Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold127
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: 3416254
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 147187 characters in sequence are not A, C, G, or T
File 5 of 10
Found at i:1414265 original size:50 final size:50
Alignment explanation
Indices: 1414190--1414488 Score: 305
Period size: 50 Copynumber: 5.7 Consensus size: 50
1414180 TTTCTTGTAC
* * **
1414190 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
1414240 TGCCCAA-GCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATAATCTCAATGA
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* * * *
1414296 CGCCAATGCCATGTCCCAGACATGTTCTTATGA-GGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTA-CATGGGACCTCTCATATCGG
* *
1414346 TGCCAACGCCATGTCCCAGACATGGTCTTACATTGGACCTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * *
1414396 TGCCAACGCCATGTCCCTGACATGGCCTTACATGGGACCTCTAATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
1414452 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1414489 TCTTATTTCC
Statistics
Matches: 207, Mismatches: 26, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
49 1 0.00
50 119 0.57
51 6 0.03
53 6 0.03
55 4 0.02
56 70 0.34
57 1 0.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:1414339 original size:106 final size:106
Alignment explanation
Indices: 1414191--1414484 Score: 307
Period size: 106 Copynumber: 2.8 Consensus size: 106
1414181 TTCTTGTACT
* **
1414191 GCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCAA-GCCATGTC
1 GCCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG-CCAACGCCATGTC
1414255 CCAGACATGGTCTTACATAGGACCTCTCATAATCTCAATGAC
65 CCAGACATGGTCTTACATAGGACCTCTCATAATCTCAATGAC
* * * *
1414297 GCCAATGCCATGTCCCAGACATGTTCTTATGA-GGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 GCCAATGCCATATCCCAGACATGGTCTTA-CATGGGACCTCTCATATCGGTGCCAACGCCATGTC
* **
1414361 CCAGACATGGTCTTACATTGGACCTCTCAT-A--TC---GGT
65 CCAGACATGGTCTTACATAGGACCTCTCATAATCTCAATGAC
* * * * * * *
1414397 GCCAACGCCATGTCCCTGACATGGCCTTACATGGGACCTCTAATAATCTCAATGATGCCAATGCC
1 GCCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTGCCAACGCC
1414462 ATGTCCCAGACATGGTCTTACAT
60 ATGTCCCAGACATGGTCTTACAT
1414485 GGGATCTTAT
Statistics
Matches: 160, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
99 1 0.01
100 37 0.23
103 4 0.03
105 5 0.03
106 112 0.70
107 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (106 bp):
GCCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCC
CAGACATGGTCTTACATAGGACCTCTCATAATCTCAATGAC
Found at i:1414373 original size:156 final size:156
Alignment explanation
Indices: 1414190--1414481 Score: 460
Period size: 156 Copynumber: 1.9 Consensus size: 156
1414180 TTTCTTGTAC
* * **
1414190 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCAA-GCCATGT
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG-CCAACGCCATGT
* *
1414254 CCCAGACATGGTCTTACATAGGACCTCTCATAATCTCAATGACGCCAATGCCATGTCCCAGACAT
65 CCCAGACATGGCCTTACATAGGACCTCTAATAATCTCAATGACGCCAATGCCATGTCCCAGACAT
*
1414319 GTTCTTATGAGGGACCTCTCATCTCGG
130 GGTCTTATGAGGGACCTCTCATCTCGG
* *
1414346 TGCCAACGCCATGTCCCAGACATGGTCTTACATTGGACCTCTCATATCGGTGCCAACGCCATGTC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTC
* * *
1414411 CCTGACATGGCCTTACATGGGACCTCTAATAATCTCAATGATGCCAATGCCATGTCCCAGACATG
66 CCAGACATGGCCTTACATAGGACCTCTAATAATCTCAATGACGCCAATGCCATGTCCCAGACATG
1414476 GTCTTA
131 GTCTTA
1414482 CATGGGATCT
Statistics
Matches: 123, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
155 4 0.03
156 119 0.97
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (156 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTC
CCAGACATGGCCTTACATAGGACCTCTAATAATCTCAATGACGCCAATGCCATGTCCCAGACATG
GTCTTATGAGGGACCTCTCATCTCGG
Found at i:1416052 original size:4 final size:4
Alignment explanation
Indices: 1416043--1416193 Score: 293
Period size: 4 Copynumber: 37.8 Consensus size: 4
1416033 CTTTTTAGCA
1416043 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
1416091 ACAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1416139 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1416187 ATAC ATA
1 ATAC ATA
1416194 TCATTAATTG
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 145 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:1426312 original size:159 final size:159
Alignment explanation
Indices: 1426018--1426354 Score: 597
Period size: 159 Copynumber: 2.1 Consensus size: 159
1426008 AACAATTCAC
* *
1426018 TATAT-TACATTCGGCCATAGCTTATGTAACTTCAAATAATTTATTTCAATGCATAACAAATATA
1 TATATATACATTCGGCCATAACCTATGTAACTTCAAATAATTTATTTCAATGCATAACAAATATA
* **
1426082 TCTATGCATTCGGCCATAGTTTCTTTCATTTCTCTGCATAACAATTACATATACATTCAGCTATA
66 TATATGCATTCGGCCATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAGCTATA
1426147 GATTAATTCATTTCAATGTATAACAAATA
131 GATTAATTCATTTCAATGTATAACAAATA
*
1426176 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
1 TATATATACATTCGGCCATAACCTATGTAACTTCAAATAATTTATTTCAATGCATAACAAATATA
1426241 TATATGCATTCGGCCATAGTTTAAATT-ATTTCTCTGCATAACAATTACATATACATTCAGCTAT
66 TATATGCATTCGGCCATAGTTT-AATTCATTTCTCTGCATAACAATTACATATACATTCAGCTAT
1426305 AGATTAATTCATTTCAATGTATAACAAATA
130 AGATTAATTCATTTCAATGTATAACAAATA
1426335 TATATATACATTCGGCCATA
1 TATATATACATTCGGCCATA
1426355 GTTTAATTNN
Statistics
Matches: 171, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
158 5 0.03
159 164 0.96
160 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (159 bp):
TATATATACATTCGGCCATAACCTATGTAACTTCAAATAATTTATTTCAATGCATAACAAATATA
TATATGCATTCGGCCATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAGCTATA
GATTAATTCATTTCAATGTATAACAAATA
Found at i:1426361 original size:49 final size:48
Alignment explanation
Indices: 1426217--1426362 Score: 188
Period size: 49 Copynumber: 3.0 Consensus size: 48
1426207 TTCAAATAAT
*
1426217 TTATTTCAATGCATAACAAATATATATATGCATTCGGCCATAGTTTAAA
1 TTATTTCAATGCATAACAAATATATATATACATTCGGCCATAGTTT-AA
** * * * *
1426266 TTATTTCTCTGCATAAC-AAT-TACATATACATTCAGCTATAGATTAA
1 TTATTTCAATGCATAACAAATATATATATACATTCGGCCATAGTTTAA
*
1426312 TTCATTTCAATGTATAACAAATATATATATACATTCGGCCATAGTTTAA
1 TT-ATTTCAATGCATAACAAATATATATATACATTCGGCCATAGTTTAA
1426361 TT
1 TT
1426363 NNNNNNNNNN
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
46 4 0.05
47 31 0.39
48 6 0.08
49 39 0.49
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (48 bp):
TTATTTCAATGCATAACAAATATATATATACATTCGGCCATAGTTTAA
Found at i:1440934 original size:13 final size:13
Alignment explanation
Indices: 1440916--1440946 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1440906 TTTCATTTTC
*
1440916 AACAAAGTAACTT
1 AACAAAGTAACTA
1440929 AACAAAGTAACTA
1 AACAAAGTAACTA
1440942 AACAA
1 AACAA
1440947 CAACCTTGTT
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:0.61, C:0.16, G:0.06, T:0.16
Consensus pattern (13 bp):
AACAAAGTAACTA
Found at i:1442970 original size:17 final size:17
Alignment explanation
Indices: 1442933--1442970 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1442923 TCCAAATGTG
* *
1442933 CGAGCTCACCAAGACTG
1 CGAGCTCACCAAAACTA
1442950 CGAGCTCACCAAAACTA
1 CGAGCTCACCAAAACTA
1442967 CGAG
1 CGAG
1442971 GTCGCTAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.34, G:0.21, T:0.11
Consensus pattern (17 bp):
CGAGCTCACCAAAACTA
Found at i:1447573 original size:127 final size:126
Alignment explanation
Indices: 1447286--1447809 Score: 716
Period size: 127 Copynumber: 4.2 Consensus size: 126
1447276 AAATCAAAGT
* * * * * *
1447286 AGGATGATTTATCAGAAGGATTTTTGAAGTCGCACCCACGTGTACGCGCTTTTGCTACAGTAGGT
1 AGGATGCTTTATAAGAAGAATTTATGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
*
1447351 CCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTT-AAAAAACGCTTCAAGC
66 CCTGGAAAAATAATTTCGACTTGACGTTTCTAAGCAAATAGTTTAAAAAAACGCTTCAAGC
* * * * * * *
1447411 AGGATACTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTTCTACAGTTGGT
1 AGGATGCTTTATAAGAAGAATTTATGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
* * *
1447476 CTTGGAAGAAATAATTTCGAGTTGACGTTTTTAAGCAAATAGTTTAAAAAAACGCTTCAAGC
66 CCTGGAA-AAATAATTTCGACTTGACGTTTCTAAGCAAATAGTTTAAAAAAACGCTTCAAGC
* * *
1447538 AGGATGCTTTATAAGAATAATTTATGAAGTCGCGCCCACGTGGACGCGCTTTTTCTACAGTTGGT
1 AGGATGCTTTATAAGAAGAATTTATGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
* * *
1447603 CTTGGAAGAAATAATTTCGAGTTGACGTTTTTAAGCAAATAGTTTAAAAAAACGCTTCAAGC
66 CCTGGAA-AAATAATTTCGACTTGACGTTTCTAAGCAAATAGTTTAAAAAAACGCTTCAAGC
*
1447665 AGGATGCTTTATAAGAATAATTTATGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
1 AGGATGCTTTATAAGAAGAATTTATGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
* * * ** *
1447730 CCT-GCAAAATAATTTCGACTT-ACGTTTCTGAGCAAATAG--TATAAAATGGCTTCTAGC
66 CCTGGAAAAATAATTTCGACTTGACGTTTCTAAGCAAATAGTTTAAAAAAACGCTTCAAGC
*
1447787 AGGATGCTTTATGAGAAGAATTT
1 AGGATGCTTTATAAGAAGAATTT
1447810 GGGTTAAGGG
Statistics
Matches: 363, Mismatches: 34, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
122 35 0.10
124 16 0.04
125 74 0.20
126 36 0.10
127 202 0.56
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (126 bp):
AGGATGCTTTATAAGAAGAATTTATGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
CCTGGAAAAATAATTTCGACTTGACGTTTCTAAGCAAATAGTTTAAAAAAACGCTTCAAGC
Found at i:1447853 original size:22 final size:22
Alignment explanation
Indices: 1447812--1447852 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1447802 AAGAATTTGG
1447812 GTTAAGGGTTTATGGGTTTTAA
1 GTTAAGGGTTTATGGGTTTTAA
1447834 GTTAAGGGTTTA-GGGTTTT
1 GTTAAGGGTTTATGGGTTTT
1447853 TTTGTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (22 bp):
GTTAAGGGTTTATGGGTTTTAA
Found at i:1448426 original size:18 final size:18
Alignment explanation
Indices: 1448400--1448442 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1448390 GACTCGAAAA
* *
1448400 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
1448418 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
1448436 AGGAAAC
1 AGGAAAC
1448443 GCACCTGGCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:1449283 original size:20 final size:20
Alignment explanation
Indices: 1449246--1449283 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1449236 TTTATTTTTA
*
1449246 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
1449266 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
1449284 TACCTCGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:1450468 original size:11 final size:11
Alignment explanation
Indices: 1450454--1450530 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
1450444 ATAAATATGG
1450454 ATTTGAGAGAA
1 ATTTGAGAGAA
*
1450465 ATTTTGA-AGGA
1 A-TTTGAGAGAA
1450476 ATTTGAGAGCAA
1 ATTTGAGAG-AA
1450488 A-TTGAGAGGAA
1 ATTTGAGA-GAA
1450499 ATTT-AGAAGAA
1 ATTTGAG-AGAA
*
1450510 A-CTGAGAGCAA
1 ATTTGAGAG-AA
1450521 ATTTGAGAGA
1 ATTTGAGAGA
1450531 GGATTAGTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
10 8 0.15
11 28 0.53
12 17 0.32
ACGTcount: A:0.44, C:0.04, G:0.27, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:1450493 original size:33 final size:33
Alignment explanation
Indices: 1450454--1450530 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
1450444 ATAAATATGG
* **
1450454 ATTTGAGAGAAATTTTGAAGGAATTTGAGAGCAA
1 ATTTGAGAGAAATTTAGAA-GAAACTGAGAGCAA
1450488 A-TTGAGAGGAAATTTAGAAGAAACTGAGAGCAA
1 ATTTGAGA-GAAATTTAGAAGAAACTGAGAGCAA
1450521 ATTTGAGAGA
1 ATTTGAGAGA
