Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold76
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: 1973630
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 106294 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1655815 original size:40 final size:40
Alignment explanation
Indices: 1655724--1655869 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
1655714 TTTTTTGTGA
* * *
1655724 CATTTTTCAAAAAGCGCCGCTAATGGTCGACCTATAGCGG
1 CATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGG
** * * * *
1655764 TGTTTTGCAAAACGCACCGGTAATGCTCGATCTATAGTGG
1 CATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGG
* *
1655804 CATTTTTCAAAAGGCGCCGCTAATGCTCGATCTATAGTAG
1 CATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGG
* *
1655844 CATTTTTCAAAAAGTGCTGCTAATGC
1 CATTTTTCAAAAAGCGCCGCTAATGC
1655870 CACTAAAGCT
Statistics
Matches: 87, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (40 bp):
CATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGG
Found at i:1655994 original size:40 final size:40
Alignment explanation
Indices: 1655915--1656280 Score: 183
Period size: 40 Copynumber: 9.3 Consensus size: 40
1655905 TAATTTTTTT
* * * *
1655915 GCGGCATTTTTCGAA-AAGTGCTGCTAATGGTCGACCTATA
1 GCGGCATTTTTC-AAGAAGCGCCGCTAATGCTCGATCTATA
* * *
1655955 GCGGCGTTTTTCAAGAAGCGCCGCTAGTGCTCTATCTATA
1 GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
* *
1655995 GCGGCATTTTTCATGAAGCGCCGCTAATTCTCGATCTATA
1 GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
* * * * *
1656035 ACGGTATTTTCCAAGAAACGCCGCTAATGC-C-A-CTAAA
1 GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
* *** * * * ** ** * * *
1656072 GC-TCA-ACAT-AAAATAGGGGCG-TTGTGCTTAATTTTTTT
1 GCGGCATTTTTCAAGA-AGCGCCGCTAATGCTCGA-TCTATA
** * * * *
1656110 GCGGTGTTTTTCAAAAAGAGCCGCTAATGGTCGACCTATA
1 GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
* * *
1656150 GCAGCGTTTTTCAAGAAGCGCCGCGAATGCTCGATCTATA
1 GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
* ** *
1656190 GAGGTGTTTTTCAA-AAGGCGCCACTAATGCTCGATCTATA
1 GCGGCATTTTTCAAGAA-GCGCCGCTAATGCTCGATCTATA
* * * * * * *
1656230 ACTGCATTTTTTAAAAAGCGTCACTAATGCTAGATCTATA
1 GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
* *
1656270 ACGGCGTTTTT
1 GCGGCATTTTT
1656281 TTATCCAAAC
Statistics
Matches: 238, Mismatches: 76, Indels: 24
0.70 0.22 0.07
Matches are distributed among these distances:
34 7 0.03
35 4 0.02
36 2 0.01
37 5 0.02
38 4 0.02
39 5 0.02
40 200 0.84
41 11 0.05
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (40 bp):
GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
Found at i:1655994 original size:195 final size:194
Alignment explanation
Indices: 1655648--1656259 Score: 764
Period size: 195 Copynumber: 3.1 Consensus size: 194
1655638 TCGAAAAGCG
* * * * *
1655648 GCATTTTCCGAAAAGCGACGCTAATGCCACTAAAGCTCAACATAAAATGATGGTGTTATGCTTAA
1 GCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAATGACGGTGTTGTGCTTAA
* * * * *
1655713 TTTTTTTGTGACATTTTTCAAAAAGCGCCGCTAATGGTCGACCTATAGCGGTGTTTTGCAA-AAC
66 TTTTTTTGCGGCATTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAGAA-
* * * *
1655777 GCACCGGTAATGCTCGATCTATAGTGGCATTTTTCAAAAGGCGCCGCTAATGCTCGATCTATAGT
130 GCGCCGCTAATGCTCGATCTATAGAGGCATTTTTCAAAAGGCGCCGCTAATGCTCGATCTATAAT
* * * *
1655842 AGCATTTTTCAAAAAGTGCTGCTAATGCCACTAAAGCTCAACATAAAATGACAGTGTTGCGCTTA
1 -GCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAATGACGGTGTTGTGCTTA
* * *
1655907 ATTTTTTTGCGGCATTTTTCGAAAAGTGCTGCTAATGGTCGACCTATAGCGGCGTTTTTCAAGAA
65 ATTTTTTTGCGGCATTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAGAA
* * * * *
1655972 GCGCCGCTAGTGCTCTATCTATAGCGGCATTTTTCATGAA-GCGCCGCTAATTCTCGATCTATAA
130 GCGCCGCTAATGCTCGATCTATAGAGGCATTTTTCA-AAAGGCGCCGCTAATGCTCGATCTATAA
*
1656036 CG
194 -T
* * * *
1656038 GTATTTTCCAAGAAA-CGCCGCTAATGCCACTAAAGCTCAACATAAAAT-AGGGGCGTTGTGCTT
1 GCATTTTTCAA-AAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAATGA-CGGTGTTGTGCTT
** *
1656101 AATTTTTTTGCGGTGTTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCAGCGTTTTTCAAGA
64 AATTTTTTTGCGGCATTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAGA
* ** *
1656166 AGCGCCGCGAATGCTCGATCTATAGAGGTGTTTTTCAAAAGGCGCCACTAATGCTCGATCTATAA
129 AGCGCCGCTAATGCTCGATCTATAGAGGCATTTTTCAAAAGGCGCCGCTAATGCTCGATCTATAA
1656231 CT
194 -T
* * *
1656233 GCATTTTTTAAAAAGCGTCACTAATGC
1 GCATTTTTCAAAAAGCGCCGCTAATGC
1656260 TAGATCTATA
Statistics
Matches: 356, Mismatches: 54, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
194 6 0.02
195 343 0.96
196 7 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (194 bp):
GCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAATGACGGTGTTGTGCTTAA
TTTTTTTGCGGCATTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAGAAG
CGCCGCTAATGCTCGATCTATAGAGGCATTTTTCAAAAGGCGCCGCTAATGCTCGATCTATAAT
Found at i:1661173 original size:27 final size:27
Alignment explanation
Indices: 1661143--1661197 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1661133 AAGCTATTGC
1661143 ATTTAAACATAACTCTTTTTGGAACTA
1 ATTTAAACATAACTCTTTTTGGAACTA
*
1661170 ATTTAAACATAATTCTTTTTGGAACTA
1 ATTTAAACATAACTCTTTTTGGAACTA
1661197 A
1 A
1661198 CCACATGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (27 bp):
ATTTAAACATAACTCTTTTTGGAACTA
Found at i:1689389 original size:25 final size:24
Alignment explanation
Indices: 1689353--1689429 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 24
1689343 TATCATTTCT
* *
1689353 GCTCTTTTGAGCTATGATCGGTAA
1 GCTCTTTCGAGCTATGAACGGTAA
*
1689377 GCTCATTTCGAGCTGAAGAACGGTAA
1 GCTC-TTTCGAGCT-ATGAACGGTAA
*
1689403 GCTCTATCGAG-T-TGAAACGGTAA
1 GCTCTTTCGAGCTATG-AACGGTAA
1689426 GCTC
1 GCTC
1689430 ATAAGAGCTG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
22 1 0.02
23 12 0.27
24 5 0.11
25 14 0.31
26 13 0.29
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (24 bp):
GCTCTTTCGAGCTATGAACGGTAA
Found at i:1689425 original size:23 final size:26
Alignment explanation
Indices: 1689371--1689440 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 26
1689361 GAGCTATGAT
*
1689371 CGGTAAGCTCATTTCGAGCTGAAGAA
1 CGGTAAGCTCATATCGAGCTGAAGAA
*
1689397 CGGTAAGCTC-TATCGAGTTG-A-AA
1 CGGTAAGCTCATATCGAGCTGAAGAA
*
1689420 CGGTAAGCTCATA-AGAGCTGA
1 CGGTAAGCTCATATCGAGCTGA
1689441 TATATTGGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 17 0.45
24 3 0.08
25 8 0.21
26 10 0.26
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (26 bp):
CGGTAAGCTCATATCGAGCTGAAGAA
Found at i:1701956 original size:215 final size:215
Alignment explanation
Indices: 1701579--1702009 Score: 792
Period size: 215 Copynumber: 2.0 Consensus size: 215
1701569 GCTTTTGCAA
* *
1701579 AAACTTCATCACAACCTTAGCATCGCTCTTCAGATATGCCTTGGCCTCAACCCACTTAGACACGT
1 AAACTTCATCACAACCTTAGCATCGCTCGTCAGATATGCCTTGGCCTCAACCCACTTAGAAACGT
* *
1701644 AATCTACTGCTACCAATATGTACTTGTGATCGAAAGACGGAGGGAAAGGACCAAGGAAGTAAATA
66 AATCTACTACTACCAATATGTACTTGTGATCGAAAGACAGAGGGAAAGGACCAAGGAAGTAAATA
*
1701709 CCCAAAACATCGACTAATTCTGCCTTAATGATGTTTGTCTGGGGTATTTCATTTCTTTGGTGACG
131 CCCAAAACATCGACTAATTCTGCCTCAATGATGTTTGTCTGGGGTATTTCATTTCTTTGGTGACG
1701774 TTTCCAACCTTTTGGCATCG
196 TTTCCAACCTTTTGGCATCG
*
1701794 AAACTTCATCACAACCTTAGCATCGTTCGTCAGATATGCCTTGGCCTCAACCCACTTAGAAACGT
1 AAACTTCATCACAACCTTAGCATCGCTCGTCAGATATGCCTTGGCCTCAACCCACTTAGAAACGT
1701859 AATCTACTACTACCAATATGTACTTGTGA-CTGAAAGACAGAGGGAAAGGACCAAGGAAGTAAAT
66 AATCTACTACTACCAATATGTACTTGTGATC-GAAAGACAGAGGGAAAGGACCAAGGAAGTAAAT
1701923 ACCCAAAACATCGACTAATTCTGCCTCAATGATGTTTGTCTGGGGTATTTCATTTCTTTGGTGAC
