Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 2 of 141
Found at i:291011 original size:22 final size:22
Alignment explanation
Indices: 290977--291020 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
290967 TTTTCACTTA
* *
290977 AATTATTAATATATTTAATTTT
1 AATTATTAATATAATAAATTTT
**
290999 AATTATTTGTATAATAAATTTT
1 AATTATTAATATAATAAATTTT
291021 CACAAATTTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
AATTATTAATATAATAAATTTT
Found at i:299849 original size:50 final size:50
Alignment explanation
Indices: 299736--299976 Score: 268
Period size: 50 Copynumber: 4.7 Consensus size: 50
299726 GGTAAAAAGA
* *
299736 TCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCCTTAAGATCATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-CA--AGAGG
*
299792 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACAAGATG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACAAGAGG
* * **
299842 TCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACAAGAGG
* * ** **
299892 TCTCC-TGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACAAGAGG
* * *
299942 TCCCATGTAAGACCATATCTGGGATATGGAATTGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG
299977 TAGTATAAGA
Statistics
Matches: 165, Mismatches: 18, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
49 2 0.01
50 118 0.72
51 2 0.01
52 2 0.01
53 3 0.02
55 2 0.01
56 36 0.22
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACAAGAGG
Found at i:299920 original size:100 final size:103
Alignment explanation
Indices: 299736--299976 Score: 301
Period size: 100 Copynumber: 2.3 Consensus size: 103
299726 GGTAAAAAGA
*
299736 TCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCCTTAAGATCATGAGAGGTCCCATGTA
1 TCCCATGTAAGACCATGTCTAGGACATGGAATTGGCATCC---AGATCATGAGAGGTCCCATGTA
* **
299801 AGACCATGTCTGGGACATGGCATTGGCACCGAGACAAGATG
63 AGACCATGTCTGGGACATGGCATGGGCACCGAGACAAGAAC
** *
299842 TCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCTCC-TGTAAG
1 TCCCATGTAAGACCATGTCTAGGACATGGAATTGGCATCCAGATCATGAGAGGTC-CCATGTAAG
* **
299903 ACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
65 ACCATGTCTGGGACATGGCATGGGCACCGAGACAAGAAC
* * *
299942 TCCCATGTAAGACCATATCTGGGATATGGAATTGG
1 TCCCATGTAAGACCATGTCTAGGACATGGAATTGG
299977 TAGTATAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
100 79 0.66
101 4 0.03
105 2 0.02
106 34 0.29
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (103 bp):
TCCCATGTAAGACCATGTCTAGGACATGGAATTGGCATCCAGATCATGAGAGGTCCCATGTAAGA
CCATGTCTGGGACATGGCATGGGCACCGAGACAAGAAC
Found at i:318022 original size:50 final size:50
Alignment explanation
Indices: 317955--318126 Score: 281
Period size: 50 Copynumber: 3.4 Consensus size: 50
317945 ATTTGGGTAA
*
317955 AGAGCTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
* * *
318005 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
*
318055 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
**
318105 AGAGGTCCCCCGTAAGACCATG
1 AGAGGTCCCATGTAAGACCATG
318127 GCATGGGCAC
Statistics
Matches: 112, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 112 1.00
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
Found at i:324830 original size:50 final size:50
Alignment explanation
Indices: 324755--324887 Score: 257
Period size: 50 Copynumber: 2.7 Consensus size: 50
324745 ATTTGGGTAA
*
324755 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
324805 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
324855 AGAGGTCCCATGTAAGACCATGTCTGGGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATG
324888 TAGCGCATTT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.26, C:0.22, G:0.32, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:328346 original size:14 final size:15
Alignment explanation
Indices: 328319--328348 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
328309 TTATTAACCC
328319 TTTTAAAACTCCTTT
1 TTTTAAAACTCCTTT
328334 TTTTAAAAC-CCTTT
1 TTTTAAAACTCCTTT
328348 T
1 T
328349 CTTTGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTAAAACTCCTTT
Found at i:333864 original size:50 final size:50
Alignment explanation
Indices: 333777--333956 Score: 148
Period size: 50 Copynumber: 3.5 Consensus size: 50
333767 CAATGCTATA
* ** * * *
333777 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCA-TGCCATG
1 TCCCAGAAATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACT-CCATG
* * *
333827 TCCTAGACATGGTCTTACGA-GGGACCTCTTATCTCGGTGCCAACTTCATG
1 TCCCAGAAATGGTCTTAC-ATGGGACCTCTTATCTCGGTGCCAACTCCATG
* * *
333877 TCCCAGAAATGGTCTTACATGGGACCTCTCGTAATCTAAATGATGCCAATTCCATG
1 TCCCAGAAATGGTCTTACATGGGACCTCT--T-ATCT---CGGTGCCAACTCCATG
* *
333933 TCTCAGACATGGTCTTACATGGGA
1 TCCCAGAAATGGTCTTACATGGGA
333957 TCTCATTCCC
Statistics
Matches: 105, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
49 1 0.01
50 63 0.60
51 2 0.02
52 1 0.01
53 4 0.04
56 34 0.32
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (50 bp):
TCCCAGAAATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACTCCATG
Found at i:344164 original size:22 final size:21
Alignment explanation
Indices: 344139--344182 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
344129 TGATAAACTT
344139 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
344161 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
344182 T
1 T
344183 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:348628 original size:20 final size:20
Alignment explanation
Indices: 348605--348643 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
348595 CATCTCTAAA
348605 TTCTCTATT-CATTCTCCTTT
1 TTCTCTATTCCATT-TCCTTT
*
348625 TTCTCTCTTCCATTTCCTT
1 TTCTCTATTCCATTTCCTT
348644 CCTTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.08, C:0.33, G:0.00, T:0.59
Consensus pattern (20 bp):
TTCTCTATTCCATTTCCTTT
Found at i:352491 original size:16 final size:16
Alignment explanation
Indices: 352470--352504 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
352460 TTTTAGATGA
352470 TTTAATTGAGGAAGAG
1 TTTAATTGAGGAAGAG
*
352486 TTTAATTGAGGAGGAG
1 TTTAATTGAGGAAGAG
352502 TTT
1 TTT
352505 GCAGTGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.37
Consensus pattern (16 bp):
TTTAATTGAGGAAGAG
Found at i:368646 original size:9 final size:10
Alignment explanation
Indices: 368622--368655 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
368612 AGACATATAA
368622 ATTTTTAATG
1 ATTTTTAATG
368632 ATTTTTAATG
1 ATTTTTAATG
368642 ATTTTTAATG
1 ATTTTTAATG
368652 ATTT
1 ATTT
368656 CCTAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (10 bp):
ATTTTTAATG
Found at i:369287 original size:20 final size:20
Alignment explanation
Indices: 369262--369301 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
369252 TACTTTCTTC
369262 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
369282 TTTACTTACTTGCTTACTTG
1 TTTACTTACTTGCTTACTTG
369302 AATAACTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.15, C:0.23, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:369626 original size:50 final size:50
Alignment explanation
Indices: 369555--369680 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 50
369545 TTGTACTGCA
* * * * **
369555 AATGTCATATCCCATATATGGTCTTACATGAGAGTTCTCATATCGATGCC
1 AATGTCATGTCCCAGACATGGTCTTACAAGAGACCTCTCATATCGATGCC
* * *
369605 CATGTCATGTCCCAGACATGGTCTTACAAGGGACCTCTCATCTCGATGCC
1 AATGTCATGTCCCAGACATGGTCTTACAAGAGACCTCTCATATCGATGCC
* *
369655 AACGCCATGTCCCAGACATGGTCTTA
1 AATGTCATGTCCCAGACATGGTCTTA
369681 TGTGGGACCT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (50 bp):
AATGTCATGTCCCAGACATGGTCTTACAAGAGACCTCTCATATCGATGCC
Found at i:369688 original size:50 final size:50
Alignment explanation
Indices: 369572--369696 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 50
369562 TATCCCATAT
* * ** * * *
369572 ATGGTCTTACATGAGAGTTCTCATATCGATGCCCATGTCATGTCCCAGAC
1 ATGGTCTTACAAGGGACCTCTCATATCGATGCCAACGCCATGTCCCAGAC
*
369622 ATGGTCTTACAAGGGACCTCTCATCTCGATGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACAAGGGACCTCTCATATCGATGCCAACGCCATGTCCCAGAC
***
369672 ATGGTCTTATGTGGGACCTCTCATA
1 ATGGTCTTACAAGGGACCTCTCATA
369697 ACCTCAATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACAAGGGACCTCTCATATCGATGCCAACGCCATGTCCCAGAC
Found at i:388859 original size:25 final size:25
Alignment explanation
Indices: 388825--388895 Score: 133
Period size: 25 Copynumber: 2.8 Consensus size: 25
388815 CAGGCCCATT
388825 TTCACAGCTCATGTGAGCATACTTA
1 TTCACAGCTCATGTGAGCATACTTA
*
388850 TTCATAGCTCATGTGAGCATACTTA
1 TTCACAGCTCATGTGAGCATACTTA
388875 TTCACAGCTCATGTGAGCATA
1 TTCACAGCTCATGTGAGCATA
388896 TATGTAAAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (25 bp):
TTCACAGCTCATGTGAGCATACTTA
Found at i:395789 original size:20 final size:20
Alignment explanation
Indices: 395753--395790 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
395743 ATCTCTCAAT
*
395753 TCTCTCTTTATTCTCCTTTC
1 TCTCTCTTTAGTCTCCTTTC
395773 TCTCTCTTCTAGT-TCCTT
1 TCTCTCTT-TAGTCTCCTT
395791 CCTTGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.05, C:0.34, G:0.03, T:0.58
Consensus pattern (20 bp):
TCTCTCTTTAGTCTCCTTTC
Found at i:399107 original size:20 final size:20
Alignment explanation
Indices: 398986--399112 Score: 94
Period size: 20 Copynumber: 6.3 Consensus size: 20
398976 TTGTGTGGGA
*
398986 TTTGCACTTTGGTGCCCCTA
1 TTTGCACTTTGGTGCCCCTG
* * *
399006 TTTTCACTTTGATGCCTCTG
1 TTTGCACTTTGGTGCCCCTG
* * * * * *
399026 TATACACTTCGGTGTCTCTA
1 TTTGCACTTTGGTGCCCCTG
** **
399046 TTCACACTACGGTGCCCCTG
1 TTTGCACTTTGGTGCCCCTG
*
399066 TTTGCACATTT-GTGCCCTTG
1 TTTGCAC-TTTGGTGCCCCTG
399086 TTTGCACTTTGGTGCCCCTG
1 TTTGCACTTTGGTGCCCCTG
399106 TTATGCA
1 TT-TGCA
399113 TCTATGATGC
Statistics
Matches: 82, Mismatches: 22, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
19 3 0.04
20 74 0.90
21 5 0.06
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.40
Consensus pattern (20 bp):
TTTGCACTTTGGTGCCCCTG
Found at i:401031 original size:40 final size:40
Alignment explanation
Indices: 400933--401195 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
