Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 135 of 230
Found at i:39527437 original size:15 final size:15
Alignment explanation
Indices: 39527419--39527449 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
39527409 TGCAAAACTT
39527419 GGGCTTGGAAAAAGA
1 GGGCTTGGAAAAAGA
39527434 GGGCTTGGAAAAAGA
1 GGGCTTGGAAAAAGA
39527449 G
1 G
39527450 ATGATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.42, T:0.13
Consensus pattern (15 bp):
GGGCTTGGAAAAAGA
Found at i:39532102 original size:49 final size:48
Alignment explanation
Indices: 39532020--39532177 Score: 246
Period size: 49 Copynumber: 3.2 Consensus size: 48
39532010 CTTACTTTGA
* *
39532020 GAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGACCGATGTGAT
1 GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
39532067 GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
* *
39532116 GGATGTGAAAATGTGTATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
39532165 GAATGTGATAAGT
1 GAATGTGA-AAGT
39532178 CCCGAAGGGC
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
47 13 0.13
49 85 0.84
50 3 0.03
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (48 bp):
GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
Found at i:39532351 original size:37 final size:37
Alignment explanation
Indices: 39532295--39532373 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
39532285 CCGAGCTCTA
* *
39532295 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTTTGTCCGGGT
*
39532332 AAGACCCGATAACTTCGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTTTGTCCGGGT
*
39532369 GAGAC
1 AAGAC
39532374 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTTTGTCCGGGT
Found at i:39536215 original size:49 final size:49
Alignment explanation
Indices: 39536110--39536399 Score: 250
Period size: 49 Copynumber: 5.8 Consensus size: 49
39536100 AATAATAACA
* *
39536110 TGCCAAAGCCATGTCCTAGACATGGTCTTACAT-GGATGTTTTCTGTAC
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATGTTATCTGTAC
*
39536158 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATGTTTTCTGTAC
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATGTTATCTGTAC
* * * * **
39536207 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGA-GTTCTCATATTGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATGTTATC-T-GTAC
* * ** * * *
39536257 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG--G
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA--TGTTATCT-GTAC
* * *
39536307 TG-CAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCT-TAA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA--TGT--T-ATCTGTAC
39536359 TGATTCCAATGCCATGTCCTAGACATGGTCTTACATGGGAT
1 TG---CCAATGCCATGTCCTAGACATGGTCTTACATGGGAT
39536400 CTCTTTACCC
Statistics
Matches: 201, Mismatches: 26, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
48 37 0.18
49 85 0.42
50 35 0.17
52 7 0.03
53 3 0.01
54 1 0.00
56 33 0.16
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (49 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATGTTATCTGTAC
Found at i:39536225 original size:97 final size:99
Alignment explanation
Indices: 39536110--39536399 Score: 250
Period size: 99 Copynumber: 2.9 Consensus size: 99
39536100 AATAATAACA
* *
39536110 TGCCAAAGCCATGTCCTAGACATGGTCTTACAT-GGATGTTTTC-T-GTACTGCCAATGCCATGT
1 TGCCAAAGCCATATCCTAGACATGGTCTTACATGGGA-GTTCTCATAGTACTGCCAATGCCATGT
*
39536172 CCTAGACATGGTCTTACATGGGATGTTTTCTGTAC
65 CCCAGACATGGTCTTACATGGGATGTTTTCTGTAC
* * * ** *
39536207 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATGTC
1 TGCCAAAGCCATATCCTAGACATGGTCTTACATGGGAGTTCTCATAGTACTGCCAATGCCATGTC
** * ** *
39536272 CCAGACATGGTCTTACGGGGGACCTCTCATCTCG--G
66 CCAGACATGGTCTTACATGGGA--TGTTTTCT-GTAC
* * ** * *
39536307 TG-CAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTTAATGATTCCAATGC
1 TGCCAAAGCCATATCCTAGACATGGTCTTACATGGGAGTTCTCAT-A--GTACTG---CCAATGC
*
39536371 CATGTCCTAGACATGGTCTTACATGGGAT
60 CATGTCCCAGACATGGTCTTACATGGGAT
39536400 CTCTTTACCC
Statistics
Matches: 155, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
97 35 0.23
98 4 0.03
99 71 0.46
100 3 0.02
101 5 0.03
102 5 0.03
103 1 0.01
105 31 0.20
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (99 bp):
TGCCAAAGCCATATCCTAGACATGGTCTTACATGGGAGTTCTCATAGTACTGCCAATGCCATGTC
CCAGACATGGTCTTACATGGGATGTTTTCTGTAC
Found at i:39543810 original size:50 final size:50
Alignment explanation
Indices: 39543682--39543969 Score: 294
Period size: 50 Copynumber: 5.8 Consensus size: 50
39543672 GATAATAACA
* * * ** * * *
39543682 TGCCAAAGCCATGTCCCGGACATGGTCTTACATAGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * ** *
39543731 TGCCAATGCCATATCCCAGATATGATCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * ***
39543781 TGCCCATGCCATGTCCAAGACATGGTCTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * *
39543831 TGCTAACGCCATGT-CCAGACATGGTCTTACATGGGACCTGTTATCTAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
39543880 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
39543930 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT
39543970 TTTTACCCAA
Statistics
Matches: 196, Mismatches: 40, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
48 1 0.01
49 76 0.39
50 119 0.61
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:39543860 original size:99 final size:100
Alignment explanation
Indices: 39543731--39543969 Score: 302
Period size: 99 Copynumber: 2.4 Consensus size: 100
39543721 TTTCTTGTAC
* * * * ** * *
39543731 TGCCAATGCCATATCCCAGATATGATCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGT-
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAATGCCATGTC
**
39543795 CCAAGACATGGTCTTATGGGGGACCTCTCATCTCGG
66 CCAA-ACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * *
39543831 TGCTAACGCCATGT-CCAGACATGGTCTTACATGGGACCTGTTATCTAGGTGCCAATGCCATGTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAATGCCATGTC
* *
39543895 CCAAACATGGTCTTACATGGGACCTCTTATCTCGG
66 CCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
*
39543930 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCT
39543970 TTTTACCCAA
Statistics
Matches: 119, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
99 80 0.67
100 39 0.33
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (100 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAATGCCATGTC
CCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:39543959 original size:149 final size:148
Alignment explanation
Indices: 39543689--39543959 Score: 357
Period size: 149 Copynumber: 1.8 Consensus size: 148
39543679 ACATGCCAAA
* * * *
39543689 GCCATGTCCCGGACATGGTCTTACATAGGATGTTTCTTGTACTGCCAATGCCATATCCCAGATAT
1 GCCATGTCCCAGACATGGTCTTACATAGGATGTTTCTAG-ACTGCCAATGCCATATCCCAAACAT
** * *
39543754 GATCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCAAGACATGGTCTTATGGGGGAC
65 GATCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCAAGACATGGTCTTATGGGGGAC
39543819 CTCTCATCTCGGTGCTAAC
130 CTCTCATCTCGGTGCTAAC
* * *
39543838 GCCATGT-CCAGACATGGTCTTACATGGGACCTGTTATCTAG-GTGCCAATGCCATGTCCCAAAC
1 GCCATGTCCCAGACATGGTCTTACATAGGA--TGTT-TCTAGACTGCCAATGCCATATCCCAAAC
* * * *
39543901 ATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTA
63 ATGATCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCAAGACATGGTCTTA
39543960 CATAGGACCT
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
148 20 0.19
149 76 0.73
150 4 0.04
151 4 0.04
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (148 bp):
GCCATGTCCCAGACATGGTCTTACATAGGATGTTTCTAGACTGCCAATGCCATATCCCAAACATG
ATCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCAAGACATGGTCTTATGGGGGACC
TCTCATCTCGGTGCTAAC
Found at i:39550353 original size:50 final size:48
Alignment explanation
Indices: 39550230--39550364 Score: 132
Period size: 50 Copynumber: 2.8 Consensus size: 48
39550220 GATAATAACA
* * *
39550230 TGCCAAAGCCATGTCCCAGACATGGTCTTACAT--GATTTTTTTTGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATTTATATTG-AC
* * * *
39550277 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATTG-G
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-TT-T-ATATTGAC
* *
39550327 TGCCTATGCCATGTCCCAGACATGGTCCTACATGGGAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT
39550365 ATCTTTACCC
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
47 29 0.41
49 3 0.04
50 34 0.48
51 1 0.01
52 4 0.06
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.33
Consensus pattern (48 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATTTATATTGAC
Found at i:39554509 original size:30 final size:30
Alignment explanation
Indices: 39554470--39554531 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
39554460 TACATGAAAT
39554470 ACATAGAAAT-GAT-ATTACATGATATATTGAA
1 ACATAGAAATGGATGA-TACATG-TATA-TGAA
39554501 ACAT-GAAATGGATGATACATGTATATGAA
1 ACATAGAAATGGATGATACATGTATATGAA
39554530 AC
1 AC
39554532 TTGCTTAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 6 0.21
30 9 0.31
31 13 0.45
32 1 0.03
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (30 bp):
ACATAGAAATGGATGATACATGTATATGAA
Found at i:39554932 original size:107 final size:107
Alignment explanation
Indices: 39554744--39554957 Score: 374
Period size: 107 Copynumber: 2.0 Consensus size: 107
39554734 TTTCCGTGTT
* *
39554744 TTATAGTGAATTAGAAGCTCGTTCGGGTTGGAAGCTTGTCGAAACTATATCACACTATCCATCGG
1 TTATAGTGAATCAAAAGCTCGTTCGGGTTGGAAGCTTGTCGAAACTATATCACACTATCCATCGG
* *
39554809 CTCTTTTGGTATTTTCAGTTGGTTTATGTTTGGTTATAATGG
66 CTCTTTTGGTACTTTCAGTTGGTTTAGGTTTGGTTATAATGG
*
39554851 TTATAGTGAATCAAAAGCTCGTTCGGGTTGGAAGCTTGTCGGAACTATATCACACTATCCATCGG
1 TTATAGTGAATCAAAAGCTCGTTCGGGTTGGAAGCTTGTCGAAACTATATCACACTATCCATCGG
*
39554916 CTCTTTTTGTACTTTCAGTTGGTTTAGGTTTGGTTATAATGG
66 CTCTTTTGGTACTTTCAGTTGGTTTAGGTTTGGTTATAATGG
39554958 CATGTATAGG
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 101 1.00
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.39
Consensus pattern (107 bp):
TTATAGTGAATCAAAAGCTCGTTCGGGTTGGAAGCTTGTCGAAACTATATCACACTATCCATCGG
CTCTTTTGGTACTTTCAGTTGGTTTAGGTTTGGTTATAATGG
Found at i:39558530 original size:50 final size:50
Alignment explanation
Indices: 39558417--39558713 Score: 310
Period size: 50 Copynumber: 5.8 Consensus size: 50
39558407 ATTTGGGTAA
* *
39558417 AGAGATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCCTTGAGATTTAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA--T-G
* * *
39558473 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