130 ACCCAAAACATCGACTAATTCTGCCTCAATGATGTTTGTCTGGGGTATTTCATTTCTTTGGTGAC
1701988 GTTTCCAACCTTTTGGCATCG
195 GTTTCCAACCTTTTGGCATCG
1702009 A
1 A
1702010 TCACAACCCT
Statistics
Matches: 209, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
214 1 0.00
215 208 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (215 bp):
AAACTTCATCACAACCTTAGCATCGCTCGTCAGATATGCCTTGGCCTCAACCCACTTAGAAACGT
AATCTACTACTACCAATATGTACTTGTGATCGAAAGACAGAGGGAAAGGACCAAGGAAGTAAATA
CCCAAAACATCGACTAATTCTGCCTCAATGATGTTTGTCTGGGGTATTTCATTTCTTTGGTGACG
TTTCCAACCTTTTGGCATCG
Found at i:1712809 original size:344 final size:344
Alignment explanation
Indices: 1712182--1712869 Score: 1376
Period size: 344 Copynumber: 2.0 Consensus size: 344
1712172 CATTTATTTT
1712182 ACTTAAAGAGCATCTTACTAATGCCCTTTTACTAGCTTTACTTGATTTCAATAAAACGTTTGAAA
1 ACTTAAAGAGCATCTTACTAATGCCCTTTTACTAGCTTTACTTGATTTCAATAAAACGTTTGAAA
1712247 TTGAATGTGATGCTTCAGGTGTGGGCATAGGAGCCGTGTTGACACAAGATGGAAGGCCAGTTGCC
66 TTGAATGTGATGCTTCAGGTGTGGGCATAGGAGCCGTGTTGACACAAGATGGAAGGCCAGTTGCC
1712312 TACTTTAGCAAGAATTAAGTGGAGCTGCCCTCAACTACCCCATTTACGAGAAGGAGATGTACACT
131 TACTTTAGCAAGAATTAAGTGGAGCTGCCCTCAACTACCCCATTTACGAGAAGGAGATGTACACT
1712377 TTAGTTCGAGCCCTAGAGACGTGGCAACATTATTTATGGCCGAAGGAGTTCGTGATTCACTCTGA
196 TTAGTTCGAGCCCTAGAGACGTGGCAACATTATTTATGGCCGAAGGAGTTCGTGATTCACTCTGA
1712442 TCACGAAGCTTTGAAGCACATTAAGGGCCAGCATAGTAGAAAAGGAGATGCCAAACATAATCACT
261 TCACGAAGCTTTGAAGCACATTAAGGGCCAGCATAGTAGAAAAGGAGATGCCAAACATAATCACT
1712507 CATTAAAGAAATTTTGGCA
326 CATTAAAGAAATTTTGGCA
1712526 ACTTAAAGAGCATCTTACTAATGCCCTTTTACTAGCTTTACTTGATTTCAATAAAACGTTTGAAA
1 ACTTAAAGAGCATCTTACTAATGCCCTTTTACTAGCTTTACTTGATTTCAATAAAACGTTTGAAA
1712591 TTGAATGTGATGCTTCAGGTGTGGGCATAGGAGCCGTGTTGACACAAGATGGAAGGCCAGTTGCC
66 TTGAATGTGATGCTTCAGGTGTGGGCATAGGAGCCGTGTTGACACAAGATGGAAGGCCAGTTGCC
1712656 TACTTTAGCAAGAATTAAGTGGAGCTGCCCTCAACTACCCCATTTACGAGAAGGAGATGTACACT
131 TACTTTAGCAAGAATTAAGTGGAGCTGCCCTCAACTACCCCATTTACGAGAAGGAGATGTACACT
1712721 TTAGTTCGAGCCCTAGAGACGTGGCAACATTATTTATGGCCGAAGGAGTTCGTGATTCACTCTGA
196 TTAGTTCGAGCCCTAGAGACGTGGCAACATTATTTATGGCCGAAGGAGTTCGTGATTCACTCTGA
1712786 TCACGAAGCTTTGAAGCACATTAAGGGCCAGCATAGTAGAAAAGGAGATGCCAAACATAATCACT
261 TCACGAAGCTTTGAAGCACATTAAGGGCCAGCATAGTAGAAAAGGAGATGCCAAACATAATCACT
1712851 CATTAAAGAAATTTTGGCA
326 CATTAAAGAAATTTTGGCA
1712870 TGCCAACAAC
Statistics
Matches: 344, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
344 344 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (344 bp):
ACTTAAAGAGCATCTTACTAATGCCCTTTTACTAGCTTTACTTGATTTCAATAAAACGTTTGAAA
TTGAATGTGATGCTTCAGGTGTGGGCATAGGAGCCGTGTTGACACAAGATGGAAGGCCAGTTGCC
TACTTTAGCAAGAATTAAGTGGAGCTGCCCTCAACTACCCCATTTACGAGAAGGAGATGTACACT
TTAGTTCGAGCCCTAGAGACGTGGCAACATTATTTATGGCCGAAGGAGTTCGTGATTCACTCTGA
TCACGAAGCTTTGAAGCACATTAAGGGCCAGCATAGTAGAAAAGGAGATGCCAAACATAATCACT
CATTAAAGAAATTTTGGCA
Found at i:1717103 original size:106 final size:106
Alignment explanation
Indices: 1716918--1717129 Score: 415
Period size: 106 Copynumber: 2.0 Consensus size: 106
1716908 CAATAAAGTG
*
1716918 AGTTGTAAACTCAGTGCACAAATAAGCTTGTTCACATAAACACATTTACCAAATAGTGTCCATAT
1 AGTTGTAAACTCAGTGCACAAAGAAGCTTGTTCACATAAACACATTTACCAAATAGTGTCCATAT
1716983 TCAAAGATTCGATCTGATAACAGAACATTTCTAGTTCAGAT
66 TCAAAGATTCGATCTGATAACAGAACATTTCTAGTTCAGAT
1717024 AGTTGTAAACTCAGTGCACAAAGAAGCTTGTTCACATAAACACATTTACCAAATAGTGTCCATAT
1 AGTTGTAAACTCAGTGCACAAAGAAGCTTGTTCACATAAACACATTTACCAAATAGTGTCCATAT
1717089 TCAAAGATTCGATCTGATAACAGAACATTTCTAGTTCAGAT
66 TCAAAGATTCGATCTGATAACAGAACATTTCTAGTTCAGAT
1717130 CCAAGACAGA
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.30
Consensus pattern (106 bp):
AGTTGTAAACTCAGTGCACAAAGAAGCTTGTTCACATAAACACATTTACCAAATAGTGTCCATAT
TCAAAGATTCGATCTGATAACAGAACATTTCTAGTTCAGAT
Found at i:1719165 original size:69 final size:71
Alignment explanation
Indices: 1719035--1719169 Score: 193
Period size: 69 Copynumber: 1.9 Consensus size: 71
1719025 ACTCATTCAT
* * *
1719035 GGTTCCTAAGTGCTGATTCCACCGTATCCTTGAATATAAAAAGGGGTTGCTAAGTGTTGATTCCC
1 GGTTCCTAAGTGCTGATCCCACCGTATCCTTAAATATAAAAAGGGGTTGCTAAGTGCTGATTCCC
1719100 CCAAGG
66 CCAAGG
* * * *
1719106 GGTTGCTAAGTGCTGATCCCACCGTAT-TTTAAATGT-GAAAGGGGTTGCTAAGTGCTGATTCCC
1 GGTTCCTAAGTGCTGATCCCACCGTATCCTTAAATATAAAAAGGGGTTGCTAAGTGCTGATTCCC
1719169 C
66 C
1719170 GAATTACTGG
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 26 0.46
70 6 0.11
71 25 0.44
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (71 bp):
GGTTCCTAAGTGCTGATCCCACCGTATCCTTAAATATAAAAAGGGGTTGCTAAGTGCTGATTCCC
CCAAGG
Found at i:1719190 original size:33 final size:33
Alignment explanation
Indices: 1719148--1719299 Score: 169
Period size: 33 Copynumber: 4.4 Consensus size: 33
1719138 ATGTGAAAGG
1719148 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
1719181 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
* ** * *
1719214 GGTTGCTAAGTGCTGATCCCACCATGTCTTAAATGTGAAGG
1 GGTTGCTAAGTGCTGATTCC-CC--GAATT--A-CTG--GT
* *
1719255 GGTTGCTAAGTGCTAATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
1719288 GGTTGCTAAGTG
1 GGTTGCTAAGTG
1719300 TTGAATCCAC
Statistics
Matches: 99, Mismatches: 12, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
33 65 0.66
34 2 0.02
35 2 0.02
36 4 0.04
38 3 0.03
39 2 0.02
40 2 0.02
41 19 0.19
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
Found at i:1719286 original size:107 final size:108
Alignment explanation
Indices: 1719106--1719299 Score: 336
Period size: 107 Copynumber: 1.8 Consensus size: 108
1719096 TCCCCCAAGG
* * *
1719106 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCG
1 GGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGCTAATTCCCCG
*
1719171 AATTACTGGTGGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
66 AATCACTGGTGGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
*
1719214 GGTTGCTAAGTGCTGATCCCACCATGTCTTAAATGTG-AAGGGGTTGCTAAGTGCTAATTCCCCG
1 GGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGCTAATTCCCCG
1719278 AATCACTGGTGGTTGCTAAGTG
66 AATCACTGGTGGTTGCTAAGTG
1719300 TTGAATCCAC
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
107 47 0.58
108 34 0.42
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (108 bp):
GGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGCTAATTCCCCG
AATCACTGGTGGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
Found at i:1725922 original size:27 final size:27
Alignment explanation
Indices: 1725892--1725944 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1725882 TTGAATACAA
*
1725892 AAGGGGCTGCTAAGTGTTGATTCCCCC
1 AAGGGGCTGCTAAGTGCTGATTCCCCC
*
1725919 AAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGCTGCTAAGTGCTGATTCCCC
1725945 GACTCATTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.25, G:0.30, T:0.26
Consensus pattern (27 bp):
AAGGGGCTGCTAAGTGCTGATTCCCCC
Found at i:1725965 original size:33 final size:33
Alignment explanation
Indices: 1725923--1726226 Score: 158
Period size: 33 Copynumber: 8.4 Consensus size: 33
1725913 TCCCCCAAGG
*
1725923 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTAATTGGT
* * *
1725956 GGTTGCTAAGTGTTGATTCCACAGTATCCTTGAATATAAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--C-T-AAT-T----GGT
*
1726000 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTAATTGGT
* * *
1726033 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--CT-AAT-TG---GT
* * * *
1726075 GGTTGCTAAGTGCTGATTCACCGAATTACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTAATTGGT
* * * * *
1726108 GGTTGCTAAGTGTTGATTCCCCGAATTACTAGT