1450531 GGATTAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 21 0.55
34 17 0.45
ACGTcount: A:0.44, C:0.04, G:0.27, T:0.25
Consensus pattern (33 bp):
ATTTGAGAGAAATTTAGAAGAAACTGAGAGCAA
Found at i:1450966 original size:17 final size:17
Alignment explanation
Indices: 1450912--1450970 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
1450902 TTATATCTAC
1450912 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
* **
1450929 TAAATTTAACATT-TTGTAT
1 T--ATTT-ATATTATTAAAT
1450948 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
1450965 TATTTA
1 TATTTA
1450971 ATCATATTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 4 0.12
17 15 0.47
19 9 0.28
20 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTATATTATTAAAT
Found at i:1461447 original size:17 final size:17
Alignment explanation
Indices: 1461393--1461451 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
1461383 TTATATCTAC
1461393 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
* **
1461410 TAAATTTAACATT-TTGTAT
1 T--ATTT-ATATTATTAAAT
1461429 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
1461446 TATTTA
1 TATTTA
1461452 ATCATATTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 4 0.12
17 15 0.47
19 9 0.28
20 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTATATTATTAAAT
Found at i:1463901 original size:18 final size:18
Alignment explanation
Indices: 1463878--1463917 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1463868 TTTTAAATAC
* *
1463878 ATTTATTTCATTTTATTT
1 ATTTATATCATTTTATAT
*
1463896 ATTTATATCTTTTTATAT
1 ATTTATATCATTTTATAT
1463914 ATTT
1 ATTT
1463918 TCGAACTCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTATATCATTTTATAT
Found at i:1464040 original size:19 final size:21
Alignment explanation
Indices: 1464016--1464065 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
1464006 ATTCGTTCCA
*
1464016 TTAGTTTTTTT-TTTA-TATT
1 TTAGTTTTTTTACTTATTATT
1464035 TTAGTTTCTTTTACTTATTATT
1 TTAGTTT-TTTTACTTATTATT
*
1464057 TTACTTTTT
1 TTAGTTTTT
1464066 ATTAGCGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 7 0.27
20 4 0.15
21 5 0.19
22 10 0.38
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.74
Consensus pattern (21 bp):
TTAGTTTTTTTACTTATTATT
Found at i:1467607 original size:426 final size:426
Alignment explanation
Indices: 1466814--1467667 Score: 1708
Period size: 426 Copynumber: 2.0 Consensus size: 426
1466804 ATGCAAATTG
1466814 AAGGAGTCTTCAAGGGCCATTTTGCAAGCCAAGTAATCAGCCAACAAGCTAATTGGGTCAGCATG
1 AAGGAGTCTTCAAGGGCCATTTTGCAAGCCAAGTAATCAGCCAACAAGCTAATTGGGTCAGCATG
1466879 TAGGACGGTTTTGGGCTGCCCAGTGTTCGGTTGGATCGATTTTCTCGGTTTAGCTCAACTAGGCC
66 TAGGACGGTTTTGGGCTGCCCAGTGTTCGGTTGGATCGATTTTCTCGGTTTAGCTCAACTAGGCC
1466944 CCTTTTCATAATTAATTAACAATAATTTATTTAACCCAATTAAATTGGATTAAAATTAAAATTAA
131 CCTTTTCATAATTAATTAACAATAATTTATTTAACCCAATTAAATTGGATTAAAATTAAAATTAA
1467009 TTATATTATGATTTAATATTCATAATTTGGACTATCTTCGGCTGAAAATATAATTCGCCTTGATG
196 TTATATTATGATTTAATATTCATAATTTGGACTATCTTCGGCTGAAAATATAATTCGCCTTGATG
1467074 CTTCAAAATTGCTTCTCGGTTTTGTGCTTTTAGTAGTGTCTGCCGAGCCGTTTTTCGCCCTTTGT
261 CTTCAAAATTGCTTCTCGGTTTTGTGCTTTTAGTAGTGTCTGCCGAGCCGTTTTTCGCCCTTTGT
1467139 GCGAATCTGTCGAAAATGATCAAAATTAATCAAAATTTATTATAAAATTAAATAAAACTCTACAT
326 GCGAATCTGTCGAAAATGATCAAAATTAATCAAAATTTATTATAAAATTAAATAAAACTCTACAT
1467204 GTTAATAATTTAAGTACAATTTAATTATTTTATAAT
391 GTTAATAATTTAAGTACAATTTAATTATTTTATAAT
1467240 AAGGAGTCTTCAAGGGCCATTTTGCAAGCCAAGTAATCAGCCAACAAGCTAATTGGGTCAGCATG
1 AAGGAGTCTTCAAGGGCCATTTTGCAAGCCAAGTAATCAGCCAACAAGCTAATTGGGTCAGCATG
1467305 TAGGACGGTTTTGGGCTGCCCAGTGTTCGGTTGGATCGATTTTCTCGGTTTAGCTCAACTAGGCC
66 TAGGACGGTTTTGGGCTGCCCAGTGTTCGGTTGGATCGATTTTCTCGGTTTAGCTCAACTAGGCC
1467370 CCTTTTCATAATTAATTAACAATAATTTATTTAACCCAATTAAATTGGATTAAAATTAAAATTAA
131 CCTTTTCATAATTAATTAACAATAATTTATTTAACCCAATTAAATTGGATTAAAATTAAAATTAA
1467435 TTATATTATGATTTAATATTCATAATTTGGACTATCTTCGGCTGAAAATATAATTCGCCTTGATG
196 TTATATTATGATTTAATATTCATAATTTGGACTATCTTCGGCTGAAAATATAATTCGCCTTGATG
1467500 CTTCAAAATTGCTTCTCGGTTTTGTGCTTTTAGTAGTGTCTGCCGAGCCGTTTTTCGCCCTTTGT
261 CTTCAAAATTGCTTCTCGGTTTTGTGCTTTTAGTAGTGTCTGCCGAGCCGTTTTTCGCCCTTTGT
1467565 GCGAATCTGTCGAAAATGATCAAAATTAATCAAAATTTATTATAAAATTAAATAAAACTCTACAT
326 GCGAATCTGTCGAAAATGATCAAAATTAATCAAAATTTATTATAAAATTAAATAAAACTCTACAT
1467630 GTTAATAATTTAAGTACAATTTAATTATTTTATAAT
391 GTTAATAATTTAAGTACAATTTAATTATTTTATAAT
1467666 AA
1 AA
1467668 TTATATAATT
Statistics
Matches: 428, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
426 428 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (426 bp):
AAGGAGTCTTCAAGGGCCATTTTGCAAGCCAAGTAATCAGCCAACAAGCTAATTGGGTCAGCATG
TAGGACGGTTTTGGGCTGCCCAGTGTTCGGTTGGATCGATTTTCTCGGTTTAGCTCAACTAGGCC
CCTTTTCATAATTAATTAACAATAATTTATTTAACCCAATTAAATTGGATTAAAATTAAAATTAA
TTATATTATGATTTAATATTCATAATTTGGACTATCTTCGGCTGAAAATATAATTCGCCTTGATG
CTTCAAAATTGCTTCTCGGTTTTGTGCTTTTAGTAGTGTCTGCCGAGCCGTTTTTCGCCCTTTGT
GCGAATCTGTCGAAAATGATCAAAATTAATCAAAATTTATTATAAAATTAAATAAAACTCTACAT
GTTAATAATTTAAGTACAATTTAATTATTTTATAAT
Found at i:1470464 original size:41 final size:40
Alignment explanation
Indices: 1470405--1470727 Score: 342
Period size: 41 Copynumber: 7.9 Consensus size: 40
1470395 CTTACCTTTA
* *
1470405 GGGGCTTTCGTGGCGTTTTCAAAAAAGCGCCGCTAATGCTC
1 GGGGCTTTAGCGGCGTTTTC-AAAAAGCGCCGCTAATGCTC
* * * * * *
1470446 AGGGATTTAGCGGTGTTTTTGAGAAAGCGCTGCTAATGCTC
1 GGGGCTTTAGCGGCG-TTTTCAAAAAGCGCCGCTAATGCTC
* * * *
1470487 GGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAACGCTG
1 GGGGCTTTAGCGGCG-TTTTCAAAAAGCGCCGCTAATGCTC
* *
1470528 GGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCT-
1 GGGGCTTTAGCGGC-GTTTTCAAAAAGCGCCGCTAATGCTC
* *
1470568 GAGGGCTTTAACGGCGTTTTTCAAAAAGCGCCGCTAATGCTG
1 G-GGGCTTTAGCGGCG-TTTTCAAAAAGCGCCGCTAATGCTC
*
1470610 GGGGCTTTAGCGGCGTTTTTCAAAAAGCACCGCTAATGCTC
1 GGGGCTTTAGCGGCG-TTTTCAAAAAGCGCCGCTAATGCTC
* * * *
1470651 GGGGTTTTAGCGGCGTTTTTCAAAAAGCGTCACTAATGCTT
1 GGGGCTTTAGCGGCG-TTTTCAAAAAGCGCCGCTAATGCTC
* * *
1470692 GGGGTTTTAGCGACATTTTTCAAAAAGCGCCGCTAA
1 GGGGCTTTAGCGGC-GTTTTCAAAAAGCGCCGCTAA
1470728 AAACATTTTA
Statistics
Matches: 243, Mismatches: 33, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
40 1 0.00
41 237 0.98
42 5 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
GGGGCTTTAGCGGCGTTTTCAAAAAGCGCCGCTAATGCTC
Found at i:1470555 original size:82 final size:82
Alignment explanation
Indices: 1470416--1470727 Score: 412
Period size: 82 Copynumber: 3.8 Consensus size: 82
1470406 GGGCTTTCGT
** * ** * * *
1470416 GGCG-TTTTCAAAAAAGCGCCGCTAATGCTCAGGGATTTAGCGGTGTTTTTGAGAAAGCGCTGCT
1 GGCGTTTTTC-AAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGGCATTTTTCAAAAAGCGCCGCT
1470480 AATGCTCGGGGTTTTAGC
65 AATGCTCGGGGTTTTAGC
* * *
1470498 GGCGTTTTTGAAAAAGCGCCGCTAACGCTGGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTA
1 GGCGTTTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGGCATTTTTCAAAAAGCGCCGCTA
* *
1470563 ATGCT-GAGGGCTTTAAC
66 ATGCTCG-GGGTTTTAGC
* *
1470580 GGCGTTTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGGCGTTTTTCAAAAAGCACCGCTA
1 GGCGTTTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGGCATTTTTCAAAAAGCGCCGCTA
1470645 ATGCTCGGGGTTTTAGC
66 ATGCTCGGGGTTTTAGC
* * * * *
1470662 GGCGTTTTTCAAAAAGCGTCACTAATGCTTGGGGTTTTAGCGACATTTTTCAAAAAGCGCCGCTA
1 GGCGTTTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGGCATTTTTCAAAAAGCGCCGCTA
1470727 A
66 A
1470728 AAACATTTTA
Statistics
Matches: 202, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
81 1 0.00
82 196 0.97
83 5 0.02
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (82 bp):
GGCGTTTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGGCATTTTTCAAAAAGCGCCGCTA
ATGCTCGGGGTTTTAGC
Found at i:1470624 original size:123 final size:123
Alignment explanation
Indices: 1470420--1470727 Score: 402
Period size: 123 Copynumber: 2.5 Consensus size: 123
1470410 TTTCGTGGCG
* * * * *
1470420 TTTTCAAAAAAGCGCCGCTAATGCTCAGGGATTTAGCGGTGTTTTTGAGAAAGCGCTGCTAATGC
1 TTTTC-AAAAAGCGCCGCTAATGCTGAGGGATTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGC
* * * *
1470485 TCGGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAACGCTGGGGGCTTTAGCGGCAT
65 TCGGGGCTTTAGCGGCGTTTTTCAAAAAGCACCGCTAACGCTCGGGGCTTTAGCGGCAT
* * *
1470544 TTTTGAAAAAGCGCCGCTAATGCTGAGGGCTTTAACGGCGTTTTTCAAAAAGCGCCGCTAATGCT
1 TTTTCAAAAAGCGCCGCTAATGCTGAGGGATTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCT
* * * *
1470609 GGGGGCTTTAGCGGCGTTTTTCAAAAAGCACCGCTAATGCTCGGGGTTTTAGCGGCGT
66 CGGGGCTTTAGCGGCGTTTTTCAAAAAGCACCGCTAACGCTCGGGGCTTTAGCGGCAT
* * * * *
1470667 TTTTCAAAAAGCGTCACTAATGCTTG-GGGTTTTAGCGACATTTTTCAAAAAGCGCCGCTAA
1 TTTTCAAAAAGCGCCGCTAATGC-TGAGGGATTTAGCGGCGTTTTTCAAAAAGCGCCGCTAA
1470728 AAACATTTTA
Statistics
Matches: 160, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
123 154 0.96
124 6 0.04
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (123 bp):
TTTTCAAAAAGCGCCGCTAATGCTGAGGGATTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCT
CGGGGCTTTAGCGGCGTTTTTCAAAAAGCACCGCTAACGCTCGGGGCTTTAGCGGCAT
Found at i:1471110 original size:15 final size:15
Alignment explanation
Indices: 1471090--1471131 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1471080 TATTTTAAGG
*
1471090 TTTAGGGAGTATGAA
1 TTTAGGGATTATGAA
*
1471105 TTTAGGGATTATGGA
1 TTTAGGGATTATGAA
1471120 -TTAGGGATTATG
1 TTTAGGGATTATG
1471132 GTTTAAGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.29, C:0.00, G:0.33, T:0.38
Consensus pattern (15 bp):
TTTAGGGATTATGAA
Found at i:1471125 original size:14 final size:15
Alignment explanation
Indices: 1471090--1471136 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
1471080 TATTTTAAGG
* *
1471090 TTTAGGGAGTATGAA
1 TTTAGGGATTATGGA
1471105 TTTAGGGATTATGGA
1 TTTAGGGATTATGGA
1471120 -TTAGGGATTATGG-
1 TTTAGGGATTATGGA
1471133 TTTA
1 TTTA
1471137 AGGGTTGGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:1471157 original size:21 final size:20
Alignment explanation
Indices: 1471123--1471195 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
1471113 TTATGGATTA
*
1471123 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
1471143 GGGATTTAAGGTTTAAGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
* * * *
1471164 AGGGGTTAGGGGTTAGGGGTTT
1 -GGGATTAAGGTTTAAGGG-TT
1471186 AGGGATTAAG
1 -GGGATTAAG
1471196 AGTTAGAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 4 0.09
21 26 0.60
22 13 0.30
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:1471178 original size:14 final size:15
Alignment explanation
Indices: 1471152--1471189 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
1471142 TGGGATTTAA
*
1471152 GGTTTAAGGGTTAGG
1 GGTTTAGGGGTTAGG
1471167 GG-TTAGGGGTTAGG
1 GGTTTAGGGGTTAGG
1471181 GGTTTAGGG
1 GGTTTAGGG
1471190 ATTAAGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.16, C:0.00, G:0.53, T:0.32
Consensus pattern (15 bp):
GGTTTAGGGGTTAGG
Found at i:1471189 original size:8 final size:7
Alignment explanation
Indices: 1471159--1471189 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
1471149 TAAGGTTTAA
1471159 GGGTTAG
1 GGGTTAG
1471166 GGGTTAG
1 GGGTTAG
1471173 GGGTTAG
1 GGGTTAG
1471180 GGGTTTAG
1 GGG-TTAG
1471188 GG
1 GG
1471190 ATTAAGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.74
8 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.58, T:0.29
Consensus pattern (7 bp):
GGGTTAG
Found at i:1471294 original size:25 final size:25
Alignment explanation
Indices: 1471251--1471306 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
