Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold432
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: 1706767
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 187295 characters in sequence are not A, C, G, or T
File 3 of 8
Found at i:416262 original size:55 final size:55
Alignment explanation
Indices: 415995--417527 Score: 1604
Period size: 61 Copynumber: 26.4 Consensus size: 55
415985 ATAAAGTGCA
* **
415995 TCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT------GAAAGGCG
* * *
416056 TCCTGATTTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGCAAAGGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT------GAAAGGCG
* * *
416117 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTACAAAGAAGAAGCA
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-----GAA-AGGCG
* *
416178 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAGCTTCTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
416233 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
416288 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTCAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* ** *
416343 TCCTCCTCTTTGAGGACTAAAAAACTGCCACCAACTAGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
416399 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTATGAAAAGGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCT-T-----TGAAAGGCG
* *
416460 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTG--AA-AG---GCG
*
416521 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTCTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
416576 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTGGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
** *
416631 TCCTGCTCTTTGAGGACTAAAAAAGTGCCACCAACTGGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
416687 TCCTACTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT------GAAAGGCG
** *
416748 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG--AA-AG---GCG
* *
416809 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTCTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
416864 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTGGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* ** *
416919 TCCTGCTCTTTGAGGGCTAAAAAAGTGCCACCAACTGGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
416975 TCCTGCTCTTTGAGGACAGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT------GAAAGGCG
** *
417036 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG--AA-AG---GCG
*
417097 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
417152 TCATGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
417207 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTCGTGCGGGCTTTGAAAAGGAAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAA-G----GCG
* * * *
417268 TCCTACTCCTTGAGGGCTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGACG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAA-G---G-CG
** * *
417329 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTATGTGGGCTTTGCAAAAGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT------GA-AAGGCG
* * ** * *
417390 TCTTGCTCTTTGAGGACT-GAAAGTGCCACCGGCTTGTGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
417444 TCCTGCTCTTTGAGGACTAGG-AAGTGCGACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCG
417505 TCCTGCTCTTTGAGGACT-GAAAA
1 TCCTGCTCTTTGAGGACTGGAAAA
417528 GTGGAAGAAG
Statistics
Matches: 1289, Mismatches: 115, Indels: 137
0.84 0.07 0.09
Matches are distributed among these distances:
54 22 0.02
55 467 0.36
56 159 0.12
57 7 0.01
58 12 0.01
59 7 0.01
60 43 0.03
61 555 0.43
62 12 0.01
65 2 0.00
66 3 0.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:416584 original size:288 final size:288
Alignment explanation
Indices: 415995--417527 Score: 2137
Period size: 288 Copynumber: 5.3 Consensus size: 288
415985 ATAAAGTGCA
* * *
415995 TCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAGGCGTCC
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTCGTGTGGGCTTT------GAAAGGCATCC
* * ** *
416059 TGATTTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTTGCAAAGGAAAGGCGTCCTGC
59 TGCTCTTTGAGGACTAAAAAAGTGCCACCAACTGGTGTGGGCTTT------GAAAGGCGTCCTGC
* * * *
416123 TCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-ACAAA-GAAGAAGCATCCTGCT
118 TCTTTGAGGACTGGAAA-ATGCCACCAACTCGTGTGGGCTTTGA-AAAGGAA-AGGCGTCCTGCT
* * * *
416185 CTTTGAGGACTGGAAA-ATGCCACCAGCTTCTGTGGGCTTTG--AA-AG---GCGTCCTGCTCTT
180 CTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTT
416243 TGAGGACTGGAAAATGCCACCAAC-TCGTGTGGGCTTTGAAAGGCG
244 TGAGGACTGGAAAATGCCACCAACTTC-TGTGGGCTTTGAAAGGCG
* * *
416288 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTCAAAGGCGTCCTCCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCATCCTGCTCTT
* *
416353 TGAGGACTAAAAAACTGCCACCAACTAGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTG
66 TGAGGACTAAAAAAGTGCCACCAACTGGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTG
*
416418 GAAAATGCCACCAACTCGTGTGGGCTATGAAAAGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAG
131 GAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAG
416483 GTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTGAGGACTGGAAAATGC
196 GTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTGAGGACTGGAAAATGC
416548 CACCAACTTCTGTGGGCTTTGAAAGGCG
261 CACCAACTTCTGTGGGCTTTGAAAGGCG
*
416576 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTGGTGTGGGCTTTGAAAGGCATCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCATCCTGCTCTT
*
416641 TGAGGACTAAAAAAGTGCCACCAACTGGTGTGGGCTTTGAAAGGCGTCCTACTCTTTGAGGACTG
66 TGAGGACTAAAAAAGTGCCACCAACTGGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTG
* *
416706 GAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCATCCTGCTCTTTGAGGACTGGAAG
131 GAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAG
416771 GTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTGAGGACTGGAAAATGC
196 GTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTGAGGACTGGAAAATGC
*
416836 CACCAACTTCTGTGGGCTTTGAAAGGTG
261 CACCAACTTCTGTGGGCTTTGAAAGGCG
*
416864 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTGGTGTGGGCTTTGAAAGGCATCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCATCCTGCTCTT
* *
416929 TGAGGGCTAAAAAAGTGCCACCAACTGGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACAG
66 TGAGGACTAAAAAAGTGCCACCAACTGGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTG
*
416994 GAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTTTGAGGACTGGAAG
131 GAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAG
417059 GTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTGAGGACTGGAAAATGC
196 GTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTGAGGACTGGAAAATGC
* *
417124 CACCAACTTGTGTGGGCTTTGAAAGGTG
261 CACCAACTTCTGTGGGCTTTGAAAGGCG
* *
417152 TCATGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCATCCTGCTCTT
* * * * * *
417217 TGAGGACTGAAAAA-TGCCACCAACTCGTGCGGGCTTTGAAAAGGAAAAGCATCCTACTCCTTGA
66 TGAGGACTAAAAAAGTGCCACCAACTGGTGTGGGCTTTG-AAA-G----GCGTCCTGCTCTTTGA
* *
417281 GGGCTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGACGTCCTGCTCTTTGAGGAC
125 GGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTTTGAGGAC
* * * * *
417346 TG-AAGGTGCCACCAGCTTATGTGGGCTTTGCAAAAGAGAAGGCGTCTTGCTCTTTGAGGACT-G
190 TGAAAGGTGCCACCAACTTGTGTGGGCTTTGC-AAAGAGAAAGCATCCTGCTCTTTGAGGACTGG
* ** * * *
417409 AAAGTGCCACCGGCTTGTGTGGGCTTTAAAAGGCA
254 AAAATGCCACCAACTTCTGTGGGCTTTGAAAGGCG
* * *
417444 TCCTGCTCTTTGAGGACTAGG-AAGTGCGACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
1 TCCTGCTCTTTGAGGACT-GGAAAATGCCACCAACTCGTGTGGGCTTT-----G-AAAGGCATCC
*
417508 TGCTCTTTGAGGACTGAAAA
59 TGCTCTTTGAGGACTAAAAA
417528 GTGGAAGAAG
Statistics
Matches: 1152, Mismatches: 61, Indels: 49
0.91 0.05 0.04
Matches are distributed among these distances:
281 4 0.00
282 93 0.08
283 8 0.01
284 2 0.00
285 2 0.00
287 44 0.04
288 717 0.62
289 3 0.00
292 98 0.09
293 146 0.13
294 4 0.00
297 1 0.00
298 30 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (288 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCATCCTGCTCTT
TGAGGACTAAAAAAGTGCCACCAACTGGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTG
GAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAG
GTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTGAGGACTGGAAAATGC
CACCAACTTCTGTGGGCTTTGAAAGGCG
Found at i:418503 original size:1 final size:1
Alignment explanation
Indices: 418497--418572 Score: 71
Period size: 1 Copynumber: 76.0 Consensus size: 1
418487 TAGATTCTTC
** * * * * * * *
418497 TTTTTTTTTTCCTTTTTTTTGTTTTTGTTTTTTTTGTTTTTTTTTTGTTTTTTGTTTTTTTGTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
418562 TTTTTTTTTTT
1 TTTTTTTTTTT
418573 GAAAAAAGAA
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:418527 original size:26 final size:27
Alignment explanation
Indices: 418497--418571 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
418487 TAGATTCTTC
*
418497 TTTTTTTTTTCCTTTTTTTTG-TTTTTG
1 TTTTTTTTGT-CTTTTTTTTGTTTTTTG
*
418524 TTTTTTTTGTTTTTTTTTTGTTTTTTG
1 TTTTTTTTGTCTTTTTTTTGTTTTTTG
*
418551 TTTTTTTGTTGTTTTTTTTTT
1 -TTTTTT-TTGTCTTTTTTTT
418572 TGAAAAAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.21
27 15 0.35
28 6 0.14
29 13 0.30
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (27 bp):
TTTTTTTTGTCTTTTTTTTGTTTTTTG
Found at i:418527 original size:27 final size:27
Alignment explanation
Indices: 418509--418571 Score: 101
Period size: 29 Copynumber: 2.3 Consensus size: 27
418499 TTTTTTTTCC
418509 TTTTTTTTG-TTTTTGTTTTTTTTGTT
1 TTTTTTTTGTTTTTTGTTTTTTTTGTT
418535 TTTTTTTTGTTTTTTGTTTTTTTGTTGTT
1 TTTTTTTTGTTTTTTG-TTTTTT-TTGTT
418564 TTTTTTTT
1 TTTTTTTT
418572 TGAAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 9 0.26
27 6 0.18
28 6 0.18
29 13 0.38
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (27 bp):
TTTTTTTTGTTTTTTGTTTTTTTTGTT
Found at i:418572 original size:15 final size:15
Alignment explanation
Indices: 418509--418573 Score: 84
Period size: 15 Copynumber: 4.5 Consensus size: 15
418499 TTTTTTTTCC
418509 TTTTTT-TTGTTTTT
1 TTTTTTGTTGTTTTT
418523 GTTTTTT-TTG-TTTT
1 -TTTTTTGTTGTTTTT
418537 TTTTTTGTT-TTTTGT
1 TTTTTTGTTGTTTT-T
418552 TTTTTTGTTGTTTTT
1 TTTTTTGTTGTTTTT
418567 TTTTTTG
1 TTTTTTG
418574 AAAAAAGAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.13
14 9 0.20
15 27 0.59
16 4 0.09
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (15 bp):
TTTTTTGTTGTTTTT
Found at i:430980 original size:52 final size:51
Alignment explanation
Indices: 430924--431022 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
430914 ATACTTCTCG
* * * *
430924 ATGAGAAATTTAATATTTTGGAGATAATA-ACGGGGTTGGAGTATCCCCAATT
1 ATGAGAAA-TCAATATTTTGAAAATAA-AGACGAGGTTGGAGTATCCCCAATT
*
430976 ATGAGAAATCAATATTTTGAAAATAAAGCCGAGGTTGGAGTATCCCC
1 ATGAGAAATCAATATTTTGAAAATAAAGACGAGGTTGGAGTATCCCC
431023 TCGGAGGTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 1 0.02
51 32 0.78
52 8 0.20
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (51 bp):
ATGAGAAATCAATATTTTGAAAATAAAGACGAGGTTGGAGTATCCCCAATT
Found at i:431127 original size:52 final size:52
Alignment explanation
Indices: 431065--431408 Score: 220
Period size: 52 Copynumber: 6.6 Consensus size: 52
431055 AAATAACGAG
* * * *
431065 GTTGGGGTATCCTCGATTCTGAAAAATTGGTGTTTTTGGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
* * * * *
431117 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTG-TTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
* *** * * * *
431169 GTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTTGGGAATAAAACCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
* ** * ***
431220 GTTGGAGTATCCCCTCGGACGTAATG--AGGTTGGAGTATCCCCGATGAAAT--AA-C-GA
1 GTTGGAGTAT-CCC-C-GA--TTATGAAAAATTGGTGT-T-TTTG--GAAATAAAATCGGA
* * *
431275 GGTTAGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
1 -GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
* * * *
431328 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTG-TTTTGAAAATAAAATCGGG
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
* *
431380 GTTGGATTATCCCCGATTATGAACAATTG
1 GTTGGAGTATCCCCGATTATGAAAAATTG
431409 AGAAACTTAA
Statistics
Matches: 221, Mismatches: 51, Indels: 41
0.71 0.16 0.13
Matches are distributed among these distances:
49 5 0.02
51 48 0.22
52 104 0.47
53 34 0.15
54 5 0.02
55 3 0.01
56 15 0.07
57 3 0.01
59 4 0.02
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
Found at i:431318 original size:211 final size:211
Alignment explanation
Indices: 430954--431401 Score: 754
Period size: 211 Copynumber: 2.1 Consensus size: 211
430944 GAGATAATAA
* *