400923 TCCTCGTTCA
* * * * *
400933 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
400972 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
401012 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
401052 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
401092 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
401132 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
401172 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
401196 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:406026 original size:17 final size:19
Alignment explanation
Indices: 405986--406027 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
405976 ATATGATTCT
*
405986 TGATGTGAGTTTTGAATCG
1 TGATGAGAGTTTTGAATCG
*
406005 AGATGAGAGTTTTG-AT-G
1 TGATGAGAGTTTTGAATCG
406022 TGATGA
1 TGATGA
406028 TTTTTACTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
18 2 0.10
19 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.33, T:0.38
Consensus pattern (19 bp):
TGATGAGAGTTTTGAATCG
Found at i:407802 original size:20 final size:19
Alignment explanation
Indices: 407779--407817 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
407769 CGCACTACAT
*
407779 TGCCCCTGTTTGCACATTTG
1 TGCCCCTGTCTGCAC-TTTG
407799 TGCCCCTGTCTGCACTTTG
1 TGCCCCTGTCTGCACTTTG
407818 GGGCCTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.08, C:0.33, G:0.21, T:0.38
Consensus pattern (19 bp):
TGCCCCTGTCTGCACTTTG
Found at i:411420 original size:29 final size:28
Alignment explanation
Indices: 411384--411461 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
411374 TCATGAGATT
411384 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
411414 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
411441 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
411462 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:411679 original size:174 final size:174
Alignment explanation
Indices: 411414--411741 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
411404 AAATTGTACA
*
411414 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* * *
411479 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTATCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
411544 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
411588 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
411653 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
411718 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
411742 ACCTTGAGTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:415342 original size:51 final size:51
Alignment explanation
Indices: 415283--415403 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 51
415273 ATGTGTACTG
* *
415283 CTATGTGCAGGCTACTATGCGTA-CTGGATAGT-TTCGATCACGTATGTAGTA
1 CTATGTGCAGGCTACTATGCGTATC-GGATAGTAAT-GATCACATATGTAGTA
*** * * *
415334 CTATGTGCAGGCTACTACATGTATCGGATGGTAATGGTCACATGTGTAGTA
1 CTATGTGCAGGCTACTATGCGTATCGGATAGTAATGATCACATATGTAGTA
415385 CTATGTGCAGGCTACTATG
1 CTATGTGCAGGCTACTATG
415404 TGAACCGAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
51 56 0.97
52 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (51 bp):
CTATGTGCAGGCTACTATGCGTATCGGATAGTAATGATCACATATGTAGTA
Found at i:422273 original size:22 final size:24
Alignment explanation
Indices: 422247--422309 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 24
422237 TAATGAACAA
422247 AGAGCACTGAA-GTGCT-AT-ACAG
1 AGAGCA-TGAATGTGCTAATCACAG
422269 AGAGCATGAATGTGCTAATCAC--
1 AGAGCATGAATGTGCTAATCACAG
422291 AGAGCA-GTAATGTGCTAAT
1 AGAGCATG-AATGTGCTAAT
422310 AATTGGAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
21 5 0.14
22 28 0.76
23 2 0.05
24 2 0.05
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (24 bp):
AGAGCATGAATGTGCTAATCACAG
Found at i:440321 original size:17 final size:16
Alignment explanation
Indices: 440291--440325 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
440281 AATTAATTTA
440291 AATTAATTAATTTCTC
1 AATTAATTAATTTCTC
*
440307 AATTCAATTATTTTCTC
1 AATT-AATTAATTTCTC
440324 AA
1 AA
440326 CCTAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAATTAATTTCTC
Found at i:442589 original size:77 final size:77
Alignment explanation
Indices: 442461--442606 Score: 229
Period size: 77 Copynumber: 1.9 Consensus size: 77
442451 TGACCTTGTC
* ***
442461 CTTAATCTCTTTGGGAGAATATTTTTTCTCCCAATATGCTCCTATTGTATCTCATGGTAACCATT
1 CTTAATCTCTTTGGGACAATATCCATTCTCCCAATATGCTCCTATTGTATCTCATGGTAACCATT
442526 ACATAGAATATT
66 ACATAGAATATT
* * *
442538 CTTAATCTCTTTGGGACAATATCCATTCTTCCAATATGCTCCTATTTTATCTCATGGTAATCATT
1 CTTAATCTCTTTGGGACAATATCCATTCTCCCAATATGCTCCTATTGTATCTCATGGTAACCATT
442603 ACAT
66 ACAT
442607 CTTCCTTCAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 62 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (77 bp):
CTTAATCTCTTTGGGACAATATCCATTCTCCCAATATGCTCCTATTGTATCTCATGGTAACCATT
ACATAGAATATT
Found at i:444306 original size:40 final size:40
Alignment explanation
Indices: 444208--444470 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
444198 TCCTCGTTCA
* * * * *
444208 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
444247 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
444287 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
444327 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
444367 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
444407 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
444447 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
444471 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:452258 original size:40 final size:40
Alignment explanation
Indices: 452160--452422 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
452150 TCCTCGTTCA
* * * * *
452160 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
452199 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
452239 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
452279 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
452319 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
452359 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
452399 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
452423 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:455860 original size:15 final size:16
Alignment explanation
Indices: 455835--455867 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
455825 GTTCAAATAT
455835 ATAGAAAAATAATTAC
1 ATAGAAAAATAATTAC
455851 ATAG-AAAATAATTAC
1 ATAGAAAAATAATTAC
455866 AT
1 AT
455868 GTTTACTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (16 bp):
ATAGAAAAATAATTAC
Found at i:489073 original size:22 final size:22
Alignment explanation
Indices: 489043--489085 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
489033 ACACCAAAAC
*
489043 AGGCTTTTAGCGCCGCTTTTTT
1 AGGCCTTTAGCGCCGCTTTTTT
*
489065 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGCCGCTTTTT
489086 AGCGTCGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.23, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGCCGCTTTTTT
Found at i:489535 original size:43 final size:43
Alignment explanation
Indices: 489149--489536 Score: 305
Period size: 43 Copynumber: 9.0 Consensus size: 43
489139 AGAAATAAAT
* * ** *
489149 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTAACCACAAAT
1 GCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCCACAAAC
* * * *
489192 GCCGCTGAAGGCCATGGTCTTCAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCCACAAAC
** * *
489235 GCCGCTAAAGGTCATGGTCTTCAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCCACAAAC
* ** * * * * * *
489278 TCCGCTAAAGGTCATGCTCTTTAGCGGCACTTTTACGAAAAAT
1 GCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCCACAAAC
* ** * * * **
489321 ACCGCTAAAGGTCATGGTTTTTAGCGGCGC-TTACAAAACAAAC
1 GCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTC-CCACAAAC
* ** * * * *
489364 GCCGCTAACGATAATGACCTTTAGCGGCGCTTCT-CCAGAAAAT
1 GCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCCA-CAAAC
* * * * *
489407 GCCGCTAAAGACCCTGATCGTTAGCGGTGCCTTTCCAACAAAC
1 GCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCCACAAAC
* * * *
489450 GCCACTAAAGCCCCTGATCTTTAGCGGCG-TTTTCCTCTCAAAC
1 GCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCC-CACAAAC
*
489493 GCCGCTGAAGACCATGATCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCCACAAAC
489536 G
1 G
489537 GCACTAATTT
Statistics
Matches: 273, Mismatches: 66, Indels: 12
0.78 0.19 0.03
Matches are distributed among these distances:
42 8 0.03
43 256 0.94
44 9 0.03
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (43 bp):
GCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:489918 original size:21 final size:21
Alignment explanation
Indices: 489863--489933 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
489853 TTTTACGCTG
* *
489863 CTCTACTTCCCTCACTACAGC
1 CTCTACTTCCCTCGCTGCAGC
*
489884 CCCTACTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
* *
489905 CTCTACTTCTCTCGCTGCCGC
1 CTCTACTTCCCTCGCTGCAGC
*
489926 ATCTACTT
1 CTCTACTT
489934 TAAGCTGCTG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.13, C:0.46, G:0.10, T:0.31
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTGCAGC
Found at i:489994 original size:66 final size:66
Alignment explanation
Indices: 489910--490050 Score: 205
Period size: 66 Copynumber: 2.1 Consensus size: 66
489900 GCAGCCTCTA
489910 CTTCTCTCGCTGCCGCATCTACTTTAAGCTGCT-GCTAGAGTTCTTCATA-CTTTCGTTGAACCT
1 CTTCTCTCGCTGCCGCATCTACTTTAAGCTG-TAGCTAGAGTTCTTCATATCTTT-GTTGAACCT
489973 CAG
64 CAG
* * * * *
489976 CTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACCTCA
1 CTTCTCTCGCTGCCGCATCTACTTTAAGCTGTAGCTAGAGTTCTTCATATCTTTGTTGAACCTCA
490041 G
66 G
490042 CTTCTCTCG
1 CTTCTCTCG
490051 ATGTTGCCTC
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
65 1 0.01
66 63 0.93
67 4 0.06
ACGTcount: A:0.15, C:0.28, G:0.17, T:0.40
Consensus pattern (66 bp):
CTTCTCTCGCTGCCGCATCTACTTTAAGCTGTAGCTAGAGTTCTTCATATCTTTGTTGAACCTCA
G
Found at i:490067 original size:66 final size:66
Alignment explanation
