Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 194 of 206
Found at i:58646755 original size:43 final size:42
Alignment explanation
Indices: 58646708--58646799 Score: 130
Period size: 43 Copynumber: 2.2 Consensus size: 42
58646698 CTTAGGAAAA
*
58646708 AAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTCATCTAC
1 AAACGCCGCTAAAAGTAACGTTCTTTAGCGGCGCTTCATC-AC
* * **
58646751 AAACGCCGCTAAAAGTAGCGTTCTTTCGCGGCGCTTTTTCAC
1 AAACGCCGCTAAAAGTAACGTTCTTTAGCGGCGCTTCATCAC
58646793 AAACGCC
1 AAACGCC
58646800 ACTATATGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 9 0.20
43 35 0.80
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (42 bp):
AAACGCCGCTAAAAGTAACGTTCTTTAGCGGCGCTTCATCAC
Found at i:58647286 original size:21 final size:21
Alignment explanation
Indices: 58647218--58647276 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
58647208 TTCTTTTGAA
58647218 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCTCTCGCTGCAG
58647239 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCTCTCGCTGCAG
*
58647260 CCTCTGCTTCCCTCGCT
1 CCTCTGCTTCTCTCGCT
58647277 ACCGCTTCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.03, C:0.46, G:0.17, T:0.34
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCAG
Found at i:58652810 original size:9 final size:9
Alignment explanation
Indices: 58652796--58653016 Score: 160
Period size: 9 Copynumber: 25.4 Consensus size: 9
58652786 TTTTTATGTA
58652796 TTATGTAAG
1 TTATGTAAG
58652805 TTATGTAAG
1 TTATGTAAG
58652814 -TACTGTAAG
1 TTA-TGTAAG
58652823 TTATGTAAG
1 TTATGTAAG
*
58652832 TAATGT-A-
1 TTATGTAAG
58652839 TTATGTAAG
1 TTATGTAAG
*
58652848 TTGTGTATA-
1 TTATGTA-AG
*
58652857 ATAT-TAA-
1 TTATGTAAG
*
58652864 TTATGTGAG
1 TTATGTAAG
*
58652873 TTGTGT-A-
1 TTATGTAAG
* *
58652880 TAATGTTAG
1 TTATGTAAG
*
58652889 TTAAG-AAGG
1 TTATGTAA-G
58652898 TTATGT-A-
1 TTATGTAAG
*
58652905 TAATGTAAG
1 TTATGTAAG
**
58652914 TTATGCCAG
1 TTATGTAAG
* *
58652923 TTATTTAAT
1 TTATGTAAG
58652932 TTATGTAAG
1 TTATGTAAG
58652941 TTATGTAAG
1 TTATGTAAG
* *
58652950 TTATTTAAT
1 TTATGTAAG
58652959 TTATGTAAG
1 TTATGTAAG
58652968 TTATGTAAG
1 TTATGTAAG
* *
58652977 TTATTTAAT
1 TTATGTAAG
*
58652986 TTTTGTAAG
1 TTATGTAAG
58652995 TTATGTAA-
1 TTATGTAAG
58653003 TTAATGTAAG
1 TT-ATGTAAG
58653013 TTAT
1 TTAT
58653017 TTAATTTGTG
Statistics
Matches: 163, Mismatches: 34, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
7 18 0.11
8 14 0.09
9 126 0.77
10 5 0.03
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:58656861 original size:114 final size:115
Alignment explanation
Indices: 58656658--58656939 Score: 331
Period size: 114 Copynumber: 2.5 Consensus size: 115
58656648 GTGTTTTACC
* * * *
58656658 ATAAGCGCCAC-AACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTT--GATATTTTG
1 ATAAGCGCCACTAA-TCCTAATATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAGAAATATTG
* *
58656720 CGGCGCTTTACAATAAGCGCTGCTAATACTATGCTTTAGCGGCATTTTCAA-
65 CGGCGCTTTACAATAAGCGCCGCTAATACTATACTTTAGCGGCATTTT-AAT
* * * * * *
58656771 ATATGCTCCACTAATCCTAATGTACCTCAATACCAAA-CTCTGCGTTTTGGTTAAGAAATATTGC
1 ATAAGCGCCACTAATCCTAATATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAGAAATATTGC
* * ** * *
58656835 GGCGCTTTTCACTACTCGCCGTTAATACTATACTTTAGCGGCGTTTTAAT
66 GGCGCTTTACAATAAGCGCCGCTAATACTATACTTTAGCGGCATTTTAAT
* *
58656885 ATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAA
1 ATAAGCGCCACTAATCCTAATATACATCAAGACCAAAGCGCTGCGTTTTGGTTAA
58656940 TCTTTTGCGG
Statistics
Matches: 138, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
112 14 0.10
113 29 0.21
114 79 0.57
115 16 0.12
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (115 bp):
ATAAGCGCCACTAATCCTAATATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAGAAATATTGC
GGCGCTTTACAATAAGCGCCGCTAATACTATACTTTAGCGGCATTTTAAT
Found at i:58656983 original size:74 final size:73
Alignment explanation
Indices: 58656867--58657012 Score: 197
Period size: 74 Copynumber: 2.0 Consensus size: 73
58656857 TAATACTATA
* *
58656867 CTTTAGCGGCGTTTTAATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCGCTGCGTT
1 CTTTAGCGGCGTTTTAATATAAGCGCCACTAATGCTAATATACAGCAAGACCAAA-CGCTGCGTT
58656932 TTGGTTAAT
65 TTGGTTAAT
* * * *
58656941 CTTTTGCGGCGATTTTCA-ATAAGCGCCACTAA-GCCTAATATACCGCAAGACCAAACTCTGCGT
1 CTTTAGCGGCG-TTTTAATATAAGCGCCACTAATG-CTAATATACAGCAAGACCAAACGCTGCGT
58657004 TTTGGTTAA
64 TTTGGTTAA
58657013 GAAATCTTGC
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
73 17 0.27
74 42 0.66
75 5 0.08
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (73 bp):
CTTTAGCGGCGTTTTAATATAAGCGCCACTAATGCTAATATACAGCAAGACCAAACGCTGCGTTT
TGGTTAAT
Found at i:58657099 original size:188 final size:188
Alignment explanation
Indices: 58656753--58657160 Score: 622
Period size: 188 Copynumber: 2.2 Consensus size: 188
58656743 TAATACTATG
* * * * * * *
58656753 CTTTAGCGGC-ATTTTCAAATATGCTCCACTAATCCTAATGTACCTCAATACCAAACTCTGCGTT
1 CTTTTGCGGCGATTTTC-AATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTT
*
58656817 TTGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGTTAATACTATACTTTAGCGGCGTTTT
65 TTGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATACTTTAGCGGCGTTTT
58656882 AATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
130 AATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
58656941 CTTTTGCGGCGATTTTCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
1 CTTTTGCGGCGATTTTCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
* * *
58657006 TGGTTAAGAAATCTTGCGTCGTTTTTCACTACTCGCCGCTAATACTATGA-TTTAGCGGCGTTTT
66 TGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTAT-ACTTTAGCGGCGTTTT
* *
58657070 AATATAAGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
130 AATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
* * * * *
58657129 ATTTTGCGGTGCTTTACAATAAGCGCCGCTAA
1 CTTTTGCGGCGATTTTCAATAAGCGCCACTAA
58657161 TACTATGCTT
Statistics
Matches: 200, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
188 193 0.96
189 7 0.04
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (188 bp):
CTTTTGCGGCGATTTTCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
TGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTA
ATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
Found at i:58657295 original size:114 final size:112
Alignment explanation
Indices: 58656941--58657428 Score: 546
Period size: 114 Copynumber: 4.3 Consensus size: 112
58656931 TTTGGTTAAT
* * * *
58656941 CTTTTGCGGCGATTTTCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
1 CTTTAGCGGCG-TTTTAAATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTT
* * *
58657006 TGGTTAAGAAATCTTGCGTCGTTTTTCACTACTCGCCGCTAATACTATG
65 TGGTTAAG-AATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATG
* * * * * *
58657055 ATTTAGCGGCGTTTTAATATAAGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTT
1 CTTTAGCGGCGTTTTAA-ATAAGCGCCACTAATCCTAATATACCTCAAGACCAAA-CTCTGCGTT
* * * * * **
58657120 TTGGTTAA-TATTTTGCGGTGCTTTACAATAAGCGCCGCTAATACTATG
64 TTGGTTAAGAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATG
** *
58657168 CTTTAGCGGCGTTTTCCGATAAGCGCCAGTAATCCTAATATACCTCAAGACCAAACTCTGCGTTT
1 CTTTAGCGGCGTTTT-AAATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTT
*
58657233 TGGTTAAGAACTATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATT
65 TGGTTAAGAA-TATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATG
** * * * *
58657282 CTTTAGCGGCGTTTTTGTATAAGCGCCACTAATGCTAGTGTACCTCAAGACCAAACTCTACGTTT
1 CTTTAGCGGCG-TTTTAAATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTT
* * ** * * *
58657347 TGGTTAAGATGTATTACGGCGCTTTTTGCGACTCGCCGCTAATTCTATC
65 TGGTTAAGA-ATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATG
*
58657396 CTTTAGTGGCGATTTTAAATAAGCGCCACTAAT
1 CTTTAGCGGCG-TTTTAAATAAGCGCCACTAAT
58657429 ACTTTCTTTA
Statistics
Matches: 313, Mismatches: 54, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
112 16 0.05
113 83 0.27
114 194 0.62
115 20 0.06
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (112 bp):
CTTTAGCGGCGTTTTAAATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTTT
GGTTAAGAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATG
Found at i:58659008 original size:5 final size:5
Alignment explanation
Indices: 58658998--58659023 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
58658988 CGTCATACTT
58658998 TCTGC TCTGC TCTGC TCTGC TCTGC T
1 TCTGC TCTGC TCTGC TCTGC TCTGC T
58659024 TCTCTCGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.19, T:0.42
Consensus pattern (5 bp):
TCTGC
Found at i:58659106 original size:21 final size:21
Alignment explanation
Indices: 58659082--58659132 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
58659072 TTCTTTTGAA
*
58659082 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
58659103 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
