Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold148
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: 1464219
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 85296 characters in sequence are not A, C, G, or T
File 7 of 9
Found at i:1001946 original size:39 final size:39
Alignment explanation
Indices: 1001873--1002034 Score: 137
Period size: 39 Copynumber: 3.9 Consensus size: 39
1001863 ATCATTAAAA
* * *
1001873 CCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAGC
**
1001912 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTCTAAAA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA---------C-AAGC
* * * *
1001961 CCAATGA-CGCTGGCCTTGAATCGGTATATTAGCATAAGC
1 CCAAT-ATCGCTGGCCTTGAATCAGCATATTGGCACAAGC
1002000 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1002035 CTTGTCTCTA
Statistics
Matches: 96, Mismatches: 15, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
38 1 0.01
39 62 0.65
48 1 0.01
49 31 0.32
50 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (39 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAGC
Found at i:1002284 original size:39 final size:39
Alignment explanation
Indices: 1002230--1002394 Score: 132
Period size: 39 Copynumber: 4.0 Consensus size: 39
1002220 ACTCTTCTTC
* *
1002230 AAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCAT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAT
* * * *
1002269 AAGTCCGATATCGCTGGCATCGAATCAGCATATTGGCACCGT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA---T
* * * *
1002311 CATCATTAAAACCAATGTCACTGGCCTTGAATCAGCACATTGGCAC
1 -A--AGT----CCAATATCGCTGGCCTTGAATCAGCACATTGGCAT
* *
1002357 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA
1002395 CCTTTTTCTC
Statistics
Matches: 97, Mismatches: 19, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
39 63 0.65
42 1 0.01
43 2 0.02
45 3 0.03
49 28 0.29
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (39 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAT
Found at i:1002395 original size:39 final size:39
Alignment explanation
Indices: 1002322--1002483 Score: 128
Period size: 39 Copynumber: 3.9 Consensus size: 39
1002312 ATCATTAAAA
* * *
1002322 CCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAGC
**
1002361 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTCTAAAA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA---------C-AAGC
* * * * *
1002410 CCAATGA-CGTTGGCCTTGAATCGGTATATTAGCATAAGC
1 CCAAT-ATCGCTGGCCTTGAATCAGCATATTGGCACAAGC
1002449 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1002484 CTTGTCTCTA
Statistics
Matches: 94, Mismatches: 17, Indels: 24
0.70 0.13 0.18
Matches are distributed among these distances:
38 1 0.01
39 61 0.65
48 1 0.01
49 30 0.32
50 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (39 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAGC
Found at i:1002535 original size:449 final size:449
Alignment explanation
Indices: 1001697--1002672 Score: 1827
Period size: 449 Copynumber: 2.2 Consensus size: 449
1001687 CTAATATCGC
1001697 TGGCCTTGAATCAGTATATTGGCATCTTTAACATTCCTAAGCCCAATATCGCTGGCTTGTATCAG
1 TGGCCTTGAATCAGTATATTGGCATCTTTAACATTCCTAAGCCCAATATCGCTGGCTTGTATCAG
1001762 CACATTGGCACTCTTCTTCAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGTCCG
66 CACATTGGCACTCTTCTTCAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGTCCG
1001827 ATATCGCTGGCATCGAATCAGCATATTGGCACCGTCATCATTAAAACCAATGTCACTGGCCTTGA
131 ATATCGCTGGCATCGAATCAGCATATTGGCACCGTCATCATTAAAACCAATGTCACTGGCCTTGA
1001892 ATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTCT
196 ATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTCT
1001957 AAAACCAATGACGCTGGCCTTGAATCGGTATATTAGCATAAGCCCAATATCGCTGGCCTTGAATC
261 AAAACCAATGACGCTGGCCTTGAATCGGTATATTAGCATAAGCCCAATATCGCTGGCCTTGAATC
1002022 AGCATATTGGCACCTTGTCTCTAAAACCAATGACGCTGGCCTTGAATCGGTACATTAGCATAAGC
326 AGCATATTGGCACCTTGTCTCTAAAACCAATGACGCTGGCCTTGAATCGGTACATTAGCATAAGC
*
1002087 CCAATATCGCTAGCCTTGAATCAACATATTGCCACCTTCATCTTTAAGACTGATGTCAT
391 CCAATATCGCTAGCCTTGAATCAACATATTGCCACCTTCATCTTTAAGACCGATGTCAT
1002146 TGGCCTTGAATCAGTATATTGGCATCTTTAACATTCCTAAGCCCAATATCGCTGGCTTGTATCAG
1 TGGCCTTGAATCAGTATATTGGCATCTTTAACATTCCTAAGCCCAATATCGCTGGCTTGTATCAG
1002211 CACATTGGCACTCTTCTTCAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGTCCG
66 CACATTGGCACTCTTCTTCAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGTCCG
1002276 ATATCGCTGGCATCGAATCAGCATATTGGCACCGTCATCATTAAAACCAATGTCACTGGCCTTGA
131 ATATCGCTGGCATCGAATCAGCATATTGGCACCGTCATCATTAAAACCAATGTCACTGGCCTTGA
1002341 ATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTCT
196 ATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTCT
*
1002406 AAAACCAATGACGTTGGCCTTGAATCGGTATATTAGCATAAGCCCAATATCGCTGGCCTTGAATC
261 AAAACCAATGACGCTGGCCTTGAATCGGTATATTAGCATAAGCCCAATATCGCTGGCCTTGAATC
*
1002471 AGCATATTGGCACCTTGTCTCTAAAACCAATGACGCTGGCCTTGAATCGGTACATTGGCATAAGC
326 AGCATATTGGCACCTTGTCTCTAAAACCAATGACGCTGGCCTTGAATCGGTACATTAGCATAAGC
1002536 CCAATATCGCTAGCCTTGAATCAACATATTGCCACCTTCATCTTTAAGACCGATGTCAT
391 CCAATATCGCTAGCCTTGAATCAACATATTGCCACCTTCATCTTTAAGACCGATGTCAT
* * * * *
1002595 TGGCCTTGAATCAGTACATTGGCA-CGTT--CA-TCTTTAAGTCCAATATCGCTGGCCTTGAATC
1 TGGCCTTGAATCAGTATATTGGCATCTTTAACATTC-CTAAGCCCAATATCGCTGG-CTTGTATC
1002656 AGCACATTGGCAC-CTTC
64 AGCACATTGGCACTCTTC
1002673 ATCTTTAAGT
Statistics
Matches: 517, Mismatches: 8, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
445 2 0.00
446 23 0.04
447 20 0.04
448 3 0.01
449 469 0.91
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (449 bp):
TGGCCTTGAATCAGTATATTGGCATCTTTAACATTCCTAAGCCCAATATCGCTGGCTTGTATCAG
CACATTGGCACTCTTCTTCAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGTCCG
ATATCGCTGGCATCGAATCAGCATATTGGCACCGTCATCATTAAAACCAATGTCACTGGCCTTGA
ATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTCT
AAAACCAATGACGCTGGCCTTGAATCGGTATATTAGCATAAGCCCAATATCGCTGGCCTTGAATC
AGCATATTGGCACCTTGTCTCTAAAACCAATGACGCTGGCCTTGAATCGGTACATTAGCATAAGC
CCAATATCGCTAGCCTTGAATCAACATATTGCCACCTTCATCTTTAAGACCGATGTCAT
Found at i:1002625 original size:49 final size:49
Alignment explanation
Indices: 1002539--1002716 Score: 212
Period size: 49 Copynumber: 3.6 Consensus size: 49
1002529 CATAAGCCCA
* * * * *
1002539 ATATCGCTAGCCTTGAATCAACATATTGCCACCTTCATCTTTAAGACCG
1 ATATCGTTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGTCCG
* * ** * *
1002588 ATGTCATTGGCCTTGAATCAGTACATTGGCACGTTCATCTTTAAGTCCA
1 ATATCGTTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGTCCG
* *
1002637 ATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCG
1 ATATCGTTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGTCCG
* * *
1002686 ATATCGTTGGCCTGGAATCAATATATTGGCA
1 ATATCGTTGGCCTTGAATCAACACATTGGCA
1002717 TCTTTAATAT
Statistics
Matches: 107, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 107 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (49 bp):
ATATCGTTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGTCCG
Found at i:1002705 original size:98 final size:100
Alignment explanation
Indices: 1002531--1002764 Score: 292
Period size: 98 Copynumber: 2.4 Consensus size: 100
1002521 TACATTGGCA
* * * *
1002531 TAAGCCCAATATCGCTAGCCTTGAATCAACATATTGCCACCTTCATCTTTAAGACCGATGTCATT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGCCACCTTCATCTTTAAGACCGATATCATT
* * * *
1002596 GGCCTTGAATCAGTACATTGGCA-CGTTCATCTT-
66 GGCCTGGAATCAATACATTGGCATCGTTAATATTC
* * * *
1002629 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGCCACCTTCATCTTTAAGACCGATATCATT
* *
1002694 GGCCTGGAATCAATATATTGGCATCTTTAATATTCC
66 GGCCTGGAATCAATACATTGGCATCGTTAATATT-C
* **
1002730 TAAGCCCAATGTCGCTGGCCTTGTCTCAGCACATT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCACATT
1002765 AGCATTCTTC
Statistics
Matches: 115, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
98 77 0.67
99 7 0.06
101 31 0.27
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (100 bp):
TAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGCCACCTTCATCTTTAAGACCGATATCATT
GGCCTGGAATCAATACATTGGCATCGTTAATATTC
Found at i:1009904 original size:13 final size:13
Alignment explanation
Indices: 1009886--1009912 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1009876 CAATTCTTTA
1009886 TGTATCGATACAT
1 TGTATCGATACAT
1009899 TGTATCGATACAT
1 TGTATCGATACAT
1009912 T
1 T
1009913 ATGCCATGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1009998 original size:13 final size:13
Alignment explanation
Indices: 1009980--1010006 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1009970 TACAATGAAC
1009980 ATGTATTGATACA
1 ATGTATTGATACA
1009993 ATGTATTGATACA
1 ATGTATTGATACA
1010006 A
1 A
1010007 AGCATAATGT
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:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:1010024 original size:33 final size:32
Alignment explanation
Indices: 1009964--1010025 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
1009954 CAGTTTCATT
* *
1009964 TATTGATACAATGAACATGTATTGATACAATG
1 TATTGATACAAAGAACATGTATCGATACAATG
1009996 TATTGATACAAAGCATA-ATGTATCGATACA
1 TATTGATACAAAG-A-ACATGTATCGATACA
1010026 TCTGAAAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 12 0.46
33 13 0.50
34 1 0.04
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (32 bp):
TATTGATACAAAGAACATGTATCGATACAATG
Found at i:1015223 original size:27 final size:27
Alignment explanation
Indices: 1015192--1015246 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1015182 TTTAAATCAA
1015192 AAGTGTGCATATGAGGTACAGGCTCAT
1 AAGTGTGCATATGAGGTACAGGCTCAT
1015219 AAGTGTGCATATGAGGTACAGGCTCAT
1 AAGTGTGCATATGAGGTACAGGCTCAT
