13920 AAATATCTATATTCATCTACCCAAATCTCATCCAAAGTGGATTTAAGGATATGTTTTTACGATCA
1 AAATATCTATATTCATCTACCCAAATCTCA-GCAAAATGGATTTAAGGATATGTTTTTACGAGCA
**
13985 TCTGAATCTAGTTTCGATTTAAATAGAAATTAATATACAAAAAAAATTGGAAAAATGATATTAGA
65 TCTGAATCTAGTTTCGATTTAAATAGAAATTAATAT-GGAAAAAAATTGG-AAAATGATATTAGA
* *
14050 AAGGTTAGAAGCCCTTCAATCTTTTTTGCGTTAAATTATCTA-TTTTTATGAGTATTTTGGCCAA
128 AAGGTTAGAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAA
* * *
14114 AAATTGAGGAAAAATATTTCGGTTCAGTTTTTGCAAAATTTTAGTTGAAATCGTGTACTAACCAT
193 AAATTGAGGAAAAATTTTTCGGATCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCAT
* ** * **
14179 CACGGTTTTTAGCGAAAACCGCGTTGCCGGGCCCC-GCTCAGTTTTGCTTAATGTTTGGCGCC-A
258 CACGGTTTTTAGCTAAAACCGCGTTTTCGGGCCCCGGCTCAGTTTTGCATAAACTTTGGCGCCAA
*
14242 GGACTCCTTA
323 GGACTCCTTG
* * * * * * *
14252 AAATCTCCATATTCATATACCCAAATATCAGCAACAATGGTTTTAAGGATATGTTTTTATGAACA
1 AAATATCTATATTCATCTACCCAAATCTCAGCAA-AATGGATTTAAGGATATGTTTTTACGAGCA
* *
14317 TCAGAATCTTGTTT
65 TCTGAATCTAGTTT
14331 TAGTCAAAAT
Statistics
Matches: 1780, Mismatches: 237, Indels: 127
0.83 0.11 0.06
Matches are distributed among these distances:
329 11 0.01
330 121 0.07
331 153 0.09
332 717 0.40
333 94 0.05
334 227 0.13
335 221 0.12
336 22 0.01
337 22 0.01
338 5 0.00
342 13 0.01
343 14 0.01
344 10 0.01
345 150 0.08
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (332 bp):
AAATATCTATATTCATCTACCCAAATCTCAGCAAAATGGATTTAAGGATATGTTTTTACGAGCAT
CTGAATCTAGTTTCGATTTAAATAGAAATTAATATGGAAAAAAATTGGAAAATGATATTAGAAAG
GTTAGAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAA
TTGAGGAAAAATTTTTCGGATCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCAC
GGTTTTTAGCTAAAACCGCGTTTTCGGGCCCCGGCTCAGTTTTGCATAAACTTTGGCGCCAAGGA
CTCCTTG
Found at i:13736 original size:664 final size:664
Alignment explanation
Indices: 11855--14330 Score: 3141
Period size: 664 Copynumber: 3.7 Consensus size: 664
11845 TGAAATCGTG
* * * * **
11855 AAAGCAATTCGAAGCCCCGGCTCACTTTTACTTGACTTTTGGCGCCAAAGATTCTCAAAATATCT
1 AAAGCAATTCGGAGTCCCGGCTCAGTTTTGCTTGACTTTTGGCGCCAAAGATTCTTGAAATATCT
* * *
11920 ATATTTATGTACCCAAATCTCAGCGAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATC
66 ATATTCATCTACCCAAATCTCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATC
* *
11985 TAGTTTCGATTTAAATAGAAATTAATATGG-AAAAAATTGAAAAAATGATATTAGAAAGTTTAGA
131 TAGTTTCGATTTAAATAGAAATTAATATGGAAAAAAATTGGAAAAATGATATTAGAAAGGTTAGA
* * * *
12049 AGCCCTTCAATCTTTTTTGCGTTGAATTTTATTTTTTATTTTATCAATATTTTGGCCAAAAAATG
196 AGCCCTTCAATCTTTTTTGCATTGAA-TTTATATATT-TTTTATCAGTATTTTGGCCAAAAAATG
** *
12114 AGGAAAAATTTTTCGGGTCAGTTTTTTTTTTTTAAAAAAAAGTTTTAGTCGAAATCGTCTACTAA
259 AGGAAAAATTTTTCGGGTCAG-------TTTTT--GCAAAA-TTTTAGTCGAAATCGTGTACTAA
* * *
12179 CCATCACGGA-TTTTAGCTAAAACCGTGTTTCCAGGCCCCGACTCAGTTTTGCATAATTTTTGGC
314 CCATCAC-GATTTTTAGCTAAAACCGCGTTTCCGGGCCCCGGCTCAGTTTTGCATAATTTTTGGC
* * *
12243 GCCAAGACTCCTTGAAATATCCATA-TCAATCTACCCAAATCTCAACAACAATGTATTTAAGAAT
378 GCCAAGACTCCTTGAAATATCCATATTC-ATCTACCCAAATCTCAGCAACAATGGATTTAAGGAT
* * *
12307 ATGTTTCTACGAGCATCAGAATATTGTTTCGATTTACTGAAAAATTAATTAGG-AAAAAATTGGA
442 ATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAAT-AAAAATTAATTAGGAAAAAAATTGG-
* * *
12371 AAAATGATATTAGAAGCGTCAGAAGCCCTTCAATCTTTTTTGCGTTGTATTATATATTTTTTATG
505 AAAATGATATTAGAAGCGTTAGAAGTCCTTCAATC-TTTTTGCGTTGAATTATATATTTTTTATG
** *
12436 AGTATTTTGGGTAAAAAATTTTGCGGAAAAATTTTTCGAGTCAGTTTTTGCAAAATTTTAGTCGA
