Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011425.1 Corchorus capsularis cultivar CVL-1 contig11446, 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: 24575
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:96 original size:34 final size:32
Alignment explanation
Indices: 23--108 Score: 109
Period size: 32 Copynumber: 2.6 Consensus size: 32
13 AAAGTAGTCG
**
23 AGCCGCCCCACCGGGGCGGCCTGCCCCGGCGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCCCGGCGA
* *
55 AGCCGCCCCAGTGGGGCGGCCTGCCCAATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCC--CGGCGA
*
89 AGCCGCCCAAGTGGGGCGGC
1 AGCCGCCCCAGTGGGGCGGC
109 ACTGGACATC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 24 0.51
34 23 0.49
ACGTcount: A:0.13, C:0.41, G:0.40, T:0.07
Consensus pattern (32 bp):
AGCCGCCCCAGTGGGGCGGCCTGCCCCGGCGA
Found at i:5267 original size:38 final size:38
Alignment explanation
Indices: 5225--5305 Score: 162
Period size: 38 Copynumber: 2.1 Consensus size: 38
5215 GTATCTTGGG
5225 TGCAGGTATCTTGGGTACACCTTTGAGTATCCCACCGT
1 TGCAGGTATCTTGGGTACACCTTTGAGTATCCCACCGT
5263 TGCAGGTATCTTGGGTACACCTTTGAGTATCCCACCGT
1 TGCAGGTATCTTGGGTACACCTTTGAGTATCCCACCGT
5301 TGCAG
1 TGCAG
5306 AGATATAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.31
Consensus pattern (38 bp):
TGCAGGTATCTTGGGTACACCTTTGAGTATCCCACCGT
Found at i:6612 original size:7 final size:7
Alignment explanation
Indices: 6600--6643 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
6590 GAAAATCAGA
6600 TCCAATT
1 TCCAATT
6607 TCCAATT
1 TCCAATT
6614 TCCAATT
1 TCCAATT
6621 TCCAATT
1 TCCAATT
6628 TCCAATT
1 TCCAATT
6635 TCCAATT
1 TCCAATT
6642 TC
1 TC
6644 TACTGGGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (7 bp):
TCCAATT
Found at i:10523 original size:19 final size:19
Alignment explanation
Indices: 10499--10537 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
10489 AAGTCCCAAG
10499 CTCTTAACCATTGTGGTGT
1 CTCTTAACCATTGTGGTGT
10518 CTCTTAACCATTGTGGTGT
1 CTCTTAACCATTGTGGTGT
10537 C
1 C
10538 CCGTTGGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (19 bp):
CTCTTAACCATTGTGGTGT
Found at i:13627 original size:333 final size:329
Alignment explanation
Indices: 12658--14837 Score: 1785
Period size: 333 Copynumber: 6.7 Consensus size: 329
12648 ACCCATAATG
* * * * *
12658 GCAAAAA-TGACCTGAAATATTTTTCTTAAATTTTTGG-TAAAAATACTCAT--AAAATATATAA
1 GCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCT-AAAATACTCATAAAAAATATATAA
** * * * * * ** **
12719 TTTAATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTCTCATAATTTTCTGAAT
65 TTTAACACCAAAAAGATTGAAGGGCTTTTCACACTTCTAATATCGTTTTTCATTTTTTTCCAAAT
* * * * * *
12784 TAATTTCTAATTAAATCGAAACAAGAATCAAATGCACATAAAAAC-AA-CCTTAAGTCCAATGTG
130 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTG
* * * * **
12847 GCTGAGATTTGATTAAATGAATAAAGATATTTCAAGGAGTCTCAGTGCC--AAA--AT-----A-
195 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT-TGACCCAAAAATCATGAAAAAC
* * * * *
12902 -GAGCCGTGG-TCCTGAAACGTGTTTTTAGACTAAAAACCATGATGGTTAGTAAATGATTTCGGC
259 TGAGCCG-GGCTCC-GGAACGCGTTTTTAG-CCAAAAACCATGATGGTTAGTACACGATTTCGGC
12965 TAAAATTTT
321 TAAAATTTT
* *
12974 GAAAAAATTGACCCTG-AAGATATTTCCTCAATTTTTGGCTAGAATACTCATAAAAAATATATAA
1 GCAAAAATTGACCC-GAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAA
* * * * * * *
13038 TTTGACATCAAAAAGATTTAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTT-C---
65 TTTAACACCAAAAAGATTGAAGGGCTTTTCACACTTCTAATATCGTTTTTCAT-TTTTTTCCAAA
* * * *
13099 ------T-GAATTAAATCGAGACAAGATTTAGATGCTCGTAAAAACAAATTCTTAAATCTAATGT
129 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGT
** *
13157 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGACACCAAAAATCATTCAGAA
194 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGAC-CCAAAAATCATGAAAAA
* * * * * *
13222 CTGAGTCAGGCCCCGGAACGCATTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTA
258 CTGAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCTA
13287 AAATTTT
323 AAATTTT
* * *
13294 GCAAAAATTGACCCGAAAGATATTTCCTCAATGTTTGGCTAGAATACTCATAAAAAAAATATAAT
1 GCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAAT
* * * * * *
13359 TTGACATCAAAAAGATTTAAGGGCTTTTAACACTTCTAATATTGTTTTTCCTATTTTTTTTTCCG
66 TTAACACCAAAAAGATTGAAGGGCTTTTCACACTTCTAATATCGTTTTT-C-A--TTTTTTTCCA
*
13424 AATTAATTTCTAATTAAATCGAGACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAAT
127 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAAT
*
13489 GTGGCTGAGATTTGGTT-GATGAATATAGATATTTTAAGGAGTCTTGACCCAAAAAATCATGAAA
192 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGACCC-AAAAATCATGAAA
* * * * *
13553 AACTTAGTCGGGCTCCGGAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGT
256 AACTGAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGC
13618 TAAAATTTT
321 TAAAATTTT
* * * * ** ** *
13627 GCAAATATTGACCCAAAAGATTTTTCCTCTATTTTAAGAGAAAATACTCAT-AAAAATATATCAT
1 GCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAAT
* * * * * * *
13691 TCAA-AGCTAAAAA-AATAAAAGTCTTTGTCGA-GCTTCTAATATCGTTTTTCCTATTTTATTTC
66 TTAACA-CCAAAAAGATTGAAGGGCTTT-TC-ACACTTCTAATATCGTTTTT-C-ATTTT-TTTC
* * * ** *
13753 CAAATTAATTTATGATTAAATCGAAACAAGATTTAGAAACTCATAAAAACAAATCCTTAAATAC-
125 CAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CT
* * * * *
13817 AATGTGGCAGAGATTTAGTTAGATGAATATAAATATATTTTAAGGAGTCTTGTCGCC-AAAATCA
189 AATGTGGCTGAGATTTGGTTAGATGAATAT--AGATATTTCAAGGAGTCTTGAC-CCAAAAATCA
* * * * *
13881 TGCAAAACTGACCCAAGG-TCCCAGAACGCGTTTTTAGCCTAAAAATCATGAT-G--A-TACACG
251 TGAAAAACTGAGCC-GGGCT-CCGGAACGCGTTTTTAGCC-AAAAACCATGATGGTTAGTACACG
*
13941 ATTTCGGTTAAAATTTT
313 ATTTCGGCTAAAATTTT
* * * *
13958 GCAAAAATTGACCTG-AA-ATACTTTCATCAATTTTTAGGC-ACAATACTCATTAAAAATATATA
1 GCAAAAATTGACCCGAAAGATA-TTTCCTCAATTTTT-GGCTAAAATACTCATAAAAAATATATA
*
14020 ATTCAACACCAAAAAGATTGAAGGG-TTTCTCACGA-TTCTAATATC-----T--TTTTTTT--A
64 ATTTAACACCAAAAAGATTGAAGGGCTTT-TCAC-ACTTCTAATATCGTTTTTCATTTTTTTCCA
* ** * * *
14074 AATTAATTTTTAATTAAATCGAAACATTATTCAAATACTCGTAACAACAAATCCTTAAATCTAAT
127 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAAT
* * * * *
14139 GTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGG-GATTTTGCCACCAAAAACCATG-C
192 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG-TCTTGAC-CCAAAAATCATGAA
* * * * ** *
14202 AAACTGACCCGGGGTCTCGAAACGCGTTTTTAGCAAAAATAAAAAAGTGAAAAATCGTGATAGTA
255 AAACTGAGCCGGGCTC-CGGAACGCGTTTTTAGC--CAA-AAACCA-TG----AT-G-GTTAGTA
*
14267 CACGATTTTGGCTAAAATTTT
309 CACGATTTCGGCTAAAATTTT
* * * * * * * *
14288 G-TAAAATTGACCCGAAATATTTTTCCTCACTTTTTAGCCACAATACTCAT--AAAATATATGAT
1 GCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAAT
* * * * * * *
14350 TTAACGCCAAAACA-ATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTAAAT
66 TTAACACCAAAA-AGATTGAAGGGCTTTTCACACTTCTAATATCGTTTTTCATTTTTTTCCAAAT
*
14414 TAATTTCTAATTAAATCGAAACAAGATTCACATGCTCGTAAAAACAAATCCTTAAAT-TCAATGT
130 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCT-AATGT
* * * * * **
14478 GGCTAAAATTTGATTAGATTAATATATAGATATTTCAAAAGGAAT-TTCGGGGCCAAAAATCAT-
194 GGCTGAGATTTGGTTAGA-TGA-ATATAGATATTTC--AAGGAGTCTT--GACCCAAAAATCATG
* * * * **
14541 ACAAAACTAAGCCGGGGCCCCGAAACGCATTTTTAGCCAAAAACCATGATGGTTAGTACATAATT
253 A-AAAACTGAGCC-GGGCTCCGGAACGCGTTTTTAGCCAAAAACCATGATGGTTAGTACACGATT
*
14606 TCTGCTAAAATTTT
316 TCGGCTAAAATTTT
* * * * *
14620 GCAAAAAATGACCGGAAA-ACTTTTTCCGTCAATTTTTGGCTAAAATACTCATAAAATATATACA
1 GCAAAAATTGACCCGAAAGA-TATTTCC-TCAATTTTTGGCTAAAATACTCATAAAAAATATATA