*
58659124 CATCTGCTT
1 CCTCTGCTT
58659133 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.04, C:0.45, G:0.18, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:58659185 original size:87 final size:87
Alignment explanation
Indices: 58659017--58659176 Score: 248
Period size: 87 Copynumber: 1.8 Consensus size: 87
58659007 CTCTGCTCTG
* * *
58659017 CTCTGCTTCTCTCGCTGCAACCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGAA
1 CTCTGCTTCCCTCGCTGCAACATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
** *
58659082 CCTCTGCTTCTCTCGCTGCAGC
66 CCTCAACTTCGCTCGCTGCAGC
**
58659104 CTCTGCTTCCCTCGCTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
1 CTCTGCTTCCCTCGCTGCAACATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
58659169 CCTCAACT
66 CCTCAACT
58659177 GTGGTCGCTT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 66 1.00
ACGTcount: A:0.14, C:0.30, G:0.17, T:0.39
Consensus pattern (87 bp):
CTCTGCTTCCCTCGCTGCAACATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
CCTCAACTTCGCTCGCTGCAGC
Found at i:58659622 original size:28 final size:28
Alignment explanation
Indices: 58659576--58659632 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
58659566 TATAGTTTTT
58659576 ATAATATTTATAAAGGTTATAATAATAA
1 ATAATATTTATAAAGGTTATAATAATAA
*
58659604 ATAATATATTATAAA-GTTATTATAATAA
1 ATAATAT-TTATAAAGGTTATAATAATAA
58659632 A
1 A
58659633 AACAAACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40
Consensus pattern (28 bp):
ATAATATTTATAAAGGTTATAATAATAA
Found at i:58660790 original size:64 final size:64
Alignment explanation
Indices: 58660706--58660853 Score: 226
Period size: 64 Copynumber: 2.3 Consensus size: 64
58660696 ATATATATTT
* * *
58660706 AAAGTTCTTGAGTTGCATTTAAGGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAAGGTATGAATTTTACATACATATGTGGTTCAAATATAGGTTAC
* * *
58660770 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTACATACATATGTGGTTCGAGTATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAAGGTATGAATTTTACATACATATGTGGTTCAAATATAGGTTAC
58660834 AAA-TTCTTTGAGCTGAATTT
1 AAAGTTC-TTGAGCTGAATTT
58660854 TAATGTTGTA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
63 3 0.04
64 74 0.96
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.41
Consensus pattern (64 bp):
AAAGTTCTTGAGCTGAATTTAAGGTATGAATTTTACATACATATGTGGTTCAAATATAGGTTAC
Found at i:58661896 original size:14 final size:15
Alignment explanation
Indices: 58661872--58661906 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
58661862 TATTTTAATC
58661872 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
58661887 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
58661902 ATGGT
1 ATGGT
58661907 AATGTGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:58668418 original size:7 final size:7
Alignment explanation
Indices: 58668406--58668445 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
58668396 TTAAACACTG
58668406 AAACCCT
1 AAACCCT
58668413 AAACCCT
1 AAACCCT
58668420 AAACCCT
1 AAACCCT
*
58668427 AAACACTAT
1 AAAC-C-CT
58668436 AAACCCT
1 AAACCCT
58668443 AAA
1 AAA
58668446 TCCAAAACGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 22 0.76
8 2 0.07
9 5 0.17
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (7 bp):
AAACCCT
Found at i:58668425 original size:14 final size:16
Alignment explanation
Indices: 58668397--58668445 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 16
58668387 AAATAGTAAT
*
58668397 TAAACACT-GAAACCC
1 TAAACACTATAAACCC
*
58668412 TAAAC-C-CTAAACCC
1 TAAACACTATAAACCC
58668426 TAAACACTATAAACCC
1 TAAACACTATAAACCC
58668442 TAAA
1 TAAA
58668446 TCCAAAACGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 12 0.41
15 6 0.21
16 11 0.38
ACGTcount: A:0.49, C:0.33, G:0.02, T:0.16
Consensus pattern (16 bp):
TAAACACTATAAACCC
Found at i:58669390 original size:21 final size:20
Alignment explanation
Indices: 58669366--58669406 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
58669356 CTCTAAACCT
*
58669366 TAAACCTCAATCTCCAAGCCC
1 TAAACCT-AAACTCCAAGCCC
*
58669387 TAAACCTAAACTCTAAGCCC
1 TAAACCTAAACTCCAAGCCC
58669407 AGGACACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.37, C:0.39, G:0.05, T:0.20
Consensus pattern (20 bp):
TAAACCTAAACTCCAAGCCC
Found at i:58670070 original size:133 final size:132
Alignment explanation
Indices: 58669759--58670129 Score: 459
Period size: 133 Copynumber: 2.8 Consensus size: 132
58669749 AACCGTTTCT
* * *
58669759 GGCGTTTTTTAACATTTCGCCACTAAAGC-ATAAAAAGGAAACAACAAAACGGTACCGTTTTGCT
1 GGCGTTTTTTAA-A-TGCGCCACTAAAGCAAT-AAAATGAAACAATAAAACGGTA-CGTTTTGCT
* * *
58669823 CAAAATTTTTCCTCAAATTAGATATCTTTACCGACGTTTCTCCAATAACGCCACTATATCCCAAT
62 CAAATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTCTCCAATAACGCCACCATATCCCAAT
58669888 ATTTGC
127 ATTTGC
* * *
58669894 GGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAATAAAATGGTAGCATTTTG-TCC
1 GGCGTTTTTTA-AATGCGCCACTAAAGCAATAAAATGAAACAATAAAACGGTA-CGTTTTGCT-C
* *
58669958 AAATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTC-CCTGAA-AACGCCGCCA-AT-TCAA
63 AAATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTCTCC--AATAACGCCACCATATCCCAA
*
58670019 TCTTTTGC
126 T-ATTTGC
58670027 GGCGTTTTTTAGAATGCGCCACTAAAGCAATAAAATGAAACAATAAAACGGTACTGTTTTGCTCA
1 GGCGTTTTTTA-AATGCGCCACTAAAGCAATAAAATGAAACAATAAAACGGTAC-GTTTTGCTCA
*
58670092 AATTTTTTCCTCAAATTCA-TTATCTTTACCGGCGTTTC
64 AATTTTTTCCTCAAATT-AGATATCTTTACCGGCGTTTC
58670130 GCTAGATTCC
Statistics
Matches: 209, Mismatches: 18, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
132 5 0.02
133 102 0.49
134 85 0.41
135 16 0.08
136 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (132 bp):
GGCGTTTTTTAAATGCGCCACTAAAGCAATAAAATGAAACAATAAAACGGTACGTTTTGCTCAAA
TTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTCTCCAATAACGCCACCATATCCCAATATTT
GC
Found at i:58673889 original size:2 final size:2
Alignment explanation
Indices: 58673882--58673911 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
58673872 TAGTTGGTAA
58673882 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
58673912 TTTTAATCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58677009 original size:3 final size:3
Alignment explanation
Indices: 58677001--58677027 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
58676991 TTTCCCTACT
58677001 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
58677028 TGTCACTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:58681889 original size:143 final size:143
Alignment explanation
Indices: 58681631--58682216 Score: 843
Period size: 143 Copynumber: 4.1 Consensus size: 143
58681621 TTAGGCTGAT
* * *
58681631 AAGTTTCAGCGGAGCT-GACTGAAGACAGCGAATCTTATTTCCCTGGCGTTACAGTGGAGCAGAT
1 AAGTTGCAGCGGAG-TAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGAT
* * *
58681695 TAAAGCTACAAATTATGGCAGATCTTATCATCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAGCA
65 TAAAGCTACAAATTATGGCAGATCTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAGCCACCA
*
58681760 GCCTTATCTCCCTA
130 GCCTTATCTCCCTG
* * * *
58681774 AAGTTGCAGCGAAGTAGACTGAAGACAGCGAATATTATTTCCCTAGCGTTGCAGTGGAACAGATG
1 AAGTTGCAGCGGAGTAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATT
* **
58681839 AGAGCTACAAATTATGGTGGATCTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAGCCACCAG
66 AAAGCTACAAATTATGGCAGATCTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAGCCACCAG
58681904 CCTTATCTCCCTG
131 CCTTATCTCCCTG
* * * * * * *
58681917 AAGTTGCAGCGGAGCAAACTGAAAACAACGAATCTTATTTCCCTGGCGTTGAAATGGAACAAATT
1 AAGTTGCAGCGGAGTAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATT
* * * *
58681982 AAAGTTACAAATTATGGCGGATCTTATCTTCCTAAAGTTGCAATGGAGCAGATTGAAGCCACCGG
66 AAAGCTACAAATTATGGCAGATCTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAGCCACCAG
*
58682047 CCTTATCTCTCTG
131 CCTTATCTCCCTG
* * *
58682060 AAGTTGCAGCGGAGTAGACTGAAGACAGAGAATCTTATTTCTCTGGCGTTGCAGTGGAATAGATT
1 AAGTTGCAGCGGAGTAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATT
* *
58682125 AATGCTACAAATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAA
66 AAAGCTACAAATTATGGCAGATCTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAGCCACC-A
*
58682190 TCC-TATCTCCCTG
130 GCCTTATCTCCCTG
*
58682203 AAGTTGCAGTGGAG
1 AAGTTGCAGCGGAG
58682217 CGGATTAAAA
Statistics
Matches: 391, Mismatches: 50, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
142 1 0.00
143 388 0.99
144 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (143 bp):
AAGTTGCAGCGGAGTAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATT
AAAGCTACAAATTATGGCAGATCTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAGCCACCAG
CCTTATCTCCCTG
Found at i:58684100 original size:15 final size:15
Alignment explanation
Indices: 58684082--58684112 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
58684072 ACATTATTAC
58684082 TATTATTATTATCAT
