Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold222
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: 1154749
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.31
Warning! 71027 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:306342 original size:44 final size:44
Alignment explanation
Indices: 306294--306432 Score: 120
Period size: 44 Copynumber: 3.2 Consensus size: 44
306284 ATTGGCGAAA
*
306294 TAGATCGAAGATACA-AGTCTTATCTCCCTGAAGTTGTAGTGGAG
1 TAGATCGAAGA-ACACAGTCTTATCTCCCTGAAGTTGCAGTGGAG
* * * * * * *
306338 TAGATAGAAGAAAATAATCCTATCTCCTTGAAGTTGCAATGGAG
1 TAGATCGAAGAACACAGTCTTATCTCCCTGAAGTTGCAGTGGAG
* * * * * *
306382 TAGGT-TAAGACCACAGATCTCATCTCTCTGAAGTTGCAGTAGAG
1 TAGATCGAAGAACACAG-TCTTATCTCCCTGAAGTTGCAGTGGAG
306426 TAGATCG
1 TAGATCG
306433 CATCAAGATT
Statistics
Matches: 71, Mismatches: 21, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
43 8 0.11
44 63 0.89
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (44 bp):
TAGATCGAAGAACACAGTCTTATCTCCCTGAAGTTGCAGTGGAG
Found at i:307808 original size:15 final size:15
Alignment explanation
Indices: 307790--307819 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
307780 TTACAATTCA
*
307790 TTGTTTTTTTTTATT
1 TTGTTTTTATTTATT
307805 TTGTTTTTATTTATT
1 TTGTTTTTATTTATT
307820 ATTTCCATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (15 bp):
TTGTTTTTATTTATT
Found at i:315159 original size:23 final size:24
Alignment explanation
Indices: 315128--315172 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
315118 ATATCCCCAC
*
315128 ATGGAGTGTAG-GGTTGGATGGAG
1 ATGGAGTGTAGAGGCTGGATGGAG
*
315151 ATGGTGTGTAGAGGCTGGATGG
1 ATGGAGTGTAGAGGCTGGATGG
315173 GTAGGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.20, C:0.02, G:0.51, T:0.27
Consensus pattern (24 bp):
ATGGAGTGTAGAGGCTGGATGGAG
Found at i:318690 original size:42 final size:42
Alignment explanation
Indices: 318599--318696 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
318589 ATTAATTGAT
*
318599 ATTTGATTTGCATGTTAAGCATGCCGACTATGATAAACTAAG
1 ATTTGATTTGCATGTTAAGCATCCCGACTATGATAAACTAAG
* * * * * *
318641 ATCTGATTTGCATGTTAAGCATCCCGATTATGTTGATCTTAG
1 ATTTGATTTGCATGTTAAGCATCCCGACTATGATAAACTAAG
*
318683 ATTTGATTCGCATG
1 ATTTGATTTGCATG
318697 ATAACTTTAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (42 bp):
ATTTGATTTGCATGTTAAGCATCCCGACTATGATAAACTAAG
Found at i:319656 original size:56 final size:56
Alignment explanation
Indices: 319590--319706 Score: 225
Period size: 56 Copynumber: 2.1 Consensus size: 56
319580 AAGAAATTCA
*
319590 AAAGGTTTTACCTTAGTTTTTCTCAAGCAAAATAACTCACTGATTTTGATTTTATT
1 AAAGGTTTTACCTTAGTTTTTCTCAAGCAAAACAACTCACTGATTTTGATTTTATT
319646 AAAGGTTTTACCTTAGTTTTTCTCAAGCAAAACAACTCACTGATTTTGATTTTATT
1 AAAGGTTTTACCTTAGTTTTTCTCAAGCAAAACAACTCACTGATTTTGATTTTATT
319702 AAAGG
1 AAAGG
319707 AGATAACGAC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (56 bp):
AAAGGTTTTACCTTAGTTTTTCTCAAGCAAAACAACTCACTGATTTTGATTTTATT
Found at i:324704 original size:51 final size:51
Alignment explanation
Indices: 324642--324741 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
324632 CTCAATTTCC
324642 TCTCAAATTGCTCGCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAAATTGCTCGCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* * * * *
324693 TCTCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCTTATTT
1 TCTCAAATTGCTCGCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
324742 TTAATTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (51 bp):
TCTCAAATTGCTCGCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:327975 original size:24 final size:24
Alignment explanation
Indices: 327903--327977 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
327893 GTAATATATG
*
327903 TGTGAACTATCTTTGCAAAGAGTA
1 TGTGAACTATCTTTGCAAAGAATA
* ** * ** *
327927 TGCGAACTATCAATGTATTGTATA
1 TGTGAACTATCTTTGCAAAGAATA
327951 TGTGAACTATCTTTGCAAAGAATA
1 TGTGAACTATCTTTGCAAAGAATA
327975 TGT
1 TGT
327978 AAATTGTGAT
Statistics
Matches: 36, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (24 bp):
TGTGAACTATCTTTGCAAAGAATA
Found at i:327992 original size:48 final size:48
Alignment explanation
Indices: 327864--327997 Score: 169
Period size: 48 Copynumber: 2.8 Consensus size: 48
327854 ATGTGAGAGT
* * * *
327864 TCTTTTCAAAGAATATGCAAACTGTCAATGTAATATATGTGTGAACTA
1 TCTTTGCAAAGAATATGCAAACTGTCAATGTATTGTATATGTGAACTA
* * *
327912 TCTTTGCAAAGAGTATGCGAACTATCAATGTATTGTATATGTGAACTA
1 TCTTTGCAAAGAATATGCAAACTGTCAATGTATTGTATATGTGAACTA
* * * *
327960 TCTTTGCAAAGAATATGTAAATTGTGATTGTATTGTAT
1 TCTTTGCAAAGAATATGCAAACTGTCAATGTATTGTAT
327998 GCATGAATTG
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (48 bp):
TCTTTGCAAAGAATATGCAAACTGTCAATGTATTGTATATGTGAACTA
Found at i:333683 original size:13 final size:13
Alignment explanation
Indices: 333665--333693 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
333655 TAATTTTTCA
333665 ACACTTGAGTGGT
1 ACACTTGAGTGGT
333678 ACACTTGAGTGGT
1 ACACTTGAGTGGT
333691 ACA
1 ACA
333694 ATTGTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (13 bp):
ACACTTGAGTGGT
Found at i:334707 original size:20 final size:18
Alignment explanation
Indices: 334660--334708 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
334650 CAAGAAAAAC
334660 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
334677 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
334697 ATTAAATTAATA
1 ATTAAATTAATA
334709 AAATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:335762 original size:21 final size:21
Alignment explanation
Indices: 335703--335767 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
335693 CAAAAGCAGT
*
335703 ATACGACACATAAAGTGCCTG
1 ATACGACACATATAGTGCCTG
* ** *
335724 AAACGACACACGTGGTGCCT-
1 ATACGACACATATAGTGCCTG
335744 ATTACGACACATATAGTGCCTG
1 A-TACGACACATATAGTGCCTG
335766 AT
1 AT
335768 CGGCAAAACC
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (21 bp):
ATACGACACATATAGTGCCTG
Found at i:336250 original size:17 final size:18
Alignment explanation
Indices: 336216--336251 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
336206 GAATTTTTTA
336216 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
336234 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
336251 T
1 T
336252 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:337284 original size:30 final size:32
Alignment explanation
Indices: 337250--337319 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 32
337240 NGTCATGTTT
*
337250 TAATATAAATATCT-TTTTCTT-AATAATAAA
1 TAATATAAATATCTATTTACTTAAATAATAAA
*
337280 T-A-ATAAATATCTATTTACTTAAATAATAAG
1 TAATATAAATATCTATTTACTTAAATAATAAA
*
337310 TAATTTAAAT
1 TAATATAAAT
337320 CCATGAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 10 0.30
29 7 0.21
30 10 0.30
31 1 0.03
32 5 0.15
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (32 bp):
TAATATAAATATCTATTTACTTAAATAATAAA
Found at i:337471 original size:13 final size:12
Alignment explanation
Indices: 337417--337472 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 12
337407 ATTTAATAAG
*
337417 ATAATATCAATT
1 ATAATATTAATT
*
337429 A-AATAATAATTT
1 ATAATATTAA-TT
337441 ATAATATTATATT
1 ATAATATTA-ATT
*
337454 CTAATATTAATT
1 ATAATATTAATT
337466 AATAATA
1 -ATAATA
337473 ACTTAAATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
11 6 0.17
12 7 0.20
13 21 0.60
14 1 0.03
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (12 bp):
ATAATATTAATT
Found at i:343080 original size:20 final size:20
Alignment explanation
Indices: 343053--343104 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
343043 TATGAACCAC
343053 TCCATTTACTTACTTTCCAT
1 TCCATTTACTTACTTTCCAT
*
343073 TTCATTTACTTACTTTCCAT
1 TCCATTTACTTACTTTCCAT
343093 TCCATTTACTTA
1 TCCATTTACTTA
343105 GCATAAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.27, G:0.00, T:0.52
Consensus pattern (20 bp):
TCCATTTACTTACTTTCCAT
Found at i:346518 original size:37 final size:38
Alignment explanation
Indices: 346467--346541 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
346457 TTATTTCAAG
346467 ATAGGTACCTCGAATGTTGAAAGACCCGAGGAGTTTTA
1 ATAGGTACCTCGAATGTTGAAAGACCCGAGGAGTTTTA
346505 ATAGG-ACCTCGAATGTTGAAAGACCCGAGGAGTTTTA
1 ATAGGTACCTCGAATGTTGAAAGACCCGAGGAGTTTTA
346542 CTATTCCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 32 0.86
38 5 0.14
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (38 bp):
ATAGGTACCTCGAATGTTGAAAGACCCGAGGAGTTTTA
Found at i:363547 original size:12 final size:12
Alignment explanation
Indices: 363530--363555 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
363520 AATGGAATTG
363530 TAAATCGTGAGA
1 TAAATCGTGAGA
363542 TAAATCGTGAGA
1 TAAATCGTGAGA
363554 TA
1 TA
363556 TAATAAGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (12 bp):
TAAATCGTGAGA
Found at i:371153 original size:25 final size:24
Alignment explanation
Indices: 371111--371162 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
371101 ACATACCGTA
371111 GCTCTTTATGAACGTCCTGATATAG
1 GCTCTTTATGAACGTCCTGATAT-G
* * *
371136 GCTCTTTGTGAGCTTCCTGATATG
1 GCTCTTTATGAACGTCCTGATATG
371160 GCT
1 GCT
371163 TGGTTGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (24 bp):
GCTCTTTATGAACGTCCTGATATG
Found at i:376595 original size:25 final size:25