* * * * ** * * **
14684 ATTTAACGCCAAAAATATTGGAGGACTTTTCACGTTTTTAATATCGTTTTTCATATTTTTCTGAA
64 ATTTAACACCAAAAAGATTGAAGGGCTTTTCACACTTCTAATATCGTTTTTCATTTTTTTCCAAA
* * *
14749 TTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAA-AATTTCTTAAATCTAATGT
129 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGT
* * *
14813 AGCTGAGATATGATTAGATGAATAT
194 GGCTGAGATTTGGTTAGATGAATAT
14838 GTAAAACTTA
Statistics
Matches: 1538, Mismatches: 217, Indels: 201
0.79 0.11 0.10
Matches are distributed among these distances:
309 31 0.02
310 4 0.00
311 54 0.04
313 3 0.00
315 2 0.00
316 10 0.01
317 77 0.05
318 13 0.01
319 136 0.09
320 153 0.10
321 18 0.01
322 10 0.01
323 6 0.00
324 4 0.00
326 1 0.00
327 1 0.00
328 41 0.03
329 20 0.01
330 75 0.05
331 161 0.10
332 83 0.05
333 196 0.13
334 134 0.09
335 47 0.03
336 113 0.07
337 76 0.05
338 4 0.00
339 17 0.01
340 4 0.00
341 15 0.01
342 25 0.02
343 4 0.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (329 bp):
GCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAAT
TTAACACCAAAAAGATTGAAGGGCTTTTCACACTTCTAATATCGTTTTTCATTTTTTTCCAAATT
AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGG
CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGACCCAAAAATCATGAAAAACTG
AGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCTAAAA
TTTT
Found at i:15117 original size:297 final size:296
Alignment explanation
Indices: 14543--15134 Score: 719
Period size: 297 Copynumber: 2.0 Consensus size: 296
14533 AAAATCATAC
* * * *
14543 AAAACTAAGCCGGGGCCCCGAAACGCATTTTTAGCCAAAAACCATGATGGTTAGTACATAATTTC
1 AAAACTAAGCCGGGGCCCCAAAACACATTGTTAGCCAAAAACCATGATGGTTAGTACACAATTTC
* * *
14608 TGCTAAAATTTTGCAAAAAATGACCGGAAAACTTTTTCCGTCAATTTTTGGCTAAAATACTCATA
66 GGCTAAAATTTTGCAAAAAATGACC-GAAAACTTTTTCCGTCAATTTTTAGCCAAAATACTCATA
* * * *
14673 AAATATATACAATTTAACGCCAAAAATATTGGAGGACTTTTCACGTTTTTAATATCGTTTTTCAT
130 AAATATATACAATTCAACGCCAAAAATATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCAT
* *
14738 ATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAAATTTCTTA
195 ATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAAATTCCTTA
* *
14803 AATCTAATGTAGCTGAGA-TATGATTAGATGAATATGT
260 AATCCAATATAGCTGAGATTATG-TTAGATGAATATGT
* * * * * * *
14840 AAAACTTAGCCGGGG-CCCAAAACACGTTGTTAGCCAAAAACCGTGATGTTTATTACCCGATTTC
1 AAAACTAAGCCGGGGCCCCAAAACACATTGTTAGCCAAAAACCATGATGGTTAGTACACAATTTC
* * * * * *
14904 GGTTAGAATTTTGCAAAAATTGACTC-AAAAGTTATTTCC-TCAATTTTTATCCACAATACTCAT
66 GGCTAAAATTTTGCAAAAAATGAC-CGAAAACTT-TTTCCGTCAATTTTTAGCCAAAATACTCAT
* *
14967 AAAA-ATTATATAATTCAACGCCAAAAATATTGAAGGACTTTTCATGCTTCTAATATCGTTTTTC
129 AAAATA-TATACAATTCAACGCCAAAAATATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTC
* ** * ** *
15031 CTATTATTTGCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGTTTTACAAA-T
193 ATATT-TTT-CCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCG-TAAAAAAATT
* *
15095 CCTTAAATCCAATATGGCTGAGATTTTGTTAGATGAATAT
255 CCTTAAATCCAATATAGCTGAGATTATGTTAGATGAATAT
15135 AGACATTTCA
Statistics
Matches: 249, Mismatches: 39, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
294 1 0.00
295 86 0.35
296 67 0.27
297 87 0.35
298 8 0.03
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (296 bp):
AAAACTAAGCCGGGGCCCCAAAACACATTGTTAGCCAAAAACCATGATGGTTAGTACACAATTTC
GGCTAAAATTTTGCAAAAAATGACCGAAAACTTTTTCCGTCAATTTTTAGCCAAAATACTCATAA
AATATATACAATTCAACGCCAAAAATATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCATA
TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAAATTCCTTAA
ATCCAATATAGCTGAGATTATGTTAGATGAATATGT
Found at i:16065 original size:332 final size:332
Alignment explanation
Indices: 14850--16768 Score: 1528
Period size: 332 Copynumber: 5.9 Consensus size: 332
