Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 182 of 335
Found at i:54704360 original size:33 final size:33
Alignment explanation
Indices: 54704322--54704384 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
54704312 AGTTTAGATC
*
54704322 ATTTCATATCATAACTTTACTCATATTAATTGG
1 ATTTCATATCAGAACTTTACTCATATTAATTGG
54704355 ATTTCATATCAGAACTTTACTCATATTAAT
1 ATTTCATATCAGAACTTTACTCATATTAAT
54704385 CGGAATATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (33 bp):
ATTTCATATCAGAACTTTACTCATATTAATTGG
Found at i:54725021 original size:46 final size:47
Alignment explanation
Indices: 54724923--54725097 Score: 229
Period size: 46 Copynumber: 3.8 Consensus size: 47
54724913 GGTTATTGTG
* *
54724923 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACG-A
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGA-GTA
*
54724970 GAGCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCTCGAGATGTA
1 -AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGA-GTA
54725017 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CTACGAGA-TA
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGAGAGTA
*
54725061 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
54725098 ATCCTACCCC
Statistics
Matches: 116, Mismatches: 6, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
44 14 0.12
45 16 0.14
46 59 0.51
47 14 0.12
48 13 0.11
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (47 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAGTA
Found at i:54727862 original size:20 final size:20
Alignment explanation
Indices: 54727833--54727877 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
54727823 AGCTCATGTA
*
54727833 TTCATAAAATTTCATAATTT
1 TTCATAAAATTTCATAACTT
* *
54727853 TTCATCAAATTTTATAACTT
1 TTCATAAAATTTCATAACTT
54727873 TTCAT
1 TTCAT
54727878 TTTAGTCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (20 bp):
TTCATAAAATTTCATAACTT
Found at i:54731470 original size:21 final size:21
Alignment explanation
Indices: 54731444--54731487 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
54731434 ACACACTCAG
54731444 CTTAATTGAGCT-ATTAAAGAA
1 CTTAATTGAGCTAATTAAA-AA
54731465 CTTAATTGAGCTAATTAAAAA
1 CTTAATTGAGCTAATTAAAAA
54731486 CT
1 CT
54731488 ACAAGACCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (21 bp):
CTTAATTGAGCTAATTAAAAA
Found at i:54736080 original size:25 final size:25
Alignment explanation
Indices: 54736046--54736100 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
54736036 TTCTCTCACC
* * *
54736046 AAAAACGACTTATTTTCCTAATTAA
1 AAAAACGACTTATATGCCAAATTAA
*
54736071 AAAAATGACTTATATGCCAAATTAA
1 AAAAACGACTTATATGCCAAATTAA
54736096 AAAAA
1 AAAAA
54736101 AAGGCATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (25 bp):
AAAAACGACTTATATGCCAAATTAA
Found at i:54737664 original size:9 final size:9
Alignment explanation
Indices: 54737650--54737775 Score: 64
Period size: 9 Copynumber: 13.7 Consensus size: 9
54737640 GTCACATGTG
54737650 ATAAAAATT
1 ATAAAAATT
54737659 ATAAAAA--
1 ATAAAAATT
*
54737666 AT-AAAATCA
1 ATAAAAAT-T
54737675 ATAAAAATT
1 ATAAAAATT
*
54737684 AT-TAAATGT
1 ATAAAAAT-T
*
54737693 -TAATAAAAT
1 ATAA-AAATT
54737702 ATAAAAAATTT
1 AT-AAAAA-TT
*
54737713 ATAAAAATC
1 ATAAAAATT
* *
54737722 GTAAAAAAT
1 ATAAAAATT
54737731 ATAAAAAATT
1 AT-AAAAATT
* *
54737741 GTAAAATTT
1 ATAAAAATT
*
54737750 ATAAAAATC
1 ATAAAAATT
54737759 ATAGAAAAGTT
1 ATA-AAAA-TT
54737770 ATAAAA
1 ATAAAA
54737776 TGCATCAAAA
Statistics
Matches: 87, Mismatches: 17, Indels: 25
0.67 0.13 0.19
Matches are distributed among these distances:
6 4 0.05
7 2 0.02
8 5 0.06
9 36 0.41
10 31 0.36
11 9 0.10
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (9 bp):
ATAAAAATT
Found at i:54737726 original size:20 final size:20
Alignment explanation
Indices: 54737703--54737775 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
54737693 TAATAAAATA
54737703 TAAAAAATTTATAAAAATCG
1 TAAAAAATTTATAAAAATCG
* *
54737723 TAAAAAATATA-AAAAATTG
1 TAAAAAATTTATAAAAATCG
*
54737742 T--AAAATTTATAAAAATCA
1 TAAAAAATTTATAAAAATCG
* *
54737760 TAGAAAAGTTATAAAA
1 TAAAAAATTTATAAAA
54737776 TGCATCAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
17 7 0.16
18 7 0.16
19 8 0.18
20 22 0.50
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAAATTTATAAAAATCG
Found at i:54737756 original size:29 final size:29
Alignment explanation
Indices: 54737697--54737775 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
54737687 AAATGTTAAT
*
54737697 AAAATATAAAAAATTTATAAAAATCGTAA
1 AAAATATAAAAAATTTATAAAAATCATAA
* * *
54737726 AAAATATAAAAAA-TTGTAAAATTTAT-A
1 AAAATATAAAAAATTTATAAAAATCATAA
* *
54737753 AAAATCATAGAAAAGTTATAAAA
1 AAAAT-ATAAAAAATTTATAAAA
54737776 TGCATCAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
27 6 0.14
28 16 0.38
29 20 0.48
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (29 bp):
AAAATATAAAAAATTTATAAAAATCATAA
Found at i:54737970 original size:9 final size:9
Alignment explanation
Indices: 54737956--54738084 Score: 77
Period size: 9 Copynumber: 13.9 Consensus size: 9
54737946 TTTTGGTACA
54737956 ATAATTTTT
1 ATAATTTTT
54737965 ATAATTCTTTT
1 ATAA-T-TTTT
*
54737976 ATGAA-TTGT
1 AT-AATTTTT
*
54737985 ATATTTCTTT
1 ATAATT-TTT
* *
54737995 ACATTTTTT
1 ATAATTTTT
54738004 ATAATTTTGT
1 ATAATTTT-T
* *
54738014 ATGA-CTTT
1 ATAATTTTT
*
54738022 ATAAAATTTT
1 AT-AATTTTT
54738032 ATAATTTTT
1 ATAATTTTT
54738041 AT-ATTTTT
1 ATAATTTTT
54738049 AT-ATATTTT
1 ATAAT-TTTT
54738058 ATAATTTTT
1 ATAATTTTT
*
54738067 ATGATTTTAT
1 ATAATTTT-T
*
54738077 AAAATTTT
1 ATAATTTT
54738085 ACATTTTTTT
Statistics
Matches: 95, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
8 14 0.15
9 47 0.49
10 26 0.27
11 6 0.06
12 2 0.02
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:54738050 original size:17 final size:18
Alignment explanation
Indices: 54737956--54738084 Score: 77
Period size: 19 Copynumber: 6.9 Consensus size: 18
54737946 TTTTGGTACA
54737956 ATAATTTTTATAATTCTTTT
1 ATAATTTTTATAA-T-TTTT
* *
54737976 ATGAA-TTGTATATTTCTTT
1 AT-AATTTTTATAATT-TTT
* *
54737995 ACATTTTTTATAATTTTGT
1 ATAATTTTTATAATTTT-T
* * *
54738014 ATGA-CTTTATAAAATTTT
1 ATAATTTTTAT-AATTTTT