1015246 A
1 A
1015247 TGCTCAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (27 bp):
AAGTGTGCATATGAGGTACAGGCTCAT
Found at i:1015616 original size:424 final size:425
Alignment explanation
Indices: 1014827--1015643 Score: 1255
Period size: 424 Copynumber: 1.9 Consensus size: 425
1014817 AAACAAGAAT
* * * *
1014827 AAATTATGTTAGAATCTAACTTTAAATGATCTTGAGAAATTCTCCTAAATGCATAAGTATAAGGC
1 AAATTATGTTAGAATCTAACTTCAAATGATCATGAAAAATTCTCCTAAATGCACAAGTATAAGGC
*
1014892 CCATTATATTTTCTAATCTCCCATACTTGTTTTTTTTCAATAATGTTGCTCTTATACTGCAATTG
66 CCATTATATTTTCTAATCTCCCATACTTGTTTTTTTTCAATAATGTTGCTCTTATACTCCAATTG
1014957 CACCATTGCCCATACATTAGACACTTACCATGGTATTGCTTCGGGTTAGATTCTATTACTCTGTA
131 CACCATTGCCCATACATTAGACACTTACCATGGTATTGCTTCGGGTTAGATTCTATTACTCTGTA
1015022 ATCTACTGATTTTTTGATGTTATAATACTTTATAACTGAAACCATGGCCTCCTTCATTGCGAATT
196 ATCTACTGATTTTTTGATGTTATAATACTTTATAACTGAAACCATGGCCTCCTTCATTGCGAATT
* * *
1015087 GCAACCGAACACAGAGATCACCGCTAGATGAATTCCAGCTTATTGGCACACCTAATGTATGAACA
261 GCAACCAAACACAGAAATCACCGCTAAATGAATTCCAGCTTATTGGCACACCTAATGTATGAACA
*
1015152 TATTTTGGAAACTCTGGCACATGCATTGCCTTTAAATCAAAAGTGTGCATATGAGGTACAGGCTC
326 TATTTTGGAAACTCTGGCACATGCATTGCCTTTAAATCAAAAGTGCGCATATGAGGTACAGGCTC
1015217 ATAAGTGTGCATATGAGGTACAGGCTCATATGCTC
391 ATAAGTGTGCATATGAGGTACAGGCTCATATGCTC
** *
1015252 AAATTATGTTAGAATCTAACTTCAAATGATCATGAAAAATTCT-CTGGGATGCACACGTATAAGG
1 AAATTATGTTAGAATCTAACTTCAAATGATCATGAAAAATTCTCCT-AAATGCACAAGTATAAGG
* * *
1015316 CCTATTATATTTTCTATTCTCTCATACTT-TTTTTTTTCAATAATGTTGCTCTTATACTCCAATT
65 CCCATTATATTTTCTAATCTCCCATACTTGTTTTTTTTCAATAATGTTGCTCTTATACTCCAATT
* * * *
1015380 GCACCCTTGCCCATACATTAGACACTTACTATGGTATTGCTTCGGGTTAGATTTTATTACTTTGT
130 GCACCATTGCCCATACATTAGACACTTACCATGGTATTGCTTCGGGTTAGATTCTATTACTCTGT
* * * * * *
1015445 AATCTA-TATATTTTTTGATGTTATAGTGCTTTATAGCTGAAACCATGGCCTCTTTCGTTGCGAA
195 AATCTACT-GATTTTTTGATGTTATAATACTTTATAACTGAAACCATGGCCTCCTTCATTGCGAA
* * ** * * *
1015509 TTGCATCCAAACATAGAAATCGTCGCTAAATGGATTCCAGCTTGTTGGCACACCTAATGTTTGAA
259 TTGCAACCAAACACAGAAATCACCGCTAAATGAATTCCAGCTTATTGGCACACCTAATGTATGAA
* * **
1015574 CATATTTTGGAAATTTTGGCACATGCATTG-CTTCTAAATCAAAAGTGCGCATATGAGGTGTAGG
324 CATATTTTGGAAACTCTGGCACATGCATTGCCTT-TAAATCAAAAGTGCGCATATGAGGTACAGG
1015638 CTCATA
388 CTCATA
1015644 CTGATGAAGA
Statistics
Matches: 353, Mismatches: 36, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
423 4 0.01
424 269 0.76
425 80 0.23
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (425 bp):
AAATTATGTTAGAATCTAACTTCAAATGATCATGAAAAATTCTCCTAAATGCACAAGTATAAGGC
CCATTATATTTTCTAATCTCCCATACTTGTTTTTTTTCAATAATGTTGCTCTTATACTCCAATTG
CACCATTGCCCATACATTAGACACTTACCATGGTATTGCTTCGGGTTAGATTCTATTACTCTGTA
ATCTACTGATTTTTTGATGTTATAATACTTTATAACTGAAACCATGGCCTCCTTCATTGCGAATT
GCAACCAAACACAGAAATCACCGCTAAATGAATTCCAGCTTATTGGCACACCTAATGTATGAACA
TATTTTGGAAACTCTGGCACATGCATTGCCTTTAAATCAAAAGTGCGCATATGAGGTACAGGCTC
ATAAGTGTGCATATGAGGTACAGGCTCATATGCTC
Found at i:1016886 original size:90 final size:90
Alignment explanation
Indices: 1016776--1016940 Score: 233
Period size: 89 Copynumber: 1.8 Consensus size: 90
1016766 ATCTTTCAAC
* * *
1016776 TGTAATATTTACAATCAATCAATTTTTCAGTTTTTTTATCAAAAAGAATTTGATTCTCAAATATA
1 TGTAATACTTACAATCAATCAATTTTTC-GTTTTTTTATCAAAAAGAATTCGATTCTCAAATACA
1016841 ATT-ATGCATTGTTTAATCTTTGCAG
65 ATTCATGCATTGTTTAATCTTTGCAG
* * * * * *
1016866 TGTAATACTTATAATTAATCAATTTTTCTTTTTTTTATCAAAAGGAATTCGATTTTCATATACAA
1 TGTAATACTTACAATCAATCAATTTTTCGTTTTTTTATCAAAAAGAATTCGATTCTCAAATACAA
1016931 TTCATGCATT
66 TTCATGCATT
1016941 ATCTAATCCT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
89 33 0.51
90 32 0.49
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.47
Consensus pattern (90 bp):
TGTAATACTTACAATCAATCAATTTTTCGTTTTTTTATCAAAAAGAATTCGATTCTCAAATACAA
TTCATGCATTGTTTAATCTTTGCAG
Found at i:1016948 original size:90 final size:90
Alignment explanation
Indices: 1016754--1016948 Score: 232
Period size: 90 Copynumber: 2.2 Consensus size: 90
1016744 TCAAAATATC
* *
1016754 TGCATTTATCTCATCTTTCAACTGTAATATTTACAATCAATCAATTTTTCAGTTTTTTTATCAAA
1 TGCA-TTATCTAATCTTTCAACTGTAATACTTACAATCAATCAATTTTTCAGTTTTTTTATCAAA
* *
1016819 AAGAATTTGATTCTCAAATATAATTA
65 AAGAATTCGATTCTCAAATACAATTA
* * * * * *
1016845 TGCATTGTTTAATCTTTGC-AGTGTAATACTTATAATTAATCAATTTTTC-TTTTTTTTATCAAA
1 TGCATTATCTAATCTTT-CAACTGTAATACTTACAATCAATCAATTTTTCAGTTTTTTTATCAAA
* * *
1016908 AGGAATTCGATTTTCATATACAATTCA
65 AAGAATTCGATTCTCAAATACAATT-A
1016935 TGCATTATCTAATC
1 TGCATTATCTAATC
1016949 CTTGTAGTCT
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
89 33 0.38
90 49 0.56
91 5 0.06
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (90 bp):
TGCATTATCTAATCTTTCAACTGTAATACTTACAATCAATCAATTTTTCAGTTTTTTTATCAAAA
AGAATTCGATTCTCAAATACAATTA
Found at i:1016985 original size:65 final size:65
Alignment explanation
Indices: 1016892--1017022 Score: 165
Period size: 65 Copynumber: 2.0 Consensus size: 65
1016882 AATCAATTTT
* * * * *
1016892 TCTTTTTTTTATCAAAAGGAATTCGATTTTCATATACAATTCATGCATTA-TCTAATCCTTGTAG
1 TCTTTTTTTTATAAAAAAGAATCCGATTTTCAGATACAATTCATGCATTAGTCTAATCCTTCTAG
* * * *
1016956 TCTTTTTTTCTATAAAAAAGAATCCGATTTTTAGATATAATTTATGCATTAGTCTAATTCTTCTA
1 TCTTTTTTT-TATAAAAAAGAATCCGATTTTCAGATACAATTCATGCATTAGTCTAATCCTTCTA
1017021 G
65 G
1017022 T
1 T
1017023 TTAACATTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
64 9 0.16
65 34 0.61
66 13 0.23
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.47
Consensus pattern (65 bp):
TCTTTTTTTTATAAAAAAGAATCCGATTTTCAGATACAATTCATGCATTAGTCTAATCCTTCTAG
Found at i:1017195 original size:92 final size:91
Alignment explanation
Indices: 1016956--1017287 Score: 417
Period size: 92 Copynumber: 3.7 Consensus size: 91
1016946 ATCCTTGTAG
** * * *
1016956 TCTTTTTTTCTATAAAAAAGAATCCGATTTTTAGATATAATTTATGCATTAGTCTAATTCTTCTA
1 TCTTTTTTTCTATAAAAAAGAATTTGATTCTCAGATATAATTTATGCATTAGTCTAATCCTTC-A
*
1017021 GTTTAACATTTATAATCAATCAACTTT
65 GTTTAACATTTAAAATCAATCAACTTT
* *
1017048 TCTTTTTTT-TATAAAAAAGAATTTGATTCTCATATATAATTCATGCATTAGTCTAATCCTTACA
1 TCTTTTTTTCTATAAAAAAGAATTTGATTCTCAGATATAATTTATGCATTAGTCTAATCCTT-CA
**
1017112 GTCAAACATTTAAAATCAATCAACTTT
65 GTTTAACATTTAAAATCAATCAACTTT
**
1017139 TCTTTTTTTCTATAAAAAAGAATTTGATTCTCAGATATAATTTATGCATTAGTCTAATTTTTGCA
1 TCTTTTTTTCTATAAAAAAGAATTTGATTCTCAGATATAATTTATGCATTAGTCTAATCCTT-CA
* * *
1017204 GTTTGAGATTTACAATCAATCAACTTT
65 GTTTAACATTTAAAATCAATCAACTTT
* * * *
1017231 TC--TTTTCCTAT---AAA-AATTTGATTTTCAGATATAATTTATGTATTAGTGTAATCCTTC
1 TCTTTTTTTCTATAAAAAAGAATTTGATTCTCAGATATAATTTATGCATTAGTCTAATCCTTC
1017288 TAATATGACA
Statistics
Matches: 212, Mismatches: 26, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
85 1 0.00
86 37 0.17
87 3 0.01
90 8 0.04
91 79 0.37
92 84 0.40
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (91 bp):
TCTTTTTTTCTATAAAAAAGAATTTGATTCTCAGATATAATTTATGCATTAGTCTAATCCTTCAG
TTTAACATTTAAAATCAATCAACTTT
Found at i:1017733 original size:38 final size:38
Alignment explanation
Indices: 1017691--1017780 Score: 94
Period size: 38 Copynumber: 2.4 Consensus size: 38
1017681 TAATCTTATT
*
1017691 TTTTAAATTTTAATAAATAATCTAT-AATTA-CTAATATC
1 TTTTAAATTTTAATAAA-AATATATGAATTATC-AATATC
* * * *
1017729 TTTTAAAATCTAATAAAAATATATGCATTATCCATATC
1 TTTTAAATTTTAATAAAAATATATGAATTATCAATATC
*
1017767 TTTTAGATTTTAAT
1 TTTTAAATTTTAAT
1017781 TAATTTTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
37 6 0.14
38 35 0.83
39 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (38 bp):
TTTTAAATTTTAATAAAAATATATGAATTATCAATATC
Found at i:1019062 original size:34 final size:36
Alignment explanation
Indices: 1018989--1019061 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
1018979 TTTTTTAGTA
* *
1018989 TTATTATTAACATAATTTTTAAAATTAAAAATTATTT
1 TTATTATAAACATAATTTTTAAAACTAAAAA-TATTT
*
1019026 TTATTATAAATATAA-TTTTAACAACTAAAAA-ATTT
1 TTATTATAAACATAATTTTTAA-AACTAAAAATATTT
1019061 T
1 T
1019062 AATTTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 5 0.16
36 6 0.19
37 21 0.66
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (36 bp):
TTATTATAAACATAATTTTTAAAACTAAAAATATTT
Found at i:1019317 original size:15 final size:16
Alignment explanation
Indices: 1019289--1019329 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
1019279 TATTTTTATC
1019289 ATATTTTATTTAAC-TA
1 ATATTTT-TTTAACTTA
1019305 ATATTTTTTTAACTTA
1 ATATTTTTTTAACTTA
1019321 ATATATTTT
1 ATAT-TTTT
1019330 CAACAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.26
16 13 0.57
17 4 0.17
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTTTTTTAACTTA
Found at i:1019721 original size:26 final size:27
Alignment explanation
Indices: 1019692--1019743 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1019682 TAAATAAATT
1019692 TTAAATAGTTTT-TAA-TTTTTATTTAG
1 TTAAATA-TTTTATAATTTTTTATTTAG
*
1019718 TTAATTATTTTATAATTTTTTATTTA
1 TTAAATATTTTATAATTTTTTATTTA
1019744 AATATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 9 0.39
27 10 0.43
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (27 bp):
TTAAATATTTTATAATTTTTTATTTAG
Found at i:1019737 original size:33 final size:32
Alignment explanation
Indices: 1019665--1019742 Score: 77
Period size: 33 Copynumber: 2.3 Consensus size: 32
1019655 TTTTAAAAAT
1019665 ATTTTTAAATTTTTATTTAAATAAATTTTAAATA
1 ATTTTT-AATTTTTATTTAAATAAATTTT-AATA
* **
1019699 GTTTTTAATTTTTATTTAGTTAATTATTTT-ATA
1 ATTTTTAATTTTTATTTAAATAA--ATTTTAATA
*
1019732 ATTTTTTATTT
1 ATTTTTAATTT
1019743 AAATATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
33 27 0.73
34 5 0.14
35 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (32 bp):
ATTTTTAATTTTTATTTAAATAAATTTTAATA