14840 AAAACTTAGC
* * * * * * *
14850 CGGGG-CCCAAAACACGTTGTTAGCCAAAAACCGTGATGTTTATTACCCGATTTCGGTTAGAATT
1 CGGGGTCCCAAAACGCGTTTTTAGCCAAAAACAGTGATG-ATATTACACGATTTCGGCTAAAATT
* * *
14914 TTGCAAAAATTGACTCA-AAAGT-TATTTCCTCAATTTTTATCCACAATACTCATAAAAATTATA
65 TTGCAAAAATTGAC-CAGAAA-TATATTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATA
* * * * * * *
14977 TAATTCAACGCCAAAAATATTGAAGGACTTTTCATGCTTCTAATATCGTTTTTCCT-ATTATTTG
128 TAATTCAAAGCCAAAAAAATTGAAGGGCTTTTCACGTTTCTAATATCGTTTTTCATAATT-TTTT
* * * *** *
15041 CCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGT-TTTACAAATCCTTAAATCC
192 CCGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGC
* * * * * * **
15105 AATATGGCTGAGATTTTG-TTAGATGAATATAGACATTTCAAGGAGTCTCGGCACCAAAAATCAT
257 AATGTGGCTGA-AATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGACGTCAAAAATCAT
* *
15169 GCAACAGTGAAC-
321 GCAAAACTG-ACT
* * * * * * * * *
15181 CAGGGCCCCAGAATGCGTTTTTAGACAAAAACCGCGATTTCGACTAACATACACGATTTCGGTTA
1 CGGGGTCCCAAAACGCGTTTTTAGCCAAAAACAGTGA--T-GA-T-A-TTACACGATTTCGGCTA
* **
15246 ATATTTTGCAAAAATTGACCAGAAATAT-TTTCC-C------T---C--AAT-CT-A-AAATGAT
60 AAATTTTGCAAAAATTGACCAGAAATATATTTCCTCAATTTTTAGCCAAAATACTCATAAAAAAT
* * ** * * **
15295 CATGTAGTTCAACTCCAAAAAGATTGGAA-GACTTTTCACGCTTT-TAATA-CCATTTTCAT-A-
125 -ATATAATTCAAAGCCAAAAAAATT-GAAGGGCTTTTCACG-TTTCTAATATCGTTTTTCATAAT
* *
15355 TTTTTCCGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
187 TTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * *
15420 AATGCAATGTGGATGAGATTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAA
252 AATGCAATGTGGCTGAAATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGACGTCAAAAA
*
15485 TCATGCAAAGCTGAGC-
317 TCATGCAAAACTGA-CT
** * * *
15501 CGGGACCCCGAAACGCGTTTTTAG-CAAAAAAACGTGATG-T-GTACACGATTTCGGCTAAAATT
1 CGGGGTCCCAAAACGCGTTTTTAGCCAAAAACA-GTGATGATATTACACGATTTCGGCTAAAATT
* * * ** * * * *
15563 TTGCAAAAAATGATCAGAGAA-AT-TTTCCTCAATTTTTGGATAAAATACTCGTGAAATATATGT
65 TTGCAAAAATTGACCAGA-AATATATTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATAT
* * * * * *
15626 AATTTAAAGTCAAAAAGATTGGAGGACTTTTCACACTTT-TCATATATCGTTTTTCAT-A-TTTT
129 AATTCAAAGCCAAAAAAATTGAAGGGCTTTTCAC-GTTTCT-A-ATATCGTTTTTCATAATTTTT
*
15688 TCTGAATTAATTTCTAATTAAATCGAAACT-AGATTCAGATGCTCGTAAAAACAAATCCTTAAAT
191 TCCGAATTAATTTCTAATTAAATCGAAA-TAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT
* * *
15752 GCAATGTGGCTGAAATTTGATTAGATGAAT-TGGAAATCTCAAGGAGTCTTGACGTCAAAAATAA
255 GCAATGTGGCTGAAATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGACGTCAAAAATCA
15816 TGCAAAACTGACT
320 TGCAAAACTGACT
* * * * *
15829 CGGGGTCCTAAAACACTTTTTTAGCCAAAAACCGTGATGGATATTACACGTTTTCGGCTAAAATT
1 CGGGGTCCCAAAACGCGTTTTTAGCCAAAAACAGTGAT-GATATTACACGATTTCGGCTAAAATT
* * * **
15894 TTGCAAAAATTGATC-GAAAATATATTTCCTCAAATTTTGGTTAAAATACTCATAAAAAATATAT
65 TTGCAAAAATTGACCAG-AAATATATTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATAT
* * * * *
15958 AATTCAACA-CCGAAAATATTGAAGGGTTTTTTACGTTTCTAATATCGTTTTTCCTAATTTTTTC
129 AATTCAA-AGCCAAAAAAATTGAAGGGCTTTTCACGTTTCTAATATCGTTTTTCATAATTTTTTC
* *
16022 CGAATTAATTTCTAATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCA
193 CGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCA
* * * * *
16087 ATGTGGCTGAAATTTAATTAGATGAATATAGATATCTCAAGGAGTCTTGGCGTAAAAAATCCTTC
258 ATGTGGCTGAAATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGACGTCAAAAATCATGC
* *
16152 AAAACTTACC
323 AAAACTGACT
* * * * * * * * *
16162 CAGGG-CTTCGAAGCGCGATTTTAGCCCAAAAAAAAAATCG-TGATATTACACGATTTTGGTTAA
1 CGGGGTC-CCAAAACGCGTTTTTAG-CC--AAAAACAGT-GATGATATTACACGATTTCGGCTAA
* * * * *
16225 TATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTAGCCACAATAATCATAAAAAATA
61 AATTTTGCAAAAATTGACCAGAAATATATTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATA
* * ** * * **
16290 TATAATTTAAAGCCAAAAAAATT-AAAGTATTTTCACGCTTCTAATTTCGTTTTTC-TTTTTTTT
126 TATAATTCAAAGCCAAAAAAATTGAAGGGCTTTTCACGTTTCTAATATCGTTTTTCATAATTTTT
** * * * *
16353 TTAGAATTAATTTCTAATTAAAACGAAACATGATTCAGATGCTTGT-------AA-----AAA--
191 TCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATG
* * * *
16404 CAA--TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGACG-CAAAAAATCA
256 CAATGTGGCTGAAATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGACGTC-AAAAATCA
* *
16466 TTCAAAATTGAACT
320 TGCAAAACTG-ACT
* * * * * * *
16480 ---AGTCCCAGGAACGCG-TTTTAGTCAAAAACATTGATGATTATTATACGATTTCAGCTCAAAT
1 CGGGGTCCCA-AAACGCGTTTTTAGCCAAAAACAGTGATGA-TATTACACGATTTCGGCTAAAAT
* * * * *
16541 TTTACAAAAATTGACCTGAAAGATATTTCCTCAATTTTTAGCCATAATACTCATATAAAATATAT
64 TTTGCAAAAATTGACCAGAAATATATTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATAT
* * *
16606 AATTCAACA-CCAAAAAAATTAAAGTGCTTTTCACGTTTTTAATATCGTTTTTCATATATTTTTT
129 AATTCAA-AGCCAAAAAAATTGAAGGGCTTTTCACGTTTCTAATATCGTTTTTCATA-ATTTTTT
* * * * *
16670 --GAATTAATTTCTAATTAAATTGAAATAATATTTATATGCTCGTAAAAACAAATCCTTAAATGT
192 CCGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGC
* * *
16733 AATGTGGCTAAAATTTTATTAGATCAATATAGATAT
257 AATGTGGCTGAAATTTGATTAGATGAATATAGATAT
16769 ATTTAAAGGA
Statistics
Matches: 1283, Mismatches: 220, Indels: 171
0.77 0.13 0.10
Matches are distributed among these distances:
311 1 0.00
312 52 0.04
313 95 0.07
314 62 0.05
315 10 0.01
316 12 0.01
317 59 0.05
318 3 0.00
319 59 0.05
320 96 0.07
321 17 0.01
322 36 0.03
323 7 0.01
324 6 0.00
325 4 0.00
326 39 0.03
327 6 0.00
328 67 0.05
329 108 0.08
330 44 0.03
331 47 0.04
332 177 0.14
333 98 0.08
334 30 0.02
335 94 0.07
336 17 0.01
337 37 0.03
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (332 bp):
CGGGGTCCCAAAACGCGTTTTTAGCCAAAAACAGTGATGATATTACACGATTTCGGCTAAAATTT
TGCAAAAATTGACCAGAAATATATTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAA
TTCAAAGCCAAAAAAATTGAAGGGCTTTTCACGTTTCTAATATCGTTTTTCATAATTTTTTCCGA
ATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATG
TGGCTGAAATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGACGTCAAAAATCATGCAAA
ACTGACT
Found at i:16186 original size:661 final size:646
Alignment explanation
Indices: 15355--16768 Score: 1584
Period size: 661 Copynumber: 2.2 Consensus size: 646
15345 CATTTTCATA
* *
15355 TTTTTCCGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
1 TTTTTCCGAATTAATTTCTAATTAAATTGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTA
* * * *
15420 AATGCAATGTGGATGAGATTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAA
66 AATGCAATGTGGCTGAAATTTTATTAGATGAATATAGATATCTCAAGGAGTCTTGACGCAAAAAA
* * * *
15485 TCATGCAAAGCTGAGCCGGGACCCCGAAACGCGTTTTTAG-C-AAAAAAA-CGTGATGTGTACAC
131 TCATGCAAAACTGACCCGGGACCCCGAAACGCGATTTTAGCCAAAAAAAATCGTGATAT-TACAC
* * *
15547 GATTTCGGCTAAAATTTTGCAAAAAATGATCAGAGAA-A-TTTTCCTCAATTTTTGGATAAAATA
195 GATTTCGGCTAAAATTTTGCAAAAAATGACCAGA-AATATTTTTCCTCAATTTTTAGACAAAATA
* * * * * * * ** *
15610 CTCGTGAAATATATGTAATTTAAAGTCAAAAAGATTGGAGGACTTTTCACACTTTTCATATATCG
259 ATCATAAAAAATATATAATTTAAAGCCAAAAAAATTAAAGGA-TTTTCACACTTCT-A-ATATCG
*
15675 TTTTTCATATTTTTCT-GAATTAATTTCTAATTAAATCGAAAC-TAGATTCAGATGCTCGTAAAA
321 TTTTTCATATTTTTCTAGAATTAATTTCTAATTAAAACGAAACAT-GATTCAGATGCTCGT----
* *
15738 ACAAATCCTTAAATGCAATGTGGCTGAAATTTGATTAGATGAAT-TGGAAATCTCAAGGAGTCTT
381 ---AA-----AAA--CAA--TGGCTGAAATTTGATTAGATGAATATAGAAATCTCAAGGAGTCTC
* * * *
15802 GACGTC-AAAAATAATGCAAAACTG-ACTCGGGGTCCTA-AAACACTTTTTTAGCCAAAAACCGT
434 GACG-CAAAAAATAATGCAAAACTGAACT---AGTCCCAGAAACAC-GTTTTAGCCAAAAACAGT
* * * * *