54738032 ATAATTTTTAT-ATTTTT
1 ATAATTTTTATAATTTTT
54738049 AT-ATATTTTATAATTTTT
1 ATAAT-TTTTATAATTTTT
* *
54738067 ATGATTTTATAAAATTTT
1 ATAATTTT-TATAATTTT
54738085 ACATTTTTTT
Statistics
Matches: 84, Mismatches: 15, Indels: 21
0.70 0.12 0.17
Matches are distributed among these distances:
16 2 0.02
17 13 0.15
18 24 0.29
19 35 0.42
20 8 0.10
21 2 0.02
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (18 bp):
ATAATTTTTATAATTTTT
Found at i:54738092 original size:26 final size:27
Alignment explanation
Indices: 54738000--54738085 Score: 122
Period size: 26 Copynumber: 3.2 Consensus size: 27
54737990 TCTTTACATT
*
54738000 TTTTATAATTTTGTATGACTTTATAAAA
1 TTTTATAATTTT-TATGATTTTATAAAA
*
54738028 TTTTATAATTTTTAT-ATTTT-TATATA
1 TTTTATAATTTTTATGATTTTATA-AAA
54738054 TTTTATAATTTTTATGATTTTATAAAA
1 TTTTATAATTTTTATGATTTTATAAAA
54738081 TTTTA
1 TTTTA
54738086 CATTTTTTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.04
26 21 0.40
27 15 0.29
28 14 0.27
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (27 bp):
TTTTATAATTTTTATGATTTTATAAAA
Found at i:54742177 original size:23 final size:23
Alignment explanation
Indices: 54742151--54742221 Score: 133
Period size: 23 Copynumber: 3.0 Consensus size: 23
54742141 TTAAGGTAGC
54742151 TAAGGGTTAAATTAGCGACGGTA
1 TAAGGGTTAAATTAGCGACGGTA
54742174 TAAGGGTTAAATTAGCGACGGTA
1 TAAGGGTTAAATTAGCGACGGTA
54742197 TTAAGGGTTAAATTAGCGACGGTA
1 -TAAGGGTTAAATTAGCGACGGTA
54742221 T
1 T
54742222 TAAACGGTAC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
23 24 0.51
24 23 0.49
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (23 bp):
TAAGGGTTAAATTAGCGACGGTA
Found at i:54742237 original size:24 final size:24
Alignment explanation
Indices: 54742151--54742224 Score: 141
Period size: 24 Copynumber: 3.1 Consensus size: 24
54742141 TTAAGGTAGC
54742151 TAAGGGTTAAATTAGCGACGGTA-
1 TAAGGGTTAAATTAGCGACGGTAT
54742174 TAAGGGTTAAATTAGCGACGGTAT
1 TAAGGGTTAAATTAGCGACGGTAT
54742198 TAAGGGTTAAATTAGCGACGGTAT
1 TAAGGGTTAAATTAGCGACGGTAT
54742222 TAA
1 TAA
54742225 ACGGTACATT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 23 0.46
24 27 0.54
ACGTcount: A:0.35, C:0.08, G:0.28, T:0.28
Consensus pattern (24 bp):
TAAGGGTTAAATTAGCGACGGTAT
Found at i:54742543 original size:5 final size:5
Alignment explanation
Indices: 54742535--54742559 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54742525 AACTTTTATT
54742535 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
54742560 CTTAGTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:54743028 original size:31 final size:30
Alignment explanation
Indices: 54742971--54743029 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
54742961 GTAAGTACTC
* * * *
54742971 AAAATTTGAGGGATTAAAGTGTAAATATGA
1 AAAAGTTGAAGGACTAAAGTGAAAATATGA
54743001 AAAAGTTGAAGGACTAATAGTGAAAATAT
1 AAAAGTTGAAGGACTAA-AGTGAAAATAT
54743030 TTTAATGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.49, C:0.02, G:0.22, T:0.27
Consensus pattern (30 bp):
AAAAGTTGAAGGACTAAAGTGAAAATATGA
Found at i:54743291 original size:8 final size:8
Alignment explanation
Indices: 54743280--54743311 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
54743270 TTTAATAAGA
54743280 TATTTTAT
1 TATTTTAT
54743288 TA-TTTAT
1 TATTTTAT
54743295 TATTTTAT
1 TATTTTAT
54743303 TATTTTAT
1 TATTTTAT
54743311 T
1 T
54743312 TAGTCTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTTTAT
Found at i:54746760 original size:2 final size:2
Alignment explanation
Indices: 54746753--54746785 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54746743 GTGGTTTTTC
54746753 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54746786 GTCCAAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54746955 original size:20 final size:20
Alignment explanation
Indices: 54746916--54746956 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54746906 AGGAACTATC
* * *
54746916 CTAGAATTAGGGGATTACAA
1 CTAGAATTAGAGAATCACAA
54746936 CTAGAATTAGAGAATCACAA
1 CTAGAATTAGAGAATCACAA
54746956 C
1 C
54746957 AAATTATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.22
Consensus pattern (20 bp):
CTAGAATTAGAGAATCACAA
Found at i:54754969 original size:39 final size:39
Alignment explanation
Indices: 54754881--54755047 Score: 212
Period size: 40 Copynumber: 4.2 Consensus size: 39
54754871 TGAATGATAC
* *
54754881 CCGGGCTAA-ACCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGA-CCCGAAGGCATTTGTGCGAGTG-TTATAT
54754921 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGTTATAT
* *
54754960 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* * **
54755000 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGT-GTTATAT
54755040 CC-GGCTAA
1 CCGGGCTAA
54755048 ATTCCGAAGA
Statistics
Matches: 113, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
39 43 0.38
40 69 0.61
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGTTATAT
Found at i:54755012 original size:79 final size:80
Alignment explanation
Indices: 54754881--54755048 Score: 218
Period size: 79 Copynumber: 2.1 Consensus size: 80
54754871 TGAATGATAC
* * * *
54754881 CCGGGCTAAACCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAACCCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCAATTG
54754946 TGCGAGT-GTTATAT
66 TGCGAGTGGTTATAT
* *
54754960 CCGGGCTAAGA-CCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGCAAT
1 CCGGGCTAA-ACCCCGAAGGCATTTATGCGAG-TGACTATACCCGGGCTAAGACCCGAAGGCAAT
**
54755023 TGTGCTTGTGGTTATAT
64 TGTGCGAGTGGTTATAT
54755040 CC-GGCTAAA
1 CCGGGCTAAA
54755049 TTCCGAAGAA
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
78 1 0.01
79 65 0.83
80 12 0.15
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAACCCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCAATTG
TGCGAGTGGTTATAT
Found at i:54763013 original size:40 final size:40
Alignment explanation
Indices: 54762954--54763120 Score: 230
Period size: 40 Copynumber: 4.2 Consensus size: 40
54762944 TGAATGATAC
* * *
54762954 CCGGGCTAAG-CCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTTATAT
54762993 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTTATAT
* * *
54763033 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTTATAT
* * **
54763073 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTTATAT
54763113 CC-GGCTAA
1 CCGGGCTAA
54763121 ATTCCGAAGA
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
39 15 0.13
40 98 0.87
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTTATAT
Found at i:54765592 original size:28 final size:28
Alignment explanation
Indices: 54765554--54765630 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
54765544 AATCAAATAT
* * *
54765554 GGCACTCAGTGTACGAAATATTGAGAAA
1 GGCACTTAGTGTGCGAGATATTGAGAAA
*
54765582 GGCACTTAGTGTGCGAGATATTGAGAAT
1 GGCACTTAGTGTGCGAGATATTGAGAAA
*
54765610 GACACTTAGTGTGCGAGATAT
1 GGCACTTAGTGTGCGAGATAT
54765631 CAAATGATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (28 bp):
GGCACTTAGTGTGCGAGATATTGAGAAA
Found at i:54766070 original size:25 final size:25
Alignment explanation
Indices: 54766020--54766070 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
54766010 AAGGTAAGTA
*
54766020 TATGTGCAAAGAATATATTGTGATG
1 TATGTGCAAAGAATATATGGTGATG
* *
54766045 TATGTGGAAATGAA-ATATGGTTATG
1 TATGTGCAAA-GAATATATGGTGATG
54766070 T
1 T
54766071 GCCAATGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.37
Consensus pattern (25 bp):
TATGTGCAAAGAATATATGGTGATG
Found at i:54767064 original size:2 final size:2
Alignment explanation
Indices: 54767057--54767085 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54767047 ATTGTGCACT
54767057 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54767086 GCATCATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54770611 original size:22 final size:20
Alignment explanation
Indices: 54770567--54770613 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
54770557 ATTTTTTTAA
* *
54770567 ATTTTTAATATTTAACTGTT
1 ATTTTTAATAATAAACTGTT
54770587 ATTTTTAATGAATAAACATGTT
1 ATTTTTAAT-AATAAAC-TGTT
54770609 ATTTT
1 ATTTT
54770614 CAAATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
21 5 0.22
22 9 0.39
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (20 bp):
ATTTTTAATAATAAACTGTT
Found at i:54772270 original size:104 final size:104
Alignment explanation
Indices: 54772086--54772276 Score: 265
Period size: 104 Copynumber: 1.8 Consensus size: 104
54772076 TGAGTCACAT
* * * * * *
54772086 GGCCTGGGCACACGCACGTGTCCCTGGCCGTATGGTCTTAAATCATAAATAGTGAGTTACACGGC
1 GGCCTGGGCACACACACATGTCCCTGGCCGTATCGTCCTAAATCATAAACAGTGAGTTACAAGGC
**
54772151 CTGGACACATGCCCATGTCCTTGCCTGTGTGGCTCAAAC
66 CTGGACACACACCCATGTCCTTGCCTGTGTGGCTCAAAC
** * *
54772190 GGCCTGGGCACACACTTATGTCCCTGGCTGTGTCGTCCTAAATCATAAACAGTGAGTTACAAGGC
1 GGCCTGGGCACACACACATGTCCCTGGCCGTATCGTCCTAAATCATAAACAGTGAGTTACAAGGC
*
54772255 TTGGACACACACCCATGTCCTT
66 CTGGACACACACCCATGTCCTT
54772277 ACTCGTGTGG
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
104 74 1.00
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.25
Consensus pattern (104 bp):
GGCCTGGGCACACACACATGTCCCTGGCCGTATCGTCCTAAATCATAAACAGTGAGTTACAAGGC
CTGGACACACACCCATGTCCTTGCCTGTGTGGCTCAAAC
Found at i:54775993 original size:43 final size:42
Alignment explanation
Indices: 54775902--54776024 Score: 165
Period size: 43 Copynumber: 2.9 Consensus size: 42
54775892 TTAGGGTTAG
54775902 TTGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGAT
1 TTGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGAT
* * * * *
54775944 ATGAGATTTCGTGTAAGACTATAGCTGGGCTATTGGCATCGAT
1 TTGAGATTACGTGTAAGACCATATCTGGGATA-TGGCATCGAT
** *
54775987 TTGAGATCCCATGTAAGACCATATCTGGGATATGGCAT
1 TTGAGATTACGTGTAAGACCATATCTGGGATATGGCAT
54776025 TGGTATGGTA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 33 0.49
43 35 0.51
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (42 bp):
TTGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGAT
Found at i:54784716 original size:55 final size:53
Alignment explanation
Indices: 54784629--54784883 Score: 243
Period size: 55 Copynumber: 4.8 Consensus size: 53
54784619 ATTAGGGTTT
* *
54784629 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAAGTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-GTTTCTAAGGC
* * * * * *
54784684 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT--TCTAAGGC
* * *
54784739 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTC-TAAGGC
* *
54784792 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCTAAGGC
* * * * * *
54784841 AATGATACCACGTAAGACCATGACAAGTCATGGAAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
54784884 GTACCCGTGT
Statistics
Matches: 169, Mismatches: 25, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
49 38 0.22
52 7 0.04
53 42 0.25
54 9 0.05
55 69 0.41
56 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCTAAGGC
Found at i:54785096 original size:16 final size:16
Alignment explanation
Indices: 54785075--54785105 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54785065 ATAAATTTGA
54785075 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
54785091 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
54785106 ATTGAAGAAG
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:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:54786939 original size:42 final size:42
Alignment explanation
Indices: 54786829--54786973 Score: 175
Period size: 42 Copynumber: 3.5 Consensus size: 42
54786819 AAACAGTGAG
* *
54786829 TCACATGGCCTAGGCACACACCCATGTCCTTGCCCGTGTGGC
1 TCACACGGCCTAGGCACACACCCATGTCCTTGCTCGTGTGGC
* * * * *
54786871 TTACATGGCTTGGGCATAC-CCACATGTCCTTGCTCGTGTGGC
1 TCACACGGCCTAGGCACACACC-CATGTCCTTGCTCGTGTGGC
* * * *
54786913 TCACACGGCCTAGGCACACACCCATGTTCTTACTCGTATGAC
1 TCACACGGCCTAGGCACACACCCATGTCCTTGCTCGTGTGGC
54786955 TCACACGGCCTAGGCACAC
1 TCACACGGCCTAGGCACAC
54786974 GCCTATATTC
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.02
42 83 0.95
43 2 0.02
ACGTcount: A:0.19, C:0.35, G:0.22, T:0.23
Consensus pattern (42 bp):
TCACACGGCCTAGGCACACACCCATGTCCTTGCTCGTGTGGC
Found at i:54786994 original size:84 final size:84
Alignment explanation
Indices: 54786829--54786998 Score: 191
Period size: 84 Copynumber: 2.0 Consensus size: 84
54786819 AAACAGTGAG
* * * * * * * * *
54786829 TCACATGGCCTAGGCACACACCCATGTCCTTGCCCGTGTGGCTTACATGGCTTGGGCATACCCAC
