Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012848.1 Corchorus olitorius cultivar O-4 contig12881, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 52150
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Found at i:5599 original size:3 final size:3
Alignment explanation
Indices: 5591--5626 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
5581 AAATAAAAAT
5591 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-A GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
5627 GAAAAGAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:8613 original size:31 final size:31
Alignment explanation
Indices: 8575--8714 Score: 129
Period size: 31 Copynumber: 4.5 Consensus size: 31
8565 TTTGTTCATG
* *
8575 TGGCATGCCACATGTCATTTTTTGGAACACA
1 TGGCGTGCCACATGTCATTTTTTGGTACACA
* ** * * *
8606 TGGCATGCCATGTGTCACTTTTGGGTATACA
1 TGGCGTGCCACATGTCATTTTTTGGTACACA
* ** * * *
8637 TGACGTGATACGTGTCATCTTTTGGTACACG
1 TGGCGTGCCACATGTCATTTTTTGGTACACA
*
8668 TGGCGTGCCACATGTC-TCTTTTTGGTACACG
1 TGGCGTGCCACATGTCAT-TTTTTGGTACACA
8699 TGGCGTGCCACATGTC
1 TGGCGTGCCACATGTC
8715 GCTTTTTTTA
Statistics
Matches: 87, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
30 1 0.01
31 86 0.99
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.34
Consensus pattern (31 bp):
TGGCGTGCCACATGTCATTTTTTGGTACACA
Found at i:8729 original size:30 final size:31
Alignment explanation
Indices: 8656--8739 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
8646 ACGTGTCATC
*
8656 TTTTGGTACACGTGGCGTGCCACATGTCTCT
1 TTTTGGTACACGTGGCGTGCCACATGTCGCT
8687 TTTTGGTACACGTGGCGTGCCACATGTCGCT
1 TTTTGGTACACGTGGCGTGCCACATGTCGCT
* * *
8718 TTTT-TTACACGTGACATGCCAC
1 TTTTGGTACACGTGGCGTGCCAC
8740 GTCGGACATC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 15 0.31
31 34 0.69
ACGTcount: A:0.15, C:0.26, G:0.24, T:0.35
Consensus pattern (31 bp):
TTTTGGTACACGTGGCGTGCCACATGTCGCT
Found at i:9858 original size:56 final size:56
Alignment explanation
Indices: 9790--9902 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
9780 AAAATTATTA
9790 CACAATCAGTGGAGTTTAGCAGACTTGTCCTTCCTACCAGGAATCAGGCACTGCAT
1 CACAATCAGTGGAGTTTAGCAGACTTGTCCTTCCTACCAGGAATCAGGCACTGCAT
9846 CACAATCAGTGGAGTTTAGCAGACTTGTCCTTCCTACCAGGAATCAGGCACTGCAT
1 CACAATCAGTGGAGTTTAGCAGACTTGTCCTTCCTACCAGGAATCAGGCACTGCAT
9902 C
1 C
9903 CGAACCACTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (56 bp):
CACAATCAGTGGAGTTTAGCAGACTTGTCCTTCCTACCAGGAATCAGGCACTGCAT
Found at i:11832 original size:31 final size:29
Alignment explanation
Indices: 11794--11870 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
11784 AATCCGTATA
11794 GGTCCCTCTATTTACAAAAAAGGATCAATTT
1 GGTCCCTCTA-TTACAAAAAAGG-TCAATTT
* * **
11825 GGTCCCTCTACTATAAAAACTGTCAATTT
1 GGTCCCTCTATTACAAAAAAGGTCAATTT
*
11854 GATCCCTCTACTTACAA
1 GGTCCCTCTA-TTACAA
11871 TTTGGTGTCG
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 16 0.42
30 12 0.32
31 10 0.26
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.32
Consensus pattern (29 bp):
GGTCCCTCTATTACAAAAAAGGTCAATTT
Found at i:11916 original size:31 final size:31
Alignment explanation
Indices: 11795--11914 Score: 97
Period size: 31 Copynumber: 3.9 Consensus size: 31
11785 ATCCGTATAG
* ***
11795 GTCCCTCTATTTACAAAAAAGGATCAATTTG-
1 GTCCCTCTACTTACAAAATCTG-TCAATTTGA
11826 GTCCCTCTACTATA-AAAA-CTGTCAATTTGA
1 GTCCCTCTACT-TACAAAATCTGTCAATTTGA
** * *
11856 -TCCCTCTACTTACAATTTGGTGTCGA-TTGA
1 GTCCCTCTACTTACAAAAT-CTGTCAATTTGA
11886 GTCCCTCTACTTAGCAAAATCTGTCAATT
1 GTCCCTCTACTTA-CAAAATCTGTCAATT
11915 GATTATATAT
Statistics
Matches: 70, Mismatches: 11, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
28 2 0.03
29 20 0.29
30 5 0.07
31 36 0.51
32 7 0.10
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.35
Consensus pattern (31 bp):
GTCCCTCTACTTACAAAATCTGTCAATTTGA
Found at i:12199 original size:29 final size:30
Alignment explanation
Indices: 12142--12214 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 30
12132 CACCAAATTG
* *
12142 TAAGTAGAGGGATCAAATTGACAGTTTTTA
1 TAAGTAGAGGGACCAAATTGACACTTTTTA
* *
12172 T-AGTA-AGGGACCAAATTGATCCCTTTTTG
1 TAAGTAGAGGGACCAAATTGA-CACTTTTTA
12201 TAAGTAGAGGGACC
1 TAAGTAGAGGGACC
12215 TGTACGGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 13 0.36
29 11 0.31
30 5 0.14
31 7 0.19
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (30 bp):
TAAGTAGAGGGACCAAATTGACACTTTTTA
Found at i:14747 original size:26 final size:26
Alignment explanation
Indices: 14711--14762 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
14701 CCATGCAGTC
*
14711 AACTATACTAATCTGGGAAGAAATTA
1 AACTATACTAAACTGGGAAGAAATTA
14737 AACTATACTAAACTGGGAAGAAATTA
1 AACTATACTAAACTGGGAAGAAATTA
14763 GAGGGTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (26 bp):
AACTATACTAAACTGGGAAGAAATTA
Found at i:20979 original size:24 final size:24
Alignment explanation
Indices: 20947--20994 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
20937 GGCCCTTTAG
20947 TTCAATGTAGTTCAATATGCAGAA
1 TTCAATGTAGTTCAATATGCAGAA
*
20971 TTCAATGTAGTTCCATATGCAGAA
1 TTCAATGTAGTTCAATATGCAGAA
20995 GTTAGCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (24 bp):
TTCAATGTAGTTCAATATGCAGAA
Found at i:27064 original size:31 final size:31
Alignment explanation
Indices: 27026--27189 Score: 170
Period size: 31 Copynumber: 5.3 Consensus size: 31
27016 TTATGCACGA
27026 GGCATGCCACGTGTCACTTTTTGGTATACAT
1 GGCATGCCACGTGTCACTTTTTGGTATACAT
*
27057 GGCATGCCACATGTCACTTTTTGGTATACAT
1 GGCATGCCACGTGTCACTTTTTGGTATACAT
*
27088 GGCATGCCATGTGTCACTTTTT-GT-TACATGT
1 GGCATGCCACGTGTCACTTTTTGGTATACA--T
* * * **
27119 GGCGTGCCATGTGTCACTTTTTGGTACATGT
1 GGCATGCCACGTGTCACTTTTTGGTATACAT
* * * * * *
27150 GGCGTGTCACATGTCGCTTTTTGATACACAT
1 GGCATGCCACGTGTCACTTTTTGGTATACAT
*
27181 GTCATGCCA
1 GGCATGCCA
27190 TGTCGGACAC
Statistics
Matches: 112, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
29 4 0.04
30 2 0.02
31 103 0.92
32 2 0.02
33 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (31 bp):
GGCATGCCACGTGTCACTTTTTGGTATACAT
Found at i:28887 original size:13 final size:13
Alignment explanation
Indices: 28869--28894 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28859 CTTCCTGCTC
28869 TTATTTCTTGCAA
1 TTATTTCTTGCAA
28882 TTATTTCTTGCAA
