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 65 of 187
Found at i:19019768 original size:54 final size:52
Alignment explanation
Indices: 19019710--19019826 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 52
19019700 TTAGTGGTGA
* *
19019710 ATATTCTTCTTCATCTTCGTTTTCTTCTGCTGGATGTAATGATTCCATCAATGG
1 ATATTCTTC-T-ATCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGG
19019764 ATA------T-TCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGG
1 ATATTCTTCTATCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGG
19019809 ATATTCTTCATAATCTTC
1 ATATTCTTC-T-ATCTTC
19019827 TTCCCCTGCT
Statistics
Matches: 52, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
45 42 0.81
47 1 0.02
52 1 0.02
54 8 0.15
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (52 bp):
ATATTCTTCTATCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGG
Found at i:19019787 original size:45 final size:45
Alignment explanation
Indices: 19019723--19019817 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
19019713 TTCTTCTTCA
* *
19019723 TCTTCGTTTTCTTCTGCTGGATGTAATGATTCCATCAATGGATAT
1 TCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGGATAT
19019768 TCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGGATAT
1 TCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGGATAT
19019813 TCTTC
1 TCTTC
19019818 ATAATCTTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (45 bp):
TCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGGATAT
Found at i:19019826 original size:45 final size:45
Alignment explanation
Indices: 19019732--19019827 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
19019722 ATCTTCGTTT
* * * **
19019732 TCTTCTGCTGGATGTAATGATTCCATCAATGGATATTCTTCGTTT
1 TCTTCTGCTGGATATAATGATTCCATCAAAGGATATTCTTCATAA
19019777 TCTTCTGCTGGATATAATGATTCCATCAAAGGATATTCTTCATAA
1 TCTTCTGCTGGATATAATGATTCCATCAAAGGATATTCTTCATAA
19019822 TCTTCT
1 TCTTCT
19019828 TCCCCTGCTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.43
Consensus pattern (45 bp):
TCTTCTGCTGGATATAATGATTCCATCAAAGGATATTCTTCATAA
Found at i:19022996 original size:43 final size:42
Alignment explanation
Indices: 19022929--19023151 Score: 268
Period size: 43 Copynumber: 5.2 Consensus size: 42
19022919 ACGTTTGCGG
* *
19022929 CGCCGCTATAGATCAGGACATTTAGCGGCGATTTTTCCACAAA
1 CGCCGCTATAGATCAAGACCTTTAGCGGCG-TTTTTCCACAAA
* * ** *
19022972 TGCCGCTATAGATCAATACCTTTAGCAACGCTTTTCACACAAA
1 CGCCGCTATAGATCAAGACCTTTAGCGGCGTTTTTC-CACAAA
* *
19023015 CGCCGCTATAGATCAATACCTTTAGCGGCG-CTTTCGACACAAA
1 CGCCGCTATAGATCAAGACCTTTAGCGGCGTTTTTC--CACAAA
* *
19023058 CGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTCTCCACAAA
1 CGCCGCTATAGATCAAGACCTTTAGCGGCG-TTTTTCCACAAA
* *
19023101 CGCCGCTATAGATCAAGAGCTTTAGCGGCGCTTTTCACACAAA
1 CGCCGCTATAGATCAAGACCTTTAGCGGCGTTTTTC-CACAAA
19023144 CGCCGCTA
1 CGCCGCTA
19023152 AAAACATATC
Statistics
Matches: 156, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
42 13 0.08
43 140 0.90
45 3 0.02
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (42 bp):
CGCCGCTATAGATCAAGACCTTTAGCGGCGTTTTTCCACAAA
Found at i:19023079 original size:86 final size:85
Alignment explanation
Indices: 19022929--19023151 Score: 297
Period size: 86 Copynumber: 2.6 Consensus size: 85
19022919 ACGTTTGCGG
* * * * *
19022929 CGCCGCTATAGATCAGGACATTTAGCGGCGATTTTTC-CACAAATGCCGCTATAGATCAATACCT
1 CGCCGCTATAGATCAAGACCTTTAGCGGCG--CTTTCACACAAACGCCGCTATAGATCAAGACCT
19022993 TTAGCAACGCTTT-TCACACAAA
64 TTAGCAACGCTTTCTC-CACAAA
* *
19023015 CGCCGCTATAGATCAATACCTTTAGCGGCGCTTTCGACACAAACGCCGCTATAGCTCAAGACCTT
1 CGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTC-ACACAAACGCCGCTATAGATCAAGACCTT
**
19023080 TAGCGGCGCTTTCTCCACAAA
65 TAGCAACGCTTTCTCCACAAA
*
19023101 CGCCGCTATAGATCAAGAGCTTTAGCGGCGCTTTTCACACAAACGCCGCTA
1 CGCCGCTATAGATCAAGACCTTTAGCGGCGC-TTTCACACAAACGCCGCTA
19023152 AAAACATATC
Statistics
Matches: 122, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
84 4 0.03
86 112 0.92
87 6 0.05
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (85 bp):
CGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTCACACAAACGCCGCTATAGATCAAGACCTTT
AGCAACGCTTTCTCCACAAA
Found at i:19023480 original size:43 final size:43
Alignment explanation
Indices: 19023416--19023500 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
19023406 ATATGCAAGA
* * *
19023416 TAATAAAACATACAATTCATTTTCTTAATCAAGTAAATCTTGG
1 TAATAAAACATACAATACATTTACTTAATCAAGAAAATCTTGG
* *
19023459 TAATAAAAGATATAATACATTTACTTAATCAAGAAAATCTTG
1 TAATAAAACATACAATACATTTACTTAATCAAGAAAATCTTG
19023501 TACATCATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (43 bp):
TAATAAAACATACAATACATTTACTTAATCAAGAAAATCTTGG
Found at i:19027688 original size:21 final size:22
Alignment explanation
Indices: 19027649--19027689 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
19027639 ATCTAACCCC
19027649 TAAACCCCTAACCCCTAAACAT
1 TAAACCCCTAACCCCTAAACAT
* *
19027671 TAAATCCC-AACCCTTAAAC
1 TAAACCCCTAACCCCTAAAC
19027690 CATAATCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (22 bp):
TAAACCCCTAACCCCTAAACAT
Found at i:19027707 original size:14 final size:14
Alignment explanation
Indices: 19027690--19027733 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
19027680 ACCCTTAAAC
19027690 CATAATCCCTAATT
1 CATAATCCCTAATT
*
19027704 CATAATCCCTAAATC
1 CATAATCCCT-AATT
19027719 CATACA-CCCTAATT
1 CATA-ATCCCTAATT
19027733 C
1 C
19027734 TTAAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 14 0.54
15 11 0.42
16 1 0.04
ACGTcount: A:0.36, C:0.34, G:0.00, T:0.30
Consensus pattern (14 bp):
CATAATCCCTAATT
Found at i:19027951 original size:15 final size:15
Alignment explanation
Indices: 19027931--19028017 Score: 56
Period size: 15 Copynumber: 5.9 Consensus size: 15
19027921 CCTAGCACGT
19027931 CTAACCCCTAAACCC
1 CTAACCCCTAAACCC
19027946 CTAACCCTCT-AACCC
1 CTAACCC-CTAAACCC
* * **
19027961 CTAAACCTTAAATAC
1 CTAACCCCTAAACCC
*
19027976 C-AACCCCT-AATCC
1 CTAACCCCTAAACCC
* *
19027989 ATAATCCCTAAACCC
1 CTAACCCCTAAACCC
*
19028004 AT-ACTCCCTAAACC
1 CTAAC-CCCTAAACC
19028018 TTAAAATATG
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
13 4 0.07
14 13 0.23
15 37 0.66
16 2 0.04
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.20
Consensus pattern (15 bp):
CTAACCCCTAAACCC
Found at i:19027967 original size:8 final size:7
Alignment explanation
Indices: 19027931--19027964 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 7
19027921 CCTAGCACGT
19027931 CTAACCC
1 CTAACCC
19027938 CTAAACCC
1 CT-AACCC
19027946 CTAACCC
1 CTAACCC
19027953 TCTAACCC
1 -CTAACCC
19027961 CTAA
1 CTAA
19027965 ACCTTAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 11 0.44
8 14 0.56
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAACCC
Found at i:19028471 original size:114 final size:114
Alignment explanation
Indices: 19028271--19028773 Score: 704
Period size: 114 Copynumber: 4.4 Consensus size: 114
19028261 ATTTTTAGCA
* * ** *
19028271 GCGCTTTCCGAAAAACGCCGCTAAAGACCTGCGCATTAGCGGCACTTTCATAAAAACGCCGCTAA
1 GCGCTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTTCATAAAAACGCCGCTAA
* * *
19028336 ATCCCTGAAAGCTCATAAAACGGCGTCATTGGACTGAGGTGATTTTGCG
66 ATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGACTGAGGTGATTTTGCG
*
19028385 GCGCTTTCCCAAAAATGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTTCATAAAAACGCCGCTAA
1 GCGCTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTTCATAAAAACGCCGCTAA
*
19028450 ATCCCCGAAAGCTCATAAAACGGCGTCGTTGGACTGAGGTGATTTTGCG
66 ATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGACTGAGGTGATTTTGCG
* * *
19028499 GCGCTTTCCCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCATAAAAACACCGCTAA
1 GCGCTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTTCATAAAAACGCCGCTAA
*** *
19028564 ATTTTCAAAAGCTCAGAAAACGGCGTCGTTGGACTGAGGTGATTTTGCG
66 ATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGACTGAGGTGATTTTGCG
* *
19028613 GCGCTTTTCCCAAAAACGCCGCTAAAGCTCTGAA-CATTAGCGGCGCTTTCTTAAAAACGCCGCT
1 GCGC-TTTCCCAAAAACGCCGCTAAAGCCCT-AAGCATTAGCGGCGCTTTCATAAAAACGCCGCT
* * * * * **
19028677 AAATCCTCGAAAGCTCAGGAAATGGCGTCGTTGGGCTTAGGTTTTTTTGCG
64 AAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGACTGAGGTGATTTTGCG
* * *
19028728 GCGCTTCCCCAAAAATGCCGCTAAAGGCCTGAA-CATTAGCGGCGCT
1 GCGCTTTCCCAAAAACGCCGCTAAAGCCCT-AAGCATTAGCGGCGCT
19028774 CCGAAAGCTC
Statistics
Matches: 352, Mismatches: 35, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
114 253 0.72
115 98 0.28
116 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (114 bp):
GCGCTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTTCATAAAAACGCCGCTAA
ATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGACTGAGGTGATTTTGCG
Found at i:19028690 original size:229 final size:228
Alignment explanation
Indices: 19028271--19028773 Score: 724
Period size: 229 Copynumber: 2.2 Consensus size: 228
19028261 ATTTTTAGCA
* * *
19028271 GCGCTTT-CCGAAAAACGCCGCTAAAGACCTGCGCATTAGCGGCACTTTCATAAAAACGCCGCTA
1 GCGCTTTCCCG-AAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTCATAAAAACACCGCTA
* *
19028335 AATCCCTGAAAGCTCATAAAACGGCGTCATTGGACTGAGGTGATTTTGCGGCGCTTTCCCAAAAA
65 AATCCCTAAAAGCTCAGAAAACGGCGTCATTGGACTGAGGTGATTTTGCGGCGCTTTCCCAAAAA
*
19028400 TGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTTCATAAAAACGCCGCTAAATCCCCGAAAGCTCA
130 CGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTTCATAAAAACGCCGCTAAATCCCCGAAAGCTCA
*
19028465 TAAAACGGCGTCGTTGGACTGAGGTGATTTTGCG
195 GAAAACGGCGTCGTTGGACTGAGGTGATTTTGCG
*
19028499 GCGCTTTCCCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCATAAAAACACCGCTAA
1 GCGCTTTCCCGAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTCATAAAAACACCGCTAA
** *
19028564 AT-TTTCAAAAGCTCAGAAAACGGCGTCGTTGGACTGAGGTGATTTTGCGGCGCTTTTCCCAAAA
66 ATCCCT-AAAAGCTCAGAAAACGGCGTCATTGGACTGAGGTGATTTTGCGGCGC-TTTCCCAAAA
* * *