Found at i:1019744 original size:23 final size:23
Alignment explanation
Indices: 1019713--1019757 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1019703 TTAATTTTTA
* *
1019713 TTTAGTTAATTATTTTATAATTT
1 TTTAGTTAAATATTTTAAAATTT
*
1019736 TTTATTTAAATATTTTAAAATT
1 TTTAGTTAAATATTTTAAAATT
1019758 ATTCATTCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTAGTTAAATATTTTAAAATTT
Found at i:1021666 original size:35 final size:35
Alignment explanation
Indices: 1021604--1021672 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
1021594 CATGCAATAT
* * * *
1021604 ATATACCCACCTAGTTTAGTCTACAGATTTTCTGC
1 ATATACCCACCTAGCTCAGTCCACAGATGTTCTGC
* *
1021639 ATATACCCATCTAGCTCAGTCCGCAGATGTTCTG
1 ATATACCCACCTAGCTCAGTCCACAGATGTTCTG
1021673 GACCGGATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (35 bp):
ATATACCCACCTAGCTCAGTCCACAGATGTTCTGC
Found at i:1023858 original size:23 final size:23
Alignment explanation
Indices: 1023832--1023880 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
1023822 TATTCAAATT
1023832 TTAATATACATCAAATAAAA-AAA
1 TTAA-ATACATCAAATAAAATAAA
**
1023855 TTAAATATTTCAAATAAAATAAA
1 TTAAATACATCAAATAAAATAAA
1023878 TTA
1 TTA
1023881 CAAGAGCGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (23 bp):
TTAAATACATCAAATAAAATAAA
Found at i:1025194 original size:2 final size:2
Alignment explanation
Indices: 1025189--1025227 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1025179 ACACACACAC
1025189 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1025228 GTGATCATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1027630 original size:13 final size:13
Alignment explanation
Indices: 1027612--1027638 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1027602 ACAACATTCC
1027612 TTGTATCGATACA
1 TTGTATCGATACA
1027625 TTGTATCGATACA
1 TTGTATCGATACA
1027638 T
1 T
1027639 GGGTTACTAT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1030220 original size:20 final size:20
Alignment explanation
Indices: 1030197--1030251 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
1030187 ACATTATGCT
1030197 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
1030217 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
1030237 TTGTATCGATACATG
1 TTGTATCGATACATG
1030252 AAACTAGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:1031193 original size:67 final size:67
Alignment explanation
Indices: 1031091--1031269 Score: 168
Period size: 67 Copynumber: 2.7 Consensus size: 67
1031081 CATCATGCTT
* * * * * *
1031091 TTTAAGGACTGAAGTAGG-TAGGTGACATCAACTTGTATAGGCTTTAAGGTAGGTAAGTGTCCCG
1 TTTAAGGACTAAAGT-GGATAGGTGCCACCAGCTTGTGTAGGCTTTAAGGTAGGTAAGCGTCCCG
1031155 CTC
65 CTC
** **
1031158 TTTAAGGACTAAAGTGGATAGGTGCCACCAGCTTGTGT-GAGCTTTGGGGTAGGTAAGCGTCTTG
1 TTTAAGGACTAAAGTGGATAGGTGCCACCAGCTTGTGTAG-GCTTTAAGGTAGGTAAGCGTCCCG
1031222 CTC
65 CTC
* ** *
1031225 TTTGAA-GATTACGGT-AAGTAGGTGCCACCAGCTTGTGTAGGCTTT
1 TTT-AAGGACTAAAGTGGA-TAGGTGCCACCAGCTTGTGTAGGCTTT
1031270 GTGTAAGGCT
Statistics
Matches: 93, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
66 4 0.04
67 86 0.92
68 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (67 bp):
TTTAAGGACTAAAGTGGATAGGTGCCACCAGCTTGTGTAGGCTTTAAGGTAGGTAAGCGTCCCGC
TC
Found at i:1031600 original size:71 final size:71
Alignment explanation
Indices: 1031429--1031603 Score: 199
Period size: 71 Copynumber: 2.5 Consensus size: 71
1031419 GGTGGGTAAG
* * * * *
1031429 CATCTTACTCTTTGAGGACTGGAGAAGATATGTGATGCCACTAGCTTGTATGGGCTTTGTAGATA
1 CATCCTACTCTTTGAGGACTGGAGAAGATAAGTGATGCCACCAGCTTGTATAGGCTTTGAAGATA
*
1031494 AAAAGG
66 AAAAGA
** * ** ** *
1031500 TGTCCCACTCTTTGAAAACTAAAGTAGATAAGTGATGCCACCAGCTTGTATAGGCTTTGAAGA-A
1 CATCCTACTCTTTGAGGACTGGAGAAGATAAGTGATGCCACCAGCTTGTATAGGCTTTGAAGATA
1031564 GAAAAGA
66 -AAAAGA
*
1031571 CATCCTACTATTTGAGGACTGGAGAAGATAAGT
1 CATCCTACTCTTTGAGGACTGGAGAAGATAAGT
1031604 TTAGACACCT
Statistics
Matches: 80, Mismatches: 23, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
70 1 0.01
71 79 0.99
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (71 bp):
CATCCTACTCTTTGAGGACTGGAGAAGATAAGTGATGCCACCAGCTTGTATAGGCTTTGAAGATA
AAAAGA
Found at i:1035834 original size:194 final size:194
Alignment explanation
Indices: 1035505--1035896 Score: 775
Period size: 194 Copynumber: 2.0 Consensus size: 194
1035495 ATGTCCTCAA
1035505 CTACTATTTTGATTTGATTATAGCCTAAAAAACCCATCCATGAAGGAAAATAATGCATTTTTAGT
1 CTACTATTTTGATTTGATTATAGCCTAAAAAACCCATCCATGAAGGAAAATAATGCATTTTTAGT
1035570 AGTGTTGTCTACTAAAGGTATCGATGTGAGGCAGAGAAAAATTATCCTTAAGGCTGGCTCAGTTT
66 AGTGTTGTCTACTAAAGGTATCGATGTGAGGCAGAGAAAAATTATCCTTAAGGCTGGCTCAGTTT
1035635 AAGTCCTTGTAGTCCATACACATCCACACTTTGCCATCCTTTTTGGGGATTGAGACTATATTGG
131 AAGTCCTTGTAGTCCATACACATCCACACTTTGCCATCCTTTTTGGGGATTGAGACTATATTGG
1035699 CTACTATTTTGATTTGATTATAGCCTAAAAAACCCATCCATGAAGGAAAATAATGCATTTTTAGT
1 CTACTATTTTGATTTGATTATAGCCTAAAAAACCCATCCATGAAGGAAAATAATGCATTTTTAGT
1035764 AGTGTTGTCTACTAAAGGTATCGATGTGAGGCAGAGAAAAATTATCCTTAAGGCTGGCTCAGTTT
66 AGTGTTGTCTACTAAAGGTATCGATGTGAGGCAGAGAAAAATTATCCTTAAGGCTGGCTCAGTTT
*
1035829 AAGTCCTTGTAGTCCATACACATCCACATTTTGCCATCCTTTTTGGGGATTGAGACTATATTGG
131 AAGTCCTTGTAGTCCATACACATCCACACTTTGCCATCCTTTTTGGGGATTGAGACTATATTGG
1035893 CTAC
1 CTAC
1035897 CCATTTTGGA
Statistics
Matches: 197, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
194 197 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (194 bp):
CTACTATTTTGATTTGATTATAGCCTAAAAAACCCATCCATGAAGGAAAATAATGCATTTTTAGT
AGTGTTGTCTACTAAAGGTATCGATGTGAGGCAGAGAAAAATTATCCTTAAGGCTGGCTCAGTTT
AAGTCCTTGTAGTCCATACACATCCACACTTTGCCATCCTTTTTGGGGATTGAGACTATATTGG
Found at i:1039164 original size:13 final size:13
Alignment explanation
Indices: 1039146--1039172 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1039136 ACATGCTGCT
1039146 TTGTATCGATACA
1 TTGTATCGATACA
1039159 TTGTATCGATACA
1 TTGTATCGATACA
1039172 T
1 T
1039173 GGTCAAATTG
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1039260 original size:13 final size:13
Alignment explanation
Indices: 1039239--1039269 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1039229 CGATACATGG
*
1039239 TACAATGTATCGA
1 TACATTGTATCGA
1039252 TACATTGTATCGA
1 TACATTGTATCGA
1039265 TACAT
1 TACAT
1039270 GAAGGAATGT
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:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1039265 original size:33 final size:33
Alignment explanation
Indices: 1039223--1039289 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
1039213 CTATCACTAT
*
1039223 TTGTATCGATACATGGTA-CAATGTATCGATACA
1 TTGTATCGATACAT-GAAGCAATGTATCGATACA
*
1039256 TTGTATCGATACATGAAGGAATGTATCGATACA
1 TTGTATCGATACATGAAGCAATGTATCGATACA
1039289 T
1 T
1039290 AGCATGTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 2 0.06
33 29 0.94
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (33 bp):
TTGTATCGATACATGAAGCAATGTATCGATACA
Found at i:1047292 original size:35 final size:36
Alignment explanation
Indices: 1047226--1047329 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
1047216 TAAAAAGGGG
*
1047226 GAGAA-ATAATCGTTTAAGGGGGATAATTTTTTTTA
1 GAGAAGATAATCGTTTAAGGGGGAGAATTTTTTTTA
1047261 GAGAAGATAATCGTTTAAGGGGGAGAATTTTTTTTA
1 GAGAAGATAATCGTTTAAGGGGGAGAATTTTTTTTA
* * *
1047297 GAGGAGATAATCATTTAA-GGGGAGAATATTTTT
1 GAGAAGATAATCGTTTAAGGGGGAGAATTTTTTT
1047330 AAGGGGAGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.30
36 45 0.70
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.37
Consensus pattern (36 bp):
GAGAAGATAATCGTTTAAGGGGGAGAATTTTTTTTA
Found at i:1047330 original size:17 final size:17
Alignment explanation
Indices: 1047274--1047339 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
1047264 AAGATAATCG
*
1047274 TTTAAGGGGGAGAATTTT
1 TTTAA-GGGGAGAATATT
* * *
1047292 TTTTAGAGGAG-ATAATCA
1 TTTAAGGGGAGAAT-AT-T
1047310 TTTAAGGGGAGAATATT
1 TTTAAGGGGAGAATATT
1047327 TTTAAGGGGAGAA
1 TTTAAGGGGAGAA
1047340 AAACGACAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
16 2 0.05
17 19 0.50
18 15 0.39
19 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (17 bp):
TTTAAGGGGAGAATATT
Found at i:1047900 original size:13 final size:13
Alignment explanation
Indices: 1047882--1047908 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1047872 ACATGTTGCT
1047882 TTGTATCGATACA
1 TTGTATCGATACA
1047895 TTGTATCGATACA
1 TTGTATCGATACA
1047908 T
1 T
1047909 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1047905 original size:33 final size:32
Alignment explanation
Indices: 1047863--1047927 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
1047853 CACACCCATA
*
1047863 TGTATCGATACATGTTGCTTTGTATCGATACAT
1 TGTATCGATACATGTT-CATTGTATCGATACAT
*
1047896 TGTATCGATACATGTTCATTGTATTGATACAT
1 TGTATCGATACATGTTCATTGTATCGATACAT
1047928 GGTTAAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATACAT
Found at i:1047917 original size:19 final size:20
Alignment explanation
Indices: 1047891--1047949 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
1047881 TTTGTATCGA
1047891 TACATTGTATCGATACATGT
1 TACATTGTATCGATACATGT
*
1047911 T-CATTGTATTGATACATGGT
1 TACATTGTATCGATACAT-GT
*
1047931 TAAATTGTATCGATACATG
1 TACATTGTATCGATACATG
1047950 AAACTGGTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 15 0.44
20 5 0.15
21 14 0.41
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.41
Consensus pattern (20 bp):
TACATTGTATCGATACATGT
Found at i:1047939 original size:21 final size:20
Alignment explanation
Indices: 1047894--1047949 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
1047884 GTATCGATAC
*
1047894 ATTGTATCGATACAT-GTTC
1 ATTGTATCGATACATGGTTA
