Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006135.1 Corchorus capsularis cultivar CVL-1 contig06153, 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: 31496
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:780 original size:367 final size:363
Alignment explanation
Indices: 1--684 Score: 885
Period size: 367 Copynumber: 1.9 Consensus size: 363
* * * * * * * *
1 CCCCGAAACGCGATTTTAGCAAGAATCCGTGATGG-TAGTACACGATTTTGTTTAAATTTTTGCA
1 CCCCGAAAAGCGAATTTACCAAAAAACCGGGATGGTTAGTACACGATTTTGGTTAAAATTTTG-A
*
65 CAAAAAAAATGATGGAAAAAAAATCTTGCAAAAAATTAACCGAAATTTTTTCCCTCAATTTTTTG
65 -AAAAAAAATGATGGAAAAAAAATCTTGCAAAAAATTAACAGAAATTTTTTCCCTCAATTTTTTG
* **
130 TCAAAATACTCATAAAATATTTATAATTCAAGCCCAAAAAGATTGAAGGGTTTTTCACACTTCTA
129 CCAAAATACTCATAAAATATTTATAATTCAAGCCCAAAAAGATTGAAGGACTTTTCACACTTCTA
* * *
195 ATATCGTTTTTCCTAAATTTTCCGAATTAATTTCTAATTAAATCAAAACCGGATTGAGAAGCTCG
194 ATATCATTTTTCCTAAATTTTCCGAATTAATTTCTAATTAAATCAAAACCGGATTCAGAAGCTCC
* * *
260 TAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGGTTAGATTAACATAGATATTACAATGA
259 TAAAAACAAATCCTTAAATCCAATATGGATGAGATTTGGTTAGATGAACATAGATATTACAAGGA
325 GTCTTGACACCAAAAATACAATCAAAACGTAACGCAAAGG
324 GTCTTGACACCAAAAATACAATCAAAACGTAACGCAAAGG
* *
365 CCCCGAAAAGCGAATTTACCAAAAATCCGTGATGGTTAGTACACGATTTTGGTTAAAATTTTGTA
1 CCCCGAAAAGCGAATTTACCAAAAAACCGGGATGGTTAGTACACGATTTTGGTTAAAATTTTG-A
*
430 AAAAAAAATTAGATGG-AAAAAAATACTTGC-AAAAATTAACAG-ATTTGGTTTTCCCTCTAATT
65 AAAAAAAA-T-GATGGAAAAAAAAT-CTTGCAAAAAATTAACAGAAATT--TTTTCCCTC-AATT
* * ** * *
492 TTTTGCCAAAATACTCATAAAATTTTTATAATTCAAGGCCAAAAATCTTGAATGACTTTTCACGC
124 TTTTGCCAAAATACTCATAAAATATTTATAATTCAAGCCCAAAAAGATTGAAGGACTTTTCACAC
** ** *
557 TTCTAATATCATTTTTCCTATTTTATTCTTAATTAATTTC-AATTAAATCGAAA-CGAGATTCAG
189 TTCTAATATCATTTTTCCTAAATT-TTCCGAATTAATTTCTAATTAAATCAAAACCG-GATTCAG
* * * * * *
620 ATGCTCCTACAAACAAATCCTTAAATCCATTATGGATTATATTTGGTTAGATGAATATAGATATT
252 AAGCTCCTAAAAACAAATCCTTAAATCCAATATGGATGAGATTTGGTTAGATGAACATAGATATT
685 TTGAGGAGTC
Statistics
Matches: 277, Mismatches: 34, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
364 42 0.15
365 46 0.17
366 21 0.08
367 155 0.56
368 13 0.05
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (363 bp):
CCCCGAAAAGCGAATTTACCAAAAAACCGGGATGGTTAGTACACGATTTTGGTTAAAATTTTGAA
AAAAAAATGATGGAAAAAAAATCTTGCAAAAAATTAACAGAAATTTTTTCCCTCAATTTTTTGCC
AAAATACTCATAAAATATTTATAATTCAAGCCCAAAAAGATTGAAGGACTTTTCACACTTCTAAT
ATCATTTTTCCTAAATTTTCCGAATTAATTTCTAATTAAATCAAAACCGGATTCAGAAGCTCCTA
AAAACAAATCCTTAAATCCAATATGGATGAGATTTGGTTAGATGAACATAGATATTACAAGGAGT
CTTGACACCAAAAATACAATCAAAACGTAACGCAAAGG
Found at i:3911 original size:18 final size:19
Alignment explanation
Indices: 3888--3923 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3878 GATTTTGGTT
*
3888 AAAATTT-TGTAAAAAAAA
1 AAAATTTATGGAAAAAAAA
3906 AAAATTTATGGAAAAAAA
1 AAAATTTATGGAAAAAAA
3924 TCTTGCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (19 bp):
AAAATTTATGGAAAAAAAA
Found at i:9119 original size:323 final size:324
Alignment explanation
Indices: 8641--9268 Score: 834
Period size: 323 Copynumber: 1.9 Consensus size: 324
8631 TTTTTGGATG
* * *
8641 AATATAGATACTTCAATGAATCTTGGCATCAGAAATCAAGCAAAACTGAGCCGGGACCCCGAAAT
1 AATATAGATACTTCAATGAATCTTGGCATCAAAAATCAAGCAAAACTGAGCCGGGACCCCAAAAC
* * * *
8706 GAGCTTTTAGCCAAAAACCGTATTGGGTTAGTACACAATTTCGGCCAAATTTTTTCAAAAATCTA
66 GAGCTTTTAGCCAAAAACCATATTGCGTAAGTACACAATTTCGGCCAAATTTTTCCAAAAATCTA
* * *
8771 ACCGAAAGTTTTTTCCTCAAGTTTTAGCCAAAAATACAGATAAAATATATATAATTCAAG-CCAA
131 ACCGAAAGTTTTTCCCTCAAGTTTTAGCCAAAAATACACATAAAATATACATAATTCAAGTCC--
* * * * *
8835 AAAAAATACTGAAGTGCTTTTCACGCTTCTAATCTCGTTTTTCCTAAATTTAC-GAATTAATTTG
194 -AAAAAGACTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCCTAAATTTACTGAATTAATTTC
*
8899 TAATTAAATCGAAA-CTGGATTGAGATGCTCGTAACAACAAATCCTTAAGATGAGATTTGGTTAG
258 TAATTAAATCGAAATC-GGATTGAGATGCTCGTAAAAACAAATCCTTAAGATGAGATTTGGTTAG
8963 ATT
322 ATT
* * * * * * *
8966 AATATAGATATTTCAATGATTTTTGGCGTCAAAAATCATGCAAAACTGTGTCGGG-CCCCAAAAC
1 AATATAGATACTTCAATGAATCTTGGCATCAAAAATCAAGCAAAACTGAGCCGGGACCCCAAAAC
* * * * * * * *
