Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008143.1 Hibiscus syriacus cultivar Beakdansim tig00110705_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1142845
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:7650 original size:137 final size:138
Alignment explanation
Indices: 7398--7658 Score: 411
Period size: 137 Copynumber: 1.9 Consensus size: 138
7388 TTAAGGTCAA
*
7398 TTGACCTTTCTGATTGCAAGAGACTAAGGAAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
1 TTGACCTTTCTCATTGCAAGAGACTAAGGAAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
* *
7463 ACCCTTTGCTGCAATGGATGTGAAAATTTGGTTGAACTATCTTCTCTCAATCAATTGACATCTCT
66 ACCCTTTGCTGCAATGGATGTGAAAATTTGATTGAACTACCTTCTCTCAATCAATTGACATCTCT
7528 TCAACGTC
131 TCAACGTC
* *
7536 TTGACCTTTCTCATTGCAAGAGTCTAAGG-AGATCCCTAATCTATCAGGAGCCGTCAACCTTCAA
1 TTGACCTTTCTCATTGCAAGAGACTAAGGAAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
* * *
7600 AGCCTTTGCTGCCATAGG-TGTGAAAATTTGATTGAACTACCTTGC-GTCAATCAATTGAC
66 ACCCTTTGCTGCAAT-GGATGTGAAAATTTGATTGAACTACCTT-CTCTCAATCAATTGAC
7659 CTTTCTCATT
Statistics
Matches: 113, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
137 83 0.73
138 30 0.27
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (138 bp):
TTGACCTTTCTCATTGCAAGAGACTAAGGAAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
ACCCTTTGCTGCAATGGATGTGAAAATTTGATTGAACTACCTTCTCTCAATCAATTGACATCTCT
TCAACGTC
Found at i:10252 original size:29 final size:30
Alignment explanation
Indices: 10172--10255 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
10162 ATTCTTCCTT
* * *
10172 CCCTTCTCCTCAGTTGAATTGTTTTCTCTC
1 CCCTTCTCCTCAGTTGAAGTATTTTCTATC
* * *
10202 CCCTCCTCGC-CAATTCAAGTATTTTC-ATC
1 CCCTTCTC-CTCAGTTGAAGTATTTTCTATC
*
10231 CTCTTCTCCTCAGTTGAAGTATTTT
1 CCCTTCTCCTCAGTTGAAGTATTTT
10256 TCTTGAGAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
28 1 0.02
29 21 0.50
30 19 0.45
31 1 0.02
ACGTcount: A:0.15, C:0.32, G:0.10, T:0.43
Consensus pattern (30 bp):
CCCTTCTCCTCAGTTGAAGTATTTTCTATC
Found at i:10683 original size:30 final size:29
Alignment explanation
Indices: 10648--10752 Score: 86
Period size: 30 Copynumber: 3.6 Consensus size: 29
10638 ATTTTTCTTG
10648 TCAATTCAAGTATTCTTCCTTCCCTTCTCC
1 TCAATTCAAGTATT-TTCCTTCCCTTCTCC
* * * * * *
10678 TCAATTGAATTGTTTTCTCTCCCCTCCTCG
1 TCAATTCAAGTATTTTC-CTTCCCTTCTCC
* *
10708 TCGATTCAAGTATTTT-CATCCTCTTCTCC
1 TCAATTCAAGTATTTTCCTTCC-CTTCTCC
* *
10737 TCAGTTGAAGTATTTT
1 TCAATTCAAGTATTTT
10753 TCTTGAGAAC
Statistics
Matches: 56, Mismatches: 17, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
28 3 0.05
29 21 0.38
30 32 0.57
ACGTcount: A:0.17, C:0.30, G:0.09, T:0.45
Consensus pattern (29 bp):
TCAATTCAAGTATTTTCCTTCCCTTCTCC
Found at i:12757 original size:23 final size:24
Alignment explanation
Indices: 12731--12786 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
12721 TTTATAACTG
* *
12731 TAAAAAATAATTAAATAA-AATAC
1 TAAAAAAAAAATAAATAATAATAC
*
12754 TAAAAAAAAAATAAATAATAATAT
1 TAAAAAAAAAATAAATAATAATAC
*
12778 TAAATAAAA
1 TAAAAAAAA
12787 TACTAACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAAAAAAAATAAATAATAATAC
Found at i:12781 original size:36 final size:35
Alignment explanation
Indices: 12740--12811 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
12730 GTAAAAAATA
12740 ATTAAATAAAATACTAAAAAAAAAATAAATAATAAT
1 ATTAAATAAAATACTAAAAAAAAAATAAAT-ATAAT
* * *
12776 ATTAAATAAAATACTAACAAAATATTAAATATAAT
1 ATTAAATAAAATACTAAAAAAAAAATAAATATAAT
12811 A
1 A
12812 AAATATACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 6 0.18
36 27 0.82
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (35 bp):
ATTAAATAAAATACTAAAAAAAAAATAAATATAAT
Found at i:12816 original size:17 final size:18
Alignment explanation
Indices: 12784--12817 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12774 ATATTAAATA
12784 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
12802 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
12818 ACCTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:14390 original size:30 final size:30
Alignment explanation
Indices: 14363--14552 Score: 204
Period size: 30 Copynumber: 6.3 Consensus size: 30
14353 GCTCTTCTTC
*
14363 TCAATTGAAGTGTTTTTCATCCCCTTCTCG
1 TCAATTGAAGTATTTTTCATCCCCTTCTCG
* * *
14393 TCAGTTGAAGTGTTTTCTC-TCCCCTTCTAG
1 TCAATTGAAGTATTTT-TCATCCCCTTCTCG
* **
14423 TCAATTGAAGTATTCTTCATCCTTTTCTCG
1 TCAATTGAAGTATTTTTCATCCCCTTCTCG
* * *
14453 TCAACTGAAGTATTTTTTC-TCCCCGTCTCA
1 TCAATTGAAGTA-TTTTTCATCCCCTTCTCG
* * *
14483 TCAATTAAAGTATTTTTCATCCTCTACTCG
1 TCAATTGAAGTATTTTTCATCCCCTTCTCG
* * *
14513 CCAATTAAAGTATTTTTCATCCCCTTCTTG
1 TCAATTGAAGTATTTTTCATCCCCTTCTCG
14543 TCAATTGAAG
1 TCAATTGAAG
14553 GGAACTTCCT
Statistics
Matches: 130, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
29 8 0.06
30 115 0.88
31 7 0.05
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.43
Consensus pattern (30 bp):
TCAATTGAAGTATTTTTCATCCCCTTCTCG
Found at i:19730 original size:20 final size:20
Alignment explanation
Indices: 19707--19746 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
19697 TTGAATAACT
*
19707 AATAACATTATAAAATAAAA
1 AATAACATAATAAAATAAAA
* *
19727 AATATCATAATAAATTAAAA
1 AATAACATAATAAAATAAAA
19747 TACACAAGCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AATAACATAATAAAATAAAA
Found at i:26265 original size:34 final size:34
Alignment explanation
Indices: 26222--26345 Score: 194
Period size: 34 Copynumber: 3.6 Consensus size: 34
26212 TTTATTAATT
26222 AACCTGAATTACATAAGATACAAAATGCACTCTA
1 AACCTGAATTACATAAGATACAAAATGCACTCTA
26256 AACCTGAATTACATAAGATACAAAATGCACTCTA
1 AACCTGAATTACATAAGATACAAAATGCACTCTA
* * * *
26290 AACCTGAATTACATAAGATACACATTACTCTCTA
1 AACCTGAATTACATAAGATACAAAATGCACTCTA
* *
26324 ATCCTGAAATACATAAGATACA
1 AACCTGAATTACATAAGATACA
26346 CATTACACTA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 84 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (34 bp):
AACCTGAATTACATAAGATACAAAATGCACTCTA
Found at i:48730 original size:41 final size:41
Alignment explanation
Indices: 48684--48839 Score: 276
Period size: 41 Copynumber: 3.8 Consensus size: 41
48674 TAGTGGAAAA
* *
48684 TCGCGTTGCAATAGTCTACAGTGTCGTTGCTATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
48725 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
* *
48766 TCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATC
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
48807 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGAT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGAT
48840 AGTCTAAAAA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 110 1.00
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
Found at i:48754 original size:21 final size:21
Alignment explanation
Indices: 48728--48845 Score: 95
Period size: 21 Copynumber: 5.7 Consensus size: 21
48718 TTCCATTTCG
48728 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
48749 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
*
48767 CGCGTTGCGATAGTGTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
* * *
48790 CGTTGCGAT--TTTCCA-TCT
1 CGTTGCGATAGTCTACAGTGT
48808 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
48831 CGTTGCGATAGTCTA
1 CGTTGCGATAGTCTA
48846 AAAATATTAA
Statistics
Matches: 75, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
18 4 0.05
19 8 0.11
20 18 0.24
21 33 0.44
22 8 0.11
23 4 0.05
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:48774 original size:20 final size:20
Alignment explanation
Indices: 48708--48818 Score: 68
Period size: 20 Copynumber: 5.5 Consensus size: 20
48698 TCTACAGTGT
* *
48708 CGTTGCTATTTTCCATTTCG
1 CGTTGCGATTTTCCATGTCG
* *
48728 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATGTCG
*
48748 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATGTCG
* *
48769 CGTTGCGATAGTGTACA-GT-G
1 CGTTGCGAT--TTTCCATGTCG
*
48789 TCGTTGCGATTTTCCATCTCG
1 -CGTTGCGATTTTCCATGTCG
48810 CGTTGCGAT
1 CGTTGCGAT
48819 AGTCTACAGT
Statistics
Matches: 68, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
19 8 0.12
20 30 0.44
21 22 0.32
22 8 0.12
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCCATGTCG
Found at i:49303 original size:41 final size:40
Alignment explanation
Indices: 49258--49362 Score: 146
Period size: 36 Copynumber: 2.7 Consensus size: 40
49248 TAATTTACTT
49258 TAGACTATCGCAACGCGAAATGGAAAATAGCAACGACACTG
1 TAGACTATC-CAACGCGAAATGGAAAATAGCAACGACACTG
*
49299 TAGACTAT----CGCGAAATGGAAAATCGCAACGACACTG
1 TAGACTATCCAACGCGAAATGGAAAATAGCAACGACACTG
*
49335 TAGACTATCACAACACGAAATGGAAAAT
1 TAGACTATC-CAACGCGAAATGGAAAAT
49363 CGCGTTGCGA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
36 35 0.61
41 22 0.39
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.16
Consensus pattern (40 bp):
TAGACTATCCAACGCGAAATGGAAAATAGCAACGACACTG
Found at i:49523 original size:17 final size:17