1 TTATTTCTTGCAA
28895 CTTACAGCAT
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:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
TTATTTCTTGCAA
Found at i:35298 original size:325 final size:328
Alignment explanation
Indices: 33279--35638 Score: 2224
Period size: 330 Copynumber: 7.2 Consensus size: 328
33269 TCTGTTTTTT
* * * * * * **
33279 GCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGACGTCGAGACTCCTCAAA
1 GCTAAAAACGCGTTTCGGGG-CACGGCTCAGTTTTGCATGAATTTTGGCGCCAAGACTCCTTGAA
* *
33344 ATAT-T-TA-T-AT-T----AAATCTCAGCCACATTGCATTTAATGATTTGTTTTTACGAGCATC
65 ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* *
33400 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGTGA
130 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCA-AAAAATATGAAAAACGATATTAAAAGCGT
* * * **
33465 GAAAAGTCCTCCAAT-TTTTTGGA-GTTGAATTATATATATCTTGTGAGTATTTTAGAAAAAAAT
194 GAAAAGTCCTCCAATCTTTTT-GACGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAAT
* * * * * * *
33528 TGAGGAAAAATATTTCTGGTCAATTTTTGCAAAATATTAACCGAAATCGTGTATGTTAGTCGAAA
258 TGAGGAAAAATCTTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTA--CTA-AC--CA
**
33593 TCACGGTTTTTA
317 TCACGGTTTTCG
* * * * * * *
33605 GCTAAAAACGCATTTCGGGACCACGGTTCAGTGTTGCATGATTTTTTGCGCCGAGACTCCTTGAA
1 GCTAAAAACGCGTTTCGGG-GCACGGCTCAGTTTTGCATGAATTTTGGCGCCAAGACTCCTTGAA
* * *** * *
33670 ATATCTACATTCATCCAACCAAATCTCAGCCACATTGGATTTAAGGATTTG-TAAAACAAACATC
65 ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * * * *
33734 TGAATCATGTTTCGATTTAATTAGAAATTAATCCCGAAAATAATAGGAAAACCGATATTAGAAGC
130 TGAATCTTGTTTCGATTTAATTAGAAATTAAT-TC-AAAA-AATATGAAAAACGATATTAAAAGC
* * * * * * * *** *
33799 ATGAAAA-ACCCCTCAATATTTTTGGCGTTGATTTATATAATTTTTATGAGTATTGCGGATAAAA
192 GTGAAAAGTCCTC-CAATCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAA
* * * * * * * *
33863 ATTAAGGAAATAA-CTTTTGAGTCAATTTTTGTAAAATTCTAGCCGAAATCGTATAATAATCATC
256 ATTGAGGAAA-AATCTTTCG-GTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATC
* *
33927 ATGGTTTTTG
319 ACGGTTTTCG
* * * * * *
33937 GCTAAAAACGCGTTCCGGGGCCCCGGCT-AGGTTTTGCATGATTTTTGGCGCCAGGACT-TTTTA
1 GCTAAAAACGCGTTTCGGGG-CACGGCTCA-GTTTTGCATGAATTTTGGCGCCAAGACTCCTTGA
* * * * * * **
34000 AGATATCCATATTCATTTAATCTAATCTCAGCTACATTGGATTGAACAATTTGTTTTTACGAGCA
64 A-ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
* *
34065 TCTGAATCTTATTTCGATTTAACTAGAAATTAATTCAAAAAATATGAAAAACGATATTAAAAGCG
128 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAATATGAAAAACGATATTAAAAGCG
* *
34130 TGAAAA-TCCTCCAATCTTTTTGACGTTAAATTATATATATTTTATGAGTATTTTAGGC-AAAAA
193 TGAAAAGTCCTCCAATCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTTTA-GCTAAAAA
* *
34193 TTGATGATAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAGATCATGTACACTAACCAT
257 TTGAGGA-AAAATCTTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCATGT--ACTAACCAT
*
34258 CACGGTTTTCT
318 CACGGTTTTCG
* * * * * *
34269 GCTAAAAATGCATTTCGAGGCCCTGTTCAGTTTTGC----A-TTT--CG---AGACTCCTTGAAA
1 GCTAAAAACGCGTTTCGGGGCACGGCTCAGTTTTGCATGAATTTTGGCGCCAAGACTCCTTGAAA
* * * * * * *
34324 GATCTATATTCATCTAATCAAATCTCAGCCACACTGAATTTAATGATTTGTTTTTATGAGCATTT
66 TATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
*
34389 GAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATAAAAAACGATATTAAAAGCGT
131 GAATCTTGTTTCGATTTAATTAGAAATTAATTC--AAAAAATATGAAAAACGATATTAAAAGCGT
* * * * ** *
34454 GAAAAAGGCTTTCAATTTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTTTCA-CTAGAAA
194 G-AAAAGTCCTCCAATCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTTT-AGCTAAAAA
** * * *
34518 TCAAGGAAAATTCTTTCGAGTCAATTTTTGTAAAATTTTAGCTGAAATCATG---T----A-CAC
257 TTGAGGAAAAATCTTTCG-GTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCAC
34575 GGTTTTCG
321 GGTTTTCG
** * * *
34583 GCT-AAAACAGCGTTTCGGGGTTCCGCTCAGTTTTGCATG-ATTTTTGTGCCAAGACTCCTTGAA
1 GCTAAAAAC-GCGTTTCGGGGCACGGCTCAGTTTTGCATGAATTTTGGCGCCAAGACTCCTTGAA
*
34646 ATATCTATATTCATCTAACCAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
65 ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * * * * *
34711 TAAATCTTATTTCGATTTAATTAGAAAGTTAATTTGAAAAAAT-TCAAAAAACAATATTAGAAGC
130 TGAATCTTGTTTCGATTTAATTAGAAA-TTAA-TTCAAAAAATAT-GAAAAACGATATTAAAAGC
* * * * * * * * * *
34775 GTTAAAAGCCCTTCAATATTTTTGATGTCGAATTATATATTTTCTATGACTATATTAGCCAAAAA
192 GTGAAAAGTCCTCCAATCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAA
* *
34840 TTGAGGAAATATCTTTCGGATCAA-TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC
257 TTGAGGAAAAATCTTTCGG-TCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCAC
* *
34904 AGTTTTTG
321 GGTTTTCG
* * * * * * *
34912 GCTAAAAACGCGTTCCAGGGCCACAGCTCTGTTTTGCATGATTTTTGGCGCCGATACTCCTTGAA
1 GCTAAAAACGCGTTTC-GGGGCACGGCTCAGTTTTGCATGAATTTTGGCGCCAAGACTCCTTGAA
* * * * * * * * *
34977 ATATCTTTATTCATCTAATCAAATCTCAGGCACATTAGATTTAAGAATTTG-TTTAATGTGAATC
65 ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* *
35041 TGAATCTTGTTTCAATTTAATTAGAAATT-A-T-AAAAAATATGAGAAACGATATTAAAAGCGTG
130 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAATATGAAAAACGATATTAAAAGCGTG
* ** * *
35103 AAAAGTCCTCCAATCCTTTTGACGTTGAATTATATATTTTTTATGAGTATTTTCTCTAGAAATCG
195 AAAAGTCCTCCAATCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTG
* *
35168 AGGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTAGTAACCATCATGGT
260 AGGAAAAATCTTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGT
35233 TTTCG
324 TTTCG
* ** * *
35238 GCTAAAACCGCG-TTCTGGGGTTCGGCTCAGTTTTGCTTGAATTTTGGTGCCAAGACTCCTTGAA
1 GCTAAAAACGCGTTTC-GGGGCACGGCTCAGTTTTGCATGAATTTTGGCGCCAAGACTCCTTGAA
** *
35302 ATATCTATATTCATCTAACCAAATCTCAGCCACATTAAATTTAAGGATTTGTTTTTACGAGCATT
65 ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * * *
35367 TGAATCTTGTTTCGATTTTATTAGAAATTAATTTGAAAAAATA-GAAAAAACAATATTAGAAGCG
130 TGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCAAAAAATATG-AAAAACGATATTAAAAGCG
* * * * * *
35431 TTAAAAGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAAT
193 TGAAAAGTCCTCCAATCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAAT
* * * *
35496 TGAAGAAATATTTTTCGGGTCAATTTTTGCAAAATCTTAGCCGAAAT-AGTGTACTAACCATCAC
258 TGAGGAAAAATCTTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCA-TGTACTAACCATCAC
** *
35560 AATTTTTG
