Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 9 of 230
Found at i:2798014 original size:90 final size:87
Alignment explanation
Indices: 2797732--2798196 Score: 346
Period size: 87 Copynumber: 5.3 Consensus size: 87
2797722 AAAAAATTTC
* ** ** *
2797732 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTG-AAGCCAGAGATCTTATCTCCCTGAGAT
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAATTC--AGATCTTATCTCCCTGAGGT
** * *
2797796 TACAGCAGAGCAGATTAAAGATAG
64 TACAGTGGAGCAGATTGAAGACAG
* * * * ** * *
2797820 TA-ATCCTATCTCCTTGAGATTACAATGGAGCGGA-TTAAA---AGATCTTATCTCTCTGAAGTT
1 -AGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAATTCAGATCTTATCTCCCTGAGGTT
* * * *
2797880 ACAGTAGAGAAGA-TCACA-TCAG
65 ACAGTGGAGCAGATTGA-AGACAG
* * *
2797902 -G-TCTTATTTCCCTGAGGTTACAGTGGAGTAGACCAGAGAATTCCAGATCTTATCTCCCTGAGG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGACC-GA-AATT-CAGATCTTATCTCCCTGAGG
*
2797965 TTACAGTGGAGCAGATTGAAGCCAG
63 TTACAGTGGAGCAGATTGAAGACAG
* * * *
2797990 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGA--CACTATCCTATCTCCCTGAAGT
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAA-ATTCA-GATCTTATCTCCCTGAGGT
* * * * *
2798053 TACAGTGGAGCGGA-TCAAAATGAT
64 TACAGTGGAGCAGATTGAAGA-CAG
* *
2798077 AGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGA
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCG--AAA-TTCAGATCTTATCTCCCTGAGG
* *
2798142 TTACAATGGAGCAGATTGAAGATAG
63 TTACAGTGGAGCAGATTGAAGACAG
*
2798167 TA-ATCTTATCTCCCTGAGATTACAGCGGAG
1 -AGATCTTATCTCCCTGAGATTACAGTGGAG
2798197 TAGATTGAAG
Statistics
Matches: 296, Mismatches: 56, Indels: 47
0.74 0.14 0.12
Matches are distributed among these distances:
80 24 0.08
82 5 0.02
83 32 0.11
86 5 0.02
87 97 0.33
88 36 0.12
89 7 0.02
90 83 0.28
91 7 0.02
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (87 bp):
AGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAATTCAGATCTTATCTCCCTGAGGTTA
CAGTGGAGCAGATTGAAGACAG
Found at i:2798133 original size:177 final size:172
Alignment explanation
Indices: 2797730--2798251 Score: 513
Period size: 177 Copynumber: 3.0 Consensus size: 172
2797720 AAAAAAAATT
* * ** *
2797730 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGA-TTG--AA-GCCAGAGATCTTATCTCCCT
1 TCAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCAGAAAATTCC--AGATCTTATCTCCCT
** * * * * * *
2797791 GAGATTACAGCAGAGCAGATTAAAGATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATT
64 GAGATTACAGTGGAGCAGATTGAAGATAGTAATCTTATCTCCCTGAGATTACAGTGGAGCAGATG
* * * * * *
2797856 AA-AAGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATC-ACA
129 AAGAATATCCTATCTCCCTGAAGTTACAGTGGAGAGGATCAAAA
* * * ** *
2797898 TCAGGTCTTATTTCCCTGAGGTTACAGTGGAGTAGACCAGAGAATTCCAGATCTTATCTCCCTGA
1 TCAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCAGAAAATTCCAGATCTTATCTCCCTGA
* **
2797963 GGTTACAGTGGAGCAGATTGAAGCCAG-AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCG
66 GATTACAGTGGAGCAGATTGAAGATAGTA-ATCTTATCTCCCTGAGATTACAGTGGAGCAGAT-G
*
2798027 AAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATCAAAA
129 AAGA-A-TATCCTATCTCCCTGAAGTTACAGTGGAGAGGATCAAAA
* *
2798073 TGATAGATCTTATCTCCCTGAGATTACAGTGGAACAGACC-GAAAAATTTCAGATCTTATCTCCC
1 T--CAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCAG-AAAATTCCAGATCTTATCTCCC
* * *
2798137 TGAGATTACAATGGAGCAGATTGAAGATAGTAATCTTATCTCCCTGAGATTACAGCGGAGTAGAT
63 TGAGATTACAGTGGAGCAGATTGAAGATAGTAATCTTATCTCCCTGAGATTACAGTGGAGCAGA-
* * * *
2798202 TGAAGATAGTAATCCTATCTGCCTG-AGATTACAGCGGAGTGGATTAAAA
127 TGAAGA-A-T-ATCCTATCTCCCTGAAG-TTACAGTGGAGAGGATCAAAA
2798251 T
1 T
2798252 AAAGGATCTT
Statistics
Matches: 293, Mismatches: 44, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
168 33 0.11
169 2 0.01
170 67 0.23
171 4 0.01
172 3 0.01
173 1 0.00
174 29 0.10
175 3 0.01
176 1 0.00
177 116 0.40
178 34 0.12
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (172 bp):
TCAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCAGAAAATTCCAGATCTTATCTCCCTGA
GATTACAGTGGAGCAGATTGAAGATAGTAATCTTATCTCCCTGAGATTACAGTGGAGCAGATGAA
GAATATCCTATCTCCCTGAAGTTACAGTGGAGAGGATCAAAA
Found at i:2798714 original size:8 final size:8
Alignment explanation
Indices: 2798703--2798727 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2798693 CCACCTACCC
2798703 CCCACTTG
1 CCCACTTG
2798711 CCCACTTG
1 CCCACTTG
2798719 CCCACTTG
1 CCCACTTG
2798727 C
1 C
2798728 GCCGAACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.52, G:0.12, T:0.24
Consensus pattern (8 bp):
CCCACTTG
Found at i:2799224 original size:22 final size:24
Alignment explanation
Indices: 2799199--2799244 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2799189 GGCCGGATTC
2799199 CCCTTC-CCCCTCCCT-TCTCTCT
1 CCCTTCTCCCCTCCCTCTCTCTCT
* *
2799221 CCCTTCTCTCTTCCCTCTCTCTCT
1 CCCTTCTCCCCTCCCTCTCTCTCT
2799245 TCTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 7 0.35
24 7 0.35
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (24 bp):
CCCTTCTCCCCTCCCTCTCTCTCT
Found at i:2799241 original size:13 final size:12
Alignment explanation
Indices: 2799209--2799246 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
2799199 CCCTTCCCCC
2799209 TCCCTTCTCTC-
1 TCCCTTCTCTCT
2799220 TCCCTTCTCTCT
1 TCCCTTCTCTCT
2799232 TCCCTCTCTCTCT
1 TCCCT-TCTCTCT
2799245 TC
1 TC
2799247 TTTTTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.44
12 5 0.20
13 9 0.36
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (12 bp):
TCCCTTCTCTCT
Found at i:2799735 original size:3 final size:3
Alignment explanation
Indices: 2799711--2799781 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
2799701 AATATCCTTG
* * * *
2799711 TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
2799758 TGTA TTA GTA TATA TTT TTA TTA T
1 T-TA TTA TTA T-TA TTA TTA TTA T
2799782 GTACGCGTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2799778 original size:23 final size:22
Alignment explanation
Indices: 2799723--2799784 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
2799713 ATTTTTATAT
*
2799723 TATTAGTATTATTA-GTATTAC
1 TATTATTATTATTATGTATTAC
*
2799744 TATTATTATTATTATGTATTAG
1 TATTATTATTATTATGTATTAC
*
2799766 TATATATTTTTATTATGTA
1 TAT-TATTATTATTATGTA
2799785 CGCGTATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 13 0.36
22 9 0.25
23 14 0.39
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TATTATTATTATTATGTATTAC
Found at i:2799791 original size:23 final size:23
Alignment explanation
Indices: 2799747--2799792 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2799737 GTATTACTAT
**
2799747 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTACGAGTATA
* *
2799770 TATTTTTATTATGTACGCGTATA
1 TATTATTATTATGTACGAGTATA
2799793 CATGTATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (23 bp):
TATTATTATTATGTACGAGTATA
Found at i:2802206 original size:32 final size:32
Alignment explanation
Indices: 2802157--2802217 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
2802147 GGCCATTAAA
*
2802157 TTTTTAGTTAAATTTGACTAAAACATTAATTT
1 TTTTTAGTGAAATTTGACTAAAACATTAATTT
2802189 TTTTTAG-GAAATATTGACTAAAACATTAA
1 TTTTTAGTGAAAT-TTGACTAAAACATTAA
2802218 AATTTTAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (32 bp):
TTTTTAGTGAAATTTGACTAAAACATTAATTT
Found at i:2805441 original size:24 final size:24
Alignment explanation
Indices: 2805413--2805464 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2805403 TTAGTAAGTC
* *
2805413 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2805437 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2805461 AAAT
1 AAAT
2805465 TTTTTCTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2809894 original size:41 final size:37
Alignment explanation
Indices: 2809799--2809895 Score: 86
Period size: 37 Copynumber: 2.5 Consensus size: 37
2809789 CGCAATAAAG
*
2809799 TGACACCCAGTGTCTCATCGGCCAAACCGAAGTAAGT
1 TGACACCCAGTGTCTCATCGACCAAACCGAAGTAAGT
** ** * * *
2809836 TGGTACCCAGTACCTCATCGAATCTATCCGAAGTAACAGT
1 TGACACCCAGTGTCTCATCG-ACCAAACCGAAGT-A-AGT
2809876 ATGACACCCAGTGTCTCATC
1 -TGACACCCAGTGTCTCATC
2809896 AACTCAAGGT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
37 16 0.36
38 9 0.20
39 1 0.02
40 3 0.07
41 15 0.34
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.23
Consensus pattern (37 bp):
TGACACCCAGTGTCTCATCGACCAAACCGAAGTAAGT
Found at i:2810202 original size:27 final size:27
Alignment explanation
Indices: 2810171--2810224 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2810161 CCACACATAA
*
2810171 TCATA-ATTTAATTCACTTTTATTCAAT
1 TCATATATTTAATTCA-TTTAATTCAAT
*
2810198 TCATATTTTTAATTCATTTAATTCAAT
1 TCATATATTTAATTCATTTAATTCAAT
2810225 ATCAACATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (27 bp):
TCATATATTTAATTCATTTAATTCAAT
Found at i:2811079 original size:8 final size:8
Alignment explanation
Indices: 2811066--2811098 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
2811056 TGTTTTATAG
2811066 ATATAATA
1 ATATAATA
2811074 ATATAATA
1 ATATAATA
2811082 ATATAATTA
1 ATATAA-TA
2811091 ATATAATA
1 ATATAATA
2811099 CTTATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:2815862 original size:27 final size:27
Alignment explanation
Indices: 2815831--2815884 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2815821 CCACAAATAA
*
2815831 TCATA-ATTTAATTCACTTTTATTCAAT
1 TCATATATTTAATTCA-TTTAATTCAAT
*
2815858 TCATATTTTTAATTCATTTAATTCAAT
1 TCATATATTTAATTCATTTAATTCAAT
2815885 ATCGACATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (27 bp):
TCATATATTTAATTCATTTAATTCAAT
Found at i:2816645 original size:13 final size:13
Alignment explanation
Indices: 2816627--2816653 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2816617 TTAATTTTTC
2816627 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
2816640 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
2816653 C
1 C
2816654 CTTCTTTCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
CTTTTCTTTCTTT
Found at i:2816745 original size:8 final size:8
Alignment explanation
Indices: 2816732--2816764 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
2816722 TGTTTTTTAT
2816732 ATATAATA
1 ATATAATA
2816740 ATATAATA
1 ATATAATA
2816748 ATATAATTA
1 ATATAA-TA
2816757 ATATAATA
1 ATATAATA
2816765 CTTATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:2817794 original size:13 final size:13
Alignment explanation
Indices: 2817776--2817802 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2817766 ACTGTCAAAC
2817776 GTTTCAGTTGTAA
1 GTTTCAGTTGTAA
2817789 GTTTCAGTTGTAA
1 GTTTCAGTTGTAA
2817802 G
1 G
2817803 CTGTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.44
Consensus pattern (13 bp):
GTTTCAGTTGTAA
Found at i:2817815 original size:20 final size:20
Alignment explanation
Indices: 2817790--2817830 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2817780 CAGTTGTAAG
2817790 TTTCAGTTGTAAGCTGTTAA
1 TTTCAGTTGTAAGCTGTTAA
2817810 TTTCAGTTGTAAGCTGTTAA
1 TTTCAGTTGTAAGCTGTTAA
2817830 T
1 T
2817831 AGGTTAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (20 bp):
TTTCAGTTGTAAGCTGTTAA
Found at i:2821844 original size:23 final size:24
Alignment explanation
Indices: 2821811--2821866 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
2821801 ACTAAAAGTA
*
2821811 TATATTTAATACTAATTAATTTTT
1 TATATTTAATAATAATTAATTTTT
*
2821835 TATA-TTAATAATGATTAA-TTTT
1 TATATTTAATAATAATTAATTTTT
*
2821857 AATATTTAAT
1 TATATTTAAT
2821867 TTTTTTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.25
