Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397269.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.1, 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: 5666189
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 144833 characters in sequence are not A, C, G, or T
File 1 of 14
Found at i:715 original size:137 final size:138
Alignment explanation
Indices: 359--726 Score: 422
Period size: 138 Copynumber: 2.7 Consensus size: 138
349 CACCGAATTG
* * * * * *
359 TTAGATGTCGATGACATCTTGTGGTGACATGTTGAGTGATAGCAGATTTATGGGGTAACACGCTG
1 TTAGATGTCGATGACATCTTGTGGTGACACGCTAAGTGGTAGCAGATTTATGGGGTGACACGCTA
* * ** * * *
424 AGTGGTAGCAAAATTAT-GGCGTGACTTGCTGAATTGTTGTGGCATTGTGGGTTGACACGCCACG
66 AGTTGTAGCAGAATTATAGG-GTGACACGCTGAATTGTTATAGCATTGTGGGGTGACACGCCACG
**
488 CCCCAATTT
130 CCCCAATCA
* *
497 TTAGATGTCGATAACATCTTGTGGTGACACGCTAAGTGGTAGCAGATTTATGGGGTGACACGCCA
1 TTAGATGTCGATGACATCTTGTGGTGACACGCTAAGTGGTAGCAGATTTATGGGGTGACACGCTA
* * * * *
562 CA-TAGTAGTAGAATTATAAGGG-GACACGCTGAGTTGTTATAGTATTGTGGGGTGACATGCCAC
66 -AGTTGTAGCAGAATTAT-AGGGTGACACGCTGAATTGTTATAGCATTGTGGGGTGACACGCCAC
625 G-CCCAATCA
129 GCCCCAATCA
* * * *
634 TTGGATGTCGATGACATCTTGTGGTGACACACTAAGTGGTAGCAGATTTATGAGGTGACACACTA
1 TTAGATGTCGATGACATCTTGTGGTGACACGCTAAGTGGTAGCAGATTTATGGGGTGACACGCTA
*
699 AGTTGTTA-CAGTATTATAGGGTGACACG
66 AGTTG-TAGCAGAATTATAGGGTGACACG
727 TCACGTCCCA
Statistics
Matches: 194, Mismatches: 30, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
136 5 0.03
137 80 0.41
138 105 0.54
139 2 0.01
140 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (138 bp):
TTAGATGTCGATGACATCTTGTGGTGACACGCTAAGTGGTAGCAGATTTATGGGGTGACACGCTA
AGTTGTAGCAGAATTATAGGGTGACACGCTGAATTGTTATAGCATTGTGGGGTGACACGCCACGC
CCCAATCA
Found at i:769 original size:107 final size:106
Alignment explanation
Indices: 566--801 Score: 292
Period size: 107 Copynumber: 2.2 Consensus size: 106
556 ACGCCACATA
* * * * * * * * *
566 GTAGTAGAATTATAAGGGGACACGCTGAGTTGTTATAGTATTGTGGGGTGACATGCCACGCCCAA
1 GTAGCAGATTTATAAGGTGACACACTAAGTTGTTACAGTATTATAGGGTGACACGCCACGCCCAA
* * *
631 TCATTGGATGTCGATGACATCTTGTGGTGACACACTAAGTG
66 TCATTAGATATCGATGACATCTTGTAGTGACACACTAAGTG
* *
672 GTAGCAGATTTATGAGGTGACACACTAAGTTGTTACAGTATTATAGGGTGACACGTCACGTCCCA
1 GTAGCAGATTTATAAGGTGACACACTAAGTTGTTACAGTATTATAGGGTGACACGCCACG-CCCA
** **
737 ATTGTTAGATATCGATGACATCTTGTAGTGACATGCTAAGTG
65 ATCATTAGATATCGATGACATCTTGTAGTGACACACTAAGTG
779 GTAGCAGATTTAATAAGGTGACA
1 GTAGCAGATTT-ATAAGGTGACA
802 TCTGAGTGGT
Statistics
Matches: 109, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
106 49 0.45
107 50 0.46
108 10 0.09
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (106 bp):
GTAGCAGATTTATAAGGTGACACACTAAGTTGTTACAGTATTATAGGGTGACACGCCACGCCCAA
TCATTAGATATCGATGACATCTTGTAGTGACACACTAAGTG
Found at i:812 original size:31 final size:31
Alignment explanation
Indices: 764--839 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
754 ACATCTTGTA
* *
764 GTGACATGCTAAGTGGTAGCAGATTTAATAAG
1 GTGACATGCTGAGTGGTAGCAGAATT-ATAAG
**
796 GTGACAT-CTGAGTGGTAGCAGAATTATGGG
1 GTGACATGCTGAGTGGTAGCAGAATTATAAG
826 GTGACATGCTGAGT
1 GTGACATGCTGAGT
840 TGTTGCCGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 10 0.26
31 22 0.56
32 7 0.18
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.28
Consensus pattern (31 bp):
GTGACATGCTGAGTGGTAGCAGAATTATAAG
Found at i:829 original size:138 final size:137
Alignment explanation
Indices: 668--938 Score: 362
Period size: 138 Copynumber: 2.0 Consensus size: 137
658 TGACACACTA
* ** *
668 AGTGGTAGCAGATTTATGAGGTGACACACTAAGTTGTTACAGTATTATAGGGTGACACGTCACGT
1 AGTGGTAGCAGAATTATGAGGTGACACACTAAGTTGTTACAGTATTATAGGGTGACACACCACGC
*
733 CCCAATTGTTAGATATCGATGACATCTTGTAGTGACATGCTAAGTGGTAGCAGATTTAATAAGGT
66 CCCAATTGTTAGATATCGATGACATCTTGTAGTGACATCCTAAGTGGTAGCAG-TTTAATAAGGT
798 GACATCTG
130 GACATCTG
* ** * * * * * *
806 AGTGGTAGCAGAATTATGGGGTGACATGCTGAGTTGTTGCCGTATTGTGGGGTGACACACCATGC
1 AGTGGTAGCAGAATTATGAGGTGACACACTAAGTTGTTACAGTATTATAGGGTGACACACCACGC
* * * * *
871 CCCAATTGTTAGATGTCGATGACATCTTGTGGTGACATCCTGAGTGGTAGCAGTTTTATTAGGTG
66 CCCAATTGTTAGATATCGATGACATCTTGTAGTGACATCCTAAGTGGTAGCAGTTTAATAAGGTG
936 ACA
131 ACA
939 CACCACGTGA
Statistics
Matches: 114, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
137 13 0.11
138 101 0.89
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (137 bp):
AGTGGTAGCAGAATTATGAGGTGACACACTAAGTTGTTACAGTATTATAGGGTGACACACCACGC
CCCAATTGTTAGATATCGATGACATCTTGTAGTGACATCCTAAGTGGTAGCAGTTTAATAAGGTG
ACATCTG
Found at i:853 original size:244 final size:244
Alignment explanation
Indices: 476--983 Score: 623
Period size: 244 Copynumber: 2.1 Consensus size: 244
466 CATTGTGGGT
* * *
476 TGACACGCCACGCCCCAATTTTTAGATGTCGATAACATCTTGTGGTGACACGCTAAGTGGTAGCA
1 TGACACGCCACGCCCCAATTGTTAGATATCGATAACATCTTGTAGTGACACGCTAAGTGGTAGCA
** * *
541 GATTTATGGGGTGACACGCCACATAGTAGTAGAATTATAAGGGGACACGCTGAGTTGTTATAGTA
66 GATTTATAAGGTGACACG-CACATAGTAGCAGAATTATAAGGGGACACGCTGAGTTGTTACAGTA
** *
606 TTGTGGGGTGACATGCCACG-CCCAATCATTGGATGTCGATGACATCTTGTGGTGACA-CACTAA
130 TTGTGGGGTGACACACCACGCCCCAATCATTAGATGTCGATGACATCTTGTGGTGACATC-CTAA
669 GTGGTAGCAGATTTATGAGGTGACACACTAAGTTGTTACAGTATTATAGGG
194 GTGGTAGCAGATTTATGAGGTGACACACTAAGTTGTTACAGTATTATAGGG
* * * *
720 TGACACGTCACGTCCCAATTGTTAGATATCGATGACATCTTGTAGTGACATGCTAAGTGGTAGCA
1 TGACACGCCACGCCCCAATTGTTAGATATCGATAACATCTTGTAGTGACACGCTAAGTGGTAGCA
* * * * * *
785 GATTTAATAAGGTGACATCTG-A-GTGGTAGCAGAATTAT-GGGGTGACATGCTGAGTTGTTGCC
66 GATTT-ATAAGGTGACA-C-GCACATAGTAGCAGAATTATAAGGG-GACACGCTGAGTTGTTACA
* **
847 GTATTGTGGGGTGACACACCATGCCCCAATTGTTAGATGTCGATGACATCTTGTGGTGACATCCT
127 GTATTGTGGGGTGACACACCACGCCCCAATCATTAGATGTCGATGACATCTTGTGGTGACATCCT
* * * * * ** *
912 GAGTGGTAGCAGTTTTATTAGGTGACACACCACG-TGATTGTAGTATTATGGGG
192 AAGTGGTAGCAGATTTATGAGGTGACACACTAAGTTG-TTACAGTATTATAGGG
*
965 TGACACGCCATGCCCCAAT
1 TGACACGCCACGCCCCAAT
984 GAGGTGACAT
Statistics
Matches: 223, Mismatches: 34, Indels: 13
0.83 0.13 0.05
Matches are distributed among these distances:
243 3 0.01
244 113 0.51
245 104 0.47
246 2 0.01
247 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (244 bp):
TGACACGCCACGCCCCAATTGTTAGATATCGATAACATCTTGTAGTGACACGCTAAGTGGTAGCA
GATTTATAAGGTGACACGCACATAGTAGCAGAATTATAAGGGGACACGCTGAGTTGTTACAGTAT
TGTGGGGTGACACACCACGCCCCAATCATTAGATGTCGATGACATCTTGTGGTGACATCCTAAGT
GGTAGCAGATTTATGAGGTGACACACTAAGTTGTTACAGTATTATAGGG
Found at i:857 original size:31 final size:30
Alignment explanation
Indices: 764--862 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
754 ACATCTTGTA
* * **
764 GTGACATGCTAAGTGGTAGCAGATTTAATAAG
1 GTGACAT-CTGAGTGGTAGCAGAATT-ATGGG
796 GTGACATCTGAGTGGTAGCAGAATTATGGG
1 GTGACATCTGAGTGGTAGCAGAATTATGGG
* * * * *
826 GTGACATGCTGAGTTGTTGCCGTATTGTGGG
1 GTGACAT-CTGAGTGGTAGCAGAATTATGGG
857 GTGACA
1 GTGACA
863 CACCATGCCC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
30 10 0.18
31 40 0.70
32 7 0.12
ACGTcount: A:0.25, C:0.11, G:0.34, T:0.29
Consensus pattern (30 bp):
GTGACATCTGAGTGGTAGCAGAATTATGGG
Found at i:5074 original size:31 final size:31
Alignment explanation
Indices: 5031--5136 Score: 124
Period size: 31 Copynumber: 3.4 Consensus size: 31
5021 AGAAAGAAAT
*
5031 AAATGTTATTACATGCTATGCATACTAAGTA
1 AAATGTTGTTACATGCTATGCATACTAAGTA
* * *
5062 AAATATTGTTACACGCCATGCATA-TCAAGTA
1 AAATGTTGTTACATGCTATGCATACT-AAGTA
** * *
5093 AAATGTTGTTACATGCTAAACATACCAAGTC
1 AAATGTTGTTACATGCTATGCATACTAAGTA
5124 AAATGTTGTTACA
1 AAATGTTGTTACA
5137 CGTTAATGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
30 1 0.02
31 61 0.98
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (31 bp):
AAATGTTGTTACATGCTATGCATACTAAGTA
Found at i:6011 original size:23 final size:23
Alignment explanation
Indices: 5975--6029 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
