Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011279.1 Kokia drynarioides strain JFW-HI SEQ_126258, 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: 4592
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Found at i:329 original size:62 final size:62
Alignment explanation
Indices: 244--433 Score: 188
Period size: 62 Copynumber: 3.0 Consensus size: 62
234 TCGATGAATT
* * * * * * *
244 AAAAATTTATTTACGTGAAAATTGGTTCTCTC-TTGGTTGTTGGCCGAAGTTTCGAACTTGTC
1 AAAAACTTATTTACGTGAAAATTGCTTCTCTCATT-ATTCTTGGACGAACTTCCGAACTTGTC
* *
306 AAAAACTTGTTTACGTGAGAATTGCTTCTCTCATTATTCTTGGACGAACTTCCGAACTTGTC
1 AAAAACTTATTTACGTGAAAATTGCTTCTCTCATTATTCTTGGACGAACTTCCGAACTTGTC
** * * * *
368 AAAAACTTATTTTATAT-AACAATGGTTTCTCTC-TTAATTCTTGGACGAACATCTGAACTTGTC
1 AAAAACTTA-TTTACGTGAA-AATTGCTTCTCTCATT-ATTCTTGGACGAACTTCCGAACTTGTC
431 AAA
1 AAA
434 CTTTTACGAT
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
62 61 0.57
63 46 0.43
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.38
Consensus pattern (62 bp):
AAAAACTTATTTACGTGAAAATTGCTTCTCTCATTATTCTTGGACGAACTTCCGAACTTGTC
Found at i:414 original size:63 final size:61
Alignment explanation
Indices: 269--433 Score: 168
Period size: 63 Copynumber: 2.6 Consensus size: 61
259 TGAAAATTGG
* * * * * * * * *
269 TTCTCTCTTGGTTGTTGGCCGAAGTTTCGAACTTGTCAAAAACTTGTTTACGTGAGAATTGC
1 TTCTCTCTT-ATTCTTGGACGAACTTCCGAACTTGTCAAAAACTTGTTTACATAACAATGGC
* * *
331 TTCTCTCATTATTCTTGGACGAACTTCCGAACTTGTCAAAAACTTATTTTATATAACAATGGT
1 TTCTCTC-TTATTCTTGGACGAACTTCCGAACTTGTCAAAAACTT-GTTTACATAACAATGGC
* *
394 TTCTCTCTTAATTCTTGGACGAACATCTGAACTTGTCAAA
1 TTCTCTCTT-ATTCTTGGACGAACTTCCGAACTTGTCAAA
434 CTTTTACGAT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
62 39 0.45
63 47 0.55
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (61 bp):
TTCTCTCTTATTCTTGGACGAACTTCCGAACTTGTCAAAAACTTGTTTACATAACAATGGC
Found at i:919 original size:62 final size:62
Alignment explanation
Indices: 817--996 Score: 297
Period size: 62 Copynumber: 2.9 Consensus size: 62
807 AATAACTTAG
817 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTATCAAAAACATAT
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTATCAAAAACATAT
* * * * *
879 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGACAAACTTCCAAACTTGTCAAAAACTTAT
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTATCAAAAACATAT
* *
941 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCCGAACTTTTCAAAA
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTATCAAAA
997 TTTTACGGTT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 108 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (62 bp):
TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTATCAAAAACATAT
Found at i:1224 original size:340 final size:340
Alignment explanation
Indices: 583--1510 Score: 1086
Period size: 340 Copynumber: 2.7 Consensus size: 340
573 TCTTTGAATT
* * * * **
583 AAAAACTTATTTACGTGAGAACTATTTCTCTCTTGGTTCTTGGAAGAACTTCCGAAATTCTGAAA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAAGAACATCCGAACTT-TTCAA
* * *
648 AACTTATTTACGTGAGAATTGTTTTATAACTT-AGGTTCCTTAAAGTATTCAAGACGATCCATTC
65 AA--T-TTTAC--G-G-TTTCTTTTATAACTTCA-GTTCCTGAAAGTATTCAAGACGATCCATTC
* * * * *
712 CTTTGAGCAAATTTCCAAACATTCCGTGCTCGAGAAATCACACCATTTGGTC-AAAATAGTTTGT
122 CTTTGAGCTAATTTTCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAAA-AGTTTGT
* * * * * **
776 CATTTTGTAAACAAGTTTTGG--ACTGTTAGTTAATAACTTAGTTACGTGAGAATTGTTTCTCTC
186 CATTTTGTAAACAAGTTTTGGTCACTG--AATTAAAAATTTATTTACATGAGAATTGAATCTCTC
*
839 TTGGTTCTTGGACGAACTTCCGAACTTATCAAAAACATATTTACGTGAGAATTG-TTTCTCTCTT
249 TTGGTTCTTGGACAAACTTCCGAACTTATCAAAAACATATTTACGTGAGAATTGCTTT-TCTCTT
*
903 GGTTCTTAGACAAACTTCCAAACTTGTC
313 AGTTCTTAGACAAACTTCCAAACTTGTC
*
931 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCCGAACTTTTCAAA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAAGAACATCCGAACTTTTCAAA
* *
996 ATTTTACGGTTTTTTTTATAACTTCAGTTCCTGAAAGTATTCAAGAGGATCCATTCCTTTGAG-T
66 ATTTTACGGTTTCTTTTATAACTTCAGTTCCTGAAAGTATTCAAGACGATCCATTCCTTTGAGCT
** * * * *
1060 AATTCTTTGAACATTCCATGCTTGGGAAATCGCATAATTTGGTCTAAAAAGTTTATC-TTTCTGT
131 AATT-TTCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTT-TGT
1124 AAACAAGTTTTGGTCACTGAATTAAAAATTTATTTACATGAGAATTGAATCTCTCTTGGTTCTTG
194 AAACAAGTTTTGGTCACTGAATTAAAAATTTATTTACATGAGAATTGAATCTCTCTTGGTTCTTG
* * * * * * *
1189 GACAAACTTTCGAACTTGTCGAAAACTTGTTTACGTGAGAATTGCTTTTCTCTTAGTTCTTGGAT