19028628 ACGCCGCTAAAGCTCTGAA-CATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCTCGAAAGCT
129 ACGCCGCTAAAGCCCT-AAGCATTAGCGGCGCTTTCATAAAAACGCCGCTAAATCCCCGAAAGCT
* * * * **
19028692 CAGGAAATGGCGTCGTTGGGCTTAGGTTTTTTTGCG
193 CAGAAAACGGCGTCGTTGGACTGAGGTGATTTTGCG
* * * * *
19028728 GCGCTTCCCCAAAAATGCCGCTAAAGGCCTGAACATTAGCGGCGCT
1 GCGCTTTCCCGAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCT
19028774 CCGAAAGCTC
Statistics
Matches: 246, Mismatches: 25, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
227 1 0.00
228 103 0.42
229 140 0.57
230 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (228 bp):
GCGCTTTCCCGAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTCATAAAAACACCGCTAA
ATCCCTAAAAGCTCAGAAAACGGCGTCATTGGACTGAGGTGATTTTGCGGCGCTTTCCCAAAAAC
GCCGCTAAAGCCCTAAGCATTAGCGGCGCTTTCATAAAAACGCCGCTAAATCCCCGAAAGCTCAG
AAAACGGCGTCGTTGGACTGAGGTGATTTTGCG
Found at i:19028839 original size:91 final size:91
Alignment explanation
Indices: 19028684--19028864 Score: 265
Period size: 91 Copynumber: 2.0 Consensus size: 91
19028674 GCTAAATCCT
** * * * * *
19028684 CGAAAGCTCAGGAAATGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTCCCCAAAAATGCCGC
1 CGAAAGCTCACAAAACGACGTCGTTGGGCTTAGATTTTTTTGCGGCACTTCCCCAAAAACGCCGC
*
19028749 TAAAGGCCTGAACATTAGCGGCGCTC
66 TAAAGCCCTGAACATTAGCGGCGCTC
19028775 CGAAAGCTCACAAAACGACGTCGTTGGGCTTAGATTTTTTTGCGGCACTTCCTCC-AAAACGCCG
1 CGAAAGCTCACAAAACGACGTCGTTGGGCTTAGATTTTTTTGCGGCACTTCC-CCAAAAACGCCG
*
19028839 CTAAAGCCCTGAGCATTAGCGGCGCT
65 CTAAAGCCCTGAACATTAGCGGCGCT
19028865 TTCTTAAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 78 0.98
92 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (91 bp):
CGAAAGCTCACAAAACGACGTCGTTGGGCTTAGATTTTTTTGCGGCACTTCCCCAAAAACGCCGC
TAAAGCCCTGAACATTAGCGGCGCTC
Found at i:19029312 original size:14 final size:15
Alignment explanation
Indices: 19029283--19029323 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
19029273 GGGGTTGTTA
*
19029283 ATTTTGATTTTAATTT
1 ATTTTG-TTTTTATTT
19029299 A-TTTGTTTTTATTT
1 ATTTTGTTTTTATTT
19029313 ATTTTGTTTTT
1 ATTTTGTTTTT
19029324 TCAAAATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 9 0.39
15 13 0.57
16 1 0.04
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (15 bp):
ATTTTGTTTTTATTT
Found at i:19038813 original size:40 final size:40
Alignment explanation
Indices: 19038758--19038869 Score: 154
Period size: 40 Copynumber: 2.8 Consensus size: 40
19038748 GGCGTTTGGA
*
19038758 TAAAAAAACACCGCTAAAAATCAAGCATTAGCGACGCTTT
1 TAAAAAAACACCGCTAAAAATCGAGCATTAGCGACGCTTT
* * *
19038798 TAAAAAAACACCGCTAAAGATCGAGCATTAGTGGCGCTTT
1 TAAAAAAACACCGCTAAAAATCGAGCATTAGCGACGCTTT
** *
19038838 TTGAAAAACGCCGCTAAAAAT-GAGCATTAGCG
1 TAAAAAAACACCGCTAAAAATCGAGCATTAGCG
19038870 GCTTTTCTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
39 10 0.16
40 53 0.84
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (40 bp):
TAAAAAAACACCGCTAAAAATCGAGCATTAGCGACGCTTT
Found at i:19038884 original size:40 final size:40
Alignment explanation
Indices: 19038761--19038884 Score: 137
Period size: 40 Copynumber: 3.1 Consensus size: 40
19038751 GTTTGGATAA
* * *
19038761 AAAAACACCGCTAAAAATCAAGCATTAGCGACGC-TTTTAA
1 AAAAACACCGCTAAAAATCGAGCATTAGCGGC-CTTTTTAG
* *
19038801 AAAAACACCGCTAAAGATCGAGCATTAGTGGCGCTTTTT-G
1 AAAAACACCGCTAAAAATCGAGCATTAGCGGC-CTTTTTAG
* *
19038841 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCTTTTCTTAG
1 AAAAACACCGCTAAAAATCGAGCATTAGCGGCCTTT-TTAG
19038881 AAAA
1 AAAA
19038885 GCGCCGCAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
38 3 0.04
39 14 0.19
40 51 0.71
41 4 0.06
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.23
Consensus pattern (40 bp):
AAAAACACCGCTAAAAATCGAGCATTAGCGGCCTTTTTAG
Found at i:19039034 original size:42 final size:40
Alignment explanation
Indices: 19038934--19039082 Score: 201
Period size: 41 Copynumber: 3.6 Consensus size: 40
19038924 ACCTTTCGGG
* * *
19038934 GCTTTAGCCGCGTTTTTGAAAAAACGTCGCTAATGCTCAAA
1 GCTTTAGCGGCGTTTTTGGAAAAGCGTCGCTAATGCTC-AA
19038975 GCTTTAGCGGCGTTTTTGGAAAAGCG-CTGCTAATGCTCAGA
1 GCTTTAGCGGCGTTTTTGGAAAAGCGTC-GCTAATGCTCA-A
19039016 GCTTTAGCGGCGTTTTTTGGAAAAGCGTCGCTAATGCTCAA
1 GCTTTAGCGGCG-TTTTTGGAAAAGCGTCGCTAATGCTCAA
* **
19039057 GATTTAGCGGCGTTTTTAAAAAAGCG
1 GCTTTAGCGGCGTTTTTGGAAAAGCG
19039083 CCGCAAAAAC
Statistics
Matches: 98, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
40 14 0.14
41 58 0.59
42 25 0.26
43 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (40 bp):
GCTTTAGCGGCGTTTTTGGAAAAGCGTCGCTAATGCTCAA
Found at i:19039513 original size:15 final size:14
Alignment explanation
Indices: 19039493--19039536 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
19039483 AAGGTTTATA
19039493 GATTATGGAATTAAG
1 GATTATGG-ATTAAG
*
19039508 GATTATGGATTAGG
1 GATTATGGATTAAG
* *
19039522 GATTCTGGTTTAAG
1 GATTATGGATTAAG
19039536 G
1 G
19039537 GTTGTGATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (14 bp):
GATTATGGATTAAG
Found at i:19039684 original size:7 final size:7
Alignment explanation
Indices: 19039672--19039765 Score: 116
Period size: 7 Copynumber: 13.4 Consensus size: 7
19039662 TAAATAATGT
19039672 TTAGGGG
1 TTAGGGG
19039679 TTAGGGG
1 TTAGGGG
*
19039686 TTGGGGG
1 TTAGGGG
**
19039693 TTAGTAG
1 TTAGGGG
19039700 TTAGGGG
1 TTAGGGG
19039707 TTAGGGG
1 TTAGGGG
*
19039714 TTGGGGG
1 TTAGGGG
**
19039721 TTAGTAG
1 TTAGGGG
19039728 TTAGGGG
1 TTAGGGG
19039735 TTAGGGG
1 TTAGGGG
*
19039742 TTTGGGG
1 TTAGGGG
19039749 TTAGGGG
1 TTAGGGG
*
19039756 TTAGAGG
1 TTAGGGG
19039763 TTA
1 TTA
19039766 AGAGTTAGTA
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 72 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:19039765 original size:28 final size:28
Alignment explanation
Indices: 19039672--19039752 Score: 153
Period size: 28 Copynumber: 2.9 Consensus size: 28
19039662 TAAATAATGT
19039672 TTAGGGGTTAGGGGTTGGGGGTTAGTAG
1 TTAGGGGTTAGGGGTTGGGGGTTAGTAG
19039700 TTAGGGGTTAGGGGTTGGGGGTTAGTAG
1 TTAGGGGTTAGGGGTTGGGGGTTAGTAG
*
19039728 TTAGGGGTTAGGGGTTTGGGGTTAG
1 TTAGGGGTTAGGGGTTGGGGGTTAG
19039753 GGGTTAGAGG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.14, C:0.00, G:0.53, T:0.33
Consensus pattern (28 bp):
TTAGGGGTTAGGGGTTGGGGGTTAGTAG
Found at i:19039890 original size:7 final size:7
Alignment explanation
Indices: 19039878--19039931 Score: 72
Period size: 7 Copynumber: 7.6 Consensus size: 7
19039868 ATTGTAAAAG
19039878 AGGGGTT
1 AGGGGTT
19039885 AGGGGTT
1 AGGGGTT
*
19039892 AGAGGTT
1 AGGGGTT
19039899 AGGGGTT
1 AGGGGTT
*
19039906 AAGGGTT
1 AGGGGTT
*
19039913 AGTGGTT
1 AGGGGTT
19039920 AGGGGTTT
1 AGGGG-TT
19039928 AGGG
1 AGGG
19039932 TTTATGTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
7 34 0.85
8 6 0.15
ACGTcount: A:0.19, C:0.00, G:0.52, T:0.30
Consensus pattern (7 bp):
AGGGGTT
Found at i:19039904 original size:21 final size:21
Alignment explanation
Indices: 19039878--19039931 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
19039868 ATTGTAAAAG
19039878 AGGGGTTAGGGGTTAGAGGTT
1 AGGGGTTAGGGGTTAGAGGTT
* *
19039899 AGGGGTTAAGGGTTAGTGGTT
1 AGGGGTTAGGGGTTAGAGGTT
19039920 AGGGGTTTAGGG
1 AGGGG-TTAGGG
19039932 TTTATGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.19, C:0.00, G:0.52, T:0.30
Consensus pattern (21 bp):
AGGGGTTAGGGGTTAGAGGTT
Found at i:19040697 original size:113 final size:115
Alignment explanation
Indices: 19040515--19040741 Score: 361
Period size: 113 Copynumber: 2.0 Consensus size: 115
19040505 ACCGCAAAAG
19040515 GTAAGCAATAGCGGCGTTTTATAAAAAACGCCACAAAAAATAATTTTACTATAAAAAATAGCACC
1 GTAAGCAATAGCGGCG-TTTATAAAAAACGCCACAAAAAATAATTTTACTATAAAAAATAGCACC
* *
19040580 ATTTTATATAGCAAAATAGTATCGTTTTATTCCAAATGAAATAATTTTTGC
65 ATTTTACATAGCAAAACAGTATCGTTTTATTCCAAATGAAATAATTTTTGC
* *
19040631 GTAAGCAATAGCGGCG-TT-T-AAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAGCGCC
1 GTAAGCAATAGCGGCGTTTATAAAAAACGCCACAAAAAATAATTTTACTAT-AAAAAATAGCACC
* *
19040693 ATTTTACATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATATTTTTT
65 ATTTTACATAGCAAAACAGTATCGTTTTATTCCAAATGAAATAATTTTT
19040742 TGCGGCGTTT
Statistics
Matches: 104, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
112 28 0.27
113 58 0.56
114 2 0.02
116 16 0.15
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.32
Consensus pattern (115 bp):
GTAAGCAATAGCGGCGTTTATAAAAAACGCCACAAAAAATAATTTTACTATAAAAAATAGCACCA
TTTTACATAGCAAAACAGTATCGTTTTATTCCAAATGAAATAATTTTTGC
Found at i:19041257 original size:11 final size:11
Alignment explanation
Indices: 19041241--19041266 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19041231 TTTTCCTCAT
19041241 TTTTCTTTTTG
1 TTTTCTTTTTG
19041252 TTTTCTTTTTG
1 TTTTCTTTTTG
19041263 TTTT
1 TTTT
19041267 GTTCTACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:19044022 original size:43 final size:43
Alignment explanation
Indices: 19043929--19044050 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
19043919 AATTTTTTTT
19043929 AAAAAGTCATGT-TTTTAGCGGCGTTTGT-GAAAAAGCATCGC
1 AAAAAGTCATGTCTTTTAGCGGCGTTTGTGGAAAAAGCATCGC
* * * * *
19043970 TAAAGGTCAT-TCTTTATAGTGGCGTTTGTGGTAGAAGCATCGC
1 AAAAAGTCATGTCTTT-TAGCGGCGTTTGTGGAAAAAGCATCGC
*
19044013 AAAAAGTCATGATC-TTTAGCGGCGTTTGTGGGAAAAGC
1 AAAAAGTCATG-TCTTTTAGCGGCGTTTGTGGAAAAAGC
19044051 GCCGCAAATG
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
40 1 0.02
41 11 0.17
42 12 0.18
43 38 0.58
44 2 0.03
45 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (43 bp):
AAAAAGTCATGTCTTTTAGCGGCGTTTGTGGAAAAAGCATCGC
Found at i:19046054 original size:3 final size:3
Alignment explanation
Indices: 19046048--19046098 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
19046038 TATTATTATT
*
19046048 ATC ATC AAC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
19046096 ATC
1 ATC
19046099 GCAACTATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:19047827 original size:23 final size:23
Alignment explanation