Alignment explanation
Indices: 376567--376650 Score: 114
Period size: 25 Copynumber: 3.4 Consensus size: 25
376557 AGCTATAAAT
376567 GGTAAGCTCCTCCAAGTTGAATAAC
1 GGTAAGCTCCTCCAAGTTGAATAAC
* * *
376592 GGTAAGCTCATCCAAGCTGAATAAT
1 GGTAAGCTCCTCCAAGTTGAATAAC
* *
376617 GGTAAGCTCCTACGAGTTGAATAAC
1 GGTAAGCTCCTCCAAGTTGAATAAC
*
376642 AGTAAGCTC
1 GGTAAGCTC
376651 ATACGAGTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (25 bp):
GGTAAGCTCCTCCAAGTTGAATAAC
Found at i:376655 original size:25 final size:25
Alignment explanation
Indices: 376581--376687 Score: 115
Period size: 25 Copynumber: 4.3 Consensus size: 25
376571 AGCTCCTCCA
* * *
376581 AGTTGAATAACGGTAAGCTCATCCA
1 AGTTGAATAACAGTAAGCTCATACG
* ** *
376606 AGCTGAATAATGGTAAGCTCCTACG
1 AGTTGAATAACAGTAAGCTCATACG
376631 AGTTGAATAACAGTAAGCTCATACG
1 AGTTGAATAACAGTAAGCTCATACG
* * *
376656 AGTTGAGTACCAGTAAGCTCATAAG
1 AGTTGAATAACAGTAAGCTCATACG
*
376681 AGCTGAA
1 AGTTGAA
376688 ATCGGTAACC
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 68 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (25 bp):
AGTTGAATAACAGTAAGCTCATACG
Found at i:376672 original size:50 final size:50
Alignment explanation
Indices: 376568--376675 Score: 126
Period size: 50 Copynumber: 2.2 Consensus size: 50
376558 GCTATAAATG
* * * **
376568 GTAAGCTCCTCCAAGTTGAATAACGGTAAGCTCATCCAAGCTGAATAATG
1 GTAAGCTCCTACAAGTTGAATAACAGTAAGCTCATACAAGCTGAATAACA
* * * * *
376618 GTAAGCTCCTACGAGTTGAATAACAGTAAGCTCATACGAGTTGAGTACCA
1 GTAAGCTCCTACAAGTTGAATAACAGTAAGCTCATACAAGCTGAATAACA
376668 GTAAGCTC
1 GTAAGCTC
376676 ATAAGAGCTG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (50 bp):
GTAAGCTCCTACAAGTTGAATAACAGTAAGCTCATACAAGCTGAATAACA
Found at i:380472 original size:26 final size:25
Alignment explanation
Indices: 380408--380473 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
380398 AAGTGAGAAC
*
380408 TAATGGGAAGCTCACAAAGAGCCTT
1 TAATGGGAAGCTCACAAAGAGCCTA
* *
380433 TAATCAGGAAGCTCACGAAGAGCCATA
1 TAAT-GGGAAGCTCACAAAGAGCC-TA
*
380460 TAATGGGACGCTCA
1 TAATGGGAAGCTCA
380474 TAAGAGCTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 4 0.12
26 25 0.74
27 5 0.15
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.18
Consensus pattern (25 bp):
TAATGGGAAGCTCACAAAGAGCCTA
Found at i:380947 original size:21 final size:21
Alignment explanation
Indices: 380921--380960 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
380911 TATACGATTA
380921 AATTTAACA-TCAATTTAATAC
1 AATTT-ACATTCAATTTAATAC
380942 AATTTACATTCAATTTAAT
1 AATTTACATTCAATTTAAT
380961 CCAAGTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTTACATTCAATTTAATAC
Found at i:380971 original size:21 final size:21
Alignment explanation
Indices: 380930--380971 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
380920 AAATTTAACA
* *
380930 TCAATTTAATACAATTTACAT
1 TCAATTTAATACAAGTCACAT
*
380951 TCAATTTAATCCAAGTCACAT
1 TCAATTTAATACAAGTCACAT
380972 CTTAGGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (21 bp):
TCAATTTAATACAAGTCACAT
Found at i:381165 original size:29 final size:29
Alignment explanation
Indices: 381105--381158 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
381095 AATAGCAGCA
*
381105 CATGAATTCCAATAAATTTTAGAATTTTC
1 CATGAATTCCAATAAATTTTACAATTTTC
*
381134 CATGAATT-CAATAACTTTT-CAATTT
1 CATGAATTCCAATAAATTTTACAATTT
381159 AATCCATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 10 0.43
29 8 0.35
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (29 bp):
CATGAATTCCAATAAATTTTACAATTTTC
Found at i:386207 original size:25 final size:25
Alignment explanation
Indices: 386164--386228 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
386154 TGAGCACTTA
* *
386164 AACAGGAAGCTCTTTTGAGTCATAT
1 AACAGGAAGCTCATGTGAGTCATAT
* *
386189 AACAGGAAGCTGATGTGAGTCATGT
1 AACAGGAAGCTCATGTGAGTCATAT
*
386214 AATAGGGAAGCTCAT
1 AACA-GGAAGCTCAT
386229 AAGAGCTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 24 0.73
26 9 0.27
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (25 bp):
AACAGGAAGCTCATGTGAGTCATAT
Found at i:388033 original size:12 final size:12
Alignment explanation
Indices: 388016--388040 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
388006 CGGAACTTCA
388016 ACACAACAATTC
1 ACACAACAATTC
388028 ACACAACAATTC
1 ACACAACAATTC
388040 A
1 A
388041 TTCAATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (12 bp):
ACACAACAATTC
Found at i:389929 original size:18 final size:18
Alignment explanation
Indices: 389906--389940 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
389896 CATAAAATTT
389906 CAAGAAAATCGATACCAC
1 CAAGAAAATCGATACCAC
389924 CAAGAAAATCGATACCA
1 CAAGAAAATCGATACCA
389941 ATCTAGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.26, G:0.11, T:0.11
Consensus pattern (18 bp):
CAAGAAAATCGATACCAC
Found at i:393905 original size:20 final size:20
Alignment explanation
Indices: 393870--393922 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
393860 GAGTTACCGG
*
393870 AGTATAACCA-GGGTACCAA
1 AGTATAAACAGGGGTACCAA
* *
393889 GGTATAATCAGGGGTACCAA
1 AGTATAAACAGGGGTACCAA
*
393909 AGTACAAACAGGGG
1 AGTATAAACAGGGG
393923 CATGTAAGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.40, C:0.17, G:0.28, T:0.15
Consensus pattern (20 bp):
AGTATAAACAGGGGTACCAA
Found at i:393931 original size:20 final size:20
Alignment explanation
Indices: 393908--393971 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
393898 AGGGGTACCA
393908 AAGTACAAACAGGGGCATGT
1 AAGTACAAACAGGGGCATGT
* * *
393928 AAGTGCAATCAGGGGTATCG-
1 AAGTACAAACAGGGGCAT-GT
*
393948 AAGTACAAACAGGGGCACGT
1 AAGTACAAACAGGGGCATGT
393968 AAGT
1 AAGT
393972 GTAATAAGGG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.31, T:0.16
Consensus pattern (20 bp):
AAGTACAAACAGGGGCATGT
Found at i:393938 original size:40 final size:40
Alignment explanation
Indices: 393894--394018 Score: 178
Period size: 40 Copynumber: 3.1 Consensus size: 40
393884 ACCAAGGTAT
* *
393894 AATCAGGGGTACCAAAGTACAAACAGGGGCATGTAAGTGC
1 AATCAGGGGTACCGAAGTACAAACAGGGGCACGTAAGTGC
* *
393934 AATCAGGGGTATCGAAGTACAAACAGGGGCACGTAAGTGT
1 AATCAGGGGTACCGAAGTACAAACAGGGGCACGTAAGTGC
* * * *
393974 AATAAGGGGTACCGAATTACAAATAGGGGCACATAAGTGC
1 AATCAGGGGTACCGAAGTACAAACAGGGGCACGTAAGTGC
394014 AATCA
1 AATCA
394019 TTCAATAATT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.17
Consensus pattern (40 bp):
AATCAGGGGTACCGAAGTACAAACAGGGGCACGTAAGTGC
Found at i:396039 original size:9 final size:10
Alignment explanation
Indices: 396009--396042 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
395999 CAACTGGGAA
396009 TTTCTCACTT
1 TTTCTCACTT
*
396019 TTTTTCACTT
1 TTTCTCACTT
396029 TTTCTCA-TT
1 TTTCTCACTT
396038 TTTCT
1 TTTCT
396043 TTTTCACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTCTCACTT
Found at i:397737 original size:44 final size:45
Alignment explanation
Indices: 397674--397764 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
397664 TGCATGAAGA
397674 AAATCAAAACCAAAGCTT-CCCCCCCTTTAATGGTGATTTCAGCC
1 AAATCAAAACCAAAGCTTCCCCCCCCTTTAATGGTGATTTCAGCC
397718 AAATCAAAACCAAAGCTTCCCCCCCCTTTAATGGTGATTTCAGCC
1 AAATCAAAACCAAAGCTTCCCCCCCCTTTAATGGTGATTTCAGCC
397763 AA
1 AA
397765 GGAATAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 18 0.39
45 28 0.61
ACGTcount: A:0.33, C:0.32, G:0.11, T:0.24
Consensus pattern (45 bp):
AAATCAAAACCAAAGCTTCCCCCCCCTTTAATGGTGATTTCAGCC
Found at i:397830 original size:16 final size:16
Alignment explanation
Indices: 397809--397855 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
397799 CATCTTTTGT
397809 TTAATTAACATTTAAC
1 TTAATTAACATTTAAC
* *
397825 TTAATTATCAAATT-AC
1 TTAATTAAC-ATTTAAC
*
397841 TTAATTAACCTTTAA
1 TTAATTAACATTTAA
397856 AAATTGTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
15 2 0.08
16 19 0.79
17 3 0.12
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAATTAACATTTAAC
Found at i:398603 original size:33 final size:33
Alignment explanation
Indices: 398557--398663 Score: 115
Period size: 33 Copynumber: 3.5 Consensus size: 33
398547 ACCGAGACAA
*
398557 TAAACATGAAACAGAGTAAGTTCGTCGGGATAG
1 TAAACATGGAACAGAGTAAGTTCGTCGGGATAG
* *
398590 TAAACATGGAACAGAG-ATAGTTTG-CTGG---G
1 TAAACATGGAACAGAGTA-AGTTCGTCGGGATAG
398619 ---AC-TGGAACAGAGTAAGTTCGTCGGGATAG
1 TAAACATGGAACAGAGTAAGTTCGTCGGGATAG
398648 TAAACATGGAACAGAG
1 TAAACATGGAACAGAG
398664 ATAGTAAACA
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
25 15 0.25
26 6 0.10
29 2 0.03
32 6 0.10
33 30 0.51
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (33 bp):
TAAACATGGAACAGAGTAAGTTCGTCGGGATAG
Found at i:398679 original size:20 final size:20
Alignment explanation
Indices: 398643--398682 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
398633 AGTTCGTCGG
**
398643 GATAGTAAACATGGAACAGA
1 GATAGTAAACACAGAACAGA
398663 GATAGTAAACACAGAACAGA
1 GATAGTAAACACAGAACAGA
398683 TAAAGTCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.23, T:0.12
Consensus pattern (20 bp):
GATAGTAAACACAGAACAGA
Found at i:404200 original size:27 final size:27
Alignment explanation
Indices: 404170--404226 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
404160 AATGAATTCT
404170 GCTAAAGGTAAATAATGTTCCCAAATA
1 GCTAAAGGTAAATAATGTTCCCAAATA
*
404197 GCTAAGGGTAAATAATGTTCCCAAATA
