Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 43 of 318
Found at i:12047342 original size:47 final size:48
Alignment explanation
Indices: 12047272--12047413 Score: 220
Period size: 47 Copynumber: 3.0 Consensus size: 48
12047262 GAGGAAGTGC
12047272 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
12047320 -AAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
*
12047366 AAAAAGGGCTT-TGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATTAAAAG-GGCTTATGCC-CCAGTTAT
12047414 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 1, Indels: 9
0.90 0.01 0.09
Matches are distributed among these distances:
46 23 0.26
47 36 0.41
48 18 0.20
49 11 0.12
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
Found at i:12047640 original size:31 final size:31
Alignment explanation
Indices: 12047605--12047668 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
12047595 CGTTTACAGT
12047605 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
12047636 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
12047667 AA
1 AA
12047669 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:12054052 original size:18 final size:17
Alignment explanation
Indices: 12054029--12054062 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
12054019 TAGCTGTGCC
12054029 GTTTTCTCTTCTGTATTA
1 GTTTTCTCTTCT-TATTA
12054047 GTTTTCTCTTCTTATT
1 GTTTTCTCTTCTTATT
12054063 TTCTTCCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.09, C:0.18, G:0.09, T:0.65
Consensus pattern (17 bp):
GTTTTCTCTTCTTATTA
Found at i:12055313 original size:11 final size:11
Alignment explanation
Indices: 12055277--12055332 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
12055267 CATGGTATGT
12055277 ATGATATGCAC
1 ATGATATGCAC
* *
12055288 ATGACATG--T
1 ATGATATGCAC
12055297 ATGATATGCAC
1 ATGATATGCAC
12055308 ATGATATG-A-
1 ATGATATGCAC
*
12055317 ATGACATGCAC
1 ATGATATGCAC
12055328 ATGAT
1 ATGAT
12055333 GTATTTATGA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 14 0.40
10 2 0.06
11 19 0.54
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:12055332 original size:20 final size:20
Alignment explanation
Indices: 12055266--12055332 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
12055256 ATTTTGATAA
*
12055266 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
12055286 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
12055306 ACATGATATGAATGACATGC
1 ACATGATATGTATGATATGC
12055326 ACATGAT
1 ACATGAT
12055333 GTATTTATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:12055451 original size:47 final size:48
Alignment explanation
Indices: 12055381--12055523 Score: 195
Period size: 47 Copynumber: 3.0 Consensus size: 48
12055371 GAGGAAGTGC
*
12055381 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
12055429 -AAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
* *
12055475 AAAAAAGGGCTT-TTCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 --AAAAGGGCTTATGCCCCAGTTATTAAAAG-GGCTTATGCC-CCAGTTAT
12055524 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
46 22 0.26
47 23 0.27
48 12 0.14
49 18 0.21
50 11 0.13
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
Found at i:12055519 original size:25 final size:24
Alignment explanation
Indices: 12055381--12055523 Score: 195
Period size: 23 Copynumber: 6.0 Consensus size: 24
12055371 GAGGAAGTGC
12055381 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
12055405 AAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
12055429 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
12055452 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
12055475 AAAAAAGGGCTT-TTCCCCAGTTATT
1 --AAAAGGGCTTATGCCCCAGTTATT
*
12055500 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
12055524 ATGATAAAGC
Statistics
Matches: 108, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
23 51 0.47
24 28 0.26
25 20 0.19
26 9 0.08
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:12055751 original size:31 final size:31
Alignment explanation
Indices: 12055716--12055779 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
12055706 CGTTTACAGT
12055716 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
12055747 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
12055778 AA
1 AA
12055780 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:12057875 original size:31 final size:34
Alignment explanation
Indices: 12057832--12057915 Score: 102
Period size: 37 Copynumber: 2.5 Consensus size: 34
12057822 CATTATGTGA
*
12057832 TGTGTGAGTAAGACCA-TG-G-CATTGATATATG
1 TGTGCGAGTAAGACCATTGTGACATTGATATATG
*
12057863 TGTGCGAGTAAGACCACGTTTGTGACTTTGATATATG
1 TGTGCGAGTAAGACCA---TTGTGACATTGATATATG
12057900 TGTGCGAGTAAGACCA
1 TGTGCGAGTAAGACCA
12057916 CGTTTTATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
31 15 0.33
35 2 0.04
36 1 0.02
37 27 0.60
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (34 bp):
TGTGCGAGTAAGACCATTGTGACATTGATATATG
Found at i:12062684 original size:48 final size:48
Alignment explanation
Indices: 12062632--12062865 Score: 193
Period size: 48 Copynumber: 4.9 Consensus size: 48
12062622 ATGTCAGTAT
* **
12062632 TGAGATCCCATATAAGACCATATCTGGGATATGAAATCGGCATCGAGA
1 TGAGATCCCGTATAAGACCATATCTGGGATATGGCATCGGCATCGAGA
* * * * * *
12062680 TGAGATTCCGTGTAAGACCATATCTGGAATATGGCATCAGCATTGATA
1 TGAGATCCCGTATAAGACCATATCTGGGATATGGCATCGGCATCGAGA
* * * * *
12062728 AGAGATCCCGTA-AATGACCTTGTTTGGGACATGGCATCGGCATC-AGTA
1 TGAGATCCCGTATAA-GACCATATCTGGGATATGGCATCGGCATCGAG-A
* * * * * ** *
12062776 TGAAATCCCATGTAAGACCATATTTGGGATATGGCATTGGCATTAATA
1 TGAGATCCCGTATAAGACCATATCTGGGATATGGCATCGGCATCGAGA
* * * * *
12062824 TGAGGTCCCGTATAAGACCATGTCTAGGACATTGCATCGGCA
1 TGAGATCCCGTATAAGACCATATCTGGGATATGGCATCGGCA
12062866 CCATTATGAG
Statistics
Matches: 142, Mismatches: 40, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
47 3 0.02
48 136 0.96
49 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (48 bp):
TGAGATCCCGTATAAGACCATATCTGGGATATGGCATCGGCATCGAGA
Found at i:12062769 original size:96 final size:96
Alignment explanation
Indices: 12062633--12062874 Score: 254
Period size: 96 Copynumber: 2.5 Consensus size: 96
12062623 TGTCAGTATT
* * * * ** * * *
12062633 GAGATCCCATATAAGACCATATCTGGGATATGAAATCGGCATCGAG-ATGAGATTCCGTGTAAGA
1 GAGATCCCGTATAAGACCATGTCTAGGACATGGCATCGGCATC-AGTATGAAATCCCATGTAAGA
*
12062697 CCATATCTGGAATATGGCATCAGCATTGATAA
65 CCATATCTGGAATATGGCATCAGCATTAATAA
* * *
12062729 GAGATCCCGTA-AATGACCTTGTTTGGGACATGGCATCGGCATCAGTATGAAATCCCATGTAAGA
1 GAGATCCCGTATAA-GACCATGTCTAGGACATGGCATCGGCATCAGTATGAAATCCCATGTAAGA
* * ** *
12062793 CCATATTTGGGATATGGCATTGGCATTAATAT
65 CCATATCTGGAATATGGCATCAGCATTAATAA
* * * *
12062825 GAGGTCCCGTATAAGACCATGTCTAGGACATTGCATCGGCACCATTATGA
1 GAGATCCCGTATAAGACCATGTCTAGGACATGGCATCGGCATCAGTATGA
12062875 GACTTTGTGT
Statistics
Matches: 120, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
95 4 0.03
96 114 0.95
97 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (96 bp):
GAGATCCCGTATAAGACCATGTCTAGGACATGGCATCGGCATCAGTATGAAATCCCATGTAAGAC
CATATCTGGAATATGGCATCAGCATTAATAA
Found at i:12063518 original size:21 final size:19
Alignment explanation
Indices: 12063486--12063524 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
12063476 CCCCTATCTT
12063486 AAATTTAGAAAATCATTAA
1 AAATTTAGAAAATCATTAA
*
12063505 AAATTGTATGAAAATGATTA
1 AAATT-TA-GAAAATCATTA
12063525 TGGGTTAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.33
Consensus pattern (19 bp):
AAATTTAGAAAATCATTAA
Found at i:12067797 original size:42 final size:40
Alignment explanation
Indices: 12067737--12067866 Score: 111
Period size: 39 Copynumber: 3.2 Consensus size: 40
12067727 GGGCCATGAG
* ** ** *
12067737 CCTAGCAGGCATAATGCCGGTGAATGAGTTTCAGACTTAATG
1 CCTAGCAGGCCTCGTGCCGGTGAAT-AAATTCAG-CTTAATA
* * * *
12067779 TCTAGCAGGCCTCGTGCCGATG-ATAAATTCAGGTTTATA
1 CCTAGCAGGCCTCGTGCCGGTGAATAAATTCAGCTTAATA
* * *
12067818 CCTAGCAGGCCTCGTGCCGGTG-ATAAGTTCAGGTTTATA
1 CCTAGCAGGCCTCGTGCCGGTGAATAAATTCAGCTTAATA
12067857 CCTAGCAGGC
1 CCTAGCAGGC
12067867 TAATTGCCGG
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
39 50 0.67
40 6 0.08
41 2 0.03
42 17 0.23
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (40 bp):
CCTAGCAGGCCTCGTGCCGGTGAATAAATTCAGCTTAATA
Found at i:12067830 original size:39 final size:39
Alignment explanation
Indices: 12067780--12067866 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
12067770 GACTTAATGT
12067780 CTAGCAGGCCTCGTGCCGATGATAAATTCAGGTTTATAC
1 CTAGCAGGCCTCGTGCCGATGATAAATTCAGGTTTATAC
* *
12067819 CTAGCAGGCCTCGTGCCGGTGATAAGTTCAGGTTTATAC
1 CTAGCAGGCCTCGTGCCGATGATAAATTCAGGTTTATAC
12067858 CTAGCAGGC
1 CTAGCAGGC
12067867 TAATTGCCGG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.26
Consensus pattern (39 bp):
CTAGCAGGCCTCGTGCCGATGATAAATTCAGGTTTATAC
Found at i:12067875 original size:39 final size:39
Alignment explanation
Indices: 12067780--12067879 Score: 139
Period size: 39 Copynumber: 2.6 Consensus size: 39
12067770 GACTTAATGT
* *
12067780 CTAGCAGGCCTCGTGCCGATGATAAATTCAGGTTTATAC
1 CTAGCAGGCCTAGTGCCGGTGATAAATTCAGGTTTATAC
* *
12067819 CTAGCAGGCCTCGTGCCGGTGATAAGTTCAGGTTTATAC
1 CTAGCAGGCCTAGTGCCGGTGATAAATTCAGGTTTATAC
*
12067858 CTAGCAGG-CTAATTGCCGGTGA
1 CTAGCAGGCCT-AGTGCCGGTGA
12067880 AAAAATAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
38 2 0.04
39 54 0.96
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (39 bp):
CTAGCAGGCCTAGTGCCGGTGATAAATTCAGGTTTATAC
Found at i:12075920 original size:40 final size:39
Alignment explanation
