Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014695.1 Corchorus olitorius cultivar O-4 contig14728, 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: 107884
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:769 original size:320 final size:321
Alignment explanation
Indices: 70--2299 Score: 1305
Period size: 320 Copynumber: 6.8 Consensus size: 321
60 ATGTGTTTCG
* * *
70 GGCCCCGG-TTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATAGCTATATTCATCTA
1 GGCCCCGGCTT-AGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGA
* * * * * *
134 ACCAAATCTCAGTCACAATGGATTTAAGGACTTT-TTTTTACGAGTATCTCAATCTTTGTTTCAA
65 ACCAAATCTCAGCCACATTGGATATAAGGA-TTTGTTTTTACGAGCATCTGAATC-TTGTTTCGA
* *
198 TTTAATTAGAAATAAATTC-G---CAAA---AAAAACGATATTAGAAGCGTGAAAACCCTTCAAT
128 TTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAACCCGTCAAT
* * * * * **
256 ATTTTTGGCGTTGAATTATTTATTCTTTCTGAGTATTGTGGCAAAAAATTTAGGAAAAACCCTTC
193 TTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTC
** * * * * *
321 GGGTCAATTTTTGCAAAATTTTAGCCAAAATCTTGTACCAACCATCAC-GATTTTTGCCTAAAAA
258 GGG-------TT---AGTTTTTAGCCGAAATCGTATACTAACCATCACAG-TTTTTGGCTAAAAA
**
385 CGCG-TTCCG
312 CGCGTTTCAT
* * * * * ** * *
394 GAGTCTCGGCTCAATTTTGTATGATTTTTTCCACAAAGACTCCTTGAAATATCTATATTCAACGA
1 G-GCCCCGGCTTAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGA
* * * *
459 ACCAAATCTCAGCCACATTGTATATAAGAATTTGTTTTTACGATCATCTAAATCTTGTTTCGATT
65 ACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATT
* * *
524 TAATTA-ATAATGAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGGCCGTCAAT
130 TAATTAGA-AATAAATTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA-CCCGTCAAT
* * * * * *
588 CTTTTTGGCTTTGAATTATATA-TTTTTATGAATATT-TTGCAAAAATTTGAGAAAAAACTTTTC
193 TTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTC
** * * *
651 GGGTTAGTTTTTAGCCGAAATCGTATACTAACCATCATGGTTTTTGGTTAAAAATGTGTTTCAT
258 GGGTTAGTTTTTAGCCGAAATCGTATACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCAT
* * * *
715 GGCCCCGACTTAGTTATGAATGATTTTTGGCAGAAAGACTCCTAGAAATATCTATATTCATCTAA
1 GGCCCCGGCTTAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAA
* * * * * * *
780 CCAGATCTCAACCACAATGGATTTAAGGATTTGATTTTACGAGCATCTGAATCTTTATTTTGATT
66 CCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATC-TTGTTTCGATT
* *
845 TAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAACCCTTCAATTT
130 TAATTAGAAATAAATTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAACCCGTCAATTT
* *
910 TTTTGGCGTTGAATTATATATTTTTTCTCAGTATTGTGGCAAAAAATTTGAGTAAAAA-TATTTC
195 TTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAA-TTGAGAAAAAACT-TTTC
* * * ** * ** * *
974 GGGTCAATTTTT-G-CAAAATTTTA-ACCGAA--ATCA-AGTACTTTTTTTCCAATGAAA-TCG-
258 GGGTTAGTTTTTAGCCGAAATCGTATA-CTAACCATCACAG---TTTTTGGCTAA--AAACGCGT
*
1031 TGCACT
317 TTCA-T
** ** * * ** * *** * *
1037 AACTATCATGGTTTA-TTTTGGCTAAAAACGCGTTTCGG-AGTCCCGACTCAATTTTGCATGATT
1 GGC---CCCGGCTTAGTTTT-G-----AATGATTTTTGGCAG-AAAGACTC---CTTG-A--A-A
* * * * * **** * * * * *
1100 TTTGGCGTAAAGATTCCTTGAA--ATATCT-ATATTCATTGTATCAAATCTCAGCCACGTTGTAT
49 TAT--C-T--ATATTCATCGAACCAAATCTCAGCCACATTGGAT---A--TAAG-GA-TTTGTTT
* * * * * * * *
1162 ATA--AGGATTTG-TTTTTACGAGCATAT-GAATCTTATTTCGATTTAATTAGAAATTAATTCAG
102 TTACGAGCATCTGAATCTT----G--TTTCG-AT-TTAATTAGA---AA-T--AA----ATTCAG
* * ***
1223 AAAAAAATGGAAAAACGATATTAGAAGCATTAACAGTACGTCAATTTTTTTGGCGTTGAATTATA
149 AAAAAAATGGAAAAACGATATTAGAAGCGTGAA-AACCCGTCAATTTTTTTGGCGTTGAATTATA
* * * *
1288 TATTTTTTCTAAATATT-TTGCAAAAAATTGAG-AAAAACTTTTCGAGTTAGTTTTTAGCCGAAA
213 TATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTTAGTTTTTAGCCGAAA
* * * * *
1351 TTGTGTACTAACTAACACAGTTTTTGGCTAAAAACGCGTTTC-G
278 TCGTATACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCAT
* * * *
1394 GGCCCCGGCTTAGTTTTGCATGATTTTTGGCTGAAAGACTCCTTGAAATAGCTATATTCATCTAA
1 GGCCCCGGCTTAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAA
* * * * * *
1459 CCAAATCTCAGTCACAATCGATTTAAGGATTTGCTTTTACGAGCATCTCAATCTTTGTTTCGATT
66 CCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATC-TTGTTTCGATT
** * *
1524 TAATTAGAAATAAATTCAGAAAAAAAAAG-AAAACGATATTAGAAACGTGAAAACCCTTCAACTT
130 TAATTAGAAATAAATTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAACCCGTCAA-TT
* * *
1588 TTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTG-GGAAAAACTTTTTG
194 TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCG
* * * *
1652 GGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGCTTTTGGCTAAAAACG
259 GGTTAG----T------TTTTAGCCGAAATCGTATACTAACCATCACAGTTTTTGGCTAAAAACG
*
1717 CGTTCCGGA-
314 CGTTTC--AT
* * * * *
1726 GG-CCCGGCTCAATTTTGTATAATTTTTGGC-GCAAAGACTCTTTGAAATATCTATATTCATCGA
1 GGCCCCGGCTTAGTTTTGAATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCGA
* * *
1789 ACCAAATGTCAGCCACATGGGATATAGGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATT
65 ACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATT
* * * * * * **
1854 TAATTAGAAATTAATTC-GGATAAAATGGAAAAACAATATTAGAAGCATGAAAAGCCTGTCAACC
130 TAATTAGAAATAAATTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA-CCCGTCAATT
* *
1918 TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAATAAACGTTTCG
194 TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCG
* * * *
1983 GGTTAGTTTTTAG-C-----C----A-T---CAT--GA-TTTTTGACTAAAAACGC-CTAC-T
259 GGTTAGTTTTTAGCCGAAATCGTATACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCAT
* * ** **** *
2027 GGGGTCGCGGCTCT-GTTTTCCATGATTTTTGGCTCTGAGACTCCTTGAAATATCTTTATTCATC
1 --GGCCCCGGCT-TAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATC
* * * * *
2091 TAATCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGTGCATCTGAAT-TCTGTTTCG
63 GAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCT-TGTTTCG
* * * * *
2155 ATTTAATTAGAAATTAATTCATAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC-TC
127 ATTTAATTAGAAATAAATTCAGAAAAAAAT-GGAAAAACGATATTAGAAGCGTGAAAA-CCCGT-
* * * * * * *
2219 CAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTTGCCAAAAATTGATAAAAAA-T
189 CAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACT
*
2283 CTTTCGGGTCA-TTTTTA
254 -TTTCGGGTTAGTTTTTA
2300 CCATCATGGT
Statistics
Matches: 1467, Mismatches: 314, Indels: 269
0.72 0.15 0.13
Matches are distributed among these distances:
303 5 0.00
304 135 0.09
305 13 0.01
306 89 0.06
307 3 0.00
310 1 0.00
311 1 0.00
315 1 0.00
318 7 0.00
319 59 0.04
320 205 0.14
321 100 0.07
322 14 0.01
323 30 0.02
324 34 0.02
325 99 0.07
326 2 0.00
327 3 0.00
328 3 0.00
329 9 0.01
330 190 0.13
331 157 0.11
332 29 0.02
333 9 0.01
334 2 0.00
335 8 0.01
336 2 0.00
337 12 0.01
339 14 0.01
340 13 0.01
342 11 0.01
343 2 0.00
344 9 0.01
345 2 0.00
346 9 0.01
347 1 0.00
348 4 0.00
349 19 0.01
350 1 0.00
352 2 0.00
353 1 0.00
354 7 0.00
355 6 0.00
357 22 0.01
358 9 0.01
359 65 0.04
360 43 0.03
361 3 0.00
362 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (321 bp):
GGCCCCGGCTTAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAA
CCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
AATTAGAAATAAATTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAACCCGTCAATTTT
TTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGG
TTAGTTTTTAGCCGAAATCGTATACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCAT
Found at i:1896 original size:330 final size:331
Alignment explanation
Indices: 1339--1993 Score: 899
Period size: 330 Copynumber: 2.0 Consensus size: 331
1329 TCGAGTTAGT
* * * *
1339 TTTTAGCCGAAATTGTGTACTAACTAACACAGTTTTTGGCTAAAAACGCGTTTCGGGCCCCGGCT
1 TTTTAGCCGAAATCGTGTACTAACCAACACAGCTTTTGGCTAAAAACGCGTTCCGGGCCCCGGCT
* * * *
1404 TAGTTTTGCATGATTTTTGGCTGAAAGACTCCTTGAAATAGCTATATTCATCTAACCAAATCTCA
66 CAATTTTGCATAATTTTTGGCTGAAAGACTCCTTGAAATAGCTATATTCATCGAACCAAATCTCA
* *
1469 GTCACAATCGATTTAAGGATTTGCTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAA
131 GCCACAATCGATATAAGGATTTGCTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAA
* * *
1534 TAAATTCAGAAAAAAAAAGAAAACGATATTAGAAACGTGAAAACCCT-TCAACTTTTTTTGGCGT
196 TAAATTCAGAAAAAAAAAGAAAACAATATTAGAAACATGAAAACCCTGTCAAC-CTTTTTGGCGT
* * *
1598 TAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGGGAA-AAACTTTTTGGGTCAGTTTT
260 TAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAATAAACGTTTCGGGTCAGTTTT
1662 TGCAAAA
325 TGCAAAA
* * *
1669 TTTTAGCCGAAATCGTGTACTAACCATCACGGCTTTTGGCTAAAAACGCGTTCCGGAGGCCCGGC
1 TTTTAGCCGAAATCGTGTACTAACCAACACAGCTTTTGGCTAAAAACGCGTTCCGG-GCCCCGGC
* * * *
1734 TCAATTTTGTATAATTTTTGGC-GCAAAGACTCTTTGAAATATCTATATTCATCGAACCAAATGT
65 TCAATTTTGCATAATTTTTGGCTG-AAAGACTCCTTGAAATAGCTATATTCATCGAACCAAATCT
* * * *
1798 CAGCCAC-ATGGGATATAGGGATTTGTTTTTACGAGCATCTGAATC-TTGTTTCGATTTAATTAG
129 CAGCCACAAT-CGATATAAGGATTTGCTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAG
* * * ** * *
1861 AAATTAATTC-GGATAAAATGGAAAAACAATATTAGAAGCATGAAAAGCCTGTCAACCTTTTTGG
193 AAATAAATTCAGAAAAAAAAAG-AAAACAATATTAGAAACATGAAAACCCTGTCAACCTTTTTGG
* *
1925 CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAATAAACGTTTCGGGTTAGT
257 CGTTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAATAAACGTTTCGGGTCAGT
1990 TTTT
322 TTTT
1994 AGCCATCATG
Statistics
Matches: 283, Mismatches: 36, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
329 7 0.02
330 156 0.55
331 120 0.42
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (331 bp):
TTTTAGCCGAAATCGTGTACTAACCAACACAGCTTTTGGCTAAAAACGCGTTCCGGGCCCCGGCT
CAATTTTGCATAATTTTTGGCTGAAAGACTCCTTGAAATAGCTATATTCATCGAACCAAATCTCA
GCCACAATCGATATAAGGATTTGCTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAA
TAAATTCAGAAAAAAAAAGAAAACAATATTAGAAACATGAAAACCCTGTCAACCTTTTTGGCGTT
AAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAATAAACGTTTCGGGTCAGTTTTT
GCAAAA
Found at i:2306 original size:304 final size:304