23 17 0.61
24 4 0.14
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TATATTTAATAATAATTAATTTTT
Found at i:2822061 original size:43 final size:43
Alignment explanation
Indices: 2821902--2822156 Score: 203
Period size: 43 Copynumber: 5.9 Consensus size: 43
2821892 GCGTTTTTAT
** *
2821902 GTAAAA-CGCCGCTAAAGAACAGTAAT-TTTAGCGGCGTTTGTG
1 GTAAAAGCGCCGCTAAAGGTCA-TGATCTTTAGCGGCGTTTGTG
* ** * * * *
2821944 ATCAAAA-CTGTTGCTAAAGGTCATGTTCTTTAGCGACATTTGTT
1 GT-AAAAGC-GCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTG
* ** *
2821988 ATAAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTGTG
1 GTAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTG
** * *
2822031 GTAAAAGCGATGCTAAAGGTCATGACCTTTAGCGGTGTTTGTG
1 GTAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTG
* * * *
2822074 AG-GAAAGCGCCGCTAAAAGCCATGATCTATAGCGGCGTTTGTG
1 -GTAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTG
* * * * *
2822117 GGAGAAGCGCCGCTAAAGTTCATGACCTTTAGCAGCGTTT
1 GTAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTT
2822157 ATTTCTAAAA
Statistics
Matches: 165, Mismatches: 42, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
42 2 0.01
43 136 0.82
44 27 0.16
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (43 bp):
GTAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTG
Found at i:2822072 original size:86 final size:86
Alignment explanation
Indices: 2821903--2822149 Score: 259
Period size: 86 Copynumber: 2.9 Consensus size: 86
2821893 CGTTTTTATG
* * *
2821903 TAAAA-CGCCGCTAAAGAACAGTAAT-TTTAGCGGCGTTTGTGATCAAAA-CTGTTGCTAAAGGT
1 TAAAAGCGCCGCTAAAGAACA-TGATCTTTAGCGGCGTTTGTGGT-AAAAGC-GATGCTAAAGGT
** *
2821965 CATGTTCTTTAGCGACATTTGTTA
63 CATGACCTTTAGCGACATTTGTGA
*
2821989 TAAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGATGCTAAAGGTCAT
1 TAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTGGTAAAAGCGATGCTAAAGGTCAT
***
2822054 GACCTTTAGCGGTGTTTGTGA
66 GACCTTTAGCGACATTTGTGA
** * * * * ** *
2822075 GGAAAGCGCCGCTAAA-AGCCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGTTCA
1 TAAAAGCGCCGCTAAAGA-ACATGATCTTTAGCGGCGTTTGTGGTAAAAGCGATGCTAAAGGTCA
2822139 TGACCTTTAGC
65 TGACCTTTAGC
2822150 AGCGTTTATT
Statistics
Matches: 137, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
85 1 0.01
86 103 0.75
87 33 0.24
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (86 bp):
TAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTGGTAAAAGCGATGCTAAAGGTCAT
GACCTTTAGCGACATTTGTGA
Found at i:2824364 original size:17 final size:16
Alignment explanation
Indices: 2824344--2824383 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
2824334 ATTTAAGTCT
2824344 ATAATTCAATTAATATC
1 ATAATTCAATTAATA-C
*
2824361 ATAAGTCAATTAATAC
1 ATAATTCAATTAATAC
2824377 -TAATTCA
1 ATAATTCA
2824384 GTTGAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 6 0.29
16 1 0.05
17 14 0.67
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (16 bp):
ATAATTCAATTAATAC
Found at i:2824906 original size:26 final size:26
Alignment explanation
Indices: 2824870--2824925 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
2824860 TTTTTTATTT
2824870 ATCTACCAGAGCGAG-CTCAATAATTA
1 ATCTACCAGAGCGAGCCT-AATAATTA
*
2824896 ATCTACCAGAGCGAGCCTATTAATTA
1 ATCTACCAGAGCGAGCCTAATAATTA
2824922 ATCT
1 ATCT
2824926 TCCGTATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (26 bp):
ATCTACCAGAGCGAGCCTAATAATTA
Found at i:2825469 original size:21 final size:21
Alignment explanation
Indices: 2825439--2825480 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2825429 CAGATAGCTG
* *
2825439 CATCTGTTTACATTATGCAAT
1 CATCTATTTACATTATACAAT
2825460 CATCTATTTACATTATACAAT
1 CATCTATTTACATTATACAAT
2825481 TATATGATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (21 bp):
CATCTATTTACATTATACAAT
Found at i:2825689 original size:93 final size:92
Alignment explanation
Indices: 2825531--2825719 Score: 360
Period size: 93 Copynumber: 2.0 Consensus size: 92
2825521 ATATGTTGAT
*
2825531 TTTAACATAGTTAATTGGGTTTAGAATTATCTATGATAACATCTTATTTATTCAGTCAAATAGGC
1 TTTAACATAGTTAATTGGATTTAGAATTATCTATGATAACATCTTATTTATTCAGTCAAATAGGC
2825596 ACACAATTATTATAACAGTTCAATCAA
66 ACACAATTATTATAACAGTTCAATCAA
2825623 TTTAACATAGTTAATTGGATTTAGAATTTATCTATGATAACATCTTATTTATTCAGTCAAATAGG
1 TTTAACATAGTTAATTGGATTTAGAA-TTATCTATGATAACATCTTATTTATTCAGTCAAATAGG
2825688 CACACAATTATTATAACAGTTCAATCAA
65 CACACAATTATTATAACAGTTCAATCAA
2825716 TTTA
1 TTTA
2825720 CATTATACTA
Statistics
Matches: 95, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 25 0.26
93 70 0.74
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (92 bp):
TTTAACATAGTTAATTGGATTTAGAATTATCTATGATAACATCTTATTTATTCAGTCAAATAGGC
ACACAATTATTATAACAGTTCAATCAA
Found at i:2836676 original size:11 final size:9
Alignment explanation
Indices: 2836638--2836678 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
2836628 ATATAAAGTA
2836638 AAATAAAAG
1 AAATAAAAG
*
2836647 AAACAAAAG
1 AAATAAAAG
2836656 AAATAAAAG
1 AAATAAAAG
2836665 AACATAAAAAG
1 AA-AT-AAAAG
2836676 AAA
1 AAA
2836679 CAGAGAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 18 0.64
10 3 0.11
11 7 0.25
ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07
Consensus pattern (9 bp):
AAATAAAAG
Found at i:2837283 original size:39 final size:40
Alignment explanation
Indices: 2837240--2837327 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 40
2837230 CGAATTATGG
* * *
2837240 AATACTGGATATTGTTTTG-ATTACTG-AGTGAATTGTGAA
1 AATACTGAATATTGTTATGTA-TAATGCAGTGAATTGTGAA
*
2837279 AATACTGAATATTGTTATGTATAATGCATTGAATTGTGAA
1 AATACTGAATATTGTTATGTATAATGCAGTGAATTGTGAA
*
2837319 ATTACTGAA
1 AATACTGAA
2837328 GTAAAGAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 21 0.50
40 21 0.50
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (40 bp):
AATACTGAATATTGTTATGTATAATGCAGTGAATTGTGAA
Found at i:2837574 original size:39 final size:41
Alignment explanation
Indices: 2837512--2837628 Score: 114
Period size: 45 Copynumber: 2.8 Consensus size: 41
2837502 TTACTGATCA
* * *
2837512 GGCAC-TTATGTGCCGACTACTGTTACTGTTAC-C-GATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTCAGATTC
2837550 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACAGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTAC---T-CAGATTC
** * *
2837595 AACACTTTGTGTGTTGAATACTGTCACTGTTACT
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACT
2837629 GTTACTGTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
38 5 0.08
39 24 0.37
42 1 0.02
44 1 0.02
45 34 0.52
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
GGCACTTTGTGTGTCGAATACTGTTACTGTTACTCAGATTC
Found at i:2837629 original size:6 final size:6
Alignment explanation
Indices: 2837613--2837666 Score: 81
Period size: 6 Copynumber: 8.8 Consensus size: 6
2837603 GTGTGTTGAA
* *
2837613 TACTGT CACTGT TACTGT TACTGT TACTGT TACCGT TACTGAT TACTGT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT
2837662 TACTG
1 TACTG
2837667 GTGTATTTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
6 37 0.86
7 6 0.14
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (6 bp):
TACTGT
Found at i:2837639 original size:51 final size:45
Alignment explanation
Indices: 2837529--2837633 Score: 165
Period size: 45 Copynumber: 2.3 Consensus size: 45
2837519 ATGTGCCGAC
* **
2837529 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGT
*
2837574 TACTGTTACTGTTACAGATTCAACACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGT
*
2837619 CACTGTTACTGTTAC
1 TACTGTTACTGTTAC
2837634 TGTTACTGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGT
Found at i:2841483 original size:41 final size:41
Alignment explanation
Indices: 2841438--2841635 Score: 288
Period size: 41 Copynumber: 4.8 Consensus size: 41
2841428 TTGTATATAA
** * * *
2841438 CACCGGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* * *
2841479 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
*
2841520 CACCGGTATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
*
2841561 CACCGGCATAAAGCCTGCTAGACATAAAGCCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
**
2841602 CACCGGCATAAAGCCTGCTAGGCACCAAGCCTGA
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGA
2841636 ACTTACAAAA
Statistics
Matches: 140, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 140 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (41 bp):
CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:2841575 original size:82 final size:82
Alignment explanation
Indices: 2841438--2841635 Score: 324
Period size: 82 Copynumber: 2.4 Consensus size: 82
2841428 TTGTATATAA
* *
2841438 CACCGGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTTCACCGGCACAAAGCCTGCTAGACA
1 CACCGGCATAAAGCCTGCTAGGCACCAAGCCTGATACAATTCACCGGCACAAAGCCTGCTAGACA
*
2841503 TAAAGTCTGATATAATT
66 TAAAGCCTGATATAATT
* ** * *
2841520 CACCGGTATAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACCGGCATAAAGCCTGCTAGACA
1 CACCGGCATAAAGCCTGCTAGGCACCAAGCCTGATACAATTCACCGGCACAAAGCCTGCTAGACA
2841585 TAAAGCCTGATATAATT
66 TAAAGCCTGATATAATT
2841602 CACCGGCATAAAGCCTGCTAGGCACCAAGCCTGA
1 CACCGGCATAAAGCCTGCTAGGCACCAAGCCTGA
2841636 ACTTACAAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 105 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (82 bp):
CACCGGCATAAAGCCTGCTAGGCACCAAGCCTGATACAATTCACCGGCACAAAGCCTGCTAGACA
TAAAGCCTGATATAATT
Found at i:2842840 original size:41 final size:41
Alignment explanation
Indices: 2842746--2842900 Score: 127
Period size: 41 Copynumber: 3.7 Consensus size: 41
2842736 GGCTCGTACA
** *
2842746 ATGCCAATGTCCCAGAC-GTGGTCTTACATGTAATCACATAAG
1 ATGCCAATGTCCCAGACAG-GGTCTTACA-CAAATCAAATAAG
* *
2842788 ATGCCACTGTCCCAGACAGGGTCTTACACAAATCAAATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACAAATCAAATAAG
* * * ** *
2842829 ATGCTAATGTCCCGGACATGGTCTTACACGTATACACAAGTCA-
1 ATGCCAATGTCCCAGACAGGGTCTTACACAAAT-CA-AA-TAAG
*
2842872 ATGCCAACGTCCCAGAC-GTGGTCTTACAC
1 ATGCCAATGTCCCAGACAG-GGTCTTACAC
2842901 GAAAATACAT
Statistics
Matches: 91, Mismatches: 17, Indels: 9
0.78 0.15 0.08
Matches are distributed among these distances:
41 36 0.40
42 27 0.30
43 27 0.30
44 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (41 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACAAATCAAATAAG
Found at i:2843667 original size:24 final size:24
Alignment explanation
Indices: 2843635--2843685 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
2843625 TTGGTTTTAT
* *
2843635 TATTATTATAATAACTTTATAATA
1 TATTATTATAAAAACTATATAATA
2843659 TATTATTATAAAAACTATATAATA
1 TATTATTATAAAAACTATATAATA
2843683 TAT
1 TAT
2843686 ACATAGTGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTATTATAAAAACTATATAATA
Found at i:2843882 original size:14 final size:15
Alignment explanation
Indices: 2843863--2843891 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2843853 TCACGAAACT
2843863 TTCACACAT-ATAAA
1 TTCACACATAATAAA
2843877 TTCACACATAATAAA
1 TTCACACATAATAAA
2843892 CACAGAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:2852107 original size:14 final size:14
Alignment explanation
Indices: 2852088--2852126 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2852078 TGTTATTGTG
2852088 TTTTAGTTTTAGAC
1 TTTTAGTTTTAGAC
*
2852102 TTTTAGTTTTAGAT
1 TTTTAGTTTTAGAC
*
2852116 TTTTATTTTTA
1 TTTTAGTTTTA
2852127 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.67
Consensus pattern (14 bp):
TTTTAGTTTTAGAC
Found at i:2852169 original size:5 final size:5