Indices: 12075755--12075938 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
12075745 AAATTGAATG
* * *
12075755 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
12075795 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
12075835 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
12075875 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
12075914 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
12075939 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:12075963 original size:80 final size:81
Alignment explanation
Indices: 12075795--12075983 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
12075785 GCTGGAAATT
* * * *
12075795 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
12075860 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
12075876 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
12075939 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
12075955 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
12075984 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:12081985 original size:40 final size:39
Alignment explanation
Indices: 12081820--12082003 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
12081810 AAATTGAATG
* * *
12081820 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
12081860 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
12081900 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
12081940 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
12081979 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
12082004 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:12082028 original size:80 final size:81
Alignment explanation
Indices: 12081860--12082048 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
12081850 GCTGGAAATT
* * * *
12081860 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
12081925 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
12081941 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
12082004 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
12082020 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
12082049 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:12084172 original size:14 final size:15
Alignment explanation
Indices: 12084155--12084183 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12084145 TCATTAAAAT
12084155 TTCACACAT-ATAAA
1 TTCACACATAATAAA
12084169 TTCACACATAATAAA
1 TTCACACATAATAAA
12084184 CATAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:12088562 original size:68 final size:70
Alignment explanation
Indices: 12088490--12088687 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
12088480 ACACCCTGTA
* * * *
12088490 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
12088552 ATAAAT
65 ATAAAT
*
12088558 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
12088623 ATAAAT
65 ATAAAT
*
12088629 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
12088688 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:12088601 original size:41 final size:41
Alignment explanation
Indices: 12088556--12088673 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
12088546 TGAAAGATAA
12088556 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
12088597 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
12088627 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
12088668 ATGTAG
1 ATGTAG
12088674 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:12088613 original size:71 final size:71
Alignment explanation
Indices: 12088524--12088687 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
12088514 GAGATGTATC
12088524 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
12088589 AGGACA
66 AGGACA
12088595 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
12088660 AGGACA
66 AGGACA
12088666 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
12088688 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:12093129 original size:28 final size:28
Alignment explanation
Indices: 12093074--12093161 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 28
12093064 AGCATGGCTG
* * *
12093074 CCAG-AACAGAT-ATTGTGACTGAGTCA
1 CCAGAAACAGATAATTGTGGCAGAGCCA
* *
12093100 CCAGATACAGATAATTGTGGCAGGGCCA
1 CCAGAAACAGATAATTGTGGCAGAGCCA
*
12093128 CCAGAAACAGATATTTGTGGCAGAGCCA
1 CCAGAAACAGATAATTGTGGCAGAGCCA
12093156 CCAGAA
1 CCAGAA
12093162 TGCTTCCTCC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
26 4 0.08
27 6 0.12
28 42 0.81
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (28 bp):
CCAGAAACAGATAATTGTGGCAGAGCCA
Found at i:12096677 original size:27 final size:28
Alignment explanation
Indices: 12096647--12096716 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
12096637 ATAGTGAATC
*
12096647 CGCACACTTAGTGCTATAAAATC-AGCT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
12096674 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATAAAATCAAACT
12096702 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
12096717 GTACAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:12096788 original size:42 final size:42
Alignment explanation
Indices: 12096724--12096830 Score: 187
Period size: 42 Copynumber: 2.5 Consensus size: 42
12096714 GCTGTACAAT
* *
12096724 TTTAAACCCGCACACGTAGTGCCAATATTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATATTGTCACCGTGTCCA
*
12096766 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATATTGTCACCGTGTCCA
12096808 TTTATACCCGCACACTTAGTGCC
1 TTTATACCCGCACACTTAGTGCC
12096831 GAGACCAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (42 bp):
TTTATACCCGCACACTTAGTGCCAATATTGTCACCGTGTCCA
Found at i:12099910 original size:15 final size:15
Alignment explanation
Indices: 12099890--12099920 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12099880 CTAAAAATTC
12099890 CAATCCAAAACATAT
1 CAATCCAAAACATAT
12099905 CAATCCAAAACATAT
1 CAATCCAAAACATAT
12099920 C
1 C
12099921 TTTCATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATCCAAAACATAT
Found at i:12103067 original size:2 final size:2
Alignment explanation
Indices: 12103060--12103087 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12103050 AAATGGCATA
12103060 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
12103088 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12103742 original size:40 final size:40
Alignment explanation
Indices: 12103687--12103950 Score: 347
Period size: 40 Copynumber: 6.5 Consensus size: 40
12103677 TATTCGGATG
* *
12103687 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
12103727 ATATCCGGGCTAAGTCCCGAAGGCATTCT-TGCGAGTAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATT-TGTGC---TAG-TGACT
*
12103770 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* **
12103810 ATATCCGAGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
**
12103850 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
12103890 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
12103930 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
12103951 ATACTTGGGT
Statistics
Matches: 202, Mismatches: 14, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
39 15 0.07
40 149 0.74
41 3 0.01
42 1 0.00
43 33 0.16
44 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:12110862 original size:22 final size:22
Alignment explanation
Indices: 12110834--12110878 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
12110824 AATGCTCATA
12110834 TATTTTCAGGTACATTATGTCG
1 TATTTTCAGGTACATTATGTCG
12110856 TATTTTCAGGTACATTATGTCG
1 TATTTTCAGGTACATTATGTCG
12110878 T
1 T
12110879 CATCAAGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (22 bp):
TATTTTCAGGTACATTATGTCG
Found at i:12112142 original size:22 final size:22
Alignment explanation
Indices: 12112114--12112175 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
12112104 TGACTCCTCC
*
12112114 TATTTTTTTTATTA-TTTATTCT
1 TATTTTTATT-TTATTTTATTCT
*
12112136 TATTTTTATTTTATTTTATTTT
1 TATTTTTATTTTATTTTATTCT
12112158 TATTTTTATTTTGATTTT
1 TATTTTTATTTT-ATTTT
12112176 TAATTTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 3 0.08
22 28 0.78
23 5 0.14
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (22 bp):
TATTTTTATTTTATTTTATTCT
Found at i:12112144 original size:6 final size:6
Alignment explanation
Indices: 12112119--12112177 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
12112109 CCTCCTATTT
*
12112119 TTTTTA TTATTTA TTCTTA TTTTTA -TTTTA -TTTTA TTTTTA TTTTTA
1 TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
12112166 TTTTGA TTTTTA
1 TTTTTA TTTTTA
12112178 ATTTCATTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
5 10 0.21
6 31 0.66
7 6 0.13
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:12112144 original size:16 final size:15
Alignment explanation
Indices: 12112114--12112206 Score: 80
Period size: 17 Copynumber: 5.7 Consensus size: 15
12112104 TGACTCCTCC
*
12112114 TATTTTTTTTATTATT
1 TATTTTATTT-TTATT
12112130 TATTCTTATTTTTATTT
1 TATT-TTATTTTTA-TT
12112147 TATTTTATTTTTATTTT
1 TATTTTATTTTTA--TT
12112164 TATTTTGATTTTTAATT
1 TATTTT-ATTTTT-ATT
* *
12112181 TCATTTCAATTTTA-T
1 T-ATTTTATTTTTATT
12112196 TATTTTATTTT
1 TATTTTATTTT
12112207 GAAAGACATA
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
14 8 0.12
15 2 0.03
16 17 0.26
17 28 0.42
18 10 0.15
19 1 0.02
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.75
Consensus pattern (15 bp):
TATTTTATTTTTATT
Found at i:12112149 original size:5 final size:5
Alignment explanation
Indices: 12112114--12112206 Score: 57
Period size: 5 Copynumber: 17.2 Consensus size: 5