Alignment explanation
Indices: 1760--2314 Score: 778
Period size: 304 Copynumber: 1.8 Consensus size: 304
1750 TTTGGCGCAA
* * *
1760 AGACTCTTTGAAATATCTATATTCATCGAACCAAATGTCAGCCACATGGGATATAGGGATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATGGGATATAAGGATTTGTT
* *
1825 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGATAAAATGGAAAAACAA
66 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATGGAAAAACAA
* * * *
1890 TATTAGAAGCATGAAAAGCCTGTCAACCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTG
131 TATTAAAAGCATGAAAAGCCTGCCAACCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTG
* *
1955 TGGCAAAAAATTGAGAATAAACGTTTCGGGTTAGTTTTTAGCCATCATGATTTTTGACTAAAAAC
196 TGGCAAAAAATTGAGAAAAAACGTTTCGGGTCAGTTTTTAGCCATCATGATTTTTGACTAAAAAC
2020 GCCTACTGGGGTCGCGGCTCTGTTTTCCATGATTTTTGGCTCTG
261 GCCTACTGGGGTCGCGGCTCTGTTTTCCATGATTTTTGGCTCTG
* * * * * *
2064 AGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTTAGCCACATTGGATTTAAGGATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATGGGATATAAGGATTTGTT
* * *
2129 TTTACGTGCATCTGAAT-TCTGTTTCGATTTAATTAGAAATTAATTCATAAAAAAATATGAAAAA
66 TTTACGAGCATCTGAATCT-TGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAAT-GGAAAAA
* * *
2193 CGATATTAAAAGCGTGAAAAGTCCT-CCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGT
128 CAATATTAAAAGCATGAAAAG-CCTGCCAACCTTTTTGGCGTTGAATTATATATATTTTATGAGT
* * * * *
2257 ATTTTTGCCAAAAATTGATAAAAAATC-TTTCGGGTCA-TTTTTA-CCATCATGGTTTTTG
192 ATTGTGGCAAAAAATTGAGAAAAAA-CGTTTCGGGTCAGTTTTTAGCCATCATGATTTTTG
2315 GAAAAACGTA
Statistics
Matches: 218, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
303 1 0.00
304 113 0.52
305 12 0.06
306 88 0.40
307 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (304 bp):
AGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATGGGATATAAGGATTTGTT
TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATGGAAAAACAA
TATTAAAAGCATGAAAAGCCTGCCAACCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTG
TGGCAAAAAATTGAGAAAAAACGTTTCGGGTCAGTTTTTAGCCATCATGATTTTTGACTAAAAAC
GCCTACTGGGGTCGCGGCTCTGTTTTCCATGATTTTTGGCTCTG
Found at i:2860 original size:123 final size:128
Alignment explanation
Indices: 2730--2976 Score: 396
Period size: 131 Copynumber: 1.9 Consensus size: 128
2720 AAACTTTTAT
2730 AGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T-TA-TGATTTT
1 AGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTATTGATTTT
2790 TACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTAAC
66 TACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTAAC
* *
2853 AGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTTTAT
1 AGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTAT--CTA-TTGAT
* *
2918 TTTTACCATTTTACTATTTTATTTTAAAAACTTATATATATTAGAATTTTTTAAATATA
63 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATA
2977 TTTCTTAAAT
Statistics
Matches: 112, Mismatches: 4, Indels: 8
0.90 0.03 0.06
Matches are distributed among these distances:
123 47 0.42
124 1 0.01
125 1 0.01
126 1 0.01
129 2 0.02
131 60 0.54
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (128 bp):
AGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTATTGATTTT
TACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTAAC
Found at i:10069 original size:331 final size:330
Alignment explanation
Indices: 9415--11362 Score: 1794
Period size: 321 Copynumber: 5.9 Consensus size: 330
9405 TTAAATACTC
* * * *
9415 AAACAAATCCTTAAATCCAATATGTCTAAGATTTGATTAGAT-AATATAGATATTTCAAGGAGTC
1 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
** * * * ** * * * * ** * *
9479 TCGGCGCAAAAAATTATAC-ATTTTCAGTTCCGTGGCCCCGGAACGTATTTTTAGTCAAAAACCG
66 TTTGTGCAAAAAATCATGCAAAATTGAG--ACGGGGCTCCGGAACGCGTTTTTAGCCAAAAACAG
*
9543 TGATGGTTAGTACACAATTTCGGCTAAAA---AC-----TGACCCGAAATA-TTTATT-CTCAAT
129 TGATGGTTAGTACACGATTTCGGCTAAAATTTACAAAAATGACCCGAAA-AGTTT-TTCCTCAAT
* **
9598 TTTTTGCCACAATACTCAG-AAAAATATATAATTCAACGCCAAAAAGATTGGTGGGCTTTTCACG
192 TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGG-TTTTCACG
* * *
9662 GTTCTAATATCGTTTTTCC-ATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAG
256 CTTCTAATATCGTTTTTCCTTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAG
9726 ATGCTCGTAA
321 ATGCTCGTAA
* * * * * * *
9736 AAACAAATCCTTATATCCAATGTGGCTGACATTTGTTTCGATGAATATAGATATTTTAATGACTC
1 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* * * * * * * *
9801 TTTGTGCTAAAAGTTATGCAAAATTGAGTCTGGGCTCTGGAACGCGTTTTTAGTCAAAAGTC-GT
66 TTTGTGCAAAAAATCATGCAAAATTGAGACGGGGCTCCGGAACGCGTTTTTAGCCAAAA-ACAGT
*
9865 GATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAAGTTTTTCCCCAATT
130 GATGGTTAGTACACGATTTCGGCTAAAA-TTTACAAAAA-TGACCCGAAAAGTTTTTCCTCAATT
* * *
9930 TTTTGCCACAATACTCAG-AAAAATATATAATTTAACGTCAAAAAAATTGAAGGGTTTTCACGTT
193 TTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTCACGCT
* * *