1 GCTAAAGGTAAATAATGTTCCCAAATA
404224 GCT
1 GCT
404227 TCAAACTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (27 bp):
GCTAAAGGTAAATAATGTTCCCAAATA
Found at i:408031 original size:16 final size:16
Alignment explanation
Indices: 408006--408039 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
407996 AAAATAATAT
* *
408006 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
408022 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
408038 AT
1 AT
408040 TGGATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:409355 original size:48 final size:48
Alignment explanation
Indices: 409284--409380 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
409274 ACGGGTTGAA
*
409284 TGACCCCTACAGTTGAATTTTTTAACTTTTTCCTCAAATTTTCAAATG
1 TGACCCCTACAGTTGAATTTTTTAACTTTTTCCTCAAATCTTCAAATG
409332 TGACCCCTACAGTTGAATTTTTTAACTTTTTCCTCAAATCTTCAAATG
1 TGACCCCTACAGTTGAATTTTTTAACTTTTTCCTCAAATCTTCAAATG
409380 T
1 T
409381 TCCTGATTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (48 bp):
TGACCCCTACAGTTGAATTTTTTAACTTTTTCCTCAAATCTTCAAATG
Found at i:417229 original size:15 final size:15
Alignment explanation
Indices: 417206--417237 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
417196 GTGGTAAGAA
417206 TTTAATACTTAATTT
1 TTTAATACTTAATTT
*
417221 TTTAGTACTTAATTT
1 TTTAATACTTAATTT
417236 TT
1 TT
417238 AATTGATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTAATACTTAATTT
Found at i:427860 original size:43 final size:43
Alignment explanation
Indices: 427807--428036 Score: 320
Period size: 43 Copynumber: 5.3 Consensus size: 43
427797 GTTTTTAGAA
*
427807 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTTCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTTCC
* *
427850 ACAAACGCCGCTAAATACCAAGACCATTAGCGACGCTTTTTCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTTCC
* * * *
427893 ACAAACGTCGCTAAAGACCCAGACCTTTAGCGACGATTTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTTCC
*
427936 ACAAACGCCGCTAAAGACCAGGACCTTTAGCGACGC-TTTTCTC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTTC-C
* * *
427979 ACAAACGCCGCTAAAGACCCAA-ACCTCTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGA-CCAAGACCTTTAGCGACGCTTTTTCC
*
428022 AGAAACGCCGCTAAA
1 ACAAACGCCGCTAAA
428037 AATATATCTT
Statistics
Matches: 165, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
42 4 0.02
43 154 0.93
44 7 0.04
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.19
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTTCC
Found at i:428345 original size:43 final size:43
Alignment explanation
Indices: 428297--428387 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
428287 ACATATGCAA
* * * *
428297 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
428340 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
428383 -GTAAT
1 GGTAAT
428388 GAACTCAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:432658 original size:11 final size:11
Alignment explanation
Indices: 432644--432703 Score: 56
Period size: 10 Copynumber: 5.7 Consensus size: 11
432634 AAAATAAAAG
*
432644 TTTAAAATCTT
1 TTTAAAATCAT
432655 TTTAAAAT--T
1 TTTAAAATCAT
* *
432664 TTTAAAA-AAA
1 TTTAAAATCAT
432674 TTTAAAATC-T
1 TTTAAAATCAT
432684 TTTAAAATTCAT
1 TTTAAAA-TCAT
432696 TTTAAAAT
1 TTTAAAAT
432704 TTTAAATCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
9 8 0.20
10 14 0.34
11 11 0.27
12 8 0.20
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (11 bp):
TTTAAAATCAT
Found at i:432702 original size:29 final size:29
Alignment explanation
Indices: 432637--432711 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 29
432627 TATTATAAAA
432637 ATAAAAGTTTAAAATCTTTTTAAAATTTTT
1 ATAAAA-TTTAAAATCTTTTTAAAATTTTT
*
432667 AAAAAAATTTAAAATC-TTTTAAAATTCATTT
1 -ATAAAATTTAAAATCTTTTTAAAATT--TTT
*
432698 -TAAAATTTTAAATC
1 ATAAAATTTAAAATC
432712 ATGAAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 22 0.56
30 9 0.23
31 8 0.21
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (29 bp):
ATAAAATTTAAAATCTTTTTAAAATTTTT
Found at i:432708 original size:30 final size:30
Alignment explanation
Indices: 432637--432709 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
432627 TATTATAAAA
*
432637 ATAAAAGTTTAAAATCTTTTTAAAATTTTT
1 ATAAAAATTTAAAATCTTTTTAAAATTTTT
*
432667 AAAAAAATTTAAAATC-TTTTAAAATTCATTT
1 ATAAAAATTTAAAATCTTTTTAAAATT--TTT
*
432698 -TAAAATTTTAAA
1 ATAAAAATTTAAA
432710 TCATGAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.27
30 24 0.65
31 3 0.08
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (30 bp):
ATAAAAATTTAAAATCTTTTTAAAATTTTT
Found at i:432709 original size:20 final size:20
Alignment explanation
Indices: 432644--432706 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
432634 AAAATAAAAG
*
432644 TTTAAAATCTTTTTAAAATT
1 TTTAAAATCATTTTAAAATT
* *
432664 TTTAAAA-AAATTTAAAATCT
1 TTTAAAATCATTTTAAAAT-T
432684 TTTAAAATTCATTTTAAAATT
1 TTTAAAA-TCATTTTAAAATT
432705 TT
1 TT
432707 AAATCATGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 8 0.23
20 15 0.43
21 3 0.09
22 9 0.26
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAAATCATTTTAAAATT
Found at i:433167 original size:27 final size:27
Alignment explanation
Indices: 433103--433167 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
433093 CTAAAATGTA
*
433103 AACTCTAAACCTTAAACCCCAATCCCC
1 AACTCTAAACCTTAAACCCCAAACCCC
*
433130 AAGCCCTAAACC-TAAACCCCAAACCCC
1 AA-CTCTAAACCTTAAACCCCAAACCCC
*
433157 GAACTCAAAAC
1 -AACTCTAAAC
433168 TGTAATCCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 22 0.69
28 10 0.31
ACGTcount: A:0.42, C:0.43, G:0.03, T:0.12
Consensus pattern (27 bp):
AACTCTAAACCTTAAACCCCAAACCCC
Found at i:434334 original size:41 final size:41
Alignment explanation
Indices: 434276--434463 Score: 286
Period size: 41 Copynumber: 4.6 Consensus size: 41
434266 GCTAAAGTCA
**
434276 AGCATTAGCGGCGCTTTTTCAAAAACGTCGCTAAAGGCCCG
1 AGCATTAGCGGCGCTTTTGAAAAAACGTCGCTAAAGGCCCG
* * *
434317 AGCATTAGCGGCACTTTTGAAAAAACGCCGCTAAAGGACCG
1 AGCATTAGCGGCGCTTTTGAAAAAACGTCGCTAAAGGCCCG
* *
434358 AGCATTAGCGGCGCTTTTGAAAAAACGCCGCTAAAGCCCCG
1 AGCATTAGCGGCGCTTTTGAAAAAACGTCGCTAAAGGCCCG
*
434399 AGCATTAGCGGCGCTTTTGAAAAAACGTCGCTAAAGCCCCG
1 AGCATTAGCGGCGCTTTTGAAAAAACGTCGCTAAAGGCCCG
* *
434440 AACATTAGCTGCGCTTTTGAAAAA
1 AGCATTAGCGGCGCTTTTGAAAAA
434464 GCACGGCTAA
Statistics
Matches: 136, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 136 1.00
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (41 bp):
AGCATTAGCGGCGCTTTTGAAAAAACGTCGCTAAAGGCCCG
Found at i:434625 original size:40 final size:40
Alignment explanation
Indices: 434522--434666 Score: 145
Period size: 40 Copynumber: 3.6 Consensus size: 40
434512 GGTTTTTTGC
* *
434522 GGCGCTTTTTGGAAAA-CGCCGCTAATGCTT-ATTTTTAGC
1 GGCG-TTTTTGCAAAAGCGCCGCTAATGCTTGATTTTTAGT
* * *
434561 AGCGTTTTT-CAATATGCGCCGCTAATGCTTGATCTTTAGT
1 GGCGTTTTTGCAA-AAGCGCCGCTAATGCTTGATTTTTAGT
* *
434601 GGCGTTTTTGTAAAAGCGCTGCTAATGCTTGATTTTTAGT
1 GGCGTTTTTGCAAAAGCGCCGCTAATGCTTGATTTTTAGT
* *
434641 GGCATTTTTTGTCCAAA-CGCCGCTAA
1 GGC-GTTTTTG-CAAAAGCGCCGCTAA
434667 AAATGCCACT
Statistics
Matches: 86, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
37 2 0.02
38 6 0.07
39 17 0.20
40 42 0.49
41 16 0.19
42 3 0.03
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (40 bp):
GGCGTTTTTGCAAAAGCGCCGCTAATGCTTGATTTTTAGT
Found at i:444817 original size:20 final size:21
Alignment explanation
Indices: 444784--444823 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
444774 CAGCTTGTTG
444784 AGCTCAATTGAGCTCATTTCT
1 AGCTCAATTGAGCTCATTTCT
*
444805 AGCTCAA-TGAGCTCCTTTC
1 AGCTCAATTGAGCTCATTTC
444824 CATCTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.35
Consensus pattern (21 bp):
AGCTCAATTGAGCTCATTTCT
Found at i:447422 original size:20 final size:21
Alignment explanation
Indices: 447389--447430 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
447379 CAGCTTGTTG
447389 AGCTCAATTGAGCTCATTTCC
1 AGCTCAATTGAGCTCATTTCC
*
447410 AGCTCAA-TGAGCTCGTTTCC
1 AGCTCAATTGAGCTCATTTCC
447430 A
1 A
447431 TCTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (21 bp):
AGCTCAATTGAGCTCATTTCC
Found at i:451087 original size:20 final size:20
Alignment explanation
Indices: 451062--451105 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
451052 ATAACGATTC
451062 AAAAGAAAAAAAATTGAGAG
1 AAAAGAAAAAAAATTGAGAG
* *
451082 AAAAGAACAAAAATTGTGAG
1 AAAAGAAAAAAAATTGAGAG
451102 AAAA
1 AAAA
451106 ACAAGAGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.68, C:0.02, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAAGAAAAAAAATTGAGAG
Found at i:451133 original size:21 final size:23
Alignment explanation
Indices: 451100--451144 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
451090 AAAAATTGTG
*
451100 AGAAAAACAAGAGTG-GAGAAAA
1 AGAAAAACAAGAGTGAAAGAAAA
*
451122 AGAAAAA-GAGAGTGAAAGAAAA
1 AGAAAAACAAGAGTGAAAGAAAA
451144 A
1 A
451145 TGAATGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.67, C:0.02, G:0.27, T:0.04
Consensus pattern (23 bp):
AGAAAAACAAGAGTGAAAGAAAA
Found at i:451915 original size:42 final size:42
Alignment explanation
Indices: 451856--452025 Score: 340
Period size: 42 Copynumber: 4.0 Consensus size: 42
451846 CCTGGCCCAC
451856 ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