259 GACAAACTTCCGAACTTATCAAAAACATATTTACGTGAGAATTGCTTTTCTCTTAGTTCTTAGAC
* *
1254 GAACTTCCGAACTTGTC
324 AAACTTCCAAACTTGTC
* * * * ** *
1271 AAAAACTTATTTTATGTAAGAATTGTTTCTCTCTTGCTTCTTGGATGAACATATGAACTTGTCAA
1 AAAAACTTA-TTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAAGAACATCCGAACTTTTCAA
* * *
1336 ACA-TTTACGATTTCTTTTATAACTTCGGTTCCTGAAAGTATTCATGACGATCCATTCCTTTGAG
65 A-ATTTTACGGTTTCTTTTATAACTTCAGTTCCTGAAAGTATTCAAGACGATCCATTCCTTTGAG
* * *
1400 CT-ATTTTCCAAACATTCCTTGCTCGAAAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
129 CTAATTTT-CAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTG
* ** *
1464 -AAA-AATATTTTGGTCTTTGAATTAAAAATTTATTTACATGAAAATTG
193 TAAACAA-GTTTTGGTCACTGAATTAAAAATTTATTTACATGAGAATTG
1511 GTCTTAAAAG
Statistics
Matches: 502, Mismatches: 65, Indels: 34
0.84 0.11 0.06
Matches are distributed among these distances:
339 9 0.02
340 258 0.51
341 160 0.32
342 10 0.02
344 5 0.01
345 1 0.00
347 5 0.01
348 54 0.11
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (340 bp):
AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAAGAACATCCGAACTTTTCAAA
ATTTTACGGTTTCTTTTATAACTTCAGTTCCTGAAAGTATTCAAGACGATCCATTCCTTTGAGCT
AATTTTCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAA
ACAAGTTTTGGTCACTGAATTAAAAATTTATTTACATGAGAATTGAATCTCTCTTGGTTCTTGGA
CAAACTTCCGAACTTATCAAAAACATATTTACGTGAGAATTGCTTTTCTCTTAGTTCTTAGACAA
ACTTCCAAACTTGTC
Found at i:1259 original size:62 final size:61
Alignment explanation
Indices: 1147--1336 Score: 188
Period size: 62 Copynumber: 3.0 Consensus size: 61
1137 TCACTGAATT
* * * * **
1147 AAAAATTTA-TTTACATGAGAATTGAATCTCTCTTGGTTCTTGGACAAACTTTCGAACTTGTC
1 AAAAACTTAGTTTACGTGAGAATTG-TTTTCTCTT-GTTCTTGGATGAACTTTCGAACTTGTC
* *
1209 GAAAACTT-GTTTACGTGAGAATTGCTTTTCTCTTAGTTCTTGGATGAACTTCCGAACTTGTC
1 AAAAACTTAGTTTACGTGAGAATTG-TTTTCTCTT-GTTCTTGGATGAACTTTCGAACTTGTC
* * * *
1271 AAAAACTTATTTTATGTAAGAATTGTTTCTCTCTTGCTTCTTGGATGAACATAT-GAACTTGTC
1 AAAAACTTAGTTTACGTGAGAATTGTTT-TCTCTTG-TTCTTGGATGAAC-TTTCGAACTTGTC
1334 AAA
1 AAA
1337 CATTTACGAT
Statistics
Matches: 107, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
62 62 0.58
63 44 0.41
64 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (61 bp):
AAAAACTTAGTTTACGTGAGAATTGTTTTCTCTTGTTCTTGGATGAACTTTCGAACTTGTC
Found at i:1524 original size:69 final size:70
Alignment explanation
Indices: 1439--1582 Score: 206
Period size: 70 Copynumber: 2.1 Consensus size: 70
1429 ATCGCATCAT
** *
1439 TTGGTCTAAATAGTTTGTCATTT-TG-AAA-AATATTTTGGTCTTTGAATTAAAAATTTATTTAC
1 TTGGTCTAAATAGTTTGTC-TTTCTGTAAACAA-ATTTTGGTCGCTGAATTAAAAACTTATTTAC
1501 ATGAAAA
64 ATGAAAA
1508 TTGGTCTTAAA-AGTTTGTCTTTCTGTAAACAAATTTTGGTCGCTGAATTAAAAACTTATTTACA
1 TTGGTC-TAAATAGTTTGTCTTTCTGTAAACAAATTTTGGTCGCTGAATTAAAAACTTATTTACA
1572 TGAAAA
65 TGAAAA
1578 TTGGT
1 TTGGT
1583 TCTCTCTTGG
Statistics
Matches: 68, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
68 3 0.04
69 16 0.24
70 47 0.69
71 2 0.03
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (70 bp):
TTGGTCTAAATAGTTTGTCTTTCTGTAAACAAATTTTGGTCGCTGAATTAAAAACTTATTTACAT
GAAAA
Found at i:1870 original size:62 final size:62
Alignment explanation
Indices: 1772--1961 Score: 256
Period size: 62 Copynumber: 3.0 Consensus size: 62
1762 TCTTTAAATT
* * * * * *
1772 AAAAACTTATTTACATGACAACTGTTTCTCTCTTGGTTCTTGGAAGAACTTCCGAACTTATC
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTGTC
*
1834 AAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTTCGAACTTGTC
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTGTC
* * * *
1896 AAAAACTTATTTTATGTAAGAATTGTTTCTCTCTTT-GTTCTTGGACGAACATCTGAACTTGTC
1 AAAAACTTA-TTTACGTGAGAATTGTTTCTCT-TTTGGTTCTTGGACGAACTTCCGAACTTGTC
1959 AAA
1 AAA
1962 CTTTTACGAT
Statistics
Matches: 114, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
62 64 0.56
63 47 0.41
64 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (62 bp):
AAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTGTC
Found at i:2124 original size:625 final size:617
Alignment explanation
Indices: 869--2855 Score: 2391
Period size: 625 Copynumber: 3.2 Consensus size: 617
859 CGAACTTATC
* * ** * * * ** *
869 AAAAACATATTTACGTGAGAATT-GTTTCTCTCTTGGTTCTTAGACAAACTTCCAAACTTGTCAA
1 AAAAACTTATTTACATGAGAATTGGTTTAACTCTTGGTTCGTAGAAAAACTTCCGAACTAATTAA
* * *
933 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCCGAACTTTTCAAAAT
66 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCTGAACTTGTCAAACT
* * *
998 TTTACGGTTTTTTTTATAACTTCAGTTCCTGAAAGTATTCAAGAGGATCCATTCCTTTGAG-TAA
131 TTTAC-GATTCTTTTATAACTTCAGTTCCTGAAAGTATTCAAGACGATCCATTCCTTTGAGCT-A
** * * * *
1062 TTCTT-TGAACATTCCATGCTTGGGAAATCGCATAATTTGGTCTAAAAAGTTTATC-TTTCTGTA
194 TT-TTCCAAACATTCCATGCTCGGAAAATCGCATAATTTGGTCTAAATAGTTTGTCATTT-TGTA
* * * * **
1125 AACAAGTTTTGGTCACTGAATTAAAAATTTATTTACATGAGAATTGAATCTCTCTTGGTTCTTGG
257 AACAAATTTTGGTC-TTTAATTAAAAACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGG
* * * * *
1190 ACA-AACTTTCGAACTTGTCGAAAACTTGTTTACGTGAGAATTGCTTT-TCTCTTAGTTCTTGGA
321 A-AGAACTTCCGAACTTATCAAAAACTTATTTACGTGAGAATTG-TTTCTCTCTTGGTTCTTGGA
* *
1253 TGAACTTCCGAACTTGTCAAAAACTTATTTTATGTAAGAATTGTTTCTCTC-TTGCTTCTTGGAT
384 CGAACTTCCGAACTTGTCAAAAACTTATTTTATGTAAGAATTGTTTCTCTCTTTG-TTCTTGGAC
* *
1317 GAACATATGAACTTGTCAAACATTTACGATTTCTTTTATAACTTCGGTTCCTGAAAGTATTCATG
448 GAACATCTGAACTTGTCAAACTTTTACGATTTCTTTTATAACTTCGGTTCCTGAAAGTATTCATG
**
1382 ACGATCCATTCCTTTGAGCTATTTTCCAAACATTCCTTGCTCGAAAAATCGCATCATTTGGTCTA
513 ACGATCCATTCCTTTGAGCTATTTTCCAAACATTCCTTGCTCGGGAAATCGCATCATTTGGTCTA
1447 AATAGTTTGTCATTTTGAAAAATATTTTGGTCTTTGAATT
578 AATAGTTTGTCATTTTGAAAAATATTTTGGTCTTTGAATT
* * * * * ** **
1487 AAAAATTTATTTACATGAAAATTGGTCTTAAAAGT-TTGTCTTTCTGTA-AACAAATTTTGGTCG
1 AAAAACTTATTTACATGAGAATTGGT-TT--AACTCTTG--GTTC-GTAGAA-AAACTTCCG-AA
* * *
1550 CTGAATTAAAAACTTATTTACATGAAAATTGGTTCTCTCTTGGTTCTTGGACGAACATCTGAACT
58 CT-AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCTGAACT
*
1615 TGTCAAACTTTTACGATTACTTTTATAACTTCAGTTCCTGAAAGTATTCATGACGATCCATTCCT
122 TGTCAAACTTTTACGATT-CTTTTATAACTTCAGTTCCTGAAAGTATTCAAGACGATCCATTCCT
* *
1680 TTGAGCTATTTTCCAAACATTCCTTGCTCGGAAAATCGCATGATTTGGTCTAAATAGTTTGTCAT
186 TTGAGCTATTTTCCAAACATTCCATGCTCGGAAAATCGCATAATTTGGTCTAAATAGTTTGTCAT
* *
1745 TTTG-AAA-AATATTTTGGTCTTTAAATTAAAAACTTATTTACATGACAACTGTTTCTCTCTTGG
251 TTTGTAAACAA-ATTTTGGTCTTT-AATTAAAAACTTATTTACATGAGAATTGTTTCTCTCTTGG
*
1808 TTCTTGGAAGAACTTCCGAACTTATCAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTC
314 TTCTTGGAAGAACTTCCGAACTTATCAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTC
*
1873 TTGGACGAACTTTCGAACTTGTCAAAAACTTATTTTATGTAAGAATTGTTTCTCTCTTTGTTCTT
379 TTGGACGAACTTCCGAACTTGTCAAAAACTTATTTTATGTAAGAATTGTTTCTCTCTTTGTTCTT
1938 GGACGAACATCTGAACTTGTCAAACTTTTACGATTTCTTTTATAACTTCGGTTCCTGAAAGTATT
444 GGACGAACATCTGAACTTGTCAAACTTTTACGATTTCTTTTATAACTTCGGTTCCTGAAAGTATT
* * *
2003 CATGACGATCCATTCCTTCGAGCTATTTTCCAAACCTTCCTTGCTCGGGAAATCGCATCAGTTGG
509 CATGACGATCCATTCCTTTGAGCTATTTTCCAAACATTCCTTGCTCGGGAAATCGCATCATTTGG
2068 TCTAAATAGTTTGTCATTTTGAAAAATATTTTGGTCTTTGAATT
574 TCTAAATAGTTTGTCATTTTGAAAAATATTTTGGTCTTTGAATT
* * ** * * *
2112 AAAAACTTATTTACGTGAGAACT-GTTTCTCTCTTGGTTCGTAGAAGAACTTCCGAACTTATTGA
1 AAAAACTTATTTACATGAGAATTGGTTTAACTCTTGGTTCGTAGAAAAACTTCCGAACTAATTAA
* *
2176 AAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAAC-TTTCGAACTTGTCAAAC
66 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCT-GAACTTGTCAAAC
* * * * *
2240 TTTCACTAGTTCTTTTATAACTT-AGGTTCCTTAAAGTATACAAGACGATCCATTCCTTTGAGCA
130 TTTTACGA-TTCTTTTATAACTTCA-GTTCCTGAAAGTATTCAAGACGATCCATTCCTTTGAGCT
* * * ** *
2304 AATTTCCAAACATTCCCTGCTC-GAGAAATCACACCATTTGGTCAAAATAGTTTGTCATTTTGTA
193 ATTTTCCAAACATTCCATGCTCGGA-AAATCGCATAATTTGGTCTAAATAGTTTGTCATTTTGTA
* * * * ** * *
2368 AACAACTTTTGGACTGTTAATTAATAACTTAGTTATGTAAGAATTGTTTCTCTCTTGGTTCTGGG
257 AACAAATTTTGGTCT-TTAATTAAAAACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGG
* *
2433 ACGAACTTCCAAACTTATCAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACG
321 AAGAACTTCCGAACTTATCAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACG
* * * *
2498 AACTTCCAAACTTGTCAAAAACTTA-TTTACGTGAGAATTGTTTCTCTCTTGGTT-TTGGACGAA
386 AACTTCCGAACTTGTCAAAAACTTATTTTATGTAAGAATTGTTTCTCTCTTTGTTCTTGGACGAA
* * * * * * *
2561 CATCCGTACTTTTCAAACTTTTACGATTTCTTCTATAACTTCGGTTCCTAAAAGTATTCAAGAGG
451 CATCTGAACTTGTCAAACTTTTACGATTTCTTTTATAACTTCGGTTCCTGAAAGTATTCATGACG
* *** * * *
2626 ATCCATTCCTTTGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATAATTTGGTCTAAAA
516 ATCCATTCCTTTGAGCTATTTTCCAAACATTCCTTGCTCGGGAAATCGCATCATTTGGTCTAAAT
* * * **
2691 ATTTTGTCTTTTTGTAAACAA-CTTTTGGTCGCTGAATT
581 AGTTTGTCATTTTG-AAA-AATATTTTGGTCTTTGAATT
** * *
2729 AAAAACTTATTTACATGAGAATTGGTTCT--CTCTTGGATCTCG--GACGAACTTTCGAACTTGA