9994 TTTAATATCG-TTTTCCTTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAGATTGAGA
258 TCTAATATCGTTTTTCCTTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAAC-AAGATTCAGA
* *
10058 TGATTGTAA
322 TGCTCGTAA
* *
10067 AAACAAATCCTTAAATCCATTGTGGCTGAGAAATT-GTTAGATGAATATAGATATTTCAAGGAGT
1 AAACAAATCCTTAAATCCAATGTGGCTGAG-ATTTGGTTAGATGAATATAGATATTTCAAGGAGT
* * * * *
10131 TTTTTTGCAAAAAAATCATGCAAAACTGAGACGGGGCT-CGAAACGCGTTTTTAGCCAACAACAG
65 CTTTGTGC-AAAAAATCATGCAAAATTGAGACGGGGCTCCGGAACGCGTTTTTAGCCAAAAACAG
* * * *
10195 TGATGGTAAGTATACGATTTAGGCTAAAA---AC-----TGATCCGAAAA-TTTTT-CTCAATTT
129 TGATGGTTAGTACACGATTTCGGCTAAAATTTACAAAAATGACCCGAAAAGTTTTTCCTCAATTT
* * * * *
10250 TTCG-CAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAACATTGACGGCCTTTTTCACGC
194 TTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGG--GTTTTCACGC
* * * ** *
10314 TTCTCATATCGTTTTTCCATTCTTTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTTAGA
257 TTCTAATATCGTTTTTCCTTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
10379 TGCTCGTAA
322 TGCTCGTAA
* * * *
10388 AAACAAAGTCC-TATATACAATATGACTGAGATTTGGTTCA-ATGAATATAGATATTTCAAGGAG
1 AAACAAA-TCCTTAAATCCAATGTGGCTGAGATTTGGTT-AGATGAATATAGATATTTCAAGGAG
* * * * * * * * *
10451 TCTTGGCGGAAAAAATCATGCAAAATTGAGCCGAGACTCCGGAATGCGTTTTTAGGCAAAAACCG
64 TCTTTGTGCAAAAAATCATGCAAAATTGAGACGGGGCTCCGGAACGCGTTTTTAGCCAAAAACAG
* * * * *
10516 TGATGATTAGTACACGATTTCGTCTAAAATTTTGCAAAAAATTGACTCGAAAGGTTTTTCCTCAA
129 TGATGGTTAGTACACGATTTCGGCTAAAA-TTTAC-AAAAA-TGACCCGAAAAGTTTTTCCTCAA
* * * * * *
10581 TTTTTTGCCATAATAATCAGAAAGAATAAATAATTGAACGCCAACAAAAATTGAAAGGTTTTTCA
191 TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAA-AAAAATTG-AAGGGTTTTCA
* *
10646 CGCTTCTAATATCGTTTTTCAATTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAGAT
254 CGCTTCTAATATCGTTTTTC-CTTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAAC-AAGAT
* *
10711 TTAGATGCTCTTAA
317 TCAGATGCTCGTAA
* * * * *
10725 AAACAAATCCTTAAATCTATTGTGCCTGAGATTTGGTTAGATGAATGTAGATATTTTAAGGAGTC
1 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* * * ** ** * *
10790 TTT-TAGCCAAAAATCTTGGAAAACCGACTCGGGGCCCCGAAACGCG-TTTTAGCCAAAAAAAAA
66 TTTGT-GCAAAAAATCATGCAAAATTGAGACGGGGCTCCGGAACGCGTTTTTAGCC------AAA
* * * * * * *
10853 AACAG-GTATAGTTAAGTATATGATTTTGGCTAAAA---AC-----TGACCTGAAAATTTTTTTC
124 AACAGTG-ATGGTT-AGTACACGATTTCGGCTAAAATTTACAAAAATGACCCGAAAAGTTTTTCC
* * * * * *
10909 TTAATTTTTTG-CAAAATATTCAGAAAAAATGTATAATTCAATGCCAAAAGAAATTG-ACGGTCT
187 TCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAA-AAATTGAAGGGT-T
*
10972 TTCACGCTTCTAATATCGTTTTTCCATTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
250 TTCACGCTTCTAATATCGTTTTTCC-TTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
*
11037 GATTCAAATGCTCGTAA
314 GATTCAGATGCTCGTAA
* * * *
11054 AAACAAATCCTTACATCCAATGTAGATGAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTC
1 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* * * * * * * *
11119 TTTGCGCCAAAAATCATGCAAAATTGAGACAGGACTCCTTG-ATGCGTTTTTAGTCAAAAACTGT
66 TTTGTGCAAAAAATCATGCAAAATTGAGACGGGGCTCC-GGAACGCGTTTTTAGCCAAAAACAGT
* ** * *
11183 AATGGTTAGTACACGATTTCCACTAAAATATTGCAAAAACTGACCCGAAAAGTTTTTTCCTCGAT
130 GATGGTTAGTACACGATTTCGGCTAAAAT-TTACAAAAA-TGACCCGAAAAG-TTTTTCCTCAAT
* *
11248 TTTTTGCCACAATACTCAGAAAAAATATATAATTTAACACCAAAAAAATTTGAAGGGTTTTTTCA
192 TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAA-TTGAAGGG--TTTTCA
*** * ** * *
11313 CAAATCAAATATCG-TTTTCCCATTTTTTTCCGAATTTATTTCTAAGTAAA
254 CGCTTCTAATATCGTTTTTCCTTTTTTTTTCCGAATTAATTTCTAATTAAA
11363 CACACACACA
Statistics
Matches: 1309, Mismatches: 238, Indels: 146
0.77 0.14 0.09
Matches are distributed among these distances:
318 11 0.01
319 41 0.03
320 33 0.03
321 227 0.17
322 75 0.06
323 21 0.02
324 12 0.01
325 3 0.00
327 3 0.00
329 112 0.09
330 124 0.09
331 221 0.17
332 58 0.04
333 15 0.01
334 29 0.02
335 117 0.09
336 59 0.05
337 117 0.09
338 1 0.00
339 1 0.00
341 1 0.00
342 11 0.01
343 17 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (330 bp):
AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
TTTGTGCAAAAAATCATGCAAAATTGAGACGGGGCTCCGGAACGCGTTTTTAGCCAAAAACAGTG
ATGGTTAGTACACGATTTCGGCTAAAATTTACAAAAATGACCCGAAAAGTTTTTCCTCAATTTTT
TGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTCACGCTTCT
AATATCGTTTTTCCTTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
CGTAA
Found at i:11086 original size:666 final size:651
Alignment explanation
Indices: 9526--11362 Score: 2263
Period size: 666 Copynumber: 2.8 Consensus size: 651
9516 CCGGAACGTA
* * * * * * *
9526 TTTTTAGTCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACTGACCCG-AAATATTTA
1 TTTTTAGCCAAAAACAGTGATGGTAAGTATACGATTTAGGCTAAAAACTGA-CCGAAAAT-TTTT
* * ** *
9590 TTCTCAATTTTTTGCCACAATACTCAG-AAAAATATATAATTCAACGCCAAAAAGATTGGTGGGC
64 TTCTCAATTTTTTG-CAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGACGGTC
*
9654 TTTTCACGGTTCTAATATCGTTTTTCCA-TTTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
128 -TTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTC-GAATTAATTTCTAATTAAATCGAAACA
* * *
9718 AGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGTTTCGATGAATA
191 AGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGT-GATGAGATTTGGTTCGATGAATA
* * * * * * * * * * *
9783 TAGATATTTTAATGACTCTTTGTGCTAAAAGTTATGCAAAATTGAGTCTG-GGCTCTGGAACGCG
255 TAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAATTGAG-CCGAGACTCCGGAATGCG
** * *
9847 TTTTTAGTCAAAAGTCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCG
319 TTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAATTTTGCAAAAATTGACCCG
* * *
9912 AAAAGTTTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATATATAATTTAACGTCAAAAAAAT
384 AAAGGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAATATATAATTTAACGCCAAAAAAAT
* * * *
9977 TG-AAGGGTTTTCACGTTTTTAATATCG-TTTTCCTTTTTTTTTCCGAATTTATTTCTAATTAAA
449 TGAAAGGTTTTTCACGATTCTAATATCGTTTTTCATTTTTTTTTCCGAATTTATTTCTAATTAAA
*
10040 TCGAAACAAAGATTGAGATGATTGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGAAATTGTT
514 TCGAAACAAAGATTGAGATGATTGTAAAAACAAATCCTTAAATCCATTGTGCCTGAGAAATTGTT
* * * * *
10105 AGATGAATATAGATATTTCAAGGAGTTTTTTTGCAAAAAAATCATGCAAAACTGAGACGGGGCTC
579 AGATGAATATAGATATTTCAAGGAGTCTTTTAGCAAAAAAATCATGCAAAACCGACACGGGGCCC
10170 GAAACGCG
644 GAAACGCG
*
10178 TTTTTAGCCAACAACAGTGATGGTAAGTATACGATTTAGGCTAAAAACTGATCCGAAAA--TTTT
1 TTTTTAGCCAAAAACAGTGATGGTAAGTATACGATTTAGGCTAAAAACTGA-CCGAAAATTTTTT
* * *
10241 TCTCAATTTTTCGCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAACATTGACGGCCTT
65 TCTCAATTTTTTGCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGACGG--TC
*
10306 TTTCACGCTTCTCATATCGTTTTTCCATTCTTTTTAT-GAATTAATTTCTAATTAAATCGAAACA
128 TTTCACGCTTCTAATATCGTTTTTCCATT-TTTTT-TCGAATTAATTTCTAATTAAATCGAAACA
* * * *
10370 AGATTTAGATGCTCGTAAAAACAAAGTCC-TATATACAATATGACTGAGATTTGGTTCAATGAAT
191 AGATTCAGATGCTCGTAAAAACAAA-TCCTTATATCCAATGTGA-TGAGATTTGGTTCGATGAAT
* *
10434 ATAGATATTTCAAGGAGTCTTGGCGGAAAAAATCATGCAAAATTGAGCCGAGACTCCGGAATGCG
254 ATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAATTGAGCCGAGACTCCGGAATGCG
* * * *
10499 TTTTTAGGCAAAAACCGTGATGATTAGTACACGATTTCGTCTAAAATTTTGCAAAAAATTGACTC
319 TTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAATTTTGC-AAAAATTGACCC
* * * *
10564 GAAAGGTTTTTCCTCAATTTTTTGCCATAATAATCAGAAAGAATAAATAATTGAACGCCAACAAA
383 GAAAGGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAA-AATATATAATTTAACGCCAA-AAA
*
10629 AATTGAAAGGTTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTTTCCGAATTTATTTCTAAT
446 AATTGAAAGGTTTTTCACGATTCTAATATCGTTTTTC-ATTTTTTTTTCCGAATTTATTTCTAAT
* * * *
10694 TAAATCGAAACAAAGATTTAGATGCTCT-TAAAAACAAATCCTTAAATCTATTGTGCCTGAG-AT
510 TAAATCGAAACAAAGATTGAGATGAT-TGTAAAAACAAATCCTTAAATCCATTGTGCCTGAGAAA
* * * * * *
10757 TTGGTTAGATGAATGTAGATATTTTAAGGAGTCTTTTAGC-CAAAAATCTTGGAAAACCGACTCG
574 TT-GTTAGATGAATATAGATATTTCAAGGAGTCTTTTAGCAAAAAAATCATGCAAAACCGACACG
10821 GGGCCCCGAAACGCG
638 GGG-CCCGAAACGCG
* * *
10836 -TTTTAGCCAAAAAAAAAAACAG-GTATAGTTAAGTATATGATTTTGGCTAAAAACTGACCTGAA
1 TTTTTAGCC------AAAAACAGTG-AT-GGTAAGTATACGATTTAGGCTAAAAACTGACC-GAA
* * * *
10899 AATTTTTTTCTTAATTTTTTGCAAAATATTCAGAAAAAATGTATAATTCAATGCCAAAAGAAATT
57 AATTTTTTTCTCAATTTTTTGCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAA-AAATT
10964 GACGGTCTTTCACGCTTCTAATATCGTTTTTCCATTATTTTTTCCGAATTAATTTCTAATTAAAT
121 GACGGTCTTTCACGCTTCTAATATCGTTTTTCCATT-TTTTTT-CGAATTAATTTCTAATTAAAT
* * *
11029 CGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTACATCCAATGTAGATGAGATTTGGTTTG
184 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGT-GATGAGATTTGGTTCG
* *
11094 ATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGAC-AGGACTCCT
248 ATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAATTGAGCCGA-GACTCC-
* * * * *
11158 TG-ATGCGTTTTTAGTCAAAAACTGTAATGGTTAGTACACGATTTCCACTAAAATATTGCAAAAA
311 GGAATGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAATTTTGCAAAAA
* * * *
11222 CTGACCCGAAAAGTTTTTTCCTCGATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAACA
376 TTGACCCG-AAAGGTTTTTCCTCAATTTTTTGCCACAATACTCAG-AAAAATATATAATTTAACG
* * * * *
11287 CCAAAAAAATTTGAAGGGTTTTTTCACAAATCAAATATCGTTTTCCCA--TTTTTTTCCGAATTT
439 CCAAAAAAA-TTGAAAGG-TTTTTCACGATTCTAATATCGTTTT-TCATTTTTTTTTCCGAATTT
*
11350 ATTTCTAAGTAAA
501 ATTTCTAATTAAA
11363 CACACACACA
Statistics
Matches: 1023, Mismatches: 120, Indels: 71
0.84 0.10 0.06
Matches are distributed among these distances:
649 11 0.01
650 47 0.05
651 28 0.03
652 221 0.22
653 58 0.06
654 18 0.02
655 8 0.01
656 22 0.02
657 37 0.04
658 124 0.12
659 1 0.00
662 1 0.00
663 11 0.01
664 33 0.03
665 81 0.08
666 284 0.28
667 37 0.04
668 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (651 bp):
TTTTTAGCCAAAAACAGTGATGGTAAGTATACGATTTAGGCTAAAAACTGACCGAAAATTTTTTT
CTCAATTTTTTGCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGACGGTCTTT
CACGCTTCTAATATCGTTTTTCCATTTTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATT
CAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGATGAGATTTGGTTCGATGAATATAGATA
TTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAATTGAGCCGAGACTCCGGAATGCGTTTTTAG
TCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAATTTTGCAAAAATTGACCCGAAAGGTT
TTTCCTCAATTTTTTGCCACAATACTCAGAAAAATATATAATTTAACGCCAAAAAAATTGAAAGG
TTTTTCACGATTCTAATATCGTTTTTCATTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAAC
AAAGATTGAGATGATTGTAAAAACAAATCCTTAAATCCATTGTGCCTGAGAAATTGTTAGATGAA
TATAGATATTTCAAGGAGTCTTTTAGCAAAAAAATCATGCAAAACCGACACGGGGCCCGAAACGC
G
Found at i:12364 original size:528 final size:531
Alignment explanation
Indices: 11639--12621 Score: 1497
Period size: 528 Copynumber: 1.8 Consensus size: 531
11629 GAAACAAGAA
* * * * *
11639 TCAGATGTTTGTAAAAAGAAATCGTTAAATCCAATGTGGCTGGGATTTGGTTCGATGAGGATGGA
1 TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGAT--GGA--GA
* * *
11704 TATAGATATTTTAAGGAGTCTTTACGCAAAAAAAATCATGCAAAACTAAGTTGGGACCCTAGAAT
62 TATAGATATTTCAAGGAGTCTTTACGCAAAAAAAACCATGCAAAACTAAGTTGGGACCCTAGAAC
11769 GCGTTTTTAACTAAAAACCATGAATGAGTAAATGATTTCGACTAAAATTTTGCAAAAACTGACCC
127 GCGTTTTTAACTAAAAACCATGAATGAGTAAATGATTTCGACTAAAATTTTGCAAAAACTGACCC
* * * *
11834 GAAAATTTTTTCCTCAATTCTTTGCAACAATACTCAGAACAAATATGTAATTCAACGCCAAAAAA
192 GAAAAGTTTTTCCTCAATTCTTTGCAACAATACTCAGAAAAAATATATAATTCAACGACAAAAAA
* * ** *
11899 AT-TGACGGGTTTTTCACGCTTCTAATATCGTTTTTCC-TTTTTTTTTGAATTTATTTCTTATTA
257 ATAT-AAGGGTTTTTCAAGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTA
* * * * * **
11962 AATTGAAACAAGATTCACATGCTCGTAAAAATAAATCCTTAAATCCATTGTGGCTTAGATTTGGT
321 AATCGAAACAAGATTCACATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAAATTTAAT
* * *
12027 TAGATCAATATAGATGTTTCAAGTAGTCTTTCGGCCAAAAATCATGCAAAACTGAGCCGGGGCCC
386 TAGATCAATATAGATATTTCAAGGAGTCTTTCGACCAAAAATCATGCAAAACTGAGCCGGGGCCC
12092 CAAAACACGTTTTTAGCCGAAAACCGTGATTTCGACTAAAAACTGACCAGAAAAGTTTTTTCTCA
451 CAAAACACGTTTTTAGCCGAAAACCGTGATTTCGACTAAAAACTGACCAGAAAAGTTTTTTCTCA
12157 ATTTTTTACGAAATAT
516 ATTTTTTACGAAATAT
* *
12173 TCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGATATTTGGTTCGAT-GA-ATATA
1 TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGGAGATATA
* * *
12236 GATATTTCAAGGAGTCTTTGCGCCAAAAAAACCATGCAAAACTGAGTTGGGACCCTAGAACGCGT
66 GATATTTCAAGGAGTCTTTACGCAAAAAAAACCATGCAAAACTAAGTTGGGACCCTAGAACGCGT
12301 TTTTAACTAAAAACCATGAATGAGTAAATGATTTCGACTAAAATTTTGCAAAAACTGACCCGAAA
131 TTTTAACTAAAAACCATGAATGAGTAAATGATTTCGACTAAAATTTTGCAAAAACTGACCCGAAA
* * * *
12366 AGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGATAAACAAATAT
196 AGTTTTTCCTCAATTCTTTGCAACAATACTCAGAAAAAATATATAATTCAACGACAAAAAAATAT
* *
12431 AAGTGTTTTTCAAGCTTTTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCG
261 AAGGGTTTTTCAAGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCG
* *
12496 AAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTAAAATTTAATTAGAT
326 AAACAAGATTCACATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAAATTTAATTAGAT
* * * *
12561 GAATATAGATATTTCAAGGAGTCTTTCTACCTAAAATCATGCAAAACTGCGCCGGGGCCCC
391 CAATATAGATATTTCAAGGAGTCTTTCGACCAAAAATCATGCAAAACTGAGCCGGGGCCCC
12622 GAAGCTTGTT
Statistics
Matches: 403, Mismatches: 44, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
528 213 0.53
529 139 0.34
531 2 0.00
534 49 0.12
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (531 bp):
TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGGAGATATA
GATATTTCAAGGAGTCTTTACGCAAAAAAAACCATGCAAAACTAAGTTGGGACCCTAGAACGCGT
TTTTAACTAAAAACCATGAATGAGTAAATGATTTCGACTAAAATTTTGCAAAAACTGACCCGAAA
AGTTTTTCCTCAATTCTTTGCAACAATACTCAGAAAAAATATATAATTCAACGACAAAAAAATAT
AAGGGTTTTTCAAGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCG
AAACAAGATTCACATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAAATTTAATTAGAT
CAATATAGATATTTCAAGGAGTCTTTCGACCAAAAATCATGCAAAACTGAGCCGGGGCCCCAAAA
CACGTTTTTAGCCGAAAACCGTGATTTCGACTAAAAACTGACCAGAAAAGTTTTTTCTCAATTTT
TTACGAAATAT
Found at i:14965 original size:8 final size:8
Alignment explanation
Indices: 14952--14995 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
14942 TTTTAAATAG
14952 TAGTAAGA
1 TAGTAAGA
*
14960 TAGTAAAA
1 TAGTAAGA
14968 TAGTAAGA
1 TAGTAAGA
*
14976 TAAGATAAAA
1 T-AG-TAAGA
14986 TAGTAAGA
1 TAGTAAGA
14994 TA
1 TA
14996 TATATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 21 0.70
9 4 0.13
10 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.18, T:0.25
Consensus pattern (8 bp):
TAGTAAGA
Found at i:14984 original size:18 final size:17
Alignment explanation
Indices: 14952--14995 Score: 72
Period size: 18 Copynumber: 2.6 Consensus size: 17
14942 TTTTAAATAG
14952 TAGTAAGAT-AGTAAAA
1 TAGTAAGATAAGTAAAA