1 ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
451898 ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
1 ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
451940 ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
1 ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
451982 ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
1 ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
452024 AT
1 AT
452026 GGTGAAGGTG
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 128 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (42 bp):
ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
Found at i:452441 original size:20 final size:21
Alignment explanation
Indices: 452408--452449 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
452398 TAGCTTGTTA
452408 AGCTCAATTGAGCTCATTTCC
1 AGCTCAATTGAGCTCATTTCC
*
452429 AGCTCAA-TGAGCTCGTTTCC
1 AGCTCAATTGAGCTCATTTCC
452449 A
1 A
452450 TCTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (21 bp):
AGCTCAATTGAGCTCATTTCC
Found at i:456282 original size:27 final size:27
Alignment explanation
Indices: 456252--456305 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
456242 AGAACTCTTA
456252 GCTTAGATATTACAACTCGACTTGTAT
1 GCTTAGATATTACAACTCGACTTGTAT
456279 GCTTAGATATTACAACTCGACTTGTAT
1 GCTTAGATATTACAACTCGACTTGTAT
456306 AGTAGCAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (27 bp):
GCTTAGATATTACAACTCGACTTGTAT
Found at i:468259 original size:17 final size:17
Alignment explanation
Indices: 468237--468270 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
468227 AAGTGAGAAA
468237 CAAATGAAGGACTAAAG
1 CAAATGAAGGACTAAAG
* *
468254 CAAATGAGGGGCTAAAG
1 CAAATGAAGGACTAAAG
468271 GAAGGAGAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.29, T:0.12
Consensus pattern (17 bp):
CAAATGAAGGACTAAAG
Found at i:470327 original size:13 final size:13
Alignment explanation
Indices: 470309--470333 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
470299 AAAATTTGAT
470309 TTGATTATGTAAA
1 TTGATTATGTAAA
470322 TTGATTATGTAA
1 TTGATTATGTAA
470334 TCTTATAAAT
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:474801 original size:28 final size:28
Alignment explanation
Indices: 474761--474818 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
474751 AATCATACAT
*
474761 CAACAACTTCAAAAGAGAGGAAAAACAC
1 CAACAACATCAAAAGAGAGGAAAAACAC
474789 CAACAACATCAAAAGAGAGGAAAAACAC
1 CAACAACATCAAAAGAGAGGAAAAACAC
474817 CA
1 CA
474819 GCTGGAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.59, C:0.22, G:0.14, T:0.05
Consensus pattern (28 bp):
CAACAACATCAAAAGAGAGGAAAAACAC
Found at i:476409 original size:6 final size:6
Alignment explanation
Indices: 476367--476406 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
476357 CAGTATTCTT
*
476367 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTCC TTTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
476407 CCTCCTCTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.17, G:0.12, T:0.70
Consensus pattern (6 bp):
TTTTGC
Found at i:477097 original size:28 final size:29
Alignment explanation
Indices: 477065--477119 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
477055 AGCAAAGAAA
*
477065 TAAAA-GATTATT-AAATTTTAAAAAAAAC
1 TAAAACGATT-TTAAAATTATAAAAAAAAC
477093 TAAAACGATTTTAAAATTATAAAAAAA
1 TAAAACGATTTTAAAATTATAAAAAAA
477120 CAAGTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (29 bp):
TAAAACGATTTTAAAATTATAAAAAAAAC
Found at i:477715 original size:6 final size:6
Alignment explanation
Indices: 477704--477730 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
477694 TTTGTTCTTA
477704 TTAATT TTAATT TTAATT TTAATT TTA
1 TTAATT TTAATT TTAATT TTAATT TTA
477731 TAAAAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTAATT
Found at i:478198 original size:30 final size:30
Alignment explanation
Indices: 478158--478237 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
478148 TTAAATTAAA
*
478158 TAAAAAAATTTATTTAATTACATATTA--TT
1 TAAAATAATTTATTTAATTA-ATATTATGTT
* *
478187 TATAAATAATTTTTTTAAGTTAATTTTATGTT
1 TA-AAATAATTTATTTAA-TTAATATTATGTT
*
478219 TAAAATAA-ATATTTAATTA
1 TAAAATAATTTATTTAATTA
478238 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
29 5 0.12
30 24 0.57
31 9 0.21
32 4 0.10
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (30 bp):
TAAAATAATTTATTTAATTAATATTATGTT
Found at i:478673 original size:23 final size:23
Alignment explanation
Indices: 478647--478690 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
478637 ATTTTAACCT
478647 ATTATAAAAATATGAATATTTTA
1 ATTATAAAAATATGAATATTTTA
* *
478670 ATTATATAAATATGAGTATTT
1 ATTATAAAAATATGAATATTT
478691 GTTTAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (23 bp):
ATTATAAAAATATGAATATTTTA
Found at i:478798 original size:17 final size:17
Alignment explanation
Indices: 478778--478815 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
478768 TTAAGTTTTA
478778 ATTAAGTATAATTTATT
1 ATTAAGTATAATTTATT
* *
478795 ATTAAGTATATTTTCTT
1 ATTAAGTATAATTTATT
478812 ATTA
1 ATTA
478816 TGAAATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (17 bp):
ATTAAGTATAATTTATT
Found at i:485642 original size:27 final size:27
Alignment explanation
Indices: 485612--485673 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
485602 AACAATGTTT
485612 CTGGCAATAAAATCCTGAACAGAGTTC
1 CTGGCAATAAAATCCTGAACAGAGTTC
* * * *
485639 CTGG-AGATAAGATTCTTAATAGAGTTC
1 CTGGCA-ATAAAATCCTGAACAGAGTTC
*
485666 CTGTCAAT
1 CTGGCAAT
485674 CGCAACTCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
26 1 0.04
27 26 0.93
28 1 0.04
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (27 bp):
CTGGCAATAAAATCCTGAACAGAGTTC
Found at i:485882 original size:35 final size:35
Alignment explanation
Indices: 485801--485925 Score: 146
Period size: 35 Copynumber: 3.6 Consensus size: 35
485791 CACATGGTTA
* *
485801 ACCATCCAACACACCAGATACTCATAAGAG-TCAGT
1 ACCATCCAGCACACCAGTTACTCATAAGAGCT-AGT
485836 ACCATCCAGCACACCAGTTACTCATAAGAGCTAGT
1 ACCATCCAGCACACCAGTTACTCATAAGAGCTAGT
** * * * *
485871 ACCATTTAGCACACCA-TTCGCTCATACGAACCAGT
1 ACCATCCAGCACACCAGTT-ACTCATAAGAGCTAGT
485906 ACCATCCAGCACACCAGTTA
1 ACCATCCAGCACACCAGTTA
485926 ACACTATAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.03
35 71 0.93
36 3 0.04
ACGTcount: A:0.35, C:0.34, G:0.12, T:0.19
Consensus pattern (35 bp):
ACCATCCAGCACACCAGTTACTCATAAGAGCTAGT
Found at i:488251 original size:25 final size:25
Alignment explanation
Indices: 488223--488277 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
488213 AAATACGAAT
*
488223 AAAAATTGTAATACAAAATTAATTAA
1 AAAAATT-TAATACAAAATTAATAAA
* **
488249 AAAAACTTAATACAATTTTAATAAA
1 AAAAATTTAATACAAAATTAATAAA
488274 AAAA
1 AAAA
488278 TAAGAGTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAAATTTAATACAAAATTAATAAA
Found at i:488306 original size:11 final size:11
Alignment explanation
Indices: 488290--488345 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
488280 AGAGTGAACT
488290 GAGAGAATTGA
1 GAGAGAATTGA
* *
488301 GTGAGAATTAA
1 GAGAGAATTGA
*
488312 GAGAGGATTGA
1 GAGAGAATTGA
488323 GA-ATGAATTGA
1 GAGA-GAATTGA
* *
488334 GAAAGAGTTGA
1 GAGAGAATTGA
488345 G
1 G
488346 TGAATTGAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
10 1 0.03
11 34 0.94
12 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (11 bp):
GAGAGAATTGA
Found at i:492861 original size:115 final size:116
Alignment explanation
Indices: 492724--492966 Score: 373
Period size: 116 Copynumber: 2.1 Consensus size: 116
492714 TAAGTTTGTG
* *
492724 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATAATTAA
* ** *
492789 TTGTT-GTATCA-GTCAAAACATTTTTCAAAATCTAAAATTATGTGAATGTA
65 TTGTTAGTACCAGGAAAAAACATTTTTCAAAATCTAAAATTATGTGAAAGTA
492839 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATAATTAAT
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATAATTAAT
* * * *
492904 TGTTAGTACCAGGAAAAAATATTTTTCCAAATCTAACATTATTTGAAAGTA
66 TGTTAGTACCAGGAAAAAACATTTTTCAAAATCTAAAATTATGTGAAAGTA
492955 AAATTATTAATT
1 AAATTATTAATT
492967 TAGTTTAGGG
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
114 33 0.28
115 39 0.34
116 44 0.38
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (116 bp):
AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATAATTAAT
TGTTAGTACCAGGAAAAAACATTTTTCAAAATCTAAAATTATGTGAAAGTA
Found at i:493001 original size:23 final size:23
Alignment explanation
Indices: 492961--493881 Score: 849
Period size: 23 Copynumber: 41.4 Consensus size: 23
492951 AGTAAAATTA
* *
492961 TTAATTTAGTTTAGGGTTTTTAAT
1 TTAA-TTAGGTTAGGGTTTTTAAG
*
492985 TTAATTAGGTTAAGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* *
493008 TTAA--GGGTTAGGATTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* *
493029 TTAA--GGGTTTAGTGTTTTTAAG
1 TTAATTAGG-TTAGGGTTTTTAAG
*
493051 TTAA--GGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
**
493072 TTAA-GGGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
** *
493094 -TAA-CGGGTTAGGGTTTTTAAC
1 TTAATTAGGTTAGGGTTTTTAAG
* *
493115 TAAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
493138 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
*
493161 TTAATTAGGTTAGGGTTTTTAAC
1 TTAATTAGGTTAGGGTTTTTAAG
***
493184 TTAAGGGGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* *