1 GGTTGCTAAGTGCTGATTCCCCGACTAATTGGT
* *
1726141 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-C-T-AAT-TG--GT
* * *
1726182 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTAATTGGT
1726215 GGTTGCTAAGTG
1 GGTTGCTAAGTG
1726227 TTGAATCCAC
Statistics
Matches: 210, Mismatches: 33, Indels: 56
0.70 0.11 0.19
Matches are distributed among these distances:
33 102 0.49
34 8 0.04
35 5 0.02
36 3 0.01
37 6 0.03
38 7 0.03
39 7 0.03
40 6 0.03
41 23 0.11
42 20 0.10
43 2 0.01
44 21 0.10
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGACTAATTGGT
Found at i:1726230 original size:107 final size:108
Alignment explanation
Indices: 1726000--1726239 Score: 383
Period size: 108 Copynumber: 2.2 Consensus size: 108
1725990 TATAAAAGGG
* * * * *
1726000 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTTTAA
1 GGTTGCTAAGTGTTGATTCCCCGAATCACTAGTGGTTGCTAAGTGCTGATCCCACCGTATCTTAA
*
1726065 ATGTGAAAGGGGTTGCTAAGTGCTGATTCACCGAATTACTGGT
66 ATGTGAAAGGGGTTGCTAAGTGCTGATTCACCGAATCACTGGT
*
1726108 GGTTGCTAAGTGTTGATTCCCCGAATTACTAGTGGTTGCTAAGTGCTGATCCCACCGTATCTTAA
1 GGTTGCTAAGTGTTGATTCCCCGAATCACTAGTGGTTGCTAAGTGCTGATCCCACCGTATCTTAA
*
1726173 ATGTG-AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
66 ATGTGAAAGGGGTTGCTAAGTGCTGATTCACCGAATCACTGGT
*
1726215 GGTTGCTAAGTGTTGAATCCACCGA
1 GGTTGCTAAGTGTTGATTCC-CCGA
1726240 TAACGGATAA
Statistics
Matches: 122, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
107 54 0.44
108 68 0.56
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (108 bp):
GGTTGCTAAGTGTTGATTCCCCGAATCACTAGTGGTTGCTAAGTGCTGATCCCACCGTATCTTAA
ATGTGAAAGGGGTTGCTAAGTGCTGATTCACCGAATCACTGGT
Found at i:1734008 original size:22 final size:22
Alignment explanation
Indices: 1733949--1734010 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
1733939 TATGAAATAT
*
1733949 GAAAATAAATATATAAAAATTCA
1 GAAAAAAAATATAT-AAAATTCA
* * *
1733972 GAAAACATATGTATAAAA-TCTA
1 GAAAAAAAATATATAAAATTC-A
1733994 GAAAAAAAATATATAAA
1 GAAAAAAAATATATAAA
1734011 TTATAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 2 0.06
22 19 0.59
23 11 0.34
ACGTcount: A:0.65, C:0.05, G:0.06, T:0.24
Consensus pattern (22 bp):
GAAAAAAAATATATAAAATTCA
Found at i:1734408 original size:15 final size:15
Alignment explanation
Indices: 1734388--1734416 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1734378 GTCAATGGTC
1734388 AGTCAACAACTAGTT
1 AGTCAACAACTAGTT
1734403 AGTCAACAACTAGT
1 AGTCAACAACTAGT
1734417 CAAAGTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (15 bp):
AGTCAACAACTAGTT
Found at i:1734457 original size:21 final size:20
Alignment explanation
Indices: 1734433--1734484 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
1734423 CAATAGTATT
1734433 TTTTAATATTTAAATATTTAA
1 TTTTAATATTT-AATATTTAA
**
1734454 TTTT-ATAATTTTTTATTTAA
1 TTTTAAT-ATTTAATATTTAA
*
1734474 ATTTAATATTT
1 TTTTAATATTT
1734485 TTATTTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAATATTTAATATTTAA
Found at i:1734486 original size:21 final size:20
Alignment explanation
Indices: 1734447--1734490 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1734437 AATATTTAAA
*
1734447 TATTTAATTTTATAATTTTT
1 TATTTAATTTAATAATTTTT
1734467 TATTTAAATTTAAT-A-TTTT
1 TATTT-AATTTAATAATTTTT
1734486 TATTT
1 TATTT
1734491 TAAGTAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 6 0.27
21 7 0.32
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTTAATTTAATAATTTTT
Found at i:1754898 original size:61 final size:61
Alignment explanation
Indices: 1754824--1754963 Score: 147
Period size: 61 Copynumber: 2.3 Consensus size: 61
1754814 ATCAATTTGA
* * * * ** * *
1754824 TCCTAAATATAAAAAGTTCAACAAATTTAGCTCTTAA-AGTTTACAAAATTTGTCATTTTAG
1 TCCTAACTCTAAAAAGTTCAACAAATTTAGCCCTCAATA-TTTACAAAATTAATAAATTTAG
* * * * *
1754885 TTCTAATTCTAAAAAATTCAATAAATTTGGCCCTCAATATTTACAAAATTAATAAATTTAG
1 TCCTAACTCTAAAAAGTTCAACAAATTTAGCCCTCAATATTTACAAAATTAATAAATTTAG
1754946 TCCTAACTCTAAAAAGTT
1 TCCTAACTCTAAAAAGTT
1754964 AAAAATATTT
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
61 62 0.98
62 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.37
Consensus pattern (61 bp):
TCCTAACTCTAAAAAGTTCAACAAATTTAGCCCTCAATATTTACAAAATTAATAAATTTAG
Found at i:1762921 original size:18 final size:18
Alignment explanation
Indices: 1762900--1762934 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1762890 CTATTATAAT
1762900 TATTAGTATTAT-TGTTTG
1 TATTAGT-TTATATGTTTG
1762918 TATTAGTTTATATGTTT
1 TATTAGTTTATATGTTT
1762935 ATTTACCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (18 bp):
TATTAGTTTATATGTTTG
Found at i:1767690 original size:9 final size:9
Alignment explanation
Indices: 1767676--1767713 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
1767666 TGAGTTTCAA
1767676 AAAAAAATC
1 AAAAAAATC
1767685 AAAAAAATC
1 AAAAAAATC
1767694 --AAAAATC
1 AAAAAAATC
*
1767701 AAACAAATC
1 AAAAAAATC
1767710 AAAA
1 AAAA
1767714 TGAAAATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
7 7 0.28
9 18 0.72
ACGTcount: A:0.76, C:0.13, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAATC
Found at i:1767699 original size:16 final size:16
Alignment explanation
Indices: 1767678--1767713 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1767668 AGTTTCAAAA
1767678 AAAAATCAAAAAAATC
1 AAAAATCAAAAAAATC
*
1767694 AAAAATCAAACAAATC
1 AAAAATCAAAAAAATC
1767710 AAAA
1 AAAA
1767714 TGAAAATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.75, C:0.14, G:0.00, T:0.11
Consensus pattern (16 bp):
AAAAATCAAAAAAATC
Found at i:1768653 original size:46 final size:45
Alignment explanation
Indices: 1768584--1768672 Score: 115
Period size: 46 Copynumber: 2.0 Consensus size: 45
1768574 AAGGAGAGGG
** * *
1768584 GACCAAGGTGAAAACCCGTAAAGGGCGCTTTGATTCCTAAAAAAAA
1 GACCAAGGTGAAAACCCACAAAGGGCACTTTGAGTCC-AAAAAAAA
* *
1768630 GACCAAGGTGAAAACTCACAAAGGGCATTTTGAGTCCAAAAAA
1 GACCAAGGTGAAAACCCACAAAGGGCACTTTGAGTCCAAAAAA
1768673 TAATAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 6 0.16
46 31 0.84
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (45 bp):
GACCAAGGTGAAAACCCACAAAGGGCACTTTGAGTCCAAAAAAAA
Found at i:1770044 original size:45 final size:45
Alignment explanation
Indices: 1769977--1770313 Score: 512
Period size: 45 Copynumber: 7.5 Consensus size: 45
1769967 GCAGCAGTGG
* * * * *
1769977 AGTAGGTTGAAAACAGCAGATCTTGTCTTCCTGTATTGGTAGTGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * *
1770022 AGTAGATCGAAGATATCAGATCTTGTCTTCTTGTATTGGCAGCGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
** *
1770067 AGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
**
1770112 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAATGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
1770157 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
1770202 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * *
1770247 AGAAGATCGAAGTTAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* *
1770292 AATAGATTAAAGATAGCAGATC
1 AGTAGATTGAAGATAGCAGATC
1770314 CGCGAGGTGT
Statistics
Matches: 265, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 265 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (45 bp):
AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
Found at i:1770759 original size:18 final size:18
Alignment explanation
Indices: 1770738--1770772 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1770728 CTATTATAAT
1770738 TATTAGTATTAT-TGTTTG
1 TATTAGT-TTATATGTTTG
1770756 TATTAGTTTATATGTTT
1 TATTAGTTTATATGTTT