430954 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGAAAATAAAGCCGAGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGAAAATAAAACCGAGGTTGGAGTAT
* * * *
431019 CCCCTCGGAGGTAACGGAGTTGGAGTATCCTCGATGAAATAACGAGGTTGGGGTATCCTCGATTC
66 CCCCTCGGACGTAACGGAGTTGGAGTATCCCCGATGAAATAACGAGGTTAGAGTATCCTCGATTC
431084 TGAAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
131 TGAAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
431149 GTTTTGAAAATAAAAC
196 GTTTTGAAAATAAAAC
** *
431165 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGGAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGAAAATAAAACCGAGGTTGGAGTAT
*
431230 CCCCTCGGACGTAA-TGAGGTTGGAGTATCCCCGATGAAATAACGAGGTTAGAGTATCCTCGATT
66 CCCCTCGGACGTAACGGA-GTTGGAGTATCCCCGATGAAATAACGAGGTTAGAGTATCCTCGATT
* *
431294 GTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGG
130 CTGAAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGG
*
431359 TGTTTTGAAAATAAAAT
195 TGTTTTGAAAATAAAAC
*
431376 CGGGGTTGGATTATCCCCGATTATGA
1 CGGGGTTGGAGTATCCCCGATTATGA
431402 ACAATTGAGA
Statistics
Matches: 222, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
210 2 0.01
211 220 0.99
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.28
Consensus pattern (211 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGAAAATAAAACCGAGGTTGGAGTAT
CCCCTCGGACGTAACGGAGTTGGAGTATCCCCGATGAAATAACGAGGTTAGAGTATCCTCGATTC
TGAAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
GTTTTGAAAATAAAAC
Found at i:431835 original size:13 final size:13
Alignment explanation
Indices: 431817--431873 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
431807 TTCAATGATT
431817 TGTATCGATACAA
1 TGTATCGATACAA
431830 TGTATCGATACATAA
1 TGTATCGATAC--AA
431845 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
431862 TGTATCGATACA
1 TGTATCGATACA
431874 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:431854 original size:19 final size:18
Alignment explanation
Indices: 431830--431892 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
431820 ATCGATACAA
431830 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
431849 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
431862 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
431881 TGTATCGATACA
1 TGTATCGATACA
431893 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:431857 original size:32 final size:32
Alignment explanation
Indices: 431816--431900 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
431806 TTTCAATGAT
431816 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
431848 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
431880 TTGTATCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
431901 CTACTACCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:431954 original size:13 final size:13
Alignment explanation
Indices: 431936--431960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
431926 ATTACTCAAA
431936 TGTATCGATACAT
1 TGTATCGATACAT
431949 TGTATCGATACA
1 TGTATCGATACA
431961 CTATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:431975 original size:33 final size:34
Alignment explanation
Indices: 431915--431981 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
431905 TACCAAAAAA
* *
431915 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCGATACACTACTAAAATGTATCGATACAT
431949 TGTATCGATACACTA-TAAAATGTATCGATACAT
1 TGTATCGATACACTACTAAAATGTATCGATACAT
431982 GCAGGCAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (34 bp):
TGTATCGATACACTACTAAAATGTATCGATACAT
Found at i:437380 original size:21 final size:21
Alignment explanation
Indices: 437354--437394 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
437344 ACAAAGATCG
437354 ATGTATCGATACATTTCCTTA
1 ATGTATCGATACATTTCCTTA
437375 ATGTATCGATACATTTCCTT
1 ATGTATCGATACATTTCCTT
437395 GGCAGTAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATTTCCTTA
Found at i:437460 original size:32 final size:32
Alignment explanation
Indices: 437419--437479 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
437409 GCCGATACAT
* *
437419 TGTATCGATACCAA-ATTTATGTATTGATATAA
1 TGTATCGATA-CAACAATTATGTATCGATATAA
437451 TGTATCGATACAACAATTATGTATCGATA
1 TGTATCGATACAACAATTATGTATCGATA
437480 CATTTACGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 3 0.12
32 23 0.88
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (32 bp):
TGTATCGATACAACAATTATGTATCGATATAA
Found at i:439307 original size:31 final size:30
Alignment explanation
Indices: 439261--439428 Score: 196
Period size: 31 Copynumber: 5.5 Consensus size: 30
439251 CTTCAAATAC
* *
439261 CTTCTTAAAGTCCACGACTCAATGGCAATCT
1 CTTCTCAAAGTCCACGACTCAGTGGC-ATCT
*
439292 CTTCTCAAAGCCCACGACTCAGTGGCAT-T
1 CTTCTCAAAGTCCACGACTCAGTGGCATCT
* *
439321 TTGTCCCAAAGTCCACGACTCAGTGGCATCT
1 CT-TCTCAAAGTCCACGACTCAGTGGCATCT
* * *
439352 ATTCTTCAATGTCCACGACTCAGTGGCATTT
1 CTTC-TCAAAGTCCACGACTCAGTGGCATCT
*
439383 TTTCTTCAAAGTCCACGACTCAGTGGCATCT
1 CTTC-TCAAAGTCCACGACTCAGTGGCATCT
439414 CTT-TCCAAAGTCCAC
1 CTTCT-CAAAGTCCAC
439429 AATTCCGTGA
Statistics
Matches: 119, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
29 3 0.03
30 38 0.32
31 78 0.66
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.29
Consensus pattern (30 bp):
CTTCTCAAAGTCCACGACTCAGTGGCATCT
Found at i:439427 original size:61 final size:61
Alignment explanation
Indices: 439262--439428 Score: 223
Period size: 61 Copynumber: 2.7 Consensus size: 61
439252 TTCAAATACC
* *
439262 TTCTT-AAAGTCCACGACTCAATGGCAATCTC-TTCTCAAAGCCCACGACTCAGTGGCATTTT
1 TTCTTCAAAGTCCACGACTCAGTGGC-ATCTCTTTC-CAAAGTCCACGACTCAGTGGCATTTT
* * * * *
439323 GTC-CCAAAGTCCACGACTCAGTGGCATCTATTCTTCAATGTCCACGACTCAGTGGCATTTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTCTT-TCCAAAGTCCACGACTCAGTGGCATTTT
439384 TTCTTCAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCAC
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCAC
439429 AATTCCGTGA
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
60 4 0.04
61 58 0.64
62 28 0.31
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.29
Consensus pattern (61 bp):
TTCTTCAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCATTTT
Found at i:439427 original size:92 final size:91
Alignment explanation
Indices: 439262--439428 Score: 232
Period size: 92 Copynumber: 1.8 Consensus size: 91
439252 TTCAAATACC
439262 TTCTTAAAGTCCACGACTCAATGGCAATCTCTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCC
1 TTCTTAAAGTCCACGACTCAATGGCAATCTCTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCC
439327 CAAAGTCCACGACTCAGTGGCATCTA
66 CAAAGTCCACGACTCAGTGGCATCTA
* * * * *
439353 TTCTTCAATGTCCACGACTCAGTGGC-ATTTTTTCTTCAAAGTCCACGACTCAGTGGCATCTCTT
1 TTCTT-AAAGTCCACGACTCAATGGCAATCTCTTC-TCAAAGCCCACGACTCAGTGGCAT-T-TT
439417 -T-CCAAAGTCCAC
62 GTCCCAAAGTCCAC
439429 AATTCCGTGA
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
91 11 0.16
92 52 0.78
93 2 0.03
94 2 0.03
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.29
Consensus pattern (91 bp):
TTCTTAAAGTCCACGACTCAATGGCAATCTCTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCC
CAAAGTCCACGACTCAGTGGCATCTA
Found at i:439457 original size:34 final size:34
Alignment explanation
Indices: 439413--439569 Score: 147
Period size: 34 Copynumber: 4.5 Consensus size: 34
439403 CAGTGGCATC
* * *
439413 TCTTTCCAAAGTCCACAATTCCGTGACACCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGACACCTTTT
*
439447 TCTTTTCAAAGCCCACCACTCCGTGACACCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGACACCTTTT
* * *
439481 TCTTTTTAAAGCCCACAACTCAGTGGCACTCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGACAC-CTTTT
* * * *
439516 TCCCTTTT--AAGTCCACAACTTCGTGGCAACTTTCT
1 T--CTTTTCAAAGCCCACAACTCCGTGACACCTTT-T
*
439551 CCTTTTCAAAAGCCCACAA
1 TCTTTTC-AAAGCCCACAA
439570 GTCAGTGGCA
Statistics
Matches: 102, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
33 5 0.05
34 59 0.58
35 24 0.24
36 9 0.09
37 5 0.05
ACGTcount: A:0.24, C:0.33, G:0.10, T:0.34
Consensus pattern (34 bp):
TCTTTTCAAAGCCCACAACTCCGTGACACCTTTT
Found at i:439532 original size:35 final size:34
Alignment explanation
Indices: 439329--439579 Score: 111
Period size: 34 Copynumber: 7.6 Consensus size: 34
439319 TTTTGTCCCA
* * *
439329 AAGTCCACGACTCAGTGGCA-TC-TATT-C-TTC
1 AAGTCCACAACTCAGTGGCACTCTTTTTCCTTTT
* **
439359 AATGTCCACGACTCAGTGGCA-T-TTTTT-CTTCA
1 AA-GTCCACAACTCAGTGGCACTCTTTTTCCTTTT
* * *
439391 AAGTCCACGACTCAGTGGCA-TCTCTTTCC---A
1 AAGTCCACAACTCAGTGGCACTCTTTTTCCTTTT
* * *
439421 AAGTCCACAATTCCGTGACAC-CTTTTT-CTTTT
1 AAGTCCACAACTCAGTGGCACTCTTTTTCCTTTT
* * * * *
439453 CAAAGCCCACCACTCCGTGACAC-CTTTTTCTTTTT
1 --AAGTCCACAACTCAGTGGCACTCTTTTTCCTTTT
*
439488 AAAGCCCACAACTCAGTGGCACTCTTTTTCCCTTTT
1 -AAGTCCACAACTCAGTGGCACTCTTTTT-CCTTTT
* *
439524 AAGTCCACAACTTC-GTGGCA-ACTTTCTCCTTTT
1 AAGTCCACAAC-TCAGTGGCACTCTTTTTCCTTTT
* *
439557 CAAAAGCCCACAAGTCAGTGGCA
1 ---AAGTCCACAACTCAGTGGCA
439580 ACCTTCAAAA
Statistics
Matches: 179, Mismatches: 23, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
29 1 0.01
30 24 0.13
31 42 0.23
32 7 0.04
33 7 0.04
34 48 0.27
35 28 0.16
36 22 0.12
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.32
Consensus pattern (34 bp):
AAGTCCACAACTCAGTGGCACTCTTTTTCCTTTT
Found at i:439578 original size:36 final size:35
Alignment explanation
Indices: 439448--439581 Score: 105
Period size: 35 Copynumber: 3.8 Consensus size: 35
439438 ACACCTTTTT
* * * * *
439448 CTTTTCAAAGCCCACCACTCCGTGACACCTTT-TTC
1 CTTTT-AAAGCCCACAACTCAGTGGCAACTTTCTCC
* * *
439483 TTTTTAAAGCCCACAACTCAGTGGCACTCTTTTTCC
1 CTTTTAAAGCCCACAACTCAGTGGCA-ACTTTCTCC
*
439519 CTTTT-AAGTCCACAACTTC-GTGGCAACTTTCT-C
1 CTTTTAAAGCCCACAAC-TCAGTGGCAACTTTCTCC
*
439552 CTTTTCAAAAGCCCACAAGTCAGTGGCAAC
1 CTTTT--AAAGCCCACAACTCAGTGGCAAC
439582 CTTCAAAAGC
Statistics
Matches: 80, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
33 6 0.08
34 23 0.29
35 26 0.32
36 25 0.31
ACGTcount: A:0.24, C:0.33, G:0.12, T:0.31
Consensus pattern (35 bp):
CTTTTAAAGCCCACAACTCAGTGGCAACTTTCTCC
Found at i:439792 original size:92 final size:92
Alignment explanation
Indices: 439616--440260 Score: 1020
Period size: 92 Copynumber: 7.0 Consensus size: 92
439606 GGCATCTTCT
* * * *
439616 TTTAAGTCCAATATTGCTGGCCTTGAATCAACATATTGGCGCCTTTTTCATCTTTAAGACCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--TTT-GTCTTTAAGACCAATG
439681 TCGCTGGCCTTGAATCAGCACATTGGCACC
63 TCGCTGGCCTTGAATCAGCACATTGGCACC
* *
439711 TTTAAGCCCACTATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
*
439776 CTGGCCTTGAATCAGCACATTAGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* *
439803 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGAACCTTTGTCTTTAAGACCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
439868 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
*
439895 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTTGTCTTTAAGACCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
439960 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* ** * *
439987 TTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGTGCCTTTGTCTTTAAGGCCAATGTCA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
* * *
440052 CTGGCCTTCAATCAGCACATTAGCACT
66 CTGGCCTTGAATCAGCACATTGGCACC
* * *
440079 TTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTGTCTTTAAGTCTAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
440144 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * * *
440171 TTTAAGTCCATTATCGCTGGCCTTGAATTAGCATATTGGCACCTTTGTCTTTAAGCCCGATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
**
440236 CTGGCCTTGCCTCAGCACATTGGCA
66 CTGGCCTTGAATCAGCACATTGGCA
440261 TTTTTCTTCA
Statistics
Matches: 510, Mismatches: 40, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
92 469 0.92
93 3 0.01
95 38 0.07
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (92 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
CTGGCCTTGAATCAGCACATTGGCACC
Found at i:441044 original size:13 final size:13
Alignment explanation
Indices: 441026--441115 Score: 63
Period size: 13 Copynumber: 6.0 Consensus size: 13
441016 TTCAACGATT
441026 TGTATCGATACAA
1 TGTATCGATACAA
441039 TGTATCGATACATAA
1 TGTATCGATAC--AA
441054 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
441071 TGTATCGATACATAA
1 TGTATCGATAC--AA
441086 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
441103 TGTATCGCTACAA
1 TGTATCGATACAA
441116 AGCTACTGCC
Statistics
Matches: 64, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:441063 original size:19 final size:18
Alignment explanation
Indices: 441039--441101 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
441029 ATCGATACAA
441039 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
