Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 53 of 187
Found at i:15846524 original size:25 final size:25
Alignment explanation
Indices: 15846508--15846594 Score: 90
Period size: 25 Copynumber: 3.5 Consensus size: 25
15846498 AAGCTCTTGC
15846508 GAGCAAATTATCGGGAAGCTCAAGA
1 GAGCAAATTATCGGGAAGCTCAAGA
* *
15846533 GAGCCAATTATCGGGAAGCTCATA-C
1 GAGCAAATTATCGGGAAGCTCA-AGA
* * *
15846558 GAGC-CATAAACGGGAAGCTCAAGA
1 GAGCAAATTATCGGGAAGCTCAAGA
15846582 GAGCCAAA-TATCG
1 GAG-CAAATTATCG
15846595 CGATGCTCTG
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
23 1 0.02
24 17 0.35
25 29 0.59
26 2 0.04
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (25 bp):
GAGCAAATTATCGGGAAGCTCAAGA
Found at i:15846585 original size:24 final size:24
Alignment explanation
Indices: 15846519--15846587 Score: 86
Period size: 24 Copynumber: 2.8 Consensus size: 24
15846509 AGCAAATTAT
* *
15846519 CGGGAAGCTCAAGAGAGCCAATTAT
1 CGGGAAGCTCAAGAGAGCC-ATAAA
*
15846544 CGGGAAGCTCATA-CGAGCCATAAA
1 CGGGAAGCTCA-AGAGAGCCATAAA
15846568 CGGGAAGCTCAAGAGAGCCA
1 CGGGAAGCTCAAGAGAGCCA
15846588 AATATCGCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 1 0.03
24 20 0.53
25 16 0.42
26 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.29, T:0.12
Consensus pattern (24 bp):
CGGGAAGCTCAAGAGAGCCATAAA
Found at i:15846609 original size:74 final size:73
Alignment explanation
Indices: 15846531--15846667 Score: 168
Period size: 74 Copynumber: 1.9 Consensus size: 73
15846521 GGAAGCTCAA
* * **
15846531 GAGAGCCAATT-ATCGGGAAGCTCATACGAGCCATAAACGGGAAGCTCAAGAGAGCCAAATATCG
1 GAGAG-CAATTAATCGGGAAACTCATAAGAGCCATAAACCAGAAGCTCAAGAGAGCC-AATATCG
15846595 CGATGCTCTG
64 CGATGCTCTG
* * * * *
15846605 GAGAGCTATTAATCGGGAAACTCATAAGAGCCGTAATCCAGAAGCTCATGCGAGCCAATATCG
1 GAGAGCAATTAATCGGGAAACTCATAAGAGCCATAAACCAGAAGCTCAAGAGAGCCAATATCG
15846668 AGAAGCTCGT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
73 11 0.21
74 42 0.79
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.18
Consensus pattern (73 bp):
GAGAGCAATTAATCGGGAAACTCATAAGAGCCATAAACCAGAAGCTCAAGAGAGCCAATATCGCG
ATGCTCTG
Found at i:15855876 original size:17 final size:17
Alignment explanation
Indices: 15855843--15855876 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15855833 TTGTGTTTTG
*
15855843 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
15855860 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
15855877 GTTAGGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:15856472 original size:2 final size:2
Alignment explanation
Indices: 15856465--15856489 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15856455 ATGATATGAA
15856465 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
15856490 AAAGAGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15856897 original size:41 final size:41
Alignment explanation
Indices: 15856840--15856942 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 41
15856830 NNNNNNNNNC
* * *
15856840 CTAGCAGGCTTGATGCCGGTGAAATAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* * * *
15856881 CTAGCAGGCTTAATGCCGGTGATACATTTCGGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* *
15856922 CTAGCAGGCTAAAAGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
15856943 TACTGAATCA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
Found at i:15859653 original size:46 final size:46
Alignment explanation
Indices: 15859600--15859754 Score: 231
Period size: 46 Copynumber: 3.4 Consensus size: 46
15859590 ATTGCTATAG
* * *
15859600 CTCAGTATGATTTTCTTCACGAAAATATCATACCTACTTTTCATAA
1 CTCAGTATGATTTTCTTCACGAAAACACCATACCTACTTTTCACAA
*
15859646 CTCAGTATGGTTTTCTTCACTG-AAACACCATACCTACTTTTCACAA
1 CTCAGTATGATTTTCTTCAC-GAAAACACCATACCTACTTTTCACAA
* * *
15859692 CTCAGTATGGTTTTCTTCACTAAAACACCATACCTATTTTTCACAA
1 CTCAGTATGATTTTCTTCACGAAAACACCATACCTACTTTTCACAA
15859738 CTCAGTATGATTTTCTT
1 CTCAGTATGATTTTCTT
15859755 TATCGAAATA
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
46 99 0.99
47 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.39
Consensus pattern (46 bp):
CTCAGTATGATTTTCTTCACGAAAACACCATACCTACTTTTCACAA
Found at i:15859773 original size:46 final size:45
Alignment explanation
Indices: 15859600--15859782 Score: 224
Period size: 46 Copynumber: 4.0 Consensus size: 45
15859590 ATTGCTATAG
* *
15859600 CTCAGTATGATTTTCTTCACGAAAATATCATACCTACTTTTCATAA
1 CTCAGTATGATTTTCTTCACG-AAATACCATACCTACTTTTCACAA
* *
15859646 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
1 CTCAGTATGATTTTCTTCAC-GAAATACCATACCTACTTTTCACAA
* * * *
15859692 CTCAGTATGGTTTTCTTCACTAAAACACCATACCTATTTTTCACAA
1 CTCAGTATGATTTTCTTCAC-GAAATACCATACCTACTTTTCACAA
* *
15859738 CTCAGTATGATTTTCTTTATCGAAATACC-TAACCTACATTTCACA
1 CTCAGTATGATTTTCTTCA-CGAAATACCAT-ACCTACTTTTCACA
15859783 CTTTGTCATG
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
45 1 0.01
46 119 0.98
47 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (45 bp):
CTCAGTATGATTTTCTTCACGAAATACCATACCTACTTTTCACAA
Found at i:15861874 original size:30 final size:30
Alignment explanation
Indices: 15861818--15861886 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
15861808 TACCCTTAAA
* * *
15861818 ATATTTACACTATTGATCCTTCAAATTTTTG
1 ATATTTACACTATTAACCCCTCAAA-TTTTG
15861849 ATATTTACACT-TTAACCCCTCAAATTTTG
1 ATATTTACACTATTAACCCCTCAAATTTTG
15861878 AGTATTTAC
1 A-TATTTAC
15861887 TCTTGGATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 6 0.18
30 17 0.50
31 11 0.32
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (30 bp):
ATATTTACACTATTAACCCCTCAAATTTTG
Found at i:15865872 original size:21 final size:20
Alignment explanation
Indices: 15865844--15865907 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 20
15865834 TTCAGGTGGA
*
15865844 TCAGCTCTTTCGAGCTTCTGT
1 TCAGCTCTTT-GAGCTTCTAT
*
15865865 TTAGCTCTTTTGAGCTTCTAT
1 TCAGCTC-TTTGAGCTTCTAT
15865886 TCAGCTCTTATGAGCTTCTAT
1 TCAGCTCTT-TGAGCTTCTAT
15865907 T
1 T
15865908 GACGATGTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 2 0.05
21 33 0.87
22 3 0.08
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (20 bp):
TCAGCTCTTTGAGCTTCTAT
Found at i:15869177 original size:22 final size:23
Alignment explanation
Indices: 15869142--15869205 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
15869132 AATAAGATTT
15869142 AATATTAAATTTAATCTAATATA
1 AATATTAAATTTAATCTAATATA
* *
15869165 AATATTATA-TTAATTTAATATTA
1 AATATTAAATTTAATCTAATA-TA
*
15869188 AAGTGATTAAGTTTAATC
1 AA-T-ATTAAATTTAATC
15869206 ATAGTTGAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 10 0.31
23 12 0.38
24 1 0.03
25 4 0.12
26 5 0.16
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (23 bp):
AATATTAAATTTAATCTAATATA
Found at i:15886055 original size:45 final size:44
Alignment explanation
Indices: 15885949--15886187 Score: 162
Period size: 44 Copynumber: 5.4 Consensus size: 44
15885939 ATGGTGAATA
* * * * *
15885949 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACACAAATC
* *
15885993 TTACCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATATCAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACA-CAAATC
* * * * *
15886038 TTATCTCCCTGAAGTTGCAGTGGAGTATATTGAAGTCACTAAA-C
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAC-AAATC
* * * * * * * *
15886082 ATATCCCCCTAAAGTTACAGTGGGGCA-AGTTGAA-AC-CAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAAGACACAAATC
* * * * * *
15886124 TTATCTCTCTAAAGTTACAGTGGAGCAGACTGAAGATAGCGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACA-CAAATC
* *
15886169 TTATTTCCCTAAAGTTGCA
1 TTATCTCCCTGAAGTTGCA
15886188 ATAAAACAGA
Statistics
Matches: 154, Mismatches: 33, Indels: 15
0.76 0.16 0.07
Matches are distributed among these distances:
41 2 0.01
42 29 0.19
43 4 0.03
44 61 0.40
45 58 0.38
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACACAAATC
Found at i:15886287 original size:41 final size:40
Alignment explanation
Indices: 15886219--15886325 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
15886209 AATTACCGAT
* * * * *
15886219 CTTATCTCGCTGAAGTTGTAATAGAGCAAATCATAGCAAAC
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAAATCA-AACAAAC
* * * *
15886260 CTTATCTCTCTGAAGTTGCAGTGGAGCAATTTAAACCAAT
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAAATCAAACAAAC
*
15886300 CTTCTCTCTCTGAAGTTGCAGTGGAG
1 CTTATCTCTCTGAAGTTGCAGTGGAG
15886326 TAGACTGAAG
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 29 0.52
41 27 0.48
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (40 bp):
CTTATCTCTCTGAAGTTGCAGTGGAGCAAATCAAACAAAC
Found at i:15886333 original size:177 final size:177
Alignment explanation
Indices: 15886093--15886498 Score: 571
Period size: 177 Copynumber: 2.3 Consensus size: 177
15886083 TATCCCCCTA
* * * * *
15886093 AAGTTACAGTGGGGCAAGTTGAAACCAAGTCTTATCTCTCTAAAGTTACAGTGGAGCAGACTGAA
1 AAGTTGCAGTGGAGCAA-TTTAAACCAA-TCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAA
15886158 GATAGCGAATCTTATTTCCCTAAAGTTGCAATAAAACAGATTAAAACTATAAATTACCGATCTTA
64 GATAGCGAATCTTATTTCCCTAAAGTTGCAATAAAACAGATTAAAACTATAAATTACCGATCTTA
* * *
15886223 TCTCGCTGAAGTTGTAATAGAGCAAATCATAGCAAACCTTATCT-CTCTG
129 TCTCACTAAAGTTATAATAGAGCAAATCATAGCAAACCTTATCTCCT-TG
* *
15886272 AAGTTGCAGTGGAGCAATTTAAACCAATCTTCTCTCTCTGAAGTTGCAGTGGAGTAGACTGAAGA
1 AAGTTGCAGTGGAGCAATTTAAACCAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGA
** ** * * *
15886337 TAGCGAATCTTATTTCCCTAAAGTTGCGGTGGAACAGTTTAAAGCTATAAATTGCCGATCTTATC
66 TAGCGAATCTTATTTCCCTAAAGTTGCAATAAAACAGATTAAAACTATAAATTACCGATCTTATC
* * * *
15886402 TTACTAAAGTTATAGTAGAGCATATTATAGCAAACCTTATCTCCTTG
