Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016338.1 Corchorus olitorius cultivar O-4 contig16371, 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: 103062
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:703 original size:205 final size:206
Alignment explanation
Indices: 351--743 Score: 653
Period size: 205 Copynumber: 1.9 Consensus size: 206
341 TCCTTGACCC
* *
351 AAATTGGATCTAAAGATTTGATTTTAAAATCATTAGAATCATGTTTCGATTTAATCAGAAATTAA
1 AAATTGGATCTAAAGATTTGATTTTAAAAGCATCAGAATCATGTTTCGATTTAATCAGAAATTAA
* *
416 TTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGTAAAACCCTTCAATCTTTTTGGCATTAA
66 TTCGGAAAGATATAGGAAAATCGATATTAGAAACGTGAAAAACCCTTCAATCTTTTTGGCATTAA
* * *
481 ATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGG-TAAAATTTTTCGGGTCATCTAACC
131 ATTATACATATTCTATAAGTGTTTTGGCCAAAGATTATGGAAAAAATATTTCGGGTCATCTAACC
545 AAATCTCAGCG
196 AAATCTCAGCG
* * ** * *
556 AAATTGGATTTAAGGATTTGATTTTATGAGCGTCAGTATCATGTTTCGATTTAATCAGAAATTAA
1 AAATTGGATCTAAAGATTTGATTTTAAAAGCATCAGAATCATGTTTCGATTTAATCAGAAATTAA
*
621 TTCGGAAAGATATAGGAAAATCGATATTAGAAACGTGAAAAACCCTTCAATCTTTTTGGCATTGA
66 TTCGGAAAGATATAGGAAAATCGATATTAGAAACGTGAAAAACCCTTCAATCTTTTTGGCATTAA
686 ATTATACATATTCTATAAGTGTTTTGGCCAAAGATTATGGAAAAAATATTTCGGGTCA
131 ATTATACATATTCTATAAGTGTTTTGGCCAAAGATTATGGAAAAAATATTTCGGGTCA
744 ATTTTTGCAA
Statistics
Matches: 173, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
205 158 0.91
206 15 0.09
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (206 bp):
AAATTGGATCTAAAGATTTGATTTTAAAAGCATCAGAATCATGTTTCGATTTAATCAGAAATTAA
TTCGGAAAGATATAGGAAAATCGATATTAGAAACGTGAAAAACCCTTCAATCTTTTTGGCATTAA
ATTATACATATTCTATAAGTGTTTTGGCCAAAGATTATGGAAAAAATATTTCGGGTCATCTAACC
AAATCTCAGCG
Found at i:1411 original size:40 final size:40
Alignment explanation
Indices: 1352--1428 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
1342 CGAATTATAT
* *
1352 ATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAATAA
1 ATATTCTATAAGCGATTTGGCCAAAGATTGTGGAAAATAA
* *
1392 ATATTCTATTAGCGATTTGGCCAACGATTGTGGAAAA
1 ATATTCTATAAGCGATTTGGCCAAAGATTGTGGAAAA
1429 ATCTTTCGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.34
Consensus pattern (40 bp):
ATATTCTATAAGCGATTTGGCCAAAGATTGTGGAAAATAA
Found at i:2323 original size:333 final size:332
Alignment explanation
Indices: 535--4658 Score: 4587
Period size: 333 Copynumber: 12.4 Consensus size: 332
525 ATTTTTCGGG
* * * * *
535 TCATCTAACCAAATCTCAGCGAAATTGGATTTAAGGATTTGATTTTATGAGCGTCAGTATCATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
*
600 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAACGTGAAAAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
* * *
665 CTTCAATCTTTTTGGCATTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTATGGAAAA
131 CTTCAATCTTTTTGGCGTTGAATTAT-TAT-TTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAA
* * * ** *
730 AATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTAAATATCACGGTTTTTGG
194 AATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATAGTGTACTAACCATCACGTTTTTTGG
* * * *
795 CTAAAAACGCGTTCTGGGGCCCCGACTTAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGACA
259 CTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACA
860 TATCTATAT
324 TATCTATAT
* * *
869 TCATCTAACCAAATCTCAGCCTAATTGGATTTAAGGATTTGATTTTAAGAGCATCAGAATCATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* * *
934 TTCGATTTAATCAGCAATTAATTCGGAAACATATAGGAAAATCGATATTAGAAACGTGAAAAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
* * * *
999 C-T--ATATATAT----AT--A-TA-TATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAA
131 CTTCAATCTTTTTGGCGTTGAATTATTAT-TTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAA
* *
1053 A-CTTTCAGGTCAATTTTTGCAAAAACTTTAGCCGAAATCA-TGTACTAACCATCACGGTTTTTT
195 ATCTTTCGGGTCAATTTTTGC-AAAATTTTAGCCGAAAT-AGTGTACTAACCATCAC-G--TTTT
* * * *
1116 TTGGCTAAAAAGGCGTTCTGGGGCCCCGGCTTAGTTTTTAATGATTTATGGCCCCGAGACTCCTT
255 TTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTT
1181 GACATATCTATAT
320 GACATATCTATAT
*** **
1194 TCATCTAATTGAATCTCAGCCAAAACGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* * *
1259 TTCGATTTAATTAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGGAAATCC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
* *
1324 TTTCAATCTTTTTGGCGTCGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAA
131 CTTCAATCTTTTTGGCGTTGAATTAT-TAT-TTCTATAAGTGTTTTGGCCAAAGATTGTGG-AAA
* * * * * * ** ** **
1389 TAAAT-ATTC---T--A--TTAGC--GA-TTTGGCC-AACGATTGTGGAAAAATCTTTCGGGTCA
193 -AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAA--ATAGTGTACTAA-CCATCACGT--
* * ** * ** * * * *
1442 ATTTTT-G-TAAAATCTTAGCCGAAAT-CGTGTACTAACCATCACGGGTTTTGGTTAAAAACGCG
252 -TTTTTGGCTAAAAAC---G-CG--TTCCG-GGGC--CCCGGCTC-AG-TTT--TT---AATG-A
*** * * *
1504 TTCCGGGGCCCCG-G-CTCAGTTTTTA-ATGATTTATGGCCACGAGACT
299 TT-TTTGGCCCCGAGACTC---CTTGACAT-ATCTAT---------A-T
* * * ** *
1550 CCTTGACATATCTATATTCATCTAACCGAATCTCAGCCAAAACGGATTTATGGATTTGATTTTAC
1 TCAT--C-TAAC---------C--A---AATCTCAGCCAAATTGGATTTAAGGATTTGATTTTAC
*
1615 GGGCATCAGAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGGAAAATCGATAT
49 GGGCATCAGAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATAT
* * * *
1680 TAGAAACGTG-AAAA----T--A--TATAT----AT--A-TA-TA-TTCTATAAGTGTTTTGGCC