441058 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
441071 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
441090 TGTATCGATACA
1 TGTATCGATACA
441102 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:441066 original size:32 final size:32
Alignment explanation
Indices: 441025--441114 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
441015 TTTCAACGAT
441025 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
441057 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
441089 TTGTATCGATACAATGTATCGCTACA
1 TTGTATCGATACAATGTATCGATACA
441115 AAGCTACTGC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:441209 original size:52 final size:52
Alignment explanation
Indices: 441166--441294 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
441156 CACTGATCTT
*
441166 TGTATCAATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATGAAA
** * *
441218 TGTATCGATACATATAGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATGAAA
441270 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
441295 TCATATGTCT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATGAAA
Found at i:451339 original size:34 final size:34
Alignment explanation
Indices: 451296--451366 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
451286 GAAATCCCAA
451296 AGTAAGCTTAATAAAAGGCATGCCAAATGGCTAG
1 AGTAAGCTTAATAAAAGGCATGCCAAATGGCTAG
*
451330 AGTAAGCTTAATAAAAGGCATGCCAAATGGTTAG
1 AGTAAGCTTAATAAAAGGCATGCCAAATGGCTAG
451364 AGT
1 AGT
451367 TTATTGAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.23
Consensus pattern (34 bp):
AGTAAGCTTAATAAAAGGCATGCCAAATGGCTAG
Found at i:453136 original size:52 final size:53
Alignment explanation
Indices: 453069--453176 Score: 173
Period size: 52 Copynumber: 2.1 Consensus size: 53
453059 GAGGTTGAGT
453069 CCAAACACGACACCTACGTCCTCTCTCCTCGACACTT-CCTTATTGAGTATTA
1 CCAAACACGACACCTACGTCCTCTCTCCTCGACACTTGCCTTATTGAGTATTA
** * *
453121 CCAAACACGGTACCTATGTCCTCTCTCCTCGGCACTTGCCTTATTGAGTATTA
1 CCAAACACGACACCTACGTCCTCTCTCCTCGACACTTGCCTTATTGAGTATTA
453174 CCA
1 CCA
453177 CAATCCACTA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
52 33 0.65
53 18 0.35
ACGTcount: A:0.23, C:0.35, G:0.12, T:0.30
Consensus pattern (53 bp):
CCAAACACGACACCTACGTCCTCTCTCCTCGACACTTGCCTTATTGAGTATTA
Found at i:453804 original size:20 final size:20
Alignment explanation
Indices: 453774--453828 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
453764 CTTTTAGTTT
*
453774 CATGTATCGATACAAATGAG
1 CATGCATCGATACAAATGAG
*
453794 TATGCATCGATAC-AATGAG
1 CATGCATCGATACAAATGAG
*
453813 CATGTATCGATACAAA
1 CATGCATCGATACAAA
453829 GCATAATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (20 bp):
CATGCATCGATACAAATGAG
Found at i:453839 original size:20 final size:18
Alignment explanation
Indices: 453775--453843 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 18
453765 TTTTAGTTTC
453775 ATGTATCGATACAAATGAGT
1 ATGTATCGATACAAA-GA-T
* * *
453795 ATGCATCGATACAATGAGC
1 ATGTATCGATACAAAGA-T
453814 ATGTATCGATACAAAGCAT
1 ATGTATCGATACAAAG-AT
453833 AATGTATCGAT
1 -ATGTATCGAT
453844 CATCTAGATG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 17 0.41
20 24 0.59
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (18 bp):
ATGTATCGATACAAAGAT
Found at i:454620 original size:41 final size:41
Alignment explanation
Indices: 454560--454668 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
454550 TCTTTTTATA
**
454560 AAAATTT-TTTTCAGTAATTTCTCCCCCTTTGTCAAATGCC
1 AAAATTTATTTTCAAAAATTTCTCCCCCTTTGTCAAATGCC
454600 AAAATTTATTTTCAAAAATTTCTCCCCCTTTGTCAAATGCC
1 AAAATTTATTTTCAAAAATTTCTCCCCCTTTGTCAAATGCC
* *
454641 AAACTTTATTTTCAAAAATTTCTTCCCC
1 AAAATTTATTTTCAAAAATTTCTCCCCC
454669 ATTTTGTTGT
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
40 7 0.11
41 57 0.89
ACGTcount: A:0.29, C:0.25, G:0.05, T:0.41
Consensus pattern (41 bp):
AAAATTTATTTTCAAAAATTTCTCCCCCTTTGTCAAATGCC
Found at i:456192 original size:21 final size:21
Alignment explanation
Indices: 456149--456192 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
456139 AAGATGAGTG
* *
456149 GAAAGGAACCTAAATCTCTAA
1 GAAAGGAACCTAAAACGCTAA
456170 GAAAGGCAACCTAAAACGC-AA
1 GAAAGG-AACCTAAAACGCTAA
456191 GA
1 GA
456193 TTTGAAGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.50, C:0.20, G:0.18, T:0.11
Consensus pattern (21 bp):
GAAAGGAACCTAAAACGCTAA
Found at i:460709 original size:217 final size:217
Alignment explanation
Indices: 460326--460754 Score: 752
Period size: 217 Copynumber: 2.0 Consensus size: 217
460316 TTTTCATTAG
460326 TTAGGATTTTATTAATATCTTGCATTTCATTTAATTGATTTTCTAATTTGACCAATTTCACTTTA
1 TTAGGATTTTATTAATATCTTGCATTTCATTTAATTGATTTTCTAATTTGACCAATTTCACTTTA
*
460391 AGCTTATCATTCTCTAAACTTACGGATTTATTTTCATCATTTAGTTTAGAGAGAGCTTCCTTTTC
66 AGCTCATCATTCTCTAAACTTACGGATTTATTTTCATCATTTAGTTTAGAGAGAGCTTCCTTTTC
* * *
460456 TAATTCGACAATTTTCTTTTCAAGAGTTTTATTCTCAATAAATTTTGATTTATTTTCTTCTTTCA
131 TAATTCGACAATTTTCTTTTCAAGAATTTCATTCTCAATAAATTTTGATTTATTTTCTTCCTTCA
460521 ATTTTAAAATTGTCTTTAATTT
196 ATTTTAAAATTGTCTTTAATTT
*
460543 TTAGGATTTTATTAATATCTTGCATTTCATTTAATTGATTTTCTAATTTGACCAATTTCATTTTA
1 TTAGGATTTTATTAATATCTTGCATTTCATTTAATTGATTTTCTAATTTGACCAATTTCACTTTA
* * *
460608 AGCTCATTATTCTCTAAACTTACGGATTTATTTTCATTATTTAGTTTAGAGAGAGTTTCCTTTTC
66 AGCTCATCATTCTCTAAACTTACGGATTTATTTTCATCATTTAGTTTAGAGAGAGCTTCCTTTTC
* *
460673 TAGTTTTG-CAATTTTCTTTTCAAGAATTTCATTCTCAATAAATTTTGATTTATTTTCTTCCTTC
131 TA-ATTCGACAATTTTCTTTTCAAGAATTTCATTCTCAATAAATTTTGATTTATTTTCTTCCTTC
460737 AATTTTAAAATTGTCTTT
195 AATTTTAAAATTGTCTTT
460755 TTATGCCTTA
Statistics
Matches: 201, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
217 198 0.99
218 3 0.01
ACGTcount: A:0.26, C:0.14, G:0.08, T:0.52
Consensus pattern (217 bp):
TTAGGATTTTATTAATATCTTGCATTTCATTTAATTGATTTTCTAATTTGACCAATTTCACTTTA
AGCTCATCATTCTCTAAACTTACGGATTTATTTTCATCATTTAGTTTAGAGAGAGCTTCCTTTTC
TAATTCGACAATTTTCTTTTCAAGAATTTCATTCTCAATAAATTTTGATTTATTTTCTTCCTTCA
ATTTTAAAATTGTCTTTAATTT
Found at i:461152 original size:3 final size:3
Alignment explanation
Indices: 461144--461175 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
461134 CGAGTCAACT
*
461144 TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
461176 TTTGATGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:463939 original size:37 final size:36
Alignment explanation
Indices: 463837--463959 Score: 138
Period size: 37 Copynumber: 3.3 Consensus size: 36
463827 CTGTCGATGT
* *
463837 TGGTTTTTTTTATCGTGGACTGGAGGCTGCTAGAAGC
1 TGGTTTTTTTTATCGTGGA-TGGAGGCTGTTGGAAGC
* *
463874 TGGGTTTTCTTTTATCGTGGACGAGAGGCCGTTGGAAGC
1 T-GGTTTT-TTTTATCGTGGATG-GAGGCTGTTGGAAGC
* * *
463913 TAGTTTTTTTTATTGTGGATTGGAGGCTATTGGAAGC
1 TGGTTTTTTTTATCGTGGA-TGGAGGCTGTTGGAAGC
463950 TGGTTTTTTT
1 TGGTTTTTTT
463960 CCTTTGAGTT
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
37 34 0.47
38 13 0.18
39 25 0.35
ACGTcount: A:0.15, C:0.11, G:0.32, T:0.42
Consensus pattern (36 bp):
TGGTTTTTTTTATCGTGGATGGAGGCTGTTGGAAGC
Found at i:464831 original size:17 final size:17
Alignment explanation
Indices: 464805--464839 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
464795 CTACGTGTTC
*
464805 TTTCACATTTTTTTATT
1 TTTCAAATTTTTTTATT
464822 TTTCAAATTTTTTTATT
1 TTTCAAATTTTTTTATT
464839 T
1 T
464840 ATTTGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCAAATTTTTTTATT
Found at i:464848 original size:26 final size:25
Alignment explanation
Indices: 464811--464870 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
464801 GTTCTTTCAC
*
464811 ATTTTTTTATTTTTCAAATTTTTTT
1 ATTTTTTGATTTTTCAAATTTTTTT
**
464836 ATTTATTTGATTTTTGGAATTTTTTT
1 ATTT-TTTGATTTTTCAAATTTTTTT
464862 GAATTTTTT
1 --ATTTTTT
464871 AAGTTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 4 0.14
26 18 0.62
27 3 0.10
28 4 0.14
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.72
Consensus pattern (25 bp):
ATTTTTTGATTTTTCAAATTTTTTT
Found at i:465432 original size:42 final size:41
Alignment explanation
Indices: 465373--466403 Score: 400
Period size: 42 Copynumber: 24.5 Consensus size: 41
465363 AAGATTTTCT
* *
465373 TGGGTCAAAGCTGACAGGCAGACTTTAGATAAGGTAGTCTCC
1 TGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCT-C
* * * *
465415 TGGGTTAAAGCTGACAGGCAGAC-TAAGGGAT-AGGAAAGTCTCC
1 TGGGTCAAAGCCGACAGGCAGACTTTA--GATAAGG-CAGTCT-C
* * * * *
465458 AGGGTCAAAGACAACAGGCAGACTTTAGATGAGGTAGTCTC
1 TGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTC
* * *
465499 TGGGGTCAAAGCCGATAGGCAGAC-TAAGGGAT-AGGAAAGTCTC
1 T-GGGTCAAAGCCGACAGGCAGACTTTA--GATAAGG-CAGTCTC
** * * *
465542 TAGGGTCAAAGCTAACTA-GTAGACTTTAGATGAGGCAGTCGC
1 T-GGGTCAAAGCCGAC-AGGCAGACTTTAGATAAGGCAGTCTC
** * * ** * **
465584 TAGGGAAAAAGCCGACTGACAGACTAAAGGT-AGAAAAGTCTC
1 T-GGGTCAAAGCCGACAGGCAGACTTTAGATAAG-GCAGTCTC
** * * *
465626 TAGGGTCAAAGTTGATAGGCAGACTTTAGAGGAA-ACAGTCTCC
1 T-GGGTCAAAGCCGACAGGCAGACTTTAGA-TAAGGCAGTCT-C
* *
465669 GGGGTCAAAGCCAACAGGC-GAACTTTAGATGAA-GCAGTCTCC
1 TGGGTCAAAGCCGACAGGCAG-ACTTTAGAT-AAGGCAGTCT-C
** * *
465711 AAGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCTC
1 TGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTC
* * * * *
465752 TAGGGTCAAAGCCAACAAGCAAACTTTAGATGAA-GCAATGTC
1 T-GGGTCAAAGCCGACAGGCAGACTTTAGAT-AAGGCAGTCTC
** *
465794 TAGGGTCAAAGCCGACAGGCAGACTTTAGATGTGGCAGCCTC
1 T-GGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTC
* *
465836 TAGGGTCAAAGCCGACAGGCAGAC-TGAGGGAT-AGGAAAGTCTTC
1 T-GGGTCAAAGCCGACAGGCAGACTTTA--GATAAGG-CAGTC-TC
** * * *
465880 AAGGTCAAAGCCAACAGGCGGACTTTAGATGAGGCAGTCTCC
1 TGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCT-C
* * * * *** **
465922 AGGATCAAAGCTGATAGGCAGACTAGGGGATAAGAAAGTCTC
1 TGGGTCAAAGCCGACAGGCAGACT-TTAGATAAGGCAGTCTC
*
465964 TAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTCC
1 T-GGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCT-C
** * * * *
466007 AAGGTCAAAGCCGACAAGCAAAC-TAAGGGTAA---AGTCTC
1 TGGGTCAAAGCCGACAGGCAGACTTTA-GATAAGGCAGTCTC
* * * *
466045 TAGGGTCAAAGCCAACAGGTAGATTTTAGATGAGGCAGTCTC
1 T-GGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTC
** * * * *
466087 TAGGGTCAAAGCTAACAGGCAGAC-TAAGGGAT-TGGAAAGTCTT
1 T-GGGTCAAAGCCGACAGGCAGACTTTA--GATAAGG-CAGTCTC
* ** * **
466130 TAGGGTCAAACCCGACAGGCAGACTAAAGGT-AGAAAAGTCTCC
1 T-GGGTCAAAGCCGACAGGCAGACTTTAGATAAG-GCAGTCT-C
** * * *
466173 AAGGTCAAAGTCGACAGGCAGACTTTAAATGAGGCAGTCTCC
1 TGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCT-C
* * * * *
466215 AGGGTC-AAGCCGATAGAG-AGA-TTGAGGGAT-AGGAAATTCTCC
1 TGGGTCAAAGCCGACAG-GCAGACTTTA--GATAAGG-CAGTCT-C
*** *
466257 AAAGTCAAAGCCGATAGGCAGACTTTAGATAAGGCAGTCTCC
1 TGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCT-C
** * * ***
466299 AAGGTGAAAGCCGATAGGCAGAC-TTAGGGATAAAAAAGTCTC
1 TGGGTCAAAGCCGACAGGCAGACTTTA--GATAAGGCAGTCTC
** * * * *
466341 TAGGGTCAAAGTTGATAGGTAGACTTTAGATAAAGCAGTTTCC
1 T-GGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCT-C
* *
466384 AGGGTCAAAGCCGAAAGGCA
1 TGGGTCAAAGCCGACAGGCA
466404 AACTGAAGTA
Statistics
Matches: 748, Mismatches: 181, Indels: 120
0.71 0.17 0.11
Matches are distributed among these distances:
38 1 0.00
39 24 0.03
40 5 0.01
41 34 0.05
42 470 0.63
43 196 0.26
44 18 0.02
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (41 bp):
TGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTC
Found at i:465519 original size:85 final size:85
Alignment explanation
Indices: 465374--466154 Score: 766
Period size: 85 Copynumber: 9.3 Consensus size: 85
465364 AGATTTTCTT
* * * * *
465374 GGGTCAAAGCTGACAGGCAGACTTTAGATAAGGTAGTCTCCT-GGGTTAAAGCTGACAGGCAGAC
1 GGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCT-CTAGGGTCAAAGCCGACAGGCAGAC
*
465438 TAAGGGATAGGAAAGTCTCCA
65 TAAGGGATAGGAAAGTCTCTA
* * * * *
465459 GGGTCAAAGACAACAGGCAGACTTTAGATGAGGTAGTCTCTGGGGTCAAAGCCGATAGGCAGACT
1 GGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
465524 AAGGGATAGGAAAGTCTCTA
66 AAGGGATAGGAAAGTCTCTA
** * * ** * *
465544 GGGTCAAAGCTAACTA-GTAGACTTTAGATGAGGCAGTCGCTAGGGAAAAAGCCGACTGACAGAC
1 GGGTCAAAGCCGAC-AGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAGAC
* *
465608 TAAAGG-TAGAAAAGTCTCTA
65 TAAGGGATAGGAAAGTCTCTA
** * * ** ** *
465628 GGGTCAAAGTTGATAGGCAGACTTTAGAGGAAACAGTCTCCGGGGTCAAAGCCAACAGGC-GAAC
1 GGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAG-AC
* *
465692 TTTA--GAT--GAAGCAGTCTCCA
65 -TAAGGGATAGGAA--AGTCTCTA
* * * * *
465712 AGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCAACAAGCAAACT
1 GGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAGAC-
* * * *
465777 TTA--GATGAAGCAA-TGTCTA
65 TAAGGGAT-AGGAAAGTCTCTA
* *
465796 GGGTCAAAGCCGACAGGCAGACTTTAGATGTGGCAGCCTCTAGGGTCAAAGCCGACAGGCAGACT