1770773 ATTTACCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (18 bp):
TATTAGTTTATATGTTTG
Found at i:1772650 original size:28 final size:29
Alignment explanation
Indices: 1772558--1772650 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
1772548 GCACTAGGTG
1772558 CCGGTGATTACAGTTTCTAGGTACTATGTA
1 CCGGTGA-TACAGTTTCTAGGTACTATGTA
* * * * * *
1772588 CCAGTGTTACAGTTTCCAGGCACTCTGTG
1 CCGGTGATACAGTTTCTAGGTACTATGTA
*
1772617 CCGGTGATATA-TTTCTAGGTACTATGTA
1 CCGGTGATACAGTTTCTAGGTACTATGTA
*
1772645 TCGGTG
1 CCGGTG
1772651 GTGGATACCA
Statistics
Matches: 49, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
28 18 0.37
29 26 0.53
30 5 0.10
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (29 bp):
CCGGTGATACAGTTTCTAGGTACTATGTA
Found at i:1776134 original size:14 final size:14
Alignment explanation
Indices: 1776104--1776143 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
1776094 TGAGAGATGA
1776104 GAGGGATGATAGGAT
1 GAGGGATGAT-GGAT
1776119 GAGGGATGATGGAT
1 GAGGGATGATGGAT
*
1776133 GATGGATGATG
1 GAGGGATGATG
1776144 AGAAATGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (14 bp):
GAGGGATGATGGAT
Found at i:1776142 original size:7 final size:7
Alignment explanation
Indices: 1776107--1776143 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
1776097 GAGATGAGAG
1776107 GGATGAT
1 GGATGAT
*
1776114 AGGATGAG
1 -GGATGAT
1776122 GGATGAT
1 GGATGAT
1776129 GGATGAT
1 GGATGAT
1776136 GGATGAT
1 GGATGAT
1776143 G
1 G
1776144 AGAAATGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.46, T:0.24
Consensus pattern (7 bp):
GGATGAT
Found at i:1796831 original size:18 final size:18
Alignment explanation
Indices: 1796808--1796842 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1796798 ATTTATTGCA
1796808 TGAAAACTATATAATAAC
1 TGAAAACTATATAATAAC
*
1796826 TGAAAACTTTATAATAA
1 TGAAAACTATATAATAA
1796843 AACATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (18 bp):
TGAAAACTATATAATAAC
Found at i:1806673 original size:7 final size:7
Alignment explanation
Indices: 1806663--1806691 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1806653 GAGATGAGAG
1806663 GGATGAT
1 GGATGAT
1806670 GGATGAT
1 GGATGAT
1806677 GGATGAT
1 GGATGAT
1806684 GGATGAT
1 GGATGAT
1806691 G
1 G
1806692 AGAAATGAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.28
Consensus pattern (7 bp):
GGATGAT
Found at i:1810707 original size:68 final size:69
Alignment explanation
Indices: 1810587--1810716 Score: 208
Period size: 68 Copynumber: 1.9 Consensus size: 69
1810577 AACTTAACCG
* *
1810587 CTTTAATATTAAATTAATATAATATTTATCAAGATAAATATGAAATTCAATTTAATATTAAAGAT
1 CTTTAATATTAAATTAATAAAATATCTATCAAGATAAATATGAAATTCAATTTAATATTAAAGAT
1810652 ATCA
66 ATCA
* * *
1810656 CTTTAATATTAAATTAATAAAATA-CTATTAAGATAAATATTAAATTTAATTTAATATTAAA
1 CTTTAATATTAAATTAATAAAATATCTATCAAGATAAATATGAAATTCAATTTAATATTAAA
1810717 CTATTAGAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
68 33 0.59
69 23 0.41
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (69 bp):
CTTTAATATTAAATTAATAAAATATCTATCAAGATAAATATGAAATTCAATTTAATATTAAAGAT
ATCA
Found at i:1820163 original size:20 final size:22
Alignment explanation
Indices: 1820136--1820191 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
1820126 CCTAATCAGT
*
1820136 ATACGACACATAAGTGCCT-GA
1 ATACGACACATAAGTGCCTAAA
*
1820157 A-ACGACACACGAAGTGCCTAAA
1 ATACGACACA-TAAGTGCCTAAA
1820179 ATACGACACATAA
1 ATACGACACATAA
1820192 AGTGTCTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 8 0.28
21 9 0.31
22 4 0.14
23 8 0.28
ACGTcount: A:0.45, C:0.25, G:0.16, T:0.14
Consensus pattern (22 bp):
ATACGACACATAAGTGCCTAAA
Found at i:1820554 original size:26 final size:25
Alignment explanation
Indices: 1820523--1820572 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1820513 TAGTTCAATA
1820523 ATTCAATTCAAAC-CATTTCAATTTCT
1 ATTCAA-T-AAACACATTTCAATTTCT
*
1820549 ATTCAATAATCACATTTCAATTTC
1 ATTCAATAAACACATTTCAATTTC
1820573 ACTTTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.59
26 6 0.27
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTCAATAAACACATTTCAATTTCT
Found at i:1820920 original size:11 final size:11
Alignment explanation
Indices: 1820904--1820937 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1820894 AAACCCTAGT
1820904 TTTTCCTTTTC
1 TTTTCCTTTTC
1820915 TTTTCCTTTTC
1 TTTTCCTTTTC
*
1820926 TTCTTTCTTTTC
1 TT-TTCCTTTTC
1820938 CCCTGTTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCCTTTTC
Found at i:1828433 original size:17 final size:17
Alignment explanation
Indices: 1828407--1828460 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
1828397 TAAACCATAT
1828407 ATTT-ATTCTATAATTA
1 ATTTAATTCTATAATTA
1828423 ATTTAATTC--T-A-TA
1 ATTTAATTCTATAATTA
1828436 A-TTAATTCTATAATTA
1 ATTTAATTCTATAATTA
1828452 ATTTAATTC
1 ATTTAATTC
1828461 AAGCGACCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
12 7 0.22
13 3 0.09
14 2 0.06
15 2 0.06
16 7 0.22
17 11 0.34
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTAATTCTATAATTA
Found at i:1828442 original size:12 final size:12
Alignment explanation
Indices: 1828425--1828454 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1828415 TATAATTAAT
1828425 TTAATTCTATAA
1 TTAATTCTATAA
1828437 TTAATTCTATAA
1 TTAATTCTATAA
1828449 TTAATT
1 TTAATT
1828455 TAATTCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAATTCTATAA
Found at i:1842173 original size:17 final size:17
Alignment explanation
Indices: 1842151--1842185 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1842141 TGATCCTGTC
1842151 TCACTAAAATTCAAATA
1 TCACTAAAATTCAAATA
1842168 TCACTAAAATTCAAATA
1 TCACTAAAATTCAAATA
1842185 T
1 T
1842186 TACAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (17 bp):
TCACTAAAATTCAAATA
Found at i:1842758 original size:16 final size:16
Alignment explanation
Indices: 1842733--1842769 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1842723 ATCACGATCT
*
1842733 TTACTTTCTTCTTTAC
1 TTACTCTCTTCTTTAC
*
1842749 TTACTCTCTTGTTTAC
1 TTACTCTCTTCTTTAC
1842765 TTACT
1 TTACT
1842770 TGCTTACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.03, T:0.59
Consensus pattern (16 bp):
TTACTCTCTTCTTTAC
Found at i:1844803 original size:11 final size:11
Alignment explanation
Indices: 1844780--1844808 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1844770 TGAAGATGGT
1844780 TGTTTTG-GCA
1 TGTTTTGAGCA
1844790 TGTTTTGAGCA
1 TGTTTTGAGCA
1844801 TGTTTTGA
1 TGTTTTGA
1844809 ATAGGTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.14, C:0.07, G:0.28, T:0.52
Consensus pattern (11 bp):
TGTTTTGAGCA
Found at i:1851342 original size:17 final size:17
Alignment explanation
Indices: 1851320--1851352 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1851310 ACATATATGG
*
1851320 ATTGAATCCCAAAATTT
1 ATTGAAACCCAAAATTT
1851337 ATTGAAACCCAAAATT
1 ATTGAAACCCAAAATT
1851353 AACAAATCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.30
Consensus pattern (17 bp):
ATTGAAACCCAAAATTT
Found at i:1851809 original size:22 final size:22
Alignment explanation
Indices: 1851768--1851810 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1851758 ACAACAGAAC
* *
1851768 AGGTTTTTAGCGGCATTTTTTT
1 AGGTCTTTAGCGGCACTTTTTT
*
1851790 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCACTTTTT
1851811 AACGCCACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCACTTTTTT
Found at i:1851953 original size:43 final size:42
Alignment explanation
Indices: 1851900--1852068 Score: 234
Period size: 43 Copynumber: 4.0 Consensus size: 42
1851890 GCGCTTACAT