114 TAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATTATTTCTATAAGTGTTTTGGCC
* ** *
1727 AAAGATTGTTGAAAAAA-CTTTCAAGTCAATTTTTGCAAAAACTTTAGCCGAAATCA-TGTACTA
179 AAAGATTGTGGAAAAAATCTTTCGGGTCAATTTTTGC-AAAATTTTAGCCGAAAT-AGTGTACTA
* * *
1790 ACCATCTCGGTTTTGTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTAAGTTTTTAATGATTTTTG
242 ACCATCAC-GTTTT-TTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTG
1855 GCCCCGAGACTCCTTGACATATCTATAT
305 GCCCCGAGACTCCTTGACATATCTATAT
1883 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* *
1948 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCAATATTAGAAGCATGAAAAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
* * * * * *
2013 TTTCAATCTTTTTGGTGTTCAATTATTCATTCCTATTAGTGTTTTGGCCAAAGATTATGGAAAAA
131 CTTCAATCTTTTTGGCGTTGAATTATT-ATTTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAA
* *
2078 ATCTTTCGGGTCAATTTTTGCTAAATTTTAGCCGAAATAGTGTACTAACCATCACGATTTTTGGC
195 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATAGTGTACTAACCATCACGTTTTTTGGC
* * * * *
2143 TAAAAACGCATTCCAGGGCCCCGGCTCAGTTTTTGATAATTTTTGTCCCCGAGACTCCTTGACAT
260 TAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACAT
2208 ATCTATAT
325 ATCTATAT
* * *
2216 TCATGTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGAGCATCAGAATCAAGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* * *
2281 TTCGATTTAGTCAGAAATTAATTCGAAAAGATATAGGAAAATCGATATTAGAAACGTTG-AAAAC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCG-TGAAAAAC
* * * * * * *
2345 CTTTCAATCTTTTTGTCGTTGAATTTTTCTTTTCTATTATTGTTTTGTG-CAAAGATTATGG-AA
130 CCTTCAATCTTTTTGGCGTTGAATTATT-ATTTCTATAAGTGTTTTG-GCCAAAGATTGTGGAAA
* * * *
2408 AATTCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-CCCATCAATGTTTTTT
193 AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATAGTGTACTAACCATC-ACG-TTTTT
* * * *
2472 TGGCTAAAAACGCGTTCTGGGGCCCCGACTCAGTTTTTAATGAATTTTGGCCCCAAGACTCCTTG
256 TGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTG
*
2537 GCATATCTATAT
321 ACATATCTATAT
* * * *
2549 TCATTTAACCAAATCTCAGCAAAATTGGATTTAAGGATTTGATTTTACGGGTATCAGAATAATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* *
2614 TT-GAATTTAATCAGAAATTAATTAGGAAAGATATAGGAAAATCGATACTAGAAGCGTGAAAAAC
66 TTCG-ATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAAC
* * * * *
2678 CCTTTAAACTTTTTGGTGTTGAATTATATATATTCTATAAGTGTTTTGGCCAGAGATAGT-GAGA
130 CCTTCAATCTTTTTGGCGTTGAATTAT-TAT-TTCTATAAGTGTTTTGGCCAAAGATTGTGGA-A
* * * * ***
2742 AAAA-CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATTGTGTGCCATCACAGT-TTTTTTT
192 AAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATAGTGTACTAAC-CA-TCACGTTTT
* * * * * *
2805 TTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTGTATTAATTTTTGTCCTCGAGACTCCTT
255 TTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTT
2870 GACATATCTATAT
320 GACATATCTATAT
* * * *
2883 TCATCTAGCAAAATATCAGCCAAATTGGATTTAAAGATTTGATTTTACGGGCATCAGAATCATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* *
2948 TTCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTAAAAAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
* * * *
3013 TTTCAATCTTTTTGGCGTTGAATTATTCTTTTCTATTAGTGTTTTGGCCAAAGATTATGG-AAAA
131 CTTCAATCTTTTTGGCGTTGAATTATT-ATTTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAA
* * *
3077 ATCTTTCGAGTCAATTTTTGCTAAATTTTAGCCGAAATAGTGTACCAACCATCACGGTTTTTTGG
195 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATAGTGTACTAACCATCAC-GTTTTTTGG
* * * * *
3142 CCAAAAACGTGTTCCGGGGCCTCGTCTCAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGACA
259 CTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACA
3207 TATCTATAT
324 TATCTATAT
*
3216 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGC
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* * * * *
3281 TTCGATTTAATTAGAAATTAATTCGGAAACATATTGGAAAATCGATATTAGAAGCTTGAATAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
* *
3346 CTTCAATCTTTTTGGCATTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAA
131 CTTCAATCTTTTTGGCGTTGAATTAT-TAT-TTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAA
*
3411 AATCTTTCGGG--------T-C--AATTTTAGCCGAAATCA-TGTAC---GCATCACGGTTTTTT
194 AATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT-AGTGTACTAACCATCAC-GTTTTTT
* * * *
3461 GGCTAAAAATGTGTTCTGGGGCCCCGGCTCAATTTTTAATGATTTTTGGCCCCGAGACTCCTTGA
257 GGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGA
3526 CATATCTATAT
322 CATATCTATAT
* * *
3537 TCATCTAACCAAATCTCAGCCAAGTTGGATGTAAGGATTTGATTTTACGAGCATCAGAATCATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* * * * * *
3602 TTCGATTTAATTAGAAATTAATTCGGAAACATATTGAAAAATTGATATTAGAAGCTTGAAAAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
*
3667 CTTCAATCTTTTTTGGCGTTGAATTATATATATTCTATAAGCGTTTTGGCCAAAGATTGTGGAAA
131 CTTCAATC-TTTTTGGCGTTGAATTAT-TAT-TTCTATAAGTGTTTTGGCCAAAGATTGTGGAAA
* * * ** *
3732 AAATCTTTCGGGTCAATTATTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCACGGGTTTCG
193 AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATAGTGTACTAACCATCACGTTTTTTG
* *
3797 GCTAAAAACGCGTTCCGAGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGAT
258 GCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGAC
3862 ATATCTATAT
323 ATATCTATAT
3872 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* * * *