9030 GCGTTTTTAGCCAAAAACCATGTT-CGTAAGTACACGATTTCTGCTAAATTTTTCCAAATATTTA
66 GAGCTTTTAGCCAAAAACCATATTGCGTAAGTACACAATTTCGGCCAAATTTTTCCAAAAATCTA
* * **
9094 ACCGAAAGTTTTTCCCTCAAGTTTTAGCCTAAAATACTCATATTATATACATAATTCAAGTCCAA
131 ACCGAAAGTTTTTCCCTCAAGTTTTAGCCAAAAATACACATAAAATATACATAATTCAAGTCCAA
* * * *
9159 AAAGACTGAAGGGCTTTTTACGCTTCTCATATCATTTTTCCTAAATTTTCTGAATTAATTTCTAG
196 AAAGACTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCCTAAATTTACTGAATTAATTTCTAA
9224 TTAAATCGAAATCGGATTGAGATGCTCGTAAAAACAAATCCTTAA
261 TTAAATCGAAATCGGATTGAGATGCTCGTAAAAACAAATCCTTAA
9269 ATCCAATGTG
Statistics
Matches: 261, Mismatches: 39, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
321 45 0.17
322 54 0.21
323 86 0.33
324 29 0.11
325 47 0.18
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (324 bp):
AATATAGATACTTCAATGAATCTTGGCATCAAAAATCAAGCAAAACTGAGCCGGGACCCCAAAAC
GAGCTTTTAGCCAAAAACCATATTGCGTAAGTACACAATTTCGGCCAAATTTTTCCAAAAATCTA
ACCGAAAGTTTTTCCCTCAAGTTTTAGCCAAAAATACACATAAAATATACATAATTCAAGTCCAA
AAAGACTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCCTAAATTTACTGAATTAATTTCTAA
TTAAATCGAAATCGGATTGAGATGCTCGTAAAAACAAATCCTTAAGATGAGATTTGGTTAGATT
Found at i:9780 original size:364 final size:362
Alignment explanation
Indices: 9103--9785 Score: 840
Period size: 364 Copynumber: 1.9 Consensus size: 362
9093 AACCGAAAGT
** *
9103 TTTTCCCTCAAGTTTTAGCCTAAAATACTCATATTATATACATAATTCAAGTCCAAAAAGACTGA
1 TTTTCCCTCAAGTTTTAGCCTAAAATACTCATAAAATATACATAATTCAAGGCCAAAAAGACTGA
* * * *
9168 AGGGCTTTTTACGCTTCTCATATCATTTTTCCTAAATTTTCTGAATTAATTTCTAGTTAAATCGA
66 AGGACTTTTCACGCTTCTAATATCATTTTTCCTAAATTTTCTGAATTAATTTCTAATTAAATCGA
* * * *
9233 AATCGGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGGTTAGATT
131 AATCGGATTCAGATGCTCCTAAAAACAAATCCTTAAATCCAATATGGATGAGATTTGGTTAGATA
*
9298 AACATAGATATTACAATGAGTCTTGACACCAAAAATCATCAAAAACTAAGCAAAGGCCCCGAAAA
196 AACATAGATATTACAAGGAGTCTTGACACCAAAAATCATCAAAAACTAAGCAAA-GCCCCGAAAA
*
9363 GCGAATTTACCAAAAATCCGTGATGGTTAGTACACGATTTTGGTTAAAATTTTGTAAAAAAAAAA
260 GCGAATTTACCAAAAATCCGTGATGGTTAGTACACGATTTTCGTTAAAATTTTG-AAAAAAAAAA
9428 TTGATGGAAAAAAAATCTTGCAAAAAATTAACAGATTGG
324 TTGATGGAAAAAAAATCTTGCAAAAAATTAACAGATTGG
* * * ** *
9467 TTTTCCCTCAATTTTTTGCC-AAAATACTCATAAAATTTTTATAATTCAAGGCCAAAAA-TCTTG
1 TTTTCCCTCAAGTTTTAGCCTAAAATACTCATAAAATATACATAATTCAAGGCCAAAAAGAC-TG
* ** *
9530 AATGACTTTTCACGCTTCTAATATCATTTTTCCTATTTTATTCTTAATTAATTTCTAATTAAATC
65 AAGGACTTTTCACGCTTCTAATATCATTTTTCCTAAATT-TTCTGAATTAATTTCTAATTAAATC
* * * *
9595 GAAA-CGAGATTCAGATGCTCCTACAAACAAATCCTTAAATCCATTATGGATTATATTTGGTTAG
129 GAAATCG-GATTCAGATGCTCCTAAAAACAAATCCTTAAATCCAATATGGATGAGATTTGGTTAG
** * * *** *
9659 ATAAATGTAGATATTTCGAGGAGTCTTGGTGCCAAAAATCATGC-AAAACTGAGCCTAAA-CCCC
193 ATAAACATAGATATTACAAGGAGTCTTGACACCAAAAATCAT-CAAAAACTAAG-C-AAAGCCCC
* * * ** * * *
9722 GGAACGTGTTTTTAGCAAAAAGT-TGTGATGGTTAGTACACGA-TTTCGTCTACAATTTTGAAAA
255 GAAAAGCGAATTTACCAAAAA-TCCGTGATGGTTAGTACACGATTTTCGT-TAAAATTTTGAAAA
9785 A
318 A
9786 TTTTACCCGA
Statistics
Matches: 268, Mismatches: 43, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
362 1 0.00
363 79 0.29
364 182 0.68
365 3 0.01
366 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (362 bp):
TTTTCCCTCAAGTTTTAGCCTAAAATACTCATAAAATATACATAATTCAAGGCCAAAAAGACTGA
AGGACTTTTCACGCTTCTAATATCATTTTTCCTAAATTTTCTGAATTAATTTCTAATTAAATCGA
AATCGGATTCAGATGCTCCTAAAAACAAATCCTTAAATCCAATATGGATGAGATTTGGTTAGATA
AACATAGATATTACAAGGAGTCTTGACACCAAAAATCATCAAAAACTAAGCAAAGCCCCGAAAAG
CGAATTTACCAAAAATCCGTGATGGTTAGTACACGATTTTCGTTAAAATTTTGAAAAAAAAAATT
GATGGAAAAAAAATCTTGCAAAAAATTAACAGATTGG
Found at i:12051 original size:334 final size:329
Alignment explanation
Indices: 11417--12542 Score: 1149
Period size: 333 Copynumber: 3.4 Consensus size: 329
11407 TTGTACACGA
* * *
11417 TTCTAGTTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTATATCTATTATGGACT
1 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCTATTATGGATT
* * *
11482 AGATCTAGTTGGATGAATATATATATTTCGAGGAGTCTTGAC-ACAAAAAATCATGCAAAACTGA
66 AGATTTGGTTGGATGAATATAGATATTTCGAGGAGTCTTG-CGACAAAAAATCATGCAAAACTGA
* * * * * * * *