321 GGTTTTCG
* * * * * * * * *
35568 GCTAAAAACACGCTCCAGGGCCACGTCTCTGTTTTGCATGATTTTTGGCACCGAGACTCCTTGAA
1 GCTAAAAACGCGTTTC-GGGGCACGGCTCAGTTTTGCATGAATTTTGGCGCCAAGACTCCTTGAA
35633 ATATCT
65 ATATCT
35639 CGGGCATATT
Statistics
Matches: 1653, Mismatches: 307, Indels: 143
0.79 0.15 0.07
Matches are distributed among these distances:
313 4 0.00
314 34 0.02
315 1 0.00
317 1 0.00
318 3 0.00
319 1 0.00
320 1 0.00
321 115 0.07
322 73 0.04
323 151 0.09
324 51 0.03
325 228 0.14
326 154 0.09
327 2 0.00
328 3 0.00
329 71 0.04
330 272 0.16
331 133 0.08
332 131 0.08
333 37 0.02
334 39 0.02
335 38 0.02
336 32 0.02
337 76 0.05
338 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (328 bp):
GCTAAAAACGCGTTTCGGGGCACGGCTCAGTTTTGCATGAATTTTGGCGCCAAGACTCCTTGAAA
TATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
GAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAATATGAAAAACGATATTAAAAGCGTGA
AAAGTCCTCCAATCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGA
GGAAAAATCTTTCGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTT
TCG
Found at i:35632 original size:656 final size:652
Alignment explanation
Indices: 33355--35638 Score: 2492
Period size: 656 Copynumber: 3.5 Consensus size: 652
33345 TATTTATATT
* * *
33355 AAATCTCAGCCACATTGCATTTAATGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
1 AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAA
* * * *
33420 TTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGTGAGAAAAGTCCTCCAAT-TTTT
66 TTAGAAATTAATTCA-AAAAATATGAAAAACAATATTAAAAGCGTGAAAAGCCCTCCAATCTTTT
* * * ** * *
33484 TGGA-GTTGAATTATATATATCTTGTGAGTATTTTAGAAAAAAATTGAGGAAAAATATTTCTGGT
130 T-GATGTCGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGT
* * * * * * * *
33548 CAATTTTTGCAAAATATTAACCGAAATCGTGTATGTTAGTCGAAATCACGGTTTTTAGCTAAAAA
194 CAATTTTTGCAAAATTTTAGCCGAAATAGTGTA--CTA-AC--CATCACAGTTTTTGGCTAAAAA
* * * * * *
33613 CGCATTTC-GGGACCACGGTTCAGTGTTGCATGATTTTTTGCGCCGAGACTCCTTGAAATATCTA
254 CACGTTCCAGGG-CCACAGTTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTA
* * * * ** * *
33677 CATTCATCCAACCAAATCTCAGCCACATTGGATTTAAGGATTTG-TAAAACAAACATCTGAATCA
318 TATTCATCTAATCAAATCTCAGCCACATT-GATTTAA-GATTTGTTTAATGAGA-ATCTGAATCT
* * *
33741 TGTTTCGATTTAATTAGAAATTAATCCCGAAAATAATAGGAAAACCGATATTAGAAGCATGAAAA
380 TGTTTCGATTTAATTAGAAATTAAT--C-AAAA-AATATGAAAA-CGATATTAAAAGCGTGAAAA
* * * * * *
33806 -ACCCCTCAATATTTTTGGCGTTGATTTATATAATTTTTATGAGTA-TTGCGGA-TAAAAATTAA
440 GACCTC-CAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTC--ACTAGAAATCAA
* * * *
33868 GGAAATAA-CTTTTGAGTCAATTTTTGTAAAATTCTAGCCGAAATCGTATAATAATCATCATGGT
502 GGAAA-AATCTTTCGAGTCAATTTTTGTAAAATTTTAGCCGAAATCAT-TAGTAA-CATCATGGT
* * * ** * * *
33932 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCT-AGGTTTTGCATGATTTTTGGCGCCAGGACT-
564 TTTCGGCTAAAACCGCGTTCTGGGG-TTCGGCTCA-GTTTTGCATGAATTTTGGTGCCAAGACTC
* * * * *
33995 TTTTAAGATATCCATATTCATTTAATC
627 CTTGAA-ATATCTATATTCATCTAACC
* * * **
34022 TAATCTCAGCTACATTGGATTGAACAATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAA
1 AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAA
* * *
34087 CTAGAAATTAATTCAAAAAATATGAAAAACGATATTAAAAGCGTGAAAA-TCCTCCAATCTTTTT
66 TTAGAAATTAATTCAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTT
* ** * * *
34151 GACGTTAAATTATATATATTTTATGAGTATTTTAGGCAAAAATTGATGATAAAATCTTTCAGGTC
131 GATGTCGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGA-AAAATCTTTCGGGTC
* *
34216 AATTTTTGCAAAATTTTAGCCGAGATCA-TGTACACTAACCATCACGGTTTTCT-GCTAAAAATG
195 AATTTTTGCAAAATTTTAGCCGAAAT-AGTGT--ACTAACCATCACAGTTTT-TGGCTAAAAA--
* * * *
34279 CA-TTTCGA-GGCC-CTGTTCAGTTTTGC---A--TTT-----CGAGACTCCTTGAAAGATCTAT
254 CACGTTCCAGGGCCACAGTTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTAT
* * * *
34331 ATTCATCTAATCAAATCTCAGCCACACTGAATTTAATGATTTGTTTTTATGAGCATTTGAATCTT
319 ATTCATCTAATCAAATCTCAGCCACATTG-ATTTAA-GATTTG-TTTAATGAGAATCTGAATCTT
*
34396 GTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATAAAAAACGATATTAAAAGCGTGAAAAAG
381 GTTTCGATTTAATTAGAAATTAA-TC--AAAAAATAT-GAAAACGATATTAAAAGCGTG-AAAAG
* * * * *
34461 GCTTTCAATTTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTTTCACTAGAAATCAAGGAA
441 ACCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCACTAGAAATCAAGGAA
* *
34526 AATTCTTTCGAGTCAATTTTTGTAAAATTTTAGCTGAAATCA-T-GT-ACA-C--GGTTTTCGGC
506 AAATCTTTCGAGTCAATTTTTGTAAAATTTTAGCCGAAATCATTAGTAACATCATGGTTTTCGGC
* * *
34585 TAAAACAGCGTT-TCGGGGTTCCGCTCAGTTTTGCATG-ATTTTTGTGCCAAGACTCCTTGAAAT
571 TAAAACCGCGTTCT-GGGGTTCGGCTCAGTTTTGCATGAATTTTGGTGCCAAGACTCCTTGAAAT
34648 ATCTATATTCATCTAACC
635 ATCTATATTCATCTAACC
* *
34666 AAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAA
1 AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAA
* * * * * *
34731 TTAGAAAGTTAATTTGAAAAAAT-TCAAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATATT
66 TTAGAAA-TTAA-TTCAAAAAATAT-GAAAAACAATATTAAAAGCGTGAAAAGCCCTCCAATCTT
* * *
34795 TTTGATGTCGAATTATATAT-TTTCTATGACTATATTAGCCAAAAATTGAGGAAATATCTTTCGG
128 TTTGATGTCGAATTATATATATTT-TATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGG
* * *
34859 ATCAA-TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGC
192 GTCAATTTTTGCAAAATTTTAGCCGAAATAGTGTACTAACCATCACAGTTTTTGGCTAAAAACAC
* * * *
34923 GTTCCAGGGCCACAGCTCTGTTTTGCATGATTTTTGGCGCCGATACTCCTTGAAATATCTTTATT
257 GTTCCAGGGCCACAGTTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATT
* *
34988 CATCTAATCAAATCTCAGGCACATTAGATTTAAGAATTTGTTTAATGTGAATCTGAATCTTGTTT
322 CATCTAATCAAATCTCAGCCACATT-GATTTAAG-ATTTGTTTAATGAGAATCTGAATCTTGTTT
* *
35053 CAATTTAATTAGAAATT-AT-AAAAAATATGAGAAACGATATTAAAAGCGTGAAAAGTCCTCCAA
385 CGATTTAATTAGAAATTAATCAAAAAATATGA-AAACGATATTAAAAGCGTGAAAAGACCTCCAA
** * * *
35116 TCCTTTTGACGTTGAATTATATATTTTTTATGAGTATTTTCTCTAGAAATCGAGGAAAAATCTTT
449 TATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCACTAGAAATCAAGGAAAAATCTTT
*
35181 C-AGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTAGTAACCATCATGGTTTTCGGCTAAAA
514 CGA-GTCAATTTTTGTAAAATTTTAGCCGAAATCAT-TAGTAA-CATCATGGTTTTCGGCTAAAA
*
35245 CCGCGTTCTGGGGTTCGGCTCAGTTTTGCTTGAATTTTGGTGCCAAGACTCCTTGAAATATCTAT
576 CCGCGTTCTGGGGTTCGGCTCAGTTTTGCATGAATTTTGGTGCCAAGACTCCTTGAAATATCTAT
35310 ATTCATCTAACC
641 ATTCATCTAACC