3937 TTCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCAATATTCGAATCGTGAAAAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
* * * *
4002 CTTCAAACTTTTTGGCGTTGAATTACATATATTCTATAATTTTTTTGGCCAAAGATTGTGGAAAA
131 CTTCAATCTTTTTGGCGTTGAATTA-TTAT-TTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAA
*
4067 AA-CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCA-TGTATTAACCATCACGGTTTTTT
194 AATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT-AGTGTACTAACCATCAC-GTTTTTT
* * *
4130 -GCTAAAAATGCGTTCCGGAGCCCCGGCTCAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGA
257 GGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGA
4194 CATATCTATAT
322 CATATCTATAT
* *
4205 TCATCTATCCAAATCTCAGCCAAATTGGATTTAAGAATTTGATTTTACGGGCATCAGAATCATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* * *
4270 TTCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTCGAATCGTGAAAAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
* * *
4335 CTTCAAACTTTTTGGCGTTGAAATATATATATTCTATAAGTGTTTTGGCCAAAGAATGTGGAAAA
131 CTTCAATCTTTTTGGCGTTGAATTAT-TAT-TTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAA
* * * **
4400 AA-CTTTCAGGTCAAATTTTGTAAAATTTTAGCCG-AA-A---T-C--ACGGT----TTTTTTGG
194 AATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATAGTGTACTAACCATCACGTTTTTTGG
* * * * **
4452 CTAAAAACGCGTTCTGGGACCTCGGCTCAGTTTTTAATGAATTTTGGCCCTAAGACTCCTTGACA
259 CTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACA
4517 TATCTATAT
324 TATCTATAT
* * * * *
4526 TCATCTAACCAAATTTCAGCCAAATTGGATTTATGGATTTAATTTTACGGGCATCAAAATTATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
4591 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
4656 CTT
131 CTT
4659 AGAACCTAAG
Statistics
Matches: 3248, Mismatches: 378, Indels: 341
0.82 0.10 0.09
Matches are distributed among these distances:
316 105 0.03
317 4 0.00
319 1 0.00
320 6 0.00
321 422 0.13
322 131 0.04
323 2 0.00
324 22 0.01
325 201 0.06
326 2 0.00
327 5 0.00
328 17 0.01
329 11 0.00
330 13 0.00
331 15 0.00
332 69 0.02
333 1090 0.34
334 499 0.15
335 281 0.09
336 29 0.01
337 36 0.01
338 6 0.00
339 6 0.00
340 2 0.00
343 14 0.00
344 12 0.00
345 12 0.00
346 14 0.00
349 2 0.00
351 9 0.00
352 4 0.00
353 32 0.01
354 1 0.00
355 6 0.00
356 5 0.00
357 4 0.00
358 10 0.00
359 4 0.00
360 4 0.00
361 16 0.00
362 6 0.00
363 2 0.00
364 3 0.00
366 1 0.00
368 1 0.00
372 3 0.00
373 108 0.03
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (332 bp):
TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
CTTCAATCTTTTTGGCGTTGAATTATTATTTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAA
TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATAGTGTACTAACCATCACGTTTTTTGGCT
AAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATA
TCTATAT
Found at i:3044 original size:667 final size:665
Alignment explanation
Indices: 535--4658 Score: 4961
Period size: 667 Copynumber: 6.2 Consensus size: 665
525 ATTTTTCGGG
* * * * *
535 TCATCTAACCAAATCTCAGCGAAATTGGATTTAAGGATTTGATTTTATGAGCGTCAGTATCATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
*
600 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAACGTGAAAAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
* * *
665 CTTCAATCTTTTTGGCATTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTA-TGGAAA
131 CTTCAAACTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGA-TAGTGGAAA
* * * *
729 AAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTAAATATCACGG-TTTTT
195 AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATTGTGTAC----CATCACGGTTTTTT
* * * *
793 GGCTAAAAACGCGTTCTGGGGCCCCGACTTAG-TTTTCAATGATTTTTGGCCCCGAGACTCCTTG
256 GGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTCAATAATTTTTGGCCCCGAGACTCCTTG
* * *
857 ACATATCTATATTCATCTAACCAAATCTCAGCCTAATTGGATTTAAGGATTTGATTTTAAGAGCA
321 ACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAAGATTTGATTTTACGAGCA
* * *
922 TCAGAATCATGTTTCGATTTAATCAGCAATTAATTCGGAAACATATAGGAAAATCGATATTAGAA
386 TCAGAATCATGTTTCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAA
* * * *
987 ACGTGAAAAACCC-T--A--TATAT----AT--A-TATATATATTCTATAAGTGTTTTGGCCAAA
451 GCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAA
* * * * *
1040 GATTGTGGAAAAAACTTTCAGGTCAATTTTTGCAAAAACTTTAGCCGAAATCATGTACTAACCAT
516 GATTATGGAAAAATCTTTCGGGTCAATTTTTGC-AAAATTTTAGCCGAAATCGTGTACT-ACCAT
* * *
1105 CACGGTTTTTTTTGGCTAAAAAGGCGTTCTGGGGCCCCGGCTTAGTTTTTAATGATTTATGGCCC
579 CAC-G-TTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCC
1170 CGAGACTCCTTGACATATCTATAT
642 CGAGACTCCTTGACATATCTATAT
*** **
1194 TCATCTAATTGAATCTCAGCCAAAACGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* * *
1259 TTCGATTTAATTAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGGAAATCC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
* * * *
1324 TTTCAATCTTTTTGGCGTCGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAA
131 CTTCAAACTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATAGTGG--AA
* * * * * * * *
1389 TAAATATTCTATTAGCGATTTGGCCAACGATTGTGGAAAAATCTTTCG-GGTCAATTTTTGTAAA
194 -AAA-A-TCT-TT--CG----GGTC-A--ATTTTTGCAAAAT-TTTAGCCG--AAATTGTGT---
* * *
1453 ATCTTAGCCGAAATCGTGTACTAACCATCACGGGTTTTGGTTAAAAACGCGTTCCGGGGCCCCGG
240 A-C-CA-TC---A-CG-G---T-----T------TTTTGGCTAAAAACGCGTTCCGGGGCCCCGG