5965 TAAACCCTGT
*
5975 CGTGTCACATATTATCACCATAC
1 CGTGTCACACATTATCACCATAC
* *
5998 CGTTTCACACATTATCACCCTAC
1 CGTGTCACACATTATCACCATAC
6021 CGTGTCACA
1 CGTGTCACA
6030 GATTCCCCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.35, G:0.09, T:0.29
Consensus pattern (23 bp):
CGTGTCACACATTATCACCATAC
Found at i:6073 original size:93 final size:94
Alignment explanation
Indices: 5885--6076 Score: 253
Period size: 93 Copynumber: 2.1 Consensus size: 94
5875 CATAGTCATA
* * *** *
5885 TCACATATTATCACCGTACCGTCTCACACATTATCACCTTTGTTGTGTCACAGATTCTCTCCATG
1 TCACATATTATCACCATACCGTCTCACACATTATCACCTCTACCGTGTCACAGATTCCCTCCATG
*
5950 GCATGTCAAAAACTCTAAACCCTGTCGTG
66 GCATGTCAAAAACTCTAAACCCTATCGTG
*
5979 TCACATATTATCACCATACCGTTTCACACATTATCACC-CTACCGTGTCACAGATTCCC-CTCAT
1 TCACATATTATCACCATACCGTCTCACACATTATCACCTCTACCGTGTCACAGATTCCCTC-CAT
* * * *
6042 GGCTTGTTACAAACTCTAAACCCTATTGTG
65 GGCATGTCAAAAACTCTAAACCCTATCGTG
6072 TCACA
1 TCACA
6077 GCCATGTCAC
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
92 1 0.01
93 48 0.56
94 36 0.42
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.31
Consensus pattern (94 bp):
TCACATATTATCACCATACCGTCTCACACATTATCACCTCTACCGTGTCACAGATTCCCTCCATG
GCATGTCAAAAACTCTAAACCCTATCGTG
Found at i:6103 original size:23 final size:23
Alignment explanation
Indices: 6077--6122 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6067 TTGTGTCACA
*
6077 GCCATGTCACATACGCTCACCAT
1 GCCATCTCACATACGCTCACCAT
**
6100 GCCATCTCACATATTCTCACCAT
1 GCCATCTCACATACGCTCACCAT
6123 AGCGTGTCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.26, C:0.39, G:0.09, T:0.26
Consensus pattern (23 bp):
GCCATCTCACATACGCTCACCAT
Found at i:6569 original size:23 final size:23
Alignment explanation
Indices: 6324--6570 Score: 92
Period size: 23 Copynumber: 10.8 Consensus size: 23
6314 GTTGAATATG
* * *
6324 CTCACCATGCCATATCATATATT
1 CTCACCATGCCATGTCACACATT
* * *
6347 CTCATCATGCTATGTCACATATT
1 CTCACCATGCCATGTCACACATT
* *
6370 CACACCATGGCATG-C-CACATT
1 CTCACCATGCCATGTCACACATT
* * *
6391 CTCA-CATTGGCGTGTCACATATT
1 CTCACCA-TGCCATGTCACACATT
* * *
6414 CTCACCATGTCATCTCACATATT
1 CTCACCATGCCATGTCACACATT
* * * * *
6437 CCCTCCAAG-TAGTGTCACATATT
1 CTCACCATGCCA-TGTCACACATT
* * *
6460 TTCACTC-TACCATGTCACATATT
1 CTCAC-CATGCCATGTCACACATT
* * * * * *
6483 CCCTCTATGGCATGTCACAAACT
1 CTCACCATGCCATGTCACACATT
* ** **
6506 CTTACGTTGTTATGTCACACATT
1 CTCACCATGCCATGTCACACATT
* *
6529 CTCACTATGCCGTGTCACACATT
1 CTCACCATGCCATGTCACACATT
*
6552 C-CTACCATGCCATTTCACA
1 CTC-ACCATGCCATGTCACA
6571 AACTCAAAAC
Statistics
Matches: 163, Mismatches: 52, Indels: 18
0.70 0.22 0.08
Matches are distributed among these distances:
20 2 0.01
21 14 0.09
22 4 0.02
23 139 0.85
24 4 0.02
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.33
Consensus pattern (23 bp):
CTCACCATGCCATGTCACACATT
Found at i:9427 original size:205 final size:210
Alignment explanation
Indices: 9119--9527 Score: 639
Period size: 205 Copynumber: 2.0 Consensus size: 210
9109 ATTACCTTTC
* * *
9119 TTATTTCTAATTTATTAGTTTTTTGAAATAAATAAAAAATTCTTGATATTGAAAATTTCTCAAAT
1 TTATTTCTAATTTATTAGTTCTTTGAAATAAATAAAAAATTCTTAATATTAAAAATTTCTCAAAT
* * * *
9184 ATCTCCCAAACACTTATGGTAAAATTTTGGAAAATTCTCACCTAGAAATTCTCAAGAAGCCACTT
66 ACCTCCCAAACACTCATGGTAAAATTTTGAAAAATTCTCACCTAGAAATTCCCAAGAAGCCACTT
* *
9249 TTGGTTTTCTTTAGATTTCATTATTGGAGAACTTATTATTTAATTCTATAAATTTATCTT-TTCT
131 TTGGTTTTCTTGAGATTTCATCATTGGAGAACTTATTATTTAATTCTATAAATTTATCTTCTTCT
9313 ATTTTATTTCTTTAT
196 ATTTTATTTCTTTAT
*
9328 TTATTT-TATTTTATTAGTTCTTTGAAATAAAT-AAAAATTCTTAATATTAAAAATTT-TCAAA-
1 TTATTTCTAATTTATTAGTTCTTTGAAATAAATAAAAAATTCTTAATATTAAAAATTTCTCAAAT
* * *
9389 ACCTCCCAAACGCTCATGGTAAAATTTTGAAAAATTCTCACCTATAAATTCCCAAGAAGCTACTT
66 ACCTCCCAAACACTCATGGTAAAATTTTGAAAAATTCTCACCTAGAAATTCCCAAGAAGCCACTT
* * *
9454 TTGGTTTTCTTGATATTTCATCATTGGAGAACTTATTATTTAATTCTATAATTTTATCTTCTTTT
131 TTGGTTTTCTTGAGATTTCATCATTGGAGAACTTATTATTTAATTCTATAAATTTATCTTCTTCT
9519 ATTTTATTT
196 ATTTTATTT
9528 AAATATTTAT
Statistics
Matches: 183, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
205 114 0.62
206 17 0.09
207 22 0.12
208 24 0.13
209 6 0.03
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (210 bp):
TTATTTCTAATTTATTAGTTCTTTGAAATAAATAAAAAATTCTTAATATTAAAAATTTCTCAAAT
ACCTCCCAAACACTCATGGTAAAATTTTGAAAAATTCTCACCTAGAAATTCCCAAGAAGCCACTT
TTGGTTTTCTTGAGATTTCATCATTGGAGAACTTATTATTTAATTCTATAAATTTATCTTCTTCT
ATTTTATTTCTTTAT
Found at i:12116 original size:35 final size:35
Alignment explanation
Indices: 12077--12145 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
12067 TTTACTAGGA
* * *
12077 TCAAGTGTAACCTCTACAACATGTCTTTTGCAAGG
1 TCAAGCGTAACCTCTACAACATGCCATTTGCAAGG
*
12112 TCAAGCGTAACGTCTACAACATGCCATTTGCAAG
1 TCAAGCGTAACCTCTACAACATGCCATTTGCAAG
12146 ATTAGGTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (35 bp):
TCAAGCGTAACCTCTACAACATGCCATTTGCAAGG
Found at i:18141 original size:30 final size:31
Alignment explanation
Indices: 18079--18142 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
18069 TCAAGTCCTC
* **
18079 ATATGTTTTATTTTGAGTCAAATAAGTTTTT
1 ATATGTTTTATTTTAAGTCAAATAAGCATTT
18110 ATAT-TTTTATTTTAAGTCAAATAAGCATTT
1 ATATGTTTTATTTTAAGTCAAATAAGCATTT
18140 ATA
1 ATA
18143 ATTAATAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (31 bp):
ATATGTTTTATTTTAAGTCAAATAAGCATTT
Found at i:56782 original size:4 final size:4
Alignment explanation
Indices: 56775--56840 Score: 114
Period size: 4 Copynumber: 16.5 Consensus size: 4
56765 TATATATGTA
* *
56775 TATG TATG TATG TATG TATG TATA TATG TATG TATG TATG TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
56823 TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TA
56841 CCAAGTAAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:56805 original size:24 final size:24
Alignment explanation
Indices: 56773--56840 Score: 136
Period size: 24 Copynumber: 2.8 Consensus size: 24
56763 CATATATATG
56773 TATATGTATGTATGTATGTATGTA
1 TATATGTATGTATGTATGTATGTA
56797 TATATGTATGTATGTATGTATGTA
1 TATATGTATGTATGTATGTATGTA
56821 TATATGTATGTATGTATGTA
1 TATATGTATGTATGTATGTA
56841 CCAAGTAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (24 bp):
TATATGTATGTATGTATGTATGTA
Found at i:59335 original size:3 final size:3
Alignment explanation
Indices: 59327--59352 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
59317 TATGTAGTTC
59327 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
59353 AGGGCTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:60503 original size:18 final size:19
Alignment explanation
Indices: 60480--60521 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
60470 GCTTCCGCGT
*
60480 TCTCTCCCTCC-TTCTCTC
1 TCTCTCCCTCCTTTCTATC
*
60498 TCTCT-CGTCCTTTCTATC
1 TCTCTCCCTCCTTTCTATC
60516 TCTCTC
1 TCTCTC
60522 ATTGTCTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.02, C:0.48, G:0.02, T:0.48
Consensus pattern (19 bp):
TCTCTCCCTCCTTTCTATC
Found at i:69258 original size:29 final size:29
Alignment explanation
Indices: 69203--69258 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
69193 ACTAAATAAA
*
69203 ATTTAAATAAATTTTTATTTTTCTATTAT
1 ATTTAAATAAATTTTTATCTTTCTATTAT
*
69232 ATTTAATTAAATTTTTATACTTT-TATT
1 ATTTAAATAAATTTTTAT-CTTTCTATT
69259 TTAAAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTAAATAAATTTTTATCTTTCTATTAT
Found at i:72281 original size:2 final size:2
Alignment explanation
Indices: 72276--72300 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
72266 CTCTCCTCTT
72276 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 T
72301 TAAATGCCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:76662 original size:3 final size:3
Alignment explanation
Indices: 76654--76680 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
76644 CACTACAAAA