1 AAAAACTTATTTACATGAGAATTGGTT-TAACTCTTGG-T-TCGTAGAAAAACTTCCGAAC-TAA
* * * * ** * * *
2790 -CAAAAACTTATTCACGTAAGTATTGTTTCTCTCTCAGTTCTTGGACGAACTTCCGAGCTTGTCA
62 TTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCTGAACTTGTCA
2854 AA
127 AA
2856 AACTTATTTT
Statistics
Matches: 1183, Mismatches: 150, Indels: 73
0.84 0.11 0.05
Matches are distributed among these distances:
616 139 0.12
617 303 0.26
618 167 0.14
619 18 0.02
620 7 0.01
621 4 0.00
622 4 0.00
623 6 0.01
624 16 0.01
625 350 0.30
626 165 0.14
627 4 0.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (617 bp):
AAAAACTTATTTACATGAGAATTGGTTTAACTCTTGGTTCGTAGAAAAACTTCCGAACTAATTAA
AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCTGAACTTGTCAAACT
TTTACGATTCTTTTATAACTTCAGTTCCTGAAAGTATTCAAGACGATCCATTCCTTTGAGCTATT
TTCCAAACATTCCATGCTCGGAAAATCGCATAATTTGGTCTAAATAGTTTGTCATTTTGTAAACA
AATTTTGGTCTTTAATTAAAAACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGGAAGAA
CTTCCGAACTTATCAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTT
CCGAACTTGTCAAAAACTTATTTTATGTAAGAATTGTTTCTCTCTTTGTTCTTGGACGAACATCT
GAACTTGTCAAACTTTTACGATTTCTTTTATAACTTCGGTTCCTGAAAGTATTCATGACGATCCA
TTCCTTTGAGCTATTTTCCAAACATTCCTTGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTT
GTCATTTTGAAAAATATTTTGGTCTTTGAATT
Found at i:2202 original size:340 final size:339
Alignment explanation
Indices: 1557--2238 Score: 1186
Period size: 340 Copynumber: 2.0 Consensus size: 339
1547 TCGCTGAATT
1557 AAAAACTTATTTACATGAAAATTGGTTCTCTCTTGGTTCTTGGACGAACATCTGAACTTGTCAAA
1 AAAAACTTATTTACATGAAAATTGGTTCTCTCTTGGTTCTTGGACGAACATCTGAACTTGTCAAA
*
1622 CTTTTACGATTACTTTTATAACTTCAGTTCCTGAAAGTATTCATGACGATCCATTCCTTTGAGCT
66 CTTTTACGATTACTTTTATAACTTCAGTTCCTGAAAGTATTCATGACGATCCATTCCTTCGAGCT
* *
1687 ATTTTCCAAACATTCCTTGCTCGGAAAATCGCATGATTTGGTCTAAATAGTTTGTCATTTTGAAA
131 ATTTTCCAAACATTCCTTGCTCGGAAAATCGCATCAGTTGGTCTAAATAGTTTGTCATTTTGAAA
* *
1752 AATATTTTGGTCTTTAAATTAAAAACTTATTTACATGACAACTGTTTCTCTCTTGGTTCTTGGAA
196 AATATTTTGGTCTTTAAATTAAAAACTTATTTACATGACAACTGTTTCTCTCTTGGTTCGTAGAA
1817 GAACTTCCGAACTTATCAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAA
261 GAACTTCCGAACTTATCAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAA
1882 CTTTCGAACTTGTC
326 CTTTCGAACTTGTC
* * *
1896 AAAAACTTATTT-TATGTAAGAATTGTTTCTCTCTTTGTTCTTGGACGAACATCTGAACTTGTCA
1 AAAAACTTATTTACATG-AA-AATTGGTTCTCTCTTGGTTCTTGGACGAACATCTGAACTTGTCA
* *
1960 AACTTTTACGATTTCTTTTATAACTTCGGTTCCTGAAAGTATTCATGACGATCCATTCCTTCGAG
64 AACTTTTACGATTACTTTTATAACTTCAGTTCCTGAAAGTATTCATGACGATCCATTCCTTCGAG
* *
2025 CTATTTTCCAAACCTTCCTTGCTCGGGAAATCGCATCAGTTGGTCTAAATAGTTTGTCATTTTGA
129 CTATTTTCCAAACATTCCTTGCTCGGAAAATCGCATCAGTTGGTCTAAATAGTTTGTCATTTTGA
* * *
2090 AAAATATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAACTGTTTCTCTCTTGGTTCGTAG
194 AAAATATTTTGGTCTTTAAATTAAAAACTTATTTACATGACAACTGTTTCTCTCTTGGTTCGTAG
**
2155 AAGAACTTCCGAACTTATTGAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACG
259 AAGAACTTCCGAACTTATCAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACG
2220 AACTTTCGAACTTGTC
324 AACTTTCGAACTTGTC
2236 AAA
1 AAA
2239 CTTTCACTAG
Statistics
Matches: 324, Mismatches: 17, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
338 3 0.01
339 14 0.04
340 307 0.95
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (339 bp):
AAAAACTTATTTACATGAAAATTGGTTCTCTCTTGGTTCTTGGACGAACATCTGAACTTGTCAAA
CTTTTACGATTACTTTTATAACTTCAGTTCCTGAAAGTATTCATGACGATCCATTCCTTCGAGCT
ATTTTCCAAACATTCCTTGCTCGGAAAATCGCATCAGTTGGTCTAAATAGTTTGTCATTTTGAAA
AATATTTTGGTCTTTAAATTAAAAACTTATTTACATGACAACTGTTTCTCTCTTGGTTCGTAGAA
GAACTTCCGAACTTATCAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAA
CTTTCGAACTTGTC
Found at i:2210 original size:62 final size:62
Alignment explanation
Indices: 2113--2232 Score: 186
Period size: 62 Copynumber: 1.9 Consensus size: 62
2103 CTTTGAATTA
2113 AAAACTTATTTACGTGAGAACTGTTTCTCTCTTGGTTCGTAGAAGAACTTCCGAACTTATTG
1 AAAACTTATTTACGTGAGAACTGTTTCTCTCTTGGTTCGTAGAAGAACTTCCGAACTTATTG
* * * * * *
2175 AAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTTCGAACTT
1 AAAACTTATTTACGTGAGAACTGTTTCTCTCTTGGTTCGTAGAAGAACTTCCGAACTT
2233 GTCAAACTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (62 bp):
AAAACTTATTTACGTGAGAACTGTTTCTCTCTTGGTTCGTAGAAGAACTTCCGAACTTATTG
Found at i:2477 original size:62 final size:62
Alignment explanation
Indices: 2393--2561 Score: 286