Indices: 19047774--19047817 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
19047764 CACCAATGTG
19047774 CCAAAATGAATTGCACCGTAGAT
1 CCAAAATGAATTGCACCGTAGAT
*
19047797 CCAAAATGAATTGCATCGTAG
1 CCAAAATGAATTGCACCGTAG
19047818 TGCTAGAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (23 bp):
CCAAAATGAATTGCACCGTAGAT
Found at i:19048691 original size:30 final size:30
Alignment explanation
Indices: 19048655--19048754 Score: 111
Period size: 30 Copynumber: 3.5 Consensus size: 30
19048645 TTCAAACCAA
* *
19048655 ATCATATCATAACAAAACATATTATAATGT
1 ATCATATCATATCATAACATATTATAATGT
* * *
19048685 ATCATATCATATCGTAACGTA--A-CA--T
1 ATCATATCATATCATAACATATTATAATGT
*
19048710 AGCATATCATATCATAACATATTATAATGT
1 ATCATATCATATCATAACATATTATAATGT
19048740 ATCATATCATATCAT
1 ATCATATCATATCAT
19048755 GTCATACCGT
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
25 19 0.35
27 2 0.04
28 2 0.04
30 32 0.58
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (30 bp):
ATCATATCATATCATAACATATTATAATGT
Found at i:19048692 original size:5 final size:5
Alignment explanation
Indices: 19048684--19048784 Score: 69
Period size: 5 Copynumber: 20.2 Consensus size: 5
19048674 TATTATAATG
* * * * * * *
19048684 TATCA TATCA TATCG TAACG TAACA TAGCA TATCA TATCA TAACA TATTA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
* * * * * *
19048734 TAAT-G TATCA TATCA TATCA TGTCA TACCG TAACA TAACA TATCA TATCA
1 T-ATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
19048784 T
1 T
19048785 GTCCTACCCC
Statistics
Matches: 77, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
4 2 0.03
5 73 0.95
6 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.35
Consensus pattern (5 bp):
TATCA
Found at i:19048742 original size:25 final size:25
Alignment explanation
Indices: 19048659--19048750 Score: 78
Period size: 25 Copynumber: 3.5 Consensus size: 25
19048649 AACCAAATCA
* *
19048659 TATCATAACAAAACATATTATAATG
1 TATCATATCATAACATATTATAATG
* * *
19048684 TATCATATCATATCGTAACGTA-ACATAG
1 TATCATATCATAACAT-A-TTATA-AT-G
19048712 CATATCATATCATAACATATTATAATG
1 --TATCATATCATAACATATTATAATG
19048739 TATCATATCATA
1 TATCATATCATA
19048751 TCATGTCATA
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
25 24 0.46
26 2 0.04
27 5 0.10
28 5 0.10
29 2 0.04
30 14 0.27
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (25 bp):
TATCATATCATAACATATTATAATG
Found at i:19048787 original size:30 final size:30
Alignment explanation
Indices: 19048684--19048784 Score: 103
Period size: 30 Copynumber: 3.4 Consensus size: 30
19048674 TATTATAATG
* * *
19048684 TATCATATCATATCGTAACGTAACATAGCA
1 TATCATATCATATCATACCGTAACATAACA
* *** ** *
19048714 TATCATATCATAACATATTATAATGTATCA
1 TATCATATCATATCATACCGTAACATAACA
*
19048744 TATCATATCATGTCATACCGTAACATAACA
1 TATCATATCATATCATACCGTAACATAACA
19048774 TATCATATCAT
1 TATCATATCAT
19048785 GTCCTACCCC
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.35
Consensus pattern (30 bp):
TATCATATCATATCATACCGTAACATAACA
Found at i:19052968 original size:7 final size:7
Alignment explanation
Indices: 19052956--19052985 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
19052946 AATGTGAAAT
19052956 TTGGATA
1 TTGGATA
19052963 TTGGATA
1 TTGGATA
19052970 TTGGATA
1 TTGGATA
19052977 TTGGATA
1 TTGGATA
19052984 TT
1 TT
19052986 TGTTGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (7 bp):
TTGGATA
Found at i:19055230 original size:27 final size:27
Alignment explanation
Indices: 19055200--19055429 Score: 180
Period size: 27 Copynumber: 8.5 Consensus size: 27
19055190 CCCAACGGAT
* *
19055200 TACCCCGTGTTTACTGTCTTGGTGGAC
1 TACCCTGTGTTTACTGTCTCGGTGGAC
* * *
19055227 TACCCTGTATTTACTGTCCCGGTGAAC
1 TACCCTGTGTTTACTGTCTCGGTGGAC
** *
19055254 TACCCCATGTTTACTGT-TCCGATGGAC
1 TACCCTGTGTTTACTGTCT-CGGTGGAC
* * ***
19055281 TACCATATGTTTACTGTAC-CGACAGAC
1 TACCCTGTGTTTACTGT-CTCGGTGGAC
* *
19055308 TACCCTGTGTTTACTGTCCCGGTGAAC
1 TACCCTGTGTTTACTGTCTCGGTGGAC
**
19055335 TACCCCATGTTTACTGT-TCCGGTGGAC
1 TACCCTGTGTTTACTGTCT-CGGTGGAC
* * *
19055362 TACCATGTGTTTACTGTAC-CGATAGAC
1 TACCCTGTGTTTACTGT-CTCGGTGGAC
* *
19055389 TACCCTGTGTTTATTGTCTCGGTAGAC
1 TACCCTGTGTTTACTGTCTCGGTGGAC
* *
19055416 TACTCTATGTTTAC
1 TACCCTGTGTTTAC
19055430 ACATTAGACC
Statistics
Matches: 159, Mismatches: 36, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
26 2 0.01
27 157 0.99
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.35
Consensus pattern (27 bp):
TACCCTGTGTTTACTGTCTCGGTGGAC
Found at i:19055311 original size:81 final size:81
Alignment explanation
Indices: 19055224--19055429 Score: 324
Period size: 81 Copynumber: 2.5 Consensus size: 81
19055214 TGTCTTGGTG
*
19055224 GACTACCCTGTATTTACTGTCCCGGTGAACTACCCCATGTTTACTGTTCCGATGGACTACCATAT
1 GACTACCCTGTGTTTACTGTCCCGGTGAACTACCCCATGTTTACTGTTCCGATGGACTACCATAT
19055289 GTTTACTGTACCGACA
66 GTTTACTGTACCGACA
* *
19055305 GACTACCCTGTGTTTACTGTCCCGGTGAACTACCCCATGTTTACTGTTCCGGTGGACTACCATGT
1 GACTACCCTGTGTTTACTGTCCCGGTGAACTACCCCATGTTTACTGTTCCGATGGACTACCATAT
*
19055370 GTTTACTGTACCGATA
66 GTTTACTGTACCGACA
* * * *
19055386 GACTACCCTGTGTTTATTGTCTCGGT-AGACTACTCTATGTTTAC
1 GACTACCCTGTGTTTACTGTCCCGGTGA-ACTACCCCATGTTTAC
19055430 ACATTAGACC
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 1 0.01
81 115 0.99
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (81 bp):
GACTACCCTGTGTTTACTGTCCCGGTGAACTACCCCATGTTTACTGTTCCGATGGACTACCATAT
GTTTACTGTACCGACA
Found at i:19056696 original size:114 final size:114
Alignment explanation
Indices: 19056457--19056661 Score: 322
Period size: 114 Copynumber: 1.8 Consensus size: 114
19056447 AACCCTCAAT
* *
19056457 CCTTAATCATTTTGTCTTCTACTTTGGAACCAGCCAGTTCCATCCTAAGGGAACTAGAATTGAGA
1 CCTTAACCATTTTGTCTTCTACTTTGGAACCAGCCAGTTCCATCCTAAGAGAACTAGAATTGAGA
* ** * * *
19056522 TCCAAATAATCTCAATTTTGTCTTCTACTTTGGAACCAGCCAGTTCCAT
66 TCCAAATAATCTCAATTTTGGCCACTACTTTGGAACCAGCCAGGTACAG
*
19056571 CCTTAATCATTTTGTCTTCTACTTTGGAACCAGCCAGTTCCATCCTAAGAGAACTAGAATTGAGA
1 CCTTAACCATTTTGTCTTCTACTTTGGAACCAGCCAGTTCCATCCTAAGAGAACTAGAATTGAGA
19056636 TCCAAATAATCTCAA-TTTGGCCACTA
66 TCCAAATAATCTCAATTTTGGCCACTA
19056662 AAACTTTTTA
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
113 8 0.09
114 79 0.91
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (114 bp):
CCTTAACCATTTTGTCTTCTACTTTGGAACCAGCCAGTTCCATCCTAAGAGAACTAGAATTGAGA
TCCAAATAATCTCAATTTTGGCCACTACTTTGGAACCAGCCAGGTACAG
Found at i:19074870 original size:159 final size:159
Alignment explanation
Indices: 19074657--19074976 Score: 550
Period size: 159 Copynumber: 2.0 Consensus size: 159
19074647 CGGACTAAAA
* * **
19074657 TCGATCTTGACTTTCTATCGAATAGCCTTATCAGTTATTCTCAAATTACGAACTGCTTTGAGTGT
1 TCGATCTTGACTTTCTATCGAACAACCTTATCAGTTATTCTCAAACCACGAACTGCTTTGAGTGT
* * *
19074722 GTGCTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTTACTTTCAGTAGGAAGGC
66 GTACTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTAACTTTCAGAAGGAAGGC
19074787 TAATTCTCTCTATAAACGAAAACTATGCG
131 TAATTCTCTCTATAAACGAAAACTATGCG
19074816 TCGATCTTGACTTTCTATCGAACAACCTTATCAGTTATTCTCAAACCACGAACTGCTTTGAGTGT
1 TCGATCTTGACTTTCTATCGAACAACCTTATCAGTTATTCTCAAACCACGAACTGCTTTGAGTGT
*
19074881 GTACTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTAACTTTCAGAAGGAAGGT
66 GTACTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTAACTTTCAGAAGGAAGGC
* *
19074946 TAATTCTCTCTATGAACGGAAACTATGCG
131 TAATTCTCTCTATAAACGAAAACTATGCG
19074975 TC
1 TC
19074977 TTTGAAATTA
Statistics
Matches: 151, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
159 151 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34
Consensus pattern (159 bp):
TCGATCTTGACTTTCTATCGAACAACCTTATCAGTTATTCTCAAACCACGAACTGCTTTGAGTGT
GTACTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTAACTTTCAGAAGGAAGGC
TAATTCTCTCTATAAACGAAAACTATGCG
Found at i:19075361 original size:16 final size:17
Alignment explanation
Indices: 19075332--19075367 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
19075322 TTAATCAATT
19075332 AATTAAATTAATTTCTC
1 AATTAAATTAATTTCTC
*
19075349 AATTAAA-TAATTTTTC
1 AATTAAATTAATTTCTC
19075365 AAT
1 AAT
19075368 CCAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAATTAATTTCTC
Found at i:19075512 original size:14 final size:15
Alignment explanation
Indices: 19075493--19075526 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
19075483 CTTTGAGTTT
*
19075493 TAATTATTTAATT-A
1 TAATTAATTAATTAA
19075507 TAATTAATTAATTAA
1 TAATTAATTAATTAA
19075522 TAATT
1 TAATT
19075527 TGAAGAACTT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTAATTAATTAA
Found at i:19077518 original size:43 final size:43
Alignment explanation
Indices: 19077409--19077523 Score: 117
Period size: 43 Copynumber: 2.7 Consensus size: 43
19077399 AGCTCGTACA
* * * * * *
19077409 ATGCCAACGTCTCATACATGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAAACGTGGTCTTACACGTAAACACAAATCG
*
19077452 ATGCC-ACTGTCCCAAATAG-GGTCTTACACGTAAACACAAATCG
1 ATGCCAAC-GTCCCAAA-CGTGGTCTTACACGTAAACACAAATCG
* *
19077495 ATGCCAACATCCCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAAACGTGGTCTTACAC
19077524 AAAAAACACA
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
42 3 0.05
43 53 0.91
44 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAAACGTGGTCTTACACGTAAACACAAATCG
Found at i:19082738 original size:24 final size:25
Alignment explanation
Indices: 19082710--19082763 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
19082700 TGGAAGTAAA
19082710 GAAAAAAACTATG-TTAATTACACC
1 GAAAAAAACTATGTTTAATTACACC
*** *
19082734 GAAAATCCCTCTGTTTAATTACACC
1 GAAAAAAACTATGTTTAATTACACC
19082759 GAAAA
1 GAAAA
19082764 TCCCTCCGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.26
Consensus pattern (25 bp):
GAAAAAAACTATGTTTAATTACACC
Found at i:19082756 original size:25 final size:25
Alignment explanation
Indices: 19082723--19082774 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