1 TCACACGGCCTAGGCACACACCCATGTCCTTACCCGTATGACTCACACGGCCTAGGCACACCCAC
*
54786894 ATGTCCTTGCTCGTGTGGC
66 ATGTCCTGGCTCGTGTGGC
* *
54786913 TCACACGGCCTAGGCACACACCCATGTTCTTACTCGTATGACTCACACGGCCTAGGCACACGCCT
1 TCACACGGCCTAGGCACACACCCATGTCCTTACCCGTATGACTCACACGGCCTAGGCACAC-CC-
*
54786978 ATAT-TCCTGGCT-GTGTGGC
64 ACATGTCCTGGCTCGTGTGGC
54786997 TC
1 TC
54786999 TTAATCATGG
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
84 59 0.83
85 9 0.13
86 3 0.04
ACGTcount: A:0.18, C:0.34, G:0.23, T:0.25
Consensus pattern (84 bp):
TCACACGGCCTAGGCACACACCCATGTCCTTACCCGTATGACTCACACGGCCTAGGCACACCCAC
ATGTCCTGGCTCGTGTGGC
Found at i:54788539 original size:19 final size:18
Alignment explanation
Indices: 54788502--54788541 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
54788492 CATAATGATA
* *
54788502 TATATAATATATTTTTAT
1 TATATAATACATATTTAT
54788520 TATATAATTACATATTTAT
1 TATATAA-TACATATTTAT
54788539 TAT
1 TAT
54788542 TTTATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATAATACATATTTAT
Found at i:54788944 original size:21 final size:21
Alignment explanation
Indices: 54788904--54788945 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
54788894 TTTTGTCTAC
*
54788904 TTATTTTACATATAATTAATT
1 TTATTTTACATATAAATAATT
54788925 TTATTTTA-ATATATAATAATT
1 TTATTTTACATATA-AATAATT
54788946 ATTTACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTTTACATATAAATAATT
Found at i:54791929 original size:78 final size:80
Alignment explanation
Indices: 54791809--54791990 Score: 228
Period size: 78 Copynumber: 2.3 Consensus size: 80
54791799 TACTCGTTCA
* *
54791809 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGG-CTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
*
54791872 ATTTAATAAC-TCGCAC
64 ATTTAATAACTTAGCAC
**
54791888 AATGCCTTCGGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
* *
54791952 TTAGTCACTTAGCAC
66 TTAATAACTTAGCAC
* *
54791967 AAAGCCTTCAGGACTTAGCCCGGA
1 AATGCCTTC-GGGCTTAGCCCGGA
54791991 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
77 3 0.03
78 48 0.53
79 26 0.29
80 13 0.14
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
TTAATAACTTAGCAC
Found at i:54791990 original size:40 final size:39
Alignment explanation
Indices: 54791807--54791990 Score: 221
Period size: 40 Copynumber: 4.6 Consensus size: 39
54791797 GCTACTCGTT
*
54791807 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAACTCGCA
* *
54791847 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTAACTCGCA
* *
54791887 C-AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
54791925 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
54791966 CAAA-GCCTTCAGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
54791991 CATCATTCGA
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
38 25 0.20
39 20 0.16
40 68 0.54
41 13 0.10
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:54795668 original size:20 final size:20
Alignment explanation
Indices: 54795640--54795677 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
54795630 TAGGAAATTA
54795640 TGTGATCTGAGCTCATGAGT
1 TGTGATCTGAGCTCATGAGT
*
54795660 TGTGGTCTGAGCTCATGA
1 TGTGATCTGAGCTCATGA
54795678 TATATGTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (20 bp):
TGTGATCTGAGCTCATGAGT
Found at i:54798534 original size:28 final size:28
Alignment explanation
Indices: 54798494--54798552 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
54798484 GTTCAGCTAC
54798494 ATATATGGCTAATAAATGCAATATTCTA
1 ATATATGGCTAATAAATGCAATATTCTA
* *
54798522 ATATATGGCTAATAAATGCATTTTTCTA
1 ATATATGGCTAATAAATGCAATATTCTA
54798550 ATA
1 ATA
54798553 AATGTTAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (28 bp):
ATATATGGCTAATAAATGCAATATTCTA
Found at i:54802682 original size:20 final size:19
Alignment explanation
Indices: 54802659--54802705 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
54802649 CATTTCTTAA
54802659 AATTAAAACTCAATTCTACC
1 AATTAAAACTCAATTC-ACC
* *
54802679 AATTCAAAACTCCATTCAGC
1 AATT-AAAACTCAATTCACC
54802699 AATTAAA
1 AATTAAA
54802706 CATGAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (19 bp):
AATTAAAACTCAATTCACC
Found at i:54816598 original size:2 final size:2
Alignment explanation
Indices: 54816548--54816589 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
54816538 TGGGATAAAG
* *
54816548 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54816590 GCATATATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:54816791 original size:29 final size:29
Alignment explanation
Indices: 54816758--54816819 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
54816748 GTATAAATTA
* *
54816758 GTTTATTTGAAATATGAAGATAATTATAT
1 GTTTACTTGAAATATCAAGATAATTATAT
*
54816787 GTTTACTTGAAATATCAAGATGATTATAT
1 GTTTACTTGAAATATCAAGATAATTATAT
54816816 GTTT
1 GTTT
54816820 TTGTGATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (29 bp):
GTTTACTTGAAATATCAAGATAATTATAT
Found at i:54817619 original size:35 final size:33
Alignment explanation
Indices: 54817524--54817633 Score: 105
Period size: 35 Copynumber: 3.2 Consensus size: 33
54817514 CCAACATTTA
*
54817524 AAAAAGGTTGGAATAAACCCATCTAAAGCAACCTT
1 AAAAAGG-TGGAATAGACCCATCT-AAGCAACCTT
* **
54817559 AAAAAGGTAAGG-ATTGACCTGTCTAATGCAACCTT
1 AAAAAGGT--GGAATAGACCCATCTAA-GCAACCTT
*
54817594 TAAAAGGCTGGAATAGACCCATCTAAGACAACCTT
1 AAAAAGG-TGGAATAGACCCATCTAAG-CAACCTT
54817629 AAAAA
1 AAAAA
54817634 AGTTGAGATA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
34 6 0.10
35 51 0.85
36 3 0.05
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (33 bp):
AAAAAGGTGGAATAGACCCATCTAAGCAACCTT
Found at i:54817645 original size:35 final size:35
Alignment explanation
Indices: 54817521--54817660 Score: 99
Period size: 35 Copynumber: 4.0 Consensus size: 35
54817511 AGGCCAACAT
*
54817521 TTAAAAAAGGTTGGAATAAACCCATCTAA-AGCAACC
1 TTAAAAAA-GTTGGAATAGACCCATCTAAGA-CAACC
* * * **
54817557 TTAAAAAGGTAAGG-ATTGACCTGTCTAATG-CAACC
1 TTAAAAAAGT-TGGAATAGACCCATCTAA-GACAACC
* * *
54817592 TTTAAAAGGCTGGAATAGACCCATCTAAGACAACC
1 TTAAAAAAGTTGGAATAGACCCATCTAAGACAACC
* * *
54817627 TTAAAAAAGTT-GAGATAGACACGTTTAAGACAAC
1 TTAAAAAAGTTGGA-ATAGACCCATCTAAGACAAC
54817661 TTTTAAAAGA
Statistics