Indices: 489910--490073 Score: 199
Period size: 66 Copynumber: 2.5 Consensus size: 66
489900 GCAGCCTCTA
* * * * *
489910 CTTCTCTCGCTGCCGCATCTACTTTAAGCTGCT-GCTAGAGTTCTTCATACTTTCGTTGAACCTC
1 CTTCTCTCGATGCTGCATCTGCTTTAAGTTG-TAGCTGGAGTTCTTCATACTTTCGTTGAACCTC
489974 AG
65 AG
* *
489976 CTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTT-TTTGAACCTC
1 CTTCTCTCGATGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATA-CTTTCGTTGAACCTC
490040 AG
65 AG
* *
490042 CTTCTCTCGATGTTGCCTCCT-CTTTAAGTTGT
1 CTTCTCTCGATGCTGCAT-CTGCTTTAAGTTGT
490074 GTAATTTGCT
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
65 1 0.01
66 80 0.92
67 6 0.07
ACGTcount: A:0.15, C:0.27, G:0.17, T:0.41
Consensus pattern (66 bp):
CTTCTCTCGATGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATACTTTCGTTGAACCTCA
G
Found at i:490292 original size:66 final size:66
Alignment explanation
Indices: 490203--490329 Score: 186
Period size: 66 Copynumber: 1.9 Consensus size: 66
490193 GCTGCTGCTA
*
490203 GAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGTTACAT-CTACTTTAAGTTGTAGT
1 GAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGTTACATCCT-CTTTAAGTTGTAGT
490267 TG
65 TG
* * *
490269 GAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATGTTGCCTCCTCTTTAAGTTGT
1 GAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGATGTTACATCCTCTTTAAGTTGT
490330 GTAATTTGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
66 49 0.89
67 6 0.11
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.44
Consensus pattern (66 bp):
GAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGTTACATCCTCTTTAAGTTGTAGTT
G
Found at i:490385 original size:256 final size:256
Alignment explanation
Indices: 489930--490442 Score: 990
Period size: 256 Copynumber: 2.0 Consensus size: 256
489920 TGCCGCATCT
*
489930 ACTTTAAGCTGCTGCTAGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATC
1 ACTTTAAGCTGCTGCTAGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTACATC
*
489995 TGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACCTCAGCTTCTCTCGATGTTGCCT
66 TACTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACCTCAGCTTCTCTCGATGTTGCCT
490060 CCTCTTTAAGTTGTGTAATTTGCTCAATTGTTGTCGCTTGCATCTGAGCCATCTGGTCTCTTAAC
131 CCTCTTTAAGTTGTGTAATTTGCTCAATTGTTGTCGCTTGCATCTGAGCCATCTGGTCTCTTAAC
490125 CTCTAAAATTCAGTTTGAGCCTGACTCCTCGAAGGCATGTATTGTTGCGAGCTAGATCCAA
196 CTCTAAAATTCAGTTTGAGCCTGACTCCTCGAAGGCATGTATTGTTGCGAGCTAGATCCAA
*
490186 ACTTTAAGCTGCTGCTAGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGTTACATC
1 ACTTTAAGCTGCTGCTAGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTACATC
*
490251 TACTTTAAGTTGTAGTTGGAGTTCTTCATATCTTTTTTGAACCTCAGCTTCTCTCGATGTTGCCT
66 TACTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACCTCAGCTTCTCTCGATGTTGCCT
490316 CCTCTTTAAGTTGTGTAATTTGCTCAATTGTTGTCGCTTGCATCTGAGCCATCTGGTCTCTTAAC
131 CCTCTTTAAGTTGTGTAATTTGCTCAATTGTTGTCGCTTGCATCTGAGCCATCTGGTCTCTTAAC
490381 CTCTAAAATTCAGTTTGAGCCTGACTCCTCGAAGGCATGTATTGTTGCGAGCTAGATCCAA
196 CTCTAAAATTCAGTTTGAGCCTGACTCCTCGAAGGCATGTATTGTTGCGAGCTAGATCCAA
490442 A
1 A
490443 ATATTGGGAT
Statistics
Matches: 253, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
256 253 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (256 bp):
ACTTTAAGCTGCTGCTAGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTACATC
TACTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACCTCAGCTTCTCTCGATGTTGCCT
CCTCTTTAAGTTGTGTAATTTGCTCAATTGTTGTCGCTTGCATCTGAGCCATCTGGTCTCTTAAC
CTCTAAAATTCAGTTTGAGCCTGACTCCTCGAAGGCATGTATTGTTGCGAGCTAGATCCAA
Found at i:495775 original size:9 final size:9
Alignment explanation
Indices: 495758--495883 Score: 90
Period size: 9 Copynumber: 14.9 Consensus size: 9
495748 TAAGTATAAT
*
495758 TAAGCTATG
1 TAAGTTATG
495767 TAAGTTATG
1 TAAGTTATG
*
495776 TAAGTTATA
1 TAAGTTATG
*
495785 TAAGTTGTG
1 TAAGTTATG
*
495794 T-A-TAATG
1 TAAGTTATG
495801 TAAGTTATG
1 TAAGTTATG
*
495810 AAAGTTATG
1 TAAGTTATG
495819 T-A-TTATG
1 TAAGTTATG
495826 TAAGTTACT-
1 TAAGTTA-TG
*
495835 TAAGTTGTG
1 TAAGTTATG
*
495844 T-A-TTATA
1 TAAGTTATG
*
495851 TAAGTCATG
1 TAAGTTATG
* *
495860 TAGGCTATG
1 TAAGTTATG
495869 T-A-TTATG
1 TAAGTTATG
495876 TAAGTTAT
1 TAAGTTAT
495884 AATAAGTAAG
Statistics
Matches: 88, Mismatches: 19, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
7 19 0.22
8 8 0.09
9 60 0.68
10 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:495805 original size:25 final size:25
Alignment explanation
Indices: 495771--495890 Score: 127
Period size: 25 Copynumber: 4.8 Consensus size: 25
495761 GCTATGTAAG
*
495771 TTATGTAAGTTATATAAGTTGTGTA
1 TTATGTAAGTTATATAAGTTATGTA
*
495796 TAATGTAAGTTATGA-AAGTTATGTA
1 TTATGTAAGTTAT-ATAAGTTATGTA
*
495821 TTATGTAAGTTACT-TAAGTTGTGTA
1 TTATGTAAGTTA-TATAAGTTATGTA
* * * * *
495846 TTATATAAGTCATGTAGGCTATGTA
1 TTATGTAAGTTATATAAGTTATGTA
495871 TTATGTAAGTTATAATAAGT
1 TTATGTAAGTTAT-ATAAGT
495891 AAGTTATGAA
Statistics
Matches: 76, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
24 1 0.01
25 70 0.92
26 5 0.07
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (25 bp):
TTATGTAAGTTATATAAGTTATGTA
Found at i:495826 original size:50 final size:50
Alignment explanation
Indices: 495759--495890 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 50
495749 AAGTATAATT
* *
495759 AAGCTATGTAAGTTATGTAAGTTATATAAGTTGTGTATAATGTAAGTTATGA
1 AAGCTATGT-A-TTATGTAAGTTATATAAGTTGTGTATAATATAAGTCATGA
* * *
495811 AAGTTATGTATTATGTAAGTTACT-TAAGTTGTGTATTATATAAGTCATGT
1 AAGCTATGTATTATGTAAGTTA-TATAAGTTGTGTATAATATAAGTCATGA
*
495861 AGGCTATGTATTATGTAAGTTATAATAAGT
1 AAGCTATGTATTATGTAAGTTAT-ATAAGT
495891 AAGTTATGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
49 1 0.01
50 54 0.77
51 7 0.10
52 8 0.11
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (50 bp):
AAGCTATGTATTATGTAAGTTATATAAGTTGTGTATAATATAAGTCATGA
Found at i:495914 original size:34 final size:34
Alignment explanation
Indices: 495875--495951 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 34
495865 TATGTATTAT
495875 GTAAGTTATA-ATAAGTAAGTTATG-AAAGTTATATA
1 GTAAGTTATATAT-A-TAAGTTATGTAAA-TTATATA
495910 -TAAGTT-TATATATAAGTTATGTAAATTATATA
1 GTAAGTTATATATATAAGTTATGTAAATTATATA
495942 TGTAAGTTAT
1 -GTAAGTTAT
495952 GTGTTGTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
32 16 0.43
33 6 0.16
34 14 0.38
35 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (34 bp):
GTAAGTTATATATATAAGTTATGTAAATTATATA
Found at i:495921 original size:10 final size:11
Alignment explanation
Indices: 495900--496047 Score: 70
Period size: 12 Copynumber: 12.6 Consensus size: 11
495890 TAAGTTATGA
495900 AAGTTATATAT
1 AAGTTATATAT
495911 AAGTTTATATAT
1 AAG-TTATATAT
*
495923 AAGTTATGTA-
1 AAGTTATATAT
495933 AA-TTATATATGT
1 AAGTTATATA--T
* *
495945 AAGTTATGTGTTGTGT
1 AAGTTA-----TATAT
495961 AAGTTTATATAT
1 AAG-TTATATAT
* * *
495973 AAATTTTATTT
1 AAGTTATATAT
*
495984 AAGTTATGTATGT
1 AAGTTA--TATAT
495997 AAGTTATATAT
1 AAGTTATATAT
496008 AAGTTTATATAT
1 AAG-TTATATAT
*
496020 AAG-T-TATGT
1 AAGTTATATAT
*
496029 AAGTTATTATGT
1 AAGTTA-TATAT
496041 AAGTTAT
1 AAGTTAT
496048 GTGTTGTGTA
Statistics
Matches: 106, Mismatches: 14, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
9 13 0.12
10 4 0.04
11 27 0.25
12 40 0.38
13 13 0.12
16 4 0.04
17 3 0.03
18 2 0.02
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (11 bp):
AAGTTATATAT
Found at i:495927 original size:32 final size:31
Alignment explanation
Indices: 495890--496045 Score: 115
Period size: 32 Copynumber: 4.8 Consensus size: 31
495880 TTATAATAAG
495890 TAAGTTATGAAAGTTATATATAAGTTTATATA
1 TAAGTTATGAAAGTTATATATAAGTTT-TATA
*
495922 TAAGTTATGTAAA-TTATATATGTAAG--TTATG
1 TAAGTTATG-AAAGTTATATA--TAAGTTTTATA
* * * *
495953 T--GTTGTGTAAGTTTATATATAAATTTTATT
1 TAAGTTATGAAAG-TTATATATAAGTTTTATA
495983 TAAGTTATGTATGTAAGTTATATATAAGTTTATATA
1 TAAGTTATG-A---AAGTTATATATAAGTTT-TATA
* *
496019 TAAGTTATGTAAGTTATTATGTAAGTT
1 TAAGTTATGAAAGTTA-TATATAAGTT
496046 ATGTGTTGTG
Statistics
Matches: 98, Mismatches: 11, Indels: 29
0.71 0.08 0.21
Matches are distributed among these distances:
28 5 0.05
29 5 0.05
30 12 0.12
31 4 0.04
32 28 0.29
33 12 0.12
34 4 0.04
35 13 0.13
36 15 0.15
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (31 bp):
TAAGTTATGAAAGTTATATATAAGTTTTATA
Found at i:496023 original size:36 final size:36
Alignment explanation
Indices: 495958--496029 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
495948 TTATGTGTTG
*
495958 TGTAAGTTTATATATAAATTTTATTTAAGTTATGTA
1 TGTAAGTTTATATATAAATTTTATATAAGTTATGTA
*
495994 TGTAAG-TTATATATAAGTTTATATATAAGTTATGTA
1 TGTAAGTTTATATATAAATTT-TATATAAGTTATGTA
496030 AGTTATTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 13 0.39
36 20 0.61
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (36 bp):
TGTAAGTTTATATATAAATTTTATATAAGTTATGTA
Found at i:496038 original size:12 final size:12
Alignment explanation
Indices: 495869--496047 Score: 62
Period size: 12 Copynumber: 15.2 Consensus size: 12
495859 GTAGGCTATG
495869 TATTATGTAAGT
1 TATTATGTAAGT
*
495881 TA-TA-ATAAGT
1 TATTATGTAAGT
* *
495891 AAGTTATGAAAGT
1 TA-TTATGTAAGT
*
495904 TA-TATATAAGT
1 TATTATGTAAGT
*
495915 T-TATATATAAG-
1 TAT-TATGTAAGT
*
495926 --TTATGTAAAT
1 TATTATGTAAGT
495936 TATATATGTAAGT
1 TAT-TATGTAAGT
*
495949 TATGTGTTGTGTAAGT
1 TA----TTATGTAAGT
* *
495965 T-TATATATAAAT
1 TAT-TATGTAAGT
*
495977 T-TTATTTAAGT
1 TATTATGTAAGT
495988 TATGTATGTAAGT
1 TAT-TATGTAAGT
*
496001 TA-TATATAAGT
1 TATTATGTAAGT
*
496012 T-TATATATAAG-
1 TAT-TATGTAAGT
496023 --TTATGTAAGT
1 TATTATGTAAGT
496033 TATTATGTAAGT
1 TATTATGTAAGT
496045 TAT
1 TAT
496048 GTGTTGTGTA
Statistics
Matches: 127, Mismatches: 19, Indels: 42
0.68 0.10 0.22
Matches are distributed among these distances:
9 13 0.10
10 8 0.06
11 28 0.22
12 43 0.34
13 25 0.20
16 9 0.07
17 1 0.01
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (12 bp):
TATTATGTAAGT
Found at i:496074 original size:96 final size:96
Alignment explanation
Indices: 495895--496103 Score: 348
Period size: 97 Copynumber: 2.2 Consensus size: 96
495885 ATAAGTAAGT