493207 TTAA--GGGTTATGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
** *
493228 -TAA-CGGGTTAGAGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
***
493249 -T--TTAGGGTTTAAAATTTTTAA-
1 TTAATTA-GG-TTAGGGTTTTTAAG
493270 TTAAATTAGGTTAGGGTTTTTAAG
1 TT-AATTAGGTTAGGGTTTTTAAG
* * * *
493294 TTAA--GGGTTAGGATTTTCAAT
1 TTAATTAGGTTAGGGTTTTTAAG
*
493315 TTAATTAGGTTAAGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
*
493338 TTAATTAGGTTAGGGTTTTTAAC
1 TTAATTAGGTTAGGGTTTTTAAG
***
493361 TTAAGGGGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* *
493384 TTAA--GGGTTATGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
** *
493405 -TAA-CGGGTTAGAGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
***
493426 -T--TTAGGGTTTAAAATTTTTAA-
1 TTAATTA-GG-TTAGGGTTTTTAAG
493447 TTAAATTAGGTTAGGGTTTTTAAG
1 TT-AATTAGGTTAGGGTTTTTAAG
* * * *
493471 TTAA--GGGTTAGGATTTTCAAT
1 TTAATTAGGTTAGGGTTTTTAAG
*
493492 TTAATTAGGTTAAGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
493515 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
*** *
493538 TTAAGGGGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
*
493561 TTAATTAGGTTGGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* *
493584 TTAA--GGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
*
493605 TTAATTATGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* * *
493628 TTAA--GGGTTAGAGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
493649 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
*
493672 TTAATTAGGTTAGAGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* * *
493695 TTAA--GGGTTAGAGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
493716 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
*
493739 TTAATTAGGTTAGAGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* * *
493762 TTAA--GGGTTAGAGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
493783 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
*
493806 TTAATTAGGTTAGAGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* * *
493829 TTAA--GGGTTAGAGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
493850 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
493873 TTAATTAGG
1 TTAATTAGG
493882 NNNNNNNNNN
Statistics
Matches: 754, Mismatches: 107, Indels: 73
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.01
21 251 0.33
22 62 0.08
23 417 0.55
24 12 0.02
25 6 0.01
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (23 bp):
TTAATTAGGTTAGGGTTTTTAAG
Found at i:493159 original size:67 final size:67
Alignment explanation
Indices: 492971--493881 Score: 982
Period size: 67 Copynumber: 13.7 Consensus size: 67
492961 TTAATTTAGT
* * *
492971 TTAGGGTTTTTAATTTAATTAGGTTAAGGTTTTTAAGTTAA--GGGTTAGGATTTTTAAGTTAAG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAG
493034 GG
66 GG
* * * **
493036 TTTAGTGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAGTTAA-GGGGTTAGGGTTTTTAAG-TAA
1 -TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAA
493097 CGGG
65 -GGG
* * *
493101 TTAGGGTTTTTAACTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAT
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAA-
*
493166 TAGG
65 -GGG
* *** * *
493170 TTAGGGTTTTTAACTTAAGGGGGTTAGGGTTTTTAAGTTAA--GGGTTATGGTTTTTAAG-TAAC
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAA-
493232 GGG
65 GGG
* * ***
493235 TTAGAGTTTTTAAGTTT-A--GGGTTTAAAATTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTT
1 TTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGTT
493296 AAGGG
63 AAGGG
* * * *
493301 TTAGGATTTTCAATTTAATTAGGTTAAGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAACTTAAG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAA-
493366 GGGG
65 -GGG
* * * ** * *
493370 TTAGGGTTTTTAAGTTAA--GGGTTATGGTTTTTAAG-TAA-CGGGTTAGAGTTTTTAAGTTTAG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAG
493431 GG
66 GG
*** * * * * *
493433 TTTAAAATTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGATTTTCAATTTAA
1 -TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAA
*
493496 TTAGG
65 --GGG
* * *** *
493501 TTAAGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAGGGGGTTAGGGTTTTTAATTTAAT
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAA-
*
493566 TAGG
65 -GGG
* * * * *
493570 TTGGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAATTTAATTATGTTAGGGTTTTTAAGTTAAG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAG
493633 GG
66 GG
* *
493635 TTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGAGTTTTTAAGTTAAG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAG
493700 GG
66 GG
* *
493702 TTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGAGTTTTTAAGTTAAG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAG
493767 GG
66 GG
* *
493769 TTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGAGTTTTTAAGTTAAG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAG
493834 GG
66 GG
*
493836 TTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGG
493882 NNNNNNNNNN
Statistics
Matches: 733, Mismatches: 83, Indels: 57
0.84 0.10 0.07
Matches are distributed among these distances:
63 8 0.01
64 62 0.08
65 71 0.10
66 103 0.14
67 384 0.52
68 9 0.01
69 96 0.13
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (67 bp):
TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAG
GG
Found at i:493305 original size:177 final size:176
Alignment explanation
Indices: 492961--493881 Score: 1078
Period size: 177 Copynumber: 5.2 Consensus size: 176
492951 AGTAAAATTA
* * * * *
492961 TTAATTTAGTTTAGGGTTTTTAATTTAATTAGGTTAAGGTTTTTAAGTTAA--GGGTTAGGATTT
1 TTAA-TTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAACTTAAGGGGGTTAGGGTTT
* * *
493024 TTAAGTTAAGGGTT-TAGTGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTT
65 TTAAGTTAAGGGTTAT-G-GTTTTTAAGTTAAGGGTTAGAGTTTTTAAGTTTAGGGTTTAGGGTT
* ** * * *
493088 TTTAAGTAA-CGGGTTAGGGTTTTTAACTAAATTAGGTTAGGGTTTTTAAT
128 TTTAATTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAT
493138 TTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAACTTAAGGGGGTTAGGGTTTT
1 TTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAACTTAAGGGGGTTAGGGTTTT
***
493203 TAAGTTAAGGGTTATGGTTTTTAAG-TAACGGGTTAGAGTTTTTAAGTTTAGGGTTTAAAATTTT
66 TAAGTTAAGGGTTATGGTTTTTAAGTTAA-GGGTTAGAGTTTTTAAGTTTAGGGTTTAGGGTTTT
* *
493267 TAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGATTTTCAAT
130 TAATT-AATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAT
*
493315 TTAATTAGGTTAAGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAACTTAAGGGGGTTAGGGTTTT
1 TTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAACTTAAGGGGGTTAGGGTTTT
***
493380 TAAGTTAAGGGTTATGGTTTTTAAG-TAACGGGTTAGAGTTTTTAAGTTTAGGGTTTAAAATTTT
66 TAAGTTAAGGGTTATGGTTTTTAAGTTAA-GGGTTAGAGTTTTTAAGTTTAGGGTTTAGGGTTTT
* *
493444 TAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGATTTTCAAT
130 TAATT-AATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAT
* *
493492 TTAATTAGGTTAAGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAGGGGGTTAGGGTTTT
1 TTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAACTTAAGGGGGTTAGGGTTTT
* * ** * ***
493557 TAATTTAATTAGGTTGGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAA-TTTAATTATGTTAGGGT
66 TAAGTTAA--GGGTTATGGTTTTTAAGTTAAGGGTTAGAGTTTTTAAGTTT-AGGGT-TTAGGGT
* * * * *
493621 TTTTAAGTTAA--GGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAG
127 TTTTAA-TTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAT
* * * * ***
493672 TTAATTAGGTTAGAGTTTTTAAGTTAA--GGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTT
1 TTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAACTTAAGGGGGTTAGGGTTTT
* *
493735 TAAGTTAATTAGGTTA-GAGTTTTTAAGTTAAGGGTTAGAGTTTTTAA-TTTAATTAGG-TTAGG
66 TAAGTTAA--GGGTTATG-GTTTTTAAGTTAAGGGTTAGAGTTTTTAAGTTT-A--GGGTTTAGG
* *
493797 GTTTTTAAGTTAATTAGGTTAGAGTTTTTAAGTTAAGGGTTAGAGTTTTTAAT
125 GTTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAT
493850 TTAATTAGGTTAGGGTTTTTAAGTTAATTAGG
1 TTAATTAGGTTAGGGTTTTTAAGTTAATTAGG
493882 NNNNNNNNNN
Statistics
Matches: 663, Mismatches: 60, Indels: 39
0.87 0.08 0.05
Matches are distributed among these distances:
176 45 0.07
177 308 0.46
178 184 0.28
179 50 0.08
180 74 0.11
181 2 0.00
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (176 bp):
TTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAACTTAAGGGGGTTAGGGTTTT
TAAGTTAAGGGTTATGGTTTTTAAGTTAAGGGTTAGAGTTTTTAAGTTTAGGGTTTAGGGTTTTT
AATTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAT
Found at i:494692 original size:25 final size:25
Alignment explanation
Indices: 494658--494705 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
494648 TATGAAAAAT
*
494658 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACACCAAATAAAC
494683 TTCTATTTTATTACACCAAATAA
1 TTCTATTTTATTACACCAAATAA
494706 TATCAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.44
Consensus pattern (25 bp):
TTCTATTTTATTACACCAAATAAAC
Found at i:494722 original size:9 final size:9
Alignment explanation
Indices: 494704--494744 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
494694 TACACCAAAT
494704 AATA-TCAA
1 AATATTCAA
494712 AATATTCAA
1 AATATTCAA
494721 AATATTCAA
1 AATATTCAA
494730 AATATT-AA