1 GGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
*
465861 GAGGGATAGGAAAGTCT-TCA
66 AAGGGATAGGAAAGTCTCT-A
* * * * * * *
465881 AGGTCAAAGCCAACAGGCGGACTTTAGATGAGGCAGTCTCCAGGATCAAAGCTGATAGGCAGACT
1 GGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
* *
465946 AGGGGATAAGAAAGTCTCTA
66 AAGGGATAGGAAAGTCTCTA
* * * * * *
465966 AGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAGCCGACAAGCAAACT
1 GGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
466031 AAGGG-T---AAAGTCTCTA
66 AAGGGATAGGAAAGTCTCTA
* * * **
466047 GGGTCAAAGCCAACAGGTAGATTTTAGATGAGGCAGTCTCTAGGGTCAAAGCTAACAGGCAGACT
1 GGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
* *
466112 AAGGGATTGGAAAGTCTTTA
66 AAGGGATAGGAAAGTCTCTA
*
466132 GGGTCAAACCCGACAGGCAGACT
1 GGGTCAAAGCCGACAGGCAGACT
466155 AAAGGTAGAA
Statistics
Matches: 574, Mismatches: 101, Indels: 42
0.80 0.14 0.06
Matches are distributed among these distances:
81 69 0.12
82 3 0.01
83 5 0.01
84 195 0.34
85 298 0.52
86 2 0.00
87 2 0.00
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.19
Consensus pattern (85 bp):
GGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
AAGGGATAGGAAAGTCTCTA
Found at i:465708 original size:84 final size:84
Alignment explanation
Indices: 465620--466222 Score: 300
Period size: 85 Copynumber: 7.2 Consensus size: 84
465610 AAGGTAGAAA
* * *
465620 AGTCTCTAGGGTCAAAGTTGATAGGCAGACTTTAGAGGAAACAGTCTCCGGGGTCAAAGCCAACA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTTTAGAGGAAACAGTCTCCAGGGTCAAAGCCAACA
* *
465685 GGCGAACTTTAGATGAAGC
66 AGCAAACTTTAGATGAAGC
* * * ** *
465704 AGTCTCCAAGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCAACA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTTTAGAGGAAACAGTCTCCAGGGTCAAAGCCAACA
465769 AGCAAACTTTAGATGAAGC
66 AGCAAACTTTAGATGAAGC
* * * * *** * * *
465788 AATGTCTAGGGTCAAAGCCGACAGGCAGACTTTAGATGTGGCAGCCTCTAGGGTCAAAGCCGACA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTTTAGAGGAAACAGTCTCCAGGGTCAAAGCCAACA
* * *
465853 GGCAGAC-TGAGGGATAGGAA--
66 AGCAAACTTTA--GAT--GAAGC
* ** * * ** * ** *
465873 AGTCT-TCAAGGTCAAAGCCAACAGGCGGACTTTAGATGAGGCAGTCTCCAGGATCAAAGCTGAT
1 AGTCTCT-AGGGTCAAAGCTGACAGGCAGACTTTAGAGGAAACAGTCTCCAGGGTCAAAGCCAAC
* * *** *
465937 AGGCAGACTAGGGGAT-AAGAA
65 AAGCAAACT-TTAGATGAAG-C
* * * * * *
465958 AGTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGA-TAAGGCAGTCTCCAAGGTCAAAGCCGAC
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTTTAGAGGAA-ACAGTCTCCAGGGTCAAAGCCAAC
* *
466022 AAGCAAAC-TAAG-GGTAA--
65 AAGCAAACTTTAGATG-AAGC
** * * * ** * *
466039 AGTCTCTAGGGTCAAAGCCAACAGGTAGATTTTAGATGAGGCAGTCTCTAGGGTCAAAGCTAACA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTTTAGAGGAAACAGTCTCCAGGGTCAAAGCCAACA
* * *
466104 GGCAGAC-TAAGGGATTGGAA--
66 AGCAAACTTTA--GA-T-GAAGC
* * * * * * * *
466124 AGTCTTTAGGGTCAAACCCGACAGGCAGAC--TAAAGGTAGAAAAGTCTCCAAGGTCAAAGTCGA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTTTAGAGG-A-AACAGTCTCCAGGGTCAAAGCCAA
* * * *
466187 CAGGCAGACTTTAAATGAGGC
64 CAAGCAAACTTTAGATGAAGC
*
466208 AGTCTCCAGGGTCAA
1 AGTCTCTAGGGTCAA
466223 GCCGATAGAG
Statistics
Matches: 412, Mismatches: 82, Indels: 50
0.76 0.15 0.09
Matches are distributed among these distances:
81 61 0.15
82 5 0.01
83 9 0.02
84 154 0.37
85 175 0.42
86 4 0.01
87 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (84 bp):
AGTCTCTAGGGTCAAAGCTGACAGGCAGACTTTAGAGGAAACAGTCTCCAGGGTCAAAGCCAACA
AGCAAACTTTAGATGAAGC
Found at i:466351 original size:85 final size:84
Alignment explanation
Indices: 466131--466403 Score: 291
Period size: 85 Copynumber: 3.2 Consensus size: 84
466121 GAAAGTCTTT
* * * * *
466131 AGGGTCAAACCCGACAGGCAGACTAAAGG-TAGAAAAGTCTCCAAGGTCAAAGTCGACAGGCAGA
1 AGGGT-AAAGCCGATAGGCAGACTTAGGGATAGAAAAGTCTCCAAGGTCAAAGTCGATAGGCAGA
* *
466195 CTTTAAATGAGGCAGTCTCC
65 CTTTAGATAAGGCAGTCTCC
* * * * *
466215 AGGGTCAAGCCGATAGAG-AGA-TTGAGGGATAGGAAATTCTCCAAAGTCAAAGCCGATAGGCAG
1 AGGGTAAAGCCGATAG-GCAGACTT-AGGGATAGAAAAGTCTCCAAGGTCAAAGTCGATAGGCAG
466278 ACTTTAGATAAGGCAGTCTCC
64 ACTTTAGATAAGGCAGTCTCC
* * * * * *
466299 AAGGTGAAAGCCGATAGGCAGACTTAGGGATAAAAAAGTCTCTAGGGTCAAAGTTGATAGGTAGA
1 AGGGT-AAAGCCGATAGGCAGACTTAGGGATAGAAAAGTCTCCAAGGTCAAAGTCGATAGGCAGA
* *
466364 CTTTAGATAAAGCAGTTTCC
65 CTTTAGATAAGGCAGTCTCC
*
466384 AGGGTCAAAGCCGAAAGGCA
1 AGGGT-AAAGCCGATAGGCA
466404 AACTGAAGTA
Statistics
Matches: 155, Mismatches: 28, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
82 1 0.01
83 14 0.09
84 59 0.38
85 79 0.51
86 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (84 bp):
AGGGTAAAGCCGATAGGCAGACTTAGGGATAGAAAAGTCTCCAAGGTCAAAGTCGATAGGCAGAC
TTTAGATAAGGCAGTCTCC
Found at i:466893 original size:21 final size:22
Alignment explanation
Indices: 466856--466902 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
466846 TCATGATTTG
*
466856 ATTTGATTCTTTCTATGTC-TT
1 ATTTGATTCTTTCTATGGCTTT
*
466877 ATTTG-TTCATTTTTATGGCTTT
1 ATTTGATTC-TTTCTATGGCTTT
466899 ATTT
1 ATTT
466903 AGTCTACCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 3 0.14
21 13 0.59
22 6 0.27
ACGTcount: A:0.15, C:0.11, G:0.11, T:0.64
Consensus pattern (22 bp):
ATTTGATTCTTTCTATGGCTTT
Found at i:470733 original size:33 final size:33
Alignment explanation
Indices: 470677--470742 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
470667 AAATTCCCAG
*
470677 ATGTATCGATACAAAGATCAATGTATTGATACA
1 ATGTATCGATACAAAGATCAATGTATCGATACA
**
470710 ATGTATCGATACATTGAGT-AATGTATCGATACA
1 ATGTATCGATACAAAGA-TCAATGTATCGATACA
470743 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAATGTATCGATACA
Found at i:470784 original size:13 final size:13
Alignment explanation
Indices: 470766--470817 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
470756 AGCTTTGGAG
470766 CGATACATTGTAT
1 CGATACATTGTAT
470779 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
470798 CGATACATTGTAT
1 CGATACATTGTAT
470811 CGATACA
1 CGATACA
470818 AAACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:470798 original size:19 final size:19
Alignment explanation
Indices: 470774--470836 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
470764 AGCGATACAT
470774 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
470793 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
470806 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
470825 TGTATCGATACA
1 TGTATCGATACA
470837 TTTACTATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 5 0.14
18 1 0.03
19 21 0.57
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:470807 original size:32 final size:32
Alignment explanation
Indices: 470766--470838 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
470756 AGCTTTGGAG
*
470766 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
470798 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
470830 CGATACATT
1 CGATACATT
470839 TACTATTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:472355 original size:19 final size:20
Alignment explanation
Indices: 472331--472384 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
472321 ATATTATGCT
**
472331 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGGACAA
472350 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
472370 TTGTATCGATACATG
1 TTGTATCGATACATG
472385 AAATTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:478595 original size:15 final size:15
Alignment explanation
Indices: 478575--478606 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
478565 ATATCGATAC
478575 ATCTGGATAACCCAG
1 ATCTGGATAACCCAG
478590 ATCTGGATAACCCAG
1 ATCTGGATAACCCAG
478605 AT
1 AT
478607 GTATCGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (15 bp):
ATCTGGATAACCCAG
Found at i:481175 original size:20 final size:19
Alignment explanation
Indices: 481129--481185 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
481119 TTGTATTGAT
*
481129 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
481148 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
481167 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
481186 AAATTGGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:481275 original size:33 final size:33
Alignment explanation
Indices: 481214--481282 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
481204 CTTCCACTGT
*
481214 TTGTATCGATACATGGTACAATGAATCGATACA
1 TTGTATCGATACATGATACAATGAATCGATACA
* *
481247 TTGTATCGATACATGATGA-ATTGTATCGATACA
1 TTGTATCGATACATGAT-ACAATGAATCGATACA
481280 TTG
1 TTG
481283 CTTGTAACGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATGAATCGATACA
Found at i:487759 original size:4 final size:4
Alignment explanation
Indices: 487745--487776 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
487735 GTACAAAACA
487745 AAAT AAAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAA
487777 CACATCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:489498 original size:13 final size:13
Alignment explanation
Indices: 489480--489505 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
489470 CAATTTTTTG
489480 TGTATCGATACAT
1 TGTATCGATACAT
489493 TGTATCGATACAT
1 TGTATCGATACAT
489506 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:492069 original size:13 final size:13
Alignment explanation
Indices: 492051--492076 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
492041 ATAATCACCC
492051 TGTATCGATACAA
1 TGTATCGATACAA
492064 TGTATCGATACAA
1 TGTATCGATACAA
492077 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:494175 original size:15 final size:15
Alignment explanation
Indices: 494155--494185 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
494145 ATTTCGTTTG
*
494155 GAGCTTCTTCATTTT
1 GAGCTTCGTCATTTT
494170 GAGCTTCGTCATTTT
1 GAGCTTCGTCATTTT
494185 G
1 G
494186 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
GAGCTTCGTCATTTT
Found at i:496018 original size:21 final size:21
Alignment explanation
Indices: 495989--496033 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
495979 AAGTTTTCAT
*
495989 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
496009 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
496031 TTT
1 TTT
496034 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:498669 original size:21 final size:22
Alignment explanation
Indices: 498614--498685 Score: 89
Period size: 21 Copynumber: 3.4 Consensus size: 22
498604 CACTGTTCAT
498614 ACTGTTCATGTATCGATACAT-
1 ACTGTTCATGTATCGATACATC
**
498635 --TGTGAATAGTATCGATACATC
1 ACTGTTCAT-GTATCGATACATC
498656 ACT-TTCATGTATCGATACATC
1 ACTGTTCATGTATCGATACATC
498677 ACTGTTCAT
1 ACTGTTCAT
498686 AGGTCACTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
19 5 0.12
20 12 0.29
21 16 0.38
22 8 0.19
23 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (22 bp):
ACTGTTCATGTATCGATACATC
Found at i:499329 original size:34 final size:35
Alignment explanation
Indices: 499266--499332 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
499256 CTAAGTGATT
499266 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
499302 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
499333 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:500101 original size:13 final size:13
Alignment explanation
Indices: 500083--500108 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
500073 ACATATTTGT
500083 GTGTATCGATACA
1 GTGTATCGATACA
500096 GTGTATCGATACA
1 GTGTATCGATACA
500109 TCATAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:502399 original size:79 final size:79
Alignment explanation
Indices: 502259--502676 Score: 412
Period size: 79 Copynumber: 5.3 Consensus size: 79
502249 ATTTAATATT
* * **** * *
502259 TTGGTGTA-CCCCTTCGAAAATAACGGGGTTGGAGTATCTTTGATTGTGAAAATTTAGTGTTTTG
1 TTGGAGTATCCCC-TCGAAAATAACGAGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTG
502323 GAAATAAAACCGGGG
65 GAAATAAAACCGGGG
* *
502338 TTGGAGTATCCCCTCAAAAATAACGA-GTTTGAGGTATCCCCAATTGTGAAAAATTGGTGTTTTG
1 TTGGAGTATCCCCTCGAAAATAACGAGGTTGGA-GTATCCCCAATTGTGAAAAATTGGTGTTTTG
* * *
502402 GATATAAAACCAGGA
65 GAAATAAAACCGGGG
* * * * *
502417 TTAGAGTATCCCTTCGAAAATAACAAGGTTGGAGTATCCTCGAA-TGTGAAAATTTGGTGTTTTG
1 TTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCC-CCAATTGTGAAAAATTGGTGTTTTG
* **
502481 AAAATAAAACCACGG
65 GAAATAAAACCGGGG
* * * * * *
502496 TTGAAGTATCCTCTCGGAAATAAAGCGGTTGGAGTATCCTCAATTGCTG-AAAATTGGTGTTTTG
1 TTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCAATTG-TGAAAAATTGGTGTTTTG
** * *
502560 GAAATAAAATTGTGC
65 GAAATAAAACCGGGG
* * * ** * *
502575 TTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCTGATTGTGAAAAATTGATGCTTTGG
1 TTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGG
*
502640 GAATAAAACCGGGG
66 AAATAAAACCGGGG
*
502654 TTGGAGTATCCCCTCGTAAATAA
1 TTGGAGTATCCCCTCGAAAATAA