1471241 TTGGGTTTAG
*
1471251 ATTAATTAT-TTTTTT-ATTTATAT
1 ATTAAATATGTTTTTTAATTTATAT
*
1471274 TTTAAATATGTTTTTTAATTTATAT
1 ATTAAATATGTTTTTTAATTTATAT
1471299 ATTAAATA
1 ATTAAATA
1471307 ATTTCATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 7 0.25
24 6 0.21
25 15 0.54
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
ATTAAATATGTTTTTTAATTTATAT
Found at i:1471491 original size:14 final size:15
Alignment explanation
Indices: 1471461--1471498 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1471451 GGGGATTATA
*
1471461 TATGGATTTAGGGAT
1 TATGGATTTACGGAT
1471476 TATGGA-TTACGGAT
1 TATGGATTTACGGAT
1471490 TATGG-TTTA
1 TATGGATTTA
1471499 AGGGTTGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (15 bp):
TATGGATTTACGGAT
Found at i:1471555 original size:12 final size:12
Alignment explanation
Indices: 1471538--1471587 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
1471528 AAATATTTAA
1471538 TAATTCTTTATG
1 TAATTCTTTATG
1471550 TAATTCTTTATG
1 TAATTCTTTATG
* *
1471562 TAAAAT-TTTA-A
1 T-AATTCTTTATG
1471573 TAATTCTTTATG
1 TAATTCTTTATG
1471585 TAA
1 TAA
1471588 AATTTATAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 3 0.10
11 5 0.16
12 20 0.65
13 3 0.10
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (12 bp):
TAATTCTTTATG
Found at i:1473051 original size:9 final size:9
Alignment explanation
Indices: 1473022--1473066 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
1473012 TTAAGTTAAA
1473022 TATAAATAT
1 TATAAATAT
**
1473031 TATATGTA-
1 TATAAATAT
1473039 TATAAATAT
1 TATAAATAT
1473048 TATAAATAT
1 TATAAATAT
*
1473057 TATAATTAT
1 TATAAATAT
1473066 T
1 T
1473067 TATTCAAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 6 0.20
9 24 0.80
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (9 bp):
TATAAATAT
Found at i:1484375 original size:13 final size:11
Alignment explanation
Indices: 1484339--1484369 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1484329 CTGTCCGTAT
1484339 TAATTTTTATA
1 TAATTTTTATA
*
1484350 TTATTTTTATA
1 TAATTTTTATA
1484361 TAATTTTTA
1 TAATTTTTA
1484370 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:1485882 original size:101 final size:102
Alignment explanation
Indices: 1485749--1486029 Score: 426
Period size: 101 Copynumber: 2.8 Consensus size: 102
1485739 TATTGATGAA
1485749 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTAC
1485814 TAAGTG-AGGCTACAATGTGTACCGAGAAA-CTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGA-AAAGCTTTGGT
1485850 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTAC
* *
1485915 TAAGTGAAGGCTACTATGTGTGCCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
* * * *** * *
1485952 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTAC
1486016 TATA-TGAAGGCTAC
66 TA-AGTGAAGGCTAC
1486030 TACGTGTATC
Statistics
Matches: 167, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
101 106 0.63
102 61 0.37
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
Found at i:1485901 original size:51 final size:51
Alignment explanation
Indices: 1485749--1486037 Score: 336
Period size: 51 Copynumber: 5.7 Consensus size: 51
1485739 TATTGATGAA
* * *
1485749 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGTTGGT
* * * * *
1485800 CACATGTGTAGTACTAAGTG-AGGCTACAATGTGTACCGAGAAACT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA-TGTTGGT
* * *
1485850 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGTTGGT
* * * *
1485901 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTGCCGA-AAA-GCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATG--TTGGT
* ** *
1485952 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGTTGGT
*
1486002 CACGTGTGTAGTACTATATGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1486038 TCGAATGATA
Statistics
Matches: 199, Mismatches: 32, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.01
50 82 0.41
51 116 0.58
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGTTGGT
Found at i:1485934 original size:26 final size:26
Alignment explanation
Indices: 1485854--1485935 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
1485844 TTTGGTCACG
**
1485854 TGTGTAGTACTGTGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
* * *
1485880 CGTGTA-T-CGATAAATGATGG-TCAC-A
1 TGTGTAGTAC--TAAGTGAAGGCT-ACTA
1485905 TGTGTAGTACTAAGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
1485931 TGTGT
1 TGTGT
1485936 GCCGAAAAGC
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
24 1 0.02
25 18 0.44
26 21 0.51
27 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGAAGGCTACTA
Found at i:1486024 original size:152 final size:152
Alignment explanation
Indices: 1485753--1486041 Score: 388
Period size: 152 Copynumber: 1.9 Consensus size: 152
1485743 GATGAACACG
** *
1485753 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGATAAATGATGGTCACATGTGTAGTACTAAG
* * * * *
1485818 TGAGGCTACAATGTGTACCGAGAAACTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGT
66 TGAGGCTACAACGTGAACCGAGAAACTTTGATCACGTGTGTAGTACTATATGAAGGCTACTACGT
1485883 GTATCGATAAATGATGGTCACA
131 GTATCGATAAATGATGGTCACA
* * * *
1485905 TGTGTAGTACTAAGTGAAGGCTACTATGTGTGCCGA-AAA-GCTTTGGTCACGTGTGTAGTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGATAAATG--ATGGTCACATGTGTAGTACTA
* *
1485968 TGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGATCACGTGTGTAGTACTATATGAAGGCTACT
64 AGTG-AGGCTACAACGTGAACCG-AGAAACTTTGATCACGTGTGTAGTACTATATGAAGGCTACT
1486031 ACGTGTATCGA
127 ACGTGTATCGA
1486042 ATGATAAAAG
Statistics
Matches: 119, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
150 1 0.01
151 3 0.03
152 95 0.80
153 19 0.16
154 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (152 bp):
TGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGATAAATGATGGTCACATGTGTAGTACTAAG
TGAGGCTACAACGTGAACCGAGAAACTTTGATCACGTGTGTAGTACTATATGAAGGCTACTACGT
GTATCGATAAATGATGGTCACA
Found at i:1486073 original size:101 final size:102
Alignment explanation
Indices: 1485756--1486074 Score: 279
Period size: 101 Copynumber: 3.1 Consensus size: 102
1485746 GAACACGTGT
* * ** *
1485756 GTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTACTAAGTG-
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
* * * *** * * *
1485820 AGGCTACAATGTGTACCGAGAAA-CTTTGGTCACGTGT
66 AGGCTACTACGTGTACCGA-AAAGATAAAGTAACATGG
* * ** *
1485857 GTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
* * * *** * * *
1485922 AGGCTACTATGTGTGCCGAAAAGCTTTGGTCACGTGT
66 AGGCTACTACGTGTACCGAAAAGATAAAGTAACATGG
* * *
1485959 GTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTACTATA-TG
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTA-AGTG
* *
1486022 AAGGCTACTACGTGTATCG-AATGATAAAAGTAACATGG
65 AAGGCTACTACGTGTACCGAAAAGAT-AAAGTAACATGG
1486060 GTAGTACTGTGTGAA
1 GTAGTACTGTGTGAA
1486075 AAACCCCAAA
Statistics
Matches: 192, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
100 4 0.02
101 127 0.66
102 61 0.32
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29
Consensus pattern (102 bp):
GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
AGGCTACTACGTGTACCGAAAAGATAAAGTAACATGG
Found at i:1486074 original size:152 final size:152
Alignment explanation
Indices: 1485756--1486074 Score: 378
Period size: 152 Copynumber: 2.1 Consensus size: 152
1485746 GAACACGTGT
*
1485756 GTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
* * * * *
1485821 GGCTACAATGTGTACCGAGAAACTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTA
66 GGCTACAACGTGAACCGAGAAACTTTGATCACGTGTGTAGTACTATATGAAGGCTACTACGTGTA
* ** * *
1485886 TCGATAAATGATGGTCACATGT
131 TCGATAAATAAAAGTAACATGG
** * * * * *
1485908 GTAGTACTAAGTGAAGGCTACTATGTGTGCCGA-AAA-GCTTTGGTCACGTGTGTAGTACTATGT
1 GTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATG--ATGGTCACATGTGTAGTACTAAGT
*
1485971 GAAGGCTACTACGTGAACCGTA-AAAC-TTGATCACGTGTGTAGTACTATATGAAGGCTACTACG
64 G-AGGCTACAACGTGAACCG-AGAAACTTTGATCACGTGTGTAGTACTATATGAAGGCTACTACG
*
1486034 TGTATCGA-ATGATAAAAGTAACATGG
127 TGTATCGATA-AATAAAAGTAACATGG
1486060 GTAGTACTGTGTGAA
1 GTAGTACTGTGTGAA
1486075 AAACCCCAAA
Statistics
Matches: 140, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
150 1 0.01
151 4 0.03
152 115 0.82
153 19 0.14
154 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29
Consensus pattern (152 bp):
GTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
GGCTACAACGTGAACCGAGAAACTTTGATCACGTGTGTAGTACTATATGAAGGCTACTACGTGTA
TCGATAAATAAAAGTAACATGG
Found at i:1488886 original size:22 final size:22
Alignment explanation
Indices: 1488858--1488902 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1488848 TAGGAAGATA
1488858 AATTGTCGGTAATAATAATGTC
1 AATTGTCGGTAATAATAATGTC
1488880 AATTGTCGGTAATAATAATGTC
1 AATTGTCGGTAATAATAATGTC
1488902 A
1 A
1488903 TCCACATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
AATTGTCGGTAATAATAATGTC
Found at i:1493436 original size:45 final size:45
Alignment explanation
Indices: 1493378--1493465 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
1493368 ACAGATACTC
*
1493378 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATAATGTCT
1 GGTGGATTCAGCACATAGCAACCACCTTACTAATCAATAATGTCT
*
1493423 GGTGGAATT-AGCACATAGCAACCACCTTACTAATCAATGATGT
1 GGTGG-ATTCAGCACATAGCAACCACCTTACTAATCAATAATGT
1493466 TCGGTTCACA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 37 0.93
46 3 0.08
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (45 bp):
GGTGGATTCAGCACATAGCAACCACCTTACTAATCAATAATGTCT
Found at i:1493530 original size:51 final size:51
Alignment explanation
Indices: 1493465--1493662 Score: 231
Period size: 51 Copynumber: 3.9 Consensus size: 51
1493455 ATCAATGATG
* *
1493465 TTCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTTACCATTACC-
1 TTCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCA
* * * * ** *
1493515 GTCTGATACACATAGTAGCCTGCACGTAGTACTACACATGTGATCAAAACTA
1 TTC-GGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCA
* * *
1493567 TTCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC--TATCA
1 TTCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCA
* *
1493616 TTTCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 -TTCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCAT
1493663 CACTTTCACT
Statistics
Matches: 121, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
49 2 0.02
50 42 0.35
51 75 0.62
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (51 bp):
TTCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCA
Found at i:1493682 original size:101 final size:102
Alignment explanation
Indices: 1493472--1493661 Score: 249
Period size: 101 Copynumber: 1.9 Consensus size: 102
1493462 ATGTTCGGTT
** *
1493472 CACATAGTAGCCTGCACATAGTACTACACATGTTACCATTACCGTCTGATACACATAGTAGCCTG
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACCGTCTGATACACATAGTAGCCTG
* * * *
1493537 CACGTAGTACTACACATGTGATCAAAACTATTCGGTA
66 CACATAGTACTACACACGTGACCAAAACTATTCCGTA
* ** * *
1493574 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-TTTC-GGTACACGTAGTAGCCT
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACCGTCTGATACACATAGTAGCCT
1493637 GCACATAGTACTACACACGTGACCA
65 GCACATAGTACTACACACGTGACCA
1493662 TCACTTTCAC
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
101 37 0.49
102 36 0.47
103 3 0.04
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (102 bp):
CACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACCGTCTGATACACATAGTAGCCTG
CACATAGTACTACACACGTGACCAAAACTATTCCGTA