*
495895 TATGAAAGTTATATATAAGTTTATATATAAGTTATGTAAATTATATATGTAAGTTATGTGTTGTG
1 TATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAATTATATATGTAAGTTATGTGTTGTG
*
495960 TAAGTTTATATATAAATTTTATTTAAGTTATG
66 TAAGTTTATATATAAA-TTTATATAAGTTATG
*
495992 TATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTAT-TATGTAAGTTATGTGTTGTG
1 TATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAATTATATATGTAAGTTATGTGTTGTG
*
496056 TAAGTTTATATATAAATTTATATATGTTATG
66 TAAGTTTATATATAAATTTATATAAGTTATG
*
496087 TATGTAAATTATGATAT
1 TATGTAAGTTAT-ATAT
496104 GATTGATAAA
Statistics
Matches: 106, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
95 24 0.23
96 40 0.38
97 42 0.40
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (96 bp):
TATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAATTATATATGTAAGTTATGTGTTGTG
TAAGTTTATATATAAATTTATATAAGTTATG
Found at i:496148 original size:19 final size:19
Alignment explanation
Indices: 496109--496170 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
496099 GATATGATTG
*
496109 ATAAATTTTTCAA-ATATAT
1 ATAAAATTTT-AATATATAT
496128 ATAAAATTTTAATATATAT
1 ATAAAATTTTAATATATAT
* *
496147 ATTAAAATTGTATATAAATAT
1 A-TAAAATTTTA-ATATATAT
496168 ATA
1 ATA
496171 TCAAAGATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.05
19 16 0.43
20 11 0.30
21 8 0.22
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAAAATTTTAATATATAT
Found at i:496348 original size:9 final size:9
Alignment explanation
Indices: 496331--496635 Score: 124
Period size: 9 Copynumber: 35.9 Consensus size: 9
496321 TAAGTATAAT
*
496331 TAAGCTATG
1 TAAGTTATG
496340 TAAGTTATG
1 TAAGTTATG
*
496349 TAAGTTATA
1 TAAGTTATG
*
496358 TAAGTTGTG
1 TAAGTTATG
*
496367 T-A-TAATG
1 TAAGTTATG
496374 TAAGTTATG
1 TAAGTTATG
*
496383 AAAGTTATG
1 TAAGTTATG
496392 T-A-TTATG
1 TAAGTTATG
*
496399 TAAGTTATT
1 TAAGTTATG
*
496408 TAAGTTGTG
1 TAAGTTATG
*
496417 T-A-TTATA
1 TAAGTTATG
*
496424 TAAGTCATG
1 TAAGTTATG
* * *
496433 TAGGCTATA
1 TAAGTTATG
*
496442 TAAGTTTATATA
1 TAAG--T-TATG
496454 TAAGTTATG
1 TAAGTTATG
496463 TAAGTTA--
1 TAAGTTATG
496470 T-A--TATG
1 TAAGTTATG
496476 TAAGTTATG
1 TAAGTTATG
*
496485 T--GTTGTG
1 TAAGTTATG
*
496492 TAAGTTTATATA
1 TAAG--T-TATG
*
496504 TAAATTTTAT-
1 T-AA-GTTATG
496514 TCAAGTTATG
1 T-AAGTTATG
496524 --A---ATG
1 TAAGTTATG
496528 TAAGTTATG
1 TAAGTTATG
*
496537 TAAGTTGTG
1 TAAGTTATG
*
496546 T--GTAATG
1 TAAGTTATG
496553 TAAGTTATG
1 TAAGTTATG
496562 T-A-TTATG
1 TAAGTTATG
*
496569 TAAGTTATT
1 TAAGTTATG
*
496578 TAAGTTATT
1 TAAGTTATG
*
496587 TAAGTTGTG
1 TAAGTTATG
496596 T-A-TTATG
1 TAAGTTATG
*
496603 TAAGTCATG
1 TAAGTTATG
* *
496612 TAGGCTATG
1 TAAGTTATG
496621 T--GTTATG
1 TAAGTTATG
496628 TAAGTTAT
1 TAAGTTAT
496636 TATAAGTAAG
Statistics
Matches: 219, Mismatches: 42, Indels: 70
0.66 0.13 0.21
Matches are distributed among these distances:
4 5 0.02
6 3 0.01
7 45 0.21
8 10 0.05
9 134 0.61
10 4 0.02
11 4 0.02
12 12 0.05
13 2 0.01
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:496378 original size:25 final size:25
Alignment explanation
Indices: 496344--496428 Score: 118
Period size: 25 Copynumber: 3.4 Consensus size: 25
496334 GCTATGTAAG
496344 TTATGTAAGTTATATAAGTTGTGTA
1 TTATGTAAGTTATATAAGTTGTGTA
* *
496369 TAATGTAAGTTATGA-AAGTTATGTA
1 TTATGTAAGTTAT-ATAAGTTGTGTA
*
496394 TTATGTAAGTTATTTAAGTTGTGTA
1 TTATGTAAGTTATATAAGTTGTGTA
*
496419 TTATATAAGT
1 TTATGTAAGT
496429 CATGTAGGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
25 51 0.98
26 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (25 bp):
TTATGTAAGTTATATAAGTTGTGTA
Found at i:496477 original size:13 final size:13
Alignment explanation
Indices: 496459--496483 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
496449 ATATATAAGT
496459 TATGTAAGTTATA
1 TATGTAAGTTATA
496472 TATGTAAGTTAT
1 TATGTAAGTTAT
496484 GTGTTGTGTA
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):
TATGTAAGTTATA
Found at i:496479 original size:22 final size:21
Alignment explanation
Indices: 496442--496485 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
496432 GTAGGCTATA
496442 TAAGTTTATATATAAGTTATG
1 TAAGTTTATATATAAGTTATG
*
496463 TAAGTTATATATGTAAGTTATG
1 TAAGTT-TATATATAAGTTATG
496485 T
1 T
496486 GTTGTGTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (21 bp):
TAAGTTTATATATAAGTTATG
Found at i:496500 original size:50 final size:50
Alignment explanation
Indices: 496442--496754 Score: 152
Period size: 55 Copynumber: 5.9 Consensus size: 50
496432 GTAGGCTATA
496442 TAAGTTTATATATAAGTTATGTAAGTTATATATGTAAGTTATGTGTTGTG
1 TAAGTTTATATATAAGTTATGTAAGTTATATATGTAAGTTATGTGTTGTG
*
496492 TAAGTTTATATATAAATTTTAT-TCAAGTTATGA-ATGTAAGTTATGTAAGTTGTGTG
1 TAAGTTTATATAT-AA-GTTATGT-AAGTTAT-ATATGTAAGTTATGT--G-T-TGTG
* * * * * *
496548 TAA-TGTA-AGT-TATGTATTATGTAAGTTATTTAAGTTATTTAAGTTGTGTATTATG
1 TAAGTTTATA-TATAAG--TTATGTAAGTTA--T-A--TATGTAAGTTATGTGTTGTG
** ** * * * *
496603 TAAGTCATGTAGGCTATGTGTTATGTAAGTTATTATAAGTAAGTTATGAAAGTTATATA
1 TAAGT--T-TA-TATATAAGTTATGTAAGTTA-TATATGTAAGTTATG--TG-T-TGTG
* *
496662 TAAGTTTATATATAAGTTATGTAAGTT-TTTGTGTAAGTTATGTGTTGTG
1 TAAGTTTATATATAAGTTATGTAAGTTATATATGTAAGTTATGTGTTGTG
* * * * *
496711 TAAGTTTATATATAAATTTATATATGTTATGTATGTAAATTATG
1 TAAGTTTATATAT-AAGTTATGTAAGTTATATATGTAAGTTATG
496755 ATATGATTGA
Statistics
Matches: 199, Mismatches: 34, Indels: 59
0.68 0.12 0.20
Matches are distributed among these distances:
49 15 0.08
50 25 0.13
51 16 0.08
52 24 0.12
53 14 0.07
54 13 0.07
55 37 0.19
56 13 0.07
57 2 0.01
58 3 0.02
59 33 0.17
60 1 0.01
61 3 0.02
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.48
Consensus pattern (50 bp):
TAAGTTTATATATAAGTTATGTAAGTTATATATGTAAGTTATGTGTTGTG
Found at i:496520 original size:52 final size:51
Alignment explanation
Indices: 496442--496546 Score: 135
Period size: 52 Copynumber: 2.0 Consensus size: 51
496432 GTAGGCTATA
496442 TAAGTTTATATATAAGTTATGTAAGTTAT-ATATGTAAGTTATGT-GTTGTG
1 TAAGTTTATATATAAGTTATGTAAGTTATGA-ATGTAAGTTATGTAGTTGTG
*
496492 TAAGTTTATATATAAATTTTAT-TCAAGTTATGAATGTAAGTTATGTAAGTTGTG
1 TAAGTTTATATAT-AA-GTTATGT-AAGTTATGAATGTAAGTTATGT-AGTTGTG
496546 T
1 T
496547 GTAATGTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
50 13 0.27
51 3 0.06
52 24 0.50
53 1 0.02
54 7 0.15
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (51 bp):
TAAGTTTATATATAAGTTATGTAAGTTATGAATGTAAGTTATGTAGTTGTG
Found at i:496555 original size:16 final size:16
Alignment explanation
Indices: 496534--496613 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 16
496524 AATGTAAGTT
* *
496534 ATGTAAGTTGTGTGTA
1 ATGTAAGTTATGTATA
*
496550 ATGTAAGTTATGTATT
1 ATGTAAGTTATGTATA
* *
496566 ATGTAAGTTATTTAAGTT
1 ATGTAAGTTATGT-A-TA
* * *
496584 ATTTAAGTTGTGTATT
1 ATGTAAGTTATGTATA
*
496600 ATGTAAGTCATGTA
1 ATGTAAGTTATGTA
496614 GGCTATGTGT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
16 38 0.73
17 2 0.04
18 12 0.23
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.47
Consensus pattern (16 bp):
ATGTAAGTTATGTATA
Found at i:496557 original size:25 final size:25
Alignment explanation
Indices: 496525--496635 Score: 109
Period size: 25 Copynumber: 4.4 Consensus size: 25
496515 CAAGTTATGA
* *
496525 ATGTAAGTTATGTAAGTTGTGTGTA
1 ATGTAAGTTATGTAAGTTATGTGTT
496550 ATGTAAGTTATGT-A-TTATGTAAGTT
1 ATGTAAGTTATGTAAGTTATGT--GTT
* * * *
496575 ATTTAAGTTATTTAAGTTGTGTATT
1 ATGTAAGTTATGTAAGTTATGTGTT
* * *
496600 ATGTAAGTCATGTAGGCTATGTGTT
1 ATGTAAGTTATGTAAGTTATGTGTT
496625 ATGTAAGTTAT
1 ATGTAAGTTAT
496636 TATAAGTAAG
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
23 5 0.07
24 1 0.01
25 56 0.82
26 1 0.01
27 5 0.07
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.47
Consensus pattern (25 bp):
ATGTAAGTTATGTAAGTTATGTGTT
Found at i:496655 original size:23 final size:24
Alignment explanation
Indices: 496622--496666 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
496612 TAGGCTATGT
*
496622 GTTATGTAAGTTAT-TATAAGTAA
1 GTTATGAAAGTTATATATAAGTAA
496645 GTTATGAAAGTTATATATAAGT
1 GTTATGAAAGTTATATATAAGT
496667 TTATATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (24 bp):
GTTATGAAAGTTATATATAAGTAA
Found at i:496673 original size:10 final size:11
Alignment explanation
Indices: 496652--496681 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
496642 TAAGTTATGA
496652 AAGTTATATAT
1 AAGTTATATAT
496663 AAGTTTATATAT
1 AAG-TTATATAT
496675 AAGTTAT
1 AAGTTAT
496682 GTAAGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (11 bp):
AAGTTATATAT
Found at i:496686 original size:21 final size:21
Alignment explanation
Indices: 496662--496704 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
496652 AAGTTATATA
496662 TAAGTTTATATATAAGTTATG
1 TAAGTTTATATATAAGTTATG
* * *
496683 TAAGTTTTTGTGTAAGTTATG
1 TAAGTTTATATATAAGTTATG
496704 T
1 T
496705 GTTGTGTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (21 bp):
TAAGTTTATATATAAGTTATG
Found at i:496803 original size:19 final size:19
Alignment explanation
Indices: 496764--496808 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
496754 GATATGATTG
*
496764 ATAAATTTTTCAAATATAT
1 ATAAAATTTTCAAATATAT
496783 ATAAAATTTT-AATATATAT
1 ATAAAATTTTCAA-ATATAT
496802 ATTAAAA
1 A-TAAAA
496809 CTGTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 16 0.70
20 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAAATTTTCAAATATAT
Found at i:496803 original size:21 final size:22
Alignment explanation
Indices: 496775--496827 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
496765 TAAATTTTTC
* *
496775 AAATATATATAAAATTTTA-AT
1 AAATATATATAAAACTGTATAT
*
496796 ATATATAT-TAAAACTGTATAT
1 AAATATATATAAAACTGTATAT
496817 AAATATATATA
1 AAATATATATA
496828 TCAAAGATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.31
21 16 0.62
22 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATATATATAAAACTGTATAT
Found at i:498878 original size:45 final size:45
Alignment explanation
Indices: 498829--499014 Score: 122
Period size: 45 Copynumber: 4.0 Consensus size: 45
498819 AATATCTGCT
498829 ATCTTCAGTCTATTCTACTGCAACCTCAGTGAGATAAGACTTGTA