*
1047913 ATTGTATTGATACATGGTTAA
1 ATTGTATCGATACATGGTT-A
1047934 ATTGTATCGATACATG
1 ATTGTATCGATACATG
1047950 AAACTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 14 0.44
20 3 0.09
21 15 0.47
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTGTATCGATACATGGTTA
Found at i:1048015 original size:13 final size:13
Alignment explanation
Indices: 1047994--1048024 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1047984 CGATACATGG
*
1047994 TACAATGTATCGA
1 TACATTGTATCGA
1048007 TACATTGTATCGA
1 TACATTGTATCGA
1048020 TACAT
1 TACAT
1048025 GAAGAAATGT
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:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1048015 original size:33 final size:32
Alignment explanation
Indices: 1047978--1048044 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
1047968 CTATCACTAT
1047978 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
1048011 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
1048044 T
1 T
1048045 AGCATGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:1050742 original size:33 final size:32
Alignment explanation
Indices: 1050705--1050772 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
1050695 CGTTACAAGC
* * *
1050705 CAATGTATCGATATATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGACA
*
1050738 CAATGTATCGATACATATTGTGTGTATCGACA
1 CAATGTATCGATACATATTGGGTGTATCGACA
1050770 CAA
1 CAA
1050773 ACAGTTAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGACA
Found at i:1050745 original size:13 final size:13
Alignment explanation
Indices: 1050727--1050752 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1050717 ATATTTTGGG
1050727 ATGTATCGATACA
1 ATGTATCGATACA
1050740 ATGTATCGATACA
1 ATGTATCGATACA
1050753 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1050860 original size:20 final size:21
Alignment explanation
Indices: 1050813--1050865 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1050803 GCCAATGACC
*
1050813 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
1050834 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
1050854 TGTATCGATACA
1 TGTATCGATACA
1050866 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:1050871 original size:13 final size:13
Alignment explanation
Indices: 1050853--1050877 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1050843 ACATTTGGTC
1050853 ATGTATCGATACA
1 ATGTATCGATACA
1050866 ATGTATCGATAC
1 ATGTATCGATAC
1050878 TGTGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1053320 original size:13 final size:13
Alignment explanation
Indices: 1053298--1053335 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1053288 ATAAACCCTT
* *
1053298 TGTATTGATACAC
1 TGTATCGATACAA
1053311 TGTATCGATACAA
1 TGTATCGATACAA
1053324 TGTATCGATACA
1 TGTATCGATACA
1053336 GAGAATGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1058809 original size:13 final size:13
Alignment explanation
Indices: 1058791--1058816 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1058781 ACATTTTGGG
1058791 ATGTATCGATACA
1 ATGTATCGATACA
1058804 ATGTATCGATACA
1 ATGTATCGATACA
1058817 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1058811 original size:33 final size:32
Alignment explanation
Indices: 1058769--1058836 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1058759 CGTTACAAGC
*
1058769 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
*
1058802 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
1058834 CAA
1 CAA
1058837 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:1058913 original size:20 final size:21
Alignment explanation
Indices: 1058866--1058920 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1058856 GCCAAGGACC
*
1058866 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
1058887 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
1058907 TGTATCGATACATT
1 TGTATCGATACATT
1058921 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:1059841 original size:89 final size:89
Alignment explanation
Indices: 1059739--1060102 Score: 271
Period size: 88 Copynumber: 4.1 Consensus size: 89
1059729 GAAGTTGGAG
* *
1059739 TATCCCCTCAGAGGAATAAGGATGAAGTTTCCCCAAGAATAAAATTATACAAAAGAAAATTTTAA
1 TATCCCTTCAGAGGAATAAGGATGAAGTTTCCCCAAGAATAAAATTATACAAAAGAAAAATTTAA
* *
1059804 ATTTTTGTTAGAATGGGACTAGAG
66 ATTTTTGTTAGAATGGGATTAGAA
* * * ** * * *** *
1059828 TATCCCTTTAGAGGTATGAGGATGGTGTTTCCCTAAAGACT-AAATTATGTGAAAG-AAAATTTG
1 TATCCCTTCAGAGGAATAAGGATGAAGTTTCCC-CAAGAATAAAATTATACAAAAGAAAAATTTA
*** *
1059891 AATTTTTGTTAGAACAAGATTATAA
65 AATTTTTGTTAGAATGGGATTAGAA
** * * * *
1059916 TAT-CCTCTCAGAATAGT-AGAGAT-AGAGTTTCCCTAAGGATAAAATTATA-AGAAGAAAAATT
1 TATCCCT-TCAGAGGAATAAG-GATGA-AGTTTCCCCAAGAATAAAATTATACAAAAGAAAAATT
* * *
1059977 TAAATTTTTATTAGAATGGGGTTGGAA
63 TAAATTTTTGTTAGAATGGGATTAGAA
* ** * * * * *
1060004 TATCTCC-TCGGAATAGTAAGGATGGAGTTTCCCCAAGGATAAAATTATAC-GAAGAAAAATTTG
1 TATC-CCTTCAGAGGAATAAGGATGAAGTTTCCCCAAGAATAAAATTATACAAAAGAAAAATTTA
*
1060067 AATTTTTGTTAG-ACGGGATT-GAA
65 AATTTTTGTTAGAATGGGATTAGAA
1060090 GTATCCCTTCAGA
1 -TATCCCTTCAGA
1060103 ATAGTGGGAT
Statistics
Matches: 214, Mismatches: 48, Indels: 28
0.74 0.17 0.10
Matches are distributed among these distances:
86 5 0.02
87 26 0.12
88 136 0.64
89 40 0.19
90 7 0.03
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (89 bp):
TATCCCTTCAGAGGAATAAGGATGAAGTTTCCCCAAGAATAAAATTATACAAAAGAAAAATTTAA
ATTTTTGTTAGAATGGGATTAGAA
Found at i:1060155 original size:16 final size:16
Alignment explanation
Indices: 1060131--1060166 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1060121 CTTGAAAGTG
*
1060131 AAAATTTTTTATTTTA
1 AAAAATTTTTATTTTA
*
1060147 AAAAATTTTTCTTTTA
1 AAAAATTTTTATTTTA
1060163 AAAA
1 AAAA
1060167 GGATTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAAATTTTTATTTTA
Found at i:1063103 original size:66 final size:65
Alignment explanation
Indices: 1063028--1063243 Score: 177
Period size: 66 Copynumber: 3.3 Consensus size: 65
1063018 ATGATGAAAC
* ** * *
1063028 CGATGAAGTCAACTAAAATTGACTAGGACGAGACCTAAATTGAAAAGAGG-TTGACCAAGGCAAA
1 CGATAAAGTCAACTAAAAGGGACAAGGACGA-ACCTAAATCGAAAAG-GGATTGACCAAGGCAAA
1063092 AT
64 AT
** * *
1063094 CGATAAAGTCAACTAAAAGGGACAAGGTGGAACCTAAGTCGAAAAGGGTATTGACCAGGGCAAAA
1 CGATAAAGTCAACTAAAAGGGACAAGGACGAACCTAAATCGAAAAGGG-ATTGACCAAGGCAAAA
1063159 T
65 T
* * * ** * * * * *
1063160 CGATAAAGTTAACAAAAAGAGG-CTAGGGTGAAACTTAAGTCGAAAAGGG-TGTGACTAGGGTAA
1 CGATAAAGTCAACTAAAAG-GGACAAGGACG-AACCTAAATCGAAAAGGGAT-TGACCAAGGCAA
1063223 AAT
63 AAT
*
1063226 CAATAAAGTCAACTAAAA
1 CGATAAAGTCAACTAAAA
1063244 AAGACCAAGG
Statistics
Matches: 125, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
64 2 0.02
65 14 0.11
66 90 0.72
67 19 0.15
ACGTcount: A:0.44, C:0.13, G:0.25, T:0.18
Consensus pattern (65 bp):
CGATAAAGTCAACTAAAAGGGACAAGGACGAACCTAAATCGAAAAGGGATTGACCAAGGCAAAAT
Found at i:1063244 original size:67 final size:67
Alignment explanation
Indices: 1063079--1063244 Score: 205
Period size: 66 Copynumber: 2.5 Consensus size: 67
1063069 GAAAAGAGGT
* *
1063079 TGACCAAGGCAAAATCGATAAAGTCAACT-AAAAGGGACAAGGTGGAACCTAAGTCGAAAAGGGT
1 TGACCAGGGCAAAATCGATAAAGTCAACTAAAAAGGGACAAGGTGAAACCTAAGTCGAAAAGGGT
*
1063143 AT
66 AG
* * *
1063145 TGACCAGGGCAAAATCGATAAAGTTAAC-AAAAAGAGG-CTAGGGTGAAACTTAAGTCGAAAAGG
1 TGACCAGGGCAAAATCGATAAAGTCAACTAAAAAG-GGAC-AAGGTGAAACCTAAGTCGAAAAGG
1063208 GT-G
64 GTAG
* * *
1063211 TGACTAGGGTAAAATCAATAAAGTCAACTAAAAA
1 TGACCAGGGCAAAATCGATAAAGTCAACTAAAAA
1063245 AGACCAAGGC
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
66 56 0.65
67 30 0.35
ACGTcount: A:0.45, C:0.13, G:0.25, T:0.17
Consensus pattern (67 bp):
TGACCAGGGCAAAATCGATAAAGTCAACTAAAAAGGGACAAGGTGAAACCTAAGTCGAAAAGGGT
AG
Found at i:1063516 original size:40 final size:42
Alignment explanation
Indices: 1063412--1063524 Score: 106
Period size: 42 Copynumber: 2.7 Consensus size: 42
1063402 GAAAAAGGTA
* * * **
1063412 TTGACCAGAGCAAAATTGATAAAGCCAACAAGTTAGGGGGGG
1 TTGACTAGGGCAAAATCGATAAAGCCAACAAGTTAGAAGGGG
* * *
1063454 TTGACTAGGGCAAAA-CTAATAAAGTCAAGAAGTTA-AAGGGG
1 TTGACTAGGGCAAAATC-GATAAAGCCAACAAGTTAGAAGGGG
* *
1063495 TT-AGTAGGGCAAAATCGATAAAGCTAACAA
1 TTGACTAGGGCAAAATCGATAAAGCCAACAA
1063525 AACGAGACCA
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
40 21 0.38
41 7 0.12
42 28 0.50
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (42 bp):
TTGACTAGGGCAAAATCGATAAAGCCAACAAGTTAGAAGGGG
Found at i:1064344 original size:67 final size:67
Alignment explanation
Indices: 1064120--1064332 Score: 207
Period size: 67 Copynumber: 3.2 Consensus size: 67
1064110 TTAATGGCCA
* * * * * *
1064120 AAACTAATAACAACCTGAAGTAAAAGATCATAATAGGGAATATGTGGCTCCCATAAAAAGTTGAA
1 AAACTGATAACAAGCTGAAGTAAAAGATCATAATGGGGAATATGTGGTTCCCATAAATAGTCGAA
1064185 AC
66 AC
* * * * ** * *
1064187 AAACTGATAACAAGCT-AGAGTAAAATATCATGATGGGAAATATTTAATTCCCATCAATA-ACTG
1 AAACTGATAACAAGCTGA-AGTAAAAGATCATAATGGGGAATATGTGGTTCCCATAAATAGTC-G
1064250 AAAC
64 AAAC
* * * * *
1064254 AAACTGATAACAAGTTGGAGTAGAAA-ATCATAATGGGGAGTATGTGGTTCCCATTAATAGTCAA
1 AAACTGATAACAAGCTGAAGTA-AAAGATCATAATGGGGAATATGTGGTTCCCATAAATAGTCGA
1064318 AAC
65 AAC
1064321 AAACTGATAACA
1 AAACTGATAACA
1064333 GACTCAAGTA
Statistics
Matches: 116, Mismatches: 25, Indels: 10
0.77 0.17 0.07
Matches are distributed among these distances:
66 1 0.01
67 111 0.96
68 4 0.03
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (67 bp):
AAACTGATAACAAGCTGAAGTAAAAGATCATAATGGGGAATATGTGGTTCCCATAAATAGTCGAA
AC
Found at i:1065041 original size:13 final size:13
Alignment explanation
Indices: 1065020--1065054 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1065010 CCTTTTTGGG