19082713 AAAAACTATG
*
19082723 TTAATTACACCGAAAATCCCTCTGT
1 TTAATTACACCGAAAATCCCTCCGT
19082748 TTAATTACACCGAAAATCCCTCCGT
1 TTAATTACACCGAAAATCCCTCCGT
19082773 TT
1 TT
19082775 TTTCCTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.33
Consensus pattern (25 bp):
TTAATTACACCGAAAATCCCTCCGT
Found at i:19083158 original size:17 final size:18
Alignment explanation
Indices: 19083121--19083158 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19083111 CTAAAACCTT
*
19083121 AAACCCTAATTCCTAAAA
1 AAACCCTAATCCCTAAAA
19083139 AAACCCTAA-CCCTAACAA
1 AAACCCTAATCCCTAA-AA
19083157 AA
1 AA
19083159 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.16
Consensus pattern (18 bp):
AAACCCTAATCCCTAAAA
Found at i:19083158 original size:18 final size:18
Alignment explanation
Indices: 19083121--19083158 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
19083111 CTAAAACCTT
*
19083121 AAACCCTAATTCCTAAAA
1 AAACCCTAATCCCTAAAA
*
19083139 AAACCCTAA-CCCTAACA
1 AAACCCTAATCCCTAAAA
19083156 AAA
1 AAA
19083159 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.16
Consensus pattern (18 bp):
AAACCCTAATCCCTAAAA
Found at i:19090468 original size:83 final size:83
Alignment explanation
Indices: 19090329--19090490 Score: 288
Period size: 83 Copynumber: 2.0 Consensus size: 83
19090319 TAAAGGAACG
19090329 GTTTTACAAAATAGGGAAGGATAGTGGATGAAAAGTAACTTGGAGAAAAAATTCAAACCCACTTG
1 GTTTTACAAAATAGGGAAGGATAGTGGATGAAAAGTAACTTGGAGAAAAAATTCAAACCCACTTG
19090394 AATGCCCCTCTTAGACTA
66 AATGCCCCTCTTAGACTA
* * * *
19090412 GTTTTACAAAATAGGGGAGGATGGTGGATGAGAAGTAACTTGGAGAAAAATTTCAAACCCACTTG
1 GTTTTACAAAATAGGGAAGGATAGTGGATGAAAAGTAACTTGGAGAAAAAATTCAAACCCACTTG
19090477 AATGCCCCTCTTAG
66 AATGCCCCTCTTAG
19090491 GCTTCCTCCA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 75 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (83 bp):
GTTTTACAAAATAGGGAAGGATAGTGGATGAAAAGTAACTTGGAGAAAAAATTCAAACCCACTTG
AATGCCCCTCTTAGACTA
Found at i:19094723 original size:20 final size:20
Alignment explanation
Indices: 19094682--19094724 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
19094672 ATTTTTTATC
* *
19094682 TTTTCCTTCTTTCTTTTTTT
1 TTTTCCTTCTTTCTATTCTT
19094702 TTTTCC-TCTTTTCTATTCTT
1 TTTTCCTTC-TTTCTATTCTT
19094722 TTT
1 TTT
19094725 GCCATCCCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTCCTTCTTTCTATTCTT
Found at i:19095300 original size:41 final size:40
Alignment explanation
Indices: 19095255--19095383 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 40
19095245 AGCGGCATTT
19095255 TTAGCGGCG-TTTGGATAAAAAACGCCGCTAAAGATCGAGCA
1 TTAGCGGCGCTTT--ATAAAAAACGCCGCTAAAGATCGAGCA
* * * *
19095296 TTAGCGGCGCTTTTTAGAAAATGCCGCTAAAGATCGAGTA
1 TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGATCGAGCA
* * * * *
19095336 TTAGTGGCGCTTTATGAAAAACGCTGCTAAA-AACAAGCA
1 TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGATCGAGCA
*
19095375 TTAGTGGCG
1 TTAGCGGCG
19095384 TTTTCCAGAA
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
39 14 0.19
40 48 0.65
41 9 0.12
42 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.24
Consensus pattern (40 bp):
TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGATCGAGCA
Found at i:19095326 original size:40 final size:40
Alignment explanation
Indices: 19095273--19095401 Score: 129
Period size: 40 Copynumber: 3.2 Consensus size: 40
19095263 GTTTGGATAA
19095273 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTTAG
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTTAG
* * * *
19095313 AAAATGCCGCTAAAGATCGAGTATTAGTGGCGCTTTAT-G
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTTAG
* * * * *
19095352 AAAAACGCTGCTAAA-AACAAGCATTAGTGGCG-TTTTCCAG
1 -AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTT-TAG
*
19095392 AAAGCGCCGC
1 AAAACGCCGC
19095402 AAAAAACCTA
Statistics
Matches: 73, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
38 3 0.04
39 23 0.32
40 47 0.64
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTTAG
Found at i:19095378 original size:39 final size:39
Alignment explanation
Indices: 19095272--19095387 Score: 137
Period size: 40 Copynumber: 3.0 Consensus size: 39
19095262 CGTTTGGATA
* *
19095272 AAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTT
1 AAAAACGCCGCTAAAGATCGAGCATTAGTGGCGCTTTTG
* *
19095311 AGAAAATGCCGCTAAAGATCGAGTATTAGTGGCGCTTTATG
1 A-AAAACGCCGCTAAAGATCGAGCATTAGTGGCGCTTT-TG
* * *
19095352 AAAAACGCTGCTAAA-AACAAGCATTAGTGGCG-TTTT
1 AAAAACGCCGCTAAAGATCGAGCATTAGTGGCGCTTTT
19095388 CCAGAAAGCG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
37 1 0.02
38 3 0.05
39 15 0.23
40 45 0.68
41 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (39 bp):
AAAAACGCCGCTAAAGATCGAGCATTAGTGGCGCTTTTG
Found at i:19095499 original size:41 final size:41
Alignment explanation
Indices: 19095442--19095776 Score: 471
Period size: 41 Copynumber: 8.2 Consensus size: 41
19095432 TGAGCTTTCG
*
19095442 GGGCTTTAGCGGCGTTTTTGGGAAAGCGCTGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCA
19095483 GGGCTTTAGCGGCG-TTTTGGGAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCA
*
19095523 GGGCTTTAG-GTGCGTTTTTGGGTAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCG-GCGTTTTTGGGAAAGCGCCGCTAATGCTCA
* *
19095564 GGGCTTTAGCGGTGTTTTTGGGGAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCA
19095605 GGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCA
*
19095646 GGGCTTTAGCGGCGTTTTTGGGAAAGCGCCACTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCA
*** *
19095687 GGGCTTTTAGCGGCGTTTTTGATTAAGCGCCGCGAATGCTCTA
1 GGGC-TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTC-A
** *** *
19095730 --TTTTTAGCGGCGTTTTTTAAAAAGCGTCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCA
*
19095769 GGGGTTTA
1 GGGCTTTA
19095777 AAATAATTTA
Statistics
Matches: 266, Mismatches: 21, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.01
40 68 0.26
41 163 0.61
42 32 0.12
43 1 0.00
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCA
Found at i:19096005 original size:22 final size:21
Alignment explanation
Indices: 19095980--19096027 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
19095970 GTGTTACCAT
* *
19095980 TTTAAGGTTTGTGGATTATGGG
1 TTTAAGGGTTATGGATTAT-GG
* *
19096002 TTTAGGGGTTATGGTTTATGG
1 TTTAAGGGTTATGGATTATGG
19096023 TTTAA
1 TTTAA
19096028 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:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (21 bp):
TTTAAGGGTTATGGATTATGG
Found at i:19096099 original size:20 final size:21
Alignment explanation
Indices: 19096065--19096104 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
19096055 TGTGTTAAGG
*
19096065 GTTTATGGTTTTAGGGTTTAA
1 GTTTATGGTTTTAGGATTTAA
19096086 GTTTATGG-TTTAGGATTTA
1 GTTTATGGTTTTAGGATTTA
19096105 GATTAACTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.53
Consensus pattern (21 bp):
GTTTATGGTTTTAGGATTTAA
Found at i:19096400 original size:21 final size:20
Alignment explanation
Indices: 19096367--19096407 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
19096357 TATGGATTTA
*
19096367 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
19096387 GGGATCTAAGGTTTAAGGGTT
1 GGGAT-TAAGGTTTAAGGGTT
19096408 AAGAGTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.22, C:0.02, G:0.39, T:0.37
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:19096954 original size:23 final size:23
Alignment explanation
Indices: 19096905--19096955 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
19096895 TTTTATCAAT
*
19096905 TATTTTCTTATTAAAATATCATT
1 TATTTTCTTATTAAAATATCATA
19096928 TATTTTCTTATTAAAATAT-ATAA
1 TATTTTCTTATTAAAATATCAT-A
19096951 TATTT
1 TATTT
19096956 ATTTTAAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTTTCTTATTAAAATATCATA
Found at i:19096960 original size:27 final size:23
Alignment explanation
Indices: 19096898--19096946 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
19096888 ACAACCATTT
*
19096898 TATCAATTATTTTCTTATTAAAA
1 TATCATTTATTTTCTTATTAAAA
19096921 TATCATTTATTTTCTTATTAAAA
1 TATCATTTATTTTCTTATTAAAA
19096944 TAT
1 TAT
19096947 ATAATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (23 bp):
TATCATTTATTTTCTTATTAAAA
Found at i:19097968 original size:14 final size:14
Alignment explanation
Indices: 19097949--19097979 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
19097939 ATGATCGTAC
19097949 AACTTATTTGTAGT
1 AACTTATTTGTAGT
19097963 AACTTATTTGTAGT
1 AACTTATTTGTAGT
19097977 AAC
1 AAC
19097980 GTGCTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (14 bp):
AACTTATTTGTAGT
Found at i:19099661 original size:43 final size:43
Alignment explanation
Indices: 19099582--19099834 Score: 291
Period size: 43 Copynumber: 5.9 Consensus size: 43
19099572 TTAAAGATTA
* ** *
19099582 TGTT-TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGT-T
1 TGTTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCT
19099623 TGTTCTTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCAT
1 TGTTCTTTAGCGGCGTTTGT-GGAAAAAGCGCCGCTAAAGGTC-T
* * *
19099668 GGTT-TATAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAGGTCA
1 TGTTCTTTAGCGGCGTTTGTGGA-AAAAGCGCCGCTAAAGGTCT
* * *
19099710 TGGTCTATAGCGGCGTTTGTGGAAATAGCGCCGCTAAAGGTCT
1 TGTTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCT
* * * ** *
19099753 TGGTCTTTAACGGCGTTTGTGGGAGTAGCGCCGCTAAAAGTCT
1 TGTTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCT
19099796 T-TGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAG
1 TGT-TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAG
19099835 TTAGTGACCG
Statistics
Matches: 182, Mismatches: 22, Indels: 14
0.83 0.10 0.06
Matches are distributed among these distances:
41 4 0.02
42 18 0.10
43 140 0.77
44 16 0.09
45 4 0.02
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (43 bp):
TGTTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCT
Found at i:19099734 original size:86 final size:85
Alignment explanation
Indices: 19099585--19099834 Score: 340
Period size: 86 Copynumber: 2.9 Consensus size: 85
19099575 AAGATTATGT
* * *
19099585 TTTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGT-TTGTTCTTTAGCGGCGTTTGTGGGAAA
1 TTTTAGCGGCGTTTGTGATAGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT-GGAAA
19099649 AAGCGCCGCTAAAGGTCATGG
65 AAGCGCCGCTAAAGGTCATGG
* * *
19099670 TTTATAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAA
1 TTT-TAGCGGCGTTTGTGATAGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGAAA
* *
19099735 TAGCGCCGCTAAAGGTCTTGG
65 AAGCGCCGCTAAAGGTCATGG
* ** * * *
19099756 TCTTTAACGGCGTTTGTGGGAGTAGCGCCGCTAAAAGTCTTTGTCTTTAGCGGCGTTTGTGGAAA
1 T-TTTAGCGGCGTTTGTGATAGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGAAA
19099821 AAGCGCCGCTAAAG
65 AAGCGCCGCTAAAG
19099835 TTAGTGACCG
Statistics
Matches: 144, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
85 3 0.02
86 121 0.84
87 20 0.14
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (85 bp):
TTTTAGCGGCGTTTGTGATAGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGAAAA
AGCGCCGCTAAAGGTCATGG
Found at i:19100939 original size:44 final size:44
Alignment explanation
Indices: 19100756--19100922 Score: 132
Period size: 43 Copynumber: 3.9 Consensus size: 44
19100746 AACTCATTCA
* * * *
19100756 ATGCCAACGTCCCAGACGTGGTCTTACATG-AAATCA-AATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCACAA-ATGG
* * * * *
19100799 ATGCCACTGTCCCCGACAGGGTTTTACACG-AACTC-CTATAA--G
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCAC-A-AATGG
* * * * *
19100841 ATGTCGATGTCCCAGATATGGTCTTACACGTAAATCGCAAATTG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCACAAATGG
19100885 ATGCCAATGTCCCAGACATGGTCTTACACGT-AATCACA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCACA
19100923 TATCGGAATC
Statistics
Matches: 97, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
42 26 0.27
43 38 0.39
44 32 0.33
45 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCACAAATGG
Found at i:19104087 original size:18 final size:18
Alignment explanation
Indices: 19104066--19104103 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
19104056 TAAAGTTAGT
*
19104066 AATTATGGTTTTGTTAAC
1 AATTATGGTTTTATTAAC
19104084 AATTATGGTTTTATTAAC
1 AATTATGGTTTTATTAAC
19104102 AA
1 AA
19104104 ATTGTGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (18 bp):
AATTATGGTTTTATTAAC
Found at i:19104976 original size:13 final size:13
Alignment explanation
Indices: 19104958--19104990 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
19104948 CCTTTCCCTC
19104958 CTTTTCTTTCTTG
1 CTTTTCTTTCTTG
19104971 CTTTTCCTTTCTTG
1 CTTTT-CTTTCTTG
19104985 -TTTTCT
1 CTTTTCT
19104991 CTTATTTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 9 0.47
14 8 0.42
ACGTcount: A:0.00, C:0.24, G:0.06, T:0.70
Consensus pattern (13 bp):
CTTTTCTTTCTTG
Found at i:19104980 original size:14 final size:14
Alignment explanation
Indices: 19104958--19105002 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
19104948 CCTTTCCCTC
19104958 CTTTT-CTTTCTTG
1 CTTTTCCTTTCTTG
19104971 CTTTTCCTTTCTTG
1 CTTTTCCTTTCTTG
19104985 -TTTTCTCTTAT-TTG
1 CTTTTC-CTT-TCTTG
19104999 CTTT
1 CTTT
19105003 GAAACTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 10 0.36
14 14 0.50
15 4 0.14
ACGTcount: A:0.02, C:0.22, G:0.07, T:0.69
Consensus pattern (14 bp):
CTTTTCCTTTCTTG
Found at i:19107700 original size:165 final size:161
Alignment explanation
Indices: 19107427--19107753 Score: 401
Period size: 165 Copynumber: 2.0 Consensus size: 161
19107417 ATCAAGTCAG
** * * *
19107427 TCAAGCATATGATTGTCAAATCTCAAAATCTAAAATATCTTCATTGCAAAACTCGCATAATTCTT
1 TCAAGCATACAATTGTCAAATCGCAAAATCTAAAATATCTTCATTGCAAAACTCACATAATTCAT
* * *
19107492 ATCTATAATTTTTATAGTCTTAGGAAATAAAGAGATTTGGCCTTTCAAATGAGTAGTGCAGAAAA
66 ATCTATAATTTTTATAGTCATAGGAAATAAAAAGAATTGGCCTTTCAAATGAGTAGTGCAGAAAA
*
19107557 TTTACAGATTCAGA-TTTTG-AAGCGTTGAAA
131 TTTACACATTCA-ATTTTTGTAAGCGTTGAAA
* * * * *
19107587 TCAAGCATACAATTTTCCAATCGCAAAGTCTAAGAATATTTTTCATTGCAAAAACTCACCTAATT
1 TCAAGCATACAATTGTCAAATCGCAAAATCTAA-AATA-TCTTCATTGC-AAAACTCACATAATT
* *
19107652 CATA-CTTATAA-TTTTAGTGAAGTCATATGAAATAAAAAGAATTGGCCTTTCAAATGATTAGTG
63 CATATC-TATAATTTTTA-T--AGTCATAGGAAATAAAAAGAATTGGCCTTTCAAATGAGTAGTG
*
19107715 CAGAAAATTTACACATTCAATTTTTGTAAGTGTTGAAA
124 CAGAAAATTTACACATTCAATTTTTGTAAGCGTTGAAA
19107753 T
1 T
19107754 TAAATGAATG
Statistics
Matches: 141, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
160 27 0.19
161 4 0.03
162 15 0.11
163 22 0.16
164 1 0.01
165 61 0.43
166 11 0.08
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (161 bp):
TCAAGCATACAATTGTCAAATCGCAAAATCTAAAATATCTTCATTGCAAAACTCACATAATTCAT
ATCTATAATTTTTATAGTCATAGGAAATAAAAAGAATTGGCCTTTCAAATGAGTAGTGCAGAAAA
TTTACACATTCAATTTTTGTAAGCGTTGAAA
Found at i:19123025 original size:11 final size:10
Alignment explanation
Indices: 19122998--19123070 Score: 74
Period size: 11 Copynumber: 6.7 Consensus size: 10
19122988 ACTTAAATCC
19122998 TTTCTCTCAA
1 TTTCTCTCAA
*
19123008 ATTCTCTCATA
1 TTTCTCTCA-A
19123019 TTTCTCTCCAA
1 TTTCTCT-CAA
19123030 TATTCTCTCATA
1 T-TTCTCTCA-A
19123042 TTTCTCTCAAA
1 TTTCTCTC-AA
*
19123053 TTCCTCTCAAA
1 TTTCTCTC-AA
19123064 TTTCTCT
1 TTTCTCT
19123071 TAAAACTCTC
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
10 8 0.15
11 35 0.65
12 11 0.20
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.48
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:19123034 original size:23 final size:21
Alignment explanation
Indices: 19122998--19123070 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 21
19122988 ACTTAAATCC
19122998 TTTCTCTCAAATTCTCTCATA
1 TTTCTCTCAAATTCTCTCATA
19123019 TTTCTCTCCAATATTCTCTCATA
1 TTTCTCT-CAA-ATTCTCTCATA
*
19123042 TTTCTCTCAAATTCCTCTCAAA
1 TTTCTCTCAAATT-CTCTCATA
19123064 TTTCTCT
1 TTTCTCT
19123071 TAAAACTCTC
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
21 10 0.21
22 20 0.42
23 18 0.38
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTCTCTCAAATTCTCTCATA
Found at i:19124245 original size:7 final size:7
Alignment explanation
Indices: 19124233--19124261 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
19124223 CGATTCATGC
19124233 TTAGTAT
1 TTAGTAT
19124240 TTAGTAT
1 TTAGTAT
19124247 TTAGTAT
1 TTAGTAT
19124254 TTAGTAT
1 TTAGTAT
19124261 T
1 T
19124262 ATGTATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (7 bp):
TTAGTAT
Found at i:19124847 original size:30 final size:30
Alignment explanation
Indices: 19124789--19124847 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
19124779 ATAATTATTC
* * *
19124789 GGCTCATCAACAGCGCCCATACAATCACCA
1 GGCTCAGCAACAGCACCCACACAATCACCA
* *
19124819 GGCTCAGCAACAGCACCGACACAGTCACC
1 GGCTCAGCAACAGCACCCACACAATCACC
19124848 CGACCCAACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.41, G:0.17, T:0.10
Consensus pattern (30 bp):
GGCTCAGCAACAGCACCCACACAATCACCA
Found at i:19124931 original size:18 final size:18
Alignment explanation
Indices: 19124908--19124950 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
19124898 TGCCAGGTGC
* *
19124908 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
19124926 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
19124944 GTTTCCT
1 GTATCCT
19124951 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:19125437 original size:61 final size:61
Alignment explanation
Indices: 19125358--19125577 Score: 242
Period size: 61 Copynumber: 3.7 Consensus size: 61
19125348 TTGTACAAAC
* * * *
19125358 ATTTTGAATATTTTTATATTATTTTATGTAATAAAATAGAAATTCTTTTAAATAAGACAAT
1 ATTTTGAATATTTCTATATTATTTCATTTAATAAAATATAAATTCTTTTAAATAAGACAAT
* * **
19125419 ATTTTGAATATTTCTATATTATTTCATTTAATAAAATA-AAACGTTGTTTTGAATAA-AGTA-
1 ATTTTGAATATTTCTATATTATTTCATTTAATAAAATATAAA--TTCTTTTAAATAAGACAAT
* * * *
19125479 ATTGT-AAT-TTGCTTTAATATTTTCA---AATAAAATATAAATTCTTTTAAATAAGACAAT
1 ATTTTGAATATTTCTATATTA-TTTCATTTAATAAAATATAAATTCTTTTAAATAAGACAAT
19125536 ATTTTGAATATTTCTATATTATTTCATTTAA-AAAATATAAAT
1 ATTTTGAATATTTCTATATTATTTCATTTAATAAAATATAAAT
19125578 AATACAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 23
0.75 0.11 0.13
Matches are distributed among these distances:
55 11 0.09
56 11 0.09
57 7 0.05
58 16 0.12
59 16 0.12
60 18 0.14
61 39 0.30
62 11 0.09
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (61 bp):
ATTTTGAATATTTCTATATTATTTCATTTAATAAAATATAAATTCTTTTAAATAAGACAAT
Found at i:19126987 original size:320 final size:320
Alignment explanation
Indices: 19126392--19127036 Score: 1157
Period size: 320 Copynumber: 2.0 Consensus size: 320
19126382 AACGTAAAAC
*
19126392 TGCCAACATATCATGAAAACGGTCTTTACTTATTTCATACCCTACCAATATAAGTTCATATCGAA
1 TGCCAACATATCATGAAAACGGTCTTTACTTATTTCATACCCTACCAATATAAGTTCATAGCGAA
19126457 TATTACATACCACACTTTCATTTAGAATAAATCCAAAATGACAAACGAAATTATATTAATAGAGG
66 TATTACATACCACACTTTCATTTAGAATAAATCCAAAATGACAAACGAAATTATATTAATAGAGG
* *
19126522 CTAAATACTCATGTTGGTTACTTTTCGTCGTTCACTTTTAGATGGATATTGCCTGTAGTAGTTGG
131 CTAAATACTCATGTTGGTTACTTTTCGTCGTTCACTTTTAGATGAATATTACCTGTAGTAGTTGG
19126587 AAGCAACGTGCCTTAGGCAATACCAATGGTGTGTACGCTGCCATAAGCTTCCCTGTCGCTCAATT
196 AAGCAACGTGCCTTAGGCAATACCAATGGTGTGTACGCTGCCATAAGCTTCCCTGTCGCTCAATT
*
19126652 ACAGCTAGAATTTTGGTGTCCCGA-TCTGAAATAACGCAGATATCAGGTTGGTGGCACACA
261 ACAGCTAGAATTTTGGTGTCCCGATTC-GAAATAACGCAGATATCAGGTTGGGGGCACACA
* * *
19126712 TGCCAATATATCATGAAAATGGTCTTTACTTATTTCATACCCTGCCAATATAAGTTCATAGCGAA
1 TGCCAACATATCATGAAAACGGTCTTTACTTATTTCATACCCTACCAATATAAGTTCATAGCGAA
* *
19126777 TATTACATACCACACTTTCATTTAGAATAAATTCAAAATGACAAAGGAAATTATATTAATAGAGG
66 TATTACATACCACACTTTCATTTAGAATAAATCCAAAATGACAAACGAAATTATATTAATAGAGG
19126842 CTAAATACTCATGTTGGTTACTTTTCGTCGTTCACTTTTAGATGAATATTACCTGTAGTAGTTGG
131 CTAAATACTCATGTTGGTTACTTTTCGTCGTTCACTTTTAGATGAATATTACCTGTAGTAGTTGG
* *