Matches: 80, Mismatches: 18, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
34 5 0.06
35 66 0.82
36 9 0.11
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (35 bp):
TTAAAAAAGTTGGAATAGACCCATCTAAGACAACC
Found at i:54818588 original size:15 final size:15
Alignment explanation
Indices: 54818568--54818601 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
54818558 CATAAAGGCT
54818568 TAAAGGTAAAATCAA
1 TAAAGGTAAAATCAA
*
54818583 TAAAGGTGAAATCAA
1 TAAAGGTAAAATCAA
54818598 TAAA
1 TAAA
54818602 CTGTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.59, C:0.06, G:0.15, T:0.21
Consensus pattern (15 bp):
TAAAGGTAAAATCAA
Found at i:54818617 original size:16 final size:16
Alignment explanation
Indices: 54818596--54818642 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
54818586 AGGTGAAATC
54818596 AATAAACTGTTAAAAA
1 AATAAACTGTTAAAAA
*
54818612 AATAAATTGTTAAAAA
1 AATAAACTGTTAAAAA
*
54818628 AATAAACTATTAAAA
1 AATAAACTGTTAAAA
54818643 GCTGTTAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (16 bp):
AATAAACTGTTAAAAA
Found at i:54843072 original size:53 final size:53
Alignment explanation
Indices: 54843008--54843141 Score: 198
Period size: 53 Copynumber: 2.5 Consensus size: 53
54842998 TCATACTGAA
* *
54843008 GCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTATCACATTATACCGAT
1 GCCATAACCCAG-CTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
* * *
54843061 GCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATTGCACCGAT
1 GCCATAACCCAGCTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
*
54843114 GCCATAACCCAGCTATGGTCTTAAACGG
1 GCCATAACCCAGCTATGGTCTTATACGG
54843142 GCGCACTTAT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
52 1 0.01
53 73 0.99
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
GCCATAACCCAGCTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
Found at i:54848115 original size:20 final size:21
Alignment explanation
Indices: 54848075--54848115 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
54848065 ATGCCTTATA
*
54848075 TTTTGAAAATTTTTCTAAGTT
1 TTTTGAAAATTTTCCTAAGTT
*
54848096 TTTTGAAAA-TTTCCTGAGTT
1 TTTTGAAAATTTTCCTAAGTT
54848116 ATCAGTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.27, C:0.07, G:0.12, T:0.54
Consensus pattern (21 bp):
TTTTGAAAATTTTCCTAAGTT
Found at i:54854529 original size:79 final size:81
Alignment explanation
Indices: 54854428--54854612 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
54854418 ACGACTCGCT
** * *
54854428 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
54854491 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* **
54854508 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
54854572 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
54854588 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54854613 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:54854612 original size:40 final size:39
Alignment explanation
Indices: 54854421--54854612 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
54854411 GGATATAACG
* ** * *
54854421 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
54854461 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
54854501 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
54854540 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
54854580 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
54854613 CATCATTCGA
Statistics
Matches: 121, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 79 0.65
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:54858343 original size:13 final size:13
Alignment explanation
Indices: 54858327--54858351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54858317 AGTCAACAGA
54858327 ATTAGATATACAT
1 ATTAGATATACAT
54858340 ATTAGATATACA
1 ATTAGATATACA
54858352 GAATCCTACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
ATTAGATATACAT
Found at i:54860337 original size:140 final size:140
Alignment explanation
Indices: 54860097--54860640 Score: 630
Period size: 140 Copynumber: 4.0 Consensus size: 140
54860087 AAAAGTCGGT
* * * * * *
54860097 ATAGTGTTAGACAAAGCTGAATCTTATTGAAGTGTTGCCTTAGTCATGCATATCCCAACCCTTAT
1 ATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTAT
*
54860162 ACAAAGAGTTGGCCAAAGCATATGTCGGTAAGTCTATCCCAACACTTAGGAAAGTGTCGGCCCAA
66 ACAAAGAGTTGGCCAAAGCATATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCCCAA
54860227 AAATGTCGAC
131 AAATGTCGAC
* *
54860237 ATAGTGTTGGACAAAGCTGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTAAT
1 ATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTAT
* * * * * * *
54860302 ATAAAGGGTTGGCTAAAGCGTATGCCGACAAGTCTATCCCAACACTTAGGAAAGTGTCCGCCCAA
66 ACAAAGAGTTGGCCAAAGCATATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCCCAA
* *
54860367 AAGTGTCTGGC
131 AAATGTC-GAC
* * *
54860378 ATAGTGTTGGACAAAGCCAACTCTAATTTAAGCCTTGCCTTAGGCATGCATATCCCAACCCTTAT
1 ATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTAT
** * * * *
54860443 ACAAAGAGTAAGCCAAATCATGTGTTGGCAAGTCTATCCCAACACTCAGGAAAGTGTCGG--C--
66 ACAAAGAGTTGGCCAAAGCATATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCCCAA
*
54860504 ATA-GT--AC
131 AAATGTCGAC
* *
54860511 -TA------GACAAAGCCGACTCTTATTTAATCGTTGCCTTAGGCATGTATATCCCAACCCTTAT
1 ATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTAT
* * * ** * * * *
54860569 ACAAAGAGTTGGGCAAAACGTGGGTAGGCAAGTCTATCCTAACACTTAGAAAAGTGTCAGCCCAA
66 ACAAAGAGTTGGCCAAAGCATATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCCCAA
54860634 AAATGTC
131 AAATGTC
54860641 ATCTTAGGAC
Statistics
Matches: 343, Mismatches: 54, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
126 100 0.29
128 1 0.00
130 2 0.01
131 2 0.01
132 2 0.01
133 1 0.00
136 2 0.01
137 1 0.00
139 1 0.00
140 122 0.36
141 109 0.32
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (140 bp):
ATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTAT
ACAAAGAGTTGGCCAAAGCATATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCCCAA
AAATGTCGAC
Found at i:54860438 original size:141 final size:140
Alignment explanation
Indices: 54860131--54860640 Score: 571
Period size: 141 Copynumber: 3.7 Consensus size: 140