*
1065020 TTTTCATTTGATT
1 TTTTTATTTGATT
1065033 TTTTTATTTGATT
1 TTTTTATTTGATT
1065046 TTTTTATTT
1 TTTTTATTT
1065055 TTTGATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (13 bp):
TTTTTATTTGATT
Found at i:1065054 original size:8 final size:8
Alignment explanation
Indices: 1065043--1065118 Score: 59
Period size: 8 Copynumber: 9.9 Consensus size: 8
1065033 TTTTTATTTG
1065043 ATTTTTTT
1 ATTTTTTT
*
1065051 ATTTTTTG
1 ATTTTTTT
*
1065059 A-TTTTTG
1 ATTTTTTT
1065066 A--TTTTT
1 ATTTTTTT
**
1065072 GGTTTTTT
1 ATTTTTTT
1065080 ATTTTTTT
1 ATTTTTTT
* *
1065088 AATTTTTC
1 ATTTTTTT
*
1065096 ACTTTTTT
1 ATTTTTTT
*
1065104 CTTTTTTT
1 ATTTTTTT
1065112 ATTTTTT
1 ATTTTTT
1065119 AGACATAATA
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
6 4 0.07
7 7 0.13
8 43 0.80
ACGTcount: A:0.12, C:0.04, G:0.05, T:0.79
Consensus pattern (8 bp):
ATTTTTTT
Found at i:1065057 original size:7 final size:7
Alignment explanation
Indices: 1065032--1065119 Score: 61
Period size: 7 Copynumber: 12.0 Consensus size: 7
1065022 TTCATTTGAT
1065032 TTTTTTA
1 TTTTTTA
**
1065039 TTTGAT-
1 TTTTTTA
1065045 TTTTTTA
1 TTTTTTA
1065052 TTTTTTGA
1 TTTTTT-A
*
1065060 TTTTTGA
1 TTTTTTA
**
1065067 TTTTTGG
1 TTTTTTA
1065074 TTTTTTA
1 TTTTTTA
1065081 TTTTTTTAA
1 -TTTTTT-A
*
1065090 TTTTTCA
1 TTTTTTA
*
1065097 CTTTTTTCT
1 -TTTTTT-A
1065106 TTTTTTA
1 TTTTTTA
1065113 TTTTTTA
1 TTTTTTA
1065120 GACATAATAT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
6 4 0.06
7 30 0.48
8 28 0.44
9 1 0.02
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.78
Consensus pattern (7 bp):
TTTTTTA
Found at i:1065062 original size:29 final size:28
Alignment explanation
Indices: 1065026--1065118 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 28
1065016 TGGGTTTTCA
*
1065026 TTTGATTTTT-TTATTTGATTTTTTTATTT
1 TTTGATTTTTATT-TTTG-GTTTTTTATTT
1065055 TTTGATTTTTGATTTTTGGTTTTTTATTTT
1 TTTGATTTTT-ATTTTTGGTTTTTTA-TTT
* **
1065085 TTTAATTTTTCACTTTTTTCTTTTTTTATTT
1 TTTGATTTTT-A--TTTTTGGTTTTTTATTT
1065116 TTT
1 TTT
1065119 AGACATAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
29 17 0.31
30 17 0.31
31 8 0.15
32 12 0.22
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.78
Consensus pattern (28 bp):
TTTGATTTTTATTTTTGGTTTTTTATTT
Found at i:1071874 original size:21 final size:21
Alignment explanation
Indices: 1071838--1071900 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1071828 TAATTTTTCT
1071838 ATTTCATTTGTT-TTTATTTTA
1 ATTT-ATTTGTTATTTATTTTA
1071859 ATTTATTTGTTATTTATTTTTA
1 ATTTATTTGTTATTTA-TTTTA
* **
1071881 A-TTAATTAATATTTATTTTA
1 ATTTATTTGTTATTTATTTTA
1071901 TTTTGGTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 12 0.32
21 19 0.51
22 6 0.16
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (21 bp):
ATTTATTTGTTATTTATTTTA
Found at i:1071875 original size:4 final size:4
Alignment explanation
Indices: 1071859--1072038 Score: 52
Period size: 4 Copynumber: 44.5 Consensus size: 4
1071849 TTTTATTTTA
* * *
1071859 ATTT ATTT -GTT ATTT ATTT -TTA ATTA ATTAAT ATTT ATTTT ATTT -TGGTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT--T ATTT A-TTT ATTT AT--TT
* * * * * * *
1071909 ATTT GTTT ATTT ATAT ATTT -TTGT ATTT CTTT CTTT CTTT CTTT -CTT
1 ATTT ATTT ATTT ATTT ATTT ATT-T ATTT ATTT ATTT ATTT ATTT ATTT
* * * * * *
1071956 ATCT ATTC ATTT ATTT -TTT A-TT GTTT ATCT ATTT ACTT ATTT GTTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* *
1072002 -TATT ATTTT GTTT CATTT ATTT ATCTA ATTT ATTT AT
1 AT-TT A-TTT ATTT -ATTT ATTT AT-TT ATTT ATTT AT
1072039 ATAATTTTTA
Statistics
Matches: 132, Mismatches: 26, Indels: 36
0.68 0.13 0.19
Matches are distributed among these distances:
3 15 0.11
4 96 0.73
5 16 0.12
6 5 0.04
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:1071875 original size:11 final size:11
Alignment explanation
Indices: 1071837--1071877 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1071827 TTAATTTTTC
1071837 TATTTCATTTGT
1 TATTT-ATTTGT
1071849 T-TTTATTT-T
1 TATTTATTTGT
*
1071858 AATTTATTTGT
1 TATTTATTTGT
1071869 TATTTATTT
1 TATTTATTT
1071878 TTAATTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 11 0.44
11 12 0.48
12 1 0.04
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (11 bp):
TATTTATTTGT
Found at i:1071983 original size:26 final size:26
Alignment explanation
Indices: 1071954--1072023 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
1071944 TCTTTCTTTC
*
1071954 TTATCTATTCATTTATTTTTTATTGT
1 TTATCTATTCATTTATTTTTTATTAT
* *
1071980 TTATCTATTTACTTATTTGTTTTATTAT
1 TTATCTATTCATTTA-TT-TTTTATTAT
*
1072008 TT-TGT-TTCATTTATTT
1 TTATCTATTCATTTATTT
1072024 ATCTAATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
24 1 0.03
25 2 0.06
26 19 0.53
27 4 0.11
28 10 0.28
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.70
Consensus pattern (26 bp):
TTATCTATTCATTTATTTTTTATTAT
Found at i:1072032 original size:13 final size:13
Alignment explanation
Indices: 1072016--1072045 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1072006 ATTTTGTTTC
*
1072016 ATTTATTTATCTA
1 ATTTATTTATATA
1072029 ATTTATTTATATA
1 ATTTATTTATATA
1072042 ATTT
1 ATTT
1072046 TTAATGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTTATTTATATA
Found at i:1074050 original size:17 final size:16
Alignment explanation
Indices: 1074028--1074060 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1074018 CTTTAGACAT
1074028 TTTTTTTAATATTTTTA
1 TTTTTTTAAT-TTTTTA
1074045 TTTTTTTAATTTTTTA
1 TTTTTTTAATTTTTTA
1074061 AGTTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTAATTTTTTA
Found at i:1074061 original size:8 final size:8
Alignment explanation
Indices: 1074029--1074070 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
1074019 TTTAGACATT
1074029 TTTTTTAA
1 TTTTTTAA
*
1074037 TATTTTTAT
1 T-TTTTTAA
1074046 TTTTTTAA
1 TTTTTTAA
1074054 TTTTTTAA
1 TTTTTTAA
*
1074062 -GTTTTAA
1 TTTTTTAA
1074069 TT
1 TT
1074071 CTATTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 6 0.21
8 15 0.54
9 7 0.25
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (8 bp):
TTTTTTAA
Found at i:1074066 original size:17 final size:17
Alignment explanation
Indices: 1074029--1074066 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1074019 TTTAGACATT
*
1074029 TTTTTTAATATTTTTAT
1 TTTTTTAATATTTTTAG
1074046 TTTTTTAAT-TTTTTAAG
1 TTTTTTAATATTTTT-AG
1074063 TTTT
1 TTTT
1074067 AATTCTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTTAATATTTTTAG
Found at i:1075808 original size:21 final size:21
Alignment explanation
Indices: 1075779--1075824 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1075769 TCACTTCAAC
1075779 TTAA-ACTTTATTAGATCATT
1 TTAATACTTTATTAGATCATT
*
1075799 TTAATACTTTATTAGATTATT
1 TTAATACTTTATTAGATCATT
1075820 TTAAT
1 TTAAT
1075825 TTTGGGCCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (21 bp):
TTAATACTTTATTAGATCATT
Found at i:1075868 original size:3 final size:3
Alignment explanation
Indices: 1075862--1075887 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1075852 ATAATATATA
1075862 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1075888 ATACATCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1078735 original size:27 final size:27
Alignment explanation
Indices: 1078703--1078758 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
1078693 TTTAATAAAG
1078703 ACTAAATTTTCCATTTCCAAATAAACA
1 ACTAAATTTTCCATTTCCAAATAAACA
*
1078730 ACTAAATTTTCCATTTCCAAATGAACA
1 ACTAAATTTTCCATTTCCAAATAAACA
1078757 AC
1 AC
1078759 AATAACCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.32
Consensus pattern (27 bp):
ACTAAATTTTCCATTTCCAAATAAACA
Found at i:1083399 original size:20 final size:20
Alignment explanation
Indices: 1083374--1083515 Score: 106
Period size: 20 Copynumber: 6.5 Consensus size: 20
1083364 TTTTAACTAG
*
1083374 ATGTATTGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
1083394 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
1083414 ATGTATCGATACATCCGGGTAAAAATACAGA
1 ATGTATCGATACAT-----T---GA-A-A-A
*
1083445 ATGTATCGATATATTGAAAA
1 ATGTATCGATACATTGAAAA
* * * *
1083465 ATATATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
1083485 ATGTATCGATACATT-AAAGA
1 ATGTATCGATACATTGAAA-A
1083505 ATGTATCGATA
1 ATGTATCGATA
1083516 TATTTGGGTA
Statistics
Matches: 98, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
19 2 0.02
20 74 0.76
21 1 0.01
22 1 0.01
23 1 0.01
25 1 0.01
26 1 0.01
28 1 0.01
29 1 0.01
30 1 0.01
31 14 0.14
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:1084205 original size:57 final size:56
Alignment explanation
Indices: 1084074--1084954 Score: 1076
Period size: 57 Copynumber: 15.4 Consensus size: 56
1084064 AAAAAAATAC
* * *
1084074 TGCCACTAACTTGTGTGGGCTTTAAAAAGAGTTGCCACCGACTCATGTGGGCTTTGAAAAGAA
1 TGCCACTAAC-T-TGTGGGCTTT-GAAAGAG-TGCCACTGACT--TGTGGGCTTTG-AAAGGA
* * * *
1084137 TGCCACTAACTTGTGGGCTTTGAAAGTGGTGCCACTGACTTATTGGCTTTGAAAAGA
1 TGCCACTAACTTGTGGGCTTTGAAAG-AGTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1084194 TGCCACTAACTTATGGGCTTTGAAAAGAGTGCCATTGACTTGTGGGCTTTGAAAGGA
1 TGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1084251 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * *
1084308 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTAGGTTTTGAAAGGG
1 TGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
1084365 TGCCACTGACCTGTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTGAAAGGA
1 TGCCACT-AACT-TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * **
1084423 TGCCACTAACTT-TTGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTT-AAAAAA
1 TGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
