Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold260
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: 1006324
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 4 of 7
Found at i:494514 original size:123 final size:123
Alignment explanation
Indices: 494275--494791 Score: 639
Period size: 123 Copynumber: 4.2 Consensus size: 123
494265 AATGAAATGG
* * * * **
494275 GTCCTGCTCCTTGGGGACTA-AAAAGTGCCACCAACTTGTATGGGCTTTGCAAGGAGAAA-GCAT
1 GTCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCAT
* * * *
494338 CCTGCTCTTTGAGGACTAGAAGGTACCACCAACTTATGTGGGCTTAAAAAGGAAAAGGC
65 CCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * **
494397 GTCCTATTCTTTGAGGACTATAAAAGTGCCACCAATTTGTGTGGGCTTTAAAAGGAAAAGGTGTC
1 GTCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC
* *
494462 CTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAATGT
66 CTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * * *
494520 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTAGGCTTTAAAAAGAAAAGACGTC
1 GTCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC
* * * *
494585 CTACTCTTTGAGGACT-GAAGGTGCCACTAGCTTGTATGGGCTTTAAAAGGAAATGGC
66 CTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * *
494642 ATCTTACTCCTTGAGGACT-GAAAAGTGCCATCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC
1 GTCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC
* * * * * *
494706 CTGCTTTTTGAGGACTAAAAAAGTGCCACCAACTTGCGTGGGCTTTAAAAGGAGAAGGC
66 CTACTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* *
494765 GTCTTGCTCTTTGAGGACT-GAAAAGTG
1 GTCCTACTCTTTGAGGACTAGAAAAGTG
494792 AAAGAAGAAA
Statistics
Matches: 339, Mismatches: 52, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
121 54 0.16
122 69 0.20
123 216 0.64
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (123 bp):
GTCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC
CTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
Found at i:495582 original size:21 final size:21
Alignment explanation
Indices: 495539--495591 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
495529 TAAAACCCAG
*
495539 AATGTATCAAT-ACAATGAAA
1 AATGTATCGATAACAATGAAA
495559 AATGTATCGATAACAAT-AATA
1 AATGTATCGATAACAATGAA-A
*
495580 AATGTATTGATA
1 AATGTATCGATA
495592 CATTTACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (21 bp):
AATGTATCGATAACAATGAAA
Found at i:495680 original size:13 final size:13
Alignment explanation
Indices: 495662--495688 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
495652 AGTTTAGGCA
495662 TGTATCGATACAT
1 TGTATCGATACAT
495675 TGTATCGATACAT
1 TGTATCGATACAT
495688 T
1 T
495689 TACCATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:499371 original size:13 final size:13
Alignment explanation
Indices: 499353--499378 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
499343 TACACACAAG
499353 ATGTATCGATACA
1 ATGTATCGATACA
499366 ATGTATCGATACA
1 ATGTATCGATACA
499379 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:505329 original size:8 final size:8
Alignment explanation
Indices: 505316--505341 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
505306 ATTTGATTAA
505316 ATTTTGTG
1 ATTTTGTG
505324 ATTTTGTG
1 ATTTTGTG
505332 ATTTTGTG
1 ATTTTGTG
505340 AT
1 AT
505342 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:505562 original size:13 final size:13
Alignment explanation
Indices: 505544--505581 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
505534 CAACATTCTC
* *
505544 TGTATCCATACAT
1 TGTATCGATACAG
505557 TGTATCGATACAG
1 TGTATCGATACAG
505570 TGTATCGATACA
1 TGTATCGATACA
505582 AAGGGTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:505748 original size:20 final size:20
Alignment explanation
Indices: 505713--505754 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
505703 CAAATTTCTT
505713 ATTTTTCACTTCAAAATACATC
1 ATTTTTCAC-TCAAAAT-CATC
505735 ATTTTTCA-TCAAAATCATC
1 ATTTTTCACTCAAAATCATC
505754 A
1 A
505755 ACAAAAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
22 8 0.40
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTTTCACTCAAAATCATC
Found at i:508192 original size:13 final size:13
Alignment explanation
Indices: 508174--508199 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
508164 TACACACAAG
508174 ATGTATCGATACA
1 ATGTATCGATACA
508187 ATGTATCGATACA
1 ATGTATCGATACA
508200 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:509741 original size:36 final size:36
Alignment explanation
Indices: 509682--509759 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 36
509672 TCCTTTAAGG
* *
509682 ATATTTTAGCAAAAGCTTTCAAAG-CTTCTCTTGAGA
1 ATATTTTAGCAAAAGCTTACAAAGTC-TCTATTGAGA
** * *
509718 ATATTTTATTAAAGGCTTACAAAGTCTCTATTGAGC
1 ATATTTTAGCAAAAGCTTACAAAGTCTCTATTGAGA
509754 ATATTT
1 ATATTT
509760 CTTCAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 34 0.97
37 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (36 bp):
ATATTTTAGCAAAAGCTTACAAAGTCTCTATTGAGA
Found at i:510064 original size:36 final size:35
Alignment explanation
Indices: 509923--510166 Score: 163
Period size: 36 Copynumber: 6.8 Consensus size: 35
509913 TTTTGAAGAC
* *
509923 ATTTCATTAAAAACTTTTAAAGCTTCTTTTGTA-GAT
1 ATTTCATAAAAAAC-TTTAAAGCTTCTCTTG-AGGAT
* * ** *
509959 ATTTTATCAAAAACCTCCAAA-ATATCTCTTGAGGAT
1 ATTTCAT-AAAAAACTTTAAAGCT-TCTCTTGAGGAT
* * * * *
509995 ATTTTATTAAAAACCTCTAAAGCCTCTCTTGAGGAC
1 ATTTCA-TAAAAAACTTTAAAGCTTCTCTTGAGGAT
*
510031 ATTTCATAAAAAACTTTAAGAGCTTCTCCTGAGGAT
1 ATTTCATAAAAAACTTTAA-AGCTTCTCTTGAGGAT
* *
510067 ATTTCA-ACAAAACTTCTAAAGCTTCTTTTGAGGAT
1 ATTTCATAAAAAACTT-TAAAGCTTCTCTTGAGGAT
** * * *
510102 ATTTCACCAAAAACTTTCTAAA-TTTTTCTTGATGAT
1 ATTTCATAAAAAAC-TT-TAAAGCTTCTCTTGAGGAT
** *
510138 ATTTCATATGAAACTTTCAAAGCCTCTCT
1 ATTTCATAAAAAACTTT-AAAGCTTCTCT
510167 CAAGTATATT
Statistics
Matches: 164, Mismatches: 33, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
34 1 0.01
35 46 0.28
36 104 0.63
37 13 0.08
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.38
Consensus pattern (35 bp):
ATTTCATAAAAAACTTTAAAGCTTCTCTTGAGGAT
Found at i:510090 original size:35 final size:35
Alignment explanation
Indices: 509794--510143 Score: 160
Period size: 36 Copynumber: 9.8 Consensus size: 35
509784 CAACATAGAC
* * *
509794 CTTC-AAAGCCTCTCTTAAGGACT-TTTCATCAAAAA
1 CTTCTAAAGCTTCTCTTGAGGA-TATTTCAAC-AAAA
* * * * * *
509829 ATTCCAAAGCTTCTCTTAAGAATATTTTAGCAAAA
1 CTTCTAAAGCTTCTCTTGAGGATATTTCAACAAAA
* * * * *
509864 CCTCTAAAACCTCCCTTGAGAATA-TTCAATCAAAAA
1 CTTCTAAAGCTTCTCTTGAGGATATTTCAA-C-AAAA
* * * * * *
509900 TTTCTAAAACCTCTTTTGAAGACATTTCATTA-AAAA
1 CTTCTAAAGCTTCTCTTGAGGATATTTCA--ACAAAA
* * * *
509936 CTTTTAAAGCTTCTTTTGTA-GATATTTTATCAAAAA
1 CTTCTAAAGCTTCTCTTG-AGGATATTTCAAC-AAAA
* * * *
509972 CCTCCAAA-ATATCTCTTGAGGATATTTTATTA-AAAA
1 CTTCTAAAGCT-TCTCTTGAGGATATTTCA--ACAAAA
* * * *
510008 CCTCTAAAGCCTCTCTTGAGGACATTTCATAAAAAA
1 CTTCTAAAGCTTCTCTTGAGGATATTTCA-ACAAAA
*
510044 CTT-TAAGAGCTTCTCCTGAGGATATTTCAACAAAA
1 CTTCTAA-AGCTTCTCTTGAGGATATTTCAACAAAA
* *
510079 CTTCTAAAGCTTCTTTTGAGGATATTTCACCAAAAA
1 CTTCTAAAGCTTCTCTTGAGGATATTTCAAC-AAAA
* * *
510115 CTTTCTAAA-TTTTTCTTGATGATATTTCA
1 C-TTCTAAAGCTTCTCTTGAGGATATTTCA
510144 TATGAAACTT
Statistics
Matches: 244, Mismatches: 51, Indels: 39
0.73 0.15 0.12
Matches are distributed among these distances:
34 3 0.01
35 62 0.25
36 166 0.68
37 12 0.05
39 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (35 bp):
CTTCTAAAGCTTCTCTTGAGGATATTTCAACAAAA
Found at i:510122 original size:108 final size:106
Alignment explanation
Indices: 509798--510123 Score: 302
Period size: 108 Copynumber: 3.0 Consensus size: 106
509788 ATAGACCTTC
* * * * * *
509798 AAAGCCTCTCTTAAGGACTTTTCATCAAAAAA-TTCCAAAGCTTCTCTTAAGAATATTTTAGCAA
1 AAAGCCTCTCTTGAGGACATTTCAT-AAAAAACTT-TAAAGCTTCTCTTGAGGATATTTTAACAA
* * *
509862 AACCTCTAAAACCTCCCTTGAGAATA-TTCAATCAAAAA-TTTCT
64 AACCTCT-AAACTTCTCTTGAGGATATTTC-ATCAAAAACTTTCT
* * * * * *
509905 AAAACCTCTTTTGAAGACATTTCATTAAAAACTTTTAAAGCTTCTTTTGTA-GATATTTTATCAA
1 AAAGCCTCTCTTGAGGACATTTCATAAAAAAC-TTTAAAGCTTCTCTTG-AGGATATTTTAAC-A
* * * * *
509969 AAACCTCCAAAATATCTCTTGAGGATATTTTATTAAAAAC-CTCT
63 AAACCTCTAAACT-TCTCTTGAGGATATTTCATCAAAAACTTTCT
* *
510013 AAAGCCTCTCTTGAGGACATTTCATAAAAAACTTTAAGAGCTTCTCCTGAGGATATTTCAACAAA
1 AAAGCCTCTCTTGAGGACATTTCATAAAAAACTTTAA-AGCTTCTCTTGAGGATATTTTAACAAA
* * *
510078 ACTTCTAAAGCTTCTTTTGAGGATATTTCACCAAAAACTTTCT
65 ACCTCTAAA-CTTCTCTTGAGGATATTTCATCAAAAACTTTCT
510121 AAA
1 AAA
510124 TTTTTCTTGA
Statistics
Matches: 173, Mismatches: 35, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
106 5 0.03
107 81 0.47
108 85 0.49
109 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (106 bp):
AAAGCCTCTCTTGAGGACATTTCATAAAAAACTTTAAAGCTTCTCTTGAGGATATTTTAACAAAA
CCTCTAAACTTCTCTTGAGGATATTTCATCAAAAACTTTCT
Found at i:510139 original size:71 final size:70
Alignment explanation
Indices: 509879--510145 Score: 209
Period size: 72 Copynumber: 3.7 Consensus size: 70
509869 AAAACCTCCC
* * ** * * * *
509879 TTGAGAATA-TTCAATCAAAAATTTCTAAAACCTCTTTTGAAGACATTTCATTAAAAACTTTTAA
1 TTGAGGATATTTC-ATCAAAAACTTCT-AAATTTCTCTTGAGGATATTTCA-TAAAAACTTCTAA
509943 AGCTTCTT
63 AGCTTCTT
* * * * * *
509951 TTGTA-GATATTTTATCAAAAACCTCCAAAATATCTCTTGAGGATATTTTATTAAAAACCTCTAA
1 TTG-AGGATATTTCATCAAAAA-CTTCTAAATTTCTCTTGAGGATATTTCA-TAAAAACTTCTAA
* *
510015 AGCCTCTC
63 AGCTTCTT
* * * *
510023 TTGAGGACATTTCATAAAAAACTT-TAAGAGCTTCTCCTGAGGATATTTCA-ACAAAACTTCTAA
1 TTGAGGATATTTCATCAAAAACTTCTAA-A-TTTCTCTTGAGGATATTTCATA-AAAACTTCTAA
510086 AGCTTCTT
63 AGCTTCTT
* * *
510094 TTGAGGATATTTCACCAAAAACTTTCTAAATTTTTCTTGATGATATTTCATA
1 TTGAGGATATTTCATCAAAAAC-TTCTAAATTTCTCTTGAGGATATTTCATA
510146 TGAAACTTTC
Statistics
Matches: 151, Mismatches: 34, Indels: 20
0.74 0.17 0.10
Matches are distributed among these distances:
70 3 0.02
71 55 0.36
72 85 0.56
73 8 0.05
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (70 bp):
TTGAGGATATTTCATCAAAAACTTCTAAATTTCTCTTGAGGATATTTCATAAAAACTTCTAAAGC
TTCTT
Found at i:510757 original size:51 final size:51
Alignment explanation
Indices: 510697--511070 Score: 329
Period size: 51 Copynumber: 7.3 Consensus size: 51
510687 TTCACCTATG
* * * * *
510697 TATAAAGTCAAAGTCCACATTAGCTAACACTTGTATAAAGAGGCCAAGCCA
1 TATAAAGTCAAAGTCCACATTAGCTAGCACCTGTATAGAGAGGTCAAGCCT
* * * *
510748 TATAAAGTCAAAGTACACATTAGTTTGCACCTATATAGAGAGGTCAAGCCT
1 TATAAAGTCAAAGTCCACATTAGCTAGCACCTGTATAGAGAGGTCAAGCCT
* * * * * ** *
510799 TTTAGAGTTAAAATCCACACTAAATGGCACCTGTATAGAGAGGTCAAGCCT
1 TATAAAGTCAAAGTCCACATTAGCTAGCACCTGTATAGAGAGGTCAAGCCT
* * ** * * * * * *
510850 TATAGAGTCAAATTATACATTAGTTAGCACCTATAAAGGGAGGTTAAGCCC
1 TATAAAGTCAAAGTCCACATTAGCTAGCACCTGTATAGAGAGGTCAAGCCT
* * * * *
510901 TATAGAGACCATGTCCACATTAGCTAGCACCTATATAG-GAAGGTCAAGCCT
1 TATAAAGTCAAAGTCCACATTAGCTAGCACCTGTATAGAG-AGGTCAAGCCT
* * * * *
510952 TATAAAGTCTAAGTCCACATTAACTCGCA-CTGGTATAGGGAGGTCAAGCCC
1 TATAAAGTCAAAGTCCACATTAGCTAGCACCT-GTATAGAGAGGTCAAGCCT
* * ** *
511003 TGTAGAGTCAAAGTCCACATTAATTAGCACCCGTATAGAGAGGTCAAGCCT
1 TATAAAGTCAAAGTCCACATTAGCTAGCACCTGTATAGAGAGGTCAAGCCT
*
511054 TATAAAGTCCAAGTCCA
1 TATAAAGTCAAAGTCCA
511071 TGTTAGCTGG
Statistics
Matches: 257, Mismatches: 62, Indels: 8
0.79 0.19 0.02
Matches are distributed among these distances:
50 3 0.01
51 252 0.98
52 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (51 bp):
TATAAAGTCAAAGTCCACATTAGCTAGCACCTGTATAGAGAGGTCAAGCCT
Found at i:511070 original size:102 final size:102
Alignment explanation
Indices: 510697--511067 Score: 386
Period size: 102 Copynumber: 3.6 Consensus size: 102
510687 TTCACCTATG
* * * * * * *
510697 TATAAAGTCAAAGTCCACATTAGCTAACACTTGTATAAAGAGGCCAAGCCATATAAAGTCAAAGT
1 TATAGAGTCAAAGTCCACATTAACTAGCACCTGTATAGAGAGGTCAAGCCTTATAAAGTCAAAGT
* * *
510762 ACACATTAGTTTGCACCTATATAGAGAGGTCAAGCCT
66 ACACATTAGTTAGCACCTATATAGGGAGGTCAAGCCC
* * * * * * * *
510799 TTTAGAGTTAAAATCCACACTAAATGGCACCTGTATAGAGAGGTCAAGCCTTATAGAGTCAAATT
1 TATAGAGTCAAAGTCCACATTAACTAGCACCTGTATAGAGAGGTCAAGCCTTATAAAGTCAAAGT
* * *
510864 ATACATTAGTTAGCACCTATAAAGGGAGGTTAAGCCC
66 ACACATTAGTTAGCACCTATATAGGGAGGTCAAGCCC
* * * * * *
510901 TATAGAGACCATGTCCACATTAGCTAGCACCTATATAG-GAAGGTCAAGCCTTATAAAGTCTAAG
1 TATAGAGTCAAAGTCCACATTAACTAGCACCTGTATAGAG-AGGTCAAGCCTTATAAAGTCAAAG
* ** * *
510965 TCCACATTAACTCGCA-CTGGTATAGGGAGGTCAAGCCC
65 TACACATTAGTTAGCACCT-ATATAGGGAGGTCAAGCCC
* * * *
511003 TGTAGAGTCAAAGTCCACATTAATTAGCACCCGTATAGAGAGGTCAAGCCTTATAAAGTCCAAGT
1 TATAGAGTCAAAGTCCACATTAACTAGCACCTGTATAGAGAGGTCAAGCCTTATAAAGTCAAAGT
511068 CCATGTTAGC
Statistics
Matches: 214, Mismatches: 52, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
101 3 0.01
102 210 0.98
103 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (102 bp):
TATAGAGTCAAAGTCCACATTAACTAGCACCTGTATAGAGAGGTCAAGCCTTATAAAGTCAAAGT
ACACATTAGTTAGCACCTATATAGGGAGGTCAAGCCC
Found at i:511078 original size:153 final size:153
Alignment explanation
Indices: 510697--511070 Score: 403
Period size: 153 Copynumber: 2.4 Consensus size: 153
510687 TTCACCTATG
* * * * * * *
510697 TATAAAGTCAAAGTCCACATTAGCTAACACTTGTATAAAGAGGCCAAGCCATATAAAGTCAAAGT
1 TATAGAGTCAAAGTCCACATTAGTTAGCACCTGTATAGAGAGGTCAAGCCATATAAAGTCCAAGT
* * * * * *
510762 ACACATTAGTTTGCACCTATATAGAGAGGTCAAGCCTTTTAGAGTTAAAATCCACACTAAATGGC
66 CCACATTAGCTAGCACCTATATAGAGAGGTCAAGCCTTATAAAGTTAAAATCCACACTAAATCGC
*
510827 ACCTGTATAGAGAGGTCAAGCCT
131 ACCTGTATAGAGAGGTCAAGCCC
* ** * * * * * * * *
510850 TATAGAGTCAAATTATACATTAGTTAGCACCTATAAAGGGAGGTTAAGCCCTATAGAGACCATGT
1 TATAGAGTCAAAGTCCACATTAGTTAGCACCTGTATAGAGAGGTCAAGCCATATAAAGTCCAAGT
* * *
510915 CCACATTAGCTAGCACCTATATAG-GAAGGTCAAGCCTTATAAAGTCT-AAGTCCACATTAACTC
66 CCACATTAGCTAGCACCTATATAGAG-AGGTCAAGCCTTATAAAGT-TAAAATCCACACTAAATC
*
510978 GCA-CTGGTATAGGGAGGTCAAGCCC
129 GCACCT-GTATAGAGAGGTCAAGCCC
* * * *
511003 TGTAGAGTCAAAGTCCACATTAATTAGCACCCGTATAGAGAGGTCAAGCCTTATAAAGTCCAAGT
1 TATAGAGTCAAAGTCCACATTAGTTAGCACCTGTATAGAGAGGTCAAGCCATATAAAGTCCAAGT
511068 CCA
66 CCA
511071 TGTTAGCTGG
Statistics
Matches: 175, Mismatches: 43, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
152 3 0.02
153 171 0.98
154 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (153 bp):
TATAGAGTCAAAGTCCACATTAGTTAGCACCTGTATAGAGAGGTCAAGCCATATAAAGTCCAAGT
CCACATTAGCTAGCACCTATATAGAGAGGTCAAGCCTTATAAAGTTAAAATCCACACTAAATCGC
ACCTGTATAGAGAGGTCAAGCCC
Found at i:511960 original size:22 final size:22
Alignment explanation
Indices: 511932--511982 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
511922 TAAACAAAAA
*
511932 GAAAAAGCTTTCCTTTTTGGCT
1 GAAAAAGCTCTCCTTTTTGGCT
511954 GAAAAAGCTCTCCTTTTTGGCT
1 GAAAAAGCTCTCCTTTTTGGCT
*
511976 AAAAAAG
1 GAAAAAG
511983 ATTGTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (22 bp):
GAAAAAGCTCTCCTTTTTGGCT
Found at i:517122 original size:21 final size:21
Alignment explanation
Indices: 517089--517133 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
517079 TTGCAAGTTG
*
517089 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
517111 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
517131 AAA
1 AAA
517134 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:521060 original size:20 final size:20
Alignment explanation
Indices: 520981--521060 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
520971 AATGTCCAAA
*
520981 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
521001 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
521026 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
521046 TTGTATCGATACATT
1 ATGTATCGATACATT
521061 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:521064 original size:13 final size:13
Alignment explanation
Indices: 521046--521084 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
521036 ACATTTTTCT
521046 TTGTATCGATACA
1 TTGTATCGATACA
521059 TTGTATCGATACA
1 TTGTATCGATACA
*
521072 CTGTATCGATACA
1 TTGTATCGATACA
521085 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:524835 original size:77 final size:77
Alignment explanation
Indices: 524724--524922 Score: 213
Period size: 77 Copynumber: 2.6 Consensus size: 77
524714 GTAAAATAAG
* * * * *
524724 AAAATTAAGTAACTTGGTAACTAACAGATTTAAATATAATAAAATGCATGAATAATAGTTTTT-A
1 AAAATTAAGTAATTTGATAACTAATAGATGTAAATATAATAAAA-GAATGAATAATAGTTTTTAA
**
524788 T-TTAAAAGAGTAA
65 TAGAAAAAGAGT-A
* * * *
524801 AAAATTAAGTAATTTGATAAATAATAGATGTAAATATAATTAAAAGAATTAATATTATTTTTTAA
1 AAAATTAAGTAATTTGATAACTAATAGATGTAAATATAA-TAAAAGAATGAATAATAGTTTTTAA
524866 TAGAAAAAGAGTA
65 TAGAAAAAGAGTA
* * * * *
524879 AAAATAAAATAATTTGATATCTAATATATGTAAAAATAATAAAA
1 AAAATTAAGTAATTTGATAACTAATAGATGTAAATATAATAAAA
524923 AAACATTGAC
Statistics
Matches: 102, Mismatches: 17, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
77 53 0.52
78 41 0.40
79 8 0.08
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.34
Consensus pattern (77 bp):
AAAATTAAGTAATTTGATAACTAATAGATGTAAATATAATAAAAGAATGAATAATAGTTTTTAAT
AGAAAAAGAGTA
Found at i:525193 original size:2 final size:2
Alignment explanation
Indices: 525150--525183 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
525140 AAATCTTTTT
525150 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
525184 GTTAATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:526438 original size:5 final size:5
Alignment explanation
Indices: 526428--526479 Score: 65
Period size: 5 Copynumber: 10.6 Consensus size: 5
526418 GTAAATTTTT
526428 TTATA TTATA -TATA TTATA TTATA TTATA CGTTATA TTATA -TATA -TATA
1 TTATA TTATA TTATA TTATA TTATA TTATA --TTATA TTATA TTATA TTATA
526477 TTA
1 TTA
526480 ATATAAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
4 12 0.28
5 26 0.60
7 5 0.12
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (5 bp):
TTATA
Found at i:526439 original size:2 final size:2
Alignment explanation
Indices: 526429--526523 Score: 53
Period size: 2 Copynumber: 51.0 Consensus size: 2
526419 TAAATTTTTT
**
526429 TA TA T- TA TA TA TA T- TA TA T- TA TA T- TA TA CG T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
526465 TA TA TA TA TA TA T- TA -A TA TA AA TA TA TA TA AA AA AA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
526505 TA TA TA GTG TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA
526524 ACATATAATA
Statistics
Matches: 74, Mismatches: 10, Indels: 18
0.73 0.10 0.18
Matches are distributed among these distances:
1 8 0.11
2 65 0.88
3 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:526462 original size:12 final size:10
Alignment explanation
Indices: 526428--526479 Score: 65
Period size: 9 Copynumber: 5.3 Consensus size: 10
526418 GTAAATTTTT
526428 TTATATTATA
1 TTATATTATA
526438 -TATATTATA
1 TTATATTATA
526447 TTATATTATA
1 TTATATTATA
526457 CGTTATATTATA
1 --TTATATTATA
526469 -TATA-TATA
1 TTATATTATA
526477 TTA
1 TTA
526480 ATATAAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
8 4 0.11
9 15 0.39
10 9 0.24
12 10 0.26
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (10 bp):
TTATATTATA
Found at i:530169 original size:89 final size:89
Alignment explanation
Indices: 530011--530714 Score: 695
Period size: 89 Copynumber: 7.9 Consensus size: 89
530001 TTTGTCGTAT
* * * * *
530011 CATTAGTCAAATATTTTTTATCGTGTCAGAAAGAATCTAATACCCGCATACATCTGTCATATCTT
1 CATTAGTCAAATATTTTATGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
*
530076 TTGGGTTTCAAGAAATTTATTAGG
66 TCGGGTTTCAAGAAATTTATTAGG
*
530100 CATTAGTCAAATATTTTATGTCGTGTCAGAAAGAATTTGATACCCGCATGCATCTGTCACATCTG
1 CATTAGTCAAATATTTTATGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCT-
* * *
530165 TT-GGGTTCCAAAAAATTTATTAAG
65 TTCGGGTTTCAAGAAATTTATTAGG
* * * * * * * * * *
530189 CATTAGTTATATATTTTCTATCATATCA-TAAGAAACCTGATACCCACATGCATCTATCACATCT
1 CATTAGTCAAATATTTTATGTCGTGTCAGAAAG-AATCTGATACCCGCATGCATCTGTCACATCT
* * * * * *
530253 TTCAGCTTCCCACAAATTTATTAAG
65 TTCGGGTTTCAAGAAATTTATTAGG
* * * * *
530278 CATTAATCAAATATTTTTTGTCATGTCAGAAAAAATCTGATATCCGCATGCATCTGTCACATCTT
1 CATTAGTCAAATATTTTATGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
* * *
530343 TCGGGTTTTAAAAAAATTATTAGG
66 TCGGGTTTCAAGAAATTTATTAGG
* * * ** *
530367 CATTAGTCAAATATTTTATGTTGTGTCAGAAGGAATCTGCTACCCGCATATATCTGTCACATTTT
1 CATTAGTCAAATATTTTATGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
*
530432 TCGAGTTTCAAGAAATTTATTAGG
66 TCGGGTTTCAAGAAATTTATTAGG
* * * * * ** * *
530456 CATTAGTCATATATTTTTTGTCATGTCAGAATGAACCT-ATTATTCGCATGCGTCTGTCACATTT
1 CATTAGTCAAATATTTTATGTCGTGTCAGAAAGAATCTGA-TACCCGCATGCATCTGTCACATCT
* *
530520 TTCGAG-TTCGAAGAAATTTATTAGA
65 TTCGGGTTTC-AAGAAATTTATTAGG
* *
530545 CATTAATCAAATA-TTTATGTCGTGTCA-AAAGGAATCTGATACCCGCATGCATCTGTCACGTCT
1 CATTAGTCAAATATTTTATGTCGTGTCAGAAA-GAATCTGATACCCGCATGCATCTGTCACATCT
* * ***
530608 TTC-GGATTCTAAGAATTTTATTTTA
65 TTCGGGTTTC-AAGAAATTTATTAGG
* * * * * *
530633 CATTAGTCAAATATTTTCTGTCTTGTCAGAAAAAATCTGATATCCGCATGTATCTGTCACATTTT
1 CATTAGTCAAATATTTTATGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
* *
530698 TCGAGTTCCAA-AAATTT
66 TCGGGTTTCAAGAAATTT
530715 TTTATATTAA
Statistics
Matches: 503, Mismatches: 100, Indels: 25
0.80 0.16 0.04
Matches are distributed among these distances:
87 3 0.01
88 79 0.16
89 411 0.82
90 10 0.02
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (89 bp):
CATTAGTCAAATATTTTATGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
TCGGGTTTCAAGAAATTTATTAGG
Found at i:530539 original size:267 final size:266
Alignment explanation
Indices: 530011--530714 Score: 848
Period size: 267 Copynumber: 2.6 Consensus size: 266
530001 TTTGTCGTAT
* * * * *
530011 CATTAGTCAAATATTTTTTATCGTGTCAGAAAGAATCTAATACCCGCATACATCTGTCATATCTT
1 CATTAATCAAATATTTTTTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
* * * *
530076 TTGGGTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTATGTCGTGTCAGAAAGAATTTGAT
66 TCGGGTTTTAAGAAATTTATTAGGCATTAGTCAAATATTTTATGTTGTGTCAGAAAGAATCTGAT
* * * *
530141 ACCCGCATGCATCTGTCACATCTGTT-GGGTTCCAAAAAATTTATTAAGCATTAGTTATATATTT
131 ACCCGCATGTATCTGTCACAT-TTTTCGAGTTCC-AAAAATTTATTAAGCATTAGTCATATATTT
* *
530205 TCTATCATATCATAAGAAACCTGATACCCACATGCATCTATCACATCTTTCAGCTTCCCACAAAT
194 TCTATCATATCAGAAGAAACCTGATACCCACATGCATCTATCACATCTTTCAGCTTCCAACAAAT
530270 TTATTA-A
259 TTATTAGA
* * *
530277 GCATTAATCAAATATTTTTTGTCATGTCAGAAAAAATCTGATATCCGCATGCATCTGTCACATCT
1 -CATTAATCAAATATTTTTTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCT
* * * *
530342 TTCGGGTTTTAAAAAAATTATTAGGCATTAGTCAAATATTTTATGTTGTGTCAGAAGGAATCTGC
65 TTCGGGTTTTAAGAAATTTATTAGGCATTAGTCAAATATTTTATGTTGTGTCAGAAAGAATCTGA
* * *