Found at i:1495518 original size:12 final size:12
Alignment explanation
Indices: 1495501--1495525 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1495491 ACATATTCTT
1495501 TGATAAGGTGCA
1 TGATAAGGTGCA
1495513 TGATAAGGTGCA
1 TGATAAGGTGCA
1495525 T
1 T
1495526 ATTCTTGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.28
Consensus pattern (12 bp):
TGATAAGGTGCA
Found at i:1496333 original size:854 final size:854
Alignment explanation
Indices: 1494686--1496358 Score: 3319
Period size: 854 Copynumber: 2.0 Consensus size: 854
1494676 ATAATGAAAA
1494686 TAAAATTTTTTCTCATCAAATTTGTGGCCTCGAAACCACTATTTCGACTAGCCCCAAATTCGGGT
1 TAAAATTTTTTCTCATCAAATTTGTGGCCTCGAAACCACTATTTCGACTAGCCCCAAATTCGGGT
1494751 TATTGCAATAAACTCTAATAGCAGCAAGCCTATGTGCATGATAAAGTGCAGGCTCAAACCCATAG
66 TATTGCAATAAACTCTAATAGCAGCAAGCCTATGTGCATGATAAAGTGCAGGCTCAAACCCATAG
1494816 TGAAACTATGACCCAAATGATAGCCCATAACTAACACCATCAGCTCTGTCTAAGTATGAATTAGA
131 TGAAACTATGACCCAAATGATAGCCCATAACTAACACCATCAGCTCTGTCTAAGTATGAATTAGA
1494881 ACCTCTAGGATGTTGAGGCGTAGCAGTCGACCAAAACAATTCTCCCGAACTAGCGCCTTGCGACT
196 ACCTCTAGGATGTTGAGGCGTAGCAGTCGACCAAAACAATTCTCCCGAACTAGCGCCTTGCGACT
1494946 CCATCAACCCCGGGACATGAGGCGGACCAGAGAACGGTGACGAGACATAAGGCGAACCAGAGAAT
261 CCATCAACCCCGGGACATGAGGCGGACCAGAGAACGGTGACGAGACATAAGGCGAACCAGAGAAT
1495011 GGCGATTCACTAGCGCCATAATGATCAATCAGATTCGCTGCTCGAATCGTCGACGACCCTTTATA
326 GGCGATTCACTAGCGCCATAATGATCAATCAGATTCGCTGCTCGAATCGTCGACGACCCTTTATA
1495076 ACCCCGATTATAACGAAAGAAACACCGTTGGGCTATATGGCCGAACCTTCCAAAGATTTGGCACT
391 ACCCCGATTATAACGAAAGAAACACCGTTGGGCTATATGGCCGAACCTTCCAAAGATTTGGCACT
1495141 GTAGGCGGGATCGAAACCCTCTCCTACATTCTTCAGACAAAATACGAGCACCACGAACGGAGCCC
456 GTAGGCGGGATCGAAACCCTCTCCTACATTCTTCAGACAAAATACGAGCACCACGAACGGAGCCC
1495206 ACTGGAACCGATGATAGCCCATCCTCCAGATTCGACAGCGAACCAGTCTTCAAAAGATTAGCATG
521 ACTGGAACCGATGATAGCCCATCCTCCAGATTCGACAGCGAACCAGTCTTCAAAAGATTAGCATG
*
1495271 AAGGGGTACATTCTAGATCGTACGCTCTTGACGACTTTCATACTTGACCAGTACCTTAACAAGCC
586 AAGGGGTACATTCTAGATCGTACGCTCTTGACGACTTTCATACTTGACCAGTACATTAACAAGCC
*
1495336 GTTAAAACGGTAAAGGTTCTGAAGAGAACGAAGATAAAGTGATAATTACATCGAAATATGGAGGT
651 ATTAAAACGGTAAAGGTTCTGAAGAGAACGAAGATAAAGTGATAATTACATCGAAATATGGAGGT
1495401 AACCTGGTAAGGACGATTTCTACCTTCTCTTCGTCTGATATTCGAGAATCGGACGCCTCTAACAA
716 AACCTGGTAAGGACGATTTCTACCTTCTCTTCGTCTGATATTCGAGAATCGGACGCCTCTAACAA
1495466 GACACTAATATTTTGAATCTTGGAAACATATTCTTTGATAAGGTGCATGATAAGGTGCATATTCT
781 GACACTAATATTTTGAATCTTGGAAACATATTCTTTGATAAGGTGCATGATAAGGTGCATATTCT
1495531 TGGAAACAC
846 TGGAAACAC
1495540 TAAAATTTTTTCTCATCAAATTTGTGGCCTCGAAACCACTATTTCGACTAGCCCCAAATTCGGGT
1 TAAAATTTTTTCTCATCAAATTTGTGGCCTCGAAACCACTATTTCGACTAGCCCCAAATTCGGGT
*
1495605 TATTGCAATAAACTCTAATAGCAGCAAGCCTATGTGCATGATAAGGTGCAGGCTCAAACCCATAG
66 TATTGCAATAAACTCTAATAGCAGCAAGCCTATGTGCATGATAAAGTGCAGGCTCAAACCCATAG
1495670 TGAAACTATGACCCAAATGATAGCCCATAACTAACACCATCAGCTCTGTCTAAGTATGAATTAGA
131 TGAAACTATGACCCAAATGATAGCCCATAACTAACACCATCAGCTCTGTCTAAGTATGAATTAGA
1495735 ACCTCTAGGATGTTGAGGCGTAGCAGTCGACCAAAACAATTCTCCCGAACTAGCGCCTTGCGACT
196 ACCTCTAGGATGTTGAGGCGTAGCAGTCGACCAAAACAATTCTCCCGAACTAGCGCCTTGCGACT
1495800 CCATCAACCCCGGGACATGAGGCGGACCAGAGAACGGTGACGAGACATAAGGCGAACCAGAGAAT
261 CCATCAACCCCGGGACATGAGGCGGACCAGAGAACGGTGACGAGACATAAGGCGAACCAGAGAAT
1495865 GGCGATTCACTAGCGCCATAATGATCAATCAGATTCGCTGCTCGAATCGTCGACGACCCTTTATA
326 GGCGATTCACTAGCGCCATAATGATCAATCAGATTCGCTGCTCGAATCGTCGACGACCCTTTATA
1495930 ACCCCGATTATAACGAAAGAAACACCGTTGGGCTATATGGCCGAACCTTCCAAAGATTTGGCACT
391 ACCCCGATTATAACGAAAGAAACACCGTTGGGCTATATGGCCGAACCTTCCAAAGATTTGGCACT
1495995 GTAGGCGGGATCGAAACCCTCTCCTACATTCTTCAGACAAAATACGAGCACCACGAACGGAGCCC
456 GTAGGCGGGATCGAAACCCTCTCCTACATTCTTCAGACAAAATACGAGCACCACGAACGGAGCCC
1496060 ACTGGAACCGATGATAGCCCATCCTCCAGATTCGACAGCGAACCAGTCTTCAAAAGATTAGCATG
521 ACTGGAACCGATGATAGCCCATCCTCCAGATTCGACAGCGAACCAGTCTTCAAAAGATTAGCATG
1496125 AAGGGGTACATTCTAGATCGTACGCTCTTGACGACTTTCATACTTGACCAGTACATTAACAAGCC
586 AAGGGGTACATTCTAGATCGTACGCTCTTGACGACTTTCATACTTGACCAGTACATTAACAAGCC
1496190 ATTAAAACGGTAAAGGTTCTGAAGAGAACGAAGATAAAGTGATAATTACATCGAAATATGGAGGT
651 ATTAAAACGGTAAAGGTTCTGAAGAGAACGAAGATAAAGTGATAATTACATCGAAATATGGAGGT
1496255 AACCTGGTAAGGACGATTTCTACCTTCTCTTCGTCTGATATTCGAGAATCGGACGCCTCTAACAA
716 AACCTGGTAAGGACGATTTCTACCTTCTCTTCGTCTGATATTCGAGAATCGGACGCCTCTAACAA
1496320 GACACTAATATTTTGAATCTTGGAAACATATTCTTTGAT
781 GACACTAATATTTTGAATCTTGGAAACATATTCTTTGAT
1496359 CGAATAACTG
Statistics
Matches: 816, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
854 816 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (854 bp):
TAAAATTTTTTCTCATCAAATTTGTGGCCTCGAAACCACTATTTCGACTAGCCCCAAATTCGGGT
TATTGCAATAAACTCTAATAGCAGCAAGCCTATGTGCATGATAAAGTGCAGGCTCAAACCCATAG
TGAAACTATGACCCAAATGATAGCCCATAACTAACACCATCAGCTCTGTCTAAGTATGAATTAGA
ACCTCTAGGATGTTGAGGCGTAGCAGTCGACCAAAACAATTCTCCCGAACTAGCGCCTTGCGACT
CCATCAACCCCGGGACATGAGGCGGACCAGAGAACGGTGACGAGACATAAGGCGAACCAGAGAAT
GGCGATTCACTAGCGCCATAATGATCAATCAGATTCGCTGCTCGAATCGTCGACGACCCTTTATA
ACCCCGATTATAACGAAAGAAACACCGTTGGGCTATATGGCCGAACCTTCCAAAGATTTGGCACT
GTAGGCGGGATCGAAACCCTCTCCTACATTCTTCAGACAAAATACGAGCACCACGAACGGAGCCC
ACTGGAACCGATGATAGCCCATCCTCCAGATTCGACAGCGAACCAGTCTTCAAAAGATTAGCATG
AAGGGGTACATTCTAGATCGTACGCTCTTGACGACTTTCATACTTGACCAGTACATTAACAAGCC
ATTAAAACGGTAAAGGTTCTGAAGAGAACGAAGATAAAGTGATAATTACATCGAAATATGGAGGT
AACCTGGTAAGGACGATTTCTACCTTCTCTTCGTCTGATATTCGAGAATCGGACGCCTCTAACAA
GACACTAATATTTTGAATCTTGGAAACATATTCTTTGATAAGGTGCATGATAAGGTGCATATTCT
TGGAAACAC
Found at i:1504474 original size:17 final size:18
Alignment explanation
Indices: 1504454--1504489 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1504444 TTGTTAGGCG
1504454 TCTGT-TTTTAATGTTGC
1 TCTGTCTTTTAATGTTGC
*
1504471 TCTGTCTTTTCATGTTGC
1 TCTGTCTTTTAATGTTGC
1504489 T
1 T
1504490 TTACAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.08, C:0.17, G:0.17, T:0.58
Consensus pattern (18 bp):
TCTGTCTTTTAATGTTGC
Found at i:1506531 original size:20 final size:20
Alignment explanation
Indices: 1506508--1506565 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
1506498 ATTTTTCTTG
1506508 TAAAAACTCAAGTTTTCCTA
1 TAAAAACTCAAGTTTTCCTA
* **
1506528 TAAAAACCCACTTAATTTCCTA
1 TAAAAACTCAAGT--TTTCCTA
*
1506550 TAAAACCTCAAGTTTT
1 TAAAAACTCAAGTTTT
1506566 TGCTTCTCTT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 13 0.45
22 16 0.55
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.34
Consensus pattern (20 bp):
TAAAAACTCAAGTTTTCCTA
Found at i:1506830 original size:31 final size:31
Alignment explanation
Indices: 1506795--1506853 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1506785 TTAACGGTGG
1506795 GTGACTAAAATAATAAAAGAATGTAACGACA
1 GTGACTAAAATAATAAAAGAATGTAACGACA
* *
1506826 GTGACTAAAATGATAAAAGTATGTAACG
1 GTGACTAAAATAATAAAAGAATGTAACG
1506854 GAAGTGCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.22
Consensus pattern (31 bp):
GTGACTAAAATAATAAAAGAATGTAACGACA
Found at i:1507772 original size:24 final size:26
Alignment explanation
Indices: 1507719--1507773 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1507709 AATCACAATC
**
1507719 ATTTTCAGAAAATAATCTTTTGTTTG
1 ATTTTCAGAAAATAATCTTTTAATTG
1507745 ATTTTCA-AATAATAAT-TTTTAATT-
1 ATTTTCAGAA-AATAATCTTTTAATTG
1507769 ATTTT
1 ATTTT
1507774 ATTTAAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 5 0.19
25 8 0.31
26 13 0.50
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (26 bp):
ATTTTCAGAAAATAATCTTTTAATTG
Found at i:1534298 original size:44 final size:43
Alignment explanation
Indices: 1534198--1534743 Score: 252
Period size: 44 Copynumber: 12.7 Consensus size: 43
1534188 GCTTAATTAG
* * * * * *
1534198 TCTGCTCCACTACAATTTCAGGTAGATAAGA--CTAGGTGTGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCCTAGTTTTAA
* * *
1534239 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCCCAAGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-CCTAGTTTTAA
* ** * *
1534282 TCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCCT-AGTTTTAA
* * * *
1534326 CCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTCT-GTCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA--TCCTAGT-TTTAA
* * *
1534371 TCTAC-CTCACTGCAACTTCA-GGAGGATAAGA--CTTGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGATCCTAG-TT--TTAA
* * * ***
1534415 TTTGCTCCACTGTAACTTCAGGGAGATAAGA--CTAGATGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCCTAGTTTTAA
* * *
1534456 TCTGCT-CTCTGCAACTTCAGAGAGATAACATCCTAGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCCTA-GTTTTAA
* * * ** * *
1534499 TCCGCTCCACTACAACTTCAGGGAGATAGGATTATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TCCTAGTTTTAA
* * *
1534543 -CTTGCTCCACTGCAAATTCAGGGAGATAAGATTTGCC-A-TCTTCAG
1 TC-TGCTCCACTGCAACTTCAGGGAGATAAGA--T-CCTAGT-TTTAA
* * *
1534588 TCTGC-CTCACTGTAACTTCA-GGAGGATAAGACTTGCCTA--CTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGA--T-CCTAGTTTTAA
* * * ***
1534632 TCTGCTCCCCTGCAACTTCAGGGAGATAAGA--CGAGATGGGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCCTAGTTTTAA
* * *
1534673 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCCAATGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCCTA-GTTTTAA
* *
1534716 TCTGCTCCACTGCAACTTTAGAGAGATA
1 TCTGCTCCACTGCAACTTCAGGGAGATA
1534744 GGATTATTGG
Statistics
Matches: 382, Mismatches: 86, Indels: 71
0.71 0.16 0.13
Matches are distributed among these distances:
39 2 0.01
40 61 0.16
41 19 0.05
42 7 0.02
43 32 0.08
44 189 0.49
45 67 0.18
46 5 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATCCTAGTTTTAA
Found at i:1534616 original size:45 final size:44
Alignment explanation
Indices: 1534545--1534663 Score: 145
Period size: 45 Copynumber: 2.7 Consensus size: 44
1534535 GGCTTTAACT
* *
1534545 TGCTCCACTGCAAATTCAGGGAGATAAGATTTGCC-ATCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCTA-CTT-AGTC
*
1534590 TGC-CTCACTGTAACTTCA-GGAGGATAAGACTTGCCTACTTAGTC
1 TGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCCTACTTAGTC
*
1534634 TGCTCCCCTGCAACTTCAGGGAGATAAGAC
1 TGCTCCACTGCAACTTCAGGGAGATAAGAC
1534664 GAGATGGGAT
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
44 30 0.47
45 33 0.52
46 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (44 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCTACTTAGTC
Found at i:1534751 original size:217 final size:216
Alignment explanation
Indices: 1534118--1534754 Score: 968
Period size: 217 Copynumber: 2.9 Consensus size: 216
1534108 GATCTGCTCT
* * * * *
1534118 CTGCAACTTCAGGGAGATAAGATTTGCCATCTTGAGTTTGCCTTATTGCAACTTCAGGAGGAGAA
1 CTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAA
* * * * * *
1534183 GACTTGCTTAATTAGTCTGCTCCACTACAATTTCAGGTAGATAAGACTAGGTGTGATCTGCTCTC
66 GACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTC
1534248 TGCAACTTCAGAGAGATAAGATCCCAAGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGA
131 TGCAACTTCAGAGAGATAAGAT-CCAAGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGA
*
1534313 TTATCGGCTTTAACCTGCTCCA
195 TTATTGGCTTTAACCTGCTCCA
* ** *
1534335 CTGCAACTTCAGGGAGATAAGATTTTCTGTCTTCAGTCTACCTCACTGCAACTTCAGGAGGATAA
1 CTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAA
* *
1534400 GACTTGCTTACTTAGTTTGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTC
66 GACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTC
* * * *
1534465 TGCAACTTCAGAGAGATAACATCCTAGGTTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGA
131 TGCAACTTCAGAGAGATAAGATCC-AAGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGA
*
1534530 TTATTGGCTTTAACTTGCTCCA
195 TTATTGGCTTTAACCTGCTCCA
* *
1534552 CTGCAAATTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGTAACTTCAGGAGGATAA
1 CTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAA
* * * *
1534617 GACTTGCCTACTTAGTCTGCTCCCCTGCAACTTCAGGGAGATAAGACGAGATGGGATCTGCTCTC
66 GACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTC
* *
1534682 TGCAACTTCAGAGAGATAAGATCCAATGTTTTAATCTGCTCCACTGCAACTTTAGAGAGATAGGA
131 TGCAACTTCAGAGAGATAAGATCCAA-GTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGA
1534747 TTATTGGC
195 TTATTGGC
1534755 CATGGATCTG
Statistics
Matches: 377, Mismatches: 41, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
216 3 0.01
217 374 0.99
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (216 bp):
CTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAA
GACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTC
TGCAACTTCAGAGAGATAAGATCCAAGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT
TATTGGCTTTAACCTGCTCCA
Found at i:1547021 original size:22 final size:22
Alignment explanation
Indices: 1546996--1547042 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1546986 TAAAAAACAT
* *
1546996 ATATTTTCATTTTTAAAAATAA
1 ATATATTCATTTATAAAAATAA
*
1547018 ATATATTCATTTATATAAATAA
1 ATATATTCATTTATAAAAATAA
1547040 ATA
1 ATA
1547043 AAAATTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATATTCATTTATAAAAATAA
Found at i:1547036 original size:24 final size:25
Alignment explanation
Indices: 1546982--1547036 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 25
1546972 AATTATAAAG
*
1546982 TATATAAAAAACATATATTTTCATT
1 TATATAAAAAACATATATATTCATT
1547007 T-T-TAAAAATA-A-ATATATTCATT
1 TATATAAAAA-ACATATATATTCATT
1547029 TATATAAA
1 TATATAAA
1547037 TAAATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 11 0.42
23 8 0.31
24 6 0.23
25 1 0.04
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (25 bp):
TATATAAAAAACATATATATTCATT
Found at i:1560577 original size:114 final size:114
Alignment explanation
Indices: 1560285--1560918 Score: 1029
Period size: 114 Copynumber: 5.6 Consensus size: 114
1560275 AAAGCGCCGT
* * * *
1560285 AAAAAACCTAAGCCCAATGACGCCGTTTTCTGAGCTTTCGGGGATTTAG-CAGTGTTTTTAAGAA
1 AAAAAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGA-CGTTTTTAAGAA
* * **
1560349 AGCACCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGGGAAAGCGCCGC-
65 AGCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGAGAAAATGCCGCA
* * * * *
1560398 AAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCTTTCGGGGATTTTGCGGCGTTTTTAAGAAA
1 AAAAAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGACGTTTTTAAGAAA
1560463 GCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGAGAAAATGCCGCA
66 GCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGAGAAAATGCCGCA
*
1560512 AAAAAAACTAAGCCCAACGACGCCGTTTTTTGAGCTTTCGGGGATTTAGTGACGTTTTTAAGAAA
1 AAAAAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGACGTTTTTAAGAAA
* **
1560577 GCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGGGAAAGCGCCGCA
66 GCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGAGAAAATGCCGCA
* ** * *
1560626 AAAAAACCTAAGCCCAACGACGTTGTTTTCTAAGCTTTCGGGGATTTAGTGGCGTTTTTAAGAAA
1 AAAAAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGACGTTTTTAAGAAA
1560691 GCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGAGAAAATGCCGCA
66 GCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGAGAAAATGCCGCA
*
1560740 AAAAAAACTAAGCCCAACGACGCCGTTTTTTGAGCTTTCGGGGATTTAGTGACGTTTTTAAGAAA
1 AAAAAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGACGTTTTTAAGAAA
1560805 GCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGAGAAAATGCCGCA
66 GCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGAGAAAATGCCGCA
*
1560854 AAAAAAACTAAGCCCAACGACGCCGTTTTTTGAGCTTTCGGGGATTTAGTGACGTTTTTAAGAAA
1 AAAAAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGACGTTTTTAAGAAA
1560919 TTTAGCGGTG
Statistics
Matches: 485, Mismatches: 34, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
113 102 0.21
114 383 0.79
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (114 bp):
AAAAAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGACGTTTTTAAGAAA
GCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGAGAAAATGCCGCA
Found at i:1560923 original size:21 final size:21
Alignment explanation
Indices: 1560897--1560939 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1560887 GCTTTCGGGG
*
1560897 ATTTAGTGACGTTTTTAAGAA
1 ATTTAGCGACGTTTTTAAGAA
**
1560918 ATTTAGCGGTGTTTTTAAGAA
1 ATTTAGCGACGTTTTTAAGAA
1560939 A
1 A
1560940 GGACTGCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.42
Consensus pattern (21 bp):
ATTTAGCGACGTTTTTAAGAA
Found at i:1561072 original size:9 final size:9
Alignment explanation
Indices: 1561058--1561147 Score: 60
Period size: 9 Copynumber: 9.6 Consensus size: 9
1561048 ATAATTTGTC
1561058 TATTTAATT
1 TATTTAATT
1561067 TATTTAA-T
1 TATTTAATT
*
1561075 TGTTT-ATT
1 TATTTAATT
1561083 TATTTAATT
1 TATTTAATT
*
1561092 TATTTAGTTTTT
1 TATTTA---ATT
*
1561104 CTGTTTAATT
1 -TATTTAATT
1561114 TATTT-ATT
1 TATTTAATT
1561122 TATATTAATT
1 TAT-TTAATT
*
1561132 AAAATTTAATT
1 --TATTTAATT
1561143 TATTT
1 TATTT
1561148 TTAATTGAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
7 1 0.02
8 16 0.25
9 26 0.41
10 5 0.08
11 6 0.10
12 4 0.06
13 5 0.08
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (9 bp):
TATTTAATT
Found at i:1561077 original size:21 final size:21
Alignment explanation
Indices: 1561053--1561093 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1561043 TTTTAATAAT
1561053 TTGTCTATTTAATTT-ATTTAA
1 TTGTCTATTT-ATTTAATTTAA
*
1561074 TTGTTTATTTATTTAATTTA
1 TTGTCTATTTATTTAATTTA
1561094 TTTAGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (21 bp):
TTGTCTATTTATTTAATTTAA
Found at i:1561084 original size:4 final size:4
Alignment explanation
Indices: 1561058--1561124 Score: 55
Period size: 4 Copynumber: 15.8 Consensus size: 4
1561048 ATAATTTGTC
* * *
1561058 TATT TAATT TATT TAAT TGTT TATT TATT TAATT TATT TAGTT T-TT CTGTT
1 TATT T-ATT TATT TATT TATT TATT TATT T-ATT TATT TA-TT TATT -TATT
1561109 TAATT TATT TATT TAT
1 T-ATT TATT TATT TAT
1561125 ATTAATTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
3 2 0.04
4 34 0.65
5 16 0.31
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:1565610 original size:43 final size:43
Alignment explanation
Indices: 1565553--1565639 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
1565543 GAGTTCATTG
* * * *
1565553 CAAGATTTTCTTGATTAAGTAGATGTATTATATCTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
* * *
1565596 CAAGGTTTACTTGATTAAGAAAATGCATTGTATTTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
1565639 C
1 C
1565640 TTGCAATATG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (43 bp):
CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
Found at i:1566064 original size:43 final size:42
Alignment explanation
Indices: 1566011--1566260 Score: 284
Period size: 43 Copynumber: 5.9 Consensus size: 42
1566001 TTTCTGTGAG
* *
1566011 AAGCGTCGCTAAAGGTCCTGATCTTTAGCGGCGTTTGTGGAA
1 AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAA
* *
1566053 TAAGCGCCGCTAAAGGTCCTGATCTTTAGCAGCGTTTGTGGGAA
1 -AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGT-GGAA
* ** * * *
1566097 AAGCGCCGCTAAAGATCAGGATCTTTAGCGGCGTTTGAGAAAA
1 AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTG-GAA
* * * *
1566140 AAGCGTCACTAAAGCTCCTGATCTATAGCAGCGTTTGTGGAA
1 AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAA
* * * *
1566182 AAGCGCCGCTAAAGGTCCTAACCTATAGCGGCATTTGTGGGGA
1 AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGT-GGAA
* *
1566225 AAGCGCCGCTAAAGATCATGATCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTT
1566261 ATTTCTAAAA
Statistics
Matches: 174, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
42 34 0.20
43 136 0.78
44 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (42 bp):
AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAA
Found at i:1566241 original size:128 final size:129
Alignment explanation
Indices: 1566011--1566260 Score: 385
Period size: 128 Copynumber: 1.9 Consensus size: 129
1566001 TTTCTGTGAG
* * * * * *
1566011 AAGCGTCGCTAAAGGTCCTGATCTTTAGCGGCGTTTGTGGAATAAGCGCCGCTAAAGGTCCTGAT
1 AAGCGTCACTAAAGCTCCTGATCTATAGCAGCGTTTGTGGAATAAGCGCCGCTAAAGGTCCTAAC
* * *
1566076 CTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGATCTTTAGCGGCGTTTGAGAAAA
66 CTATAGCAGCATTTGTGGGAAAAGCGCCGCTAAAGATCAGGATCTATAGCGGCGTTTGAGAAAA
1566140 AAGCGTCACTAAAGCTCCTGATCTATAGCAGCGTTTGTGGAA-AAGCGCCGCTAAAGGTCCTAAC
1 AAGCGTCACTAAAGCTCCTGATCTATAGCAGCGTTTGTGGAATAAGCGCCGCTAAAGGTCCTAAC
* * *
1566204 CTATAGCGGCATTTGTGGGGAAAGCGCCGCTAAAGATCATGATCTATAGCGGCGTTT
66 CTATAGCAGCATTTGTGGGAAAAGCGCCGCTAAAGATCAGGATCTATAGCGGCGTTT
1566261 ATTTCTAAAA
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
128 71 0.65
129 38 0.35
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (129 bp):
AAGCGTCACTAAAGCTCCTGATCTATAGCAGCGTTTGTGGAATAAGCGCCGCTAAAGGTCCTAAC
CTATAGCAGCATTTGTGGGAAAAGCGCCGCTAAAGATCAGGATCTATAGCGGCGTTTGAGAAAA
Found at i:1566466 original size:43 final size:42
Alignment explanation
Indices: 1566433--1566638 Score: 243
Period size: 43 Copynumber: 4.9 Consensus size: 42
1566423 TTATTACGAG
* *
1566433 AAGCGTCGCTAAAGGTCCTGATCTTTAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGT-GGAA
* * * * * *
1566476 AAACCCCGCTAAAGGTCCTGATCTTTAGCGGTGTTTGAGAAAA
1 AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTG-GAA
* *
1566519 AAACG-CGCTAAAGGTCCTGATCTATAGCGGTGTTTGTGGAA
1 AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAA
* * *
1566560 AAGCGCCGCTAAAGGTCCTAACCTATAGCGGCGTTTGTGGGGA
1 AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGT-GGAA
* *
1566603 AAGCGACGCTAAAGGTCATGATCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTT
1566639 ATTTCTAAAA
Statistics
Matches: 141, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
41 6 0.04
42 61 0.43
43 74 0.52
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (42 bp):
AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAA
Found at i:1566533 original size:42 final size:43
Alignment explanation
Indices: 1566433--1566638 Score: 238
Period size: 42 Copynumber: 4.8 Consensus size: 43
1566423 TTATTACGAG
* *
1566433 AAGCGTCGCTAAAGGTCCTGATCTTTAGCGGCGTTTGTGGGAAA
1 AAGCGACGCTAAAGGTCCTGATCTATAGCGGCGTTTGT-GGAAA
** * * * *
1566477 AA-CCCCGCTAAAGGTCCTGATCTTTAGCGGTGTTTGAGAAAA
1 AAGCGACGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAA
* *
1566519 AAACG-CGCTAAAGGTCCTGATCTATAGCGGTGTTTGTGG-AA
1 AAGCGACGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAA
* * * **
1566560 AAGCGCCGCTAAAGGTCCTAACCTATAGCGGCGTTTGTGGGGA
1 AAGCGACGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAA
*
1566603 AAGCGACGCTAAAGGTCATGATCTATAGCGGCGTTT
1 AAGCGACGCTAAAGGTCCTGATCTATAGCGGCGTTT
1566639 ATTTCTAAAA
Statistics
Matches: 141, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
41 6 0.04
42 68 0.48
43 65 0.46
44 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (43 bp):
AAGCGACGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAA
Found at i:1566613 original size:85 final size:85
Alignment explanation
Indices: 1566433--1566638 Score: 261
Period size: 85 Copynumber: 2.4 Consensus size: 85
1566423 TTATTACGAG
* * *
1566433 AAGCGTCGCTAAAGGTCCTGATCTTTAGCGGCGTTTGTGGGAAAAACCCCGCTAAAGGTCCTGAT