131 TCACTAAAGTTATAATAGAGCAAATCATAGCAAACCTTATCTCCTTG
* *
15886449 AAGTTGCAGTGGAGCAGTTTAAACCAATCTTATCTCCCTGAAGTTGCAGT
1 AAGTTGCAGTGGAGCAATTTAAACCAATCTTATCTCTCTGAAGTTGCAGT
15886499 AAAATAGATT
Statistics
Matches: 202, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
177 176 0.87
178 11 0.05
179 15 0.07
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (177 bp):
AAGTTGCAGTGGAGCAATTTAAACCAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGA
TAGCGAATCTTATTTCCCTAAAGTTGCAATAAAACAGATTAAAACTATAAATTACCGATCTTATC
TCACTAAAGTTATAATAGAGCAAATCATAGCAAACCTTATCTCCTTG
Found at i:15888336 original size:28 final size:26
Alignment explanation
Indices: 15888302--15888357 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 26
15888292 TATTCCATTT
* *
15888302 AATTAATTTATTATTCTTTGTTTTTAAA
1 AATTAATTAATTAAT-TTT-TTTTTAAA
15888330 AATTAATTAATTAATTTTTTTTTAAA
1 AATTAATTAATTAATTTTTTTTTAAA
15888356 AA
1 AA
15888358 GGGCTCTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 10 0.38
27 3 0.12
28 13 0.50
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
AATTAATTAATTAATTTTTTTTTAAA
Found at i:15910088 original size:6 final size:6
Alignment explanation
Indices: 15910077--15910121 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
15910067 ACGATCATCT
*
15910077 CTTTAC CTTTAC CTTTAC CTTTAC CTTTAC CTTCAC CTTTAC CTT
1 CTTTAC CTTTAC CTTTAC CTTTAC CTTTAC CTTTAC CTTTAC CTT
15910122 GTGCCCAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.49
Consensus pattern (6 bp):
CTTTAC
Found at i:15916375 original size:37 final size:37
Alignment explanation
Indices: 15916279--15916377 Score: 108
Period size: 37 Copynumber: 2.7 Consensus size: 37
15916269 TGAGAGAATA
* * * *
15916279 TTTGTAGATAATCCTTACTATTCATCTTGGTCTTTTC
1 TTTGTAGAAAATCATTACTATTCATCTTCGTATTTTC
* * **
15916316 TTTGCATAAAATTTTTACTATTCATCTTCGTATTTTC
1 TTTGTAGAAAATCATTACTATTCATCTTCGTATTTTC
* *
15916353 TTTGTAGAGAATCATTATTATTCAT
1 TTTGTAGAAAATCATTACTATTCAT
15916378 GTAACTTTCA
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (37 bp):
TTTGTAGAAAATCATTACTATTCATCTTCGTATTTTC
Found at i:15917403 original size:3 final size:3
Alignment explanation
Indices: 15917393--15917428 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
15917383 AAAAATCTGC
15917393 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
15917429 ATGATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:15918500 original size:43 final size:43
Alignment explanation
Indices: 15918448--15918585 Score: 213
Period size: 43 Copynumber: 3.2 Consensus size: 43
15918438 TTTAAAAAAT
* * *
15918448 GCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTTCGACAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCACAAAC
** *
15918491 ATCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCACAAAC
*
15918534 GCCGCTAAAGACCATGACCTTTAGCAGCGCTTTTACCACAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCACAAAC
15918577 GCCGCTAAA
1 GCCGCTAAA
15918586 ACCTTTACCG
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 86 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (43 bp):
GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCACAAAC
Found at i:15923033 original size:14 final size:14
Alignment explanation
Indices: 15923016--15923065 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
15923006 ATAAACCGTA
*
15923016 AACCCTTAATCCCT
1 AACCCTTAAACCCT
* *
15923030 AACCCCTAACCCCT
1 AACCCTTAAACCCT
*
15923044 AACCCTTAAACCCC
1 AACCCTTAAACCCT
15923058 AACCCTTA
1 AACCCTTA
15923066 TAACTGTCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.20
Consensus pattern (14 bp):
AACCCTTAAACCCT
Found at i:15924079 original size:13 final size:13
Alignment explanation
Indices: 15924061--15924088 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15924051 ACCCTGAGCA
15924061 TTAGCGGCGCTTC
1 TTAGCGGCGCTTC
15924074 TTAGCGGCGCTTC
1 TTAGCGGCGCTTC
15924087 TT
1 TT
15924089 TAAAAACGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.29, G:0.29, T:0.36
Consensus pattern (13 bp):
TTAGCGGCGCTTC
Found at i:15924079 original size:53 final size:54
Alignment explanation
Indices: 15924021--15924129 Score: 195
Period size: 53 Copynumber: 2.0 Consensus size: 54
15924011 AGCCTGAGCA
15924021 TTAGCGGCGCTT-TTTCAAAAACGCCGCTAAA-CCCTGAGCATTAGCGGCGCTTC
1 TTAGCGGCGCTTCTTT-AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC
15924074 TTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC
1 TTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC
15924128 TT
1 TT
15924130 CAAAAACGCC
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
53 27 0.50
54 27 0.50
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (54 bp):
TTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC
Found at i:15924253 original size:40 final size:39
Alignment explanation
Indices: 15924205--15924323 Score: 127
Period size: 40 Copynumber: 3.0 Consensus size: 39
15924195 TGCTTTTTGG
*
15924205 AAAA-CGCCGCTAATGCTCATTTTTAGCGGCGTTTTTTAA
1 AAAAGCGCCGCTAATGCTCATTTTTAGTGGCGTTTTTT-A
* * *
15924244 AAAAGCGCCGCTAATACTCGATCTTTAGTGGTGTTTTTGT-
1 AAAAGCGCCGCTAATGCTC-ATTTTTAGTGGCGTTTTT-TA
*
15924284 AAAAGCGCCTG-TAATGCTTGATTTTTAGTGGCGTTTTTTA
1 AAAAGCGCC-GCTAATGC-TCATTTTTAGTGGCGTTTTTTA
15924324 TCCAAATGCC
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
39 5 0.08
40 43 0.65
41 17 0.26
42 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.39
Consensus pattern (39 bp):
AAAAGCGCCGCTAATGCTCATTTTTAGTGGCGTTTTTTA
Found at i:15927443 original size:44 final size:44
Alignment explanation
Indices: 15927380--15927466 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
15927370 GTATTTTGCC
15927380 CCTTTTACTAAAATAAATGGGCAAATTAACCCTTATACGTTAGA
1 CCTTTTACTAAAATAAATGGGCAAATTAACCCTTATACGTTAGA
15927424 CCTTTTACTAAAATAAATGGGCAAATTAACCCTTATACGTTAG
1 CCTTTTACTAAAATAAATGGGCAAATTAACCCTTATACGTTAG
15927467 GAAAACTGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (44 bp):
CCTTTTACTAAAATAAATGGGCAAATTAACCCTTATACGTTAGA
Found at i:15928496 original size:50 final size:52
Alignment explanation
Indices: 15928436--15928534 Score: 157
Period size: 53 Copynumber: 1.9 Consensus size: 52
15928426 AAAATAATAA
* *
15928436 TTCTTATAAATTTT-A-GTTTTTAAATAATTTTCTATAATGTTTTTAATCAT
1 TTCTTATAAATTTTAATATTTTTAAACAATTTTCTATAATGTTTTTAATCAT
15928486 TTCTTATAAATTTTAATTATTTTTAAACAATTTTCTATAATGTTTTTAA
1 TTCTTATAAATTTTAA-TATTTTTAAACAATTTTCTATAATGTTTTTAA
15928535 AAACCATGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 14 0.32
51 1 0.02
53 29 0.66
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (52 bp):
TTCTTATAAATTTTAATATTTTTAAACAATTTTCTATAATGTTTTTAATCAT
Found at i:15928517 original size:20 final size:20
Alignment explanation
Indices: 15928476--15928519 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
15928466 TCTATAATGT
*
15928476 TTTTAATCATTTCTTATAAA
1 TTTTAATCATTTCTTAAAAA
*
15928496 TTTTAATTATTT-TTAAACAA
1 TTTTAATCATTTCTTAAA-AA
15928516 TTTT
1 TTTT
15928520 CTATAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAATCATTTCTTAAAAA
Found at i:15929904 original size:2 final size:2
Alignment explanation
Indices: 15929897--15929934 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
15929887 AATATAAAAG
15929897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15929935 ATAAAACAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15930106 original size:20 final size:20
Alignment explanation
Indices: 15930083--15930123 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
15930073 AATAAGAAAG
15930083 ATATAAATAATAT-AATATAA
1 ATAT-AATAATATCAATATAA
*
15930103 ATATAGTAATATCAATATAA
1 ATATAATAATATCAATATAA
15930123 A
1 A
15930124 AACAAATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAATAATATCAATATAA
Found at i:15930120 original size:14 final size:14
Alignment explanation
Indices: 15930083--15930121 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
15930073 AATAAGAAAG
15930083 ATATAAATAATA-TA
1 ATATAAAT-ATAGTA
15930097 ATATAAATATAGTA
1 ATATAAATATAGTA
*
15930111 ATATCAATATA
1 ATATAAATATA
15930122 AAAACAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 3 0.13
14 20 0.87
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (14 bp):
ATATAAATATAGTA
Found at i:15937455 original size:5 final size:5
Alignment explanation
Indices: 15937447--15937474 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
15937437 TTAAGTATAA
15937447 ATATT ATATT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATA
15937475 AAAGAAATAA
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):
ATATT
Found at i:15938446 original size:25 final size:25
Alignment explanation
Indices: 15938418--15938552 Score: 124
Period size: 25 Copynumber: 5.6 Consensus size: 25
15938408 ACTTTAGCGC
* *
15938418 GCTCTCAGATTATTAGCACATCAGT
1 GCTCTCTGATTATTAGCACGTCAGT
**
15938443 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTCAGT
*
15938468 GCTCTCTGATTACTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACGTCAGT
*
15938493 GCTCTCTG--T-TTAGCACAT-ATGT
1 GCTCTCTGATTATTAGCACGTCA-GT
* *
15938515 GCTCTCTG--TA-TAGCACTTTAGT
1 GCTCTCTGATTATTAGCACGTCAGT
15938537 GCTCTCTG-TTCATTAG
1 GCTCTCTGATT-ATTAG
15938553 TGCATAATAA
Statistics
Matches: 94, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
21 1 0.01
22 35 0.37
23 3 0.03
24 1 0.01
25 54 0.57
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTCAGT
Found at i:15938493 original size:50 final size:48
Alignment explanation
Indices: 15938418--15938552 Score: 145
Period size: 50 Copynumber: 2.8 Consensus size: 48