530407 TACCCGCATATATCTGTCACATTTTTCGAGTTTCAAGAAATTTATTAGGCATTAGTCATATATTT
130 TACCCGCATGTATCTGTCACATTTTTCGAGTTCCAA-AAATTTATTAAGCATTAGTCATATATTT
* * * ** * * * * * *
530472 TTTGTCATGTCAGAATG-AACCT-ATTATTCGCATGCGTCTGTCACATTTTTCGAG-TTCGAAGA
194 TCTATCATATCAGAA-GAAACCTGA-TACCCACATGCATCTATCACATCTTTC-AGCTTCCAACA
530534 AATTTATTAGA
256 AATTTATTAGA
* *
530545 CATTAATCAAATA-TTTATGTCGTGTCA-AAAGGAATCTGATACCCGCATGCATCTGTCACGTCT
1 CATTAATCAAATATTTTTTGTCGTGTCAGAAA-GAATCTGATACCCGCATGCATCTGTCACATCT
* * * *** * *
530608 TTCGGATTCTAAGAATTTTATTTTACATTAGTCAAATATTTTCTGTCT-TGTCAGAAAAAATCTG
65 TTCGGGTTTTAAGAAATTTATTAGGCATTAGTCAAATATTTTATGT-TGTGTCAGAAAGAATCTG
*
530672 ATATCCGCATGTATCTGTCACATTTTTCGAGTTCCAAAAATTT
129 ATACCCGCATGTATCTGTCACATTTTTCGAGTTCCAAAAATTT
530715 TTTATATTAA
Statistics
Matches: 373, Mismatches: 56, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
265 9 0.02
266 131 0.35
267 229 0.61
268 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (266 bp):
CATTAATCAAATATTTTTTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
TCGGGTTTTAAGAAATTTATTAGGCATTAGTCAAATATTTTATGTTGTGTCAGAAAGAATCTGAT
ACCCGCATGTATCTGTCACATTTTTCGAGTTCCAAAAATTTATTAAGCATTAGTCATATATTTTC
TATCATATCAGAAGAAACCTGATACCCACATGCATCTATCACATCTTTCAGCTTCCAACAAATTT
ATTAGA
Found at i:530821 original size:7 final size:7
Alignment explanation
Indices: 530806--530874 Score: 61
Period size: 7 Copynumber: 9.6 Consensus size: 7
530796 AATAAATAAA
530806 ATATTAT
1 ATATTAT
*
530813 ATGTTAT
1 ATATTAT
530820 ATATTAT
1 ATATTAT
530827 ATTATTAT
1 A-TATTAT
530835 ATATTAT
1 ATATTAT
530842 -TA-TAT
1 ATATTAT
530847 ATTATATAT
1 A-TAT-TAT
* *
530856 GTTTTAT
1 ATATTAT
530863 ATATTTAT
1 ATA-TTAT
530871 ATAT
1 ATAT
530875 AACATATAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
5 3 0.06
6 2 0.04
7 26 0.52
8 16 0.32
9 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (7 bp):
ATATTAT
Found at i:530875 original size:10 final size:11
Alignment explanation
Indices: 530810--530875 Score: 70
Period size: 10 Copynumber: 6.4 Consensus size: 11
530800 AATAAAATAT
*
530810 TATATGTTATA
1 TATATATTATA
530821 TATTATATTAT-
1 TA-TATATTATA
530832 TATATATTAT-
1 TATATATTATA
530842 TATATATTATA
1 TATATATTATA
*
530853 TATGT-TT-TA
1 TATATATTATA
530862 TATAT-TTATA
1 TATATATTATA
530872 TATA
1 TATA
530876 ACATATAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
9 8 0.16
10 26 0.53
11 8 0.16
12 7 0.14
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
TATATATTATA
Found at i:530932 original size:9 final size:9
Alignment explanation
Indices: 530918--530982 Score: 55
Period size: 9 Copynumber: 7.6 Consensus size: 9
530908 AGTTTTTTTT
530918 TTTAATTTA
1 TTTAATTTA
*
530927 TTTAATTTT
1 TTTAATTTA
**
530936 TTTAAAATA
1 TTTAATTTA
*
530945 TTTAATATA
1 TTTAATTTA
*
530954 -TAAATTT-
1 TTTAATTTA
*
530961 TTTTATTT-
1 TTTAATTTA
530969 TTTAATTTA
1 TTTAATTTA
530978 TTTAA
1 TTTAA
530983 ATAAATTATA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
8 17 0.39
9 27 0.61
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTAATTTA
Found at i:533459 original size:2 final size:2
Alignment explanation
Indices: 533452--533483 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
533442 TAGATAACTC
533452 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
533484 GATCCATTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:535225 original size:2 final size:2
Alignment explanation
Indices: 535218--535254 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
535208 TTAAATATTT
535218 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
535255 TCATTCTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:535887 original size:2 final size:2
Alignment explanation
Indices: 535880--535922 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
535870 CTTATTCTTT
535880 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
535922 T
1 T
535923 GTTAAAACTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:537406 original size:26 final size:28
Alignment explanation
Indices: 537377--537431 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
537367 GTTTTAAATA
537377 ATTTT-AT-AATTATTTATATAATTATT
1 ATTTTGATAAATTATTTATATAATTATT
* *
537403 ATTTTGATCAAATTATTTATGTTATTATT
1 ATTTTGAT-AAATTATTTATATAATTATT
537432 TAATATTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 2 0.08
29 17 0.71
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (28 bp):
ATTTTGATAAATTATTTATATAATTATT
Found at i:537507 original size:21 final size:19
Alignment explanation
Indices: 537481--537520 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
537471 TGTAGTATTA
537481 TTTTTTAAATATAATAATAAT
1 TTTTTTAAATA-AA-AATAAT
537502 TTTTTTAAATAAAAATAAT
1 TTTTTTAAATAAAAATAAT
537521 CGTATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 2 0.11
21 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTTTAAATAAAAATAAT
Found at i:537513 original size:19 final size:20
Alignment explanation
Indices: 537480--537520 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
537470 ATGTAGTATT
*
537480 ATTTTTTAAATATAATAATA
1 ATTTTTTAAATATAAAAATA
*
537500 ATTTTTTTAA-ATAAAAATA
1 ATTTTTTAAATATAAAAATA
537519 AT
1 AT
537521 CGTATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTTTAAATATAAAAATA
Found at i:539943 original size:19 final size:20
Alignment explanation
Indices: 539908--539947 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
539898 GATTGTTTTC
539908 TTCCATCTCATAAATCTTAT
1 TTCCATCTCATAAATCTTAT
539928 TTCCATCTCA-AAATCTTAT
1 TTCCATCTCATAAATCTTAT
539947 T
1 T
539948 CTCAGATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (20 bp):
TTCCATCTCATAAATCTTAT
Found at i:548848 original size:33 final size:33
Alignment explanation
Indices: 548811--548875 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
548801 TAAAATATAT
548811 AAAA-TAAAA-AATTATTATTATTTAATAGAATTG
1 AAAATTAAAATAA-TATTATTA-TTAATAGAATTG
*
548844 AAAATTAAAATAATATTATTATTAATATAATT
1 AAAATTAAAATAATATTATTATTAATAGAATT
548876 ATTTATAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 14 0.48
34 13 0.45
35 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (33 bp):
AAAATTAAAATAATATTATTATTAATAGAATTG
Found at i:549346 original size:21 final size:20
Alignment explanation
Indices: 549322--549369 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
549312 AGCTTACAAG
549322 TTTAATTAAATTTTGTTAATT
1 TTTAATTAAATTTT-TTAATT
*
549343 TTTAATTTATATTTTTTAATT
1 TTTAA-TTAAATTTTTTAATT
549364 TTTAAT
1 TTTAAT
549370 AGTTTTAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.64
22 8 0.32
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTAATTAAATTTTTTAATT
Found at i:549998 original size:32 final size:32
Alignment explanation
Indices: 549959--550019 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
549949 ATAGAAAAAG
549959 GTATCAAA-ATTTATATAAA-ATAAACTATTAAC
1 GTATCAAATA-TTATATAAATATAAA-TATTAAC
549991 GTATCAAATATTATATAAATATAAATATT
1 GTATCAAATATTATATAAATATAAATATT
550020 TTAAATATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (32 bp):
GTATCAAATATTATATAAATATAAATATTAAC
Found at i:550161 original size:29 final size:29
Alignment explanation
Indices: 550127--550202 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 29
550117 AACATAAATG
*
550127 ATATAAAAAAATAATTAAAATACGATATA
1 ATATAAAAAAATAATTAAAATACAATATA
* *
550156 ATAT--AAAAATAATTTAAATATAATATA
1 ATATAAAAAAATAATTAAAATACAATATA
* * *
550183 A-ATAATAAAATTATAAAAAT
1 ATATAAAAAAATAATTAAAAT
550203 TTAAATTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 2 0.05
27 21 0.55
28 11 0.29
29 4 0.11
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (29 bp):
ATATAAAAAAATAATTAAAATACAATATA
Found at i:550187 original size:20 final size:20
Alignment explanation
Indices: 550151--550265 Score: 64
Period size: 16 Copynumber: 6.3 Consensus size: 20
550141 TTAAAATACG
550151 ATATAATATAAAAATAATTTAA
1 ATATAATAT--AAATAATTTAA
550173 ATATAATATAAATAA--TAA
1 ATATAATATAAATAATTTAA
550191 A-AT--TATAAA-AATTTAA
1 ATATAATATAAATAATTTAA
*
550207 AT-TAA-ATAAATTA-TT-A
1 ATATAATATAAATAATTTAA
*
550223 ATAT-AT-T-AA-AATTTAT
1 ATATAATATAAATAATTTAA
550239 ATA-AATATATAAT-ATATTAA
1 ATATAATATA-AATAAT-TTAA
550259 ATATAAT
1 ATATAAT
550266 TATGATAATC
Statistics
Matches: 72, Mismatches: 4, Indels: 35
0.65 0.04 0.32
Matches are distributed among these distances:
14 3 0.04
15 10 0.14
16 15 0.21
17 11 0.15
18 5 0.07
19 4 0.06
20 12 0.17
21 3 0.04
22 9 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATAATATAAATAATTTAA
Found at i:551132 original size:10 final size:9
Alignment explanation
Indices: 551103--551136 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
551093 ATCAATAAAT
*
551103 TATTTCTAA
1 TATTTTTAA
551112 TATTTTTAA
1 TATTTTTAA
551121 TATTTATTAA
1 TATTT-TTAA
551131 TATTTT
1 TATTTT
551137 AAAATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (9 bp):
TATTTTTAA
Found at i:551148 original size:19 final size:19
Alignment explanation
Indices: 551134--551174 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
551124 TTATTAATAT
551134 TTTAAAAT-TAAATTAAAA
1 TTTAAAATATAAATTAAAA
*
551152 TTTAAAATATAAAAATAAAA
1 TTTAAAATAT-AAATTAAAA
551172 TTT
1 TTT
551175 TTTTCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTAAAATATAAATTAAAA
Found at i:551708 original size:2 final size:2
Alignment explanation
Indices: 551701--551732 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
551691 GCGTCCCTTG
551701 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
551733 GTCTGTGGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:555321 original size:311 final size:311
Alignment explanation
Indices: 554758--555385 Score: 1256
Period size: 311 Copynumber: 2.0 Consensus size: 311
554748 GGCTACCCCA
554758 GTTGCTGTGTAAGATCAAATCAATTTTTCCCCACCCTGTTTACTTTATTTGTTCGGTTTTGTAAT
1 GTTGCTGTGTAAGATCAAATCAATTTTTCCCCACCCTGTTTACTTTATTTGTTCGGTTTTGTAAT
554823 CGAGAAATGAAACGTTTTTGGAAGAAATGAGTTCTTGTTGTAAATGCACACGTTACTTCAAAAGA
66 CGAGAAATGAAACGTTTTTGGAAGAAATGAGTTCTTGTTGTAAATGCACACGTTACTTCAAAAGA
554888 AGGGGGCCATTTCCACCTCTTCCTTTCTTGCTTGTGCCTTAAGTTGCCAGAAGAGTGTTAATAAT
131 AGGGGGCCATTTCCACCTCTTCCTTTCTTGCTTGTGCCTTAAGTTGCCAGAAGAGTGTTAATAAT
554953 GGGCAGACAGAACCTTGAGAATGATTCCAAATAAATTGGTTTATTTTATCAAAAGCATTTTCTTG
196 GGGCAGACAGAACCTTGAGAATGATTCCAAATAAATTGGTTTATTTTATCAAAAGCATTTTCTTG
555018 CATTATGCTTATATTGTTCTGAATGTCCTTTTTCTTATACTTTTATTCTAT
261 CATTATGCTTATATTGTTCTGAATGTCCTTTTTCTTATACTTTTATTCTAT
555069 GTTGCTGTGTAAGATCAAATCAATTTTTCCCCACCCTGTTTACTTTATTTGTTCGGTTTTGTAAT
1 GTTGCTGTGTAAGATCAAATCAATTTTTCCCCACCCTGTTTACTTTATTTGTTCGGTTTTGTAAT
555134 CGAGAAATGAAACGTTTTTGGAAGAAATGAGTTCTTGTTGTAAATGCACACGTTACTTCAAAAGA
66 CGAGAAATGAAACGTTTTTGGAAGAAATGAGTTCTTGTTGTAAATGCACACGTTACTTCAAAAGA
555199 AGGGGGCCATTTCCACCTCTTCCTTTCTTGCTTGTGCCTTAAGTTGCCAGAAGAGTGTTAATAAT
131 AGGGGGCCATTTCCACCTCTTCCTTTCTTGCTTGTGCCTTAAGTTGCCAGAAGAGTGTTAATAAT
555264 GGGCAGACAGAACCTTGAGAATGATTCCAAATAAATTGGTTTATTTTATCAAAAGCATTTTCTTG
196 GGGCAGACAGAACCTTGAGAATGATTCCAAATAAATTGGTTTATTTTATCAAAAGCATTTTCTTG
555329 CATTATGCTTATATTGTTCTGAATGTCCTTTTTCTTATACTTTTATTCTAT
261 CATTATGCTTATATTGTTCTGAATGTCCTTTTTCTTATACTTTTATTCTAT
555380 GTTGCT
1 GTTGCT
555386 CTGACTGTTC
Statistics
Matches: 317, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