39558523 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
39558573 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** ** * * **
39558623 AGAATTCCCATGTAAGACCAAATCTGAGATATGGCATTGGCA--GTTCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * *
39558672 AAACATCCCATGTAAGACCATGTCTGGGACTTGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39558714 TGTTATTATC
Statistics
Matches: 208, Mismatches: 32, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
48 1 0.00
49 36 0.17
50 127 0.61
51 1 0.00
53 3 0.01
55 2 0.01
56 38 0.18
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:39560328 original size:19 final size:19
Alignment explanation
Indices: 39560296--39560332 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39560286 CATTTTACGA
* *
39560296 CTCATCTTTTCTCTTTTCT
1 CTCATATTTCCTCTTTTCT
39560315 CTCATATTTCCTCTTTTC
1 CTCATATTTCCTCTTTTC
39560333 CACCATATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.59
Consensus pattern (19 bp):
CTCATATTTCCTCTTTTCT
Found at i:39562961 original size:20 final size:20
Alignment explanation
Indices: 39562936--39562975 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39562926 TTTATTGACT
* *
39562936 CCATTTTTGGTGATTTTTCA
1 CCATTTTTAGTGAATTTTCA
39562956 CCATTTTTAGTGAATTTTCA
1 CCATTTTTAGTGAATTTTCA
39562976 AAGTCACACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.53
Consensus pattern (20 bp):
CCATTTTTAGTGAATTTTCA
Found at i:39563340 original size:51 final size:52
Alignment explanation
Indices: 39563278--39563405 Score: 188
Period size: 52 Copynumber: 2.5 Consensus size: 52
39563268 GGATACCCGT
* * *
39563278 TGGCCTACACATAGTATCACCCTTGT-AGCCAAAGCTA-CCTTCTTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTGA-CCAAAGCTATCCTTCTTCACAAAG
* *
39563329 TGGCCTTCACATAGTACCACACTTGTGACCTAAGCTATCTTTCTTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCCTTCTTCACAAAG
39563381 TGGCCTTCACATAGTACCACACTTG
1 TGGCCTTCACATAGTACCACACTTG
39563406 AGTCATTAGT
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 31 0.44
52 39 0.56
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.28
Consensus pattern (52 bp):
TGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCCTTCTTCACAAAG
Found at i:39569907 original size:28 final size:28
Alignment explanation
Indices: 39569875--39569932 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
39569865 CGAATATGAT
*
39569875 CTCCCACGGTCTCGGTGTGAATACCCAA
1 CTCCCACGGTCTCGGTGCGAATACCCAA
39569903 CTCCCACGGTCTCGGTGCGAATACCCAA
1 CTCCCACGGTCTCGGTGCGAATACCCAA
39569931 CT
1 CT
39569933 GAAGCAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (28 bp):
CTCCCACGGTCTCGGTGCGAATACCCAA
Found at i:39572352 original size:51 final size:52
Alignment explanation
Indices: 39572275--39572403 Score: 163
Period size: 52 Copynumber: 2.5 Consensus size: 52
39572265 CGGATACCTG
* * *
39572275 GTGGCCTGCACATTGTACCACCCTTGT-AGCCAAAAATA-CCTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGA-CCAAAAATATCCTTCTTCACAAA
** * *
39572326 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTCTTCATAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAAATATCCTTCTTCACAAA
*
39572378 GTGGCCTTCACATGGTACCACACTTG
1 GTGGCCTTCACATAGTACCACACTTG
39572404 AGTCACTAGT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
51 31 0.46
52 37 0.54
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (52 bp):
GTGGCCTTCACATAGTACCACACTTGTGACCAAAAATATCCTTCTTCACAAA
Found at i:39574478 original size:40 final size:40
Alignment explanation
Indices: 39574434--39574531 Score: 187
Period size: 40 Copynumber: 2.5 Consensus size: 40
39574424 TATAACCAGA
39574434 GGCACGAGAGTGCAATCAGGGGTACTGAAGTACAAATAGG
1 GGCACGAGAGTGCAATCAGGGGTACTGAAGTACAAATAGG
39574474 GGCACGAGAGTGCAATCAGGGGTACTGAAGTACAAATAGG
1 GGCACGAGAGTGCAATCAGGGGTACTGAAGTACAAATAGG
*
39574514 GGCACGAGAGTGTAATCA
1 GGCACGAGAGTGCAATCA
39574532 TTCAATAATC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.35, C:0.15, G:0.35, T:0.15
Consensus pattern (40 bp):
GGCACGAGAGTGCAATCAGGGGTACTGAAGTACAAATAGG
Found at i:39574494 original size:20 final size:20
Alignment explanation
Indices: 39574434--39574531 Score: 87
Period size: 20 Copynumber: 4.9 Consensus size: 20
39574424 TATAACCAGA
39574434 GGCACGAGAGTGCAATCAGG
1 GGCACGAGAGTGCAATCAGG
* *
39574454 GGTACTGA-AGTACAAAT-AGG
1 GGCAC-GAGAGTGC-AATCAGG
39574474 GGCACGAGAGTGCAATCAGG
1 GGCACGAGAGTGCAATCAGG
* *
39574494 GGTACTGA-AGTACAAAT-AGG
1 GGCAC-GAGAGTGC-AATCAGG
*
39574514 GGCACGAGAGTGTAATCA
1 GGCACGAGAGTGCAATCA
39574532 TTCAATAATC
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
19 10 0.16
20 41 0.67
21 10 0.16
ACGTcount: A:0.35, C:0.15, G:0.35, T:0.15
Consensus pattern (20 bp):
GGCACGAGAGTGCAATCAGG
Found at i:39577127 original size:60 final size:61
Alignment explanation
Indices: 39576977--39577127 Score: 155
Period size: 60 Copynumber: 2.5 Consensus size: 61
39576967 GGCATACCTT
* * * *
39576977 TCTAGAGTTTTGCCATAAAGGCTGCCTTTTACATGTAGTACTCACCACAAAAGCTTTTATG
1 TCTAGAGTTTTGCCATAAAGGCTGCCCTTTACATCTAGTACTCACCAAAAAAGCTTTTATA
* * * * * * **
39577038 TCTAGATTTTTGCCACAAATGTTGTCCTTTACATCTAGT-TTC-GTAAAAAAGGCTTTCT-TA
1 TCTAGAGTTTTGCCATAAAGGCTGCCCTTTACATCTAGTACTCACCAAAAAA-GCTTT-TATA
39577098 TCTAGAGTTTTGCCATAAAGGCTGCCCTTT
1 TCTAGAGTTTTGCCATAAAGGCTGCCCTTT
39577128 TTTACTAGTG
Statistics
Matches: 71, Mismatches: 17, Indels: 5
0.76 0.18 0.05
Matches are distributed among these distances:
59 5 0.07
60 33 0.46
61 33 0.46
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (61 bp):
TCTAGAGTTTTGCCATAAAGGCTGCCCTTTACATCTAGTACTCACCAAAAAAGCTTTTATA
Found at i:39578737 original size:79 final size:78
Alignment explanation
Indices: 39578652--39578807 Score: 231
Period size: 79 Copynumber: 2.0 Consensus size: 78
39578642 CCATTGAACG
* *
39578652 ATCAATTAATTTGATTCATTCAGCTCAACTCCTTAAGTCCGCTCCAATGGCTGTTCGGGAACTCC
1 ATCAATTAATTTGATTCATTCAGCTCAACTCCTTAAGTCCACTCCAATGGCTATTCGGGAACTCC
39578717 AAATGTCCAAGCTA
66 AAATGT-CAAGCTA
* * * * *
39578731 ATCAATTAATTTGATTTATTTAGCTCAACTCTTTAAGTCCACTCTAATGGCTATTCGGGAACTTC
1 ATCAATTAATTTGATTCATTCAGCTCAACTCCTTAAGTCCACTCCAATGGCTATTCGGGAACTCC
*
39578796 AAGTGTCAAGCT
66 AAATGTCAAGCT
39578808 TCCAAGACTG
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
78 6 0.09
79 63 0.91
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (78 bp):
ATCAATTAATTTGATTCATTCAGCTCAACTCCTTAAGTCCACTCCAATGGCTATTCGGGAACTCC
AAATGTCAAGCTA
Found at i:39586960 original size:20 final size:20
Alignment explanation
Indices: 39586935--39586999 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
39586925 TACATTATCT
*
39586935 ACATTACTGGTGGCTTGTCC
1 ACATTACTGGTAGCTTGTCC
*
39586955 ACATTACT-GTCAGCTTGTCT
1 ACATTACTGGT-AGCTTGTCC
* * *
39586975 ACAATACTGGTAGCTAGTTC
1 ACATTACTGGTAGCTTGTCC
39586995 ACATT
1 ACATT
39587000 TCTTGCAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (20 bp):
ACATTACTGGTAGCTTGTCC
Found at i:39598438 original size:38 final size:38
Alignment explanation
Indices: 39598396--39598578 Score: 251
Period size: 38 Copynumber: 4.8 Consensus size: 38
39598386 ACACCAACAT
* * * * *
39598396 AAAGCCTGCTAGGAATAAAGCCTGAATAACACCAGCAC
1 AAAGCCTGCTAGGCACATAGCCTGAATATCACCGGCAC
39598434 AAAGCCTGCTAGGCACATAGCCCT-AATATCACCGGCAC
1 AAAGCCTGCTAGGCACATAG-CCTGAATATCACCGGCAC
39598472 AAAGCCTGCTAGGCACATAGCCTGAATATCACCGGCAC
1 AAAGCCTGCTAGGCACATAGCCTGAATATCACCGGCAC
* * * *
39598510 AAAGCCTACTAGGCACACAGCTTGAATATCACCGGTAC
1 AAAGCCTGCTAGGCACATAGCCTGAATATCACCGGCAC
* *
39598548 AAAGCCTACTAGGCACATAGCCCGAATATCA
1 AAAGCCTGCTAGGCACATAGCCTGAATATCA
39598579 TTACGTTTTT
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
37 3 0.02
38 125 0.95
39 3 0.02
ACGTcount: A:0.36, C:0.30, G:0.19, T:0.16
Consensus pattern (38 bp):
AAAGCCTGCTAGGCACATAGCCTGAATATCACCGGCAC
Found at i:39598515 original size:22 final size:22
Alignment explanation
Indices: 39598445--39598516 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
39598435 AAGCCTGCTA
*
39598445 GGCACATAGCCCT-AATATCACC
1 GGCACAAAG-CCTGAATATCACC
*
39598467 GGCACAAAGCCTG---CT-A--
1 GGCACAAAGCCTGAATATCACC
*
39598483 GGCACATAGCCTGAATATCACC
1 GGCACAAAGCCTGAATATCACC
39598505 GGCACAAAGCCT
1 GGCACAAAGCCT
39598517 ACTAGGCACA
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
16 12 0.32
18 1 0.03
19 2 0.05
20 1 0.03
21 3 0.08
22 19 0.50
ACGTcount: A:0.32, C:0.33, G:0.19, T:0.15
Consensus pattern (22 bp):
GGCACAAAGCCTGAATATCACC
Found at i:39604943 original size:19 final size:19
Alignment explanation
Indices: 39604934--39604972 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
39604924 TTTATCTTTG
39604934 TCTTTAATTTTAATTTTAA
1 TCTTTAATTTTAATTTTAA
39604953 TCTTTAATTTTAATTTTAA
1 TCTTTAATTTTAATTTTAA
39604972 T
1 T
39604973 GATAGTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
TCTTTAATTTTAATTTTAA
Found at i:39604945 original size:6 final size:6
Alignment explanation
Indices: 39604936--39604972 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
39604926 TATCTTTGTC
39604936 TTTAAT TTTAAT TTTAAT CTTTAAT TTTAAT TTTAAT
1 TTTAAT TTTAAT TTTAAT -TTTAAT TTTAAT TTTAAT
39604973 GATAGTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTAAT
Found at i:39605391 original size:13 final size:13
Alignment explanation
Indices: 39605373--39605397 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39605363 CCAAAATCTC
39605373 AAAATTTCTTCCA
1 AAAATTTCTTCCA
39605386 AAAATTTCTTCC
1 AAAATTTCTTCC
39605398 TTGTCGTAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATTTCTTCCA
Found at i:39611483 original size:29 final size:29
Alignment explanation
Indices: 39611442--39611682 Score: 93
Period size: 29 Copynumber: 8.3 Consensus size: 29
39611432 ACAAAGGTTT
*
39611442 ACAC-AAGACATTCCTTTAACTGAGATAG
1 ACACAAAGGCATTCCTTTAACTGAGATAG
* * *
39611470 ATACAAAGGTATTCATTTAACTGAGATAG
1 ACACAAAGGCATTCCTTTAACTGAGATAG
* * * * *
39611499 CCATAAAGGCATCCCTTTAACAGAGAT-C
1 ACACAAAGGCATTCCTTTAACTGAGATAG
** * * *
39611527 AC-CATAGAGATATTCATTTTACTAAGATAG
1 ACACA-A-AGGCATTCCTTTAACTGAGATAG
* * **
39611557 CCATAAAGGCACCCCTTTAA-TAGAGATCA-
1 ACACAAAGGCATTCCTTTAACT-GAGAT-AG
* * **
39611586 CCACAAAGACATTTGTTTAACTGAGATAG
1 ACACAAAGGCATTCCTTTAACTGAGATAG
* * *
39611615 TCATAAAGGCA-TCCTCTTAA-TAGAGATCG
1 ACACAAAGGCATTCCT-TTAACT-GAGATAG
* ** *
39611644 CCACAAAGGC-TTCCTTATAACAAAGATTG
1 ACACAAAGGCATTCCTT-TAACTGAGATAG
*
39611673 CCACAAAGGC
1 ACACAAAGGC
39611683 TACCTTTCAG
Statistics
Matches: 151, Mismatches: 48, Indels: 27
0.67 0.21 0.12
Matches are distributed among these distances:
27 1 0.01