1 TATTATTATTATCAT
*
58684097 TATTATTTTTATCAT
1 TATTATTATTATCAT
58684112 T
1 T
58684113 TAAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTATTATTATCAT
Found at i:58689818 original size:22 final size:25
Alignment explanation
Indices: 58689793--58689846 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
58689783 TTATAGATTC
58689793 AATTTAAAAG-ATA-TAAT-ACAAT
1 AATTTAAAAGCATATTAATAACAAT
*
58689815 AATTT-CAAGCATATTTAATAACAAT
1 AATTTAAAAGCATA-TTAATAACAAT
58689840 AATTTAA
1 AATTTAA
58689847 TCATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
24 4 0.16
25 10 0.40
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTTAAAAGCATATTAATAACAAT
Found at i:58703137 original size:11 final size:11
Alignment explanation
Indices: 58703121--58703153 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
58703111 ATATTAATTT
58703121 AAAATAATATA
1 AAAATAATATA
*
58703132 AAAATAA-CTA
1 AAAATAATATA
58703142 AAAATAATATA
1 AAAATAATATA
58703153 A
1 A
58703154 GCGGGTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATAATATA
Found at i:58703820 original size:18 final size:19
Alignment explanation
Indices: 58703786--58703823 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
58703776 AAATTATAAA
58703786 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
58703805 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
58703823 A
1 A
58703824 TTTTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:58730876 original size:22 final size:22
Alignment explanation
Indices: 58730846--58730900 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
58730836 TATCCAAACA
58730846 ATAACAACAAAAT-AGTAACAAC
1 ATAACAACAAAATGAG-AACAAC
* *
58730868 ATAATAACAAAATGAGAACAAA
1 ATAACAACAAAATGAGAACAAC
*
58730890 ACAACAACAAA
1 ATAACAACAAA
58730901 CAGCAAACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.67, C:0.16, G:0.05, T:0.11
Consensus pattern (22 bp):
ATAACAACAAAATGAGAACAAC
Found at i:58735431 original size:24 final size:22
Alignment explanation
Indices: 58735404--58735472 Score: 59
Period size: 24 Copynumber: 3.0 Consensus size: 22
58735394 ACTTAGAATT
58735404 AATTGAAATCTAAATCTAAATTTG
1 AATT-AAATC-AAATCTAAATTTG
* *
58735428 AATTATA-CAAATAATAAATTTG
1 AATTAAATCAAAT-CTAAATTTG
*
58735450 AATTAATTCAAAATCTTAAATTT
1 AATTAAATC-AAATC-TAAATTT
58735473 CAAATATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
21 4 0.11
22 14 0.39
23 3 0.08
24 15 0.42
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.39
Consensus pattern (22 bp):
AATTAAATCAAATCTAAATTTG
Found at i:58735733 original size:21 final size:23
Alignment explanation
Indices: 58735687--58735733 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
58735677 AATATTATTT
58735687 ATTTTAATTAATTTTGAACATAA
1 ATTTTAATTAATTTTGAACATAA
*
58735710 ATTTT-ATTAATTTTG-ACATTA
1 ATTTTAATTAATTTTGAACATAA
58735731 ATT
1 ATT
58735734 GATCATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 10 0.43
23 5 0.22
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (23 bp):
ATTTTAATTAATTTTGAACATAA
Found at i:58738959 original size:16 final size:16
Alignment explanation
Indices: 58738940--58738970 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58738930 TATTTTTATT
*
58738940 AATATTTTTGTTAAAA
1 AATATTTTTGGTAAAA
58738956 AATATTTTTGGTAAA
1 AATATTTTTGGTAAA
58738971 TTACACTAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (16 bp):
AATATTTTTGGTAAAA
Found at i:58743512 original size:12 final size:13
Alignment explanation
Indices: 58743476--58743513 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
58743466 ATTTTCTTAC
58743476 TAAATAATTTTGAA
1 TAAATAATTTT-AA
58743490 TAAATAA-TTTAA
1 TAAATAATTTTAA
58743502 TAAA-AATTTTAA
1 TAAATAATTTTAA
58743514 AAAAGTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 11 0.48
13 3 0.13
14 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (13 bp):
TAAATAATTTTAA
Found at i:58747482 original size:184 final size:179
Alignment explanation
Indices: 58747113--58747475 Score: 543
Period size: 186 Copynumber: 2.0 Consensus size: 179
58747103 CAATTAACAC
* *
58747113 GTAGACTTTTGATTTTATAAGTGGTAGGATGATCGACTTCCATTAATTGGTTTAAAGTTTGTATT
1 GTAGACTTATGATTTTATAAGTGGTAGGATGATAGACTTCCATTAATTGGTTTAAAGTTTGTATT
* * * **
58747178 TGTCATGTAATTGAATTTTGGGTGTTGGTTTGCCATGACTAGGTCAGTGGCCGTCTCCCTTGGAT
66 CGTCATGTAATTGAATTTTGGGTGCTGATTTGCCATGACTAGGTCAGTGGCCGTCTCCCAAGGAT
*
58747243 ATTGACAAGTTCAAAAGTATTTAGTTTTTTTTTTTTATATGTAAGGACATTTTT
131 A-T-ACAAGTTCAAAAGTATTTAG---TTTATTTTTATATGTAAGGACATTTTT
*
58747297 GTAGACTTATGATTTTATAAGTGGTAGGATGCTAGACTTCCATTAATTGGTTTAAAGTTTGTGTA
1 GTAGACTTATGATTTTATAAGTGGTAGGATGATAGACTTCCATTAATTGGTTTAAAG-TT-TGTA
*
58747362 TTCGTCATGTAATTGAATTTTGGGTGCTGATTTGCCATGACTAGGTC-GATGGTCGTCTCCCAAG
64 TTCGTCATGTAATTGAATTTTGGGTGCTGATTTGCCATGACTAGGTCAG-TGGCCGTCTCCCAAG
58747426 GATA-ACAAGTTCAAAAGTATTTAG-TTATTTTTATATGTAAGGACATTTTT
128 GATATACAAGTTCAAAAGTATTTAGTTTATTTTTATATGTAAGGACATTTTT
58747476 TTTTTGTCTT
Statistics
Matches: 166, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
179 25 0.15
183 20 0.12
184 54 0.33
185 3 0.02
186 64 0.39
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (179 bp):
GTAGACTTATGATTTTATAAGTGGTAGGATGATAGACTTCCATTAATTGGTTTAAAGTTTGTATT
CGTCATGTAATTGAATTTTGGGTGCTGATTTGCCATGACTAGGTCAGTGGCCGTCTCCCAAGGAT
ATACAAGTTCAAAAGTATTTAGTTTATTTTTATATGTAAGGACATTTTT
Found at i:58755979 original size:20 final size:18
Alignment explanation
Indices: 58755951--58755994 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
58755941 AGGTTTAAAA
* *
58755951 TAGTAGTTAACTGTTATAGT
1 TAGTTGTTAACAGTTA-A-T
58755971 TAGTTGTTAACAGTTAAT
1 TAGTTGTTAACAGTTAAT
58755989 TAGTTG
1 TAGTTG
58755995 ATAGTAGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 1 0.05
20 14 0.64
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (18 bp):
TAGTTGTTAACAGTTAAT
Found at i:58760477 original size:18 final size:18
Alignment explanation
Indices: 58760454--58760488 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
58760444 TTAACTGTTA
*
58760454 TAGTTAGTTGTTAGCAGT
1 TAGTTAGTTGATAGCAGT
58760472 TAGTTAGTTGATAGCAG
1 TAGTTAGTTGATAGCAG
58760489 GTACTGGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.40
Consensus pattern (18 bp):
TAGTTAGTTGATAGCAGT
Found at i:58765108 original size:101 final size:102
Alignment explanation
Indices: 58764988--58765172 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
58764978 AAAGTGATGG
* *
58764988 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGG-ATGATAATGGTCACATGTATAGT
58765051 ACTATGTGCAGGCTACTATGCATACCGGATAGTTTCGA
65 ACTATGTGCAGGCTACTATGCATACCGGATAGTTTCGA
* ** * *
58765089 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATTGGATGGTAATGGTTACATGTATAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGATGATAATGGTCACATGTATAGTA
58765154 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
58765173 TGAACCGAAC
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.52
102 32 0.43
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGATGATAATGGTCACATGTATAGTA
CTATGTGCAGGCTACTATGCATACCGGATAGTTTCGA
Found at i:58765118 original size:51 final size:49
Alignment explanation
Indices: 58764988--58765120 Score: 162
Period size: 50 Copynumber: 2.7 Consensus size: 49
58764978 AAAGTGATGG
*
58764988 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACA-GTACCGGAATGATAGA
* * * *
58765038 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCA-TACCGG-ATAGTTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA--CAGTACCGGAAT-G-ATAGA
58765089 TCACGTGTGTAGTACTATGTGCAGGCTACTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTAC
58765121 GTGTATTGGA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
49 3 0.04
50 36 0.50
51 31 0.43
52 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (49 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACAGTACCGGAATGATAGA
Found at i:58765153 original size:51 final size:50
Alignment explanation
Indices: 58764984--58765179 Score: 205
Period size: 51 Copynumber: 3.9 Consensus size: 50
58764974 AGTGAAAGTG
* * *
58764984 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGGT
* * ** *
58765035 A-GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCATACCGGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
* * * **
58765084 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATTGGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
* * * *
58765135 AATGGTTACATGTATAGTACTATGTGCAGGCTACTATGTGAACCG
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
58765180 AACATCATTG
Statistics
Matches: 115, Mismatches: 27, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
49 3 0.03
50 37 0.32
51 74 0.64
52 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
Found at i:58779555 original size:2 final size:2
Alignment explanation
Indices: 58779548--58779592 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