Alignment explanation
Indices: 2852160--2852193 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
2852150 TATGATTGAG
* *
2852160 TTGGG TTGGG TTGGA TTGGA TTGGA TTGGA TTGG
1 TTGGA TTGGA TTGGA TTGGA TTGGA TTGGA TTGG
2852194 GTACTTGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.12, C:0.00, G:0.47, T:0.41
Consensus pattern (5 bp):
TTGGA
Found at i:2855628 original size:18 final size:18
Alignment explanation
Indices: 2855587--2855622 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2855577 AACAATTAAA
2855587 TAAA-TTGGAAATAAGAT
1 TAAATTTGGAAATAAGAT
2855604 TAAATTTGGAAATAA-AT
1 TAAATTTGGAAATAAGAT
2855621 TA
1 TA
2855623 GGATTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (18 bp):
TAAATTTGGAAATAAGAT
Found at i:2857211 original size:4 final size:4
Alignment explanation
Indices: 2857204--2857245 Score: 66
Period size: 4 Copynumber: 10.0 Consensus size: 4
2857194 AAATTGAGCC
2857204 TTTA TTTA TTTA TTTA TTTCA TTTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTT-A -TTTA TTTA TTTA TTTA TTTA
2857246 CAAGCAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 31 0.86
5 2 0.06
6 3 0.08
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:2857231 original size:18 final size:17
Alignment explanation
Indices: 2857204--2857244 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
2857194 AAATTGAGCC
2857204 TTTA-TTTATTTATTTA
1 TTTATTTTATTTATTTA
2857220 TTTCATTTTATTTATTTA
1 TTT-ATTTTATTTATTTA
2857238 TTTATTT
1 TTTATTT
2857245 ACAAGCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.13
17 5 0.22
18 15 0.65
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTATTTATTTA
Found at i:2866852 original size:501 final size:502
Alignment explanation
Indices: 2865817--2866876 Score: 1881
Period size: 501 Copynumber: 2.1 Consensus size: 502
2865807 TAATCCTACA
* ** *
2865817 ATATTGATGCCCTAAATGAAGGTTAGAGCCCCCCTTCACATCATAATTATTTCTATCCTTGGAAA
1 ATATTGTTGCCCTAAATGAAGGTTAGAG-CCCCCTTCACATGGTAATTATTTCTATCATTGGAAA
* * *
2865882 GTGACTGGTTATGCATTTTCCAATGCTGCTTGTCATTGTATTTGGTTTGCTCTAAATGAAGGTTA
65 GTGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTA
* * *
2865947 GTGCTATCATAATTATTCCTATCCTTGTAAATTGACTTATTTTTCATTTGCGCGTACTGCTTGTC
130 GTGCCATCATAATTATTCCTATCCTTGTAAATTGACTGATTTTTCATTTGCGCGTAATGCTTGTC
* * *
2866012 TTTGCGTTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACATCCTGTATAT
195 ATTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACATCCTGTATAA
*
2866077 AACTTGAGTAATGCTAAGGTACAAAGAAGTCTGAGTGGTTGTGTGAAAATGTCTTCCTTTTTCCA
260 AACTTGAGTAATGCTAAGGTACAAAGAAGTCTGAGTCGTTGTGTGAAAATGTCTTCCTTTTTCCA
*
2866142 AGATGAATGAGTGGACTCAGTTTTGTTAGGACTATATGTCGTGCTCTTCTTGTTGTTTTGAATGG
325 AGATGAATGAGTGGACTCAGTTTTGTCAGGACTATATGTCGTGCTCTTCTTGTTGTTTTGAATGG
2866207 GTACGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTT
390 GTACGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTT
2866272 TAACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAT
455 TAACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAT
2866320 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTCTATCATTGGAAAG
1 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTCTATCATTGGAAAG
* *
2866385 TGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAATGTTGG
66 TGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTAG
2866450 TGCCATCATAATTATTCCTATCCTTGTAAATTGACTGATTTTTCATTTGC-CAGTAATGCTTGTC
131 TGCCATCATAATTATTCCTATCCTTGTAAATTGACTGATTTTTCATTTGCGC-GTAATGCTTGTC
*
2866514 ATTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACTTCCTGTATAA
195 ATTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACATCCTGTATAA
*
2866579 AACTTGAGTAATGCTAAGGTACAAAGAAGTC-GAGTCGTTGTGTGAAAATGTGTTCCTTTTTCCA
260 AACTTGAGTAATGCTAAGGTACAAAGAAGTCTGAGTCGTTGTGTGAAAATGTCTTCCTTTTTCCA
*
2866643 AGATGAATGAGTGGACTCAGTTTTGTCAGGACTATGTGTCGTGCTCTTCTTGTTGTTTTGAATGG
325 AGATGAATGAGTGGACTCAGTTTTGTCAGGACTATATGTCGTGCTCTTCTTGTTGTTTTGAATGG
* *
2866708 GTACGAGGCTCCTAGCACCTTTAGGGAACTGGAGCTGAAGTTCGTTAGCTTTGGGCAGAGAATTT
390 GTACGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTT
2866773 TAACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAT
455 TAACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAT
*
2866821 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCATATGGTAATTATTTCTATC
1 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTCTATC
2866877 CTTGAACTTC
Statistics
Matches: 533, Mismatches: 23, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
501 261 0.49
502 245 0.46
503 27 0.05
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (502 bp):
ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTCTATCATTGGAAAG
TGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTAG
TGCCATCATAATTATTCCTATCCTTGTAAATTGACTGATTTTTCATTTGCGCGTAATGCTTGTCA
TTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACATCCTGTATAAA
ACTTGAGTAATGCTAAGGTACAAAGAAGTCTGAGTCGTTGTGTGAAAATGTCTTCCTTTTTCCAA
GATGAATGAGTGGACTCAGTTTTGTCAGGACTATATGTCGTGCTCTTCTTGTTGTTTTGAATGGG
TACGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTTT
AACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAT
Found at i:2867304 original size:96 final size:96
Alignment explanation
Indices: 2867135--2867308 Score: 240
Period size: 96 Copynumber: 1.8 Consensus size: 96
2867125 CCCGTTCACA
* * * *
2867135 TCATAATTATTTCTATCCTTGGAAAGTGACTGATTAAGCATTTGCCAATGCTGCTTGTCATTATA
1 TCATAATTAATCCTATCCTTGGAAAGTGACTGATTAAGCATTTGCCAATACTGCTTGTCATTACA
2867200 TTTGGTTTGCTCTGAATGAAGGTTGGTGCCC
66 TTTGGTTTGCTCTGAATGAAGGTTGGTGCCC
* * *** * *
2867231 TCATAATTAATCCTATCCTTGTAAATTGACTGATTTTTCATTTGCCAGTACTGCTTGTCATTGCA
1 TCATAATTAATCCTATCCTTGGAAAGTGACTGATTAAGCATTTGCCAATACTGCTTGTCATTACA
*
2867296 TTTTGTTTGCTCT
66 TTTGGTTTGCTCT
2867309 TGTTGTCAGT
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 66 1.00
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (96 bp):
TCATAATTAATCCTATCCTTGGAAAGTGACTGATTAAGCATTTGCCAATACTGCTTGTCATTACA
TTTGGTTTGCTCTGAATGAAGGTTGGTGCCC
Found at i:2869799 original size:29 final size:29
Alignment explanation
Indices: 2869750--2869849 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
2869740 AAAAATAAAA
* *
2869750 ATTTACTAAAACATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
*
2869779 ATTGACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
2869808 ATTTACCAAAATATATA-AAC-TTTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTTT
2869836 ATTTACCAAAATAT
1 ATTTACCAAAATAT
2869850 ATAAAAAACA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
28 22 0.33
29 42 0.64
30 2 0.03
ACGTcount: A:0.38, C:0.13, G:0.01, T:0.48
Consensus pattern (29 bp):
ATTTACCAAAATATTACAACTTTTTTTTT
Found at i:2870457 original size:18 final size:19
Alignment explanation
Indices: 2870406--2870466 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
2870396 CTGATATTTC
*
2870406 TATTAATTTAAAATA-TAGT
1 TATTAAATTAAAATAGTA-T
* *
2870425 TATTAAATGAGAATAGT-T
1 TATTAAATTAAAATAGTAT
*
2870443 TATTAAATTAAAATAGAAT
1 TATTAAATTAAAATAGTAT
2870462 TATTA
1 TATTA
2870467 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 15 0.44
19 18 0.53
20 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (19 bp):
TATTAAATTAAAATAGTAT
Found at i:2871003 original size:27 final size:26
Alignment explanation
Indices: 2870965--2871021 Score: 96
Period size: 27 Copynumber: 2.2 Consensus size: 26
2870955 TTTTAATCCT
2870965 TTGGCACATTGGTGCCGCCAATGGCA
1 TTGGCACATTGGTGCCGCCAATGGCA
*
2870991 TTGGCACCTTTGGTGCCGCCAATGGCA
1 TTGGCA-CATTGGTGCCGCCAATGGCA
2871018 TTGG
1 TTGG
2871022 GGTGATCAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.16, C:0.26, G:0.32, T:0.26
Consensus pattern (26 bp):
TTGGCACATTGGTGCCGCCAATGGCA
Found at i:2871110 original size:28 final size:29
Alignment explanation
Indices: 2871058--2871134 Score: 122
Period size: 28 Copynumber: 2.7 Consensus size: 29
2871048 TTATTTTTAT
2871058 TTTATATATTTTGGTAAATAAAAAAAAAAG
1 TTTATATATTTTGGTAAAT-AAAAAAAAAG
2871088 TTTATATATTTTGGTAAAT-AAAAAAAAG
1 TTTATATATTTTGGTAAATAAAAAAAAAG
2871116 TTGTA-ATATTTTGGTAAAT
1 TT-TATATATTTTGGTAAAT
2871135 TTTTATTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
28 25 0.54
29 2 0.04
30 19 0.41
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.42
Consensus pattern (29 bp):
TTTATATATTTTGGTAAATAAAAAAAAAG
Found at i:2888377 original size:17 final size:17
Alignment explanation
Indices: 2888355--2888393 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2888345 ATTACAATCA
*
2888355 ATTAAATCTTTTGACCG
1 ATTAAACCTTTTGACCG
2888372 ATTAAACCTTTTGACCG
1 ATTAAACCTTTTGACCG
2888389 -TTAAA
1 ATTAAA
2888394 GTAAACGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (17 bp):
ATTAAACCTTTTGACCG
Found at i:2889029 original size:20 final size:19
Alignment explanation
Indices: 2888985--2889029 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2888975 TTTTACTTTT
* *
2888985 AAAAAATATATAATATGAA
1 AAAAAATAAATAAAATGAA
2889004 ATAAAAATAAATTAAAATGAA
1 A-AAAAATAAA-TAAAATGAA
2889025 AAAAA
1 AAAAA
2889030 GAAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 12 0.55
21 9 0.41
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (19 bp):
AAAAAATAAATAAAATGAA
Found at i:2889862 original size:21 final size:22
Alignment explanation
Indices: 2889838--2889885 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
2889828 TAACTTAATT
*
2889838 TTTAAAATG-AAAATATTTAAA
1 TTTAAAATGTAAAATATATAAA
*
2889859 TTT-AACTGTAAAATATATAAA
1 TTTAAAATGTAAAATATATAAA
2889880 TATTAA
1 T-TTAA
2889886 TATAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.18
21 15 0.68
22 2 0.09
23 1 0.05
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (22 bp):
TTTAAAATGTAAAATATATAAA
Found at i:2896678 original size:96 final size:96
Alignment explanation
Indices: 2896509--2896682 Score: 233
Period size: 96 Copynumber: 1.8 Consensus size: 96
2896499 CCCGTTCACA
* * * *
2896509 TCATAATTATTTCTATCCTTGGAAAGTGACTGTTTAAGCATTTGCCAATGCTGCTTGTCATTATA
1 TCATAATTAATCCTATCCTTGGAAAGTGACTGTTTAAGCATTTGCCAATACTGCTTGTCATTACA
2896574 TTTGGTTTGCTCTGAATGAAGGTTGGTGCCC
66 TTTGGTTTGCTCTGAATGAAGGTTGGTGCCC
* * ** * *
2896605 TCATAATTAATCCTATCCTTGTAAATTGACTGATTT-TTCATTTGCCAGTACTGCTTGTCATTGC
1 TCATAATTAATCCTATCCTTGGAAAGTGACTG-TTTAAGCATTTGCCAATACTGCTTGTCATTAC
*
2896669 ATTTTGTTTGCTCT
65 ATTTGGTTTGCTCT
2896683 TGTTGTCAGT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
96 63 0.95
97 3 0.05
ACGTcount: A:0.21, C:0.18, G:0.17, T:0.44
Consensus pattern (96 bp):
TCATAATTAATCCTATCCTTGGAAAGTGACTGTTTAAGCATTTGCCAATACTGCTTGTCATTACA
TTTGGTTTGCTCTGAATGAAGGTTGGTGCCC
Found at i:2898818 original size:3 final size:3
Alignment explanation
Indices: 2898810--2898840 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2898800 TTTTACTATC
2898810 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2898841 CTACTTATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2898950 original size:26 final size:24
Alignment explanation
Indices: 2898921--2898979 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
2898911 CTACTTTTTT
2898921 ATATATAC-TTTATAATTTATATATAC
1 ATATATACATTT-TAA-TT-TATATAC
* *
2898947 ATATACACATTTTAATTTATGTAC
1 ATATATACATTTTAATTTATATAC
2898971 ATATATACA
1 ATATATACA
2898980 CACATTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 14 0.48
25 2 0.07
26 10 0.34
27 3 0.10
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (24 bp):
ATATATACATTTTAATTTATATAC
Found at i:2898980 original size:26 final size:27