Alignment explanation
Indices: 49501--49534 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
49491 CAAAATCGTA
49501 TATTATCTGAGATTTTT
1 TATTATCTGAGATTTTT
49518 TATTATCTGAGATTTTT
1 TATTATCTGAGATTTTT
49535 GGTCACTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.59
Consensus pattern (17 bp):
TATTATCTGAGATTTTT
Found at i:50023 original size:138 final size:141
Alignment explanation
Indices: 49769--50024 Score: 403
Period size: 138 Copynumber: 1.8 Consensus size: 141
49759 TTACCTTTCA
* * *
49769 TATAAAATATTGTCTTCTTTATTTTTTATATACGTATATACATTGGTGACGAAGTTAATTATACT
1 TATAAAATATTGTCTTCTTTATTTTTGATATACGTATATACATTAGTGACAAAGTTAATTATACT
* *
49834 AAAGTAATTGTCTTTTTTATTTATATATTTATAACACTCATTTTTTCTCATTTACCTTTCATATG
66 AAAGTAATTGTCTTCTTTATTTATATATTTATAACACTCAATTTTTCTCATTTACCTTTCATATG
49899 ATCTCTTTATT
131 ATCTCTTTATT
* *
49910 TATAAAAT-TGTGTCTTCTTTATTTTTGATGTATGTATATACATTAGTGACAAAGTT-ATT-T-C
1 TATAAAATAT-TGTCTTCTTTATTTTTGATATACGTATATACATTAGTGACAAAGTTAATTATAC
*
49971 TAAATTAATTGTCTTCTTTATTTATATATTTATAACACTCAATTTTTCTCATTT
65 TAAAGTAATTGTCTTCTTTATTTATATATTTATAACACTCAATTTTTCTCATTT
50025 TATATTTATA
Statistics
Matches: 106, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
138 52 0.49
139 1 0.01
140 4 0.04
141 49 0.46
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.52
Consensus pattern (141 bp):
TATAAAATATTGTCTTCTTTATTTTTGATATACGTATATACATTAGTGACAAAGTTAATTATACT
AAAGTAATTGTCTTCTTTATTTATATATTTATAACACTCAATTTTTCTCATTTACCTTTCATATG
ATCTCTTTATT
Found at i:50102 original size:22 final size:24
Alignment explanation
Indices: 50072--50116 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
50062 AGATTACTTT
50072 ATTTGTATATTTATAAAA-AAATC
1 ATTTGTATATTTATAAAATAAATC
50095 ATTT-TATATTTATAAAATAAAT
1 ATTTGTATATTTATAAAATAAAT
50117 TAATTATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTTGTATATTTATAAAATAAATC
Found at i:50123 original size:22 final size:22
Alignment explanation
Indices: 50077--50124 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
50067 ACTTTATTTG
*
50077 TATATTTATAAAAAAATCATTT
1 TATATTTATAAAAAAATCATAT
*
50099 TATATTTATAAAATAAATTA-AT
1 TATATTTATAAAA-AAATCATAT
50121 TATA
1 TATA
50125 ACTAAGTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TATATTTATAAAAAAATCATAT
Found at i:50157 original size:74 final size:74
Alignment explanation
Indices: 50019--50157 Score: 208
Period size: 74 Copynumber: 1.9 Consensus size: 74
50009 TCAATTTTTC
* * *
50019 TCATTTTATATTTATAAAATAAATTGATTATAACTAAGTGACTAGATTACTTTATTTGTATATTT
1 TCATTTTATATTTATAAAATAAATTAATTATAACTAAGTGACTAGATTAATTTATTTCTATATTT
50084 ATAAAAAAA
66 ATAAAAAAA
* * *
50093 TCATTTTATATTTATAAAATAAATTAATTATAACTAAGTGAGTATATTAATTGT-TTTCTTTATT
1 TCATTTTATATTTATAAAATAAATTAATTATAACTAAGTGACTAGATTAATT-TATTTCTATATT
50157 T
65 T
50158 CTGCTGTGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 57 0.98
75 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.48
Consensus pattern (74 bp):
TCATTTTATATTTATAAAATAAATTAATTATAACTAAGTGACTAGATTAATTTATTTCTATATTT
ATAAAAAAA
Found at i:64354 original size:128 final size:129
Alignment explanation
Indices: 64124--64361 Score: 288
Period size: 128 Copynumber: 1.9 Consensus size: 129
64114 CTAGGAGACC
* ** * * *
64124 CAACTCCAACACAATAGAGCTTGCTTTTTAAGGCATTCATCTGCATTCCTCTTAGTTTCCTTCAG
1 CAACTCCAACACAATAAAGCTTGCTTTTTAAGGCATTCAGATGCACTCCCCTTAGATTCCTTCAG
* *
64189 TCTGTCGCCCCCTCCCTCCCTCCCCTTTGACTGTAGACCCTAGACCCTAGCTCCGAATGAGCTA
66 TCTGTCGCCCCCTCCCTCCCTCCCCTGTGACTCTAGACCCTAGACCCTAGCTCCGAATGAGCTA
*
64253 CAACTCCAACACAATAAAGC-T-CATTTTTAAGGCATTCAGATGCACTCCCCTTA-ATTCCTT-G
1 CAACTCCAACACAATAAAGCTTGC-TTTTTAAGGCATTCAGATGCACTCCCCTTAGATTCCTTCA
* * * *
64314 GTCTGCTTGTCTCCCTCCCTCCCTCTCCC-GTGATTCTAGACCTTAGAC
65 GTCTG-TCG-CCCCCTCCCTCCCTC-CCCTGTGACTCTAGACCCTAGAC
64362 TCCAATCACC
Statistics
Matches: 92, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
126 5 0.05
127 9 0.10
128 56 0.61
129 22 0.24
ACGTcount: A:0.21, C:0.35, G:0.13, T:0.31
Consensus pattern (129 bp):
CAACTCCAACACAATAAAGCTTGCTTTTTAAGGCATTCAGATGCACTCCCCTTAGATTCCTTCAG
TCTGTCGCCCCCTCCCTCCCTCCCCTGTGACTCTAGACCCTAGACCCTAGCTCCGAATGAGCTA
Found at i:65793 original size:107 final size:107
Alignment explanation
Indices: 65607--65822 Score: 414
Period size: 107 Copynumber: 2.0 Consensus size: 107
65597 TTCATAGAAG
*
65607 TATGTATTGGTTATGATTTATATGTGTGCATGAGTATATGTGTTATTGATATGAATATGGTAAGT
1 TATGTATTGGTCATGATTTATATGTGTGCATGAGTATATGTGTTATTGATATGAATATGGTAAGT
*
65672 AAAATGGATTAATGGTGATGATAAGAATAATAATAAAGATAA
66 AAAATGGATTAATGGTGAGGATAAGAATAATAATAAAGATAA
65714 TATGTATTGGTCATGATTTATATGTGTGCATGAGTATATGTGTTATTGATATGAATATGGTAAGT
1 TATGTATTGGTCATGATTTATATGTGTGCATGAGTATATGTGTTATTGATATGAATATGGTAAGT
65779 AAAATGGATTAATGGTGAGGATAAGAATAATAATAAAGATAA
66 AAAATGGATTAATGGTGAGGATAAGAATAATAATAAAGATAA
65821 TA
1 TA
65823 AAATGATAGG
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (107 bp):
TATGTATTGGTCATGATTTATATGTGTGCATGAGTATATGTGTTATTGATATGAATATGGTAAGT
AAAATGGATTAATGGTGAGGATAAGAATAATAATAAAGATAA
Found at i:66415 original size:103 final size:103
Alignment explanation
Indices: 66190--66407 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
66180 GTCGAGGGTC
66190 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
66255 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCACTAGCATATGTATATGATTCTTAAGGAATGA
*
66293 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
66358 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCACTAGCATATGTATATGATTCTTAAGGAATGA
66396 TATGTGGTCCTT
1 TATGTGGTCCTT
66408 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCACTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:66458 original size:23 final size:23
Alignment explanation
Indices: 66423--66489 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
66413 CATTATTATA
* *
66423 TGGCACTACGGTGTAATTCTACG
1 TGGCACTACGGTGCAATTATACG
66446 TGGCACT-CGGGTGCAATTATACG
1 TGGCACTAC-GGTGCAATTATACG
*
66469 TGGCACTTCGGTGCAATTATA
1 TGGCACTACGGTGCAATTATA
66490 TGAGCTGTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.03
23 38 0.95
24 1 0.03
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:80527 original size:17 final size:17
Alignment explanation
Indices: 80505--80545 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
80495 ATTTTTAACG
*
80505 TTTGATTAAATAATCAC
1 TTTGATCAAATAATCAC
80522 TTTGATCAAATAATCAC
1 TTTGATCAAATAATCAC
80539 TTTGATC
1 TTTGATC
80546 CTTATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (17 bp):
TTTGATCAAATAATCAC
Found at i:90270 original size:23 final size:22
Alignment explanation
Indices: 90227--90271 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
90217 GTCAAAATAT
* *
90227 AAAAATTAGAGGTTAGTTTTAA
1 AAAAAATAGAGGTTAGATTTAA
90249 AAAAAATAGAGGTTAGAATTTAA
1 AAAAAATAGAGGTTAG-ATTTAA
90272 TTTATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (22 bp):
AAAAAATAGAGGTTAGATTTAA
Found at i:94277 original size:157 final size:153
Alignment explanation
Indices: 93995--94308 Score: 522
Period size: 157 Copynumber: 2.0 Consensus size: 153
93985 TAGAAAGAAA
*
93995 ATAGATCAAGGTAATGAAAGTTGAGGAGATTCACACCCAATTACTTTATTGCTTTCAATCATATT
1 ATAGATCAAAGTAATGAAAGTTGAGGAGATTCACACCCAATTACTTTATTGCTTTCAATCATATT
*
94060 CCCAACACAACCCATTAGCCTTAAACCCTAAATGAAAGTTGATCAACTTTCCTTCTACC-AACCC
66 CCCAACACAACCCATTAGCCTTAAACCCTAAATGAAAGTTGATCAACTTTCCTTCCACCAAACCC
94124 CCCACAAAGTAATTAAACAAAAT
131 CCCACAAAGTAATTAAACAAAAT
94147 ATAGATCAAAGTAATGAAAGTTGAGGAGATTCACACCCAAATTTATTACTTTATTGCTTTCAATC
1 ATAGATCAAAGTAATGAAAGTTGAGGAGATTCACACCC--A---ATTACTTTATTGCTTTCAATC
*
94212 ATATTCCCAACACAGCCCATTAGCCTTAAACCCTAAATGAAAGTTGATCAACTTTCCTTCCACCA
61 ATATTCCCAACACAACCCATTAGCCTTAAACCCTAAATGAAAGTTGATCAACTTTCCTTCCACC-
* *
94277 AAACCGCCCACAAAGTAATTAAACAATAT
125 AAACCCCCCACAAAGTAATTAAACAAAAT
94306 ATA
1 ATA
94309 TATAAAACCA
Statistics
Matches: 150, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
152 37 0.25
154 1 0.01
157 83 0.55
159 29 0.19
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (153 bp):
ATAGATCAAAGTAATGAAAGTTGAGGAGATTCACACCCAATTACTTTATTGCTTTCAATCATATT
CCCAACACAACCCATTAGCCTTAAACCCTAAATGAAAGTTGATCAACTTTCCTTCCACCAAACCC
CCCACAAAGTAATTAAACAAAAT
Found at i:103153 original size:16 final size:16
Alignment explanation
Indices: 103132--103165 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
103122 TAAATTATAA
*
103132 AAAAAACACTTCAAAT
1 AAAAAACAATTCAAAT
*
103148 AAAAAACAATTTAAAT
1 AAAAAACAATTCAAAT
103164 AA
1 AA
103166 TTAATTCCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAAACAATTCAAAT
Found at i:108908 original size:6 final size:6
Alignment explanation
Indices: 108897--108924 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
108887 ACTTTTATCT
108897 GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACC
108925 CGAGACGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:109612 original size:20 final size:20