Period size: 62 Copynumber: 2.7 Consensus size: 62
2383 GTTAATTAAT
* * * *
2393 AACTTAGTTATGTAAGAATTGTTTCTCTCTTGGTTCTGGGACGAACTTCCAAACTTATCAAA
1 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTATCAAA
*
2455 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGTCAAA
1 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTATCAAA
2517 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTT-TTGGACGAAC
1 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAC
2562 ATCCGTACTT
Statistics
Matches: 102, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
61 10 0.10
62 92 0.90
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (62 bp):
AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTATCAAA
Found at i:2512 original size:278 final size:277
Alignment explanation
Indices: 1834--2516 Score: 931
Period size: 278 Copynumber: 2.5 Consensus size: 277
1824 CGAACTTATC
* * * *
1834 AAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTTCGAACTTGTCAAA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTGGGACGAACTTCCGAACTTATCAAA
* * * * *
1899 AACTTATTTTATGTAAGAATTGTTTCTCTCTTTGTTCTTGGACGAACATCTGAACTTGTCAAACT
66 AACTTA-TTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACT
* * * * * * *
1964 TTTACGATTTCTTTTATAACTTCGGTTCCTGAAAGTATTCATGACGATCCATTCCTTCGAGCTAT
130 TTCACGAGTTCTTTTATAACTTAGGTTCCTGAAAGTATACAAGACGATCCATTCCTTCGAGCAAA
* * * * * *
2029 TTTCCAAACCTTCCTTGCTCGGGAAATCGCATCAGTTGGTCTAAATAGTTTGTCATTTTGAAAAA
195 TTTCCAAACATTCCCTGCTCGAGAAATCACACCAGTTGGTCAAAATAGTTTGTCATTTTGAAAAA
*
2094 TATTTTGGTCTTTGAATT
260 TATTTTGGACTTTGAATT
* * * **
2112 AAAAACTTATTTACGTGAGAACTGTTTCTCTCTTGGTTC-GTAGAAGAACTTCCGAACTTATTGA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTG-GGACGAACTTCCGAACTTATCAA
* *
2176 AAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACT
65 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACT
* * *
2241 TTCACTAGTTCTTTTATAACTTAGGTTCCTTAAAGTATACAAGACGATCCATTCCTTTGAGCAAA
130 TTCACGAGTTCTTTTATAACTTAGGTTCCTGAAAGTATACAAGACGATCCATTCCTTCGAGCAAA
*
2306 TTTCCAAACATTCCCTGCTCGAGAAATCACACCATTTGGTCAAAATAGTTTGTCATTTTGTAAAC
195 TTTCCAAACATTCCCTGCTCGAGAAATCACACCAGTTGGTCAAAATAGTTTGTCATTTTG-AAA-
*
2371 AA-CTTTTGGACTGTT-AATT
258 AATATTTTGGACT-TTGAATT
* * * * *
2390 AATAACTTAGTTATGTAAGAATTGTTTCTCTCTTGGTTCTGGGACGAACTTCCAAACTTATCAAA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTGGGACGAACTTCCGAACTTATCAAA
*
2455 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGTCAAA
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAA
2517 AACTTATTTA
Statistics
Matches: 352, Mismatches: 48, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
277 159 0.45
278 188 0.53
279 5 0.01
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (277 bp):
AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTGGGACGAACTTCCGAACTTATCAAA
AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTT
TCACGAGTTCTTTTATAACTTAGGTTCCTGAAAGTATACAAGACGATCCATTCCTTCGAGCAAAT
TTCCAAACATTCCCTGCTCGAGAAATCACACCAGTTGGTCAAAATAGTTTGTCATTTTGAAAAAT
ATTTTGGACTTTGAATT
Found at i:2752 original size:339 final size:339
Alignment explanation
Indices: 2112--3110 Score: 1327
Period size: 339 Copynumber: 3.0 Consensus size: 339
2102 TCTTTGAATT
* * * * * **
2112 AAAAACTTATTTACGTGAGAACTGTTTCTCTCTTGGTTCGTAGAAGAACTTCCGAACTTATTGAA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAA
* * *
2177 AACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTT
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCCGAACTTGTCAAACTT
* * * * * * * *
2242 TCACTAGTTCTTTTATAACTTAGGTTCCTTAAAGTATACAAGACGATCCATTCCTTTGAGCAAAT
131 TTACGATTTCTTTTATAACTTCGGTTCCTAAAAGTATTCAAGAGGATCCATTCCTTTGAGCAATT
*** * * * ** *
2307 TTCCAAACATTCCCTGCTCGAGAAATCACACCATTTGGTC-AAAATAGTTTGTCATTTTGTAAAC
196 TTTTGAACATTCCATGCTCGGGAAATCGCATAATTTGGTCTAAAA-A-TTTGTCTTTTTGTAAAC
* * * * * *
2371 AACTTTTGGACTG-TTAATTAATAACTTAGTTATGTAAGAATTGTTTCTCTCTTGGTTCTGGGAC
259 AACTTTTGGTC-GCTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCTCGGAC
2435 GAACTTCCAAACTT-ATC
323 GAACTTCCAAACTTGA-C
*
2452 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGTCAAA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAA
* *
2517 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTT-TTGGACGAACATCCGTACTTTTCAAACTT
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCCGAACTTGTCAAACTT
*
2581 TTACGATTTCTTCTATAACTTCGGTTCCTAAAAGTATTCAAGAGGATCCATTCCTTTGAGCAATT