15938408 ACTTTAGCGC
* *
15938418 GCTCTCAGATTATTAGCACATCAGTGCTCTCTGATTATTAGCACGT-TGGT
1 GCTCTCTGATTA-TAGCACATCAGTGCTCTCTG-TTATTAGCACATAT-GT
*
15938468 GCTCTCTGATTACTAGCACGTCAGTGCTCTCTG-T-TTAGCACATATGT
1 GCTCTCTGATTA-TAGCACATCAGTGCTCTCTGTTATTAGCACATATGT
* *
15938515 GCTCTCTG--TATAGCACTTTAGTGCTCTCTGTTCATTAG
1 GCTCTCTGATTATAGCACATCAGTGCTCTCTGTT-ATTAG
15938553 TGCATAATAA
Statistics
Matches: 75, Mismatches: 6, Indels: 11
0.82 0.07 0.12
Matches are distributed among these distances:
44 18 0.24
45 3 0.04
47 22 0.29
48 2 0.03
50 30 0.40
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (48 bp):
GCTCTCTGATTATAGCACATCAGTGCTCTCTGTTATTAGCACATATGT
Found at i:15945652 original size:21 final size:21
Alignment explanation
Indices: 15945628--15945680 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
15945618 CATTGTTTCT
*
15945628 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
15945649 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
15945670 AATCTCACCGC
1 AATCTCACCGC
15945681 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:15948144 original size:38 final size:38
Alignment explanation
Indices: 15948099--15948177 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
15948089 TTTTAGGAAA
15948099 GTTAACCATGATAAATAGTTTTTTCTTCTTTTTTATAG
1 GTTAACCATGATAAATAGTTTTTTCTTCTTTTTTATAG
15948137 GTTAACCATGATAAATAGTTTTTTCTTCTTTTTTATAG
1 GTTAACCATGATAAATAGTTTTTTCTTCTTTTTTATAG
15948175 GTT
1 GTT
15948178 GTTATTATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.25, C:0.10, G:0.11, T:0.53
Consensus pattern (38 bp):
GTTAACCATGATAAATAGTTTTTTCTTCTTTTTTATAG
Found at i:15950290 original size:20 final size:20
Alignment explanation
Indices: 15950267--15950304 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
15950257 ATAATATTTA
15950267 TATTTTATTAAATTATATAT
1 TATTTTATTAAATTATATAT
*
15950287 TATTTTATTAATTTATAT
1 TATTTTATTAAATTATAT
15950305 TTAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTATTAAATTATATAT
Found at i:15950305 original size:15 final size:15
Alignment explanation
Indices: 15950237--15950306 Score: 59
Period size: 17 Copynumber: 4.2 Consensus size: 15
15950227 ATATTGTAAT
*
15950237 TTTTATTAATTCATA
1 TTTTATTAATTTATA
*
15950252 TTTTAATAATATTTATA
1 TTTT-ATTA-ATTTATA
15950269 TTTTATTAAATTATATATTA
1 TTTTATT-AA-T-T-TA-TA
15950289 TTTTATTAATTTATA
1 TTTTATTAATTTATA
15950304 TTT
1 TTT
15950307 AATAAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
15 9 0.20
16 8 0.18
17 13 0.29
18 2 0.04
19 4 0.09
20 9 0.20
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTATTAATTTATA
Found at i:15950547 original size:16 final size:16
Alignment explanation
Indices: 15950534--15950592 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
15950524 TAATTACAGA
15950534 TCTATTCCATTACAAC
1 TCTATTCCATTACAAC
*
15950550 TCTATTACATTACAAC
1 TCTATTCCATTACAAC
15950566 TCTATTCCATTACAAC
1 TCTATTCCATTACAAC
* *
15950582 CCTATTTCATT
1 TCTATTCCATT
15950593 CCCCCCAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.41
Consensus pattern (16 bp):
TCTATTCCATTACAAC
Found at i:15950570 original size:32 final size:32
Alignment explanation
Indices: 15950526--15950592 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
15950516 TGAAGTACTA
*
15950526 ATTACAGATCTATTCCATTACAACTCTATTAC
1 ATTACAGATCTATTCCATTACAACCCTATTAC
*
15950558 ATTACA-ACTCTATTCCATTACAACCCTATTTC
1 ATTACAGA-TCTATTCCATTACAACCCTATTAC
15950590 ATT
1 ATT
15950593 CCCCCCAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 1 0.03
32 31 0.97
ACGTcount: A:0.33, C:0.27, G:0.01, T:0.39
Consensus pattern (32 bp):
ATTACAGATCTATTCCATTACAACCCTATTAC
Found at i:15953140 original size:18 final size:20
Alignment explanation
Indices: 15953124--15953163 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
15953114 ATACACATAT
15953124 ACATTTGTTTGCACATATCTC
1 ACATTTGTTTGCACATA-CTC
*
15953145 AGATTTGTTTGCACATACT
1 ACATTTGTTTGCACATACT
15953164 TTTGTGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (20 bp):
ACATTTGTTTGCACATACTC
Found at i:15955684 original size:34 final size:32
Alignment explanation
Indices: 15955603--15955685 Score: 82
Period size: 34 Copynumber: 2.5 Consensus size: 32
15955593 TATTTTAATT
15955603 GATATTTTTAATTTTTATTTTGAATAAAACAA
1 GATATTTTTAATTTTTATTTTGAATAAAACAA
* *
15955635 GATCAATTTTT--TTTTTAGTTTTGACTAAAAACTTA
1 GAT--ATTTTTAATTTTTA-TTTTGAAT-AAAAC-AA
15955670 -ATATTTTTAATTTTTA
1 GATATTTTTAATTTTTA
15955686 ATTTATATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
32 15 0.36
33 7 0.17
34 19 0.45
35 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (32 bp):
GATATTTTTAATTTTTATTTTGAATAAAACAA
Found at i:15956503 original size:114 final size:112
Alignment explanation
Indices: 15956320--15956646 Score: 404
Period size: 114 Copynumber: 2.9 Consensus size: 112
15956310 AAAATAAGCA
* * *
15956320 TTAGCGGCGTTTTCCAGTAAGCGCCGC-AAAAAACCTAAGCCCAACGATGCCGGTTTTCGAGCTT
1 TTAGCGGCGTTTT-GAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCC-GTTTTCGAGCTT
* * * *
15956384 TCGGGGATTTAGCGGTGTTTTTATGAAAGCCCCGCTAATTCTCAGGGCT
64 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAGGGCT
* * * *
15956433 TTAGCGGCGTTTCTGAGCAAGCACCGCAAAAAAACCTAAGCTCAACGACGCCGTTTTCTGATCTT
1 TTAGCGGCGTTT-TGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTC-GAGCTT
*
15956498 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCACTGCTAATGCTCAGGGCT
64 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAGGGCT
* * * * * *
15956547 TTAGTGGCATTTTTGAGAAACCGCCGCAAAAAAACCTAAGCCCAATGACACCGTTTTCCGAGCTG
1 TTAGCGGC-GTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTT-CGAGCTT
* * *
15956612 TCGGGGATTTAGTGGCATTTTTAAGAAAGCGCCGC
64 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGC
15956647 AAAAAAAACC
Statistics
Matches: 184, Mismatches: 25, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
113 28 0.15
114 152 0.83
115 4 0.02
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (112 bp):
TTAGCGGCGTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCGAGCTTTC
GGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAGGGCT
Found at i:15956684 original size:74 final size:73
Alignment explanation
Indices: 15956546--15956720 Score: 260
Period size: 74 Copynumber: 2.4 Consensus size: 73
15956536 TGCTCAGGGC
* *
15956546 TTTAGTGGCATTTTTGAGAAACCGCCGCAAAAAAACCTAAGCCCAATGACACCGTTTTCCGAGCT
1 TTTAGTGGCATTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAATGACACCGTTTTCCGAGCT
15956611 GTCGGGGA
66 GTCGGGGA
* **
15956619 TTTAGTGGCATTTTTAAGAAAGCGCCGCAAAAAAAACCTAAGCCCAATGACGCCGTTTTTTGAGC
1 TTTAGTGGCATTTTTAAGAAAGCGCCGC-AAAAAAACCTAAGCCCAATGACACCGTTTTCCGAGC
*
15956684 TTTCGGGGA
65 TGTCGGGGA
* * *
15956693 TTTTGCGGCGTTTTTAAGAAAGCGCCGC
1 TTTAGTGGCATTTTTAAGAAAGCGCCGC
15956721 TAATGCTCAG
Statistics
Matches: 92, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 26 0.28
74 66 0.72
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.26
Consensus pattern (73 bp):
TTTAGTGGCATTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAATGACACCGTTTTCCGAGCT
GTCGGGGA
Found at i:15956689 original size:188 final size:187
Alignment explanation
Indices: 15956432--15956834 Score: 572
Period size: 188 Copynumber: 2.1 Consensus size: 187
15956422 TTCTCAGGGC
* * * * * * *
15956432 TTTAGCGGCGTTTCTGAGCAAGCACCGCAAAAAAACCTAAGCTCAACGACGCCGTTTTCTGATCT
1 TTTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* *
15956497 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACTGCTAATGCTCAGGGCTTTAGTGGCATTTTTG
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAGGGCTTTAGCGGCATTTTTG
* * * *
15956562 AGAAACCGCCGCAAAAAAACCTAAGCCCAATGACACCGTTTTCCGAGCTGTCGGGGA
131 AGAAACCGCCGCAAAAAAACCTAAGCCCAACGACACCATTTTCCGAGCTGTCAGAGA
* * *
15956619 TTTAGTGGCATTTTTAAGAAAGCGCCGCAAAAAAAACCTAAGCCCAATGACGCCGTTTTTTGAGC
1 TTTAGCGGCATTTTTAAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC
* * **
15956684 TTTCGGGGATTTTGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGTGTTTTT
65 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAGGGCTTTAGCGGCATTTTT
* * * *
15956749 GAGAAAGCGCCGCAAAAAAACCTACGCCCAACGACACCATTTTCTGAGCTTTCAGAGA
130 GAGAAACCGCCGCAAAAAAACCTAAGCCCAACGACACCATTTTCCGAGCTGTCAGAGA
*
15956807 TTTAGCGGCGTTTTTAAGAAAGCGCCGC
1 TTTAGCGGCATTTTTAAGAAAGCGCCGC
15956835 TAATGCTCAT
Statistics
Matches: 189, Mismatches: 26, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
187 22 0.12
188 167 0.88
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (187 bp):
TTTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAGGGCTTTAGCGGCATTTTTG
AGAAACCGCCGCAAAAAAACCTAAGCCCAACGACACCATTTTCCGAGCTGTCAGAGA
Found at i:15956820 original size:114 final size:114
Alignment explanation
Indices: 15956619--15957330 Score: 1095
Period size: 114 Copynumber: 6.2 Consensus size: 114
15956609 CTGTCGGGGA
* * * * *
15956619 TTTAGTGGCATTTTTAAGAAAGCGCCGCAAAAAAAACCTAAGCCCAATGACGCCGTTTTTTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC
*
15956684 TTTCGGGGATTTTGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
65 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * * *
15956734 TTTAGCGGTGTTTTTGAGAAAGCGCCGCAAAAAAACCTACGCCCAACGACACCATTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
15956799 TTCAGAGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCATGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
*
15956848 TTTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
** * *
15956912 TTCGGGGATTTAGCGATGTTTTTTAATAAAGCACCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCG-TTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* *