Alignment explanation
Indices: 109587--109665 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
109577 CTATCGCAAC
109587 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAA
**
109607 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAA
** * *
109627 TTCAACTATCGCAACGCGAAC
1 TGGAA-AATCGCAACGCGAAA
109648 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
109666 TTTTCGCAAC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 33 0.69
21 15 0.31
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:109652 original size:41 final size:40
Alignment explanation
Indices: 109593--109761 Score: 183
Period size: 41 Copynumber: 4.3 Consensus size: 40
109583 CAACTGGAAA
*
109593 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTT-AACT
109634 ATCGCAACGCGAACTGGAAAATCGCAACGCGA--TT---T
1 ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTAACT
* * * *
109669 -TCGCAA--CGAATTTGGAAAATCGCAACGACAACTGTAGACT
1 ATCGCAACGCGAA-CTGGAAAATCGCAACG-CGATTTTA-ACT
*
109709 ATCGCAACGCGAACTGAAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTT-AACT
109750 ATCGCAACGCGA
1 ATCGCAACGCGA
109762 TTTTCAATTA
Statistics
Matches: 107, Mismatches: 9, Indels: 24
0.76 0.06 0.17
Matches are distributed among these distances:
32 4 0.04
33 15 0.14
34 8 0.07
35 1 0.01
36 1 0.01
39 2 0.02
40 1 0.01
41 56 0.52
42 15 0.14
43 4 0.04
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (40 bp):
ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTAACT
Found at i:109673 original size:75 final size:75
Alignment explanation
Indices: 109602--109745 Score: 213
Period size: 75 Copynumber: 1.9 Consensus size: 75
109592 AATCGCAACG
* * * *
109602 CGAA-ATGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAACTGGAAAATCGCAACGC
1 CGAATATGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAACTGAAAAATCGCAACGC
109664 GATTTTCGCAA
65 GATTTTCGCAA
*
109675 CGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGAAAAATCGCAACGCG
1 CGAATATGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGAAAAATCGCAACGCG
109740 ATTTTC
66 ATTTTC
109746 AACTATCGCA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
73 4 0.06
74 16 0.25
75 43 0.68
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.19
Consensus pattern (75 bp):
CGAATATGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGAAAAATCGCAACGCG
ATTTTCGCAA
Found at i:109723 original size:22 final size:21
Alignment explanation
Indices: 109687--109783 Score: 67
Period size: 21 Copynumber: 4.6 Consensus size: 21
109677 AATTTGGAAA
109687 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTGTA-ACT
**
109709 ATCGCAACGCGAACTG-AAAA
1 ATCGCAACGCGAACTGTAACT
* *
109729 ATCGCAACGCG-ATTTTCAACT
1 ATCGCAACGCGAACTGT-AACT
* * *
109750 ATCGCAACGCG-ATTTTCAATT
1 ATCGCAACGCGAACTGT-AACT
109771 ATCGCAACGCGAA
1 ATCGCAACGCGAA
109784 ATGCAATGCG
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
19 2 0.03
20 12 0.19
21 35 0.55
22 15 0.23
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTGTAACT
Found at i:109755 original size:21 final size:21
Alignment explanation
Indices: 109729--109782 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
109719 GAACTGAAAA
109729 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
109750 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
109771 ATCGCAACGCGA
1 ATCGCAACGCGA
109783 AATGCAATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:109790 original size:21 final size:21
Alignment explanation
Indices: 109708--109790 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
109698 AACTGTAGAC
* *
109708 TATCGCAACGCGAACTG-AAA
1 TATCGCAACGCGAATTGCAAT
* * * *
109728 AATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGAATTGCAAT
* *
109749 TATCGCAACGCGATTTTCAAT
1 TATCGCAACGCGAATTGCAAT
*
109770 TATCGCAACGCGAAATGCAAT
1 TATCGCAACGCGAATTGCAAT
109791 GCGAATTTGC
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
20 13 0.25
21 39 0.75
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (21 bp):
TATCGCAACGCGAATTGCAAT
Found at i:109843 original size:19 final size:19
Alignment explanation
Indices: 109808--109844 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
109798 TGCGATAGTG
*
109808 GAGATCGCAATGTGAATTA
1 GAGATCGCAATGCGAATTA
*
109827 GAGATCGCATTGCGAATT
1 GAGATCGCAATGCGAATT
109845 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (19 bp):
GAGATCGCAATGCGAATTA
Found at i:118202 original size:20 final size:21
Alignment explanation
Indices: 118164--118203 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
118154 ATATAATATT
118164 AATAATTTAAAATTCAATTAA
1 AATAATTTAAAATTCAATTAA
*
118185 AATATTTTAAAATT-AATTA
1 AATAATTTAAAATTCAATTA
118204 TAACATGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
AATAATTTAAAATTCAATTAA
Found at i:131155 original size:9 final size:9
Alignment explanation
Indices: 131138--131177 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
131128 AATATTATTT
*
131138 TAATAAAAA
1 TAATTAAAA
131147 TAATTAAAA
1 TAATTAAAA
131156 TAATTAAAA
1 TAATTAAAA
131165 TATATTTAAAA
1 TA-A-TTAAAA
131176 TA
1 TA
131178 TAATATACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
9 19 0.68
10 1 0.04
11 8 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAATTAAAA
Found at i:131367 original size:22 final size:21
Alignment explanation
Indices: 131333--131373 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
131323 ATTCTAATAT
131333 TTTTAAAATAATAATATTAAG
1 TTTTAAAATAATAATATTAAG
*
131354 TTTTATAATAAATAATATTA
1 TTTTAAAAT-AATAATATTA
131374 TTTATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTTAAAATAATAATATTAAG
Found at i:131381 original size:22 final size:20
Alignment explanation
Indices: 131330--131382 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
131320 ATTATTCTAA
*
131330 TATTTTTAAAATAATAATAT
1 TATTTTTATAATAATAATAT
*
131350 TAAGTTTTATAATAAATAATAT
1 T-ATTTTTATAAT-AATAATAT
131372 TATTTATTATA
1 TATTT-TTATA
131383 TTTCATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 12 0.44
22 14 0.52
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TATTTTTATAATAATAATAT
Found at i:132817 original size:13 final size:12
Alignment explanation
Indices: 132799--132832 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
132789 ATGGTCGATG
132799 TTTTTTATTATTA
1 TTTTTTATT-TTA
132812 TTTTTTATTTTA
1 TTTTTTATTTTA
132824 TGTTTTTAT
1 T-TTTTTAT
132833 CTTTTAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:140058 original size:53 final size:53
Alignment explanation
Indices: 139943--140182 Score: 318
Period size: 53 Copynumber: 4.5 Consensus size: 53
139933 AACAAATCAT
* * * *
139943 AATAGCTTACCTATGAATATAAGCATGCAGCTGTATCCTTCTGATAAACTATAAATA
1 AATAGCTTACCTATGAATGTAAGCA-G-A--TATATCCTTATAATAAACTATAAATA
* *
140000 AATAGCTTACCTATGAGTGTAAGCAGATATATCCTTATAATAAACTATAAACA
1 AATAGCTTACCTATGAATGTAAGCAGATATATCCTTATAATAAACTATAAATA
* * *
140053 TATAGCTTACCTATGAGTGTAAGCAGCTATATCCTTATAATAAACTATAAATA
1 AATAGCTTACCTATGAATGTAAGCAGATATATCCTTATAATAAACTATAAATA
* * *
140106 AATAGCTTACCTATGAATATAAGTAGATGTATCCTTATAATAAACTATAAATA
1 AATAGCTTACCTATGAATGTAAGCAGATATATCCTTATAATAAACTATAAATA
* *
140159 AATAGTTTACCTATTAATGTAAGC
1 AATAGCTTACCTATGAATGTAAGC
140183 CGTTGGATCA
Statistics
Matches: 164, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
53 139 0.85
55 1 0.01
56 1 0.01
57 23 0.14
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (53 bp):
AATAGCTTACCTATGAATGTAAGCAGATATATCCTTATAATAAACTATAAATA
Found at i:144323 original size:2 final size:2
Alignment explanation
Indices: 144311--144343 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
144301 GGTAAGTACA
144311 AT AT A- 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 AT
144344 TAAATGCTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:144574 original size:13 final size:13
Alignment explanation
Indices: 144556--144580 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
144546 TTTGACTGTT
144556 TTTTTTATTTTTA
1 TTTTTTATTTTTA
144569 TTTTTTATTTTT
1 TTTTTTATTTTT
144581 CTACGTTGTC
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:145559 original size:2 final size:2
Alignment explanation
Indices: 145552--145588 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
145542 TGTCTTATAA
145552 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
145589 TATTGTTCGA
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:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:153786 original size:14 final size:14
Alignment explanation
Indices: 153748--153797 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
153738 TTTTATAACT
*
153748 TTAAAATTATT-TA
1 TTAACATTATTATA
*
153761 TTGACA-TATTATA
1 TTAACATTATTATA
153774 TGTAA-ATTATTATA
1 T-TAACATTATTATA
153788 TTAACATTAT
1 TTAACATTAT
153798 AAAAGAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
12 4 0.13