** * * *
35322 AAATCTCAGCCACATTAAATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTTA
1 AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAA
* * * *
35387 TTAGAAATTAATTTGAAAAAATA-GAAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTT
66 TTAGAAATTAA-TTCAAAAAATATG-AAAAACAATATTAAAAGCGTGAAAAGCCCTCCAATCTTT
* * * *
35451 TTGATGTCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAAGAAATATTTTTCGGGT
129 TTGATGTCGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGT
* * *
35516 CAATTTTTGCAAAATCTTAGCCGAAATAGTGTACTAACCATCACAATTTTTGGCTAAAAACACGC
194 CAATTTTTGCAAAATTTTAGCCGAAATAGTGTACTAACCATCACAGTTTTTGGCTAAAAACACGT
* *
35581 TCCAGGGCCAC-GTCTCTGTTTTGCATGATTTTTGGCACCGAGACTCCTTGAAATATCT
259 TCCAGGGCCACAGT-TCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCT
35639 CGGGCATATT
Statistics
Matches: 1388, Mismatches: 166, Indels: 137
0.82 0.10 0.08
Matches are distributed among these distances:
641 1 0.00
642 5 0.00
643 29 0.02
644 105 0.08
645 48 0.03
646 73 0.05
647 150 0.11
648 29 0.02
649 6 0.00
650 3 0.00
651 3 0.00
652 5 0.00
653 117 0.08
654 183 0.13
655 164 0.12
656 221 0.16
658 3 0.00
660 1 0.00
663 12 0.01
664 21 0.02
665 16 0.01
666 79 0.06
667 113 0.08
669 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (652 bp):
AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAA
TTAGAAATTAATTCAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTT
GATGTCGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCA
ATTTTTGCAAAATTTTAGCCGAAATAGTGTACTAACCATCACAGTTTTTGGCTAAAAACACGTTC
CAGGGCCACAGTTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATC
TAATCAAATCTCAGCCACATTGATTTAAGATTTGTTTAATGAGAATCTGAATCTTGTTTCGATTT
AATTAGAAATTAATCAAAAAATATGAAAACGATATTAAAAGCGTGAAAAGACCTCCAATATTTTT
GGCGTTGAATTATATATTTTTTATGAGTATTTTCACTAGAAATCAAGGAAAAATCTTTCGAGTCA
ATTTTTGTAAAATTTTAGCCGAAATCATTAGTAACATCATGGTTTTCGGCTAAAACCGCGTTCTG
GGGTTCGGCTCAGTTTTGCATGAATTTTGGTGCCAAGACTCCTTGAAATATCTATATTCATCTAA
CC
Found at i:37616 original size:18 final size:18
Alignment explanation
Indices: 37593--37628 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
37583 TTTTGTTGCT
37593 TCACCATTTCTCAACAAA
1 TCACCATTTCTCAACAAA
*
37611 TCACCATTTCTCATCAAA
1 TCACCATTTCTCAACAAA
37629 GATGTATCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (18 bp):
TCACCATTTCTCAACAAA
Found at i:48247 original size:334 final size:330
Alignment explanation
Indices: 45900--48248 Score: 2052
Period size: 334 Copynumber: 7.0 Consensus size: 330
45890 ATTGCATCAA
* ** ** * * *
45900 CTAACCAAATCTCAGTAACATTGGATTTAAAAATTTGTTTTTACGAGTATATGAATCTTGTTTCG
1 CTAACCAAATTTCAGCCAC-TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * * *
45965 ATTTAATTAGAAATTAATTTACAAAAAATAAGAAATACGATATTAAAAGCGTGAAAAGCCCTCCA
65 ATTTAATTAGAAATTAATTCAGAAAAAAT-TGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCA
* * * * * *
46030 ATCTTTTTAGCGTTGAAATATATATATTTTTATAAGTATTTTAGCCAAAAATTGAGCAGAAATCT
129 ATCTTTTTGGCGTTGAATTATATATA-TTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAAT-T
* * * * * **
46095 TTCGTGTCAATTTTTGCATAATTTTAGCCGAAATTGTGTACTAACTAACCATCACGGTTTTTGGC
192 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT---TATCCATCACGATTTTAAGC
* * * * ** * * * * *
46160 TGAAAATGCATTCCGAGGCCATGGCTCAATTTAGCATAATTTTTGGCGCTG-AGACTCCTTGAAA
254 TAAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTTGCAC-GAAGACTCCTTGAAA
46224 TATCTATATTCAT
318 TATCTATATTCAT
** * * * *
46237 CTAATAAAATGTT-AGCCGCATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTC
1 CTAACCAAAT-TTCAGCCAC-TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTC
* ** * *
46301 GATTTAATTAGAAATTAAATCAGAAAAAAAGGAAAAACGATATTAAAAGCGTGAAAAACACTTCA
64 GATTTAATTAGAAATTAATTCAGAAAAAATTGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCA
* * * * * *
46366 ATCTTTTTGGTGTTGAATTATAT-TATTTTTATGACTATTTTAGCTAAAAATTAAGGAAATATCT
129 ATCTTTTTGGCGTTGAATTATATATA-TTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAAT-T
* * * * * * * *
46430 TTCGAGTCAATTTTTACAAAATTTTAGTCAAAATCGTGTA-ATAACCATCACAACTTTT-GGCTA
192 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTATCCATCACGA-TTTTAAGCTA
* * *** * * * * * * *
46493 ACAAA-GCGTTGCAAGGCTGTGGCACAGTTTTGCATGATTTTTGGCCCCAAGCCTCCTTCAGATA
256 A-AAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTTGCACGAAGACTCCTTGAAATA
*
46557 TCCATATTCAT
320 TCTATATTCAT
* * * ** * *
46568 CTAATCAAATCTCAGCCAAATTGGATTTAAAAATTTGTTTTTACGAGTATCTGAATCTTGTTTCG
1 CTAACCAAATTTCAGCC-ACTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * ** * ** *
46633 ATTTAATTAAAAATTAATTTAGAAAAAAATAAGAAAAAATAAATTAAAAGCGTGAAAAGTGCTCC
65 ATTTAATTAGAAATTAATTCAG-AAAAAAT-TGAAAAACGATATTAAAAGCGTGAAAAGCCCTTC
* * *** *
46698 AATCTTTTTGGCGTTAAATTATATATATTTAATGAGTATTTTATTCAAAAACTGAGGAAAAAAAA
128 AATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTGGCCAAAAATTGAGG---AAAAA
* * * * * **
46763 TTTT-GTGG-C-ATCTTTTGCAAAATTTTAGCCAAAATTGTGTAC-TAACCATCATGGTTTTTGG
190 TTTTCG-GGTCAAT-TTTTGCAAAATTTTAGCCGAAATCGTGTACTTATCCATCACGATTTTAAG
* * * * * *
46824 ATAAAAACGTGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCTG-AGACTCCTTGAA
253 CTAAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTTGCAC-GAAGACTCCTTGAA
46888 ATATCTATATTCAT
317 ATATCTATATTCAT
** * * * * * * * *
46902 CTAATAAAACGTT-GGCCGCATTGCAATTAAGGATTTATTTTTACGAGCATATGAATCTTGTTTC
1 CTAACCAAA-TTTCAGCCAC-TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTC
* * * *
46966 GATTTATTTAGAGATTAATTCAGAAAAAAAATGAAAAACGATATTAAAATCGTGAAAAGCCCTTC
64 GATTTAATTAGAAATTAATTCAG-AAAAAATTGAAAAACGATATTAAAAGCGTGAAAAGCCCTTC
* * * * *
47031 AATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAATTTGAGGAAATATCT
128 AATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAAT-T
* *
47096 TTCGGGTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTAATAATCATTTTCCATCAC-AGTTTT
192 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---T-A-C-TTATCCATCACGA-TTTT
* * * * *
47160 AAGCTTAAAAA-GCGTATCGGGGCCCCGGCTTAGTTTTGCATGA-TTTTTG-GC-AAGACTTCTT
250 AAGC-TAAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTTGCACGAAGACTCCTT
* *
47221 GAAATATTTATATTTAT
314 GAAATATCTATATTCAT
* * ** * *
47238 CTAACTAAATCTCAGCCACATTGGATTTAACAATTTTGTTTTTATGATCATCTGAATCATGTTTC