11546 GCCGGTGCCCCGAAAACGCGTTTTT-GCCAACAACAGTGATAGTTAGTACACAATTTCGGT-TAA
130 GCCTGAGCCCC-AGAACGTGTTTTTAGCAAAAAACTGTGATAGTTAGTAAACAATTTC-GTCTAA
* * * ** *
11609 ATATTTGCAAAAAATTTAACCG-AAAGTTTTTCCCTCAATTTTTTGCCACAATACTCATAATATA
193 AT-TTTGC-AAAAATTTACCCGAAAAGTTTTT--CTCAATTTTTGGACATGATACTCATAA-AAA
* * * * * *
11673 TATATAATTCAAGGCCA-AAAAGATTGAATGACTTTTCACGCTTCTAATATCGTTTTTCCTATTT
253 TATATAATTCAACGCCAGAAAAG-TTGAAAGGCTTTTCTCGCTTCTAATATCATTTTTACTATTT
*
11737 GTTTCCGAATTAAT
317 -TTTGCGAATTAAT
* * * * *
11751 TTCTAATTAATTTGAAACAAGATTTAGA-GCTCGTACAAAC-AATACTTTATATCTATTATGGAT
1 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT-CCTTATATCTATTATGGAT
** *
11814 TATTTTTGGTTGGATGAATATAGATATTTCTAGGAGTCTTGCTGTA-AAAAAATCATGCAAAACT
65 TAGATTTGGTTGGATGAATATAGATATTTCGAGGAGTCTTGC-G-ACAAAAAATCATGCAAAACT
11878 GAGCCTGAGCCCCAGAACGTGTTTTTAGCAAAAAAACTGTGATAGTTAGTAAACAATTTCGTCTA
128 GAGCCTGAGCCCCAGAACGTGTTTTTAGC-AAAAAACTGTGATAGTTAGTAAACAATTTCGTCT-
* * *
11943 AAATTTTGCAAAGATTTACCCGAAAAGGTTTTTCTCAATTTTTGGTCATGATACTTATAAAGAAT
191 AAATTTTGCAAAAATTTACCCGAAAA-GTTTTTCTCAATTTTTGGACATGATACTCATAAA-AAT
* * *
12008 ATATAATTCAACGCCAGAAAAGTTCAAGGGCTTTTCTCGCTTCTAATATTATTTTTACTATTTTT
254 ATATAATTCAACGCCAGAAAAGTTGAAAGGCTTTTCTCGCTTCTAATATCATTTTTACTATTTTT
*
12073 TGCGAATTGAT
319 TGCGAATTAAT
*
12084 TTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATC-ATTTATGGAT
1 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCTA-TTATGGAT
** * * * * * *
12148 TAGATTTGGTCAGATGAGTATAGCTATTTCGAGAAGTCCTG-GCACCAAATATCATGCAAAACTG
65 TAGATTTGGTTGGATGAATATAGATATTTCGAGGAGTCTTGCG-ACAAAAAATCATGCAAAACTG
** * * * * * ** *
12212 AGTTTGGGCCCCGGAATGTGTTTTTAGCAAAAAACTGTGATGGTTAGTATATGATTTTGTCTAAA
129 AGCCTGAGCCCCAGAACGTGTTTTTAGCAAAAAACTGTGATAGTTAGTAAACAATTTCGTCTAAA
** *
12277 TTTTGCAAAAATTTACCTAAAAATTTTCTTTTCTCAATTTTTGGACATGATACTCATAAAAAATA
194 TTTTGCAAAAATTTACCCGAAAA--GT-TTTTCTCAATTTTTGGACATGATACTCAT-AAAAATA
* * * * * *
12342 TTTAATTCAACGCTAGAAAAATTGAAAGGTTTTTCTCGCTTCTATTATCAATTTTACTATTTTTT
255 TATAATTCAACGCCAGAAAAGTTGAAAGGCTTTTCTCGCTTCTAATATCATTTTTACTATTTTTT
12407 GCGAATTAAT
320 GCGAATTAAT
* * * * * * * * * * * *
12417 TTCTAATTAAAGCGAAACATGATTTAGATTCTTGTAAAAACAAATCTTTAAATCCAATCTGGGTG
1 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCTATTATGGATT
* * * * * ** *
12482 GGACTTGGTTAGATGAATATAGATATTTCAATGACACTTGGCGAC-AAAAATCAAGCAAAAC
66 AGATTTGGTTGGATGAATATAGATATTTCGAGGAGTCTT-GCGACAAAAAATCATGCAAAAC
12543 AAACCAGGAC
Statistics
Matches: 660, Mismatches: 110, Indels: 45
0.81 0.13 0.06
Matches are distributed among these distances:
331 23 0.03
332 36 0.05
333 339 0.51
334 207 0.31
335 45 0.07
336 10 0.02
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (329 bp):
TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCTATTATGGATT
AGATTTGGTTGGATGAATATAGATATTTCGAGGAGTCTTGCGACAAAAAATCATGCAAAACTGAG
CCTGAGCCCCAGAACGTGTTTTTAGCAAAAAACTGTGATAGTTAGTAAACAATTTCGTCTAAATT
TTGCAAAAATTTACCCGAAAAGTTTTTCTCAATTTTTGGACATGATACTCATAAAAATATATAAT
TCAACGCCAGAAAAGTTGAAAGGCTTTTCTCGCTTCTAATATCATTTTTACTATTTTTTGCGAAT
TAAT
Found at i:13265 original size:331 final size:332
Alignment explanation
Indices: 12595--13354 Score: 846
Period size: 332 Copynumber: 2.3 Consensus size: 332
12585 ATTTGTACAC
* * * * *
12595 GATTT-TAATTAAATCGAAACAAGATTTAGATGCTCATAAAAATAAATCCTTGTATCTATTATGG
1 GATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTATATCTATTATGG
* * *
12659 ACTAGATCTGGTTGGATGAATATAGATATTTCGAGGAGTCTTGGCACAAAAAATCATGCAAAACT
66 ATTAGATTTGGTTAGATGAATATAGATATTTCGAGGAGTCTTGGCACAAAAAATCATGCAAAACT
* * * * * * * *
12724 GAGGCGGTGTCCCGAAACACGTTTTTGCCAACAACCGTGATAGTTAATACACGATTTCGGTTAAA
131 GAGGCGCTGACCCCAAACACGTTTTTGCAAAAAACCGTGATAGTTAATAAACAATTTCGGTAAAA
*
12789 TATTTGCAAAAAATTTAACCGAAAGTTTTTCCCTCAATTTTTAGTCACAATACTCATAAAATATA
196 TATTTGCAAAAAATTTAACCGAAAGTTTTT-CCTCAATTTTTAGCCACAATACTCATAAAATATA
* * * *
12854 TATAATTCAAGGCCAAAAAGATTGAATGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTAT
260 TATAATTCAAGGCCAAAAAGATTCAAGGACTTTTCACGCTTCTAATATCATTTTTACTATTTTAT
12919 TCTGAATT
325 TCTGAATT
*