13 11 0.37
14 15 0.50
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (14 bp):
TTAACATTATTATA
Found at i:159352 original size:23 final size:23
Alignment explanation
Indices: 159326--159381 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
159316 CAGTTCATAT
*
159326 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* **
159349 AATTGCACCGGAGTGCCGTGTAG
1 AATTGCACCGAAGTGCCACGTAG
159372 AATTGCACCG
1 AATTGCACCG
159382 TAGTTCCATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:159534 original size:103 final size:103
Alignment explanation
Indices: 159409--159622 Score: 410
Period size: 103 Copynumber: 2.1 Consensus size: 103
159399 GTCCATAAGG
159409 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACC
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACC
159474 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
*
159512 ACCATATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACC
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACC
*
159577 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
159615 ACCACATA
1 ACCACATA
159623 GACCCTCTAC
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACC
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
Found at i:160182 original size:64 final size:67
Alignment explanation
Indices: 160071--160198 Score: 192
Period size: 64 Copynumber: 2.0 Consensus size: 67
160061 ATTTTCATCT
*
160071 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTG
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATACATAAATCATATTCGATGTTTG
160136 TA
66 TA
* *
160138 TTTAATGG-GG-ATGCATCGATGCACT-C-CTTATGCATCGATACATAAATCCTATTCGATGTTT
1 TTTAATGGAGGTATGCATCGATGCACTACAC-CATGCATCGATACATAAATCATATTCGATGTTT
160199 TCATTTTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
63 1 0.02
64 31 0.54
65 15 0.26
66 2 0.04
67 8 0.14
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATACATAAATCATATTCGATGTTTG
TA
Found at i:160216 original size:64 final size:62
Alignment explanation
Indices: 160083--160240 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 62
160073 TAATGGAGGT
* * *
160083 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATACATAAATCATATTCGATGTTTGTATTTAAT-GGA
* *
160148 ATGCATCGATGCACTCCTTATGCATCGATACATAAATCCTATTCGATGTTT-TCATTTTAAAT-T
1 ATGCATCGATGCACTCC-TATGCATCGATACATAAATCATATTCGATGTTTGT-A-TTT-AATGG
160211 A
62 A
* *
160212 ATGCATCGATGCACTGCATGTGCATCGAT
1 ATGCATCGATGCACT-CCTATGCATCGAT
160241 GCACTGCATG
Statistics
Matches: 81, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
63 2 0.02
64 57 0.70
65 19 0.23
66 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATACATAAATCATATTCGATGTTTGTATTTAATGGA
Found at i:160237 original size:19 final size:19
Alignment explanation
Indices: 160213--160282 Score: 140
Period size: 19 Copynumber: 3.7 Consensus size: 19
160203 TTTAAATTAA
160213 TGCATCGATGCACTGCATG
1 TGCATCGATGCACTGCATG
160232 TGCATCGATGCACTGCATG
1 TGCATCGATGCACTGCATG
160251 TGCATCGATGCACTGCATG
1 TGCATCGATGCACTGCATG
160270 TGCATCGATGCAC
1 TGCATCGATGCAC
160283 CTTAAACAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCACTGCATG
Found at i:163981 original size:15 final size:15
Alignment explanation
Indices: 163944--163981 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
163934 ATATTTAATT
*
163944 GGGCGGGCGGATGCA
1 GGGCGGGTGGATGCA
*
163959 GGGCGGGTGGATGCG
1 GGGCGGGTGGATGCA
163974 GGGCGGGT
1 GGGCGGGT
163982 AATGTCTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.16, G:0.66, T:0.11
Consensus pattern (15 bp):
GGGCGGGTGGATGCA
Found at i:164755 original size:6 final size:6
Alignment explanation
Indices: 164744--164774 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
164734 GACACATATT
*
164744 ACCACG ACCACG ACCACG ACCACG AGCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
164775 GCCGAGCCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.35, C:0.45, G:0.19, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:164782 original size:5 final size:5
Alignment explanation
Indices: 164766--164795 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
164756 ACCACGACCA
164766 CGAGC ACGAGC CGAGC CGAGC CGAGC CGAG
1 CGAGC -CGAGC CGAGC CGAGC CGAGC CGAG
164796 ACGGACGGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.23, C:0.37, G:0.40, T:0.00
Consensus pattern (5 bp):
CGAGC
Found at i:166645 original size:2 final size:2
Alignment explanation
Indices: 166638--166662 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
166628 ATTCACTTCA
166638 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
166663 ATTAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:168440 original size:21 final size:21
Alignment explanation
Indices: 168400--168440 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
168390 ACCTTTATGT
**
168400 CACGTTTCTTTTATTTTTTAG
1 CACGTTTCTTTTATAGTTTAG
*
168421 CACGTTTTTTTTATAGTTTA
1 CACGTTTCTTTTATAGTTTA
168441 ATAGTTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.61
Consensus pattern (21 bp):
CACGTTTCTTTTATAGTTTAG
Found at i:172445 original size:5 final size:5
Alignment explanation
Indices: 172435--172459 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
172425 GTATTTTCTC
172435 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
172460 TTCTACTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:176567 original size:22 final size:22
Alignment explanation
Indices: 176538--176585 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
176528 TATAACTGAT
176538 TATT-TATTATAATATTAAAAA
1 TATTATATTATAATATTAAAAA
* *
176559 TATTATATTATATTATTAGAAA
1 TATTATATTATAATATTAAAAA
176581 TATTA
1 TATTA
176586 ATAAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TATTATATTATAATATTAAAAA
Found at i:176604 original size:52 final size:53
Alignment explanation
Indices: 176485--176605 Score: 128
Period size: 52 Copynumber: 2.3 Consensus size: 53
176475 ATAATTTATT
* * *
176485 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAACTGA
1 ATATATTATTAAATATTAAAAATAT-ATATATTATATTATTAAAATATAACTAA
*
176537 TTAT-TTATTATAATATTAAAAATAT-TATATTATATTATTAGAAATATTAA-TAA
1 ATATATTATTA-AATATTAAAAATATATATATTATATTATTA-AAATA-TAACTAA
176590 ATATATT-TTAAATATT
1 ATATATTATTAAATATT
176606 TTAATAATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
51 6 0.10
52 25 0.43
53 13 0.22
54 14 0.24
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (53 bp):
ATATATTATTAAATATTAAAAATATATATATTATATTATTAAAATATAACTAA
Found at i:191703 original size:29 final size:30
Alignment explanation
Indices: 191661--191721 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
191651 ATGCCAGTTT
* *
191661 TTTTAGTTTAGTGCCTAACGTTT-ATTTCG
1 TTTTAATTTAGTGCCTAACGTTTCATTCCG
*
191690 TTTTAATTTGGTGCCTAACGTTTCATTCCG
1 TTTTAATTTAGTGCCTAACGTTTCATTCCG
191720 TT
1 TT
191722 GCTCAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (30 bp):
TTTTAATTTAGTGCCTAACGTTTCATTCCG
Found at i:191830 original size:20 final size:20
Alignment explanation
Indices: 191807--191846 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
191797 TTAAATTTTT
191807 TATATAAAATTTAAAAAAAA
1 TATATAAAATTTAAAAAAAA
** *
191827 TATATGTATTTTAAAAAAAA
1 TATATAAAATTTAAAAAAAA
191847 AGAAAATACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
TATATAAAATTTAAAAAAAA
Found at i:195666 original size:23 final size:21
Alignment explanation
Indices: 195639--195681 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
195629 ATATAAAAAA
195639 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
195660 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
195681 T
1 T
195682 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:197928 original size:28 final size:28
Alignment explanation
Indices: 197894--197968 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
197884 TTATATTGTC
*
197894 GTCGAGCTGGTACTTGAAATATTAGATT
1 GTCGAGCTGGTGCTTGAAATATTAGATT
*
197922 GTCGAGCTGGTGCTTAAAATATTAGATT
1 GTCGAGCTGGTGCTTGAAATATTAGATT
*
197950 GTCGAGCTAGTGCTTGAAA
1 GTCGAGCTGGTGCTTGAAA
197969 GCAATGAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.33
Consensus pattern (28 bp):
GTCGAGCTGGTGCTTGAAATATTAGATT
Found at i:207376 original size:50 final size:49
Alignment explanation
Indices: 207260--207376 Score: 110
Period size: 50 Copynumber: 2.3 Consensus size: 49
207250 AAGCGCGTCA
* * *
207260 CCTGAACCGCGCTATATGCTGATTTGACTCCACGTGGATATAACGCGCCC
1 CCTG-ACCGCGCTATACGCTGATCTGACGCCACGTGGATATAACGCGCCC
* * * * **
207310 CCTG-CCTCGCAATATACGGTGATCTGGCGCCACGTGGGTATAGTGCGCCC
1 CCTGACCGCGC--TATACGCTGATCTGACGCCACGTGGATATAACGCGCCC
207360 CCTGATCCGCGCTATAC
1 CCTGA-CCGCGCTATAC
207377 CTAGATATCT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
48 5 0.09
50 43 0.81
52 5 0.09
ACGTcount: A:0.19, C:0.33, G:0.25, T:0.23
Consensus pattern (49 bp):
CCTGACCGCGCTATACGCTGATCTGACGCCACGTGGATATAACGCGCCC
Found at i:207845 original size:111 final size:111