15956962 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACAACGCCGTTTTTTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
15957027 TTCGGGGATTTAGCGGCTTTTTTAAGAATGCGCCGCTAATGCTTAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* *
15957076 TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
15957141 TTCGGGGATTTAGCTGCTTTTTTAAGAATGCGCCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
*
15957190 TTTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCTGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * * *
15957254 TTTGGGGATTTAGCAGTGTTTTTAATAAAGCGCCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
15957303 TTTAGCGGCGTTTTTGAGAAAGCGCCGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGC
15957331 TAATGCTCAA
Statistics
Matches: 549, Mismatches: 46, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
113 153 0.28
114 324 0.59
115 72 0.13
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:15956937 original size:302 final size:300
Alignment explanation
Indices: 15956320--15956926 Score: 883
Period size: 302 Copynumber: 2.0 Consensus size: 300
15956310 AAAATAAGCA
* ** * *
15956320 TTAGCGGCGTTTTCCAGTAAGCGCCGCAAAAAACCTAAGCCCAACGATGCCGGTTTTCGAGCTTT
1 TTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGGTTTTCGAGCTTT
* * *
15956385 CGGGGATTTAGCGGTGTTTTTATGAAAGCCCCGCTAATTCTCAGGGCTTTAGCGGCGTTTCTGAG
66 CGGGGATTTAGCGGCGTTTTTAAGAAAGCCCCGCTAATGCTCAGGGCTTTAGCGGCGTTTCTGAG
* * * * * * *
15956450 CAAGCACCGCAAAAAAACCTAAGCTCAACGACGCCGTTTTCTGATCTTTCGGGGATTTAGCGGCG
131 AAAGCACCGCAAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTTTCAGAGATTTAGCGGCG
* *
15956515 TTTTTAAGAAAGCACTGCTAATGCTCAGGGCTTTAGTGGCATTTTTGAGAAACCGCCGCAAAAAA
196 TTTTTAAGAAAGCACCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAAACCGCCGCAAAAAA
*
15956580 ACCTAAGCCCAATGACACCGTTTTCCGAGCTGTCGGGGAT
261 ACCTAAGCCCAACGACACCGTTTTCCGAGCTGTCGGGGAT
* * * *
15956620 TTAGTGGCATTTTTAAGAAAGCGCCGCAAAAAAAACCTAAGCCCAATGACGCCGTTTTTTGAGCT
1 TTAGCGGCATTTTTAAGAAAGCGCCGC--AAAAAACCTAAGCCCAACGACGCCGGTTTTCGAGCT
* * * *
15956685 TTCGGGGATTTTGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGTGTTTTTG
64 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCCCCGCTAATGCTCAGGGCTTTAGCGGCGTTTCTG
* *
15956750 AGAAAGCGCCGCAAAAAAACCTACGCCCAACGACACCATTTTCTGAGCTTTCAGAGATTTAGCGG
129 AGAAAGCACCGCAAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTTTCAGAGATTTAGCGG
* * * *
15956815 CGTTTTTAAGAAAGCGCCGCTAATGCTCATGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGC-AAA
194 CGTTTTTAAGAAAGCACCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAAACCGCCGCAAAA
* *
15956879 AAACCTAAGCCCAACGACACCGTTTTCTGAGCTTTCGGGGAT
259 AAACCTAAGCCCAACGACACCGTTTTCCGAGCTGTCGGGGAT
15956921 TTAGCG
1 TTAGCG
15956927 ATGTTTTTTA
Statistics
Matches: 270, Mismatches: 35, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
300 22 0.08
301 47 0.17
302 201 0.74
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.26
Consensus pattern (300 bp):
TTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGGTTTTCGAGCTTT
CGGGGATTTAGCGGCGTTTTTAAGAAAGCCCCGCTAATGCTCAGGGCTTTAGCGGCGTTTCTGAG
AAAGCACCGCAAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTTTCAGAGATTTAGCGGCG
TTTTTAAGAAAGCACCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAAACCGCCGCAAAAAA
ACCTAAGCCCAACGACACCGTTTTCCGAGCTGTCGGGGAT
Found at i:15957325 original size:41 final size:41
Alignment explanation
Indices: 15957262--15957339 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
15957252 CTTTTGGGGA
* *
15957262 TTTAGCAGTGTTTTTAATAAAGCGCCGCTAATGCTCAGGGC
1 TTTAGCAGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* *
15957303 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
1 TTTAGCAGCGTTTTTAAGAAAGCGCCGCTAATGCTCA
15957340 AGGATTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (41 bp):
TTTAGCAGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:15957591 original size:22 final size:21
Alignment explanation
Indices: 15957566--15957613 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
15957556 GTGTTACCAT
* *
15957566 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGGTTAGGGATTAT-GG
* *
15957588 TTTAGGGGTTAGGGTTTATGG
1 TTTAAGGGTTAGGGATTATGG
15957609 TTTAA
1 TTTAA
15957614 AGGCTGGGGT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (21 bp):
TTTAAGGGTTAGGGATTATGG
Found at i:15957648 original size:21 final size:22
Alignment explanation
Indices: 15957607--15957655 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
15957597 TAGGGTTTAT
*
15957607 GGTTTAAAGGCTGGGGTTTAA-
1 GGTTTAAAGGCTGAGGTTTAAG
*
15957628 GGTTTAAAGG-TGATGTGTTAAG
1 GGTTTAAAGGCTGAGGT-TTAAG
15957650 GGTTTA
1 GGTTTA
15957656 TGGTTTATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.17
21 14 0.58
22 6 0.25
ACGTcount: A:0.24, C:0.02, G:0.37, T:0.37
Consensus pattern (22 bp):
GGTTTAAAGGCTGAGGTTTAAG
Found at i:15957693 original size:28 final size:29
Alignment explanation
Indices: 15957648--15957703 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
15957638 TGATGTGTTA
*
15957648 AGGGTTTATGGTTTATGGTTTAGGGTTTT
1 AGGGTTTATAGTTTATGGTTTAGGGTTTT
15957677 AGGGTTTA-AGTTTATGGTTTAGGGTTT
1 AGGGTTTATAGTTTATGGTTTAGGGTTT
15957704 AGATTAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (29 bp):
AGGGTTTATAGTTTATGGTTTAGGGTTTT
Found at i:15957705 original size:7 final size:7
Alignment explanation
Indices: 15957648--15957705 Score: 64
Period size: 7 Copynumber: 8.3 Consensus size: 7
15957638 TGATGTGTTA
15957648 AGGGTTT
1 AGGGTTT
*
15957655 ATGGTTT
1 AGGGTTT
*
15957662 ATGGTTT
1 AGGGTTT
15957669 AGGGTTTT
1 AGGG-TTT
15957677 AGGGTTT
1 AGGGTTT
*
15957684 A-AGTTT
1 AGGGTTT
*
15957690 ATGGTTT
1 AGGGTTT
15957697 AGGGTTT
1 AGGGTTT
15957704 AG
1 AG
15957706 ATTAACTAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
6 5 0.11
7 32 0.73
8 7 0.16
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.48
Consensus pattern (7 bp):
AGGGTTT
Found at i:15957820 original size:21 final size:20
Alignment explanation
Indices: 15957786--15957826 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
15957776 TATGGATTTA
*
15957786 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
15957806 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
15957827 AGTAGTTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:15957848 original size:14 final size:14
Alignment explanation
Indices: 15957797--15957905 Score: 57
Period size: 14 Copynumber: 7.8 Consensus size: 14
15957787 GGATTATGGT
*
15957797 TTAAGGGTT-GGGAT
1 TTAAGGGTTAGGG-G
*
15957811 TTAAGGTTTAGGGG
1 TTAAGGGTTAGGGG
*
15957825 TT-AGTAGTTAGGGG
1 TTAAG-GGTTAGGGG
* *
15957839 TTAAGGGTTAAGAG
1 TTAAGGGTTAGGGG
15957853 TT-AGGGATTTAGGGG
1 TTAAGGG--TTAGGGG
** *
15957868 TTAAGATTTAGGGA
1 TTAAGGGTTAGGGG
15957882 TTCAAGGGTT--GGG
1 TT-AAGGGTTAGGGG
*
15957895 TTAAGGTTTAG
1 TTAAGGGTTAG
15957906 ATTAATTAGT
Statistics
Matches: 70, Mismatches: 16, Indels: 18
0.67 0.15 0.17
Matches are distributed among these distances:
12 6 0.09
13 10 0.14
14 35 0.50
15 17 0.24
16 2 0.03
ACGTcount: A:0.25, C:0.01, G:0.39, T:0.35
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:15957871 original size:22 final size:22
Alignment explanation
Indices: 15957817--15957883 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
15957807 GGATTTAAGG
15957817 TTTAGGGGTT-AGTAGTTAGGG-
1 TTTAGGGGTTAAG-AGTTAGGGA
* *
15957838 GTTAAGGGTTAAGAGTTAGGGA
1 TTTAGGGGTTAAGAGTTAGGGA
*
15957860 TTTAGGGGTTAAGATTTAGGGA
1 TTTAGGGGTTAAGAGTTAGGGA
15957882 TT
1 TT
15957884 CAAGGGTTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 16 0.41
22 23 0.59
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.36
Consensus pattern (22 bp):
TTTAGGGGTTAAGAGTTAGGGA
Found at i:15957890 original size:22 final size:21
Alignment explanation
Indices: 15957822--15957891 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 21
15957812 TAAGGTTTAG
*
15957822 GGGTT-AGTAGTTAGGGGTTAA
1 GGGTTAAG-AGTTAGGGATTAA
*
15957843 GGGTTAAGAGTTAGGGATTTAG
1 GGGTTAAGAGTTAGGGA-TTAA
*
15957865 GGGTTAAGATTTAGGGATTCAA
1 GGGTTAAGAGTTAGGGATT-AA
15957887 GGGTT
1 GGGTT
15957892 GGGTTAAGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 15 0.36
22 27 0.64
ACGTcount: A:0.26, C:0.01, G:0.40, T:0.33
Consensus pattern (21 bp):
GGGTTAAGAGTTAGGGATTAA
Found at i:15961854 original size:43 final size:43
Alignment explanation
Indices: 15961787--15961925 Score: 235
Period size: 43 Copynumber: 3.2 Consensus size: 43
15961777 TTTTTATGAC
*
15961787 CTTTAGTGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTT
* *
15961830 CTTTAGCGGCGTTTCT-GGTAAAAGCGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTTGTGGGT-AAAGCGCCGCTAAAGATCATGTT
15961873 CTTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTT
15961916 CTTTAGCGGC
1 CTTTAGCGGC
15961926 ATAAATGCCG
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
42 3 0.03
43 83 0.93
44 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.31
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTT
Found at i:15962297 original size:26 final size:25
Alignment explanation
Indices: 15962245--15962297 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
15962235 ATAAAGATAT
* *
15962245 TAATTTTTATATAGAATTTCTGAAA
1 TAATTTTTATATAGAATATCTAAAA
15962270 TAATTTTT-TATAGAATAATCTAAGAA
1 TAATTTTTATATAGAAT-ATCTAA-AA
15962296 TA
1 TA
15962298 TAAAATATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 12 0.50
26 4 0.17
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (25 bp):