28 11 0.07
29 134 0.89
30 4 0.03
31 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.25
Consensus pattern (29 bp):
ACACAAAGGCATTCCTTTAACTGAGATAG
Found at i:39611525 original size:58 final size:58
Alignment explanation
Indices: 39611454--39611642 Score: 193
Period size: 58 Copynumber: 3.3 Consensus size: 58
39611444 ACAAGACATT
* *
39611454 CCTTTAACTGAGAT-AGATACAAAGGTATTCATTTAACTGAGATAGCCATAAAGGCATC
1 CCTTTAACAGAGATCA-ATACAAAGATATTCATTTAACTGAGATAGCCATAAAGGCATC
** * * * * *
39611512 CCTTTAACAGAGATCACCATAGAGATATTCATTTTACTAAGATAGCCATAAAGGCACC
1 CCTTTAACAGAGATCAATACAAAGATATTCATTTAACTGAGATAGCCATAAAGGCATC
* ** * ** *
39611570 CCTTTAATAGAGATCACCACAAAGACATTTGTTTAACTGAGATAGTCATAAAGGCAT-
1 CCTTTAACAGAGATCAATACAAAGATATTCATTTAACTGAGATAGCCATAAAGGCATC
*
39611627 CCTCTTAATAGAGATC
1 CCT-TTAACAGAGATC
39611643 GCCACAAAGG
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
57 3 0.03
58 106 0.96
59 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (58 bp):
CCTTTAACAGAGATCAATACAAAGATATTCATTTAACTGAGATAGCCATAAAGGCATC
Found at i:39611648 original size:58 final size:58
Alignment explanation
Indices: 39611480--39611651 Score: 229
Period size: 58 Copynumber: 3.0 Consensus size: 58
39611470 ATACAAAGGT
* * * *
39611480 ATTCATTTAACTGAGATAGCCATAAAGGCATCCCTTTAACAGAGATCACCATAGAGAT
1 ATTCATTTAACTGAGATAGCCATAAAGGCATCCCTTTAATAGAGATCACCACAAAGAC
* * *
39611538 ATTCATTTTACTAAGATAGCCATAAAGGCACCCCTTTAATAGAGATCACCACAAAGAC
1 ATTCATTTAACTGAGATAGCCATAAAGGCATCCCTTTAATAGAGATCACCACAAAGAC
** * *
39611596 ATTTGTTTAACTGAGATAGTCATAAAGGCAT-CCTCTTAATAGAGATCGCCACAAAG
1 ATTCATTTAACTGAGATAGCCATAAAGGCATCCCT-TTAATAGAGATCACCACAAAG
39611652 GCTTCCTTAT
Statistics
Matches: 99, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
57 3 0.03
58 96 0.97
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (58 bp):
ATTCATTTAACTGAGATAGCCATAAAGGCATCCCTTTAATAGAGATCACCACAAAGAC
Found at i:39623995 original size:25 final size:25
Alignment explanation
Indices: 39623961--39624016 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
39623951 TAAAACTCAT
*
39623961 CATAAATTGACCTGTATCACTTCAA
1 CATAAATTGACCTATATCACTTCAA
39623986 CATAAATTGACCTATATCACTTCAA
1 CATAAATTGACCTATATCACTTCAA
39624011 CATAAA
1 CATAAA
39624017 CTTACAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.30
Consensus pattern (25 bp):
CATAAATTGACCTATATCACTTCAA
Found at i:39632243 original size:25 final size:25
Alignment explanation
Indices: 39632209--39632264 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
39632199 CAAAACTCAT
*
39632209 CATAAATTGACCTGTATCACTTCAA
1 CATAAATTGACCTATATCACTTCAA
39632234 CATAAATTGACCTATATCACTTCAA
1 CATAAATTGACCTATATCACTTCAA
39632259 CATAAA
1 CATAAA
39632265 CTTACCATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.30
Consensus pattern (25 bp):
CATAAATTGACCTATATCACTTCAA
Found at i:39635524 original size:5 final size:5
Alignment explanation
Indices: 39635514--39635541 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
39635504 TTTTTTTATA
39635514 AATTT AATTT AATTT AATTT AATTT AAT
1 AATTT AATTT AATTT AATTT AATTT AAT
39635542 CTTGTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:39641730 original size:20 final size:20
Alignment explanation
Indices: 39641705--39641745 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
39641695 AAAAATGAGA
39641705 AAAGATTCTATTTTTGTTGT
1 AAAGATTCTATTTTTGTTGT
39641725 AAAGATTCTATTTTTGTTGT
1 AAAGATTCTATTTTTGTTGT
39641745 A
1 A
39641746 GTGGATCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.54
Consensus pattern (20 bp):
AAAGATTCTATTTTTGTTGT
Found at i:39649746 original size:95 final size:94
Alignment explanation
Indices: 39649574--39649754 Score: 218
Period size: 95 Copynumber: 1.9 Consensus size: 94
39649564 CATTACCGAG
* * * * ** *
39649574 CTATGGTCTTACACAATCTACCCTATGTTTAACGTCTTGGCGGACTACCTCATGTTTATTGTCCC
1 CTATGGTCATACACAATCTACCCCATGTTTAACATCATGGCGGACTACAACATATTTATTGTCCC
* *
39649639 GACGGACTCCATATACTACCAAAGCCAAC
66 AACGAACTCCATATACTACCAAAGCCAAC
* * * *
39649668 CTATGGTCATACACAATCTAACCCCATGTTTAACATCATGGCTGATTATAACTTATTTATTGTCC
1 CTATGGTCATACACAATCT-ACCCCATGTTTAACATCATGGCGGACTACAACATATTTATTGTCC
* *
39649733 CAATGAACTCCATATGCTACCA
65 CAACGAACTCCATATACTACCA
39649755 TAGTCAAGCA
Statistics
Matches: 71, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
94 18 0.25
95 53 0.75
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (94 bp):
CTATGGTCATACACAATCTACCCCATGTTTAACATCATGGCGGACTACAACATATTTATTGTCCC
AACGAACTCCATATACTACCAAAGCCAAC
Found at i:39652862 original size:14 final size:14
Alignment explanation
Indices: 39652843--39652869 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39652833 CATTTCTTGG
39652843 TCGGTTCAGTTCAC
1 TCGGTTCAGTTCAC
39652857 TCGGTTCAGTTCA
1 TCGGTTCAGTTCA
39652870 ACTGGACCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (14 bp):
TCGGTTCAGTTCAC
Found at i:39672270 original size:21 final size:21
Alignment explanation
Indices: 39672246--39672291 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
39672236 TTTTAAAGGT
39672246 TAAATT-ATAAAGTTAT-TTAAG
1 TAAATTGATAAA--TATGTTAAG
39672267 TAAATTGATAAATATGTTAAG
1 TAAATTGATAAATATGTTAAG
39672288 TAAA
1 TAAA
39672292 AAAATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.13
21 15 0.65
22 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (21 bp):
TAAATTGATAAATATGTTAAG
Found at i:39680215 original size:5 final size:5
Alignment explanation
Indices: 39680205--39680240 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
39680195 TTTATACGTT
39680205 TTATA TTATA TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA T
39680241 CATTATACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:39681088 original size:16 final size:18
Alignment explanation
Indices: 39681054--39681090 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
39681044 ATTCTTATTT
*
39681054 AAATAAAATATAATCGTA
1 AAATAAAATATAATAGTA
39681072 AAATAAAATA-AA-AGTA
1 AAATAAAATATAATAGTA
39681088 AAA
1 AAA
39681091 ATTCATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
18 10 0.56
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (18 bp):
AAATAAAATATAATAGTA
Found at i:39684447 original size:16 final size:16
Alignment explanation
Indices: 39684426--39684457 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39684416 AACTTATTGC
*
39684426 AAAATTTTCCTTAGCA
1 AAAATTGTCCTTAGCA
39684442 AAAATTGTCCTTAGCA
1 AAAATTGTCCTTAGCA
39684458 GTGGATTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (16 bp):
AAAATTGTCCTTAGCA
Found at i:39690864 original size:35 final size:35
Alignment explanation
Indices: 39690818--39690887 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
39690808 AATAGATGAA
39690818 AGAATTATTGGTTTGTTTGGGTTATGTTTGACATT
1 AGAATTATTGGTTTGTTTGGGTTATGTTTGACATT
39690853 AGAATTATTGGTTTGTTTGGGTTATGTTTGACATT
1 AGAATTATTGGTTTGTTTGGGTTATGTTTGACATT
39690888 GTCATGTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.03, G:0.26, T:0.51
Consensus pattern (35 bp):
AGAATTATTGGTTTGTTTGGGTTATGTTTGACATT
Found at i:39692574 original size:51 final size:49
Alignment explanation
Indices: 39692404--39692590 Score: 187
Period size: 51 Copynumber: 3.7 Consensus size: 49
39692394 AGTGAAAGTG
* * *
39692404 ATGGTCACGTGTGTAGTATTATGTGCAGGCTACTACGTGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGG-ATGGT
** * * * * *
39692455 A-GGTTGCATGTGTAGTACTATGTGTAGGCTATTATGCGTACTGGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTAC-GGATGGT
* * *
39692504 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGGATGGT
*
39692555 AATGGTCACATGTGCAGTACTATGTGCAGGCTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
39692591 TGTGAACTAA
Statistics
Matches: 107, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
49 4 0.04
50 33 0.31
51 68 0.64
52 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.33
Consensus pattern (49 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACGGATGGT
Found at i:39692665 original size:45 final size:45
Alignment explanation
Indices: 39692601--39692686 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
39692591 TGTGAACTAA
* * *
39692601 ACATCATTGATTAGTAAGGTGGTTGTTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
39692646 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCA
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCA
39692687 TCGAGTATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
Found at i:39697772 original size:33 final size:33
Alignment explanation
Indices: 39697733--39697799 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
39697723 AGTTTTTGTA
39697733 TGTCTACAGAACTAAAGAATGATATCTAGATTT
1 TGTCTACAGAACTAAAGAATGATATCTAGATTT
39697766 TGTCTACAGAACTAAAGAATGATATCTAGATTT
1 TGTCTACAGAACTAAAGAATGATATCTAGATTT
39697799 T
1 T
39697800 TCTCCCTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTCTACAGAACTAAAGAATGATATCTAGATTT
Found at i:39701691 original size:17 final size:18
Alignment explanation
Indices: 39701650--39701691 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
39701640 CCTAACATAG
39701650 AAAAAAGAAAAATTAAGC
1 AAAAAAGAAAAATTAAGC
39701668 AAGAAAAG-AAAATT-AGC
1 AA-AAAAGAAAAATTAAGC
39701685 ATAAAAA
1 A-AAAAA
39701692 TTAGAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.36
18 9 0.41
19 5 0.23
ACGTcount: A:0.71, C:0.05, G:0.12, T:0.12
Consensus pattern (18 bp):
AAAAAAGAAAAATTAAGC
Found at i:39706811 original size:29 final size:29
Alignment explanation
Indices: 39706779--39707070 Score: 254
Period size: 29 Copynumber: 10.0 Consensus size: 29
39706769 TTCGACTATT
*
39706779 GAATATGAAAAGGGATGGTGACGAGCATC
1 GAATATGAAAAGGGATGGTGACGACCATC
* * * *
39706808 GAATATG-AAAGGAATAGCT-TCGACTATC
1 GAATATGAAAAGGGAT-GGTGACGACCATC
* * * * *
39706836 GAAATGTGAAAAGGGATAGCT-TCGGCTATC
1 G-AATATGAAAAGGGAT-GGTGACGACCATC
*
39706866 GATTATGAAAAGGGATGGTGACGACCATC
1 GAATATGAAAAGGGATGGTGACGACCATC
* *
39706895 -AACTATGGAAAGGAATGGTGACGACCATC
1 GAA-TATGAAAAGGGATGGTGACGACCATC
* * * *
39706924 GATTAATGAAAAGGGATAGCT-TCGACTATC
1 GAAT-ATGAAAAGGGAT-GGTGACGACCATC
*
39706954 GATTATGAAAAGGGATGGTGACGACCATC
1 GAATATGAAAAGGGATGGTGACGACCATC
*
39706983 -AACTATGGAAAGGGATGGTGACGACCATC
1 GAA-TATGAAAAGGGATGGTGACGACCATC
* **
39707012 GATTAATGAAAAGGGATGGTTTCGACCATC
1 GAAT-ATGAAAAGGGATGGTGACGACCATC
* *
39707042 GAATATGAAAAGGGATGGTTACAACCATC
1 GAATATGAAAAGGGATGGTGACGACCATC
39707071 ATTTAGCACA
Statistics
Matches: 216, Mismatches: 35, Indels: 24
0.79 0.13 0.09
Matches are distributed among these distances:
28 20 0.09
29 126 0.58
30 68 0.31
31 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (29 bp):
GAATATGAAAAGGGATGGTGACGACCATC
Found at i:39706936 original size:59 final size:58
Alignment explanation
Indices: 39706782--39707071 Score: 246
Period size: 59 Copynumber: 5.0 Consensus size: 58
39706772 GACTATTGAA
* * * * * * *
39706782 TATGAAAAGGGATGGTGACGAGCATCGAATATG-AAAGGAATAGCT-TCGACTATCGAAA
1 TATGAAAAGGGATGGTGACGACCATCGATTATGAAAAGGGAT-GGTGACGACCATC-AAT
* * * * * *
39706840 TGTGAAAAGGGATAGCT-TCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCAAC
1 TATGAAAAGGGAT-GGTGACGACCATCGATTATGAAAAGGGATGGTGACGACCATCAAT
* * * * * *
39706898 TATGGAAAGGAATGGTGACGACCATCGATTAATGAAAAGGGATAGCT-TCGACTATCGAT
1 TATGAAAAGGGATGGTGACGACCATCGATT-ATGAAAAGGGAT-GGTGACGACCATCAAT
* * * *
39706957 TATGAAAAGGGATGGTGACGACCATCAACTATGGAAAGGGATGGTGACGACCATCGAT
1 TATGAAAAGGGATGGTGACGACCATCGATTATGAAAAGGGATGGTGACGACCATCAAT
** * * *
39707015 TAATGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGATGGTTACAACCATCA
1 T-ATGAAAAGGGATGGTGACGACCATCGATTATGAAAAGGGATGGTGACGACCATCA
39707072 TTTAGCACAC
Statistics
Matches: 184, Mismatches: 40, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
57 4 0.02
58 69 0.38
59 109 0.59
60 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (58 bp):
TATGAAAAGGGATGGTGACGACCATCGATTATGAAAAGGGATGGTGACGACCATCAAT
Found at i:39706946 original size:88 final size:88
Alignment explanation
Indices: 39706755--39707071 Score: 437
Period size: 88 Copynumber: 3.6 Consensus size: 88
39706745 CATCGACCAC
* *
39706755 TGAAAAGGGATAGCTTCGACTATTGAATATGAAAAGGGATGGTGACGAGCATCGAA-TAT-GAAA
1 TGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATGGTGACGACCATC-AACTATGGAAA
* * *
39706818 GGAATAGCT-TCGACTATCGA--AA
65 GGAAT-GGTGACGACCATCGATTAA
* *
39706840 TGTGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGGAA
1 --TGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATGGTGACGACCATCAACTATGGAA
39706905 AGGAATGGTGACGACCATCGATTAA
64 AGGAATGGTGACGACCATCGATTAA
*
39706930 TGAAAAGGGATAGCTTCGACTATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGGAAAG
1 TGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATGGTGACGACCATCAACTATGGAAAG
*
39706995 GGATGGTGACGACCATCGATTAA
66 GAATGGTGACGACCATCGATTAA
* * * * *
39707018 TGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGATGGTTACAACCATCA
1 TGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATGGTGACGACCATCA
39707072 TTTAGCACAC
Statistics
Matches: 210, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
86 2 0.01
87 54 0.26
88 152 0.72
90 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (88 bp):
TGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATGGTGACGACCATCAACTATGGAAAG
GAATGGTGACGACCATCGATTAA
Found at i:39716816 original size:39 final size:39
Alignment explanation
Indices: 39716695--39716904 Score: 307
Period size: 39 Copynumber: 5.3 Consensus size: 39
39716685 GCTCCTCGTT
* * *
39716695 CAAATGACTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
39716735 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
*
39716775 CAAATGCCTTCGGGCTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
39716814 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
39716853 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
39716892 CAAATGCCTTCGG
1 CAAATGCCTTCGG
39716905 ATCTTAGTCC
Statistics
Matches: 159, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 112 0.70
40 45 0.28
41 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:39716949 original size:78 final size:79
Alignment explanation
Indices: 39716695--39716955 Score: 299
Period size: 78 Copynumber: 3.3 Consensus size: 79
39716685 GCTCCTCGTT
* * * *
39716695 CAAATGACTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGACTTAGCCC
39716758 GGAT-TTAGTAAC-TCGCA
62 GGATATTAGT-ACTTCGCA
* *
39716775 CAAATGCCTTCGGGCTTAGCCCGAAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGA-
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGACTTAGCCCGGAT
39716839 ATTAGTA-TCTCGCA
66 ATTAGTACT-TCGCA
*
39716853 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGA-CTTAGCCCGGA
*
39716918 TATT-GTCACTTAGCA
65 TATTAGT-ACTTCGCA
39716933 C-AA-G-CTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
39716956 CATCATTCAA
Statistics
Matches: 161, Mismatches: 10, Indels: 22
0.83 0.05 0.11
Matches are distributed among these distances:
77 8 0.05
78 87 0.54
79 42 0.26
80 23 0.14
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGACTTAGCCCGGAT
ATTAGTACTTCGCA
Found at i:39724568 original size:39 final size:39
Alignment explanation
Indices: 39724447--39724656 Score: 307
Period size: 39 Copynumber: 5.3 Consensus size: 39
39724437 GCTCCTCGTT
* *
39724447 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * * *
39724487 CAAATGCCTTCGGGACTTAACTCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
*
39724527 CAAATGCCTTCGGGCTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
39724566 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
39724605 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
39724644 CAAATGCCTTCGG
1 CAAATGCCTTCGG
39724657 ATCTTAGTCC
Statistics
Matches: 158, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 111 0.70
40 45 0.28
41 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:39724701 original size:78 final size:79
Alignment explanation
Indices: 39724447--39724707 Score: 292
Period size: 78 Copynumber: 3.3 Consensus size: 79
39724437 GCTCCTCGTT
* *
39724447 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTA-ACT
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGACTTAGAC-
39724509 CGGAT-TTAGTAAC-TCGCA
61 CGGATATTAGT-ACTTCGCA
* * *
39724527 CAAATGCCTTCGGGCTTAGCCCGAAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGA-
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGACTTAGACCGGAT
39724591 ATTAGTA-TCTCGCA
66 ATTAGTACT-TCGCA
*
39724605 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGA-CTTAGACCGGA
*
39724670 TATT-GTCACTTAGCA
65 TATTAGT-ACTTCGCA
39724685 C-AA-G-CTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
39724708 CATCATTCAA
Statistics
Matches: 161, Mismatches: 9, Indels: 24
0.83 0.05 0.12
Matches are distributed among these distances:
77 8 0.05
78 85 0.53
79 43 0.27
80 24 0.15
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGACTTAGACCGGAT
ATTAGTACTTCGCA
Found at i:39727175 original size:49 final size:51
Alignment explanation
Indices: 39727048--39727198 Score: 189
Period size: 51 Copynumber: 3.0 Consensus size: 51
39727038 TCGTCCATCC
* * * * *
39727048 ATAACACCATTTGTAGACAAGTCACCACTGATTTGCAGATAAACTACCACTA
1 ATAACA-CTTTTGTGGACAAGCCACCACTGATTTGCACATATACTACCACTA
* *
39727100 ATAACACTTTTGTGGACAAGCCACCACTGATATGAACATATACTACCACTA
1 ATAACACTTTTGTGGACAAGCCACCACTGATTTGCACATATACTACCACTA
* * *
39727151 TTAA-A-TTTTGTGGACAAGCCACCACTGATTTGCATATATACTGCCACT
1 ATAACACTTTTGTGGACAAGCCACCACTGATTTGCACATATACTACCACT
39727199 GCTTCCCCCT
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
49 39 0.45
50 1 0.01
51 41 0.47
52 6 0.07
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.28
Consensus pattern (51 bp):
ATAACACTTTTGTGGACAAGCCACCACTGATTTGCACATATACTACCACTA
Found at i:39757134 original size:50 final size:50
Alignment explanation
Indices: 39757026--39757223 Score: 189
Period size: 50 Copynumber: 3.8 Consensus size: 50
39757016 ATTTGGGTAA
* * * * *
39757026 AGAGATCCCATGTAAAACCATGTCTGGGACATGACATTGGCATCATTGAGGTTATG
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
* *
39757082 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
39757132 AGAGGTCCCCCGTAAGATCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * * *
39757182 CGAACTCCCACGTAAGACCATATCTGGGATATGCCATTGGCA
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
39757224 GTATAAGAAA
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 80 0.66
52 1 0.01
53 2 0.02
55 1 0.01
56 38 0.31
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:39758697 original size:20 final size:20
Alignment explanation
Indices: 39758672--39758711 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39758662 CGTAAAATGA
*
39758672 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
39758692 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
39758712 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:39758701 original size:34 final size:35
Alignment explanation
Indices: 39758657--39758723 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
39758647 CAGTAAAATA
*
39758657 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
39758691 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
39758724 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:39758727 original size:14 final size:15
Alignment explanation
Indices: 39758651--39758727 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
39758641 GATTGCCAGT
* *
39758651 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
39758665 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
39758679 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
39758699 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
39758714 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
39758728 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:39765364 original size:50 final size:50
Alignment explanation
Indices: 39765241--39765413 Score: 172
Period size: 50 Copynumber: 3.5 Consensus size: 50
39765231 AAGGTCCTAT
* * ** *
39765241 GTAAGACCATGTCTGGGACATAGCGTTGGCACCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCAC
* * *
39765291 GTAAGACCATGTCTGGGACATGGCATGGGCATCGATATGAGAACTCCCAC
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCAC
* * * * *
39765341 GTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAGA-AACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAAC-TCCCAC
* *
39765390 GTAATACTATGTCTGGGACATGGC
1 GTAAGACCATGTCTGGGACATGGC
39765414 TTTGACATGT
Statistics
Matches: 103, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
48 4 0.04
49 29 0.28
50 70 0.68
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCAC
Found at i:39765413 original size:49 final size:50
Alignment explanation
Indices: 39765179--39765413 Score: 165
Period size: 50 Copynumber: 4.6 Consensus size: 50
39765169 GGTAAAGAGA
* * * *
39765179 TCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCATTGAGGTTATGA-AAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATGGGCATC---GA---TATGAGAA-C
* * * * * * * **