Alignment explanation
Indices: 207651--207872 Score: 354
Period size: 111 Copynumber: 2.0 Consensus size: 111
207641 TGGAAATCAT
* *
207651 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTAAAATGAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTAAAATGAAATTATTAGTAA
* * *
207716 TATTTAGTTGATTGATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATACATGATTATTAGATTAAGAATTAA
* * *
207762 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTAAAATGAAATTATTAGTAA
* *
207827 TAATTAGTTTATTCATTTAATACATGATTATTATATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATACATGATTATTAGATTAAGAATTAA
207873 TTTTTGTAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTAAAATGAAATTATTAGTAA
TAATTAGTTGATTCATTTAATACATGATTATTAGATTAAGAATTAA
Found at i:209980 original size:35 final size:33
Alignment explanation
Indices: 209941--210025 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
209931 ATATTTTAGT
209941 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
* *
209976 TAATTTGGTTATCATTTACCATTTTATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
210011 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
210026 TAAATATCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:219064 original size:22 final size:23
Alignment explanation
Indices: 219034--219082 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
219024 GAGGTTTCGG
*
219034 TTTTGTAAGGAAGAACAAA-GGT
1 TTTTATAAGGAAGAACAAAGGGT
219056 TTTTATAAGGAAGAACAAAGGGT
1 TTTTATAAGGAAGAACAAAGGGT
219079 TTTT
1 TTTT
219083 TGTAAAAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (23 bp):
TTTTATAAGGAAGAACAAAGGGT
Found at i:219091 original size:22 final size:21
Alignment explanation
Indices: 219034--219091 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 21
219024 GAGGTTTCGG
219034 TTTTGTAAGGAAGAACAAAGGT
1 TTTTGTAA-GAAGAACAAAGGT
*
219056 TTTTATAAGGAAGAACAAAGGGTT
1 TTTTGTAA-GAAGAACAAA-GG-T
219080 TTTTGTAA-AAGA
1 TTTTGTAAGAAGA
219092 TGTTTTCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 22 0.69
23 2 0.06
24 8 0.25
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (21 bp):
TTTTGTAAGAAGAACAAAGGT
Found at i:228737 original size:17 final size:17
Alignment explanation
Indices: 228715--228747 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
228705 GATACGACTC
228715 AATTTTTTAATTTTTTT
1 AATTTTTTAATTTTTTT
*
228732 AATTTTTTCATTTTTT
1 AATTTTTTAATTTTTT
228748 CAAAGCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
AATTTTTTAATTTTTTT
Found at i:269616 original size:21 final size:21
Alignment explanation
Indices: 269592--269632 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
269582 TTAGAAATTA
* *
269592 GGTAGAAAAATTAATATTTTC
1 GGTAAAAAAAATAATATTTTC
269613 GGTAAAAAAAATAATATTTT
1 GGTAAAAAAAATAATATTTT
269633 AGATAATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (21 bp):
GGTAAAAAAAATAATATTTTC
Found at i:279192 original size:2 final size:2
Alignment explanation
Indices: 279187--279212 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
279177 AAAGTCCGTC
279187 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
279213 TAAAATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:279615 original size:15 final size:14
Alignment explanation
Indices: 279592--279632 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
279582 ATTAAATACT
*
279592 AAATACATAAAAGA
1 AAATTCATAAAAGA
279606 AATATTCATAAAA-A
1 AA-ATTCATAAAAGA
279620 AAATT-ATAAAAGA
1 AAATTCATAAAAGA
279633 TCAAATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 6 0.25
13 4 0.17
14 5 0.21
15 9 0.38
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (14 bp):
AAATTCATAAAAGA
Found at i:281653 original size:40 final size:38
Alignment explanation
Indices: 281609--281683 Score: 105
Period size: 40 Copynumber: 1.9 Consensus size: 38
281599 GTTGCACACA
*
281609 TTCTTAATAACATTTTCGGTTGGCAACCGAAAATGTTTCC
1 TTCTTAATAACATTTTCAGTT--CAACCGAAAATGTTTCC
* *
281649 TTCTTCATAACATTTTCAGTTCAATCGAAAATGTT
1 TTCTTAATAACATTTTCAGTTCAACCGAAAATGTT
281684 ACAAATTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 13 0.41
40 19 0.59
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (38 bp):
TTCTTAATAACATTTTCAGTTCAACCGAAAATGTTTCC
Found at i:287206 original size:645 final size:647
Alignment explanation
Indices: 285967--287259 Score: 2509
Period size: 645 Copynumber: 2.0 Consensus size: 647
285957 AGATTAGATC
285967 GGTTTCTATTAAGTGGTGCTTTTTTTCAGGTATTTCCAAAAGTTATTCAGAAACTGTTGCCGAAA
1 GGTTTCTATTAAGTGGTGCTTTTTTTCAGGTATTTCCAAAAGTTATTCAGAAACTGTTGCCGAAA
286032 TCTATTTCTGATCATAACCCTATAGTACTTGAGGATGATTTCAAAAACTGGGGTCCTAAACCTTT
66 TCTATTTCTGATCATAACCCTATAGTACTTGAGGATGATTTCAAAAACTGGGGTCCTAAACCTTT
*
286097 CCGGTTTTTTAATTATTTACTAGAGGAGGATGGGTTTGATGGGGTGGTTAAGAATGTTGTGTATG
131 CCGGTTTTTTAATTATTTACTAGAGGAGGATGGGTTTGATGGGGTGGTTAAGAATGATGTGTATG
*
286162 ATTTAAAGAGGGAAAATGCACGTAGGGGTATGTTGAGTATTCTTCAAGGAACTAAGAAAGTGATT
196 ATTTAAAGAGGGAAAATGCACGTAGGGGTATGTTGAGTATTCTTCAAGGAACAAAGAAAGTGATT
286227 AAAAAGTGGCCCAATAGTAATAATATGGGGTTTTCCAAACAGATTTCAGATTTGGAGAATAGGAT
261 AAAAAGTGGCCCAATAGTAATAATATGGGGTTTTCCAAACAGATTTCAGATTTGGAGAATAGGAT
286292 AAATGAGTTGGAATTGAGGTGTCAGGGGGGGTTTCGGCACAAGATTGGGGTCAACTATTGACGTG
326 AAATGAGTTGGAATTGAGGTGTCAGGGGGGGTTTCGGCACAAGATTGGGGTCAACTATTGACGTG
286357 GAGGAATGAATTGTGGGGTTTGCATAGGAAGGAGGAGAGCATTTGGTTTCAAAAATCAAGACTTA
391 GAGGAATGAATTGTGGGGTTTGCATAGGAAGGAGGAGAGCATTTGGTTTCAAAAATCAAGACTTA
286422 AATAGATCAAGGATAGGGACAGAAATACCAGATTTTATCATTTATGTGCTCTTAATAGGAGTCGA
456 AATAGATCAAGGATAGGGACAGAAATACCAGATTTTATCATTTATGTGCTCTTAATAGGAGTCGA
286487 GTGAATGCCATTTCATCTTTGAAAGTGGATGGGGTAGATATTGTTAATCCTAATCAGATTAGATC
521 GTGAATGCCATTTCATCTTTGAAAGTGGATGGGGTAGATATTGTTAATCCTAATCAGATTAGATC
*
286552 AGTTATTTCTGAGTTTTTTAAAGCCAATTACAACTCGAATGCAGCTCTGGAAGTGGATGACT
586 AGCTATTTCTGAGTTTTTTAAAGCCAATTACAACTCGAATGCAGCTCTGGAAGTGGATGACT
286614 GGTTTCTATTAAGTGGTGCTTTTTTTCAGGTATTTCCAAAAGTTATTCAGAAACTGTTGCCGAAA
1 GGTTTCTATTAAGTGGTGCTTTTTTTCAGGTATTTCCAAAAGTTATTCAGAAACTGTTGCCGAAA
286679 TCTATTTCTGATCATAACCCTATAGTACTTGAGGATGATTTCAAAAACTGGGGTCCTAAACCTTT
66 TCTATTTCTGATCATAACCCTATAGTACTTGAGGATGATTTCAAAAACTGGGGTCCTAAACCTTT
286744 CCGGTTTTTTAATTATTTACTAGAGGAGGAT-GGTTTGATGGGGTGGTTAAGAATGATGTGTATG
131 CCGGTTTTTTAATTATTTACTAGAGGAGGATGGGTTTGATGGGGTGGTTAAGAATGATGTGTATG
286808 ATTTAAAGAGGGAAAATGCACGTAGGGGTATGTTGAGTATTCTTCAAGGAACAAAGAAAGTGATT
196 ATTTAAAGAGGGAAAATGCACGTAGGGGTATGTTGAGTATTCTTCAAGGAACAAAGAAAGTGATT
* *
286873 AAAAAGTGGCCCAATAGTAATAATATGGGGTTTTCCGAACAGATTTTAGATTTGGAGAATAGGAT
261 AAAAAGTGGCCCAATAGTAATAATATGGGGTTTTCCAAACAGATTTCAGATTTGGAGAATAGGAT
286938 AAATGAGTTGGAATTGAGGTGTCA-GGGGGGTTTCGGCACAAGATTGGGGTCAACTATTGACGTG
326 AAATGAGTTGGAATTGAGGTGTCAGGGGGGGTTTCGGCACAAGATTGGGGTCAACTATTGACGTG
287002 GAGGAATGAATTGTGGGGTTTGCATAGGAAGGAGGAGAGCATTTGGTTTCAAAAATCAAGACTTA
391 GAGGAATGAATTGTGGGGTTTGCATAGGAAGGAGGAGAGCATTTGGTTTCAAAAATCAAGACTTA
* *
287067 AATGGATCAAGGATGGGGACAGAAATACCAGATTTTATCATTTATGTGCTCTTAATAGGAGTCGA
456 AATAGATCAAGGATAGGGACAGAAATACCAGATTTTATCATTTATGTGCTCTTAATAGGAGTCGA
287132 GTGAATGCCATTTCATCTTTGAAAGTGGATGGGGTAGATATTGTTAATCCTAATCAGATTAGATC
521 GTGAATGCCATTTCATCTTTGAAAGTGGATGGGGTAGATATTGTTAATCCTAATCAGATTAGATC
287197 AGCTATTTCTGAGTTTTTTAAAGCCAATTACAACTCGAATGCAGCTCTGGAAGTGGATGACT
586 AGCTATTTCTGAGTTTTTTAAAGCCAATTACAACTCGAATGCAGCTCTGGAAGTGGATGACT
287259 G
1 G
287260 TAATCTGAAT
Statistics
Matches: 639, Mismatches: 7, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
645 295 0.46
646 183 0.29
647 161 0.25
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.32
Consensus pattern (647 bp):
GGTTTCTATTAAGTGGTGCTTTTTTTCAGGTATTTCCAAAAGTTATTCAGAAACTGTTGCCGAAA
TCTATTTCTGATCATAACCCTATAGTACTTGAGGATGATTTCAAAAACTGGGGTCCTAAACCTTT
CCGGTTTTTTAATTATTTACTAGAGGAGGATGGGTTTGATGGGGTGGTTAAGAATGATGTGTATG
ATTTAAAGAGGGAAAATGCACGTAGGGGTATGTTGAGTATTCTTCAAGGAACAAAGAAAGTGATT
AAAAAGTGGCCCAATAGTAATAATATGGGGTTTTCCAAACAGATTTCAGATTTGGAGAATAGGAT
AAATGAGTTGGAATTGAGGTGTCAGGGGGGGTTTCGGCACAAGATTGGGGTCAACTATTGACGTG
GAGGAATGAATTGTGGGGTTTGCATAGGAAGGAGGAGAGCATTTGGTTTCAAAAATCAAGACTTA
AATAGATCAAGGATAGGGACAGAAATACCAGATTTTATCATTTATGTGCTCTTAATAGGAGTCGA
GTGAATGCCATTTCATCTTTGAAAGTGGATGGGGTAGATATTGTTAATCCTAATCAGATTAGATC
AGCTATTTCTGAGTTTTTTAAAGCCAATTACAACTCGAATGCAGCTCTGGAAGTGGATGACT
Found at i:287537 original size:11 final size:11
Alignment explanation
Indices: 287518--287558 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
287508 TCCCTAAGAA
287518 AGCGAATCCTG
1 AGCGAATCCTG
*
287529 AGGGAATCCTG
1 AGCGAATCCTG
287540 AGCGAATCCTG
1 AGCGAATCCTG
*
287551 AGTGAATC
1 AGCGAATC
287559 ATTCATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (11 bp):
AGCGAATCCTG
Found at i:307710 original size:588 final size:589
Alignment explanation
Indices: 306593--307774 Score: 2357
Period size: 588 Copynumber: 2.0 Consensus size: 589
306583 TTATTATATA