502677 AAACATGAAT
Statistics
Matches: 274, Mismatches: 58, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
78 9 0.03
79 251 0.92
80 14 0.05
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGG
AAATAAAACCGGGG
Found at i:502556 original size:158 final size:160
Alignment explanation
Indices: 502267--502677 Score: 496
Period size: 158 Copynumber: 2.6 Consensus size: 160
502257 TTTTGGTGTA
* * *
502267 CCCCTTCGAAAATAACGGGGTTGGAGTATCTTTGATTGTGAAAATTTAGTGTTTTGGAAATAAAA
1 CCCCTTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAATTTGGTGTTTTGGAAATAAAA
* *
502332 CCGGGGTTGGAGTATCCCCTCAAAAAT-AACGAGTTTGAGGTATCCCCAATTGTGAAAAATTGGT
66 CCGGGGTTGGAGTATCCCCTCGAAAATAAACGAGTTGGAGGTATCCCCAATTGTGAAAAATTGGT
*
502396 GTTTTGGATATAAAACCAG-GATTAGAGTAT
131 GTTTTGGAAATAAAA-CAGTGATTAGAGTAT
** * *
502426 -CCCTTCGAAAATAACAAGGTTGGAGTATCCTCGAATGTGAAAATTTGGTGTTTTGAAAATAAAA
1 CCCCTTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAATTTGGTGTTTTGGAAATAAAA
** * * * *
502490 CCACGGTTGAAGTATCCTCTCGGAAATAAAGCG-GTTGGA-GTATCCTCAATTGCTG-AAAATTG
66 CCGGGGTTGGAGTATCCCCTCGAAAATAAA-CGAGTTGGAGGTATCCCCAATTG-TGAAAAATTG
** * *
502552 GTGTTTTGGAAATAAAATTGTGCTTGGAGTAT
129 GTGTTTTGGAAATAAAACAGTGATTAGAGTAT
* * * * *
502584 CCCCTT-GGAAATAACGGGGTTGGAGTATCC-CTGATTGTGAAAAATTGATGCTTTGGGAATAAA
1 CCCCTTCGAAAATAACGGGGTTGGAGTATCCTC-GATTGTGAAAATTTGGTGTTTTGGAAATAAA
*
502647 ACCGGGGTTGGAGTATCCCCTCGTAAATAAA
65 ACCGGGGTTGGAGTATCCCCTCGAAAATAAA
502678 AACATGAATG
Statistics
Matches: 212, Mismatches: 34, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
157 2 0.01
158 194 0.92
159 14 0.07
160 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (160 bp):
CCCCTTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAATTTGGTGTTTTGGAAATAAAA
CCGGGGTTGGAGTATCCCCTCGAAAATAAACGAGTTGGAGGTATCCCCAATTGTGAAAAATTGGT
GTTTTGGAAATAAAACAGTGATTAGAGTAT
Found at i:505080 original size:30 final size:30
Alignment explanation
Indices: 505044--505113 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
505034 ATACACTAAG
505044 GAATGTATCGATACATCTGGGTAAAACCCA
1 GAATGTATCGATACATCTGGGTAAAACCCA
* *
505074 GAATGTATCGATACATTTGGGTAAAATCCA
1 GAATGTATCGATACATCTGGGTAAAACCCA
*
505104 GAATATATCG
1 GAATGTATCG
505114 TTATAATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (30 bp):
GAATGTATCGATACATCTGGGTAAAACCCA
Found at i:509184 original size:20 final size:20
Alignment explanation
Indices: 509159--509206 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
509149 CATGCATTCT
* *
509159 GATACATTCATACATGTATC
1 GATACATTCAAAAATGTATC
*
509179 GATACATTGAAAAATGTATC
1 GATACATTCAAAAATGTATC
509199 GATACATT
1 GATACATT
509207 TGGGTAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (20 bp):
GATACATTCAAAAATGTATC
Found at i:510936 original size:19 final size:19
Alignment explanation
Indices: 510912--510977 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
510902 ACGTTATGCT
510912 TTGTATCGATACATGTTAA
1 TTGTATCGATACATGTTAA
510931 TTGTATCGATAC------A
1 TTGTATCGATACATGTTAA
510944 TTGTATCGATACATGTTAA
1 TTGTATCGATACATGTTAA
510963 TTGTATCGATACATG
1 TTGTATCGATACATG
510978 AGATTGGCAG
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 13 0.32
19 28 0.68
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (19 bp):
TTGTATCGATACATGTTAA
Found at i:510948 original size:13 final size:13
Alignment explanation
Indices: 510930--510957 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
510920 ATACATGTTA
510930 ATTGTATCGATAC
1 ATTGTATCGATAC
510943 ATTGTATCGATAC
1 ATTGTATCGATAC
510956 AT
1 AT
510958 GTTAATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:510953 original size:32 final size:32
Alignment explanation
Indices: 510912--510976 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
510902 ACGTTATGCT
510912 TTGTATCGATACATGTTAATTGTATCGATACA
1 TTGTATCGATACATGTTAATTGTATCGATACA
510944 TTGTATCGATACATGTTAATTGTATCGATACA
1 TTGTATCGATACATGTTAATTGTATCGATACA
510976 T
1 T
510977 GAGATTGGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (32 bp):
TTGTATCGATACATGTTAATTGTATCGATACA
Found at i:511066 original size:33 final size:33
Alignment explanation
Indices: 511006--511074 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
510996 CTACCACTGT
* *
511006 TTGTATCGATACATGGTACAATATATCGATACA
1 TTGTATCGATACATGATACAATATATCGACACA
* *
511039 TTGTATCGATACATGATGA-ATTGTATCGACACA
1 TTGTATCGATACATGAT-ACAATATATCGACACA
511072 TTG
1 TTG
511075 CTTGTAATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATATATCGACACA
Found at i:515333 original size:34 final size:35
Alignment explanation
Indices: 515295--515361 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
515285 CCTTACAACA
515295 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
515329 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
515362 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:515839 original size:13 final size:13
Alignment explanation
Indices: 515821--515846 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
515811 CAATTTTTTG
515821 TGTATCGATACAT
1 TGTATCGATACAT
515834 TGTATCGATACAT
1 TGTATCGATACAT
515847 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:515861 original size:32 final size:33
Alignment explanation
Indices: 515801--515864 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
515791 TACAAGCCAA
** *
515801 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
515834 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
515865 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:522255 original size:16 final size:16
Alignment explanation
Indices: 522236--522276 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
522226 GCATCCTTCT
*
522236 TAAAAAAAATAAAAAA
1 TAAAAAAAACAAAAAA
*
522252 TAAAATAAACAAAAAA
1 TAAAAAAAACAAAAAA
*
522268 CAAAAAAAA
1 TAAAAAAAA
522277 AAATAAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (16 bp):
TAAAAAAAACAAAAAA
Found at i:522272 original size:23 final size:23
Alignment explanation
Indices: 522239--522283 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
522229 TCCTTCTTAA
* *
522239 AAAAAATAAAAAATAAAATAAAC
1 AAAAAACAAAAAAAAAAATAAAC
522262 AAAAAACAAAAAAAAAAATAAA
1 AAAAAACAAAAAAAAAAATAAA
522284 AACCTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.87, C:0.04, G:0.00, T:0.09
Consensus pattern (23 bp):
AAAAAACAAAAAAAAAAATAAAC
Found at i:523613 original size:28 final size:29
Alignment explanation
Indices: 523581--524131 Score: 607
Period size: 28 Copynumber: 19.6 Consensus size: 29
523571 AATACGACCT
*
523581 CTTTTCAAAGCACA-AAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
*
523609 CTTTTCAAAGCCCACAAGTTAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
* * * * *
523638 CTTCTCAAAGCCTATAAGTTAGTGCCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
*
523667 C-TCTCAAAGCCCACAAGTCAGTGGCA-C
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
* *
523694 CTTCTCAAAGCCCACAAGTTAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
* *
523723 CTTTTTAAAGCCCACAAGTCAATGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
*
523752 ATTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
* *
523781 CTCTT-AAAGCCCATAAGTCAGTGGCA-C
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
* * *
523808 CTTCTCAAAGCCCATAAGTCAATGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
* *
523837 CTCTT-AAAGCCCACAAGTCAGTAGCA--
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
* * *
523863 CTTTCTCAAAGCCCGCAAGTCAGTAGTATC
1 CTTT-TCAAAGCCCACAAGTCAGTGGCATC
* * *
523893 C-TCTCCAAGCCCACAAGTTAGTGGCA-C
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
* *
523920 CTTTTCAAAACCCACAAGTTAGTGGCA-C
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
* *
523948 CTTCTCAAAGCCCACAAGTTAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
*
523977 C-TCTCAAAGCCCACAAGTCAGTGGCA-C
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
*
524004 CTTCTT-AAAGCCCACAAGTTAGTGGCA-C
1 CTT-TTCAAAGCCCACAAGTCAGTGGCATC
* **
524032 CTTCTCAAAGCCCACGTGTCAGTGGCA-C
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
* * * *
524060 CTTCTCAAAGCTCACAAGTTAGTAGCA-C
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
524088 CTTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCATC
524117 C-TTTCAAAGCCCACA
1 CTTTTCAAAGCCCACA
524132 CAAGTCGGTG
Statistics
Matches: 449, Mismatches: 59, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
26 3 0.01
27 12 0.03
28 329 0.73
29 104 0.23
30 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (29 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCATC
Found at i:523717 original size:56 final size:57
Alignment explanation
Indices: 523585--524131 Score: 673
Period size: 56 Copynumber: 9.7 Consensus size: 57
523575 CGACCTCTTT
* *
523585 TCAAAGCACA-AAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTC
1 TCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTTAGTGGCA-CCTTC
* * * * *
523642 TCAAAGCCTATAAGTTAGTGCCATCC-TCTCAAAGCCCACAAGTCAGTGGCACCTTC
1 TCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTTAGTGGCACCTTC
* * * * * * *
523698 TCAAAGCCCACAAGTTAGTGGCATCCTTTTTAAAGCCCACAAGTCAATGGCATCATTT
1 TCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTTAGTGGCA-CCTTC
* * *
523756 TCAAAGCCCACAAGTCAGTGGCATCC-TCTTAAAGCCCATAAGTCAGTGGCACCTTC
1 TCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTTAGTGGCACCTTC
* * * * * *
523812 TCAAAGCCCATAAGTCAATGGCATCC-TCTTAAAGCCCACAAGTCAGTAGCACTTTC
1 TCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTTAGTGGCACCTTC
* * * * *
523868 TCAAAGCCCGCAAGTCAGTAGTATCC-TCTCCAAGCCCACAAGTTAGTGGCACCTTT
1 TCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTTAGTGGCACCTTC
* *
523924 TCAAAACCCACAAGTTAGTGGCA-CCTTCTCAAAGCCCACAAGTTAGTGGCATCC-TC
1 TCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTTAGTGGCA-CCTTC
*
523980 TCAAAGCCCACAAGTCAGTGGCA-CCTTCTTAAAGCCCACAAGTTAGTGGCACCTTC
1 TCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTTAGTGGCACCTTC
** * * *
524036 TCAAAGCCCACGTGTCAGTGGCA-CCTTCTCAAAGCTCACAAGTTAGTAGCACCTTT
1 TCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTTAGTGGCACCTTC
524092 TCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAGCCCACA
1 TCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACA
524132 CAAGTCGGTG
Statistics
Matches: 428, Mismatches: 55, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
55 4 0.01
56 302 0.71
57 81 0.19
58 41 0.10
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (57 bp):
TCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTTAGTGGCACCTTC
Found at i:524167 original size:32 final size:33
Alignment explanation
Indices: 524090--524178 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 33
524080 AGTAGCACCT
* *
524090 TTTCAAAGC-C-CACAAGTCAGTGGC-A--TCC
1 TTTCAAAGCACACACAAGTCGGTGGCAACTTTC
*
524118 TTTCAAAGCCCACACAAGTCGGTGGCAACTTTC
1 TTTCAAAGCACACACAAGTCGGTGGCAACTTTC
* *
524151 TTT-AAAGCACATACAAGTTGGTGGCAAC
1 TTTCAAAGCACACACAAGTCGGTGGCAAC
524179 CCTTCTAAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 9 0.18
29 1 0.02
30 13 0.25
31 1 0.02
32 22 0.43
33 5 0.10
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (33 bp):
TTTCAAAGCACACACAAGTCGGTGGCAACTTTC
Found at i:525837 original size:20 final size:21
Alignment explanation
Indices: 525798--525837 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
525788 CAGCCCCTAA
*
525798 TCATGCATTTTTTACTATGTT
1 TCATGCATTTTTAACTATGTT
525819 TCATGCATTTTTAAC-ATGT
1 TCATGCATTTTTAACTATGT
525838 CCAGCACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.53
Consensus pattern (21 bp):
TCATGCATTTTTAACTATGTT
Found at i:526581 original size:128 final size:127
Alignment explanation
Indices: 526344--526587 Score: 285
Period size: 128 Copynumber: 1.9 Consensus size: 127
526334 GCCAGTTGGT
* * * *
526344 TAGAAGGTTGACTAAGGCAAAACCGACAAAATCAATCAAATAAAGGTTGGCCAGGGCAAAACTCA
1 TAGAAGGTTGACTAAGGCAAAACCAACAAAATCAATCAAATAAAGGTTAGCCAAGGCAAAACTAA
* * * * *
526409 TAAAGCCCACAGGTTTGAAAGGTTGACCAAGGCAAAACTAATAAAGTCAACCAACTAGAAGG
66 TAAAGCCAACAAGTTAGAAAGGTGGACCAAGGCAAAACCAATAAAGTCAACCAACTAGAAGG
* * *
526471 TAGAAGGGTTGACTAA-GCAAAACCAATAAAGTCAA-CTAATTAAAAGGTTAGCCAAGGCAAAAC
1 TAGAA-GGTTGACTAAGGCAAAACCAACAAAATCAATC-AAAT-AAAGGTTAGCCAAGGCAAAAC
* * * ** *
526534 TAATAAAGCCAAGAAGTTAGAAGGGTGGACTAAGGTGAAACCGATAAAGTCAAC
63 TAATAAAGCCAACAAGTTAGAAAGGTGGACCAAGGCAAAACCAATAAAGTCAAC
526588 TAATTAGTAT
Statistics
Matches: 96, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
126 1 0.01
127 24 0.25
128 71 0.74
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (127 bp):
TAGAAGGTTGACTAAGGCAAAACCAACAAAATCAATCAAATAAAGGTTAGCCAAGGCAAAACTAA
TAAAGCCAACAAGTTAGAAAGGTGGACCAAGGCAAAACCAATAAAGTCAACCAACTAGAAGG