1851900 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCGTTGA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTGA
*
1851943 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTGAA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-CTTG-A
* *
1851987 AAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTGT
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGA
**
1852029 TCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTT
1 AAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTT
1852069 ATTTCACAAA
Statistics
Matches: 115, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
41 2 0.02
42 33 0.29
43 43 0.37
44 37 0.32
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGA
Found at i:1852003 original size:87 final size:86
Alignment explanation
Indices: 1851900--1852065 Score: 255
Period size: 87 Copynumber: 1.9 Consensus size: 86
1851890 GCGCTTACAT
*
1851900 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCGTTGAAAAAAAACGCCGCT-AAAGATC
1 AAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGC-TTGAAAAAAAACGCCGCTAAAAG-T-
1851964 A-TGTTCTTTAGCGGCGTTTTGAA
63 AGTGTTCTTTAGCGGCGTTTTGAA
***
1851987 AAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTGTTCAAAAACGCCGCTAAAAGTAGT
1 AAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTGAAAAAAAACGCCGCTAAAAGTAGT
1852052 GTTCTTTAGCGGCG
66 GTTCTTTAGCGGCG
1852066 CTTATTTCAC
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
85 1 0.01
86 31 0.42
87 41 0.56
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (86 bp):
AAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTGAAAAAAAACGCCGCTAAAAGTAGT
GTTCTTTAGCGGCGTTTTGAA
Found at i:1852507 original size:12 final size:12
Alignment explanation
Indices: 1852490--1852535 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1852480 TTTTGAACCT
*
1852490 CTGCTTCTATTG
1 CTGCTTCTCTTG
*
1852502 CTGCTTCTCTCG
1 CTGCTTCTCTTG
*
1852514 CCGCTTCTCTTG
1 CTGCTTCTCTTG
*
1852526 TTGCTTCTCT
1 CTGCTTCTCT
1852536 CCTGCGGCCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.02, C:0.35, G:0.15, T:0.48
Consensus pattern (12 bp):
CTGCTTCTCTTG
Found at i:1852556 original size:20 final size:21
Alignment explanation
Indices: 1852527--1852593 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
1852517 CTTCTCTTGT
*
1852527 TGCTTCTCTC-CTGCGGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
* *
1852547 TGCTTGTCTCGCTGTAGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
* * *
1852568 TGCTTCCCTCGCTGCCGTCTC
1 TGCTTCTCTCGCTGCAGCCTC
1852589 TGCTT
1 TGCTT
1852594 TAAGTTGCTG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 9 0.24
21 29 0.76
ACGTcount: A:0.01, C:0.40, G:0.21, T:0.37
Consensus pattern (21 bp):
TGCTTCTCTCGCTGCAGCCTC
Found at i:1861879 original size:25 final size:25
Alignment explanation
Indices: 1861851--1861899 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1861841 TAGGAAAGAA
1861851 AAAAATAAGTTAGGGATTTAGGGAT
1 AAAAATAAGTTAGGGATTTAGGGAT
* *
1861876 AAAACTAAGTTAGGGATTTGGGGA
1 AAAAATAAGTTAGGGATTTAGGGA
1861900 AAATGATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.31, T:0.27
Consensus pattern (25 bp):
AAAAATAAGTTAGGGATTTAGGGAT
Found at i:1863031 original size:14 final size:14
Alignment explanation
Indices: 1863012--1863041 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1863002 AGTGAGAGAC
*
1863012 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
1863026 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
1863040 GA
1 GA
1863042 ATGAGGGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:1863617 original size:20 final size:22
Alignment explanation
Indices: 1863592--1863639 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1863582 CGAATCTCTA
1863592 AAAAATAA-T-CAAAATTCACT
1 AAAAATAATTGCAAAATTCACT
* *
1863612 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGCAAAATTCACT
1863634 AAAAAT
1 AAAAAT
1863640 TAACATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATAATTGCAAAATTCACT
Found at i:1863865 original size:24 final size:25
Alignment explanation
Indices: 1863824--1863870 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1863814 AAATTTTGGA
*
1863824 AAGAATTTTTCAGAAAC-ACTTTTG
1 AAGAATTCTTCAGAAACAACTTTTG
1863848 AAGAATTCCTTCAG-AACAACTTT
1 AAGAATT-CTTCAGAAACAACTTT
1863871 CTTCTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (25 bp):
AAGAATTCTTCAGAAACAACTTTTG
Found at i:1874685 original size:18 final size:18
Alignment explanation
Indices: 1874662--1874799 Score: 276
Period size: 18 Copynumber: 7.7 Consensus size: 18
1874652 TAATACAATG
1874662 TAATTATTTTATAAAAAT
1 TAATTATTTTATAAAAAT
1874680 TAATTATTTTATAAAAAT
1 TAATTATTTTATAAAAAT
1874698 TAATTATTTTATAAAAAT
1 TAATTATTTTATAAAAAT
1874716 TAATTATTTTATAAAAAT
1 TAATTATTTTATAAAAAT
1874734 TAATTATTTTATAAAAAT
1 TAATTATTTTATAAAAAT
1874752 TAATTATTTTATAAAAAT
1 TAATTATTTTATAAAAAT
1874770 TAATTATTTTATAAAAAT
1 TAATTATTTTATAAAAAT
1874788 TAATTATTTTAT
1 TAATTATTTTAT
1874800 GACAAAAATT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 120 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTATTTTATAAAAAT
Found at i:1885964 original size:6 final size:6
Alignment explanation
Indices: 1885941--1885975 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
1885931 TTTCAAATAA
1885941 TTTCAT TTCTCTAT TTTCAT TTTCAT TTTCAT TTT
1 TTTCAT TT-TC-AT TTTCAT TTTCAT TTTCAT TTT
1885976 AGAGAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCAT
Found at i:1886898 original size:30 final size:30
Alignment explanation
Indices: 1886864--1886926 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1886854 ACTTAACAAG
1886864 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
1886894 CAAATGCCTTTAAAATAATATCAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
1886924 CAA
1 CAA
1886927 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:1886979 original size:14 final size:14
Alignment explanation
Indices: 1886960--1886986 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1886950 CAAACAATAA
1886960 CAACATAATAGTAG
1 CAACATAATAGTAG
1886974 CAACATAATAGTA
1 CAACATAATAGTA
1886987 AAATGGTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (14 bp):
CAACATAATAGTAG
Found at i:1892627 original size:37 final size:37
Alignment explanation
Indices: 1892575--1892665 Score: 137
Period size: 37 Copynumber: 2.5 Consensus size: 37
1892565 CGAAGTTTCC
** *
1892575 AGCTTAACTTGGCTAACTCAAATAACTGGAGGTTGCG
1 AGCTTAACTCAGCTAACTCAAATAACTGGAGGTTGCA
*
1892612 AGCTTAACTCAGCTAACTCAAATAACTGGATGTTGCA
1 AGCTTAACTCAGCTAACTCAAATAACTGGAGGTTGCA
*
1892649 AGCTTAACTCAACTAAC
1 AGCTTAACTCAGCTAAC
1892666 CTTTAATCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (37 bp):
AGCTTAACTCAGCTAACTCAAATAACTGGAGGTTGCA
Found at i:1892790 original size:104 final size:105
Alignment explanation
Indices: 1892601--1892790 Score: 310
Period size: 104 Copynumber: 1.8 Consensus size: 105
1892591 CTCAAATAAC
* * *
1892601 TGGAGGTTGCGAGCTTAACTCAGCTAACTCAAATAACTGGATGTTGCAAGCTTAACTCAACTAAC
1 TGGAGGTTACGAGCTTAACTCAACTAACTCAAATAACTGGAGGTTGCAAGCTTAACTCAACTAAC
1892666 CTTTAATCATCAGTTGGGAACATAGGTCCGCAAGCTATTT
66 CTTTAATCATCAGTTGGGAACATAGGTCCGCAAGCTATTT
* * *
1892706 TGGA-GTTACGAGCTTAACTCAACTAACTCAAATAATTGGAGGTTGCGAGCTTAACTCATCTAAC
1 TGGAGGTTACGAGCTTAACTCAACTAACTCAAATAACTGGAGGTTGCAAGCTTAACTCAACTAAC
*
1892770 CTTTAATCATTAGTTGGGAAC
66 CTTTAATCATCAGTTGGGAAC
1892791 GTAAGTGTAA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
104 74 0.95
105 4 0.05