76654 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
76681 AATAATAATA
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:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:76685 original size:3 final size:3
Alignment explanation
Indices: 76679--76754 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
76669 CATCATCATC
76679 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
76727 ATA ATA ATA ATA ATA ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
76755 CAAATCTTGT
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 70 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:76801 original size:68 final size:68
Alignment explanation
Indices: 76729--76941 Score: 293
Period size: 68 Copynumber: 3.0 Consensus size: 68
76719 TAATAATAAT
76729 AATAATAATAATAATAATAATATAATCAAATCTTGTTCAAATCAAATTTAAGATTTGTTGTAACA
1 AATAATAATAATAATAATAATATAATCAAATCTTGTTCAAATCAAATTTAAGATTTGTTGTAACA
76794 TTC
66 TTC
* * *
76797 AATAATAATAATAATAATAATACAACCAAATCTTGTTCAAATCAAATTTAAGATTTGTTGTAATA
1 AATAATAATAATAATAATAATATAATCAAATCTTGTTCAAATCAAATTTAAGATTTGTTGTAACA
*
76862 GTC
66 TTC
* *
76865 AATAATAATAATAATAATAATCATCATCATCATCAAATATTGTTCAAAGCAAATTTAA-ACTTTG
1 AATAATAATAATAATAAT-A--AT-AT-A--ATCAAATCTTGTTCAAATCAAATTTAAGA-TTTG
76929 TTGTAACATTC
58 TTGTAACATTC
76940 AA
1 AA
76942 GTTCATTACC
Statistics
Matches: 127, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
68 82 0.65
69 1 0.01
71 2 0.02
72 1 0.01
73 1 0.01
74 1 0.01
75 39 0.31
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (68 bp):
AATAATAATAATAATAATAATATAATCAAATCTTGTTCAAATCAAATTTAAGATTTGTTGTAACA
TTC
Found at i:80019 original size:2 final size:2
Alignment explanation
Indices: 80012--80039 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
80002 TTTTGATTTG
80012 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
80040 TTGATTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82046 original size:2 final size:2
Alignment explanation
Indices: 82039--82071 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
82029 GCGTACATAG
*
82039 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
82072 ACTATTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:105137 original size:22 final size:21
Alignment explanation
Indices: 105111--105156 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
105101 GTTTCAATGA
* * *
105111 TTTTTGAAAAGAAAGGAAGCT
1 TTTTTTAAAAGAAAAGAAGAT
105132 TTTTTTAAAAGAAAAGAAGAT
1 TTTTTTAAAAGAAAAGAAGAT
105153 TTTT
1 TTTT
105157 ATCAGGGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.37
Consensus pattern (21 bp):
TTTTTTAAAAGAAAAGAAGAT
Found at i:108067 original size:2 final size:2
Alignment explanation
Indices: 108055--108089 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
108045 TGAGAAGTGC
108055 AT AT A- 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
108090 TCTGTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:110181 original size:4 final size:5
Alignment explanation
Indices: 110156--110189 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
110146 GACTGACTCT
110156 TTTTA TTTTA TTTTA TTTTA -TTTA TTTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTT
110190 CAACAGACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:118005 original size:25 final size:24
Alignment explanation
Indices: 117951--118016 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
117941 CCGACCCTTA
*
117951 TCTTCTCCTTCTTC-CTTCCTACCT
1 TCTTCTCCTTCTTCTC-ACCTACCT
*
117975 TTTTCTCCTTCTTCTCACCTTACCT
1 TCTTCTCCTTCTTCTCACC-TACCT
* *
118000 TCTTCTCTTTTTTCTCA
1 TCTTCTCCTTCTTCTCA
118017 GTGTTTGCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 15 0.43
25 20 0.57
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (24 bp):
TCTTCTCCTTCTTCTCACCTACCT
Found at i:122294 original size:2 final size:2
Alignment explanation
Indices: 122287--122311 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
122277 TTAAAAACAA
122287 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
122312 CACACACACA
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:139492 original size:2 final size:2
Alignment explanation
Indices: 139479--139510 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
139469 ACCCATCAAA
*
139479 AT AT AA 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
139511 TACATATAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:144559 original size:8 final size:7
Alignment explanation
Indices: 144546--144594 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
144536 TTAAAGTCTA
144546 AAAAAAGT
1 AAAAAA-T
144554 AAAAAAT
1 AAAAAAT
144561 --AAAAT
1 AAAAAAT
144566 AAAAAAT
1 AAAAAAT
*
144573 AAAATA-
1 AAAAAAT
*
144579 AAAAAAG
1 AAAAAAT
144586 AAAAAAT
1 AAAAAAT
144593 AA
1 AA
144595 TACCTGAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
5 5 0.14
6 5 0.14
7 19 0.54
8 6 0.17
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:144570 original size:12 final size:12
Alignment explanation
Indices: 144548--144583 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
144538 AAAGTCTAAA
144548 AAAAGTAAAAAAT
1 AAAA-TAAAAAAT
144561 AAAATAAAAAAT
1 AAAATAAAAAAT
144573 AAAATAAAAAA
1 AAAATAAAAAA
144584 AGAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:144592 original size:20 final size:19
Alignment explanation
Indices: 144546--144594 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
144536 TTAAAGTCTA
* *
144546 AAAAAAGTAAAAAATAAAAT
1 AAAAAA-TAAAAAAAAAAAG
144566 AAAAAATAAAATAAAAAAAG
1 AAAAAATAAAA-AAAAAAAG
144586 AAAAAATAA
1 AAAAAATAA
144595 TACCTGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.12
Consensus pattern (19 bp):
AAAAAATAAAAAAAAAAAG
Found at i:159247 original size:19 final size:19
Alignment explanation
Indices: 159211--159248 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
159201 ATTTGATTAT
159211 TTATTTTTTTAATTTCAAAA
1 TTATTTTTTTAA-TTCAAAA
159231 TTATTTTTTCTAA-TCAAA
1 TTATTTTTT-TAATTCAAA
159249 GTTTTTCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 9 0.53
21 3 0.18
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATTTTTTTAATTCAAAA
Found at i:160046 original size:3 final size:3
Alignment explanation
Indices: 160038--160063 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
160028 TGTTTTATAG
160038 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
160064 ACAATTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:166226 original size:15 final size:15
Alignment explanation
Indices: 166206--166244 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
166196 TAATGTTATT
166206 TTTTTAATAATCACA
1 TTTTTAATAATCACA
*
166221 TTTTT-ATAATCATA
1 TTTTTAATAATCACA
166235 TTTTTAATAA
1 TTTTTAATAA
166245 AACATCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTTTAATAATCACA
Found at i:168206 original size:20 final size:20
Alignment explanation
Indices: 168172--168212 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
168162 TCCCAAGAAC
168172 AAAGAGAGAAAAAAAAAATAA
1 AAAGAGAG-AAAAAAAAATAA
*
168193 AAAGA-AGAAGAAAAAATAA
1 AAAGAGAGAAAAAAAAATAA
168212 A
1 A
168213 CATAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 2 0.11
21 5 0.26
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAGAGAGAAAAAAAAATAA
Found at i:177842 original size:16 final size:17
Alignment explanation
Indices: 177818--177850 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
177808 CGTATTCGTA
177818 TTTAATTTTAAT-ATAT
1 TTTAATTTTAATCATAT
*
177834 TTTATTTTTAATCATAT
1 TTTAATTTTAATCATAT
177851 CTAATATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAATTTTAATCATAT
Found at i:180656 original size:2 final size:2
Alignment explanation
Indices: 180649--180674 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
180639 TTAGACATAA
180649 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
180675 TATGCTTCAA