19126907 AAGCAACGTGCCTTAGGCAATACCGATGGTGTGTACGCTGCCATAAGCTTTCCTGTCGCTCAATT
196 AAGCAACGTGCCTTAGGCAATACCAATGGTGTGTACGCTGCCATAAGCTTCCCTGTCGCTCAATT
* *
19126972 ACAGCTAGTATTTTGGTGTCCCGATTCGAAATAACGCAGATATCAGGTTGGGGGCACGCA
261 ACAGCTAGAATTTTGGTGTCCCGATTCGAAATAACGCAGATATCAGGTTGGGGGCACACA
19127032 TGCCA
1 TGCCA
19127037 CTTTAACCTA
Statistics
Matches: 311, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
320 309 0.99
321 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (320 bp):
TGCCAACATATCATGAAAACGGTCTTTACTTATTTCATACCCTACCAATATAAGTTCATAGCGAA
TATTACATACCACACTTTCATTTAGAATAAATCCAAAATGACAAACGAAATTATATTAATAGAGG
CTAAATACTCATGTTGGTTACTTTTCGTCGTTCACTTTTAGATGAATATTACCTGTAGTAGTTGG
AAGCAACGTGCCTTAGGCAATACCAATGGTGTGTACGCTGCCATAAGCTTCCCTGTCGCTCAATT
ACAGCTAGAATTTTGGTGTCCCGATTCGAAATAACGCAGATATCAGGTTGGGGGCACACA
Found at i:19128397 original size:125 final size:125
Alignment explanation
Indices: 19128175--19128455 Score: 447
Period size: 125 Copynumber: 2.2 Consensus size: 125
19128165 TCAGGCCAAA
* * *
19128175 TAGGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCCTCTTTCAGTACTTTTGCAGACAAAGC
1 TAGGAACTACTGTAGCAAAAGAGCGTCCACGTAGAAGCCTCTTTCAGTACTTTTACAGACAAAGC
* *
19128240 ATCCTGCTTAAAGTGTTTTTGACACTATTTGCTCAGAAACATCTTCTCGAAATTATTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTT
* *
19128300 TAGGAACTACTGTAGCAAAAGAGCGTCCACGTAGAAGCTTCTTTCAGTACTTTTACTA-ACAATG
1 TAGGAACTACTGTAGCAAAAGAGCGTCCACGTAGAAGCCTCTTTCAGTACTTTTAC-AGACAAAG
* * *
19128364 CATCCTGCTTAAAGCGTTTTTGCCACTATTTGCTTAGAAACGTCTTCTCAAAATTATTTTT
65 CATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTT
19128425 TCAGGAACTACTGTAGCAAAAGAGCGTCCAC
1 T-AGGAACTACTGTAGCAAAAGAGCGTCCAC
19128456 ATGGGAGCTT
Statistics
Matches: 144, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
125 114 0.79
126 30 0.21
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (125 bp):
TAGGAACTACTGTAGCAAAAGAGCGTCCACGTAGAAGCCTCTTTCAGTACTTTTACAGACAAAGC
ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTT
Found at i:19128643 original size:97 final size:98
Alignment explanation
Indices: 19128508--19128806 Score: 401
Period size: 96 Copynumber: 3.1 Consensus size: 98
19128498 CCTAAATCCC
*
19128508 AAACCCTAATTTATTTAAGTTTTTCCTTAAAAAC-CTTAAACACTAAACCCTAATCAAATTTTTT
1 AAACCCTAATTTATTTAAGTTTTTCCTTAAAAACTCTTAAACACTAAACCCTAATCTAATTTTTT
* * * *
19128572 TAAAACTTATAATTAATTTACTTAGGTAACCTT
66 AAAAATTTATAATTAATTTACTTAAGTAACCCT
* *
19128605 AAACCCTAATTTATTTGA-TTTTTCCTTAAAAACTCTT-AACACTAAACCCTAATCTGATTTTTT
1 AAACCCTAATTTATTTAAGTTTTTCCTTAAAAACTCTTAAACACTAAACCCTAATCTAATTTTTT
*
19128668 AAAAATTTATAATTAATTTACTCAAGTAACCCT
66 AAAAATTTATAATTAATTTACTTAAGTAACCCT
* * * * * * *
19128701 AAACCCTAATTTAATTAATTTTTTTCTTAAAAACT-ATAAACACGAAAACCTAATCTAA-TTTTG
1 AAACCCTAATTTATTTAAGTTTTTCCTTAAAAACTCTTAAACACTAAACCCTAATCTAATTTTTT
* * *
19128764 AATAATTTATAATTAATTTAATTAAGAAACCCT
66 AAAAATTTATAATTAATTTACTTAAGTAACCCT
19128797 AAACCCTAAT
1 AAACCCTAAT
19128807 CCCTTATTTA
Statistics
Matches: 179, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
96 127 0.71
97 52 0.29
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (98 bp):
AAACCCTAATTTATTTAAGTTTTTCCTTAAAAACTCTTAAACACTAAACCCTAATCTAATTTTTT
AAAAATTTATAATTAATTTACTTAAGTAACCCT
Found at i:19128845 original size:7 final size:7
Alignment explanation
Indices: 19128833--19128882 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
19128823 TTTTTCTTTA
19128833 AAACCCT
1 AAACCCT
*
19128840 AAACCCAA
1 AAACCC-T
19128848 AAACCCT
1 AAACCCT
*
19128855 -AGCCCT
1 AAACCCT
*
19128861 AAACCTT
1 AAACCCT
19128868 AAACCCT
1 AAACCCT
19128875 -AACCCT
1 AAACCCT
19128881 AA
1 AA
19128883 CGCAGGAAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
6 11 0.32
7 17 0.50
8 6 0.18
ACGTcount: A:0.44, C:0.40, G:0.02, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:19134421 original size:24 final size:24
Alignment explanation
Indices: 19134388--19134438 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
19134378 CAATAAGTAA
*
19134388 TAATACTTAAAAAATGTAGATTTT
1 TAATACTTAAAAAATGTAGATTAT
* *
19134412 TAATAGTTAAAAGATGTAGATTAT
1 TAATACTTAAAAAATGTAGATTAT
19134436 TAA
1 TAA
19134439 CCTTGGTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39
Consensus pattern (24 bp):
TAATACTTAAAAAATGTAGATTAT
Found at i:19141770 original size:5 final size:5
Alignment explanation
Indices: 19141760--19141785 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19141750 CTCGAAAATT
19141760 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
19141786 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:19150145 original size:28 final size:28
Alignment explanation
Indices: 19150113--19150169 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
19150103 CAAGAGAGAT
19150113 TATCAAAGCAAAATTTTTAATCAATCAA
1 TATCAAAGCAAAATTTTTAATCAATCAA
19150141 TATCAAAGCAAAATTTTTAATCAATCAA
1 TATCAAAGCAAAATTTTTAATCAATCAA
19150169 T
1 T
19150170 CTTTGTACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (28 bp):
TATCAAAGCAAAATTTTTAATCAATCAA
Found at i:19150633 original size:27 final size:27
Alignment explanation
Indices: 19150603--19150655 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
19150593 TCGTAAGGAG
19150603 TCCTATTGAAACCAAGAAATAGAGGCA
1 TCCTATTGAAACCAAGAAATAGAGGCA
19150630 TCCTATTGAAACCAAGAAATAGAGGC
1 TCCTATTGAAACCAAGAAATAGAGGC
19150656 CTGCCTGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (27 bp):
TCCTATTGAAACCAAGAAATAGAGGCA
Found at i:19151007 original size:18 final size:19
Alignment explanation
Indices: 19150981--19151026 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
19150971 ATTTTAAGCA
*
19150981 TTAACTTTATAGCAA-ATT
1 TTAATTTTATAGCAATATT
* *
19150999 TTAATTTTA-ATCAATTTT
1 TTAATTTTATAGCAATATT
19151017 TTAATTTTAT
1 TTAATTTTAT
19151027 TTTTTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (19 bp):
TTAATTTTATAGCAATATT
Found at i:19153496 original size:4 final size:4
Alignment explanation
Indices: 19153487--19153513 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
19153477 GGTATATTAG
19153487 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
19153514 TATCTATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:19156535 original size:14 final size:15
Alignment explanation
Indices: 19156516--19156544 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19156506 ACCCTTGAAT
19156516 CCCTAAAT-CCTAAC
1 CCCTAAATCCCTAAC
19156530 CCCTAAATCCCTAAC
1 CCCTAAATCCCTAAC
19156545 TCTTAACCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCCCTAAC
Found at i:19156538 original size:22 final size:22
Alignment explanation
Indices: 19156513--19156557 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
19156503 CCGACCCTTG
19156513 AATCCCTAAATCCTAACCCCTA
1 AATCCCTAAATCCTAACCCCTA
* *
19156535 AATCCCTAACTCTTAACCCCTA
1 AATCCCTAAATCCTAACCCCTA
19156557 A
1 A
19156558 CTACTAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (22 bp):
AATCCCTAAATCCTAACCCCTA
Found at i:19156866 original size:7 final size:7
Alignment explanation
Indices: 19156854--19156905 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
19156844 ACTAGTTAAT
19156854 CTAAACC
1 CTAAACC
19156861 CTAAACC
1 CTAAACC
*
19156868 ATAAA-C
1 CTAAACC
*
19156874 TTAAACC
1 CTAAACC
19156881 CTAAAACC
1 CT-AAACC
*
19156889 TTAAACC
1 CTAAACC
19156896 CATAAACC
1 C-TAAACC
19156904 CT
1 CT
19156906 TAACACATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
6 5 0.14
7 19 0.51
8 13 0.35
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:19156893 original size:15 final size:15
Alignment explanation
Indices: 19156856--19156908 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 15
19156846 TAGTTAATCT
* *
19156856 AAACCCTAAACCAT-
1 AAACCTTAAACCCTA
19156870 AAA-CTTAAACCCTA
1 AAACCTTAAACCCTA
19156884 AAACCTTAAACCCATA
1 AAACCTTAAACCC-TA
*
19156900 AACCCTTAA
1 AAACCTTAA
19156909 CACATAACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 8 0.24
14 6 0.18
15 9 0.27
16 10 0.30
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (15 bp):
AAACCTTAAACCCTA
Found at i:19160627 original size:7 final size:7
Alignment explanation
Indices: 19160612--19160648 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
19160602 TGAGTACTTT
*
19160612 TGATCAG
1 TGATAAG
19160619 TGATAAG
1 TGATAAG
19160626 TGATAAG
1 TGATAAG
19160633 TGATAAG
1 TGATAAG
19160640 TGATAAG
1 TGATAAG
19160647 TG
1 TG
19160649 GTAGCTTAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.38, C:0.03, G:0.30, T:0.30
Consensus pattern (7 bp):
TGATAAG
Found at i:19160729 original size:51 final size:50
Alignment explanation
Indices: 19160619--19160896 Score: 403
Period size: 51 Copynumber: 5.5 Consensus size: 50
19160609 TTTTGATCAG
* * *
19160619 TGATAAGTGATAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATC
1 TGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATC
* ** *
19160669 TGATCAGTGACAAGTGCCAAGTGATAAGTGAAAGATTCAGCTACACTTATC
1 TGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTT-AGCTACACTTATC
* * *
19160720 TGATTAGTGACAAGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATC
1 TGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTT-AGCTACACTTATC
19160771 TGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATC
1 TGATCAGTGACAAGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATC
**
19160822 TGATCAGTGACAAGTGGTAAGTGATAAGTGGTAGCTTAGCTACACTTATC
1 TGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATC
* *
19160872 TGATCAGGGACAAGTGATAAGTGAT
1 TGATCAGTGACAAGTGACAAGTGAT
19160897 CATACGTAAG
Statistics
Matches: 208, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
50 68 0.33
51 138 0.66
52 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (50 bp):
TGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATC
Found at i:19168498 original size:4 final size:4
Alignment explanation
Indices: 19168489--19168515 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