1 ATCTTCAGTCTATTCTACTGCAACCTCAGTGAGATAAGACTTGTA
* ** ** * * * * **
498874 ATCTTTAACCTGCTCCACTGCAACTTCGGGGAGATAAGGTTTG-A
1 ATCTTCAGTCTATTCTACTGCAACCTCAGTGAGATAAGACTTGTA
** * * ** * * *
498918 TATGATAAGATCTAATTCGACCTACTGCAACTTCAAAGAGATGAGATTTGTT
1 -ATCTTCAG-TCT-ATT----CTACTGCAACCTCAGTGAGATAAGACTTGTA
498970 ATCTTCAGTCTATTCTACTGCAACCTCAGTGAGATAAGACTTGTA
1 ATCTTCAGTCTATTCTACTGCAACCTCAGTGAGATAAGACTTGTA
499015 GCCTCAATAA
Statistics
Matches: 99, Mismatches: 34, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
44 1 0.01
45 61 0.62
46 2 0.02
47 1 0.01
49 3 0.03
50 3 0.03
51 28 0.28
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (45 bp):
ATCTTCAGTCTATTCTACTGCAACCTCAGTGAGATAAGACTTGTA
Found at i:500117 original size:46 final size:46
Alignment explanation
Indices: 499762--500101 Score: 475
Period size: 46 Copynumber: 7.4 Consensus size: 46
499752 TTCTTAGGGT
* * * *
499762 GACAAAATCTG-TAATCTTCAACCTACTCCACTGCCAAATACAGGAA
1 GACAAGATCTGCT-ATCTTCGATCTACTCCGCTGCCAAATACAGGAA
* * *
499808 GACAAGATCTACTATCTACGATCTACTCCACTGCCAAATACAGGAA
1 GACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAA
* **
499854 GACAAGATCTGCTATCTTCAATCTACTTTGCTGCCAAATACAGGAA
1 GACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAA
* * *
499900 GACAATATCTGCTATCTTCGATCTACTCCGCTGCCAAAAATAGGAA
1 GACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAA
* *
499946 GACAAGATCTGCTATCTACAATCTACTCCGCTGCCAAATACAGGAA
1 GACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAA
* * * * *
499992 GGCAAGATCTGTTATCTACGATCTACTCCTCTACCAAATACAGGAA
1 GACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAA
*
500038 GAAAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAA
1 GACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAA
500084 GACAAGATCTGCTATCTT
1 GACAAGATCTGCTATCTT
500102 TAATCTGTTC
Statistics
Matches: 259, Mismatches: 34, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
46 258 1.00
47 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (46 bp):
GACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAA
Found at i:501622 original size:13 final size:12
Alignment explanation
Indices: 501601--501647 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
501591 AGGCCTCTCC
501601 TTTTT-TTTTCT
1 TTTTTCTTTTCT
501612 TCTTTTCTTTTCT
1 T-TTTTCTTTTCT
501625 TTTTTCCTTTT-T
1 TTTTT-CTTTTCT
501637 TTTCTTCTTTT
1 TTT-TTCTTTT
501648 TTGTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.03
12 17 0.53
13 14 0.44
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:501629 original size:20 final size:20
Alignment explanation
Indices: 501603--501658 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
501593 GCCTCTCCTT
*
501603 TTTTTTTCTTCTTTTCTT-TTC
1 TTTTTTCCTT-TTTT-TTCTTC
501624 TTTTTTCCTTTTTTTTCTTC
1 TTTTTTCCTTTTTTTTCTTC
*
501644 TTTTTT-GTTTTTTTT
1 TTTTTTCCTTTTTTTT
501659 AACATTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 10 0.31
20 13 0.41
21 9 0.28
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (20 bp):
TTTTTTCCTTTTTTTTCTTC
Found at i:501636 original size:27 final size:27
Alignment explanation
Indices: 501605--501656 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
501595 CTCTCCTTTT
501605 TTTTTCTTCTT-TTCTTTTCTTTTTTCC
1 TTTTTCTTCTTCTT-TTTTCTTTTTTCC
* *
501632 TTTTTTTTCTTCTTTTTTGTTTTTT
1 TTTTTCTTCTTCTTTTTTCTTTTTT
501657 TTAACATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (27 bp):
TTTTTCTTCTTCTTTTTTCTTTTTTCC
Found at i:501648 original size:13 final size:13
Alignment explanation
Indices: 501600--501658 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
501590 TAGGCCTCTC
501600 CTTTTTTTTTCTT
1 CTTTTTTTTTCTT
*
501613 CTTTTCTTTTCTT
1 CTTTTTTTTTCTT
*
501626 -TTTTCCTTTTTTTT
1 CTTTT--TTTTTCTT
* *
501640 CTTCTTTTTTGTT
1 CTTTTTTTTTCTT
501653 -TTTTTT
1 CTTTTTT
501659 AACATTCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
12 9 0.24
13 19 0.51
14 6 0.16
15 3 0.08
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (13 bp):
CTTTTTTTTTCTT
Found at i:504137 original size:19 final size:20
Alignment explanation
Indices: 504113--504159 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
504103 TGTGAAAATC
*
504113 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGCAATG
*
504132 TAATGCAAATGCATGGAATG
1 TAATGCAAATGCATGCAATG
504152 -AATGCAAA
1 TAATGCAAA
504160 AAAGAAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.26
Consensus pattern (20 bp):
TAATGCAAATGCATGCAATG
Found at i:507467 original size:30 final size:29
Alignment explanation
Indices: 507433--507530 Score: 85
Period size: 30 Copynumber: 3.2 Consensus size: 29
507423 ACCTTTCATC
507433 TGTTTTCTATTTTGTATTTGTTTCTCTTAA
1 TGTTTTCTATTTT-TATTTGTTTCTCTTAA
* *
507463 TGTTTT-T-TTTTTCTTT-TTTACCACCTTTCATA
1 TGTTTTCTATTTTTATTTGTTT--C-TC-TT-A-A
507495 TGTTTTCTATTTTATATTTGTTTCTCTTAA
1 TGTTTTCTATTTT-TATTTGTTTCTCTTAA
507525 TGTTTT
1 TGTTTT
507531 TTTTCTTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
26 3 0.06
27 4 0.07
28 5 0.09
29 2 0.04
30 15 0.28
31 2 0.04
32 9 0.17
33 2 0.04
34 5 0.09
35 4 0.07
36 3 0.06
ACGTcount: A:0.13, C:0.12, G:0.07, T:0.67
Consensus pattern (29 bp):
TGTTTTCTATTTTTATTTGTTTCTCTTAA
Found at i:507500 original size:62 final size:60
Alignment explanation
Indices: 507423--507545 Score: 210
Period size: 62 Copynumber: 2.0 Consensus size: 60
507413 GGAAAAGAAA
* *
507423 ACCTTTCATCTGTTTTCTATTTTGTATTTGTTTCTCTTAATGTTTTTTTTTTCTTTTTTACC
1 ACCTTTCATATGTTTTCTATTTTATATTTGTTTCTCTTAATG--TTTTTTTTCTTTTTTACC
507485 ACCTTTCATATGTTTTCTATTTTATATTTGTTTCTCTTAATGTTTTTTTTCTTTTTTACC
1 ACCTTTCATATGTTTTCTATTTTATATTTGTTTCTCTTAATGTTTTTTTTCTTTTTTACC
507545 A
1 A
507546 AATATCGGGA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
60 19 0.32
62 40 0.68
ACGTcount: A:0.14, C:0.15, G:0.06, T:0.65
Consensus pattern (60 bp):
ACCTTTCATATGTTTTCTATTTTATATTTGTTTCTCTTAATGTTTTTTTTCTTTTTTACC
Found at i:509629 original size:19 final size:20
Alignment explanation
Indices: 509605--509644 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
509595 AAATTTTAAG
509605 TAAATAAT-TATT-AAAGTTT
1 TAAATAATAT-TTAAAAGTTT
509624 TAAATAATATTTAAAAGTTT
1 TAAATAATATTTAAAAGTTT
509644 T
1 T
509645 TGATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TAAATAATATTTAAAAGTTT
Found at i:509659 original size:21 final size:21
Alignment explanation
Indices: 509593--509659 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
509583 TATGTTTCAT
*
509593 TAAAA-TTTTAAGTAAATAATTA
1 TAAAAGTTTTAAAT-AA-AATTA
* *
509615 TTAAAGTTTTAAATAATATT-
1 TAAAAGTTTTAAATAAAATTA
**
509635 TAAAAGTTTTTGATAAAATTA
1 TAAAAGTTTTAAATAAAATTA
509656 TAAA
1 TAAA
509660 TTTTAGTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
20 16 0.44
21 7 0.19
22 6 0.17
23 7 0.19
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (21 bp):
TAAAAGTTTTAAATAAAATTA
Found at i:509691 original size:10 final size:10
Alignment explanation
Indices: 509678--509710 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
509668 TTTTGTTTCC
509678 TTTTTTATAT
1 TTTTTTATAT
509688 TTTTTTAT-T
1 TTTTTTATAT
509697 TTTTCTTATAT
1 TTTT-TTATAT
509708 TTT
1 TTT
509711 GGTCCTGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.24
10 12 0.57
11 4 0.19
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:509895 original size:2 final size:2
Alignment explanation
Indices: 509888--509921 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
509878 TAAAGTGATC
*
509888 TA TA TA TA TA TA TA TA TA TA TA TC TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
509922 CTCTTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:510399 original size:23 final size:22
Alignment explanation
Indices: 510342--510402 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
510332 TAACTTGTGT
*
510342 ACCCTTGACACCCT-AAACCCTA
1 ACCCTTAAC-CCCTAAAACCCTA
*
510364 AACCTATAA-CCCTAAAATCCCTA
1 ACCCT-TAACCCCTAAAA-CCCTA
510387 ACCCTTAACCCCTAAA
1 ACCCTTAACCCCTAAA
510403 CCTCAATCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 4 0.12
22 10 0.31
23 18 0.56
ACGTcount: A:0.38, C:0.41, G:0.02, T:0.20
Consensus pattern (22 bp):
ACCCTTAACCCCTAAAACCCTA
Found at i:510742 original size:14 final size:15
Alignment explanation
Indices: 510725--510757 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
510715 CTTAAATCAG
510725 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
510739 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
510754 AATC
1 AATC
510758 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:511221 original size:41 final size:41
Alignment explanation
Indices: 511151--511475 Score: 307
Period size: 41 Copynumber: 8.0 Consensus size: 41
511141 TGCGCATTTT
** *
511151 CAAAAACGCCGCTAAATCTCGGAGCATTAGCGGCGCTTTAC
1 CAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTAC
* * *
511192 CAAAAACGCTGCTAAAGATCTGAGTATTAGCGGCGCTTTTC
1 CAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTAC
* * * * * **
511233 TATAAACGCCGCTAAAGATTTGAGCA-TCGCGGCGATTTTG
1 CAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTAC
* * * * *
511273 GAAAAACACCGATAAAGATCTGAGCTTTAGCAGCGCTTCTA-
1 CAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTT-TAC
* * * * **
511314 CAGAAACGCCGCTAAATATCTTAGCATTACCGGCGCTTTTT
1 CAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTAC
* *
511355 CAAAAACGCAGCTAAAGATCTGAGCATCAGCGGCGCTTCT-C
1 CAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTT-TAC
* *
511396 AAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGATTTTA-
1 CAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCG-CTTTAC
* * * *
511437 CAAAAACACCGCTAAAGATCTGGGAACTAGCGGCGCTTT
1 CAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTT
511476 TTTTTAAAAC
Statistics
Matches: 227, Mismatches: 51, Indels: 13
0.78 0.18 0.04
Matches are distributed among these distances:
40 35 0.15
41 188 0.83
42 4 0.02
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (41 bp):
CAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTAC
Found at i:511856 original size:17 final size:17
Alignment explanation
Indices: 511834--511868 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