311 317 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (311 bp):
GTTGCTGTGTAAGATCAAATCAATTTTTCCCCACCCTGTTTACTTTATTTGTTCGGTTTTGTAAT
CGAGAAATGAAACGTTTTTGGAAGAAATGAGTTCTTGTTGTAAATGCACACGTTACTTCAAAAGA
AGGGGGCCATTTCCACCTCTTCCTTTCTTGCTTGTGCCTTAAGTTGCCAGAAGAGTGTTAATAAT
GGGCAGACAGAACCTTGAGAATGATTCCAAATAAATTGGTTTATTTTATCAAAAGCATTTTCTTG
CATTATGCTTATATTGTTCTGAATGTCCTTTTTCTTATACTTTTATTCTAT
Found at i:556356 original size:2 final size:2
Alignment explanation
Indices: 556349--556379 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
556339 ATTTCAACCT
556349 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
556380 GTTCACGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:560727 original size:6 final size:7
Alignment explanation
Indices: 560710--560735 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
560700 GAAATCATTA
560710 AAAAAAT
1 AAAAAAT
560717 AAAAAAT
1 AAAAAAT
560724 AAAAAAT
1 AAAAAAT
560731 AAAAA
1 AAAAA
560736 CACAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:561948 original size:11 final size:11
Alignment explanation
Indices: 561932--561958 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
561922 TGTATGATTA
561932 TATTTATATTT
1 TATTTATATTT
561943 TATTTATATTT
1 TATTTATATTT
561954 TATTT
1 TATTT
561959 TTTATATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TATTTATATTT
Found at i:562230 original size:26 final size:27
Alignment explanation
Indices: 562200--562250 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
562190 ATAGTTATTC
562200 AATTATGAAG-TTTATTTTTATTAATT
1 AATTATGAAGTTTTATTTTTATTAATT
***
562226 AATTATTTTGTTTTATTTTTATTAA
1 AATTATGAAGTTTTATTTTTATTAA
562251 GAATAAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (27 bp):
AATTATGAAGTTTTATTTTTATTAATT
Found at i:562976 original size:25 final size:23
Alignment explanation
Indices: 562948--562993 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
562938 TACTTTTAAA
562948 TAAAAATAACATAATATATTAATAT
1 TAAAAATAACAT-ATA-ATTAATAT
* *
562973 TAAAATTAATATATAATTAAT
1 TAAAAATAACATATAATTAAT
562994 TAAAAAAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 3 0.16
25 10 0.53
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAAAATAACATATAATTAATAT
Found at i:563210 original size:17 final size:18
Alignment explanation
Indices: 563176--563210 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
563166 AATTTGATAA
*
563176 TAATTAAAGATAATTTTG
1 TAATTAAAAATAATTTTG
563194 TAATTAAAAAT-ATTTTG
1 TAATTAAAAATAATTTTG
563211 AGTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (18 bp):
TAATTAAAAATAATTTTG
Found at i:563779 original size:13 final size:13
Alignment explanation
Indices: 563761--563795 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
563751 AAATTTATTT
563761 TTTATAATTAAAA
1 TTTATAATTAAAA
*
563774 TTTATAAATAAAA
1 TTTATAATTAAAA
*
563787 ATTATAATT
1 TTTATAATT
563796 TAATAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATAATTAAAA
Found at i:563811 original size:15 final size:16
Alignment explanation
Indices: 563784--563813 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
563774 TTTATAAATA
563784 AAAATTATAATTTAAT
1 AAAATTATAATTTAAT
563800 AAAATT-TAATTTAA
1 AAAATTATAATTTAA
563814 AATTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATTATAATTTAAT
Found at i:564032 original size:12 final size:12
Alignment explanation
Indices: 564015--564045 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
564005 TAATATTTAC
564015 ATATTATATTTT
1 ATATTATATTTT
564027 ATATTATATTTT
1 ATATTATATTTT
564039 ATTATTA
1 A-TATTA
564046 ATATAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:564074 original size:26 final size:28
Alignment explanation
Indices: 564041--564101 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 28
564031 TATATTTTAT
*
564041 TATT-AATATAATATAATTATTTAAT-A
1 TATTAAATATAATATAATTAATTAATCA
*
564067 TA-TAAATATGATATAATTAATTAATCA
1 TATTAAATATAATATAATTAATTAATCA
564094 TATTAAAT
1 TATTAAAT
564102 TTTAAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 1 0.03
26 21 0.70
27 3 0.10
28 5 0.17
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
TATTAAATATAATATAATTAATTAATCA
Found at i:564180 original size:14 final size:15
Alignment explanation
Indices: 564152--564191 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
564142 CGTAATATAA
564152 TAAAATTAATACATT
1 TAAAATTAATACATT
564167 TAAAATTAAT-CATT
1 TAAAATTAATACATT
*
564181 TAAATTTAATA
1 TAAAATTAATA
564192 TAATAAGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAATTAATACATT
Found at i:564376 original size:19 final size:20
Alignment explanation
Indices: 564354--564398 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
564344 TAATTTATTA
**
564354 AAATTATTATATTTTA-AAT
1 AAATTATTATATAATATAAT
*
564373 AAATAATTATATAATATAAT
1 AAATTATTATATAATATAAT
564393 AAATTA
1 AAATTA
564399 ATCTTGTCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTATTATATAATATAAT
Found at i:569146 original size:14 final size:14
Alignment explanation
Indices: 569127--569155 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
569117 TTTGCATGTT
569127 AAACTTGAAAGTAA
1 AAACTTGAAAGTAA
569141 AAACTTGAAAGTAA
1 AAACTTGAAAGTAA
569155 A
1 A
569156 TTTTTTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
AAACTTGAAAGTAA
Found at i:569966 original size:41 final size:41
Alignment explanation
Indices: 569920--570004 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
569910 GGTGATTGGT
* *
569920 TTTGAATTTTAATATAGTTAATGATTAAGATTGGTATGTGA
1 TTTGAATTTGAATATAGTTAATAATTAAGATTGGTATGTGA
* * *
569961 TTTGAATTTGAGTATAGTTCATAATTAAGATTGGTCTGTGA
1 TTTGAATTTGAATATAGTTAATAATTAAGATTGGTATGTGA
570002 TTT
1 TTT
570005 TTAAATATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (41 bp):
TTTGAATTTGAATATAGTTAATAATTAAGATTGGTATGTGA
Found at i:571200 original size:15 final size:14
Alignment explanation
Indices: 571163--571205 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
571153 TAAAAATTTA
571163 AATAAACATATTAAT
1 AATAAA-ATATTAAT
571178 AA-AAAATATGTAAT
1 AATAAAATAT-TAAT
571192 AATAAAATA-TAAT
1 AATAAAATATTAAT
571205 A
1 A
571206 TTATTAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 9 0.35
14 9 0.35
15 8 0.31
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (14 bp):
AATAAAATATTAAT
Found at i:571242 original size:3 final size:3
Alignment explanation
Indices: 571234--571259 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
571224 AATATTAATA
571234 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
571260 ACCAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:574419 original size:14 final size:14
Alignment explanation
Indices: 574400--574427 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
574390 AACACATCTT
574400 TTCTTTAACAACAA
1 TTCTTTAACAACAA
574414 TTCTTTAACAACAA
1 TTCTTTAACAACAA
574428 CTTGATCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (14 bp):
TTCTTTAACAACAA
Found at i:575956 original size:19 final size:19
Alignment explanation
Indices: 575929--575965 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
575919 AGCTAGTGGC
575929 GTATCTACAAACTTTGTTG
1 GTATCTACAAACTTTGTTG
*
575948 GTATTTACAAACTTTGTT
1 GTATCTACAAACTTTGTT
575966 ACCTAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.46
Consensus pattern (19 bp):
GTATCTACAAACTTTGTTG
Found at i:578670 original size:97 final size:97
Alignment explanation
Indices: 578521--578742 Score: 288
Period size: 97 Copynumber: 2.3 Consensus size: 97
578511 AAAATGGGAC
* * * * * *
578521 TGGAGTA-CCCCCTCGAAGGAATGTGGTTAGAGTATCATTGACGATGAAAATTTGAGCAAAAATG
1 TGGAGTATCCCCTTCGAAAGAATGGGGTTAAAGTATCA-TAACGATGAAAATTTGAGCAAAAATA
* ** *
578585 AGATTTAAATCTTGACAAATTTAAAAGTAGGGT
65 AGATTTAAATCTTAACAAATTTAAAAACAAGGT
*
578618 TGGAGTATCCCCTTCGAAAGAATGGGGTTAAAGTATCCA-AACGTTGAAAATTTGAGCAAAAATA
1 TGGAGTATCCCCTTCGAAAGAATGGGGTTAAAGTAT-CATAACGATGAAAATTTGAGCAAAAATA
*
578682 AGATTTAAATCTTAACAAGTTTAAAAACAAGGT
65 AGATTTAAATCTTAACAAATTTAAAAACAAGGT
*
578715 TGGAGTAT-CTCTTCGAAAGAATGGGGTT
1 TGGAGTATCCCCTTCGAAAGAATGGGGTT
578743 GGAGCAACCT
Statistics
Matches: 110, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
96 19 0.17
97 65 0.59
98 24 0.22
99 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.28
Consensus pattern (97 bp):
TGGAGTATCCCCTTCGAAAGAATGGGGTTAAAGTATCATAACGATGAAAATTTGAGCAAAAATAA
GATTTAAATCTTAACAAATTTAAAAACAAGGT
Found at i:578767 original size:97 final size:96
Alignment explanation
Indices: 578561--578824 Score: 303
Period size: 97 Copynumber: 2.7 Consensus size: 96
578551 AGTATCATTG
* * **
578561 ACGATGAAAATTTGAGCAAAAATGAGATTTAAATCTTGACAAATTTAAAAGTAGGGTTGGAGTAT
1 ACGATGAAAATTTGAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAACAGGGTTGGAGTAT
* *
578626 CCCCTTCGAAAGAATGGGGTTAAAGTATCCAA
66 -CCCTTCGAAAGAATGGGGTTAAAGCAACCAA
* * *
578658 ACGTTGAAAATTTGAGCAAAAATAAGATTTAAATCTTAACAAGTTTAAAAACAAGGTTGGAGTAT
1 ACGATGAAAATTTGAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAACAGGGTTGGAGTAT
* ** **
578723 CTCTTCGAAAGAATGGGGTTGGAGCAACCTCG
66 CCCTTCGAAAGAATGGGGTTAAAGCAACC-AA
* * * * * * * * *
578755 ATGATGACAATTTAAACCAAAATAAGGTGTAAATCTTGACAAGCTTAAAAACGGGGTTGGAGTAT
1 ACGATGAAAATTTGAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAACAGGGTTGGAGTAT
578820 CCCTT
66 CCCTT
578825 AAAAAAATAA
Statistics
Matches: 139, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
96 24 0.17
97 115 0.83
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.27
Consensus pattern (96 bp):
ACGATGAAAATTTGAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAACAGGGTTGGAGTAT
CCCTTCGAAAGAATGGGGTTAAAGCAACCAA
Found at i:581288 original size:52 final size:53
Alignment explanation
Indices: 581232--581349 Score: 150
Period size: 53 Copynumber: 2.2 Consensus size: 53
581222 ACATTGAAGG
* * * *
581232 ATGTATCGATACATTTGGGTCAAAAATC-CAG-AATGTATTGATACAATGAAAA
1 ATGTATCAATACATTTGGGTCAAAAA-CACAGAAATGCATCGATACAATAAAAA
* * *
581284 ATGTATCAATACATTTGGGTTAAAAACATAGAAATGCATCGATATAATAAAAA
1 ATGTATCAATACATTTGGGTCAAAAACACAGAAATGCATCGATACAATAAAAA
581337 ATGTATCAATACA
1 ATGTATCAATACA
581350 ATTTTTTTCC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
51 1 0.02
52 26 0.46
53 30 0.53
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (53 bp):
ATGTATCAATACATTTGGGTCAAAAACACAGAAATGCATCGATACAATAAAAA
Found at i:581436 original size:18 final size:20
Alignment explanation
Indices: 581390--581438 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
581380 ACAAGGTCTA
*
581390 GTATCGATACATTCACTTAT
1 GTATCGATACATTAACTTAT
*
581410 GTATTGATACATTAAC-T-T
1 GTATCGATACATTAACTTAT
581428 GTATCGATACA
1 GTATCGATACA
581439 AATTGTAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
19 1 0.04
20 14 0.54
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (20 bp):
GTATCGATACATTAACTTAT
Found at i:581536 original size:21 final size:21
Alignment explanation
Indices: 581487--581539 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
581477 GTAGCGATAC
*
581487 ATGCATGAAAGGCATGTATCG
1 ATGCATGTAAGGCATGTATCG
581508 ATGCATGTAAGGCATGTATCG
1 ATGCATGTAAGGCATGTATCG
*
581529 ATTCATGTAAG
1 ATGCATGTAAG
581540 CAAAAATGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (21 bp):
ATGCATGTAAGGCATGTATCG
Found at i:581626 original size:64 final size:64