54860121 TATTGAAGTG
* *
54860131 TTGCCTTAGTCATGCATATCCCAACCCTTATACAAAGAGTTGGCCAAAGCATATGTCGGTAAGTC
1 TTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAGTTGGCCAAAGCATATGTCGGCAAGTC
* **
54860196 TATCCCAACACTTAGGAAAGTGTCGGCCCAAAAATGTCGACATAGTGTTGGACAAAGCTGACTCT
66 TATCCCAACACTTAGGAAAGTGTCCGCCCAAAAATGTCGACATAGTGTTGGACAAAGCCAACTCT
* *
54860261 TATTTAAGCG
131 AATTTAAGCC
* * * * * * *
54860271 TTGCCTTAGGCATGCATATCCCAACCCTAATATAAAGGGTTGGCTAAAGCGTATGCCGACAAGTC
1 TTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAGTTGGCCAAAGCATATGTCGGCAAGTC
* *
54860336 TATCCCAACACTTAGGAAAGTGTCCGCCCAAAAGTGTCTGGCATAGTGTTGGACAAAGCCAACTC
66 TATCCCAACACTTAGGAAAGTGTCCGCCCAAAAATGTC-GACATAGTGTTGGACAAAGCCAACTC
54860401 TAATTTAAGCC
130 TAATTTAAGCC
** * * *
54860412 TTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAGTAAGCCAAATCATGTGTTGGCAAGTC
1 TTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAGTTGGCCAAAGCATATGTCGGCAAGTC
* * * *
54860477 TATCCCAACACTCAGGAAAGTGT-CG-GC--ATA-GT--AC-TA------GACAAAGCCGACTCT
66 TATCCCAACACTTAGGAAAGTGTCCGCCCAAAAATGTCGACATAGTGTTGGACAAAGCCAACTCT
* * *
54860528 TATTTAATCG
131 AATTTAAGCC
* * * * ** *
54860538 TTGCCTTAGGCATGTATATCCCAACCCTTATACAAAGAGTTGGGCAAAACGTGGGTAGGCAAGTC
1 TTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAGTTGGCCAAAGCATATGTCGGCAAGTC
* * *
54860603 TATCCTAACACTTAGAAAAGTGTCAGCCCAAAAATGTC
66 TATCCCAACACTTAGGAAAGTGTCCGCCCAAAAATGTC
54860641 ATCTTAGGAC
Statistics
Matches: 312, Mismatches: 51, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
126 98 0.31
127 1 0.00
128 1 0.00
130 2 0.01
131 2 0.01
132 2 0.01
133 1 0.00
136 2 0.01
137 1 0.00
139 1 0.00
140 94 0.30
141 107 0.34
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (140 bp):
TTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAGTTGGCCAAAGCATATGTCGGCAAGTC
TATCCCAACACTTAGGAAAGTGTCCGCCCAAAAATGTCGACATAGTGTTGGACAAAGCCAACTCT
AATTTAAGCC
Found at i:54860600 original size:126 final size:127
Alignment explanation
Indices: 54860365--54860626 Score: 355
Period size: 126 Copynumber: 2.1 Consensus size: 127
54860355 GTGTCCGCCC
** *
54860365 AAAAGTGTCTGGCATAGTGTTGGACAAAGCCAACTCTAATTTAAGCCTTGCCTTAGGCATGCATA
1 AAAAGTGTCTGGCATAGTACTAGACAAAGCCAACTCTAATTTAAGCCTTGCCTTAGGCATGCATA
* * *
54860430 TCCCAACCCTTATACAAAGAGTAAGCCAAATCATGTGTTGGCAAGTCTATCCCAACACTCAG
66 TCCCAACCCTTATACAAAGAGTAAGCCAAAACATGGGTAGGCAAGTCTATCCCAACACTCAG
* * * * * *
54860492 GAAAGTGTC-GGCATAGTACTAGACAAAGCCGACTCTTATTTAATCGTTGCCTTAGGCATGTATA
1 AAAAGTGTCTGGCATAGTACTAGACAAAGCCAACTCTAATTTAAGCCTTGCCTTAGGCATGCATA
** * * * *
54860556 TCCCAACCCTTATACAAAGAGTTGGGCAAAACGTGGGTAGGCAAGTCTATCCTAACACTTAG
66 TCCCAACCCTTATACAAAGAGTAAGCCAAAACATGGGTAGGCAAGTCTATCCCAACACTCAG
54860618 AAAAGTGTC
1 AAAAGTGTC
54860627 AGCCCAAAAA
Statistics
Matches: 116, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
126 108 0.93
127 8 0.07
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (127 bp):
AAAAGTGTCTGGCATAGTACTAGACAAAGCCAACTCTAATTTAAGCCTTGCCTTAGGCATGCATA
TCCCAACCCTTATACAAAGAGTAAGCCAAAACATGGGTAGGCAAGTCTATCCCAACACTCAG
Found at i:54860905 original size:23 final size:24
Alignment explanation
Indices: 54860879--54860926 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
54860869 ACAATAATTT
* *
54860879 TTTATTTTTATATGTTTTT-AAAA
1 TTTATTATTATATATTTTTGAAAA
54860902 TTTATTATTATATATTTTTGAAAA
1 TTTATTATTATATATTTTTGAAAA
54860926 T
1 T
54860927 ATTTATGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTATTATTATATATTTTTGAAAA
Found at i:54860932 original size:23 final size:22
Alignment explanation
Indices: 54860881--54860932 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
54860871 AATAATTTTT
*
54860881 TATTT-TTATATGTTTTTAAAA
1 TATTTATTATATATTTTTAAAA
*
54860902 TTTATTATTATATATTTTTGAAAA
1 TAT-TTATTATATATTTTT-AAAA
54860926 TATTTAT
1 TATTTAT
54860933 GTATTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 2 0.08
22 2 0.08
23 15 0.60
24 6 0.24
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
TATTTATTATATATTTTTAAAA
Found at i:54861437 original size:12 final size:11
Alignment explanation
Indices: 54861416--54861449 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
54861406 GGCTGTTTTC
*
54861416 TTTTCTTTCTT
1 TTTTTTTTCTT
54861427 TTTTTTGTTCTT
1 TTTTTT-TTCTT
54861439 TTTTTTTTCTT
1 TTTTTTTTCTT
54861450 CTTGTTTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:54861442 original size:14 final size:14
Alignment explanation
Indices: 54861411--54861452 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
54861401 CGAGGGGCTG
*
54861411 TTTTCTTTTCTT-T
1 TTTTTTTTTCTTCT
* *
54861424 CTTTTTTTTGTTCT
1 TTTTTTTTTCTTCT
54861438 TTTTTTTTTCTTCT
1 TTTTTTTTTCTTCT
54861452 T
1 T
54861453 GTTTAGGCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTCTTCT
Found at i:54861689 original size:38 final size:38
Alignment explanation
Indices: 54861638--54861720 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 38
54861628 TGAAAAATTT
* *
54861638 GCATTTGAATTTGTCTTTCCTTCACTAAAATTGGTATA
1 GCATTTGAATTTGTCTTTCCTTCAATAAAAGTGGTATA
54861676 GCATTTGAATTTGTCTTTCCTTCAATAAAAGTGGTATA
1 GCATTTGAATTTGTCTTTCCTTCAATAAAAGTGGTATA
54861714 -C-TTTGAA
1 GCATTTGAA
54861721 GCCATGCGCG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 6 0.14
37 1 0.02
38 36 0.84
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.43
Consensus pattern (38 bp):
GCATTTGAATTTGTCTTTCCTTCAATAAAAGTGGTATA
Found at i:54864768 original size:3 final size:3
Alignment explanation
Indices: 54864760--54864804 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
54864750 TGTTTTAATG
54864760 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54864805 CCTTTGAATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54869082 original size:23 final size:22
Alignment explanation
Indices: 54869049--54869091 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
54869039 CTAATCATTC
* *
54869049 ATTTAATTTTAATATTTTTTAAT
1 ATTTAAATTT-ATATTATTTAAT
54869072 ATTTAAATTTATATTATTTA
1 ATTTAAATTTATATTATTTA
54869092 TTAAATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTAAATTTATATTATTTAAT
Found at i:54869202 original size:17 final size:18
Alignment explanation