12112104 TGACTCCTCC
12112114 TATTT T-TTT TATTATT TATTCT TATTTT TATTT TATTT TATTTT TATTTT
1 TATTT TATTT TA-T-TT TATT-T TA-TTT TATTT TATTT TA-TTT TA-TTT
* *
12112164 TATTT TGATTTT TAATTT CATTT CAATTT TA--T TATTT TATTT T
1 TATTT T-A-TTT T-ATTT TATTT -TATTT TATTT TATTT TATTT T
12112207 GAAAGACATA
Statistics
Matches: 73, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
3 3 0.04
4 4 0.05
5 28 0.38
6 27 0.37
7 11 0.15
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:12112159 original size:28 final size:28
Alignment explanation
Indices: 12112114--12112176 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
12112104 TGACTCCTCC
12112114 TATTTTTTTTATTATTTATTCTTATTTT
1 TATTTTTTTTATTATTTATTCTTATTTT
*
12112142 TATTTTATTTTATT-TTTATTTTTATTTT
1 TATTTT-TTTTATTATTTATTCTTATTTT
*
12112170 GATTTTT
1 TATTTTT
12112177 AATTTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.75
29 7 0.22
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (28 bp):
TATTTTTTTTATTATTTATTCTTATTTT
Found at i:12112160 original size:35 final size:36
Alignment explanation
Indices: 12112119--12112208 Score: 114
Period size: 35 Copynumber: 2.5 Consensus size: 36
12112109 CCTCCTATTT
* *
12112119 TTTTTATTATTTATTCTT-ATTTTT-ATTTTATTTTA
1 TTTTTATTATTTATT-TTGATTTTTAATTTCATTTCA
12112154 TTTTTATT-TTTATTTTGATTTTTAATTTCATTTCA
1 TTTTTATTATTTATTTTGATTTTTAATTTCATTTCA
*
12112189 ATTTTATTATTTTATTTTGA
1 TTTTTATTA-TTTATTTTGA
12112209 AAGACATATC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
33 2 0.04
34 12 0.25
35 24 0.50
37 10 0.21
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.73
Consensus pattern (36 bp):
TTTTTATTATTTATTTTGATTTTTAATTTCATTTCA
Found at i:12112186 original size:12 final size:12
Alignment explanation
Indices: 12112120--12112206 Score: 67
Period size: 11 Copynumber: 7.3 Consensus size: 12
12112110 CTCCTATTTT
12112120 TTTTATTATTT-A
1 TTTTATT-TTTAA
12112132 TTCTTATTTTT-A
1 TT-TTATTTTTAA
*
12112144 TTTTA-TTTTAT
1 TTTTATTTTTAA
12112155 TTTTATTTTT-A
1 TTTTATTTTTAA
12112166 TTTTGATTTTTAA
1 TTTT-ATTTTTAA
* *
12112179 TTTCA-TTTCAA
1 TTTTATTTTTAA
*
12112190 TTTTATTATTTTA
1 TTTTATT-TTTAA
12112203 TTTT
1 TTTT
12112207 GAAAGACATA
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
10 4 0.07
11 21 0.34
12 20 0.33
13 16 0.26
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (12 bp):
TTTTATTTTTAA
Found at i:12112904 original size:58 final size:59
Alignment explanation
Indices: 12112813--12112926 Score: 212
Period size: 58 Copynumber: 1.9 Consensus size: 59
12112803 TTTTTTAGAT
*
12112813 TATTTTCTAAATTGAGGTATTATCTTGAAATCTTAAGTATACAGGAATGACATCAATTA
1 TATTTTCTAAATTGAGGTATTATCTTGAAATCTTAAGTAAACAGGAATGACATCAATTA
12112872 TATTTT-TAAATTGAGGTATTATCTTGAAATCTTAAGTAAACAGGAATGACATCAA
1 TATTTTCTAAATTGAGGTATTATCTTGAAATCTTAAGTAAACAGGAATGACATCAA
12112927 AAACCCAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
58 48 0.89
59 6 0.11
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (59 bp):
TATTTTCTAAATTGAGGTATTATCTTGAAATCTTAAGTAAACAGGAATGACATCAATTA
Found at i:12115189 original size:17 final size:17
Alignment explanation
Indices: 12115143--12115190 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
12115133 TCTCTTTGCT
* *
12115143 TTAATTAAATCAGTTAA
1 TTAATTAAAACAATTAA
* * *
12115160 TTAGTTTAAACAATTAG
1 TTAATTAAAACAATTAA
12115177 TTAATTAAAACAAT
1 TTAATTAAAACAAT
12115191 CCCTTTTATT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (17 bp):
TTAATTAAAACAATTAA
Found at i:12125248 original size:24 final size:23
Alignment explanation
Indices: 12125221--12125271 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
12125211 TTCTGATTTA
12125221 GATTAAGGGAGAAACAAGGTGTTG
1 GATTAA-GGAGAAACAAGGTGTTG
**
12125245 GATT-AGTTGAAACAAGGTGTTG
1 GATTAAGGAGAAACAAGGTGTTG
12125267 GATTA
1 GATTA
12125272 GTTGATCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 19 0.79
23 1 0.04
24 4 0.17
ACGTcount: A:0.35, C:0.04, G:0.33, T:0.27
Consensus pattern (23 bp):
GATTAAGGAGAAACAAGGTGTTG
Found at i:12125258 original size:22 final size:22
Alignment explanation
Indices: 12125231--12125276 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
12125221 GATTAAGGGA
12125231 GAAACAAGGTGTTGGATTAGTT
1 GAAACAAGGTGTTGGATTAGTT
12125253 GAAACAAGGTGTTGGATTAGTT
1 GAAACAAGGTGTTGGATTAGTT
12125275 GA
1 GA
12125277 TCTACTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.30
Consensus pattern (22 bp):
GAAACAAGGTGTTGGATTAGTT
Found at i:12125387 original size:50 final size:50
Alignment explanation
Indices: 12125328--12125429 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
12125318 ATAAGCATTG
*
12125328 TTATATTTATGTTTTAAATGCTTTAATATTGCATAAATTGTGAATACGAT
1 TTATATTTATGTTTTAAATGCTTTAATATTGCATAAATTGTGAATACAAT
*
12125378 TTATATTTATGTTTTAAATGCTTTAATATTGTATAAATTGTGAATACAAT
1 TTATATTTATGTTTTAAATGCTTTAATATTGCATAAATTGTGAATACAAT
12125428 TT
1 TT
12125430 TGCAGACATA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (50 bp):
TTATATTTATGTTTTAAATGCTTTAATATTGCATAAATTGTGAATACAAT
Found at i:12128986 original size:39 final size:39
Alignment explanation
Indices: 12128905--12128986 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
12128895 ATGAGTTTTA
* *
12128905 GTGATAAATTCAGGTTTATACCTAGCAGGCCTCGTGCTG
1 GTGATAAATTCAGGTTTATACCTAGCAGGCCTAGTGCCG
* *
12128944 GTGATAAGTTCAGGTTTATACCTAGCAGG-CTAATTGCCG
1 GTGATAAATTCAGGTTTATACCTAGCAGGCCT-AGTGCCG
12128983 GTGA
1 GTGA
12128987 AATAATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 2 0.05
39 36 0.95
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (39 bp):
GTGATAAATTCAGGTTTATACCTAGCAGGCCTAGTGCCG
Found at i:12132981 original size:6 final size:6
Alignment explanation
Indices: 12132970--12133071 Score: 95
Period size: 6 Copynumber: 16.8 Consensus size: 6
12132960 AACCAAAATG
*
12132970 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* * *
12133018 AGTAAT- AGAATC AGAATC AGAATC AAAATT AG-GTGAC AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
12133067 AGAAT
1 AGAAT
12133072 GTGAATGTAA
Statistics
Matches: 80, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
5 7 0.09
6 65 0.81
7 6 0.08
8 2 0.03
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.21
Consensus pattern (6 bp):
AGAATC
Found at i:12133022 original size:30 final size:29
Alignment explanation
Indices: 12132970--12133071 Score: 141
Period size: 30 Copynumber: 3.4 Consensus size: 29
12132960 AACCAAAATG
*
12132970 AGAATCAGAATCAGAATCAGTAACAGAATC
1 AGAATCAGAATCA-AATTAGTAACAGAATC
*
12133000 AGAATCAGAATCAATATTAGTAATAGAATC
1 AGAATCAGAATCAA-ATTAGTAACAGAATC
*
12133030 AGAATCAGAATCAAAATTAGGTGACAGAATC
1 AGAATCAGAATC-AAATTA-GTAACAGAATC
12133061 AGAATCAGAAT
1 AGAATCAGAAT
12133072 GTGAATGTAA
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
29 1 0.02
30 42 0.65
31 22 0.34
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.21
Consensus pattern (29 bp):
AGAATCAGAATCAAATTAGTAACAGAATC
Found at i:12133252 original size:27 final size:27
Alignment explanation
Indices: 12133207--12133262 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
12133197 GATATCATGA
* *
12133207 CAGAGTCACCAGATACAGACATTGTGG
1 CAGAGCCACCAGATACAGACAATGTGG
*
12133234 CAGAGCCACCAGA-ATCAGATAATGTGG
1 CAGAGCCACCAGATA-CAGACAATGTGG
12133261 CA
1 CA
12133263 AACCCACCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (27 bp):
CAGAGCCACCAGATACAGACAATGTGG
Found at i:12133475 original size:22 final size:22
Alignment explanation
Indices: 12133427--12133485 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
12133417 GTAAATACGT
*
12133427 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
12133449 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
12133471 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
12133486 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:12133652 original size:27 final size:26
Alignment explanation
Indices: 12133573--12133655 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
12133563 TCAATCGATC
* * *
12133573 AACAGATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
12133599 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
12133626 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
12133653 AAC
1 AAC
12133656 GCTTCCTCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 8 0.16
27 43 0.84
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:12134003 original size:27 final size:27
Alignment explanation
Indices: 12133854--12134022 Score: 180
Period size: 27 Copynumber: 6.3 Consensus size: 27
12133844 GGGGCAAAAT
* *
12133854 GGTAATTTTAACCC-ACAAGGGTATCTC
1 GGTAATTCT-ACCCTACAAGGGTATTTC
* *
12133881 GGTAATTCTACCTTACAGGGGTATCTT-
1 GGTAATTCTACCCTACAAGGGTAT-TTC
* *
12133908 GGTATTTCTACCCTACAAGGGTACTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
12133935 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
12133962 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
12133989 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
12134016 AGTAATT
1 GGTAATT
12134023 TCACAATTGA
Statistics
Matches: 120, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
26 5 0.04
27 114 0.95
28 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:12134066 original size:27 final size:27
Alignment explanation
Indices: 12134034--12134195 Score: 209
Period size: 27 Copynumber: 6.0 Consensus size: 27
12134024 CACAATTGAA
*
12134034 GGTAAAACGGTAATTCTATAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* * *
12134061 GGTAAAATGATAATTTTGTAAA-CTGAG
1 GGTAAAACGGTAATTCTGTAAATC-GAG
* * *