Alignment explanation
Indices: 581520--581645 Score: 207
Period size: 64 Copynumber: 2.0 Consensus size: 64
581510 GCATGTAAGG
* * * *
581520 CATGTATCGATTCATGTAAGCAAAAATGTGCCAAAAATACTTTTTCGTCAGGCGCTAATGTCAA
1 CATGCATCGATACATGTAAGAAAAAATGTGCCAAAAATACTTTTTCGTCAGGCGCCAATGTCAA
*
581584 CATGCATCGATACATGTAAGAAAAAATGTGCCAAAAATACTTTTTCGTCGGGCGCCAATGTC
1 CATGCATCGATACATGTAAGAAAAAATGTGCCAAAAATACTTTTTCGTCAGGCGCCAATGTC
581646 GACCCCTCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
CATGCATCGATACATGTAAGAAAAAATGTGCCAAAAATACTTTTTCGTCAGGCGCCAATGTCAA
Found at i:584791 original size:19 final size:18
Alignment explanation
Indices: 584741--584803 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
584731 TAGCTACTAC
*
584741 CAATTTCATGTATCGATA
1 CAATGTCATGTATCGATA
584759 CAATTGTACATGTATCGATA
1 CAA-TGT-CATGTATCGATA
*
584779 CAATGATCATGTATCGAAA
1 CAATG-TCATGTATCGATA
584798 CAATGT
1 CAATGT
584804 ATCGGTACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.10
19 20 0.50
20 16 0.40
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (18 bp):
CAATGTCATGTATCGATA
Found at i:587360 original size:12 final size:13
Alignment explanation
Indices: 587323--587361 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
587313 ATAGTAACTC
587323 ATGTATCGATACA
1 ATGTATCGATACA
* *
587336 TTGTATGGATACA
1 ATGTATCGATACA
587349 AT-TATCGATACA
1 ATGTATCGATACA
587361 A
1 A
587362 AGAACATTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:593684 original size:19 final size:18
Alignment explanation
Indices: 593634--593696 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 18
593624 TAGCTACTGC
*
593634 CAATTTCATGTATCGATA
1 CAATGTCATGTATCGATA
593652 CAATTGTACATGTATCGATA
1 CAA-TGT-CATGTATCGATA
593672 CAATGATCATGTATCGATA
1 CAATG-TCATGTATCGATA
593691 CAATGT
1 CAATGT
593697 ATCGATACTA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
18 4 0.10
19 21 0.51
20 16 0.39
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (18 bp):
CAATGTCATGTATCGATA
Found at i:593698 original size:13 final size:13
Alignment explanation
Indices: 593680--593704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
593670 TACAATGATC
593680 ATGTATCGATACA
1 ATGTATCGATACA
593693 ATGTATCGATAC
1 ATGTATCGATAC
593705 TAAGCATAAT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:593722 original size:33 final size:32
Alignment explanation
Indices: 593661--593725 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
593651 ACAATTGTAC
*
593661 ATGTATCGATACAATGATCATGTATCGATACA
1 ATGTATCGATACAATGATAATGTATCGATACA
593693 ATGTATCGATACTAA-GCATAATGTATCGATACA
1 ATGTATCGATAC-AATG-ATAATGTATCGATACA
593726 TCTGGATGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (32 bp):
ATGTATCGATACAATGATAATGTATCGATACA
Found at i:593878 original size:21 final size:21
Alignment explanation
Indices: 593854--593897 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
593844 AAAATATTCG
593854 ATTTAA-AGCTCGAAAACATTT
1 ATTTAAGA-CTCGAAAACATTT
* *
593875 ATTTATGACTCTAAAACATTT
1 ATTTAAGACTCGAAAACATTT
593896 AT
1 AT
593898 AAATATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (21 bp):
ATTTAAGACTCGAAAACATTT
Found at i:598048 original size:34 final size:34
Alignment explanation
Indices: 597948--598163 Score: 265
Period size: 34 Copynumber: 6.4 Consensus size: 34
597938 AGGGTATCAG
* *
597948 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * * *
597981 TGTTGATTAAA-CGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
598014 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
598048 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
598082 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
598116 TGATGACTAAATGGTAGATTTGGTAGGTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
598150 TGTTGATTAAATGG
1 TGTTGATTAAATGG
598164 TGGTTTTTAC
Statistics
Matches: 156, Mismatches: 25, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
33 40 0.26
34 116 0.74
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:598125 original size:102 final size:100
Alignment explanation
Indices: 597948--598163 Score: 324
Period size: 102 Copynumber: 2.1 Consensus size: 100
597938 AGGGTATCAG
** * * * *
597948 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAACGGTGATTTGGTGGTTTGCCA
1 TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAACGGTGATTTGGTGGCTTACCA
*
598013 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
66 TTGATGACTAAATGGGAGATTTGGTAGCTTACCAT
*
598048 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAA-CGGTGATTTGGTGGCTTAC
* *
598113 CATTGATGACTAAATGGTAGATTTGGTAGGTTACCAT
64 CATTGATGACTAAATGGGAGATTTGGTAGCTTACCAT
598150 TGTTGATTAAATGG
1 TGTTGATTAAATGG
598164 TGGTTTTTAC
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
100 13 0.12
101 28 0.27
102 63 0.61
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (100 bp):
TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAACGGTGATTTGGTGGCTTACCA
TTGATGACTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:602628 original size:34 final size:34
Alignment explanation
Indices: 602571--602789 Score: 289
Period size: 34 Copynumber: 6.5 Consensus size: 34
602561 AAGTGGGAGA
*
602571 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
602604 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
602638 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
602672 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
602706 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
602740 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
602774 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
602790 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
33 17 0.10
34 144 0.89
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:602714 original size:102 final size:101
Alignment explanation
Indices: 602571--602789 Score: 348
Period size: 102 Copynumber: 2.2 Consensus size: 101
602561 AAGTGGGAGA
** * * * *
602571 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
602636 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
602672 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
602737 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
602774 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
602790 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 92 0.85
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:603894 original size:20 final size:19
Alignment explanation
Indices: 603871--603925 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
603861 AAAAAAATCA
603871 GATTTTTTTTAATTTTTTCT
1 GATTTTTTTTAATTTTTT-T
603891 GATTTTTATCTT-ATTTTTTT
1 GATTTTT-T-TTAATTTTTTT
*
603911 GAATTTTTCTTAATT
1 G-ATTTTTTTTAATT
603926 ACTTAATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 2 0.07
20 12 0.40
21 14 0.47
22 2 0.07
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
GATTTTTTTTAATTTTTTT
Found at i:604132 original size:22 final size:20
Alignment explanation
Indices: 604106--604159 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
604096 AGATCTATTG
*
604106 TTTTATATTAATATTTATATAA
1 TTTTATATTAA-ATTTA-AAAA
604128 TTTTATAATTAAATTTAAAAA
1 TTTTAT-ATTAAATTTAAAAA
604149 TTTTATTATTA
1 TTTTA-TATTA
604160 TTTAACAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 12 0.41
22 12 0.41
23 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATATTAAATTTAAAAA
Found at i:604897 original size:17 final size:18
Alignment explanation
Indices: 604859--604899 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
604849 TTTGAATTTT
604859 AAAATAATAATAATTATA
1 AAAATAATAATAATTATA
604877 AAAATAA-AA-AATTATTA
1 AAAATAATAATAATTA-TA
604894 AAAATA
1 AAAATA
604900 TAAGATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 10 0.45
18 7 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATAATAATAATTATA
Found at i:605912 original size:19 final size:19
Alignment explanation
Indices: 605870--605912 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
605860 TACATATTTT
* *
605870 TATTATTATTATACATACA
1 TATTATAATTATACATAAA
605889 TATTATAATT-TACATAAA
1 TATTATAATTATACATAAA
605907 TCATTA
1 T-ATTA
605913 AAATATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTATAATTATACATAAA
Found at i:606253 original size:20 final size:20
Alignment explanation
Indices: 606228--606322 Score: 120
Period size: 20 Copynumber: 4.8 Consensus size: 20
606218 TTTTCACAAT
*
606228 TTGTATCGATATATTGTTCA
1 TTGTATCGATACATTGTTCA
*
606248 TTGTATCGATACATTGTTTA
1 TTGTATCGATACATTGTTCA
* *
606268 TTGTATCGATACATGGCTCA
1 TTGTATCGATACATTGTTCA
606288 TTGTATCGATACATT-TTACA
1 TTGTATCGATACATTGTT-CA
* *
606308 ATGTATTGATACATT
1 TTGTATCGATACATT
606323 CACGCATTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
19 1 0.02
20 64 0.98
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:609718 original size:21 final size:23
Alignment explanation
Indices: 609692--609741 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 23
609682 AACATGCTAT
609692 AAATGCATGAAGCAT-AGC-TCA
1 AAATGCATGAAGCATGAGCGTCA
*
609713 AAATGCATGAATCATGAGCTGTCA
1 AAATGCATGAAGCATGAGC-GTCA
609737 AAATG
1 AAATG
609742 ATGGAGATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 14 0.56
22 3 0.12
24 8 0.32
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (23 bp):
AAATGCATGAAGCATGAGCGTCA
Found at i:610725 original size:13 final size:13
Alignment explanation
Indices: 610707--610790 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
610697 AGCTTCGTAG
610707 CGATACATTGTAT
1 CGATACATTGTAT
610720 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
610739 CGATACATTGTAT
1 CGATACATTGTAT
610752 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
610771 CGATACATTGTAT
1 CGATACATTGTAT
610784 CGATACA
1 CGATACA
610791 AATTGTTGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:610739 original size:19 final size:18
Alignment explanation
Indices: 610715--610777 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
610705 AGCGATACAT
610715 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
610734 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
610747 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
610766 TGTATCGATACA
1 TGTATCGATACA
610778 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:610748 original size:32 final size:32
Alignment explanation
Indices: 610707--610792 Score: 163
Period size: 32 Copynumber: 2.7 Consensus size: 32
610697 AGCTTCGTAG
610707 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
610739 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
610771 CGATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
610793 TTGTTGAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:611895 original size:43 final size:43
Alignment explanation
Indices: 611636--612473 Score: 640
Period size: 43 Copynumber: 18.1 Consensus size: 43
611626 CTTAGGAATG
* * * * * *
611636 TTAAAGATGCCAATATGCTGATGCAAGGCTAACGATATTGGGC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
611679 TTAAAGATGAGTGCGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
1 TT-AA-A-G-GT--GCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* ***
611728 TTAAAGATGACAGTGCCAATATGCTGATTCAAGGCCAGCGATACCAGAC
1 TT-AA-A-G---GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * * *
611777 TTAAAGATGAAGATACCAATGTGCTGATTCATGGCCAGCGACATTAGTC
1 TT-AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
611826 TTAAAGACAAAGGTGCCAATATGCTGATCCAAGGCCAGCGATATTGGAC
1 TT------AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * *
611875 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGTC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
611918 TTAAAGACAAAGGTGCCAATATGCTGATCCAAGGCCAGCGATATTGGAC
1 TT------AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
611967 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGAC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * *
612010 TTAAAGATGAAAAAGGCGCTAATATGCTGATTCAAGGTCAGCGATATTGGAC
1 TTAAAG--G-----TGC-C-AATATGCTGATTCAAGGCCAGCGACATTGGAC
*
612062 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * *
612105 TTAAAGATGCCAATGTACTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * *
612148 TTAAAGATGACAAAGGCGCCAATATGCTGATTCAAAGCCAGCGATATTGGAC
1 -T-----T---AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* **
612200 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAATGACATTGGAC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
*
612243 TTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TT----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * *
612291 TTAAAGGTGCCAATGTACTGATTCAAGGCCAACGACATTGGTC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
*
612334 TTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TT----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * *
612382 TT----GTGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGTC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
*
612421 TTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TT----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
612469 TTAAA
1 TTAAA
612474 AGAAGATGCC
Statistics
Matches: 650, Mismatches: 88, Indels: 114
0.76 0.10 0.13
Matches are distributed among these distances:
39 35 0.05
43 229 0.35
44 6 0.01
45 4 0.01
46 2 0.00
47 3 0.00
48 112 0.17
49 177 0.27
50 4 0.01
51 5 0.01
52 70 0.11
53 1 0.00
54 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (43 bp):
TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
Found at i:611930 original size:92 final size:92
Alignment explanation
Indices: 611638--612373 Score: 619
Period size: 95 Copynumber: 7.8 Consensus size: 92
611628 TAGGAATGTT
* * * * *
611638 AAAGATGCCAATATGCTGATGCAAGGCTAACGATATTGGGCTTAAAGATGAGTGCGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G-GT--GCCAATGTGC
* *
611703 TGATTCAAGGCCAGCGACATTGGTCTTAAAGATG
60 TGATTCAAGGCCAGCGACATTAGTCTTAAAGA-C
* *** *
611737 ACA-GTGCCAATATGCTGATTCAAGGCCAGCGATACCAGACTTAAAGATGAAGATACCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATGTGC
*
611801 TGATTCATGGCCAGCGACATTAGTCTTAAAGAC
60 TGATTCAAGGCCAGCGACATTAGTCTTAAAGAC
*
611834 AAAGGTGCCAATATGCTGATCCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
611899 AAGGCCAGCGACATTAGTCTTAAAGAC
66 AAGGCCAGCGACATTAGTCTTAAAGAC
*
611926 AAAGGTGCCAATATGCTGATCCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
* *
611991 AAGGCCAGCGACATTAGACTTAAAGATGAA
66 AAGGCCAGCGACATTAGTCTT-AA-A-GAC
* * *
612021 AAAGGCGCTAATATGCTGATTCAAGGTCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
* *
612086 AAGGCCAGCGACATTGGACTTAAAG--
66 AAGGCCAGCGACATTAGTCTTAAAGAC
* * * * *
612111 --A--TGCCAATGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---AAAGGTGCCAATG
* * * *
612172 TGCTGATTCAAAGCCAGCGATATTGGACTT------
57 TGCTGATTCAAGGCCAGCGACATTAGTCTTAAAGAC
* ** * *
612202 AAAGGTGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTAAAGACAAGGTGCCAATATGCT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAGGTGCCAATGTGCT
* * *
612267 GATTCAAGGCCAGCGATATTGGACTT------
61 GATTCAAGGCCAGCGACATTAGTCTTAAAGAC
* * * * * *
612293 AAAGGTGCCAATGTACTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAGGTGCCAATGTGCT
612358 GATTCAAGGCCAGCGA
61 GATTCAAGGCCAGCGA
612374 TATTGGACTT
Statistics
Matches: 569, Mismatches: 47, Indels: 50
0.85 0.07 0.08
Matches are distributed among these distances:
86 30 0.05
87 1 0.00
88 1 0.00
89 1 0.00
90 2 0.00
91 118 0.21
92 129 0.23
93 5 0.01
94 4 0.01
95 156 0.27
96 1 0.00
97 4 0.01
98 112 0.20
99 4 0.01
100 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (92 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
AAGGCCAGCGACATTAGTCTTAAAGAC
Found at i:612106 original size:138 final size:136
Alignment explanation
Indices: 611636--612473 Score: 721
Period size: 138 Copynumber: 6.0 Consensus size: 136
611626 CTTAGGAATG
* * * * * *
611636 TTAAAGATGCCAATATGCTGATGCAAGGCTAACGATATTGGGCTTAAAGATGAGTGCGCCAATGT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A-G-GT--GCCAATGT
* * *
611701 GCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATG-ACA-GTGCCAATATGCTGATTCAAGGCC
60 GCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-GAAAAGGCGCCAATATGCTGATTCAAGGCC
***
611764 AGCGATACCAGAC
124 AGCGATATTGGAC
* * * * *
611777 TTAAAGATGAAGATACCAATGTGCTGATTCATGGCCAGCGACATTAGTCTTAAAGACAAAGGTGC
1 TT-AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT------AAAGGTGC
* * * * *
611842 CAATATGCTGATCCAAGGCCAGCGATATTGGACTT-------AAAGGTGCCAATGTGCTGATTCA
54 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAGAAAAGGCGCCAATATGCTGATTCA
* * *
611900 AGGCCAGCGACATTAGTC
119 AGGCCAGCGATATTGGAC
* *
611918 TTAAAGACAAAGGTGCCAATATGCTGATCCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGT
1 TT------AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATGT
* * *
611983 GCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAAAAAGGCGCTAATATGCTGATTCAAGGT
60 GCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-G-AAAAGGCGCCAATATGCTGATTCAAGGC
612048 CAGCGATATTGGAC
123 CAGCGATATTGGAC
* * *
612062 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGCCAATGTACTGAT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATGTGCTGAT
*
612127 TCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAAGCCAGCGA
66 TCAAGGCCAGCGACATTGGACTTAAAGA-GA-AAAGGCGCCAATATGCTGATTCAAGGCCAGCGA
612192 TATTGGAC
129 TATTGGAC
* ** *
612200 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTAAAGACAAGGTGCCAATATG
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT----A-AAGGTGCCAATGTG
* * * * *
612265 CTGATTCAAGGCCAGCGATATTGGACTT-------AAAGGTGCCAATGTACTGATTCAAGGCCAA
61 CTGATTCAAGGCCAGCGACATTGGACTTAAAGAGAAAAGGCGCCAATATGCTGATTCAAGGCCAG
* *
612323 CGACATTGGTC
126 CGATATTGGAC
*
612334 TTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----GTGCCAATGTG
1 TT----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATGTG
* * * *
612395 CTGAGTCAAGGCCAGCGACATTGGTCTT-AA-AGACAAGGTGCCAATATGCTGATTCAAGGCCAG
61 CTGATTCAAGGCCAGCGACATTGGACTTAAAGAGAAAAGGCGCCAATATGCTGATTCAAGGCCAG
612458 CGATATTGGAC
126 CGATATTGGAC
612469 TTAAA
1 TTAAA
612474 AGAAGATGCC
Statistics
Matches: 579, Mismatches: 76, Indels: 95
0.77 0.10 0.13
Matches are distributed among these distances:
130 37 0.06
131 1 0.00
134 36 0.06
135 76 0.13
137 1 0.00
138 169 0.29
139 38 0.07
140 2 0.00
141 67 0.12
142 4 0.01
143 39 0.07
144 38 0.07
145 1 0.00
146 2 0.00
147 62 0.11
149 2 0.00
150 1 0.00
151 1 0.00
152 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (136 bp):
TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATGTGCTGAT
TCAAGGCCAGCGACATTGGACTTAAAGAGAAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATA
TTGGAC
Found at i:612300 original size:91 final size:91
Alignment explanation
Indices: 612065--612473 Score: 637
Period size: 91 Copynumber: 4.5 Consensus size: 91
612055 ATTGGACTTA
* * *
612065 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGCCAATGTACTGATTCA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTACTGATTCA
*
612130 AGGCCAGCGACATTGGACTTAAAGATGAC
66 AGGCCAACGACATTGGACTT-AA-A-GAC
* * *
612159 AAAGGCGCCAATATGCTGATTCAAAGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
1 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTACTGATTC
*
612224 AAGGCCAATGACATTGGACTTAAAGAC
65 AAGGCCAACGACATTGGACTTAAAGAC
612251 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTACTGATTCA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTACTGATTCA
*
612316 AGGCCAACGACATTGGTCTTAAAGAC
66 AGGCCAACGACATTGGACTTAAAGAC
* *
612342 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----GTGCCAATGTGCTGAGTCA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTACTGATTCA
* *
612403 AGGCCAGCGACATTGGTCTTAAAGAC
66 AGGCCAACGACATTGGACTTAAAGAC
612429 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
612474 AGAAGATGCC
Statistics
Matches: 295, Mismatches: 16, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
87 84 0.28
91 128 0.43
92 3 0.01
93 1 0.00
94 2 0.01
95 77 0.26
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (91 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTACTGATTCA
AGGCCAACGACATTGGACTTAAAGAC
Found at i:612668 original size:34 final size:33
Alignment explanation
Indices: 612566--613558 Score: 935
Period size: 33 Copynumber: 29.8 Consensus size: 33
612556 TTGTGGACTT
* *
612566 AAAAGGGTGCGACGGAGTTGTGGACTTAAAAGGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAA-GG
* *
612600 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAG-GTGCCACGGAGTTGTGGAC-TTAAAAGG
* * *
612635 AAAAAGGTGTCATGGAGTCGTGGACTT---A-G
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
* * ** *
612664 AAAAGAGATGTCATTGAGTTGTGGACTT-ACAGG
1 AAAA-AGGTGCCACGGAGTTGTGGACTTAAAAGG
* **
612697 AAAAAGGGATGCCACTGAGTTGTGGACTTTGAAGG
1 AAAAA-GG-TGCCACGGAGTTGTGGACTTAAAAGG
* * *
612732 AAAGAGATGCCACGGAGTTGTGGACTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGAC-TTAAAAGG
*
612766 AAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAAG
1 AAAAAG-GTGCCACGGAGTTGTGGAC-TTAAAAGG
* *
612801 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGG
1 AAAAAG-GTGCCACGGAGTTGTGGACTTAAAAGG
* * *
612835 AAAAAGATGCTATGGAGTTGTGGACTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
*
612868 AACAAGGTGCCACGGAGTTGTGGACTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
**
612901 ATCAAGGATGCCACGGAGTTGTGGACTTAAAAAGG
1 AAAAAGG-TGCCACGGAGTTGTGGACTT-AAAAGG
* *
612936 AACAAGGATGCCACAGAGTTGTGGACTTAAAAGG
1 AAAAAGG-TGCCACGGAGTTGTGGACTTAAAAGG
* * * *
612970 AACAAGGTGCCATGGAGGTGTGGGCTTAAAAGGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAA-GG
**
613004 AAAAAGGTTGCCACGGAGTCATGGACTTAAAAGG
1 AAAAAGG-TGCCACGGAGTTGTGGACTTAAAAGG
* *
613038 -AAAAGGTGCTACGGAGTTGTGGACTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGAC-TTAAAAGG
* *
613071 AAAAAGATGCCACAGAGTTGTGGACTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
*
613104 AACAAGGATGCCACGGAGTTGTGGACTTAAAAAGG
1 AAAAAGG-TGCCACGGAGTTGTGGACTT-AAAAGG
* * * **
613139 AACAAGGATGCCACAGAGGTGTGGGTTTAAAAGG
1 AAAAAGG-TGCCACGGAGTTGTGGACTTAAAAGG
* *
613173 AACAAGGTGCCACGGAGGTGTGGACTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
*
613206 AACAAGGATGCCACGGAGTTGTGGACTTAAAAGG
1 AAAAAGG-TGCCACGGAGTTGTGGACTTAAAAGG
* ** *
613240 AACAAGGTGCCATAGAGTTGTGGGCTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
* * ** * *
613273 GACAAGGTGCCATAGAGGTGTGGGCTTAAAAGGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAA-GG
*
613307 AAAAAAGGTGCCACGGAGTCGTGGACTTAAAAGG
1 -AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