19168479 GGTATATTAG
19168489 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
19168516 TATCTATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:19170896 original size:113 final size:113
Alignment explanation
Indices: 19170466--19171022 Score: 674
Period size: 113 Copynumber: 4.9 Consensus size: 113
19170456 NNNAAGCCCC
* * * * * *
19170466 GAGCATCAGCGGCGCTATTCTTAGATAACACCGCTAAATCCCCGACTACTCAGAAAACGACGTCG
1 GAGCATTAGCGGCGCT-TTCTTA-AAAACGCCGCTAAAT-CCCGAATGCTCAGAAAACGGCGTCG
* * * *
19170531 TTGGGCTTAGGTTTTTTTGCGGCACTTTCTAAAAAACGTCGCTAAAGCC-C
63 TTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCTT
* * * **
19170581 AAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAAGATGCACAGAAAACGGAATCGTT
1 GAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCGA-ATGCTCAGAAAACGGCGTCGTT
* *
19170646 GGGCTTAGGTTTTTTTTGCGTCGCTTTCTCAAAAACGCCGCTAAAGCCCT
65 GGGCTTAGG-TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCTT
* *
19170696 GAGCATTAGCGGCGCTTTCTTAAAAACGCCCCTAAATCCACGAAGGCTCAGAAAACGGCGTCGTT
1 GAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCC-CGAATGCTCAGAAAACGGCGTCGTT
* * * *
19170761 GGGATTCGGTTTTTTTACGGCGCTTTCTCAAAAACACCGCTAAAGCCTT
65 GGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCTT
* *
19170810 GAGCATTAGCGGCAC-TT-TTAGAAAGCGCCGCTAAATCCTCGAATGCTCAGAAAACGGCGTCGT
1 GAGCATTAGCGGCGCTTTCTTA-AAAACGCCGCTAAATCC-CGAATGCTCAGAAAACGGCGTCGT
* * * *
19170873 TGGGCTTAGGTTTTTTTGCGGCGCTTTTTCAAAATCGCCGCTAATG-CTCA
64 TGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCT-T
* *
19170923 GGGCTTTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACGGCGTCGTT
1 GAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCC-GAATGCTCAGAAAACGGCGTCGTT
* * * *
19170988 GGACTTAGG-TTTTTTGCGGGGCTTTTTGAAAAACG
65 GGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACG
19171023 TAGCTAATGC
Statistics
Matches: 383, Mismatches: 50, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
112 9 0.02
113 153 0.40
114 140 0.37
115 79 0.21
116 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.27
Consensus pattern (113 bp):
GAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCGAATGCTCAGAAAACGGCGTCGTTG
GGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCTT
Found at i:19172611 original size:7 final size:7
Alignment explanation
Indices: 19172599--19172630 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
19172589 ACTTTCGATC
19172599 AGTGATA
1 AGTGATA
19172606 AGTGATA
1 AGTGATA
19172613 AGTGATA
1 AGTGATA
19172620 AGTGATA
1 AGTGATA
19172627 AGTG
1 AGTG
19172631 GTAGCTTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (7 bp):
AGTGATA
Found at i:19172711 original size:51 final size:50
Alignment explanation
Indices: 19172601--19172738 Score: 222
Period size: 51 Copynumber: 2.7 Consensus size: 50
19172591 TTTCGATCAG
* * *
19172601 TGATAAGTGATAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATC
1 TGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATC
* *
19172651 TGATCAGTGACAAGTGCCAAGTGATAAGTGATAGCTTCAGCTACACTTATC
1 TGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTT-AGCTACACTTATC
19172702 TGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTT
1 TGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTT
19172739 TNNNNNNNNN
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 32 0.40
51 48 0.60
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (50 bp):
TGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATC
Found at i:19179689 original size:46 final size:45
Alignment explanation
Indices: 19179622--19179912 Score: 456
Period size: 46 Copynumber: 6.6 Consensus size: 45
19179612 TTTGAGTACT
19179622 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
* *
19179668 TCTGATCAAGTGACAAAGTGATGAGTGGTAGCTTAGCTTCACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
19179713 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
19179759 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC----CT---CTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
19179797 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
19179843 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
19179888 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
19179913 ATCATACGTA
Statistics
Matches: 230, Mismatches: 6, Indels: 21
0.89 0.02 0.08
Matches are distributed among these distances:
38 36 0.16
41 2 0.01
43 14 0.06
44 5 0.02
45 62 0.27
46 111 0.48
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:19179771 original size:38 final size:38
Alignment explanation
Indices: 19179728--19179855 Score: 100
Period size: 38 Copynumber: 3.2 Consensus size: 38
19179718 TCAAGTGACA
19179728 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
* * * *
19179766 AAGTGACAAAGTGATAAG-TGGTAGC--CTCTTATCTGATCAAGTGAC
1 AAGTGA-TAAGTGGT-AGCT-TTAGCTACACTTATCTG----A-T--C
19179811 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 -AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
19179850 AAGTGA
1 AAGTGA
19179856 CAAAGTGATA
Statistics
Matches: 68, Mismatches: 8, Indels: 28
0.65 0.08 0.27
Matches are distributed among these distances:
38 21 0.31
39 8 0.12
40 6 0.09
41 1 0.01
42 2 0.03
43 1 0.01
44 6 0.09
45 8 0.12
46 15 0.22
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (38 bp):
AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:19179777 original size:91 final size:90
Alignment explanation
Indices: 19179622--19179912 Score: 481
Period size: 91 Copynumber: 3.3 Consensus size: 90
19179612 TTTGAGTACT
19179622 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
*
19179687 GATGAGTGGTAGCTTAGCTTCACTTA
66 GATAAGTGGTAGC-TAGCTTCACTTA
19179713 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
19179778 GATAAGTGGTAGC---C-T--CTTA
66 GATAAGTGGTAGCTAGCTTCACTTA
19179797 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
*
19179862 GATAAGTGGTAGCCTAGCTACACTTA
66 GATAAGTGGTAG-CTAGCTTCACTTA
*
19179888 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
19179913 ATCATACGTA
Statistics
Matches: 190, Mismatches: 3, Indels: 16
0.91 0.01 0.08
Matches are distributed among these distances:
84 81 0.43
85 1 0.01
86 1 0.01
87 1 0.01
88 1 0.01
89 12 0.06
90 5 0.03
91 88 0.46
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (90 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
GATAAGTGGTAGCTAGCTTCACTTA
Found at i:19179801 original size:84 final size:84
Alignment explanation
Indices: 19179709--19179876 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
19179699 CTTAGCTTCA
19179709 CTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACA
1 CTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACA
19179774 AAGTGATAAGTGGTAGCCT
66 AAGTGATAAGTGGTAGCCT
19179793 CTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACA
1 CTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACA
19179858 AAGTGATAAGTGGTAGCCT
66 AAGTGATAAGTGGTAGCCT
19179877 AGCTACACTT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (84 bp):
CTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACA
AAGTGATAAGTGGTAGCCT
Found at i:19182627 original size:27 final size:27
Alignment explanation
Indices: 19182571--19182627 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
19182561 CCACATCAAC
* * *
19182571 AAATAATTTAAAAATTATAAAAATAGA
1 AAATAATATAAAAAGTATAAAAATACA
* *
19182598 AAATAATATAAAAAGTATAAGAATTCA
1 AAATAATATAAAAAGTATAAAAATACA
19182625 AAA
1 AAA
19182628 AAGTAGCATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (27 bp):
AAATAATATAAAAAGTATAAAAATACA
Found at i:19182917 original size:44 final size:44
Alignment explanation
Indices: 19182863--19182950 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
19182853 TATACCTTCT
*
19182863 AAAATTTATCATATAAGCTATTTTATATCATTATTACTTATTAG
1 AAAAGTTATCATATAAGCTATTTTATATCATTATTACTTATTAG
* *
19182907 AAAAGTTATCATGTAAGCTATTTTATATCATTATTGCTTATTAG
1 AAAAGTTATCATATAAGCTATTTTATATCATTATTACTTATTAG
19182951 GCATATTCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (44 bp):
AAAAGTTATCATATAAGCTATTTTATATCATTATTACTTATTAG
Found at i:19183352 original size:31 final size:31
Alignment explanation
Indices: 19183273--19183353 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
19183263 TATTTGAGAA
*
19183273 GCTCTTATTTGAACACTTTTAAAAAGGTGTG
1 GCTCTTATTTGAACACTTTCAAAAAGGTGTG
* * *
19183304 GCTCTTACTAGAACACTTTCAAAAA-CTGTTG
1 GCTCTTATTTGAACACTTTCAAAAAGGTG-TG
* *
19183335 GCTCGTATTTGAGCACTTT
1 GCTCTTATTTGAACACTTT
19183354 GAAAGTTTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 2 0.05
31 39 0.95
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (31 bp):
GCTCTTATTTGAACACTTTCAAAAAGGTGTG
Found at i:19185424 original size:15 final size:15
Alignment explanation
Indices: 19185404--19185432 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19185394 AAGAGAAAAT
19185404 GATGATGAAGATGAA
1 GATGATGAAGATGAA
19185419 GATGATGAAGATGA
1 GATGATGAAGATGA
19185433 CGAGGGGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.21
Consensus pattern (15 bp):
GATGATGAAGATGAA
Found at i:19188365 original size:14 final size:14
Alignment explanation
Indices: 19188346--19188385 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
19188336 TTGTTTGGCA
19188346 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
19188360 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
19188374 GGAAAATGTTTT
1 GTAAAATGTTTT
19188386 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:19188394 original size:20 final size:20
Alignment explanation
Indices: 19188369--19188408 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19188359 CGTAAAATGA
*
19188369 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
19188389 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
19188409 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:19188398 original size:34 final size:35