1 AAGCG-CGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAACCCCGCTAAAGGTCCTAAC
* *
1566498 CTTTAGCGGTGTTTGAGAAAA
65 CTATAGCGGCGTTTGAGAAAA
* * * *
1566519 AAACGCGCTAAAGGTCCTGATCTATAGCGGTGTTTGT-GGAAAAGCGCCGCTAAAGGTCCTAACC
1 AAGCGCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAACCCCGCTAAAGGTCCTAACC
* ***
1566583 TATAGCGGCGTTTGTGGGGA
66 TATAGCGGCGTTTGAGAAAA
*
1566603 AAGCGACGCTAAAGGTCATGATCTATAGCGGCGTTT
1 AAGCG-CGCTAAAGGTCCTGATCTATAGCGGCGTTT
1566639 ATTTCTAAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
84 41 0.40
85 58 0.56
86 4 0.04
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (85 bp):
AAGCGCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAACCCCGCTAAAGGTCCTAACC
TATAGCGGCGTTTGAGAAAA
Found at i:1568888 original size:3 final size:3
Alignment explanation
Indices: 1568880--1568913 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1568870 TTAAGATCAC
1568880 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1568914 GAGGGACTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1574723 original size:23 final size:23
Alignment explanation
Indices: 1574696--1574741 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1574686 AGAAAAAAGA
1574696 AAGAAAAATAAGAACACACAGAT
1 AAGAAAAATAAGAACACACAGAT
1574719 AAGAAAAATAAGAACACACAGAT
1 AAGAAAAATAAGAACACACAGAT
1574742 TTTATGTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.65, C:0.13, G:0.13, T:0.09
Consensus pattern (23 bp):
AAGAAAAATAAGAACACACAGAT
Found at i:1574923 original size:23 final size:23
Alignment explanation
Indices: 1574897--1574947 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
1574887 GAAGTATAGT
*
1574897 TGTAATACCCTGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
1574920 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
1574943 AGTAA
1 TGTAA
1574948 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:1575427 original size:11 final size:13
Alignment explanation
Indices: 1575403--1575434 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1575393 TAGTTTATTA
1575403 ATATTTTAATTTG
1 ATATTTTAATTTG
1575416 AT-TTTTAA-TTG
1 ATATTTTAATTTG
1575427 ATATTTTA
1 ATATTTTA
1575435 TTATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (13 bp):
ATATTTTAATTTG
Found at i:1580555 original size:59 final size:60
Alignment explanation
Indices: 1580419--1580558 Score: 160
Period size: 59 Copynumber: 2.4 Consensus size: 60
1580409 CATTTTTTTC
* * * *
1580419 CTAATTTGGTATTTGAACATAAAATTTATTCCTAATTTGGTACTTAATATTTTTTTAGGT
1 CTAATTTGGTACTTGAACTTGAAATTTATTCCTAATTTGGTACCTAATATTTTTTTAGGT
* * * *
1580479 CTAATTTAGTACCTGAACTTGATATTT-TTCCTAATTTGGTACCTAATCTTTTTCTT-GGT
1 CTAATTTGGTACTTGAACTTGAAATTTATTCCTAATTTGGTACCTAATATTTTT-TTAGGT
*
1580538 -TCGATTTGGTACTTGAACTTG
1 CT-AATTTGGTACTTGAACTTG
1580559 TCAAATGTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
58 1 0.01
59 43 0.64
60 23 0.34
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.49
Consensus pattern (60 bp):
CTAATTTGGTACTTGAACTTGAAATTTATTCCTAATTTGGTACCTAATATTTTTTTAGGT
Found at i:1583325 original size:94 final size:93
Alignment explanation
Indices: 1583028--1583585 Score: 532
Period size: 94 Copynumber: 5.9 Consensus size: 93
1583018 GTGTCACAGT
* * * * * * *
1583028 TTCATCTTGATCCATTGTAACTTCATGGAGATAAGATTTGATGTTATAGTTTCACTT-CAACCCA
1 TTCATCTTGCTCCACTGCAACTTTA-GGAGATAAGATTTGCTATTGTAGTTTCA-TTCCAACCCA
* * *
1583092 CTACAACTTCAAGGGTATATGATTTGCAGC
64 CTACAACTTTAAGGGTATAGGATTTGTAGC
* * * * * * * ** *
1583122 TTCATCTTGCTCCATTGTAACTTTAGGGAGATCAGATTTTCCATTGT-CTTTGA-TCTGATCCAC
1 TTCATCTTGCTCCACTGCAACTTTA-GGAGATAAGATTTGCTATTGTAGTTTCATTCCAACCCAC
* * *
1583185 TGCATCTTT-AGGGAAATAGGATTTTGTAGC
65 TACAACTTTAAGGG-TATAGGA-TTTGTAGC
* * *
1583215 TTCATCTTGCTCCACTGCAACTTCATGGAGATAAGATTTGCCATTGTAGTTTCATTCCAACCTAC
1 TTCATCTTGCTCCACTGCAACTTTA-GGAGATAAGATTTGCTATTGTAGTTTCATTCCAACCCAC
* *
1583280 TATAACTTTAAAGGTATAGGATTTGTAGC
65 TACAACTTTAAGGGTATAGGATTTGTAGC
* * * * *
1583309 TTCGTCTTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTATGGTAGCTTCAATCCGACCCAC
1 TTCATCTTGCTCCACTGCAACTTTA-GGAGATAAGATTTGCTATTGTAGTTTCATTCCAACCCAC
* *
1583374 TACAACTTCAGGGGTATAGGATTTGTAGC
65 TACAACTTTAAGGGTATAGGATTTGTAGC
* * * *
1583403 TTCATCTTTCTCCACTGCAACTTTAGAGAGATAAGATTTGCTGTTGTAGTTTTATTCCAACCCAT
1 TTCATCTTGCTCCACTGCAACTTTAG-GAGATAAGATTTGCTATTGTAGTTTCATTCCAACCCAC
* *
1583468 TTCAACTTTAGGGGTATAGGATTTGTAGC
65 TACAACTTTAAGGGTATAGGATTTGTAGC
* * ** * *
1583497 TTCGTCTTGCTCCACTACAACTTTAGAGAGATAAGATTCACTATGGTAGCTTCAATT-CAACCCA
1 TTCATCTTGCTCCACTGCAACTTTAG-GAGATAAGATTTGCTATTGTAGTTTC-ATTCCAACCCA
* * *
1583561 CTGCAACTTCAGGGGGTATAGGATT
64 CTACAACTTTA-AGGGTATAGGATT
1583586 CACTATTTCA
Statistics
Matches: 382, Mismatches: 73, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
91 5 0.01
92 16 0.04
93 53 0.14
94 271 0.71
95 34 0.09
96 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (93 bp):
TTCATCTTGCTCCACTGCAACTTTAGGAGATAAGATTTGCTATTGTAGTTTCATTCCAACCCACT
ACAACTTTAAGGGTATAGGATTTGTAGC
Found at i:1583347 original size:44 final size:44
Alignment explanation
Indices: 1583112--1583534 Score: 135
Period size: 44 Copynumber: 9.1 Consensus size: 44
1583102 AAGGGTATAT
* * * * *
1583112 GATTTGCAGCTTCATCTTGCTCCATTGTAACTTTAGGGAGATCA
1 GATTTGTAGCTTCGTCTTGCTCCACTGCAACTTTAGGGAGATAA
* * * * *
1583156 GATTT-TCCATTGTCTTTGATC-TGATCCACTGCATCTTTAGGGAAATAG
1 GATTTGT--A--G-CTTCG-TCTTGCTCCACTGCAACTTTAGGGAGATAA
* * *
1583204 GATTTTGTAGCTTCATCTTGCTCCACTGCAACTTCATGGAGATAA
1 GA-TTTGTAGCTTCGTCTTGCTCCACTGCAACTTTAGGGAGATAA
* * * * * ** * * *
1583249 GATTTGCCA-TTGTAGTTTCATTCCAACCTACTATAACTTTAAAGG-TATAG
1 GATTTG-TAGCT-TCG--TC-TTGC-TCC-ACTGCAACTTT-AGGGAGATAA
1583299 GATTTGTAGCTTCGTCTTGCTCCACTGCAACTTTAGGGAGATAA
1 GATTTGTAGCTTCGTCTTGCTCCACTGCAACTTTAGGGAGATAA
* * * * *
1583343 GATTTGCTATGGTAGCTTCAATC-CGAC-CCACTACAACTTCAGGG-GTATAG
1 GA--T--T-T-GTAGCTTC-GTCTTG-CTCCACTGCAACTTTAGGGAG-ATAA
* * *
1583393 GATTTGTAGCTTCATCTTTCTCCACTGCAACTTTAGAGAGATAA
1 GATTTGTAGCTTCGTCTTGCTCCACTGCAACTTTAGGGAGATAA
* * * ** * *
1583437 GATTTGCT-GTTGTAGTTTTATTCCAACCCATTTCAACTTTAGGG-GTATAG
1 GATTTG-TAGCT-TCGTCTTGCTCC-A--C--TGCAACTTTAGGGAG-ATAA
* *
1583487 GATTTGTAGCTTCGTCTTGCTCCACTACAACTTTAGAGAGATAA
1 GATTTGTAGCTTCGTCTTGCTCCACTGCAACTTTAGGGAGATAA
1583531 GATT
1 GATT
1583535 CACTATGGTA
Statistics
Matches: 270, Mismatches: 68, Indels: 82
0.64 0.16 0.20
Matches are distributed among these distances:
43 7 0.03
44 77 0.29
45 42 0.16
46 8 0.03
47 5 0.02
48 33 0.12
49 22 0.08
50 70 0.26
51 6 0.02
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (44 bp):
GATTTGTAGCTTCGTCTTGCTCCACTGCAACTTTAGGGAGATAA
Found at i:1583441 original size:188 final size:188
Alignment explanation
Indices: 1583028--1583585 Score: 676
Period size: 188 Copynumber: 3.0 Consensus size: 188
1583018 GTGTCACAGT
* * * * *
1583028 TTCATCTTGATCCATTGTAACTTCATGGAGATAAGATTTGATGTTATAGTTTCACTT-CAACCCA
1 TTCATCTTGCTCCACTGCAACTTCATGGAGATAAGATTTGCTGTTGTAGTTTCA-TTCCAACCCA
* * * * * * * *
1583092 CTACAACTTCAAGGGTATATGATTTGCAGCTTCATCTTGCTCCATTGTAACTTTAGGGAGATCAG
65 CTATAACTTTAAGGGTATAGGATTTGTAGCTTCGTCTTGCTCCACTGCAACTTTAGGGAGATAAG
* * * ** * * * * **
1583157 ATTTTCCATTGT--CTTTGATCTGATCCACTGCATCTTTAGGGAAATAGGATTTTGTAGC
130 ATTTACTATGGTAGCTTCAATCCGACCCACTGCAACTTCAGGGGTATAGGA-TTTGTAGC
** *
1583215 TTCATCTTGCTCCACTGCAACTTCATGGAGATAAGATTTGCCATTGTAGTTTCATTCCAACCTAC
1 TTCATCTTGCTCCACTGCAACTTCATGGAGATAAGATTTGCTGTTGTAGTTTCATTCCAACCCAC
*
1583280 TATAACTTTAAAGGTATAGGATTTGTAGCTTCGTCTTGCTCCACTGCAACTTTAGGGAGATAAGA
66 TATAACTTTAAGGGTATAGGATTTGTAGCTTCGTCTTGCTCCACTGCAACTTTAGGGAGATAAGA
* *
1583345 TTTGCTATGGTAGCTTCAATCCGACCCACTACAACTTCAGGGGTATAGGATTTGTAGC
131 TTTACTATGGTAGCTTCAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGTAGC
* * *
1583403 TTCATCTTTCTCCACTGCAACTTTA-GAGAGATAAGATTTGCTGTTGTAGTTTTATTCCAACCCA
1 TTCATCTTGCTCCACTGCAACTTCATG-GAGATAAGATTTGCTGTTGTAGTTTCATTCCAACCCA
* * * *
1583467 -TTTCAACTTTAGGGGTATAGGATTTGTAGCTTCGTCTTGCTCCACTACAACTTTAGAGAGATAA
65 CTAT-AACTTTAAGGGTATAGGATTTGTAGCTTCGTCTTGCTCCACTGCAACTTTAGGGAGATAA
* * *
1583531 GATTCACTATGGTAGCTTCAATTCAACCCACTGCAACTTCAGGGGGTATAGGATT
129 GATTTACTATGGTAGCTTCAATCCGACCCACTGCAACTTCA-GGGGTATAGGATT
1583586 CACTATTTCA
Statistics
Matches: 320, Mismatches: 45, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
186 2 0.01
187 121 0.38
188 156 0.49
189 41 0.13
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (188 bp):
TTCATCTTGCTCCACTGCAACTTCATGGAGATAAGATTTGCTGTTGTAGTTTCATTCCAACCCAC
TATAACTTTAAGGGTATAGGATTTGTAGCTTCGTCTTGCTCCACTGCAACTTTAGGGAGATAAGA
TTTACTATGGTAGCTTCAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGTAGC
Found at i:1592630 original size:29 final size:29
Alignment explanation
Indices: 1592588--1592648 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
1592578 CCAATCGTAT
1592588 TCTAGGGTCGTCATAGGATTTGCAACAAA
1 TCTAGGGTCGTCATAGGATTTGCAACAAA
*
1592617 TCTAGGGTCGTCATAGGATTTGTAACAAA
1 TCTAGGGTCGTCATAGGATTTGCAACAAA
1592646 TCT
1 TCT
1592649 CTTCATTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (29 bp):
TCTAGGGTCGTCATAGGATTTGCAACAAA
Found at i:1596440 original size:23 final size:24
Alignment explanation
Indices: 1596399--1596444 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
1596389 ATCTAGCCTG
1596399 TACATGCCATAATTAAAATTTAAT
1 TACATGCCATAATTAAAATTTAAT
1596423 TACATGCCAT-ATTAAAATTTAA
1 TACATGCCATAATTAAAATTTAA
1596445 ACAGTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (24 bp):
TACATGCCATAATTAAAATTTAAT
Found at i:1614228 original size:15 final size:16
Alignment explanation
Indices: 1614199--1614236 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1614189 CCCTAATCAA
*
1614199 AATTTT-CATTCTTTT
1 AATTTTACATTATTTT
1614214 -ATTTTACATTATTTT
1 AATTTTACATTATTTT
1614229 AATTTTAC
1 AATTTTAC
1614237 CAAATATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 5 0.25
15 8 0.40
16 7 0.35
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTTTACATTATTTT
Found at i:1615554 original size:5 final size:5
Alignment explanation
Indices: 1615544--1615581 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
1615534 TCCAACTCTC
1615544 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA
1615582 CACTATTGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:1620076 original size:16 final size:17
Alignment explanation
Indices: 1620036--1620069 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1620026 ATGGCTTCCA
1620036 TAAACAT-GGAAAGAAT
1 TAAACATAGGAAAGAAT
*
1620052 TAAACATAGGAATGAAT
1 TAAACATAGGAAAGAAT
1620069 T
1 T
1620070 GAAATAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (17 bp):
TAAACATAGGAAAGAAT
Found at i:1620226 original size:14 final size:15
Alignment explanation
Indices: 1620191--1620233 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
1620181 CATTTGTTTG
1620191 CTAGTAAAAT-ATTTT
1 CTAG-AAAATGATTTT
1620206 CTAGAAAATGATTTT
1 CTAGAAAATGATTTT
*
1620221 C-GGAAAATGATTT
1 CTAGAAAATGATTT
1620234 ACTTTTCTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40
Consensus pattern (15 bp):
CTAGAAAATGATTTT
Found at i:1621702 original size:32 final size:32
Alignment explanation
Indices: 1621661--1621733 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 32
1621651 TCATTTTAAT
* *
1621661 ATCCGACAAGCTTAAAACATAATAAATTCAAT
1 ATCCAACAAGCTTAAAACATAATAAATTCAAA
* * *
1621693 ATCTAACAAGTTTAAAACATAATAATTTCAAA
1 ATCCAACAAGCTTAAAACATAATAAATTCAAA
1621725 ATCCAACAA
1 ATCCAACAA