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:183855 original size:21 final size:22
Alignment explanation
Indices: 183823--183872 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
183813 AAAAAATTAA
*
183823 TTTTCTTAAACTAATTACCATT
1 TTTTCTTAAACTAATTACCATC
* *
183845 TTTTCTT-AACTGATTACTATC
1 TTTTCTTAAACTAATTACCATC
183866 TTTTCTT
1 TTTTCTT
183873 CTTCTTTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.24, C:0.18, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTTCTTAAACTAATTACCATC
Found at i:184123 original size:15 final size:15
Alignment explanation
Indices: 184103--184132 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
184093 TTAAAAAATA
184103 TTGAAGAAAGGGAAG
1 TTGAAGAAAGGGAAG
*
184118 TTGAAGAAAGTGAAG
1 TTGAAGAAAGGGAAG
184133 GTGTTTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.00, G:0.37, T:0.17
Consensus pattern (15 bp):
TTGAAGAAAGGGAAG
Found at i:184670 original size:16 final size:16
Alignment explanation
Indices: 184649--184684 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
184639 GTGAAAATAA
*
184649 ATATATATGTATGTGT
1 ATATATATGTATGTAT
184665 ATATATATGTATGTAT
1 ATATATATGTATGTAT
184681 ATAT
1 ATAT
184685 GTTAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (16 bp):
ATATATATGTATGTAT
Found at i:185166 original size:12 final size:13
Alignment explanation
Indices: 185151--185180 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
185141 GCAAAATTAT
185151 AAATAAAAAAT-A
1 AAATAAAAAATGA
185163 AAATAAAAAATGA
1 AAATAAAAAATGA
185176 AAATA
1 AAATA
185181 TTACTACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (13 bp):
AAATAAAAAATGA
Found at i:193406 original size:2 final size:2
Alignment explanation
Indices: 193356--193387 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
193346 GAGTTATTGA
*
193356 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
193388 TAATTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:195947 original size:1 final size:1
Alignment explanation
Indices: 195909--195938 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
195899 TCCTGCTCTT
*
195909 CCCCCTCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
195939 ACACCCCCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:214294 original size:30 final size:31
Alignment explanation
Indices: 214238--214299 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
214228 AATAAAATTT
* *
214238 TATTTTTTTATTACATTGAATCAAGTTATTA
1 TATTTTTTTATTAAATTAAATCAAGTTATTA
*
214269 TATTTTTATT-TTAAATTAAAT-AAGTTTTTA
1 TATTTTT-TTATTAAATTAAATCAAGTTATTA
214299 T
1 T
214300 GATTAATAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 9 0.33
31 16 0.59
32 2 0.07
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (31 bp):
TATTTTTTTATTAAATTAAATCAAGTTATTA
Found at i:216607 original size:7 final size:7
Alignment explanation
Indices: 216591--216632 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
216581 AAACTATAAC
216591 AATAAAT
1 AATAAAT
*
216598 AATAATT
1 AATAAAT
*
216605 AATTAAT
1 AATAAAT
216612 AAATAAAT
1 -AATAAAT
216620 AATAAA-
1 AATAAAT
216626 AATAAAT
1 AATAAAT
216633 TAGAGCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 17 0.59
8 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AATAAAT
Found at i:216613 original size:11 final size:11
Alignment explanation
Indices: 216591--216625 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
216581 AAACTATAAC
216591 AATAAATAATA
1 AATAAATAATA
* *
216602 ATTAATTAATA
1 AATAAATAATA
216613 AATAAATAATA
1 AATAAATAATA
216624 AA
1 AA
216626 AATAAATTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AATAAATAATA
Found at i:219346 original size:27 final size:28
Alignment explanation
Indices: 219315--219369 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
219305 CCTCTCAAAA
*
219315 TATTTT-AAATGACATTTTGACTTTTTT
1 TATTTTAAAATGACATTTTGAATTTTTT
* *
219342 TATTTTAAAATGATATTTTTAATTTTTT
1 TATTTTAAAATGACATTTTGAATTTTTT
219370 ACTGTTCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (28 bp):
TATTTTAAAATGACATTTTGAATTTTTT
Found at i:219370 original size:27 final size:27
Alignment explanation
Indices: 219315--219370 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
219305 CCTCTCAAAA
*
219315 TATTTTAAATGACATTTTGACTTTTTT
1 TATTTTAAATGACATTTTGACATTTTT
* *
219342 TATTTTAAAATGATATTTTTA-ATTTTT
1 TATTTT-AAATGACATTTTGACATTTTT
219369 TA
1 TA
219371 CTGTTCATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (27 bp):
TATTTTAAATGACATTTTGACATTTTT
Found at i:221578 original size:5 final size:5
Alignment explanation
Indices: 221568--221617 Score: 82
Period size: 5 Copynumber: 9.8 Consensus size: 5
221558 ATACATAAGA
*
221568 AAAAG AAAAG AAAAG AAAAG AAACG AAAAG AAAAG AAAAG AAAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAA
221618 CCCACGACGG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 37 0.88
6 5 0.12
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:222237 original size:18 final size:19
Alignment explanation
Indices: 222205--222247 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
222195 TGGGAATTTG
*
222205 GGAAAAGAGGAGGGGAGGA
1 GGAAAGGAGGAGGGGAGGA
*
222224 GTAAAGGAGG-GGGGAGGA
1 GGAAAGGAGGAGGGGAGGA
222242 GGAAAG
1 GGAAAG
222248 AGAAGGTGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.40, C:0.00, G:0.58, T:0.02
Consensus pattern (19 bp):
GGAAAGGAGGAGGGGAGGA
Found at i:228451 original size:17 final size:17
Alignment explanation
Indices: 228429--228461 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
228419 TGATTTTACT
228429 TTCACATTACATTATAA
1 TTCACATTACATTATAA
*
228446 TTCACATTGCATTATA
1 TTCACATTACATTATA
228462 GTATTTTTTT
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:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (17 bp):
TTCACATTACATTATAA
Found at i:231983 original size:17 final size:16
Alignment explanation
Indices: 231948--231986 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
231938 TATATACATA
**
231948 AAAATAAATAAAATTT
1 AAAATAAATAAAAAAT
231964 AAAATAAATTAAAAAAT
1 AAAATAAA-TAAAAAAT
231981 AAAATA
1 AAAATA
231987 CTAATGAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAAATAAAAAAT
Found at i:233884 original size:2 final size:2
Alignment explanation
Indices: 233877--233901 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
233867 CTGTACAAAT
233877 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 T
233902 TAATTCTTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:239840 original size:14 final size:14
Alignment explanation
Indices: 239821--239850 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
239811 AACAAATGCA
239821 ATTAATTCAGTTTG
1 ATTAATTCAGTTTG
*
239835 ATTAATTTAGTTTG
1 ATTAATTCAGTTTG
239849 AT
1 AT
239851 GCAGTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.53
Consensus pattern (14 bp):
ATTAATTCAGTTTG
Found at i:240274 original size:13 final size:13
Alignment explanation
Indices: 240248--240287 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
240238 AAATTAATAA
*
240248 TATATTAACATAT
1 TATATTAACTTAT
240261 TA-ATGTAACTTAT
1 TATAT-TAACTTAT
240274 TATATTAACTTAT
1 TATATTAACTTAT
240287 T
1 T
240288 TTTATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (13 bp):
TATATTAACTTAT
Found at i:240309 original size:16 final size:16
Alignment explanation
Indices: 240250--240312 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
240240 ATTAATAATA
*
240250 TATTAACATATTAATGT
1 TATTAATATATTAA-GT
* * *
240267 AACTTATTATATTAACT
1 TA-TTAATATATTAAGT
**
240284 TATTTTTATATTAAGT
1 TATTAATATATTAAGT
240300 TATTAATATATTA
1 TATTAATATATTA
240313 TTCTTTATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
16 23 0.64
17 3 0.08
18 10 0.28
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (16 bp):
TATTAATATATTAAGT