Indices: 54869182--54869223 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
54869172 ATTACTTTTT
54869182 TTAAAATTTAAAAAA-AA
1 TTAAAATTTAAAAAAGAA
* *
54869199 TTAAAA-ATAAAAAAGTA
1 TTAAAATTTAAAAAAGAA
54869216 TTAAAATT
1 TTAAAATT
54869224 ATTATCAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
TTAAAATTTAAAAAAGAA
Found at i:54870227 original size:3 final size:3
Alignment explanation
Indices: 54870221--54870245 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54870211 TTAATAATAA
54870221 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
54870246 TAAAAATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:54872774 original size:12 final size:11
Alignment explanation
Indices: 54872742--54872776 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
54872732 GCTACACTAG
*
54872742 TTTAGTTTTCC
1 TTTAGTTTTCT
54872753 TTTAGTTTTCT
1 TTTAGTTTTCT
54872764 TTTAGGTTTTCT
1 TTTA-GTTTTCT
54872776 T
1 T
54872777 CCCTATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.09, C:0.11, G:0.11, T:0.69
Consensus pattern (11 bp):
TTTAGTTTTCT
Found at i:54874498 original size:45 final size:45
Alignment explanation
Indices: 54874412--54874498 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
54874402 TATGTGATCT
* *
54874412 GAACTCATTGAGTTGCGGTCTGAGTTCATGATATATGTGACATCC
1 GAACTCATTGAGTTACGGTCTGAGTTCATGATATATATGACATCC
* * *
54874457 GAACTCATTGAGTTATGGTCTGAGTTCGTGATATTTATGACA
1 GAACTCATTGAGTTACGGTCTGAGTTCATGATATATATGACA
54874499 CATGTTTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (45 bp):
GAACTCATTGAGTTACGGTCTGAGTTCATGATATATATGACATCC
Found at i:54883506 original size:19 final size:20
Alignment explanation
Indices: 54883462--54883508 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
54883452 GCAACTCAAT
* *
54883462 TTTATTTTATTTATTTTCCA
1 TTTATTTTAGTAATTTTCCA
54883482 TTTATTTTAGTAATTTTCC-
1 TTTATTTTAGTAATTTTCCA
54883501 TTTATTTT
1 TTTATTTT
54883509 TATTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTATTTTAGTAATTTTCCA
Found at i:54888674 original size:17 final size:18
Alignment explanation
Indices: 54888638--54888674 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
54888628 ACTTTCAAGG
54888638 AAAACTTCCCATTCTAAA
1 AAAACTTCCCATTCTAAA
54888656 AAAACTTCCCATTCTAAA
1 AAAACTTCCCATTCTAAA
54888674 A
1 A
54888675 GGAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAACTTCCCATTCTAAA
Found at i:54889135 original size:23 final size:22
Alignment explanation
Indices: 54889102--54889146 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
54889092 AGATATGGTA
*
54889102 TGTAATCTTAGAAGATATGATTT
1 TGTAATATTAGAA-ATATGATTT
*
54889125 TGTAATATTAGAAATTTGATTT
1 TGTAATATTAGAAATATGATTT
54889147 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (22 bp):
TGTAATATTAGAAATATGATTT
Found at i:54889386 original size:15 final size:16
Alignment explanation
Indices: 54889360--54889389 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54889350 TTCATCCTCA
54889360 TTTGGATTTGAGTTGC
1 TTTGGATTTGAGTTGC
54889376 TTTGG-TTTGAGTTG
1 TTTGGATTTGAGTTG
54889390 GATTTTATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.10, C:0.03, G:0.33, T:0.53
Consensus pattern (16 bp):
TTTGGATTTGAGTTGC
Found at i:54897627 original size:33 final size:33
Alignment explanation
Indices: 54897585--54897677 Score: 87
Period size: 33 Copynumber: 2.8 Consensus size: 33
54897575 TATAGTTGGA
* *
54897585 CTATAGCATCCTGATGATAAGATCATAGCTGAG
1 CTATGGCATCATGATGATAAGATCATAGCTGAG
* * * * * *
54897618 TTATGGCATCTTAATGATAAAATCATAGTTGGG
1 CTATGGCATCATGATGATAAGATCATAGCTGAG
* * *
54897651 CTATGACATTATGATGATAAGACCATA
1 CTATGGCATCATGATGATAAGATCATA
54897678 ACCAGGTTAC
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (33 bp):
CTATGGCATCATGATGATAAGATCATAGCTGAG
Found at i:54899410 original size:39 final size:39
Alignment explanation
Indices: 54899363--54899545 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
54899353 AATGTTCGAG
54899363 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
54899402 TGATATCCGGGCTAAGCCCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
54899441 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
54899480 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
54899520 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
54899546 GTTTGAACGA
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:54906843 original size:39 final size:39
Alignment explanation
Indices: 54906796--54906978 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
54906786 AATGTTCGAG
54906796 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
54906835 TGATATCCGGGCTAAGCCCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
54906874 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
54906913 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
54906953 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
54906979 GTTTGAACGA
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:54911448 original size:39 final size:39
Alignment explanation
Indices: 54911384--54911499 Score: 169
Period size: 39 Copynumber: 3.0 Consensus size: 39
54911374 TTTATCCGGG
* *
54911384 CTTAGGGTCAGCAGGCTATGTGCTGGAATTATATCTGGA
1 CTTAAGGTCCGCAGGCTATGTGCTGGAATTATATCTGGA
* *
54911423 CTTAAGGTCCGCAGGCTATGTGCTGGAATTATAACCGGA
1 CTTAAGGTCCGCAGGCTATGTGCTGGAATTATATCTGGA
* * *
54911462 CTTAAGGTCCGCAGGCTACGTGCTGGAAATATGTCTGG
1 CTTAAGGTCCGCAGGCTATGTGCTGGAATTATATCTGG
54911500 GCTAAAGTCC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (39 bp):
CTTAAGGTCCGCAGGCTATGTGCTGGAATTATATCTGGA
Found at i:54919764 original size:37 final size:37
Alignment explanation
Indices: 54919714--54919822 Score: 137
Period size: 37 Copynumber: 2.9 Consensus size: 37
54919704 TTTGAGTATG
*
54919714 TAATTATGTCATAATTTGAACATCGTTAATATGATTT
1 TAATTATGTCATAATTTGAACATCTTTAATATGATTT
* * *
54919751 TAATTATGTCATAATCTGAACATCTTTAATAAGGGTTTT
1 TAATTATGTCATAATTTGAACATCTTTAAT-A-TGATTT
* *
54919790 TAATTATGTCATAGTTTAGGACATCTTTAATAT
1 TAATTATGTCATAATTT-GAACATCTTTAATAT
54919823 ATGTTTTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
37 28 0.46
38 1 0.02
39 20 0.33
40 12 0.20