Alignment explanation
Indices: 19188354--19188420 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
19188344 CAGTAAAATG
*
19188354 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
19188388 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
19188421 CTACTGTTTG
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:19188498 original size:21 final size:22
Alignment explanation
Indices: 19188472--19188533 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
19188462 TTGTTTTTAC
19188472 ATATATTTT-ACATATATTAAT
1 ATATATTTTAACATATATTAAT
*
19188493 ATATATTTATTAATATATATTAAT
1 ATATA-TT-TTAACATATATTAAT
* *
19188517 AAATTATTTTGACATAT
1 ATA-TATTTTAACATAT
19188534 GTTGTAATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 5 0.15
22 2 0.06
23 9 0.27
24 15 0.45
25 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATATTTTAACATATATTAAT
Found at i:19188505 original size:14 final size:14
Alignment explanation
Indices: 19188486--19188513 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19188476 ATTTTACATA
19188486 TATTAATATATATT
1 TATTAATATATATT
19188500 TATTAATATATATT
1 TATTAATATATATT
19188514 AATAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTAATATATATT
Found at i:19188825 original size:72 final size:72
Alignment explanation
Indices: 19188704--19188847 Score: 234
Period size: 72 Copynumber: 2.0 Consensus size: 72
19188694 ATAATAATAT
* *
19188704 TATCCAAATACATAATTAATGGTACACAACATAATAATAACATTGTCCAAGTGAATAATATTACA
1 TATCCAAATACATAATTAATGGTACACAACATAATAAGAACATTATCCAAGTGAATAATATTACA
*
19188769 TCACATA
66 CCACATA
* * *
19188776 TATCCAAATACATAATTAATGGTACACCACATAGTAAGAACATTATCCAAGTGCATAATATTACA
1 TATCCAAATACATAATTAATGGTACACAACATAATAAGAACATTATCCAAGTGAATAATATTACA
19188841 CCACATA
66 CCACATA
19188848 AATGTATCAA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.28
Consensus pattern (72 bp):
TATCCAAATACATAATTAATGGTACACAACATAATAAGAACATTATCCAAGTGAATAATATTACA
CCACATA
Found at i:19189832 original size:35 final size:36
Alignment explanation
Indices: 19189786--19189854 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
19189776 ATTCAACCAT
19189786 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
19189821 TTCAATATCCAACAAGCTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
19189855 TCTAACAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:19189852 original size:27 final size:28
Alignment explanation
Indices: 19189822--19189891 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
19189812 AATAATAAAT
*
19189822 TCAATATCCAACAAGCTT-AAAACATA-A
1 TCAATATCCAACAA-ATTCAAAACATATA
* *
19189849 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAACAAATTCAAAACATATA
*
19189877 TCAAAATCCAACAAA
1 TCAATATCCAACAAA
19189892 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.06
27 20 0.56
28 14 0.39
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.23
Consensus pattern (28 bp):
TCAATATCCAACAAATTCAAAACATATA
Found at i:19191296 original size:27 final size:26
Alignment explanation
Indices: 19191266--19191327 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
19191256 AGTTATAATT
19191266 TTTAATATCAAAATTTATAGAGACCAA
1 TTTAATATCAAAA-TTATAGAGACCAA
* * *
19191293 TTTAAAATCTAGATTATAGAGACCAA
1 TTTAATATCAAAATTATAGAGACCAA
*
19191319 TTTGATATC
1 TTTAATATC
19191328 TAGATTCTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 20 0.67
27 10 0.33
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (26 bp):
TTTAATATCAAAATTATAGAGACCAA
Found at i:19191313 original size:26 final size:26
Alignment explanation
Indices: 19191280--19191333 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
19191270 ATATCAAAAT
19191280 TTATAGAGACCAATTTAAAATCTAGA
1 TTATAGAGACCAATTTAAAATCTAGA
* *
19191306 TTATAGAGACCAATTTGATATCTAGA
1 TTATAGAGACCAATTTAAAATCTAGA
19191332 TT
1 TT
19191334 CTAGTTTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (26 bp):
TTATAGAGACCAATTTAAAATCTAGA
Found at i:19191678 original size:14 final size:13
Alignment explanation
Indices: 19191653--19191687 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
19191643 TTAACCTTAC
*
19191653 TTAAAATTAAATT
1 TTAAATTTAAATT
19191666 TTAATATTTAAATT
1 TTAA-ATTTAAATT
19191680 TTAAATTT
1 TTAAATTT
19191688 GGTTAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAAATTTAAATT
Found at i:19191702 original size:24 final size:22
Alignment explanation
Indices: 19191675--19191728 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 22
19191665 TTTAATATTT
*
19191675 AAATTTTAAATTTGGTTAATAAAA
1 AAATTTTAAAGTTGG-TAA-AAAA
19191699 AAATTTTAAAGTTGGTAAAAAA
1 AAATTTTAAAGTTGGTAAAAAA
19191721 AAATTTTA
1 AAATTTTA
19191729 GTATTGTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 12 0.41
23 3 0.10
24 14 0.48
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTTAAAGTTGGTAAAAAA
Found at i:19192369 original size:14 final size:13
Alignment explanation
Indices: 19192340--19192366 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19192330 AGAAGGTAAG
19192340 ACAGATACTTAAA
1 ACAGATACTTAAA
19192353 ACAGATACTTAAA
1 ACAGATACTTAAA
19192366 A
1 A
19192367 ACATGAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
ACAGATACTTAAA
Found at i:19194141 original size:12 final size:12
Alignment explanation
Indices: 19194124--19194156 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
19194114 AAACCAAATC
*
19194124 AAGGGAGAACGA
1 AAGGGAGAACAA
19194136 AAGGGAGAACAA
1 AAGGGAGAACAA
19194148 AAGGGAGAA
1 AAGGGAGAA
19194157 GGGAGAACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.55, C:0.06, G:0.39, T:0.00
Consensus pattern (12 bp):
AAGGGAGAACAA
Found at i:19194394 original size:14 final size:14
Alignment explanation
Indices: 19194375--19194402 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19194365 TGGAAAAGGT
19194375 GGAAAATATTTTCC
1 GGAAAATATTTTCC
19194389 GGAAAATATTTTCC
1 GGAAAATATTTTCC
19194403 ACCAAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
GGAAAATATTTTCC
Found at i:19199220 original size:5 final size:5
Alignment explanation
Indices: 19199210--19199242 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
19199200 GAGATAGATG
19199210 GAGGT GAGGT GAGGT GAGGT GAGGT GAGGT GAG
1 GAGGT GAGGT GAGGT GAGGT GAGGT GAGGT GAG
19199243 AGAGATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.61, T:0.18
Consensus pattern (5 bp):
GAGGT
Found at i:19199747 original size:20 final size:20
Alignment explanation
Indices: 19199701--19199749 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
19199691 AAATTTAAAC
*
19199701 TAAAAATGTTACTAAATTTA
1 TAAAAATATTACTAAATTTA
*
19199721 CATAAAATATTA-TAAATTCTA
1 TA-AAAATATTACTAAATT-TA
19199742 TAAAAATA
1 TAAAAATA
19199750 AATCAAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAAATATTACTAAATTTA
Found at i:19202579 original size:16 final size:17
Alignment explanation
Indices: 19202561--19202601 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
19202551 AAAATTTTAA
19202561 TTTAAATCTTTTATAATT
1 TTTAAATCTTTTATAA-T
*
19202579 TTTAAATTTTTTA-AAT
1 TTTAAATCTTTTATAAT
19202595 TTTAAAT
1 TTTAAAT
19202602 TAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 2 0.09
18 12 0.55
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAAATCTTTTATAAT
Found at i:19202581 original size:9 final size:8
Alignment explanation
Indices: 19202561--19202602 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
19202551 AAAATTTTAA
19202561 TTTAAATCT
1 TTTAAAT-T
19202570 TTTATAATT
1 TTTA-AATT
19202579 TTTAAATTT
1 TTTAAA-TT
19202588 TTTAAA-T
1 TTTAAATT
19202595 TTTAAATT
1 TTTAAATT
19202603 AATAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 7 0.23
8 3 0.10
9 17 0.57
10 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (8 bp):
TTTAAATT
Found at i:19202602 original size:16 final size:17
Alignment explanation
Indices: 19202561--19202602 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
19202551 AAAATTTTAA
*
19202561 TTTAAATCTTTTATAATT
1 TTTAAAT-TTTTATAAAT
19202579 TTTAAATTTTT-TAAAT
1 TTTAAATTTTTATAAAT
19202595 TTTAAATT
1 TTTAAATT
19202603 AATAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.52
17 4 0.17
18 7 0.30
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAAATTTTTATAAAT
Found at i:19203906 original size:15 final size:15
Alignment explanation
Indices: 19203886--19203917 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19203876 ACCCCAAGTC
19203886 AGAGGCAATTCTAGG
1 AGAGGCAATTCTAGG
19203901 AGAGGCAATTCTAGG
1 AGAGGCAATTCTAGG
19203916 AG
1 AG
19203918 GGCTGGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.19
Consensus pattern (15 bp):
AGAGGCAATTCTAGG
Found at i:19207391 original size:19 final size:18
Alignment explanation
Indices: 19207367--19207416 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
19207357 AATTATTTTT
19207367 TTAAAAAAATTATAAAAAA
1 TTAAAAAAATT-TAAAAAA
**
19207386 TTAAAATTATTTAAAAAA
1 TTAAAAAAATTTAAAAAA
19207404 TATAAAAAAATTT
1 T-TAAAAAAATTT
19207417 TTAATTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAAAAAATTTAAAAAA
Found at i:19207413 original size:10 final size:9
Alignment explanation
Indices: 19207367--19207415 Score: 53
Period size: 10 Copynumber: 5.2 Consensus size: 9
19207357 AATTATTTTT
19207367 TTAAAAAAA
1 TTAAAAAAA
19207376 TTATAAAAAA
1 TTA-AAAAAA
**
19207386 TTAAAATTA
1 TTAAAAAAA
*
19207395 TTTAAAAAA
1 TTAAAAAAA
19207404 TATAAAAAAA
1 T-TAAAAAAA
19207414 TT
1 TT
19207416 TTTAATTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 15 0.47
10 17 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:19207437 original size:17 final size:16
Alignment explanation
Indices: 19207406--19207439 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19207396 TTAAAAAATA
*
19207406 TAAAAAAATTTTTAAT
1 TAAAAAAATTATTAAT
19207422 TAAAAAAATTAATTAAT
1 TAAAAAAATT-ATTAAT
19207439 T
1 T
19207440 GCTAATGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAAAAATTATTAAT
Done.