569 AGTATTTT-GGCCAAAAA--TTGAGGAAAAATTTTTCGAGTCAGTTTTTGCAAAATTTTAGTCGA
* *
12501 AATCGTGTACTAACCATCACGGTTTTTGGCGAAA
631 AATCGTGTACTAACCATCACGGTTTTTAGCTAAA
*
12535 AAAGCAATTCGGAATCCCGGCTCAGTTTTGCTTGACTTTTGGCGCCAAAGA-TCTTTGAAATATC
1 AAAGCAATTCGGAGTCCCGGCTCAGTTTTGCTTGACTTTTGGCGCCAAAGATTC-TTGAAATATC
* * * *
12599 TATATTCATCCACCCAAATCTCAGCCAAAGTGGATTTAAGGATACGTTTTTATGAGCATTTGAAT
65 TATATTCATCTACCCAAATCTCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGAAT
* ** *
12664 CTAGTTTCGATTTATATAGATTTTAAT-TAGAAAAAAATTGGAAAAATGATATTAGAAAGGTTAG
130 CTAGTTTCGATTTAAATAGAAATTAATATGGAAAAAAATTGGAAAAATGATATTAGAAAGGTTAG
* * *
12728 AAGCCCTTCAATTTTTTTTGCATTGAATTATATATATTTTTTATCAGTATTTTAGCCAAAAATTG
195 AAGCCCTTCAATCTTTTTTGCATTGAATT-TATATATTTTTTATCAGTATTTTGGCCAAAAAATG
* * * * *
12793 AGGAAATATTTTTCGGATAAGTTTTTGCAAAATTTTAGTCGAAATCGTATACTAACCATCACGGT
259 AGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGAT
* * * ** * *
12858 TTTTAGCTAAAACCGCGTTTTCGGGTCTCGGCTCAGTTTTGCATAAACTGTGGC-ACAAGGACTC
324 TTTTAGCTAAAACCGCGTTTCCGGGCCCCGGCTCAGTTTTGCATAATTTTTGGCGCCAA-GACTC
* * * *
12922 CTTCAAATATCTATATTCATCTACCCAAATCTAAGCTAA-AACGGATTTAAGGATATGTTTTTAC
388 CTTGAAATATCCATATTCATCTACCCAAATCTCAGC-AACAATGGATTTAAGGATATGTTTTTAC
** * * **
12986 GATTATCTGAATCTAGTTTCGATTTAAATTGAAATTAA-TATGGAAAAAAATTGGAAAATGATAT
452 GAGCATCAGAATCTTGTTTCGATTT-AATAAAAATTAATTA-GGAAAAAAATTGGAAAATGATAT
* *
13050 TAGAAAG-TTTAGAA-TCCCTTCAATCTTTTTGCGTTGAATTATATATTTTTTTATCAGTATTTT
515 TAG-AAGCGTTAGAAGT-CCTTCAATCTTTTTGCGTTGAATTATATA-TTTTTTATGAGTATTTT
* * *
13113 AGCCAAAAATTGAGGAAATATTTTTCG-GATCAGTTTTTGCAAAATTTTAGTCGAAATCGTATAC
577 GGCCAAAAATTGAGGAAAAATTTTTCGAG-TCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTAC
* *
13177 TGACCGTCACGGTTTTTAGCTAAA
641 TAACCATCACGGTTTTTAGCTAAA
** ** * ** * * * *
13201 ACCGCGTTTTCGG-GTCTCGGCTCAGTTTTGCATAAAC-TGTGGC-ACAAGGACTTCTTCAAATA
1 AAAGC-AATTCGGAGTCCCGGCTCAGTTTTGC-TTGACTTTTGGCGCCAAAGA-TTCTTGAAATA
* * ** **
13263 TCTATATTCATCTACCGAAATCTCAGCTAAAACGGATTTAAGGATATGTTTTTACGATTATCTGA
63 TCTATATTCATCTACCCAAATCTCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGA
*
13328 ATCTAGTTTCGATTTAAATTGAAATTAATATGGAAAAAAATTGG-AAAATGATATTAGAAA-GTG
128 ATCTAGTTTCGATTTAAATAGAAATTAATATGGAAAAAAATTGGAAAAATGATATTAGAAAGGT-
* * * *
13391 TAGAATCCCTTCAATCTTTTTTTCATTGAATTT-TGTATTTTTTATGAGTATTTTGGCCAAAAAA
192 TAGAAGCCCTTCAATCTTTTTTGCATTGAATTTATATATTTTTTATCAGTATTTTGGCCAAAAAA
* *
13455 TGAGGAAAAATTTTTCGGGTCAGGTTTTGCAAAATTTTAGTCGAAATCGTGTATTAACCATCACG
257 TGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACG
* *
13520 ATTTTTAGCTAAAACTGAGTTTCCGGGCCCCGGCTCAGTTTTGCATAATTTTTGGCGCCAAGACT
322 ATTTTTAGCTAAAACCGCGTTTCCGGGCCCCGGCTCAGTTTTGCATAATTTTTGGCGCCAAGACT
* * *
13585 CCTTGAAATATCCATATTCATCTACCCAATTTTCAGCAACAATGGATTTAAGGAT-TTTTTTTAC
387 CCTTGAAATATCCATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTAC
*
13649 GAGCATCAGAATCTTTTTTCGATTTAATCAAAAATTAATTAGGAAAAAAAATTGGAAAATGATAT
452 GAGCATCAGAATCTTGTTTCGATTTAAT-AAAAATTAATTAGG-AAAAAAATTGGAAAATGATAT
* * *
13714 TAGAAGCGTTAGAAGTCCTTCAATATTTTTTGCGTAGAATTATATATTTTTTATGAGTATTTCGG
515 TAGAAGCGTTAGAAGTCCTTCAAT-CTTTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGG
* *
13779 CCAAAAATTGTGGAAAAATTTTTCGAGTC--TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
579 CCAAAAATTGAGGAAAAATTTTTCGAGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAA
* * *
13842 TCATCACGG-TTTTCGGTGAAA
644 CCATCACGGTTTTTAGCT-AAA
* *
13863 AAAGCAATTCGGAGCCCCGTG-TCAGTTTTGCTTGACTTTTGGCGCCAAAGATCCTTGAAATATC
1 AAAGCAATTCGGAGTCCCG-GCTCAGTTTTGCTTGACTTTTGGCGCCAAAGATTCTTGAAATATC
* *
13927 TATATTCATCTACCCAAATCTCATCCAAAGTGGATTTAAGGATATGTTTTTACGATCATCTGAAT
65 TATATTCATCTACCCAAATCTCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGAAT
**
13992 CTAGTTTCGATTTAAATAGAAATTAATATACAAAAAAAATTGGAAAAATGATATTAGAAAGGTTA
130 CTAGTTTCGATTTAAATAGAAATTAATAT-GGAAAAAAATTGGAAAAATGATATTAGAAAGGTTA
* * * * *
14057 GAAGCCCTTCAATCTTTTTTGCGTT-AAATTATCTA-TTTTTATGAGTATTTTGGCCAAAAATTG
194 GAAGCCCTTCAATCTTTTTTGCATTGAATTTATATATTTTTTATCAGTATTTTGGCCAAAAAATG
* * * *
14120 AGGAAAAATATTTCGGTTCAGTTTTTGCAAAATTTTAGTTGAAATCGTGTACTAACCATCACGGT
259 AGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGAT
* * * * *
14185 TTTTAGCGAAAACCGCGTTGCCGGGCCCC-GCTCAGTTTTGCTTAATGTTTGGCGCCAGGACTCC
324 TTTTAGCTAAAACCGCGTTTCCGGGCCCCGGCTCAGTTTTGCATAATTTTTGGCGCCAAGACTCC
* * * * * *
14249 TTAAAATCTCCATATTCATATACCCAAATATCAGCAACAATGGTTTTAAGGATATGTTTTTATGA
389 TTGAAATATCCATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGA
*
14314 ACATCAGAATCTTGTTT
454 GCATCAGAATCTTGTTT
14331 TAGTCAAAAT
Statistics
Matches: 1552, Mismatches: 205, Indels: 95
0.84 0.11 0.05
Matches are distributed among these distances:
661 14 0.01
662 243 0.16
663 198 0.13
664 307 0.20
665 35 0.02
666 226 0.15
667 23 0.01
668 31 0.02
669 201 0.13
670 23 0.01
672 5 0.00
679 48 0.03
680 198 0.13
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (664 bp):
AAAGCAATTCGGAGTCCCGGCTCAGTTTTGCTTGACTTTTGGCGCCAAAGATTCTTGAAATATCT
ATATTCATCTACCCAAATCTCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATC
TAGTTTCGATTTAAATAGAAATTAATATGGAAAAAAATTGGAAAAATGATATTAGAAAGGTTAGA
AGCCCTTCAATCTTTTTTGCATTGAATTTATATATTTTTTATCAGTATTTTGGCCAAAAAATGAG
GAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGATTT
TTAGCTAAAACCGCGTTTCCGGGCCCCGGCTCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTT
GAAATATCCATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGAGC
ATCAGAATCTTGTTTCGATTTAATAAAAATTAATTAGGAAAAAAATTGGAAAATGATATTAGAAG
CGTTAGAAGTCCTTCAATCTTTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAA
TTGAGGAAAAATTTTTCGAGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCAC
GGTTTTTAGCTAAA
Found at i:14451 original size:176 final size:176
Alignment explanation
Indices: 14152--14486 Score: 408
Period size: 176 Copynumber: 1.9 Consensus size: 176
14142 TTTTGCAAAA
** ** * *
14152 TTTTAGTTGAAATCGTGTACTAACCATCACGGTTTTTAGCGAAAACCGCGTTGCCGGGCCCCGCT
1 TTTTAGTCAAAATCGTGTACTAACCATCACGGTTTTTAGCGAAAAAAGCATTGCCGAGCCCCGCT
* * *
14217 CAGTTTTGCTTAATGTTTGGCGCCAGGACTCCTTAAAATCTCCATATTCATATACCCAAATATCA
66 CAGTTTTGCTTAATGTTTGGCGCAAAGACTCCTTAAAATATCCATATTCATATACCCAAATATCA
*
14282 G-CAACAATGGTTTTAAGGATATGTTTTTATGAACATCAGAATCTTG
131 GCCAA-AATGGATTTAAGGATATGTTTTTATGAACATCAGAATCTTG
* * ** *
14328 TTTTAGTCAAAATCGTGTATTAACCATCACGGTTTTTGGCGAAAAAAGCATT-TTGAAGCCCGGC
1 TTTTAGTCAAAATCGTGTACTAACCATCACGGTTTTTAGCGAAAAAAGCATTGCCG-AGCCCCGC
* * ** * *
14392 TCAGTTTTGCTTGACT-TTTGGCGGCAAAGA-TCCTTGAAATATTTATATTCATCTACCCAAATC
65 TCAGTTTTGCTT-AATGTTTGGC-GCAAAGACTCCTTAAAATATCCATATTCATATACCCAAATA
*
14455 TCAGCCAAAGTGGATTTAAGGATATGTTTTTA
128 TCAGCCAAAATGGATTTAAGGATATGTTTTTA
14487 CGAGGATCTG
Statistics
Matches: 133, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
175 1 0.01