58779538 GAAAATTTTA
58779548 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
58779590 AT A
1 AT A
58779593 AAAGTAACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58779899 original size:2 final size:2
Alignment explanation
Indices: 58779892--58779934 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
58779882 AAAAATTTTG
58779892 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
58779934 A
1 A
58779935 GCTACGTGAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58781966 original size:19 final size:19
Alignment explanation
Indices: 58781916--58781966 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
58781906 TATAACTTTT
*
58781916 TTTTTTTA-AATTTTATTTA
1 TTTTTTTATAA-TTTATTGA
* *
58781935 GTTTTTAAT-ATTTATTGA
1 TTTTTTTATAATTTATTGA
58781953 TTTTTTTATAATTT
1 TTTTTTTATAATTT
58781967 TTATAATTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTTTTTATAATTTATTGA
Found at i:58783314 original size:18 final size:20
Alignment explanation
Indices: 58783277--58783319 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
58783267 CTATTAATGT
58783277 TTCTTTGTTTTGCTTCTTCG
1 TTCTTTGTTTTGCTTCTTCG
*
58783297 TTCTTT-TTTTTCTT-TTCG
1 TTCTTTGTTTTGCTTCTTCG
58783315 TTCTT
1 TTCTT
58783320 CCGTTAGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 6 0.27
ACGTcount: A:0.00, C:0.19, G:0.09, T:0.72
Consensus pattern (20 bp):
TTCTTTGTTTTGCTTCTTCG
Found at i:58787281 original size:32 final size:31
Alignment explanation
Indices: 58787215--58787283 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
58787205 ACAATAAAGT
*
58787215 ATAAAATTGTACTATGTTACACGTCATAAGA
1 ATAAAATTGTACTATGTTACACGTCATAACA
* *
58787246 ATAATAATTGTACTATGTTGCATG-CTATAACA
1 ATAA-AATTGTACTATGTTACACGTC-ATAACA
58787278 ATAAAA
1 ATAAAA
58787284 AAAAATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 7 0.21
32 26 0.79
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (31 bp):
ATAAAATTGTACTATGTTACACGTCATAACA
Found at i:58790333 original size:17 final size:16
Alignment explanation
Indices: 58790294--58790330 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
58790284 TTTCTTTAAT
58790294 TAAAATATATAATTTC
1 TAAAATATATAATTTC
58790310 TAAAATATATAATTTC
1 TAAAATATATAATTTC
58790326 TAAAA
1 TAAAA
58790331 ATAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATATATAATTTC
Found at i:58800563 original size:24 final size:24
Alignment explanation
Indices: 58800536--58800586 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
58800526 TCCAGTGCTT
*
58800536 CCCGTTAAGTGCTTTTCGGAGCTA
1 CCCGTTAAGTGCTCTTCGGAGCTA
* *
58800560 CCCGTTAATTGCTCTTCGGCGCTA
1 CCCGTTAAGTGCTCTTCGGAGCTA
58800584 CCC
1 CCC
58800587 ATTATAAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.33, G:0.22, T:0.31
Consensus pattern (24 bp):
CCCGTTAAGTGCTCTTCGGAGCTA
Found at i:58800848 original size:26 final size:26
Alignment explanation
Indices: 58800818--58800871 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
58800808 CATGAGAACA
58800818 TGTGAAATCAAAATGAAACTATTATC
1 TGTGAAATCAAAATGAAACTATTATC
58800844 TGTGAAATCAAAATGAAACTATTATC
1 TGTGAAATCAAAATGAAACTATTATC
58800870 TG
1 TG
58800872 ACATGAGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (26 bp):
TGTGAAATCAAAATGAAACTATTATC
Found at i:58811678 original size:19 final size:18
Alignment explanation
Indices: 58811610--58811679 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
58811600 AAATTACAAA
*
58811610 AAAAATTAAAAATATTTT
1 AAAAATTCAAAATATTTT
*
58811628 CAAAAATTCAAATTATTTTTT
1 -AAAAATTCAAA--ATATTTT
* *
58811649 TAAAATACAAAATATTTAT
1 AAAAATTCAAAATATTT-T
58811668 AAAAATTCAAAA
1 AAAAATTCAAAA
58811680 GAATATATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
18 5 0.12
19 21 0.51
20 9 0.22
21 6 0.15
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAATTCAAAATATTTT
Found at i:58812649 original size:31 final size:31
Alignment explanation
Indices: 58812613--58812717 Score: 115
Period size: 31 Copynumber: 3.4 Consensus size: 31
58812603 TAATCACATT
58812613 AATATTAAATTAATAAAATATTATCTAGATA
1 AATATTAAATTAATAAAATATTATCTAGATA
* ** * * * *
58812644 AATATTTAATT--TAATTTAATGTCTCATATT
1 AATATTAAATTAATAAAATATTATCT-AGATA
58812674 AATATTAAATTAATAAAATATTATCTAGATA
1 AATATTAAATTAATAAAATATTATCTAGATA
*
58812705 AATAGTAAATTAA
1 AATATTAAATTAA
58812718 ATTTAATATT
Statistics
Matches: 56, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
29 9 0.16
30 13 0.23
31 25 0.45
32 9 0.16
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (31 bp):
AATATTAAATTAATAAAATATTATCTAGATA
Found at i:58812705 original size:61 final size:61
Alignment explanation
Indices: 58812610--58812724 Score: 203
Period size: 61 Copynumber: 1.9 Consensus size: 61
58812600 AATTAATCAC
* * *
58812610 ATTAATATTAAATTAATAAAATATTATCTAGATAAATATTTAATTTAATTTAATGTCTCAT
1 ATTAATATTAAATTAATAAAATATTATCTAGATAAATAGTAAATTAAATTTAATGTCTCAT
58812671 ATTAATATTAAATTAATAAAATATTATCTAGATAAATAGTAAATTAAATTTAAT
1 ATTAATATTAAATTAATAAAATATTATCTAGATAAATAGTAAATTAAATTTAAT
58812725 ATTAAATTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (61 bp):
ATTAATATTAAATTAATAAAATATTATCTAGATAAATAGTAAATTAAATTTAATGTCTCAT
Found at i:58813398 original size:23 final size:23
Alignment explanation
Indices: 58813372--58813417 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
58813362 ATGCAATCTT
58813372 AGATATGA-TATGTAAATCTTAGA
1 AGATATGATTATGT-AATCTTAGA
*
58813395 AGATATGATTCTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
58813418 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:58819110 original size:2 final size:2
Alignment explanation
Indices: 58819105--58819129 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58819095 TATAGACTAC
58819105 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
58819130 GGTCAGGAAT
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:58822782 original size:11 final size:12
Alignment explanation
Indices: 58822759--58822807 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 12
58822749 AATTTATTTA
58822759 ATTAAATTA-AAT
1 ATTAAA-TAGAAT
58822771 ATTAAATA-AAT
1 ATTAAATAGAAT
58822782 AAATTAAATAGAA-
1 --ATTAAATAGAAT
58822795 ATTAAATAGAAT
1 ATTAAATAGAAT
58822807 A
1 A
58822808 AGAATATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 16 0.48
12 7 0.21
13 8 0.24
14 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (12 bp):
ATTAAATAGAAT
Found at i:58822800 original size:20 final size:21
Alignment explanation
Indices: 58822756--58822802 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
58822746 CGTAATTTAT
* *
58822756 TTAATTAAATTAAATATTAAA
1 TTAAATAAATTAAATATGAAA
58822777 -TAAATAAATTAAATA-GAAA
1 TTAAATAAATTAAATATGAAA
58822796 TTAAATA
1 TTAAATA
58822803 GAATAAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TTAAATAAATTAAATATGAAA
Found at i:58823481 original size:15 final size:15
Alignment explanation
Indices: 58823440--58823497 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 15
58823430 TAACTTATTC
*
58823440 TAATTAATAATTTATA
1 TAATTAA-AATATATA
58823456 CTAACTTAAAACTA-ATA
1 -TAA-TTAAAA-TATATA
58823473 TAATTAAAATATATA
1 TAATTAAAATATATA
58823488 TAATATAAAA
1 TAAT-TAAAA
58823498 GCTCCTTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 2 0.06
15 13 0.36
16 8 0.22
17 8 0.22
18 5 0.14
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATTAAAATATATA
Found at i:58823653 original size:16 final size:15
Alignment explanation
Indices: 58823627--58823665 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
58823617 ATTAATCCCC
58823627 TTATCTTATTTTGATAT
1 TTAT-TTATTTT-ATAT
58823644 TTATTTATTTTATAT
1 TTATTTATTTTATAT
58823659 TT-TTTAT
1 TTATTTAT
58823666 ATAAAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.23
15 6 0.27
16 7 0.32
17 4 0.18
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (15 bp):
TTATTTATTTTATAT
Found at i:58829159 original size:12 final size:12
Alignment explanation
Indices: 58829144--58829216 Score: 51
Period size: 12 Copynumber: 6.0 Consensus size: 12
58829134 AAATTTATTT
58829144 TAAAAATTAAAA
1 TAAAAATTAAAA
58829156 TAAAAATTAAAA
1 TAAAAATTAAAA
*
58829168 -AAAGTATTTTAAAA
1 TAAA--A-ATTAAAA
**
58829182 -AAATTTTAAAA
1 TAAAAATTAAAA
* * *
58829193 TTAAATTTAAAT
1 TAAAAATTAAAA
58829205 TAAAAATTAAAA
1 TAAAAATTAAAA
58829217 AATTTTAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
11 10 0.20
12 29 0.59
13 1 0.02
14 9 0.18
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (12 bp):
TAAAAATTAAAA
Found at i:58829222 original size:34 final size:33
Alignment explanation
Indices: 58829179--58829252 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 33
58829169 AAGTATTTTA
* *
58829179 AAAAAATTTTAAAATTAAATTTAAATT-AAAAATT
1 AAAAAATTTTAAAA--AATTTAAAATTAAAAAATT
58829213 AAAAAATTTTAAAAAATTTAAAATTAAAAAAATT
1 AAAAAATTTTAAAAAATTTAAAATT-AAAAAATT
58829247 AAAAAA
1 AAAAAA