Found at i:242930 original size:19 final size:19
Alignment explanation
Indices: 242891--242925 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
242881 CGAAATAACT
242891 ATAGCAACAAATAAAAATC
1 ATAGCAACAAATAAAAATC
242910 ATAGCAA-AAA-AAAAAT
1 ATAGCAACAAATAAAAAT
242926 TTCATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (19 bp):
ATAGCAACAAATAAAAATC
Found at i:243977 original size:20 final size:21
Alignment explanation
Indices: 243935--243995 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
243925 TATTCTTATT
*
243935 AATATACTAATTA-ATCAATAAC
1 AATATACT-ATTATA-CTATAAC
*
243957 AATATATTATTATA-TATAAC
1 AATATACTATTATACTATAAC
243977 AATATACTATTATACTATA
1 AATATACTATTATACTATA
243996 TATTACATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 18 0.53
21 8 0.24
22 8 0.24
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (21 bp):
AATATACTATTATACTATAAC
Found at i:244049 original size:19 final size:21
Alignment explanation
Indices: 244025--244065 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
244015 ATACTTATAT
244025 ACTATATA-AGT-ATATATTA
1 ACTATATATAGTAATATATTA
244044 ACTATATATAGTAATATATTA
1 ACTATATATAGTAATATATTA
244065 A
1 A
244066 TACTTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
ACTATATATAGTAATATATTA
Found at i:252620 original size:12 final size:12
Alignment explanation
Indices: 252603--252632 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
252593 TGCATGGCTA
252603 TTTTTCTTTCTT
1 TTTTTCTTTCTT
*
252615 TTTTTCTTTTTT
1 TTTTTCTTTCTT
252627 TTTTTC
1 TTTTTC
252633 ATTTTGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:254577 original size:16 final size:16
Alignment explanation
Indices: 254552--254584 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
254542 ATAAATTTAA
254552 CTTGTATATTTAAATT
1 CTTGTATATTTAAATT
*
254568 CTTGTTTATTTAAATT
1 CTTGTATATTTAAATT
254584 C
1 C
254585 CAATCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (16 bp):
CTTGTATATTTAAATT
Found at i:258095 original size:17 final size:18
Alignment explanation
Indices: 258064--258101 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
258054 TGAGATAGAT
*
258064 AGAAGAAAAGCAG-AAAG
1 AGAAGAAAAGAAGAAAAG
*
258081 AGAAGAAAGGAAGAAAAG
1 AGAAGAAAAGAAGAAAAG
258099 AGA
1 AGA
258102 GACAGGGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.66, C:0.03, G:0.32, T:0.00
Consensus pattern (18 bp):
AGAAGAAAAGAAGAAAAG
Found at i:271998 original size:20 final size:21
Alignment explanation
Indices: 271974--272028 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
271964 AAATTTTTGA
271974 AATTTTTTATTTATT-ATAAAT
1 AATTTTTTATTTATTCA-AAAT
* *
271995 -ATTTTTTGTATTCTTCAAAAT
1 AATTTTTTAT-TTATTCAAAAT
272016 AATTTTTTATTTA
1 AATTTTTTATTTA
272029 ATAATTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
20 8 0.30
21 10 0.37
22 9 0.33
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
AATTTTTTATTTATTCAAAAT
Found at i:273961 original size:3 final size:3
Alignment explanation
Indices: 273953--273980 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
273943 TTTTTATTTA
273953 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
273981 TCTTTCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:274150 original size:15 final size:16
Alignment explanation
Indices: 274132--274161 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
274122 TTGTTATGTG
274132 GATTTT-ATTTTTAAC
1 GATTTTAATTTTTAAC
274147 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
274162 AAATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (16 bp):
GATTTTAATTTTTAAC
Found at i:279488 original size:208 final size:211
Alignment explanation
Indices: 279121--279522 Score: 530
Period size: 208 Copynumber: 1.9 Consensus size: 211
279111 CCTGTCTTTG
279121 ACGAAATGTCTTTTCCTTGTCCCATTTTCCTTTTAATTTGGATGAGCAAGCTTTTTTATTAAAGA
1 ACGAAATGTCTTTTCCTTGTCCCATTTTCCTTTTAATTTGGATGAGCAAGCTTTTTTATTAAAGA
* * *
279186 TCCGTATATTTTGACTTAAAACCTTTTTTGAAAAATATTTGTAAAATTTAAACCTATTTAAAAAA
66 TCCATATATTTTGACTTAAAACCTTTTTTAAAAAATATTTGTAAAACTTAAACCTATTTAAAAAA
* * * *
279251 TTCAAAATTAAATCGAAATTGATAAGATTTAATAAATTTCTACTAGTGTAAGATTGTTTTTCTTG
131 TTCAAAATTAAATCGAAATGGAAAAGATTTAATAAATTTCTACTAGTGTAAGATTCTTCTTCTTG
279316 ATTGCGTATGTTTTCA
196 ATTGCGTATGTTTTCA
* * * * * * *
279332 ACGAAGTGTCTTTTTCTTGTCCTA-TTTCCTTTTTAATTTGGATGAAG-AA-TTTTTTTGTTTAG
1 ACGAAATGTCTTTTCCTTGTCCCATTTTCC-TTTTAATTTGGATG-AGCAAGCTTTTTTATTAAA
* *
279394 GAT-CATATATTTTGA-TCTAAAACC-TTTTTAAAAAATATTT-TCAAAACTTAAACCTGTTTGA
64 GATCCATATATTTTGACT-TAAAACCTTTTTTAAAAAATATTTGT-AAAACTTAAACCTATTTAA
* * * * *
279455 AAGATTGAAAATTAAATCGAAATGGAAAAGATTTAATGAATTTTTACTTGTGTAAGATTCTTCTT
127 AAAATTCAAAATTAAATCGAAATGGAAAAGATTTAATAAATTTCTACTAGTGTAAGATTCTTCTT
279520 CTT
192 CTT
279523 CACTATAACA
Statistics
Matches: 166, Mismatches: 21, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
207 1 0.01
208 91 0.55
209 18 0.11
210 17 0.10
211 37 0.22
212 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (211 bp):
ACGAAATGTCTTTTCCTTGTCCCATTTTCCTTTTAATTTGGATGAGCAAGCTTTTTTATTAAAGA
TCCATATATTTTGACTTAAAACCTTTTTTAAAAAATATTTGTAAAACTTAAACCTATTTAAAAAA
TTCAAAATTAAATCGAAATGGAAAAGATTTAATAAATTTCTACTAGTGTAAGATTCTTCTTCTTG
ATTGCGTATGTTTTCA
Found at i:279608 original size:28 final size:28
Alignment explanation
Indices: 279552--279608 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
279542 GCATCTTCCA
* *
279552 TTTTCTTTTAATTTAGATGAGGAAGCTT
1 TTTTCTTTTAATTTAGATAAGAAAGCTT
*
279580 TTTTCTTTTAA-TTAGATAAAGAAATCTT
1 TTTTCTTTTAATTTAGAT-AAGAAAGCTT
279608 T
1 T
279609 CCATTGTGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (28 bp):
TTTTCTTTTAATTTAGATAAGAAAGCTT
Found at i:279855 original size:20 final size:19
Alignment explanation
Indices: 279826--279875 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
279816 ATTTTGTTAT
279826 TTTTAGTTTTT-TTATAATTA
1 TTTTA-TTTTTATTA-AATTA
*
279846 TTTTATTTTTATTAAGTTA
1 TTTTATTTTTATTAAATTA
*
279865 TTTTAATTTTA
1 TTTTATTTTTA
279876 ATTTAGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTTATTTTTATTAAATTA
Found at i:279883 original size:20 final size:20
Alignment explanation
Indices: 279805--279886 Score: 69
Period size: 20 Copynumber: 4.1 Consensus size: 20
279795 AGTTCTTAAT
* *
279805 TTTTAATTATAATTTTGTTA
1 TTTTAATTTTAATTTAGTTA
* * *
279825 TTTTTAGTTTT-TTTATAATTA
1 -TTTTAATTTTAATT-TAGTTA
* *
279846 TTTT-ATTTTTATTAAGTTA
1 TTTTAATTTTAATTTAGTTA
279865 TTTTAATTTTAATTTAGTTA
1 TTTTAATTTTAATTTAGTTA
279885 TT
1 TT
279887 ATTTATTAGT
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
19 12 0.26
20 23 0.49
21 12 0.26
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTAATTTTAATTTAGTTA
Found at i:281007 original size:30 final size:29
Alignment explanation
Indices: 280939--281007 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 29
280929 TTATCTTATT
*
280939 ATTTTAATTTTTAATTAAATTAGTTTTAG
1 ATTTTAATTTTTAATTAAATTAGATTTAG
* * *
280968 -TTGAGTAATTTTTAGTTTAATTAGAATTTAG
1 ATT--TTAATTTTTAATTAAATTAG-ATTTAG
280999 ATTTTAATT
1 ATTTTAATT
281008 ATTTGAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
28 2 0.06
30 22 0.71
31 5 0.16
32 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (29 bp):
ATTTTAATTTTTAATTAAATTAGATTTAG
Found at i:281452 original size:17 final size:17
Alignment explanation
Indices: 281427--281459 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
281417 AGGTTTAGAA
*
281427 ATAATTGAAAAAAAATG
1 ATAAATGAAAAAAAATG
281444 ATAAATGAAAAAAAAT
1 ATAAATGAAAAAAAAT
281460 TATTTATTAT
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:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (17 bp):
ATAAATGAAAAAAAATG
Found at i:282246 original size:32 final size:32
Alignment explanation
Indices: 282205--282268 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
282195 TCAATTTTAC