* * * *
1518 CTCAGTTTTT-AATGATTTATGGCCACGAGACTCCTTGACATATCTATATTCATCTAACCGAATC
283 CTCAGTTTTTCAATAATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATC
** ** * *
1582 TCAGCCAAAACGGATTTATGGATTTGATTTTACGGGCATCAGAATCATGTTTCGATTTAATCAGA
348 TCAGCCAAATTGGATTTAAAGATTTGATTTTACGAGCATCAGAATCATGTTTCGATTTATTCAGA
* *
1647 AATTAATTCGGAAACATATAGGAAAATCGATATTAGAAACGTG-AAAA----T--A------T--
413 AATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGG
* * * * **
1697 --AT--A-TATATATATTCTATAAGTGTTTTGGCCAAAGATTGTTGAAAAAACTTTCAAGTCAAT
478 CGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTATGGAAAAATCTTTCGGGTCAAT
* * * *
1757 TTTTGCAAAAACTTTAGCCGAAATCATGTACTAACCATCTCGGTTTTGTTGGCTAAAAACGCGTT
543 TTTTGC-AAAATTTTAGCCGAAATCGTGTACT-ACCATCAC-GTTTTTTTGGCTAAAAACGCGTT
*
1822 CTGGGGCCCCGGCTAAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATAT
605 CTGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATAT
1883 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* *
1948 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCAATATTAGAAGCATGAAAAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
* * * * * *
2013 TTTCAATCTTTTTGGTGTTCAATTAT-TCAT-TCCTATTAGTGTTTTGGCCAAAGATTA-TGGAA
131 CTTCAAACTTTTTGGCGTTGAATTATAT-ATATTCTATAAGTGTTTTGGCCAAAGA-TAGTGGAA
* * *
2075 AAAATCTTTCGGGTCAATTTTTGCTAAATTTTAGCCGAAATAGTGTACTAACCATCAC-GATTTT
194 AAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT--TGT-GT-ACCATCACGGTTTTT
* * * *
2139 TGGCTAAAAACGCATTCCAGGGCCCCGGCTCAGTTTTT-GATAATTTTTGTCCCCGAGACTCCTT
255 TGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTCAATAATTTTTGGCCCCGAGACTCCTT
* *
2203 GACATATCTATATTCATGTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGAGC
320 GACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAAGATTTGATTTTACGAGC
* * *
2268 ATCAGAATCAAGTTTCGATTTAGTCAGAAATTAATTCGAAAAGATATAGGAAAATCGATATTAGA
385 ATCAGAATCATGTTTCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGA
* * * * * * * *
2333 AACGTTG-AAAACCTTTCAATCTTTTTGTCGTTGAATT-TTTCTTTTCTATTATTGTTTTGTG-C
450 AGCG-TGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTG-GCC
* *
2395 AAAGATTATGGAAAATTCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTCCCA
513 AAAGATTATGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTACCA
* * *
2460 TCAATGTTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGACTCAGTTTTTAATGAATTTTGGCCC
578 TC-ACGTTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCC
* *
2525 CAAGACTCCTTGGCATATCTATAT
642 CGAGACTCCTTGACATATCTATAT
* * * *
2549 TCATTTAACCAAATCTCAGCAAAATTGGATTTAAGGATTTGATTTTACGGGTATCAGAATAATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* *
2614 TT-GAATTTAATCAGAAATTAATTAGGAAAGATATAGGAAAATCGATACTAGAAGCGTGAAAAAC
66 TTCG-ATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAAC
* * *
2678 CCTTTAAACTTTTTGGTGTTGAATTATATATATTCTATAAGTGTTTTGGCCAGAGATAGT-GAGA
130 CCTTCAAACTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATAGTGGA-A
* *
2742 AAAA-CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATTGTGTGCCATCACAGTTTTTTTTT
194 AAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATTGTGTACCATCAC-G---GTTTTT
* * * * *
2806 TGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTGT-ATTAATTTTTGTCCTCGAGACTCCTT
255 TGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTCAATAATTTTTGGCCCCGAGACTCCTT
* * * *
2870 GACATATCTATATTCATCTAGCAAAATATCAGCCAAATTGGATTTAAAGATTTGATTTTACGGGC
320 GACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAAGATTTGATTTTACGAGC
2935 ATCAGAATCATGTTTCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGA
385 ATCAGAATCATGTTTCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGA
* * * * *
3000 AGCGTAAAAAACCTTTCAATCTTTTTGGCGTTGAATTAT-TCTTTTCTATTAGTGTTTTGGCCAA
450 AGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAA
* * * *
3064 AGATTATGGAAAAATCTTTCGAGTCAATTTTTGCTAAATTTTAGCCGAAATAGTGTACCAACCAT
515 AGATTATGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-CTACCAT
* * * * * * *
3129 CACGGTTTTTTGGCCAAAAACGTGTTCCGGGGCCTCGTCTCAGTTTTCAATGATTTTTGGCCCCG
579 CACGTTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCG
3194 AGACTCCTTGACATATCTATAT
644 AGACTCCTTGACATATCTATAT
*
3216 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGC
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* * * * *
3281 TTCGATTTAATTAGAAATTAATTCGGAAACATATTGGAAAATCGATATTAGAAGCTTGAATAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
* * * *
3346 CTTCAATCTTTTTGGCATTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAA
131 CTTCAAACTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATAGTGGAAAA
**
3411 AATCTTTCGGG--------T-C--AATTTTAGCCGAAATCATGTACGCATCACGGTTTTTTGGCT
196 AATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATTGTGTAC-CATCACGGTTTTTTGGCT
* * * * *
3465 AAAAATGTGTTCTGGGGCCCCGGCTCAATTTTT-AATGATTTTTGGCCCCGAGACTCCTTGACAT
260 AAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTCAATAATTTTTGGCCCCGAGACTCCTTGACAT
* * *
3529 ATCTATATTCATCTAACCAAATCTCAGCCAAGTTGGATGTAAGGATTTGATTTTACGAGCATCAG
325 ATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAAGATTTGATTTTACGAGCATCAG
* * * * *
3594 AATCATGTTTCGATTTAATT-AGAAATTAATTCGGAAACATATTGAAAAATTGATATTAGAAGCT
390 AATCATGTTTCGATTT-ATTCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCG
*