TAATTTTTATATAGAATATCTAAAA
Found at i:15962716 original size:23 final size:23
Alignment explanation
Indices: 15962686--15962731 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
15962676 GTTATAACTT
15962686 TTTTTTATTTACCAAAAAATATA
1 TTTTTTATTTACCAAAAAATATA
*
15962709 TTTTTTATTTACCAAAATATATA
1 TTTTTTATTTACCAAAAAATATA
15962732 AAAAAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTTTATTTACCAAAAAATATA
Found at i:15962869 original size:27 final size:27
Alignment explanation
Indices: 15962801--15962870 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
15962791 CGCCAATGGG
* *
15962801 ATTGGCGGCACGAAAGGTGCCAAAGCC
1 ATTGGCGGCACCAATGGTGCCAAAGCC
15962828 ATTGGCGGCACCAATGGTGCCAATA-CC
1 ATTGGCGGCACCAATGGTGCCAA-AGCC
15962855 ATTGGCGGCACCAATG
1 ATTGGCGGCACCAATG
15962871 TTTATTAGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 39 0.98
28 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGCC
Found at i:15962953 original size:18 final size:18
Alignment explanation
Indices: 15962911--15963070 Score: 83
Period size: 18 Copynumber: 9.1 Consensus size: 18
15962901 AGAAGGAGAG
15962911 GGAAAGAAAGATAGAAAGGAGA
1 GGAAAGAAAGA-A-AAA-GA-A
15962933 GGAAAGAAAGAAAAAGAA
1 GGAAAGAAAGAAAAAGAA
**
15962951 GGAAAG-AA-AATGA-AA
1 GGAAAGAAAGAAAAAGAA
15962966 GG--AGAAGAGAAAAA-AA
1 GGAAAGAA-AGAAAAAGAA
15962982 -GAAAGAAAGAAAGAAGAA
1 GGAAAGAAAGAAA-AAGAA
* * *
15963000 GAAAAGGAAAGGAGAAGAA
1 GGAAA-GAAAGAAAAAGAA
*
15963019 -AAAAGAAAG--AAAGAA
1 GGAAAGAAAGAAAAAGAA
*
15963034 GGAAAGAAA-AAGAAAGGA
1 GGAAAGAAAGAA-AAAGAA
*
15963052 -GAAGAGAAAAAAAAAGAA
1 GGAA-AGAAAGAAAAAGAA
15963070 G
1 G
15963071 AAGAGGGAAG
Statistics
Matches: 111, Mismatches: 11, Indels: 35
0.71 0.07 0.22
Matches are distributed among these distances:
13 2 0.02
14 1 0.01
15 11 0.10
16 20 0.18
17 16 0.14
18 28 0.25
19 12 0.11
20 9 0.08
21 1 0.01
22 11 0.10
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (18 bp):
GGAAAGAAAGAAAAAGAA
Found at i:15963065 original size:44 final size:44
Alignment explanation
Indices: 15962935--15963094 Score: 174
Period size: 44 Copynumber: 3.7 Consensus size: 44
15962925 AAAGGAGAGG
*
15962935 AAAGAAAGAAAAAGAAGGAAAGAAAATGAAAGGAGAAGAGAAAAAAA
1 AAAGAAAG--AAAGAAGGAAAGAAAAAGAAAGGAGAAGAG-AAAAAA
*
15962982 GAAAGAAAGAAAGAA-G-AAGAAAAGGAAAGGAG-A-AG---AAA
1 -AAAGAAAGAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAA
15963020 AAAGAAAGAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAA
1 AAAGAAAGAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAA
*
15963064 AAAG-AAGAAGAGGGAAGGAAGGAAAAAGAAA
1 AAAGAAAGAA-A--GAAGGAAAGAAAAAGAAA
15963095 AGAAAAGAAA
Statistics
Matches: 99, Mismatches: 3, Indels: 22
0.80 0.02 0.18
Matches are distributed among these distances:
37 14 0.14
38 4 0.04
39 15 0.15
40 1 0.01
41 2 0.02
42 2 0.02
43 6 0.06
44 23 0.23
45 1 0.01
46 23 0.23
48 8 0.08
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (44 bp):
AAAGAAAGAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAA
Found at i:15963884 original size:24 final size:24
Alignment explanation
Indices: 15963857--15963902 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
15963847 TTATAAGTTT
15963857 TTTTTATTTACCAAAAAATATATA
1 TTTTTATTTACCAAAAAATATATA
*
15963881 TTTTTATTTACCAAAATATATA
1 TTTTTATTTACCAAAAAATATA
15963903 AAAAAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTTTATTTACCAAAAAATATATA
Found at i:15963961 original size:45 final size:46
Alignment explanation
Indices: 15963912--15963998 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 46
15963902 AAAAAAAAAT
*
15963912 GCAAAAAAAA-GGGTGATG-GTTATTTTTTATAGAAAATTAATACGA
1 GCAAAAAAAAGGGGT-AAGAGTTATTTTTTATAGAAAATTAATACGA
****
15963957 GCAAAGGGCAGGGGTAAGAGTTATTTTTTATAGAAAATTAAT
1 GCAAAAAAAAGGGGTAAGAGTTATTTTTTATAGAAAATTAAT
15963999 TTAAATAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
45 8 0.23
46 27 0.77
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (46 bp):
GCAAAAAAAAGGGGTAAGAGTTATTTTTTATAGAAAATTAATACGA
Found at i:15965925 original size:3 final size:3
Alignment explanation
Indices: 15965917--15965942 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
15965907 TCTTAATACT
15965917 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
15965943 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:15966029 original size:19 final size:21
Alignment explanation
Indices: 15966005--15966043 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
15965995 AGTAAAACAA
*
15966005 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
15966024 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
15966044 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:15971269 original size:2 final size:2
Alignment explanation
Indices: 15971262--15971286 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15971252 TGAAATTATG
15971262 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15971287 GTTAGATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15972246 original size:41 final size:41
Alignment explanation
Indices: 15972067--15972237 Score: 288
Period size: 41 Copynumber: 4.2 Consensus size: 41
15972057 GACTATATGT
15972067 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
*
15972108 CTAGCAAGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
15972149 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
* * * * *
15972190 CTAGCAGGCTAAGTGCCAGTGAACTGAATTAGACTTTAAAC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
15972231 CTAGCAG
1 CTAGCAG
15972238 ATGAAGTGCT
Statistics
Matches: 123, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 123 1.00
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
Found at i:15972253 original size:41 final size:41
Alignment explanation
Indices: 15972039--15972237 Score: 272
Period size: 41 Copynumber: 4.9 Consensus size: 41
15972029 TCGGATTTAT
* * * * * *
15972039 TGCCAGTGAAATTATTCAGACTATATGTCTAGCAGGCTAAG
1 TGCCAGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
* *
15972080 TGCCGGTGAACTGAATCAGGCTATAAGCCTAGCAAGCTAAG
1 TGCCAGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
*
15972121 TGCCGGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
1 TGCCAGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
*
15972162 TGCCGGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
1 TGCCAGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
* * * *
15972203 TGCCAGTGAACTGAATTAGACTTTAAACCTAGCAG
1 TGCCAGTGAACTGAATCAGGCTATAAGCCTAGCAG
15972238 ATGAAGTGCT
Statistics
Matches: 144, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 144 1.00
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.23
Consensus pattern (41 bp):
TGCCAGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
Found at i:15976985 original size:2 final size:2
Alignment explanation
Indices: 15976971--15977007 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
15976961 ATTTTTAGAA
*
15976971 AT AT AT -T AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15977008 TGAATGTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15979378 original size:16 final size:16
Alignment explanation
Indices: 15979359--15979397 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
15979349 TATGACCCAC
*
15979359 TTTAAATATAAATTTT
1 TTTAAATAGAAATTTT
*
15979375 TTTAAAAAGAAATTTT
1 TTTAAATAGAAATTTT
*
15979391 TTGAAAT
1 TTTAAAT
15979398 TCAAAAAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
TTTAAATAGAAATTTT
Found at i:15984102 original size:34 final size:34
Alignment explanation
Indices: 15984067--15984152 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 34
15984057 AGTAAGCGAA
15984067 CCCTAATGTTATATAGTATGAAGTAGTATGTGAAC
1 CCCT-ATGTTATATAGTATGAAGTAGTATGTGAAC
* *
15984102 CCCTATGTTATATAGTATGATGTAGTATGTAAAC
1 CCCTATGTTATATAGTATGAAGTAGTATGTGAAC
*
15984136 CCCTATGTTATGTAGTA
1 CCCTATGTTATATAGTA
15984153 CGTCATAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 44 0.92
35 4 0.08
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (34 bp):
CCCTATGTTATATAGTATGAAGTAGTATGTGAAC
Found at i:15984162 original size:34 final size:34
Alignment explanation
Indices: 15984067--15984183 Score: 114
Period size: 34 Copynumber: 3.4 Consensus size: 34
15984057 AGTAAGCGAA
* *
15984067 CCCTAATGTTATATAGTATGA-AGTAGTATGTGAAC
1 CCCT-ATGTTATGTAGTACGATA-TAGTATGTGAAC
* * * *
15984102 CCCTATGTTATATAGTATGATGTAGTATGTAAAC
1 CCCTATGTTATGTAGTACGATATAGTATGTGAAC
*
15984136 CCCTATGTTATGTAGTACG-TCATAGTATATGAAC
1 CCCTATGTTATGTAGTACGAT-ATAGTATGTGAAC
15984170 CCAC-ATGTTATGTA
1 CC-CTATGTTATGTA
15984184 CTTTGTGAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
33 1 0.01
34 66 0.92
35 5 0.07
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.36
Consensus pattern (34 bp):
CCCTATGTTATGTAGTACGATATAGTATGTGAAC
Found at i:15984361 original size:44 final size:43
Alignment explanation
Indices: 15984195--15984401 Score: 146
Period size: 44 Copynumber: 4.7 Consensus size: 43
15984185 TTTGTGAATT
15984195 AATATGTGTGAACCCTATATGTGCGAACCTTGTATGTGTGAACCC
1 AATATGTGTGAACCCTATATGTGCGAACC-TGTATGTGTGAA-CC
* * *** * ** ** *
15984240 TACATGTAAAAATCCTATATGTGTAAACCCTAAATGTGAGAACC
1 AATATGTGTGAACCCTATATGTGCGAA-CCTGTATGTGTGAACC
* * * * * * * *
15984284 TATACGTTTGAACACTATATGT-CTATTCTTGTATGTGCGAAACC
1 AATATGTGTGAACCCTATATGTGCGA-ACCTGTATGTGTG-AACC
15984328 AATATGTGTGAACCCTATATGTGCGAACCTGTATGTGTGAACC
1 AATATGTGTGAACCCTATATGTGCGAACCTGTATGTGTGAACC
* * * *
15984371 ATGTATGCGCGAACCCTATATGTGTGAACCT
1 A-ATATGTGTGAACCCTATATGTGCGAACCT
15984402 TACATGTGAA
Statistics