1 CTAACCAAATTTCAGCCAC-TTGGATTTAAGGA-TTTGTTTTTACGAGCATCTGAATCATGTTTC
* * * *
47303 GATTTTATTTGAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAACCCTTC
64 GATTTAATTAGAAATTAATTCAGAAAAAATT-GAAAAACGATATTAAAAGCGTGAAAAGCCCTTC
* * * *
47368 AATTTTTTTGGCTTTGAATTATATATATTTTATGAG-AGTTGTGGCCAGAAATTGA-GAAAAATT
128 AATCTTTTTGGCGTTGAATTATATATATTTTATGAGTA-TTTTGGCCAAAAATTGAGGAAAAATT
* * * * * * *
47431 TTCCGGATCAATTTTTGCAAACTTTTAGCAGAAATCGTATACTT-TCCATTACTG-CTCTAAGCT
192 TT-CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTATCCATCAC-GATTTTAAGCT
* * * * * * * *
47494 AAAAACACGTTTCG-GACACCGACTTAGGTATGCATGATTTTTTGCACAAAGACTCCTTGAAATA
255 AAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTTGCACGAAGACTCCTTGAAATA
*
47558 TTTATATTCAT
320 TCTATATTCAT
* * * * *
47569 C-AGACCAAATCTCAGCCACTTTGGATTTAAAGATTTGTTTTTACGAGCATTTGTATTATGTTTC
1 CTA-ACCAAATTTCAGCCAC-TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTC
* * * * * *
47633 TATTTAATTCA-AAATTAAATAAGAAAAAAATTGGAAAAACGATATTAAAAGCCTGAAAAACCTT
64 GATTTAATT-AGAAATTAATTCAG-AAAAAATT-GAAAAACGATATTAAAAGCGTGAAAAGCCCT
* * * * * *
47697 TCAAGCCTTTTGTCTTTGAATTATATAT-TTTCTATGAGAATTGTGGCCAAAAATTGAGGAAAAA
126 TCAATCTTTTTGGCGTTGAATTATATATATTT-TATGAGTATTTTGGCCAAAAATTGAGG-AAAA
* *
47761 ATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-TTATCCATCACGGTTTTAAG
189 ATTTT-CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTATCCATCACGATTTTAAG
* * *
47825 CTAAAAACACGTTTCGAGGCCCCGACTAAGTTTTGCATGA-TTTTTGTCACGAAGACTCCTTGAA
253 CTAAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTTG-CACGAAGACTCCTTGAA
*
47889 ATATCTATATTGAT
317 ATATCTATATTCAT
* * * * * * * *
47903 CTGACCAAATTTAAGCCACTTTTGTTTTAAGGATTTATTTTTGCGAGCATCTGGATCATGTTTCC
1 CTAACCAAATTTCAGCCAC-TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * *
47968 ATTTAATTCGAAATTAATTCAGAAAAAATTGAAACAACGATATTAGAAGCCTTAAAAGCCCTTCA
65 ATTTAATTAGAAATTAATTCAGAAAAAATTGAAA-AACGATATTAAAAGCGTGAAAAGCCCTTCA
* * * *
48033 ATCTTTTTGTCTTTGAATTATATATATTTTATGAGAATTTTGGCCAAAAAGTGAGGAAAAATTTT
129 ATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATTTT
*** * * * * *
48098 CCAAATAAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTTTTTTCAGCACGATTTTAAGCTAA
194 -CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC-TTATCCATCACGATTTTAAGCTAA
* * *
48163 AAACGTGTTTCGAGGCCCTGGCTCAATTTTGCATGATTTTTTGCACGAAGACTCCTTGAAATATC
257 AAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTTGCACGAAGACTCCTTGAAATATC
48228 TATATTCAT
322 TATATTCAT
*
48237 CTGACCAAATTT
1 CTAACCAAATTT
48249 TTTTGGCTAT
Statistics
Matches: 1662, Mismatches: 287, Indels: 129
0.80 0.14 0.06
Matches are distributed among these distances:
328 24 0.01
329 25 0.02
330 56 0.03
331 282 0.17
332 93 0.06
333 317 0.19
334 383 0.23
335 84 0.05
336 145 0.09
337 201 0.12
338 6 0.00
339 40 0.02
340 6 0.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (330 bp):
CTAACCAAATTTCAGCCACTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGA
TTTAATTAGAAATTAATTCAGAAAAAATTGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAAT
CTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATTTTCG
GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTATCCATCACGATTTTAAGCTAAAAAC
GCGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTTGCACGAAGACTCCTTGAAATATCTATA
TTCAT
Found at i:48838 original size:332 final size:333
Alignment explanation
Indices: 48289--49153 Score: 1179
Period size: 333 Copynumber: 2.6 Consensus size: 333
48279 GAGTTGTGCC
* * *
48289 AAAAA-TTTTCCGGATCAATTTTTGTAAAATATTAGCTGAAATCGTATACTTTCCATCA-AGACT
1 AAAAATTTTTCCGGATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACTTTCCATCACAG-CT
* * * * * *
48352 TTAAGCTAAAAATGCGTTTTGGGACACCAACTTAGTTTTGCATGATTTTTTGCATGAAGAATCTT
65 TTAAGCTAAAAA-ACGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTAGCAAGAAGACTCTT
* * *
48417 GGAAATATTTATATTCATCTGCCCAAAACTCAGCCACTTTGGATTTAAGGTTTTGTTTTTACGAG
129 -GAAATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAG
* *
48482 CATTTGTATCATGTTTCCATTTAATTCAAAATTAATTCAG-AAAAAATTGGAAAAACGATATTAG
193 CATCTGAATCATGTTTCCATTTAATTCAAAATTAATTCAGAAAAAAATTGGAAAAACGATATTAG
* ** * * *
48546 AAGCGTGAAAAACCC-TTCAATTTTTTTGGCTTTGAATTATATATATTT-TATGATAGTTGTGGC
258 AAGCCTGAAAAACCCTTTCAAGCTTTTTGGCTTTGAATTATATAT-TTTCTACGAGAATTGTGGC
48609 CAAAAATTGAGG
322 CAAAAATTGAGG
* * *
48621 -AAAATTTTTCCAGATCAATTTTTGCAAAATTTTATCAGAAATCGTATACTTTCCATCACTGCTT
1 AAAAATTTTTCCGGATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACTTTCCATCACAGCTT
* *
48685 TAAGCTAAAAACACGTTTCGGGACACTGACTTAGTTTTGCATGATTTTTAGCACGAAGACTCCTT
66 TAAGCTAAAAA-ACGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTAGCAAGAAGACT-CTT
*
48750 GAAATATTTATATTTATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGC
129 GAAATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGC
* * *
48815 ATCTGAATCATGTTTCCATTTAATTCGATATTAATTCTGAAAAAAATTGGAAAAACGATATTAGA
194 ATCTGAATCATGTTTCCATTTAATTCAAAATTAATTCAGAAAAAAATTGGAAAAACGATATTAGA
*
48880 AGCCTGAAAAACCCTTTCAAGCTTTTTGTCTTTGAATTATATATTTTCTACGAGAATTGTGGCCA
259 AGCCTGAAAAACCCTTTCAAGCTTTTTGGCTTTGAATTATATATTTTCTACGAGAATTGTGGCCA
*
48945 AAAATTGTGG
324 AAAATTGAGG
* * * * * * *
48955 AAAAATCTTT-CGGATCAA-TTTCGCAAAATTTTAGCCGAAATGGTGTACTTTCTATCACAGTTT
1 AAAAATTTTTCCGGATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACTTTCCATCACAGCTT
* * * *
49018 TAAGCTAAAAAAGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAAGAAGACTTCTT
66 TAAGCTAAAAAA-CGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTAGCAAGAAGAC-TCTT
* * * * *
49083 GAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACAAGC
129 GAAATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGC
49148 ATCTGA
194 ATCTGA
49154 TTAAAATGCA
Statistics
Matches: 471, Mismatches: 53, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
331 4 0.01
332 200 0.42
333 202 0.43
334 57 0.12
335 8 0.02
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (333 bp):
AAAAATTTTTCCGGATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACTTTCCATCACAGCTT
TAAGCTAAAAAACGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTAGCAAGAAGACTCTTGA
AATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCAT
CTGAATCATGTTTCCATTTAATTCAAAATTAATTCAGAAAAAAATTGGAAAAACGATATTAGAAG