1084478 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
1 -TGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
1084535 GTGCCACTGACTTGTGGGCTTTGAAAAAGTGCCATTGACTTGTGGGCTTTGAAAGGA
1 -TGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * *
1084592 TGCCACTAACTTGTGGGCTTTGAAAAGAGTG--GCTAACTTATGGGCTTTGAAAGGG
1 TGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1084647 TGCCACTAACTTGTGGGCTTTGAAAG-GATGCCACTAACTTGTGGGCTTTGAAAAGA
1 TGCCACTAACTTGTGGGCTTTGAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1084703 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGGCACTGACTTGTGGGCTTTGAAAGGA
1 -TGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * *
1084760 TGCCACTGACTTTTGGGCTTTGAAAAGAGTGCCACTAACTTATGGGCTTTGAAA-GA
1 TGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
1084816 GTGCCACTGACTTGTGGGTTTTGAAAG-GATGCTACTGACTTGTGGGCTTTGAAAGGA
1 -TGCCACTAACTTGTGGGCTTTGAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1084873 TGCCACTAACTTGTGGGCTCTGAAAAGAGTGTCACTGACTTGTGGGCTTTGAAA-GA
1 TGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1084929 GTACCACTGACTTGTGGGCTTTGAAA
1 -TGCCACTAACTTGTGGGCTTTGAAA
1084955 TGATAAACAT
Statistics
Matches: 723, Mismatches: 74, Indels: 49
0.85 0.09 0.06
Matches are distributed among these distances:
53 1 0.00
54 6 0.01
55 54 0.07
56 175 0.24
57 387 0.54
58 53 0.07
59 11 0.02
60 14 0.02
61 11 0.02
62 1 0.00
63 10 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (56 bp):
TGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:1084206 original size:28 final size:28
Alignment explanation
Indices: 1084087--1084954 Score: 1014
Period size: 28 Copynumber: 30.5 Consensus size: 28
1084077 CACTAACTTG
* *
1084087 TGTGGGCTTTAAAAAGAGTTGCCACCGACT
1 TGTGGGCTTTGAAAAGA--TGCCACTGACT
*
1084117 CATGTGGGCTTTGAAAAGAATGCCACTAACT
1 --TGTGGGCTTTGAAAAG-ATGCCACTGACT
* *
1084148 TGTGGGCTTTGAAAGTGGTGCCACTGACT
1 TGTGGGCTTTGAAA-AGATGCCACTGACT
* * *
1084177 TATTGGCTTTGAAAAGATGCCACTAACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
1084205 TATGGGCTTTGAAAAGAGTGCCATTGACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
* *
1084234 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
1084262 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
* *
1084291 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
1084319 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
* * * *
1084348 TGTAGGTTTTGAAAGGGTGCCACTGACCT
1 TGTGGGCTTTGAAAAGATGCCACTGA-CT
* *
1084377 GTGTGGGCTTTGAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
1084406 TATGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
1084434 T-TTGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
*
1084462 TGTGGGCTTT-AAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
* *
1084490 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
1084518 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
*
1084547 TGTGGGCTTTGAAAA-AGTGCCATTGACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
* *
1084575 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
1084603 TGTGGGCTTTGAAAAGAGTG--GCTAACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
* * * *
1084630 TATGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
1084658 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
1084686 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
*
1084715 TGTGGGCTTTG-AAAGAGTGGCACTGACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
*
1084743 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
1084771 TTTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
*
1084800 TATGGGCTTTG-AAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
* * *
1084828 TGTGGGTTTTGAAAGGATGCTACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
1084856 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
1084884 TGTGGGCTCTGAAAAGAGTGTCACTGACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
*
1084913 TGTGGGCTTTG-AAAGAGTACCACTGACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
1084941 TGTGGGCTTTGAAA
1 TGTGGGCTTTGAAA
1084955 TGATAAACAT
Statistics
Matches: 736, Mismatches: 79, Indels: 45
0.86 0.09 0.05
Matches are distributed among these distances:
26 2 0.00
27 33 0.04
28 429 0.58
29 222 0.30
30 25 0.03
31 9 0.01
32 15 0.02
33 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGATGCCACTGACT
Found at i:1084318 original size:85 final size:85
Alignment explanation
Indices: 1084087--1084954 Score: 1192
Period size: 85 Copynumber: 10.2 Consensus size: 85
1084077 CACTAACTTG
* ** * *
1084087 TGTGGGCTTTAAAAAGAGTTGCCACCGACTCATGTGGGCTTTGAAAAGAATGCCACTAACTTGTG
1 TGTGGGCTTTGAAAAGAG-TGCCACTAACT--TGTGGGCTTTG-AAAGAGTGCCACTGACTTGTG
*
1084152 GGCTTTGAAAGTGGTGCCACTGACT
62 GGCTTTGAAAG-GATGCCACTGACT
* * * *
1084177 TATTGGCTTTGAAAAGA-TGCCACTAACTTATGGGCTTTGAAAAGAGTGCCATTGACTTGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGC
*
1084241 TTTGAAAGGATGCCACTAACT
65 TTTGAAAGGATGCCACTGACT
* *
1084262 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCT
*
1084327 TTGAAAAGAGTGCCACTGACT
66 TTGAAAGGA-TGCCACTGACT
* * * * * *
1084348 TGTAGGTTTTG-AAAGGGTGCCACTGACCTGTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGG
1 TGTGGGCTTTGAAAAGAGTGCCACT-AACT-TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGG
*
1084412 CTTTGAAAGGATGCCACTAACT
64 CTTTGAAAGGATGCCACTGACT
* * *
1084434 T-TTGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAAAGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCT
*
1084498 TTGAAAGGGTGCCACTGACT
66 TTGAAAGGATGCCACTGACT
* * *
1084518 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAAGTGCCATTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCT
*
1084583 TTGAAAGGATGCCACTAACT
66 TTGAAAGGATGCCACTGACT
* * * *
1084603 TGTGGGCTTTGAAAAGAGTG--GCTAACTTATGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCT
*
1084666 TTGAAAGGATGCCACTAACT
66 TTGAAAGGATGCCACTGACT
* *
1084686 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGGCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCT
1084751 TTGAAAGGATGCCACTGACT
66 TTGAAAGGATGCCACTGACT
* * *
1084771 TTTGGGCTTTGAAAAGAGTGCCACTAACTTATGGGCTTTGAAAGAGTGCCACTGACTTGTGGGTT
1 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCT
*
1084836 TTGAAAGGATGCTACTGACT
66 TTGAAAGGATGCCACTGACT
* * *
1084856 TGTGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTCTGAAAAGAGTGTCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGC
*
1084920 TTTGAAA-GAGTACCACTGACT
65 TTTGAAAGGA-TGCCACTGACT
1084941 TGTGGGCTTTGAAA
1 TGTGGGCTTTGAAA
1084955 TGATAAACAT
Statistics
Matches: 697, Mismatches: 71, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
83 76 0.11
84 73 0.10
85 378 0.54
86 104 0.15
87 43 0.06
88 9 0.01
90 14 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (85 bp):
TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCT
TTGAAAGGATGCCACTGACT
Found at i:1086194 original size:18 final size:17
Alignment explanation
Indices: 1086171--1086237 Score: 72
Period size: 15 Copynumber: 4.1 Consensus size: 17
1086161 GACCCCTTTC
1086171 TGTTTTTTTCTAT-TTTTT
1 TGTTTTTTT-T-TGTTTTT
1086189 TGTTTTTTTTTGTTTTT
1 TGTTTTTTTTTGTTTTT
1086206 TG--TTTTTTTG--TTT
1 TGTTTTTTTTTGTTTTT
1086219 TGTTTTTTTTTGTGTTTT
1 TGTTTTTTTTTGT-TTTT
1086237 T
1 T
1086238 TCTGGGTCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 5 0.12
15 16 0.37
16 1 0.02
17 8 0.19
18 13 0.30
ACGTcount: A:0.01, C:0.01, G:0.12, T:0.85
Consensus pattern (17 bp):
TGTTTTTTTTTGTTTTT
Found at i:1086196 original size:17 final size:17
Alignment explanation
Indices: 1086174--1086238 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
1086164 CCCTTTCTGT
1086174 TTTTTTCTAT-TTTTTTG
1 TTTTTT-TATGTTTTTTG
*
1086191 TTTTTTTTTGTTTTTTG
1 TTTTTTTATGTTTTTTG
1086208 -TTTTTT-TGTTTTGTT-
1 TTTTTTTATGTTTT-TTG
*
1086223 TTTTTTTGTGTTTTTT
1 TTTTTTTATGTTTTTT
1086239 CTGGGTCTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
15 6 0.14
16 18 0.42
17 19 0.44
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.86
Consensus pattern (17 bp):
TTTTTTTATGTTTTTTG
Found at i:1086204 original size:15 final size:15
Alignment explanation
Indices: 1086186--1086231 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
1086176 TTTTCTATTT
1086186 TTTTGTTTTTTTTTG
1 TTTTGTTTTTTTTTG
1086201 TTTT-TTGTTTTTTTG
1 TTTTGTT-TTTTTTTG
1086216 TTTTGTTTTTTTTTG
1 TTTTGTTTTTTTTTG
1086231 T
1 T
1086232 GTTTTTTCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.07
15 25 0.86
16 2 0.07
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
TTTTGTTTTTTTTTG
Found at i:1086204 original size:25 final size:25
Alignment explanation
Indices: 1086173--1086238 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
1086163 CCCCTTTCTG
*
1086173 TTTTTTTCTATTTTTTTGTTTT-TT
1 TTTTTTTCTGTTTTTTTGTTTTGTT
*
1086197 TTTGTTTTTTGTTTTTTTGTTTTGTT
1 TTT-TTTTCTGTTTTTTTGTTTTGTT
*
1086223 TTTTTTTGTGTTTTTT
1 TTTTTTTCTGTTTTTT
1086239 CTGGGTCTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.08
25 29 0.78
26 5 0.14
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.86
Consensus pattern (25 bp):
TTTTTTTCTGTTTTTTTGTTTTGTT
Found at i:1086224 original size:10 final size:10
Alignment explanation
Indices: 1086173--1086238 Score: 80
Period size: 10 Copynumber: 6.5 Consensus size: 10
1086163 CCCCTTTCTG
* *
1086173 TTTTTTTCTA
1 TTTTTTTGTT
1086183 TTTTTTTGTT
1 TTTTTTTGTT
1086193 TTTTTTTGTT
1 TTTTTTTGTT
1086203 TTTTGTTT-TT
1 TTTT-TTTGTT
*
1086213 TTGTTTTGTT
1 TTTTTTTGTT
1086223 TTTTTTTGTGT
1 TTTTTTTGT-T
1086234 TTTTT
1 TTTTT
1086239 CTGGGTCTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