12134088 GGTAAACCAGTAATTCTGTAAATCAAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* **
12134115 GGTAAAACGGTAATTTTACAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
12134142 GGTAAAACGGTAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
*
12134169 GGTAAAACAGTAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
12134196 AGTACTTTGG
Statistics
Matches: 113, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
26 1 0.01
27 111 0.98
28 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.27
Consensus pattern (27 bp):
GGTAAAACGGTAATTCTGTAAATCGAG
Found at i:12134142 original size:81 final size:81
Alignment explanation
Indices: 12134034--12134224 Score: 249
Period size: 81 Copynumber: 2.4 Consensus size: 81
12134024 CACAATTGAA
* * * * *
12134034 GGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGATAATTTTGTAAA-CTGAGGGTAAACCAG
1 GGTAAAACGGTAATTTTACAAATCGAGGGTAAAACGATAATTCTGTAAATC-GAGGGTAAAACAG
12134098 TAATTCTGTAAATCAAG
65 TAATTCTGTAAATCAAG
*
12134115 GGTAAAACGGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGT
1 GGTAAAACGGTAATTTTACAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACAGT
*
12134180 AATTCTGTAAATCGAG
66 AATTCTGTAAATCAAG
* **** *
12134196 AGTACTTTGGTAATTTTACAAGTCGAGGG
1 GGTAAAACGGTAATTTTACAAATCGAGGG
12134225 CATTTCAGTA
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 95 0.99
82 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.28
Consensus pattern (81 bp):
GGTAAAACGGTAATTTTACAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACAGT
AATTCTGTAAATCAAG
Found at i:12134182 original size:54 final size:54
Alignment explanation
Indices: 12134015--12134183 Score: 200
Period size: 54 Copynumber: 3.1 Consensus size: 54
12134005 AGGGGTATTT
* * * *
12134015 CAGTAATTTCAC-AATTGAAGGTAAAACGGTAATTCTATAAATCGAGGGTAAAA
1 CAGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA
* ** * * *
12134068 -TGATAATTTTGTAAA-CTGAGGGTAAACCAGTAATTCTGTAAATCAAGGGTAAAA
1 CAG-TAATTTTACAAATC-GAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA
*
12134122 CGGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA
1 CAGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA
12134176 CAGTAATT
1 CAGTAATT
12134184 CTGTAAATCG
Statistics
Matches: 94, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
52 1 0.01
53 6 0.06
54 85 0.90
55 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.28
Consensus pattern (54 bp):
CAGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA
Found at i:12138397 original size:11 final size:11
Alignment explanation
Indices: 12138381--12138411 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
12138371 AGTCGAAATA
12138381 ATTATTTTATT
1 ATTATTTTATT
12138392 ATTATTTTATT
1 ATTATTTTATT
12138403 ATTATTTTA
1 ATTATTTTA
12138412 ATGTTTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:12142030 original size:40 final size:40
Alignment explanation
Indices: 12141985--12142152 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
12141975 CGGAATACAA
12141985 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
12142025 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
12142065 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
*** * ** * *
12142105 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
12142145 CCGGATAT
1 CCGGATAT
12142153 CATTCAATTG
Statistics
Matches: 105, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 3 0.03
40 100 0.95
41 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:12146199 original size:37 final size:37
Alignment explanation
Indices: 12146146--12146267 Score: 226
Period size: 37 Copynumber: 3.3 Consensus size: 37
12146136 TATAAAAGAA
*
12146146 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
12146183 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
12146220 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
12146257 GTCTCACCCGG
1 GTCTTACCCGG
12146268 AACATATTCC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 83 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:12146424 original size:49 final size:49
Alignment explanation
Indices: 12146369--12146583 Score: 340
Period size: 49 Copynumber: 4.4 Consensus size: 49
12146359 TTTTACATTA
*
12146369 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
12146418 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* * *
12146467 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* * * *
12146516 GCCATTAGGCCTCATCACATATACATCCACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* *
12146565 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTCATCACA
12146584 CATATATGTA
Statistics
Matches: 159, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 159 1.00
ACGTcount: A:0.28, C:0.33, G:0.10, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
Found at i:12149247 original size:29 final size:29
Alignment explanation
Indices: 12149211--12149432 Score: 417
Period size: 29 Copynumber: 7.7 Consensus size: 29
12149201 TGTTGAAAAA
* *
12149211 CTCGCACACACAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
12149240 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
12149269 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
12149298 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
*
12149327 CTCGCACACATGGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
12149356 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
12149385 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
12149414 CTCGCACACATAGTGCCTC
1 CTCGCACACATAGTGCCTC
12149433 AATCATTGCA
Statistics
Matches: 189, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 189 1.00
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (29 bp):
CTCGCACACATAGTGCCTCGATTACTGAT
Found at i:12151573 original size:37 final size:37
Alignment explanation
Indices: 12151520--12151641 Score: 208
Period size: 37 Copynumber: 3.3 Consensus size: 37
12151510 TATAAAAGAA
* *
12151520 GTCTTATCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
12151557 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
12151594 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCAG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
12151631 GTCTCACCCGG
1 GTCTTACCCGG
12151642 AACATATTCC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 81 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.26
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:12151798 original size:49 final size:49
Alignment explanation
Indices: 12151743--12151957 Score: 340
Period size: 49 Copynumber: 4.4 Consensus size: 49
12151733 TTTTACATTA
*
12151743 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
*
12151792 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCATATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* *
12151841 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCGCATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* * * *
12151890 GCCATTAGGCCTCATCACATATACATCCACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* *
12151939 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTCATCACA
12151958 CATATATGTA
Statistics
Matches: 157, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 157 1.00
ACGTcount: A:0.28, C:0.33, G:0.10, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
Found at i:12158119 original size:20 final size:22
Alignment explanation
Indices: 12158085--12158125 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
12158075 AGTTTATTTA
12158085 TGTTATAATTGTTGC-AAAATG
1 TGTTATAATTGTTGCTAAAATG
*
12158106 TGTT-TAATTTTTGCTAAAAT
1 TGTTATAATTGTTGCTAAAAT
12158126 TCATATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.49
Consensus pattern (22 bp):
TGTTATAATTGTTGCTAAAATG
Found at i:12159979 original size:44 final size:43
Alignment explanation
Indices: 12159946--12160045 Score: 154
Period size: 39 Copynumber: 2.4 Consensus size: 43
12159936 TAACGATCTT
12159946 GCACACTTAGTGCCATCACATTAAATCTTAGCTATCTCGATATC
1 GCACACTTAGTGCC-TCACATTAAATCTTAGCTATCTCGATATC
*
12159990 GTACACTT--TG--TCACATTAAATCTTAGCTATCTCGATATC
1 GCACACTTAGTGCCTCACATTAAATCTTAGCTATCTCGATATC
12160029 GCACACTTAGTGCCTCA
1 GCACACTTAGTGCCTCA
12160046 TATAGCTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
39 36 0.72
41 2 0.04
42 2 0.04
43 3 0.06
44 7 0.14
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (43 bp):
GCACACTTAGTGCCTCACATTAAATCTTAGCTATCTCGATATC
Found at i:12160090 original size:40 final size:40
Alignment explanation
Indices: 12160046--12160161 Score: 137
Period size: 40 Copynumber: 2.9 Consensus size: 40
12160036 TAGTGCCTCA
* *
12160046 TATAGCTGAAGCTA-TTCCAATTCGCACACTAAGTGCTATT
1 TATAGCCGAAGCTATTTCCAAAT-GCACACTAAGTGCTATT
**
12160086 TATAGCCGAAGCTATTTTGAAATGCACACTAAGTGCTATT
1 TATAGCCGAAGCTATTTCCAAATGCACACTAAGTGCTATT
* * *
12160126 TATAGCCGAAGCTACTTT-GAAACGCATACTAAGTGC
1 TATAGCCGAAGCTA-TTTCCAAATGCACACTAAGTGC
12160162 CAAACATAGT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 60 0.88
41 8 0.12
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (40 bp):
TATAGCCGAAGCTATTTCCAAATGCACACTAAGTGCTATT
Found at i:12160637 original size:28 final size:29
Alignment explanation
Indices: 12160573--12160637 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
12160563 CTTTCATTTA
* *
12160573 TTTCACAATTTAACCCCTTAATTTACACT
1 TTTCTCAATTTAACCCCTTAATATACACT
* *
12160602 TTTCTCAATTTAATCCC-TAATATGCA-T
1 TTTCTCAATTTAACCCCTTAATATACACT
12160629 TTTACTCAA
1 TTT-CTCAA
12160638 AATCACTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 4 0.13
28 12 0.39
29 15 0.48
ACGTcount: A:0.31, C:0.25, G:0.02, T:0.43
Consensus pattern (29 bp):