Matches: 120, Mismatches: 37, Indels: 11
0.71 0.22 0.07
Matches are distributed among these distances:
43 14 0.12
44 74 0.62
45 30 0.25
46 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (43 bp):
AATATGTGTGAACCCTATATGTGCGAACCTGTATGTGTGAACC
Found at i:15984409 original size:15 final size:15
Alignment explanation
Indices: 15984196--15984400 Score: 137
Period size: 15 Copynumber: 13.9 Consensus size: 15
15984186 TTGTGAATTA
15984196 ATATGTGTGAACCCT
1 ATATGTGTGAACCCT
* *
15984211 ATATGTGCGAACCTT
1 ATATGTGTGAACCCT
*
15984226 GTATGTGTGAACCCT
1 ATATGTGTGAACCCT
* *** *
15984241 ACATGTAAAAATCCT
1 ATATGTGTGAACCCT
*
15984256 ATATGTGTAAACCCT
1 ATATGTGTGAACCCT
* *
15984271 AAATGTGAGAA-CCT
1 ATATGTGTGAACCCT
* * *
15984285 ATACGTTTGAACACT
1 ATATGTGTGAACCCT
* ** *
15984300 ATATGTCT-ATTCTT
1 ATATGTGTGAACCCT
* * * *
15984314 GTATGTGCGAAACCA
1 ATATGTGTGAACCCT
15984329 ATATGTGTGAACCCT
1 ATATGTGTGAACCCT
*
15984344 ATATGTGCGAA-CCT
1 ATATGTGTGAACCCT
* *
15984358 GTATGTGTGAACCAT
1 ATATGTGTGAACCCT
* * *
15984373 GTATGCGCGAACCCT
1 ATATGTGTGAACCCT
15984388 ATATGTGTGAACC
1 ATATGTGTGAACC
15984401 TTACATGTGA
Statistics
Matches: 137, Mismatches: 50, Indels: 6
0.71 0.26 0.03
Matches are distributed among these distances:
14 29 0.21
15 108 0.79
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (15 bp):
ATATGTGTGAACCCT
Found at i:15986611 original size:17 final size:17
Alignment explanation
Indices: 15986591--15986632 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
15986581 TATAAAAGCC
15986591 TATAATATTTTAAAATA
1 TATAATATTTTAAAATA
* * *
15986608 TATAAAAATTTACAATA
1 TATAATATTTTAAAATA
15986625 TATAATAT
1 TATAATAT
15986633 ATAAAAATTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TATAATATTTTAAAATA
Found at i:15986624 original size:27 final size:26
Alignment explanation
Indices: 15986550--15986641 Score: 68
Period size: 27 Copynumber: 3.6 Consensus size: 26
15986540 CTTATTTTAA
*
15986550 AAAATATA-AAAAATATATAC-A-ATTA
1 AAAATATATAAAAAT-T-TACAATATTT
*** *
15986575 AAAATATATAAAAGCCTATAATATTTT
1 AAAATATATAAAAATTTACAATA-TTT
15986602 AAAATATATAAAAATTTACAATA--T
1 AAAATATATAAAAATTTACAATATTT
*
15986626 ATAATATATAAAAATT
1 AAAATATATAAAAATT
15986642 GATAAAAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
24 18 0.34
25 9 0.17
26 5 0.09
27 21 0.40
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (26 bp):
AAAATATATAAAAATTTACAATATTT
Found at i:15989850 original size:25 final size:25
Alignment explanation
Indices: 15989822--15989890 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
15989812 AAGTTCTTTC
15989822 GAGCCATGTAA-CGGGAAGCTCGTAA
1 GAGCCAT-TAATCGGGAAGCTCGTAA
15989847 GAGCCA-TAATCGGGAAGCTCGTAA
1 GAGCCATTAATCGGGAAGCTCGTAA
*
15989871 GAGCCA-TAATTGGGAAGCTC
1 GAGCCATTAATCGGGAAGCTC
15989891 ATGTGAGCCA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
23 3 0.07
24 33 0.79
25 6 0.14
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.17
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCGTAA
Found at i:15989864 original size:24 final size:24
Alignment explanation
Indices: 15989833--15989890 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
15989823 AGCCATGTAA
15989833 CGGGAAGCTCGTAAGAGCCATAAT
1 CGGGAAGCTCGTAAGAGCCATAAT
15989857 CGGGAAGCTCGTAAGAGCCATAAT
1 CGGGAAGCTCGTAAGAGCCATAAT
*
15989881 TGGGAAGCTC
1 CGGGAAGCTC
15989891 ATGTGAGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.17
Consensus pattern (24 bp):
CGGGAAGCTCGTAAGAGCCATAAT
Found at i:15989898 original size:24 final size:24
Alignment explanation
Indices: 15989833--15990021 Score: 96
Period size: 24 Copynumber: 7.8 Consensus size: 24
15989823 AGCCATGTAA
*
15989833 CGGGAAGCTCGTAAGAGCCATAAT
1 CGGGAAGCTCATAAGAGCCATAAT
*
15989857 CGGGAAGCTCGTAAGAGCCATAAT
1 CGGGAAGCTCATAAGAGCCATAAT
* **
15989881 TGGGAAGCTCATGTGAGCCA-ATAT
1 CGGGAAGCTCATAAGAGCCATA-AT
* * * *
15989905 CGAGAAGCTCCA-GAGAGCCTTTTAT
1 CGGGAAGCT-CATAAGAGCC-ATAAT
* *** * *
15989930 CAGGAAGCTCCGGAGATCCAATTAT
1 CGGGAAGCTCATAAGAGCC-ATAAT
* * * *
15989955 CGAGAAGCTCATACGAGCAATAAA
1 CGGGAAGCTCATAAGAGCCATAAT
* *
15989979 CGGGAAGCGCA-AGAGAGCTATTAAT
1 CGGGAAGCTCATA-AGAGCCA-TAAT
* *
15990004 CGGGATGCTCATGAGAGC
1 CGGGAAGCTCATAAGAGC
15990022 TAAATAACGG
Statistics
Matches: 124, Mismatches: 33, Indels: 15
0.72 0.19 0.09
Matches are distributed among these distances:
23 2 0.02
24 73 0.59
25 49 0.40
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.19
Consensus pattern (24 bp):
CGGGAAGCTCATAAGAGCCATAAT
Found at i:15989954 original size:25 final size:25
Alignment explanation
Indices: 15989895--15989964 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
15989885 AAGCTCATGT
15989895 GAGCCAA-TATCGAGAAGCTCCAGA
1 GAGCCAATTATCGAGAAGCTCCAGA
** *
15989919 GAGCCTTTTATC-AGGAAGCTCCGGA
1 GAGCCAATTATCGA-GAAGCTCCAGA
*
15989944 GATCCAATTATCGAGAAGCTC
1 GAGCCAATTATCGAGAAGCTC
15989965 ATACGAGCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
24 6 0.16
25 30 0.81
26 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (25 bp):
GAGCCAATTATCGAGAAGCTCCAGA
Found at i:15993931 original size:21 final size:19
Alignment explanation
Indices: 15993889--15993931 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
15993879 TAAAATGTTA
**
15993889 CTTAAATTATATTAGTTTT
1 CTTAAATTATATTAACTTT
15993908 CTTAAATTGATATTTAACTTT
1 CTTAAATT-ATA-TTAACTTT
15993929 CTT
1 CTT
15993932 TTATCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (19 bp):
CTTAAATTATATTAACTTT
Found at i:15995123 original size:14 final size:15
Alignment explanation
Indices: 15995104--15995165 Score: 76
Period size: 14 Copynumber: 4.2 Consensus size: 15
15995094 TATATTTAAA
15995104 TTTAATTTTTAAT-T
1 TTTAATTTTTAATAT
15995118 TTTAATTTTT-ATAT
1 TTTAATTTTTAATAT
15995132 TTTAATTTTTAATAT
1 TTTAATTTTTAATAT
*
15995147 GATTTGATTTTT-ATAT
1 --TTTAATTTTTAATAT
15995163 TTT
1 TTT
15995166 TATAATGTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
13 2 0.05
14 24 0.56
15 4 0.09
16 4 0.09
17 9 0.21
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTAATTTTTAATAT
Found at i:15995160 original size:31 final size:28
Alignment explanation
Indices: 15995104--15995165 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 28
15995094 TATATTTAAA
15995104 TTTAATTTTTAATTTTTAATTTTTATAT
1 TTTAATTTTTAATTTTTAATTTTTATAT
*
15995132 TTTAATTTTTAATATGATTTGATTTTTATAT
1 TTTAATTTTTAAT-T--TTTAATTTTTATAT
15995163 TTT
1 TTT
15995166 TATAATGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 13 0.43
29 1 0.03
31 16 0.53
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTAATTTTTAATTTTTAATTTTTATAT
Found at i:15995169 original size:8 final size:7
Alignment explanation
Indices: 15995104--15995167 Score: 67
Period size: 7 Copynumber: 8.6 Consensus size: 7
15995094 TATATTTAAA
15995104 TTTAATT
1 TTTAATT
15995111 TTTAATT
1 TTTAATT
15995118 TTTAATT
1 TTTAATT
15995125 TTT-ATAT
1 TTTAAT-T
15995132 TTTAATT
1 TTTAATT
15995139 TTTAATAT
1 TTTAAT-T
*
15995147 GATTTGATT
1 --TTTAATT
15995156 TTTATATT
1 TTTA-ATT
15995164 TTTA
1 TTTA
15995168 TAATGTTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
6 2 0.04
7 31 0.63
8 10 0.20
9 1 0.02
10 5 0.10
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (7 bp):
TTTAATT
Found at i:15995278 original size:22 final size:22
Alignment explanation
Indices: 15995253--15995295 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
15995243 AAGTGAATTT
15995253 TTAAATT-TAAAAAATACAAAAG
1 TTAAATTCTAAAAAATA-AAAAG
*
15995275 TTAAATTCTCAAAAATAAAAA
1 TTAAATTCTAAAAAATAAAAA
15995296 TAGAGACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (22 bp):
TTAAATTCTAAAAAATAAAAAG
Found at i:15996017 original size:3 final size:3
Alignment explanation
Indices: 15996009--15996051 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
15995999 TTTATTCTCT
15996009 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
15996052 TCGTTTTCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:15998471 original size:25 final size:22
Alignment explanation
Indices: 15998455--15998517 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
15998445 TCTCCGATTA
15998455 TTAGCACATTAGTGCTCTCCGT
1 TTAGCACATTAGTGCTCTCCGT
* * *
15998477 TTATCACATTCGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCCGT
* **
15998499 ATAGCATTTTAGTGCTCTC
1 TTAGCACATTAGTGCTCTC
15998518 AATTCAATAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.41
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCCGT
Found at i:16007065 original size:24 final size:25
Alignment explanation
Indices: 16007024--16007071 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
16007014 ATAATAATCT
*
16007024 TAATATTTTATTAAAAAA-ATATAC
1 TAATATTTTAGTAAAAAATATATAC
**
16007048 TAATATTTTAGTGGAAAATATATA
1 TAATATTTTAGTAAAAAATATATA
16007072 TTACAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (25 bp):
TAATATTTTAGTAAAAAATATATAC
Found at i:16008281 original size:17 final size:19
Alignment explanation
Indices: 16008259--16008293 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
16008249 TTATAACACT
16008259 TTCTTT-CAAC-TTTTTTG
1 TTCTTTACAACGTTTTTTG
16008276 TTCTTTACAACGTTTTTT
1 TTCTTTACAACGTTTTTT
16008294 TTTTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.14, C:0.17, G:0.06, T:0.63
Consensus pattern (19 bp):
TTCTTTACAACGTTTTTTG
Found at i:16008291 original size:18 final size:17
Alignment explanation
Indices: 16008259--16008292 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
16008249 TTATAACACT
*
16008259 TTCTTTCAACTTTTTTG
1 TTCTTTCAACGTTTTTG
16008276 TTCTTTACAACGTTTTT