CCTGAAAAACCCTTTCAAGCTTTTTGGCTTTGAATTATATATTTTCTACGAGAATTGTGGCCAAA
AATTGAGG
Found at i:49078 original size:333 final size:331
Alignment explanation
Indices: 48289--49153 Score: 1191
Period size: 332 Copynumber: 2.6 Consensus size: 331
48279 GAGTTGTGCC
* * *
48289 AAAAATTTTCCGGATCAATTTTTGTAAAATATTAGCTGAAATCGTATACTTTCCATCA-AGACTT
1 AAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACTTTCCATCACAG-CTT
* * * * * *
48353 TAAGCTAAAAATGCGTTTTGGGACACCAACTTAGTTTTGCATGATTTTTTGCATGAAGAATCTTG
65 TAAGCTAAAAAAGCGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTAGCAAGAAGACTCTT-
* * *
48418 GAAATATTTATATTCATCTGCCCAAAACTCAGCCACTTTGGATTTAAGGTTTTGTTTTTACGAGC
129 GAAATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGC
* *
48483 ATTTGTATCATGTTTCCATTTAATTCAAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAA
194 ATCTGAATCATGTTTCCATTTAATTCAAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAA
* ** * * *
48548 GCGTGAAAAACCCTTCAATTTTTTTGGCTTTGAATTATATATATTTTATGATAGTTGTGGCCAAA
259 GCCTGAAAAACCCTTCAAGCTTTTTGGCTTTGAATTATATATATTTTACGAGAATTGTGGCCAAA
48613 AATTGAGG
324 AATTGAGG
* * * *
48621 AAAATTTTTCCAGATCAATTTTTGCAAAATTTTATCAGAAATCGTATACTTTCCATCACTGCTTT
1 AAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACTTTCCATCACAGCTTT
* *
48686 AAGCTAAAAACA-CGTTTCGGGACACTGACTTAGTTTTGCATGATTTTTAGCACGAAGACTCCTT
66 AAGCTAAAAA-AGCGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTAGCAAGAAGACT-CTT
*
48750 GAAATATTTATATTTATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGC
129 GAAATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGC
* * *
48815 ATCTGAATCATGTTTCCATTTAATTCGATATTAATTCTGAAAAAAATTGGAAAAACGATATTAGA
194 ATCTGAATCATGTTTCCATTTAATTCAAAATTAATTCAG-AAAAAATTGGAAAAACGATATTAGA
*
48880 AGCCTGAAAAACCCTTTCAAGCTTTTTGTCTTTGAATTATATAT-TTTCTACGAGAATTGTGGCC
258 AGCCTGAAAAACCC-TTCAAGCTTTTTGGCTTTGAATTATATATATTT-TACGAGAATTGTGGCC
*
48944 AAAAATTGTGG
321 AAAAATTGAGG
* * * * * *
48955 AAAAATCTTT-CGGATCAA-TTTCGCAAAATTTTAGCCGAAATGGTGTACTTTCTATCACAGTTT
1 AAAAAT-TTTCCGGATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACTTTCCATCACAGCTT
* * * *
49018 TAAGCTAAAAAAGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAAGAAGACTTCTT
65 TAAGCTAAAAAAGCGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTAGCAAGAAGAC-TCTT
* * * * *
49083 GAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACAAGC
129 GAAATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGC
49148 ATCTGA
194 ATCTGA
49154 TTAAAATGCA
Statistics
Matches: 471, Mismatches: 53, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
332 204 0.43
333 202 0.43
334 62 0.13
335 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (331 bp):
AAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACTTTCCATCACAGCTTT
AAGCTAAAAAAGCGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTAGCAAGAAGACTCTTGA
AATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCAT
CTGAATCATGTTTCCATTTAATTCAAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAAGC
CTGAAAAACCCTTCAAGCTTTTTGGCTTTGAATTATATATATTTTACGAGAATTGTGGCCAAAAA
TTGAGG
Found at i:50874 original size:333 final size:331
Alignment explanation
Indices: 49433--52129 Score: 3302
Period size: 333 Copynumber: 8.2 Consensus size: 331
49423 CTGGGATTTG
* ** *** *
49433 CCCTTCAATGTTTTTGGCTTTGAATTATATATAAATTATGACCGTTGTGGCCAAAAATTGAGAAA
1 CCCTTCAATCTTTTTGGCTTTGAATTATATAT-TTTTATGAGAATTGTGGCCAAAAATTGAGGAA
* * *
49498 AAAATTTCCGGATCAATTTTTGCAAAATTTTAACAGAAATCGTATACTTTCCATCACTGG-TTTA
65 AAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTTTCCATCAC-GGTTTTA
* ** * *
49562 AGCTAAAAACGCGTTTTGGGAACCGACTTAGTTTTGCATGATTTTTTGCACAAAGACTCCTTGAA
129 AGCTAAAAACGCGTTTCGGGCCCCGACTCAGTTTTGCATGATTTTTTGCACGAAGACTCCTTGAA
*
49627 ATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATT
194 ATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATC
* * * * *
49692 TGTATCATGTTTCTATTTAATTCAAAATTAATTAAGAAAAAAATTGGAAAAACAATATTAAAAGC
259 TGAATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAAATTGGAAAAACGATATTAGAAGC
49757 CTGAAAAA
324 CTGAAAAA
* * *
49765 CCTTTCAAGCTTTTTGTCTTTGAATTATATATTTTCTATGAGAATTGTGGCCAAAAATTGAGGAA
1 CCCTTCAATCTTTTTGGCTTTGAATTATATATTTT-TATGAGAATTGTGGCCAAAAATTGAGGAA
* * *
49830 AAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGATTTT--
65 AAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTTTCCATCACGGTTTTAA
* * * *
49893 -C----GA-G-G--T-----CCCGACTCAGTTTTGCATGATTTTTGGTACGAAGACTCCTTCAAA
130 GCTAAAAACGCGTTTCGGGCCCCGACTCAGTTTTGCATGATTTTTTGCACGAAGACTCCTT-GAA
* *
49944 ATATCTATATTCATCTGACCAAATCTCAGCCACTTTTGATTTAAGGATTTGTTTTTACGAGCATC
194 ATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATC
* *
50009 TGAATCGTGTTTCTATTTAATTTGAAATTAATTCAGAAAAAAAAATTGGAAAAACGATATTAGAA
259 TGAATCATGTTTCTATTTAATTCGAAATTAATTCAG--AAAAAAATTGGAAAAACGATATTAGAA
50074 GCCTGAAAAA
322 GCCTGAAAAA
* * * *
50084 CCCTTCAATCTTTTTGTCTTTGAATT-T-TTTTTTTATGAAAATTGTGGCAAAAAATTGAGGAAA
1 CCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTATGAGAATTGTGGCCAAAAATTGAGGAAA
* * * * **
50147 AATCTTT-TGGATCAA-TTTAGCAAAATTTTAGCCGAAATCGTGTACTTTCTATCACAATTTTAA
66 AAT-TTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTTTCCATCACGGTTTTAA
* * *
50210 GCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAAGAAGACTTCTTGAA
130 GCTAAAAACGCGTTTC-GGGCCCCGACTCAGTTTTGCATGATTTTTTGCACGAAGACTCCTTGAA
* * * *
50275 ATATTTATATTTATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTATTTTTACGACCATC
194 ATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATC
* * * * * *
50340 TAAATCAGGTTTCGATTTTATTTGAAATTACA-TCAG--TAAAATTGGAAAAACGATATTAGAAG
259 TGAATCATGTTTCTATTTAATTCGAAATTA-ATTCAGAAAAAAATTGGAAAAACGATATTAGAAG
*
50402 CGTGAAAAA
323 CCTGAAAAA
* * *
50411 CCCTTCAATCGTTTTGGCTTTGAATTATATATATTTTATGAGAGTTGTGGCCAAGAATTGAGGAA
1 CCCTTCAATCTTTTTGGCTTTGAATTATATAT-TTTTATGAGAATTGTGGCCAAAAATTGAGGAA
* * * *
50476 AAATTTTCCTGATCAATTTTTGCAAAATTTTAGCCGAAATCATGA-ACTATCCATCACGATTTTA
65 AAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGT-ATACTTTCCATCACGGTTTTA
* * * *
50540 AGCTAAAAATGCCTTTCGAGGCCCCGACTCAGTTTTGCATGATTTTTAGTC-CGAAGACT-CTTT
129 AGCTAAAAACGCGTTTCG-GGCCCCGACTCAGTTTTGCATGATTTTTTG-CACGAAGACTCCTTG
* * ** *
50603 AAACTATCTATATTTATCTGAGTAAATGTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGC
192 AAA-TATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGC
* * *
50668 ATCTGAATTATGTTTCTATTTAATTCGAAATTAATTTAGAAAAAAATTGGAAAAACGATATTGGA
256 ATCTGAATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAAATTGGAAAAACGATATTAGA
50733 AGCCTGAAAAA
321 AGCCTGAAAAA
* * *
50744 CCCTTCAATCATTTTGGCTTTGAATTATATATATTTTATGAGAGTTGTGTCCAAAAATTGAGGAA
1 CCCTTCAATCTTTTTGGCTTTGAATTATATAT-TTTTATGAGAATTGTGGCCAAAAATTGAGGAA
* * * * * *
50809 AAATTTTTCGTATCAAATTTTGCAAAATTTTAGCAGAAATCGTATAATTTCCATTACGGTTTTAA
65 AAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTTTCCATCACGGTTTTAA
* * * * **
50874 GCTAAAAACACGTTTAGGGACACCGACTTAGTTTTGCATGATTTTTTGCATAAAGACTCCTTGAA
130 GCTAAAAACGCGTTTCGGG-CCCCGACTCAGTTTTGCATGATTTTTTGCACGAAGACTCCTTGAA
*
50939 ATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGGGCAT-
194 ATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATC
* * *
51003 TCGTATCATGTTTCTATTTAATTCAAAATTAATTCAGAAAAAAATTGGAAAAACGATATTAAAAG
259 T-GAATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAAATTGGAAAAACGATATTAGAAG
51068 CCTGAAAAA
323 CCTGAAAAA
* * * * * *
51077 CCCTTCAAACTGTTTT-TCTTTGAATTGTATATTGTCTATGAGAATTGTGGTCAAAATTTGAGGA
1 CCCTTCAATCT-TTTTGGCTTTGAATTATATATT-TTTATGAGAATTGTGGCCAAAAATTGAGGA
* * * * * *
51141 AAAACTTTCCGGATCAATTTTGGCAAAATTTTAGCCGAAATCGTGTTCTTTCAATCACAGTTTTA
64 AAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTTTCCATCACGGTTTTA
* * * * * *
51206 AGCTAAAAAAGCGTTTCGGGGCCCTGACTCAATTTTGCATGATTTTTGGCAAGAAGACTTCTTGA
129 AGCTAAAAACGCGTTTC-GGGCCCCGACTCAGTTTTGCATGATTTTTTGCACGAAGACTCCTTGA
* * * * * *
51271 AATATTTATATTTATCTAAGCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTAACGACCAT
193 AATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCAT
* * *
51336 C-GAATCATGTTTCGATATT-ATTTGAAATTAATTCTG-AAAAAATTGGAAAAACGATATTAGAA
258 CTGAATCATGTTTCTAT-TTAATTCGAAATTAATTCAGAAAAAAATTGGAAAAACGATATTAGAA
*
51398 GCGTGAAAAA
322 GCCTGAAAAA
* * * * *
51408 CCTTTCGATCTTTTTGGCTTTGAATTATATACATTTTATGATAGTTGTGGCCAAAAATTGAGGAA
1 CCCTTCAATCTTTTTGGCTTTGAATTATATA-TTTTTATGAGAATTGTGGCCAAAAATTGAGGAA
* * *
51473 AAATTTTCCGGATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACATTCCATCACGGCTTTAA
65 AAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTTTCCATCACGGTTTTAA
* * * *
51538 GCTAAAAA-GACGTTTCGGGACACCGACTTAGTTTTGTATGATTTTTTGCACAAAGACTCCTTGA
130 GCTAAAAACG-CGTTTCGGG-CCCCGACTCAGTTTTGCATGATTTTTTGCACGAAGACTCCTTGA
* * *
51602 AATATTTATATTCATTTGACCAAATCTAAGTCACTTTGGATTTAAGGATTTGTTTTTACGAGCAT
193 AATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCAT
* * * * * *
51667 TTGTATCATGTTTCTATCTAATTCAAAATTAATTAAGAAAAAAATTGGAAAAACGATATTAAAAG
258 CTGAATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAAATTGGAAAAACGATATTAGAAG
51732 CCTGAAAAA
323 CCTGAAAAA
* * * * * *
51741 CCTTTGAAGCTTTTTGACTTTGAATTATATATTTTCTATGAGAATTGTGACCAAAAA-TGAGTAA
1 CCCTTCAATCTTTTTGGCTTTGAATTATATATTTT-TATGAGAATTGTGGCCAAAAATTGAGGAA
* * * * ** * *
51805 AAATTTTCCTGATCAATTTTTGCAATATTTTAGCTGAATTCGTGCACTATCCATCACGATTTTAA
65 AAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTTTCCATCACGGTTTTAA
* * * * *
51870 GCTAAAAACGCGTTTCGAGGCCCCGACTCAATTTTTCATAATTTTTAGCACGAAGACTCTTTGAA
130 GCTAAAAACGCGTTTCG-GGCCCCGACTCAGTTTTGCATGATTTTTTGCACGAAGACTCCTTGAA
* * * * *
51935 CTATCTATATTTATCTGACCAAATCTCAGCCACTTTGGATTTTAGGATTTGTTTTTACGAGCAAC
194 ATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATC
*
52000 TGAATCATGTTTCTATTTAATTCGAAATTAATTCGGAAAAAAATTGGAAAAACGATATTAGAAGC
259 TGAATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAAATTGGAAAAACGATATTAGAAGC
* *
52065 TTAAAAAA
324 CTGAAAAA
** * ** *
52073 CTGTTCAAACTTTTTTTCTTTGAATTATATATTGTCTATGAGAATTGTGGCCAAAAA
1 CCCTTCAATCTTTTTGGCTTTGAATTATATATT-TTTATGAGAATTGTGGCCAAAAA
52130 ATGAAAAAAT
Statistics
Matches: 2028, Mismatches: 280, Indels: 114
0.84 0.12 0.05
Matches are distributed among these distances:
315 42 0.02
316 74 0.04
317 103 0.05
318 2 0.00
319 59 0.03
321 1 0.00
322 1 0.00
323 2 0.00
324 2 0.00
325 1 0.00
326 1 0.00
327 57 0.03
328 1 0.00
329 6 0.00
330 54 0.03
331 510 0.25
332 491 0.24
333 608 0.30
334 13 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (331 bp):
CCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTATGAGAATTGTGGCCAAAAATTGAGGAAA
AATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTTTCCATCACGGTTTTAAG
CTAAAAACGCGTTTCGGGCCCCGACTCAGTTTTGCATGATTTTTTGCACGAAGACTCCTTGAAAT
ATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATCTG
AATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAAATTGGAAAAACGATATTAGAAGCCT
GAAAAA
Found at i:51446 original size:664 final size:663
Alignment explanation
Indices: 49433--52129 Score: 3600
Period size: 664 Copynumber: 4.1 Consensus size: 663
49423 CTGGGATTTG
* ** ** *
49433 CCCTTCAATGTTTTTGGCTTTGAATTATATATAAATTATGACCGTTGTGGCCAAAAATTGAGAAA
1 CCCTTCAATCTTTTTGGCTTTGAATTATATATATTTTATGAGAGTTGTGGCCAAAAATTGAGGAA
* * * *
49498 AAAATTTCCGGATCAATTTTTGCAAAATTTTAACAGAAATCGTATACTTTCCATCACTGG-TTTA
66 AAATTTTCCGGATCAAATTTTGCAAAATTTTAGCAGAAATCGTATAATTTCCATCAC-GGTTTTA
* *
49562 AGCTAAAAACGCGTTTTGGGA-ACCGACTTAGTTTTGCATGATTTTTTGCACAAAGACTCCTTGA
130 AGCTAAAAACACGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTTGCACAAAGACTCCTTGA
49626 AATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCAT
195 AATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCAT
* *
49691 TTGTATCATGTTTCTATTTAATTCAAAATTAATTAAGAAAAAAATTGGAAAAACAATATTAAAAG
260 TCGTATCATGTTTCTATTTAATTCAAAATTAATTAAGAAAAAAATTGGAAAAACGATATTAAAAG
*
49756 CCTGAAAAACCTTTCAAGCTTTTTGTCTTTGAATTATATATTTTCTATGAGAATTGTGGCCAAAA
325 CCTGAAAAACCCTTCAAGCTTTTTGTCTTTGAATTATATATTTTCTATGAGAATTGTGGCC-AAA
49821 ATTGAGGAAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCA
389 ATTGAGGAAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCA
* * *
49886 CG------A--T--------TTTCGAGGTCCCGACTCAGTTTTGCATGATTTTTGGTACGAAGAC
454 CGATTTTAAGCTAAAAAGCGTTTCGAGGCCCCGACTCAATTTTGCATGATTTTTGGCACGAAGAC
* * *
49935 TCCTTCAAAATATCTATATTCATCTGACCAAATCTCAGCCACTTTTGATTTAAGGATTTGTTTTT
519 T-CTT-GAAATATCTATATTTATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTT
* * *
50000 ACGAGCATCTGAATCGTGTTTCTATTTAATTTGAAATTAATTCAGAAAAAAAAATTGGAAAAACG
582 ACGAGCATCTGAATCATGTTTCTATTTAATTCGAAATTAATTCTG--AAAAAAATTGGAAAAACG