306593 TATAAATATAAAATTTCAATTAAATAAATATATCTATTTAAATATTATTTGATATATTTAAATCA
1 TATAAATATAAAATTTCAATTAAATAAATATATCTATTTAAATATTATTTGATATATTTAAATCA
306658 CTTTAGATTATAAATCTTAAATTATATTTTTTTTTTCTAAATCATAATCTCATTGGTAATGAACT
66 CTTTAGATTATAAATCTTAAATTATATTTTTTTTTTCTAAATCATAATCTCATTGGTAATGAACT
306723 TTTAAACATGAAAATTTCTAGAATGCATGTCAAATATTGAAATTTACTATTAATTTTATAAGGTA
131 TTTAAACATGAAAATTTCTAGAATGCATGTCAAATATTGAAATTTACTATTAATTTTATAAGGTA
306788 AAATTCATAAATATACATTAAATTATTTTAAAATGATCTTTCTAGATACTAAACTGTCAAAACTT
196 AAATTCATAAATATACATTAAATTATTTTAAAATGATCTTTCTAGATACTAAACTGTCAAAACTT
306853 ACATAATAAACGTTAAATTTTAAATTTTATTACAAAATATGTATCATTTACCATTAAATAAGTGA
261 ACATAATAAACGTTAAATTTTAAATTTTATTACAAAATATGTATCATTTACCATTAAATAAGTGA
306918 TGTGTCATGCTAAATTAATAAAAAAAATCATTTGACCTTTCAATTGTAAATAAAATTCATTTTAT
326 TGTGTCATGCTAAATTAATAAAAAAAATCATTTGACCTTTCAATTGTAAATAAAATTCATTTTAT
306983 TGTTAATTTTAATTAAAATGATTTTTATTAGGTTCGTTGAATTGAAAGTAAAATATATAAGTTAA
391 TGTTAATTTTAATTAAAATGATTTTTATTAGGTTCGTTGAATTGAAAGTAAAATATATAAGTTAA
307048 ATACTGATTTTTAACTTCATATTATAAATATTAAATTTATATCATATAAATTACTTGATACATTA
456 ATACTGATTTTTAACTTCATATTATAAATATTAAATTTATATCATATAAATTACTTGATACATTA
307113 TTAAAACTTAAAGATTATTTCGATTATTTTTAAGTAAATTTAGATGTATTTTTCTTATTAAAGTG
521 TTAAAACTTAAAGATTATTTCGATTATTTTTAAGTAAATTTAGATGTATTTTTCTTATTAAAGTG
307178 ATAC
586 ATAC
307182 TATAAATATAAAATTTCAATTAAATAAATATATCTATTTAAATATTATTTGATATATTTAAATCA
1 TATAAATATAAAATTTCAATTAAATAAATATATCTATTTAAATATTATTTGATATATTTAAATCA
307247 CTTTAGATTATAAATCTTAAATTATA-TTTTTTTTTCTAAATCATAATCTCATTGGTAATGAACT
66 CTTTAGATTATAAATCTTAAATTATATTTTTTTTTTCTAAATCATAATCTCATTGGTAATGAACT
307311 TTTAAACATGAAAATTTCTAGAATGCATGTCAAATATTGAAATTTACTATTAATTTTATAAGGTA
131 TTTAAACATGAAAATTTCTAGAATGCATGTCAAATATTGAAATTTACTATTAATTTTATAAGGTA
307376 AAATTCATAAATATACATTAAATTATTTTAAAATGATCTTTCTAGATACTAAACTGTCAAAACTT
196 AAATTCATAAATATACATTAAATTATTTTAAAATGATCTTTCTAGATACTAAACTGTCAAAACTT
307441 ACATAATAAACGTTAAATTTTAAATTTTATTACAAAATATGTATCATTTACCATTAAATAAGTGA
261 ACATAATAAACGTTAAATTTTAAATTTTATTACAAAATATGTATCATTTACCATTAAATAAGTGA
307506 TGTGTCATGCTAAATTAATAAAAAAAATCATTTGACCTTTCAATTGTAAATAAAATTCATTTTAT
326 TGTGTCATGCTAAATTAATAAAAAAAATCATTTGACCTTTCAATTGTAAATAAAATTCATTTTAT
307571 TGTTAATTTTAATTAAAATGATTTTTATTAGGTTCGTTGAATTGAAAGTAAAATATATAAGTTAA
391 TGTTAATTTTAATTAAAATGATTTTTATTAGGTTCGTTGAATTGAAAGTAAAATATATAAGTTAA
307636 ATACTGATTTTTAACTTCATATTATAAATATTAAATTTATATCATATAAATTACTTGATACATTA
456 ATACTGATTTTTAACTTCATATTATAAATATTAAATTTATATCATATAAATTACTTGATACATTA
307701 TTAAAACTTAAAGATTATTTCGATTATTTTTAAGTAAATTTAGATGTATTTTTCTTATTAAAGTG
521 TTAAAACTTAAAGATTATTTCGATTATTTTTAAGTAAATTTAGATGTATTTTTCTTATTAAAGTG
307766 ATAC
586 ATAC
307770 TATAA
1 TATAA
307775 TTTTCTGGAT
Statistics
Matches: 593, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
588 502 0.85
589 91 0.15
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (589 bp):
TATAAATATAAAATTTCAATTAAATAAATATATCTATTTAAATATTATTTGATATATTTAAATCA
CTTTAGATTATAAATCTTAAATTATATTTTTTTTTTCTAAATCATAATCTCATTGGTAATGAACT
TTTAAACATGAAAATTTCTAGAATGCATGTCAAATATTGAAATTTACTATTAATTTTATAAGGTA
AAATTCATAAATATACATTAAATTATTTTAAAATGATCTTTCTAGATACTAAACTGTCAAAACTT
ACATAATAAACGTTAAATTTTAAATTTTATTACAAAATATGTATCATTTACCATTAAATAAGTGA
TGTGTCATGCTAAATTAATAAAAAAAATCATTTGACCTTTCAATTGTAAATAAAATTCATTTTAT
TGTTAATTTTAATTAAAATGATTTTTATTAGGTTCGTTGAATTGAAAGTAAAATATATAAGTTAA
ATACTGATTTTTAACTTCATATTATAAATATTAAATTTATATCATATAAATTACTTGATACATTA
TTAAAACTTAAAGATTATTTCGATTATTTTTAAGTAAATTTAGATGTATTTTTCTTATTAAAGTG
ATAC
Found at i:308042 original size:26 final size:25
Alignment explanation
Indices: 307988--308043 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
307978 AATTTGTAAA
*
307988 TTTTAAAAATATTTTTTTCATATATT
1 TTTTAAAAATATTTTTTT-ATATACT
*
308014 TTTTAAAATATGATTTTTTT-TTTACT
1 TTTTAAAA-AT-ATTTTTTTATATACT
308040 TTTT
1 TTTT
308044 TGAAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 16 0.62
27 2 0.08
28 8 0.31
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTTAAAAATATTTTTTTATATACT
Found at i:309053 original size:22 final size:23
Alignment explanation
Indices: 309012--309056 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
309002 TTACGATATA
309012 TTTTTCTCTACCTTTATGACATG
1 TTTTTCTCTACCTTTATGACATG
* *
309035 TTTTTCTTTATCTTT-TGACATG
1 TTTTTCTCTACCTTTATGACATG
309057 AGTTCGGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.58
Consensus pattern (23 bp):
TTTTTCTCTACCTTTATGACATG
Found at i:314364 original size:2 final size:2
Alignment explanation
Indices: 314357--314390 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
314347 TGTCAGTCAA
314357 CT 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 CT
314391 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:314395 original size:2 final size:2
Alignment explanation
Indices: 314390--314428 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
314380 TCTCTCTCTC
314390 TA 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 TA T
314429 CGTAGCCGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:314603 original size:2 final size:2
Alignment explanation
Indices: 314598--314648 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
314588 ACACACACAC
314598 AT AT AT AT AT AT AT AT -T 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 AT AT AT AT AT
314639 AT AT AT AT AT
1 AT AT AT AT AT
314649 GCATATGCAG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:318685 original size:27 final size:28
Alignment explanation
Indices: 318647--318703 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
318637 CTAAAATACT
*
318647 CATTTTGGTCCTT-ATTTTTTCCTCGAG
1 CATTTTGGTCCTTAACTTTTTCCTCGAG
*
318674 CATTTTGGTCCTTAACTTTTTCCTGGAG
1 CATTTTGGTCCTTAACTTTTTCCTCGAG
318702 CA
1 CA
318704 ATTTAACCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (28 bp):
CATTTTGGTCCTTAACTTTTTCCTCGAG
Found at i:319698 original size:12 final size:14
Alignment explanation
Indices: 319681--319717 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
319671 TTGTTTTTAT
319681 TAATTAAATAT-C-
1 TAATTAAATATACA
319693 TAATTAAATATACAA
1 TAATTAAATATAC-A
319708 TAATTAAATA
1 TAATTAAATA
319718 AATCTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.50
13 1 0.05
15 10 0.45
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATTAAATATACA
Found at i:319739 original size:16 final size:16
Alignment explanation
Indices: 319718--319765 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
319708 TAATTAAATA
319718 AATCTAAATTAATTTT
1 AATCTAAATTAATTTT
*
319734 AATCTAAATTAATTAT
1 AATCTAAATTAATTTT
*
319750 AAT-AAAATTAATTTT
1 AATCTAAATTAATTTT
319765 A
1 A
319766 CTATATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
AATCTAAATTAATTTT
Found at i:319744 original size:31 final size:28
Alignment explanation
Indices: 319709--319778 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 28
319699 AATATACAAT
*
319709 AATTAAATAAATCTAAATTAATTTTAATCTA
1 AATTAAATAAAT-AAAATTAATTTT-A-CTA
*
319740 AATTAATTATAATAAAATTAATTTTACTA
1 AATTAAATA-AATAAAATTAATTTTACTA
*
319769 TATTAAATAA
1 AATTAAATAA
319779 TTTTTATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 1 0.03
29 10 0.29
30 1 0.03
31 19 0.56
32 3 0.09
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (28 bp):
AATTAAATAAATAAAATTAATTTTACTA
Found at i:319759 original size:15 final size:16
Alignment explanation
Indices: 319709--319762 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
319699 AATATACAAT
* *
319709 AATTAAATA-AATCTA
1 AATTAATTATAATCAA
* *
319724 AATTAATTTTAATCTA
1 AATTAATTATAATCAA
319740 AATTAATTATAAT-AA
1 AATTAATTATAATCAA
319755 AATTAATT
1 AATTAATT
319763 TTACTATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 16 0.47
16 18 0.53
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTAATTATAATCAA
Found at i:319894 original size:19 final size:19
Alignment explanation
Indices: 319867--319945 Score: 79
Period size: 19 Copynumber: 4.0 Consensus size: 19
319857 TTTTATTTCC
*
319867 ATTAATTTAATATCAATTT
1 ATTATTTTAATATCAATTT
* *
319886 TTTATTTTAATTTTCAAATTT
1 ATTATTTTAA-TATC-AATTT
319907 CATTATTTTAATAAT-AATTT
1 -ATTATTTTAAT-ATCAATTT
*
319927 ATTAATTTAATATCAATTT
1 ATTATTTTAATATCAATTT
319946 TAGATTCTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
18 2 0.04
19 23 0.47
20 8 0.16
21 6 0.12
22 10 0.20
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTATTTTAATATCAATTT
Found at i:324632 original size:20 final size:20
Alignment explanation
Indices: 324604--324648 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
324594 CAATATCAAG
*
324604 CCCCTTACCACTTGAACCAA
1 CCCCCTACCACTTGAACCAA
324624 CCCCCTACCACTTGAACCAA
1 CCCCCTACCACTTGAACCAA
324644 CCCCC
1 CCCCC
324649 GTAAGGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.53, G:0.04, T:0.16
Consensus pattern (20 bp):
CCCCCTACCACTTGAACCAA
Found at i:324905 original size:43 final size:43