39765235 TCCTATGTAAGACCATGTCTGGGACATAGCGTTGGCACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATGGGCATCGATATGAGAAC
*
39765285 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCATCGATATGAGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATGGGCATCGATATGAGAAC
* * *
39765335 TCCCACGTAAGACCATATCTGGGATATGGCATTGGCAGTAC-A-A-GA-AAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATGGGCA-T-CGATATGAGAAC
* * *
39765383 ATCCCATGTAATACTATGTCTGGGACATGGC
1 -TCCCACGTAAGACCATGTCTGGGACATGGC
39765414 TTTGACATGT
Statistics
Matches: 149, Mismatches: 26, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
48 3 0.02
49 27 0.18
50 79 0.53
51 3 0.02
52 1 0.01
53 2 0.01
56 34 0.23
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATGGGCATCGATATGAGAAC
Found at i:39765773 original size:14 final size:15
Alignment explanation
Indices: 39765746--39765779 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39765736 CTTACTAAGC
39765746 TTTATTCTTACTTCT
1 TTTATTCTTACTTCT
*
39765761 TTTATT-TTCCTTCT
1 TTTATTCTTACTTCT
39765775 TTTAT
1 TTTAT
39765780 AGTATTGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTCTTACTTCT
Found at i:39769564 original size:47 final size:48
Alignment explanation
Indices: 39769425--39769564 Score: 122
Period size: 48 Copynumber: 2.9 Consensus size: 48
39769415 CCAGCACATA
* ** * ** *
39769425 TGTGGACAAAGCCACCAAATTTTTAGACAACCTACCAAAACACATAGT
1 TGTGGACAAAGCCACCAAAATCGTAGAAAAGATTCCAAAACACATAGT
** * * *
39769473 TGTGGACAAAGCCACTGAAATCGTAGGAAAGCTTCCAATACACATAGT
1 TGTGGACAAAGCCACCAAAATCGTAGAAAAGATTCCAAAACACATAGT
* * *
39769521 TGTGGTC-AAGCCACCAAAATTGTAGAAAATATGT-CAAAACACAT
1 TGTGGACAAAGCCACCAAAATCGTAGAAAAGAT-TCCAAAACACAT
39769565 TCATGGATAA
Statistics
Matches: 73, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
47 28 0.38
48 45 0.62
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (48 bp):
TGTGGACAAAGCCACCAAAATCGTAGAAAAGATTCCAAAACACATAGT
Found at i:39771749 original size:28 final size:28
Alignment explanation
Indices: 39771718--39771806 Score: 128
Period size: 28 Copynumber: 3.2 Consensus size: 28
39771708 AATAACAGTA
*
39771718 CAGTGTGGGCCCTAGCCCAATACAGAAT
1 CAGTGTGGGCCTTAGCCCAATACAGAAT
*
39771746 CAGTGTGGGCTTTAGCCCAATACAGAAT
1 CAGTGTGGGCCTTAGCCCAATACAGAAT
39771774 CAGTGTGGGCCTTAGCCTC-ATACAGTAA-
1 CAGTGTGGGCCTTAGCC-CAATACAG-AAT
39771802 CAGTG
1 CAGTG
39771807 CGATAATTGG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
28 53 0.95
29 3 0.05
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (28 bp):
CAGTGTGGGCCTTAGCCCAATACAGAAT
Found at i:39776117 original size:10 final size:10
Alignment explanation
Indices: 39776102--39776127 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
39776092 TCTAACTTCA
39776102 TCATTTATGT
1 TCATTTATGT
39776112 TCATTTATGT
1 TCATTTATGT
39776122 TCATTT
1 TCATTT
39776128 GATTCAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.08, T:0.62
Consensus pattern (10 bp):
TCATTTATGT
Found at i:39785911 original size:20 final size:20
Alignment explanation
Indices: 39785886--39785924 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39785876 AATGAGAAGA
39785886 AGAAAG-AAGAATGAAAAAAG
1 AGAAAGCAAG-ATGAAAAAAG
39785906 AGAAAGCAAGATGAAAAAA
1 AGAAAGCAAGATGAAAAAA
39785925 TCAGAATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.69, C:0.03, G:0.23, T:0.05
Consensus pattern (20 bp):
AGAAAGCAAGATGAAAAAAG
Found at i:39785930 original size:21 final size:20
Alignment explanation
Indices: 39785886--39785930 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
39785876 AATGAGAAGA
*
39785886 AGAAAGAAGAATGAAAAAAG
1 AGAAAGAAGAATGAAAAAAC
39785906 AGAAAGCAAG-ATGAAAAAATC
1 AGAAAG-AAGAATGAAAAAA-C
39785927 AGAA
1 AGAA
39785931 TGGAAAAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.67, C:0.04, G:0.22, T:0.07
Consensus pattern (20 bp):
AGAAAGAAGAATGAAAAAAC
Found at i:39788328 original size:173 final size:174
Alignment explanation
Indices: 39788026--39788350 Score: 499
Period size: 173 Copynumber: 1.9 Consensus size: 174
39788016 GTGAAGATAA
* * * *
39788026 AAAACAAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTAAAGATACCAGATTTTTCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCAGTTGCAGTGGAGCTGGTTAAAGATACCAGATCTTGCCTTCCT
* * *
39788091 GTATTAACAGCGAAGCAGATCGAAAACAAAGTCTTACCTCCATCGTTTGCATTGGAGCTGGTTAA
66 GCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTACCTCCATCGTTTGCAGTGGAGCTGGTTAA
*
39788156 AGA-AGCAGATCTTTCCGTCCTACATTAACAGCGAAGCAGATCG
131 AGATAGCAGATCTTTCCCTCCTACATTAACAGCGAAGCAGATCG
* * * *
39788199 AAAACGAAGTCTTGCCTCCATCAGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCAGTTGCAGTGGAGCTGGTTAAAGATACCAGATCTTGCCTTCCT
* * * *
39788264 GCGTTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCATCGTTTGCAGTGGAGTTGGTTAA
66 GCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTACCTCCATCGTTTGCAGTGGAGCTGGTTAA
39788329 AGATAGCAGATCTTTCCCTCCT
131 AGATAGCAGATCTTTCCCTCCT
39788351 GCGTCGACAG
Statistics
Matches: 135, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
173 118 0.87
174 17 0.13
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (174 bp):
AAAACAAAGCCTTGCCTCCATCAGTTGCAGTGGAGCTGGTTAAAGATACCAGATCTTGCCTTCCT
GCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTACCTCCATCGTTTGCAGTGGAGCTGGTTAA
AGATAGCAGATCTTTCCCTCCTACATTAACAGCGAAGCAGATCG
Found at i:39788354 original size:87 final size:87
Alignment explanation
Indices: 39788026--39788352 Score: 469
Period size: 87 Copynumber: 3.8 Consensus size: 87
39788016 GTGAAGATAA
* * * *
39788026 AAAACAAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTAAAGATACCAGATTTTTCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGTTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTTCCTTCCT
*
39788091 GTATTAACAGCGAAGCAGATCG
66 GCATTAACAGCGAAGCAGATCG
* * * *
39788113 AAAACAAAGTCTTACCTCCATCGTTTGCATTGGAGCTGGTTAAAGA-AGCAGATCTTTCCGTCCT
1 AAAACAAAGCCTTGCCTCCATCGTTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTTCCTTCCT
*
39788177 ACATTAACAGCGAAGCAGATCG
66 GCATTAACAGCGAAGCAGATCG
* * * *
39788199 AAAACGAAGTCTTGCCTCCATCAG-TTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCC
1 AAAACAAAGCCTTGCCTCCATC-GTTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTTCCTTCC
*
39788263 TGCGTTAACAGCGAAGCAGATCG
65 TGCATTAACAGCGAAGCAGATCG
* * *
39788286 AAAACGAAGCCTTGCCTCCATCGTTTGCAGTGGAGTTGGTTAAAGATAGCAGATCTTTCCCTCCT
1 AAAACAAAGCCTTGCCTCCATCGTTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTTCCTTCCT
39788351 GC
66 GC
39788353 GTCGACAGTG
Statistics
Matches: 214, Mismatches: 23, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
86 76 0.36
87 138 0.64
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (87 bp):
AAAACAAAGCCTTGCCTCCATCGTTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTTCCTTCCT
GCATTAACAGCGAAGCAGATCG
Found at i:39788562 original size:44 final size:45
Alignment explanation
Indices: 39788464--39788563 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 45
39788454 TGGAAATTGC
** *
39788464 AGATCTTATCTCATTGAGATTACAGCGGAGCGGATTGAAGCTGAT
1 AGATCTTATCTCATTGAGATTACAGCGGAGCGGATTGAAAATGAA
* * * *
39788509 A-ATCCTATCTCCTTGTGATTACAGTGGAGCGGATT-AAAAT-AA
1 AGATCTTATCTCATTGAGATTACAGCGGAGCGGATTGAAAATGAA
39788551 AGGATCTTATCTC
1 A-GATCTTATCTC
39788564 TCTGAAGTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
42 2 0.04
43 3 0.07
44 39 0.87
45 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (45 bp):
AGATCTTATCTCATTGAGATTACAGCGGAGCGGATTGAAAATGAA
Found at i:39788575 original size:44 final size:43
Alignment explanation
Indices: 39788514--39788692 Score: 114
Period size: 44 Copynumber: 4.1 Consensus size: 43
39788504 CTGATAATCC
* * *
39788514 TATCTCCTTGTGATTACAGTGGAGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-AAGGATCT
* * * *** *
39788558 TATCTCTCTGA-AGTTACAGTAGAGTAGA-TCGCATCAGG-TCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAAGGATCT
* * ** * *
39788599 TATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCT-AGTAATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAAG-GATCT
* * *
39788643 TATCTCCCTGAGATTATAGTGGAGCGGATTAAAGTAAAGGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-AAGGATCT
39788687 TATCTC
1 TATCTC
39788693 TTTGAAGTTA
Statistics
Matches: 98, Mismatches: 29, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
41 24 0.24
42 7 0.07
43 8 0.08
44 57 0.58
45 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (43 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAGGATCT
Found at i:39788699 original size:129 final size:129
Alignment explanation
Indices: 39788467--39788741 Score: 426
Period size: 129 Copynumber: 2.1 Consensus size: 129
39788457 AAATTGCAGA
** * * * *
39788467 TCTTATCTCATTGAGATTACAGCGGAGCGGATTGAAGCTGATAATCCTATCTCCTTGTGATTACA
1 TCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTGATAATCCTATCTCCCTGAGATTACA
*
39788532 GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
66 GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGG
*
39788596 TCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCT-AGTAATCCTATCTCCCTGAGATTAT
1 TCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTGA-TAATCCTATCTCCCTGAGATTAC
* * *
39788660 AGTGGAGCGGATTAAAGTAAAGGATCTTATCTCTTTGAAGTTACAGTAGAGTAGATCATATCAGG
65 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGG
*
39788725 TCTTATCTTCCTGAGAT
1 TCTTATCTCCCTGAGAT
39788742 CACGGTGGAA
Statistics
Matches: 133, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
128 1 0.01
129 132 0.99
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (129 bp):
TCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTGATAATCCTATCTCCCTGAGATTACA
GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGG
Found at i:39788856 original size:50 final size:50
Alignment explanation
Indices: 39788799--39788958 Score: 178
Period size: 50 Copynumber: 3.2 Consensus size: 50
39788789 GTAGTGGGAC
*
39788799 AGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
* * * * * * * ** ** *
39788849 AGATTAAAGCTACAACAGCGAATCTTACCTCCCAGGTGA-TGCAGTGGAAC
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCC-CGACATTGCAGTTCAAA
39788899 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
*
39788949 ATATTAAAGC
1 AGATTAAAGC
39788959 TACAACAGCG
Statistics
Matches: 82, Mismatches: 26, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
49 2 0.02
50 78 0.95
51 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
Found at i:39788943 original size:100 final size:100
Alignment explanation