Found at i:527734 original size:164 final size:165
Alignment explanation
Indices: 527564--527888 Score: 384
Period size: 164 Copynumber: 2.0 Consensus size: 165
527554 TCATCGGAGT
* *** * * * * *
527564 AAAATTTTTAAAATTCATCAAATATTGTTACCTAACTCCCATTTAATCAGTTTGGAAAAA-TTCA
1 AAAATTTTCAAAATTCATCAAATAGCATCACCTAACTCACAATAAATCAGTTT-CAAAAATTTCA
* * * * ** *
527628 TTTATTTTTATGAGTTTTTTATTTTTTT-TGAAATTCTCTTATTTTTAAAAAATCGAGTTTTCTA
65 TTTATTTTCATGAGTTTTTCATTTTTTTCTGAAATGCCCTTATTTACAAAAAATCGAATTTTCTA
* *
527692 TTCCATAAAGGTTTTCGAGGGGGTTTTTCTCAATTC
130 TTCCATAAAGGTTTTCGAGAGGATTTTTCTCAATTC
* ** * *
527728 AAAATTTTCAATATTCATCAAATAGCATCATTTAATTCATAATAAATCAGTTTCAAAAATTTCAT
1 AAAATTTTCAAAATTCATCAAATAGCATCACCTAACTCACAATAAATCAGTTTCAAAAATTTCAT
*
527793 TTATTTTCATGGGTTTTTCATTTTTTTCCATGAAATGCCCTTATTTACAAAAAATCGAATTTTCT
66 TTATTTTCATGAGTTTTTCATTTTTTT-C-TGAAATGCCCTTATTTACAAAAAATCGAATTTTCT
*
527858 ATTCCATATAGGTTTTCGAGAGGATTTTTCT
129 ATTCCATAAAGGTTTTCGAGAGGATTTTTCT
527889 TGGTTTAAAA
Statistics
Matches: 132, Mismatches: 25, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
163 5 0.04
164 69 0.52
167 58 0.44
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (165 bp):
AAAATTTTCAAAATTCATCAAATAGCATCACCTAACTCACAATAAATCAGTTTCAAAAATTTCAT
TTATTTTCATGAGTTTTTCATTTTTTTCTGAAATGCCCTTATTTACAAAAAATCGAATTTTCTAT
TCCATAAAGGTTTTCGAGAGGATTTTTCTCAATTC
Found at i:528141 original size:15 final size:17
Alignment explanation
Indices: 528113--528146 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
528103 TTTCTTGGAA
528113 TTTTATTTTAATTTATT
1 TTTTATTTTAATTTATT
528130 TTTTA-TTT-ATTTATT
1 TTTTATTTTAATTTATT
528145 TT
1 TT
528147 GCCTGGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 3 0.18
17 5 0.29
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTATTTTAATTTATT
Found at i:528483 original size:15 final size:15
Alignment explanation
Indices: 528458--528496 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
528448 TTTGGCAAGT
*
528458 GAAGAAAAAAAAAAGG
1 GAAG-AAAAAAAAAGA
528474 GAAGAAAAAAAAAGA
1 GAAGAAAAAAAAAGA
528489 GAA-AAAAA
1 GAAGAAAAA
528497 GAGAAAAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 13 0.59
16 4 0.18
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
GAAGAAAAAAAAAGA
Found at i:528585 original size:15 final size:15
Alignment explanation
Indices: 528560--528592 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
528550 TTATTTCTTT
528560 ATGATGTTATGAATAC
1 ATGATGTTATGAA-AC
528576 ATGA-GTTATGAAAC
1 ATGATGTTATGAAAC
528590 ATG
1 ATG
528593 TTGAGTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 8 0.47
16 4 0.24
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (15 bp):
ATGATGTTATGAAAC
Found at i:530560 original size:165 final size:165
Alignment explanation
Indices: 530389--530762 Score: 563
Period size: 166 Copynumber: 2.3 Consensus size: 165
530379 ATTTAATTAG
*
530389 TTTTGAAAAATTCATTTATTTTCATGAGTTTTCCATTTTTTTCCTTGAAACTCTC-TAATTACCA
1 TTTTGAAAAATTCATTTATTTTCATGAGTTTTTCATTTTTTTCCTTGAAACTCTCAT-ATTACCA
* *
530453 AAAAACTGAGTTTTTTATTCCATAAATCTTTTT-GGGGGTTTTTCTCAGTTCAAAATTTTTAATA
65 AAAAACTGAGTTTTTTATTCCATAAATCTTTTTGGGGGGTTCTTCTCAGTTAAAAATTTTTAATA
*
530517 TTCATCAAATATTATCATTTAAATCATAGTAAACCCA
130 TTCATCAAATATCATCATTTAAATCATAGTAAA-CCA
* * * *
530554 TTTTGAAAAATTCATTTATTTTCAAGAGTTTTTCATTTTTTTCCTTGAAATTCTCATGTTTCCAA
1 TTTTGAAAAATTCATTTATTTTCATGAGTTTTTCATTTTTTTCCTTGAAACTCTCATATTACCAA
* * * *
530619 AAAACTGGGTTTTTTATTCCATACATGTTTTTGGGGGGTTCTTCTCTGTTAAAAATTTTTAATAT
66 AAAACTGAGTTTTTTATTCCATAAATCTTTTTGGGGGGTTCTTCTCAGTTAAAAATTTTTAATAT
* *
530684 TCATCAAATATCATTATTTAAATCATAGTAAATCA
131 TCATCAAATATCATCATTTAAATCATAGTAAACCA
* *
530719 TTTTGGAAAATTTTATTTATTTTCATGAGTTTTTCATTTTTTTC
1 TTTT-GAAAAATTCATTTATTTTCATGAGTTTTTCATTTTTTTC
530763 TTAAAATTTC
Statistics
Matches: 189, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
165 93 0.49
166 96 0.51
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.48
Consensus pattern (165 bp):
TTTTGAAAAATTCATTTATTTTCATGAGTTTTTCATTTTTTTCCTTGAAACTCTCATATTACCAA
AAAACTGAGTTTTTTATTCCATAAATCTTTTTGGGGGGTTCTTCTCAGTTAAAAATTTTTAATAT
TCATCAAATATCATCATTTAAATCATAGTAAACCA
Found at i:530751 original size:166 final size:164
Alignment explanation
Indices: 530339--530770 Score: 582
Period size: 165 Copynumber: 2.6 Consensus size: 164
530329 TCATTGGATT
* * * * * *
530339 AAAATTTTTAAAATTCATCAAATATTATTATCT-AATCAGCATTTAATTAGTTTTGAAAAATTCA
1 AAAATTTTTAATATTCATCAAATATTATTATTTAAATCA-TAGTAAATCA-TTTTGAAAAATTCA
* *
530403 TTTATTTTCATGAGTTTTCCATTTTTTTCCTTGAAACTCTCTAATTACCAAAAAACTGAGTTTTT
64 TTTATTTTCATGAGTTTTTCATTTTTTTCCTTGAAATTCTCTAATTACCAAAAAACTGAGTTTTT
* *
530468 TATTCCATAAATCTTTTTGGGGGTTTTTCTCAGTTC
129 TATTCCATAAATCTTTTTGGGGGTTCTTCTCAGTTA
* *
530504 AAAATTTTTAATATTCATCAAATATTATCATTTAAATCATAGTAAACCCATTTTGAAAAATTCAT
1 AAAATTTTTAATATTCATCAAATATTATTATTTAAATCATAGTAAA-TCATTTTGAAAAATTCAT
* * * *
530569 TTATTTTCAAGAGTTTTTCATTTTTTTCCTTGAAATTCTC-ATGTTTCCAAAAAACTGGGTTTTT
65 TTATTTTCATGAGTTTTTCATTTTTTTCCTTGAAATTCTCTA-ATTACCAAAAAACTGAGTTTTT
* * *
530633 TATTCCATACATGTTTTTGGGGGGTTCTTCTCTGTTA
129 TATTCCATAAATCTTTTT-GGGGGTTCTTCTCAGTTA
* * *
530670 AAAATTTTTAATATTCATCAAATATCATTATTTAAATCATAGTAAATCATTTTGGAAAATTTTAT
1 AAAATTTTTAATATTCATCAAATATTATTATTTAAATCATAGTAAATCATTTT-GAAAAATTCAT
*
530735 TTATTTTCATGAGTTTTTCATTTTTTT-CTTAAAATT
65 TTATTTTCATGAGTTTTTCATTTTTTTCCTTGAAATT
530771 TCCCTATTTC
Statistics
Matches: 236, Mismatches: 26, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
164 1 0.00
165 135 0.57
166 100 0.42
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.48
Consensus pattern (164 bp):
AAAATTTTTAATATTCATCAAATATTATTATTTAAATCATAGTAAATCATTTTGAAAAATTCATT
TATTTTCATGAGTTTTTCATTTTTTTCCTTGAAATTCTCTAATTACCAAAAAACTGAGTTTTTTA
TTCCATAAATCTTTTTGGGGGTTCTTCTCAGTTA
Found at i:532250 original size:21 final size:22
Alignment explanation
Indices: 532209--532263 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
532199 AAGGGTATAG
**
532209 AAATAAAATTTTTGAAAATAAA
1 AAATAAAATTAATGAAAATAAA
*
532231 AAATAAAATTAATG-AAATAAT
1 AAATAAAATTAATGAAAATAAA
532252 AAATAAATATTA
1 AAATAAA-ATTA
532264 TTTTATCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
AAATAAAATTAATGAAAATAAA
Found at i:532601 original size:142 final size:139
Alignment explanation
Indices: 532274--532800 Score: 628
Period size: 140 Copynumber: 3.7 Consensus size: 139
532264 TTTTATCACT
* * * * * *
532274 AAATAAAAAATTATTATCTTAATTTTTAAATACTTCTAATATTCCTATGGTTTTCTATACGGGTA
1 AAAT-AAAAATTATTATCTTAATTTTTCAAGA-TTTTAATATTCCTATAGTTTTCCATAGGGGTA
* * * * * *
532339 TAGAAATCTTTAAAACTTTTTGTAT-TTTTTAGATTCCCCATTATGGTACGAAATGATTTTTTTG
64 TAGAAATCTTTAAAAATTTTCGTATCTTTTCAG-TTCTCCATTATGGTACAAAATGAATTTTTT-
*
532403 GAAACTAAAAATC
127 GAAATTAAAAATC
* ** *
532416 AAAT-AAAATTAGTATCTTAATTTTTCAAGATTTCTAATATTCCTATAGTTTTTTATAGTGGTAT
1 AAATAAAAATTATTATCTTAATTTTTCAAGATTT-TAATATTCCTATAGTTTTCCATAGGGGTAT
* * * *
532480 AGAAATTTTTAAAAATTTTCGTATCTTTTCGGTTCTCCATTATTGTACAAAATGAATTTTCTTAA
65 AGAAATCTTTAAAAATTTTCGTATCTTTTCAGTTCTCCATTATGGTACAAAATGAATTTT-TTGA
532545 TAATTAAAAATC
129 -AATTAAAAATC
* *
532557 AAATAAAAATTATTATCTTAATTTTTCAAGATTCTTAATATTCCTATGGTTTTCCGTAGGGGTAT
1 AAATAAAAATTATTATCTTAATTTTTCAAGATT-TTAATATTCCTATAGTTTTCCATAGGGGTAT
* *
532622 AGAAATCTTTAAAAATTTTCGTATCTTTTCAGTTCTCCATTAAGGTACAAAATGAATTTTTGGAA
65 AGAAATCTTTAAAAATTTTCGTATCTTTTCAGTTCTCCATTATGGTACAAAATGAATTTTTTGAA
* *
532687 GTTAAAAATT
130 ATTAAAAATC
* * * * *
532697 AAATAAAAATTCTTGTCTTAATTTTTTAAGATTTTTATGTTCCTA-AGGTTTTCCATAGGGGTAT
1 AAATAAAAATTATTATCTTAATTTTTCAAGATTTTAATATTCCTATA-GTTTTCCATAGGGGTAT
* * * *
532761 AGAAATCTTCAAAACTTTTCATATCTTTTCAGATCTCCAT
65 AGAAATCTTTAAAAATTTTCGTATCTTTTCAGTTCTCCAT
532801 GAAGGTACGA
Statistics
Matches: 334, Mismatches: 44, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
139 64 0.19
140 134 0.40
141 23 0.07
142 112 0.34
143 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (139 bp):
AAATAAAAATTATTATCTTAATTTTTCAAGATTTTAATATTCCTATAGTTTTCCATAGGGGTATA
GAAATCTTTAAAAATTTTCGTATCTTTTCAGTTCTCCATTATGGTACAAAATGAATTTTTTGAAA
TTAAAAATC
Found at i:533188 original size:177 final size:178
Alignment explanation
Indices: 532862--533204 Score: 481
Period size: 177 Copynumber: 1.9 Consensus size: 178
532852 CCTTCAGATT
* * * * *
532862 TATTTATGGATCTTTGTTTCTCACAAGGATAAAATTATCGTTTCTTTCCTTTTTTTCGAGCCCTT
1 TATTTATGGATCTTTGCTTCTCACAAGGATAAAATTATCATTTCTTTCATTCTTCTCGAGCCCTT
* * * *
532927 TAGGGGTACTAGGATACTTTCATGTCGAAGGTATACCTATAAGGGTATTTTTTTAATTTTTCTAA
66 TAGGGGTACTAAGATACTTTCATGTCGAAAGTATACCCATAAGGGTATTTTTGTAATTTTTCTAA
* * *
532992 AATCGAGTCCTAGGTTGTCATCGGGTTCGCTTTTATGCCAAGGGTGGG
131 AATCGAGTCCTAAGTTGTCATCGGGTCCACTTTTATGCCAAGGGTGGG
* * * *
533040 TATTTTTGGATTTTTGCTTCTCATAAGGATAAAATTATCATTTCTTTCATTCTTCT-GAGCCTTT
1 TATTTATGGATCTTTGCTTCTCACAAGGATAAAATTATCATTTCTTTCATTCTTCTCGAGCCCTT
* * * *
533104 TAGGGGTATTAAGATACTTTCATGTTGAAAGTATACCCATAAGGGTATTTTTGTAATTTTTTTAG
66 TAGGGGTACTAAGATACTTTCATGTCGAAAGTATACCCATAAGGGTATTTTTGTAATTTTTCTAA
* *
533169 AATCGAGTCTTAAGTTGTCATTGGGTCCACTTTTAT
131 AATCGAGTCCTAAGTTGTCATCGGGTCCACTTTTAT
533205 ATCGAACGCG
Statistics
Matches: 143, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
177 95 0.66
178 48 0.34
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (178 bp):
TATTTATGGATCTTTGCTTCTCACAAGGATAAAATTATCATTTCTTTCATTCTTCTCGAGCCCTT
TAGGGGTACTAAGATACTTTCATGTCGAAAGTATACCCATAAGGGTATTTTTGTAATTTTTCTAA
AATCGAGTCCTAAGTTGTCATCGGGTCCACTTTTATGCCAAGGGTGGG
Found at i:533338 original size:155 final size:153
Alignment explanation
Indices: 533131--533589 Score: 482
Period size: 155 Copynumber: 3.0 Consensus size: 153
533121 TTTCATGTTG
* * * *
533131 AAAGTATACCCATAAGGG-TATTTTTGTAATTTTTTTAGAA-TCGAGTCTTAAGTTGTCATTGGG
1 AAAGTAT-CCCCTAAGGGCT-TTTTTGTAA-TTTTTTAGAACT-GAGTCCTAAGTTGTCACTAGG
* * * * ** **
533194 TCCACTTTTATATCGAACGCGGGTATTTAGGATAGGTTGATCTCGCCTATAATCATTTTCGTGTC
62 TCCACTTTTAT-CCGAAAGTGGGTATTTAGGATAGGTTCATCTCATCTATAATCATTTTCAAGTC
*
533259 TTTTAAGGGTATCTAGCACTTT-TAAGTC
126 TTTTAAGGGTATCGAGCA-TTTCTAAGTC
* *
533287 AAGAGTATCCCCTAAGGGCTTTTTTGTAATTTTTTAGAACTGAGTCCTAAGTTGTCCCTAAGTCC
1 AA-AGTATCCCCTAAGGGCTTTTTTGTAATTTTTTAGAACTGAGTCCTAAGTTGTCACTAGGTCC
* * * * *
533352 ACTTTTATGCCGAATGTGGGTATTTAGGATAGGTTCACCTCATTTGTAATCATTTTTAAGTCTTT
65 ACTTTTAT-CCGAAAGTGGGTATTTAGGATAGGTTCATCTCATCTATAATCATTTTCAAGTCTTT
*
533417 TAAGGGTATCGAGCATTTCTACGTC
129 TAAGGGTATCGAGCATTTCTAAGTC
* ** * *
533442 AAAGGTATCCCCT-AGAGGCATTTTCATAATTTTCTAGAACTGAGTCCTAGGTTGTCACTAGGTC
1 AAA-GTATCCCCTAAG-GGCTTTTTTGTAATTTTTTAGAACTGAGTCCTAAGTTGTCACTAGGTC
* * * * *
533506 TACTTTTATGCTGAAAGTGGGTATTTAGGATAGGTTCATCTCATCTATAATCCTTTTTAAGTC-C
64 CACTTTTAT-CCGAAAGTGGGTATTTAGGATAGGTTCATCTCATCTATAATCATTTTCAAGTCTT
*
533570 TT--GGGTATCGAGCACTTCTA
128 TTAAGGGTATCGAGCATTTCTA
533590 CATTGAAGGT
Statistics
Matches: 260, Mismatches: 37, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
152 17 0.07
154 8 0.03
155 208 0.80
156 21 0.08
157 6 0.02
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39
Consensus pattern (153 bp):
AAAGTATCCCCTAAGGGCTTTTTTGTAATTTTTTAGAACTGAGTCCTAAGTTGTCACTAGGTCCA
CTTTTATCCGAAAGTGGGTATTTAGGATAGGTTCATCTCATCTATAATCATTTTCAAGTCTTTTA
AGGGTATCGAGCATTTCTAAGTC
Found at i:533811 original size:61 final size:61
Alignment explanation
Indices: 533736--533857 Score: 199
Period size: 61 Copynumber: 2.0 Consensus size: 61
533726 AAGTTGATGG
** *
533736 TAAACCTTAGGGATATTTTAACATTTTCCCCGGAACCTAGTCCTAAAAAACTACCAGGTCA
1 TAAACCTTAGGGATATTTTAACATTTTCCCCAAAACCTAGGCCTAAAAAACTACCAGGTCA
* *
533797 TAAACCTTAGGGATATTTTAACATTTTCCCTAAAACCTAGGCCTAAAAAACTACCATGTCA
1 TAAACCTTAGGGATATTTTAACATTTTCCCCAAAACCTAGGCCTAAAAAACTACCAGGTCA
533858 CTTTTATGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (61 bp):
TAAACCTTAGGGATATTTTAACATTTTCCCCAAAACCTAGGCCTAAAAAACTACCAGGTCA
Found at i:537870 original size:51 final size:51
Alignment explanation
Indices: 537807--537941 Score: 162
Period size: 51 Copynumber: 2.6 Consensus size: 51
537797 ATTTGCCTGT
* * * * * *
537807 ATGTATCAATACAGTGGATAATGTATCGATACATCTGGGTAAAAAATCAAA
1 ATGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAAAACCAAA
* * * * *
537858 ATGTATCGATACAATGAAGAATGTATCAACACATCTAGGTAAAAACCCAGA
1 ATGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAAAACCAAA
*
537909 ATGTATCGATACAATGAACAATGTAACGATACA
1 ATGTATCGATACAATGAACAATGTATCGATACA
537942 AACAATAAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.24
Consensus pattern (51 bp):
ATGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAAAACCAAA
Found at i:541228 original size:16 final size:16
Alignment explanation
Indices: 541207--541241 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