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (105 bp):
TGGAGGTTACGAGCTTAACTCAACTAACTCAAATAACTGGAGGTTGCAAGCTTAACTCAACTAAC
CTTTAATCATCAGTTGGGAACATAGGTCCGCAAGCTATTT
Found at i:1893287 original size:81 final size:82
Alignment explanation
Indices: 1893179--1893342 Score: 312
Period size: 81 Copynumber: 2.0 Consensus size: 82
1893169 TAAGGTTCCG
1893179 GTTAAGTGAATTTGCTTGAATTAAGAGTTATTATAGTATAAGGACTAAATCCCGTATAAGGTGAA
1 GTTAAGTGAA-TTGCTTGAATTAAGAGTTATTATAGTATAAGGACTAAATCCCGTATAAGGTGAA
1893244 AGTTGAATTATAGATTAA
65 AGTTGAATTATAGATTAA
1893262 GTTAAGTGAA-TGCTTGAATTAAGAGTTATTATAGTATAAGGACTAAATCCCGTATAAGGTGAAA
1 GTTAAGTGAATTGCTTGAATTAAGAGTTATTATAGTATAAGGACTAAATCCCGTATAAGGTGAAA
1893326 GTTGAATTATAGATTAA
66 GTTGAATTATAGATTAA
1893343 AAATTAATAT
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
81 71 0.88
83 10 0.12
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (82 bp):
GTTAAGTGAATTGCTTGAATTAAGAGTTATTATAGTATAAGGACTAAATCCCGTATAAGGTGAAA
GTTGAATTATAGATTAA
Found at i:1893591 original size:17 final size:17
Alignment explanation
Indices: 1893552--1893586 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1893542 TATGCAAATT
1893552 AAAA-AGAAAAGAAAGA
1 AAAAGAGAAAAGAAAGA
1893568 AAAAGAGAAAGAGAAAGA
1 AAAAGAGAAA-AGAAAGA
1893586 A
1 A
1893587 GAGAGGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAAGAGAAAAGAAAGA
Found at i:1898305 original size:24 final size:23
Alignment explanation
Indices: 1898245--1898317 Score: 74
Period size: 24 Copynumber: 3.1 Consensus size: 23
1898235 TCCGGGCTGT
1898245 ATAATGGGAAGCTCATAAGAGCC
1 ATAATGGGAAGCTCATAAGAGCC
* **
1898268 ATAATTGGAAAGCTCATGCGAGCC
1 ATAA-TGGGAAGCTCATAAGAGCC
* **
1898292 AATAATGGGTAGCTCCGAAGAGCC
1 -ATAATGGGAAGCTCATAAGAGCC
1898316 AT
1 AT
1898318 TAACGGAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
23 6 0.15
24 29 0.74
25 4 0.10
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (23 bp):
ATAATGGGAAGCTCATAAGAGCC
Found at i:1898418 original size:26 final size:26
Alignment explanation
Indices: 1898382--1898439 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
1898372 GTAGCTTCGG
1898382 AGAGCCGTTAATCGAGAAGCTCACAA
1 AGAGCCGTTAATCGAGAAGCTCACAA
* *
1898408 AGAGCCTTTAATCGAGAAGCTCACGA
1 AGAGCCGTTAATCGAGAAGCTCACAA
1898434 AGAGCC
1 AGAGCC
1898440 ATATATCGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (26 bp):
AGAGCCGTTAATCGAGAAGCTCACAA
Found at i:1904765 original size:12 final size:12
Alignment explanation
Indices: 1904750--1904776 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1904740 TAAAACTAAT
1904750 AATGTTTGATCG
1 AATGTTTGATCG
1904762 AATGTTTGATCG
1 AATGTTTGATCG
1904774 AAT
1 AAT
1904777 CAAGGCAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (12 bp):
AATGTTTGATCG
Found at i:1924010 original size:18 final size:18
Alignment explanation
Indices: 1923977--1924015 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1923967 TTAATTAAAC
1923977 AAAAGAAAGAAATGAAAAT
1 AAAAGAAAGAAATG-AAAT
*
1923996 AAAAGAAA-CAATGAAAT
1 AAAAGAAAGAAATGAAAT
1924013 AAA
1 AAA
1924016 GATAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (18 bp):
AAAAGAAAGAAATGAAAT
Found at i:1925092 original size:16 final size:15
Alignment explanation
Indices: 1925018--1925092 Score: 54
Period size: 16 Copynumber: 5.2 Consensus size: 15
1925008 TGGAAAATTT
*
1925018 ATTGAATTGAATTGTG
1 ATTGAATTGAA-AGTG
* *
1925034 ATTAAATTGGAA-TG
1 ATTGAATTGAAAGTG
1925048 ATTTGAATTGAAAGT-
1 A-TTGAATTGAAAGTG
1925063 A-TG-A--GAAAGTG
1 ATTGAATTGAAAGTG
1925074 ATTGAATTGAAATGTG
1 ATTGAATTGAAA-GTG
1925090 ATT
1 ATT
1925093 CAGAAACCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
10 6 0.13
11 1 0.02
12 3 0.07
13 3 0.07
14 3 0.07
15 14 0.30
16 16 0.35
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (15 bp):
ATTGAATTGAAAGTG
Found at i:1936399 original size:70 final size:70
Alignment explanation
Indices: 1936041--1937288 Score: 728
Period size: 70 Copynumber: 17.6 Consensus size: 70
1936031 TAACAAGTTC
* * * * *
1936041 AATACCGCAGCCTCCAAATAGTTAGTGAGAGTTTAAAGGTCTCAACTGTAATATTAAGGCTCGCA
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
**
1936106 TATAA
66 GGTAA
* * ** * * * * * * ***
1936111 AGTACCACAGCCCCCAAACGGTTAGCGAGAGTTCAAAGCTCCCTGTTATTAGATTAAGGCTTATA
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
1936176 GGTAA
66 GGTAA
* * * * * ** * * * * * * *
1936181 AGTACTGTAGCCCCCCAAACATTTAGAAAGAGTTAAAAGCTCCCAACTGTCATTATCAAGACTCA
1 AATACCGCAG-CCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTCG
* * **
1936246 TAAGTTC
64 CAGGTAA
* ** ** * * * * * *
1936253 AATACCGCAACCCTCCAAATAGCCAGTAAAAGTTAAAAGCTCTTAGTTGTCATTATTAAGGCTCA
1 AATACCGCAGCCC-CCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTCG
**
1936318 CAGGTTT
64 CAGGTAA
* * * * * * * *
1936325 AATATCGCAGCCCCCAAATAGTTAGCAAAATTTTAAAGCTCTCAGTTATAATGTTAAGGCTCGCA
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
1936390 GGTAA
66 GGTAA
** * * * * * ** * *
1936395 AATATTGCAGCCTCCAAAACAGTTAACGAGAGCT-AAAGCTCCCAAATGTAATCTTAAGGCTCGT
1 AATACCGCAGCC-CCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGC
* **
1936459 AGATTT
65 AGGTAA
** * * * * * * *
1936465 AATACTACAGCCCCCGAAACAGTTATCAAAAGTTAAAAGCTCTCAACTGTCATTATTAAGGCTCG
1 AATACCGCAGCCCCC-AAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTCG
**
1936530 CAGGTGC
64 CAGGTAA
* * *
1936537 AATACCGCAGCCCCCCAAACAGTTAGCGAGAGTTAAAAGCTCTCAGCTGTCATTATTAAGGCTCG
1 AATACCGCAG-CCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTCG
**
1936602 CAGGTTT
64 CAGGTAA
** * ** ** *
1936609 AATAATGCAGCCCCCAAAGAGTTATTGAGAGTTCAAAGCTC-CTAATTGTAATGTTAAGGCTCGC
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTC-AGCTGTAATATTAAGGCTCGC
*
1936673 AAGTAA
65 AGGTAA
** ** * * * * ** *
1936679 AATACTACAGCCTCTAAAATAGTTAGCGAGGGCT-GAAGCTC-CTAGCTATAA-CCTCAGGCTCG
1 AATACCGCAGCC-CCCAAATAGTTAGCGAGAGTTCAAAGCTCTC-AGCTGTAATATTAAGGCTCG
**
1936741 CAGGTTC
64 CAGGTAA
* * * * * * *
1936748 AATACCGTAGCCCCCAAATAGTTAGCGAGATTTCAAAGCTTTCATCTGTAATATTAATGTTCACA
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
*
1936813 AGTAA
66 GGTAA
* ** * * *
1936818 ATTACCTTAGCCCCCAAATAGTTAGCAAGAGTTCAAAACT-TCCAGCTGTAATATTAAGGCTCAC
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCT-CAGCTGTAATATTAAGGCTCGC
1936882 AGGTAA
65 AGGTAA
* * * * *
1936888 AGTATCACAGCCCCCAAACAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCACA
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
1936953 GGTAA
66 GGTAA
* * * * * * *
1936958 AGTACCGCAGACCCCAAATAGTTACCAAGAGTTCAAAGCTCCCAGCTGTAATATTAAGGATCACA
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
1937023 GGTAA
66 GGTAA
* ** * * ** * *
1937028 AGTACCGCAGCCCCCAAATAGTTAATGAGAGTTAAAAGCTCCCAATTGTCATTATTAAGGCTCAC
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTCGC
**
1937093 AGGTTT
65 AGGTAA
** * * * * *
1937099 AAGGCCACAGCCCCCCAAATAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCG
1 AATACCGCAG-CCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTCG
* **
1937164 CAGATTC
64 CAGGTAA
** * * * *
1937171 AATACTACAGTCCCTCAAATAGTTAG-GTAGAGTTAAAAGCTCCCAGCTGTCATTATTAAGGCTC
1 AATACCGCAG-CCCCCAAATAGTTAGCG-AGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTC
* * **
1937235 ACAGATTC
63 GCAGGTAA
* * *
1937243 AATACCGCAGCCCCTCAAATAGTTACCGAGAGTTAAAAGATCTCAG
1 AATACCGCAGCCCC-CAAATAGTTAGCGAGAGTTCAAAGCTCTCAG
1937289 TTGTCTCCCT
Statistics
Matches: 933, Mismatches: 225, Indels: 38
0.78 0.19 0.03
Matches are distributed among these distances:
68 16 0.02
69 35 0.04
70 409 0.44
71 162 0.17
72 305 0.33