3658 TGAAAAACCCTTCAATCTTTTTTGGCGTTGAATTATATATATTCTATAAGCGTTTTGGCCAAAGA
454 TGAAAAACCCTTCAATC-TTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGA
* * *
3723 TTGTGGAAAAAATCTTTCGGGTCAATTATTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCA
518 TTATGG-AAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-ACCATCA
** * * *
3788 CG-GGTTTCGGCTAAAAACGCGTTCCGAGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAG
581 CGTTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAG
*
3852 ACTCCTTGATATATCTATAT
646 ACTCCTTGACATATCTATAT
3872 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* * * *
3937 TTCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCAATATTCGAATCGTGAAAAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
* * * *
4002 CTTCAAACTTTTTGGCGTTGAATTACATATATTCTATAATTTTTTTGGCCAAAGATTGTGGAAAA
131 CTTCAAACTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATAGTGGAAAA
*
4067 AA-CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTATTAACCATCACGGTTTTTT-
196 AATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT--TGT-GT-ACCATCACGGTTTTTTG
* * *
4130 GCTAAAAATGCGTTCCGGAGCCCCGGCTCAG-TTTTCAATGATTTTTGGCCCCGAGACTCCTTGA
257 GCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTCAATAATTTTTGGCCCCGAGACTCCTTGA
* *
4194 CATATCTATATTCATCTATCCAAATCTCAGCCAAATTGGATTT-AAGAATTTGATTTTACGGGCA
322 CATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAAG-ATTTGATTTTACGAGCA
*
4258 TCAGAATCATGTTTCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTCGAA
386 TCAGAATCATGTTTCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAA
* * *
4323 TCGTGAAAAACCCTTCAAACTTTTTGGCGTTGAAATATATATATTCTATAAGTGTTTTGGCCAAA
451 GCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAA
* * * * * *
4388 GAATGTGGAAAAAACTTTCAGGTCAAATTTTGTAAAATTTTAGCCG-AA------A-T--CA-C-
516 GATTATGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTACCATCA
* * * * **
4441 GGTTTTTTTGGCTAAAAACGCGTTCTGGGACCTCGGCTCAGTTTTTAATGAATTTTGGCCCTAAG
581 CGTTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAG
4506 ACTCCTTGACATATCTATAT
646 ACTCCTTGACATATCTATAT
* * * * *
4526 TCATCTAACCAAATTTCAGCCAAATTGGATTTATGGATTTAATTTTACGGGCATCAAAATTATGT
1 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
4591 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
66 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
4656 CTT
131 CTT
4659 AGAACCTAAG
Statistics
Matches: 3036, Mismatches: 314, Indels: 235
0.85 0.09 0.07
Matches are distributed among these distances:
649 183 0.06
650 6 0.00
653 1 0.00
654 389 0.13
655 32 0.01
656 284 0.09
657 72 0.02
658 8 0.00
659 172 0.06
660 1 0.00
661 2 0.00
662 11 0.00
663 4 0.00
664 6 0.00
665 6 0.00
666 317 0.10
667 649 0.21
668 252 0.08
669 18 0.01
670 3 0.00
671 7 0.00
672 7 0.00
673 12 0.00
674 12 0.00
675 5 0.00
676 8 0.00
677 2 0.00
678 1 0.00
679 1 0.00
680 3 0.00
681 1 0.00
682 4 0.00
683 4 0.00
684 1 0.00
685 3 0.00
686 2 0.00
688 26 0.01
689 225 0.07
690 101 0.03
692 1 0.00
694 2 0.00
697 4 0.00
698 184 0.06
699 4 0.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (665 bp):
TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACC
CTTCAAACTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATAGTGGAAAA
AATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATTGTGTACCATCACGGTTTTTTGGCTA
AAAACGCGTTCCGGGGCCCCGGCTCAGTTTTTCAATAATTTTTGGCCCCGAGACTCCTTGACATA
TCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAAGATTTGATTTTACGAGCATCAGA
ATCATGTTTCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTG
AAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTA
TGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTACCATCACGTTT
TTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCC
TTGACATATCTATAT
Found at i:4147 original size:989 final size:984
Alignment explanation
Indices: 1451--4658 Score: 4375
Period size: 989 Copynumber: 3.3 Consensus size: 984
1441 AATTTTTGTA
* * * *
1451 AAATCTTAGCCGAAATCGTGTACTAAC-CATCACGG-GTTTTGGTTAAAAACGCGTTCCGGGGCC
1 AAATTTTAGCCGAAATC-TGTAC---CGCATCACGGTTTTTTGGCTAAAAACGCGTTCTGGGGCC
* * *
1514 CCGGCTCAGTTTTTAATG-ATTTATGGCCACGAGACTCCTTGACATATCTATATTCATCTAACCG
62 CCGGCTCAGTTTTTAATGAATTT-TGGCCCCAAGACTCCTTGACATATCTATATTCATCTAACCA
** * *
1578 AATCTCAGCCAAAACGGATTTATGGATTTGATTTTACGGGCATCAGAATCATGTTTCGATTTAAT
126 AATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATAATGTTTCGATTTAAT
* *
1643 CAGAAATTAATTCGGAAACATATAGGAAAATCGATATTAGAAACGTG-AAAA----T---A----
191 CAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAAACTTT
* **
1696 -T----AT--A-TATATATATTCTATAAGTGTTTTGGCCAAAGATTGTTGAAAAAACTTTCAAGT
256 TTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTG-TGAAAAAACTTTCGGGT
* *
1753 CAATTTTTGCAAAAACTTTAGCCGAAATCATGTACTAACCATCTCGGTTTTGTTGGCTAAAAACG
320 CAATTTTTGC-AAAATTTTAGCCGAAATCGTGTACTAACCATCTCGG-TTT-TTGGCTAAAAACG
* *
1818 CGTTCTGGGGCCCCGGCTAAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATAT
382 CGTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATAT
1883 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
447 TCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGT
* *
1948 TTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCAATATTAGAAGCATGAAAAACC
512 TTCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCAATATTAGAAGCGTGAAAAACC
* *
2013 TTTCAATCTTTTTGGTGTTCAATT-ATTCATTCCTATTAGTGTTTTGGCCAAAGATTATGGAAAA
577 TTTCAATCTTTTTGGCGTTGAATTAATT-ATT-CTATTAGTGTTTTGGCCAAAGATTATGGAAAA
* *
2077 AATCTTTCGGGTCAATTTTTGCTAAATTTTAGCCGAAATAGTGTACTAACCATCACGATTTTTGG
640 AA-CTTTCGGGTCAATTTTTGCTAAATTTTAGCCGAAATAGTGTACTAACCATCACGGTTTTTTG
* * ** * *
2142 CTAAAAACGCATTCCAGGGCCCCGGCTCAGTTTTTGATAATTTTTGTCCCCGAGACTCCTTGACA
704 CTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGACA
* *
2207 TATCTATATTCATGTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGAGCATCA
769 TATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCA
* * * *
2272 GAATCAAGTTTCGATTTAGTCAGAAATTAATTCGAAAAGATATAGGAAAATCGATATTAGAAACG
834 GAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAAC-
* * * * * * *
2337 TTGAAAACCTTTCAATCTTTTTGTCGTTGAATTTTTC-TTTTCTATTATTGTTTTGTG-CAAAGA
898 TTGAAAACCCTTCAATCTTTTTGGCGTTGAATTATACATATTCTATAAGTGTTTTG-GCCAAAGA
* *
2400 TTATGG-AAAATTCTTTCGGGTCAATTTTTGC
962 TTGTGGAAAAAATCTTTCGGG--------T-C
* * *
2431 AAAATTTTAGCCGAAATCGTGTACTCCCATCAATGTTTTTTTGGCTAAAAACGCGTTCTGGGGCC
1 -AAATTTTAGCCGAAATC-TGTAC-CGCATC-ACGGTTTTTTGGCTAAAAACGCGTTCTGGGGCC
* * *
2496 CCGACTCAGTTTTTAATGAATTTTGGCCCCAAGACTCCTTGGCATATCTATATTCATTTAACCAA
62 CCGGCTCAGTTTTTAATGAATTTTGGCCCCAAGACTCCTTGACATATCTATATTCATCTAACCAA
* *
2561 ATCTCAGCAAAATTGGATTTAAGGATTTGATTTTACGGGTATCAGAATAATGTTT-GAATTTAAT
127 ATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATAATGTTTCG-ATTTAAT
* * *
2625 CAGAAATTAATTAGGAAAGATATAGGAAAATCGATACTAGAAGCGTGAAAAACCCTTTAAACTTT
191 CAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAAACTTT
* * *
2690 TTGGTGTTGAATTATATATATTCTATAAGTGTTTTGGCCAGAGATAGTGAGAAAAACTTTCGGGT
256 TTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTGTGA-AAAAACTTTCGGGT
* * * * ***
2755 CAATTTTTGCAAAATTTTAGCCGAAATTGTGTGCCATCACAGT-TTTTTTTTTGGCTAAAAACGC
320 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC-CA-TCTCGGTTTTTGGCTAAAAACGC
* * * * * *
2819 GTTTCGGGGCCCCGGCTCAGTTTGTATTAATTTTTGTCCTCGAGACTCCTTGACATATCTATATT
383 GTTCCGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATT
* * * *
2884 CATCTAGCAAAATATCAGCCAAATTGGATTTAAAGATTTGATTTTACGGGCATCAGAATCATGTT
448 CATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTT
* *
2949 TCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTAAAAAACCT
513 TCGATTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCAATATTAGAAGCGTGAAAAACCT
* * *
3014 TTCAATCTTTTTGGCGTTGAATTATTCTTTTCTATTAGTGTTTTGGCCAAAGATTATGGAAAAAT
578 TTCAATCTTTTTGGCGTTGAATTAAT-TATTCTATTAGTGTTTTGGCCAAAGATTATGGAAAAAA
* * *
3079 CTTTCGAGTCAATTTTTGCTAAATTTTAGCCGAAATAGTGTACCAACCATCACGGTTTTTTGGCC
642 CTTTCGGGTCAATTTTTGCTAAATTTTAGCCGAAATAGTGTACTAACCATCACGGTTTTTT-GCT
* * *
3144 AAAAACGTGTTCCGGGGCCTCGTCTCAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATA
706 AAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATA
3209 TCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGA
771 TCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGA
* * * *
3274 ATCATGCTTCGATTTAATTAGAAATTAATTCGGAAACATATTGGAAAATCGATATTAGAAGCTTG
836 ATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAACTTG
*
3339 AATAACCCTTCAATCTTTTTGGCATTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTG
901 AA-AACCCTTCAATCTTTTTGGCGTTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTG
3404 TGGAAAAAATCTTTCGGGTC
965 TGGAAAAAATCTTTCGGGTC
* *
3424 -AATTTTAGCCGAAATCATGTA-CGCATCACGGTTTTTTGGCTAAAAATGTGTTCTGGGGCCCCG
1 AAATTTTAGCCGAAATC-TGTACCGCATCACGGTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCG
* * *
3487 GCTCAATTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATC
65 GCTCAGTTTTTAATGAATTTTGGCCCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATC
* * * * *
3552 TCAGCCAAGTTGGATGTAAGGATTTGATTTTACGAGCATCAGAATCATGTTTCGATTTAATTAGA
130 TCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATAATGTTTCGATTTAATCAGA
* * * * * *
3617 AATTAATTCGGAAACATATTGAAAAATTGATATTAGAAGCTTGAAAAACCCTTCAATCTTTTTTG
195 AATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAAAC-TTTTTG
*
3682 GCGTTGAATTATATATATTCTATAAGCGTTTTGGCCAAAGATTGTGGAAAAAATCTTTCGGGTCA
259 GCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTGT-GAAAAAA-CTTTCGGGTCA
* * * * *
3747 ATTATTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCACGGGTTTCGGCTAAAAACGCGTTC
322 ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCTCGGTTTTTGGCTAAAAACGCGTTC
* *
3812 CGAGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGATATATCTATATTCATC
387 CGGGGCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATC
3877 TAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTTTCGA
452 TAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTTTCGA
* * *
3942 TTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCAATATTCGAATCGTGAAAAACCCTTCA
517 TTTATTCAGAAATTAATTCGGAAAGATATAGGAAAATCAATATTAGAAGCGTGAAAAACCTTTCA
* * * * *
4007 AACTTTTTGGCGTTGAATTACATATATTCTATAATTTTTTTGGCCAAAGATTGTGGAAAAAACTT
582 ATCTTTTTGGCGTTGAATTA-AT-TATTCTATTAGTGTTTTGGCCAAAGATTATGGAAAAAACTT
* *
4072 TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCA-TGTATTAACCATCACGGTTTTTTGCTAAA
645 TCGGGTCAATTTTTGCTAAATTTTAGCCGAAAT-AGTGTACTAACCATCACGGTTTTTTGCTAAA
* *
4136 AATGCGTTCCGGAGCCCCGGCTCAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCT
709 AACGCGTTCCGGGGCCCCGGCTCAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCT
* *
4201 ATATTCATCTATCCAAATCTCAGCCAAATTGGATTTAAGAATTTGATTTTACGGGCATCAGAATC
774 ATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATC
* * *
4266 ATGTTTCGATTT-ATTCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTCGAATCGTGAA
839 ATGTTTCGATTTAATT-AGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAACTTG-A
* * * *
4330 AAACCCTTCAAACTTTTTGGCGTTGAAATATATATATTCTATAAGTGTTTTGGCCAAAGAATGTG
902 AAACCCTTCAATCTTTTTGGCGTTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTG
*
4395 GAAAAAA-CTTTCAGGTC
967 GAAAAAATCTTTCGGGTC
** * * * *
4412 AAATTTT-G-TAAAAT-TTTAGCCGAAATCACGGTTTTTTTGGCTAAAAACGCGTTCTGGGACCT
1 AAATTTTAGCCGAAATCTGTA-CCG-CATCACGG-TTTTTTGGCTAAAAACGCGTTCTGGGGCCC
*
4474 CGGCTCAGTTTTTAATGAATTTTGGCCCTAAGACTCCTTGACATATCTATATTCATCTAACCAAA
63 CGGCTCAGTTTTTAATGAATTTTGGCCCCAAGACTCCTTGACATATCTATATTCATCTAACCAAA
* * * * *
4539 TTTCAGCCAAATTGGATTTATGGATTTAATTTTACGGGCATCAAAATTATGTTTCGATTTAATCA
128 TCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATAATGTTTCGATTTAATCA
4604 GAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTT
193 GAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTT
4659 AGAACCTAAG
Statistics
Matches: 1966, Mismatches: 212, Indels: 90
0.87 0.09 0.04
Matches are distributed among these distances:
979 1 0.00
980 4 0.00
981 25 0.01
982 178 0.09
983 8 0.00
985 3 0.00
987 7 0.00
988 217 0.11
989 721 0.37
990 134 0.07
991 21 0.01
993 1 0.00
994 1 0.00
995 1 0.00
999 63 0.03
1000 450 0.23
1001 58 0.03
1002 72 0.04
1003 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (984 bp):
AAATTTTAGCCGAAATCTGTACCGCATCACGGTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGG
CTCAGTTTTTAATGAATTTTGGCCCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCT
CAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATAATGTTTCGATTTAATCAGAA
ATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAAACTTTTTGGC
GTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTGTGAAAAAACTTTCGGGTCAATTT
TTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCTCGGTTTTTGGCTAAAAACGCGTTCCGGG
GCCCCGGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAAC
CAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTTTCGATTTA
TTCAGAAATTAATTCGGAAAGATATAGGAAAATCAATATTAGAAGCGTGAAAAACCTTTCAATCT
TTTTGGCGTTGAATTAATTATTCTATTAGTGTTTTGGCCAAAGATTATGGAAAAAACTTTCGGGT
CAATTTTTGCTAAATTTTAGCCGAAATAGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGT
TCCGGGGCCCCGGCTCAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCA
TCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTTTC
GATTTAATTAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAACTTGAAAACCCTTC
AATCTTTTTGGCGTTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAATC
TTTCGGGTC
Found at i:17909 original size:1 final size:1
Alignment explanation
Indices: 17905--17953 Score: 80
Period size: 1 Copynumber: 49.0 Consensus size: 1
17895 TTGCTATGTC
* *
17905 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17954 CAAACAACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17981 original size:6 final size:6
Alignment explanation
Indices: 17972--18002 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
17962 AACAACAACA
17972 ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC A
1 ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC A
18003 ACTAGAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAC
Found at i:17981 original size:12 final size:12
Alignment explanation
Indices: 17943--18002 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
17933 AAAAAAAAAA
*
17943 ACAACAAAAAAC
1 ACAACAACAAAC
17955 A-AACAAC-AAC
1 ACAACAACAAAC
17965 AACAACAACAAAC
1 -ACAACAACAAAC
17978 ACAA-ACACAAAC
1 ACAACA-ACAAAC
17990 ACAA-ACACAAAC
1 ACAACA-ACAAAC
18002 A
1 A
18003 ACTAGAACAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 3 0.07
11 7 0.16
12 30 0.70
13 3 0.07
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (12 bp):
ACAACAACAAAC
Found at i:17987 original size:18 final size:17
Alignment explanation
Indices: 17945--18002 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 17
17935 AAAAAAAAAC
*
17945 AACAAAAAACAAACA-A
1 AACACAAAACAAACACA
17961 CAACAACAACAACAAACACA
1 -AAC-ACAA-AACAAACACA
17981 AACACAAACACAAACACA
1 AACACAAA-ACAAACACA
17999 AACA
1 AACA
18003 ACTAGAACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
17 4 0.11
18 20 0.56
19 11 0.31
20 1 0.03
ACGTcount: A:0.71, C:0.29, G:0.00, T:0.00
Consensus pattern (17 bp):
AACACAAAACAAACACA
Found at i:19051 original size:28 final size:29
Alignment explanation
Indices: 18981--19088 Score: 182
Period size: 29 Copynumber: 3.8 Consensus size: 29
18971 TAGCTTACTG
18981 TCGTAGAATTTTCTTTTCTTCGCTTACCA
1 TCGTAGAATTTTCTTTTCTTCGCTTACCA
* *
19010 TCGTATAATTTTCTTTTCTTCTCTTACCA
1 TCGTAGAATTTTCTTTTCTTCGCTTACCA
19039 -CGTAGAATTTTCTTTTCTTCGCTTACCA
1 TCGTAGAATTTTCTTTTCTTCGCTTACCA
*
19067 TCGTAGAATTTTCTGTTCTTCG
1 TCGTAGAATTTTCTTTTCTTCG
19089 TTTCTAGGAG
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
28 26 0.36
29 47 0.64
ACGTcount: A:0.17, C:0.23, G:0.10, T:0.50
Consensus pattern (29 bp):
TCGTAGAATTTTCTTTTCTTCGCTTACCA
Found at i:19702 original size:9 final size:9
Alignment explanation