541197 AAGAAAAAGG
541207 AAAAAGAATAAG-AAAA
1 AAAAAGAA-AAGCAAAA
541223 AAAAAGAAAAGCAAAA
1 AAAAAGAAAAGCAAAA
541239 AAA
1 AAA
541242 TGCAAAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.83, C:0.03, G:0.11, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAGCAAAA
Found at i:543044 original size:19 final size:19
Alignment explanation
Indices: 543020--543091 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
543010 AGCGATACAT
543020 TGTATCGATACAATACTTA
1 TGTATCGATACAATACTTA
*
543039 TGTATCGATACAAAACTTA
1 TGTATCGATACAATACTTA
* *
543058 TGTATCGATACATTTACTATT
1 TGTATCGATACA-ATACT-TA
543079 TGTATCGATACAA
1 TGTATCGATACAA
543092 ATTGTTGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 30 0.65
20 3 0.07
21 13 0.28
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TGTATCGATACAATACTTA
Found at i:550828 original size:13 final size:13
Alignment explanation
Indices: 550810--550836 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
550800 ACAATATTCC
550810 TTGTATCAATACA
1 TTGTATCAATACA
550823 TTGTATCAATACA
1 TTGTATCAATACA
550836 T
1 T
550837 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TTGTATCAATACA
Found at i:553374 original size:20 final size:20
Alignment explanation
Indices: 553349--553401 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
553339 TTCCACTATT
*
553349 TGTATCGATACATGGT-ACAA
1 TGTATCGATACATGATGA-AA
*
553369 TGTATCGATACATGATGAAT
1 TGTATCGATACATGATGAAA
553389 TGTATCGATACAT
1 TGTATCGATACAT
553402 TGCTTGTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGATGAAA
Found at i:559900 original size:18 final size:17
Alignment explanation
Indices: 559871--559904 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
559861 GTACAAAACA
559871 AAATAAAATAAATAAAT
1 AAATAAAATAAATAAAT
559888 AAATAATAATAAATAAA
1 AAATAA-AATAAATAAA
559905 CACATCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAATAAAT
Found at i:559916 original size:18 final size:17
Alignment explanation
Indices: 559866--559916 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
559856 TGACTGTACA
559866 AAACAAAATAAAATAAAT
1 AAAC-AAATAAAATAAAT
*
559884 AAATAAATAATAATAAAT
1 AAACAAATAA-AATAAAT
*
559902 AAACACATCAAAATA
1 AAACAAAT-AAAATA
559917 GAGATAGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 6 0.21
18 20 0.71
19 2 0.07
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.20
Consensus pattern (17 bp):
AAACAAATAAAATAAAT
Found at i:562058 original size:79 final size:79
Alignment explanation
Indices: 561955--562372 Score: 432
Period size: 79 Copynumber: 5.3 Consensus size: 79
561945 ATTTAATATT
** * *
561955 TTGGAGTA-CCCCTTCGAAAATAACGGGGTTGGAGTATCTTCGATTGTGAAAATTTAGTGTTTTG
1 TTGGAGTATCCCC-TCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTG
562019 GAAATAAAACCGAGG
65 GAAATAAAACCGAGG
* * * * *
562034 TTGGAGTATCCCCTCAAAAATAAC-GAGTTTGAGGTATCACCAATTGTGAAAAATTGGTGTTTTG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGA-GTATCCCCGATTGTGAAAAATTGGTGTTTTG
*
562098 GATATAAAACC-AGG
65 GAAATAAAACCGAGG
* * ** *
562112 ATTAGAGTATCCCTTCGAAAATAACAAGGTTGGAGTATCCCCGAATGTGAAAAATTGGTGTTTTG
1 -TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTG
*
562177 AAAATAAAACC-AGGG
65 GAAATAAAACCGA-GG
* * * * * * *
562192 TTGAAGTATCCTCTCGGAAATAAAGCGGTTGGAGTATCCTCAATTGCTG-AAAATTGGTGTTTTG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTG-TGAAAAATTGGTGTTTTG
** * *
562256 GAAATAAAATTGTGC
65 GAAATAAAACCGAGG
* * * * * *
562271 TTGGAGTATCCCTTTGGAAATAACGGGGTTGGAGTATCCCTGATTGTGAAAAATTGATGCTTTGG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGG
* *
562336 GAATAAAACCGGGG
66 AAATAAAACCGAGG
*
562350 TTGGAGTATCCCCTCGTAAATAA
1 TTGGAGTATCCCCTCGAAAATAA
562373 AAACATGAAT
Statistics
Matches: 276, Mismatches: 55, Indels: 16
0.80 0.16 0.05
Matches are distributed among these distances:
78 11 0.04
79 252 0.91
80 13 0.05
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGG
AAATAAAACCGAGG
Found at i:562246 original size:158 final size:158
Alignment explanation
Indices: 561958--562373 Score: 493
Period size: 158 Copynumber: 2.6 Consensus size: 158
561948 TAATATTTTG
* ** * *
561958 GAGTACCCCTTCGAAAATAACGGGGTTGGAGTATCTTCGATTGTGAAAATTTAGTGTTTTGGAAA
1 GAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAA
* *
562023 TAAAACCGAGGTTGGAGTATCCCCTCAAAAAT-AACGAGTTTGAGGTATCACCAATTGTGAAAAA
66 TAAAACCG-GGTTGGAGTATCCCCTCGAAAATAAACGAGTTGGAGGTATCACCAATTGTGAAAAA
*
562087 TTGGTGTTTTGGATATAAAACCAG-GATTA
130 TTGGTGTTTTGGAAATAAAA-CAGTGATTA
** * *
562116 GAGTATCCCTTCGAAAATAACAAGGTTGGAGTATCCCCGAATGTGAAAAATTGGTGTTTTGAAAA
1 GAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAA
* * *
562181 TAAAACCAGGGTTGAAGTATCCTCTCGGAAATAAAGCG-GTTGGA-GTATC-CTCAATTGCTG-A
66 TAAAACC-GGGTTGGAGTATCCCCTCGAAAATAAA-CGAGTTGGAGGTATCAC-CAATTG-TGAA
** * *
562242 AAATTGGTGTTTTGGAAATAAAATTGTGCTTG
127 AAATTGGTGTTTTGGAAATAAAACAGTGATTA
* * * * * *
562274 GAGTATCCCTTTGGAAATAACGGGGTTGGAGTATCCCTGATTGTGAAAAATTGATGCTTTGGGAA
1 GAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAA
*
562339 TAAAACCGGGGTTGGAGTATCCCCTCGTAAATAAA
66 TAAAACC-GGGTTGGAGTATCCCCTCGAAAATAAA
562374 AACATGAATG
Statistics
Matches: 219, Mismatches: 33, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
157 2 0.01
158 205 0.94
159 10 0.05
160 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (158 bp):
GAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAA
TAAAACCGGGTTGGAGTATCCCCTCGAAAATAAACGAGTTGGAGGTATCACCAATTGTGAAAAAT
TGGTGTTTTGGAAATAAAACAGTGATTA
Found at i:564778 original size:30 final size:30
Alignment explanation
Indices: 564742--564810 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
564732 TACACTAAGA
564742 AATGTATCGATACATCTGGGTAAAACCCAG
1 AATGTATCGATACATCTGGGTAAAACCCAG
* *
564772 AATGTATCGATACATTTGGGTAAAATCCAG
1 AATGTATCGATACATCTGGGTAAAACCCAG
*
564802 AATATATCG
1 AATGTATCG
564811 TTATAATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (30 bp):
AATGTATCGATACATCTGGGTAAAACCCAG
Found at i:569033 original size:20 final size:19
Alignment explanation
Indices: 569008--569075 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 19
568998 CAGAATGCAT
*
569008 GATACATTGAGGAATGTATC
1 GATACATTGA-AAATGTATC
* *
569028 GATACATTCATACATGTATC
1 GATACATTGA-AAATGTATC
569048 GATACATTGAAAAATGTATC
1 GATACATTG-AAAATGTATC
569068 GATACATT
1 GATACATT
569076 TGGGTAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 40 0.98
21 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (19 bp):
GATACATTGAAAATGTATC
Found at i:569104 original size:90 final size:90
Alignment explanation
Indices: 568951--569119 Score: 259
Period size: 90 Copynumber: 1.9 Consensus size: 90
568941 TTTTAACTAG
*
568951 ATGTATCGATACATTGAAATATGTATCAATACATCTGGGTAAAACGACAGAATGCATGATACATT
1 ATGTATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAACGACAGAATGCATGATACATT
**
569016 GAGGAATGTATCGATACATTCATAC
66 GAAAAATGTATCGATACATTCATAC
* * * *
569041 ATGTATCGATACATTGAAAAATGTATCGATACATTTGGGTAAAA-GATAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAACGACAGAATGCAT-GATACAT
569105 TGAAAAATGTATCGA
65 TGAAAAATGTATCGA
569120 AATGTCTGGG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
89 10 0.14
90 61 0.86
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (90 bp):
ATGTATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAACGACAGAATGCATGATACATT
GAAAAATGTATCGATACATTCATAC
Found at i:570800 original size:13 final size:13
Alignment explanation
Indices: 570782--570808 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
570772 ACGTTATGCT
570782 TTGTATCGATACA
1 TTGTATCGATACA
570795 TTGTATCGATACA
1 TTGTATCGATACA
570808 T
1 T
570809 GTTAATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:570917 original size:33 final size:33
Alignment explanation
Indices: 570857--570925 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
570847 CTACCACTGT
* *
570857 TTGTATCGATACATGGTACAATATATCGATACA
1 TTGTATCGATACATGATACAATATATCGACACA
* *
570890 TTGTATCGATACATGATGA-ATTGTATCGACACA
1 TTGTATCGATACATGAT-ACAATATATCGACACA
570923 TTG
1 TTG
570926 CTTGTAATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATATATCGACACA
Found at i:573686 original size:28 final size:28
Alignment explanation
Indices: 573580--573983 Score: 460
Period size: 28 Copynumber: 14.4 Consensus size: 28
573570 AGATTCATTT
* * *
573580 TCAAAGCCCACAAGTCAATGGCATCATTT
1 TCAAAGCCCACAAGTCAGTGGCA-CCTTC
*
573609 TCAAAGCCCATAAGTCAGTGGCATCC-TC
1 TCAAAGCCCACAAGTCAGTGGCA-CCTTC
*
573637 TTAAAGCCCAC-AGTCAGTGGCACCTTC
1 TCAAAGCCCACAAGTCAGTGGCACCTTC
*
573664 TCAAAGCCCACAAGTCAATGGCATCC-TC
1 TCAAAGCCCACAAGTCAGTGGCA-CCTTC
* * *
573692 TTAAAGCCCATAAGTCAGTGGCACTTTC
1 TCAAAGCCCACAAGTCAGTGGCACCTTC
* * *
573720 TCAAAGCCCGCAAGTCAGTAGTATCC-TC
1 TCAAAGCCCACAAGTCAGTGGCA-CCTTC
* *
573748 TCCAAGCCCACAAGTTAGTGGCACCTT-
1 TCAAAGCCCACAAGTCAGTGGCACCTTC
* *
573775 TCCAAAACCCACAAGTCAGTGGCACCTTT
1 T-CAAAGCCCACAAGTCAGTGGCACCTTC
*
573804 TCAAAACCCACAAGTCAGTGGCACCTTC
1 TCAAAGCCCACAAGTCAGTGGCACCTTC
573832 TCAAAGCCCACAAGTCAGTGGCACCTTC
1 TCAAAGCCCACAAGTCAGTGGCACCTTC
* *
573860 TTAAAGCCCACAAGTTAGTGGCACCTTC
1 TCAAAGCCCACAAGTCAGTGGCACCTTC
* ** *
573888 TCAAGGCCCACGTGTCAGTGGTACCTTC
1 TCAAAGCCCACAAGTCAGTGGCACCTTC
* * * * *
573916 TCAAAGCTCACAAGTTAGTAGCACATTT
1 TCAAAGCCCACAAGTCAGTGGCACCTTC
573944 TCAAAGCCCACAAGTCAGTGGCATCCTT-
1 TCAAAGCCCACAAGTCAGTGGCA-CCTTC
573972 TCAAAGCCCACA
1 TCAAAGCCCACA
573984 CAAGTCGGTG
Statistics
Matches: 317, Mismatches: 49, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
26 2 0.01
27 27 0.09
28 258 0.81
29 30 0.09
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (28 bp):
TCAAAGCCCACAAGTCAGTGGCACCTTC
Found at i:574019 original size:32 final size:33
Alignment explanation
Indices: 573942--574030 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 33
573932 AGTAGCACAT
* *
573942 TTTCAAAGC-C-CACAAGTCAGTGGC-A--TCC
1 TTTCAAAGCACACACAAGTCGGTGGCAACTTTC
*
573970 TTTCAAAGCCCACACAAGTCGGTGGCAACTTTC
1 TTTCAAAGCACACACAAGTCGGTGGCAACTTTC
* *
574003 TTT-AAAGCACATACAAGTTGGTGGCAAC
1 TTTCAAAGCACACACAAGTCGGTGGCAAC
574031 CCTTCTAAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 9 0.18
29 1 0.02
30 13 0.25
31 1 0.02
32 22 0.43
33 5 0.10
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (33 bp):
TTTCAAAGCACACACAAGTCGGTGGCAACTTTC
Found at i:575694 original size:20 final size:21
Alignment explanation
Indices: 575655--575694 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
575645 CAGCCCCTAA
*
575655 TCATGCATTTTTTACTATGTT
1 TCATGCATTTTTAACTATGTT
575676 TCATGCATTTTTAAC-ATGT
1 TCATGCATTTTTAACTATGT
575695 CCAGCACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.53
Consensus pattern (21 bp):
TCATGCATTTTTAACTATGTT
Found at i:576327 original size:81 final size:81
Alignment explanation
Indices: 576180--576330 Score: 185
Period size: 81 Copynumber: 1.9 Consensus size: 81
576170 AGCTAGGGTG
* * * * * * *
576180 AAACTGATAAAGCCAACTGGTTAGAAGGGTTGACTAAGGCAGAACCGACAAAATCAATCAAATAA
1 AAACTCATAAAGCCAACAGGTTAGAAAGGTTGACCAAGGCAAAACCAACAAAATCAACCAAATAA
576245 AAGGTTGGCCAGGGCA
66 AAGGTTGGCCAGGGCA
* * * * * *
576261 AAACTCATAAAGCCCACAGGTTTGAAAGGTTGACCAAGGCAAAACTAATAAAGTCAACCAACTAA
1 AAACTCATAAAGCCAACAGGTTAGAAAGGTTGACCAAGGCAAAACCAACAAAATCAACCAAATAA
576326 AAGGT
66 AAGGT
576331 AGAAGGGTTG
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
81 57 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.17
Consensus pattern (81 bp):
AAACTCATAAAGCCAACAGGTTAGAAAGGTTGACCAAGGCAAAACCAACAAAATCAACCAAATAA
AAGGTTGGCCAGGGCA
Found at i:576440 original size:128 final size:129
Alignment explanation
Indices: 576201--576446 Score: 298
Period size: 128 Copynumber: 1.9 Consensus size: 129
576191 GCCAACTGGT
* * * *
576201 TAGAAGGGTTGACTAAGGCAGAACCGACAAAATCAATCAAATAAAAGGTTGGCCAGGGCAAAACT
1 TAGAAGGGTTGACTAAGGCAAAACCAACAAAATCAATCAAATAAAAGGTTAGCCAAGGCAAAACT
* * * * *
576266 CATAAAGCCCACAGGTTTGAAAGGTTGACCAAGGCAAAACTAATAAAGTCAACCAACTAAAAGG
66 CATAAAGCCAACAAGTTAGAAAGGTGGACCAAGGCAAAACCAATAAAGTCAACCAACTAAAAGG
* * *
576330 TAGAAGGGTTGACTAA-GCAAAACCAATAAAGTCAA-CTAATTAAAAGGTTAGCCAAGGCAAAAC
1 TAGAAGGGTTGACTAAGGCAAAACCAACAAAATCAATC-AAATAAAAGGTTAGCCAAGGCAAAAC
* * * * ** *
576393 TGATAAAGCCAAGAAGTTAGAAGGGTGGACTAAGGTGAAACCGATAAAGTCAAC
65 TCATAAAGCCAACAAGTTAGAAAGGTGGACCAAGGCAAAACCAATAAAGTCAAC
576447 TAATTAGTAG
Statistics
Matches: 97, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
127 1 0.01
128 80 0.82
129 16 0.16
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (129 bp):
TAGAAGGGTTGACTAAGGCAAAACCAACAAAATCAATCAAATAAAAGGTTAGCCAAGGCAAAACT
CATAAAGCCAACAAGTTAGAAAGGTGGACCAAGGCAAAACCAATAAAGTCAACCAACTAAAAGG
Found at i:577597 original size:164 final size:165