9 3 0.06
10 37 0.76
11 9 0.18
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.86
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:1086238 original size:1 final size:1
Alignment explanation
Indices: 1086173--1086229 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
1086163 CCCCTTTCTG
* * * * * * *
1086173 TTTTTTTCTATTTTTTTGTTTTTTTTTGTTTTTTGTTTTTTTGTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1086230 GTGTTTTTTC
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:1089514 original size:40 final size:41
Alignment explanation
Indices: 1089459--1089541 Score: 159
Period size: 40 Copynumber: 2.0 Consensus size: 41
1089449 TATTCTTGGA
1089459 GTAAGTCAATCAGCTTAGTCC-AGTAGTCGATCTTATTGAG
1 GTAAGTCAATCAGCTTAGTCCTAGTAGTCGATCTTATTGAG
1089499 GTAAGTCAATCAGCTTAGTCCTAGTAGTCGATCTTATTGAG
1 GTAAGTCAATCAGCTTAGTCCTAGTAGTCGATCTTATTGAG
1089540 GT
1 GT
1089542 CCCAATCCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 21 0.50
41 21 0.50
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (41 bp):
GTAAGTCAATCAGCTTAGTCCTAGTAGTCGATCTTATTGAG
Found at i:1101117 original size:13 final size:13
Alignment explanation
Indices: 1101099--1101123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1101089 ATATTGCACA
1101099 GTATCGATACATT
1 GTATCGATACATT
1101112 GTATCGATACAT
1 GTATCGATACAT
1101124 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1101136 original size:20 final size:21
Alignment explanation
Indices: 1101111--1101163 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1101101 ATCGATACAT
*
1101111 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
1101131 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
1101152 TGTATCGATACA
1 TGTATCGATACA
1101164 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:1101242 original size:13 final size:13
Alignment explanation
Indices: 1101224--1101249 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1101214 ACACACAAGA
1101224 TGTATCGATACAT
1 TGTATCGATACAT
1101237 TGTATCGATACAT
1 TGTATCGATACAT
1101250 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1101265 original size:33 final size:32
Alignment explanation
Indices: 1101204--1101271 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1101194 CCTTAACTGT
*
1101204 TTGTATCGATACACACAAGATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
1101236 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
1101269 TTG
1 TTG
1101272 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:1104497 original size:13 final size:13
Alignment explanation
Indices: 1104479--1104506 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1104469 ATATAAAGAT
1104479 CAATGTATCGATA
1 CAATGTATCGATA
1104492 CAATGTATCGATA
1 CAATGTATCGATA
1104505 CA
1 CA
1104507 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1104586 original size:33 final size:33
Alignment explanation
Indices: 1104549--1104613 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1104539 TAGCTTAAAA
1104549 TGTATCGATACAAAAAAATATGTATCGATACAT
1 TGTATCGATACAAAAAAATATGTATCGATACAT
* ***
1104582 TGTATCGATACAACATTTTATGTATCGATACA
1 TGTATCGATACAAAAAAATATGTATCGATACA
1104614 AATTGTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAAAAAAATATGTATCGATACAT
Found at i:1104587 original size:13 final size:13
Alignment explanation
Indices: 1104569--1104593 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1104559 CAAAAAAATA
1104569 TGTATCGATACAT
1 TGTATCGATACAT
1104582 TGTATCGATACA
1 TGTATCGATACA
1104594 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1110800 original size:13 final size:13
Alignment explanation
Indices: 1110782--1110819 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1110772 CAGCATTCTC
*
1110782 TGTATCGATACAT
1 TGTATCGATACAG
1110795 TGTATCGATACAG
1 TGTATCGATACAG
1110808 TGTATCGATACA
1 TGTATCGATACA
1110820 AAGGTTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1113286 original size:13 final size:13
Alignment explanation
Indices: 1113268--1113292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1113258 ATATTGCACA
1113268 GTATCGATACATT
1 GTATCGATACATT
1113281 GTATCGATACAT
1 GTATCGATACAT
1113293 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1113411 original size:13 final size:13
Alignment explanation
Indices: 1113393--1113418 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1113383 ACACACAAGA
1113393 TGTATCGATACAT
1 TGTATCGATACAT
1113406 TGTATCGATACAT
1 TGTATCGATACAT
1113419 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1113414 original size:32 final size:33
Alignment explanation
Indices: 1113373--1113438 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1113363 CCTTAACTAT
*
1113373 TTGTATCGATACA-CACAAGATGTATCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
* *
1113405 TTGTATCGATACATCCCAAAATGTATTGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
1113438 T
1 T
1113439 GGGCTTGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCGATACA
Found at i:1117728 original size:12 final size:13
Alignment explanation
Indices: 1117705--1117743 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 13
1117695 TTTTAAAAAA
1117705 TAAATATTTTTAT
1 TAAATATTTTTAT
1117718 TAAAT-TTTTTAT
1 TAAATATTTTTAT
1117730 TAATATATATTTTA
1 TAA-ATAT-TTTTA
1117744 AAAATTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.43
13 7 0.30
14 1 0.04
15 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TAAATATTTTTAT
Found at i:1117739 original size:28 final size:29
Alignment explanation
Indices: 1117673--1117742 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 29
1117663 TTTTTACTTT
*
1117673 TTAA-ATATATTTTTAATTTAATTTTTAA
1 TTAATATATATTTTTAATTAAATTTTTAA
** * *
1117701 AAAATAAATATTTTT-ATTAAATTTTTTA
1 TTAATATATATTTTTAATTAAATTTTTAA
1117729 TTAATATATATTTT
1 TTAATATATATTTT
1117743 AAAAATTCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
28 24 0.73
29 9 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TTAATATATATTTTTAATTAAATTTTTAA
Found at i:1118976 original size:2 final size:2
Alignment explanation
Indices: 1118969--1118996 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1118959 TTTGCTGCAC
1118969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1118997 GTGGGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1119006 original size:2 final size:2
Alignment explanation
Indices: 1118996--1119031 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1118986 TATATATATA
*
1118996 TG TG GG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1119032 CACCCATGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.53, T:0.47
Consensus pattern (2 bp):
TG
Found at i:1120573 original size:13 final size:13
Alignment explanation
Indices: 1120555--1120579 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1120545 ATATTGCACA
1120555 GTATCGATACATT
1 GTATCGATACATT
1120568 GTATCGATACAT
1 GTATCGATACAT
1120580 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1120698 original size:13 final size:13
Alignment explanation
Indices: 1120680--1120705 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1120670 ACACATAATA
1120680 TGTATCGATACAT
1 TGTATCGATACAT
1120693 TGTATCGATACAT
1 TGTATCGATACAT
1120706 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1120721 original size:33 final size:32
Alignment explanation
Indices: 1120660--1120727 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
1120650 CCTTAACTGT
* *
1120660 TTGTATCGATACACATAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
1120692 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
1120725 TTG
1 TTG
1120728 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:1122821 original size:2 final size:2
Alignment explanation
Indices: 1122809--1122838 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1122799 GTAAATATGC
*
1122809 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1122839 GTATGTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1128663 original size:15 final size:15
Alignment explanation
Indices: 1128643--1128681 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
1128633 GGAAGTATTT
1128643 GGAGGTGTTTCTATC
1 GGAGGTGTTTCTATC
1128658 GGAGGTGTTTCTATC
1 GGAGGTGTTTCTATC
1128673 GGAGGTGTT
1 GGAGGTGTT
1128682 GAAGAGCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.13, C:0.10, G:0.38, T:0.38
Consensus pattern (15 bp):
GGAGGTGTTTCTATC
Found at i:1129220 original size:51 final size:50
Alignment explanation
Indices: 1129160--1129276 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 50
1129150 ATTTAACTAG
* * * * * *
1129160 ATGTATCGATATATTTAGGTCAAAACCCAGAATGTATCGATACGATGAAGA
1 ATGTATCGATACATTTAGATCAAAACACAGAACGTATCGATACAAT-AAAA
*
1129211 ATGTATCGATACATTTAGATCAAAATACAGAACGTATCGATACAATAAAA
1 ATGTATCGATACATTTAGATCAAAACACAGAACGTATCGATACAATAAAA
* *
1129261 ATGTATTGATTCATTT
1 ATGTATCGATACATTT
1129277 TCTTTCTAGA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
50 17 0.30
51 40 0.70
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (50 bp):
ATGTATCGATACATTTAGATCAAAACACAGAACGTATCGATACAATAAAA
Found at i:1129454 original size:141 final size:141
Alignment explanation
Indices: 1129191--1129484 Score: 367
Period size: 141 Copynumber: 2.1 Consensus size: 141
1129181 AAAACCCAGA
**
1129191 ATGTATCGATACGATGAAGAATGTATCGATACATTTAGATCAAAATACAGAACGTATCGATACAA
1 ATGTATCGATACGATGAAGAACATATCGATACATTTAGATCAAAATACAGAACGTATCGATACAA
* * * * *
1129256 TAAAAATGTATTGATTCATTTTCTTTCTAGAATACAAAATTTGCCTCAACAAAGTCCAGTATCAA
66 TAAAAATGTATCGATACATTTTCTTTCCAGAATACAAAATTTACCTCAACAAAGTCCAATATCAA
* *
1129321 TACATTTATTT
131 TACATTCACTT
* * * *