Alignment explanation
Indices: 324843--324932 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
324833 AAAGTCATGA
*
324843 TCTTTTTTTTGATAGGAATTGAAGGCCTCATTAAAAAAC-CCCT
1 TCTTTTTTTTGATAAGAATTGAAGGCCTCATT-AAAAACTCCCT
* **
324886 TCTTTTTTTTTATAAGAATTTCAGGCCTCATTAAAAACTCCCT
1 TCTTTTTTTTGATAAGAATTGAAGGCCTCATTAAAAACTCCCT
324929 TCTT
1 TCTT
324933 GATTAATGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 6 0.14
43 36 0.86
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (43 bp):
TCTTTTTTTTGATAAGAATTGAAGGCCTCATTAAAAACTCCCT
Found at i:329542 original size:20 final size:20
Alignment explanation
Indices: 329517--329561 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
329507 TATCCAGAAA
*
329517 AAAAATCCGGTCTAGGGTTT
1 AAAAATCCGGTATAGGGTTT
*
329537 AAAAATCCGGTATGGGGTTT
1 AAAAATCCGGTATAGGGTTT
329557 AAAAA
1 AAAAA
329562 ATTGGATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTATAGGGTTT
Found at i:340270 original size:39 final size:39
Alignment explanation
Indices: 340190--340266 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
340180 TCTTGGAATC
** *
340190 ATCATCACCATTGTAAATTCTTTCTCTTTCCCGCACTTT
1 ATCATCACCATCATAAATTCTTTCTCTTTCACGCACTTT
*
340229 ATCATCACCATCATGAATTCTTTCTCTTTCACGC-CTTT
1 ATCATCACCATCATAAATTCTTTCTCTTTCACGCACTTT
340267 TATCCCCGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 4 0.12
39 30 0.88
ACGTcount: A:0.21, C:0.31, G:0.05, T:0.43
Consensus pattern (39 bp):
ATCATCACCATCATAAATTCTTTCTCTTTCACGCACTTT
Found at i:341881 original size:29 final size:28
Alignment explanation
Indices: 341811--341881 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 28
341801 ATTAATAAAA
*
341811 AAAAATTATTTGATCTTTTAATTTTAATT
1 AAAAATTATTTAAT-TTTTAATTTTAATT
*
341840 AAAATTTAATTTAATTTTTAATTTTAATT
1 AAAAATT-ATTTAATTTTTAATTTTAATT
341869 GAAATAATT-TTTA
1 -AAA-AATTATTTA
341882 TTAGTTTCGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 24 0.67
30 9 0.25
31 3 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (28 bp):
AAAAATTATTTAATTTTTAATTTTAATT
Found at i:342098 original size:13 final size:15
Alignment explanation
Indices: 342067--342101 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
342057 TTATAGTTTT
342067 TTTAAATCATTGTTA
1 TTTAAATCATTGTTA
342082 TTTAAAT-ATTG-TA
1 TTTAAATCATTGTTA
342095 TTTAAAT
1 TTTAAAT
342102 TTCTTGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 4 0.20
15 7 0.35
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (15 bp):
TTTAAATCATTGTTA
Found at i:361191 original size:3 final size:3
Alignment explanation
Indices: 361183--361273 Score: 182
Period size: 3 Copynumber: 30.3 Consensus size: 3
361173 CTCCTAGAAT
361183 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
361231 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
361274 AAATATGTGC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:362903 original size:14 final size:14
Alignment explanation
Indices: 362884--362915 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
362874 ATGATCGGAA
362884 ATGGACTCCGGATG
1 ATGGACTCCGGATG
362898 ATGGACTCCGGATG
1 ATGGACTCCGGATG
362912 ATGG
1 ATGG
362916 GTCCAAGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.22
Consensus pattern (14 bp):
ATGGACTCCGGATG
Found at i:379083 original size:31 final size:31
Alignment explanation
Indices: 379045--379155 Score: 179
Period size: 31 Copynumber: 3.6 Consensus size: 31
379035 TAAGTATTAG
*
379045 AATGAAACAAAAA-TTAACGATGGTGTACTAA
1 AATGAAACAAAAAGTTAACGACGG-GTACTAA
379076 AATGAAACAAAAAGTTAACGACGGGTACTAA
1 AATGAAACAAAAAGTTAACGACGGGTACTAA
*
379107 AATGAAATAAAAAGTTAACGACGGGTACTAA
1 AATGAAACAAAAAGTTAACGACGGGTACTAA
*
379138 AATGAAATAAAAAGTTAA
1 AATGAAACAAAAAGTTAA
379156 TATTAAGTAT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
31 68 0.88
32 9 0.12
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (31 bp):
AATGAAACAAAAAGTTAACGACGGGTACTAA
Found at i:383381 original size:25 final size:26
Alignment explanation
Indices: 383335--383383 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
383325 AGTGATTTAA
* *
383335 TTTTTTCTATATTTGTATATTTAATT
1 TTTTTTCTATATTTGAAAATTTAATT
383361 TTTTTTCTATATTT-AAAATTTAA
1 TTTTTTCTATATTTGAAAATTTAA
383384 AATTTAGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTTTCTATATTTGAAAATTTAATT
Found at i:386990 original size:63 final size:62
Alignment explanation
Indices: 386889--387020 Score: 137
Period size: 63 Copynumber: 2.1 Consensus size: 62
386879 ATTCATATGC
* * * * *
386889 TTTAATTTCCACCTTTCAATTTTATTTCTTTTTCAATTT-AGTCTTCTATTTAACTTTT-TACAA
1 TTTAATTTCCACATTTCAATTTTAATTCTATTTAAATTTCAGTCCT-TATTT-A-TTTTGTACAA
*
386952 TTTAATTT-CAGCATTTCAATTTTACATT-TATTTAAATTTCAGTCCTTATTTATTTTGTATAA
1 TTTAATTTCCA-CATTTCAATTTTA-ATTCTATTTAAATTTCAGTCCTTATTTATTTTGTACAA
387014 TTTAATT
1 TTTAATT
387021 CTCCCTTTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
61 4 0.07
62 14 0.24
63 34 0.58
64 7 0.12
ACGTcount: A:0.27, C:0.14, G:0.03, T:0.57
Consensus pattern (62 bp):
TTTAATTTCCACATTTCAATTTTAATTCTATTTAAATTTCAGTCCTTATTTATTTTGTACAA
Found at i:401526 original size:2 final size:2
Alignment explanation
Indices: 401521--401582 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
401511 AAAAAAAAAA
401521 AT AT AT AT AT 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 AT AT AT AT AT
401563 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
401583 CAAATTATGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:411014 original size:17 final size:17
Alignment explanation
Indices: 410992--411026 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
410982 AGAGTTGGTG
410992 GCGAAAATATGGGGTCT
1 GCGAAAATATGGGGTCT
411009 GCGAAAATATGGGGTCT
1 GCGAAAATATGGGGTCT
411026 G
1 G
411027 TCCCCTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.37, T:0.23
Consensus pattern (17 bp):
GCGAAAATATGGGGTCT
Found at i:412414 original size:23 final size:23
Alignment explanation
Indices: 412384--412427 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
412374 AATACGTATA
412384 TGTCCCGAAAGACCACGTAGAAT
1 TGTCCCGAAAGACCACGTAGAAT
* *
412407 TGTCCCGAATGACCGCGTAGA
1 TGTCCCGAAAGACCACGTAGA
412428 CCCTCTACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAAGACCACGTAGAAT
Found at i:428115 original size:16 final size:16
Alignment explanation
Indices: 428071--428131 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
428061 ATTGGAAAAT
428071 TAATATTATAAACATAACA
1 TAATATTAT-AACAT-A-A
* *
428090 AAAAATTATAACATAA
1 TAATATTATAACATAA
*
428106 TAATATTATAACA-AT
1 TAATATTATAACATAA
428121 TATATATTATA
1 TA-ATATTATA
428132 TAAAAATAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 3 0.08
16 20 0.56
17 1 0.03
18 5 0.14
19 7 0.19
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATATTATAACATAA
Found at i:435738 original size:14 final size:14
Alignment explanation
Indices: 435719--435748 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
435709 GAGAGAACCT
435719 TGAAACTTCAACAA
1 TGAAACTTCAACAA
435733 TGAAACTTCAACAA
1 TGAAACTTCAACAA
435747 TG
1 TG
435749 CCCCATTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.23
Consensus pattern (14 bp):
TGAAACTTCAACAA
Found at i:436364 original size:53 final size:57
Alignment explanation
Indices: 436259--436379 Score: 160
Period size: 61 Copynumber: 2.1 Consensus size: 57
436249 AACCAGTGTT
* *
436259 GCCTGCAGAAAGAAACTAGACTAATCAATATATATATATATATGTATATAACCATCTTGCA
1 GCCTCCAGAAAGAAACTAGACTAATC---ATATATATATATATG-ATATAACCAGCTTGCA
436320 GCCTCCAGAAAGAAACTAGACTAA-C-TA-ATATATATATG-TATAACCAGCTTGCA
1 GCCTCCAGAAAGAAACTAGACTAATCATATATATATATATGATATAACCAGCTTGCA
436373 GCCTCCA
1 GCCTCCA
436380 TCTCATATAC
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
53 21 0.36
55 11 0.19
56 2 0.03
60 1 0.02
61 23 0.40
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (57 bp):
GCCTCCAGAAAGAAACTAGACTAATCATATATATATATATGATATAACCAGCTTGCA
Found at i:438681 original size:104 final size:104
Alignment explanation
Indices: 438501--438712 Score: 354
Period size: 104 Copynumber: 2.0 Consensus size: 104
438491 AATTGACAGG
* *
438501 CAATTTCATAAAAAGATTTTACAGTTGAAAAATGAAAACTATACAACTATACTTGTTTTACAATT
1 CAATTTCATAAAAAGATTTTACAGTTGAAAAATGAAAACTATACAACTATAATTGTTATACAATT
438566 TTTTAAAACATTTTTAC-TTTTCTTAGACCCAAAGAGTGA
66 TTTTAAAACA-TTTTACTTTTTCTTAGACCCAAAGAGTGA
* * *
438605 CAATTTCATAAAAAGATTTTACAGTTGAAAAATGAAAACTATACAATTATAATTGTTATCCATTT
1 CAATTTCATAAAAAGATTTTACAGTTGAAAAATGAAAACTATACAACTATAATTGTTATACAATT
*
438670 TTTTAAAACATTTTACTTTTTCTTAGACCCAAAGAGTGG
66 TTTTAAAACATTTTACTTTTTCTTAGACCCAAAGAGTGA
438709 CAAT
1 CAAT
438713 ACCACAGCTC
Statistics
Matches: 101, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
103 6 0.06
104 95 0.94
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (104 bp):
CAATTTCATAAAAAGATTTTACAGTTGAAAAATGAAAACTATACAACTATAATTGTTATACAATT
TTTTAAAACATTTTACTTTTTCTTAGACCCAAAGAGTGA