73 6 0.01
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (70 bp):
AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
GGTAA
Found at i:1936542 original size:284 final size:284
Alignment explanation
Indices: 1936189--1936720 Score: 674
Period size: 284 Copynumber: 1.9 Consensus size: 284
1936179 AAAGTACTGT
* * * *
1936189 AGCCCCCCAAACATTTAGAAAGAGTTAAAAGCTCCCAACTGTCATTATCAAGACTCATAAGTTCA
1 AGCCCCCCAAACAGTTACAAAGAGTTAAAAGCTCCCAACTGTCATTATCAAGACTCACAAGTGCA
* * * * *
1936254 ATACCGCAACCCTCCAAATAGCCAGTAAAAGTTAAAAGCTCTTAGTTGTCATTATTAAGGCTCAC
66 ATACCGCAACCCCCCAAACAGCCAGCAAAAGTTAAAAGCTCTCAGCTGTCATTATTAAGGCTCAC
* * * *
1936319 AGGTTTAAT-ATCGCAGCCCCCAAATAGTTAGCAAAATTTTAAAGCT-CTCAGTTATAATGTTAA
131 AGGTTTAATAAT-GCAGCCCCCAAAGAGTTAGCAAAAGTTCAAAGCTCCT-AATTATAATGTTAA
* * *
1936382 GGCTCGCAGGTAAAATATTGCAGCCTCCAAAACAGTTAACGAGAGCTAAAGCTCCCAAATGTAAT
194 GGCTCGCAAGTAAAATACTACAGCCTCCAAAACAGTTAACGAGAGCTAAAGCTCCCAAATGTAAT
1936447 CTTAAGGCTCGTAGATTTAATACTAC
259 CTTAAGGCTCGTAGATTTAATACTAC
* * * * * *
1936473 AGCCCCCGAAACAGTTATCAAA-AGTTAAAAGCTCTCAACTGTCATTATTAAGGCTCGCAGGTGC
1 AGCCCCCCAAACAGTTA-CAAAGAGTTAAAAGCTCCCAACTGTCATTATCAAGACTCACAAGTGC
* ** * * *
1936537 AATACCGCAGCCCCCCAAACAGTTAGCGAGAGTTAAAAGCTCTCAGCTGTCATTATTAAGGCTCG
65 AATACCGCAACCCCCCAAACAGCCAGCAAAAGTTAAAAGCTCTCAGCTGTCATTATTAAGGCTCA
*** * *
1936602 CAGGTTTAATAATGCAGCCCCCAAAGAGTTATTGAGAGTTCAAAGCTCCTAATTGTAATGTTAAG
130 CAGGTTTAATAATGCAGCCCCCAAAGAGTTAGCAAAAGTTCAAAGCTCCTAATTATAATGTTAAG
* * * * *
1936667 GCTCGCAAGTAAAATACTACAGCCTCTAAAATAGTTAGCGAGGGCTGAAGCTCC
195 GCTCGCAAGTAAAATACTACAGCCTCCAAAACAGTTAACGAGAGCTAAAGCTCC
1936721 TAGCTATAAC
Statistics
Matches: 207, Mismatches: 38, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
284 200 0.97
285 7 0.03
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (284 bp):
AGCCCCCCAAACAGTTACAAAGAGTTAAAAGCTCCCAACTGTCATTATCAAGACTCACAAGTGCA
ATACCGCAACCCCCCAAACAGCCAGCAAAAGTTAAAAGCTCTCAGCTGTCATTATTAAGGCTCAC
AGGTTTAATAATGCAGCCCCCAAAGAGTTAGCAAAAGTTCAAAGCTCCTAATTATAATGTTAAGG
CTCGCAAGTAAAATACTACAGCCTCCAAAACAGTTAACGAGAGCTAAAGCTCCCAAATGTAATCT
TAAGGCTCGTAGATTTAATACTAC
Found at i:1937425 original size:58 final size:58
Alignment explanation
Indices: 1937357--1937535 Score: 166
Period size: 58 Copynumber: 3.1 Consensus size: 58
1937347 AAAAACTCCC
* *
1937357 AGCTATTGATTTTAGAAAATTTTCTTAAGCTTAAAAAAGCTCGCAAACTAATATTCTT
1 AGCTATTGATTTTAGAAAATTTTCTTAAGCTCAAAAAAGCTCGCAAACTAATATTCCT
* * * * * * * * *
1937415 AGCTGTTGATTTTCGACAA-TTTCTTTAAAG-TCCAAAATAGCTCACGAACAAATCTTCCC
1 AGCTATTGATTTTAGAAAATTTTC-TT-AAGCT-CAAAAAAGCTCGCAAACTAATATTCCT
* * * *
1937474 AACTATTAAATTTAGAAAATTTCCTTAAGCTCAAAATAA-CTCGCAAACTAATATTCCT
1 AGCTATTGATTTTAGAAAATTTTCTTAAGCTCAAAA-AAGCTCGCAAACTAATATTCCT
1937532 AGCT
1 AGCT
1937536 GACAAATCTT
Statistics
Matches: 90, Mismatches: 25, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
57 4 0.04
58 44 0.49
59 39 0.43
60 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.34
Consensus pattern (58 bp):
AGCTATTGATTTTAGAAAATTTTCTTAAGCTCAAAAAAGCTCGCAAACTAATATTCCT
Found at i:1937731 original size:27 final size:27
Alignment explanation
Indices: 1937690--1937747 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
1937680 TTGGCCCGCG
*
1937690 TTGTCATTCTTAGCAAGAGGGACCACA
1 TTGTCATTCTCAGCAAGAGGGACCACA
* *
1937717 TTGTCATTCTCAGCAGGAGGGTCCACA
1 TTGTCATTCTCAGCAAGAGGGACCACA
1937744 TTGT
1 TTGT
1937748 TGTTCACAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (27 bp):
TTGTCATTCTCAGCAAGAGGGACCACA
Found at i:1937760 original size:27 final size:27
Alignment explanation
Indices: 1937706--1937761 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
1937696 TTCTTAGCAA
* *
1937706 GAGGGACCACATTGTCATTCTCAGCAG
1 GAGGGACCACATTGTCATTCACAACAG
* **
1937733 GAGGGTCCACATTGTTGTTCACAACAG
1 GAGGGACCACATTGTCATTCACAACAG
1937760 GA
1 GA
1937762 TGAGTCATGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (27 bp):
GAGGGACCACATTGTCATTCACAACAG
Found at i:1937886 original size:110 final size:110
Alignment explanation
Indices: 1937693--1938022 Score: 516
Period size: 110 Copynumber: 3.0 Consensus size: 110
1937683 GCCCGCGTTG
* * *
1937693 TCATTCTTAGCAAGAGGGACCACATTGTCATTCTCAGCAGGAGGGTCCACATTGTTGTTCACAAC
1 TCATTCTTAGCAAGAGGGACCACATTGTCATTCTCAGAAGGAGGGTCCACATTGTCGTTCACGAC
*
1937758 AGGATGAGTCATGTTGTCATTCTCAACTGGGTCATCATCTAAGTA
66 AGGATGAGTCATGTTGTCATTCTCAACTGGGTCCTCATCTAAGTA
** * * * *
1937803 TCATTCTTAGCGGGAGGGACCACATTGTCATTCCCAGTAGGAAGGTCCACATTGTCGTTCATGAC
1 TCATTCTTAGCAAGAGGGACCACATTGTCATTCTCAGAAGGAGGGTCCACATTGTCGTTCACGAC
*
1937868 AGGATGAGTCATGTTGTCATTCTCAACTAGGTCCTCATCTAAGTA
66 AGGATGAGTCATGTTGTCATTCTCAACTGGGTCCTCATCTAAGTA
* * * * *
1937913 TCATTCTTAGCAAGAGAGATCATATTGTCATTCTCAGAATGAGGGTCTACATTGTCGTTCACGAC
1 TCATTCTTAGCAAGAGGGACCACATTGTCATTCTCAGAAGGAGGGTCCACATTGTCGTTCACGAC
1937978 AGGATGAGTCATGTTGTCATTCTCAACTGGGTCCTCATCTAAGTA
66 AGGATGAGTCATGTTGTCATTCTCAACTGGGTCCTCATCTAAGTA
1938023 GGAATCCTGT
Statistics
Matches: 198, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 198 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (110 bp):
TCATTCTTAGCAAGAGGGACCACATTGTCATTCTCAGAAGGAGGGTCCACATTGTCGTTCACGAC
AGGATGAGTCATGTTGTCATTCTCAACTGGGTCCTCATCTAAGTA
Found at i:1947716 original size:24 final size:24
Alignment explanation
Indices: 1947674--1947730 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1947664 ACTGGCCATG
*
1947674 TTATATTAAATATGCTTATGTATA
1 TTATATTAAATATGCTTATATATA
*
1947698 TTATATTCATATATG-TTATATATA
1 TTATATT-AAATATGCTTATATATA
*
1947722 TTAAATTAA
1 TTATATTAA
1947731 CTAATATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.04
24 21 0.75
25 6 0.21
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (24 bp):
TTATATTAAATATGCTTATATATA
Found at i:1953295 original size:40 final size:40
Alignment explanation
Indices: 1953242--1953336 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
1953232 GCGTTTAGAT
*
1953242 AAAAAACGCCGCTAAAAATCAAGCATTAGCGTCACTTTTA
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCACTTTTA
* * * * *
1953282 AAAAAACGCCGCTAAAGATTAAGTATTAGCGGCGCTTTTT
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCACTTTTA
*
1953322 TAAAAACGCCGCTAA
1 AAAAAACGCCGCTAA
1953337 TGCTTATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCACTTTTA
Found at i:1953475 original size:41 final size:41
Alignment explanation
Indices: 1953423--1953612 Score: 211
Period size: 41 Copynumber: 4.6 Consensus size: 41
1953413 AGGCTTTAGT
* *
1953423 GTTTTTTAAAAAGTGCCGCTAATGCTCAGGGT-TTTAGCGGC
1 GTTTTTAAAAAAGCGCCGCTAATGCTC-GGGTCTTTAGCGGC
** *
1953464 GTTTTTAAAAAAGCATCGCTAATGATCGGGTCTTTAGCGGC
1 GTTTTTAAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGC
** * *
1953505 GTTTTTCGAAAAGCGCCGCTAATGATCGGGTCTTTAGCAGC
1 GTTTTTAAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGC
* * * *
1953546 GCTTTTGAGAAAGCGCCGCTAATGCTCGGGTCTTTAGTGGC
1 GTTTTTAAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGC
* ** *
1953587 GGTTTTAATGAAGCGTCGCTAATGCT
1 GTTTTTAAAAAAGCGCCGCTAATGCT
1953613 TAGGGCAATA
Statistics
Matches: 126, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
40 4 0.03
41 122 0.97
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (41 bp):
GTTTTTAAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGC
Found at i:1955108 original size:17 final size:17
Alignment explanation
Indices: 1955086--1955120 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1955076 TAGCTTTGTG
1955086 TGCTAGTATATTTTAAA
1 TGCTAGTATATTTTAAA
1955103 TGCTAGTATATTTTAAA