131 TTACGATTTCTTTTATAACTTCGGTTCCTAAAAGTATTCAAGAGGATCCATTCCTTTGAGCAATT
2646 TTTTGAACATTCCATGCTCGGGAAATCGCATAATTTGGTCTAAAAATTTTGTCTTTTTGTAAACA
196 TTTTGAACATTCCATGCTCGGGAAATCGCATAATTTGGTCTAAAAA-TTTGTCTTTTTGTAAACA
* * * *
2711 ACTTTTGGTCGCTGAATTAAAAACTTATTTACATGAGAATTGGTTCTCTCTTGGATCTCGGACGA
260 ACTTTTGGTCGCTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCTCGGACGA
* *
2776 ACTTTCGAACTTGAC
325 ACTTCCAAACTTGAC
* * * ** *
2791 AAAAACTTATTCACGTAAGTATTGTTTCTCTCTCAGTTCTTGGACGAACTTCCGAGCTTGTCAAA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAA
* * * *
2856 AACTTATTTTATGTAAGAATCGTTTCTCTCTTGGTTCTTGGACGAACATCTGAACTTGTCAAACT
66 AACTTA-TTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCCGAACTTGTCAAACT
* *
2921 TTTACGATTTATTTTATAACTTCGGTTCCTGAAAGTATTCAAGAGGATCCATTCCTTTGAGCAAT
130 TTTACGATTTCTTTTATAACTTCGGTTCCTAAAAGTATTCAAGAGGATCCATTCCTTTGAGCAAT
* * *
2986 TTTTTGACCATTCCATGCTCTGGAAATCGCATAATTTGGTCT--AAA-----CTTTTTGCAAACA
195 TTTTTGAACATTCCATGCTCGGGAAATCGCATAATTTGGTCTAAAAATTTGTCTTTTTGTAAACA
* *
3044 AGTTTTGGTCGCTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCTTGGACGA
260 ACTTTTGGTCGCTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCTCGGACGA
3109 AC
325 AC
3111 ACCTGAACTT
Statistics
Matches: 585, Mismatches: 69, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
333 73 0.12
338 1 0.00
339 262 0.45
340 122 0.21
341 127 0.22
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (339 bp):
AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAA
AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCCGAACTTGTCAAACTT
TTACGATTTCTTTTATAACTTCGGTTCCTAAAAGTATTCAAGAGGATCCATTCCTTTGAGCAATT
TTTTGAACATTCCATGCTCGGGAAATCGCATAATTTGGTCTAAAAATTTGTCTTTTTGTAAACAA
CTTTTGGTCGCTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCTCGGACGAA
CTTCCAAACTTGAC
Found at i:2895 original size:63 final size:63
Alignment explanation
Indices: 2729--2918 Score: 224
Period size: 62 Copynumber: 3.0 Consensus size: 63
2719 TCGCTGAATT
* * * * *
2729 AAAAACTTATTTACATG--AGAATTGGTTCTCTCTTGGATCTCGGACGAACTTTCGAACTTGAC
1 AAAAACTTATTT-CATGTAAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTC
* * ** *
2791 AAAAACTTA-TTCACGTAAGTATTGTTTCTCTCTCAGTTCTTGGACGAACTTCCGAGCTTGTC
1 AAAAACTTATTTCATGTAAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTC
* * * *
2853 AAAAACTTATTTTATGTAAGAATCGTTTCTCTCTTGGTTCTTGGACGAACATCTGAACTTGTC
1 AAAAACTTATTTCATGTAAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTC
2916 AAA
1 AAA
2919 CTTTTACGAT
Statistics
Matches: 106, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
60 3 0.03
61 2 0.02
62 54 0.51
63 47 0.44
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.36
Consensus pattern (63 bp):
AAAAACTTATTTCATGTAAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTC
Found at i:3233 original size:208 final size:209
Alignment explanation
Indices: 2853--3238 Score: 589
Period size: 208 Copynumber: 1.9 Consensus size: 209
2843 CGAGCTTGTC
* *
2853 AAAAACTTATTTTATGTAAGAATCGTTTCTCTCTTGGTTCTTGGACGAACATCTGAACTTGTCAA
1 AAAAACTTATTTTACGTAAGAATCGTTTCTCTCTTGGTTCTTGGACGAACACCTGAACTTGTCAA
*
2918 ACTTTTACGATTTATTTTATAACTTCGGTTCCTGAAAGTATTCAAGAGGATCCATTCCTTTGAGC
66 ACTTTTACGATTTATTTTATAACTTCGGTTCCTGAAAGTATTCAAGAGGATCCATTCCTTCGAGC
*** * *
2983 AATTTTTTGACCATTCCATGCTCTGGAAATCGCATAATTTGGTCTAAACTTTTTGCAAACAAGTT
131 AATTTTCCAAACATTCCATGCTCAGGAAATCGCATAATTTGGTCTAAACTTTTTGCAAACAAGTT
3048 TTGGTCGCTGAATT
196 TTGGTCGCTGAATT
*
3062 AAAAACTTA-TTTACGTAAGAATTGTTTCTCTCTTGGTTCTTGGACGAACACCTGAACTTGTCAA
1 AAAAACTTATTTTACGTAAGAATCGTTTCTCTCTTGGTTCTTGGACGAACACCTGAACTTGTCAA
* * *
3126 A-TTTTGACGA-TTACTTTTATAACTTCGGTTCCTGAAATTATTCATGATGATCCATTCCTTCGA
66 ACTTTT-ACGATTTA-TTTTATAACTTCGGTTCCTGAAAGTATTCAAGAGGATCCATTCCTTCGA
* * * *
3189 GCTATTTTCCAAACATTCCTTGCTCAGGAAATCTCATGATTTGGTCTAAA
129 GCAATTTTCCAAACATTCCATGCTCAGGAAATCGCATAATTTGGTCTAAA
3239 TAGTTTGTCG
Statistics
Matches: 159, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
207 7 0.04
208 143 0.90
209 9 0.06
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (209 bp):
AAAAACTTATTTTACGTAAGAATCGTTTCTCTCTTGGTTCTTGGACGAACACCTGAACTTGTCAA
ACTTTTACGATTTATTTTATAACTTCGGTTCCTGAAAGTATTCAAGAGGATCCATTCCTTCGAGC
AATTTTCCAAACATTCCATGCTCAGGAAATCGCATAATTTGGTCTAAACTTTTTGCAAACAAGTT
TTGGTCGCTGAATT
Found at i:3348 original size:62 final size:62
Alignment explanation
Indices: 3277--3402 Score: 155