58829253 AGTATTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 9 0.25
34 27 0.75
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (33 bp):
AAAAAATTTTAAAAAATTTAAAATTAAAAAATT
Found at i:58829229 original size:25 final size:25
Alignment explanation
Indices: 58829201--58829253 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
58829191 AATTAAATTT
* *
58829201 AAATTAAAAATTAAAAAATTTTAAA
1 AAATTAAAAATTAAAAAAATTAAAA
*
58829226 AAATTTAAAATTAAAAAAATTAAAA
1 AAATTAAAAATTAAAAAAATTAAAA
58829251 AAA
1 AAA
58829254 GTATTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (25 bp):
AAATTAAAAATTAAAAAAATTAAAA
Found at i:58829252 original size:9 final size:9
Alignment explanation
Indices: 58829206--58829253 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
58829196 AATTTAAATT
58829206 AAAAATTAA
1 AAAAATTAA
* *
58829215 AAAATTTTA
1 AAAAATTAA
58829224 AAAAATT--
1 AAAAATTAA
*
58829231 TAAAATTAA
1 AAAAATTAA
58829240 AAAAATTAA
1 AAAAATTAA
58829249 AAAAA
1 AAAAA
58829254 GTATTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
7 6 0.19
9 26 0.81
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAATTAA
Found at i:58829260 original size:38 final size:37
Alignment explanation
Indices: 58829196--58829290 Score: 94
Period size: 38 Copynumber: 2.6 Consensus size: 37
58829186 TTTAAAATTA
*
58829196 AATTT-AAATT-AAAAAT-TAAAAA--ATTTTAAAA-
1 AATTTAAAATTAAAAAATAAAAAAAGTATTTTAAAAG
58829227 AATTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAG
1 AATTTAAAATT-AAAAAA-TAAAAAAAGTATTTTAAAAG
* *
58829266 TATTTTAAAGTTAAAAAATAAAAAA
1 -AATTTAAAATTAAAAAATAAAAAA
58829291 TAAAAATATT
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
31 5 0.10
32 5 0.10
34 5 0.10
35 1 0.02
36 5 0.10
38 16 0.31
39 6 0.12
40 9 0.17
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (37 bp):
AATTTAAAATTAAAAAATAAAAAAAGTATTTTAAAAG
Found at i:58829264 original size:11 final size:11
Alignment explanation
Indices: 58829250--58829274 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58829240 AAAAATTAAA
58829250 AAAAGTATTTT
1 AAAAGTATTTT
58829261 AAAAGTATTTT
1 AAAAGTATTTT
58829272 AAA
1 AAA
58829275 GTTAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:58833430 original size:76 final size:76
Alignment explanation
Indices: 58833268--58833464 Score: 252
Period size: 76 Copynumber: 2.6 Consensus size: 76
58833258 TCGACTAGTG
* *
58833268 CTGGGTGCAAATCTTTGTTGATTTATTCTACTAGTGTTGGGCACACAATTAATATAGTGAGTTAA
1 CTGGGTGCAAATCTTTGTTGATTTATTCAACTAGTGTTGGGCACACAATTAATATAGTCAGTTAA
* *
58833333 TCTGACAAACG
66 TCTAACAAACA
* *
58833344 CTAGGCGCAAATCTTTGTTGATTTATTCAACTAGTGTTGGGCACACAATTAATATTA-TCAGTTA
1 CTGGGTGCAAATCTTTGTTGATTTATTCAACTAGTGTTGGGCACACAATTAATA-TAGTCAGTTA
* **
58833408 ATCTAACTAGTA
65 ATCTAACAAACA
* * * **
58833420 TTGGGTGCAAATCTTTGTCGATTTATTCGACTAGTGCAGGGCACA
1 CTGGGTGCAAATCTTTGTTGATTTATTCAACTAGTGTTGGGCACA
58833465 TCTAATGTTG
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
76 102 0.98
77 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (76 bp):
CTGGGTGCAAATCTTTGTTGATTTATTCAACTAGTGTTGGGCACACAATTAATATAGTCAGTTAA
TCTAACAAACA
Found at i:58834611 original size:160 final size:160
Alignment explanation
Indices: 58834347--58834675 Score: 570
Period size: 160 Copynumber: 2.1 Consensus size: 160
58834337 GCTGCACATG
*
58834347 GCCGTGTGTCTTATTGTCTTTAGGTGCAGGTTTTACATGGTCTGGCACACGACCCACGACATGGT
1 GCCGTGTGTCTTATTGTCTTTAGGTGCAGGTTTTACATGGTCTGGCACACGACCCACGACATGGC
58834412 CGTGTGTCTTAAAATAGTTTATTACACGATATGAGACACGGCCTGCGACACGACCGTGTGACCTT
66 CGTGTGTCTTAAAATAGTTTATTACACGATATGAGACACGGCCTGCGACACGACCGTGTGACCTT
*
58834477 AACTCGAATATCCACACGGGCTGGGACACA
131 AACTCGAATATCCACACGGGCTAGGACACA
*
58834507 GCCGTGTGTCTTATTGTCTTTAGGTGCAGGTTTTACATGG-CTTGGCACACGGCCCACGACATGG
1 GCCGTGTGTCTTATTGTCTTTAGGTGCAGGTTTTACATGGTC-TGGCACACGACCCACGACATGG
*
58834571 CCGTGTGTCTTAAAATAGTTTATTACACGATATGAGACACGGCCTGCGACACGACTGTGTGACCT
65 CCGTGTGTCTTAAAATAGTTTATTACACGATATGAGACACGGCCTGCGACACGACCGTGTGACCT
* * **
58834636 TAATTCGAATATCCACACGGTCTAGGACATG
130 TAACTCGAATATCCACACGGGCTAGGACACA
58834667 GCCGTGTGT
1 GCCGTGTGT
58834676 TTGCACTTCG
Statistics
Matches: 160, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
159 1 0.01
160 159 0.99
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.28
Consensus pattern (160 bp):
GCCGTGTGTCTTATTGTCTTTAGGTGCAGGTTTTACATGGTCTGGCACACGACCCACGACATGGC
CGTGTGTCTTAAAATAGTTTATTACACGATATGAGACACGGCCTGCGACACGACCGTGTGACCTT
AACTCGAATATCCACACGGGCTAGGACACA
Found at i:58834731 original size:160 final size:160
Alignment explanation
Indices: 58834392--58834739 Score: 409
Period size: 160 Copynumber: 2.2 Consensus size: 160
58834382 CATGGTCTGG
* * *
58834392 CACACGACCCACGACATGGTCGTGTGTCTTAAAATAGTTTATTACACGATATGAGACACGGCCTG
1 CACACGGCCCACCACATGGCCGTGTGTCTTAAAATAGTTTATTACACGATATGAGACACGGCCTG
* *
58834457 CGACACGACCGTGTGACCTTAACTCGAATATCCACACGGGCTGGGACACAGCCGTGTGTCTTATT
66 CGACACGACCGTGTGACCTTAACTCGAATATCCACACGGGCTAGGACACAGCCGTGTGTCTTACT
** * ***** * *
58834522 GTCTTTAGGTGCAGGTTTTACATGGCTTGG
131 GTCTGAAGGTCCACACAATACATGGATTGA
*
58834552 CACACGGCCCACGACATGGCCGTGTGTCTTAAAATAGTTTATTACACGATATGAGACACGGCCTG
1 CACACGGCCCACCACATGGCCGTGTGTCTTAAAATAGTTTATTACACGATATGAGACACGGCCTG
* * * **
58834617 CGACACGACTGTGTGACCTTAATTCGAATATCCACACGGTCTAGGACATGGCCGTGTGT-TTGCA
66 CGACACGACCGTGTGACCTTAACTCGAATATCCACACGGGCTAGGACACAGCCGTGTGTCTT--A
*
58834681 CT-TC-GAATGTCCACACAAT-C-TGGGATGTGA
129 CTGTCTGAAGGTCCACACAATACAT-GGAT-TGA
*
58834711 CACACGGCCCTGCCACATGGCCGTGTGTC
1 CACACGGCCC-ACCACATGGCCGTGTGTC
58834740 CCATGTTTTC
Statistics
Matches: 161, Mismatches: 22, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
157 1 0.01
158 4 0.02
159 20 0.12
160 134 0.83
161 2 0.01
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (160 bp):
CACACGGCCCACCACATGGCCGTGTGTCTTAAAATAGTTTATTACACGATATGAGACACGGCCTG
CGACACGACCGTGTGACCTTAACTCGAATATCCACACGGGCTAGGACACAGCCGTGTGTCTTACT
GTCTGAAGGTCCACACAATACATGGATTGA
Found at i:58851387 original size:17 final size:18
Alignment explanation
Indices: 58851361--58851394 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
58851351 ATTTGAATAT
58851361 AATTTATAAT-ATTTAAA
1 AATTTATAATAATTTAAA
*
58851378 AATTTGTAATAATTTAA
1 AATTTATAATAATTTAA
58851395 TTTTAGATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AATTTATAATAATTTAAA
Found at i:58855275 original size:26 final size:26
Alignment explanation
Indices: 58855219--58855268 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
58855209 AAGATGCATG
*
58855219 TATATAAAATTATAATAAATTAAAAA
1 TATATAAAATTATAAGAAATTAAAAA
* *
58855245 TATATAAAATTATTAGATATTAAA
1 TATATAAAATTATAAGAAATTAAA
58855269 TTAATATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
TATATAAAATTATAAGAAATTAAAAA
Found at i:58860216 original size:20 final size:20
Alignment explanation
Indices: 58860185--58860240 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
58860175 TAATGTGCTA
58860185 ATATAGTTTAAATTTAATAAT
1 ATATA-TTTAAATTTAATAAT
58860206 ATATATTTAAAATTTTAATAAT
1 ATATATTT-AAA-TTTAATAAT
*
58860228 ATAT-TTAAAATTT
1 ATATATTTAAATTT
58860241 TCCAAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.09
20 6 0.19
21 10 0.31
22 13 0.41
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATATTTAAATTTAATAAT
Found at i:58860241 original size:20 final size:20
Alignment explanation
Indices: 58860183--58860241 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 20
58860173 TCTAATGTGC
58860183 TAATATAGTTT-AAA-TTTAA
1 TAATATA-TTTAAAATTTTAA
58860202 TAATATATATTTAAAATTTTAA
1 T-A-ATATATTTAAAATTTTAA
58860224 TAATATATTTAAAATTTT
1 TAATATATTTAAAATTTT
58860242 CCAAAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
19 1 0.03
20 20 0.56
21 9 0.25
22 6 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TAATATATTTAAAATTTTAA
Found at i:58861433 original size:24 final size:23
Alignment explanation
Indices: 58861381--58861438 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
58861371 TGTGATGCTC
58861381 ATTATATTTTTATAATATTTGTA
1 ATTATATTTTTATAATATTTGTA
* *
58861404 AATATATTGTTTGTAATATTT-TA
1 ATTATATT-TTTATAATATTTGTA
58861427 TATTATATTTTT
1 -ATTATATTTTT
58861439 TTCATTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (23 bp):
ATTATATTTTTATAATATTTGTA
Found at i:58861567 original size:7 final size:7
Alignment explanation
Indices: 58861557--58861582 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
58861547 TCATTTACAT
58861557 ATATTAC
1 ATATTAC
58861564 ATATTAC
1 ATATTAC
58861571 ATATTAC
1 ATATTAC
58861578 ATATT
1 ATATT
58861583 GGTATTTACC
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:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (7 bp):
ATATTAC
Found at i:58862161 original size:17 final size:18
Alignment explanation
Indices: 58862124--58862161 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
58862114 TACACTAATC