Alignment explanation
Indices: 2898920--2898981 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
2898910 CCTACTTTTT
* *
2898920 TATATATAC-TTTATAATTTATATATA
1 TATATACACATTTATAATTTATATACA
* *
2898946 CATATACACATTT-TAATTTATGTACA
1 TATATACACATTTATAATTTATATACA
2898972 TATATACACA
1 TATATACACA
2898982 CATTTTCATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 27 0.90
27 3 0.10
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (27 bp):
TATATACACATTTATAATTTATATACA
Found at i:2899088 original size:24 final size:24
Alignment explanation
Indices: 2899059--2899135 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
2899049 TTTTCTTATG
* **
2899059 TATATATTTTATATTATATATATT
1 TATATATATTATACAATATATATT
* *
2899083 TTTATATATTCTACAATATATATT
1 TATATATATTATACAATATATATT
* * * *
2899107 TATATACATAATA-AATACATATC
1 TATATATATTATACAATATATATT
2899130 TATATA
1 TATATA
2899136 CGTTCTTGAT
Statistics
Matches: 42, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 14 0.33
24 28 0.67
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (24 bp):
TATATATATTATACAATATATATT
Found at i:2901502 original size:59 final size:59
Alignment explanation
Indices: 2901410--2901526 Score: 234
Period size: 59 Copynumber: 2.0 Consensus size: 59
2901400 AAGAATGCCG
2901410 AATTCAAATTTAGAACAAAGTAAACCTTCAAATCACTTGTGCTCGGTTTCATAAGAGTC
1 AATTCAAATTTAGAACAAAGTAAACCTTCAAATCACTTGTGCTCGGTTTCATAAGAGTC
2901469 AATTCAAATTTAGAACAAAGTAAACCTTCAAATCACTTGTGCTCGGTTTCATAAGAGT
1 AATTCAAATTTAGAACAAAGTAAACCTTCAAATCACTTGTGCTCGGTTTCATAAGAGT
2901527 TTAACTAAGC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.31
Consensus pattern (59 bp):
AATTCAAATTTAGAACAAAGTAAACCTTCAAATCACTTGTGCTCGGTTTCATAAGAGTC
Found at i:2903088 original size:17 final size:17
Alignment explanation
Indices: 2903066--2903099 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2903056 ATCCACTAAT
*
2903066 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2903083 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2903100 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:2907727 original size:17 final size:17
Alignment explanation
Indices: 2907705--2907738 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2907695 ATCCACTAAT
*
2907705 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2907722 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2907739 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:2916918 original size:28 final size:28
Alignment explanation
Indices: 2916878--2916932 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
2916868 ACCCGAATAG
2916878 GTACTCTATTTTTCTTGTTTGCTTTTGT
1 GTACTCTATTTTTCTTGTTTGCTTTTGT
2916906 GTACTCTATTTTTCTTGTTTGCTTTTG
1 GTACTCTATTTTTCTTGTTTGCTTTTG
2916933 CTTTGTACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.07, C:0.15, G:0.15, T:0.64
Consensus pattern (28 bp):
GTACTCTATTTTTCTTGTTTGCTTTTGT
Found at i:2919347 original size:26 final size:26
Alignment explanation
Indices: 2919313--2919362 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
2919303 GAATATAAAG
2919313 GGGGTTGCTAAGTGCTGATTCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCAA
2919339 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
2919363 GACTCATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.16, C:0.24, G:0.32, T:0.28
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCAA
Found at i:2919383 original size:33 final size:33
Alignment explanation
Indices: 2919341--2919576 Score: 108
Period size: 33 Copynumber: 6.7 Consensus size: 33
2919331 TTCCCCAAGG
2919341 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* *
2919374 GGTTGCTAAGTGCTGATTCCACCGTATCTTTGACTATAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-C--T--C-AT--TGGT
*
2919417 GGTTGCTATGTGCTGATTCCCC-A---A--GG-
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* * * * *
2919443 AGTTACTAAGTGTTGATTCCCCAAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* *
2919476 GGTTGCTAAGTGCTGATTCCACCGTATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-C--T-CAT-TG---GT
* * *
2919519 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
*
2919552 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
2919577 TAACGGTTAA
Statistics
Matches: 156, Mismatches: 19, Indels: 55
0.68 0.08 0.24
Matches are distributed among these distances:
26 18 0.12
27 3 0.02
30 1 0.01
31 1 0.01
32 2 0.01
33 57 0.37
34 9 0.06
35 2 0.01
36 3 0.02
37 1 0.01
38 3 0.02
39 2 0.01
40 4 0.03
41 3 0.02
42 5 0.03
43 42 0.27
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
Found at i:2919482 original size:102 final size:102
Alignment explanation
Indices: 2919301--2919540 Score: 392
Period size: 102 Copynumber: 2.4 Consensus size: 102
2919291 CCAGAGTACA
* * * *
2919301 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAC
1 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCAAGGAGTTACTAAGTGCTGATTCCCCAAA
2919366 TCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
66 TCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
* * *
2919403 TTGACTATAAAGGGGGTTGCTATGTGCTGATTCCCCAAGGAGTTACTAAGTGTTGATTCCCCAAA
1 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCAAGGAGTTACTAAGTGCTGATTCCCCAAA
2919468 TCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
66 TCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
*
2919505 TTGAATGTGAAA-GGGGTTGCTAAGTGCTGATTCCCC
1 TTGAATAT-AAAGGGGGTTGCTAAGTGCTGATTCCCC
2919541 GAATTACTGG
Statistics
Matches: 127, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
102 124 0.98
103 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (102 bp):
TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCAAGGAGTTACTAAGTGCTGATTCCCCAAA
TCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
Found at i:2922642 original size:19 final size:18
Alignment explanation
Indices: 2922600--2922654 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
2922590 AAACAAAAAC
*
2922600 AAAAA-AAAATGAAAAATG
1 AAAAAGAAAA-GAAAAAGG
*
2922618 -AAAAGAAGAGAAAAGAGG
1 AAAAAGAAAAGAAAA-AGG
2922636 AAAAAGAAAAGAAAAAGG
1 AAAAAGAAAAGAAAAAGG
2922654 A
1 A
2922655 GAGGCCAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 9 0.29
18 9 0.29
19 13 0.42
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGG
Found at i:2923002 original size:45 final size:44
Alignment explanation
Indices: 2922926--2923014 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 44
2922916 TTCCATTTTA
* *
2922926 TTCATTTTTATTTTGGCAAAATATGCCATCTTGATTAATTTATT
1 TTCATTTTTATCTTAGCAAAATATGCCATCTTGATTAATTTATT
* *
2922970 TTCATTTTGTATCTTAGCAAAATTTGCTATCTTGATTAATTTATT
1 TTCATTTT-TATCTTAGCAAAATATGCCATCTTGATTAATTTATT
2923015 CATTTCGAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 8 0.20
45 32 0.80
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (44 bp):
TTCATTTTTATCTTAGCAAAATATGCCATCTTGATTAATTTATT
Found at i:2923171 original size:109 final size:109
Alignment explanation
Indices: 2922978--2923179 Score: 323
Period size: 109 Copynumber: 1.9 Consensus size: 109
2922968 TTTTCATTTT
* *
2922978 GTATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTTTACTCTCAATAAAATT
1 GTATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAACCTTACTCTCAATAAAATT
* * *
2923043 CTATCTTATTCATTGTGATAATCTTTTTTCGTCTTATTCAGTTC
66 CCATCTTATCCATTGTGATAATATTTTTTCGTCTTATTCAGTTC
* *
2923087 GTATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTTGAACCTTATTCTCAATAAAATT
1 GTATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAACCTTACTCTCAATAAAATT
* *
2923152 CCATCTTGTCCATTTTGATAATATTTTT
66 CCATCTTATCCATTGTGATAATATTTTT
2923180 CAAGCATTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
109 84 1.00
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (109 bp):
GTATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAACCTTACTCTCAATAAAATT
CCATCTTATCCATTGTGATAATATTTTTTCGTCTTATTCAGTTC
Found at i:2923875 original size:16 final size:16
Alignment explanation
Indices: 2923849--2923885 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
2923839 TGACATTCAG
2923849 CATTC-ATGCAAATAT
1 CATTCAATGCAAATAT
2923864 CATTCAATGCAAATAT
1 CATTCAATGCAAATAT
2923880 CATTCA
1 CATTCA
2923886 TACACGTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (16 bp):
CATTCAATGCAAATAT
Found at i:2924648 original size:4 final size:4
Alignment explanation
Indices: 2924639--2924664 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2924629 TTATGTAATT
2924639 CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CA
2924665 GACAGACAGA
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:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:2928645 original size:14 final size:14
Alignment explanation
Indices: 2928628--2928659 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2928618 GAGCTTTAGG
2928628 AATGGAAACACTGA
1 AATGGAAACACTGA
2928642 AATGGAAACACTGA
1 AATGGAAACACTGA
2928656 AATG
1 AATG
2928660 ACTCCAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (14 bp):
AATGGAAACACTGA
Found at i:2931898 original size:10 final size:10
Alignment explanation
Indices: 2931881--2932047 Score: 68
Period size: 10 Copynumber: 17.1 Consensus size: 10
2931871 TTCCTTCCCA
2931881 CTTC-TTCTT
1 CTTCTTTCTT
2931890 CTTCTTTCTT
1 CTTCTTTCTT
* *
2931900 TTTTTTTCTT
1 CTTCTTTCTT
* *
2931910 CTCCGTTCCTT
1 CTTC-TTTCTT
* *
2931921 TTTTTTTCCTT
1 CTTCTTT-CTT
2931932 CTT-TTTCTTT
1 CTTCTTTC-TT
*
2931942 CTGTTTTTCTT
1 CT-TCTTTCTT
*
2931953 CTCCTTTCCTT
1 CTTCTTT-CTT
2931964 -TTCTTTC--
1 CTTCTTTCTT
*
2931971 CTTTTTTC-T
1 CTTCTTTCTT
*
2931980 -TTCTTTCCT
1 CTTCTTTCTT
2931989 C-TCTTTCCTT
1 CTTCTTT-CTT
2931999 -TTCTTTCTT
1 CTTCTTTCTT
*
2932008 TTTCTTTC-T
1 CTTCTTTCTT
2932017 -TTCTTTCTT
1 CTTCTTTCTT
* *
2932026 CTCCTTTCCT
1 CTTCTTTCTT
*
2932036 CTCCTTCTCTT
1 CTTCTT-TCTT
2932047 C
1 C
2932048 CCCCCCACAC
Statistics
Matches: 121, Mismatches: 20, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
8 19 0.16
9 17 0.14
10 58 0.48
11 23 0.19
12 4 0.03
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (10 bp):
CTTCTTTCTT
Found at i:2931923 original size:21 final size:21
Alignment explanation
Indices: 2931885--2931965 Score: 87
Period size: 20 Copynumber: 3.9 Consensus size: 21
2931875 TTCCCACTTC
*
2931885 TTCTTCTTCTTT-CTTTTTTT
1 TTCTTCTCCTTTCCTTTTTTT
*
2931905 TTCTTCTCCGTTCCTTTTTTT
1 TTCTTCTCCTTTCCTTTTTTT
*
2931926 TTCCTTCT--TTTTCTTTCTGTTT
1 TT-CTTCTCCTTTCCTTT-T-TTT
2931948 TTCTTCTCCTTTCCTTTT
1 TTCTTCTCCTTTCCTTTT
2931966 CTTTCCTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
20 16 0.32
21 16 0.32
22 11 0.22
23 7 0.14
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (21 bp):
TTCTTCTCCTTTCCTTTTTTT
Found at i:2931926 original size:22 final size:22
Alignment explanation
Indices: 2931885--2932035 Score: 87
Period size: 22 Copynumber: 6.7 Consensus size: 22
2931875 TTCCCACTTC
*
2931885 TTCTTCTTCTTT-C-TTTTTTT
1 TTCTTCTCCTTTCCTTTTTTTT
*
2931905 TTCTTCTCCGTTCCTTTTTTTT
1 TTCTTCTCCTTTCCTTTTTTTT
* * *
2931927 TCCTTCT--TTTTCTTTCTGTTT
1 TTCTTCTCCTTTCCTTT-TTTTT
2931948 TTCTTCTCCTTTCCTTTTCTTTCCT
1 TTCTTCTCCTTTCCTTTT-TTT--T
* * *
2931973 TTTTTCTTTCTTTCCTCTCTTTCCTT
1 TTCTTC-TCCTTTCCT-T-TTT-TTT
* * *
2931999 TTCTT-TCTTTTTCTTTCTTTCT
1 TTCTTCTCCTTTCCTTT-TTTTT
2932021 TTCTTCTCCTTTCCT
1 TTCTTCTCCTTTCCT
2932036 CTCCTTCTCT
Statistics
Matches: 97, Mismatches: 20, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
20 16 0.16
21 11 0.11
22 21 0.22
23 19 0.20
24 6 0.06
25 6 0.06
26 13 0.13