282205 CTTAAATTGTGACCTTTGAAACAAAATTCTAT
1 CTTAAATTGTGACCTTTGAAACAAAATTCTAT
282237 CTTAAATTGTGACCTTTGAAACAAAATTCTAT
1 CTTAAATTGTGACCTTTGAAACAAAATTCTAT
282269 ATTGTGAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (32 bp):
CTTAAATTGTGACCTTTGAAACAAAATTCTAT
Found at i:282958 original size:27 final size:29
Alignment explanation
Indices: 282916--282969 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
282906 ATTTCGAAAA
*
282916 ATTCAAATAATTTTTTAT-TTTTTATTAG
1 ATTCAAATAAGTTTTTATATTTTTATTAG
*
282944 ATTC-AATAAGTTTTTTTATTTTTATT
1 ATTCAAATAAGTTTTTATATTTTTATT
282970 TTTAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (29 bp):
ATTCAAATAAGTTTTTATATTTTTATTAG
Found at i:283201 original size:15 final size:17
Alignment explanation
Indices: 283181--283219 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
283171 AATAAATAAC
283181 ATTAAT-ATT-TTAATT
1 ATTAATAATTATTAATT
283196 ATTAATAATTAATTAATT
1 ATTAATAATT-ATTAATT
283214 ATTAAT
1 ATTAAT
283220 TATAAAGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 3 0.14
18 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTAATAATTATTAATT
Found at i:284634 original size:3 final size:3
Alignment explanation
Indices: 284628--284655 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
284618 TTCCTTTCAA
284628 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
284656 TTCTTTGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:308143 original size:111 final size:112
Alignment explanation
Indices: 307942--308162 Score: 318
Period size: 111 Copynumber: 2.0 Consensus size: 112
307932 GGTTTGGTCC
*
307942 ATAGGGTGTTAAAATTCTAAAACATCGAACCTACCTTACACAAAAGTCGAATTCAATTGAATAAT
1 ATAGGGTGTTAAAATTCTAAAACATCGAACCTACCTTACACAAAAATCGAATTCAATTGAATAAT
* ** * *
308007 TATACTTCATCAAATGGATAGAAATTCAAATTACTTCAATTTGTTTG
66 TATACTTAATCAAATCAATAAAAATTCAAACTACTTCAATTTGTTTG
* ** * * *
308054 ATAGGGTGTTAAAATTCT-AAACATCGAACTTATTTTATACAAAAATTGAATTGAATTGAATAAT
1 ATAGGGTGTTAAAATTCTAAAACATCGAACCTACCTTACACAAAAATCGAATTCAATTGAATAAT
*
308118 TATACTTAATCAAATCAATAAAAATTCGAACTACTTCAATTTGTT
66 TATACTTAATCAAATCAATAAAAATTCAAACTACTTCAATTTGTT
308163 CTGTCAGTTT
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
111 78 0.81
112 18 0.19
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (112 bp):
ATAGGGTGTTAAAATTCTAAAACATCGAACCTACCTTACACAAAAATCGAATTCAATTGAATAAT
TATACTTAATCAAATCAATAAAAATTCAAACTACTTCAATTTGTTTG
Found at i:308283 original size:17 final size:18
Alignment explanation
Indices: 308261--308294 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
308251 CATATTCAAG
308261 TAAATTCAATA-ATATTT
1 TAAATTCAATATATATTT
*
308278 TAAATTTAATATATATT
1 TAAATTCAATATATATT
308295 ATTGGTGTAT
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:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAATTCAATATATATTT
Found at i:310375 original size:21 final size:21
Alignment explanation
Indices: 310340--310400 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
310330 ATAAAAATTT
*
310340 ATTTAAAAA--TTTTTATATA
1 ATTTAAAAACTTTTTTAAATA
310359 ATTTAAAAACTTTTTTAAATA
1 ATTTAAAAACTTTTTTAAATA
310380 ATTTAAAAACTTTTTTAAATA
1 ATTTAAAAACTTTTTTAAATA
310401 TTATATCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 9 0.23
21 30 0.77
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTAAAAACTTTTTTAAATA
Found at i:321454 original size:3 final size:3
Alignment explanation
Indices: 321440--321478 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
321430 GAAAAGATAA
*
321440 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
321479 AAGTGCCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:326507 original size:4 final size:4
Alignment explanation
Indices: 326498--326523 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
326488 AAAAATTGCG
326498 GATT GATT GATT GATT GATT GATT GA
1 GATT GATT GATT GATT GATT GATT GA
326524 GTTTTTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (4 bp):
GATT
Found at i:328676 original size:2 final size:2
Alignment explanation
Indices: 328671--328698 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
328661 AAAATTGATC
328671 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
328699 CCATTCAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:331737 original size:19 final size:21
Alignment explanation
Indices: 331699--331737 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
331689 AGAGCTTTAG
*
331699 AGAATCAAAAACCGTATTATC
1 AGAATCAAAAACCATATTATC
331720 AGAAT-AAAAACCAT-TTAT
1 AGAATCAAAAACCATATTAT
331738 TGAGCCCTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (21 bp):
AGAATCAAAAACCATATTATC
Found at i:349470 original size:27 final size:27
Alignment explanation
Indices: 349440--349501 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
349430 ACAAGCTTTG
349440 CTTTCTTCATATATGACACTGTTAAAT
1 CTTTCTTCATATATGACACTGTTAAAT
349467 CTTTCTTCATATATGACACTGTTAAAT
1 CTTTCTTCATATATGACACTGTTAAAT
349494 CTTTCTTC
1 CTTTCTTC
349502 CTAGTTTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (27 bp):
CTTTCTTCATATATGACACTGTTAAAT
Found at i:353346 original size:2 final size:2
Alignment explanation
Indices: 353339--353378 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
353329 TGTTGTAGTG
*
353339 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA T
353379 CTTAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:373611 original size:16 final size:17
Alignment explanation
Indices: 373592--373624 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
373582 TAGAAAATAT
373592 TATTTT-ATATTACTAA
1 TATTTTAATATTACTAA
*
373608 TATTTTAATATTTCTAA
1 TATTTTAATATTACTAA
373625 GCATGTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTTAATATTACTAA
Found at i:380131 original size:15 final size:15
Alignment explanation
Indices: 380107--380136 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
380097 ATTTGAGATT
380107 ATCATAATTTTAATG
1 ATCATAATTTTAATG
*
380122 ATCATGATTTTAATG
1 ATCATAATTTTAATG
380137 TGGATTTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (15 bp):
ATCATAATTTTAATG
Found at i:380152 original size:69 final size:69
Alignment explanation
Indices: 380079--380209 Score: 262
Period size: 69 Copynumber: 1.9 Consensus size: 69
380069 TCATTTCGTG
380079 AAAAATTAAATAAATATTATTTGAGATTATCATAATTTTAATGATCATGATTTTAATGTGGATTT
1 AAAAATTAAATAAATATTATTTGAGATTATCATAATTTTAATGATCATGATTTTAATGTGGATTT
380144 CATA
66 CATA
380148 AAAAATTAAATAAATATTATTTGAGATTATCATAATTTTAATGATCATGATTTTAATGTGGA
1 AAAAATTAAATAAATATTATTTGAGATTATCATAATTTTAATGATCATGATTTTAATGTGGA
380210 AGATTGTTGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (69 bp):
AAAAATTAAATAAATATTATTTGAGATTATCATAATTTTAATGATCATGATTTTAATGTGGATTT
CATA
Found at i:380200 original size:15 final size:15
Alignment explanation
Indices: 380176--380205 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
380166 ATTTGAGATT
380176 ATCATAATTTTAATG
1 ATCATAATTTTAATG
*
380191 ATCATGATTTTAATG
1 ATCATAATTTTAATG
380206 TGGAAGATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (15 bp):
ATCATAATTTTAATG
Found at i:387342 original size:2 final size:2
Alignment explanation
Indices: 387335--387365 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
387325 CTAAATGGCT
387335 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
387366 GTATTTGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:387496 original size:29 final size:30
Alignment explanation
Indices: 387464--387527 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
387454 ACATAGCATA
*
387464 TAACAATAA-AATATTTTCAACATGATGTG
1 TAACAATAACAATATTTTCAACATGATATG
* * *
387493 TAACAATAACATTTTTTTCAACATGGTATG
1 TAACAATAACAATATTTTCAACATGATATG
387523 TAACA
1 TAACA
387528 TATTTTTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (30 bp):
TAACAATAACAATATTTTCAACATGATATG