613341 -AAAAGGTGCCACGGAGTTGTGGACTTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGAC-TTAAAAGG
* * *
613374 AAAAAGATGCCGCAGAGTTGTGGACTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
* *
613407 AACAAGGTGCCACGGAGGTT-TGGGCTTAAAAGGG
1 AAAAAGGTGCCACGGA-GTTGTGGACTTAAAA-GG
* *
613441 AAAAAGGGTGCCACAGAGTCGTGGACTTAAAA-G
1 AAAAA-GGTGCCACGGAGTTGTGGACTTAAAAGG
* * *
613474 -----GGTGCCACAGAGTTGTGGGCTT-TAA--
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
* *
613499 AAAGA-GTGCCACAGAGTTGTGGACTTTGAAAA-G
1 AAAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGG
* **
613532 AAAAAGGTGCCATGGAGTCATGGACTT
1 AAAAAGGTGCCACGGAGTTGTGGACTT
613559 TGAAGAAAAG
Statistics
Matches: 818, Mismatches: 103, Indels: 77
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.00
27 20 0.02
29 23 0.03
30 23 0.03
32 42 0.05
33 254 0.31
34 240 0.29
35 208 0.25
36 6 0.01
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (33 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
Found at i:612677 original size:30 final size:29
Alignment explanation
Indices: 612633--612692 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
612623 GGCTTTAAAA
*
612633 AGAAAAAGGTGTCATGGAGTCGTGGACTT
1 AGAAAAAGATGTCATGGAGTCGTGGACTT
* *
612662 AGAAAAGAGATGTCATTGAGTTGTGGACTT
1 AGAAAA-AGATGTCATGGAGTCGTGGACTT
612692 A
1 A
612693 CAGGAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.33, C:0.08, G:0.32, T:0.27
Consensus pattern (29 bp):
AGAAAAAGATGTCATGGAGTCGTGGACTT
Found at i:613009 original size:203 final size:200
Alignment explanation
Indices: 612566--613474 Score: 1014
Period size: 203 Copynumber: 4.5 Consensus size: 200
612556 TTGTGGACTT
* *
612566 AAAAGGGTGCGACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGC-TTAA
* * * * * **
612631 AAAGAAAAAGGTG-TCATGGAGTCGTGGACTTAGAA--AA-GAGATGTCATTGAGTTGTGGACTT
63 AAGGAAAAAGGTGCT-ATGGAGTTGTGGACTTAAAAGGAACAAGATGCCACAGAGTTGTGGACTT
* * ** *
612692 -ACAGGAAAAAGGGATGCCACTGAGTTGTGGACTTTGAAGG-AAAGAGATGCCACGGAGTTGTGG
127 AAAAGGAAAAA-GGATGCCACGGAGTTGTGGACTTAAAAGGAAAAG-GATGCCACAGAGTTGTGG
*
612755 ACTTTAAAAAG
190 ACTTTAAAAGG
* *
612766 AAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAAAAG-GTGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAG-GTGCCACGGAGTTGTGGGCTTAA
* * *
612831 AAGGAAAAAGATGCTATGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTA
63 AAGGAAAAAGGTGCTATGGAGTTGTGGACTTAAAAGGAACAAGATGCCACAGAGTTGTGGACTTA
**
612896 AAAGGATCAAGGATGCCACGGAGTTGTGGACTTAAAAAGGAACAAGGATGCCACAGAGTTGTGGA
128 AAAGGAAAAAGGATGCCACGGAGTTGTGGACTT-AAAAGGAA-AAGGATGCCACAGAGTTGTGGA
612961 C-TTAAAAGG
191 CTTTAAAAGG
* * * * ** *
612970 AACAAGGTGCCATGGAGGTGTGGGCTTAAAAGGGAAAAAGGTTGCCACGGAGTCATGGACTTAAA
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAA-GGAAAAAGG-TGCCACGGAGTTGTGGGCTTAAA
* * *
613035 AGG-AAAAGGTGCTACGGAGTTGTGGACTTTAAAAAGAAAAAGATGCCACAGAGTTGTGGACTTA
64 AGGAAAAAGGTGCTATGGAGTTGTGGAC-TTAAAAGGAACAAGATGCCACAGAGTTGTGGACTTA
* *
613099 AAAGGAACAAGGATGCCACGGAGTTGTGGACTTAAAAAGGAACAAGGATGCCACAGAGGTGTGG-
128 AAAGGAAAAAGGATGCCACGGAGTTGTGGACTT-AAAAGGAA-AAGGATGCCACAGAGTTGTGGA
*
613163 GTTTAAAAGG
191 CTTTAAAAGG
* * * *
613173 AACAAGGTGCCACGGAGGTGTGGACTTAAAAGGAACAAGGATGCCACGGAGTTGTGGACTTAAAA
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGG-TGCCACGGAGTTGTGGGCTTAAAA
* * * * * * * * *
613238 GGAACAAGGTGCCATAGAGTTGTGGGCTTAAAAGGGACAAGGTGCCATAGAGGTGTGGGCTTAAA
65 GGAAAAAGGTGCTATGGAGTTGTGGACTTAAAAGGAACAAGATGCCACAGAGTTGTGGACTTAAA
* *
613303 AGGGAAAAAAGG-TGCCACGGAGTCGTGGACTTAAAAGGAAAAGG-TGCCACGGAGTTGTGGACT
130 A-GG-AAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGAAAAGGATGCCACAGAGTTGTGGACT
613366 TTAAAAGG
193 TTAAAAGG
* * * *
613374 AAAAAGATGCCGCAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGGTT-TGGGCTTAAAA
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGGA-GTTGTGGGCTTAAAA
* ** *
613438 GGGAAAAAGGGTGCCACAGAGTCGTGGACTTAAAAGG
65 -GGAAAAA-GGTGCTATGGAGTTGTGGACTTAAAAGG
613475 GTGCCACAGA
Statistics
Matches: 616, Mismatches: 72, Indels: 40
0.85 0.10 0.05
Matches are distributed among these distances:
200 70 0.11
201 103 0.17
202 134 0.22
203 257 0.42
204 29 0.05
205 20 0.03
206 3 0.00
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.19
Consensus pattern (200 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAG
GAAAAAGGTGCTATGGAGTTGTGGACTTAAAAGGAACAAGATGCCACAGAGTTGTGGACTTAAAA
GGAAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGAAAAGGATGCCACAGAGTTGTGGACTTTA
AAAGG
Found at i:613480 original size:27 final size:28
Alignment explanation
Indices: 613441--613524 Score: 125
Period size: 27 Copynumber: 3.0 Consensus size: 28
613431 CTTAAAAGGG
*
613441 AAAAAGGGTGCCACAGAGTCGTGGACTT
1 AAAAAGGGTGCCACAGAGTTGTGGACTT
*
613469 -AAAAGGGTGCCACAGAGTTGTGGGCTTT
1 AAAAAGGGTGCCACAGAGTTGTGGAC-TT
*
613497 AAAAAGAGTGCCACAGAGTTGTGGACTT
1 AAAAAGGGTGCCACAGAGTTGTGGACTT
613525 TGAAAAGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.46
28 4 0.08
29 23 0.46
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.21
Consensus pattern (28 bp):
AAAAAGGGTGCCACAGAGTTGTGGACTT
Found at i:613511 original size:29 final size:29
Alignment explanation
Indices: 613441--613532 Score: 125
Period size: 29 Copynumber: 3.2 Consensus size: 29
613431 CTTAAAAGGG
* *
613441 AAAAAGGGTGCCACAGAGTCGTGGAC-TT
1 AAAAAGAGTGCCACAGAGTTGTGGACTTT
* *
613469 -AAAAGGGTGCCACAGAGTTGTGGGCTTT
1 AAAAAGAGTGCCACAGAGTTGTGGACTTT
613497 AAAAAGAGTGCCACAGAGTTGTGGACTTT
1 AAAAAGAGTGCCACAGAGTTGTGGACTTT
*
613526 GAAAAGA
1 AAAAAGA
613533 AAAAGGTGCC
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
27 23 0.40
28 2 0.04
29 32 0.56
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.21
Consensus pattern (29 bp):
AAAAAGAGTGCCACAGAGTTGTGGACTTT
Found at i:613559 original size:34 final size:31
Alignment explanation
Indices: 613498--613649 Score: 105
Period size: 30 Copynumber: 4.8 Consensus size: 31
613488 GTGGGCTTTA
* **
613498 AAAAGAGTGCCACAGAGTTGTGGACTTTGAAAAG
1 AAAAGA-TGCCACTGAGTCATGGACTTTG--AAG
*
613532 AAAAAGGTGCCA-TGGAGTCATGGACTTTGAAG
1 -AAAAGATGCCACT-GAGTCATGGACTTTGAAG
613564 AAAAGATGCCACTGAGTCATGGACTTTG--G
1 AAAAGATGCCACTGAGTCATGGACTTTGAAG
* * * **
613593 AATGAGATGCCACTAAATTGTGGACTTTG-AG
1 AA-AAGATGCCACTGAGTCATGGACTTTGAAG
* * * *
613624 ACAAGATGTCACTAAGTCGTGGACTT
1 AAAAGATGCCACTGAGTCATGGACTT
613650 AAAAAGGAGA
Statistics
Matches: 98, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
29 3 0.03
30 41 0.42
31 27 0.28
32 4 0.04
34 18 0.18
35 5 0.05
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (31 bp):
AAAAGATGCCACTGAGTCATGGACTTTGAAG
Found at i:613574 original size:31 final size:33
Alignment explanation
Indices: 613497--613591 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 33
613487 TGTGGGCTTT
* **
613497 AAAAAGAGTGCCACAGAGTTGTGGACTTTGAAAAG
1 AAAAAGA-TGCCACTGAGTCATGGACTTTG-AAAG
*
613532 AAAAAGGTGCCA-TGGAGTCATGGACTTTG-AAG
1 AAAAAGATGCCACT-GAGTCATGGACTTTGAAAG
613564 -AAAAGATGCCACTGAGTCATGGACTTTG
1 AAAAAGATGCCACTGAGTCATGGACTTTG
613592 GAATGAGATG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
31 25 0.47
32 4 0.08
34 18 0.34
35 6 0.11
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (33 bp):
AAAAAGATGCCACTGAGTCATGGACTTTGAAAG
Found at i:622000 original size:13 final size:13
Alignment explanation
Indices: 621982--622008 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
621972 ATAAAGATCA
621982 AATGTATCGATAC
1 AATGTATCGATAC
621995 AATGTATCGATAC
1 AATGTATCGATAC
622008 A
1 A
622009 TTTCCGTGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:622064 original size:19 final size:18
Alignment explanation
Indices: 622040--622164 Score: 109
Period size: 19 Copynumber: 7.6 Consensus size: 18
622030 AGCGATACAT
622040 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
622059 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
622072 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
622091 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
622104 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
622123 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
622136 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
622155 TGTATCGATA
1 TGTATCGATA
622165 TATTGTATCG
Statistics
Matches: 88, Mismatches: 0, Indels: 36
0.71 0.00 0.29
Matches are distributed among these distances:
13 33 0.38
14 3 0.03
16 6 0.07
18 3 0.03
19 43 0.49
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:622073 original size:32 final size:32
Alignment explanation
Indices: 622032--622180 Score: 280
Period size: 32 Copynumber: 4.7 Consensus size: 32
622022 AGCTTCATAG
*
622032 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
622064 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
622096 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
622128 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
622160 CGATATATTGTATCGATACAA
1 CGATACATTGTATCGATACAA
622181 ATTGTTGAAA
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 115 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:623815 original size:28 final size:28
Alignment explanation
Indices: 623782--623851 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
623772 TTCATAATTA
623782 GGGATACTCCAACCCCATTA-TTTC-ATTG
1 GGGATACTCCAACCCCATTATTTTCGA--G
* *
623810 GGGATATTCCAACCCCGTTATTTTCGAG
1 GGGATACTCCAACCCCATTATTTTCGAG
623838 GGGATACTCCAACC
1 GGGATACTCCAACC
623852 TCGACTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 32 0.86
29 4 0.11
30 1 0.03
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (28 bp):
GGGATACTCCAACCCCATTATTTTCGAG
Found at i:623987 original size:108 final size:107
Alignment explanation
Indices: 623733--624009 Score: 288
Period size: 108 Copynumber: 2.6 Consensus size: 107
623723 CGCAATCGGG
* * * * **
623733 GATACTCCAACTCTAATTTTATTTCCAAAACACCAATTTTTCATAATTAGGGATACTCCAACCCC
1 GATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCATAATCGGGGATACTCCAACCCC
* * * * * *
623798 ATTATTTCATTGGGGATATTCCAACCCCGTTATTTTCGAGGG
66 ATTATGTCATCGGGGATACTCCAACCCCATAATTTTCGAGGA
* * ** * * *
623840 GATACTCCAA-CCTCGACTTTATGTCTAAAATATTGATTTTTTCATAATCGGGGGTACTCCGACC
1 GATACTCCAACCCT-GATTTTATTTCTAAAATA-CCAATTTTTCATAATCGGGGATACTCCAACC
* * *
623904 CCGTTATGTCATCGGGGATACTCCAATCCCATAA-TTTCTGAGTA
64 CCATTATGTCATCGGGGATACTCCAACCCCATAATTTTC-GAGGA
* * *
623948 GATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCACAATCGAGGATACTTCAAC
1 GATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCATAATCGGGGATACTCCAAC
624010 TCCGATTTTA
Statistics
Matches: 134, Mismatches: 32, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
106 2 0.01
107 49 0.37
108 80 0.60
109 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (107 bp):
GATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCATAATCGGGGATACTCCAACCCC
ATTATGTCATCGGGGATACTCCAACCCCATAATTTTCGAGGA
Found at i:624004 original size:51 final size:50
Alignment explanation
Indices: 623948--624062 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 50
623938 TTTCTGAGTA
* * *
623948 GATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCACAATCGAG
1 GATACTCCAACCC-GATTTTATTTCCAAAACACCAATTTCTCACAATCGAG
* * *
623999 GATACTTCAACTCCGATTTTATTTCCAAAACACCAATTTCTCATAATCGGG