27 2 0.02
28 3 0.03
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.70
Consensus pattern (22 bp):
TTCTTCTCCTTTCCTTTTTTTT
Found at i:2931933 original size:48 final size:44
Alignment explanation
Indices: 2931881--2931986 Score: 119
Period size: 43 Copynumber: 2.4 Consensus size: 44
2931871 TTCCTTCCCA
* *
2931881 CTTCTTCTTCTTCTTTCTTTTTTTTTCTTCTCCGTTCCTTTTTTTTTC
1 CTTCTT-TTCTTCTTTC--TGTTTTTCTTCTCCGTTCC-TTTTCTTTC
*
2931929 CTTC-TTT-TTCTTTCTGTTTTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTCTTCTTTCTGTTTTTCTTCTCCGTTCCTTTTCTTTC
2931971 CTT-TTTTCTTTCTTTC
1 CTTCTTTTC-TTCTTTC
2931987 CTCTCTTTCC
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
42 14 0.27
43 17 0.33
44 7 0.13
45 7 0.13
46 2 0.04
47 1 0.02
48 4 0.08
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (44 bp):
CTTCTTTTCTTCTTTCTGTTTTTCTTCTCCGTTCCTTTTCTTTC
Found at i:2931948 original size:12 final size:12
Alignment explanation
Indices: 2931915--2932032 Score: 72
Period size: 12 Copynumber: 9.6 Consensus size: 12
2931905 TTCTTCTCCG
2931915 TTCCTTTTTT-T
1 TTCCTTTTTTCT
2931926 TTCCTTCTTTTTCT
1 TTCC-T-TTTTTCT
2931940 TT-CTGTTTTTCT
1 TTCCT-TTTTTCT
2931952 TCTCCTTTCCTTTTCT
1 T-TCC-TT--TTTTCT
2931968 TTCCTTTTTTCT
1 TTCCTTTTTTCT
*
2931980 TT-CTTTCCTCTCT
1 TTCCTTT--TTTCT
2931993 TTCC--TTTTCT
1 TTCCTTTTTTCT
2932003 TT-C-TTTTTCT
1 TTCCTTTTTTCT
2932013 TT-CTTTCTTTCT
1 TTCCTTT-TTTCT
2932025 TCTCCTTT
1 T-TCCTTT
2932033 CCTCTCCTTC
Statistics
Matches: 88, Mismatches: 3, Indels: 29
0.73 0.03 0.24
Matches are distributed among these distances:
9 1 0.01
10 15 0.17
11 10 0.11
12 25 0.28
13 14 0.16
14 12 0.14
15 4 0.05
16 7 0.08
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (12 bp):
TTCCTTTTTTCT
Found at i:2931964 original size:5 final size:5
Alignment explanation
Indices: 2931954--2932041 Score: 57
Period size: 5 Copynumber: 19.0 Consensus size: 5
2931944 GTTTTTCTTC
* *
2931954 TCCTT TCCTT TTCTT TCCTT T--TT T-CTT T-CTT TCCTC T-CTT TCCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
* * * *
2931999 TTCTT TCTTT TTCTT T-CTT T-CTT T-CTT CTCCTT TCCTC TCCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT -TCCTT TCCTT TCCTT
2932042 CTCTTCCCCC
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
3 3 0.04
4 21 0.31
5 40 0.60
6 3 0.04
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (5 bp):
TCCTT
Found at i:2931966 original size:28 final size:26
Alignment explanation
Indices: 2931915--2932008 Score: 99
Period size: 28 Copynumber: 3.7 Consensus size: 26
2931905 TTCTTCTCCG
* *
2931915 TTCCTTTTTT-TTTCCTTCTTTTTCT
1 TTCCTTTTTTCTTTCTTTCCTTTTCT
2931940 TT-CTGTTTTTCTTCTCCTTTCCTTTTCT
1 TTCCT-TTTTTCTT-T-CTTTCCTTTTCT
*
2931968 TTCCTTTTTTCTTTCTTTCC-TCTCT
1 TTCCTTTTTTCTTTCTTTCCTTTTCT
2931993 TTCC--TTTTCTTTCTTT
1 TTCCTTTTTTCTTTCTTT
2932009 TTCTTTCTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
23 12 0.20
24 2 0.03
25 15 0.25
26 8 0.13
27 2 0.03
28 20 0.33
29 2 0.03
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (26 bp):
TTCCTTTTTTCTTTCTTTCCTTTTCT
Found at i:2932007 original size:73 final size:73
Alignment explanation
Indices: 2931891--2932035 Score: 199
Period size: 73 Copynumber: 2.0 Consensus size: 73
2931881 CTTCTTCTTC
**
2931891 TTCTTTCTTTTTTTTTCTTCTCCGTTCCTTTTTTTTTCCTTCTTTTTCTTTCTGTT-TTTCTTCT
1 TTCTTTCTTTTTTTTTCTTCTCCGTTCCTTTCCTTTTCCTTCTTTTTCTTTCT-TTCTTTCTTCT
2931955 CCTTTCCTT
65 CCTTTCCTT
*
2931964 TTCTTTCCTTTTTTCTTTCTT-TCC--TCTCTTTCCTTTTCTTTCTTTTTCTTTCTTTCTTTCTT
1 TTCTTT-CTTTTTT-TTTCTTCTCCGTTC-CTTTCCTTTTCCTTCTTTTTCTTTCTTTCTTTCTT
2932026 CTCCTTTCCT
63 CTCCTTTCCT
2932036 CTCCTTCTCT
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
72 4 0.06
73 45 0.69
74 10 0.15
75 6 0.09
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.70
Consensus pattern (73 bp):
TTCTTTCTTTTTTTTTCTTCTCCGTTCCTTTCCTTTTCCTTCTTTTTCTTTCTTTCTTTCTTCTC
CTTTCCTT
Found at i:2932047 original size:5 final size:4
Alignment explanation
Indices: 2931891--2932025 Score: 65
Period size: 4 Copynumber: 33.2 Consensus size: 4
2931881 CTTCTTCTTC
* *
2931891 TTCT TTCT TT-T TT-T TTCT TCTCCGT TCCT TT-T TT-T TTCC TTC- TT-T
1 TTCT TTCT TTCT TTCT TTCT T-T-C-T TTCT TTCT TTCT TTCT TTCT TTCT
2931936 TTCT TTCT GTT-T TTCT TCTCCT TTCCTT TTCT TTCCT TT-T TTCT TTCT
1 TTCT TTCT -TTCT TTCT T-T-CT TT-C-T TTCT TT-CT TTCT TTCT TTCT
*
2931984 TTCCT CTCT TTCCTT TTCT TTC- TT-T TTCT TTCT TTCT TTCT T
1 TT-CT TTCT TT-C-T TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
2932026 CTCCTTTCCT
Statistics
Matches: 107, Mismatches: 5, Indels: 38
0.71 0.03 0.25
Matches are distributed among these distances:
3 25 0.23
4 52 0.49
5 18 0.17
6 10 0.09
7 2 0.02
ACGTcount: A:0.00, C:0.27, G:0.01, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:2932114 original size:27 final size:27
Alignment explanation
Indices: 2932084--2932155 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
2932074 ATTATTTGGG
*
2932084 CAGTGCCGCCTATGGCAGGGGCACCAT
1 CAGTGCCGCCTATGGCAGGGGCACAAT
* * **
2932111 CAGTGCCGCCTCTGCCATTGGCACAAT
1 CAGTGCCGCCTATGGCAGGGGCACAAT
**
2932138 TGGTGCCGCCTATGGCAG
1 CAGTGCCGCCTATGGCAG
2932156 CCCCTCCACC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.17, C:0.33, G:0.31, T:0.19
Consensus pattern (27 bp):
CAGTGCCGCCTATGGCAGGGGCACAAT
Found at i:2934005 original size:152 final size:151
Alignment explanation
Indices: 2933770--2934303 Score: 531
Period size: 152 Copynumber: 3.6 Consensus size: 151
2933760 AAAAATTAGT
* * * *
2933770 AAAAACCCTTATTTCAGCCATTTGTTCGTACTATTTTCCCGAATTATATTACTTTCAATAAAAAT
1 AAAAACCCTTATTCCAGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAAT
* * * *
2933835 AAATTACTTTCGTTTTTTATTTTACATTATTTTATTATATTATGTTTGAAGTGTATTAATTTAGT
66 ATATTATTTTTGTATTTTATTTTACATTATTTTATTATATTATGTTTGAA-TGTATTAATTTAGT
2933900 GTGTATTTTAAATAAATTTAAA
130 GTGTATTTTAAATAAATTTAAA
* *
2933922 AAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTTAATAAAAAT
1 AAAAACCCTTATTCCAGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAAT
* * **
2933987 ATATTATTTTTGTATTTTATTATT---TTATATTATT-TCAGTACATTT---TGTATTAA-TTAT
66 ATATTATTTTTGTATTTTATT-TTACATTATTTTATTAT-ATTATGTTTGAATGTATTAATTTA-
* * * * *
2934044 TTCTGAATTTTTAA-AAATTTAGTA
128 GTGTGTATTTTAAATAAATTTA-AA
* * * * * * *
2934068 AAACACCCTTACTT-CAGCCATTTGTTCGTATT-TTTTTCAGCATTTTATTACTTT--AGAAATA
1 AAAAACCCTTA-TTCCAGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAA
* ** * * * *
2934129 TCATATT-TTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTT
65 T-ATATTATTTTTGTATT-TTATTTTACATTATTTTATTATATTATGTTTG-AATGTATTAATTT
* *
2934193 AGTGAGTTTTTTAAATAAATTTAAA
127 AGTGTGTATTTTAAATAAATTTAAA
* * *
2934218 AAAAACCCTTATTCCTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAACAAT
1 AAAAACCCTTATTCCAGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAAT
2934283 ATATTATTTTAT-TATTTTATT
66 ATATTATTTT-TGTATTTTATT
2934304 ATTTTATATT
Statistics
Matches: 301, Mismatches: 58, Indels: 46
0.74 0.14 0.11
Matches are distributed among these distances:
143 14 0.05
144 10 0.03
145 29 0.10
146 59 0.20
147 2 0.01
149 3 0.01
150 56 0.19
151 29 0.10
152 86 0.29
153 13 0.04
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (151 bp):
AAAAACCCTTATTCCAGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAAT
ATATTATTTTTGTATTTTATTTTACATTATTTTATTATATTATGTTTGAATGTATTAATTTAGTG
TGTATTTTAAATAAATTTAAA
Found at i:2934297 original size:8 final size:8
Alignment explanation
Indices: 2934284--2934310 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
2934274 AATAACAATA
2934284 TATTATTT
1 TATTATTT
2934292 TATTATTT
1 TATTATTT
2934300 TATTATTT
1 TATTATTT
2934308 TAT
1 TAT
2934311 ATTATTTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TATTATTT
Found at i:2934301 original size:296 final size:298
Alignment explanation
Indices: 2933758--2934518 Score: 1020
Period size: 296 Copynumber: 2.5 Consensus size: 298
2933748 GCAAGTTCAA
* * * * * *
2933758 AAAAAAATTAGTAAAAACCCTTATTTCAGCCATTTGTTCGTACTATTTTCCCGAATTATATTACT
1 AAAAAATTTAGTAAAAACCCTTACTTCAGCCATTTGTTCGTACTTTTTTTCCGCATTTTATTACT
* ** * *
2933823 TTCAATAAAAAT-AAATTACTT-TCGTTTT-TTATTTTACATTATTTTATTATATTATGTTTGAA
66 TT--A-AAAAATCATATT--TTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAA
* * *
2933885 GTGTATTAATTTAGTGTGTATTTTAAATAAATTTAAAAAAAACCCTTATTCCTGCCATTTGCTCG
126 ATTTATTAATTTAGTGTGTTTTTTAAATAAATTTAAAAAAAACCCTTATTCCTGCCATTTGCTCG
*
2933950 TATTATTTTCCCGAATTTTATTACTTTTAATAAAAATATATTATTTTTGTATTTTATTATTTTAT
191 TATTATTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATTATTTTAT
*
2934015 ATTATTTCAGTAC-AT-TTTGTATTAATTATTTCTGAATTTTT
256 ATTATTTCAGTACTATATTTGTATTAATTATTTCTAAATTTTT
*
2934056 -AAAAATTTAGTAAAACACCCTTACTTCAGCCATTTGTTCGTA-TTTTTTTCAGCATTTTATTAC
1 AAAAAATTTAGTAAAA-ACCCTTACTTCAGCCATTTGTTCGTACTTTTTTTCCGCATTTTATTAC
*
2934119 TTTAGAAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
65 TTTA-AAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
* *
2934184 TATTAATTTAGTGAGTTTTTTAAATAAATTTAAAAAAAACCCTTATTCCTGCCCTTTGCTCGTAT
129 TATTAATTTAGTGTGTTTTTTAAATAAATTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTAT
*
2934249 TATTTTCCCGAATTTTATTACTTTCAATAACAATATATTATTTTAT-TATTTTATTATTTTATAT
194 TATTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTT-TGTATTTTATTATTTTATAT
2934313 TATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTT
258 TATTTCAGTAC--------T---ATATTTGTATTAATTATTTCTAAATTTTT
* ** *
2934365 AAAAAATGTAGTAAAAAATCTTACTTC-GACC-TTTGTTCGTATTTTTTTCTCCGCATTTTATTA
1 AAAAAATTTAGTAAAAACCCTTACTTCAG-CCATTTGTTCGTACTTTTTT-TCCGCATTTTATTA
2934428 CTTTAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
64 CTTTAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
* *
2934493 TTTTAATTTACTGTGTTTTTTAAATA
129 TATTAATTTAGTGTGTTTTTTAAATA
2934519 TACCATTTTT
Statistics
Matches: 411, Mismatches: 30, Indels: 33
0.87 0.06 0.07
Matches are distributed among these distances:
294 2 0.00
295 11 0.03
296 170 0.41
297 34 0.08
298 25 0.06
308 13 0.03
309 124 0.30
310 32 0.08
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.51
Consensus pattern (298 bp):
AAAAAATTTAGTAAAAACCCTTACTTCAGCCATTTGTTCGTACTTTTTTTCCGCATTTTATTACT
TTAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTA
TTAATTTAGTGTGTTTTTTAAATAAATTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTA
TTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATTATTTTATATTAT
TTCAGTACTATATTTGTATTAATTATTTCTAAATTTTT
Found at i:2934588 original size:17 final size:16
Alignment explanation
Indices: 2934566--2934605 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
2934556 ACAATTTCCG
2934566 TTTTTTTCTTTTCATA
1 TTTTTTTCTTTTCATA
**
2934582 TTTTTTTCTTAAACATA
1 TTTTTTTCTT-TTCATA
2934599 TTTTTTT
1 TTTTTTT
2934606 ATCTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTTCTTTTCATA
Found at i:2936698 original size:156 final size:153
Alignment explanation
Indices: 2936490--2937256 Score: 761
Period size: 156 Copynumber: 5.0 Consensus size: 153
2936480 AGTTCAAAAA
* * * * *
2936490 AAATTTAGT-AAAAACCCTTATTTCGGCCATTTATTCGTACTATTTTCTCGAATTTTATTACTTT
1 AAATTTAGTAAAAAACCCTTA-TTCTGCCCTTTGTTCGTATTATTTTCCCGAATTTTATTACTTT
* * * * *
2936554 CAATAAAAATAAATTACTTTCGTTTTTTATTATTTTACATTATTTTATTACATTATGTTTGAAGT
65 -AATAAAAATACATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
*
2936619 GTATTAATTTATGTGTTTTTTAAAT
129 TTATTAATTTATGTGTTTTTTAAAT
** *
2936644 AAATTTTTTAAAAAAACCCTTATTCCTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTT
1 AAATTTAGT-AAAAAACCCTTATT-CTGCCCTTTGTTCGTATTATTTTCCCGAATTTTATTAC-T
* * * * *
2936709 TTAATAAAAATATATTATTTTTGTATTTTATTATTTTATATTATTTCAGTA-A--AT-TTTG-TA
63 TTAATAAAAATACATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
* * **
2936769 TTAATT-ATTTCTG-AATTTTTAAA-
128 TTTATTAATTTATGTGTTTTTTAAAT
* * * * *
2936792 AAATTTAGTAAAACACTCTTACTT-TGGCCCTTTGTTCGTATTTTTTTTCCGCATTTTATTACTT
1 AAATTTAGTAAAAAACCCTTA-TTCT-GCCCTTTGTTCGTATTATTTTCCCGAATTTTATTACTT
*
2936856 TAA-AAAAAT-CA-TATTTTC-TAATTTTATTATTTTGCATTATTTTAGTACATTATGTTTGAAA
64 TAATAAAAATACATTATTTTCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
*
2936917 TTTATTAATTTAGTATGTTTTTTAAAT
128 TTTATTAATTTA-TGTGTTTTTTAAAT
* * *
2936944 AAATTTTA-AAAAAAACCCTTATTCCTGCCCTTTGCTCGTATTATTTTCCCGAATTTTTTTACTT
1 AAA-TTTAGTAAAAAACCCTTATT-CTGCCCTTTGTTCGTATTATTTTCCCGAATTTTATTACTT
* * * * *
2937008 TCAATAACAATATATTATTTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAA
64 T-AATAAAAATACATTA-TTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTG-A
* *
2937073 ATATTTTTATTAA-TTATTTCTAAATTTTTAAA-
126 A-A--TTTATTAATTTATGTGT---TTTTTAAAT
* * * *
2937105 AAATTTAGTAAAAAA-TCTTACTTC-GGCCTTTGTTCGTATTTTTTTCTCCGCATTTTATTACTT
1 AAATTTAGTAAAAAACCCTTA-TTCTGCCCTTTGTTCGTATTATTTTC-CCGAATTTTATTACTT
2937168 TAA-AAAAAT-CA-TATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
64 TAATAAAAATACATTATTTTCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
2937229 TTTATTAATTTACTGTGTTTTTTAAAT
128 TTTATTAATTTA-TGTGTTTTTTAAAT
2937256 A
1 A
2937257 TACCATTTTT
Statistics
Matches: 503, Mismatches: 71, Indels: 81
0.77 0.11 0.12
Matches are distributed among these distances:
142 1 0.00
143 30 0.06
144 2 0.00
145 6 0.01
146 8 0.02
147 46 0.09
148 15 0.03
149 12 0.02
150 15 0.03
151 23 0.05
152 54 0.11
153 13 0.03
154 15 0.03
155 44 0.09
156 89 0.18
157 43 0.09
158 8 0.02
159 25 0.05
160 27 0.05
161 19 0.04
162 8 0.02
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (153 bp):
AAATTTAGTAAAAAACCCTTATTCTGCCCTTTGTTCGTATTATTTTCCCGAATTTTATTACTTTA
ATAAAAATACATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
ATTAATTTATGTGTTTTTTAAAT
Found at i:2937189 original size:312 final size:298
Alignment explanation
Indices: 2936487--2937256 Score: 1098
Period size: 299 Copynumber: 2.5 Consensus size: 298
2936477 GCAAGTTCAA
* * * * * *
2936487 AAAAAATTTAGTAAAAACCCTTATTTCGGCCATTTATTCGTACTATTTTCT-CGAATTTTATTAC
1 AAAAAATTTAGTAAAAACTCTTACTTCGGCC-TTTGTTCGTATTTTTTTCTCCGCATTTTATTAC
* * * *
2936551 TTTCAATAAAAATAAATTACTTTCGT-TTTTTATTATTTTACATTATTTTATTACATTATGTTTG
65 TTT-AA-AAAAAT-CA-TATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTG
* * *
2936615 AAGTGTATTAATTTATGTGTTTTTTAAATAAATTTTTTAAAAAAACCCTTATTCCTGCCCTTTGC
125 AAATTTATTAATTTATGTGTTTTTTAAATAAATTTTTAAAAAAAACCCTTATTCCTGCCCTTTGC
*
2936680 TCGTATTATTTTCCCGAATTTTATTACTTTTAATAAAAATATATTATTTTTGTATTTTATTATTT
190 TCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATTATTT
*
2936745 TATATTATTTCAGTAAATTTTGTATTAATTATTTCTGAATTTTT
255 TATATTATTTCAGTAAATTTTGTATTAATTATTTCTAAATTTTT
*
2936789 AAAAAATTTAGTAAAACACTCTTACTTTGGCCCTTTGTTCGTATTTTTTT-TCCGCATTTTATTA
1 AAAAAATTTAGTAAAA-ACTCTTACTTCGG-CCTTTGTTCGTATTTTTTTCTCCGCATTTTATTA
*
2936853 CTTTAAAAAAATCATATTTTCTAATTTTATTATTTTGCATTATTTTAGTACATTATGTTTGAAAT
64 CTTTAAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
*
2936918 TTATTAATTTAGTATGTTTTTTAAATAAA-TTTTAAAAAAAACCCTTATTCCTGCCCTTTGCTCG
129 TTATTAATTTA-TGTGTTTTTTAAATAAATTTTTAAAAAAAACCCTTATTCCTGCCCTTTGCTCG
* *
2936982 TATTATTTTCCCGAATTTTTTTACTTTCAATAACAATATATTATTTTTCGTATTTTATTATTTTA
193 TATTATTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTT-GTATTTTATTATTTTA
*
2937047 TATTATTTCAGTACATTTTGTTTGAAATATTTTTATTAATTATTTCTAAATTTTT
257 TATTA-TT---T-CA----G--T-AAAT-TTTGTATTAATTATTTCTAAATTTTT
*
2937102 AAAAAATTTAGTAAAAAATCTTACTTCGGCCTTTGTTCGTATTTTTTTCTCCGCATTTTATTACT
1 AAAAAATTTAGTAAAAACTCTTACTTCGGCCTTTGTTCGTATTTTTTTCTCCGCATTTTATTACT
2937167 TTAAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
66 TTAAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
2937232 ATTAATTTACTGTGTTTTTTAAATA
131 ATTAATTTA-TGTGTTTTTTAAATA
2937257 TACCATTTTT
Statistics
Matches: 422, Mismatches: 26, Indels: 30
0.88 0.05 0.06
Matches are distributed among these distances:
298 1 0.00
299 133 0.32
300 38 0.09
301 8 0.02
302 19 0.05
303 39 0.09
304 3 0.01
305 2 0.00
309 1 0.00
311 20 0.05
312 118 0.28
313 40 0.09
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.52
Consensus pattern (298 bp):
AAAAAATTTAGTAAAAACTCTTACTTCGGCCTTTGTTCGTATTTTTTTCTCCGCATTTTATTACT
TTAAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
ATTAATTTATGTGTTTTTTAAATAAATTTTTAAAAAAAACCCTTATTCCTGCCCTTTGCTCGTAT
TATTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATTATTTTATATT
ATTTCAGTAAATTTTGTATTAATTATTTCTAAATTTTT
Found at i:2937597 original size:14 final size:14
Alignment explanation
Indices: 2937578--2937642 Score: 64
Period size: 14 Copynumber: 4.6 Consensus size: 14
2937568 TCTCCGTTCA
2937578 TTTTCTTTCCTCCT
1 TTTTCTTTCCTCCT
*
2937592 TTTTCTTT-CT-GT
1 TTTTCTTTCCTCCT
2937604 TTTTCTTCTCCTTTCC-
1 TTTTCTT-TCC--TCCT
*
2937620 TTTTCTTTCCTTCT
1 TTTTCTTTCCTCCT
2937634 TTTTCTTTC
1 TTTTCTTTC
2937643 TTTCCTCTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 8 0.19
13 5 0.12
14 18 0.43
15 3 0.07
16 8 0.19
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (14 bp):
TTTTCTTTCCTCCT
Found at i:2937600 original size:18 final size:18
Alignment explanation
Indices: 2937579--2937649 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 18
2937569 CTCCGTTCAT
2937579 TTTCTTTCCTCCTTTTTC
1 TTTCTTTCCTCCTTTTTC
*
2937597 TTTCTGTTTTTCTTCTCC-TTTCC
1 TTTC----TTTC--CTCCTTTTTC
*
2937620 TTTTCTTTCCTTCTTTTTC
1 -TTTCTTTCCTCCTTTTTC
2937639 TTTCTTTCCTC
1 TTTCTTTCCTC
2937650 TCTGTTGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
18 17 0.41
19 4 0.10
20 4 0.10
22 4 0.10
23 4 0.10
24 8 0.20
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTCTTTCCTCCTTTTTC
Found at i:2937624 original size:42 final size:42
Alignment explanation
Indices: 2937552--2937643 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
2937542 CTTCTTCTTC
*
2937552 TTTCTTT-TTTTTTTCTTCTCCGTTCATTTTCTTTCCTCCTT
1 TTTCTTTCTGTTTTTCTTCTCCGTTCATTTTCTTTCCTCCTT
* * *
2937593 TTTCTTTCTGTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTT
1 TTTCTTTCTGTTTTTCTTCTCCGTTCATTTTCTTTCCTCCTT
2937635 TTTCTTTCT
1 TTTCTTTCT
2937644 TTCCTCTCTG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 7 0.15
42 39 0.85
ACGTcount: A:0.01, C:0.27, G:0.02, T:0.70
Consensus pattern (42 bp):
TTTCTTTCTGTTTTTCTTCTCCGTTCATTTTCTTTCCTCCTT
Found at i:2937756 original size:24 final size:24
Alignment explanation
Indices: 2937724--2937772 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2937714 AGTGGGAGTC
2937724 GCCACCAATCCTTTTTATTTAGGT
1 GCCACCAATCCTTTTTATTTAGGT
2937748 GCCACCAATCCTTTTTATTTAGGT
1 GCCACCAATCCTTTTTATTTAGGT
2937772 G
1 G
2937773 TGATCGGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.41
Consensus pattern (24 bp):
GCCACCAATCCTTTTTATTTAGGT
Found at i:2938789 original size:107 final size:106
Alignment explanation
Indices: 2938589--2938808 Score: 282
Period size: 107 Copynumber: 2.1 Consensus size: 106
2938579 AAACCCATAC
* * * * *
2938589 TTTGAAGTTTTAAGAGGATATTTGGCCATTTGGTTCAACGAGAAATTGAAAACCAGCACATTAGG
1 TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
* *
2938654 GCACGTTTTCTCAAATTTTCAAATGCAAAATATCGCTTTAT
66 GCACGTTTTCTCAAATTTTCAAACGCAAAATATCGCCTTAT
* * *
2938695 TTTGAAATTTTAAAAGGATATTTTAGCTATTTGG-TCGAACGAAAAATCGAAACCCAGCACGTTA
1 TTTGAAATTTTAAAAGGATA-TTTAGCCATTTGGTTC-AACGAAAAATCGAAAACCAGCACATTA
* *
2938759 GGGCACGTTTTCTC-GATTTTCCAAACGCAAAATATTGCCTTAT
64 GGGCACGTTTTCTCAAATTTT-CAAACGCAAAATATCGCCTTAT
*
2938802 TTAGAAA
1 TTTGAAA
2938809 AAATTTCCTT
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
106 25 0.26
107 73 0.74
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (106 bp):
TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
GCACGTTTTCTCAAATTTTCAAACGCAAAATATCGCCTTAT
Found at i:2941469 original size:23 final size:23
Alignment explanation
Indices: 2941438--2941496 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
2941428 AGGCATATAT
*
2941438 ATGTGTATTTATAAAAATTAAAA
1 ATGTATATTTATAAAAATTAAAA
* *
2941461 ATGTATATTGATATATATATTAAAA
1 ATGTATATT--TATAAAAATTAAAA
2941486 A--TATATTTATA
1 ATGTATATTTATA
2941497 TGTGTTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 4 0.13
23 14 0.45
25 13 0.42
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (23 bp):
ATGTATATTTATAAAAATTAAAA
Found at i:2944596 original size:89 final size:88
Alignment explanation
Indices: 2944500--2944914 Score: 562
Period size: 89 Copynumber: 4.7 Consensus size: 88
2944490 TACCGATATA
* * * * * *
2944500 GGAAGACAGGACCTGCTATCTTTGATCTATTTCACTCCAGTACATGAAGATAAAATTTGCTCTCT
1 GGAAGACAAGATCTG-TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAAATCTGCTCTCT
2944565 TCGATCTACTCCACCACCAGTATG
65 TCGATCTACTCCACCACCAGTATG
* * *
2944589 GGGAGACAAGATCTGTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAAATCTGCTTTCTT
1 GGAAGACAAGATCTGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAAATCTGCTCTCTT
* *
2944654 CGATCTACTTCGCCACCAGTATG
66 CGATCTACTCCACCACCAGTATG
* * * * *
2944677 GGAAAACAAGATCTGGTATCTTTGATCTAGTTCACGCTAGTACATGAAGACAAGATCTGCT-TTT
1 GGAAGACAAGATCT-GTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAAATCTGCTCTCT
* * *
2944741 TCCGATCTGCTTCGCCACCAGTATG
65 T-CGATCTACTCCACCACCAGTATG
* *
2944766 GGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGATAAAATTTGCTCTCT
1 GGAAGACAAGATCTG-TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAAATCTGCTCTCT
2944831 TCGATCTACTCCACCACCAGTATG
65 TCGATCTACTCCACCACCAGTATG
* * * *
2944855 GGGAGACAAGATATGTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT
1 GGAAGACAAGATCTGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAAATCTGCT
2944915 GCTTTTCCAC
Statistics
Matches: 287, Mismatches: 35, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
88 122 0.43
89 162 0.56
90 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (88 bp):
GGAAGACAAGATCTGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAAATCTGCTCTCTT
CGATCTACTCCACCACCAGTATG
Found at i:2944615 original size:44 final size:44
Alignment explanation
Indices: 2944417--2944912 Score: 295
Period size: 44 Copynumber: 11.2 Consensus size: 44
2944407 CTTAGGGAGG
* * * *
2944417 CAAGATCTGTTTTCCTCAATCTACTTCGCCACCAGTATGGAAAGA
1 CAAGATCTG-TTTCTTCGATCTACTTCACCACCAGTATGGGAAGA
* * * * * * * *
2944462 TAAAATCTGTGTATTCGATCCACTTCGCTACC-GATATAGGAAGA
1 CAAGATCTGTTTCTTCGATCTACTTCACCACCAG-TATGGGAAGA
* * * * * * ***
2944506 CAGGACCTGCTATCTTTGATCTATTTCA-CTCCAGTACATGAAGA
1 CAAGATCTG-TTTCTTCGATCTACTTCACCACCAGTATGGGAAGA
* * * * * *
2944550 TAAAATTTGCTCTCTTCGATCTACTCCACCACCAGTATGGGGAGA
1 CAAGATCTG-TTTCTTCGATCTACTTCACCACCAGTATGGGAAGA
* * ***
2944595 CAAGATCTGTTTCTTTGATCTACTTCA-CGCCAGTACATGAAGA
1 CAAGATCTGTTTCTTCGATCTACTTCACCACCAGTATGGGAAGA
* * *
2944638 CAAAATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAAA
1 CAAGATCTG-TTTCTTCGATCTACTTCACCACCAGTATGGGAAGA
* * * * * ***
2944683 CAAGATCTGGTATCTTTGATCTAGTTCA-CGCTAGTACATGAAGA
1 CAAGATCT-GTTTCTTCGATCTACTTCACCACCAGTATGGGAAGA
* *
2944727 CAAGATCTGCTTT-TTCCGATCTGCTTCGCCACCAGTATGGGAAGA
1 CAAGATCTG-TTTCTT-CGATCTACTTCACCACCAGTATGGGAAGA
* * ***
2944772 CAAGATCTGTTATCTTTGATCTACTTCA-CGCCAGTACATGAAGA