TTTCTCAATTTAACCCCTTAATATACACT
Found at i:12161599 original size:35 final size:35
Alignment explanation
Indices: 12161560--12161629 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
12161550 CATATTTGGA
*
12161560 GCTTGGTAAATAAGGAAAGTAATCTTCAAAGATAT
1 GCTTGGAAAATAAGGAAAGTAATCTTCAAAGATAT
* * *
12161595 GCTTGGAAAATATGGAAGGTGATCTTCAAAGATAT
1 GCTTGGAAAATAAGGAAAGTAATCTTCAAAGATAT
12161630 ATGATCCTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (35 bp):
GCTTGGAAAATAAGGAAAGTAATCTTCAAAGATAT
Found at i:12163593 original size:26 final size:26
Alignment explanation
Indices: 12163564--12163616 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
12163554 TCAAACATGC
12163564 ATTTAGGTCAATTTA-CTCCTAGGGGT
1 ATTTAGGT-AATTTATCTCCTAGGGGT
* *
12163590 ATTTCGGTACTTTATCTCCTAGGGGT
1 ATTTAGGTAATTTATCTCCTAGGGGT
12163616 A
1 A
12163617 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (26 bp):
ATTTAGGTAATTTATCTCCTAGGGGT
Found at i:12165364 original size:29 final size:29
Alignment explanation
Indices: 12165331--12165406 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
12165321 GACGAGATCA
* * *
12165331 GCACTAAGTGTGCGTGCTGGAAATATATG
1 GCACTAAGTGTGCGAGCTGGAAAAATACG
*
12165360 GCACTAAGTGTGCAAGCTGGAAAAATACG
1 GCACTAAGTGTGCGAGCTGGAAAAATACG
**
12165389 GCACTGGGTGTGCGAGCT
1 GCACTAAGTGTGCGAGCT
12165407 CGGAGGGTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGCTGGAAAAATACG
Found at i:12168976 original size:23 final size:24
Alignment explanation
Indices: 12168927--12169066 Score: 218
Period size: 23 Copynumber: 6.0 Consensus size: 24
12168917 GCTTTATCAT
*
12168927 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
12168952 ATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
12168975 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
12168998 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
12169021 ATAACT-GGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
12169044 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
12169067 GCACTTCCTC
Statistics
Matches: 110, Mismatches: 1, Indels: 9
0.92 0.01 0.08
Matches are distributed among these distances:
22 12 0.11
23 61 0.55
24 29 0.26
25 8 0.07
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:12169137 original size:20 final size:20
Alignment explanation
Indices: 12169112--12169178 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
12169102 CATTATGAAC
*
12169112 ATCATGTGCATGTCATACAT
1 ATCATGTGCATATCATACAT
12169132 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
12169152 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
12169172 ACCATGT
1 ATCATGT
12169179 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:12176804 original size:31 final size:31
Alignment explanation
Indices: 12176761--12176824 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
12176751 CCTTTTCATA
12176761 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
12176792 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
12176823 TT
1 TT
12176825 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:12177063 original size:24 final size:24
Alignment explanation
Indices: 12177016--12177157 Score: 220
Period size: 24 Copynumber: 6.0 Consensus size: 24
12177006 GCTTTATCAT
*
12177016 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
12177041 ATAACTGGGGCA-AAGCCCTTTTTA
1 ATAACTGGGGCATAAGCCC-TTTTA
12177065 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
12177088 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
12177111 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
12177135 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
12177158 GCACTTCCTC
Statistics
Matches: 112, Mismatches: 1, Indels: 9
0.92 0.01 0.07
Matches are distributed among these distances:
23 47 0.42
24 51 0.46
25 14 0.12
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:12177091 original size:23 final size:23
Alignment explanation
Indices: 12177037--12177156 Score: 206
Period size: 23 Copynumber: 5.1 Consensus size: 23
12177027 CCTAGCCTCT
12177037 TTTAATAACTGGGGCA-AAGCCC
1 TTTAATAACTGGGGCATAAGCCC
12177059 TTTTTAATAACTGGGGCATAAGCCC
1 --TTTAATAACTGGGGCATAAGCCC
12177084 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
12177107 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
12177130 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
12177154 TTT
1 TTT
12177157 TGCACTTCCT
Statistics
Matches: 94, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
23 49 0.52
24 39 0.41
25 6 0.06
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:12177091 original size:47 final size:49
Alignment explanation
Indices: 12177016--12177157 Score: 222
Period size: 47 Copynumber: 3.0 Consensus size: 49
12177006 GCTTTATCAT
*
12177016 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCA-AAGCCCTTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTTA
12177065 ATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCC--TTTA
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTA
12177111 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
12177158 GCACTTCCTC
Statistics
Matches: 87, Mismatches: 1, Indels: 10
0.89 0.01 0.10
Matches are distributed among these distances:
46 23 0.26
47 39 0.45
48 11 0.13
49 14 0.16
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (49 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTA
Found at i:12177221 original size:11 final size:11
Alignment explanation
Indices: 12177206--12177261 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
12177196 TCATAAATAC
12177206 ATCATGTGCAT
1 ATCATGTGCAT
*
12177217 GTCAT-T-CAT
1 ATCATGTGCAT
12177226 ATCATGTGCAT
1 ATCATGTGCAT
*
12177237 ATCA--TACAT
1 ATCATGTGCAT
*
12177246 GTCATGTGCAT
1 ATCATGTGCAT
12177257 ATCAT
1 ATCAT
12177262 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 14 0.40
10 2 0.06
11 19 0.54
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:12177231 original size:20 final size:20
Alignment explanation
Indices: 12177206--12177272 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
12177196 TCATAAATAC
* *
12177206 ATCATGTGCATGTCATTCAT
1 ATCATGTGCATATCATACAT
12177226 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
12177246 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
12177266 ACCATGT
1 ATCATGT
12177273 TTATCAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:12177337 original size:25 final size:25
Alignment explanation
Indices: 12177309--12177356 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12177299 ATGTATAAAC
* * *
12177309 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
12177334 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
12177357 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:12178505 original size:18 final size:17
Alignment explanation
Indices: 12178478--12178511 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
12178468 TAGGGAAGAA
12178478 AATAAGAAGAGAAAACT
1 AATAAGAAGAGAAAACT
12178495 AATACAGAAGAGAAAAC
1 AATA-AGAAGAGAAAAC
12178512 GGCACAGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.65, C:0.09, G:0.18, T:0.09
Consensus pattern (17 bp):
AATAAGAAGAGAAAACT
Found at i:12181617 original size:40 final size:40
Alignment explanation
Indices: 12181558--12181775 Score: 307
Period size: 40 Copynumber: 5.5 Consensus size: 40
12181548 CGGATGATAA
* *
12181558 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
12181598 CCGGGCTAAGCCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
12181638 CCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
12181678 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
12181718 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
12181758 CC-GGCTAAATCCCAAAGG
1 CCGGGCTAAGTCCCGAAGG
12181776 TACTTGGTTT
Statistics
Matches: 163, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 16 0.10
40 146 0.90
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:12197348 original size:16 final size:16
Alignment explanation
Indices: 12197327--12197360 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12197317 ATATATAGTT
12197327 AATTAATT-AAAATATG
1 AATTAATTGAAAAT-TG
12197343 AATTAATTGAAAATTG
1 AATTAATTGAAAATTG
12197359 AA
1 AA
12197361 AAGTGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (16 bp):
AATTAATTGAAAATTG
Found at i:12197775 original size:18 final size:18
Alignment explanation
Indices: 12197716--12197906 Score: 104
Period size: 18 Copynumber: 10.6 Consensus size: 18
12197706 CAACTGATTA
*
12197716 TTACTGAATAATTGACTG
1 TTACTGGATAATTGACTG
* *
12197734 TTACTAGATAATTGATTG
1 TTACTGGATAATTGACTG
12197752 TTACTGGAT-ATTAGACTG
1 TTACTGGATAATT-GACTG
* * * * *
12197770 TTACTGAATAACTAAATA
1 TTACTGGATAATTGACTG
** *
12197788 TTACTAAATAATTGA-TCA
1 TTACTGGATAATTGACT-G
* * *
12197806 TTACTGAATAACTGATTG
1 TTACTGGATAATTGACTG
* *
12197824 TCACTGAATGAA-TGACTG
1 TTACTGGAT-AATTGACTG
* * *
12197842 TTACTGAATAACTTAATTG
1 TTACTGGATAA-TTGACTG
* *
12197861 TTACTGAAT-ATCTGA-TT
1 TTACTGGATAAT-TGACTG
*
12197878 TTACTGAATAATTGACTG
1 TTACTGGATAATTGACTG
12197896 TTACTGGATAA
1 TTACTGGATAA
12197907 CCGATCAATT
Statistics
Matches: 138, Mismatches: 25, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
17 20 0.14
18 100 0.72
19 18 0.13
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.39
Consensus pattern (18 bp):
TTACTGGATAATTGACTG
Found at i:12197780 original size:54 final size:52
Alignment explanation
Indices: 12197716--12197906 Score: 179
Period size: 54 Copynumber: 3.6 Consensus size: 52
12197706 CAACTGATTA
*