12927 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAA-CTTTATATCTATTATGG
1 GATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTATATCTATTATGG
* * * *
12990 ATTATATTTGGTTAGATGAATATAGATATTTCTAGGGGTCTTGGCGCAAAAAATTCATGCAAAAC
66 ATTAGATTTGGTTAGATGAATATAGATATTTCGAGGAGTCTTGGCACAAAAAA-TCATGCAAAAC
** * *
13055 TGA-GC-CTGAACCCCAGAACGTGTTTTTAGCAAAAAACTGTGATAGTTAGTAAACAATTTC-GT
130 TGAGGCGCTG-ACCCCA-AACACGTTTTT-GCAAAAAACCGTGATAGTTAATAAACAATTTCGGT
* * * ** *
13117 CCAAAAT-TTTGC-AAAGATTTACCCGAAAAGGTTTTT-CTCAATTTTTGGCCATGATACTTATA
192 --AAAATATTTGCAAAAAATTTAACCG-AAA-GTTTTTCCTCAATTTTTAGCCACAATACTCATA
* * * *
13179 AAGA-ATATATAATTCAATGCCAGAAAAG-TTCAAGGGCTTTTCTCGCTTCTAATATTATTTTTA
253 AA-ATATATATAATTCAAGGCCA-AAAAGATTCAAGGACTTTTCACGCTTCTAATATCATTTTTA
*
13242 TTATTTT-TTGC-GAATT
316 CTATTTTATT-CTGAATT
* * * * * *
13258 GATTTCTAATTAAAGCGAAACATA-ATTCAGATTCTCGTAAAAACAAATCTTTAAATCCAATCTG
1 GATTTCTAATTAAATCGAAACA-AGATTCAGATGCTCGTAAAAACAAATCTTTATATCTATTATG
* * * *
13322 GGTGAGACTTGGTTAGATGAATATACATATTTC
65 GATTAGATTTGGTTAGATGAATATAGATATTTC
13355 AATGAGACTT
Statistics
Matches: 361, Mismatches: 52, Indels: 29
0.82 0.12 0.07
Matches are distributed among these distances:
330 2 0.01
331 112 0.31
332 122 0.34
333 115 0.32
334 10 0.03
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (332 bp):
GATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTATATCTATTATGG
ATTAGATTTGGTTAGATGAATATAGATATTTCGAGGAGTCTTGGCACAAAAAATCATGCAAAACT
GAGGCGCTGACCCCAAACACGTTTTTGCAAAAAACCGTGATAGTTAATAAACAATTTCGGTAAAA
TATTTGCAAAAAATTTAACCGAAAGTTTTTCCTCAATTTTTAGCCACAATACTCATAAAATATAT
ATAATTCAAGGCCAAAAAGATTCAAGGACTTTTCACGCTTCTAATATCATTTTTACTATTTTATT
CTGAATT
Found at i:13369 original size:333 final size:330
Alignment explanation
Indices: 12596--13378 Score: 784
Period size: 333 Copynumber: 2.4 Consensus size: 330
12586 TTTGTACACG
* * * * ** * *
12596 ATTT-TAATTAAATCGAAACAAGATTTAGATGCTCATAAAAATAAATCCTTGTATCTATTATGGA
1 ATTTCTAATTAAAGCGAAACAAGATTCAGATGCTCGTAAAAA-AAA-CTTTAAATCCAATATGGA
* * *
12660 CT-AGA-TCTGGTTGGATGAATATAGATATTTCGAGGAGTCTTGGCACAAAAAATCATGCAAAAC
64 -TGAGACT-TGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAAC
* * * * * * * *
12723 TGAGGCGGTGTCCCGAAACACGTTTTTGCCAACAACCGTGATAGTTAATACACGATTTCGGTTAA
127 TGAGGCGCTGACCCCAAACACGTTTTTGCAAAAAACCGTGATAGTTAATAAACAATTTCGGTAAA
*
12788 ATATTTGCAAAAAATTTAACCGAAAGTTTTTCCCTCAATTTTTAGTCACAATACTCATAAAATAT
192 ATATTTGCAAAAAATTTAACCGAAAGTTTTT-CCTCAATTTTTAGCCACAATACTCATAAAATAT
* * * *
12853 ATATAATTCAAGGCCAAAAAGATTGAATGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTA
256 ATATAATTCAAGGCCAAAAAGATTCAAGGACTTTTCACGCTTCTAATATCATTTTTACTATTTTA
12918 TTCTGAATTA
321 TTCTGAATTA
* * * * *
12928 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAACTTTATATCTATTATGGATT
1 ATTTCTAATTAAAGCGAAACAAGATTCAGATGCTCGTAAAAAAAACTTTAAATCCAATATGGATG
* * * *
12993 ATATTTGGTTAGATGAATATAGATATTTCTAGGGGTCTTGGCGCAAAAAATTCATGCAAAACTGA
66 AGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAA-TCATGCAAAACTGA
** * *
13058 -GC-CTGAACCCCAGAACGTGTTTTTAGCAAAAAACTGTGATAGTTAGTAAACAATTTC-GTCCA
130 GGCGCTG-ACCCCA-AACACGTTTTT-GCAAAAAACCGTGATAGTTAATAAACAATTTCGGT--A
* * * ** *
13120 AAAT-TTTGC-AAAGATTTACCCGAAAAGGTTTTT-CTCAATTTTTGGCCATGATACTTATAAAG
190 AAATATTTGCAAAAAATTTAACCG-AAA-GTTTTTCCTCAATTTTTAGCCACAATACTCATAAA-
* * * * *
13182 A-ATATATAATTCAATGCCAGAAAAG-TTCAAGGGCTTTTCTCGCTTCTAATATTATTTTTATTA
252 ATATATATAATTCAAGGCCA-AAAAGATTCAAGGACTTTTCACGCTTCTAATATCATTTTTACTA
*
13245 TTTT-TTGC-GAATTG
316 TTTTATT-CTGAATTA
* *
13259 ATTTCTAATTAAAGCGAAACATA-ATTCAGATTCTCGTAAAAACAAATCTTTAAATCCAATCTGG
1 ATTTCTAATTAAAGCGAAACA-AGATTCAGATGCTCGTAAAAA-AAA-CTTTAAATCCAATATGG
* * * * * *
13323 GTGAGACTTGGTTAGATGAATATACATATTTCAATGAGACTTGGCGCCAAGAATCA
63 ATGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCA
13379 GACATAATAG
Statistics
Matches: 379, Mismatches: 55, Indels: 34
0.81 0.12 0.07
Matches are distributed among these distances:
330 3 0.01
331 110 0.29
332 126 0.33
333 130 0.34
334 10 0.03
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (330 bp):
ATTTCTAATTAAAGCGAAACAAGATTCAGATGCTCGTAAAAAAAACTTTAAATCCAATATGGATG
AGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGAG
GCGCTGACCCCAAACACGTTTTTGCAAAAAACCGTGATAGTTAATAAACAATTTCGGTAAAATAT
TTGCAAAAAATTTAACCGAAAGTTTTTCCTCAATTTTTAGCCACAATACTCATAAAATATATATA
ATTCAAGGCCAAAAAGATTCAAGGACTTTTCACGCTTCTAATATCATTTTTACTATTTTATTCTG
AATTA
Found at i:13519 original size:331 final size:326
Alignment explanation
Indices: 12596--13607 Score: 800
Period size: 331 Copynumber: 3.1 Consensus size: 326
12586 TTTGTACACG
* * * ** * *
12596 ATTT-TAATTAAATCGAAACAAGATTTAGATGCTCATAAAAATAAATCCTTGTATCTATTATGGA
1 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAA-CTTTAAATCCAATATGGA
* * * * *
12660 CT-AGA-TCTGGTTGGATGAATATAGATATTTCGAGGAGTCTTGGCACAAAAAA-TCATGCAAAA
64 -TGAGACT-TGGTTAGATGAATATACATATTTCAAGGAGACTTGGCGCAAAAAATTCATGCAAAA
* *** * * * * * * *
12722 CTGAGGCGGTGTCCC-GAAACACGTTTTT-GCCAACAACCGTGATAGTTAATACACGATTTCGGT
127 CTGAGCCGGAACCCCAG-AACACGTTTTTAGCAAAAAACTGTGATAGTTAGTAAACAATGTC-GT
* * * * * * *
12785 -TAAATA-TTTGCAAAAAATTTAACCG-AAAGTTTTTCCCTCAATTTTTAGTCACAATACTCATA
190 CCAAA-ACTTTGC-AAAGATTGACCCGAAAAGATTTT-GCTCAATTTTTA-CCACAATACTCATA
* * * * *
12847 AAATATATATAATTCAAGGCCAAAAAGATTGAATGACTTTTCACGCTTCTAATATCGTTTTTCCT
251 AAAAATATATAATTCAA-GCCAAAAAG-TTCAAGGACTTTTCACGCTTCTAATAT-TTTTTTCTT
12912 ATTTTATTCTGAATTA
313 ATTTT-TTC-GAATTA
* * * *
12928 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAACTTTATATCTATTATGGATT
1 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAACTTTAAATCCAATATGGATG
* * * * * *
12993 ATATTTGGTTAGATGAATATAGATATTTCTAGGGGTCTTGGCGCAAAAAATTCATGCAAAACTGA
66 AGACTTGGTTAGATGAATATACATATTTCAAGGAGACTTGGCGCAAAAAATTCATGCAAAACTGA
* ** *
13058 GCCTGAACCCCAGAACGTGTTTTTAGCAAAAAACTGTGATAGTTAGTAAACAATTTCGTCCAAAA
131 GCCGGAACCCCAGAACACGTTTTTAGCAAAAAACTGTGATAGTTAGTAAACAATGTCGTCCAAAA
* * * * * ** * *
13123 TTTTGCAAAGATTTACCCGAAAAGGTTTTTCTCAATTTTTGGCCATGATACTTATAAAGAATATA
196 CTTTGCAAAGATTGACCCGAAAAGATTTTGCTCAATTTTT-ACCACAATACTCATAAAAAATATA
* * *
13188 TAATTCAATGCCAGAAAAGTTCAAGGGCTTTTCTCGCTTCTAATATTATTTTTATTATTTTTTGC
260 TAATTCAA-GCCA-AAAAGTTCAAGGACTTTTCACGCTTCTAATATT-TTTTTCTTATTTTTT-C
*
13253 GAATTG
321 GAATTA
* * *
13259 ATTTCTAATTAAAGCGAAACATA-ATTCAGATTCTCGTAAAAACAAATCTTTAAATCCAATCTGG
1 ATTTCTAATTAAATCGAAACA-AGATTCAGATGCTCGTAAAAA-AAA-CTTTAAATCCAATATGG
* * * * *
13323 GTGAGACTTGGTTAGATGAATATACATATTTCAATGAGACTTGGCGCCAAGAA-TCA-GACATAA
63 ATGAGACTTGGTTAGATGAATATACATATTTCAAGGAGACTTGGCGCAAAAAATTCATG-CAAAA
** * * * *
13386 -TAGAGCCGGGGCCCC-GAAACACGTTTTTAGTCAAAAACCTGTGATGGTTAGTACACGA-GTC-
127 CT-GAGCCGGAACCCCAG-AACACGTTTTTAG-CAAAAAACTGTGATAGTTAGTAAACAATGTCG
* ** *
13447 TACTAAAACTTTGCAAA-ATTGACTTGAAAA-ATTTCTGCTCAATTTTTACCAACAATTCTCATA
189 T-CCAAAACTTTGCAAAGATTGACCCGAAAAGATTT-TGCTCAATTTTTACC-ACAATACTCATA
* * * * ** * *
13510 AAAAATATATCACTCAACCCTAAAAATATTCAAGGACTCCTCACGCTTCTAATATTGTTCTCTTA
251 AAAAATATATAATTCAAGCC-AAAAA-GTTCAAGGACTTTTCACGCTTCTAATATTTTTTTCTTA
13575 TTTTTTTCGAATTA
314 -TTTTTTCGAATTA
*
13589 ATTCCTAATTAAATCGAAA
1 ATTTCTAATTAAATCGAAA
13608 TCGGATTGAG
Statistics
Matches: 556, Mismatches: 98, Indels: 54
0.79 0.14 0.08
Matches are distributed among these distances:
330 41 0.07
331 182 0.33
332 172 0.31
333 161 0.29
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (326 bp):
ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAACTTTAAATCCAATATGGATG
AGACTTGGTTAGATGAATATACATATTTCAAGGAGACTTGGCGCAAAAAATTCATGCAAAACTGA
GCCGGAACCCCAGAACACGTTTTTAGCAAAAAACTGTGATAGTTAGTAAACAATGTCGTCCAAAA
CTTTGCAAAGATTGACCCGAAAAGATTTTGCTCAATTTTTACCACAATACTCATAAAAAATATAT
AATTCAAGCCAAAAAGTTCAAGGACTTTTCACGCTTCTAATATTTTTTTCTTATTTTTTCGAATT
A
Found at i:18096 original size:332 final size:331
Alignment explanation
Indices: 14121--18214 Score: 3138
Period size: 331 Copynumber: 12.4 Consensus size: 331
14111 ACCAAAAGTT
** * * * * * * *
14121 TTTC-CCTCAATTTTTACCCAAAATACTCGTAAAATATTTATAATTCAAGGCCAAAAATCTTG-A
1 TTTCTCCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAATATTGAA
* * *
14184 AGGACTTTTAACGCTTCTAATAT-TTTTTTCCTATTTTATTCCGAATTAATTTGC-AATTAAACC
66 AGG-CTTTTCACGCTTCTAATATCGTTTTTCCTA-TTT-TTCCGAATTAATTT-CTAATTAAATC