1 TTCTTT-CAACGTTTTT
16008293 TTTTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.62
Consensus pattern (17 bp):
TTCTTTCAACGTTTTTG
Found at i:16009126 original size:21 final size:21
Alignment explanation
Indices: 16009093--16009132 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16009083 CCAATAACCC
*
16009093 TAAATCATAAACCTTGAATAT
1 TAAATCATAAACCCTGAATAT
* *
16009114 TAAATCCTGAACCCTGAAT
1 TAAATCATAAACCCTGAAT
16009133 CTCAAATCTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (21 bp):
TAAATCATAAACCCTGAATAT
Found at i:16012476 original size:16 final size:16
Alignment explanation
Indices: 16012451--16012484 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16012441 TCACTTTCTC
*
16012451 AAATATTAATTAAATA
1 AAATAATAATTAAATA
*
16012467 AAATAATAATTTAATA
1 AAATAATAATTAAATA
16012483 AA
1 AA
16012485 GAATGTTAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAATAATTAAATA
Found at i:16018112 original size:13 final size:13
Alignment explanation
Indices: 16018094--16018140 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
16018084 TTAGAAGGAA
*
16018094 GTTAATGGTATTG
1 GTTAATGGTAATG
16018107 GTTAATGGTAATG
1 GTTAATGGTAATG
16018120 G-TAATGGTAAATG
1 GTTAATGGT-AATG
*
16018133 GTAAATGG
1 GTTAATGG
16018141 GGGTGTAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 7 0.23
13 18 0.60
14 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (13 bp):
GTTAATGGTAATG
Found at i:16018120 original size:19 final size:19
Alignment explanation
Indices: 16018096--16018136 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
16018086 AGAAGGAAGT
* *
16018096 TAATGGTATTGGTTAATGG
1 TAATGGTAATGGTAAATGG
16018115 TAATGGTAATGGTAAATGG
1 TAATGGTAATGGTAAATGG
16018134 TAA
1 TAA
16018137 ATGGGGGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (19 bp):
TAATGGTAATGGTAAATGG
Found at i:16018140 original size:7 final size:6
Alignment explanation
Indices: 16018096--16018136 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
16018086 AGAAGGAAGT
*
16018096 TAATGG TATTGG TTAATGG TAATGG TAATGG TAAATGG TAA
1 TAATGG TAATGG -TAATGG TAATGG TAATGG T-AATGG TAA
16018137 ATGGGGGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (6 bp):
TAATGG
Found at i:16023219 original size:27 final size:27
Alignment explanation
Indices: 16023189--16023285 Score: 131
Period size: 27 Copynumber: 3.6 Consensus size: 27
16023179 ATATAATCAA
16023189 AGTACGCCACAAAGGCAATCCATACAG
1 AGTACGCCACAAAGGCAATCCATACAG
* * *
16023216 AGTACGCCACAAAGGCTATCTATAGAG
1 AGTACGCCACAAAGGCAATCCATACAG
* * * *
16023243 GGTACGCCACAAAGGCGATTCATTCAG
1 AGTACGCCACAAAGGCAATCCATACAG
16023270 AGTACGCCACAAAGGC
1 AGTACGCCACAAAGGC
16023286 TGACAGGATG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (27 bp):
AGTACGCCACAAAGGCAATCCATACAG
Found at i:16029413 original size:23 final size:23
Alignment explanation
Indices: 16029368--16029415 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
16029358 AATAAAATAC
*
16029368 CCTAACCCGAAATACTAACTAAA
1 CCTAACCCGAAATACCAACTAAA
* * *
16029391 CCTAACCCGAATTACCCATTAAA
1 CCTAACCCGAAATACCAACTAAA
16029414 CC
1 CC
16029416 CTAGCCCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.35, G:0.04, T:0.19
Consensus pattern (23 bp):
CCTAACCCGAAATACCAACTAAA
Found at i:16035787 original size:13 final size:13
Alignment explanation
Indices: 16035746--16035775 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
16035736 AAAATAGGAG
16035746 AAAAAGAAAGAAGA
1 AAAAAGAAA-AAGA
16035760 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
16035773 AAA
1 AAA
16035776 TAAAAATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:16036615 original size:15 final size:15
Alignment explanation
Indices: 16036588--16036622 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
16036578 ACTTTGAGTC
16036588 AAAAAAATGAAAA-T
1 AAAAAAATGAAAAGT
16036602 AAAAAAATGAAAAAGT
1 AAAAAAATG-AAAAGT
16036618 AAAAA
1 AAAAA
16036623 TAGAGAGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 4 0.21
16 6 0.32
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (15 bp):
AAAAAAATGAAAAGT
Found at i:16037914 original size:48 final size:49
Alignment explanation
Indices: 16037862--16038185 Score: 179
Period size: 50 Copynumber: 6.6 Consensus size: 49
16037852 TCCCAGGCGA
16037862 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATC-GCTTCCCCGACAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTGCTTCCCCGACAT
** * * * * * ** *
16037910 TGCAGTTAAAAAGGTTAAAGCTACAACAGTGAATCTTGCTTCCTAGGCGA-
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATC-TGCTTCCCCGAC-AT
**
16037960 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATC-GCTTCCCTTACAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTGCTTCCCCGACAT
* ** * * * * * ** * * **
16038008 TGTAGTTAAAAAGGTTAAAGCTACAACAGCAAATCTTACTT-CCCTAGCGG
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATC-TGCTTCCCCGA-CAT
* *
16038058 TGCAGTGGAACAGATTAAAGCCATATAGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATC-TGCTTCCCCGACAT
** * * * * * ** * * * **
16038108 TGCAGTTAAAAAGGTTAAAGCTACAACAGCAAATCTTACTTCCCTGGCGG
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATC-TGCTTCCCCGACAT
*
16038158 TGCAATGGAACAGATTAAAGCCACATCG
1 TGCAGTGGAACAGATTAAAGCCACATCG
16038186 TGGAACAGAT
Statistics
Matches: 193, Mismatches: 75, Indels: 14
0.68 0.27 0.05
Matches are distributed among these distances:
47 1 0.01
48 60 0.31
49 4 0.02
50 123 0.64
51 5 0.03
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (49 bp):
TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTGCTTCCCCGACAT
Found at i:16038015 original size:98 final size:99
Alignment explanation
Indices: 16037843--16038185 Score: 541
Period size: 98 Copynumber: 3.5 Consensus size: 99
16037833 TGAAATCAAG
16037843 AATCTTACTTCCC-AGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCGCTTCCCCGA
1 AATCTTACTTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCGCTTCCCCGA
**
16037907 CATTGCAGTTAAAAAGGTTAAAGCTACAACAGTG
66 CATTGCAGTTAAAAAGGTTAAAGCTACAACAGCA
* **
16037941 AATCTTGCTT-CCTAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCGCTTCCCTTA
1 AATCTTACTTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCGCTTCCCCGA
*
16038005 CATTGTAGTTAAAAAGGTTAAAGCTACAACAGCA
66 CATTGCAGTTAAAAAGGTTAAAGCTACAACAGCA
* * *
16038039 AATCTTACTTCCCTA-GCGGTGCAGTGGAACAGATTAAAGCCATATAGGTGAATCTTGCTTCCCC
1 AATCTTACTTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATC--GCTTCCCC
16038103 GACATTGCAGTTAAAAAGGTTAAAGCTACAACAGCA
64 GACATTGCAGTTAAAAAGGTTAAAGCTACAACAGCA
* *
16038139 AATCTTACTTCCCT-GGCGGTGCAATGGAACAGATTAAAGCCACATCG
1 AATCTTACTTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATCG
16038186 TGGAACAGAT
Statistics
Matches: 224, Mismatches: 16, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
97 2 0.01
98 134 0.60
99 4 0.02
100 84 0.38
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (99 bp):
AATCTTACTTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCGCTTCCCCGA
CATTGCAGTTAAAAAGGTTAAAGCTACAACAGCA
Found at i:16038193 original size:23 final size:23
Alignment explanation
Indices: 16038163--16038208 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16038153 GGCGGTGCAA
16038163 TGGAACAGATTAAAGCCACATCG
1 TGGAACAGATTAAAGCCACATCG
16038186 TGGAACAGATTAAAGCCACATCG
1 TGGAACAGATTAAAGCCACATCG
16038209 GTGAATCGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (23 bp):
TGGAACAGATTAAAGCCACATCG
Found at i:16038248 original size:48 final size:48
Alignment explanation
Indices: 16038192--16038347 Score: 158
Period size: 48 Copynumber: 3.2 Consensus size: 48
16038182 ATCGTGGAAC
*
16038192 AGATTAAAGCCACATCGGTGAATCGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCGTTTCCCCGACATTGCAGTTAAAA
* * * * *
16038240 AGATTAAAGCTACAAT-AGCGAATC-TTACTCCCCAGGCGA-TGCAG-TAGAAC
1 AGATTAAAGCCAC-ATCGGTGAATCGTT--TCCCC-GAC-ATTGCAGTTA-AAA
* *
16038290 AGATTAAAGCCACATCGGTAAATCGTTTCTCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCGTTTCCCCGACATTGCAGTTAAAA
16038338 AGATTAAAGC
1 AGATTAAAGC
16038348 TACAACAACG
Statistics
Matches: 85, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
47 2 0.02
48 37 0.44
49 17 0.20
50 26 0.31
51 3 0.04
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (48 bp):
AGATTAAAGCCACATCGGTGAATCGTTTCCCCGACATTGCAGTTAAAA
Found at i:16038290 original size:121 final size:122
Alignment explanation
Indices: 16038062--16038306 Score: 384
Period size: 121 Copynumber: 2.0 Consensus size: 122
16038052 TAGCGGTGCA
* *
16038062 GTGGAACAGATTAAAGCCATATAGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGGTTAAA
1 GTGGAACAGATTAAAGCCACATAGGTGAATC-TGCTTCCCCGACATTGCAGTTAAAAAGATTAAA
* * * *
16038127 GCTACAACAGCAAATCTTACTTCCCTGGCGGTGCAATGGAACAGATTAAAGCCACATC
65 GCTACAACAGCAAATCTTACTCCCCAGGCGATGCAATAGAACAGATTAAAGCCACATC
*
16038185 GTGGAACAGATTAAAGCCACATCGGTGAATC-GCTTCCCCGACATTGCAGTTAAAAAGATTAAAG
1 GTGGAACAGATTAAAGCCACATAGGTGAATCTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAG
* * *
16038249 CTACAATAGCGAATCTTACTCCCCAGGCGATGCAGTAGAACAGATTAAAGCCACATC
66 CTACAACAGCAAATCTTACTCCCCAGGCGATGCAATAGAACAGATTAAAGCCACATC
16038306 G
1 G
16038307 GTAAATCGTT
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
121 83 0.74
123 29 0.26
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (122 bp):
GTGGAACAGATTAAAGCCACATAGGTGAATCTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAG
CTACAACAGCAAATCTTACTCCCCAGGCGATGCAATAGAACAGATTAAAGCCACATC
Found at i:16038297 original size:50 final size:50
Alignment explanation
Indices: 16038240--16038413 Score: 151