1 AATATTCAA
*
494738 AAAATTC
1 AATATTC
494745 CTATTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 11 0.37
9 19 0.63
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (9 bp):
AATATTCAA
Found at i:494739 original size:17 final size:18
Alignment explanation
Indices: 494704--494744 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
494694 TACACCAAAT
494704 AATA-TCAAAATATTCAA
1 AATATTCAAAATATTCAA
494721 AATATTCAAAATATT-AA
1 AATATTCAAAATATTCAA
*
494738 AAAATTC
1 AATATTC
494745 CTATTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (18 bp):
AATATTCAAAATATTCAA
Found at i:494788 original size:85 final size:85
Alignment explanation
Indices: 494652--494811 Score: 302
Period size: 85 Copynumber: 1.9 Consensus size: 85
494642 AAATAATATG
*
494652 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACACCAAATAATATCAAAATAT
1 AAAAATTCCTATTTTATTACATCAAATAAACTTCTATTTTATTACACCAAATAATATCAAAATAT
494717 TCAAAATATTCAAAATATTA
66 TCAAAATATTCAAAATATTA
*
494737 AAAAATTCCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAT
1 AAAAATTCCTATTTTATTACATCAAATAAACTTCTATTTTATTACACCAAATAATATCAAAATAT
494802 TCAAAATATT
66 TCAAAATATT
494812 TGTACAAATA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (85 bp):
AAAAATTCCTATTTTATTACATCAAATAAACTTCTATTTTATTACACCAAATAATATCAAAATAT
TCAAAATATTCAAAATATTA
Found at i:495242 original size:18 final size:18
Alignment explanation
Indices: 495219--495258 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
495209 GACTCGGAAA
*
495219 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
495237 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
495255 AGGA
1 AGGA
495259 AACGCACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:495903 original size:7 final size:7
Alignment explanation
Indices: 495893--495917 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
495883 TTATATACAT
495893 AATACTA
1 AATACTA
495900 AATACTA
1 AATACTA
495907 AATACTA
1 AATACTA
495914 AATA
1 AATA
495918 TCAATTGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:496125 original size:20 final size:20
Alignment explanation
Indices: 496088--496125 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
496078 TTTATTTTTA
*
496088 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
496108 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
496126 TACCTCAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:496941 original size:12 final size:12
Alignment explanation
Indices: 496917--496959 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
496907 ATTTTTATGG
496917 TTTAAAAAA-AT
1 TTTAAAAAATAT
496928 TTTAAAAAATAT
1 TTTAAAAAATAT
* *
496940 TTTTAAAATTA-
1 TTTAAAAAATAT
496951 TTTAAAAAA
1 TTTAAAAAA
496960 AAGGAGTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTTAAAAAATAT
Found at i:499041 original size:38 final size:38
Alignment explanation
Indices: 498994--499078 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 38
498984 AAATAACATA
* **
498994 AAAAATAATAAAAAATCATTAA-AATTATTAAAATTTAT
1 AAAAATAATAAAAAATAATTAATAACCA-TAAAATTTAT
* *
499032 AAAATTAATAAAAATTAATTAATAACCATAAAATTTAT
1 AAAAATAATAAAAAATAATTAATAACCATAAAATTTAT
499070 AAAAATAAT
1 AAAAATAAT
499079 TGATTAGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
38 37 0.93
39 3 0.08
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (38 bp):
AAAAATAATAAAAAATAATTAATAACCATAAAATTTAT
Found at i:499311 original size:9 final size:9
Alignment explanation
Indices: 499299--499330 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
499289 AAATTATTTT
499299 TTTTATAAA
1 TTTTATAAA
499308 TTTTATAAA
1 TTTTATAAA
499317 TTTTATAAA
1 TTTTATAAA
499326 TTTTA
1 TTTTA
499331 ATTAATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTATAAA
Found at i:499359 original size:23 final size:21
Alignment explanation
Indices: 499303--499362 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
499293 TATTTTTTTT
*
499303 ATAAATTTT-ATAAATTT-T-
1 ATAAATTTTAATTAATTTCTA
499321 ATAAATTTTAATTAATTTCTA
1 ATAAATTTTAATTAATTTCTA
499342 ATAATATTTATAATTAATTTC
1 ATAA-ATTT-TAATTAATTTC
499363 ATGACTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 9 0.25
19 7 0.19
20 1 0.03
21 4 0.11
22 4 0.11
23 11 0.31
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAAATTTTAATTAATTTCTA
Found at i:499701 original size:61 final size:61
Alignment explanation
Indices: 499621--499744 Score: 187
Period size: 61 Copynumber: 2.0 Consensus size: 61
499611 GCTTATTGGA
* * * *
499621 AAAATAATCCTTAACTTTTAAGTT-AAAAGATTTGCAATTATCTAATTTTATTTTTAGGCTT
1 AAAATAAGCCTTAAATTTTAAGTTAAAAAGATTAGCAATTATCTAATTTT-TGTTTAGGCTT
*
499682 AAAATAAGCCTTAAATTTTAAGTTAAAAAGATTAGCCATTATCTAATTTTTGTTTAGGCTT
1 AAAATAAGCCTTAAATTTTAAGTTAAAAAGATTAGCAATTATCTAATTTTTGTTTAGGCTT
499743 AA
1 AA
499745 TATGCACTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 34 0.60
62 23 0.40
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (61 bp):
AAAATAAGCCTTAAATTTTAAGTTAAAAAGATTAGCAATTATCTAATTTTTGTTTAGGCTT
Found at i:499969 original size:7 final size:8
Alignment explanation
Indices: 499958--500020 Score: 60
Period size: 9 Copynumber: 7.8 Consensus size: 8
499948 AAAAATTCTT
499958 TAAAAATA
1 TAAAAATA
499966 -AAAAATA
1 TAAAAATA
499973 TAAAAAATA
1 T-AAAAATA
499982 TTAAAAATTA
1 -TAAAAA-TA
*
499992 TTAAAATTA
1 -TAAAAATA
500001 TAAAAAT-
1 TAAAAATA
500008 T-AAAATA
1 TAAAAATA
500015 TAAAAA
1 TAAAAA
500021 AATTTACTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
6 5 0.11
7 9 0.19
8 10 0.21
9 14 0.30
10 9 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
TAAAAATA
Found at i:499977 original size:9 final size:9
Alignment explanation
Indices: 499959--500023 Score: 57
Period size: 8 Copynumber: 7.6 Consensus size: 9
499949 AAAATTCTTT
499959 AAAA-ATAA
1 AAAATATAA
499967 AAAATATAA
1 AAAATATAA
499976 AAAATATTAA
1 AAAATA-TAA
* *
499986 AAATTATTA
1 AAAATATAA
*
499995 AAATTAT-A
1 AAAATATAA
500003 AAAAT-TAA
1 AAAATATAA
*
500011 AATATA-AA
1 AAAATATAA
500019 AAAAT
1 AAAAT
500024 TTACTAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
7 1 0.02
8 20 0.42
9 19 0.40
10 8 0.17
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAATATAA
Found at i:499986 original size:19 final size:18
Alignment explanation
Indices: 499959--500023 Score: 57
Period size: 19 Copynumber: 3.8 Consensus size: 18
499949 AAAATTCTTT
499959 AAAA-ATAAAAAATATAA
1 AAAATATAAAAAATATAA
* *
499976 AAAATATTAAAAATTATTA
1 AAAATA-TAAAAAATATAA
*
499995 AAATTAT-AAAAAT-TAA
1 AAAATATAAAAAATATAA
*
500011 AATATA-AAAAAAT
1 AAAATATAAAAAAT
500024 TTACTAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
16 12 0.32
17 9 0.24
18 2 0.05
19 15 0.39
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATATAAAAAATATAA
Found at i:500012 original size:35 final size:36
Alignment explanation
Indices: 499945--500044 Score: 107
Period size: 35 Copynumber: 2.8 Consensus size: 36
499935 TAGAAAAGAA
* *
499945 ATTAAAAATTCTTTAAAAATA-AAAAATATAAAAAAT
1 ATTAAAAATT-ATTAAAATTATAAAAATATAAAAAAT
*
499981 ATTAAAAATTATTAAAATTATAAAAAT-TAAAATAT
1 ATTAAAAATTATTAAAATTATAAAAATATAAAAAAT
* * *
500016 A-AAAAAATTTACTAAAATTTTAAAAATAT
1 ATTAAAAA-TTATTAAAATTATAAAAATAT
500045 TAGATATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
34 5 0.09
35 33 0.60
36 17 0.31
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (36 bp):
ATTAAAAATTATTAAAATTATAAAAATATAAAAAAT
Found at i:500018 original size:14 final size:15
Alignment explanation
Indices: 499991--500020 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
499981 ATTAAAAATT
499991 ATTAAAATTATAAAA
1 ATTAAAATTATAAAA
500006 ATTAAAA-TATAAAA
1 ATTAAAATTATAAAA
500020 A
1 A
500021 AATTTACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAAAATTATAAAA
Found at i:500022 original size:43 final size:42
Alignment explanation
Indices: 499958--500040 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 42
499948 AAAAATTCTT
499958 TAAAAATAAAAAATATAAAAAATATTA-AAAATTATTAAAATTA
1 TAAAAATAAAAAATATAAAAAAT-TTACAAAATT-TTAAAATTA
*
500001 TAAAAAT-TAAAATATAAAAAAATTTACTAAAATTTTAAAA
1 TAAAAATAAAAAATAT-AAAAAATTTAC-AAAATTTTAAAA
500041 ATATTAGATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
42 10 0.28
43 20 0.56
44 6 0.17
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (42 bp):
TAAAAATAAAAAATATAAAAAATTTACAAAATTTTAAAATTA
Found at i:500521 original size:260 final size:262
Alignment explanation
Indices: 500048--500579 Score: 1041
Period size: 260 Copynumber: 2.0 Consensus size: 262
500038 AAAATATTAG
500048 ATATTTTAATATTTTAATAATTTTTTAAATCACATTTACTAGAACTTGAACATGATTCCTGTCCC
1 ATATTTTAATATTTTAATAATTTTTTAAATCACATTTACTAGAACTTGAACATGATTCCTGTCCC
500113 TTGGAATGATACCACATGCAATAATTGACTTATAATTCAATCAATCTAAATTTATAATTAATAGA
66 TTGGAATGATACCACATGCAATAATTGACTTATAATTCAATCAATCTAAATTTATAATTAATAGA
500178 TATTTTTAGGTGATAAATTTGGATTCGTTTAAATTTTCAAATTATTCAAATAATGGAATTAATGT
131 TATTTTTAGGTGATAAATTTGGATTCGTTTAAATTTTCAAATTATTCAAATAATGGAATTAATGT
500243 TATTTCAATTATATAATATTTTTAATTATTTCAATTGTTTTTAGACAAATTATTTGTCTCTAAAT
196 TATTTCAATTATATAATATTTTTAATTATTTCAATTGTTTTTAGACAAATTATTTGTCTCTAAAT
500308 CA
261 CA
500310 A-ATTTTAATA-TTTAATAATTTTTTAAATCACATTTACTAGAACTTGAACATGATTCCTGTCCC
1 ATATTTTAATATTTTAATAATTTTTTAAATCACATTTACTAGAACTTGAACATGATTCCTGTCCC
500373 TTGGAATGATACCACATGCAATAATTGACTTATAATTCAATCAATCTAAATTTATAATTAATAGA