15864 GATGGA-TATTACACGTTTTCGGCTAAAATTTTGCAAAAATTGATC-GAAAATATATTTCCTCAA
494 GAT-GATTATTACACGATTTCAGCTAAAATTTTACAAAAATTGACCTG-AAAGATATTTCCTCAA
* ** * * * * *
15927 ATTTTGGTTAAAATACTCATAAAAAATATATAATTCAACACCGAAAATATTGAAGGGTTTTTTAC
557 ATTTTAGCCAAAATACTCATAAAAAATATATAATTCAACACCAAAAAAATTAAAGGGCTTTTCAC
*
15992 GTTTCTAATATCGTTTTTCCTA-AT
622 GTTTCTAATATCGTTTTTCATATAT
*
16016 TTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTA
1 TTTTTCCGAATTAATTTCTAATTAAATTGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTA
* * * *
16081 AATCCAATGTGGCTGAAATTTAATTAGATGAATATAGATATCTCAAGGAGTCTTGGCGTAAAAAA
66 AATGCAATGTGGCTGAAATTTTATTAGATGAATATAGATATCTCAAGGAGTCTTGACGCAAAAAA
* * * ** *
16146 TCCTTCAAAACTTACCCAGGG-CTTCGAAGCGCGATTTTAGCCCAAAAAAAAAATCGTGATATTA
131 TCATGCAAAACTGACCC-GGGACCCCGAAACGCGATTTTAG-CC--AAAAAAAATCGTGATATTA
* * * * * * *
16210 CACGATTTTGGTTAATATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTAGCCACAA
192 CACGATTTCGGCTAAAATTTTGCAAAAAATGACCAGAAATATTTTTCCTCAATTTTTAGACAAAA
* * *
16275 TAATCATAAAAAATATATAATTTAAAGCCAAAAAAATTAAAGTATTTTCACGCTTCTAATTTCGT
257 TAATCATAAAAAATATATAATTTAAAGCCAAAAAAATTAAAGGATTTTCACACTTCTAATATCGT
* * * *
16340 TTTTCTTTTTTTTTTAGAATTAATTTCTAATTAAAACGAAACATGATTCAGATGCTTGTAAAAAC
322 TTTTCATATTTTTCTAGAATTAATTTCTAATTAAAACGAAACATGATTCAGATGCTCGTAAAAAC
* * * * * *
16405 AATGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGACGCAAAAAATCATTCA
387 AATGGCTGAAATTTGATTAGATGAATATAGAAATCTCAAGGAGTCTCGACGCAAAAAATAATGCA
* * * * * *
16470 AAATTGAACTAGTCCCAGGAACGCGTTTTAGTCAAAAACATTGATGATTATTATACGATTTCAGC
452 AAACTGAACTAGTCCCAGAAACACGTTTTAGCCAAAAACAGTGATGATTATTACACGATTTCAGC
* * * *
16535 TCAAATTTTACAAAAATTGACCTGAAAGATATTTCCTCAATTTTTAGCCATAATACTCATATAAA
517 TAAAATTTTACAAAAATTGACCTGAAAGATATTTCCTCAAATTTTAGCCAAAATACTCATAAAAA
* *
16600 ATATATAATTCAACACCAAAAAAATTAAAGTGCTTTTCACGTTTTTAATATCGTTTTTCATATAT
582 ATATATAATTCAACACCAAAAAAATTAAAGGGCTTTTCACGTTTCTAATATCGTTTTTCATATAT
* *
16665 TTTTT--GAATTAATTTCTAATTAAATTGAAATAATATTTATATGCTCGTAAAAACAAATCCTTA
1 TTTTTCCGAATTAATTTCTAATTAAATTGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTA
* * *
16728 AATGTAATGTGGCTAAAATTTTATTAGATCAATATAGATAT
66 AATGCAATGTGGCTGAAATTTTATTAGATGAATATAGATAT
16769 ATTTAAAGGA
Statistics
Matches: 640, Mismatches: 95, Indels: 50
0.82 0.12 0.06
Matches are distributed among these distances:
647 93 0.15
648 143 0.22
649 35 0.05
650 35 0.05
651 6 0.01
653 3 0.00
658 2 0.00
661 146 0.23
662 3 0.00
663 1 0.00
664 18 0.03
665 42 0.07
666 53 0.08
667 60 0.09
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.34
Consensus pattern (646 bp):
TTTTTCCGAATTAATTTCTAATTAAATTGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTA
AATGCAATGTGGCTGAAATTTTATTAGATGAATATAGATATCTCAAGGAGTCTTGACGCAAAAAA
TCATGCAAAACTGACCCGGGACCCCGAAACGCGATTTTAGCCAAAAAAAATCGTGATATTACACG
ATTTCGGCTAAAATTTTGCAAAAAATGACCAGAAATATTTTTCCTCAATTTTTAGACAAAATAAT
CATAAAAAATATATAATTTAAAGCCAAAAAAATTAAAGGATTTTCACACTTCTAATATCGTTTTT
CATATTTTTCTAGAATTAATTTCTAATTAAAACGAAACATGATTCAGATGCTCGTAAAAACAATG
GCTGAAATTTGATTAGATGAATATAGAAATCTCAAGGAGTCTCGACGCAAAAAATAATGCAAAAC
TGAACTAGTCCCAGAAACACGTTTTAGCCAAAAACAGTGATGATTATTACACGATTTCAGCTAAA
ATTTTACAAAAATTGACCTGAAAGATATTTCCTCAAATTTTAGCCAAAATACTCATAAAAAATAT
ATAATTCAACACCAAAAAAATTAAAGGGCTTTTCACGTTTCTAATATCGTTTTTCATATAT
Found at i:20626 original size:21 final size:21
Alignment explanation
Indices: 20601--20642 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20591 ATGTTTTGTG
20601 GAGATCAATCGACTCTGTAAC
1 GAGATCAATCGACTCTGTAAC
*
20622 GAGATCAATCGACTTTGTAAC
1 GAGATCAATCGACTCTGTAAC
20643 CTTGCCTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (21 bp):
GAGATCAATCGACTCTGTAAC
Found at i:23039 original size:42 final size:41