14968 TAGTAAGATAAGATAAAA
1 TAGTAAGATAAG-TAAAA
14986 TAGTAAGATA
1 TAGTAAGATA
14996 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 9 0.35
17 2 0.08
18 15 0.58
ACGTcount: A:0.57, C:0.00, G:0.18, T:0.25
Consensus pattern (17 bp):
TAGTAAGATAAGTAAAA
Found at i:15000 original size:2 final size:2
Alignment explanation
Indices: 14993--15017 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14983 AAATAGTAAG
14993 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
15018 AAGATTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45521 original size:26 final size:26
Alignment explanation
Indices: 45492--45578 Score: 76
Period size: 26 Copynumber: 3.4 Consensus size: 26
45482 CAACGTGATG
45492 ATGAAGAAGCGGAACAAGCCGAGATA
1 ATGAAGAAGCGGAACAAGCCGAGATA
* *
45518 ATGAAGAA----AACAACCACCATGA-A
1 ATGAAGAAGCGGAACAAGC-CGA-GATA
* *
45541 GATGAAGAAGCGGAACAAGCCGGGATG
1 -ATGAAGAAGCGGAACAAGCCGAGATA
45568 ATGAAGAAGCG
1 ATGAAGAAGCG
45579 AAGATAACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
22 6 0.13
23 3 0.06
24 10 0.21
26 21 0.45
27 1 0.02
28 6 0.13
ACGTcount: A:0.46, C:0.16, G:0.30, T:0.08
Consensus pattern (26 bp):
ATGAAGAAGCGGAACAAGCCGAGATA
Found at i:45556 original size:50 final size:51
Alignment explanation
Indices: 45467--45575 Score: 166
Period size: 50 Copynumber: 2.1 Consensus size: 51
45457 AAGAAGCGGC
* *
45467 TGAAGAAAACAACCACAACGTGATGATGAAGAAGCGGAACAAGCCGAGATAA
1 TGAAGAAAACAACCAC-ACATGAAGATGAAGAAGCGGAACAAGCCGAGATAA
* *
45519 TGAAGAAAACAACCAC-CATGAAGATGAAGAAGCGGAACAAGCCGGGATGA
1 TGAAGAAAACAACCACACATGAAGATGAAGAAGCGGAACAAGCCGAGATAA
45569 TGAAGAA
1 TGAAGAA
45576 GCGAAGATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 37 0.70
52 16 0.30
ACGTcount: A:0.48, C:0.17, G:0.27, T:0.09
Consensus pattern (51 bp):
TGAAGAAAACAACCACACATGAAGATGAAGAAGCGGAACAAGCCGAGATAA
Found at i:45635 original size:127 final size:131
Alignment explanation
Indices: 45460--45723 Score: 428
Period size: 127 Copynumber: 2.0 Consensus size: 131
45450 TATGATGAAG
*
45460 AAGCGGCTGAAGAAAACAACCACAACGTGATGATGAAGAAGCGGAACAAGCCGAGATAATGAAGA
1 AAGCGGCTGAAGAAAACAACCACAACGTGATAATGAAGAAGCGGAACAAGCCGAGATAATGAAGA
*
45525 AAACAACCACC-AT-GA-A-GATGAAGAAGCGGAACAAGCCGGGATGATGAAGAAGCGAAGATAA
66 AAACAACCACCAATGGAGATGATGAAGAAGCGGAACAAGCCGAGATGATGAAGAAGCGAAGATAA
45586 C
131 C
*
45587 AAGCGGCTGAAGAAAACAACCACAACGTGATAATGAAGAAGCGGAACAAGCCGGGATAATGAAGA
1 AAGCGGCTGAAGAAAACAACCACAACGTGATAATGAAGAAGCGGAACAAGCCGAGATAATGAAGA
*
45652 AAACAACCACCATAATGGGATGATGATGAAGAAGCGGAACAAGCCGAGATGATGAAGCAGCGAAG
66 AAACAACCACC--AAT-GGA-GATGATGAAGAAGCGGAACAAGCCGAGATGATGAAGAAGCGAAG
45717 ATAAC
127 ATAAC
45722 AA
1 AA
45724 CTGGTGCAAC
Statistics
Matches: 125, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
127 74 0.59
130 2 0.02
132 2 0.02
134 1 0.01
135 46 0.37
ACGTcount: A:0.46, C:0.17, G:0.27, T:0.09
Consensus pattern (131 bp):
AAGCGGCTGAAGAAAACAACCACAACGTGATAATGAAGAAGCGGAACAAGCCGAGATAATGAAGA
AAACAACCACCAATGGAGATGATGAAGAAGCGGAACAAGCCGAGATGATGAAGAAGCGAAGATAA
C
Found at i:60548 original size:38 final size:41
Alignment explanation
Indices: 60475--60557 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
60465 GATTAACTCT
*
60475 TAATAATAATATGATTAATACTTATAAATACTTATAAATT-A
1 TAATAATAATATGATTAATACTAATAAATACTTAT-AATTAA
60516 TAATAATAATATGATTAATACTAAT-AA-A-TTATAATTAA
1 TAATAATAATATGATTAATACTAATAAATACTTATAATTAA
60554 TAAT
1 TAAT
60558 GATATTCTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
37 4 0.10
38 9 0.22
39 1 0.03
40 2 0.05
41 24 0.60
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (41 bp):
TAATAATAATATGATTAATACTAATAAATACTTATAATTAA
Found at i:66523 original size:21 final size:21
Alignment explanation
Indices: 66476--66533 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 21
66466 CTGTTTAGTA
*
66476 ACTGTACAAATGAGATTACAT
1 ACTGTACAGATGAGATTACAT
* *
66497 --TGTACAGATTAGATTAGAT
1 ACTGTACAGATGAGATTACAT
66516 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
66534 TTAGAGCAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (21 bp):
ACTGTACAGATGAGATTACAT
Found at i:70381 original size:20 final size:22
Alignment explanation
Indices: 70356--70395 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
70346 CAGATATATA
70356 TATATATAGA-AG-GAAAAACT
1 TATATATAGAGAGAGAAAAACT
70376 TATATATAGAGAGAGAAAAA
1 TATATATAGAGAGAGAAAAA
70396 AGGGTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.57, C:0.03, G:0.17, T:0.23
Consensus pattern (22 bp):
TATATATAGAGAGAGAAAAACT
Found at i:72838 original size:16 final size:16
Alignment explanation
Indices: 72817--72850 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
72807 CAGGTTCATG
*
72817 TTAGGTTACTCGGGTT
1 TTAGGTCACTCGGGTT
*
72833 TTAGGTCATTCGGGTT
1 TTAGGTCACTCGGGTT
72849 TT
1 TT
72851 GGATTTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.29, T:0.47
Consensus pattern (16 bp):