* * * * * * * *
14247 GAAATAAGATTCAGATGCTCCTAAAAA-AAATCCTTAAATCCATTATGGATTAGATTTGGTTAGA
127 GAAACATGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGATTTGGTTAGA
* * * ** *
14311 TGAATATAGATATTTCGAGGAGTCTTGGCGCCAAAAATCATGCAAAATTGAGCCTG-GGCCCCGA
192 TGAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGTC-GAGGCCCCGA
* * * * *
14375 AACGTGTTTTTAG-CAAAAAGCT-GTGATGGTTTGTACACGATTTTGTCTAAAATTTTGAAAAAA
256 AACGCGTTTTTAGTC-AAAA-CTCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAA
* *
14438 TTTACCCGAAAAA
319 TTGACCTGAAAAA
* * * *
14451 GTTT-TCCTCAATTTTTGGCCACGATGA-TCATAAAAAATATATAATTCAACGCCGGAAAA-GTT
1 -TTTCTCCTCAATTTTTGGCCACAAT-ACTCATAAAAAATATATAACTCAACGCC-AAAAATATT
* * * * * * *
14513 CAAGGGTTTTTCTA-GCTTCAAATATC-ATTTTCACTGTTTTTTGCGAATTAATTTCTAATTAAA
63 GAAAGGCTTTTC-ACGCTTCTAATATCGTTTTTC-CT-ATTTTTCCGAATTAATTTCTAATTAAA
* *** * * * * * *
14576 GCGAAACATGATACTGATTCTCGT-AAAATAAATCCTTAAATCCAATTTGTGTGAGACTTGATTA
125 TCGAAACATGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGATTTGGTTA
* ** * * * * * * **
14640 GATGAATATAGATATTTCAATGAGATTTGATGCCTATAATCAGGCAAAACAAAGCCGGGGCTGC-
190 GATGAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGTCGAGGCCCCG
* * * ** * * * *
14704 AGAA-GCAATTTTTAGTCAAAAATCGTGACGGTTAGTACATAATTTCGACAAAAACTTTGCAAAT
255 A-AACGC-GTTTTTAGTCAAAACTCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAA
*
14768 ATTGACCCGAAAAA
318 ATTGACCTGAAAAA
* * * **
14782 ATTCTGCTCAATTTTTGGCCACAGTGTTCATAAAAAATATATAACTCAACGCCAGAAAA-ATTGA
1 TTTCTCCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCA-AAAATATTGA
* * * **
14846 AGGGCTTTTCTCGCTTCTAATATCGTTTTTACTATTTTTTTGAATTAATTTCTAATT-AATGCGA
65 AAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATTTCTAATTAAAT-CGA
* * * * * ** *
14910 AACATGATTCAGATTCTTGTAAAAGCAAATCCTTAAATCCAATCTCCGTGAGACTTGGTTAGATG
129 AACATGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGATTTGGTTAGATG
* * * * * * *
14975 AAGATAGATATTTCAATGAGACTTGAC-TCAAAGAATCAGGCAAAACAGAG-CCAGGGCCCTGGA
194 AATATAGATATTTCAATGAGACTTGGCGCCAAA-AATCATGCAAAACAGAGTCGA-GGCCCCGAA
* * * * * * * **
15038 ACGCCTTTTTAGTCAAAAATTGTGACGGATAATACACGATTTCGACTAAAACATTGTC-AAAATT
257 ACGCGTTTTTAGTCAAAACTCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTG-CAAAAATT
*
15102 GA-CTCCAAAAA
321 GACCT-GAAAAA
* * **
15113 TTTC-CTCTCAATTTTTTGCCACAATTCTCATAAAAAATATATAACTCAAC-CTTAAAATATTGA
1 TTTCTC-CTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAATATTGA
* * * * * **
15176 AGGGCTTCTGACGCTTCTGATATCG-TTTTCTTATTTTTTTGAATT-ATTTCCTAATTAAATCGA
65 AAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATTT-CTAATTAAATCGA
* * * * * * * *
15239 AAC-CGAATTGACATTCTCATAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTTGTTAGAA
129 AACATG-ATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGATTTGGTTAGAT
* * * * * *
15303 GAATATAGATACTTCAATGA-ATCTTGGTGCCAAAAAACATGCAACACTGAGCCGAGGCCCCGAA
193 GAATATAGATATTTCAATGAGA-CTTGGCGCCAAAAATCATGCAAAACAGAGTCGAGGCCCCGAA
* * * *
15367 A-GCGTTTTTAGCCAAAAAC-CGT-ATTGGTTAATACACGATTTCAGCTAAATTTTTGC------
257 ACGCGTTTTTAGTC-AAAACTCGTGA-TGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAT
*
15423 --ACC-G-AAAG
320 TGACCTGAAAAA
* * ** * * * *
15431 TTTTTCCCTCAATTTTTAGCCACAATACAAATAAAATATAGATAATTCAAAGCCAAAAATATTG-
1 TTTCT-CCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAATATTGA
* * * *
15495 AAGTACTTTTCACGCTTCTAATATTGTTTTTCCTATTTTATTCCAAATTAATTTCTACTTAAATC
65 AAG-GCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTT-TTCCGAATTAATTTCTAATTAAATC
* * * * * * * * *
15560 GAAACAAGATTTAGATGCTTGTAAAAA-AAATCCTTAAATTCATTGTGGATTATATCTGGTTAGA
127 GAAACATGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGATTTGGTTAGA
* * ** ** * * * *
15624 TGAATATAGAAATTTCGA-GTATCCTTATCACCAAACATCATGCAGAACTA-AGTCTG-GGCCCT
192 TGAATATAGATATTTCAATG-AGACTTGGCGCCAAAAATCATGCAAAAC-AGAGTC-GAGGCCCC
* * *
15686 GGAACGTGTTTTTAG-CAAAA-TACCGTGATGGTTAGTACACGATTTCGACTAAAATTTTGCAAA
254 GAAACGCGTTTTTAGTCAAAACT--CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* * *
15749 CATTCACCAGAAAAA
317 AATTGACCTGAAAAA
* * * *