Indices: 19688--19716 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
19678 AAGAACCAAA
19688 AACAACAAG
1 AACAACAAG
19697 AACAACAAG
1 AACAACAAG
19706 AACAACAAG
1 AACAACAAG
19715 AA
1 AA
19717 AGCACTAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.21, G:0.10, T:0.00
Consensus pattern (9 bp):
AACAACAAG
Found at i:25973 original size:8 final size:7
Alignment explanation
Indices: 25955--25991 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
25945 GACCGGAGGG
25955 AAAAATT
1 AAAAATT
25962 AAAAATT
1 AAAAATT
*
25969 AAAAAGT
1 AAAAATT
25976 AAAAA-T
1 AAAAATT
25982 AAAAA-T
1 AAAAATT
25988 AAAA
1 AAAA
25992 CCCACCTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (7 bp):
AAAAATT
Found at i:60000 original size:17 final size:17
Alignment explanation
Indices: 59980--60030 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
59970 TGATATAGTG
59980 GTACATTATTGTAATTT
1 GTACATTATTGTAATTT
*
59997 GTAC--T-CT-TAATTT
1 GTACATTATTGTAATTT
60010 GTACATTATTGTAATTT
1 GTACATTATTGTAATTT
60027 GTAC
1 GTAC
60031 TCTTAATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 10 0.36
14 1 0.04
15 2 0.07
16 1 0.04
17 14 0.50
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (17 bp):
GTACATTATTGTAATTT
Found at i:60009 original size:13 final size:13
Alignment explanation
Indices: 59991--60039 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
59981 TACATTATTG
59991 TAATTTGTACTCT
1 TAATTTGTACTCT
*
60004 TAATTTGTACATTATT
1 TAATTTGTAC--T-CT
60020 GTAATTTGTACTCT
1 -TAATTTGTACTCT
60034 TAATTT
1 TAATTT
60040 CAGTGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 16 0.53
14 1 0.03
15 2 0.07
16 1 0.03
17 10 0.33
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.55
Consensus pattern (13 bp):
TAATTTGTACTCT
Found at i:60016 original size:30 final size:30
Alignment explanation
Indices: 59980--60039 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
59970 TGATATAGTG
59980 GTACATTATTGTAATTTGTACTCTTAATTT
1 GTACATTATTGTAATTTGTACTCTTAATTT
60010 GTACATTATTGTAATTTGTACTCTTAATTT
1 GTACATTATTGTAATTTGTACTCTTAATTT
60040 CAGTGACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (30 bp):
GTACATTATTGTAATTTGTACTCTTAATTT
Found at i:66240 original size:17 final size:17
Alignment explanation
Indices: 66214--66246 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
66204 ACACGCATGA
*
66214 ACAATCTTATTAATAAG
1 ACAATATTATTAATAAG
66231 ACAATATTATTAATAA
1 ACAATATTATTAATAA
66247 ATTGGTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (17 bp):
ACAATATTATTAATAAG
Found at i:70928 original size:2 final size:2
Alignment explanation
Indices: 70921--70955 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
70911 ACGCGTCAAG
70921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
70956 TGCCTAGACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:87039 original size:18 final size:18
Alignment explanation
Indices: 87016--87050 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
87006 ACACATTCTC
87016 AAACGATTCCTATGTAGG
1 AAACGATTCCTATGTAGG
87034 AAACGATTCCTATGTAG
1 AAACGATTCCTATGTAG
87051 CAGAGTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (18 bp):
AAACGATTCCTATGTAGG
Found at i:92414 original size:30 final size:30
Alignment explanation
Indices: 92374--92439 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
92364 GGCAGGTATC
92374 ATTT-TTTTTTCAAAAAGG-TTCATAAACAA
1 ATTTCTTTTTTCAAAAAGGATT-ATAAACAA
* *
92403 ATTTCTTTTTTCAAAGAGGATTATAAGCAA
1 ATTTCTTTTTTCAAAAAGGATTATAAACAA
92433 ATTTCTT
1 ATTTCTT
92440 GTCATAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 4 0.12
30 27 0.82
31 2 0.06
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (30 bp):
ATTTCTTTTTTCAAAAAGGATTATAAACAA
Found at i:95427 original size:36 final size:36
Alignment explanation
Indices: 95380--95449 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
95370 TTCAATAACC
* * *
95380 TTACATCTTTTGTGATTTTGGTTATTATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
* *
95416 TTACATTTTTTGTAATTTTGATTATCGTATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
95450 CCAAAATCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.20, C:0.09, G:0.10, T:0.61
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:96331 original size:25 final size:25
Alignment explanation
Indices: 96277--96323 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
96267 ACGTTTGCAC
96277 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTTGAATTAAAA
96302 AAATACCTAAGAATTT-AATTAA
1 AAATACCTAAGAATTTGAATTAA
96324 TGTAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (25 bp):
AAATACCTAAGAATTTGAATTAAAA
Found at i:96373 original size:39 final size:40
Alignment explanation
Indices: 96314--96394 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
96304 ATACCTAAGA
*
96314 ATTTAATTAATGTAAATATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
* *
96353 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
96393 AT
1 AT
96395 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
Found at i:96622 original size:2 final size:2
Alignment explanation
Indices: 96610--96640 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
96600 AGTTTAGACT
96610 TA TA TA GTA 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
96641 ATTAACAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Done.