Indices: 39788770--39789012 Score: 387
Period size: 100 Copynumber: 2.4 Consensus size: 100
39788760 AGAATTACAT
* * * *
39788770 ATCTTGCCTCCCAGGTGATGTAGTGGGACAGATTAAAACCACATCGGTGAATCTTGCTTCCCCGA
1 ATCTTACCTCCCAGGTGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
39788835 CATTGCAGTTCAAAAGATTAAAGCTACAACAGCGA
66 CATTGCAGTTCAAAAGATTAAAGCTACAACAGCGA
39788870 ATCTTACCTCCCAGGTGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
1 ATCTTACCTCCCAGGTGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
*
39788935 CATTGCAGTTCAAAATATTAAAGCTACAACAGCGA
66 CATTGCAGTTCAAAAGATTAAAGCTACAACAGCGA
* ** ** *
39788970 ATCTTACCTCTCAGGCAATGCAGCAGAACATATTAAAGCCACA
1 ATCTTACCTCCCAGGTGATGCAGTGGAACAGATTAAAGCCACA
39789013 ACGGCAAATC
Statistics
Matches: 132, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 132 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (100 bp):
ATCTTACCTCCCAGGTGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
CATTGCAGTTCAAAAGATTAAAGCTACAACAGCGA
Found at i:39788972 original size:50 final size:50
Alignment explanation
Indices: 39788818--39788974 Score: 181
Period size: 50 Copynumber: 3.1 Consensus size: 50
39788808 CCACATCGGT
39788818 GAATCTTGCTTCCCCGACATTGCAGTTCAAAAGATTAAAGCTACAACAGC
1 GAATCTTGCTTCCCCGACATTGCAGTTCAAAAGATTAAAGCTACAACAGC
* * * ** ** * * * * *
39788868 GAATCTTACCTCCCAGGTGA-TGCAGTGGAACAGATTAAAGCCACATCGGT
1 GAATCTTGCTTCCC-CGACATTGCAGTTCAAAAGATTAAAGCTACAACAGC
*
39788918 GAATCTTGCTTCCCCGACATTGCAGTTCAAAATATTAAAGCTACAACAGC
1 GAATCTTGCTTCCCCGACATTGCAGTTCAAAAGATTAAAGCTACAACAGC
39788968 GAATCTT
1 GAATCTT
39788975 ACCTCTCAGG
Statistics
Matches: 80, Mismatches: 25, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
49 2 0.03
50 76 0.95
51 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (50 bp):
GAATCTTGCTTCCCCGACATTGCAGTTCAAAAGATTAAAGCTACAACAGC
Found at i:39788992 original size:50 final size:50
Alignment explanation
Indices: 39788838--39789026 Score: 166
Period size: 50 Copynumber: 3.8 Consensus size: 50
39788828 TCCCCGACAT
* **
39788838 TGCAGTTCAAAAGATTAAAGCTACAACAGCGAATCTTACCTCCCAGGTGA
1 TGCAGTTCAAAAGATTAAAGCCACAACAGCGAATCTTACCTCCCAGGCAA
** * * * * * * * * *
39788888 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTTCAAAAGATTAAAGCCACAACAGCGAATCTTACCTCCCAGGCAA
* * *
39788938 TGCAGTTCAAAATATTAAAGCTACAACAGCGAATCTTACCTCTCAGGCAA
1 TGCAGTTCAAAAGATTAAAGCCACAACAGCGAATCTTACCTCCCAGGCAA
* * *
39788988 TGCAG--CAGAACATATTAAAGCCACAACGGCAAATCTTAC
1 TGCAGTTCA-AA-AGATTAAAGCCACAACAGCGAATCTTAC
39789027 ATTCCAAAAG
Statistics
Matches: 106, Mismatches: 31, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
48 2 0.02
49 2 0.02
50 102 0.96
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (50 bp):
TGCAGTTCAAAAGATTAAAGCCACAACAGCGAATCTTACCTCCCAGGCAA
Found at i:39789288 original size:12 final size:12
Alignment explanation
Indices: 39789271--39789303 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
39789261 GCCCAAATCA
39789271 AATAAATAAAAT
1 AATAAATAAAAT
*
39789283 AATAAATATAAT
1 AATAAATAAAAT
39789295 AATAAATAA
1 AATAAATAA
39789304 TGAAAACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAAATAAAAT
Found at i:39789765 original size:16 final size:17
Alignment explanation
Indices: 39789744--39789776 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39789734 ACACACACAG
39789744 AATC-AATACAAAAAAA
1 AATCAAATACAAAAAAA
39789760 AATCAAAATACAAAAAA
1 AATC-AAATACAAAAAA
39789777 GGTGATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
18 11 0.73
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (17 bp):
AATCAAATACAAAAAAA
Found at i:39798470 original size:15 final size:16
Alignment explanation
Indices: 39798441--39798470 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39798431 CAAACATGCT
39798441 TTAACACATTATCAAA
1 TTAACACATTATCAAA
39798457 TTAACACA-TATCAA
1 TTAACACATTATCAA
39798471 TAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:39806748 original size:23 final size:23
Alignment explanation
Indices: 39806718--39806762 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
39806708 TGTTATGGAC
39806718 GAACTCATTTAAACCATGTATAT
1 GAACTCATTTAAACCATGTATAT
39806741 GAACTCATTTAAACCATGTATA
1 GAACTCATTTAAACCATGTATA
39806763 AATGTACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (23 bp):
GAACTCATTTAAACCATGTATAT
Found at i:39818779 original size:94 final size:95
Alignment explanation
Indices: 39818658--39818847 Score: 364
Period size: 95 Copynumber: 2.0 Consensus size: 95
39818648 TCTTGTTTAC
39818658 AACAATGATAGCTTAAATTTTATTTAAGCTA-GATGATTATTTTGACTAAATAATATTTATGTCA
1 AACAATGATAGCTTAAATTTTATTTAAGCTAGGATGATTATTTTGACTAAATAATATTTATGTCA
39818722 TTCATGCTTATAATGTTTGTTCCTCAATCG
66 TTCATGCTTATAATGTTTGTTCCTCAATCG
*
39818752 AACAATGATAGCTTAAATTTTATTTAAGCTAGGATGATTATTTTGACTAAATAATATTTATGTGA
1 AACAATGATAGCTTAAATTTTATTTAAGCTAGGATGATTATTTTGACTAAATAATATTTATGTCA
39818817 TTCATGCTTATAATGTTTGTTCCTCAATCG
66 TTCATGCTTATAATGTTTGTTCCTCAATCG
39818847 A
1 A
39818848 TCATGTTTTC
Statistics
Matches: 94, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 31 0.33
95 63 0.67
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (95 bp):
AACAATGATAGCTTAAATTTTATTTAAGCTAGGATGATTATTTTGACTAAATAATATTTATGTCA
TTCATGCTTATAATGTTTGTTCCTCAATCG
Found at i:39838765 original size:27 final size:27
Alignment explanation
Indices: 39838673--39838770 Score: 115
Period size: 27 Copynumber: 3.6 Consensus size: 27
39838663 CTTATTTGCG
* * *
39838673 AACACAGTTCTCCAAAACACATCTGCG
1 AACATAGTTCACCAAAACACATCTGCA
** * *
39838700 AACATAGTTCACCAAGTCAGACCTGCA
1 AACATAGTTCACCAAAACACATCTGCA
*
39838727 AACTTAGTTCACCAAAACACATCTGCA
1 AACATAGTTCACCAAAACACATCTGCA
*
39838754 AACATAGCTCACCAAAA
1 AACATAGTTCACCAAAA
39838771 GTATCTGTCA
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.41, C:0.31, G:0.10, T:0.18
Consensus pattern (27 bp):
AACATAGTTCACCAAAACACATCTGCA
Found at i:39842868 original size:54 final size:54
Alignment explanation
Indices: 39842810--39842919 Score: 177
Period size: 54 Copynumber: 2.0 Consensus size: 54
39842800 TCTGGTAAGG
*
39842810 TATCTTTCTAAGAGG-ATTTCGATTAGTATAGTTAATTAAAATTCGTGTTTATTA
1 TATCTTTCTAAGAGGAATTT-GATTAGTATAGTTAATTAAAATTCATGTTTATTA
* *
39842864 TATCTTTCTAGGAGGAATTTTATTAGTATAGTTAATTAAAATTCATGTTTATTA
1 TATCTTTCTAAGAGGAATTTGATTAGTATAGTTAATTAAAATTCATGTTTATTA
39842918 TA
1 TA
39842920 ACATTAGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 48 0.92
55 4 0.08
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (54 bp):
TATCTTTCTAAGAGGAATTTGATTAGTATAGTTAATTAAAATTCATGTTTATTA
Found at i:39846376 original size:19 final size:18
Alignment explanation
Indices: 39846347--39846391 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
39846337 ATAATATATA
*
39846347 AATAAAATTAATTTATTT
1 AATAAAATTAATTAATTT
39846365 AATAATAATTAATTAATTT
1 AATAA-AATTAATTAATTT
*
39846384 AATCAAAT
1 AATAAAAT
39846392 CCTTATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAAAATTAATTAATTT
Found at i:39848251 original size:27 final size:28
Alignment explanation
Indices: 39848193--39848261 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
39848183 AAATTTTAGA
*
39848193 TTGTTGGATTTTGATATATGTCTTGAAT
1 TTGTTGGATATTGATATATGTCTTGAAT
* *
39848221 TTGTTAGATATTGAT-TATGT-TTTAAT
1 TTGTTGGATATTGATATATGTCTTGAAT
39848247 CTTGTTGGATATTGA
1 -TTGTTGGATATTGA
39848262 ATTTATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 5 0.14
27 18 0.50
28 13 0.36
ACGTcount: A:0.23, C:0.03, G:0.20, T:0.54
Consensus pattern (28 bp):
TTGTTGGATATTGATATATGTCTTGAAT
Found at i:39848273 original size:35 final size:36
Alignment explanation
Indices: 39848229--39848305 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 36
39848219 ATTTGTTAGA
* *
39848229 TATTGATTATGTTTTAATCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAAAT
39848265 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAAAT
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAAAT
39848300 TATTGA
1 TATTGA
39848306 CAATGACAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 33 0.87
36 5 0.13
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.53
Consensus pattern (36 bp):
TATTGATTATGTTTTAAGCTTGTTGGATATTGAAAT
Found at i:39849642 original size:14 final size:15
Alignment explanation
Indices: 39849620--39849696 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 15
39849610 CAATCAAACA
39849620 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
39849634 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
39849649 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
39849669 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
39849683 CCGGAAAA-CATTTT
1 CCAGAAAATCATTTT
39849697 ACTGCCAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 23 0.45
15 14 0.27
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:39849661 original size:20 final size:20
Alignment explanation
Indices: 39849636--39849675 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39849626 AATATTTTCC
*
39849636 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
39849656 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
39849676 TCATTTTCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:39873986 original size:20 final size:20
Alignment explanation
Indices: 39873961--39874023 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
39873951 TTCAAAGTCT
39873961 TTCATACATACATATCTTGG
1 TTCATACATACATATCTTGG
* *
39873981 TTCATA-TTGA-ACA-CTAT--
1 TTCATACAT-ACATATCT-TGG
39873998 TTCATACATACATATCTTGG
1 TTCATACATACATATCTTGG
39874018 TTCATA
1 TTCATA
39874024 TTGAGCACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
17 7 0.22
18 6 0.19
19 6 0.19
20 13 0.41
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (20 bp):
TTCATACATACATATCTTGG
Found at i:39874001 original size:37 final size:37
Alignment explanation
Indices: 39873960--39874036 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
39873950 TTTCAAAGTC
*
39873960 TTTCATACATACATATCTTGGTTCATATTGAACACTA
1 TTTCATACATACATATCTTGGTTCATATTGAACACCA
*
39873997 TTTCATACATACATATCTTGGTTCATATTGAGCACCA
1 TTTCATACATACATATCTTGGTTCATATTGAACACCA
39874034 TTT
1 TTT
39874037 TTCATGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (37 bp):
TTTCATACATACATATCTTGGTTCATATTGAACACCA
Found at i:39874081 original size:26 final size:26
Alignment explanation
Indices: 39874051--39874107 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
39874041 TGTATTCATA
39874051 CATACATACACCATTTCAAAGTCTTT