1 TGCTAGTATATTTTAAA
1955120 T
1 T
1955121 TAGACTGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (17 bp):
TGCTAGTATATTTTAAA
Found at i:1957102 original size:16 final size:16
Alignment explanation
Indices: 1957081--1957111 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1957071 TGTAACCTAT
1957081 CTGATGTTTACAATAA
1 CTGATGTTTACAATAA
1957097 CTGATGTTTACAATA
1 CTGATGTTTACAATA
1957112 GTTTGGGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (16 bp):
CTGATGTTTACAATAA
Found at i:1958077 original size:43 final size:43
Alignment explanation
Indices: 1958027--1958296 Score: 416
Period size: 43 Copynumber: 6.3 Consensus size: 43
1958017 AGATTATGTT
* ** * *
1958027 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
*
1958070 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
*
1958113 TTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
* * *
1958156 TTTAGTGGCGTTTATGTGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
*
1958199 TTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
* *
1958241 TTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
1958284 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
1958297 TTTTCTAAAA
Statistics
Matches: 209, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
42 41 0.20
43 168 0.80
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
Found at i:1958269 original size:128 final size:129
Alignment explanation
Indices: 1958027--1958296 Score: 436
Period size: 128 Copynumber: 2.1 Consensus size: 129
1958017 AGATTATGTT
* *
1958027 TTTAGCGGCGTTTTTGCT-AGAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAA
1 TTTAGCGGCGTTTATG-TGAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAA
1958091 AGCGCCGCTAAAGGTCCTGGTCTTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
65 AGCGCCGCTAAAGGTCCTGGTCTTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
* * *
1958156 TTTAGTGGCGTTTATGTGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGG-AAA
1 TTTAGCGGCGTTTATGTGAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAA
* * * *
1958220 GCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCTTGGTC
66 GCGCCGCTAAAGGTCCTGGTCTTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
1958284 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
1958297 TTTTCTAAAA
Statistics
Matches: 130, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
128 76 0.58
129 54 0.42
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (129 bp):
TTTAGCGGCGTTTATGTGAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAA
GCGCCGCTAAAGGTCCTGGTCTTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
Found at i:1961141 original size:129 final size:130
Alignment explanation
Indices: 1960977--1961253 Score: 398
Period size: 130 Copynumber: 2.2 Consensus size: 130
1960967 GATTTAGATA
* * *
1960977 TTCTTAGTTCTTT--AAACTACGGTCTTTGCTTTTGTGTTTTTTCAGTTC-AATTAAAATGGGTT
1 TTCTTAGCTCTTTGCAAACTACAGTCTTTACTTTTGTGTTTTTTCAGTTCAAATTAAAATGGGTT
* **
1961039 TGTTTGTTTTTACTTTTTCTGTACTATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTGTTG
66 TGTCTGTTTTTACTTTTTCTGTACTATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTACTG
* * * *
1961104 TTCTTAGCTCTTTGCAAATTACAGTCTTTACTTTTGTGTTTTTTCGGTTCAAATTTAAATTGGTT
1 TTCTTAGCTCTTTGCAAACTACAGTCTTTACTTTTGTGTTTTTTCAGTTCAAATTAAAATGGGTT
* * *
1961169 TGTCTGTTTTTACTTTTTTTGTACTGTTTGATTCTTATTGATTGCTCCTTTTGTTGATTTTACTG
66 TGTCTGTTTTTACTTTTTCTGTACTATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTACTG
* *
1961234 TTCTTAGCTATTGGCAAACT
1 TTCTTAGCTCTTTGCAAACT
1961254 GCACAACATT
Statistics
Matches: 131, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
127 12 0.09
129 31 0.24
130 88 0.67
ACGTcount: A:0.16, C:0.13, G:0.15, T:0.56
Consensus pattern (130 bp):
TTCTTAGCTCTTTGCAAACTACAGTCTTTACTTTTGTGTTTTTTCAGTTCAAATTAAAATGGGTT
TGTCTGTTTTTACTTTTTCTGTACTATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTACTG
Found at i:1961636 original size:32 final size:30
Alignment explanation
Indices: 1961550--1961646 Score: 140
Period size: 30 Copynumber: 3.2 Consensus size: 30
1961540 GGATTGAAGT
1961550 TTTATATGAGCATGCTGGGAAGGGTATAGG
1 TTTATATGAGCATGCTGGGAAGGGTATAGG
* * *
1961580 TTTATATGAGCCTGCTGGGAAGGGTGTAAG
1 TTTATATGAGCATGCTGGGAAGGGTATAGG
*
1961610 TTTATATGAGCATATGTTGGGAAGGGTATAGG
1 TTTATATGAGC--ATGCTGGGAAGGGTATAGG
1961642 TTTAT
1 TTTAT
1961647 GTATTTAAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 38 0.66
32 20 0.34
ACGTcount: A:0.26, C:0.06, G:0.34, T:0.34
Consensus pattern (30 bp):
TTTATATGAGCATGCTGGGAAGGGTATAGG
Found at i:1963083 original size:30 final size:30
Alignment explanation
Indices: 1963049--1963107 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
1963039 CAGTAGTAGT
*
1963049 GTGTGGGCCATAGCCCAACATAGTAACAGA
1 GTGTGGGCCATAGCCCAACACAGTAACAGA
* *
1963079 GTGTGGGCCTTAGCCCAATACAGTAACAG
1 GTGTGGGCCATAGCCCAACACAGTAACAG
1963108 TGCAAATGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (30 bp):
GTGTGGGCCATAGCCCAACACAGTAACAGA
Found at i:1963244 original size:26 final size:26
Alignment explanation
Indices: 1963215--1963265 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1963205 ACACCAATAC
* *
1963215 CGCAGCAAAGCTGCCAGTAATAGTAA
1 CGCAGCAAAGCTACCAGTAACAGTAA
1963241 CGCAGCAAAGCTACCAGTAACAGTA
1 CGCAGCAAAGCTACCAGTAACAGTA
1963266 TTTGTGGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.25, G:0.22, T:0.14
Consensus pattern (26 bp):
CGCAGCAAAGCTACCAGTAACAGTAA
Found at i:1963504 original size:27 final size:27
Alignment explanation
Indices: 1963474--1963628 Score: 240
Period size: 27 Copynumber: 5.7 Consensus size: 27
1963464 TTATCTTATA
1963474 AGGGTATTTC-AGTAATTTTACCCATCG
1 AGGGTATTTCGA-TAATTTTACCCATCG
* *
1963501 AGGGTATTTCGATCATTTTACCTATCG
1 AGGGTATTTCGATAATTTTACCCATCG
* *
1963528 GGGGTATTTCGATAATTTTACCCATCA
1 AGGGTATTTCGATAATTTTACCCATCG
1963555 AGGGTATTTCGATAATTTTACCCATCG
1 AGGGTATTTCGATAATTTTACCCATCG
1963582 AGGGTATTTCGATAATTTTACCCATCG
1 AGGGTATTTCGATAATTTTACCCATCG
* *
1963609 AGGGTATTTCGGTAGTTTTA
1 AGGGTATTTCGATAATTTTA
1963629 TCCTATTTCG
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
27 116 0.99
28 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACCCATCG
Found at i:1965325 original size:6 final size:6
Alignment explanation
Indices: 1965314--1965339 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1965304 CTCAGGTAAG
1965314 TTTTCT TTTTCT TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TT
1965340 GTTATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:1966923 original size:19 final size:18
Alignment explanation
Indices: 1966888--1966937 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1966878 ATTTTAGAAA
1966888 AATTTTAATTTTTTTTAG
1 AATTTTAATTTTTTTTAG
*
1966906 AATTTTTATATTTTTTTA-
1 AATTTTAAT-TTTTTTTAG
*
1966924 AA-TATAATTTTTTT
1 AATTTTAATTTTTTT
1966938 AATATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 6 0.21
17 4 0.14
18 10 0.36
19 8 0.29
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
AATTTTAATTTTTTTTAG
Found at i:1966947 original size:18 final size:18
Alignment explanation
Indices: 1966910--1966958 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
1966900 TTTTAGAATT
1966910 TTTAT-ATTTTTTTAA-A
1 TTTATAATTTTTTTAATA
1966926 --TATAATTTTTTTAATA
1 TTTATAATTTTTTTAATA
* *
1966942 TTTATAAATATTTTAAT
1 TTTATAATTTTTTTAAT
1966959 TTTTTTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 3 0.11
15 10 0.37
16 1 0.04
18 13 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATAATTTTTTTAATA
Done.