66 TTGGAATGATACCACATGCAATAATTGACTTATAATTCAATCAATCTAAATTTATAATTAATAGA
500438 TATTTTTAGGTGATAAATTTGGATTCGTTTAAATTTTCAAATTATTCAAATAATGGAATTAATGT
131 TATTTTTAGGTGATAAATTTGGATTCGTTTAAATTTTCAAATTATTCAAATAATGGAATTAATGT
500503 TATTTCAATTATATAATATTTTTAATTATTTCAATTGTTTTTAGACAAATTATTTGTCTCTAAAT
196 TATTTCAATTATATAATATTTTTAATTATTTCAATTGTTTTTAGACAAATTATTTGTCTCTAAAT
500568 CA
261 CA
*
500570 ATATCTTAAT
1 ATATTTTAAT
500580 TCACAAATAA
Statistics
Matches: 268, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
260 251 0.94
261 16 0.06
262 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (262 bp):
ATATTTTAATATTTTAATAATTTTTTAAATCACATTTACTAGAACTTGAACATGATTCCTGTCCC
TTGGAATGATACCACATGCAATAATTGACTTATAATTCAATCAATCTAAATTTATAATTAATAGA
TATTTTTAGGTGATAAATTTGGATTCGTTTAAATTTTCAAATTATTCAAATAATGGAATTAATGT
TATTTCAATTATATAATATTTTTAATTATTTCAATTGTTTTTAGACAAATTATTTGTCTCTAAAT
CA
Found at i:505533 original size:12 final size:12
Alignment explanation
Indices: 505516--505542 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
505506 TGGATTGGAA
505516 GCAATATGAAGT
1 GCAATATGAAGT
505528 GCAATATGAAGT
1 GCAATATGAAGT
505540 GCA
1 GCA
505543 GTTTGATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.22
Consensus pattern (12 bp):
GCAATATGAAGT
Found at i:507316 original size:59 final size:59
Alignment explanation
Indices: 507224--507345 Score: 226
Period size: 59 Copynumber: 2.1 Consensus size: 59
507214 ACCAAGACTT
* *
507224 GGACAATAACTACGATACCCTTTTTGTACATGGGAATTTCTCCAAAACATACATTATAA
1 GGACAATAACTACGATACCCTTTTTGTACATGGGAATATCCCCAAAACATACATTATAA
507283 GGACAATAACTACGATACCCTTTTTGTACATGGGAATATCCCCAAAACATACATTATAA
1 GGACAATAACTACGATACCCTTTTTGTACATGGGAATATCCCCAAAACATACATTATAA
507342 GGAC
1 GGAC
507346 TTAGGATCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (59 bp):
GGACAATAACTACGATACCCTTTTTGTACATGGGAATATCCCCAAAACATACATTATAA
Found at i:534375 original size:16 final size:16
Alignment explanation
Indices: 534356--534424 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
534346 TTTGGTTCGC
534356 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
534372 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
534388 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
534405 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
534421 TGTA
1 TGTA
534425 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:534402 original size:33 final size:32
Alignment explanation
Indices: 534356--534424 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
534346 TTTGGTTCGC
534356 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
534388 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
534421 TGTA
1 TGTA
534425 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:534489 original size:44 final size:45
Alignment explanation
Indices: 534405--534495 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
534395 GGATTAGAGG
* * *
534405 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
534450 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
534494 TG
1 TG
534496 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:542403 original size:13 final size:13
Alignment explanation
Indices: 542385--542410 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
542375 TAGCTAAACT
542385 GAAACAGAAGGAA
1 GAAACAGAAGGAA
542398 GAAACAGAAGGAA
1 GAAACAGAAGGAA
542411 CGGCAGCTAA
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:0.62, C:0.08, G:0.31, T:0.00
Consensus pattern (13 bp):
GAAACAGAAGGAA
Found at i:544235 original size:15 final size:15
Alignment explanation
Indices: 544217--544259 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 15
544207 ATATCAATAA
544217 AACACATAGCTAATT
1 AACACATAGCTAATT
**
544232 AACACATAATTAA--
1 AACACATAGCTAATT
544245 AACACATAGCTAATT
1 AACACATAGCTAATT
544260 TAAACAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
13 11 0.50
15 11 0.50
ACGTcount: A:0.51, C:0.19, G:0.05, T:0.26
Consensus pattern (15 bp):
AACACATAGCTAATT
Found at i:545082 original size:99 final size:99
Alignment explanation
Indices: 544973--545157 Score: 307
Period size: 99 Copynumber: 1.9 Consensus size: 99
544963 TGATTTGTAC
*
544973 AAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATATACTAAAAAATGGACAGCAATT
1 AAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATATACTAAAAAATGGACAACAATT
* *
545038 AAGCATCAATTTGGACAGCATTAATATGCTAAAA
66 AAACACCAATTTGGACAGCATTAATATGCTAAAA
* * * *
545072 AAAAATGGACATCATTTAAGCACTAATTTGGACAGCATTAATATGCTCAAAAATGGACAACAATT
1 AAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATATACTAAAAAATGGACAACAATT
545137 AAACACCAATTTGGACAGCAT
66 AAACACCAATTTGGACAGCAT
545158 CTTATCATCA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 79 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (99 bp):
AAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATATACTAAAAAATGGACAACAATT
AAACACCAATTTGGACAGCATTAATATGCTAAAA
Found at i:545100 original size:51 final size:48
Alignment explanation
Indices: 544973--545157 Score: 246
Period size: 48 Copynumber: 3.8 Consensus size: 48
544963 TGATTTGTAC
* * *
544973 AAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATATACTA
1 AAAAATGGACAGCAATTAAGCACTAATTTGGACAGCATTAATATGCTA
545021 AAAAATGGACAGCAATTAAGCA-TCAATTTGGACAGCATTAATATGCTAAAA
1 AAAAATGGACAGCAATTAAGCACT-AATTTGGACAGCATTAATATGCT---A
* * *
545072 AAAAATGGACATCATTTAAGCACTAATTTGGACAGCATTAATATGCTC
1 AAAAATGGACAGCAATTAAGCACTAATTTGGACAGCATTAATATGCTA
* * *
545120 AAAAATGGACAACAATTAAACACCAATTTGGACAGCAT
1 AAAAATGGACAGCAATTAAGCACTAATTTGGACAGCAT
545158 CTTATCATCA
Statistics
Matches: 122, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
47 1 0.01
48 76 0.62
51 44 0.36
52 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (48 bp):
AAAAATGGACAGCAATTAAGCACTAATTTGGACAGCATTAATATGCTA
Found at i:547490 original size:19 final size:19
Alignment explanation
Indices: 547466--547506 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
547456 CTTCCACGAA
547466 GATACTTTCAAAAACACTC
1 GATACTTTCAAAAACACTC
547485 GATACTTTCAAAAACACTC
1 GATACTTTCAAAAACACTC
547504 GAT
1 GAT
547507 CCCCAATCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (19 bp):
GATACTTTCAAAAACACTC
Found at i:552910 original size:48 final size:47
Alignment explanation
Indices: 552857--553099 Score: 222
Period size: 48 Copynumber: 5.0 Consensus size: 47
552847 ACATTCGAAT
* * * *
552857 AACATTGATTTGTACAAAAATGGACAGCATTTAGGCACTAATTTGGAC
1 AACATTAATTTGTA-AAAAATGGACAACAATTAAGCACTAATTTGGAC
**
552905 AACATTAATATACTAAAAAATGGACAACAATTAAGCA-TCAATTTGGAC
1 AACATTAAT-TTGTAAAAAATGGACAACAATTAAGCACT-AATTTGGAC
* **
552953 AGCATTAATATACTAAAAAAT-GAGCAACAATTAAGC-CTCAATTTGGAC
1 AACATTAAT-TTGTAAAAAATGGA-CAACAATTAAGCACT-AATTTGGAC
* * * *
553001 AACATTAATATGCTAAAAAAAATGGACATCATTTAAGAACTAATTTGGAC
1 AACATTAATTTG-T--AAAAAATGGACAACAATTAAGCACTAATTTGGAC
* * * *
553051 AACATTAATATGCTCAATAATGGACAACAATTAAGCACCAATTTGGAC
1 AACATTAATTTG-TAAAAAATGGACAACAATTAAGCACTAATTTGGAC
553099 A
1 A
553100 GCATCTTATC
Statistics
Matches: 166, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
47 3 0.02
48 117 0.70
49 3 0.02
50 39 0.23
51 4 0.02
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.26
Consensus pattern (47 bp):
AACATTAATTTGTAAAAAATGGACAACAATTAAGCACTAATTTGGAC
Found at i:552919 original size:23 final size:23
Alignment explanation
Indices: 552893--552968 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
552883 GCATTTAGGC
552893 ACTAATTTGGACAACATTAATAT
1 ACTAATTTGGACAACATTAATAT
** *
552916 ACTAAAAAATGGACAACAATTAAGCAT
1 ACT--AATTTGGACAAC-ATTAA-TAT
*
552943 -C-AATTTGGACAGCATTAATAT
1 ACTAATTTGGACAACATTAATAT
552964 ACTAA
1 ACTAA
552969 AAAATGAGCA
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
21 2 0.05
22 6 0.15
23 14 0.35
25 10 0.25
26 6 0.15
27 2 0.05
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (23 bp):
ACTAATTTGGACAACATTAATAT
Found at i:553060 original size:98 final size:96
Alignment explanation
Indices: 552872--553099 Score: 282
Period size: 98 Copynumber: 2.4 Consensus size: 96
552862 TGATTTGTAC
* * * *
552872 AAAAATGGACAGCATTTAGGCACTAATTTGGACAACATTAATATACTAAAAAATGGACAACAATT
1 AAAAATGGACAACAATTAAGCACCAATTTGGACAACATTAATATACTAAAAAATGGACAACAATT
* *
552937 AAGCATCAATTTGGACAGCATTAATATACTA
66 AAGAATCAATTTGGACAACATTAATATACTA
* *
552968 AAAAAT-GAGCAACAATTAAGC-CTCAATTTGGACAACATTAATATGCTAAAAAAAATGGACATC
1 AAAAATGGA-CAACAATTAAGCAC-CAATTTGGACAACATTAATATACT--AAAAAATGGACAAC
* * *
553031 ATTTAAGAA-CTAATTTGGACAACATTAATATGCTC
62 AATTAAGAATC-AATTTGGACAACATTAATATACTA
*
553066 AATAATGGACAACAATTAAGCACCAATTTGGACA
1 AAAAATGGACAACAATTAAGCACCAATTTGGACA
553100 GCATCTTATC
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
95 3 0.03
96 37 0.33
97 1 0.01
98 69 0.61
99 3 0.03
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.25
Consensus pattern (96 bp):
AAAAATGGACAACAATTAAGCACCAATTTGGACAACATTAATATACTAAAAAATGGACAACAATT
AAGAATCAATTTGGACAACATTAATATACTA
Found at i:553071 original size:27 final size:26
Alignment explanation
Indices: 552992--553084 Score: 63
Period size: 27 Copynumber: 3.7 Consensus size: 26
552982 ATTAAGCCTC
*
552992 AATTTGGACAACATTAATATGCTAAAA
1 AATTTGGACAACATTAATATGCT-AAT
** * *
553019 AAAATGGACATCATT--TAAG--AACT