*
58862124 ATTTTAAATTGATTTTAA
1 ATTTTAAATTGATTCTAA
58862142 ATTTTAAATT-ATTCTAA
1 ATTTTAAATTGATTCTAA
58862159 ATT
1 ATT
58862162 ATCGAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (18 bp):
ATTTTAAATTGATTCTAA
Found at i:58870767 original size:12 final size:12
Alignment explanation
Indices: 58870727--58870782 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
58870717 TGGGGCAGAT
*
58870727 GCTGAAGCTGAA
1 GCTGGAGCTGAA
* *
58870739 GCTGCAGCTGCA
1 GCTGGAGCTGAA
58870751 GCTGGAGCTGAA
1 GCTGGAGCTGAA
* *
58870763 GCTGGAGATGGA
1 GCTGGAGCTGAA
58870775 GCTGGAGC
1 GCTGGAGC
58870783 AGCGCCAGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.23, C:0.20, G:0.41, T:0.16
Consensus pattern (12 bp):
GCTGGAGCTGAA
Found at i:58870782 original size:6 final size:6
Alignment explanation
Indices: 58870727--58870782 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
58870717 TGGGGCAGAT
* * * * * *
58870727 GCTGAA GCTGAA GCTGCA GCTGCA GCTGGA GCTGAA GCTGGA GATGGA
1 GCTGGA GCTGGA GCTGGA GCTGGA GCTGGA GCTGGA GCTGGA GCTGGA
58870775 GCTGGA GC
1 GCTGGA GC
58870783 AGCGCCAGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.23, C:0.20, G:0.41, T:0.16
Consensus pattern (6 bp):
GCTGGA
Found at i:58875256 original size:6 final size:6
Alignment explanation
Indices: 58875204--58875263 Score: 59
Period size: 6 Copynumber: 10.2 Consensus size: 6
58875194 TGGGGCAGCT
* * * * * *
58875204 GCTGAA GCTGAA GCTGAA GCTGCA CCTGGA GCTGAA GCTGGA GCTGGA
1 GCTGGA GCTGGA GCTGGA GCTGGA GCTGGA GCTGGA GCTGGA GCTGGA
58875252 GCTGGA GC-GGA G
1 GCTGGA GCTGGA G
58875264 TCAGCAGCCA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
5 4 0.08
6 44 0.92
ACGTcount: A:0.23, C:0.20, G:0.42, T:0.15
Consensus pattern (6 bp):
GCTGGA
Found at i:58875256 original size:12 final size:12
Alignment explanation
Indices: 58875204--58875259 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
58875194 TGGGGCAGCT
*
58875204 GCTGAAGCTGAA
1 GCTGGAGCTGAA
* *
58875216 GCTGAAGCTGCA
1 GCTGGAGCTGAA
*
58875228 CCTGGAGCTGAA
1 GCTGGAGCTGAA
*
58875240 GCTGGAGCTGGA
1 GCTGGAGCTGAA
58875252 GCTGGAGC
1 GCTGGAGC
58875260 GGAGTCAGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.23, C:0.21, G:0.39, T:0.16
Consensus pattern (12 bp):
GCTGGAGCTGAA
Found at i:58876739 original size:22 final size:22
Alignment explanation
Indices: 58876714--58876759 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
58876704 TAAAATCGAA
*
58876714 ATATTTATTAAAATAATAAATT
1 ATATTAATTAAAATAATAAATT
* * *
58876736 ATATTAATTATATTAATAATTT
1 ATATTAATTAAAATAATAAATT
58876758 AT
1 AT
58876760 TATATGACTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTAATTAAAATAATAAATT
Found at i:58877026 original size:22 final size:22
Alignment explanation
Indices: 58876998--58877055 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
58876988 AAAATGACTT
58876998 ATTTTCCGTTGACCTGTAAGTC
1 ATTTTCCGTTGACCTGTAAGTC
58877020 ATTTTCCGTTGACCTGTAAGTC
1 ATTTTCCGTTGACCTGTAAGTC
*
58877042 ATTTTCTGTTGACC
1 ATTTTCCGTTGACC
58877056 AAACTATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (22 bp):
ATTTTCCGTTGACCTGTAAGTC
Found at i:58880494 original size:67 final size:67
Alignment explanation
Indices: 58880386--58880513 Score: 229
Period size: 67 Copynumber: 1.9 Consensus size: 67
58880376 GTTTATATTA
* *
58880386 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTTGTGGCAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGCAGTGTGCTCTCT
58880451 TG
66 TG
*
58880453 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGCAGTGTGCT
58880514 TTCTGAATTG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.27
Consensus pattern (67 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGCAGTGTGCTCTCT
TG
Found at i:58883932 original size:36 final size:36
Alignment explanation
Indices: 58883885--58883956 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
58883875 CTACACATAT
58883885 TTTGTATAACTACTTTTATTACTATTTTCAGTATAA
1 TTTGTATAACTACTTTTATTACTATTTTCAGTATAA
58883921 TTTGTATAACTACTTTTATTACTATTTTCAGTATAA
1 TTTGTATAACTACTTTTATTACTATTTTCAGTATAA
58883957 CTATGTATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.53
Consensus pattern (36 bp):
TTTGTATAACTACTTTTATTACTATTTTCAGTATAA
Found at i:58886411 original size:6 final size:6
Alignment explanation
Indices: 58886402--58886445 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
58886392 TGGGGCAGCT
* * *
58886402 GCTGAA GCTGAA GCTGAA GCTGAA GCTGCA CCTGGA GCTGAA GC
1 GCTGAA GCTGAA GCTGAA GCTGAA GCTGAA GCTGAA GCTGAA GC
58886446 CGGAGCTGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.27, C:0.23, G:0.34, T:0.16
Consensus pattern (6 bp):
GCTGAA
Found at i:58886454 original size:18 final size:18
Alignment explanation
Indices: 58886402--58886456 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
58886392 TGGGGCAGCT
*
58886402 GCTGAAGCTGAAGCTGAA
1 GCTGAAGCTGAAGCTGGA
* *
58886420 GCTGAAGCTGCACCTGGA
1 GCTGAAGCTGAAGCTGGA
* *
58886438 GCTGAAGCCGGAGCTGGA
1 GCTGAAGCTGAAGCTGGA
58886456 G
1 G
58886457 ATGGAGCGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.25, C:0.22, G:0.38, T:0.15
Consensus pattern (18 bp):
GCTGAAGCTGAAGCTGGA
Found at i:58889448 original size:22 final size:20
Alignment explanation
Indices: 58889412--58889469 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
58889402 AGCCTGACCC
58889412 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
58889434 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
*
58889455 A-GTATTTTAAAAATA
1 ATTTATTTTAAAAATA
58889470 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 2 0.06
20 11 0.33
21 5 0.15
22 7 0.21
23 8 0.24
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:58889471 original size:11 final size:11
Alignment explanation
Indices: 58889451--58889517 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
58889441 TTAAAAATTA
58889451 AAAAAGTATTTT
1 AAAAA-TATTTT
58889463 AAAAATATTTT
1 AAAAATATTTT
*
58889474 --AAA-A-TTA
1 AAAAATATTTT
* *
58889481 AAAAATA-ATA
1 AAAAATATTTT
58889491 AAAAAGTATTTT
1 AAAAA-TATTTT
58889503 AAAAATATTTT
1 AAAAATATTTT
58889514 AAAA
1 AAAA
58889518 TTTAAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 6 0.13
10 8 0.17
11 18 0.39
12 11 0.24
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:58889500 original size:40 final size:40
Alignment explanation
Indices: 58889438--58889535 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
58889428 CCAAAAATTT
*
58889438 ATTTTAAAAAT-TAAAAAAGTATTTTAAAAATATTTTAAA
1 ATTTAAAAAATATAAAAAAGTATTTTAAAAATATTTTAAA
58889477 A-TTAAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAA
1 ATTTAAAAAAT-ATAAAAAAGTATTTTAAAAATATTTTAAA
*
58889517 ATTTAAAAAATTTAAAAAA
1 ATTTAAAAAATATAAAAAA
58889536 TAAATATATT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
38 8 0.15
39 1 0.02
40 36 0.67
41 9 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (40 bp):
ATTTAAAAAATATAAAAAAGTATTTTAAAAATATTTTAAA
Found at i:58889535 original size:18 final size:18
Alignment explanation
Indices: 58889460--58889547 Score: 63
Period size: 18 Copynumber: 4.8 Consensus size: 18
58889450 AAAAAAGTAT
*
58889460 TTTAAAAATATTTTAAAA
1 TTTAAAAATATTTAAAAA
* **
58889478 TTAAAAAATAATAAAAAAGTA
1 TTTAAAAAT-ATTTAAAA--A
*
58889499 TTTTAAAAATATTTTAAAA
1 -TTTAAAAATATTTAAAAA
58889518 TTTAAAAA-ATTTAAAAA
1 TTTAAAAATATTTAAAAA
* *
58889535 -ATAAATATATTTA
1 TTTAAAAATATTTA
58889548 TTATATCGGG
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
16 5 0.09
17 13 0.24
18 16 0.30
19 6 0.11
21 6 0.11
22 8 0.15
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (18 bp):
TTTAAAAATATTTAAAAA
Found at i:58890521 original size:2 final size:2
Alignment explanation
Indices: 58890514--58890552 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
58890504 CAAACTTTTG
58890514 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
58890553 CATCTTGTTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58892930 original size:21 final size:21
Alignment explanation
Indices: 58892904--58893020 Score: 108
Period size: 21 Copynumber: 5.1 Consensus size: 21
58892894 AACACTTATG
58892904 GCACTTTCACAATGCTATATT
1 GCACTTTCACAATGCTATATT
* *
58892925 GCACTTTCACAATGCAAACACTTATG
1 GCACTTTCACAATGC---TA--TATT
58892951 GCACTTTCACAATGCTATATT
1 GCACTTTCACAATGCTATATT
* *
58892972 GCACTTTCACAATGCAAACACTTATG
1 GCACTTTCACAATGC---TA--TATT
58892998 GCACTTTCACAATGCTATATT
1 GCACTTTCACAATGCTATATT
58893019 GC
1 GC
58893021 TTGCTTTTGT
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
21 38 0.49
23 2 0.03
24 2 0.03
26 36 0.46
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (21 bp):
GCACTTTCACAATGCTATATT
Found at i:58892958 original size:47 final size:47
Alignment explanation
Indices: 58892889--58893020 Score: 264
Period size: 47 Copynumber: 2.8 Consensus size: 47
58892879 AAAAAAAAAG