1129332 ATGTATCGATACGATGAAGAACATATCGATATATTTGGATCAAAACCTA-A-AATGTATTGATAC
1 ATGTATCGATACGATGAAGAACATATCGATACATTTAGATCAAAA--TACAGAACGTATCGATAC
* * * ** *
1129395 AATAAAAATTTATCGATACATTTTCTTTCCAGAATGCAAAATTTACTTGGACAAGGTCCAATATC
64 AATAAAAATGTATCGATACATTTTCTTTCCAGAATACAAAATTTACCTCAACAAAGTCCAATATC
*
1129460 GATACATTCACTT
129 AATACATTCACTT
*
1129473 ATGTATTGATAC
1 ATGTATCGATAC
1129485 ATTCACTTGT
Statistics
Matches: 130, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
141 127 0.98
142 1 0.01
143 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (141 bp):
ATGTATCGATACGATGAAGAACATATCGATACATTTAGATCAAAATACAGAACGTATCGATACAA
TAAAAATGTATCGATACATTTTCTTTCCAGAATACAAAATTTACCTCAACAAAGTCCAATATCAA
TACATTCACTT
Found at i:1130388 original size:59 final size:59
Alignment explanation
Indices: 1130272--1130390 Score: 148
Period size: 59 Copynumber: 2.0 Consensus size: 59
1130262 TTTAGTCCCT
* * * * * *
1130272 TTTTTTCCCATAAAATTAGAATCCAATTCTTAGCTATAGTTAAGAATGGGGATTATTTG
1 TTTTCTCCCATAAAATTAGAATCCAATTCCTAGCCATAGTCAAGAATGGGAACTATTTG
* * **
1130331 TTTTCTCCCGTAAAATTAGAATGCAATTCCTAGCCATAGTCAAGAATGTTAACTATTTG
1 TTTTCTCCCATAAAATTAGAATCCAATTCCTAGCCATAGTCAAGAATGGGAACTATTTG
1130390 T
1 T
1130391 GAGTCATATC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (59 bp):
TTTTCTCCCATAAAATTAGAATCCAATTCCTAGCCATAGTCAAGAATGGGAACTATTTG
Found at i:1131031 original size:18 final size:17
Alignment explanation
Indices: 1130990--1131031 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1130980 TAAAAAGTGG
1130990 TATTATATAAAATATTA
1 TATTATATAAAATATTA
1131007 TAGTTATATAAATTATATTA
1 TA-TTATATAAA--ATATTA
1131027 T-TTAT
1 TATTAT
1131032 TGCATACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.09
18 13 0.59
20 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TATTATATAAAATATTA
Found at i:1131152 original size:18 final size:20
Alignment explanation
Indices: 1131129--1131180 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
1131119 AAGTTAAAAA
1131129 ACATAAATTTATTAT-A-TT
1 ACATAAATTTATTATAAGTT
* *
1131147 ACATAAATTTTTTTTAAGTT
1 ACATAAATTTATTATAAGTT
*
1131167 ACATAAATATATTA
1 ACATAAATTTATTA
1131181 GCAAAGGTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 13 0.48
19 1 0.04
20 13 0.48
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (20 bp):
ACATAAATTTATTATAAGTT
Found at i:1131327 original size:17 final size:18
Alignment explanation
Indices: 1131297--1131335 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1131287 TATATTCATA
* *
1131297 TATATATATACATTATAT
1 TATATAAATACATTATAG
1131315 TATATAAAT-CATTATAG
1 TATATAAATACATTATAG
1131332 TATA
1 TATA
1131336 GATAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (18 bp):
TATATAAATACATTATAG
Found at i:1131564 original size:21 final size:20
Alignment explanation
Indices: 1131533--1131588 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1131523 ATAAAAAAAA
*
1131533 TTACGTAAAATATTATCGG-G
1 TTACATAAAATATTAT-GGAG
*
1131553 TTACATATAAATGTTATGGAG
1 TTACATA-AAATATTATGGAG
1131574 TTACATAAAATATTA
1 TTACATAAAATATTA
1131589 CCGGAACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TTACATAAAATATTATGGAG
Found at i:1132194 original size:17 final size:16
Alignment explanation
Indices: 1132172--1132206 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1132162 TTTTAAAATT
*
1132172 TTTGAGTTATTTTCGGG
1 TTTGAGTCATTTT-GGG
1132189 TTTGAGTCATTTTGGG
1 TTTGAGTCATTTTGGG
1132205 TT
1 TT
1132207 CGGATCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.11, C:0.06, G:0.29, T:0.54
Consensus pattern (16 bp):
TTTGAGTCATTTTGGG
Found at i:1134442 original size:17 final size:17
Alignment explanation
Indices: 1134391--1134444 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
1134381 CGAATATCTC
*
1134391 AAAATGTATA-AAATAT
1 AAAATTTATATAAATAT
1134407 -AAA-TTAT-TAATATATT
1 AAAATTTATATAA-ATA-T
1134423 AAAATTTATATAAATAT
1 AAAATTTATATAAATAT
1134440 AAAAT
1 AAAAT
1134445 ATATTAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
14 5 0.16
15 6 0.19
16 1 0.03
17 9 0.29
18 7 0.23
19 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AAAATTTATATAAATAT
Found at i:1134484 original size:28 final size:28
Alignment explanation
Indices: 1134431--1134486 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1134421 TTAAAATTTA
*
1134431 TATAAATATAAAATATATTAAACACAAT
1 TATAAATATAAAATATATCAAACACAAT
*
1134459 TATAAATTATAAAATATA-CAATCACAAT
1 TATAAA-TATAAAATATATCAAACACAAT
1134487 ATTAATACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (28 bp):
TATAAATATAAAATATATCAAACACAAT
Found at i:1135951 original size:27 final size:26
Alignment explanation
Indices: 1135903--1135979 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 26
1135893 AGAAAGAAAG
* *
1135903 GAAAAAACAAAAGACATCAGAGAAAAA
1 GAAAAAA-AAAAGAAATGAGAGAAAAA
*
1135930 GAAAAAAAAAAGTAAATGAGAGAGAAA
1 GAAAAAAAAAAG-AAATGAGAGAAAAA
1135957 GAAAGAAAAGAAGAGAAATGAGA
1 GAAA-AAAA-AA-AGAAATGAGA
1135980 AAGGAAAAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
26 5 0.12
27 22 0.51
28 4 0.09
29 10 0.23
30 2 0.05
ACGTcount: A:0.69, C:0.04, G:0.22, T:0.05
Consensus pattern (26 bp):
GAAAAAAAAAAGAAATGAGAGAAAAA
Found at i:1135953 original size:29 final size:30
Alignment explanation
Indices: 1135921--1135993 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 30
1135911 AAAAGACATC
1135921 AGAGA-AAAAGAAA-AAAA-AA-AGTAAATG
1 AGAGAGAAAAGAAAGAAAAGAAGAG-AAATG
1135948 AGAGAG-AAAGAAAGAAAAGAAGAGAAATG
1 AGAGAGAAAAGAAAGAAAAGAAGAGAAATG
*
1135977 AGAAAGGAAAAGAAAGA
1 AGAGA-GAAAAGAAAGA
1135994 GAGATAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 12 0.31
28 4 0.10
29 11 0.28
30 3 0.08
31 9 0.23
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (30 bp):
AGAGAGAAAAGAAAGAAAAGAAGAGAAATG
Found at i:1135989 original size:31 final size:29
Alignment explanation
Indices: 1135893--1135993 Score: 79
Period size: 27 Copynumber: 3.6 Consensus size: 29
1135883 TTTTTTATCA
* * *
1135893 AGAAAGAAAGGAAA-AAACAAAAG-ACATC
1 AGAAAGAAAAGAAAGAAA-AAAAGTAAATG
*
1135921 AGAGA-AAAAGAAA-AAAAAAAGTAAATG
1 AGAAAGAAAAGAAAGAAAAAAAGTAAATG
*
1135948 AGAGAG-AAAGAAAGAAAAGAAGAG-AAATG
1 AGAAAGAAAAGAAAGAAAA-AA-AGTAAATG
1135977 AGAAAGGAAAAGAAAGA
1 AGAAA-GAAAAGAAAGA
1135994 GAGATAAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
26 5 0.08
27 25 0.41
28 8 0.13
29 11 0.18
30 3 0.05
31 9 0.15
ACGTcount: A:0.69, C:0.03, G:0.24, T:0.04
Consensus pattern (29 bp):
AGAAAGAAAAGAAAGAAAAAAAGTAAATG
Found at i:1136333 original size:20 final size:20
Alignment explanation
Indices: 1136296--1136351 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
1136286 CCTAATTAAG
* *
1136296 AATAATTTATTATATATTTTA
1 AATATTTTA-TATTTATTTTA
1136317 AATATTTTATATTTATTTTA
1 AATATTTTATATTTATTTTA
** *
1136337 TTTATTTGATATTTA
1 AATATTTTATATTTA
1136352 AAATTTTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
AATATTTTATATTTATTTTA
Found at i:1136444 original size:21 final size:21
Alignment explanation
Indices: 1136406--1136451 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1136396 AAATACACAC
* *
1136406 ATATGTAATATAGGTATATTT
1 ATATGTAATATAGATATATAT
1136427 ATATGTGAATATA-ATATATAT
1 ATATGT-AATATAGATATATAT
1136448 ATAT
1 ATAT
1136452 ATATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (21 bp):
ATATGTAATATAGATATATAT
Found at i:1136756 original size:28 final size:28
Alignment explanation
Indices: 1136725--1136789 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
1136715 ATAAGCTTTC
*
1136725 AACTTTTATTTTGTA-TATAAT-AGTTTTT
1 AACTTTTA-TTTGTATTA-AATAAGTTATT
*
1136753 AACTTTCATTTGTATTCAAATAAGTTATT
1 AACTTTTATTTGTATT-AAATAAGTTATT
1136782 AACTTTTA
1 AACTTTTA
1136790 ATTTATACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 6 0.19
28 11 0.35
29 14 0.45
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (28 bp):
AACTTTTATTTGTATTAAATAAGTTATT
Found at i:1136933 original size:23 final size:26
Alignment explanation
Indices: 1136887--1136933 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1136877 ATTAAAATAC
1136887 AATAAAAATATAAGAGCTTATTTAAG
1 AATAAAAATATAAGAGCTTATTTAAG
*
1136913 AATAATAAT-TAAGA-CTT-TTTA
1 AATAAAAATATAAGAGCTTATTTA
1136934 GTATATTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 3 0.15
25 5 0.25
26 8 0.40
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (26 bp):
AATAAAAATATAAGAGCTTATTTAAG
Found at i:1140401 original size:2 final size:2
Alignment explanation
Indices: 1140394--1140422 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1140384 CAATTTACAA
1140394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1140423 ATTGAAGTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1140843 original size:37 final size:36
Alignment explanation
Indices: 1140801--1140877 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 36
1140791 CTTTTACTCA
* *
1140801 ATTTAAAATAAT-TTTGTGACTAAATTAATTTTTATTT
1 ATTTAAAATAATATTT-TGACCAAATTAA-TTGTATTT
1140838 ATTTAAAATAATATTTTGACCAAATTAATTGTATTT
1 ATTTAAAATAATATTTTGACCAAATTAATTGTATTT
1140874 ATTT
1 ATTT
1140878 TTAAAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 11 0.30
37 23 0.62
38 3 0.08
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (36 bp):
ATTTAAAATAATATTTTGACCAAATTAATTGTATTT
Found at i:1142125 original size:20 final size:20
Alignment explanation
Indices: 1142100--1142154 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
1142090 CTACCAAGGA
1142100 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
1142120 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
1142140 AATGTATCGATACAT
1 AATGTATCGATACAT
1142155 GTAGGTAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Done.