1 GATACTCCAAC-CCGATTTTATTTCCAAAACACCAATTTCTCACAATCGAG
624050 GATACTCCAACCC
1 GATACTCCAACCC
624063 CGTTATTATC
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
50 2 0.04
51 52 0.93
52 2 0.04
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (50 bp):
GATACTCCAACCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGAG
Found at i:624130 original size:79 final size:78
Alignment explanation
Indices: 624017--624296 Score: 273
Period size: 79 Copynumber: 3.5 Consensus size: 78
624007 AACTCCGATT
* *
624017 TTATTTCCAAAACACCAA-TTTCTCATAATCGGGGATACTCCAACCCCGTTATTATCACGGGGAT
1 TTATTTTCAAAACACCAATTTTCT-ACAATCGGGGATACTCCAACCCCGTTATT-TCACGGGGAT
624081 ACTCCAACCCC-AGCC
64 ACTCCAACCCCTA-CC
* * *
624096 TTA-TTTCTAAAGCATCGATTTTCTACAATCGGGGATACTCCAACCCCGTTATTTTCGA-GGGGA
1 TTATTTTC-AAAACACCAATTTTCTACAATCGGGGATACTCCAACCCCGTTA-TTTC-ACGGGGA
*
624159 TACTCCAACCCCTACT
63 TACTCCAACCCCTACC
* ** *
624175 TTATTTTCAAAACACCAATTTTCTATAATCAAGGATACTCCAACCCTGTTATTTC-CGAGGGGAT
1 TTATTTTCAAAACACCAATTTTCTACAATCGGGGATACTCCAACCCCGTTATTTCAC--GGGGAT
* **
624239 ACTCCAACCCCGATT
64 ACTCCAACCCCTACC
* * * * * *
624254 TTATTTTCAGAATACCGATTTTCCATAACTAGGGGATACTCCA
1 TTATTTTCAAAACACCAATTTTCTACAA-TCGGGGATACTCCA
624297 GCCCTGTTGT
Statistics
Matches: 169, Mismatches: 22, Indels: 19
0.80 0.10 0.09
Matches are distributed among these distances:
78 7 0.04
79 138 0.82
80 24 0.14
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (78 bp):
TTATTTTCAAAACACCAATTTTCTACAATCGGGGATACTCCAACCCCGTTATTTCACGGGGATAC
TCCAACCCCTACC
Found at i:626104 original size:33 final size:32
Alignment explanation
Indices: 626062--626129 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
626052 CGTTACAAGC
**
626062 CAATGTATCGATACATTTTATAGTATATCGATA
1 CAATGTATCGATACATACTAT-GTATATCGATA
*
626095 CAATGTATCGATACATACTATGTGTATCGATA
1 CAATGTATCGATACATACTATGTATATCGATA
626127 CAA
1 CAA
626130 GTTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTATATCGATA
Found at i:634870 original size:13 final size:13
Alignment explanation
Indices: 634852--634876 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
634842 CATTTTATGG
634852 TGTATCGATACAA
1 TGTATCGATACAA
634865 TGTATCGATACA
1 TGTATCGATACA
634877 TACTATGTGT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:634892 original size:32 final size:33
Alignment explanation
Indices: 634829--634896 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
634819 CGTTACAAGC
**
634829 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
634862 CAATGTATCGATACATACTAT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
634894 CAA
1 CAA
634897 GTTTAGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:635554 original size:13 final size:13
Alignment explanation
Indices: 635482--635554 Score: 53
Period size: 13 Copynumber: 5.7 Consensus size: 13
635472 TTGAATTAAC
*
635482 ATATTTATATATTT
1 ATATTAATATA-TT
*
635496 ATATT-ATTTATT
1 ATATTAATATATT
*
635508 TTATTAATATATT
1 ATATTAATATATT
* *
635521 -TTTTAATATTAGT
1 ATATTAATA-TATT
*
635534 A-ATAAATATATT
1 ATATTAATATATT
635546 ATATTAATA
1 ATATTAATA
635555 AAAATAATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
12 17 0.37
13 24 0.52
14 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (13 bp):
ATATTAATATATT
Found at i:636539 original size:21 final size:21
Alignment explanation
Indices: 636506--636546 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
636496 CTAAGTAAAA
636506 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
636527 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
636547 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:636611 original size:20 final size:19
Alignment explanation
Indices: 636586--636656 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
636576 ACCCTGAAAA
636586 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
636606 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
636625 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
636646 GTATCGATACA
1 GTATCGATACA
636657 GGACATTGGT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:636709 original size:53 final size:53
Alignment explanation
Indices: 636626--636762 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
636616 AGATTGCATA
*
636626 GTATCGATACACACAAATATGTATCGATACAGGACATTGGTAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
636680 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
636733 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
636763 TTGGTAGTAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 66 0.82
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:636838 original size:21 final size:22
Alignment explanation
Indices: 636804--636859 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
636794 CATCACTATT
636804 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
636826 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
636847 CATCACTGTTCAT
1 CATCACTGTTCAT
636860 AGGTTACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:636929 original size:13 final size:13
Alignment explanation
Indices: 636911--636935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
636901 CGTTAAAAAT
636911 TGTATCGATACAG
1 TGTATCGATACAG
636924 TGTATCGATACA
1 TGTATCGATACA
636936 TCATAAATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:637050 original size:20 final size:20
Alignment explanation
Indices: 637007--637050 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
636997 TTCAAATGCA
* *
637007 TGTATCGATACATTATAATT
1 TGTATCGATACATTAGAATG
* *
637027 TGTATCGATACATTGGAGTG
1 TGTATCGATACATTAGAATG
637047 TGTA
1 TGTA
637051 AGTGCGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTAGAATG
Found at i:638289 original size:23 final size:22
Alignment explanation
Indices: 638236--638292 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
638226 AAATTTTAAC
*
638236 ATAAAAT-TATTTTTTACTAAT
1 ATAAAATATATTTATTACTAAT
638257 AT--AATATATTTATTACTAAT
1 ATAAAATATATTTATTACTAAT
638277 ATTAAAATATATTTAT
1 A-TAAAATATATTTAT
638293 AAAATATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 3 0.10
20 14 0.45
21 3 0.10
23 11 0.35
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAAAATATATTTATTACTAAT
Found at i:638605 original size:18 final size:18
Alignment explanation
Indices: 638584--638620 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
638574 AAATATTACC
638584 TAAATTCTAAAATTTATG
1 TAAATTCTAAAATTTATG
*
638602 TAAATTCTAATATTTATG
1 TAAATTCTAAAATTTATG
638620 T
1 T
638621 GTAATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
TAAATTCTAAAATTTATG
Found at i:638982 original size:430 final size:426
Alignment explanation
Indices: 638034--639464 Score: 1434
Period size: 430 Copynumber: 3.3 Consensus size: 426
638024 GTAGTGTTTG
* * * * ** *
638034 TATGTAATCTGGTAATGTTTATA-GTAATTTGTCACATATAAACATT-GCTT--AAGATTTTTTA
1 TATGTAATCTAGTAATGTTTATATGTAATTTGTTACATACAAATATTATTTTCAAAGATTCTTTA
* * * * * ** *
638095 TACAAATATATTA-TCCATTATACATATTACATATAAACATTA--TTTACACTAATAATTTATGT
66 CACAAATACATTACT-TATTATACATATTATATATAAATATTACCTAAACTCTAATAATTTATGT
* * * * *
638157 AAATTCTAATATTTATTTGTATTTTGGTAATCTATAATT-CTAATTCTTACCAACTAATAATAAA
130 AAATTCTAATATTTATGTGTAATTTAGTAATCTTTAGTTGC-AATTCTTA-CAACTAAT-A-AAA
*
638221 AATCTAAATTTTAACATAAAATTATTTTTTACTAATATAATATATTTATTACTAATATTAAAATA
191 AATCTAAATTTTAACATAAAATTA-TTTTTATTAATATAATATATTTATTACTAATATTAAAATA
* * ** *
638286 TATTTATAAAATATAAATATAATTTTTTTAACTTTAAAAATTATTAAAAATTAATTTCATACATA
255 TATTAATAAAATAAAAATATAA-AATTTT---TTT---ACTTA--AAAAATTAA-TT--T-CATA
* *
638351 TATAATATATTTGATAGAAAATCAAAAATAATGTTT-AACAAATTATATTTAATTTTCTTAAAAT
307 TAT-AT-TA-TTAATAAAAAATCAAAAATAAT-TTTGAA-AAATTATATTTAATTTTCTTAAAAT
* * * * * *
638415 AACTTTTTACATAAATACATTACGGTTAC-AGTAATGTTTTATATAAAACTTTAATGTTTA
367 AATTTTTTACATAAATACATTAAGGTTTCGA-TAATGTTTTATGTAAAACTATAATTTTTA
* * * * ** *
638475 TATGTAATCTAGTGATGCTTATATGTAATTTATTACATACAAATATT-TTTTAAAACTTTTTTTT
1 TATGTAATCTAGTAATGTTTATATGTAATTTGTTACATACAAATATTATTTTCAAA-GATTCTTT
** * *
638539 TTACAAATACATTACTTATTATACATCTTATATATAAATATTACCTAAATTCTAA-AATTTATGT
65 ACACAAATACATTACTTATTATACATATTATATATAAATATTACCTAAACTCTAATAATTTATGT
*
638603 AAATTCTAATATTTATGTGTAATTTCAATAATCTTTAGTTGCAATTCTTACTAACTAATAAAAGA
130 AAATTCTAATATTTATGTGTAATTT-AGTAATCTTTAGTTGCAATTCTTAC-AACTAATAAAA-A
* * ** * *
638668 ATCTAAATTTTAACATAAAAATATTTCTTATTAATAAAAGGTATTTACTACTAATATTAAAATAC
192 ATCTAAATTTTAACATAAAATTATTT-TTATTAATATAATATATTTATTACTAATATTAAAATAT
*
638733 GTTAATAAAATAAAAAATATAAAATTTTTTTACTTAAAAAATTAATTTCATATATATTATTAATA
256 ATTAATAAAAT-AAAAATATAAAATTTTTTTACTTAAAAAATTAATTTCATATATATTATTAATA
* * * *
638798 AAAAATCAAAAGTAATTTTGTAAAATTATATTTAATTTTTTTAAAAGT-ATTTTTTACATAAATG
320 AAAAATCAAAAATAATTTTGAAAAATTATATTTAATTTTCTTAAAA-TAATTTTTTACATAAATA
* * *
638862 CATTATGGTTTCGATATTGTTTTATGTAAAACTGTAATTTTTA
384 CATTAAGGTTTCGATAATGTTTTATGTAAAACTATAATTTTTA
* * * * * **
638905 CATATAATCCAGTAATGTTTATATATAATTTGTTATATACAAATATTACCTTCAAAGATTCTTTA
1 TATGTAATCTAGTAATGTTTATATGTAATTTGTTACATACAAATATTATTTTCAAAGATTCTTTA
* * * * **
638970 CACAAATACATTA-TCAATTATATATATTACATATAAATATTATCTGCACTCTAATAATTTATGT
66 CACAAATACATTACT-TATTATACATATTATATATAAATATTACCTAAACTCTAATAATTTATGT
* *
639034 AAATTCTAATATTTATGTGTAATTTAGGTAATATTTAGTTGTAA-T-TTACAA-TAAATAAAAAA
130 AAATTCTAATATTTATGTGTAATTTA-GTAATCTTTAGTTGCAATTCTTACAACT-AATAAAAAA
639096 TCTAAATTTTAACATAAAATTATTTTTATTAATATAATATATTTATTACTAATATTAAAAATATA
193 TCTAAATTTTAACATAAAATTATTTTTATTAATATAATATATTTATTACTAATATT-AAAATATA
* * ** * *
639161 TTAATAAAATAAAAATATAAAA--TTTTAACTT-CAAAATT-ATTAAAAAT-TAAT-TTAAT-AA
257 TTAATAAAATAAAAATATAAAATTTTTTTACTTAAAAAATTAATTTCATATATATTATTAATAAA
* * *
639219 AAATCAAAAATAATTTTGAAAAAATATATTTAATTTTCTTAAAATAATTTTTTACACAAATAAAT
322 AAATCAAAAATAATTTTGAAAAATTATATTTAATTTTCTTAAAATAATTTTTTACATAAATACAT
* * * * * *
639284 TACAGTTTTTGACACTGTTTCATGTAAAACTATAATTTTTG
387 TA-AGGTTTCGATAATGTTTTATGTAAAACTATAATTTTTA
* * * *
639325 TATGTAATCTAATATTATTTATATGTAATTTGTTACATATAAATATTATTTTCAAAGATTCTTTA
1 TATGTAATCTAGTAATGTTTATATGTAATTTGTTACATACAAATATTATTTTCAAAGATTCTTTA
* * * * * * * *
639390 CACAAATATATTACCTATAACACATATTATATACAAATATTACCTATACTCTAATGATTTAGGTA
66 CACAAATACATTACTTATTATACATATTATATATAAATATTACCTAAACTCTAATAATTTATGTA
*
639455 AATTATAATA
131 AATTCTAATA
639465 ATTAAATTAT
Statistics
Matches: 832, Mismatches: 133, Indels: 71
0.80 0.13 0.07
Matches are distributed among these distances:
418 1 0.00
419 60 0.07
420 149 0.18
421 3 0.00
422 6 0.01
423 6 0.01
424 8 0.01
426 39 0.05
427 43 0.05
428 9 0.01
429 5 0.01
430 164 0.20
431 75 0.09
432 2 0.00
433 2 0.00
434 7 0.01
435 1 0.00
437 2 0.00
438 9 0.01
440 4 0.00
441 20 0.02
442 21 0.03
443 3 0.00
444 2 0.00
445 47 0.06
446 103 0.12
447 40 0.05
448 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (426 bp):
TATGTAATCTAGTAATGTTTATATGTAATTTGTTACATACAAATATTATTTTCAAAGATTCTTTA
CACAAATACATTACTTATTATACATATTATATATAAATATTACCTAAACTCTAATAATTTATGTA
AATTCTAATATTTATGTGTAATTTAGTAATCTTTAGTTGCAATTCTTACAACTAATAAAAAATCT
AAATTTTAACATAAAATTATTTTTATTAATATAATATATTTATTACTAATATTAAAATATATTAA
TAAAATAAAAATATAAAATTTTTTTACTTAAAAAATTAATTTCATATATATTATTAATAAAAAAT
CAAAAATAATTTTGAAAAATTATATTTAATTTTCTTAAAATAATTTTTTACATAAATACATTAAG
GTTTCGATAATGTTTTATGTAAAACTATAATTTTTA
Done.