12197716 TTACTGAATAATTGACTGTTACTAGATAATTGATTGTTACTGGATATTAGACTG
1 TTACTGAATAATTGACTGTTACTAGATAATTGATTGTTACTGAATATT-GA-TG
* * * * * ** *
12197770 TTACTGAATAACTAAATATTACTAAATAATTGATCATTACTGAATAACTGATTG
1 TTACTGAATAATTGACTGTTACTAGATAATTGATTGTTACTGAAT-ATTGA-TG
* * *
12197824 TCACTGAATGAA-TGACTGTTACT-GAATAACTTAATTGTTACTGAATATCTGATT
1 TTACTGAAT-AATTGACTGTTACTAG-ATAA-TTGATTGTTACTGAATAT-TGATG
*
12197878 TTACTGAATAATTGACTGTTACTGGATAA
1 TTACTGAATAATTGACTGTTACTAGATAA
12197907 CCGATCAATT
Statistics
Matches: 109, Mismatches: 21, Indels: 14
0.76 0.15 0.10
Matches are distributed among these distances:
53 2 0.02
54 86 0.79
55 21 0.19
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.39
Consensus pattern (52 bp):
TTACTGAATAATTGACTGTTACTAGATAATTGATTGTTACTGAATATTGATG
Found at i:12197984 original size:36 final size:36
Alignment explanation
Indices: 12197707--12197999 Score: 186
Period size: 36 Copynumber: 7.9 Consensus size: 36
12197697 GGTATAAAAC
* *
12197707 AACTGATTATTACTGAATAATTGACTGTTACT-AGAT
1 AACTGATTGTTACTGAATAATTGATTGTTACTGA-AT
* * *
12197743 AATTGATTGTTACTGGAT-ATTAGACTGTTACTGAAT
1 AACTGATTGTTACTGAATAATT-GATTGTTACTGAAT
* * * * **
12197779 AACTAAATATTACTAAATAATTGATCATTACTGAAT
1 AACTGATTGTTACTGAATAATTGATTGTTACTGAAT
* *
12197815 AACTGATTGTCACTGAATGAA-TGACTGTTACTGAAT
1 AACTGATTGTTACTGAAT-AATTGATTGTTACTGAAT
*
12197851 AACTTAATTGTTACTGAAT-ATCTGATT-TTACTGAAT
1 AAC-TGATTGTTACTGAATAAT-TGATTGTTACTGAAT
* * * *
12197887 AATTGACTGTTACTGGATAACCGATCAATTGATCGATACTGAAT
1 AACTGATTGTTACT-G---A---AT-AATTGATTGTTACTGAAT
* * * *
12197931 AACTGGTT-ATATTTGAATAATTGATTGTTACCGAAT
1 AACTGATTGTTA-CTGAATAATTGATTGTTACTGAAT
* * *
12197967 AACTGACTGTTACTGAATAAATAATTGTT-CTGA
1 AACTGATTGTTACTGAATAATTGATTGTTACTGA
12198000 GTGTTAATGA
Statistics
Matches: 195, Mismatches: 43, Indels: 39
0.70 0.16 0.14
Matches are distributed among these distances:
35 16 0.08
36 125 0.64
37 27 0.14
39 1 0.01
40 1 0.01
42 2 0.01
43 7 0.04
44 16 0.08
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (36 bp):
AACTGATTGTTACTGAATAATTGATTGTTACTGAAT
Found at i:12197995 original size:18 final size:18
Alignment explanation
Indices: 12197944--12197999 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
12197934 TGGTTATATT
*
12197944 TGAATAATTGATTGTTAC
1 TGAATAAATGATTGTTAC
* * *
12197962 CGAATAACTGACTGTTAC
1 TGAATAAATGATTGTTAC
*
12197980 TGAATAAATAATTGTT-C
1 TGAATAAATGATTGTTAC
12197997 TGA
1 TGA
12198000 GTGTTAATGA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 4 0.13
18 27 0.87
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (18 bp):
TGAATAAATGATTGTTAC
Found at i:12202663 original size:27 final size:27
Alignment explanation
Indices: 12202633--12202739 Score: 121
Period size: 27 Copynumber: 3.9 Consensus size: 27
12202623 GGCTGCTAGA
* *
12202633 ACAGATAATGTGACAGAGTCACCAGAT
1 ACAGATAATGTGGCAGAGCCACCAGAT
*
12202660 ACAGATAATCATGGCAGAGCCACCAGA-
1 ACAGATAAT-GTGGCAGAGCCACCAGAT
12202687 ACAGATATATGTGGCAGAGCCACCAGAT
1 ACAGATA-ATGTGGCAGAGCCACCAGAT
*
12202715 -CAAATAATTGTGGC-GTAGCCACCAG
1 ACAGATAA-TGTGGCAG-AGCCACCAG
12202740 GACGCTTCCT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.03
27 52 0.74
28 16 0.23
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.17
Consensus pattern (27 bp):
ACAGATAATGTGGCAGAGCCACCAGAT
Found at i:12202688 original size:54 final size:54
Alignment explanation
Indices: 12202630--12202739 Score: 143
Period size: 54 Copynumber: 2.0 Consensus size: 54
12202620 CATGGCTGCT
* *
12202630 AGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCATGGCAG-AGCCACC
1 AGAACAGATATATGTGACAGAGCCACCAGAT-CAAATAATCATGGC-GTAGCCACC
* **
12202684 AGAACAGATATATGTGGCAGAGCCACCAGATCAAATAATTGTGGCGTAGCCACC
1 AGAACAGATATATGTGACAGAGCCACCAGATCAAATAATCATGGCGTAGCCACC
12202738 AG
1 AG
12202740 GACGCTTCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 1 0.02
54 30 0.61
55 18 0.37
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (54 bp):
AGAACAGATATATGTGACAGAGCCACCAGATCAAATAATCATGGCGTAGCCACC
Found at i:12203176 original size:16 final size:15
Alignment explanation
Indices: 12203155--12203186 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
12203145 TCAAAATGCC
12203155 GGCTTTTCGGCATTTT
1 GGCTTTTCGGC-TTTT
12203171 GGCTTTTCGGCTTTT
1 GGCTTTTCGGCTTTT
12203186 G
1 G
12203187 CCGATCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.03, C:0.19, G:0.28, T:0.50
Consensus pattern (15 bp):
GGCTTTTCGGCTTTT
Found at i:12210540 original size:27 final size:26
Alignment explanation
Indices: 12210478--12210578 Score: 112
Period size: 27 Copynumber: 3.7 Consensus size: 26
12210468 AGCATGGCTG
* ** *
12210478 CCAGAATAGATAATGTAACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
12210504 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
12210532 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
12210559 CTAGATCAGATAATTGTGGC
1 CCAGAACAGATAA-TGTGGC
12210579 GTAGACACCA
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
26 6 0.09
27 43 0.66
28 16 0.25
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.19
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:12210588 original size:54 final size:54
Alignment explanation
Indices: 12210478--12210589 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 54
12210468 AGCATGGCTG
* * *
12210478 CCAGAATAGATAATGTAACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAATGTAACAGAGCCACCAGATACAGATAATCGTGGCAGAGACA
** * *
12210532 CCAGAACAGATATATGTGGCAGAGCCACTAGAT-CAGATAATTGTGGC-GTAGACA
1 CCAGAACAGATA-ATGTAACAGAGCCACCAGATACAGATAATCGTGGCAG-AGACA
12210586 CCAG
1 CCAG
12210590 GACGCTTCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
53 1 0.02
54 32 0.65
55 16 0.33
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATAATGTAACAGAGCCACCAGATACAGATAATCGTGGCAGAGACA
Found at i:12213295 original size:40 final size:40
Alignment explanation
Indices: 12213250--12213437 Score: 279
Period size: 40 Copynumber: 4.7 Consensus size: 40
12213240 ATAACCACAA
* *
12213250 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
12213290 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
12213330 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
12213370 GCACAAATGCCTTCGGGTCTTAACCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT-AGCAACTC
* * *
12213410 GCATAAATGCCTTCGGGGCTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAACCCGG
12213438 GTATCATTCA
Statistics
Matches: 136, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
40 134 0.99
41 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:12213335 original size:80 final size:79
Alignment explanation
Indices: 12213230--12213441 Score: 318
Period size: 80 Copynumber: 2.7 Consensus size: 79
12213220 TCTTCGGAAT
* *
12213230 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
12213294 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* *
12213309 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCAC
1 TTAGCCCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
12213374 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* * * *
12213389 TTAACCCGGATATAATCACTAGCATAAATGCCTTCGGGGCTTAGCCCGGGTAT
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTAT
12213442 CATTCAATTG
Statistics
Matches: 120, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
79 5 0.04
80 114 0.95
81 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
TTAGCCCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACA
AATGCCTTCGGGTC
Found at i:12216369 original size:16 final size:16
Alignment explanation
Indices: 12216348--12216400 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
12216338 TAATATAAGA
12216348 ATTATTATTATATTAT
1 ATTATTATTATATTAT
12216364 ATTATTATTATA-TAT
1 ATTATTATTATATTAT
12216379 A-TATATATATATATATAT
1 ATTAT-TAT-TATAT-TAT
12216397 ATTA
1 ATTA
12216401 AACGGGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.09
15 7 0.22
16 16 0.50
18 4 0.12
19 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTATTATTATATTAT
Found at i:12216379 original size:2 final size:2
Alignment explanation
Indices: 12216356--12216398 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
12216346 GAATTATTAT
12216356 TA TA T- TA TA T- TA T- TA T- 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 TA TA
12216394 TA TA T
1 TA TA T
12216399 TAAACGGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.11
2 33 0.89
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:12219739 original size:40 final size:40
Alignment explanation
Indices: 12219657--12219911 Score: 340
Period size: 40 Copynumber: 6.5 Consensus size: 40
12219647 AAGCCAAGTA
* * * *
12219657 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
12219695 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
12219735 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
12219775 CCTTCGGGACTTAGCCCGGATGTAATAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
12219815 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
12219855 CCTT-GGGACTTAGCCCGGA-ACAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
12219893 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
12219912 TTATCATCCG
Statistics
Matches: 194, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
38 31 0.16
39 45 0.23
40 118 0.61
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:12227828 original size:40 final size:40
Alignment explanation
Indices: 12227746--12228002 Score: 324
Period size: 40 Copynumber: 6.5 Consensus size: 40
12227736 AAGCCAAGTA
* * * *
12227746 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