50065 ATATTAGAAGCCTGAAAAA
645 ATATTAGAAGCCTGAAAAA
* * * * *
50084 CCCTTCAATCTTTTTGTCTTTGAATT-T-T-TTTTTTATGAAAATTGTGGCAAAAAATTGAGGAA
1 CCCTTCAATCTTTTTGGCTTTGAATTATATATATTTTATGAGAGTTGTGGCCAAAAATTGAGGAA
* * * * * * **
50146 AAATCTTT-TGGATC-AATTTAGCAAAATTTTAGCCGAAATCGTGTACTTTCTATCACAATTTTA
66 AAAT-TTTCCGGATCAAATTTTGCAAAATTTTAGCAGAAATCGTATAATTTCCATCACGGTTTTA
* * * * * *
50209 AGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCA-AGAAGACTTCTTG
130 AGCTAAAAACACGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTTGCACA-AAGACTCCTTG
* * * *
50273 AAATATTTATATTTATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTATTTTTACGACCA
194 AAATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCA
* * * ** * *
50338 -TC-TAAATCAGGTTTCGATTTTATTTGAAATTACA-TCAG--TAAAATTGGAAAAACGATATTA
259 TTCGT--ATCATGTTTCTATTTAATTCAAAATTA-ATTAAGAAAAAAATTGGAAAAACGATATTA
* * * * * *
50398 GAAGCGTGAAAAACCCTTCAATCGTTTTGGCTTTGAATTATATATATTT-TATGAGAGTTGTGGC
321 AAAGCCTGAAAAACCCTTCAAGCTTTTTGTCTTTGAATTATATAT-TTTCTATGAGAATTGTGGC
* * *
50462 CAAGAATTGAGGAAAAATTTTCCTGATCAATTTTTGCAAAATTTTAGCCGAAATCATGAACTATC
385 CAA-AATTGAGGAAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATC
* * *
50527 CATCACGATTTTAAGCTAAAAATGCCTTTCGAGGCCCCGACTCAGTTTTGCATGATTTTTAGTC-
449 CATCACGATTTTAAGCTAAAAA-GCGTTTCGAGGCCCCGACTCAATTTTGCATGATTTTT-GGCA
* ** *
50591 CGAAGACTCTTTAAACTATCTATATTTATCTGAGTAAATGTCAGCCACTTTGGATTTAAGGATTT
512 CGAAGACTCTTGAAA-TATCTATATTTATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTT
*
50656 GTTTTTACGAGCATCTGAATTATGTTTCTATTTAATTCGAAATTAATT-TAGAAAAAAATTGGAA
576 GTTTTTACGAGCATCTGAATCATGTTTCTATTTAATTCGAAATTAATTCT-GAAAAAAATTGGAA
*
50720 AAACGATATTGGAAGCCTGAAAAA
640 AAACGATATTAGAAGCCTGAAAAA
* *
50744 CCCTTCAATCATTTTGGCTTTGAATTATATATATTTTATGAGAGTTGTGTCCAAAAATTGAGGAA
1 CCCTTCAATCTTTTTGGCTTTGAATTATATATATTTTATGAGAGTTGTGGCCAAAAATTGAGGAA
* * *
50809 AAATTTTTCGTATCAAATTTTGCAAAATTTTAGCAGAAATCGTATAATTTCCATTACGGTTTTAA
66 AAATTTTCCGGATCAAATTTTGCAAAATTTTAGCAGAAATCGTATAATTTCCATCACGGTTTTAA
* *
50874 GCTAAAAACACGTTTAGGGACACCGACTTAGTTTTGCATGATTTTTTGCATAAAGACTCCTTGAA
131 GCTAAAAACACGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTTGCACAAAGACTCCTTGAA
*
50939 ATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGGGCATT
196 ATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATT
*
51004 CGTATCATGTTTCTATTTAATTCAAAATTAATTCAGAAAAAAATTGGAAAAACGATATTAAAAGC
261 CGTATCATGTTTCTATTTAATTCAAAATTAATTAAGAAAAAAATTGGAAAAACGATATTAAAAGC
* * * *
51069 CTGAAAAACCCTTCAAACTGTTTT-TCTTTGAATTGTATATTGTCTATGAGAATTGTGGTCAAAA
326 CTGAAAAACCCTTCAAGCT-TTTTGTCTTTGAATTATATATTTTCTATGAGAATTGTGGCCAAAA
* * * * *
51133 TTTGAGGAAAAACTTTCCGGATCAATTTTGGCAAAATTTTAGCCGAAATCGTGTTCTTTCAATCA
390 -TTGAGGAAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCA
* * *
51198 C-AGTTTTAAGCTAAAAAAGCGTTTCGGGGCCCTGACTCAATTTTGCATGATTTTTGGCAAGAAG
454 CGA-TTTTAAGCT-AAAAAGCGTTTCGAGGCCCCGACTCAATTTTGCATGATTTTTGGCACGAAG
* * * *
51262 ACTTCTTGAAATATTTATATTTATCTAAGCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
517 AC-TCTTGAAATATCTATATTTATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTT
* * * *
51327 AACGACCATC-GAATCATGTTTCGATATT-ATTTGAAATTAATTCTG-AAAAAATTGGAAAAACG
581 TACGAGCATCTGAATCATGTTTCTAT-TTAATTCGAAATTAATTCTGAAAAAAATTGGAAAAACG
*
51389 ATATTAGAAGCGTGAAAAA
645 ATATTAGAAGCCTGAAAAA
* * * *
51408 CCTTTCGATCTTTTTGGCTTTGAATTATATACATTTTATGATAGTTGTGGCCAAAAATTGAGGAA
1 CCCTTCAATCTTTTTGGCTTTGAATTATATATATTTTATGAGAGTTGTGGCCAAAAATTGAGGAA
* *
51473 AAATTTTCCGGATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACA-TTCCATCACGGCTTTA
66 AAATTTTCCGGATCAAATTTTGCAAAATTTTAGCAGAAATCGTATA-ATTTCCATCACGGTTTTA
* *
51537 AGCTAAAAAGACGTTTCGGGACACCGACTTAGTTTTGTATGATTTTTTGCACAAAGACTCCTTGA
130 AGCTAAAAACACGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTTGCACAAAGACTCCTTGA
* * *
51602 AATATTTATATTCATTTGACCAAATCTAAGTCACTTTGGATTTAAGGATTTGTTTTTACGAGCAT
195 AATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCAT
* *
51667 TTGTATCATGTTTCTATCTAATTCAAAATTAATTAAGAAAAAAATTGGAAAAACGATATTAAAAG
260 TCGTATCATGTTTCTATTTAATTCAAAATTAATTAAGAAAAAAATTGGAAAAACGATATTAAAAG
* * * *
51732 CCTGAAAAACCTTTGAAGCTTTTTGACTTTGAATTATATATTTTCTATGAGAATTGTGACCAAAA
325 CCTGAAAAACCCTTCAAGCTTTTTGTCTTTGAATTATATATTTTCTATGAGAATTGTGGCCAAAA
* * * * * * *
51797 ATGAGTAAAAATTTTCCTGATCAATTTTTGCAATATTTTAGCTGAATTCGTGCACTATCCATCAC
390 TTGAGGAAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCAC
* * *
51862 GATTTTAAGCTAAAAACGCGTTTCGAGGCCCCGACTCAATTTTTCATAATTTTTAGCACGAAGAC
455 GATTTTAAGCTAAAAA-GCGTTTCGAGGCCCCGACTCAATTTTGCATGATTTTTGGCACGAAGAC
* *
51927 TCTTTGAACTATCTATATTTATCTGACCAAATCTCAGCCACTTTGGATTTTAGGATTTGTTTTTA
519 TC-TTGAAATATCTATATTTATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTA
* *
51992 CGAGCAACTGAATCATGTTTCTATTTAATTCGAAATTAATTCGGAAAAAAATTGGAAAAACGATA
583 CGAGCATCTGAATCATGTTTCTATTTAATTCGAAATTAATTCTGAAAAAAATTGGAAAAACGATA
* *
52057 TTAGAAGCTTAAAAAA
648 TTAGAAGCCTGAAAAA
** * ** * *
52073 CTGTTCAAACTTTTTTTCTTTGAATTATATAT-TGTCTATGAGAATTGTGGCCAAAAA
1 CCCTTCAATCTTTTTGGCTTTGAATTATATATAT-TTTATGAGAGTTGTGGCCAAAAA
52130 ATGAAAAAAT
Statistics
Matches: 1782, Mismatches: 206, Indels: 102
0.85 0.10 0.05
Matches are distributed among these distances:
645 2 0.00
646 140 0.08
647 64 0.04
648 156 0.09
649 5 0.00
650 1 0.00
651 24 0.01
652 1 0.00
654 1 0.00
660 60 0.03
661 4 0.00
662 104 0.06
663 250 0.14
664 600 0.34
665 117 0.07
666 237 0.13
667 16 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (663 bp):
CCCTTCAATCTTTTTGGCTTTGAATTATATATATTTTATGAGAGTTGTGGCCAAAAATTGAGGAA
AAATTTTCCGGATCAAATTTTGCAAAATTTTAGCAGAAATCGTATAATTTCCATCACGGTTTTAA
GCTAAAAACACGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTTGCACAAAGACTCCTTGAA
ATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATT
CGTATCATGTTTCTATTTAATTCAAAATTAATTAAGAAAAAAATTGGAAAAACGATATTAAAAGC
CTGAAAAACCCTTCAAGCTTTTTGTCTTTGAATTATATATTTTCTATGAGAATTGTGGCCAAAAT
TGAGGAAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACG
ATTTTAAGCTAAAAAGCGTTTCGAGGCCCCGACTCAATTTTGCATGATTTTTGGCACGAAGACTC
TTGAAATATCTATATTTATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGA
GCATCTGAATCATGTTTCTATTTAATTCGAAATTAATTCTGAAAAAAATTGGAAAAACGATATTA
GAAGCCTGAAAAA
Done.