1 CATACATACACCATTTCAAAGTCTTT
39874077 CATACATACACCATTTCAAAGTCTTT
1 CATACATACACCATTTCAAAGTCTTT
39874103 CATAC
1 CATAC
39874108 TCAGGACCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (26 bp):
CATACATACACCATTTCAAAGTCTTT
Found at i:39877438 original size:66 final size:65
Alignment explanation
Indices: 39877324--39877449 Score: 189
Period size: 66 Copynumber: 1.9 Consensus size: 65
39877314 CTATCACACC
** *
39877324 AAATAGACTCATAGAGTCAAACATGTCCCATAAGTGAAGCATAAAGCTAACACTCTCCAAGACAA
1 AAATAGACTCATAGAGTCAAACAACTCCCAAAAGTGAAGCATAAAGCTAACACTCTCCAAGACAA
* * *
39877389 AAATTGACTCATAGAGTCGAACAACTCCCAAAAAGTGAAGCATAAAGCTAACATTCTCCAA
1 AAATAGACTCATAGAGTCAAACAACTCCC-AAAAGTGAAGCATAAAGCTAACACTCTCCAA
39877450 CATAACAAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
65 25 0.46
66 29 0.54
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.19
Consensus pattern (65 bp):
AAATAGACTCATAGAGTCAAACAACTCCCAAAAGTGAAGCATAAAGCTAACACTCTCCAAGACAA
Found at i:39883099 original size:14 final size:15
Alignment explanation
Indices: 39883076--39883109 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39883066 AATTTAGTTG
*
39883076 ATAAAGAAAA-TAAA
1 ATAAACAAAAGTAAA
39883090 ATAAACAAAAGTAAA
1 ATAAACAAAAGTAAA
39883105 ATAAA
1 ATAAA
39883110 ATATAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (15 bp):
ATAAACAAAAGTAAA
Found at i:39886975 original size:36 final size:36
Alignment explanation
Indices: 39886928--39887037 Score: 116
Period size: 41 Copynumber: 2.9 Consensus size: 36
39886918 ATTGAAGTCT
*
39886928 CGATTGCACTAGCTCGATCTCTGTGGGATCTTTAGC
1 CGATTGCACTAGCTCGATCTCTGTGGGATCTTCAGC
*
39886964 CGATTGCACTAGCTCGATTGCACCT-TACCAGGGA-CTTCAGC
1 CGATTGCACTAGCTCGA-T-C-TCTGT----GGGATCTTCAGC
*
39887005 CGATTGCACTAGCTCAATCTCTGTGGGATCTTC
1 CGATTGCACTAGCTCGATCTCTGTGGGATCTTC
39887038 TACTTACTGT
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
35 4 0.07
36 21 0.34
37 1 0.02
38 4 0.07
39 4 0.07
40 1 0.02
41 22 0.36
42 4 0.07
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (36 bp):
CGATTGCACTAGCTCGATCTCTGTGGGATCTTCAGC
Found at i:39888543 original size:28 final size:28
Alignment explanation
Indices: 39888475--39888625 Score: 178
Period size: 28 Copynumber: 5.2 Consensus size: 28
39888465 AGTGACAATA
* *
39888475 CAGTGTGGGCCTCAGCCCAATATAGTAATAGT
1 CAGTGTGGGCCTTAGCCCAATACAG--A-A-T
39888507 ACAGTGTGGGCCTTAGCCCAATACAGAAT
1 -CAGTGTGGGCCTTAGCCCAATACAGAAT
* * *
39888536 CAATGTGGGCCTTAGCCCATTGCAGAAT
1 CAGTGTGGGCCTTAGCCCAATACAGAAT
* *
39888564 TAGTGTGGGCCTTATCCCAATACAGAAT
1 CAGTGTGGGCCTTAGCCCAATACAGAAT
39888592 CAGTGTGGGCCTTAGCCCAATACAGTAAT
1 CAGTGTGGGCCTTAGCCCAATACAG-AAT
39888621 -AGTGT
1 CAGTGT
39888626 AGTGCAATAA
Statistics
Matches: 105, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
28 76 0.72
29 4 0.04
30 1 0.01
31 1 0.01
33 23 0.22
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (28 bp):
CAGTGTGGGCCTTAGCCCAATACAGAAT
Found at i:39888756 original size:26 final size:27
Alignment explanation
Indices: 39888727--39888800 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 27
39888717 ACACACCAAT
*
39888727 ATCGCAGCAAAGCGGCCAGTAAT-AGC
1 ATCGCAGCAAAGCTGCCAGTAATCAGC
* *
39888753 ATCGCAGCAGAGCTGCCAGT-ATCAGT
1 ATCGCAGCAAAGCTGCCAGTAATCAGC
* *
39888779 ATCGGAGCAAAGCTACCAGTAA
1 ATCGCAGCAAAGCTGCCAGTAA
39888801 AAATATATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 2 0.05
26 37 0.93
27 1 0.03
ACGTcount: A:0.34, C:0.26, G:0.26, T:0.15
Consensus pattern (27 bp):
ATCGCAGCAAAGCTGCCAGTAATCAGC
Found at i:39889059 original size:27 final size:27
Alignment explanation
Indices: 39889039--39889302 Score: 207
Period size: 27 Copynumber: 10.0 Consensus size: 27
39889029 GGGTATAACA
*
39889039 GTCATTTTACCCTATAAGGGTATTTTG
1 GTCATTTTACCCTATAAGGGTATTTCG
* *
39889066 GTCATTTTACCCTATGAGAGTATTTCG
1 GTCATTTTACCCTATAAGGGTATTTCG
* ***
39889093 GTCATTTTACTCTACGGGGGTATTTCG
1 GTCATTTTACCCTATAAGGGTATTTCG
*
39889120 GTCATTTTACCTTATAAGGGTATTTCG
1 GTCATTTTACCCTATAAGGGTATTTCG
* *
39889147 GTCATTCTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATAAGGGTATTTCG
* * *
39889174 GTTATTTTACCC--T---GGAATTTCA
1 GTCATTTTACCCTATAAGGGTATTTCG
* * *** *
39889196 ATTATTTTACCCTACGGGGGTATTTCA
1 GTCATTTTACCCTATAAGGGTATTTCG
* ** * *
39889223 GTTATTTTACCCTATGGGGGGAATTTTG
1 GTCATTTTACCCTAT-AAGGGTATTTCG
* * * **
39889251 ATTATTTTACCTTATTGGGGTATTTCG
1 GTCATTTTACCCTATAAGGGTATTTCG
*
39889278 GTCATTTTATCCTAT-AGGGTATTTC
1 GTCATTTTACCCTATAAGGGTATTTC
39889303 AATCATCTAT
Statistics
Matches: 194, Mismatches: 37, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
22 18 0.09
25 1 0.01
26 9 0.05
27 144 0.74
28 22 0.11
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTATAAGGGTATTTCG
Found at i:39889255 original size:28 final size:28
Alignment explanation
Indices: 39889187--39889270 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 28
39889177 ATTTTACCCT
*
39889187 GGAATTTCAATTATTTTACCCTA-CGGG
1 GGAATTTTAATTATTTTACCCTATCGGG
* * * *
39889214 GGTATTTCAGTTATTTTACCCTATGGGG
1 GGAATTTTAATTATTTTACCCTATCGGG
* * *
39889242 GGAATTTTGATTATTTTACCTTATTGGG
1 GGAATTTTAATTATTTTACCCTATCGGG
39889270 G
1 G
39889271 TATTTCGGTC
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 21 0.45
28 26 0.55
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (28 bp):
GGAATTTTAATTATTTTACCCTATCGGG
Found at i:39894214 original size:39 final size:39
Alignment explanation
Indices: 39894097--39894397 Score: 407
Period size: 39 Copynumber: 7.6 Consensus size: 39
39894087 GCTCCTCGTT
* *
39894097 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
39894137 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
39894177 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
39894216 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
39894255 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
39894294 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
39894333 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCA
39894374 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
39894398 CATCATTCAA
Statistics
Matches: 243, Mismatches: 11, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
39 171 0.70
40 61 0.25
41 11 0.05
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:39902084 original size:79 final size:80
Alignment explanation
Indices: 39901973--39902156 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 80
39901963 GCTCCTCGTT
*
39901973 CAAATGCCTTCGGGACATAGCCCGGTAATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGG-AATAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACCC
*
39902036 GGAT-TTAGTAAC-TCGCA
63 GGATATT-GTAACTTAGCA
**
39902053 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAA-TAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
*
39902117 ATATTGTCACTTAGCA
65 ATATTGTAACTTAGCA
39902133 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39902157 CATCATTCAA
Statistics
Matches: 93, Mismatches: 5, Indels: 13
0.84 0.05 0.12
Matches are distributed among these distances:
78 16 0.17
79 56 0.60
80 21 0.23
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATTGTAACTTAGCA
Found at i:39902090 original size:39 final size:41
Alignment explanation
Indices: 39901973--39902156 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 41
39901963 GCTCCTCGTT
*
39901973 CAAATGCCTTCGGGACATAGCCCGGTAA-TAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-AATTAGTAATCTCGCA
* *
39902013 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAA-CTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
39902053 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
* * *
39902092 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAATC-TCGCA
39902133 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39902157 CATCATTCAA
Statistics
Matches: 127, Mismatches: 8, Indels: 19
0.82 0.05 0.12
Matches are distributed among these distances:
38 3 0.02
39 49 0.39
40 66 0.52
41 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
Found at i:39904346 original size:30 final size:30
Alignment explanation
Indices: 39904290--39904347 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39904280 TCTGAGCTTT
*
39904290 GGGGCAAAAGTGTAATTATGTAAAAGTTTA
1 GGGGCAAAAGTGTAATTATGCAAAAGTTTA
* * *
39904320 GGGGCAAAATTGTAATTTTGCCAAAGTT
1 GGGGCAAAAGTGTAATTATGCAAAAGTT
39904348 AGAGTCAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAGTGTAATTATGCAAAAGTTTA
Found at i:39904808 original size:50 final size:50
Alignment explanation
Indices: 39904688--39904929 Score: 317
Period size: 50 Copynumber: 4.7 Consensus size: 50
39904678 GGTAAAAAGA
39904688 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATGAGAGG
* *
39904744 TCCAATGTAAGACCATGTCTGGGACATGGAATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
39904794 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * **
39904844 TCCCCA--TAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 T-CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * *
39904893 TCCCATGTAAGACCATATCTAGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39904930 TGTTATTATC
Statistics
Matches: 169, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
48 4 0.02
49 39 0.23
50 82 0.49
51 4 0.02
53 3 0.02
55 2 0.01
56 35 0.21
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:39904890 original size:99 final size:102
Alignment explanation
Indices: 39904688--39904930 Score: 323
Period size: 99 Copynumber: 2.4 Consensus size: 102
39904678 GGTAAAAAGA
39904688 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCCAATGTA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGAGA--ATGAGAGGTCCAA-GTA
* **
39904753 AGACCATGTCTGGGACATGGAATTGGCACCGAGATGAGAGG
62 AGACCATGTCTGGGACATGGAATGGGCACCGAGATGAGAAC
* *
39904794 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GAG-ATGAGAGGTCCCCA-TAAGA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGAATGAGAGGT-CCAAGTAAGA
* *
39904855 CCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
65 CCATGTCTGGGACATGGAATGGGCACCGAGATGAGAAC
* * *
39904893 TCCCATGTAAGACCATATCTAGGACATGGCTTTGGCAT
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
39904931 GTTATTATCA
Statistics
Matches: 125, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
99 72 0.58
100 9 0.07
101 3 0.02
103 3 0.02
105 2 0.02
106 36 0.29
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (102 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGAATGAGAGGTCCAAGTAAGAC
CATGTCTGGGACATGGAATGGGCACCGAGATGAGAAC