12227784 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
12227824 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
12227864 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
12227904 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * **
12227944 CCTTCGGGACTTAGCCCAGA-ACCAGTCACTAGTGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
12227984 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
12228003 TTATCATCTG
Statistics
Matches: 195, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
38 12 0.06
39 17 0.09
40 166 0.85
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:12229790 original size:18 final size:18
Alignment explanation
Indices: 12229739--12229882 Score: 98
Period size: 18 Copynumber: 8.0 Consensus size: 18
12229729 TATTAGACTG
*
12229739 TTACTGAATAACTGAACA
1 TTACTGAATAACTGATCA
*
12229757 TTACTGAATAATTGATCA
1 TTACTGAATAACTGATCA
**
12229775 TTACTGAATAACTGATTG
1 TTACTGAATAACTGATCA
** *
12229793 TCGCTGAATGAA-TGA-CTG
1 TTACTGAAT-AACTGATC-A
* **
12229811 TTACTGAATAACTTAATTG
1 TTACTGAATAAC-TGATCA
* *
12229830 TTACTGAATATCTGAT-T
1 TTACTGAATAACTGATCA
*
12229847 TTACTGAATAATTGA-CTA
1 TTACTGAATAACTGATC-A
*
12229865 TTACTGGATAACTGATCA
1 TTACTGAATAACTGATCA
12229883 ATTGATCGAT
Statistics
Matches: 98, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
17 15 0.15
18 66 0.67
19 17 0.17
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (18 bp):
TTACTGAATAACTGATCA
Found at i:12229854 original size:54 final size:55
Alignment explanation
Indices: 12229741--12229877 Score: 147
Period size: 54 Copynumber: 2.5 Consensus size: 55
12229731 TTAGACTGTT
* *
12229741 ACTGAATAACTGAAC-ATTACTGAATAA-TTGATCATTACTGAATAACTGATTGTC
1 ACTGAATAATTG-ACTATTACTGAATAACTTAATCATTACTGAATAACTGATTGTC
* * ** * *
12229795 GCTGAATGAA-TGACTGTTACTGAATAACTTAATTGTTACTGAATATCTGATT-TT
1 ACTGAAT-AATTGACTATTACTGAATAACTTAATCATTACTGAATAACTGATTGTC
*
12229849 ACTGAATAATTGACTATTACTGGATAACT
1 ACTGAATAATTGACTATTACTGAATAACT
12229878 GATCAATTGA
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
53 4 0.06
54 43 0.62
55 22 0.32
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (55 bp):
ACTGAATAATTGACTATTACTGAATAACTTAATCATTACTGAATAACTGATTGTC
Found at i:12234697 original size:55 final size:55
Alignment explanation
Indices: 12234514--12234766 Score: 251
Period size: 55 Copynumber: 4.7 Consensus size: 55
12234504 ACACGAGTAC
* *
12234514 CTTACCATTGCCATGACTT-ATCATGGTCTTACATGGTATCC-T---TT-T-GAAA
1 CTTACCAATGCCATGCCTTGA-CATGGTCTTACATGGTATCCTTGCCTTATAGAAA
* * * * *
12234563 CTTACCATTTCCATGTCTCGACATGGTCTGACATGGTATCCTTGCCTTAT-G-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAA
* * * *
12234616 CTCACCAATGCCATGCCTTGGCATGGTCTTACACGGGA-CCTTTGCCTTATAGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATAGAAA
* * *
12234671 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCC-T-TAGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAA
*
12234724 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCC
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCC
12234767 ATAAACCTTA
Statistics
Matches: 168, Mismatches: 24, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
49 35 0.21
50 2 0.01
52 2 0.01
53 48 0.29
54 11 0.07
55 68 0.40
56 2 0.01
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (55 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAA
Found at i:12234705 original size:108 final size:110
Alignment explanation
Indices: 12234559--12234758 Score: 307
Period size: 108 Copynumber: 1.8 Consensus size: 110
12234549 GTATCCTTTT
* * *
12234559 GAAACTTACCATTTCCATGTCTCGACATGGTCTGACATGGTATCCTTGCCTTATG-AA-CTCACC
1 GAAACTTACCAATGCCATGTCTCGACATGGTCTGACATGATATCCTTGCCTTA-GAAACCTCACC
12234622 AA-TGCCATGCCTTGGCATGGTCTTACACGGGACCTTTGCCTTATA
65 AATTGCCATGCCTTGGCATGGTCTTACACGGGACCTTTGCCTTATA
* * * *
12234667 GAAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTTACCA
1 GAAACTTACCAATGCCATGTCTCGACATGGTCTGACATGATATCCTTGCCTTAGAAACCTCACCA
12234732 ATTGCCATGCCTTGGCATGGTCTTACA
66 ATTGCCATGCCTTGGCATGGTCTTACA
12234759 TGGTATCCAT
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.60
109 7 0.09
110 25 0.30
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (110 bp):
GAAACTTACCAATGCCATGTCTCGACATGGTCTGACATGATATCCTTGCCTTAGAAACCTCACCA
ATTGCCATGCCTTGGCATGGTCTTACACGGGACCTTTGCCTTATA
Found at i:12235416 original size:31 final size:31
Alignment explanation
Indices: 12235352--12235416 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
12235342 TTTCAAGCTT
* *
12235352 CATATTCTACCATAAAACATCAAAATAACCA
1 CATATTCTACCATAAAACATCAAAACAAACA
*
12235383 CATATTCTACCATAAAACATCAAAGCAAACA
1 CATATTCTACCATAAAACATCAAAACAAACA
12235414 CAT
1 CAT
12235417 TTCACCTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.51, C:0.26, G:0.02, T:0.22
Consensus pattern (31 bp):
CATATTCTACCATAAAACATCAAAACAAACA
Found at i:12235746 original size:31 final size:31
Alignment explanation
Indices: 12235706--12235767 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
12235696 TTTTATCTTC
12235706 CTTTAGGTATTTTTGTCCAAACTAGTATAAT
1 CTTTAGGTATTTTTGTCCAAACTAGTATAAT
*
12235737 CTTTGGGTATTTTTGTCCAAACTAGTATAAT
1 CTTTAGGTATTTTTGTCCAAACTAGTATAAT
12235768 GGTCTAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (31 bp):
CTTTAGGTATTTTTGTCCAAACTAGTATAAT
Found at i:12235789 original size:19 final size:19
Alignment explanation
Indices: 12235765--12235804 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
12235755 AAACTAGTAT
12235765 AATGGTCTAATTACTATCC
1 AATGGTCTAATTACTATCC
12235784 AATGGTCTAATTACTATCC
1 AATGGTCTAATTACTATCC
12235803 AA
1 AA
12235805 AGAACTCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (19 bp):
AATGGTCTAATTACTATCC
Found at i:12240316 original size:9 final size:9
Alignment explanation
Indices: 12240302--12240326 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12240292 AAATGATACA
12240302 ATACATTTC
1 ATACATTTC
12240311 ATACATTTC
1 ATACATTTC
12240320 ATACATT
1 ATACATT
12240327 CCTCAGGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (9 bp):
ATACATTTC
Found at i:12242103 original size:16 final size:16
Alignment explanation
Indices: 12242084--12242114 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12242074 CTTCTTCACT
12242084 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
12242100 TACTTACTTACTTAA
1 TACTCACTTACTTAA
12242115 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:12242120 original size:20 final size:20
Alignment explanation
Indices: 12242081--12242120 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12242071 AAACTTCTTC
* *
12242081 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
12242101 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
12242121 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:12242551 original size:55 final size:53
Alignment explanation
Indices: 12242307--12242559 Score: 234
Period size: 55 Copynumber: 4.8 Consensus size: 53
12242297 ATACGGGTAC
* * * * * *
12242307 CTTACCATTTCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-GAAG
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTAGAAA
* * * * *
12242355 CTTACCATTTCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTA-GAAA
* * *
12242408 CTCACTAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTCGCCTTATAGAAA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTT-GCC-T-TAGAAA
* * * *
12242463 CTTATCAATGCCATGTCTT-GAATGGTCTTACATGATATCCTTGCCTTAGAAA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTAGAAA
12242515 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
12242560 AAACCCTAAT
Statistics
Matches: 167, Mismatches: 24, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
48 37 0.22
49 1 0.01
52 12 0.07
53 42 0.25
54 31 0.19
55 44 0.26
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTAGAAA
Found at i:12247377 original size:40 final size:40
Alignment explanation
Indices: 12247300--12247517 Score: 325
Period size: 40 Copynumber: 5.5 Consensus size: 40
12247290 AAACCAAGTA
* *
12247300 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
12247339 CCTTCGGGACTTAGCCTGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
12247379 CCTTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
12247419 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
12247459 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
12247499 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
12247518 TTATCATCCG
Statistics
Matches: 164, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
39 15 0.09
40 149 0.91
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:12247772 original size:14 final size:15
Alignment explanation
Indices: 12247755--12247783 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12247745 TCACGAAAAT
12247755 TTCACACAT-ATAAA
1 TTCACACATAATAAA
12247769 TTCACACATAATAAA
1 TTCACACATAATAAA
12247784 CACAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:12253888 original size:48 final size:48
Alignment explanation
Indices: 12253820--12254016 Score: 175
Period size: 48 Copynumber: 4.1 Consensus size: 48
12253810 TTACACGAAG
* * * * * *
12253820 TCTCATAGCGGTGCCGATGCCATGTCCAAGACATGGTTTTATACGGGG
1 TCTCATATCGATGCCGATGCCATATCCAAGATATGGTCTTATACGGGA
* * * * * * *
12253868 CCTCATATCGATGCCAATGCCATATCCCAGTTATGGTTTTACATGGGA
1 TCTCATATCGATGCCGATGCCATATCCAAGATATGGTCTTATACGGGA
* * * *
12253916 TTTCAGA-CTGATGCCGATGCCATGTCCAAGA-AGTGGTCTTATACAGGA
1 TCTCATATC-GATGCCGATGCCATATCCAAGATA-TGGTCTTATACGGGA
* *
12253964 TCTCTTATCGATGCTGATGCCATATCCCAA-ATATGGTCTTATACGGGA
1 TCTCATATCGATGCCGATGCCATAT-CCAAGATATGGTCTTATACGGGA