Period size: 50 Copynumber: 3.5 Consensus size: 50
16038230 GCAGTTAAAA
*
16038240 AGATTAAAGCTACAATAGCGAATCTTACTCCCCAGGCGATGCAGTAGAAC
1 AGATTAAAGCTACAACAGCGAATCTTACTCCCCAGGCGATGCAGTAGAAC
* * * ** * * *
16038290 AGATTAAAGCCACATCGGTAAATCGTT--TCTCC-GAC-ATTGCAGTTA-AAA
1 AGATTAAAGCTACAACAGCGAATC-TTACTCCCCAGGCGA-TGCAG-TAGAAC
* * * * *
16038338 AGATTAAAGCTACAACAACGAATCTTACTTCCCAGGCGGTGTAGTGGAAC
1 AGATTAAAGCTACAACAGCGAATCTTACTCCCCAGGCGATGCAGTAGAAC
*
16038388 AGATTGAAGCTACAACAGCGAATCTT
1 AGATTAAAGCTACAACAGCGAATCTT
16038414 GCTTCGTCGA
Statistics
Matches: 92, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
47 3 0.03
48 27 0.29
49 10 0.11
50 50 0.54
51 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCTACAACAGCGAATCTTACTCCCCAGGCGATGCAGTAGAAC
Found at i:16038360 original size:98 final size:98
Alignment explanation
Indices: 16038188--16038397 Score: 330
Period size: 98 Copynumber: 2.1 Consensus size: 98
16038178 CCACATCGTG
*
16038188 GAACAGATTAAAGCCACATCGGTGAATCGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTAC
1 GAACAGATTAAAGCCACATCGGTAAATCGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTAC
* *
16038253 AATAGCGAATCTTACTCCCCAGGCGATGCAGTA
66 AACAACGAATCTTACTCCCCAGGCGATGCAGTA
* *
16038286 GAACAGATTAAAGCCACATCGGTAAATCGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCTAC
1 GAACAGATTAAAGCCACATCGGTAAATCGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTAC
* * * *
16038351 AACAACGAATCTTACTTCCCAGGCGGTGTAGTG
66 AACAACGAATCTTACTCCCCAGGCGATGCAGTA
*
16038384 GAACAGATTGAAGC
1 GAACAGATTAAAGC
16038398 TACAACAGCG
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 102 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (98 bp):
GAACAGATTAAAGCCACATCGGTAAATCGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTAC
AACAACGAATCTTACTCCCCAGGCGATGCAGTA
Found at i:16038848 original size:23 final size:23
Alignment explanation
Indices: 16038803--16038850 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
16038793 AGTAAAATAC
*
16038803 CCTAACCCGAAATACTAACTAAA
1 CCTAACCCGAAATACCAACTAAA
* * *
16038826 CCTAACCCGAATTACCCATTAAA
1 CCTAACCCGAAATACCAACTAAA
16038849 CC
1 CC
16038851 CTAGCCCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.35, G:0.04, T:0.19
Consensus pattern (23 bp):
CCTAACCCGAAATACCAACTAAA
Found at i:16039106 original size:22 final size:24
Alignment explanation
Indices: 16039070--16039115 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
16039060 GCATACAAAC
*
16039070 AAAACAGCAAGAGAAAAGAAGAAA
1 AAAACAGCAAGAGAAAAAAAGAAA
16039094 AAAACAG-AA-AGAAAAAAAGAAA
1 AAAACAGCAAGAGAAAAAAAGAAA
16039116 TTTGTATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
23 2 0.10
24 7 0.33
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (24 bp):
AAAACAGCAAGAGAAAAAAAGAAA
Found at i:16040108 original size:17 final size:18
Alignment explanation
Indices: 16040088--16040121 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16040078 ACATTTTTTG
16040088 TATAT-ACATTATTTTAC
1 TATATAACATTATTTTAC
*
16040105 TATATAATATTATTTTA
1 TATATAACATTATTTTA
16040122 AGCGTTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATAACATTATTTTAC
Found at i:16063027 original size:13 final size:14
Alignment explanation
Indices: 16063009--16063057 Score: 66
Period size: 15 Copynumber: 3.5 Consensus size: 14
16062999 AATCAATTCC
16063009 TTTTCTTCTTTCAT
1 TTTTCTTCTTTCAT
16063023 TTTCTCTTCTTTCAT
1 TTT-TCTTCTTTCAT
16063038 TTTCTCTTCTTT--T
1 TTT-TCTTCTTTCAT
16063051 TTTTCTT
1 TTTTCTT
16063058 TTTTTCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 4 0.12
13 4 0.12
14 3 0.09
15 23 0.68
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTCTTCTTTCAT
Found at i:16063032 original size:15 final size:15
Alignment explanation
Indices: 16063012--16063049 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
16063002 CAATTCCTTT
16063012 TCTTCTTTCATTTTC
1 TCTTCTTTCATTTTC
16063027 TCTTCTTTCATTTTC
1 TCTTCTTTCATTTTC
16063042 TCTTCTTT
1 TCTTCTTT
16063050 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.68
Consensus pattern (15 bp):
TCTTCTTTCATTTTC
Found at i:16063053 original size:1 final size:1
Alignment explanation
Indices: 16063047--16063080 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
16063037 TTTTCTCTTC
* *
16063047 TTTTTTTTCTTTTTTTCTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16063081 GCATAGGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:16063058 original size:9 final size:9
Alignment explanation
Indices: 16063044--16063079 Score: 58
Period size: 8 Copynumber: 4.2 Consensus size: 9
16063034 TCATTTTCTC
16063044 TTCTTTTTT
1 TTCTTTTTT
16063053 TTC-TTTTT
1 TTCTTTTTT
16063061 TTCTTTTTT
1 TTCTTTTTT
16063070 TT-TTTTTT
1 TTCTTTTTT
16063078 TT
1 TT
16063080 TGCATAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 16 0.62
9 10 0.38
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:16063067 original size:27 final size:28
Alignment explanation
Indices: 16063009--16063080 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 28
16062999 AATCAATTCC
*
16063009 TTTTCTTCTTTCATTTTCTCTTCTTTCAT
1 TTTTCTTCTTT-TTTTTCTCTTCTTTCAT
*
16063038 TTTCTCTTCTTTTTTTTCT-TTTTTTC-T
1 TTT-TCTTCTTTTTTTTCTCTTCTTTCAT
* *
16063065 TTTTTTTTTTTTTTTT
1 TTTTCTTCTTTTTTTT
16063081 GCATAGGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 11 0.29
27 4 0.11
28 6 0.16
29 9 0.24
30 8 0.21
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (28 bp):
TTTTCTTCTTTTTTTTCTCTTCTTTCAT
Found at i:16063079 original size:17 final size:17
Alignment explanation
Indices: 16063044--16063078 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
16063034 TCATTTTCTC
16063044 TTCTTTTTTTTCTTTTT
1 TTCTTTTTTTTCTTTTT
16063061 TTCTTTTTTTT-TTTTT
1 TTCTTTTTTTTCTTTTT
16063077 TT
1 TT
16063079 TTGCATAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (17 bp):
TTCTTTTTTTTCTTTTT
Found at i:16063080 original size:20 final size:20
Alignment explanation
Indices: 16063009--16063078 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
16062999 AATCAATTCC
* *
16063009 TTTTCTTCTTTCATTTTCTCTT
1 TTTTCTT-TTTC-TCTTCTTTT
* *
16063031 CTTTCATTTTCTCTTCTTTT
1 TTTTCTTTTTCTCTTCTTTT
*
16063051 TTTTCTTTTTTTCTT-TTTT
1 TTTTCTTTTTCTCTTCTTTT
16063070 TTTT-TTTTT
1 TTTTCTTTTT
16063079 TTGCATAGGA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
18 5 0.12
19 8 0.20
20 19 0.46
21 4 0.10
22 5 0.12
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTCTTTTTCTCTTCTTTT
Found at i:16064237 original size:33 final size:34
Alignment explanation
Indices: 16064179--16064249 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
16064169 CTGAGGTGCA
16064179 AGGCGCAAAAAAAAGCGCTCACCCGAGTAAACCG
1 AGGCGCAAAAAAAAGCGCTCACCCGAGTAAACCG
*
16064213 AGGCGC-AAAAAAAGTGCT-AGCCCGAGTAAACCG
1 AGGCGCAAAAAAAAGCGCTCA-CCCGAGTAAACCG
16064246 AGGC
1 AGGC
16064250 CCAAGCATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
32 1 0.03
33 28 0.80
34 6 0.17
ACGTcount: A:0.39, C:0.27, G:0.27, T:0.07
Consensus pattern (34 bp):
AGGCGCAAAAAAAAGCGCTCACCCGAGTAAACCG
Found at i:16070002 original size:11 final size:11
Alignment explanation
Indices: 16069974--16070046 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
16069964 ATTAATCCTT
*
16069974 TCTCAATTATTT
1 TCTCAATT-TTC
16069986 TCTCAATTTTC
1 TCTCAATTTTC
16069997 TCTCAA-TTTC
1 TCTCAATTTTC
* *
16070007 TTCTCAAATTGC
1 -TCTCAATTTTC
*
16070019 TCTCAATTTCC
1 TCTCAATTTTC
*
16070030 T-TCTAAATTTC
1 TCTC-AATTTTC
16070041 TCTCAA
1 TCTCAA
16070047 ATCCATATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
10 6 0.12
11 32 0.63
12 13 0.25
ACGTcount: A:0.23, C:0.26, G:0.01, T:0.49
Consensus pattern (11 bp):
TCTCAATTTTC
Found at i:16070013 original size:22 final size:22
Alignment explanation
Indices: 16069974--16070046 Score: 94
Period size: 22 Copynumber: 3.3 Consensus size: 22
16069964 ATTAATCCTT
* *
16069974 TCTCAATTATTTTCTCAATTTTC
1 TCTCAATT-TCTTCTCAAATTTC
*
16069997 TCTCAATTTCTTCTCAAATTGC
1 TCTCAATTTCTTCTCAAATTTC
16070019 TCTCAATTTCCTTCT-AAATTTC
1 TCTCAATTT-CTTCTCAAATTTC
16070041 TCTCAA
1 TCTCAA
16070047 ATCCATATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
22 32 0.71
23 13 0.29
ACGTcount: A:0.23, C:0.26, G:0.01, T:0.49
Consensus pattern (22 bp):
TCTCAATTTCTTCTCAAATTTC
Found at i:16070025 original size:33 final size:33
Alignment explanation
Indices: 16069986--16070048 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
16069976 TCAATTATTT
* *
16069986 TCTCAATTTTC-TCTCAATTTCTTCTCAAATTGC
1 TCTCAATTTCCTTCTAAATTTC-TCTCAAATTGC
16070019 TCTCAATTTCCTTCTAAATTTCTCTCAAAT
1 TCTCAATTTCCTTCTAAATTTCTCTCAAAT
16070049 CCATATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.24, C:0.27, G:0.02, T:0.48
Consensus pattern (33 bp):
TCTCAATTTCCTTCTAAATTTCTCTCAAATTGC
Found at i:16070083 original size:11 final size:11
Alignment explanation
Indices: 16069986--16070083 Score: 62
Period size: 11 Copynumber: 9.3 Consensus size: 11
16069976 TCAATTATTT
*
16069986 TCTCAATTTTC
1 TCTCAATTTCC
*
16069997 TCTCAATTTCT
1 TCTCAATTTCC
* *
16070008 TCTCAAATTGC
1 TCTCAATTTCC
16070019 TCTCAATTTCC
1 TCTCAATTTCC
*
16070030 TTCTAAATTT-C
1 -TCTCAATTTCC
*
16070041 TCTCAA-ATCC
1 TCTCAATTTCC
* **
16070051 -AT--ATTTAA
1 TCTCAATTTCC
*
16070059 TCTCAATTTGC
1 TCTCAATTTCC
16070070 TCTCAATTTCC
1 TCTCAATTTCC
16070081 TCT
1 TCT
16070084 TAAATTTCTC
Statistics
Matches: 63, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 6 0.10
11 44 0.70
12 8 0.13
ACGTcount: A:0.23, C:0.28, G:0.02, T:0.47
Consensus pattern (11 bp):
TCTCAATTTCC
Done.