176 122 0.92
177 10 0.08
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (176 bp):
TTTTAGTCAAAATCGTGTACTAACCATCACGGTTTTTAGCGAAAAAAGCATTGCCGAGCCCCGCT
CAGTTTTGCTTAATGTTTGGCGCAAAGACTCCTTAAAATATCCATATTCATATACCCAAATATCA
GCCAAAATGGATTTAAGGATATGTTTTTATGAACATCAGAATCTTG
Found at i:14757 original size:152 final size:152
Alignment explanation
Indices: 14455--14760 Score: 413
Period size: 152 Copynumber: 2.0 Consensus size: 152
14445 TACCCAAATC
* ** *
14455 TCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGGATCTGATTCTAAGTTCGATTTAAATAGA
1 TCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATAAGAATCTAAGTTCGATTTAAATAGA
* * *
14520 AATTAATTAGGAAAAAAAATTGGAAAAATGATATTTGAAAGGTTAGAAGCCCTTCAATCTTTGTT
66 AATTAATTAGGAAAAAAAATTGGAAAAATGATATTAGAAAGGTTAAAAGCCATTCAATCTTTGTT
*
14585 GCGTTGAATTATATACTTTTTA
131 GCGTTCAATTATATACTTTTTA
* * *
14607 TCAGCCAAATTGGATTTAAGGATATGTTTTTACGAGCATAAGAATCT-TGTTTCGATTTAATTAG
1 TCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATAAGAATCTAAG-TTCGATTTAAATAG
* *
14671 AAATTAATTAGG-AAAAAATTTGGAAAAAAATTATATTAG-AAGCGTTAAAAGCCATTCAATCTA
65 AAATTAATTAGGAAAAAAAATTGG--AAAAATGATATTAGAAAG-GTTAAAAGCCATTCAATCT-
*
14734 TT-TTGCGTTCAATTATATATTTTTTA
126 TTGTTGCGTTCAATTATATACTTTTTA
14760 T
1 T
14761 GAGTATTTTA
Statistics
Matches: 135, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
151 11 0.08
152 70 0.52
153 52 0.39
154 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (152 bp):
TCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATAAGAATCTAAGTTCGATTTAAATAGA
AATTAATTAGGAAAAAAAATTGGAAAAATGATATTAGAAAGGTTAAAAGCCATTCAATCTTTGTT
GCGTTCAATTATATACTTTTTA
Found at i:20236 original size:334 final size:332
Alignment explanation
Indices: 18981--21808 Score: 3328
Period size: 334 Copynumber: 8.5 Consensus size: 332
18971 AAATATCTAT
*
18981 TTTCGATTT-AATCAAAAATTAATTAGG-AAAAACTTGGAAAAATGATATTAGAAGCGTTAGAAG
1 TTTCGATTTAAAT-AAAAATTAATTAGGAAAAAACTTGGAAAAATGATATTAGAAGCGTTAAAAG
* * *
19044 CCCTTCAATATTTTTTTGGCGTT-AATTATATAA-ATTTTATGAGTATTTTGGCCAAAAATTGAG
65 CCATTCAAT-CTTTTTT-GCGTTGAATTATA-AATTTTTTATGAGTATTTTGGCCAAAAATTGAG
* *
19107 GAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTAGCCATCACGGTTT
127 GAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTT
* * * * *
19172 TTGGCAAAAAAAACGTATTTCGGAGCTTCGACTCAGTTCTGCTTGATTTTTGGCACCAGAACTCC
192 TTGGC--GAAAAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCA-AACTCC
*
19237 TTGAAATATCCATATTCATCTACCCAAATCCCAGCAACAATGGATTTAAGGATATTTTTTTACGA
254 TTGAAATATCCATATTCATCTACCCAAATCCCAGCAACAATGGATTTAAGGATATGTTTTTACGA
* *
19302 GTATCAGAATCTTG
319 GCATCGGAATCTTG
* * * *
19316 TTTCGATTT-AATTAAAATTAATTAGGTAAAAATTTGGAAAAATGATATTAGAAGTGTTAAAAGC
1 TTTCGATTTAAATAAAAATTAATTAGGAAAAAACTTGGAAAAATGATATTAGAAGCGTTAAAAGC
* * * *
19380 CATTCAATCTATTTTGTGTTGAATTATATATTTTTTATGAGTATTTTAGCC-----------AAA
66 CATTCAATCTTTTTTGCGTTGAATTATAAATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAA
* *
19434 AA-TTTTCGGATCAGTTTTTGCAAAATTTTAGTTGAAATCGTGTACTAACCATCACGGCTTTTTT
131 AATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGG--TTTTT
* * * ** * * * * * *
19498 AGCTAAAACCGTGTTTCTGGA-CCCCGGCTCTGTTTTGCATAATTTTTGGCGCCAAGACTACTTG
194 GGCGAAAAACGCATTTC-GGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAA-ACTCCTTG
* *
19562 AAATATCTCA-ATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGTATATGTTTTTACGAGC
257 AAATATC-CATATTCATCTACCCAAATCCCAGCAACAATGGATTTAAGGATATGTTTTTACGAGC
*
19626 ATCAGAATCTTG
321 ATCGGAATCTTG
* *
19638 TTTCGATTT-AATCAAAAATTAATTAGG-AAAAACTTGGAAAAATGATATTAAAAGCGTTAGAAG
1 TTTCGATTTAAAT-AAAAATTAATTAGGAAAAAACTTGGAAAAATGATATTAGAAGCGTTAAAAG
* * * * *
19701 CCCTTCAATCTTTTTTTTGTTGCGTTAAATTATATAA-ATTGTATGAGTATTTTGGCAAAAAATT
65 CCATTCAATC----TTTT-TTGCGTTGAATTATA-AATTTTTTATGAGTATTTTGGCCAAAAATT
* * * * *
19765 GATGAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGAC-AAATTTGTGTATTAACCATCACG
124 GAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAA-TCGTGTACTAACCATCACG
* * *
19829 GTTTTTGCCGAAAAACGTATTTCGGAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCCAATGA-
188 GTTTTTGGCGAAAAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAA--AC
* * * *
19893 TCCTTGAAATATCTATATTCATCTACCAAAATCCCAACCAA-AGTGGATTTAAGGATATGTTTTT
251 TCCTTGAAATATCCATATTCATCTACCCAAATCCC-AGCAACAATGGATTTAAGGATATGTTTTT
* *
19957 ACGAGCATCTGAATCTAG
315 ACGAGCATCGGAATCTTG
* * *
19975 TTTCGATTTAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATTTTAGAAAG-GTTAAAA
1 TTTCGATTTAAATAAAAATTAATTAGGAAAAA-ACTTGGAAAAATGATATTAG-AAGCGTTAAAA
* *
20039 GCCATTCAATCTTTTTTGCGTTGAATCATAAATTTTTTATGAGTATTTTGGCCAAAAATAGAGGA
64 GCCATTCAATCTTTTTTGCGTTGAATTATAAATTTTTTATGAGTATTTTGGCCAAAAATTGAGGA
* * ** *
20104 AAAA-TTTTCGGGCCAGTTTTCTTCAAAATTTTACCCGAAATCGTATACTAACCATCACGGTTTT
129 AAAATTTTTCGGGTCAGTTTT-TGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTT
* * * * * * *
20168 TGGCGAAAAACGCATTTTGGGGTCTCGGCTCAGTTTTCCTTGATTTTTGGCGCTAGAACTCATTG
193 TGGCGAAAAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCA-AACTCCTTG
* * *
20233 AAATATCCATATTCATCAACCCAAATCTCAGCAACAATGGATTTAAGTATATGTTTTTACGAGCA
257 AAATATCCATATTCATCTACCCAAATCCCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCA
*
20298 TCGGAATATTG
322 TCGGAATCTTG
*
20309 TTTCGATTT-AATCAAAAATTAATTAGG-AAAAACTTGGAAAAATGATATTAGAAGCGTTAGAAG
1 TTTCGATTTAAAT-AAAAATTAATTAGGAAAAAACTTGGAAAAATGATATTAGAAGCGTTAAAAG
* *
20372 CCATTCAATCTTTTTTTTGCGTTAAATTATATAA-ATTTTATGAGTATTTTGGCCAAAAATTGAG
65 CCATTCAATC--TTTTTTGCGTTGAATTATA-AATTTTTTATGAGTATTTTGGCCAAAAATTGAG
* * **
20436 GAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACTATCACGAATT
127 GAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTT
* * * *
20501 TTGGCGAAAAACGTATTTCGGAGCCTCGACTCAGTTTTGCTTGACTTTTGGCACCAAAGATCCTT
192 TTGGCGAAAAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAAA-CTCCTT
* * * *
20566 GAAATATCTATATTAATCTACCCAAATCCCAGCCAA-AGTGGATTTAACGATATGTTTTTACGAG
256 GAAATATCCATATTCATCTACCCAAATCCCAG-CAACAATGGATTTAAGGATATGTTTTTACGAG
* *
20630 CATCTGAATCTAG
320 CATCGGAATCTTG
* * *
20643 TTTCGATTTAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATTTTAGAAAG-GTTAAAA
1 TTTCGATTTAAATAAAAATTAATTAGGAAAAA-ACTTGGAAAAATGATATTAG-AAGCGTTAAAA
* *
20707 GCCATTCAATCTTTTTTGCGTTGAATTATAAATTTTTTATGAGTATTTTGGACAAAAATAGAGGA
64 GCCATTCAATCTTTTTTGCGTTGAATTATAAATTTTTTATGAGTATTTTGGCCAAAAATTGAGGA
* *
20772 AAAA-TTTTCGGGTCAGTTTTCTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT
129 AAAATTTTTCGGGTCAGTTTT-TGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTT
* *
20836 TGGCGAAAAACGCATTTCGGAGTCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAGAATTCCTTG
193 TGGCGAAAAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCA-AACTCCTTG
* * * *
20901 AAATATCCATATTCATTTACCCAAATCTCAGCAACAATGGATTTAAGGATATTTTTTTACGAACA