12254012 TCTCA
1 TCTCA
12254017 ATACTCACAT
Statistics
Matches: 115, Mismatches: 29, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
47 2 0.02
48 107 0.93
49 6 0.05
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (48 bp):
TCTCATATCGATGCCGATGCCATATCCAAGATATGGTCTTATACGGGA
Found at i:12254012 original size:96 final size:96
Alignment explanation
Indices: 12253831--12254012 Score: 240
Period size: 96 Copynumber: 1.9 Consensus size: 96
12253821 CTCATAGCGG
* * *
12253831 TGCCGATGCCATGTCCAAGACATGGTTTTATACGGGGCCTCATATCGATGCCAATGCCATATCCC
1 TGCCGATGCCATGTCCAAGACATGGTCTTATACAGGACCTCATATCGATGCCAATGCCATATCCC
** * *
12253896 AGTTATGGTTTTACATGGGATTTCAGACTGA
66 AAATATGGTCTTACACGGGATTTCAGACTGA
* * **
12253927 TGCCGATGCCATGTCCAAGA-AGTGGTCTTATACAGGATCTCTTATCGATGCTGATGCCATATCC
1 TGCCGATGCCATGTCCAAGACA-TGGTCTTATACAGGACCTCATATCGATGCCAATGCCATATCC
*
12253991 CAAATATGGTCTTATACGGGAT
65 CAAATATGGTCTTACACGGGAT
12254013 CTCAATACTC
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
95 1 0.01
96 72 0.99
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (96 bp):
TGCCGATGCCATGTCCAAGACATGGTCTTATACAGGACCTCATATCGATGCCAATGCCATATCCC
AAATATGGTCTTACACGGGATTTCAGACTGA
Found at i:12258286 original size:29 final size:29
Alignment explanation
Indices: 12258151--12258282 Score: 201
Period size: 29 Copynumber: 4.6 Consensus size: 29
12258141 GTGACGAGAT
*
12258151 TGGCACTAAGTGTGCGTGCTGGAAACATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
12258180 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
12258209 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
** *
12258238 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* **
12258267 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
12258283 AGCTCGGAGG
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 95 1.00
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:12258298 original size:87 final size:86
Alignment explanation
Indices: 12258151--12258339 Score: 202
Period size: 87 Copynumber: 2.2 Consensus size: 86
12258141 GTGACGAGAT
** * * * *
12258151 TGGCACTAAGTGTGCGTGCTGGAAACATATGGCACTAAGTGTGCGTGCTGGAAATATATGGCACT
1 TGGCACTAAGTGTGCAAGCTGGAAAAATACGGCACTAAGTGTGCGAGCTGGAAAGATATGGCACT
*
12258216 AAGTGTGCGTGCTGGAAATATA-
66 AAGTGTGCGGGCT-GAAAT-TAC
** * *
12258238 TGGCACTAAGTGTGCAAGCTGGAAAAATACGGCACTGGGTGTGCGAGCTCGG-AGGGTATGGCAC
1 TGGCACTAAGTGTGCAAGCTGGAAAAATACGGCACTAAGTGTGCGAGCT-GGAAAGATATGGCAC
** *
12258302 TGTGTGTGCGGGCTTAAATTAC
65 TAAGTGTGCGGGCTGAAATTAC
12258324 GTGGCACTAAGTGTGC
1 -TGGCACTAAGTGTGC
12258340 GAAATCGAGT
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
85 2 0.02
86 4 0.05
87 77 0.91
88 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.25
Consensus pattern (86 bp):
TGGCACTAAGTGTGCAAGCTGGAAAAATACGGCACTAAGTGTGCGAGCTGGAAAGATATGGCACT
AAGTGTGCGGGCTGAAATTAC
Found at i:12265774 original size:46 final size:46
Alignment explanation
Indices: 12265707--12265881 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
12265697 TGTAACCCGC
12265707 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
12265753 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
12265803 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* *
12265846 CCATAAGTGAACTCGGACTCAACTCGACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
12265882 ATGCTCAACC
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 62 0.57
47 26 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:12265827 original size:93 final size:93
Alignment explanation
Indices: 12265715--12265885 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
12265705 GCCCATAAGT
** *
12265715 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
12265780 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* *
12265808 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCGA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
12265873 CGAGTTCGGATGC
66 CGAGCTCGGATGC
12265886 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:12273058 original size:40 final size:40
Alignment explanation
Indices: 12272973--12273123 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
12272963 AATTGAATGA
* * *
12272973 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
12273013 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
12273054 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
12273093 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
12273124 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:12273137 original size:40 final size:40
Alignment explanation
Indices: 12273010--12273139 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
12273000 ATGCTGGAAA
* * * *
12273010 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
12273050 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
12273090 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
12273130 TTATATCCGG
1 TTATATCCGG
12273140 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:12277435 original size:40 final size:40
Alignment explanation
Indices: 12277390--12277557 Score: 162
Period size: 40 Copynumber: 4.2 Consensus size: 40
12277380 CGGAATATAA
*
12277390 CCGGATATAAGCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAAGCACT-AGCACAAATGCCTTCGGGTCTTAGC
* * *
12277430 CCGGATAGAATG-ACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA-GCACTAGCACAAATGCCTTCGGGTCTTAGC
* *
12277470 CCGGATAT-AGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAAG-CACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
12277510 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAAGCACTAGCACAAATGCCTTCGGGTCTTAGC
12277550 CCGGATAT
1 CCGGATAT
12277558 CATTCAATTT
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 102 0.95
41 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAAGCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:12277540 original size:80 final size:80
Alignment explanation
Indices: 12277406--12277557 Score: 200
Period size: 80 Copynumber: 1.9 Consensus size: 80
12277396 ATAAGCATGT
* *
12277406 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
12277471 CGGATATAGCCACTA
66 CGGATATAGCCACTA
* * ** * *
12277486 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG
12277549 CCCGGATAT
64 CCCGGATAT
12277558 CATTCAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
79 3 0.05
80 59 0.95
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATATAGCCACTA
Found at i:12282968 original size:21 final size:23
Alignment explanation
Indices: 12282927--12282973 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
12282917 CATGTGAACT
*
12282927 TATATTGAAATTGTATACTTAGA
1 TATATTGAAATTGTATACTTAAA
12282950 TATATGTG-AATT-TAT-CTTAAA
1 TATAT-TGAAATTGTATACTTAAA
12282971 TAT
1 TAT
12282974 GCATATTCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 8 0.36
22 3 0.14
23 9 0.41
24 2 0.09
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (23 bp):
TATATTGAAATTGTATACTTAAA
Found at i:12290283 original size:49 final size:49
Alignment explanation
Indices: 12290209--12290417 Score: 341
Period size: 49 Copynumber: 4.3 Consensus size: 49
12290199 CCCTTCGGGA
* * * * * *
12290209 CTTATCACAT-T-TACACACTTCCACATCCATCACGTTGACCACTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
12290256 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
12290305 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
*
12290354 CTTATCACATATATACACACTTTCTCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
12290403 CTTATCACATATATA
1 CTTATCACATATATA
12290418 TATCTCATAC
Statistics
Matches: 153, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
47 10 0.07
48 1 0.01
49 142 0.93
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.31
Consensus pattern (49 bp):
CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12293205 original size:40 final size:40
Alignment explanation
Indices: 12293171--12293290 Score: 152
Period size: 40 Copynumber: 3.0 Consensus size: 40
12293161 AGCCCGGTCA
* *
12293171 TAGTGATTCGCACAATTGCCTTCGGGAATTAGCCCGGATT
1 TAGTAATTCGCACAAATGCCTTCGGGAATTAGCCCGGATT
*
12293211 TAGTAACTCGCACAAATGCCTTCGGGAATT-GACCCGGATT
1 TAGTAATTCGCACAAATGCCTTCGGGAATTAG-CCCGGATT
* * * *
12293251 TAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGAT
1 TAGT-AATTCGCACAAATGCCTTCGGGAATTAGCCCGGAT
12293291 ACCATTCGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.01
40 39 0.57
41 28 0.41
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (40 bp):
TAGTAATTCGCACAAATGCCTTCGGGAATTAGCCCGGATT
Found at i:12294083 original size:40 final size:40
Alignment explanation
Indices: 12294034--12294338 Score: 480
Period size: 40 Copynumber: 7.8 Consensus size: 40
12294024 CCAGCATGAT
* * *
12294034 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
12294074 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* **
12294114 TGCTCCTCGGAACTTAGTCCGGATATGTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* *
12294154 TGCTCTTCAGAACTTAGTCCGGATACATCACTAGCACAAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
12294194 TGCTCTTCGGAACTTAGTCCGGATACATCACT-------A
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
12294227 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
12294267 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
12294307 TGCTCTTCGGAACTTAGTCCGGATATATCACT
1 TGCTCTTCGGAACTTAGTCCGGATACATCACT
12294339 CTCAATTCTC
Statistics
Matches: 245, Mismatches: 13, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
33 33 0.13
40 212 0.87
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
Done.