15764 TTTCTGCTCAATTTTTGGCCACAATTCTCATAAAAAAAATATATAACTCAACGCTAAAAAGATTG
1 TTTCTCCTCAATTTTTGGCCACAATACTCAT--AAAAAATATATAACTCAACGCCAAAAATATTG
* * * * * * * * * *
15829 AATGACTTCTCAAGCTTTTAATATC-ATTTTCATATTTTTTTCGAATTAATTCCTAATTAAATCA
64 AAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTCCGAATTAATTTCTAATTAAATCG
* * * * * * **
15893 AAACCTTATTGAGATGTTTGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTTTTTTAGA
128 AAACATGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGA-TTTGGTTAGA
* * * * * * * * * * * *
15958 TGAATACAGACACTTCAGTGAGTCTCGGCGCCCAAAATCATGCCAAACTGAG-CCAGGGTCTCGA
192 TGAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGTCGA-GGCCCCGA
* * * * *
16022 AACGCGTTTTTAGCCAAAAAATCGTGATGATTAGTACACGATTTTCGGCTAAATTTTTTCAAAAA
256 AACGCGTTTTTAGTC-AAAACTCGTGATGGTTAGTACACGA-TTTCGGCTAAAATTTTGCAAAAA
* * *
16087 TTAATC-G-AAAG
319 TTGACCTGAAAAA
* * * * * * * * *
16098 TTTTTCCCTCAAGTTTTAGCCAAAAATACCCATAAAACATATATAATTCAA-GTTCAAAAAGATT
1 TTTCT-CCTCAATTTTTGGCC-ACAATACTCATAAAAAATATATAACTCAACG-CCAAAAATATT
* * * * * * * *
16162 GAATGACTTTTCATGCTTCTAATATCATTTTTCCTTTTTGTTACAAATTAATTTCTAATTAAATT
63 GAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTT-TTCCGAATTAATTTCTAATTAAATC
* * * ** *
16227 GAAAC-TGGACTGAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTTGACGAGACTTGGTTAG
127 GAAACAT-GATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGATTTGGTTAG
* * * *
16291 ATTAATATAGATATTTCAATGAGACTTGTCGCAAAAAATCATGCAAAACAGAG-CTAGGGCCCCG
191 ATGAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGTCGA-GGCCCCG
* * * * *
16355 GAACGCTTTTTTAGTCAAAAAC-CGTGATGGTTAGTACACGATTTCGGTTAGAATTTTACAAAAA
255 AAACGCGTTTTTAGTC-AAAACTCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGC-AAAA
**
16419 ATTGACCCAAAAAA
318 ATTGACCTGAAAAA
* * * *
16433 TTCCTCCTCGATTTTTGGCCACAATAATCATAATAAATATATAACTCAACGCCAAAAATATT-AA
1 TTTCTCCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAATATTGAA
* * * * * * * * *
16497 CGGGTTTCGCATGCTTCTAATATCG-TTTTCCTTTTTTTTCGGAATTTATTTTTAATGAAATCGA
66 AGGCTTT-TCACGCTTCTAATATCGTTTTTCC-TATTTTTCCGAATTAATTTCTAATTAAATCGA
** * * * * *
16561 AACCGGATTGAGATACTTGTAAAAA-AAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATA
129 AACATGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGATTTGGTTAGATG
* * * * *
16625 AATTTAGATATTTCAATGAGTCTTGGCGCCAAAAATAATG-AAGAACTGAGTCGGGGCCCC-AGA
194 AATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAA-AACAGAGTCGAGGCCCCGA-A
** * * * ** *
16688 ACGCGTTTTTAACCAAAAATTGTGATGATTAGTACATTATTTCAGCTAAAATTTTGCAAAAAAGT
257 ACGCGTTTTTAGTCAAAACTCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGC-AAAAA-T
* * *
16753 T-A-ATCAAAAG
320 TGACCTGAAAAA
* * * * * * * *
16763 TTTTTCGCT-TATATTTTAGCCACAATCCTCAAAAAAATATATATATAATTCAAGGCCAAAAAAA
1 TTTCTC-CTCAAT-TTTTGGCCACAATACTC-ATAAAA-A-ATATATAACTCAACGCCAAAAATA
** * * *
16827 TTGAAACCCTTTTCACGCTACTAATATTGTTTTTCCTTATTTTTTCCGAATTAATTT-TAATCAA
61 TTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCC-TA-TTTTTCCGAATTAATTTCTAATTAA
* * * * *
16891 ATCGAAACAAGATTCAGATGTTCGTAAAAA-GAA-CCTTAAATCCAATGTGGATGAGATTTGGTT
124 ATCGAAACATGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGATTTGGTT
* *
16954 AGATGAATATAGATATTTCAATGAGACTTGGCGTCAAAAATCATGCAAAACATAG-CGGAGGCCC
189 AGATGAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGTC-GAGGCCC
* * * * * *
17018 CTG-AACGCGTTTTTAGTCAAAACCCATGATAGTTAGCACACAATTTCGGTTAAAATTTTGCAAA
253 C-GAAACGCGTTTTTAGTCAAAACTCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
17082 AATTGACCTGAAAAA
317 AATTGACCTGAAAAA
* * * * * *
17097 ATTCTACTCAACTTTTTGGCCACAATTCTCATAACAAATATATAACTCAACACTAAAAA-ATT-A
1 TTTCTCCTCAA-TTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAATATTGA
* * *
17160 AAGGGTTTTTTCACGCTTCTAATATCGTTTTTCCTACTTTTTTCGAATTAATTACTAATTAAATC
65 AA-GG-CTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTCCGAATTAATTTCTAATTAAATC
** * * * ** *
17225 GAAACCGGATTGAGTTGCTCGTAAAAACAAATTCTT-ACTCCAATGTGGCAGAGATTTTGTTAGA
127 GAAACATGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGATTTGGTTAGA
* * * * ** * *
17289 TGAATATAGATATTTCAATAAGTCTTGACGCCATAAATCATGCAAAATTGAGTC-AGGGCCTCGG