Alignment explanation
Indices: 22992--23125 Score: 119
Period size: 42 Copynumber: 3.4 Consensus size: 41
22982 TGAGCATGGC
22992 CTCACCAGGTGAGTATTGTATTGGGAGAGTGTGGGTGAGTAT
1 CTCACCAGGTGAGTATTGTA-TGGGAGAGTGTGGGTGAGTAT
* * *
23034 CTCACCAAGTGAGTA-T-TA---CACCA-----GGTGAGTAT
1 CTCACCAGGTGAGTATTGTATGGGA-GAGTGTGGGTGAGTAT
*
23066 -TACACCAGGTGAGTATTGTACTGGGTGAGTGTGGGTGAGTAT
1 CT-CACCAGGTGAGTATTGTA-TGGGAGAGTGTGGGTGAGTAT
23108 CTCACCAGGTGAGTATTG
1 CTCACCAGGTGAGTATTG
23126 CACCAGGTGA
Statistics
Matches: 71, Mismatches: 7, Indels: 28
0.67 0.07 0.26
Matches are distributed among these distances:
31 1 0.01
32 21 0.30
33 1 0.01
34 2 0.03
36 1 0.01
37 2 0.03
40 2 0.03
41 1 0.01
42 39 0.55
43 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (41 bp):
CTCACCAGGTGAGTATTGTATGGGAGAGTGTGGGTGAGTAT
Found at i:23047 original size:16 final size:16
Alignment explanation
Indices: 23025--23082 Score: 91
Period size: 16 Copynumber: 3.6 Consensus size: 16
23015 GGAGAGTGTG
23025 GGTGAGTATCT-CACCA
1 GGTGAGTAT-TACACCA
*
23041 AGTGAGTATTACACCA
1 GGTGAGTATTACACCA
23057 GGTGAGTATTACACCA
1 GGTGAGTATTACACCA
23073 GGTGAGTATT
1 GGTGAGTATT
23083 GTACTGGGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
15 1 0.03
16 38 0.97
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (16 bp):
GGTGAGTATTACACCA
Found at i:23081 original size:74 final size:74
Alignment explanation
Indices: 22994--23140 Score: 258
Period size: 74 Copynumber: 2.0 Consensus size: 74
22984 AGCATGGCCT
*
22994 CACCAGGTGAGTATTGTATTGGGAGAGTGTGGGTGAGTATCTCACCAAGTGAGTATTACACCAGG
1 CACCAGGTGAGTATTGTACTGGGAGAGTGTGGGTGAGTATCTCACCAAGTGAGTATTACACCAGG
23059 TGAGTATTA
66 TGAGTATTA
* * *
23068 CACCAGGTGAGTATTGTACTGGGTGAGTGTGGGTGAGTATCTCACCAGGTGAGTATTGCACCAGG
1 CACCAGGTGAGTATTGTACTGGGAGAGTGTGGGTGAGTATCTCACCAAGTGAGTATTACACCAGG
23133 TGAGTATT
66 TGAGTATT
23141 TACCAAGTGG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (74 bp):
CACCAGGTGAGTATTGTACTGGGAGAGTGTGGGTGAGTATCTCACCAAGTGAGTATTACACCAGG
TGAGTATTA
Found at i:23093 original size:32 final size:32
Alignment explanation
Indices: 23023--23095 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
23013 TGGGAGAGTG
23023 TGGGTGAGTATCTCACCAAGTGAGTATTACAC
1 TGGGTGAGTATCTCACCAAGTGAGTATTACAC
** * **
23055 CAGGTGAGTAT-TACACCAGGTGAGTATTGTAC
1 TGGGTGAGTATCT-CACCAAGTGAGTATTACAC
23087 TGGGTGAGT
1 TGGGTGAGT
23096 GTGGGTGAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
31 1 0.03
32 32 0.97
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (32 bp):
TGGGTGAGTATCTCACCAAGTGAGTATTACAC
Found at i:23120 original size:16 final size:16
Alignment explanation
Indices: 23099--23172 Score: 80
Period size: 16 Copynumber: 4.6 Consensus size: 16
23089 GGTGAGTGTG
23099 GGTGAGTATCT-CACCA
1 GGTGAGTAT-TGCACCA
23115 GGTGAGTATTGCACCA
1 GGTGAGTATTGCACCA
*
23131 GGTGAGTATT-TACCA
1 GGTGAGTATTGCACCA
* * *
23146 AGTGGGTATTTGTACCA
1 GGTGAGTA-TTGCACCA
23163 GGTGAGTATT
1 GGTGAGTATT
23173 TATATTGGGT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
15 11 0.22
16 28 0.56
17 11 0.22
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (16 bp):
GGTGAGTATTGCACCA
Found at i:23135 original size:42 final size:42
Alignment explanation
Indices: 23057--23137 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
23047 TATTACACCA
* **
23057 GGTGAGTATTACACCAGGTGAGTATTGTACTGGGTGAGTGTG
1 GGTGAGTATTACACCAGGTGAGTATTGCACCAGGTGAGTGTG
23099 GGTGAGTATCT-CACCAGGTGAGTATTGCACCAGGTGAGT
1 GGTGAGTAT-TACACCAGGTGAGTATTGCACCAGGTGAGT
23138 ATTTACCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.22, C:0.14, G:0.36, T:0.28
Consensus pattern (42 bp):
GGTGAGTATTACACCAGGTGAGTATTGCACCAGGTGAGTGTG
Found at i:23159 original size:74 final size:74