Found at i:449232 original size:29 final size:29
Alignment explanation
Indices: 449190--449264 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
449180 AACCCAACCA
**
449190 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
449219 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
449248 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
449265 GAGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:449270 original size:29 final size:29
Alignment explanation
Indices: 449220--449278 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
449210 GCGACCTCCT
*
449220 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCAGGCGACCAAGG
* *
449249 AGGTCGCCATGCACTCGAGGCGACCAAGG
1 AGGTCGCCATGCACGCCAGGCGACCAAGG
449278 A
1 A
449279 TTCATGCATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.24, C:0.34, G:0.34, T:0.08
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCAGGCGACCAAGG
Found at i:449399 original size:36 final size:36
Alignment explanation
Indices: 449352--449448 Score: 185
Period size: 36 Copynumber: 2.7 Consensus size: 36
449342 GACCAAGGAT
449352 GACCAAGGATCGGTTCATGCATGGGGCACTCGGGGC
1 GACCAAGGATCGGTTCATGCATGGGGCACTCGGGGC
*
449388 GACCAAGGATCGATTCATGCATGGGGCACTCGGGGC
1 GACCAAGGATCGGTTCATGCATGGGGCACTCGGGGC
449424 GACCAAGGATCGGTTCATGCATGGG
1 GACCAAGGATCGGTTCATGCATGGG
449449 AAGAATGGGG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.22, C:0.24, G:0.37, T:0.18
Consensus pattern (36 bp):
GACCAAGGATCGGTTCATGCATGGGGCACTCGGGGC
Found at i:449562 original size:29 final size:29
Alignment explanation
Indices: 449529--449613 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
449519 AGCAGGGGAT
* * **
449529 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* *
449558 GTCGCCGGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
449587 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGCCGGGAGTGCATGGCGACCTACG
449614 GCTACTGTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.18
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:449805 original size:15 final size:16
Alignment explanation
Indices: 449785--449825 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
449775 AGTAAAATTC
449785 AATTTTGTTTA-AATA
1 AATTTTGTTTATAATA
*
449800 AATTTT-TTTATAATT
1 AATTTTGTTTATAATA
449815 AATTTTAGTTT
1 AATTTT-GTTT
449826 TCAATGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.18
15 15 0.68
17 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (16 bp):
AATTTTGTTTATAATA
Found at i:453983 original size:21 final size:21
Alignment explanation
Indices: 453942--453980 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
453932 ATTTGGAATT
453942 ATTTAAAACAAATATTAAATA
1 ATTTAAAACAAATATTAAATA
*
453963 ATTTTAAA-AAATATTAAA
1 ATTTAAAACAAATATTAAA
453981 ATATGGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTTAAAACAAATATTAAATA
Found at i:460038 original size:65 final size:65
Alignment explanation
Indices: 459878--460038 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 65
459868 TTGTTTAAGG
* * * **
459878 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAAGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAAGATTT
459941 A
65 A
* *
459942 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAAGATTTA
*
460006 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
460039 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAAGATTTA
Found at i:461625 original size:149 final size:149
Alignment explanation
Indices: 461452--461766 Score: 596
Period size: 149 Copynumber: 2.1 Consensus size: 149
461442 GAGTCGAGGG
461452 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
461517 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
461582 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
461601 TCTACGCGGTCTTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
461666 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
461731 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
461750 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
461767 TGCAATTATA
Statistics
Matches: 162, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 161 0.99
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:461767 original size:23 final size:23
Alignment explanation
Indices: 461734--461778 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
461724 ATTATTATAT
*
461734 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
461757 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
461779 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:481580 original size:55 final size:56
Alignment explanation
Indices: 481504--481649 Score: 215
Period size: 55 Copynumber: 2.6 Consensus size: 56
481494 GCAAAATTAT
* *
481504 CATT-TCCAATATTAGTGGATTGAGCATTATTAACATTCAATACTAATTG-ATGAG
1 CATTATCCAATACTAGTAGATTGAGCATTATTAACATTCAATACTAATTGAATGAG
* * *
481558 CATTATCCAATACTAGTAGATTGAGCATTATTACCATTTAATACTAGTTGAATGAG
1 CATTATCCAATACTAGTAGATTGAGCATTATTAACATTCAATACTAATTGAATGAG
* *
481614 CATTATCCAACACTAGTAGATTGAGCATTATCAACA
1 CATTATCCAATACTAGTAGATTGAGCATTATTAACA
481650 ATAGTGACAT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
54 4 0.05
55 40 0.49
56 38 0.46
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (56 bp):
CATTATCCAATACTAGTAGATTGAGCATTATTAACATTCAATACTAATTGAATGAG
Found at i:481586 original size:25 final size:25
Alignment explanation
Indices: 481541--481645 Score: 104
Period size: 25 Copynumber: 4.0 Consensus size: 25
481531 TATTAACATT
* *
481541 CAATACTAATTGA-TGAGCATTATC
1 CAATACTAGTAGATTGAGCATTATC
481565 CAATACTAGTAGATTGAGCATTATTAC
1 CAATACTAGTAGATTGAGCATTA-T-C
* *
481592 CATTTAATACTAGTTGAATGAGCATTATC
1 C----AATACTAGTAGATTGAGCATTATC
*
481621 CAACACTAGTAGATTGAGCATTATC
1 CAATACTAGTAGATTGAGCATTATC
481646 AACAATAGTG
Statistics
Matches: 67, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
24 11 0.16
25 30 0.45
26 1 0.01
27 2 0.03
29 2 0.03
30 1 0.01
31 20 0.30
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (25 bp):
CAATACTAGTAGATTGAGCATTATC
Found at i:481631 original size:56 final size:55
Alignment explanation
Indices: 481516--481649 Score: 205
Period size: 56 Copynumber: 2.4 Consensus size: 55
481506 TTTCCAATAT
* *
481516 TAGTGGATTGAGCATTATTAACATTCAATACTAATTGATGAGCATTATCCAATAC
1 TAGTAGATTGAGCATTATTAACATTCAATACTAATTGATGAGCATTATCCAACAC
* * *
481571 TAGTAGATTGAGCATTATTACCATTTAATACTAGTTGAATGAGCATTATCCAACAC
1 TAGTAGATTGAGCATTATTAACATTCAATACTAATTG-ATGAGCATTATCCAACAC
*
481627 TAGTAGATTGAGCATTATCAACA
1 TAGTAGATTGAGCATTATTAACA
481650 ATAGTGACAT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
55 33 0.46
56 38 0.54
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (55 bp):
TAGTAGATTGAGCATTATTAACATTCAATACTAATTGATGAGCATTATCCAACAC
Found at i:482031 original size:32 final size:33
Alignment explanation
Indices: 481990--482057 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
481980 ATTACCCGAC
*
481990 CTGTTTTCAACCTG-ATCTG-TTTTTAACCTGAT
1 CTGTTTTCAACCTGCCT-TGTTTTTTAACCTGAT
*
482022 CTGTTTTCAACCTGCCTTGTTTTTTAACCTTAT
1 CTGTTTTCAACCTGCCTTGTTTTTTAACCTGAT
482055 CTG
1 CTG
482058 ATATTTACCT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 16 0.50
33 16 0.50
ACGTcount: A:0.16, C:0.24, G:0.12, T:0.49
Consensus pattern (33 bp):
CTGTTTTCAACCTGCCTTGTTTTTTAACCTGAT
Found at i:482044 original size:16 final size:16
Alignment explanation
Indices: 481990--482035 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
481980 ATTACCCGAC
481990 CTGTTTTCAACCTGAT
1 CTGTTTTCAACCTGAT
*
482006 CTGTTTTTAACCTGAT
1 CTGTTTTCAACCTGAT
482022 CTGTTTTCAACCTG
1 CTGTTTTCAACCTG
482036 CCTTGTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.17, C:0.24, G:0.13, T:0.46
Consensus pattern (16 bp):
CTGTTTTCAACCTGAT
Found at i:482317 original size:14 final size:14
Alignment explanation
Indices: 482295--482341 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
482285 TTCAAAGGAA
*
482295 AATTAATATAGTTT
1 AATTTATATAGTTT
482309 AATTTATATA----
1 AATTTATATAGTTT
482319 AA-TTATATAGTTT
1 AATTTATATAGTTT
482332 AATTTATATA
1 AATTTATATA
482342 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:482328 original size:23 final size:24
Alignment explanation
Indices: 482294--482343 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
482284 ATTCAAAGGA
482294 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
482318 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
482341 AAA
1 AAA
482344 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:482542 original size:14 final size:14
Alignment explanation
Indices: 482525--482558 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
482515 AGGGTTTATT
482525 GTTTATGATTTAGA
1 GTTTATGATTTAGA
* *
482539 GTTTAGGGTTTAGA
1 GTTTATGATTTAGA
482553 GTTTAT
1 GTTTAT
482559 ATATATTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (14 bp):
GTTTATGATTTAGA
Done.