Alignment explanation
Indices: 577427--577751 Score: 359
Period size: 164 Copynumber: 2.0 Consensus size: 165
577417 TCATCGGAGT
* *** * * * * *
577427 AAAATTTTTAAAATTCATCAAATATTGTTACCTAACTCCCATTTAATCAGTTTGGAAAAA-TTCA
1 AAAATTTTCAAAATTCATCAAATAGCATCACCTAACTCACAATAAATCAGTTT-CAAAAATTTCA
* * * ** * *
577491 TTTATTTT-TATGAGTTTTTTATTTTTTT-TGAAATTCTCTTATTTTTAAAAAATTGAGTTTTCT
65 TTTATTTTCT-TGAGTTTTTCATTTTTTTCTGAAATGCCCTTATTTACAAAAAATCGAATTTTCT
* *
577554 ATTCCATAAAGGTTTTCGAGGGGGTTTTTCTCAATTC
129 ATTCCATAAAGGTTTTCGAGAGGATTTTTCTCAATTC
* * ** * *
577591 AAAATTTTCAATATTCATCAACTAGCATCATTTAATTCATAATAAATCAGTTTCAAAAATTTCAT
1 AAAATTTTCAAAATTCATCAAATAGCATCACCTAACTCACAATAAATCAGTTTCAAAAATTTCAT
*
577656 TTATTTTCTTGGGTTTTTCATTTTTTTCCATGAAATGCCCTTATTTACAAAAAATCGAATTTTCT
66 TTATTTTCTTGAGTTTTTCATTTTTTT-C-TGAAATGCCCTTATTTACAAAAAATCGAATTTTCT
*
577721 ATTCCATATAGGTTTTCGAGAGGATTTTTCT
129 ATTCCATAAAGGTTTTCGAGAGGATTTTTCT
577752 TGGTTTAAAA
Statistics
Matches: 130, Mismatches: 26, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
163 5 0.04
164 67 0.52
165 1 0.01
167 57 0.44
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (165 bp):
AAAATTTTCAAAATTCATCAAATAGCATCACCTAACTCACAATAAATCAGTTTCAAAAATTTCAT
TTATTTTCTTGAGTTTTTCATTTTTTTCTGAAATGCCCTTATTTACAAAAAATCGAATTTTCTAT
TCCATAAAGGTTTTCGAGAGGATTTTTCTCAATTC
Found at i:578011 original size:15 final size:16
Alignment explanation
Indices: 577983--578016 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
577973 ATTTTCGGAA
577983 TTTTATTTAAATTTATT
1 TTTTATTT-AATTTATT
578000 TTTTATTT-ATTTATT
1 TTTTATTTAATTTATT
578015 TT
1 TT
578017 GCCTAGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTATTTAATTTATT
Found at i:578443 original size:15 final size:15
Alignment explanation
Indices: 578418--578450 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
578408 TTATTTCTAT
578418 ATGATGTTATGAATAC
1 ATGATGTTATGAA-AC
578434 ATGA-GTTATGAAAC
1 ATGATGTTATGAAAC
578448 ATG
1 ATG
578451 TTGAGTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 8 0.47
16 4 0.24
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (15 bp):
ATGATGTTATGAAAC
Found at i:580699 original size:166 final size:162
Alignment explanation
Indices: 580194--580718 Score: 597
Period size: 165 Copynumber: 3.2 Consensus size: 162
580184 TTTCATTGGA
* * * * * *
580194 TTAAAATTTTTAAAATTCATCAAATATTATTATCT-AATCACCATTTAATTAGTTTTGAAAAATT
1 TTAAAATTTTTAATATTCATCAAATATTATTATTTAAATCA-TAGTAAATCA-TTTTGAAAAATT
* * * *
580258 CATTTATTTTCATGAGTTTTCCATTTTTTTCCTTGAAACTCTCTAATTACCAAAAAACTGAGTTT
64 CATTTATTTTCATGAGTTTTTCATTTTTTTCCTTGAAATTCCCT-ATT-TCAAAAAACTGAGTTT
580323 TTTATTCCATAAATGTTTTTGGGGGTTTTTCTCAGT
127 TTTATTCCATAAATGTTTTTGGGGGTTTTTCTCAGT
* * *
580359 TCAAAATTTTTAATATTCATCAAATATTATCATTTAAATCATAGTAAACCCATTTTGAAAAATTC
1 TTAAAATTTTTAATATTCATCAAATATTATTATTTAAATCATAGTAAA-TCATTTTGAAAAATTC
* * * *
580424 ATTTATTTTCAAGAGTTTTTCATTTTTTTCCTTGAAATTCTCATGTTTCCAAAAAACTGGGTTTT
65 ATTTATTTTCATGAGTTTTTCATTTTTTTCCTTGAAATTC-CCTATTT-CAAAAAACTGAGTTTT
* * *
580489 TTATTCCATACATGTTTTTGGGGGGTTCTTCTCTGT
128 TTATTCCATAAATGTTTTT-GGGGGTTTTTCTCAGT
* * * *
580525 TAAAAATTTTTAATATTCATCAAATATCATTATTTAAATCATAGTAAATCATTTTTGAAAATTTT
1 TTAAAATTTTTAATATTCATCAAATATTATTATTTAAATCATAGTAAATCA-TTTTGAAAAATTC
* * ** ** *
580590 ATTTATTTTCATGAGTTTTTCATTTTTTTTCTTAAAATTTCCCTATTTCTGAAAACCAAGTTTTC
65 ATTTATTTTCATGAGTTTTTCATTTTTTTCCTTGAAA-TTCCCTATTTCAAAAAACTGAGTTTTT
* * *
580655 TATTCCATAAATGTTTTCGAAAGGATTTTTCTCAGT
129 TATTCCATAAATGTTTTTG--GGGGTTTTTCTCAGT
580691 TTAAAATTTTT-ATAATTCAT-ATAATATT
1 TTAAAATTTTTAAT-ATTCATCA-AATATT
580719 CTCATTAAAC
Statistics
Matches: 304, Mismatches: 45, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
164 1 0.00
165 152 0.50
166 148 0.49
167 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (162 bp):
TTAAAATTTTTAATATTCATCAAATATTATTATTTAAATCATAGTAAATCATTTTGAAAAATTCA
TTTATTTTCATGAGTTTTTCATTTTTTTCCTTGAAATTCCCTATTTCAAAAAACTGAGTTTTTTA
TTCCATAAATGTTTTTGGGGGTTTTTCTCAGT
Found at i:582154 original size:21 final size:22
Alignment explanation
Indices: 582113--582162 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
582103 ATTAAGGTAG
**
582113 AAATAAAATTTTTGAAAATAAA
1 AAATAAAATTAATGAAAATAAA
*
582135 AAATAAAATTAATG-AAATAAT
1 AAATAAAATTAATGAAAATAAA
582156 AAATAAA
1 AAATAAA
582163 TATTGTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (22 bp):
AAATAAAATTAATGAAAATAAA
Found at i:582529 original size:142 final size:140
Alignment explanation
Indices: 582178--582732 Score: 686
Period size: 140 Copynumber: 4.0 Consensus size: 140
582168 TTTTATCACT
* * * * *
582178 AAATAAAAAATTATTATCTTAATTTTTAAATACTTCTAATATTCCTATGGTTTTCTATACGGGTA
1 AAAT-AAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAGGGGTA
* * * *
582243 TAGAAATCTTTAAAACTTTTCGTATTTTTTC-GATTCCCCATTATGGTACGAAATGAATTTTTTG
65 TAGAAATCTTTAAAAATTTTCGTATCTTTTCAG-TTCTCCATTATGGTACAAAATGAATTTTTT-
*
582307 GAAACTAAAAATC
128 GAAATTAAAAATC
* * ** *
582320 AAAT-AAAATTAGTATCTTAATTTTTCAAGATTTCTAATATTCCTATAGTTTTTTATAGTGGTAT
1 AAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAGGGGTAT
* * * *
582384 AGAAATTTTTAAAAATTTTCGTCTCTTTTCGGTTCTCCATTATGGTACAAAATGAATTTTCTTAA
66 AGAAATCTTTAAAAATTTTCGTATCTTTTCAGTTCTCCATTATGGTACAAAATGAATTTT-TTGA
582449 TAATTAAAAATC
130 -AATTAAAAATC
* *
582461 AAATAAAAATTATTATCTTAATTTTTCAAGATTTTTAATATTCCTATGGTTTTCCGTAGGGGTAT
1 AAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAGGGGTAT
* *
582526 AGAAATCTTTAAAAATTTTCGTATCTTTTCAGTTCTCCATTAAGGTACAAAATGAATTTTTGGAA
66 AGAAATCTTTAAAAATTTTCGTATCTTTTCAGTTCTCCATTATGGTACAAAATGAATTTTTTGAA
* *
582591 GTTAAAAATT
131 ATTAAAAATC
* * * * *
582601 AAATAAAAATTCTTGTCTTAATTTTTCAAGATTT-TTATGTTCCTAAGGTTTTCCATAGGGGTAT
1 AAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAGGGGTAT
* * * * * * * *
582665 AGAAATCTTCAAAACTTTTCATATCTTTTCAGATCTCCATGAAGGTACGAAAT-AAGATTTTTGA
66 AGAAATCTTTAAAAATTTTCGTATCTTTTCAGTTCTCCATTATGGTACAAAATGAA-TTTTTTGA
582729 AATT
130 AATT
582733 TACAACTTAT
Statistics
Matches: 362, Mismatches: 46, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
138 2 0.01
139 82 0.23
140 146 0.40
141 19 0.05
142 113 0.31
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (140 bp):
AAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAGGGGTAT
AGAAATCTTTAAAAATTTTCGTATCTTTTCAGTTCTCCATTATGGTACAAAATGAATTTTTTGAA
ATTAAAAATC
Found at i:583124 original size:177 final size:177
Alignment explanation
Indices: 582766--583129 Score: 430
Period size: 177 Copynumber: 2.1 Consensus size: 177
582756 CCTTTAGATT
* * * *
582766 TATTTATGGATCTTTGATTCTCATAAGGATAAAATTATCGTTTCTTTCCTTTTTTTCGAGCCCTT
1 TATTTATGGATCTTTGATTCTCATAAGGATAAAATTATCATTTCTTTCATTCTTCTCGAGCCCTT
* * *
582831 TAGGAGTACTAGTATACTTTCATGTCGAAGGTATACCTATAAGGGTATTTTTGTAATTTTCTAAA
66 TAGGAGTACTAGTATACTTTCATGTCGAAAGTATACCCAGAAGGGTATTTTTGTAATTTTCTAAA
* * * * ****
582896 ATCGAGTCCTAGGTTGTTATCGGGTTCGCTTTTATGCCAAGGGTGGG
131 ATCGAGTCCTAAGTTGTCATCGGGTCCACTTTTATGCCAAGCACAGG
* * *
582943 TATTTTTGGATTTTTGTTTCTCATAAGGATAAAATTATCATTTCTTTCATTCTTCT-GAGCCCTT
1 TATTTATGGATCTTTGATTCTCATAAGGATAAAATTATCATTTCTTTCATTCTTCTCGAGCCCTT
* * * *
583007 TAGGGGTATTAAG-ATACTTTCATGTTGAAAGTATACCCAGAAGGGTATTTTTGTAATTTTTTTA
66 TAGGAGTACT-AGTATACTTTCATGTCGAAAGTATACCCAGAAGGGTATTTTTGTAA-TTTTCTA
* * * * *
583071 GAATCGAGTCTTAAGTTGTCATTGGGTCCACTTTTATATCGAA-CACAGG
129 AAATCGAGTCCTAAGTTGTCATCGGGTCCACTTTTAT-GCCAAGCACAGG
583120 TATTTA-GGAT
1 TATTTATGGAT
583130 AGGTTGATCT
Statistics
Matches: 156, Mismatches: 28, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
176 59 0.38
177 94 0.60
178 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.43
Consensus pattern (177 bp):
TATTTATGGATCTTTGATTCTCATAAGGATAAAATTATCATTTCTTTCATTCTTCTCGAGCCCTT
TAGGAGTACTAGTATACTTTCATGTCGAAAGTATACCCAGAAGGGTATTTTTGTAATTTTCTAAA
ATCGAGTCCTAAGTTGTCATCGGGTCCACTTTTATGCCAAGCACAGG
Found at i:583277 original size:155 final size:155
Alignment explanation
Indices: 583053--583529 Score: 445
Period size: 155 Copynumber: 3.1 Consensus size: 155
583043 CCAGAAGGGT
* * *
583053 ATTTTTGTAATTTTTTTAGAA-TCGAGTCTTAAGTTGTCATTGGGTCCACTTTTAT-ATCGAACA
1 ATTTTTGTAA-TTTTTTAGAACT-GAGTCTTAAGTTGTCACTAGGTCCACTTTTATGCT-GAA-A
** * * ** *
583116 -CAGGTATTTAGGATAGGTTGATCTCGCCTATAATCATTTTCGTGTCTTTTAAGGGTATCGGGCA
62 GTGGGTATTTAGGATAGGTTCATCTCACCTATAATCATTTTCAAGTCTTTTAAGGGTATCGAGCA
583180 CTTT-TAAG-TCAAGAGTATCCCCTA-AGGGC
127 -TTTCTAAGTTCAAG-GTATCCCCTAGA-GGC
* * * *
583209 TTTTTTGTAATTTTTTAGAACTGAGTCTTAAGTTGTCCCTAAGTCCACTTTTATGCTGAATGTGG
1 ATTTTTGTAATTTTTTAGAACTGAGTCTTAAGTTGTCACTAGGTCCACTTTTATGCTGAAAGTGG
* ** * * *
583274 GTATTTAGGATAGGTTCACCTCATTTGTAATCCTTTTTAAGTCTTTTAAGGGTATCGAGCATTTC
66 GTATTTAGGATAGGTTCATCTCACCTATAATCATTTTCAAGTCTTTTAAGGGTATCGAGCATTTC
* * *
583339 TACGTTGAAGGTATCCCCTTGAGGC
131 TAAGTTCAAGGTATCCCCTAGAGGC
** * * * *
583364 ATTTTCATAATTTTCTAGAACTGAGTCCTAGGTTGTCACTAGGTCTACTTTTATGCTGAAAGTGG
1 ATTTTTGTAATTTTTTAGAACTGAGTCTTAAGTTGTCACTAGGTCCACTTTTATGCTGAAAGTGG
** * * * * *
583429 GTATTTAGGATAGGTTCATCTCATATATAATCCTTTTTAAGTC-CTT--GGGTATCAAGCACTTC
66 GTATTTAGGATAGGTTCATCTCACCTATAATCATTTTCAAGTCTTTTAAGGGTATCGAGCATTTC
* * *
583491 TACA-TTGAAGGT-GCCCCATAGGGGC
131 TA-AGTTCAAGGTATCCCC-TAGAGGC
583516 ATTTTTGTAATTTT
1 ATTTTTGTAATTTT
583530 AAAATCGAGT
Statistics
Matches: 268, Mismatches: 45, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
151 4 0.01
152 41 0.15
154 5 0.02
155 202 0.75
156 16 0.06
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (155 bp):
ATTTTTGTAATTTTTTAGAACTGAGTCTTAAGTTGTCACTAGGTCCACTTTTATGCTGAAAGTGG
GTATTTAGGATAGGTTCATCTCACCTATAATCATTTTCAAGTCTTTTAAGGGTATCGAGCATTTC
TAAGTTCAAGGTATCCCCTAGAGGC
Found at i:583720 original size:61 final size:61
Alignment explanation
Indices: 583644--583765 Score: 201
Period size: 61 Copynumber: 2.0 Consensus size: 61
583634 AAGTTGATGG
* *
583644 TAAACCTTAGGGATATTTTAACATTTT-CCTCAAAACCTAGTCCTAAAAAACTACCAGGTCA
1 TAAACCTTAAGGATATTTTAACATTTTCCCT-AAAACCTAGGCCTAAAAAACTACCAGGTCA
*
583705 TAAACCTTAAGGATATTTTAACATTTTCCCTAAAACCTAGGCCTAAAAAACTACCATGTCA
1 TAAACCTTAAGGATATTTTAACATTTTCCCTAAAACCTAGGCCTAAAAAACTACCAGGTCA
583766 CTTTTATGAT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 54 0.95
62 3 0.05
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (61 bp):
TAAACCTTAAGGATATTTTAACATTTTCCCTAAAACCTAGGCCTAAAAAACTACCAGGTCA
Found at i:587775 original size:51 final size:51
Alignment explanation
Indices: 587715--587849 Score: 189
Period size: 51 Copynumber: 2.6 Consensus size: 51
587705 ATTTGCCTGT
* * * *
587715 ATGTATCGATACAGTGGATAATGTATCGATACATCTGGGTAAAAAATCAAA
1 ATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAAAACCAAA
* * * *
587766 ATGTATCGATACAATGAAGAATGTATCAATACATCTGGGTAAAAACCCATA
1 ATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAAAACCAAA
*
587817 ATGTATCGATACAATGAACAATGTAACGATACA
1 ATGTATCGATACAATGAACAATGTATCGATACA
587850 AACAATAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (51 bp):
ATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAAAACCAAA
Found at i:591165 original size:16 final size:17
Alignment explanation
Indices: 591120--591168 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
591110 ATTTTCTCTA
591120 AATAAGAAAAAGGAAAAAG
1 AATAAGAAAAA--AAAAAG
591139 AATAAGAAAAAAAAAAG
1 AATAAGAAAAAAAAAAG
591156 AA-AAGCAAAAAAA
1 AATAAG-AAAAAAA
591169 TGCAAAAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.10
17 15 0.52
19 11 0.38
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (17 bp):
AATAAGAAAAAAAAAAG
Found at i:591175 original size:16 final size:16
Alignment explanation
Indices: 591147--591193 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
591137 AGAATAAGAA
*
591147 AAAAAAAAG-AAAAGC
1 AAAAAAATGCAAAAGC
591162 AAAAAAATGCAAAAGC
1 AAAAAAATGCAAAAGC
591178 ATGAAAAAAGTGCAAA
1 A--AAAAAA-TGCAAA
591194 TAGAAAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 8 0.30
16 7 0.26
18 6 0.22
19 6 0.22
ACGTcount: A:0.70, C:0.09, G:0.15, T:0.06
Consensus pattern (16 bp):
AAAAAAATGCAAAAGC
Found at i:594258 original size:13 final size:13
Alignment explanation
Indices: 594240--594322 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
594230 CATAAAGTGT
594240 TGTATCGATATAA
1 TGTATCGATATAA
594253 TGTATCGATACATAA
1 TGTATCGAT--ATAA
*
594268 GTGTTGTATCGATACAA
1 ----TGTATCGATATAA
594285 TGTATCGATACATAA
1 TGTATCGAT--ATAA
594300 GTTTGTATCGATATAA
1 ---TGTATCGATATAA
594316 TGTATCG
1 TGTATCG
594323 CTACGAAGCT
Statistics
Matches: 57, Mismatches: 2, Indels: 22
0.70 0.02 0.27
Matches are distributed among these distances:
13 25 0.44
15 7 0.12
16 4 0.07
17 3 0.05
18 9 0.16
19 9 0.16
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATATAA
Done.