Alignment explanation
Indices: 22994--23169 Score: 246
Period size: 74 Copynumber: 2.4 Consensus size: 74
22984 AGCATGGCCT
* * *
22994 CACCAGGTGAGTATTGTATTGGGAGAGTGTGGGTGAGTATCTCACCAAGTGAGTATTACACCAGG
1 CACCAAGTGAGTATTGTACTGGGTGAGTGTGGGTGAGTATCTCACCAAGTGAGTATTACACCAGG
23059 TGAGTATTA
66 TGAGTATTA
* * *
23068 CACCAGGTGAGTATTGTACTGGGTGAGTGTGGGTGAGTATCTCACCAGGTGAGTATTGCACCAGG
1 CACCAAGTGAGTATTGTACTGGGTGAGTGTGGGTGAGTATCTCACCAAGTGAGTATTACACCAGG
23133 TGAGTATT-
66 TGAGTATTA
* * **
23141 TACCAAGTGGGTATTTGTACCAGGTGAGT
1 CACCAAGTGAGTA-TTGTACTGGGTGAGT
23170 ATTTATATTG
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
73 10 0.11
74 82 0.89
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.29
Consensus pattern (74 bp):
CACCAAGTGAGTATTGTACTGGGTGAGTGTGGGTGAGTATCTCACCAAGTGAGTATTACACCAGG
TGAGTATTA
Found at i:23163 original size:32 final size:31
Alignment explanation
Indices: 23099--23174 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 31
23089 GGTGAGTGTG
* *
23099 GGTGAGTATCTCACCAGGTGAGTATTGCACCA
1 GGTGAGTAT-TTACCAAGTGAGTATTGCACCA
* *
23131 GGTGAGTATTTACCAAGTGGGTATTTGTACCA
1 GGTGAGTATTTACCAAGTGAGTA-TTGCACCA
23163 GGTGAGTATTTA
1 GGTGAGTATTTA
23175 TATTGGGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 11 0.28
32 28 0.72
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (31 bp):
GGTGAGTATTTACCAAGTGAGTATTGCACCA
Found at i:23674 original size:23 final size:22
Alignment explanation
Indices: 23598--23677 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 22
23588 TTGGGGAGAG
* * *
23598 CTCCGCACAAAAGCTGGGTGAGC
1 CTCCGCGCAAGAGCTGAGTGA-C
23621 CTCCGCGCAAGAGCAAATGAGTG--
1 CTCCGCGCAAGAGC---TGAGTGAC
*
23644 CTCAGCGCAAGAGCTGAGTGAAC
1 CTCCGCGCAAGAGCTGAGTG-AC
23667 CTCCGCGCAAG
1 CTCCGCGCAAG
23678 GAGTAAGGGA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 6 0.13
23 35 0.76
26 5 0.11
ACGTcount: A:0.28, C:0.30, G:0.30, T:0.12
Consensus pattern (22 bp):
CTCCGCGCAAGAGCTGAGTGAC
Found at i:24311 original size:33 final size:33
Alignment explanation
Indices: 24263--24375 Score: 131
Period size: 33 Copynumber: 3.4 Consensus size: 33
24253 ACGCAGTGAA
** *
24263 GGAGTCTCCTTTGAGGGAGTTTCGCATAGCAAG
1 GGAGTCTCCACTGAGGGAGTCTCGCATAGCAAG
* *
24296 GGAGTCTCCCCTGAGGGAGTCTCGCGTAGCAAG
1 GGAGTCTCCACTGAGGGAGTCTCGCATAGCAAG
*
24329 GGAGTCTCCACTGAGGGAGTATCTG--TAGCAAG
1 GGAGTCTCCACTGAGGGAGTCTC-GCATAGCAAG
*
24361 GAAAGTCTCCACTGA
1 G-GAGTCTCCACTGA
24376 AAGAACCTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
32 8 0.11
33 62 0.87
34 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.22
Consensus pattern (33 bp):
GGAGTCTCCACTGAGGGAGTCTCGCATAGCAAG
Found at i:24314 original size:15 final size:15
Alignment explanation
Indices: 24294--24348 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
24284 TCGCATAGCA
24294 AGGGAGTCTCCCCTG
1 AGGGAGTCTCCCCTG
* *
24309 AGGGAGTCTCGCGTAG
1 AGGGAGTCTCCCCT-G
*
24325 CAAGGGAGTCTCCACTG
1 --AGGGAGTCTCCCCTG
24342 AGGGAGT
1 AGGGAGT
24349 ATCTGTAGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 19 0.59
16 1 0.03
17 1 0.03
18 11 0.34
ACGTcount: A:0.20, C:0.24, G:0.38, T:0.18
Consensus pattern (15 bp):
AGGGAGTCTCCCCTG
Found at i:24332 original size:18 final size:18
Alignment explanation
Indices: 24276--24336 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
24266 GTCTCCTTTG
*
24276 AGGGAGTTTCGCATAGCA
1 AGGGAGTCTCGCATAGCA
* *
24294 AGGGAGTCTCCCCT-G--
1 AGGGAGTCTCGCATAGCA
*
24309 AGGGAGTCTCGCGTAGCA
1 AGGGAGTCTCGCATAGCA
24327 AGGGAGTCTC
1 AGGGAGTCTC
24337 CACTGAGGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 12 0.34
16 1 0.03
17 1 0.03
18 21 0.60
ACGTcount: A:0.21, C:0.23, G:0.36, T:0.20
Consensus pattern (18 bp):
AGGGAGTCTCGCATAGCA
Done.