58892889 ATGCAAACACTTATGGCACTTTCACAATGCTATATTGCACTTTCACA
1 ATGCAAACACTTATGGCACTTTCACAATGCTATATTGCACTTTCACA
58892936 ATGCAAACACTTATGGCACTTTCACAATGCTATATTGCACTTTCACA
1 ATGCAAACACTTATGGCACTTTCACAATGCTATATTGCACTTTCACA
58892983 ATGCAAACACTTATGGCACTTTCACAATGCTATATTGC
1 ATGCAAACACTTATGGCACTTTCACAATGCTATATTGC
58893021 TTGCTTTTGT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 85 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (47 bp):
ATGCAAACACTTATGGCACTTTCACAATGCTATATTGCACTTTCACA
Found at i:58896805 original size:5 final size:5
Alignment explanation
Indices: 58896795--58896822 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
58896785 TTTCGGAGAA
58896795 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
58896823 TGGTGAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:58899777 original size:73 final size:73
Alignment explanation
Indices: 58899625--58899768 Score: 227
Period size: 73 Copynumber: 2.0 Consensus size: 73
58899615 TCTCGGATTT
* ** *
58899625 AAAAAATGGATCATGCCTAGTAAGTTAGGACACAATCTTTTCTTAATTCCTGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCTAGTAAGTTAGGACACAATCGCTTCTTAATTCCCGAGATCGTTTAAAA
58899690 CTTGAGAG
66 CTTGAGAG
*
58899698 AAAAAAGGGATCATG-CTCAGTAAGTTAGGACACGATCGCTTCTTAATTCCCGAGATCGTTTAAA
1 AAAAAAGGGATCATGCCT-AGTAAGTTAGGACACAATCGCTTCTTAATTCCCGAGATCGTTTAAA
58899762 ACTTGAG
65 ACTTGAG
58899769 TTTGAAAAGA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 2 0.03
73 63 0.97
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (73 bp):
AAAAAAGGGATCATGCCTAGTAAGTTAGGACACAATCGCTTCTTAATTCCCGAGATCGTTTAAAA
CTTGAGAG
Found at i:58905478 original size:30 final size:31
Alignment explanation
Indices: 58905439--58905496 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
58905429 ATTTCTTAAG
* *
58905439 TTGAGCATTCATCCGGTATAATTTGATACTT
1 TTGAGCATTCATCCAGTACAATTTGATACTT
*
58905470 TTGA-CATTCATCCAGTACAGTTTGATA
1 TTGAGCATTCATCCAGTACAATTTGATA
58905497 TCCAAATGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.40
Consensus pattern (31 bp):
TTGAGCATTCATCCAGTACAATTTGATACTT
Found at i:58914426 original size:15 final size:13
Alignment explanation
Indices: 58914398--58914447 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 13
58914388 AATCAGCTTG
58914398 AATTAAAAAAATT
1 AATTAAAAAAATT
58914411 AATATAAAATAAATT
1 AAT-TAAAA-AAATT
*
58914426 AATTAAACAAAAAGT
1 AATT-AA-AAAAATT
58914441 AATTAAA
1 AATTAAA
58914448 TGTTTAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 4 0.12
14 8 0.25
15 18 0.56
16 2 0.06
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (13 bp):
AATTAAAAAAATT
Found at i:58916127 original size:30 final size:30
Alignment explanation
Indices: 58916093--58916152 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
58916083 TCTCCCCAAG
58916093 GACATATCAATATTAAACAAAGAGAAAGCA
1 GACATATCAATATTAAACAAAGAGAAAGCA
58916123 GACATATCAATATTAAACAAAGAGAAAGCA
1 GACATATCAATATTAAACAAAGAGAAAGCA
58916153 ATGTAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (30 bp):
GACATATCAATATTAAACAAAGAGAAAGCA
Found at i:58917710 original size:23 final size:23
Alignment explanation
Indices: 58917664--58917710 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
58917654 TACATTAATC
*
58917664 ATATTAATATTTTGTAATTTTAA
1 ATATTAATATTTTGTAATTATAA
58917687 ATATTAATATTTT-TATATTATAA
1 ATATTAATATTTTGTA-ATTATAA
58917710 A
1 A
58917711 AAATTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
ATATTAATATTTTGTAATTATAA
Found at i:58917825 original size:20 final size:21
Alignment explanation
Indices: 58917788--58917826 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
58917778 GTTTTTTAAA
*
58917788 TAAAATATTAAGAGTACTATT
1 TAAAATATTAAAAGTACTATT
*
58917809 TAAAAT-TTAAAATTACTA
1 TAAAATATTAAAAGTACTA
58917827 GTAAAGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
TAAAATATTAAAAGTACTATT
Found at i:58921844 original size:88 final size:91
Alignment explanation
Indices: 58921712--58921875 Score: 212
Period size: 88 Copynumber: 1.8 Consensus size: 91
58921702 TTCTCAACTT
* * * * * *
58921712 GTACTTGAGTTTGGCTTTAATGTTTAATTTAGTTCCTGAGTTTTT-TTTT-TCTAAATTGA-TAC
1 GTACTTAAGTTTGACTTTAATGTTTAATTTAGTACCTAAATTTTTCTTTTGTCTAAATTAAGTAC
58921774 CT-TGAGTTTTTCTTTGTCCCATACAA
66 CTATG-GTTTTTCTTTGTCCCATACAA
*
58921800 GTACTTAAGTTTGACTTTAATGTTTAATTT-GATACCTAAATTTTTCTTTTGTCTCAATTAAGTA
1 GTACTTAAGTTTGACTTTAATGTTTAATTTAG-TACCTAAATTTTTCTTTTGTCTAAATTAAGTA
58921864 CCTATGGTTTTT
65 CCTATGGTTTTT
58921876 TTACTAGAGC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
87 1 0.02
88 38 0.59
89 4 0.06
90 8 0.12
91 11 0.17
92 2 0.03
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (91 bp):
GTACTTAAGTTTGACTTTAATGTTTAATTTAGTACCTAAATTTTTCTTTTGTCTAAATTAAGTAC
CTATGGTTTTTCTTTGTCCCATACAA
Found at i:58923112 original size:33 final size:33
Alignment explanation
Indices: 58923075--58923138 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
58923065 TTGGCCCGAG
*
58923075 CCCGGCCTAGCCCGGCCCGAAAATAATAAATAT
1 CCCGGCCCAGCCCGGCCCGAAAATAATAAATAT
*
58923108 CCCGGCCCGGCCCGGCCCGAAAATAATAAAT
1 CCCGGCCCAGCCCGGCCCGAAAATAATAAAT
58923139 TTTTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.31, C:0.36, G:0.20, T:0.12
Consensus pattern (33 bp):
CCCGGCCCAGCCCGGCCCGAAAATAATAAATAT
Found at i:58923227 original size:11 final size:10
Alignment explanation
Indices: 58923180--58923270 Score: 54
Period size: 9 Copynumber: 9.4 Consensus size: 10
58923170 AAAATACTTT
58923180 TTTTTAAAT-
1 TTTTTAAATA
58923189 TTTTT-AA-A
1 TTTTTAAATA
*
58923197 TTTTAAAAT-
1 TTTTTAAATA
58923206 TTTTTAAAAATA
1 TTTTT--AAATA
58923218 CTTTTTAAAT-
1 -TTTTTAAATA
*
58923228 TTTTT-TA-A
1 TTTTTAAATA
*
58923236 TTTTAAAATA
1 TTTTTAAATA
58923246 TTTTTAAAATA
1 TTTTT-AAATA
58923257 CTTTTTAAAT-
1 -TTTTTAAATA
58923267 TTTT
1 TTTT
58923271 GTTTTAATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 24
0.68 0.06 0.26
Matches are distributed among these distances:
8 11 0.17
9 21 0.33
10 5 0.08
11 17 0.27
12 5 0.08
13 5 0.08
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:58923238 original size:39 final size:39
Alignment explanation
Indices: 58923145--58923288 Score: 182
Period size: 39 Copynumber: 3.5 Consensus size: 39
58923135 AAATTTTTTT
* *
58923145 ATTTTTTTATTTTTAAAATACTTTTAAAATACTTTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATAC---TTTTTAA
*
58923187 ATTTTTTAAATTTTAAAAT-TTTTTAAAAATACTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTT-AAAATACTTTTTAA
58923226 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
58923265 ATTTTTGTTTTAATTTTTAAAATA
1 A--TTT-TTTTAA-TTTTAAAATA
58923289 AATTTTTGAT
Statistics
Matches: 92, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
39 40 0.43
40 5 0.05
41 7 0.08
42 30 0.33
43 10 0.11
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.60
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
Found at i:58923263 original size:12 final size:11
Alignment explanation
Indices: 58923152--58923265 Score: 63
Period size: 11 Copynumber: 10.9 Consensus size: 11
58923142 TTTATTTTTT
58923152 TATTTTTAAAA
1 TATTTTTAAAA
*
58923163 TACTTTTAAAA
1 TATTTTTAAAA
*
58923174 TACTTTTTTTTAAA
1 TA---TTTTTAAAA
58923188 T-TTTTT--AA
1 TATTTTTAAAA
58923196 -A-TTTTAAAA
1 TATTTTTAAAA
58923205 T-TTTTTAAAAA
1 TATTTTT-AAAA
58923216 TACTTTTT-AAA
1 TA-TTTTTAAAA
58923227 T-TTTTT----
1 TATTTTTAAAA
*
58923233 TAATTTTAAAA
1 TATTTTTAAAA
58923244 TATTTTTAAAA
1 TATTTTTAAAA
58923255 TACTTTTTAAA
1 TA-TTTTTAAA
58923266 TTTTTGTTTT
Statistics
Matches: 81, Mismatches: 5, Indels: 33
0.68 0.04 0.28
Matches are distributed among these distances:
6 1 0.01
7 8 0.10
8 2 0.02
9 7 0.09
10 9 0.11
11 33 0.41
12 8 0.10
13 5 0.06
14 8 0.10
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:58929068 original size:15 final size:15
Alignment explanation
Indices: 58929037--58929077 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
58929027 TGATCACACA
58929037 ATAAAAATAAAATAT
1 ATAAAAATAAAATAT
58929052 ATAAATAATTAAAATAT
1 ATAAA-AA-TAAAATAT
*
58929069 ATTAAAATA
1 ATAAAAATA
58929078 CTTTATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 7 0.30
16 4 0.17
17 12 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAAAATAAAATAT
Found at i:58930046 original size:4 final size:4
Alignment explanation
Indices: 58930032--58930094 Score: 117
Period size: 4 Copynumber: 15.8 Consensus size: 4
58930022 ATGCAGCGTG
*
58930032 GAAA TAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
58930080 GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAA
58930095 CACCTGTCGG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:58936741 original size:32 final size:31
Alignment explanation
Indices: 58936691--58936750 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
58936681 ATAATGTTTC
58936691 ATTTTAAATAAAAATATTAATATATTTATTA
1 ATTTTAAATAAAAATATTAATATATTTATTA
* * * *