Period size: 62 Copynumber: 2.0 Consensus size: 62
3267 TCTTTGAATT
* *
3277 AAAAACTTATTTACGTGATAACTGTTTCTATCTTT-GTTCATGAAAGAACTTCCGAACTTATC
1 AAAAACTTATTTACGCGAGAACTGTTTCTAT-TTTGGTTCATGAAAGAACTTCCGAACTTATC
* * * * * * *
3339 AAAAACTTATTTACGCGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTTCGAACTTGTC
1 AAAAACTTATTTACGCGAGAACTGTTTCTATTTTGGTTCATGAAAGAACTTCCGAACTTATC
3401 AA
1 AA
3403 GCTTTCACTA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 3 0.06
62 51 0.94
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.39
Consensus pattern (62 bp):
AAAAACTTATTTACGCGAGAACTGTTTCTATTTTGGTTCATGAAAGAACTTCCGAACTTATC
Found at i:3678 original size:278 final size:277
Alignment explanation
Indices: 3062--3681 Score: 732
Period size: 277 Copynumber: 2.2 Consensus size: 277
3052 TCGCTGAATT
* **
3062 AAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCTTGGACGAA-CACCTGAACTTGTCAA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAATTTCC-GAACTTGTCAA
* * * * * * *
3126 ATTTTGACGATTACTTTTATAACTTCGGTTCCTGAAATTATTCATGATGATCCATTCCTTCGAGC
65 ACTTTCACAATTACTTTTATAACTTCGGTTCCTGAAAGTATACAAGACGATCCATTCCTTCGAGC
* * * ** * *
3191 TATTTTCCAAACATTCCTTGCTCAGGAAATCTCATGATTTGGTCTAAATAGTTTGTCGTTTTGAA
130 AATTTTCCAAACATTCCGTGCTCAGGAAATCACACCATTTGGTCAAAATAGTTTGTCATTTTGAA
* * * * *
3256 AAATATTTTGGTCTTTGAATTAAAAACTTATTTACGTGATAACTGTTTCTATCTTTGTTCATGAA
195 AAATATTTTGGACTTTGAATTAAAAACTTAGTTACGTAAGAACTGTTTCTATCTTGGTTCATGAA
*
3321 AGAACTTCCGAACTTATC
260 AGAACTTCCAAACTTATC
* *
3339 AAAAACTTATTTACGCGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTT-CGAACTTGTCAA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAA-TTTCCGAACTTGTCAA
* * * * *
3403 GCTTTCACTAATT-CTTTTATAACTTGGGTTCCTTAAAGTATACAAGACGATCCATTTCTTTGAG
65 ACTTTCAC-AATTACTTTTATAACTTCGGTTCCTGAAAGTATACAAGACGATCCATTCCTTCGAG
3467 CAAATTTT-CAAACATTCCGTGCTC-GAGAAATCACACCATTTGGTCAAAATAGTTTGTCATTTT
129 C-AATTTTCCAAACATTCCGTGCTCAG-GAAATCACACCATTTGGTCAAAATAGTTTGTCATTTT
* * ** * *
3530 GTAAACAA-CTTTTGGACTTTTAATTAGTAACTTAGTTACGTAAGAATTGTTTCTCTCTTGGTTC
192 G-AAA-AATATTTTGGACTTTGAATTAAAAACTTAGTTACGTAAGAACTGTTTCTATCTTGGTTC
* *
3594 -TGGGACGAACTTCCAAACTTATC
255 AT-GAAAGAACTTCCAAACTTATC
* * * * *
3617 AAAAACTTATTTACATGATAATTGTTTCTCCCTTGGTTCTTGGATGAATTTCCAAACTTGTCAAA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAATTTCCGAACTTGTCAAA
3682 AACTTATTTA
Statistics
Matches: 288, Mismatches: 46, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
276 1 0.00
277 157 0.55
278 128 0.44
279 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (277 bp):
AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAATTTCCGAACTTGTCAAA
CTTTCACAATTACTTTTATAACTTCGGTTCCTGAAAGTATACAAGACGATCCATTCCTTCGAGCA
ATTTTCCAAACATTCCGTGCTCAGGAAATCACACCATTTGGTCAAAATAGTTTGTCATTTTGAAA
AATATTTTGGACTTTGAATTAAAAACTTAGTTACGTAAGAACTGTTTCTATCTTGGTTCATGAAA
GAACTTCCAAACTTATC
Found at i:3743 original size:62 final size:62
Alignment explanation
Indices: 3558--3727 Score: 259
Period size: 62 Copynumber: 2.7 Consensus size: 62
3548 TTTAATTAGT
* * * *
3558 AACTTAGTTACGTAAGAATTGTTTCTCTCTTGGTTCTGGGACGAACTTCCAAACTTATCAAA
1 AACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTATCAAA
* * * * *
3620 AACTTATTTACATGATAATTGTTTCTCCCTTGGTTCTTGGATGAATTTCCAAACTTGTCAAA
1 AACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTATCAAA
3682 AACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAC
1 AACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAC
3728 ATCCGTACTT
Statistics
Matches: 95, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 95 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (62 bp):
AACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTATCAAA
Found at i:3918 original size:340 final size:340
Alignment explanation
Indices: 3277--4285 Score: 1225
Period size: 340 Copynumber: 3.0 Consensus size: 340
3267 TCTTTGAATT
* * * * * *
3277 AAAAACTTATTTACGTGATAACTGTTTCTATCTTTGTTCATGAAAGAACTTCCGAACTTATCAAA
1 AAAAACTTATTTACGTGATAATTGTTTCTCTCTTAGTTCTTGGAAGAACTTCCGAACTTGTCAAA
** * * * *
3342 AACTTATTTACGCGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTTCGAACTTGTCAAGCTT
66 AACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCCGAACTTGTCAAACTT
* * * * * * * * *
3407 TCACTAATTCTTTTATAACTTGGGTTCCTTAAAGTATACAAGACGATCCATTTCTTTGAGCAAAT
131 TTACGATTTCTTTTATAACTTCGGTTCCTGAAAGTATTCAAGAGGATCCATTCCTTTGAGCAATT