511824 TTTAACATTA
511834 TTTTCTTATTTTAATTT
1 TTTTCTTATTTTAATTT
*
511851 TTTTCTTATTTTGATTT
1 TTTTCTTATTTTAATTT
511868 T
1 T
511869 ATATCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTCTTATTTTAATTT
Found at i:513892 original size:19 final size:19
Alignment explanation
Indices: 513868--513906 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
513858 AAGTCAATTA
513868 ATAATT-TTAATTAAATATC
1 ATAATTATT-ATTAAATATC
*
513887 ATAATTATTTTTAAATATC
1 ATAATTATTATTAAATATC
513906 A
1 A
513907 ATTCAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAATTATTATTAAATATC
Found at i:514134 original size:22 final size:22
Alignment explanation
Indices: 514106--514148 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
514096 CAAAGATATC
514106 TTTTCATTCTTTTCTCTCTCAA
1 TTTTCATTCTTTTCTCTCTCAA
* *
514128 TTTTCATTTTTTTTTCTCTCA
1 TTTTCATTCTTTTCTCTCTCA
514149 TTCTTTTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTCATTCTTTTCTCTCTCAA
Found at i:514155 original size:24 final size:23
Alignment explanation
Indices: 514103--514155 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
514093 ACACAAAGAT
514103 ATCTTTTCATTCTTTTCTCTCTC
1 ATCTTTTCATTCTTTTCTCTCTC
* * *
514126 A-ATTTTCATTTTTTTTTCTCTC
1 ATCTTTTCATTCTTTTCTCTCTC
514148 ATTCTTTT
1 A-TCTTTT
514156 GCTTTCTTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 19 0.79
23 1 0.04
24 4 0.17
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66
Consensus pattern (23 bp):
ATCTTTTCATTCTTTTCTCTCTC
Found at i:515494 original size:55 final size:55
Alignment explanation
Indices: 515410--515576 Score: 334
Period size: 55 Copynumber: 3.0 Consensus size: 55
515400 AAAATGAGTT
515410 GATATTTTTGTTAGAAATAGTGTATTGAATAGAATTATTATTTTAGATTGAGAGC
1 GATATTTTTGTTAGAAATAGTGTATTGAATAGAATTATTATTTTAGATTGAGAGC
515465 GATATTTTTGTTAGAAATAGTGTATTGAATAGAATTATTATTTTAGATTGAGAGC
1 GATATTTTTGTTAGAAATAGTGTATTGAATAGAATTATTATTTTAGATTGAGAGC
515520 GATATTTTTGTTAGAAATAGTGTATTGAATAGAATTATTATTTTAGATTGAGAGC
1 GATATTTTTGTTAGAAATAGTGTATTGAATAGAATTATTATTTTAGATTGAGAGC
515575 GA
1 GA
515577 GTGAAAAATT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 112 1.00
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (55 bp):
GATATTTTTGTTAGAAATAGTGTATTGAATAGAATTATTATTTTAGATTGAGAGC
Found at i:515718 original size:22 final size:22
Alignment explanation
Indices: 515693--515737 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
515683 TTTTTGGATG
515693 AATGTAAATAGTTATTTATGTT
1 AATGTAAATAGTTATTTATGTT
515715 AATGTAAATAGTTATTTATGTT
1 AATGTAAATAGTTATTTATGTT
515737 A
1 A
515738 TGGTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (22 bp):
AATGTAAATAGTTATTTATGTT
Found at i:516067 original size:20 final size:20
Alignment explanation
Indices: 516024--516093 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
516014 ATAGGATTTG
*
516024 CACTTTGGTGCCTCTTTTTA
1 CACTTTGGTGCCTCTTTATA
* *
516044 CACTTCGGTGCCTCTTTATG
1 CACTTTGGTGCCTCTTTATA
* *
516064 CACTTTAGTGGCTCTTTATA
1 CACTTTGGTGCCTCTTTATA
*
516084 CACTCTGGTG
1 CACTTTGGTG
516094 TCCTTGTTCA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.13, C:0.26, G:0.19, T:0.43
Consensus pattern (20 bp):
CACTTTGGTGCCTCTTTATA
Found at i:520326 original size:9 final size:9
Alignment explanation
Indices: 520309--520345 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
520299 TGAGTTTTCA
520309 AATTCGAAT
1 AATTCGAAT
*
520318 AACTCGAAT
1 AATTCGAAT
520327 AATTCGAAT
1 AATTCGAAT
520336 AATTCGAAT
1 AATTCGAAT
520345 A
1 A
520346 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:530381 original size:27 final size:27
Alignment explanation
Indices: 530351--530406 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
530341 TCTCCACTTT
530351 CTCTCCTCTTTTTCATTCCAAAATTCC
1 CTCTCCTCTTTTTCATTCCAAAATTCC
*
530378 CTCTCTTCTTTTTCATTCCAAAATTCC
1 CTCTCCTCTTTTTCATTCCAAAATTCC
530405 CT
1 CT
530407 TACTCTCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.46
Consensus pattern (27 bp):
CTCTCCTCTTTTTCATTCCAAAATTCC
Found at i:543464 original size:26 final size:26
Alignment explanation
Indices: 543395--543454 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
543385 CGCAACATAA
543395 CTGCCAGTTGTAATAATGCAGCAGAG
1 CTGCCAGTTGTAATAATGCAGCAGAG
* *
543421 CTGCCAATTGTAATAATGCAGTAGAG
1 CTGCCAGTTGTAATAATGCAGCAGAG
543447 CTGCCAGT
1 CTGCCAGT
543455 AGTCAGAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (26 bp):
CTGCCAGTTGTAATAATGCAGCAGAG
Found at i:543637 original size:32 final size:33
Alignment explanation
Indices: 543601--543682 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 33
543591 TGAAATGAAT
*
543601 GGCACACAGCCATCGA-TAACGGTAATATGATC
1 GGCACAAAGCCATCGAGTAACGGTAATATGATC
* **
543633 GGCACAAAGCCAT-TAGTAACGGTTCTATGATC
1 GGCACAAAGCCATCGAGTAACGGTAATATGATC
*
543665 GGCATAAAGCCATC-AGTA
1 GGCACAAAGCCATCGAGTA
543683 GCATTGCAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
31 1 0.02
32 42 0.98
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (33 bp):
GGCACAAAGCCATCGAGTAACGGTAATATGATC
Found at i:543994 original size:27 final size:27
Alignment explanation
Indices: 543930--544160 Score: 232
Period size: 27 Copynumber: 8.6 Consensus size: 27
543920 ACCAGGGCAA
* * **
543930 TACAGTCATTTTATCCTATAAAGGTA-
1 TACAGTCATTTTACCCTACAGGGGTAT
* *
543956 TACGGTCATTTTACCCTACAGGGGCAT
1 TACAGTCATTTTACCCTACAGGGGTAT
* *
543983 TACAGTCATTTTACCCTAAAGGGGCAT
1 TACAGTCATTTTACCCTACAGGGGTAT
* *
544010 TACAGTCATTTTACCCTACAAGGGCAT
1 TACAGTCATTTTACCCTACAGGGGTAT
* * * *
544037 TAC-GATTATTTTACTCTAAAAGGGTAT
1 TACAG-TCATTTTACCCTACAGGGGTAT
* *
544064 TACAGTCATTTTACCCTATAGGGGTAC
1 TACAGTCATTTTACCCTACAGGGGTAT
* ** *
544091 TACGGTCATTTTACCCTGTAGAGGTAT
1 TACAGTCATTTTACCCTACAGGGGTAT
*
544118 TACGGTCATTTTACCCTACAGGGGTAT
1 TACAGTCATTTTACCCTACAGGGGTAT
**
544145 TATGGTCATTTTACCC
1 TACAGTCATTTTACCC
544161 ATCAAGGTTA
Statistics
Matches: 175, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
26 21 0.12
27 153 0.87
28 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (27 bp):
TACAGTCATTTTACCCTACAGGGGTAT
Found at i:544035 original size:54 final size:54
Alignment explanation
Indices: 543908--544160 Score: 259
Period size: 54 Copynumber: 4.7 Consensus size: 54
543898 GGGAAAAAAT
* *
543908 AGTCA-TTTACCC-ACCA-GGGCAATACAGTCATTTTATCCTATAA-AGGTA-TAC
1 AGTCATTTTACCCTA-CAGGGGCATTACAGTCATTTTACCCTA-AAGAGGTATTAC
* * *
543959 GGTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTAAAGGGGCATTAC
1 AGTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTAAAGAGGTATTAC
* * *
544013 AGTCATTTTACCCTACAAGGGCATTAC-GATTATTTTACTCTAAA-AGGGTATTAC
1 AGTCATTTTACCCTACAGGGGCATTACAG-TCATTTTACCCTAAAGA-GGTATTAC
* * * * **
544067 AGTCATTTTACCCTATAGGGGTACTACGGTCATTTTACCCTGTAGAGGTATTAC
1 AGTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTAAAGAGGTATTAC
* * **
544121 GGTCATTTTACCCTACAGGGGTATTATGGTCATTTTACCC
1 AGTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCC
544161 ATCAAGGTTA
Statistics
Matches: 170, Mismatches: 23, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
51 4 0.02
52 11 0.06
53 27 0.16
54 126 0.74
55 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (54 bp):
AGTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTAAAGAGGTATTAC
Found at i:544072 original size:81 final size:81
Alignment explanation
Indices: 543924--544160 Score: 280
Period size: 81 Copynumber: 2.9 Consensus size: 81
543914 TTACCCACCA
* * * *
543924 GGGCAATACAGTCATTTTATCCTATAAAGGTA-TACGGTCATTTTACCCTACAGGGGCATTACAG
1 GGGCAATACAGTCATTTTACCCTACAAGGGTATTACGGTCATTTTACCCTACAGGGGTATTACAG
543988 TCATTTTACCCTAAAG
66 TCATTTTACCCTAAAG
* * * * * * *
544004 GGGCATTACAGTCATTTTACCCTACAAGGGCATTACGATTATTTTACTCTAAAAGGGTATTACAG
1 GGGCAATACAGTCATTTTACCCTACAAGGGTATTACGGTCATTTTACCCTACAGGGGTATTACAG
*
544069 TCATTTTACCCTATAG
66 TCATTTTACCCTAAAG
* * * ** **
544085 GGGTACTACGGTCATTTTACCCT-GTAGAGGTATTACGGTCATTTTACCCTACAGGGGTATTATG
1 GGGCAATACAGTCATTTTACCCTACAAG-GGTATTACGGTCATTTTACCCTACAGGGGTATTACA
544149 GTCATTTTACCC
65 GTCATTTTACCC
544161 ATCAAGGTTA
Statistics
Matches: 130, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
80 29 0.22
81 101 0.78
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34
Consensus pattern (81 bp):
GGGCAATACAGTCATTTTACCCTACAAGGGTATTACGGTCATTTTACCCTACAGGGGTATTACAG
TCATTTTACCCTAAAG
Found at i:544183 original size:54 final size:54
Alignment explanation
Indices: 543963--544185 Score: 141
Period size: 54 Copynumber: 4.1 Consensus size: 54
543953 GTATACGGTC
* * * ** * * *
543963 ATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTAAAGGGGCATTAC-AGTC
1 ATTTTACCCTACAGGGGTACTACGGTCATTTTACCCTGCAGAGGTATTACGA-TA
* * * * * * * * *
544017 ATTTTACCCTACAAGGGCATTACGATTATTTTACTCT-AAAAGGGTATTAC-AGTC
1 ATTTTACCCTACAGGGGTACTACGGTCATTTTACCCTGCAGA-GGTATTACGA-TA
* * * *
544071 ATTTTACCCTATAGGGGTACTACGGTCATTTTACCCTGTAGAGGTATTACGGTC
1 ATTTTACCCTACAGGGGTACTACGGTCATTTTACCCTGCAGAGGTATTACGATA
* * **
544125 ATTTTACCCTACAGGGGTATTATGGTCATTTTACCCAT-CA-AGGTTATTTTGATA
1 ATTTTACCCTACAGGGGTACTACGGTCATTTTACCC-TGCAGAGG-TATTACGATA
544179 ATTTTAC
1 ATTTTAC
544186 AACCTTTTCG
Statistics
Matches: 138, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
53 5 0.04
54 130 0.94
55 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (54 bp):
ATTTTACCCTACAGGGGTACTACGGTCATTTTACCCTGCAGAGGTATTACGATA
Found at i:556865 original size:75 final size:75
Alignment explanation
Indices: 556776--556922 Score: 170
Period size: 75 Copynumber: 2.0 Consensus size: 75
556766 ATTATGGGTT
* * * * * * * *
556776 TTGTTTGTTAAATGCATCTTTATTTAATATTTTGCATTAGTACATTTACATCTTTTAA-AATGTG
1 TTGTTTATTAAATGCATCTTTAGTTAACACTTTACATTAATACATTCACATCCTTTAAGAAT-TG
556840 CATTATGTTTC
65 CATTATGTTTC
* * * *
556851 TTGTTTATTGAATGCGTCTTTAGTTAACACTTTACATTAATACATTCGCATCCTTTAAGACTTGC
1 TTGTTTATTAAATGCATCTTTAGTTAACACTTTACATTAATACATTCACATCCTTTAAGAATTGC
556916 ATTATGT
66 ATTATGT
556923 ATGTTTCATA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
75 57 0.97
76 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.48