1621734 ACTAATTTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.52, C:0.18, G:0.04, T:0.26
Consensus pattern (32 bp):
ATCCAACAAGCTTAAAACATAATAAATTCAAA
Found at i:1623206 original size:21 final size:21
Alignment explanation
Indices: 1623166--1623208 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1623156 CACACAAAAA
*
1623166 ATTACAAATTAATATACAATT
1 ATTACAAATCAATATACAATT
* *
1623187 ATTACAAATCAATGTGCAATT
1 ATTACAAATCAATATACAATT
1623208 A
1 A
1623209 ATTTAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.35
Consensus pattern (21 bp):
ATTACAAATCAATATACAATT
Found at i:1634302 original size:18 final size:20
Alignment explanation
Indices: 1634260--1634305 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
1634250 GAACCAACAC
**
1634260 TATCGATACTAAAATAACTT
1 TATCGATACTAAAATAAAGT
1634280 TATCGATAC-AAAA-AAAGT
1 TATCGATACTAAAATAAAGT
1634298 TATCGATA
1 TATCGATA
1634306 TCGTATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.46
19 4 0.17
20 9 0.38
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (20 bp):
TATCGATACTAAAATAAAGT
Found at i:1638002 original size:15 final size:15
Alignment explanation
Indices: 1637982--1638026 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1637972 GCCTAAAAGG
1637982 AATTTTAATTTTTTT
1 AATTTTAATTTTTTT
1637997 AATTTTAAGTTTATTTT
1 AATTTTAA-TTT-TTTT
* *
1638014 CATTTTCATTTTT
1 AATTTTAATTTTT
1638027 ATGTTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 10 0.38
16 6 0.23
17 10 0.38
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (15 bp):
AATTTTAATTTTTTT
Found at i:1639717 original size:25 final size:25
Alignment explanation
Indices: 1639661--1639718 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 25
1639651 TTCCCCAAAT
1639661 TAATAATAAATAAAACATAAGTATAAC
1 TAAT-ATAAATAAAACATAAG-ATAAC
*
1639688 TAATATAATTAAGAACATAA-ATAAC
1 TAATATAAATAA-AACATAAGATAAC
1639713 TAATAT
1 TAATAT
1639719 CACAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 11 0.38
26 7 0.24
27 11 0.38
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.29
Consensus pattern (25 bp):
TAATATAAATAAAACATAAGATAAC
Found at i:1641594 original size:51 final size:49
Alignment explanation
Indices: 1641502--1641621 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 49
1641492 ATAGAAATGG
** *
1641502 TGAAAATTGAGAAATGGGAAACATTTGGAAATTATTATGGTTTACTCCAAAA
1 TGAAAA-TGAGAAAT--GAAACATTTGGAAAGGAATATGGTTTACTCCAAAA
* *
1641554 TGAAAATGGAGAAATGAAACCATTTGGAAAGGAATGTGGTTTTCTCCAAAA
1 TGAAAAT-GAGAAATGAAA-CATTTGGAAAGGAATATGGTTTACTCCAAAA
*
1641605 TGAAAATGAAAAATGAA
1 TGAAAATGAGAAATGAA
1641622 TTTATGTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
50 13 0.22
51 34 0.57
52 13 0.22
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.27
Consensus pattern (49 bp):
TGAAAATGAGAAATGAAACATTTGGAAAGGAATATGGTTTACTCCAAAA
Found at i:1650268 original size:24 final size:24
Alignment explanation
Indices: 1650240--1650291 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
1650230 TTTCTAGAAG
*
1650240 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGTATTTATTAGCATAATAT
*
1650264 ATTTAGTATTTATTAGCATAATTT
1 ATTTAGTATTTATTAGCATAATAT
1650288 ATTT
1 ATTT
1650292 GACCTACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTTAGTATTTATTAGCATAATAT
Found at i:1650442 original size:16 final size:16
Alignment explanation
Indices: 1650423--1650457 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1650413 ATTTTGAATT
* *
1650423 TAAAAGTTTTTTGACA
1 TAAAAGTTTATTAACA
1650439 TAAAAGTTTATTAACA
1 TAAAAGTTTATTAACA
1650455 TAA
1 TAA
1650458 CAAATTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (16 bp):
TAAAAGTTTATTAACA
Found at i:1650985 original size:23 final size:23
Alignment explanation
Indices: 1650952--1650998 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
1650942 CGTTAGGTTT
1650952 TTTTGGCTTTTAGGG-TTTAGGG
1 TTTTGGCTTTTAGGGTTTTAGGG
1650974 TTTTGGCTTTTTAGGGTTTTAGGG
1 TTTTGGC-TTTTAGGGTTTTAGGG
1650998 T
1 T
1650999 CCTGGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 7 0.30
23 8 0.35
24 8 0.35
ACGTcount: A:0.09, C:0.04, G:0.34, T:0.53
Consensus pattern (23 bp):
TTTTGGCTTTTAGGGTTTTAGGG
Found at i:1651330 original size:124 final size:126
Alignment explanation
Indices: 1651020--1651354 Score: 460
Period size: 126 Copynumber: 2.7 Consensus size: 126
1651010 TAATTTCGAG
* * *
1651020 TTGACGTTTCTGATAAAATAATATAAAATTGCTTCTAGCAGGATGGTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGAAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* *
1651085 ACATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCGCGCCCTCGTAGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
* *
1651146 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGAAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * **** ***
1651211 AAATTGCGGCCTCGTCAG-CGCGCTTTTGCTACAGTAGGTCTTTTAATCTATAA-T-TTTTT
66 AAATCGCGCCCTCGT-AGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
* * *
1651270 TTGACGTTTCTGAGAAAATAATATAAAATCGCTTATACCAGGATGCTATTTGGGAAGAATTTGTG
1 TTGACGTTTCTGAGAAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
*
1651335 AAATCGCGCCCTCGTGGACG
66 AAATCGCGCCCTCGTAGACG
1651355 NNNNNNNNNN
Statistics
Matches: 183, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
123 1 0.01
124 80 0.44
125 1 0.01
126 100 0.55
127 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (126 bp):
TTGACGTTTCTGAGAAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTAGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
Found at i:1656911 original size:18 final size:18
Alignment explanation
Indices: 1656888--1656922 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1656878 CAGAAAAGGA
*
1656888 TACATAAAAGGGTTAGGG
1 TACATAAAAGGGCTAGGG
*
1656906 TACATATAAGGGCTAGG
1 TACATAAAAGGGCTAGG
1656923 AAACGCACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.09, G:0.31, T:0.23
Consensus pattern (18 bp):
TACATAAAAGGGCTAGGG
Found at i:1658722 original size:51 final size:51
Alignment explanation
Indices: 1658667--1658782 Score: 196
Period size: 51 Copynumber: 2.3 Consensus size: 51
1658657 TATTTTAAAA
* * *
1658667 AAGGAAATTGAGAAGAAATTTAAATTAAATATGGATTTGAGAGAATTTTTG
1 AAGGAAATTGAGAAGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
*
1658718 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAAGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
1658769 AAGGAAATTGAGAA
1 AAGGAAATTGAGAA
1658783 AATTTTGGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (51 bp):
AAGGAAATTGAGAAGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
Found at i:1658779 original size:22 final size:22
Alignment explanation
Indices: 1658754--1658809 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
1658744 AAATATAGAT
1658754 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
* *
1658776 TTGAGAAAATTTTGGAAGGAAT
1 TTGAGAGAATTTTGGAAGGAAA
1658798 TTGAGAGGAATT
1 TTGAGA-GAATT
1658810 GAGAGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:1659223 original size:52 final size:52
Alignment explanation
Indices: 1659166--1659271 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
1659156 TTAAAAATCC
1659166 TTAAATTCTTAATTAGGGTTTTAAAGGATTGTGTTTAAATATTATTGCATGA
1 TTAAATTCTTAATTAGGGTTTTAAAGGATTGTGTTTAAATATTATTGCATGA
1659218 TTAAATTCTTAATTAGGGTTTTAAAGGATTGTGTTTAAATATTATTGCATGA
1 TTAAATTCTTAATTAGGGTTTTAAAGGATTGTGTTTAAATATTATTGCATGA
1659270 TT
1 TT
1659272 TTTCATTGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (52 bp):
TTAAATTCTTAATTAGGGTTTTAAAGGATTGTGTTTAAATATTATTGCATGA
Found at i:1660307 original size:45 final size:45
Alignment explanation
Indices: 1660251--1660363 Score: 208
Period size: 45 Copynumber: 2.5 Consensus size: 45
1660241 ATGGATGTGT
*
1660251 AATGAAATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGG
*
1660296 AATGGAATAGAACTATAATAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGG
1660341 AATGGAATAGAACTGTAATAGTA
1 AATGGAATAGAACTGTAATAGTA
1660364 TTCTTGTGTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (45 bp):
AATGGAATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGG
Found at i:1664171 original size:27 final size:27
Alignment explanation
Indices: 1664131--1664198 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
1664121 AACACATAAG
* *
1664131 GAAAGAAAAACCTTTATGGTAAAATCT
1 GAAAGAATAGCCTTTATGGTAAAATCT
* * *
1664158 GAAAGAATAGCCTTTGTGGTGAACTCT
1 GAAAGAATAGCCTTTATGGTAAAATCT
1664185 GAAAGAATAGCCTT
1 GAAAGAATAGCCTT
1664199 AGTGGCAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (27 bp):
GAAAGAATAGCCTTTATGGTAAAATCT
Found at i:1664214 original size:27 final size:27
Alignment explanation
Indices: 1664157--1664214 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1664147 TGGTAAAATC
* ** *
1664157 TGAAAGAATAGCCTTTGTGGTGAACTC
1 TGAAAGAATAGCCTTAGTGGCAAACTA
*
1664184 TGAAAGAATAGCCTTAGTGGCAAATTA
1 TGAAAGAATAGCCTTAGTGGCAAACTA
1664211 TGAA
1 TGAA
1664215 GGGATAACCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (27 bp):
TGAAAGAATAGCCTTAGTGGCAAACTA
Found at i:1665323 original size:31 final size:31
Alignment explanation
Indices: 1665288--1665351 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
1665278 CTAAACCTAG
1665288 TTAGAATGGCTTAAAAAGGCTTTATCTGCAA
1 TTAGAATGGCTTAAAAAGGCTTTATCTGCAA
*
1665319 TTAGAATGGCTTAAAAAGGCTTTATTTGCAA
1 TTAGAATGGCTTAAAAAGGCTTTATCTGCAA
1665350 TT
1 TT
1665352 CAGTTATGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (31 bp):
TTAGAATGGCTTAAAAAGGCTTTATCTGCAA
Found at i:1667517 original size:25 final size:25
Alignment explanation
Indices: 1667489--1667568 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
1667479 TATCTCTTTC
* *
1667489 GAGCCATGTAACAGGAAGCTAATGT
1 GAGCCATGTAACAGGAAGCTCATGA
* *
1667514 GAGCCATGTAACGGGAAGCTCATAA
1 GAGCCATGTAACAGGAAGCTCATGA
*
1667539 GAGCCA--TAATCAGGAAGCTCATGC
1 GAGCCATGTAA-CAGGAAGCTCATGA
1667563 GAGCCA
1 GAGCCA
1667569 ATATCGGGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
23 3 0.06
24 17 0.36
25 27 0.57
ACGTcount: A:0.35, C:0.21, G:0.28, T:0.16
Consensus pattern (25 bp):
GAGCCATGTAACAGGAAGCTCATGA
Found at i:1669921 original size:33 final size:33
Alignment explanation
Indices: 1669884--1669948 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
1669874 GAAATAATCT
1669884 TGCATGATAATTACAATTAGTAAATGTTCACAA
1 TGCATGATAATTACAATTAGTAAATGTTCACAA
1669917 TGCATGATAATTACAATTAGTAAATGTTCACA
1 TGCATGATAATTACAATTAGTAAATGTTCACA
1669949 TTAGCATCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (33 bp):
TGCATGATAATTACAATTAGTAAATGTTCACAA
Found at i:1684880 original size:15 final size:15
Alignment explanation
Indices: 1684860--1684890 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1684850 TTTTACTTAG
*
1684860 TAGTTTTATTTAATT
1 TAGTTTAATTTAATT
1684875 TAGTTTAATTTAATT
1 TAGTTTAATTTAATT
1684890 T
1 T
1684891 TTATAGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TAGTTTAATTTAATT
Found at i:1690386 original size:17 final size:17
Alignment explanation
Indices: 1690364--1690396 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1690354 CACTAATATT
*
1690364 AAAATGCAATGACAATA
1 AAAATGCAACGACAATA
1690381 AAAATGCAACGACAAT
1 AAAATGCAACGACAAT
1690397 GTGCACTAAA
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:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (17 bp):
AAAATGCAACGACAATA
Found at i:1703740 original size:4 final size:4
Alignment explanation
Indices: 1703733--1703777 Score: 63