Found at i:387513 original size:30 final size:29
Alignment explanation
Indices: 387442--387596 Score: 107
Period size: 29 Copynumber: 5.4 Consensus size: 29
387432 AAGTATAACA
*
387442 AAATTTTTTTAAACATAGCATA--TAACAAT
1 AAATTTTTTTCAACAT-G-ATATGTAACAAT
* * *
387471 AAAATATTTTCAACATGATGTGTAACAAT
1 AAATTTTTTTCAACATGATATGTAACAAT
*
387500 AACATTTTTTTCAACATGGTATGTAAC-AT
1 AA-ATTTTTTTCAACATGATATGTAACAAT
*
387529 --ATTTTTGTT---CATGA-AGTGTAACAAC
1 AAATTTTT-TTCAACATGATA-TGTAACAAT
387554 AATATTTTTTT-AACATGGA-ATGTAACAAT
1 AA-ATTTTTTTCAACAT-GATATGTAACAAT
387583 AATATTTTTTTCAA
1 AA-ATTTTTTTCAA
387597 TATAACATAT
Statistics
Matches: 102, Mismatches: 11, Indels: 25
0.74 0.08 0.18
Matches are distributed among these distances:
23 1 0.01
24 10 0.10
25 1 0.01
26 6 0.06
27 6 0.06
28 7 0.07
29 46 0.45
30 25 0.25
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (29 bp):
AAATTTTTTTCAACATGATATGTAACAAT
Found at i:387610 original size:83 final size:83
Alignment explanation
Indices: 387491--387647 Score: 199
Period size: 83 Copynumber: 1.9 Consensus size: 83
387481 CAACATGATG
*** * * *
387491 TGTAACAATAACATTTTTTTCAACATGGTATGTAACATATTTTTGTTCAT-GAAGTGTAACAACA
1 TGTAACAATAACATTTTTTTCAACATAACATATAACATATTTTTGTACATGGAA-TGAAACAACA
387555 ATATTTTTTTAACATGGAA
65 ATATTTTTTTAACATGGAA
* * * * *
387574 TGTAACAATAATATTTTTTTCAATATAACATATAACATGTTTTTGTACATGGTATGAAACAATAA
1 TGTAACAATAACATTTTTTTCAACATAACATATAACATATTTTTGTACATGGAATGAAACAACAA
387639 TATTTTTTT
66 TATTTTTTT
387648 CAATATAACA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
83 60 0.97
84 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (83 bp):
TGTAACAATAACATTTTTTTCAACATAACATATAACATATTTTTGTACATGGAATGAAACAACAA
TATTTTTTTAACATGGAA
Found at i:387617 original size:53 final size:53
Alignment explanation
Indices: 387560--387725 Score: 269
Period size: 53 Copynumber: 3.1 Consensus size: 53
387550 CAACAATATT
*
387560 TTTTTAACATGGAATGTAACAATAATATTTTTTTCAATATAACATATAACATG
1 TTTTTAACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATG
* *
387613 TTTTTGTACATGGTATGAAACAATAATATTTTTTTCAATATAACATATAACATG
1 TTTTT-AACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATG
* * *
387667 TTTTTTACATGGCATGAAACAATAATATTTTTTTCAATATAGCATATAACATG
1 TTTTTAACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATG
387720 TTTTTA
1 TTTTTA
387726 TACGTGACGT
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 56 0.53
54 50 0.47
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (53 bp):
TTTTTAACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATG
Found at i:387635 original size:54 final size:53
Alignment explanation
Indices: 387559--387724 Score: 278
Period size: 54 Copynumber: 3.1 Consensus size: 53
387549 ACAACAATAT
*
387559 TTTTTTAACATGGAATGTAACAATAATATTTTTTTCAATATAACATATAACATG
1 TTTTTT-ACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATG
*
387613 TTTTTGTACATGGTATGAAACAATAATATTTTTTTCAATATAACATATAACATG
1 TTTTT-TACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATG
* *
387667 TTTTTTACATGGCATGAAACAATAATATTTTTTTCAATATAGCATATAACATG
1 TTTTTTACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATG
387720 TTTTT
1 TTTTT
387725 ATACGTGACG
Statistics
Matches: 107, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
53 51 0.48
54 55 0.51
55 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (53 bp):
TTTTTTACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATG
Found at i:387647 original size:30 final size:29
Alignment explanation
Indices: 387548--387700 Score: 96
Period size: 29 Copynumber: 5.6 Consensus size: 29
387538 CATGAAGTGT
* * * *
387548 AACAACAATATTTTTTTAACATGGAATGT
1 AACAATAATATTTTTTTTACATGGTATGA
*
387577 AACAATAATA-TTTTTTT-CA--ATAT--
1 AACAATAATATTTTTTTTACATGGTATGA
* *
387600 AACATATAACATGTTTTTGTACATGGTATGA
1 AACA-ATAATAT-TTTTTTTACATGGTATGA
*
387631 AACAATAATA-TTTTTTT-CA--ATAT--
1 AACAATAATATTTTTTTTACATGGTATGA
* * *
387654 AACATATAACATGTTTTTTACATGGCATGA
1 AACA-ATAATATTTTTTTTACATGGTATGA
387684 AACAATAATATTTTTTT
1 AACAATAATATTTTTTT
387701 CAATATAGCA
Statistics
Matches: 93, Mismatches: 16, Indels: 30
0.67 0.12 0.22
Matches are distributed among these distances:
23 8 0.09
24 10 0.11
25 11 0.12
26 8 0.09
27 6 0.06
28 14 0.15
29 23 0.25
30 9 0.10
31 4 0.04
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (29 bp):
AACAATAATATTTTTTTTACATGGTATGA
Found at i:387697 original size:27 final size:26
Alignment explanation
Indices: 387548--387699 Score: 68
Period size: 26 Copynumber: 5.6 Consensus size: 26
387538 CATGAAGTGT
* *
387548 AACAACAATATTTTTTTAACATGGAATGT
1 AACAATAATA-TTTTTT-ACATGG-ATGA
*
387577 AACAATAATATTTTTTTCA---AT-A
1 AACAATAATATTTTTTACATGGATGA
*
387599 TAACATATAACATGTTTTTGTACATGGTATGA
1 -AACA-AT-A-ATATTTTT-TACATGG-ATGA
*
387631 AACAATAATATTTTTTTCA---AT-A
1 AACAATAATATTTTTTACATGGATGA
*
387653 TAACATATAACATGTTTTTTACATGGCATGA
1 -AACA-AT-A-ATATTTTTTACATGG-ATGA
387684 AACAATAATATTTTTT
1 AACAATAATATTTTTT
387700 TCAATATAGC
Statistics
Matches: 94, Mismatches: 10, Indels: 40
0.65 0.07 0.28
Matches are distributed among these distances:
22 1 0.01
23 12 0.13
24 4 0.04
25 2 0.02
26 17 0.18
27 16 0.17
28 14 0.15
29 12 0.13
30 8 0.09
31 7 0.07
32 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (26 bp):
AACAATAATATTTTTTACATGGATGA
Found at i:387748 original size:107 final size:109
Alignment explanation
Indices: 387559--387758 Score: 287
Period size: 107 Copynumber: 1.9 Consensus size: 109
387549 ACAACAATAT
* *
387559 TTTTTTAACATGGAATGTAACAATAATATTTTTTTCAATATAACATATAACATGTTTTTGTACAT
1 TTTTTTAACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATGTTTTTATACAT
** *
387624 GGTATGAAACAATAATATTT-TTTTCAATATAACATATAACATG
66 GACATGAAACAAGAATATTTCTTTTCAATATAACATATAACATG
* * *
387667 TTTTTT-ACATGGCATGAAACAATAATATTTTTTTCAATATAGCATATAACATGTTTTTATACGT
1 TTTTTTAACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATGTTTTTATACAT
* * *
387731 GACGTGTAATAAGAATATTTCTTTTCAA
66 GACATGAAACAAGAATATTTCTTTTCAA
387759 CGTGACATGT
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
107 67 0.84
108 13 0.16
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (109 bp):
TTTTTTAACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATGTTTTTATACAT
GACATGAAACAAGAATATTTCTTTTCAATATAACATATAACATG
Found at i:387778 original size:107 final size:108
Alignment explanation
Indices: 387559--387789 Score: 275
Period size: 107 Copynumber: 2.1 Consensus size: 108
387549 ACAACAATAT
* *
387559 TTTTTTAACATGGAATGTAACAATAATATTTTTTTCAATATAACATATAACATGTTTTTGTACAT
1 TTTTTTAACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATGTTTTTATACAT
** * * *
387624 GGTATGAAACAATAATATTTTTTTCAATATAACATATAACATG
66 GACATGAAACAAGAATATTTTTTTCAACATAACATATAACATA
* * *
387667 TTTTTT-ACATGGCATGAAACAATAATATTTTTTTCAATATAGCATATAACATGTTTTTATACGT
1 TTTTTTAACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATGTTTTTATACAT
* * * * * * *
387731 GACGTGTAATAAGAATATTTCTTTTCAACGTGACATGTAACAATT
66 GACATGAAACAAGAATATTT-TTTTCAACATAACATATAAC-ATA
387776 TTTTTTAACCATGG
1 TTTTTTAA-CATGG
387790 CATGTAATAT
Statistics
Matches: 103, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
107 67 0.65
108 22 0.21
109 8 0.08
110 1 0.01
111 5 0.05
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.42
Consensus pattern (108 bp):
TTTTTTAACATGGAATGAAACAATAATATTTTTTTCAATATAACATATAACATGTTTTTATACAT
GACATGAAACAAGAATATTTTTTTCAACATAACATATAACATA
Found at i:387793 original size:26 final size:25
Alignment explanation
Indices: 387764--387863 Score: 69
Period size: 26 Copynumber: 3.8 Consensus size: 25
387754 TTCAACGTGA
387764 CATGTAACAATTTTTTTTAACCATGG
1 CATGTAACAATTTTTTTTAA-CATGG
* *
387790 CATGTAATATATTTTTGTATAA-ATGTG
1 CATGTAACA-ATTTTT-TTTAACATG-G
* * *
387817 TA-ATAATAATTTTTTTTTCAACATGG