Consensus pattern (75 bp):
TTGTTTATTAAATGCATCTTTAGTTAACACTTTACATTAATACATTCACATCCTTTAAGAATTGC
ATTATGTTTC
Found at i:559273 original size:40 final size:39
Alignment explanation
Indices: 559242--559451 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
559232 GGACTAAGAT
* *
559242 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
559282 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
559322 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
559362 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
559402 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
559441 CCGAAGGCATT
1 CCGAAGGCATT
559452 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:559405 original size:120 final size:120
Alignment explanation
Indices: 559189--559451 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
559179 TTGAATGCTG
* *
559189 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
559253 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
559309 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
559372 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
559428 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
559452 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:559471 original size:79 final size:80
Alignment explanation
Indices: 559190--559486 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
559180 TGAATGCTGT
* ** * * * **
559190 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
559253 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
559270 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
559334 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
559350 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
559414 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
559429 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
559487 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:569957 original size:38 final size:39
Alignment explanation
Indices: 569914--570033 Score: 188
Period size: 38 Copynumber: 3.0 Consensus size: 39
569904 GACTCATGTG
569914 ACCATCTATTTCTTTTTTTCTAGAATTTTTGGTTGGGCC
1 ACCATCTATTTCTTTTTTTCTAGAATTTTTGGTTGGGCC
* *
569953 -CCATCTATGTATTTTTTTCTAGAATTTTTGGTTGGGCC
1 ACCATCTATTTCTTTTTTTCTAGAATTTTTGGTTGGGCC
569991 AATACCATCTATTTCTTTTTTTCTAGAATTTTTGGTTGGGCC
1 ---ACCATCTATTTCTTTTTTTCTAGAATTTTTGGTTGGGCC
570033 A
1 A
570034 ATTAGTACAG
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
38 36 0.49
39 1 0.01
42 36 0.49
ACGTcount: A:0.17, C:0.17, G:0.16, T:0.50
Consensus pattern (39 bp):
ACCATCTATTTCTTTTTTTCTAGAATTTTTGGTTGGGCC
Found at i:570000 original size:42 final size:42
Alignment explanation
Indices: 569914--570035 Score: 198
Period size: 42 Copynumber: 3.0 Consensus size: 42
569904 GACTCATGTG
569914 ACCATCTATTTCTTTTTTTCTAGAATTTTTGGTTGGGCC---
1 ACCATCTATTTCTTTTTTTCTAGAATTTTTGGTTGGGCCAAT
* *
569953 -CCATCTATGTATTTTTTTCTAGAATTTTTGGTTGGGCCAAT
1 ACCATCTATTTCTTTTTTTCTAGAATTTTTGGTTGGGCCAAT
569994 ACCATCTATTTCTTTTTTTCTAGAATTTTTGGTTGGGCCAAT
1 ACCATCTATTTCTTTTTTTCTAGAATTTTTGGTTGGGCCAAT
570036 TAGTACAGTT
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
38 36 0.48
42 39 0.52
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (42 bp):
ACCATCTATTTCTTTTTTTCTAGAATTTTTGGTTGGGCCAAT
Found at i:570557 original size:190 final size:190
Alignment explanation
Indices: 570234--570612 Score: 713
Period size: 190 Copynumber: 2.0 Consensus size: 190
570224 TATGAATTTC
* *
570234 CAAAGTCGGAGCAGGGAATCTAGAAACTGTTATGGCCCTGTCCCACAAAAATCTGATTATCTCTT
1 CAAAGTCGGAGCAGAGAATCCAGAAACTGTTATGGCCCTGTCCCACAAAAATCTGATTATCTCTT
570299 AATATACTGCCCATATGATCTTTTCGTTACTTCCTCATGAAAACAGACTCATCGAGCTTCGCTTA
66 AATATACTGCCCATATGATCTTTTCGTTACTTCCTCATGAAAACAGACTCATCGAGCTTCGCTTA
570364 CATAATTTATTCATCAATTAATTCCACTCCTACTAATTTTAGTGATTTTTCAATCTCATA
131 CATAATTTATTCATCAATTAATTCCACTCCTACTAATTTTAGTGATTTTTCAATCTCATA
*
570424 CAAAGTCGGAGCAGAGAATCCAGAAACTGTTCTGGCCCTGTCCCACAAAAATCTGATTATCTCTT
1 CAAAGTCGGAGCAGAGAATCCAGAAACTGTTATGGCCCTGTCCCACAAAAATCTGATTATCTCTT
*
570489 AATATACTGCCCATATGATCTTTTCGTTACTTCCTCATGAAAATAGACTCATCGAGCTTCGCTTA
66 AATATACTGCCCATATGATCTTTTCGTTACTTCCTCATGAAAACAGACTCATCGAGCTTCGCTTA
*
570554 CATAATTTATTCATCAATTAATTCCACTTCTACTAATTTTAGTGATTTTTCAATCTCAT
131 CATAATTTATTCATCAATTAATTCCACTCCTACTAATTTTAGTGATTTTTCAATCTCAT
570613 GACACTGCTG
Statistics
Matches: 184, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
190 184 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (190 bp):
CAAAGTCGGAGCAGAGAATCCAGAAACTGTTATGGCCCTGTCCCACAAAAATCTGATTATCTCTT
AATATACTGCCCATATGATCTTTTCGTTACTTCCTCATGAAAACAGACTCATCGAGCTTCGCTTA
CATAATTTATTCATCAATTAATTCCACTCCTACTAATTTTAGTGATTTTTCAATCTCATA
Found at i:571377 original size:27 final size:27
Alignment explanation
Indices: 571347--571524 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
571337 ATATTGAGCC
* *
571347 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
571374 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
571401 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* ** ** *
571429 CGCACTCTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
571456 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
571483 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
571510 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
571525 GTACAATTTA
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.82
28 23 0.18
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:571486 original size:82 final size:81
Alignment explanation
Indices: 571368--571523 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
571358 TGCTATATAA
* *
571368 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
*
571433 CTCTTAGTGCCGCATGG
65 CCCTTAGTGCCGCATGG
* * **
571450 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
571514 CCCTTAGTGC
65 CCCTTAGTGC
571524 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 51 0.77
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
CCTTAGTGCCGCATGG
Found at i:577409 original size:90 final size:90
Alignment explanation
Indices: 577256--577435 Score: 360
Period size: 90 Copynumber: 2.0 Consensus size: 90
577246 AACATCAAGT
577256 GCCTTCAGGATTACTCCAGCCGATCATGATACCCGAGTGGAAATGGGATCGAGTCACAATGGACT
1 GCCTTCAGGATTACTCCAGCCGATCATGATACCCGAGTGGAAATGGGATCGAGTCACAATGGACT
577321 TTGTGTCCGGACTGCCCTTGTCAGC
66 TTGTGTCCGGACTGCCCTTGTCAGC
577346 GCCTTCAGGATTACTCCAGCCGATCATGATACCCGAGTGGAAATGGGATCGAGTCACAATGGACT
1 GCCTTCAGGATTACTCCAGCCGATCATGATACCCGAGTGGAAATGGGATCGAGTCACAATGGACT
577411 TTGTGTCCGGACTGCCCTTGTCAGC
66 TTGTGTCCGGACTGCCCTTGTCAGC
577436 AAGTAAGAAG
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (90 bp):
GCCTTCAGGATTACTCCAGCCGATCATGATACCCGAGTGGAAATGGGATCGAGTCACAATGGACT
TTGTGTCCGGACTGCCCTTGTCAGC
Found at i:580062 original size:40 final size:40
Alignment explanation
Indices: 579979--580241 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
579969 TTGAATGCTG
* * * * * *
579979 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
580019 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
580059 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
580099 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
580139 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
580179 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
580218 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
580242 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:580261 original size:79 final size:80
Alignment explanation
Indices: 580018--580276 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
580008 AAGTGAATAT
* * * * * *
580018 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
580082 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
580098 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
580163 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
580178 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
580242 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
580257 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
580277 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:588063 original size:80 final size:79
Alignment explanation
Indices: 587926--588150 Score: 236
Period size: 80 Copynumber: 2.8 Consensus size: 79
587916 TTGAATGCTG
* * * ** * * * * *
587926 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGCGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
587990 TGTGCGAGATATTAAA
64 TGTGCGAGATATTAAA
* * * *
588006 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTT
* *
588071 GTGCGAGTTGTTAAA
65 GTGCGAGATATTAAA
* * * *
588086 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACTGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
588151 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
79 35 0.29
80 83 0.68
81 4 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATTAAA
Found at i:588136 original size:39 final size:40
Alignment explanation
Indices: 587979--588148 Score: 234
Period size: 40 Copynumber: 4.3 Consensus size: 40
587969 GGACTAAGAT
* * * *
587979 CCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
*
588019 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
*
588059 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
* * * * *
588099 CCGAAGGCATT-GTGTGAGTTACTAAAACTGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
588138 CCGAAGGCATT
1 CCGAAGGCATT
588149 TGAACGAGGA
Statistics
Matches: 119, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 33 0.28
40 86 0.72
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
Found at i:596458 original size:50 final size:50
Alignment explanation
Indices: 596403--596524 Score: 118
Period size: 50 Copynumber: 2.4 Consensus size: 50
596393 TATCCCAAAT
** * **
596403 ATGGTCTTACATGAAAGTTCTCATATCGGTGCCCATGCCATGTCCAAGAC
1 ATGGTCTTACATGAAACCTCTCATATCGGTGCCAACACCATGTCCAAGAC
* * ** * * *
596453 ATGGTCTTAAAGGGGACCTCTCTTCTCGGTGCCAACACCATGTCCCAGAC
1 ATGGTCTTACATGAAACCTCTCATATCGGTGCCAACACCATGTCCAAGAC
**
596503 ATGGTCTTACATGGGACCTCTC
1 ATGGTCTTACATGAAACCTCTC