TTAGGTCACTCGGGTT
Found at i:78481 original size:30 final size:29
Alignment explanation
Indices: 78408--78483 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
78398 ACTTGTAGCG
*
78408 TTTGGACGTTTT-GCCTCTTGAACTTAAAT
1 TTTGGACGTTTTATCC-CTTGAACTTAAAT
* * *
78437 TTTGGACATTTTATCCCTTGAATTTTAAT
1 TTTGGACGTTTTATCCCTTGAACTTAAAT
78466 TTTGGGACGTTTTATCCC
1 TTT-GGACGTTTTATCCC
78484 CTCGGCCTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.47
Consensus pattern (29 bp):
TTTGGACGTTTTATCCCTTGAACTTAAAT
Found at i:87188 original size:2 final size:2
Alignment explanation
Indices: 87181--87206 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
87171 TTTCACGATC
87181 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
87207 GGGACTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97188 original size:29 final size:29
Alignment explanation
Indices: 97125--97196 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
97115 GTTAAGTGGG
* * *
97125 CAAAACGTCCCAAAATTGAAATTTATAGGG
1 CAAAACGT-CCAAAATTGAAATTCAGAGGA
* *
97155 TAAAATGTCCAAAATTGAAATTCAGAGGA
1 CAAAACGTCCAAAATTGAAATTCAGAGGA
97184 CAAAACGTCCAAA
1 CAAAACGTCCAAA
97197 CGCTATAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 29 0.83
30 6 0.17
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (29 bp):
CAAAACGTCCAAAATTGAAATTCAGAGGA
Found at i:101361 original size:42 final size:42
Alignment explanation
Indices: 101298--101380 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
101288 TTTTCTATTG
* *
101298 CAGAATGATTCGGAAGCTGTTGTCCCA-TGCTGCTGGCCCAGC
1 CAGAATGATTCGGAAGCTGTTGT-ACAGTGCTGCTCGCCCAGC
* *
101340 CAGAATGATTGGGAAGGTGTTGTACAGTGCTGCTCGCCCAG
1 CAGAATGATTCGGAAGCTGTTGTACAGTGCTGCTCGCCCAG
101381 GTCTTGTCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 34 0.94
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (42 bp):
CAGAATGATTCGGAAGCTGTTGTACAGTGCTGCTCGCCCAGC
Found at i:102308 original size:2 final size:2
Alignment explanation
Indices: 102301--102338 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
102291 AATTATTATG
102301 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
102339 TTAGAGAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102575 original size:2 final size:2
Alignment explanation
Indices: 102568--102602 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
102558 GAGATATTAG
*
102568 AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
102603 ATCATGTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:103497 original size:31 final size:31
Alignment explanation
Indices: 103459--103568 Score: 139
Period size: 31 Copynumber: 3.5 Consensus size: 31
103449 ACGGTGTCCG
**
103459 ATGTGGCATGCCACGTGTACCAAAAAGCGAC
1 ATGTGGCATGCCACGTGTACCAAAAAATGAC
* *
103490 ATGTGGCACGTCACGTGTACCAAAAAATGAC
1 ATGTGGCATGCCACGTGTACCAAAAAATGAC
*** *
103521 ATGCATCATGCCATGTGTACCAAAAAATGAC
1 ATGTGGCATGCCACGTGTACCAAAAAATGAC
*
103552 ACGTGGCATGCCACGTG
1 ATGTGGCATGCCACGTG
103569 CACAAAAGGA
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 64 1.00
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.19
Consensus pattern (31 bp):
ATGTGGCATGCCACGTGTACCAAAAAATGAC
Found at i:104011 original size:2 final size:2
Alignment explanation
Indices: 104000--104045 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
103990 AAATTATTCC
104000 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
104041 TA TA T
1 TA TA T
104046 GTCATTCGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:105293 original size:36 final size:35
Alignment explanation
Indices: 105246--105316 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 35
105236 ATAGTTTGAC
105246 AAATTCAAAAATACTTGATATATCTTTAACAAAAAA
1 AAATTCAAAAATACTTGATATATCTTTAA-AAAAAA
105282 AAATTCAAAAATACTTGATATATCTTTAAAAAAAA
1 AAATTCAAAAATACTTGATATATCTTTAAAAAAAA
105317 TCCCACCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 6 0.17
36 29 0.83
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (35 bp):
AAATTCAAAAATACTTGATATATCTTTAAAAAAAA
Found at i:106221 original size:6 final size:6
Alignment explanation
Indices: 106210--106238 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
106200 TTGAACTAGG
106210 GCTCGA GCTCGA GCTCGA GCTCGA -CTCGA
1 GCTCGA GCTCGA GCTCGA GCTCGA GCTCGA
106239 ATTTTCCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (6 bp):
GCTCGA
Found at i:106256 original size:20 final size:22
Alignment explanation
Indices: 106223--106280 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
106213 CGAGCTCGAG
106223 CTCGAGCTCG-ACTCGAA-TTTT
1 CTCGAG-TCGAACTCGAATTTTT
106244 C-CGAGTCGAACTCGAATTTTT
1 CTCGAGTCGAACTCGAATTTTT
*
106265 CTCGAGTCGAGCTCGA
1 CTCGAGTCGAACTCGA
106281 GTAGCTCACG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 3 0.09
20 11 0.33
21 6 0.18
22 13 0.39
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (22 bp):
CTCGAGTCGAACTCGAATTTTT
Done.