Found at i:39917553 original size:50 final size:50
Alignment explanation
Indices: 39917445--39917730 Score: 252
Period size: 50 Copynumber: 5.6 Consensus size: 50
39917435 CTATCACCAC
* * **
39917445 GTAAGACCATGTCTGGGGCATGGCATTGGCATCCTTGGGATCATGAGAGGTCTAAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GA-GATGAGAGGTCCCAT
*
39917501 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGGTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCAT
* * **
39917551 GTAAGACCATGTCTGGGACATGGCGTTAGCACCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCAT
* * * ** * ** *
39917601 ATAAGACTATGTCTGGGACATGGCATGGGCACTAATATGAGAACTCTCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCAT
* * * * * * **
39917651 GTAAGACCATATCTGGGATATGACATTGGTA--GTACATGAAACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTCCCAT
*
39917700 GTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
39917731 TGTTATTGTC
Statistics
Matches: 188, Mismatches: 41, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
49 37 0.20
50 117 0.62
51 2 0.01
55 2 0.01
56 30 0.16
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCAT
Found at i:39922698 original size:19 final size:19
Alignment explanation
Indices: 39922674--39922711 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39922664 ATAATCTCTT
39922674 GTACATATCCCTATGTCAA
1 GTACATATCCCTATGTCAA
39922693 GTACATATCCCTATGTCAA
1 GTACATATCCCTATGTCAA
39922712 TTTAAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (19 bp):
GTACATATCCCTATGTCAA
Found at i:39928669 original size:24 final size:23
Alignment explanation
Indices: 39928641--39928685 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
39928631 TCGAATTTCC
* *
39928641 TTGATTTTCTCCCCAATCTCCTCA
1 TTGATTTGCTCCACAAT-TCCTCA
39928665 TTGATTTGCTCCACAATTCCT
1 TTGATTTGCTCCACAATTCCT
39928686 TCCAAGACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.18, C:0.33, G:0.07, T:0.42
Consensus pattern (23 bp):
TTGATTTGCTCCACAATTCCTCA
Found at i:39930789 original size:19 final size:20
Alignment explanation
Indices: 39930757--39930794 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
39930747 CAAGCTGACT
39930757 TTAGCTCAATTTCAGCTCCC
1 TTAGCTCAATTTCAGCTCCC
39930777 TTAGCTC-ATTTCAGCTCC
1 TTAGCTCAATTTCAGCTCC
39930795 AATCAGCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.18, C:0.34, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGCTCAATTTCAGCTCCC
Found at i:39930802 original size:20 final size:19
Alignment explanation
Indices: 39930759--39930804 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
39930749 AGCTGACTTT
* *
39930759 AGCTCAATTTCAGCTCCCTT
1 AGCTC-ATTTCAGCTCCATC
39930779 AGCTCATTTCAGCTCCAATC
1 AGCTCATTTCAGCTCC-ATC
39930799 AGCTCA
1 AGCTCA
39930805 CTTGAGCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.24, C:0.35, G:0.11, T:0.30
Consensus pattern (19 bp):
AGCTCATTTCAGCTCCATC
Found at i:39933244 original size:18 final size:18
Alignment explanation
Indices: 39933191--39933245 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
39933181 AACAGCATGT
39933191 GAAAAAGAAA-AAGAAAAA
1 GAAAAAGAAATAA-AAAAA
* * *
39933209 TAAAAAGAAATTACAAAA
1 GAAAAAGAAATAAAAAAA
*
39933227 GAAAAAGAAATCAAAAAA
1 GAAAAAGAAATAAAAAAA
39933245 G
1 G
39933246 TGATAGAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 29 0.97
19 1 0.03
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAATAAAAAAA
Found at i:39933281 original size:27 final size:24
Alignment explanation
Indices: 39933226--39933288 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
39933216 AAATTACAAA
**
39933226 AGAAAAAGAAATCAAAAAAGTGAT
1 AGAAAAAGAAATCAAAAAAGAAAT
39933250 AGAAAAAGAAATCGAAGAAAAGAAAAT
1 AGAAAAAGAAATC-AA-AAAAG-AAAT
*
39933277 TGAAAAAGAAAT
1 AGAAAAAGAAAT
39933289 TGAAATTGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.39
25 2 0.06
26 5 0.15
27 13 0.39
ACGTcount: A:0.68, C:0.03, G:0.17, T:0.11
Consensus pattern (24 bp):
AGAAAAAGAAATCAAAAAAGAAAT
Found at i:39933289 original size:12 final size:12
Alignment explanation
Indices: 39933227--39933293 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
39933217 AATTACAAAA
39933227 GAAAAAGAAATC
1 GAAAAAGAAATC
* ** *
39933239 AAAAAAGTGATA
1 GAAAAAGAAATC
39933251 GAAAAAGAAATC
1 GAAAAAGAAATC
*
39933263 GAAGAAAAGAAAATT
1 G-A-AAAAG-AAATC
*
39933278 GAAAAAGAAATT
1 GAAAAAGAAATC
39933290 GAAA
1 GAAA
39933294 TTGAGAAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
12 26 0.60
13 6 0.14
14 6 0.14
15 5 0.12
ACGTcount: A:0.67, C:0.03, G:0.18, T:0.12
Consensus pattern (12 bp):
GAAAAAGAAATC
Found at i:39933294 original size:18 final size:18
Alignment explanation
Indices: 39933273--39933311 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
39933263 GAAGAAAAGA
39933273 AAATTGA-AAAAGAAATTG
1 AAATTGAGAAAA-AAATTG
39933291 AAATTGAGAAAAAAATTG
1 AAATTGAGAAAAAAATTG
39933309 AAA
1 AAA
39933312 AATAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (18 bp):
AAATTGAGAAAAAAATTG
Found at i:39935441 original size:20 final size:19
Alignment explanation
Indices: 39935416--39935453 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
39935406 CAAGCTGAAT
39935416 TTAGCTAAATTTCAGCTCCC
1 TTAGCT-AATTTCAGCTCCC
*
39935436 TTAGCTCATTTCAGCTCC
1 TTAGCTAATTTCAGCTCC
39935454 AATCAGCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.37
Consensus pattern (19 bp):
TTAGCTAATTTCAGCTCCC
Found at i:39936487 original size:51 final size:51
Alignment explanation
Indices: 39936373--39936551 Score: 184
Period size: 51 Copynumber: 3.5 Consensus size: 51
39936363 GATCACGTTA
* * * * * * *
39936373 GTGTAGTACTATGTGAAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCAT
1 GTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAAT-GATCACAT
* *
39936423 GTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-TTCGATCACGT
1 GTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAAT-GATCACAT
* * * * * *
39936474 GTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCATAT
1 GTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATGATCACAT
39936525 GTGTAGTACTATGTGCAGGCTACTATG
1 GTGTAGTACTATGTGCAGGCTACTATG
39936552 TGAACCGAAC
Statistics
Matches: 108, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
50 32 0.30
51 74 0.69
52 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.31
Consensus pattern (51 bp):
GTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATGATCACAT
Found at i:39936552 original size:26 final size:26
Alignment explanation
Indices: 39936473--39936553 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
39936463 TTCGATCACG
39936473 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
39936499 CGTGTA-T-CGGATG-GTAATGG-T-CATA
1 TGTGTAGTAC-TATGTG-CA-GGCTAC-TA
39936524 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
39936550 TGTG
1 TGTG
39936554 AACCGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 3 0.08
25 15 0.38
26 19 0.47
27 3 0.08
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:39936628 original size:45 final size:45
Alignment explanation
Indices: 39936555--39936649 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
39936545 TACTATGTGA
* * *
39936555 ACCGAACATCATTGATTATTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGCTGGTTGCTATGTGCTGAATCC
39936600 ACCGAACATCATTGATTAATAAGCTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGCTGGTTGCTATGTGCTGAATCC
39936645 ACCGA
1 ACCGA
39936650 GTATCTGTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGCTGGTTGCTATGTGCTGAATCC
Found at i:39943829 original size:5 final size:5
Alignment explanation
Indices: 39943819--39943857 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
39943809 ACCCTCTCTT
* *
39943819 TTCTC TTCTC TTCTC TTCTC TTTTC TTCTTC TCCTC TTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTC-TC TTCTC TTC
39943858 ATTCCAGTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TTCTC
Found at i:39944581 original size:27 final size:27
Alignment explanation
Indices: 39944551--39944788 Score: 309
Period size: 27 Copynumber: 8.8 Consensus size: 27
39944541 CAAATGACTA
* *
39944551 AAATACCCCTAGAA-GGTAAAATGACCG
1 AAATACCCCCA-AAGGGTAAAATGATCG
** *
39944578 AAATACCCCTGGAA-GGTAAAATGACCG
1 AAATACCCC-CAAAGGGTAAAATGATCG
* * *
39944605 AAATACCCTCAGAGGTTAAAATGATCG
1 AAATACCCCCAAAGGGTAAAATGATCG
*
39944632 AAATACCCCCGAAGGGTAAAATGATCG
1 AAATACCCCCAAAGGGTAAAATGATCG
*
39944659 AAATACCCCCAAAGGGTAAAATGACCG
1 AAATACCCCCAAAGGGTAAAATGATCG
*
39944686 AAGTACCCCCAAAGGGTAAAATGATCG
1 AAATACCCCCAAAGGGTAAAATGATCG
*
39944713 AAATACCCCCAAAGGGTAAAATGATTG
1 AAATACCCCCAAAGGGTAAAATGATCG
*
39944740 AAATACCCCCAAAGGGTAAAATGATTG
1 AAATACCCCCAAAGGGTAAAATGATCG
* *
39944767 AAATACCTCCATAGGGTAAAAT
1 AAATACCCCCAAAGGGTAAAAT
39944789 AACTGTTATA
Statistics
Matches: 189, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
26 1 0.01
27 188 0.99
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (27 bp):
AAATACCCCCAAAGGGTAAAATGATCG
Found at i:39945040 original size:23 final size:24
Alignment explanation
Indices: 39944990--39945037 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
39944980 ACATATACCG
*
39944990 TTACTGGCAGCTTCGTTGCGATTCTA
1 TTACTGGCAGCTTCGCTGCGA-T-TA
*
39945016 TTACTGGCAGCTTTGCTGCGAT
1 TTACTGGCAGCTTCGCTGCGAT
39945038 ATTGGTGTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
25 1 0.05
26 19 0.95
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (24 bp):
TTACTGGCAGCTTCGCTGCGATTA
Found at i:39945186 original size:28 final size:28
Alignment explanation
Indices: 39945146--39945228 Score: 130
Period size: 28 Copynumber: 3.0 Consensus size: 28
39945136 ACTGTAATGG
39945146 TTACTGTATTGGGCTAAGGCCCACACTA
1 TTACTGTATTGGGCTAAGGCCCACACTA
* *
39945174 TTACTGTATTGGGCTAAGGCCCACATTG
1 TTACTGTATTGGGCTAAGGCCCACACTA
* *
39945202 TTACTATTTTGGGCTAAGGCCCACACT
1 TTACTGTATTGGGCTAAGGCCCACACT
39945229 GTACTGTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTA
Found at i:39946004 original size:20 final size:20
Alignment explanation
Indices: 39945981--39946040 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 20
39945971 AAATATGTTT
*
39945981 TTGAGTATTGTGATATATGC
1 TTGAGTATTATGATATATGC
* * * *
39946001 TTGAATGTTATGAGATATAC
1 TTGAGTATTATGATATATGC
*
39946021 --GAGTATTTTGATATATGC
1 TTGAGTATTATGATATATGC
39946039 TT
1 TT
39946041 AAAAGTGAAT
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
18 13 0.46
20 15 0.54
ACGTcount: A:0.28, C:0.05, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGAGTATTATGATATATGC
Done.