257 AAATATCCATATTCATCTACCCAAATCCCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCA
*
20966 TCGGAATCTTC
322 TCGGAATCTTG
* * * * *
20977 TTCCGATTTAATTAGAAATTAATTAGGAAAAAATTTGCAAAAAATGATATTAGAAGCGTTAAAAG
1 TTTCGATTTAAATAAAAATTAATTAGGAAAAAACTTG-GAAAAATGATATTAGAAGCGTTAAAAG
* * * * *
21042 CCATTCAATCTATTTTGCGTTGAATTATATATTTTTTATGATTATTTT-GCCCAAAATTGAGTAA
65 CCATTCAATCTTTTTTGCGTTGAATTATAAATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAA
* *
21106 AAATTTTTCGGATCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTA
130 AAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTG
* * * * * * * *
21171 GCTAAAACCGCTTTTCCGAGCCTCGTCTCAGTTTTACAT-AGTTTTTGGCGCCAAGACTCCTTCA
195 GCGAAAAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGA-TTTTTGGCGCCAA-ACTCCTTGA
* * * *
21235 AATATCCCA-ATTCACCTACCCAAATCTCAGCAACAATGGATTTAAGTATATGTTTTTACGACCA
258 AATAT-CCATATTCATCTACCCAAATCCCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCA
21299 TCGGAATCTTG
322 TCGGAATCTTG
* * *
21310 TTTCCATTT-AATCAAAAATTAATTAGG-AAAAACTTGGAAAAATGACATTAGAAGCGTTAGAAG
1 TTTCGATTTAAAT-AAAAATTAATTAGGAAAAAACTTGGAAAAATGATATTAGAAGCGTTAAAAG
* * *
21373 CCCTTCAATCTTTTTTTATGCGTTAAATTATATAA-ATTTTATGAGTATTTTGGCCAAAAATTGA
65 CCATTCAATC--TTTTT-TGCGTTGAATTATA-AATTTTTTATGAGTATTTTGGCCAAAAATTGA
* *
21437 GGAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGTCGAAATC----A-T----GTCACGGTT
126 GGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTT
* * * * *
21493 TTTGGCAAAAAACGCATTTCGGAACCTCGACTCAGTTTTGCTTGACTTTTGGAGCCAAAGATCCT
191 TTTGGCGAAAAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAAA-CTCCT
* * * * *
21558 TGAAATATCTATATTAATCTACCTAAATCCCAGCCAA-AGTGGATTTAAGGAAATGTTTTTACGA
255 TGAAATATCCATATTCATCTACCCAAATCCCAG-CAACAATGGATTTAAGGATATGTTTTTACGA
** *
21622 GCATCTAAATCTAG
319 GCATCGGAATCTTG
* * * *
21636 TTTCGATTTAAATAGAAATTAATTAGGAAAAATAATTGGAGAAATGATTTTAGAATG-GTTAAAA
1 TTTCGATTTAAATAAAAATTAATTAGGAAAAA-ACTTGGAAAAATGATATTAGAA-GCGTTAAAA
* * * *
21700 GCCCTTCAATCTTTTTTGCGTTGAATTATAAATTTTTTATAAGTATTTTGGACAAAAATAGAGGA
64 GCCATTCAATCTTTTTTGCGTTGAATTATAAATTTTTTATGAGTATTTTGGCCAAAAATTGAGGA
* * * *
21765 AAAA-TTTCCGGGTCAGTTTTCTTCATAATTTTAGCCGAAATCGT
129 AAAATTTTTCGGGTCAGTTTT-TGCAAAATTTTAGTCGAAATCGT
21809 ACTCCTTTTC
Statistics
Matches: 2137, Mismatches: 274, Indels: 172
0.83 0.11 0.07
Matches are distributed among these distances:
321 1 0.00
322 216 0.10
323 23 0.01
324 23 0.01
325 66 0.03
326 144 0.07
327 40 0.02
328 36 0.02
329 1 0.00
330 1 0.00
331 37 0.02
332 47 0.02
333 258 0.12
334 824 0.39
335 143 0.07
336 39 0.02
337 136 0.06
338 21 0.01
339 78 0.04
340 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (332 bp):
TTTCGATTTAAATAAAAATTAATTAGGAAAAAACTTGGAAAAATGATATTAGAAGCGTTAAAAGC
CATTCAATCTTTTTTGCGTTGAATTATAAATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAA
AATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGG
CGAAAAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAAACTCCTTGAAAT
ATCCATATTCATCTACCCAAATCCCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCATCGG
AATCTTG
Found at i:22226 original size:301 final size:298
Alignment explanation
Indices: 21502--22274 Score: 984
Period size: 301 Copynumber: 2.6 Consensus size: 298
21492 TTTTGGCAAA
* *
21502 AAACGCATTTCGGAACCTCGACTCAGTTTTGCTTGACTTTTGGAGCCAAAGATCCTTGAAATATC
1 AAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCCAAAGATCCTTGAAATATC
*
21567 TATATTAATCTACCTAAATCCCAGCCAAAGTGGATTTAAGGAAATGTTTTTACGAGCATCTAAAT
66 TATATTAATCTACCTAAATCCCAGCCAAAGTGGATTTAAGGAAATGTTTTTACGAGCATCTGAAT
* * **
21632 CTAGTTTCGATTTAAATAGAAATTAATTAGGAAAAATAATTGGAGAAATGATTTTAGAATGGTTA
131 CTAGTTTCGATTTAAATAGAAATTAATTAGG-AAAA-AATTGGAAAAATAACATTAGAATGGTTA
* *
21697 AAAGCCCTTCAATCTTTTTTGCGTTGAATTATAAATTTTTTATAAGTATTTTGGACAAAAATAGA
194 AAAGCCCTTCAATCTTTTTTGCGTTAAATTATAAATATTTTATAAGTATTTTGGACAAAAATAGA
* * *
21762 GGAAAAATTTCCGGGTCAGTTTTCTTCATAATTTTAGCCG
259 GGAAAAATTTCCGGGTCAATTTTCTGCAAAATTTTAGCCG
* * * * * *
21802 AAATCGTACTCCTTTTCCGAGCCCCGGCTCAGTTTTGCAT-AGTTTTTGGCGCC-AAGACTCCTT
1 AAA-CG-----CATTTCGGAGCCTCGACTCAGTTTTGCTTGA-CTTTTGGCGCCAAAGA-TCCTT
* * * * * * * * * *
21865 CAAATATCCCA-ATTCATCAACCCAAATCTCAGCAAAAATGGATTTAAGTATATGTTTTTACGAG
58 GAAATAT-CTATATTAATCTACCTAAATCCCAGCCAAAGTGGATTTAAGGAAATGTTTTTACGAG
* * * *
21929 CATCGGAATCTTGTTTCGATTT-AATCAAAAATTAATTAGGAAAAACTTGGAAAAATAACATTAG
122 CATCTGAATCTAGTTTCGATTTAAAT-AGAAATTAATTAGGAAAAAATTGGAAAAATAACATTAG
* *
21993 AA-GCGTTAGAAGCCCTTCAATCTTTTTTTATGCGTTAAATTATATAA-ATTTTATTAGTATTTT
186 AATG-GTTAAAAGCCCTTCAATC--TTTTT-TGCGTTAAATTATA-AATATTTTATAAGTATTTT
* * * *
22056 GGCCAAAAATTGAGGAAAAATTTTTCGGGTCAATTTT-TGCAAAATTTTAGTCG
246 GGACAAAAATAGAGGAAAAA-TTTCCGGGTCAATTTTCTGCAAAATTTTAGCCG
22109 AAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCCAAAGATCCTTGAAATATC
1 AAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCCAAAGATCCTTGAAATATC
*
22174 TATATTAATCTACCTAAATCCCAGCCAAAGTGGATTTAAGGAAATTTTTTTACGAGCATCTGAAT
66 TATATTAATCTACCTAAATCCCAGCCAAAGTGGATTTAAGGAAATGTTTTTACGAGCATCTGAAT
22239 CTAGTTTCGATTTAAATAGAAATTAATTAGGAAAAA
131 CTAGTTTCGATTTAAATAGAAATTAATTAGGAAAAA
22275 TAATTAGATA
Statistics
Matches: 395, Mismatches: 58, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
300 5 0.01
301 129 0.33
302 8 0.02
303 1 0.00
304 34 0.09
305 12 0.03
306 127 0.32
307 63 0.16
308 16 0.04
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (298 bp):
AAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCCAAAGATCCTTGAAATATC
TATATTAATCTACCTAAATCCCAGCCAAAGTGGATTTAAGGAAATGTTTTTACGAGCATCTGAAT
CTAGTTTCGATTTAAATAGAAATTAATTAGGAAAAAATTGGAAAAATAACATTAGAATGGTTAAA
AGCCCTTCAATCTTTTTTGCGTTAAATTATAAATATTTTATAAGTATTTTGGACAAAAATAGAGG
AAAAATTTCCGGGTCAATTTTCTGCAAAATTTTAGCCG
Found at i:22440 original size:192 final size:192
Alignment explanation
Indices: 22112--22466 Score: 473
Period size: 192 Copynumber: 1.8 Consensus size: 192
22102 TTAGTCGAAA
* * *
22112 CGCATTTCGGAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCCAAAGATCCTTGAAATATCTAT
1 CGCATTTCGAAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCCAAAGATCATTGAAATATCCAT
* * * * * *
22177 ATTAATCTACCTAAATCCCAGCCAAAGTGGATTTAAGGAAATTTTTTTACGAGCATCTGAATCTA
66 ATTAATCAACCCAAATCCCAGCCAAAATGGATTTAAGGAAATTTTTCTACGAGCAACAGAATCTA
22242 GTTTCGATTTAAATAGAAATTAATTAGGAAAAATAATTAGATAAATGATTTTTGGCGAAAAC
131 GTTTCGATTTAAATAGAAATTAATTAGGAAAAATAATTAGATAAATGATTTTTGGCGAAAAC
* * *
22304 CGCATTTCGAAGTCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAGAA-CTCATTGAAATATCCA
1 CGCATTTCGAAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCCA-AAGATCATTGAAATATCCA
** * * * *
22368 TATTCTTCAACCCAAATCTCC-G-TAACAATGGATTTAAGGATATTTTTCTCCGGGCAACAGAAT
65 TATTAATCAACCCAAATC-CCAGCCAA-AATGGATTTAAGGAAATTTTTCTACGAGCAACAGAAT
* * *
22431 TTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAA
128 CTAGTTTCGATTTAAATAGAAATTAATTAGGAAAAA
22467 ATTTGCAAAA
Statistics
Matches: 139, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
191 2 0.01
192 133 0.96
193 4 0.03
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (192 bp):
CGCATTTCGAAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCCAAAGATCATTGAAATATCCAT
ATTAATCAACCCAAATCCCAGCCAAAATGGATTTAAGGAAATTTTTCTACGAGCAACAGAATCTA
GTTTCGATTTAAATAGAAATTAATTAGGAAAAATAATTAGATAAATGATTTTTGGCGAAAAC
Found at i:23072 original size:336 final size:332
Alignment explanation
Indices: 22288--23131 Score: 1006
Period size: 336 Copynumber: 2.5 Consensus size: 332
22278 TTAGATAAAT
* *
22288 GATTTTTGGCGAAAACCGCATTTCGAAGTCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAGAA-
1 GATTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCA-AAG
* * * * * *
22352 CTCATTGAAATATCCATATTCTTCAACCCAAATCTCC-GTAACAATGGATTTAAGGATAT-TTTT
65 ATCCTTGAAATATCTATATT-ATCTACCCAAATC-CCAGCAACAATGGATTTAAGGATATGTTTT
* * * * *
22415 CTCCGGGCAACAGAATTTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAATTTGCAAAAAAT
128 -TACGAGCATCAGAATCTTGTTTCGATTTAA-TAGAAATTAATTAGGAAAAAACTTGCAAAAAAT
**
22480 GATATTAGAAGCGTTAAAAGCCATTCAATCTATTTTACGTTGAAATATATATTTTTTATGAGTAT
191 GATATTAGAAGCGTTAAAAGCCATTCAATCTATTTTACGTTGAAATATATAAATTTTATGAGTAT
*
22545 TTTAGCCAAAAATTGACTAAAAAATTTTCGGATCAGTTTTTGCAAAATTTTAGTCGAAATCGTGT
256 TTTAGCCAAAAATTGACGAAAAAATTTTCGGATCAGTTTTTGCAAAATTTTAGTCGAAATCGTGT
*
22610 ACTAACTATCAC
321 ACTAACCATCAC
* ** * * * * *
22622 GATTTTTAGCTTAAACCGCTTTTCCGAGCCCCGTCTCAGTTTTGCAT-AGTTTTTGGCGCC-AAG
1 GATTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGA-TTTTTGGCGCCAAAG
* * *
22685 ACTCCTTCAAATATCCTA-ACTTATCTACCCAAATCTCAGCAACAATGGATTTAAGTATATGTTT
65 A-TCCTTGAAATAT-CTATA-TTATCTACCCAAATCCCAGCAACAATGGATTTAAGGATATGTTT
* * * *
22749 TTACGAGCATCGGAATCTTGTTTCGATTTAATCAAAAATTAATTAGG-ATAAACTTG-GAAAAAT
127 TTACGAGCATCAGAATCTTGTTTCGATTTAAT-AGAAATTAATTAGGAAAAAACTTGCAAAAAAT
* * *
22812 GATATTAGAAGCGTTAGAAGCCCTTCAATCTTTTTTTATGCGTT-AAATTATATAAATTTTATGA
191 GATATTAGAAGCGTTAAAAGCCATTCAATC-TATTTTA--CGTTGAAA-TATATAAATTTTATGA
* * * * *
22876 GTATTTTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAATTTTTTGCAAAATTTTAGTCGAAAT
252 GTATTTTAGCCAAAAATTGACGAAAAAATTTTCGGATC-AGTTTTTGCAAAATTTTAGTCGAAAT
22941 CGTGTACTAACCATCAC
316 CGTGTACTAACCATCAC
* * * *
22958 GGTTTTTGGCGAAAAACGCATTTCGGAGCCTCGACTCAATTTTGCTTGACTTTTGGCGCCAAAGA
1 GATTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAAAGA
* * * *
23023 TCCTTGAAATATCTATATTAATCTATCTAAATCCCAGCCAA-AGTGGATTTAAGGAAATGTTTTT
66 TCCTTGAAATATCTATATT-ATCTACCCAAATCCCAG-CAACAATGGATTTAAGGATATGTTTTT
* *
23087 ACGAGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTAGG
129 ACGAGCATCAGAATCTTGTTTCGATTT-AATAGAAATTAATTAGG
Statistics
Matches: 429, Mismatches: 62, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
332 36 0.08
333 16 0.04
334 131 0.31
335 64 0.15
336 171 0.40
337 11 0.03
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (332 bp):
GATTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAAAGA
TCCTTGAAATATCTATATTATCTACCCAAATCCCAGCAACAATGGATTTAAGGATATGTTTTTAC
GAGCATCAGAATCTTGTTTCGATTTAATAGAAATTAATTAGGAAAAAACTTGCAAAAAATGATAT
TAGAAGCGTTAAAAGCCATTCAATCTATTTTACGTTGAAATATATAAATTTTATGAGTATTTTAG
CCAAAAATTGACGAAAAAATTTTCGGATCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAA
CCATCAC
Done.