** * * * ** * *
3472 TTTCAAACATTCCGTGCTCGAGAAATCACACCATTTGGTCAAAATAGTTTGTCATTTTGTAAACA
196 TTTTGAACATTCCATGCTCGGGAAATCGCATAATTTGGTCTAAATAGTTTGTCTTTTTGTAAACA
* * ** * ** * *
3537 ACTTTTGGACTTTTAATTAGTAACTTAGTTACGTAAGAATTGTTTCTCTCTTGGTTCTGGGACGA
261 AGTTTTGGTCGCTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCTCGGACGA
3602 ACTTCCAAACTT-ATC
326 ACTTCCAAACTTGA-C
* * * * * *
3617 AAAAACTTATTTACATGATAATTGTTTCTCCCTTGGTTCTTGGATGAATTTCCAAACTTGTCAAA
1 AAAAACTTATTTACGTGATAATTGTTTCTCTCTTAGTTCTTGGAAGAACTTCCGAACTTGTCAAA
* *
3682 AACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCCGTACTTTTCAAACTT
66 AACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCCGAACTTGTCAAACTT
* * *
3747 TTACGATTTCTTCTATAACTTCGGTTCCTGAAAGTTTTCAAGAGGATCCATTCCTTTGAACAATT
131 TTACGATTTCTTTTATAACTTCGGTTCCTGAAAGTATTCAAGAGGATCCATTCCTTTGAGCAATT
* *
3812 TTTTGAACATTCCATTCTCGGGAAATCGCATAATTTGGTCTAAATAGTTTGTGTTTTTGTAAACA
196 TTTTGAACATTCCATGCTCGGGAAATCGCATAATTTGGTCTAAATAGTTTGTCTTTTTGTAAACA
* * * *
3877 AGTTTTGGTCGCTGAATTAAAAACTTATTTACATGAGAATTGGTTCTCTCTTGGATCTCGGACGA
261 AGTTTTGGTCGCTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCTCGGACGA
***
3942 ACTTTTGAACTTGAC
326 ACTTCCAAACTTGAC
* * * * *
3957 AAAAACTTATTCACGTAAGT-ATTGTTTCTCTCTCAGTTCTTGGACGAACTTCCGAGCTTGTCAA
1 AAAAACTTATTTACGTGA-TAATTGTTTCTCTCTTAGTTCTTGGAAGAACTTCCGAACTTGTCAA
* * * * *
4021 AAACCTATTT-TATGTAAGAATTGTTTCTCTCATGGTTCTTGGACGATCATCTGAACTTGTCAAA
65 AAACTTATTTACATG--AGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCCGAACTTGTCAAA
* * *
4085 CTTTTACGATTTATTTTATAACTTCGGTTCCCGAAAGTATTCAAG-GAGATCTATTCCTTTGAGC
128 CTTTTACGATTTCTTTTATAACTTCGGTTCCTGAAAGTATTCAAGAG-GATCCATTCCTTTGAGC
** * * *
4149 AATTTTTTTGTCCATTCCATGCTCTGGAAATCGCATAATTTGGCCTAAATAGTTTTTCTTTTTGT
192 AA-TTTTTTGAACATTCCATGCTCGGGAAATCGCATAATTTGGTCTAAATAGTTTGTCTTTTTGT
* *
4214 AAACAAGTTTTGGTCGCTGAATTAAAAACTTATTTATGTAAGAATTGTTTCTCTCTTGGTTCTTG
256 AAACAAGTTTTGGTCGCTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCTCG
4279 GACGAAC
321 GACGAAC
4286 ATCTGTACTT
Statistics
Matches: 569, Mismatches: 94, Indels: 10
0.85 0.14 0.01
Matches are distributed among these distances:
339 3 0.01
340 342 0.60
341 103 0.18
342 121 0.21
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (340 bp):
AAAAACTTATTTACGTGATAATTGTTTCTCTCTTAGTTCTTGGAAGAACTTCCGAACTTGTCAAA
AACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACATCCGAACTTGTCAAACTT
TTACGATTTCTTTTATAACTTCGGTTCCTGAAAGTATTCAAGAGGATCCATTCCTTTGAGCAATT
TTTTGAACATTCCATGCTCGGGAAATCGCATAATTTGGTCTAAATAGTTTGTCTTTTTGTAAACA
AGTTTTGGTCGCTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCTCGGACGA
ACTTCCAAACTTGAC
Found at i:3986 original size:62 final size:62
Alignment explanation
Indices: 3895--4084 Score: 209
Period size: 62 Copynumber: 3.0 Consensus size: 62
3885 TCGCTGAATT
* * * * * * *
3895 AAAAACTTATTTACATGAGAATTGGTTCTCTCTTGGATCTCGGACGAACTTTTGAACTTGAC
1 AAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACTTGTC
* * ** * *
3957 AAAAACTTATTCACGTAAGTATTGTTTCTCTCTCAGTTCTTGGACGAACTTCCGAGCTTGTC
1 AAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACTTGTC
* * * * *
4019 AAAAACCTATTTTATGTAAGAATTGTTTCTCTCATGGTTCTTGGACGATCATCTGAACTTGTC
1 AAAAACTTA-TTTACGTAAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACTTGTC
4082 AAA
1 AAA
4085 CTTTTACGAT
Statistics
Matches: 103, Mismatches: 24, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
62 57 0.55
63 46 0.45
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (62 bp):
AAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACTTGTC
Found at i:4051 original size:63 final size:61
Alignment explanation
Indices: 3912--4084 Score: 184
Period size: 63 Copynumber: 2.8 Consensus size: 61
3902 TATTTACATG
* * * * * *
3912 AGAATTGGTTCTCTCTTGGATCTCGGACGAACTTTTGAACTTGACAAAAACTTATTCACGTA
1 AGAATTGTTTCTCTC-TGGTTCTTGGACGAACTTCTGAACTTGTCAAAAACCTATTCACGTA
* * * * * *
3974 AGTATTGTTTCTCTCTCAGTTCTTGGACGAACTTCCGAGCTTGTCAAAAACCTATTTTATGTA
1 AGAATTGTTTCTCTCT-GGTTCTTGGACGAACTTCTGAACTTGTCAAAAACCTA-TTCACGTA
* *
4037 AGAATTGTTTCTCTCATGGTTCTTGGACGATCATCTGAACTTGTCAAA
1 AGAATTGTTTCTCTC-TGGTTCTTGGACGAACTTCTGAACTTGTCAAA
4085 CTTTTACGAT
Statistics
Matches: 90, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
61 1 0.01
62 42 0.47
63 46 0.51
64 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (61 bp):
AGAATTGTTTCTCTCTGGTTCTTGGACGAACTTCTGAACTTGTCAAAAACCTATTCACGTA
Done.