1 CATGTAACAA-TTTTTTTT-AACATGG
* *
387843 CGTGTAACAATCTTTTTTAAC
1 CATGTAACAATTTTTTTTAAC
387864 CATGACGTGC
Statistics
Matches: 57, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
25 6 0.11
26 31 0.54
27 16 0.28
28 4 0.07
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (25 bp):
CATGTAACAATTTTTTTTAACATGG
Found at i:387849 original size:79 final size:80
Alignment explanation
Indices: 387734--387921 Score: 227
Period size: 79 Copynumber: 2.4 Consensus size: 80
387724 TATACGTGAC
* * * * * * * *
387734 GTGTAATAAGAATATTTCTTTTCAACGTGACATGTAACAATTTTTTTTAACCATGGCATGTAATA
1 GTGTAATAATAAT-TTTTTTTTCAACATGGCATGTAACAATCTTTTTTAACCATGACATGCAACA
387799 TATTTTTGTATA-AAT
65 TATTTTTGTATATAAT
* *
387814 GTGTAATAATAATTTTTTTTTCAACATGGCGTGTAACAATCTTTTTTAACCATGACGTGCAACAT
1 GTGTAATAATAATTTTTTTTTCAACATGGCATGTAACAATCTTTTTTAACCATGACATGCAACAT
*
387879 ATTTTTGTATATAGT
66 ATTTTTGTATATAAT
* **
387894 GTGTAACAATAA-CATTTTTTCAACATGG
1 GTGTAATAATAATTTTTTTTTCAACATGG
387922 TAGGTAATAT
Statistics
Matches: 93, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
79 68 0.73
80 25 0.27
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (80 bp):
GTGTAATAATAATTTTTTTTTCAACATGGCATGTAACAATCTTTTTTAACCATGACATGCAACAT
ATTTTTGTATATAAT
Found at i:387883 original size:25 final size:26
Alignment explanation
Indices: 387829--387884 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
387819 ATAATAATTT
* * *
387829 TTTTTTCAACATGGCGTGTAACAATC
1 TTTTTTCAACATGACGTGCAACAATA
387855 TTTTTT-AACCATGACGTGCAAC-ATA
1 TTTTTTCAA-CATGACGTGCAACAATA
387880 TTTTT
1 TTTTT
387885 GTATATAGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (26 bp):
TTTTTTCAACATGACGTGCAACAATA
Found at i:391832 original size:2 final size:2
Alignment explanation
Indices: 391825--391852 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
391815 ACCTAATGAG
391825 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
391853 TACCAAACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:393673 original size:15 final size:15
Alignment explanation
Indices: 393646--393677 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
393636 TTCTTATATT
393646 ATATATTTTATTTTA
1 ATATATTTTATTTTA
*
393661 ATATTTTTTATTTTA
1 ATATATTTTATTTTA
393676 AT
1 AT
393678 TATAACATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:397584 original size:19 final size:20
Alignment explanation
Indices: 397562--397600 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
397552 AAATACAATT
397562 GAAAAGT-AAAAACAAAAGA
1 GAAAAGTAAAAAACAAAAGA
*
397581 GAAAATTAAAAAACAAAAGA
1 GAAAAGTAAAAAACAAAAGA
397601 CAATGTGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (20 bp):
GAAAAGTAAAAAACAAAAGA
Found at i:399573 original size:13 final size:14
Alignment explanation
Indices: 399549--399581 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
399539 GAAGCGTCAC
399549 TTAAATCTAAAATT
1 TTAAATCTAAAATT
399563 TTAAA-CTAAAATT
1 TTAAATCTAAAATT
*
399576 ATAAAT
1 TTAAAT
399582 AATAGAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAATCTAAAATT
Found at i:399709 original size:3 final size:3
Alignment explanation
Indices: 399696--399740 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
399686 CTAAGTTGAG
*
399696 TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
399741 GTTCAAGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:406588 original size:17 final size:17
Alignment explanation
Indices: 406566--406600 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
406556 ATTCGAAGTG
406566 TTTGAATTATCATATTT
1 TTTGAATTATCATATTT
* *
406583 TTTGAATTTTCTTATTT
1 TTTGAATTATCATATTT
406600 T
1 T
406601 GTTTTAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (17 bp):
TTTGAATTATCATATTT
Found at i:422639 original size:28 final size:28
Alignment explanation
Indices: 422582--422640 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
422572 GACCTAAGAC
* *
422582 AATTTGGCAGATCTTTTGTGTTCTTGTA
1 AATTTGGCAGATCTTGTGTGTTCTTATA
422610 AATTTGGCAAGATCTTGT-TG-TCTGTATA
1 AATTTGGC-AGATCTTGTGTGTTCT-TATA
422638 AAT
1 AAT
422641 CAAGAATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.11
28 16 0.59
29 8 0.30
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (28 bp):
AATTTGGCAGATCTTGTGTGTTCTTATA
Found at i:423253 original size:30 final size:30
Alignment explanation
Indices: 423195--423253 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
423185 GCCAAGGTTA
* * * *
423195 AGCACTGATCATAGAGAAAAGGCTAGAAAC
1 AGCACTGATAAGAGAGAAAAAGCAAGAAAC
*
423225 AGCACTGATAAGAGAGAAAAATCAAGAAA
1 AGCACTGATAAGAGAGAAAAAGCAAGAAA
423254 GAGTGTGGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.53, C:0.14, G:0.22, T:0.12
Consensus pattern (30 bp):
AGCACTGATAAGAGAGAAAAAGCAAGAAAC
Found at i:429496 original size:5 final size:5
Alignment explanation
Indices: 429486--429513 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
429476 TACACAAATA
429486 TTCCC TTCCC TTCCC TTCCC TTCCC TTC
1 TTCCC TTCCC TTCCC TTCCC TTCCC TTC
429514 ATTCCAACAG
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:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (5 bp):
TTCCC
Found at i:430299 original size:12 final size:12
Alignment explanation
Indices: 430282--430307 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
430272 TTCTTCTTCA
430282 TTATTATTATTC
1 TTATTATTATTC
430294 TTATTATTATTC
1 TTATTATTATTC
430306 TT
1 TT
430308 TTTCACTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTATTATTC
Found at i:431185 original size:3 final size:3
Alignment explanation
Indices: 431177--431202 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
431167 CTCATTCTTT
431177 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
431203 TCCTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:433021 original size:21 final size:21
Alignment explanation
Indices: 432996--433047 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
432986 TCGGACGTTA
432996 TTTTCTCAAACCCATTTTCTC
1 TTTTCTCAAACCCATTTTCTC
433017 TTTTCTCAAACCCATTTTCTC
1 TTTTCTCAAACCCATTTTCTC
*
433038 TTCTCTCAAA
1 TTTTCTCAAA
433048 ATCTGTTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTCTCAAACCCATTTTCTC
Found at i:434634 original size:16 final size:16
Alignment explanation
Indices: 434613--434647 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
434603 TATTTATTTT
434613 GAAATTTAAAATAACC
1 GAAATTTAAAATAACC
434629 GAAATTTAAAATAACC
1 GAAATTTAAAATAACC
434645 GAA
1 GAA
434648 GTTATTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23
Consensus pattern (16 bp):
GAAATTTAAAATAACC
Found at i:437348 original size:10 final size:10
Alignment explanation
Indices: 437312--437348 Score: 65
Period size: 10 Copynumber: 3.6 Consensus size: 10
437302 ACTGTATCCC
437312 TTTTTTCTATT
1 TTTTTTCT-TT
437323 TTTTTTCTTT
1 TTTTTTCTTT
437333 TTTTTTCTTT
1 TTTTTTCTTT
437343 TTTTTT
1 TTTTTT
437349 TGGACCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:437349 original size:11 final size:11
Alignment explanation
Indices: 437312--437349 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
437302 ACTGTATCCC
*
437312 TTTTTTCTATT
1 TTTTTTCTTTT
437323 TTTTTTC-TTT
1 TTTTTTCTTTT
437333 TTTTTTCTTTT
1 TTTTTTCTTTT
437344 TTTTTT
1 TTTTTT
437350 GGACCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:437735 original size:50 final size:50
Alignment explanation
Indices: 437672--437768 Score: 176
Period size: 50 Copynumber: 1.9 Consensus size: 50
437662 TAGTATATTT
* *
437672 GTATTTTTGGAAACCAGACTTATCCCAACTCTTTAAAACTGGGAGCACCA
1 GTATTTTTAGAAACCAAACTTATCCCAACTCTTTAAAACTGGGAGCACCA
437722 GTATTTTTAGAAACCAAACTTATCCCAACTCTTTAAAACTGGGAGCA
1 GTATTTTTAGAAACCAAACTTATCCCAACTCTTTAAAACTGGGAGCA
437769 GGTAGCTCGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (50 bp):
GTATTTTTAGAAACCAAACTTATCCCAACTCTTTAAAACTGGGAGCACCA
Done.