Period size: 4 Copynumber: 10.8 Consensus size: 4
1703723 AACAAAAAAA
*
1703733 AAAG AAAG AAAG AAAG AGAG AAAG AAAAG AAAG AAAG AAAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG -AAAG AAA
1703778 TGTAAACAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 29 0.78
5 8 0.22
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1703767 original size:13 final size:13
Alignment explanation
Indices: 1703732--1703777 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
1703722 TAACAAAAAA
1703732 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
*
1703745 -AAAGAGAGAAAG
1 AAAAGAAAGAAAG
1703757 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
1703770 AAAAGAAA
1 AAAAGAAA
1703778 TGTAAACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:1704566 original size:26 final size:27
Alignment explanation
Indices: 1704532--1704582 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
1704522 AATATGATAT
*
1704532 ACAACTTTAAATAT-AAATTGATAAAA
1 ACAACTTTAAATATCAAAGTGATAAAA
* *
1704558 ACAAGTTTAGATATCAAAGTGATAA
1 ACAACTTTAAATATCAAAGTGATAA
1704583 TTAGAACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (27 bp):
ACAACTTTAAATATCAAAGTGATAAAA
Found at i:1707353 original size:93 final size:93
Alignment explanation
Indices: 1707194--1707380 Score: 320
Period size: 93 Copynumber: 2.0 Consensus size: 93
1707184 ATCTCTTCTC
* *
1707194 CCATTCTTCATTCTTTCACTTCCCATTTGAGAGAGCAACACAAGAGTTTGAGGGAAGCATTGCAG
1 CCATTCTTCATTATTTCACTTCCCATTTGAGAGAGCAACACAAGAGTTTGAGGGAAGCATTACAG
* *
1707259 AAGTTCTTTGAGTAGAAAAATTCAGCAT
66 AAGTTCTTTGAGCAGAAAAATTCAACAT
*
1707287 CCATTCTTCATTATTTCACTTCCCATTTGAGAGAGTAACACAAGAGTTTGAGGGAAGCATTACAG
1 CCATTCTTCATTATTTCACTTCCCATTTGAGAGAGCAACACAAGAGTTTGAGGGAAGCATTACAG
*
1707352 AAGTTCTTTGAGCAGCAAAATTCAACAT
66 AAGTTCTTTGAGCAGAAAAATTCAACAT
1707380 C
1 C
1707381 TTGAAGGCAA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (93 bp):
CCATTCTTCATTATTTCACTTCCCATTTGAGAGAGCAACACAAGAGTTTGAGGGAAGCATTACAG
AAGTTCTTTGAGCAGAAAAATTCAACAT
Found at i:1709592 original size:18 final size:18
Alignment explanation
Indices: 1709564--1709611 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1709554 TAAAAGAATA
*
1709564 GAAATTAAAAATGAAAAT
1 GAAAATAAAAATGAAAAT
*
1709582 GAAAATGAAAATGAAAAT
1 GAAAATAAAAATGAAAAT
1709600 GAAAATAAAAAT
1 GAAAATAAAAAT
1709612 AAAGAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (18 bp):
GAAAATAAAAATGAAAAT
Found at i:1709622 original size:6 final size:6
Alignment explanation
Indices: 1709571--1709611 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
1709561 ATAGAAATTA
*
1709571 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATA AAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAAT
1709612 AAAGAAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:1730410 original size:23 final size:24
Alignment explanation
Indices: 1730354--1730422 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 24
1730344 TTATTAACAT
*
1730354 TGTTTGTGAATATGTTCAATTATA
1 TGTTTGTGAACATGTTCAATTATA
** *
1730378 TGTTCATGAACATGTTCATTTA-A
1 TGTTTGTGAACATGTTCAATTATA
*
1730401 TGTTTGTGAACATGTTCGATTA
1 TGTTTGTGAACATGTTCAATTA
1730423 AGTTAAATGA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 19 0.51
24 18 0.49
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.46
Consensus pattern (24 bp):
TGTTTGTGAACATGTTCAATTATA
Found at i:1733819 original size:23 final size:21
Alignment explanation
Indices: 1733783--1733827 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
1733773 AATCTAAATT
1733783 TTAAAATCTGAAAAAGTAAAAAA
1 TTAAAATCTG-AAAA-TAAAAAA
* *
1733806 TTAAAATTTTAAAATAAAAAA
1 TTAAAATCTGAAAATAAAAAA
1733827 T
1 T
1733828 GCAGAAGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 4 0.20
23 8 0.40
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
TTAAAATCTGAAAATAAAAAA
Found at i:1736236 original size:2 final size:2
Alignment explanation
Indices: 1736229--1736257 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1736219 NNNNNNNNNN
1736229 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1736258 TAATTTCTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1737876 original size:16 final size:17
Alignment explanation
Indices: 1737839--1737882 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1737829 GGATTTTGTT
1737839 ATTTTTTAAAATTTTAG
1 ATTTTTTAAAATTTTAG
1737856 ATTTTTTAAAATTTT-G
1 ATTTTTTAAAATTTTAG
*
1737872 TTTTTTTAAAA
1 ATTTTTTAAAA
1737883 GGATGTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (17 bp):
ATTTTTTAAAATTTTAG
Found at i:1737941 original size:18 final size:17
Alignment explanation
Indices: 1737914--1737947 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1737904 AATTCAATGT
*
1737914 TTAATTAATTCGTGATA
1 TTAATTAATTAGTGATA
1737931 TTAATTTAATTAGTGAT
1 TTAA-TTAATTAGTGAT
1737948 TTTAGTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (17 bp):
TTAATTAATTAGTGATA
Found at i:1744633 original size:32 final size:32
Alignment explanation
Indices: 1744597--1744660 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1744587 GTCACCACCA
* *
1744597 TCTAGCGTCCACCAGGTCACCATCATCGTTTG
1 TCTAGCATCCACCAAGTCACCATCATCGTTTG
* *
1744629 TCTAGCATCCACCAAGTTACCATCATTGTTTG
1 TCTAGCATCCACCAAGTCACCATCATCGTTTG
1744661 ACTGCCATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCTAGCATCCACCAAGTCACCATCATCGTTTG
Found at i:1745306 original size:40 final size:40
Alignment explanation
Indices: 1745257--1745333 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
1745247 AATGCTTTAC
* *
1745257 AGATTCTTAGTTGCTATGAACAATATTTGAATTATTACAT
1 AGATTCTTAGTTACTATAAACAATATTTGAATTATTACAT
* * *
1745297 AGATTCTTAGTTACTTTAAACCATATTTTAATTATTA
1 AGATTCTTAGTTACTATAAACAATATTTGAATTATTA
1745334 TAATTGTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.45
Consensus pattern (40 bp):
AGATTCTTAGTTACTATAAACAATATTTGAATTATTACAT
Found at i:1751651 original size:42 final size:42
Alignment explanation
Indices: 1751604--1751820 Score: 217
Period size: 42 Copynumber: 5.2 Consensus size: 42
1751594 GGCTGCATAG
* * * *
1751604 AAGCTCATAAGTGCTAAACAGAAACCCATAAGGGTTGAACGA
1 AAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACGA
** * * * *
1751646 AAGCTCGTAAGAGCTGAACGGAAACCCATAAAGGATAAAATG-
1 AAGCTCAAAAGAGCTGAACAGAAACCCAT-AAGGGTTAAACGA
* *
1751688 AAG-TAAAAAAGAGCTAAAC-GAAAACCCATAAGGGTTAAACTG-
1 AAGCT-CAAAAGAGCTGAACAG-AAACCCATAAGGGTTAAAC-GA
* *
1751730 AAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACTA
1 AAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACGA
* *
1751772 AAGCTTAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACTA
1 AAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACGA
*
1751814 AAACTCA
1 AAGCTCA
1751821 TATGAGTTAA
Statistics
Matches: 146, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
41 10 0.07
42 126 0.86
43 10 0.07
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (42 bp):
AAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACGA
Found at i:1751757 original size:84 final size:85
Alignment explanation
Indices: 1751616--1751820 Score: 267
Period size: 84 Copynumber: 2.4 Consensus size: 85
1751606 GCTCATAAGT
* **
1751616 GCTAAACAGAAACCCATAAGGGTTGAAC-GAAAGCTCGTAAGAGCTGAACGGAAACCCATAAAGG
1 GCTAAACAGAAACCCATAAGGGTTAAACTGAAAGCTCAAAAGAGCTGAACGGAAACCCATAAAGG
*
1751680 ATAAAATGAAG-TAAAAAAGA
66 ATAAAATAAAGCT-AAAAAGA
*
1751700 GCTAAAC-GAAAACCCATAAGGGTTAAACTG-AAGCTCAAAAGAGCTGAACGGAAACCCATAAGG
1 GCTAAACAG-AAACCCATAAGGGTTAAACTGAAAGCTCAAAAGAGCTGAACGGAAACCCATAAAG
* * *
1751763 GTTAAACTAAAGCTTAAAAGA
65 GATAAAATAAAGCTAAAAAGA
* *
1751784 GCTGAACAGAAACCCATAAGGGTTAAACT-AAAACTCA
1 GCTAAACAGAAACCCATAAGGGTTAAACTGAAAGCTCA
1751821 TATGAGTTAA
Statistics
Matches: 106, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
83 1 0.01
84 102 0.96
85 3 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (85 bp):
GCTAAACAGAAACCCATAAGGGTTAAACTGAAAGCTCAAAAGAGCTGAACGGAAACCCATAAAGG
ATAAAATAAAGCTAAAAAGA
Found at i:1751822 original size:21 final size:21
Alignment explanation
Indices: 1751702--1751822 Score: 64
Period size: 21 Copynumber: 5.8 Consensus size: 21
1751692 AAAAAAGAGC
*
1751702 TAAACGAAAACCCATAAGGGT
1 TAAACTAAAACCCATAAGGGT
* * * * * *
1751723 TAAACTGAAGCTCAAAAGAGC
1 TAAACTAAAACCCATAAGGGT
* **
1751744 TGAACGGAAACCCATAAGGGT
1 TAAACTAAAACCCATAAGGGT
* ** * * *
1751765 TAAACTAAAGCTTAAAAGAGC
1 TAAACTAAAACCCATAAGGGT
*
1751786 TGAAC-AGAAACCCATAAGGGT
1 TAAACTA-AAACCCATAAGGGT
*
1751807 TAAACTAAAACTCATA
1 TAAACTAAAACCCATA
1751823 TGAGTTAACA
Statistics
Matches: 66, Mismatches: 32, Indels: 4
0.65 0.31 0.04
Matches are distributed among these distances:
20 1 0.02
21 64 0.97
22 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.17
Consensus pattern (21 bp):
TAAACTAAAACCCATAAGGGT
Found at i:1752100 original size:45 final size:46
Alignment explanation
Indices: 1752013--1752104 Score: 116
Period size: 45 Copynumber: 2.0 Consensus size: 46
1752003 TTTTCAATTC
* * *
1752013 ATAATTTAACAATATTTCATTTTTTTAACAATAAGCTAAATACATA
1 ATAATTTAACAACATTCCATTTTTTCAACAATAAGCTAAATACATA
* *
1752059 ATAATTTAACAACATTCCA-TTTTTCAACGATATA-TTAAATACATA
1 ATAATTTAACAACATTCCATTTTTTCAACAATA-AGCTAAATACATA
1752104 A
1 A
1752105 CATCATTCGT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
45 22 0.55
46 18 0.45
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (46 bp):
ATAATTTAACAACATTCCATTTTTTCAACAATAAGCTAAATACATA
Found at i:1755145 original size:31 final size:30
Alignment explanation
Indices: 1755110--1755203 Score: 70
Period size: 31 Copynumber: 3.2 Consensus size: 30
1755100 ATTTTCCAAA
1755110 AAGGCATTCTTTTCTTTCAGAACTTGCCACG
1 AAGGCA-TCTTTTCTTTCAGAACTTGCCACG
* ** *
1755141 AAGG---C-TTTCCTTCAGATGTTTGCCACA
1 AAGGCATCTTTTCTTTCAGA-ACTTGCCACG
* * *
1755168 AAGGCATCCTCTTCTTTCAGTACTCGCCACG
1 AAGGCAT-CTTTTCTTTCAGAACTTGCCACG
1755199 AAGGC
1 AAGGC
1755204 TTTCCTTCAT
Statistics
Matches: 46, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
26 10 0.22
27 12 0.26
31 16 0.35
32 8 0.17
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (30 bp):
AAGGCATCTTTTCTTTCAGAACTTGCCACG
Found at i:1755148 original size:27 final size:27
Alignment explanation
Indices: 1755118--1755206 Score: 72
Period size: 27 Copynumber: 3.1 Consensus size: 27
1755108 AAAAGGCATT
1755118 CTTTTCTTTCAGAACTTGCCACGAAGG
1 CTTTTCTTTCAGAACTTGCCACGAAGG
* ** *
1755145 C-TTTCCTTCAGATGTTTGCCACAAAGG
1 CTTTTCTTTCAGA-ACTTGCCACGAAGG
* *
1755172 CATCCTCTTCTTTCAGTACTCGCCACGAAGG
1 C-T--T-TTCTTTCAGAACTTGCCACGAAGG
1755203 CTTT
1 CTTT
1755207 CCTTCATAGA
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
26 10 0.22
27 14 0.30
28 1 0.02
30 1 0.02
31 12 0.26
32 8 0.17
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (27 bp):
CTTTTCTTTCAGAACTTGCCACGAAGG
Found at i:1755155 original size:26 final size:26
Alignment explanation
Indices: 1755120--1755212 Score: 69
Period size: 26 Copynumber: 3.3 Consensus size: 26
1755110 AAGGCATTCT
*
1755120 TTTCTTTCAGAACTTGCCACGAAGGC
1 TTTCCTTCAGAACTTGCCACGAAGGC
** *
1755146 TTTCCTTCAGATGTTTGCCACAAAGGCATCC
1 TTTCCTTCAGA-ACTTGCCACGAAGG----C
* * *
1755177 TCTTCTTTCAGTACTCGCCACGAAGGC
1 T-TTCCTTCAGAACTTGCCACGAAGGC
1755204 TTTCCTTCA
1 TTTCCTTCA
1755213 TAGATTCACC
Statistics
Matches: 50, Mismatches: 11, Indels: 12
0.68 0.15 0.16
Matches are distributed among these distances:
26 17 0.34
27 13 0.26
31 12 0.24
32 8 0.16
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.33
Consensus pattern (26 bp):
TTTCCTTCAGAACTTGCCACGAAGGC
Done.