1 CAAGATCTGTT-TCTTCGATCTACTTCACCACCAGTATGGGAAGA
* * * * * *
2944816 TAAAATTTGCTCTCTTCGATCTACTCCACCACCAGTATGGGGAGA
1 CAAGATCTG-TTTCTTCGATCTACTTCACCACCAGTATGGGAAGA
* * * ***
2944861 CAAGATATGTTTCTTTGATCTACTTCA-CGCCAGTACATGAAGA
1 CAAGATCTGTTTCTTCGATCTACTTCACCACCAGTATGGGAAGA
2944904 CAAGATCTG
1 CAAGATCTG
2944913 CTGCTTTTCC
Statistics
Matches: 329, Mismatches: 108, Indels: 30
0.70 0.23 0.06
Matches are distributed among these distances:
43 42 0.13
44 167 0.51
45 117 0.36
46 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
CAAGATCTGTTTCTTCGATCTACTTCACCACCAGTATGGGAAGA
Found at i:2944699 original size:177 final size:178
Alignment explanation
Indices: 2944458--2944914 Score: 591
Period size: 177 Copynumber: 2.6 Consensus size: 178
2944448 CCAGTATGGA
* * * * * * * *
2944458 AAGATAAAATCTG-TGTATTCGATCCACTTCGCTACC-GATATAGGAAGACAGGACCTGCTATCT
1 AAGATAAAATCTGCTCTCTTCGATCTACTTCGCCACCAG-TATGGGAAGACAAGATCTGGTATCT
* * * *
2944521 TTGATCTATTTCACTCCAGTACATGAAGATAAAATTTGCTCTCTT-CGATCTACTCCACCACCAG
65 TTGATCTACTTCACGCCAGTACATGAAGACAAAATCTGCT-TCTTCCGATCTACTCCACCACCAG
*
2944585 TATGGGGAGACAAGATCTGTT-TCTTTGATCTACTTCACGCCAGTACATG
129 TATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATG
* * *
2944634 AAGACAAAATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAAACAAGATCTGGTATCTT
1 AAGATAAAATCTGCTCTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTT
* * * * * * *
2944699 TGATCTAGTTCACGCTAGTACATGAAGACAAGATCTGCTTTTTCCGATCTGCTTCGCCACCAGTA
66 TGATCTACTTCACGCCAGTACATGAAGACAAAATCTGCTTCTTCCGATCTACTCCACCACCAGTA
2944764 TGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATG
131 TGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATG
* * * * * *
2944812 AAGATAAAATTTGCTCTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATAT-GTTTCTT
1 AAGATAAAATCTGCTCTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTT
*
2944876 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT
66 TGATCTACTTCACGCCAGTACATGAAGACAAAATCTGCT
2944915 GCTTTTCCAC
Statistics
Matches: 245, Mismatches: 32, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
176 15 0.06
177 152 0.62
178 78 0.32
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (178 bp):
AAGATAAAATCTGCTCTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTT
TGATCTACTTCACGCCAGTACATGAAGACAAAATCTGCTTCTTCCGATCTACTCCACCACCAGTA
TGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATG
Found at i:2952325 original size:3 final size:3
Alignment explanation
Indices: 2952317--2952395 Score: 60
Period size: 3 Copynumber: 26.7 Consensus size: 3
2952307 TAAATGAGTA
* * *
2952317 AAT AAT AAT AAT GAT TAT AAT AAT ACAA AATT AAT AAT -AT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T AAT AAT AAT AAT AAT
2952362 AAT -AT AAT -AT AAT AAT -AT AAT AAT GAAT AGAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AA
2952396 ATATAAAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
2 10 0.16
3 42 0.68
4 10 0.16
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2952360 original size:5 final size:5
Alignment explanation
Indices: 2952350--2952383 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
2952340 TACAAAATTA
2952350 ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
2952384 ATGAATAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.07
4 2 0.07
5 23 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:2952398 original size:23 final size:23
Alignment explanation
Indices: 2952332--2952426 Score: 64
Period size: 22 Copynumber: 4.3 Consensus size: 23
2952322 TAATAATGAT
*
2952332 TATAATAAT-ACA-AAATTAATAA
1 TATAATAATGA-ATAAATAAATAA
2952354 TATAAT-AT-AATATAATATAATAA
1 TATAATAATGAATA-AATA-AATAA
*
2952377 TATAATAATGAATAGATAAAT-A
1 TATAATAATGAATAAATAAATAA
2952399 TA-AA-AA-GAA-AATATAAATAA
1 TATAATAATGAATAA-ATAAATAA
*
2952419 GATAATAA
1 TATAATAA
2952427 GTAGATTAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
18 1 0.02
19 9 0.15
20 5 0.08
21 8 0.13
22 14 0.23
23 14 0.23
24 5 0.08
25 4 0.07
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (23 bp):
TATAATAATGAATAAATAAATAA
Found at i:2954582 original size:15 final size:15
Alignment explanation
Indices: 2954562--2954611 Score: 100
Period size: 15 Copynumber: 3.3 Consensus size: 15
2954552 TATGTCTAAG
2954562 TTTTATTGTATTTAT
1 TTTTATTGTATTTAT
2954577 TTTTATTGTATTTAT
1 TTTTATTGTATTTAT
2954592 TTTTATTGTATTTAT
1 TTTTATTGTATTTAT
2954607 TTTTA
1 TTTTA
2954612 AGGTCATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTATTGTATTTAT
Found at i:2954728 original size:21 final size:21
Alignment explanation
Indices: 2954704--2954747 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2954694 TTTTAAAATG
*
2954704 AAAATATTTAAAT-TTAACTAT
1 AAAATATATAAATATTAA-TAT
2954725 AAAATATATAAATATTAATAT
1 AAAATATATAAATATTAATAT
2954746 AA
1 AA
2954748 TTTTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAATATATAAATATTAATAT
Found at i:2955639 original size:10 final size:10
Alignment explanation
Indices: 2955626--2955735 Score: 74
Period size: 10 Copynumber: 11.3 Consensus size: 10
2955616 TTTTTCTCTG
2955626 TTCCTTTTCT
1 TTCCTTTTCT
2955636 TTCCTTCTT-T
1 TTCCTT-TTCT
*
2955646 TT-CTTTCTTT
1 TTCCTTT-TCT
* *
2955656 TTTCTTCTCCT
1 TTCCTT-TTCT
2955667 TTCCTTTTCT
1 TTCCTTTTCT
2955677 TTCCTTCTT-T
1 TTCCTT-TTCT
2955687 TT-C-TTTCT
1 TTCCTTTTCT
*
2955695 TTCC-TCTCAT
1 TTCCTTTTC-T
2955705 TTCCTTTTCT
1 TTCCTTTTCT
*
2955715 TTCTTTTTCT
1 TTCCTTTTCT
2955725 TT-C-TTTCT
1 TTCCTTTTCT
2955733 TTC
1 TTC
2955736 TTCTCTTTTC
Statistics
Matches: 81, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
7 2 0.02
8 12 0.15
9 9 0.11
10 41 0.51
11 16 0.20
12 1 0.01
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (10 bp):
TTCCTTTTCT
Found at i:2955649 original size:41 final size:41
Alignment explanation
Indices: 2955598--2955746 Score: 179
Period size: 41 Copynumber: 3.8 Consensus size: 41
2955588 TTCCCACTTT
*
2955598 TTCTTCTTTCTTTCTTTTTTTTTCT-CTGTTCCTTTTCTTTCC
1 TTCTT-TTTCTTTCTTTTTTCTTCTCCT-TTCCTTTTCTTTCC
2955640 TTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCC
1 TTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCC
* *
2955681 TTCTTTTTCTTTC---TTTCCTCTCATTTCCTTTTC--T--
1 TTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCC
*
2955715 TTCTTTTTCTTTCTTTCTTTCTTCTCTTTTCC
1 TTCTTTTTCTTTCTTT-TTTCTTCTCCTTTCC
2955747 CTCTCATTCT
Statistics
Matches: 97, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 13 0.13
36 1 0.01
38 31 0.32
41 45 0.46
42 7 0.07
ACGTcount: A:0.01, C:0.28, G:0.01, T:0.70
Consensus pattern (41 bp):
TTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCC
Found at i:2955669 original size:31 final size:31
Alignment explanation
Indices: 2955598--2955737 Score: 103
Period size: 31 Copynumber: 4.5 Consensus size: 31
2955588 TTCCCACTTT
* * * *
2955598 TTCTTCTTTCTTTCTTTTTTTTTCTCTGTTCC
1 TTCTTCTTTCCTTCTTTTTCTTTCT-TTTTTC
2955630 TT-TTCTTTCCTTCTTTTTCTTTCTTTTTTC
1 TTCTTCTTTCCTTCTTTTTCTTTCTTTTTTC
* *
2955660 TTCTCCTTTCCTT-TTCTTTCCTTC-TTTTTC
1 TTCTTCTTTCCTTCTT-TTTCTTTCTTTTTTC
* *
2955690 -T-TTCTTTCCTCTCATTTCCTTTTCTTTCTTT-
1 TTCTTCTTTCCT-TCTTTTTC-TTTCTTT-TTTC
*
2955721 TTCTTTCTTTCTTTCTT
1 TTC-TTCTTTCCTTCTT
2955738 CTCTTTTCCC
Statistics
Matches: 86, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
28 8 0.09
29 5 0.06
30 18 0.21
31 38 0.44
32 6 0.07
33 3 0.03
34 8 0.09
ACGTcount: A:0.01, C:0.27, G:0.01, T:0.71
Consensus pattern (31 bp):
TTCTTCTTTCCTTCTTTTTCTTTCTTTTTTC
Found at i:2955717 original size:38 final size:38
Alignment explanation
Indices: 2955608--2955746 Score: 167
Period size: 38 Copynumber: 3.6 Consensus size: 38
2955598 TTCTTCTTTC
*
2955608 TTTCTTT-TTTTTTCTC-TGTTCCTTTTCTTTCCTTCTT
1 TTTCTTTCTTTCTTCTCAT-TTCCTTTTCTTTCCTTCTT
*
2955645 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTT
1 TTTCTTTC---TTTCTTCTCATTTCCTTTTCTTTCCTTCTT
* *
2955686 TTTCTTTCTTTCCTCTCATTTCCTTTTCTTT-CTTTTT
1 TTTCTTTCTTTCTTCTCATTTCCTTTTCTTTCCTTCTT
*
2955723 CTTTCTTTCTTTCTTCTCTTTTCC
1 -TTTCTTTCTTTCTTCTCATTTCC
2955747 CTCTCATTCT
Statistics
Matches: 90, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
37 12 0.13
38 42 0.47
41 35 0.39
42 1 0.01
ACGTcount: A:0.01, C:0.28, G:0.01, T:0.71
Consensus pattern (38 bp):
TTTCTTTCTTTCTTCTCATTTCCTTTTCTTTCCTTCTT
Found at i:2955745 original size:10 final size:10
Alignment explanation
Indices: 2955596--2955745 Score: 61
Period size: 10 Copynumber: 15.5 Consensus size: 10
2955586 CCTTCCCACT
*
2955596 TTTTCTTCTT
1 TTTTCTTCTC
2955606 TCTTTCTT-T-
1 T-TTTCTTCTC
2955615 TTTT-TTCTC
1 TTTTCTTCTC
* *
2955624 TGTTCCTTTTC
1 T-TTTCTTCTC
*
2955635 TTTCCTTCT-
1 TTTTCTTCTC
*
2955644 TTTTCTTTCTT
1 TTTTC-TTCTC
2955655 TTTTCTTCTCC
1 TTTTCTTCT-C
* *
2955666 TTTCCTTTTC
1 TTTTCTTCTC
*
2955676 TTTCCTTCT-
1 TTTTCTTCTC
2955685 TTTTCTT-TC
1 TTTTCTTCTC
*
2955694 -TTTCCTCTC
1 TTTTCTTCTC
* *
2955703 ATTTCCTTTTC
1 -TTTTCTTCTC
*
2955714 -TTTCTT-TT
1 TTTTCTTCTC
2955722 TCTTTCTT-TC
1 T-TTTCTTCTC
2955732 -TTTCTTCTC
1 TTTTCTTCTC
2955741 TTTTC
1 TTTTC
2955746 CCTCTCATTC
Statistics
Matches: 108, Mismatches: 16, Indels: 32
0.69 0.10 0.21
Matches are distributed among these distances:
7 2 0.02
8 17 0.16
9 21 0.19
10 39 0.36
11 29 0.27
ACGTcount: A:0.01, C:0.27, G:0.01, T:0.71
Consensus pattern (10 bp):
TTTTCTTCTC
Found at i:2958789 original size:281 final size:287
Alignment explanation
Indices: 2958358--2959006 Score: 906
Period size: 300 Copynumber: 2.2 Consensus size: 287
2958348 ATTACTTTCG
* * * * * *
2958358 TTTT-TTATTTTACATTGTTTTATTATATTATGTTTGAAGTGTATTAATTTAGTGTGTATTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
2958422 ATAAATTTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACT
66 ATAAATTTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACT
* *
2958487 TTTAATAAAAATATATTA-TT-TTA-TA-A-TATTTCAGTAC-AT-TTTGTATTAATTATTTCTG
131 TTCAATAAAAATATATTATTTATTATTATATTATTTCAGTACTATATTTGTATTAATTATTTCTA
* *
2958545 AATTTTTAAAAAATTTAGTAAAACACTCTTACTTC-AGCCATTTGTTCGTATTTTTT-TCAGCAT
196 AATTTTTAAAAAATGTAGTAAAA-AATCTTACTTCGA-CC-TTTGTTCGTATTTTTTCTCAGCAT
*
2958608 TTTATTACTTTAAAAATATCATATTTTCTAA
258 TTTATTAC-TTAAAAAAATCATATTTTCTAA
*
2958639 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGAGTTTTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
* *
2958704 ATAAA-TTTAAAAAAAACCCTTATTCCTGCCCTTTGCTTGTATTATTTTCCCGAATTTTATTACT
66 ATAAATTTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACT
*
2958768 TTCAATAACAATATATTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGT
131 TTCAATAAAAATATATTA-TTTATTA--TTATATTATTTCAGTAC--------T---ATATTTGT
2958833 ATTAATTATTTCTAAATTTTTAAAAAATGTAGTAAAAAATCTTACTTCGACCTTTGTTCGTATTT
182 ATTAATTATTTCTAAATTTTTAAAAAATGTAGTAAAAAATCTTACTTCGACCTTTGTTCGTATTT
*
2958898 TTTCTCCGCATTTTATTACTTAAAAAAATCATATTTTCTAA
247 TTTCTCAGCATTTTATTACTTAAAAAAATCATATTTTCTAA
*
2958939 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTACTGTGTTTTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
2959004 ATA
66 ATA
2959007 TACCATATTT
Statistics
Matches: 326, Mismatches: 18, Indels: 29
0.87 0.05 0.08
Matches are distributed among these distances:
281 77 0.24
282 58 0.18
283 2 0.01
284 3 0.01
287 2 0.01
288 1 0.00
289 11 0.03
300 103 0.32
301 28 0.09
302 41 0.13
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51
Consensus pattern (287 bp):
TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
ATAAATTTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACT
TTCAATAAAAATATATTATTTATTATTATATTATTTCAGTACTATATTTGTATTAATTATTTCTA
AATTTTTAAAAAATGTAGTAAAAAATCTTACTTCGACCTTTGTTCGTATTTTTTCTCAGCATTTT
ATTACTTAAAAAAATCATATTTTCTAA
Found at i:2959317 original size:19 final size:19
Alignment explanation
Indices: 2959293--2959333 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2959283 ATTCCCACCA
* *
2959293 CTTCTTCTACTTTCTTTTT
1 CTTCTTCTACGTTCCTTTT
*
2959312 CTTCTTCTCCGTTCCTTTT
1 CTTCTTCTACGTTCCTTTT
2959331 CTT
1 CTT
2959334 TCCTTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.63
Consensus pattern (19 bp):
CTTCTTCTACGTTCCTTTT
Found at i:2959440 original size:14 final size:13
Alignment explanation
Indices: 2959361--2959441 Score: 54
Period size: 14 Copynumber: 5.8 Consensus size: 13
2959351 TTTTCTTCTC
2959361 CTTTCCTTTTCTTT
1 CTTTCC-TTTCTTT
* *
2959375 CATTCTTTTTCTTT
1 CTTTC-CTTTCTTT
*
2959389 CTTTCCTCTCATTT
1 CTTTCCTTTC-TTT
*
2959403 CCTTTTCTTTCTTT
1 -CTTTCCTTTCTTT
* *
2959417 TTATTTCTTTCTTT
1 CT-TTCCTTTCTTT
2959431 CTTCTCCTTTC
1 CTT-TCCTTTC
2959442 CCTCTCCTTC
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
13 5 0.10
14 39 0.75
15 8 0.15
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (13 bp):
CTTTCCTTTCTTT
Found at i:2959455 original size:38 final size:37
Alignment explanation
Indices: 2959303--2959442 Score: 156
Period size: 38 Copynumber: 3.6 Consensus size: 37
2959293 CTTCTTCTAC
* *
2959303 TTTCTTTTTCTTCTTCTCCGTTCCTTTTCTTTCCTTTTT
1 TTTCTTTCT-TTCTTCTCCTTTCCTTTTCTTT-CTTTTT
* *
2959342 TTT-TTCAGTTTTTCTTCTCCTTTCCTTTTCTTTCATTCTT
1 TTTCTT---TCTTTCTTCTCCTTTCCTTTTCTTTC-TTTTT
* *
2959382 TTTCTTTCTTTCCTCTCATTTCCTTTTCTTTCTTTTT
1 TTTCTTTCTTTCTTCTCCTTTCCTTTTCTTTCTTTTT
2959419 ATTTCTTTCTTTCTTCTCCTTTCC
1 -TTTCTTTCTTTCTTCTCCTTTCC
2959443 CTCTCCTTCT
Statistics
Matches: 87, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
37 4 0.05
38 46 0.53
39 4 0.05
40 28 0.32
41 5 0.06
ACGTcount: A:0.03, C:0.28, G:0.01, T:0.68
Consensus pattern (37 bp):
TTTCTTTCTTTCTTCTCCTTTCCTTTTCTTTCTTTTT
Found at i:2961708 original size:155 final size:149
Alignment explanation
Indices: 2961483--2961916 Score: 415
Period size: 153 Copynumber: 2.8 Consensus size: 149
2961473 TTAAAATTTG
* * * *
2961483 GCCCTTTGTTCGTATT-TTTT-TTCGCATTTTATTACTTTAAAAATATCATATTTTCTAATTTTA
1 GCCCTCTGTACGTATTATTTTCTCCGAATTTTATTACTTTAAAAA-ATCATATTTTCTAATTTTA
2961546 TTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTATGTTTTTTAAATAAA
65 TTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTA-TATGTTTTTTAAATAAA
*
2961611 TTT-TTAAAAAAACCCTTA-TTCC
129 TTTAGT-AAAAAA-CCTTACTT-C
* *
2961633 TGCCCTCTGCT-CGTATTATTTTC-CCGAATTTT-TTATTTTCAATAACAAT-ATATTATTTTCA
1 -GCCCTCTG-TACGTATTATTTTCTCCGAATTTTATTACTTT-AA-AA-AATCATATT-TTCT-A
* * * * *
2961694 TATTTTCA-TATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAA-TTATTTCTA
59 -ATTTT-ATTATTTTACATTATTTTAGTACATTATGTTTG-AA-A-TT-TATTAATTTATATGT-
*
2961757 AATTTTT-AA-AAATTTAGTAAAAAATCTTACTTC
117 --TTTTTAAATAAATTTAGTAAAAAACCTTACTTC
* * * * *
2961790 GGCCTTTGTACTTATTTTTTTCTCCGCATTTTATTACTTTAAAAAATCATATTTTCTAATTTTAT
1 GCCCTCTGTACGTATTATTTTCTCCGAATTTTATTACTTTAAAAAATCATATTTTCTAATTTTAT
*
2961855 TATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTACTGTGTTTTTTAAATA
66 TATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTA-TATGTTTTTTAAATA
2961917 TACCATTTTT
Statistics
Matches: 231, Mismatches: 24, Indels: 57
0.74 0.08 0.18
Matches are distributed among these distances:
148 5 0.02
149 8 0.03
150 6 0.03
151 23 0.10
152 22 0.10
153 40 0.17
154 3 0.01
155 40 0.17
156 26 0.11
157 19 0.08
158 25 0.11
159 9 0.04
160 5 0.02
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.53
Consensus pattern (149 bp):
GCCCTCTGTACGTATTATTTTCTCCGAATTTTATTACTTTAAAAAATCATATTTTCTAATTTTAT
TATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTATATGTTTTTTAAATAAATT
TAGTAAAAAACCTTACTTC
Found at i:2962214 original size:10 final size:10
Alignment explanation
Indices: 2962197--2962296 Score: 59
Period size: 10 Copynumber: 10.0 Consensus size: 10
2962187 TTCCTTCCCA
2962197 CTTC-TTCTT
1 CTTCTTTCTT
2962206 CTTCTTTCTT
1 CTTCTTTCTT
* *
2962216 TTTTTTTCTT
1 CTTCTTTCTT
* *
2962226 CTCCGTTCCTT
1 CTTC-TTTCTT
2962237 -TTCTTTCCTT
1 CTTCTTT-CTT
2962247 CTT-TTTCTTT
1 CTTCTTTC-TT
2962257 CTGT-TTTCTT
1 CT-TCTTTCTT
*
2962267 CTCCTTTCCTT
1 CTTCTTT-CTT
2962278 -TTCTTTCCTT
1 CTTCTTT-CTT
2962288 CTT-TTTCTT
1 CTTCTTTCTT
2962297 TTTTCCTCTC
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
9 10 0.14
10 45 0.62
11 17 0.24
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (10 bp):
CTTCTTTCTT
Found at i:2962235 original size:44 final size:40
Alignment explanation
Indices: 2962169--2962300 Score: 122
Period size: 41 Copynumber: 3.2 Consensus size: 40
2962159 AAAAATTACC
* *
2962169 CTTTTTCTTTT-TTTTCCCTTCCTTCCCACTTCTTCTTCTTCTTT
1 CTTTTT-TTTTCTTCTCCCTTCCTT--CACTT-TCCTTCTT-TTT
* **
2962213 CTTTTTTTTTCTTCTCCGTTCCTTTTCTTTCCTTCTTTTT
1 CTTTTTTTTTCTTCTCCCTTCCTTCACTTTCCTTCTTTTT
* * **
2962253 CTTTCTGTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTT
1 CTTT-TTTTTTCTTCTCCCTTCCTTCACTTTCCTTCTTTTT
2962294 CTTTTTT
1 CTTTTTT
2962301 CCTCTCTGTT
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
40 9 0.12
41 45 0.58
42 3 0.04
43 4 0.05
44 17 0.22
ACGTcount: A:0.01, C:0.30, G:0.02, T:0.68
Consensus pattern (40 bp):
CTTTTTTTTTCTTCTCCCTTCCTTCACTTTCCTTCTTTTT
Found at i:2962248 original size:41 final size:40
Alignment explanation
Indices: 2962203--2962300 Score: 160
Period size: 41 Copynumber: 2.4 Consensus size: 40
2962193 CCCACTTCTT
2962203 CTTCTTCTTTCTTTTTTTTTCTTCTCCGTTCCTTTTCTTTC
1 CTTCTT-TTTCTTTTTTTTTCTTCTCCGTTCCTTTTCTTTC
* *
2962244 CTTCTTTTTCTTTCTGTTTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTT-TTTTTTCTTCTCCGTTCCTTTTCTTTC
2962285 CTTCTTTTTCTTTTTT
1 CTTCTTTTTCTTTTTT
2962301 CCTCTCTGTT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 9 0.17
41 44 0.83
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (40 bp):
CTTCTTTTTCTTTTTTTTTCTTCTCCGTTCCTTTTCTTTC
Found at i:2963427 original size:107 final size:106
Alignment explanation
Indices: 2963242--2963461 Score: 291
Period size: 107 Copynumber: 2.1 Consensus size: 106
2963232 AAACCCATAC
* * * * *
2963242 TTTGAAGTTTTAAGAGGATATTTGGCCATTTGGTTCAACGAGAAATTGAAAACCAGCACATTAGG
1 TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
* *
2963307 GCACGTTTTCTCGAATTTT-CAAATGCAAAATATCGCTTTAT
66 GCACGTTTTCTCG-ATTTTCCAAACGCAAAATATCGCCTTAT
* * *
2963348 TTTGAAATTTTAAAAGGATATTTTAGCTATTTGG-TCTAACGAAAAATCGAAACCCAGCACGTTA
1 TTTGAAATTTTAAAAGGATA-TTTAGCCATTTGGTTC-AACGAAAAATCGAAAACCAGCACATTA
*
2963412 GGGCACGTTTTCTCGATTTTCCAAACGCAAAATATTGCCTTAT
64 GGGCACGTTTTCTCGATTTTCCAAACGCAAAATATCGCCTTAT
*
2963455 TTAGAAA
1 TTTGAAA
2963462 AATTTTCCTT
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
106 25 0.25
107 74 0.75
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (106 bp):
TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
GCACGTTTTCTCGATTTTCCAAACGCAAAATATCGCCTTAT
Found at i:2965100 original size:19 final size:19
Alignment explanation
Indices: 2965076--2965126 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
2965066 TTTCCTCTAT
2965076 TTTGTTTGCTTGTGATTTG
1 TTTGTTTGCTTGTGATTTG
2965095 TTTGTTTGCTTGTGATTTG
1 TTTGTTTGCTTGTGATTTG
2965114 TTTGTTTGCTTGT
1 TTTGTTTGCTTGT
2965127 TGTCTGCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.04, C:0.06, G:0.25, T:0.65
Consensus pattern (19 bp):
TTTGTTTGCTTGTGATTTG
Found at i:2966102 original size:21 final size:22
Alignment explanation
Indices: 2966073--2966118 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2966063 ATGTATATTG
2966073 ATATATATATATATTA-AAAAT
1 ATATATATATATATTATAAAAT
* * *
2966094 ATATTTATATGTGTTATAAAAT
1 ATATATATATATATTATAAAAT
2966116 ATA
1 ATA
2966119 GCAAATACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATATATATATATTATAAAAT
Found at i:2966233 original size:3 final size:3
Alignment explanation
Indices: 2966225--2966298 Score: 57
Period size: 3 Copynumber: 24.7 Consensus size: 3
2966215 TAAATGAGTA
* * *
2966225 AAT AAT AAT AAT GAT TAT AAT AAT ACAA AACT AAT AAT -AT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T AAT AAT AAT AAT AAT
2966270 AAT -AT AAT AAT -AT AAT AAT GAAT AGAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AA
2966299 ATATAAAAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
2 8 0.14
3 40 0.69
4 10 0.17
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2966315 original size:13 final size:13
Alignment explanation
Indices: 2966297--2966327 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2966287 ATGAATAGAT
2966297 AAATATAAAAAGA
1 AAATATAAAAAGA
2966310 AAATATAAAAAGA
1 AAATATAAAAAGA
*
2966323 TAATA
1 AAATA
2966328 AGTAGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (13 bp):
AAATATAAAAAGA
Found at i:2967091 original size:13 final size:14
Alignment explanation
Indices: 2967070--2967098 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2967060 AAGAAAAATG
2967070 AAGAGAAAAAGAAA
1 AAGAGAAAAAGAAA
2967084 AAGA-AAAAAGAAA
1 AAGAGAAAAAGAAA
2967097 AA
1 AA
2967099 TAGATCTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAGAGAAAAAGAAA
Found at i:2968464 original size:13 final size:14
Alignment explanation
Indices: 2968448--2968490 Score: 65
Period size: 13 Copynumber: 3.3 Consensus size: 14
2968438 TATGTCTAAG
2968448 TTTTATTGTA-TTA
1 TTTTATTGTATTTA
2968461 TTTTA-TGTATTTA
1 TTTTATTGTATTTA
2968474 TTTTATT-TATTTA
1 TTTTATTGTATTTA
2968487 TTTT
1 TTTT
2968491 TAAGGTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.14
13 23 0.82
14 1 0.04
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (14 bp):
TTTTATTGTATTTA
Found at i:2968613 original size:21 final size:20
Alignment explanation
Indices: 2968578--2968624 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
2968568 TTAATTTTAA
2968578 AATG-AAAATATTAAAT-TT
1 AATGTAAAATATTAAATATT
2968596 AACTGTAAAATATATAAATATT
1 AA-TGTAAAATAT-TAAATATT
2968618 AATGTAA
1 AATGTAA
2968625 TTTTTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 7 0.28
21 10 0.40
22 4 0.16
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (20 bp):
AATGTAAAATATTAAATATT
Found at i:2969191 original size:1 final size:1
Alignment explanation
Indices: 2969187--2969258 Score: 135
Period size: 1 Copynumber: 72.0 Consensus size: 1
2969177 CTTTTTTCTA
2969187 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
2969252 ATTTTTT
1 TTTTTTT
2969259 CTCCGCATTT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.01, C:0.00, G:0.00, T:0.99
Consensus pattern (1 bp):
T
Found at i:2969694 original size:35 final size:38
Alignment explanation
Indices: 2969645--2969783 Score: 142
Period size: 40 Copynumber: 3.6 Consensus size: 38
2969635 CTCCTTCCCA
* *
2969645 CTTTTCTTCTTTCTTTCTTTTTTTTTCTCCGTTCCTTTT
1 CTTTCCTTCTTTC-TTCTTTTTTCTTCTCCGTTCCTTTT
*
2969684 CTTTCCTTCTTTTTCTTCTTTTTTCTTCTCCTTTCCTTTT
1 CTTTCCTTC--TTTCTTCTTTTTTCTTCTCCGTTCCTTTT
* **
2969724 CTTTCCTTCTTT-TTCTTTCTTTCCTCTCATTTCC-TTT
1 CTTTCCTTCTTTCTTCTTT-TTTCTTCTCCGTTCCTTTT
*
2969761 CTTT-CTT-TTTCTTTCTTTCTTCT
1 CTTTCCTTCTTTC-TTCTTTTTTCT
2969784 CTTTTCCCTC
Statistics
Matches: 88, Mismatches: 7, Indels: 13
0.81 0.06 0.12
Matches are distributed among these distances:
35 3 0.03
36 6 0.07
37 19 0.22
38 16 0.18
39 8 0.09
40 32 0.36
41 4 0.05
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.70
Consensus pattern (38 bp):
CTTTCCTTCTTTCTTCTTTTTTCTTCTCCGTTCCTTTT
Done.