192 TGAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGTCGA-GGCCCCGA
* * * * * *
17353 AACGCCCTTTTTTTTTTGTCAAAAAC-AGTGATGGTTAGTACATGATTTCGACTAAAATTTTACA
256 AACG--C---GTTTTTAGTC-AAAACTCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCA
*
17417 AAAATTGACCTAAAAAA
315 AAAATTGACCTGAAAAA
* * *
17434 TTTCTCCTCAATTTTTGGCCACAATAATCATAATAAATATATAACTCAACGCCAAAAAGATT-AA
1 TTTCTCCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAATATTGAA
* * * * * * **
17498 CGGGCTTCTCATGCTTATAATATTG-TTTTCCTATTTTT-CGAAATTAATTTCTAAATAAATTAA
66 -AGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTCCG-AATTAATTTCTAATTAAATCGA
* * *
17561 AACCA-GATTGAGATGCTCGTAAAAACAAATCCTTAGATCCAATGTTGATGAGATTT-GTTAGAT
129 AA-CATGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGATTTGGTTAGAT
* * * * * *
17624 GAATATA-ATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGACTG-GACTCCC-T
193 GAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGTC-GAGGC-CCCGA
* ** * * **
17686 AACGTGTTTTTAACCGAAGC-CGTGA----T-G--CACGATTTCAACTAAAATTTTGCAAAAATT
256 AACGCGTTTTTAGTCAAAACTCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATT
*
17743 TACCTGAAAGAA
321 GACCTGAAA-AA
** * * *
17755 TTT-TCCTCAATTTTTGGCCATGATACTTATAAAAAATATATAATTGAACGCCAAAAATATTGAA
1 TTTCTCCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAATATTGAA
* *
17819 AGGCTTTTCACGCTT-TCAATATCATTTTTCCTATTTTTCCGAATTGATTTCTAATTAAATCGAA
66 AGGCTTTTCACGCTTCT-AATATCGTTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAA
* * * * *
17883 ATATGATTTAGATGCTCATAAAAAACAAATCCTTAAATCCAATGTGGGTCACGATTTGTTTAGAT
130 ACATGATTGAGATGCTCGT-AAAAACAAATCCTTAAATCCAATGTGGGTGA-GATTTGGTTAGAT
* * *
17948 GAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCTTGCAAAACAGATTC-AGACCCCGAAA
193 GAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGTCGAGGCCCCGAAA
* * *
18012 CGCGTTTTTAGTCAAAACTTGTGATGGTTAGTACACGATTTCGGCTAAAATGTTGCAAACATTGA
258 CGCGTTTTTAGTCAAAACTCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA
18077 CCTGAAAAA
323 CCTGAAAAA
* *
18086 TTTCTCCTCAATTTTTGGCCACAATACTTATAAAAAGAATATATAACTCAACGCCAAAAAGATTG
1 TTTCTCCTCAATTTTTGGCCACAATACTCAT-AAAA-AATATATAACTCAACGCCAAAAATATTG
*
18151 -AAGGACTTCTCACGCTTCTAATATCGTTTTTCCTAATTTTTTTCCGAATTAATTTCTAATTAAA
64 AAAGG-CTTTTCACGCTTCTAATATCGTTTTTCCT-A--TTTTTCCGAATTAATTTCTAATTAAA
18215 AAATTATATT
Statistics
Matches: 2979, Mismatches: 620, Indels: 322
0.76 0.16 0.08
Matches are distributed among these distances:
318 6 0.00
319 39 0.01
320 131 0.04
321 66 0.02
322 106 0.04
323 85 0.03
324 37 0.01
325 43 0.01
327 9 0.00
328 48 0.02
329 132 0.04
330 129 0.04
331 712 0.24
332 300 0.10
333 194 0.07
334 548 0.18
335 186 0.06
336 108 0.04
337 95 0.03
338 5 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (331 bp):
TTTCTCCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAATATTGAA
AGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAA
CATGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGATTTGGTTAGATGAA
TATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGTCGAGGCCCCGAAACGC
GTTTTTAGTCAAAACTCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCT
GAAAAA
Found at i:18310 original size:54 final size:54
Alignment explanation
Indices: 18230--18332 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
18220 ATATTTTGTA
*
18230 AAAAATATATTTAAATAATATGAATTTAGAAATATATTTGAAAAAAAAGTAAAC
1 AAAAATATATTTAAATAATATCAATTTAGAAATATATTTGAAAAAAAAGTAAAC
* * * * *
18284 AAAATTATATTTTAATAATGA-CAATTTAGGAATATATTTTAAGAAAAAG
1 AAAAATATATTTAAATAAT-ATCAATTTAGAAATATATTTGAAAAAAAAG
18333 GTACAATCGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 41 0.98
55 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (54 bp):
AAAAATATATTTAAATAATATCAATTTAGAAATATATTTGAAAAAAAAGTAAAC
Found at i:31456 original size:2 final size:2
Alignment explanation
Indices: 31449--31496 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
31439 ATAATCGATC
31449 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
31491 AG AG AG
1 AG AG AG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.