58936722 ATTTATAATTAAAATTATTATTATTTTTA
1 ATTT-TAAATAAAAATATTAATATATTTA
58936751 AATATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 4 0.17
32 20 0.83
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
ATTTTAAATAAAAATATTAATATATTTATTA
Found at i:58937519 original size:108 final size:108
Alignment explanation
Indices: 58937325--58937540 Score: 405
Period size: 108 Copynumber: 2.0 Consensus size: 108
58937315 AAAGTTATAA
58937325 ATTATTGAAATCACACACAATAAAATACACACTTAGCACCGTATAATAAGTTAAACCTAACCAAT
1 ATTATTGAAATCACACACAATAAAATACACACTTAGCACCGTATAATAAGTTAAACCTAACCAAT
*
58937390 CAGTGGAAGCAAATTGCGTGTTTGCTCCTGGATAGCAGTTTCT
66 CAGTGGAAGCAAATTGCGTGTTTGCTCCTGGATAGCAGCTTCT
*
58937433 ATTATTGAAGTCACACACAATAAAATACACACTTAGCACCGTATAATAAGTTAAACCTAACCAAT
1 ATTATTGAAATCACACACAATAAAATACACACTTAGCACCGTATAATAAGTTAAACCTAACCAAT
*
58937498 CAGTGGAAGCAAATTGGGTGTTTGCTCCTGGATAGCAGCTTCT
66 CAGTGGAAGCAAATTGCGTGTTTGCTCCTGGATAGCAGCTTCT
58937541 TCATATTCAA
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 105 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (108 bp):
ATTATTGAAATCACACACAATAAAATACACACTTAGCACCGTATAATAAGTTAAACCTAACCAAT
CAGTGGAAGCAAATTGCGTGTTTGCTCCTGGATAGCAGCTTCT
Found at i:58943834 original size:11 final size:11
Alignment explanation
Indices: 58943818--58943842 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58943808 AAAAAATTAA
58943818 AATTTTAAAAT
1 AATTTTAAAAT
58943829 AATTTTAAAAT
1 AATTTTAAAAT
58943840 AAT
1 AAT
58943843 AATTTTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTTAAAAT
Found at i:58943995 original size:22 final size:22
Alignment explanation
Indices: 58943953--58944014 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
58943943 TGTAATAAGA
**
58943953 TTTTAATTTAACAT-GTTTAATT
1 TTTTAATTTAAC-TCGAATAATT
58943975 TTTTAATTTAACTCGAATAATT
1 TTTTAATTTAACTCGAATAATT
*
58943997 TTACTCAATTTAACTCGA
1 TT--TTAATTTAACTCGA
58944015 CTCGAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.03
22 20 0.59
24 13 0.38
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (22 bp):
TTTTAATTTAACTCGAATAATT
Found at i:58947314 original size:31 final size:31
Alignment explanation
Indices: 58947278--58947339 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
58947268 ATTTTTTGAA
58947278 TCCTCTTTAGGTTTTGCATTTTATTCAATTT
1 TCCTCTTTAGGTTTTGCATTTTATTCAATTT
58947309 TCCTCTTTAGGTTTTGCATTTTATTCAATTT
1 TCCTCTTTAGGTTTTGCATTTTATTCAATTT
58947340 AGTCCCTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.58
Consensus pattern (31 bp):
TCCTCTTTAGGTTTTGCATTTTATTCAATTT
Found at i:58949161 original size:2 final size:2
Alignment explanation
Indices: 58949093--58949153 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
58949083 GTAAGCATGC
58949093 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
58949135 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
58949154 TCATATATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58964663 original size:19 final size:18
Alignment explanation
Indices: 58964635--58964674 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
58964625 ATAATATTAT
58964635 ATATAAAATAGAAAAATAA
1 ATATAAAATA-AAAAATAA
* *
58964654 ATATACAATAAATAATAA
1 ATATAAAATAAAAAATAA
58964672 ATA
1 ATA
58964675 AAAGGTCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (18 bp):
ATATAAAATAAAAAATAA
Found at i:58971225 original size:16 final size:18
Alignment explanation
Indices: 58971190--58971226 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
58971180 TCAATTAAAT
*
58971190 AAATTATTAAAAGTTATA
1 AAATTATTAAAAGATATA
58971208 AAATT-TTAAAA-ATATA
1 AAATTATTAAAAGATATA
58971224 AAA
1 AAA
58971227 CTCAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AAATTATTAAAAGATATA
Found at i:58974537 original size:11 final size:11
Alignment explanation
Indices: 58974521--58974545 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58974511 ATCCATGCGC
58974521 TTTATACACAA
1 TTTATACACAA
58974532 TTTATACACAA
1 TTTATACACAA
58974543 TTT
1 TTT
58974546 CCATATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (11 bp):
TTTATACACAA
Found at i:58978299 original size:31 final size:31
Alignment explanation
Indices: 58978261--58978323 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
58978251 TTACAATTAT
*
58978261 TGAACTATTCGAAAGTTTTCATTTAAGTCAC
1 TGAACTATTCAAAAGTTTTCATTTAAGTCAC
*
58978292 TGAACTATTCAAAAGTTTTTATTTAAGTCAC
1 TGAACTATTCAAAAGTTTTCATTTAAGTCAC
58978323 T
1 T
58978324 AGGCTGTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (31 bp):
TGAACTATTCAAAAGTTTTCATTTAAGTCAC
Found at i:58983428 original size:2 final size:2
Alignment explanation
Indices: 58983421--58983462 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
58983411 CGAGGTTGTT
* * *
58983421 TA TA TA TA TA CA TA TA TA TA TA TA TA CA T- TG 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
58983462 T
1 T
58983463 TTAATATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:58983706 original size:3 final size:3
Alignment explanation
Indices: 58983698--58983737 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
58983688 CCACATCGTA
58983698 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
58983738 TCCACATAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:58984003 original size:15 final size:15
Alignment explanation
Indices: 58983959--58984003 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
58983949 TCAGTAAATA
* *
58983959 ATATATAAAATAATA
1 ATATTTAAAATAATT
*
58983974 ATATTAAAAATAATT
1 ATATTTAAAATAATT
*
58983989 ATTTTTAAAATAATT
1 ATATTTAAAATAATT
58984004 TTAAAAGGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATTTAAAATAATT
Found at i:58984388 original size:5 final size:5
Alignment explanation
Indices: 58984378--58984415 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
58984368 CAAATTACTT
*
58984378 ATATA ATATA ATATA ATATA ACATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA
58984416 GACGTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:58990165 original size:3 final size:3
Alignment explanation
Indices: 58990157--58990188 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
58990147 AACACTCAAC
58990157 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
58990189 GCATCCAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:58990678 original size:16 final size:18
Alignment explanation
Indices: 58990639--58990672 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58990629 TAAGTTTATA
58990639 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
58990656 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
58990673 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:58990808 original size:16 final size:15
Alignment explanation
Indices: 58990789--58990838 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
58990779 AAAAAATGTA
58990789 TAAAATTATTAAATAT
1 TAAAA-TATTAAATAT
*
58990805 TAAAATAATATAATA-
1 TAAAATATTA-AATAT
58990820 -AAAATATTAAATAT
1 TAAAATATTAAATAT
58990834 TAAAA
1 TAAAA
58990839 ATAATATAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 4 0.14
14 8 0.28
15 8 0.28
16 9 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATATTAAATAT
Found at i:58990827 original size:29 final size:30
Alignment explanation
Indices: 58990788--58990847 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
58990778 TAAAAAATGT
*
58990788 ATAAAATTATTAAATATT-AAAATAATATA
1 ATAAAAATATTAAATATTAAAAATAATATA
58990817 ATAAAAATATTAAATATTAAAAATAATATA
1 ATAAAAATATTAAATATTAAAAATAATATA
58990847 A
1 A
58990848 GTGGGCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (30 bp):
ATAAAAATATTAAATATTAAAAATAATATA
Found at i:58991594 original size:14 final size:13
Alignment explanation
Indices: 58991560--58991598 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
58991550 TATCCTAATT
58991560 TCTCAATTTTTTC
1 TCTCAATTTTTTC
**
58991573 TCAAAATTATTTTC
1 TCTCAATT-TTTTC
58991587 TCTCAATTTTTT
1 TCTCAATTTTTT
58991599 ATCCTAACTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.59
Consensus pattern (13 bp):
TCTCAATTTTTTC
Found at i:58996103 original size:11 final size:11
Alignment explanation
Indices: 58996072--58996114 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
58996062 AAAAATTTAT
*
58996072 TTTTAAAAAAAA
1 TTTT-AAAAATA
*
58996084 TTTAAAAAAGTA
1 TTTTAAAAA-TA
58996096 TTTTAAAAATA
1 TTTTAAAAATA
58996107 TTTTAAAA
1 TTTTAAAA
58996115 CTAAAAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 15 0.56
12 12 0.44
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:58996398 original size:3 final size:3
Alignment explanation
Indices: 58996386--58996441 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
58996376 TCCATAAATG
58996386 GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
58996433 GAA GAA GAA
1 GAA GAA GAA
58996442 ACTAAAACCA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Done.