1 AATTTGGACAACATTAATATGCTAA-T
553042 AATTTGGACAACATTAATATGCTCAAT
1 AATTTGGACAACATTAATATGCT-AAT
553069 AA--TGGACAACAATTAA
1 AATTTGGACAAC-ATTAA
553085 GCACCAATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
22 2 0.04
23 12 0.24
25 14 0.28
26 5 0.10
27 15 0.30
28 2 0.04
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (26 bp):
AATTTGGACAACATTAATATGCTAAT
Found at i:553746 original size:42 final size:43
Alignment explanation
Indices: 553679--553764 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 43
553669 ACATGTTATA
* ** * *
553679 ATATATCGATGCCACTGTCTTAGACAAGGTCTTACACGAAATC
1 ATATATCGATGCCAATGTCCCAGACAAGGTCGTACACAAAATC
* *
553722 ATATA-CGATGCCAATGTCCCAGACATGTTCGTACACAAAATC
1 ATATATCGATGCCAATGTCCCAGACAAGGTCGTACACAAAATC
553764 A
1 A
553765 CACCTCAGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 31 0.86
43 5 0.14
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (43 bp):
ATATATCGATGCCAATGTCCCAGACAAGGTCGTACACAAAATC
Found at i:565164 original size:27 final size:27
Alignment explanation
Indices: 565132--565265 Score: 155
Period size: 27 Copynumber: 5.0 Consensus size: 27
565122 AGACCCCAAA
*
565132 ATAGGGTAAAATGACTGAAATACCCCT
1 ATAGGGTAAAATGACTGAAATACCCCC
*
565159 GTAGGGTAAAATGA-TCGAAATACCCCC
1 ATAGGGTAAAATGACT-GAAATACCCCC
* *
565186 GTAGGGTAAAATGA-TCGAAATACCTCC
1 ATAGGGTAAAATGACT-GAAATACCCCC
* *
565213 ACAGGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
* **
565240 ATAGGATAAAATGACTGTTATACCCC
1 ATAGGGTAAAATGACTGAAATACCCC
565266 TAGGAGATGA
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 92 0.99
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (27 bp):
ATAGGGTAAAATGACTGAAATACCCCC
Found at i:565208 original size:54 final size:54
Alignment explanation
Indices: 565132--565256 Score: 173
Period size: 54 Copynumber: 2.3 Consensus size: 54
565122 AGACCCCAAA
** *
565132 ATAGGGTAAAATGACTGAAATACC-CCTGTAGGGTAAAATGATCGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCTCC-ACAGGGTAAAATGACCGAAATACCCCC
*
565186 GTAGGGTAAAATGA-TCGAAATACCTCCACAGGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACT-GAAATACCTCCACAGGGTAAAATGACCGAAATACCCCC
*
565240 ATAGGATAAAATGACTG
1 ATAGGGTAAAATGACTG
565257 TTATACCCCT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
53 1 0.02
54 58 0.94
55 3 0.05
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (54 bp):
ATAGGGTAAAATGACTGAAATACCTCCACAGGGTAAAATGACCGAAATACCCCC
Found at i:565427 original size:26 final size:26
Alignment explanation
Indices: 565398--565478 Score: 108
Period size: 26 Copynumber: 3.1 Consensus size: 26
565388 TGGAGGAAAT
*
565398 ATACTGTTACTGGCAGCTTTGCTACG
1 ATACTGTTACTGGCAGCTTTGCTGCG
* * *
565424 ATACTGTTATTGGCAACTTTGCTGCT
1 ATACTGTTACTGGCAGCTTTGCTGCG
* *
565450 ATACTATTACTGGTAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
565476 ATA
1 ATA
565479 TTAGTGTGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGCG
Found at i:565660 original size:33 final size:34
Alignment explanation
Indices: 565612--565679 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
565602 GGCCCACACC
* *
565612 GTTACTGTATTGGGCTAAGGCCCACACTGT-ACT
1 GTTACTGAATAGGGCTAAGGCCCACACTGTCACT
* *
565645 GTTACTGAATAGGGCTCAGGCCCAGACTGTCACT
1 GTTACTGAATAGGGCTAAGGCCCACACTGTCACT
565679 G
1 G
565680 CTTATTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.26
Consensus pattern (34 bp):
GTTACTGAATAGGGCTAAGGCCCACACTGTCACT
Found at i:579148 original size:70 final size:70
Alignment explanation
Indices: 579034--579174 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
579024 GGTTACCTCT
579034 ATGGATAAAGGTTGAAACCTTCTACAACGATTTGAATCTCTCAAGTAGGCAGTTGATCGATGCAG
1 ATGGATAAAGGTTGAAACCTTCTACAACGATTTGAATCTCTCAAGTAGGCAGTTGATCGATGCAG
579099 CAGCC
66 CAGCC
*
579104 ATGGATAAAGGTTGAAACCTTCTACAACGATTTGAATCTTTCAAGTAGGCAGTTGATCGATGCAG
1 ATGGATAAAGGTTGAAACCTTCTACAACGATTTGAATCTCTCAAGTAGGCAGTTGATCGATGCAG
579169 CAGCC
66 CAGCC
579174 A
1 A
579175 GTGGTACACT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (70 bp):
ATGGATAAAGGTTGAAACCTTCTACAACGATTTGAATCTCTCAAGTAGGCAGTTGATCGATGCAG
CAGCC
Found at i:580754 original size:29 final size:28
Alignment explanation
Indices: 580711--580807 Score: 124
Period size: 29 Copynumber: 3.4 Consensus size: 28
580701 CGACGTATTG
*
580711 ACGACCATC-ACATATGAAAATGGATGTT
1 ACGACCATCGA-ATATGAAAAGGGATGTT
*
580739 AACGACCATCGAATATGAAAAGGGATGGTG
1 -ACGACCATCGAATATGAAAAGGGAT-GTT
580769 ACGACCATCGAATATGAAAAGGGATGGTT
1 ACGACCATCGAATATGAAAAGGGAT-GTT
*
580798 TCGACCATCG
1 ACGACCATCG
580808 TTTAAAGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
29 59 0.95
30 3 0.05
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.21
Consensus pattern (28 bp):
ACGACCATCGAATATGAAAAGGGATGTT
Found at i:580803 original size:58 final size:59
Alignment explanation
Indices: 580709--580826 Score: 152
Period size: 58 Copynumber: 2.0 Consensus size: 59
580699 AACGACGTAT
* *
580709 TGACGACCATCACATATGAAAATGGATGTTAACGACCATCGAAT-ATGAAAAGGGATGG
1 TGACGACCATCACATATGAAAAGGGATGTTAACGACCATCGAATAAAGAAAAGGGATGG
* **
580767 TGACGACCATCGA-ATATGAAAAGGGATGGTT-TCGACCATCGTTTAAAGAAAAGGGATGG
1 TGACGACCATC-ACATATGAAAAGGGAT-GTTAACGACCATCGAATAAAGAAAAGGGATGG
580826 T
1 T
580827 TTCAAAAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
58 34 0.65
59 18 0.35
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.22
Consensus pattern (59 bp):
TGACGACCATCACATATGAAAAGGGATGTTAACGACCATCGAATAAAGAAAAGGGATGG
Found at i:580820 original size:30 final size:29
Alignment explanation
Indices: 580741--580829 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
580731 TGGATGTTAA
* **
580741 CGACCATCGAATATGAAAAGGGATGGTGA
1 CGACCATCGAATAAGAAAAGGGATGGTTT
*
580770 CGACCATCGAATATGAAAAGGGATGGTTT
1 CGACCATCGAATAAGAAAAGGGATGGTTT
**
580799 CGACCATCGTTTAAAGAAAAGGGATGGTTT
1 CGACCATCGAAT-AAGAAAAGGGATGGTTT
580829 C
1 C
580830 AAAAATATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 37 0.69
30 17 0.31
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (29 bp):
CGACCATCGAATAAGAAAAGGGATGGTTT
Found at i:582517 original size:26 final size:26
Alignment explanation
Indices: 582481--582530 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
582471 ATGATTTGTG
*
582481 TTCAAAGTGATAATTGT-TGGCATGGT
1 TTCAAAATGATAATT-TATGGCATGGT
*
582507 TTCAAAATGATCATTTATGGCATG
1 TTCAAAATGATAATTTATGGCATG
582531 TATTGATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (26 bp):
TTCAAAATGATAATTTATGGCATGGT
Found at i:590596 original size:22 final size:22
Alignment explanation
Indices: 590566--590617 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
590556 AATGACTAAG
* * *
590566 AGCCGTAAACAGGATAGCTATA
1 AGCCATAAACAGAATAGCTACA
* *
590588 AGCTATAAACAGAATGGCTACA
1 AGCCATAAACAGAATAGCTACA
590610 AGCCATAA
1 AGCCATAA
590618 GTACAGTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17
Consensus pattern (22 bp):
AGCCATAAACAGAATAGCTACA
Found at i:590660 original size:32 final size:31
Alignment explanation
Indices: 590622--590808 Score: 169
Period size: 32 Copynumber: 5.8 Consensus size: 31
590612 CCATAAGTAC
* *
590622 AGTAATATGATTGGCACAAAACATTCAGTAGT
1 AGTAATATGATCGGCACAAACCA-TCAGTAGT
* *
590654 AGTAATATGGTCGGCACACAGCCATCAGTAGT
1 AGTAATATGATCGGCACA-AACCATCAGTAGT
** *
590686 AGTTGTATGATCGACACAAAGCCATCAGTAGT
1 AGTAATATGATCGGCACAAA-CCATCAGTAGT
* * *
590718 AGTAATATGATCGGCATAAAGCCAGCAGTAAT
1 AGTAATATGATCGGCACAAA-CCATCAGTAGT
* * * *
590750 GGTAATATGATTGACACACAACCATCAGTAAT
1 AGTAATATGATCGGCACA-AACCATCAGTAGT
*
590782 GGTAATATGA-CTGGCACAAAGCCATCA
1 AGTAATATGATC-GGCACAAA-CCATCA
590809 ATAGCATCGC
Statistics
Matches: 128, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
31 3 0.02
32 120 0.94
33 5 0.04
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (31 bp):
AGTAATATGATCGGCACAAACCATCAGTAGT
Found at i:590704 original size:64 final size:63
Alignment explanation
Indices: 590609--590808 Score: 206
Period size: 64 Copynumber: 3.1 Consensus size: 63
590599 GAATGGCTAC
* * * *
590609 AAGCCATAAGT-ACAGTAATATGATTGGCACAAAACATTCAGTAGTAGTAATATGGTCGGCACA
1 AAGCCATCAGTAATAGTAATATGATTGACACAAACCA-TCAGTAGTAGTAATATGGTCGGCACA
* * ** * * *
590672 CAGCCATCAGTAGTAGTTGTATGATCGACACAAAGCCATCAGTAGTAGTAATATGATCGGCATA
1 AAGCCATCAGTAATAGTAATATGATTGACACAAA-CCATCAGTAGTAGTAATATGGTCGGCACA
* * * * *
590736 AAGCCAGCAGTAATGGTAATATGATTGACACACAACCATCAGTAATGGTAATAT-GACTGGCACA
1 AAGCCATCAGTAATAGTAATATGATTGACACA-AACCATCAGTAGTAGTAATATGGTC-GGCACA
590800 AAGCCATCA
1 AAGCCATCA
590809 ATAGCATCGC
Statistics
Matches: 109, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
63 10 0.09
64 95 0.87
65 4 0.04
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (63 bp):
AAGCCATCAGTAATAGTAATATGATTGACACAAACCATCAGTAGTAGTAATATGGTCGGCACA
Found at i:590832 original size:23 final size:23
Alignment explanation
Indices: 590806--590860 Score: 56
Period size: 26 Copynumber: 2.3 Consensus size: 23
590796 CACAAAGCCA
590806 TCAATAGCATCGCAGCAAAGCTG
1 TCAATAGCATCGCAGCAAAGCTG
* *
590829 TCAACAACAGTATCGCAGCAAAGCTG
1 T---CAATAGCATCGCAGCAAAGCTG
*
590855 CCAATA
1 TCAATA
590861 ACAGTATATG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
23 5 0.20
26 20 0.80
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.16
Consensus pattern (23 bp):
TCAATAGCATCGCAGCAAAGCTG
Done.