596525 GTAACCTCAA
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
ATGGTCTTACATGAAACCTCTCATATCGGTGCCAACACCATGTCCAAGAC
Found at i:613671 original size:21 final size:20
Alignment explanation
Indices: 613645--613685 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
613635 GGTACGTGTA
613645 GACAAATTTATCTTTCCTGC
1 GACAAATTTATCTTTCCTGC
613665 NGACAAATTTATCTTTCCTGC
1 -GACAAATTTATCTTTCCTGC
613686 TGACTTTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.39
Consensus pattern (20 bp):
GACAAATTTATCTTTCCTGC
Found at i:616232 original size:30 final size:30
Alignment explanation
Indices: 616176--616233 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
616166 AGCTTAGGGA
*
616176 CAAAAGTGTAAATATGTAAAAGGTTGGGGG
1 CAAAAGTGTAAATATGTAAAAAGTTGGGGG
* *
616206 CAAAATTGTAAAT-TTTCAAAAAGTTGGG
1 CAAAAGTGTAAATATGT-AAAAAGTTGGG
616234 TGGAGGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.41, C:0.05, G:0.26, T:0.28
Consensus pattern (30 bp):
CAAAAGTGTAAATATGTAAAAAGTTGGGGG
Found at i:616824 original size:102 final size:103
Alignment explanation
Indices: 616559--616812 Score: 366
Period size: 102 Copynumber: 2.5 Consensus size: 103
616549 ATTGCATATA
* * * *
616559 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGCGCTGATTCCACCGTATT
1 AAGGGGTTGCTGTGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
*
616624 TTAAATGTGAAAGGGGCTTGCTAAGTGCTGATTCCCCC
66 TGAAATGTGAAAGGGGCTTGCTAAGTGCTGATTCCCCC
* * ** * *
616662 GACGGGTTGCTAAGTGTTGATTTCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AAGGGGTTGCTGTGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
*
616727 TGAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TGAAATGTGAAAGGGGCTTGCTAAGTGCTGATTCCCCC
* **
616764 AAGGGGTTGTTGTGTGTTGATTCCCCGATTCATTGGTCATTGCTAAGTG
1 AAGGGGTTGCTGTGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTG
616813 TGGAATCCAC
Statistics
Matches: 130, Mismatches: 21, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
102 67 0.52
103 63 0.48
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (103 bp):
AAGGGGTTGCTGTGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
TGAAATGTGAAAGGGGCTTGCTAAGTGCTGATTCCCCC
Found at i:620928 original size:21 final size:21
Alignment explanation
Indices: 620904--620946 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
620894 GCCAGTGCTG
620904 GTGCAACCTGAATCAGGGAAA
1 GTGCAACCTGAATCAGGGAAA
*
620925 GTGCAACCTGAATCATGGAAA
1 GTGCAACCTGAATCAGGGAAA
620946 G
1 G
620947 AGTTTGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.19, G:0.28, T:0.16
Consensus pattern (21 bp):
GTGCAACCTGAATCAGGGAAA
Found at i:624269 original size:27 final size:27
Alignment explanation
Indices: 624231--624282 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
624221 TAAATGTGAA
624231 AGGGGTCGCTAAGTGCTGATTCCCCCG
1 AGGGGTCGCTAAGTGCTGATTCCCCCG
*
624258 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTCGCTAAGTGCTGATTCCCC
624283 TATTCATTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.15, C:0.27, G:0.33, T:0.25
Consensus pattern (27 bp):
AGGGGTCGCTAAGTGCTGATTCCCCCG
Found at i:624290 original size:102 final size:102
Alignment explanation
Indices: 624052--624356 Score: 486
Period size: 102 Copynumber: 3.0 Consensus size: 102
624042 ATTGCATATA
* *
624052 AAGGGGTTGCTGTGTGCTGATTCCTCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
*
624117 TTAAATGTGAAAGGGGGTTGCTAAATGCTGATTCCCCC
66 TTAAATGTGAAA-GGGGTTGCTAAGTGCTGATTCCCCC
*
624155 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
*
624220 TTAAATGTGAAAGGGGTCGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCC
* ** * * *
624257 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
*
624322 TGAAATGTG-AAGGGGTTGCTAAGTGCTGATTCCCC
66 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
624357 TATTCATTGG
Statistics
Matches: 189, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
101 25 0.13
102 90 0.48
103 74 0.39
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (102 bp):
AAGGGGTTGCTGTGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:624351 original size:41 final size:41
Alignment explanation
Indices: 624294--624428 Score: 187
Period size: 41 Copynumber: 3.5 Consensus size: 41
624284 ATTCATTGGT
624294 GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTGAAGG
1 GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTGAAGG
* * *
624335 GGTTGCTAAGTGCTGATTCC-CC-TAT-T--CAT-TG--GT
1 GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTGAAGG
624368 GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTGAAGG
1 GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTGAAGG
624409 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
624429 CCCAAGGGGT
Statistics
Matches: 80, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
33 21 0.26
34 2 0.03
35 4 0.05
36 3 0.04
38 3 0.04
39 4 0.05
40 2 0.03
41 41 0.51
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTGAAGG
Found at i:624379 original size:74 final size:74
Alignment explanation
Indices: 624258--624430 Score: 346
Period size: 74 Copynumber: 2.3 Consensus size: 74
624248 GATTCCCCCG
624258 AGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATCT
624323 GAAATGTGA
66 GAAATGTGA
624332 AGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATCT
624397 GAAATGTGA
66 GAAATGTGA
624406 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
624431 CAAGGGGTTG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 99 1.00
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.32
Consensus pattern (74 bp):
AGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATCT
GAAATGTGA
Found at i:624436 original size:101 final size:103
Alignment explanation
Indices: 624331--624533 Score: 320
Period size: 101 Copynumber: 2.0 Consensus size: 103
624321 CTGAAATGTG
*
624331 AAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
624396 TGAAATGTG-AAGGGG-TTGCTAAGTGCTGATTCCCCC
66 TGAAATGTGAAAGGGGCTTGCTAAGTGCTGATTCCCCC
* ** * * *
624432 AAGGGGTTGTTGTGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
*
624497 TTAAATGTGAAAGGGGCTTGCTAAGTGCTGATTCCCC
66 TGAAATGTGAAAGGGGCTTGCTAAGTGCTGATTCCCC
624534 TATTCATTGG
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 66 0.72
102 6 0.07
103 20 0.22
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.33
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
TGAAATGTGAAAGGGGCTTGCTAAGTGCTGATTCCCCC
Found at i:624579 original size:76 final size:75
Alignment explanation
Indices: 624449--624608 Score: 266
Period size: 76 Copynumber: 2.1 Consensus size: 75
624439 TGTTGTGTGT
* * *
624449 TGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAGGGGC
1 TGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATATGAAATGTG-AAGGGGC
624514 TTGCTAAGTGC
65 TTGCTAAGTGC
* *
624525 TGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATATGAAATGTGAAGGGGGT
1 TGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATATGAAATGTGAAGGGGCT
624590 TGCTAAGTGC
66 TGCTAAGTGC
624600 TGATTCCCC
1 TGATTCCCC
624609 CAAGGGGTTG
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
75 26 0.33
76 53 0.67
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (75 bp):
TGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATATGAAATGTGAAGGGGCT
TGCTAAGTGC
Found at i:628487 original size:25 final size:25
Alignment explanation
Indices: 628427--628487 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
628417 CTCCTAAATT
*
628427 TTAATTTAATTATCTAATTTTTCAA
1 TTAATTAAATTATCTAATTTTTCAA
* *
628452 TTTATTGAATTAT-TAATATTTT-ATA
1 TTAATTAAATTATCTAAT-TTTTCA-A
628477 TTAATTAAATT
1 TTAATTAAATT
628488 TTTGAGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATCTAATTTTTCAA
Found at i:647057 original size:80 final size:80
Alignment explanation
Indices: 646961--647120 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
646951 CGAAACACAC
646961 CTGGGCACTAAATGTCATGCCTGAAGGCCTTACATTTGCCCCCAGTAACACACCAGAATCACTGT
1 CTGGGCACTAAATGTCATGCCTGAAGGCCTTACATTTGCCCCCAGTAACACACCAGAATCACTGT
647026 AAATATAACACGATA
66 AAATATAACACGATA
647041 CTGGGCACTAAATGTCATGCCTGAAGGCCTTACATTTGCCCCCAGTAACACACCAGAATCACTGT
1 CTGGGCACTAAATGTCATGCCTGAAGGCCTTACATTTGCCCCCAGTAACACACCAGAATCACTGT
647106 AAATATAACACGATA
66 AAATATAACACGATA
647121 GGCCACAACA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.23
Consensus pattern (80 bp):
CTGGGCACTAAATGTCATGCCTGAAGGCCTTACATTTGCCCCCAGTAACACACCAGAATCACTGT
AAATATAACACGATA
Found at i:658724 original size:18 final size:18
Alignment explanation
Indices: 658701--658742 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
658691 GTTGTTGAGA
* *
658701 AAGAAGTTGCTGCTATAG
1 AAGAAGTTGCTACTAAAG
*
658719 AAGAAGTTGTTACTAAAG
1 AAGAAGTTGCTACTAAAG
658737 AAGAAG
1 AAGAAG
658743 AAGTTGCTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.26, T:0.24
Consensus pattern (18 bp):
AAGAAGTTGCTACTAAAG
Found at i:670225 original size:40 final size:40
Alignment explanation
Indices: 670188--670373 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
670178 GCTACTCGTT
*
670188 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
670228 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
670268 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
670308 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACCTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AACTCGCA
670349 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
670374 CATCATTCAA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 114 0.87
41 14 0.11
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:671479 original size:47 final size:47
Alignment explanation
Indices: 671410--671503 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
671400 CATTACATAG
671410 CAAAGATTTGAACCATGGGCTAATTAGAACTCAAGCTAGCAACTAAA
1 CAAAGATTTGAACCATGGGCTAATTAGAACTCAAGCTAGCAACTAAA
671457 CAAAGATTTGAACCATGGGCTAATTAGAACTCAAGCTAGCAACTAAA
1 CAAAGATTTGAACCATGGGCTAATTAGAACTCAAGCTAGCAACTAAA
671504 AACATGCATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (47 bp):
CAAAGATTTGAACCATGGGCTAATTAGAACTCAAGCTAGCAACTAAA
Done.