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (37 bp):
TAATTATGTCATAATTTGAACATCTTTAATATGATTT
Found at i:54919830 original size:39 final size:39
Alignment explanation
Indices: 54919714--54919838 Score: 141
Period size: 39 Copynumber: 3.3 Consensus size: 39
54919704 TTTGAGTATG
*
54919714 TAATTATGTCATAATTTGAACATCGTT-A-ATATGATTT
1 TAATTATGTCATAATTTGAACATCTTTAATATATGATTT
* * *
54919751 TAATTATGTCATAATCTGAACATCTTTAATA-AGGGTTTT
1 TAATTATGTCATAATTTGAACATCTTTAATATA-TGATTT
* *
54919790 TAATTATGTCATAGTTTAGGACATCTTTAATATATG-TTT
1 TAATTATGTCATAATTT-GAACATCTTTAATATATGATTT
*
54919829 TAAATATGTC
1 TAATTATGTC
54919839 TTAGTTTAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
37 25 0.34
38 2 0.03
39 32 0.43
40 14 0.19
41 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.46
Consensus pattern (39 bp):
TAATTATGTCATAATTTGAACATCTTTAATATATGATTT
Found at i:54921861 original size:161 final size:161
Alignment explanation
Indices: 54921595--54921891 Score: 459
Period size: 161 Copynumber: 1.8 Consensus size: 161
54921585 TTTCTAAGAC
* * *
54921595 AAGATCTTGGTTGTGATATCTAAAGTAATAAACCCTTAAGCAAAATTTTAGCTTTTCAATTTTTC
1 AAGATCTTGGTTGTGATATCTAAAGTAATAAACACTTAAGCAAAATTTTACCTTTTCAATTTGTC
* * * *
54921660 TAGGATGAGTGCTTCTACTGAGTAGTCTTCTTCGCTATCCTCAAGCTCACGTCTGCCGAGTGTGG
66 TAGGATGAGCGCTTCGACCGAGTAGTCTTCTCCGCTATCCTCAAGCTCACGTCTGCCGAGTGTGG
54921725 GCTTGCGTTAGTTTTAAATTTTTTCCAAAAT
131 GCTTGCGTTAGTTTTAAATTTTTTCCAAAAT
* * *
54921756 AAGATCTTGGTTGTGATATCTAAAGTAATAAAGACTTAATCAAAATTTTACCTTTTCGATTTGTC
1 AAGATCTTGGTTGTGATATCTAAAGTAATAAACACTTAAGCAAAATTTTACCTTTTCAATTTGTC
* * * **
54921821 TAGGATGAGCGCTTCGACCGAGTAGTCTTCTCCTCTATCCTTAAGCTCACGTTTGTTGAGTGTGG
66 TAGGATGAGCGCTTCGACCGAGTAGTCTTCTCCGCTATCCTCAAGCTCACGTCTGCCGAGTGTGG
54921886 GCTTGC
131 GCTTGC
54921892 TTTGAATCAG
Statistics
Matches: 121, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
161 121 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (161 bp):
AAGATCTTGGTTGTGATATCTAAAGTAATAAACACTTAAGCAAAATTTTACCTTTTCAATTTGTC
TAGGATGAGCGCTTCGACCGAGTAGTCTTCTCCGCTATCCTCAAGCTCACGTCTGCCGAGTGTGG
GCTTGCGTTAGTTTTAAATTTTTTCCAAAAT
Found at i:54922015 original size:25 final size:26
Alignment explanation
Indices: 54921972--54922024 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
54921962 AAGTTGTAAA
54921972 CTAGAAAAATATCTCTAGA-AATTTT
1 CTAGAAAAATATCTCTAGATAATTTT
* * *
54921997 CTAGAATAATCTCTTTAGATAATTTT
1 CTAGAAAAATATCTCTAGATAATTTT
54922023 CT
1 CT
54922025 CTTTACAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (26 bp):
CTAGAAAAATATCTCTAGATAATTTT
Found at i:54929767 original size:16 final size:16
Alignment explanation
Indices: 54929746--54929776 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54929736 CTATGCATGC
54929746 AAAATATAAAAGACAG
1 AAAATATAAAAGACAG
*
54929762 AAAATATAATAGACA
1 AAAATATAAAAGACA
54929777 TAATTGTGAA
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:0.68, C:0.06, G:0.10, T:0.16
Consensus pattern (16 bp):
AAAATATAAAAGACAG
Found at i:54932008 original size:30 final size:30
Alignment explanation
Indices: 54931972--54932102 Score: 180
Period size: 30 Copynumber: 4.5 Consensus size: 30
54931962 GACAAGATTG
* * * *
54931972 GCACTAAGTGTGCGGGTTTAAAATTATACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
54932002 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
54932030 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
54932060 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
54932089 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
54932103 GATTCACTAT
Statistics
Matches: 93, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.25
29 20 0.22
30 46 0.49
31 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:54932063 original size:58 final size:58
Alignment explanation
Indices: 54931972--54932102 Score: 183
Period size: 58 Copynumber: 2.2 Consensus size: 58
54931962 GACAAGATTG
* * * * *
54931972 GCACTAAGTGTGCGGGTTTAAAATTATACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
54932030 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
54932089 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
54932103 GATTCACTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
57 2 0.03
58 42 0.65
59 21 0.32
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:54934640 original size:21 final size:20
Alignment explanation
Indices: 54934616--54934654 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
54934606 AATGTTGGGG
54934616 TAAGTCTGTTAATATGGGCGT
1 TAAGTCTGTTAATA-GGGCGT
54934637 TAAGTCTGTTAATAGGGC
1 TAAGTCTGTTAATAGGGC
54934655 CTGTTATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (20 bp):
TAAGTCTGTTAATAGGGCGT
Found at i:54939882 original size:30 final size:30
Alignment explanation
Indices: 54939846--54939976 Score: 180
Period size: 30 Copynumber: 4.5 Consensus size: 30
54939836 GACAAGATTG
* * * *
54939846 GCACTAAGTGTGCGGGTTTAAAATTATACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
54939876 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
54939904 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
54939934 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
54939963 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
54939977 GATTCACTAT
Statistics
Matches: 93, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.25
29 20 0.22
30 46 0.49
31 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:54939937 original size:58 final size:58
Alignment explanation
Indices: 54939846--54939976 Score: 183
Period size: 58 Copynumber: 2.2 Consensus size: 58
54939836 GACAAGATTG
* * * * *
54939846 GCACTAAGTGTGCGGGTTTAAAATTATACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
54939904 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
54939963 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
54939977 GATTCACTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
57 2 0.03
58 42 0.65
59 21 0.32
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:54942539 original size:39 final size:39
Alignment explanation
Indices: 54942485--54942562 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
54942475 TTGGGGTAAG
54942485 TCTGTTAATAGGGCCTGTTATGGATGCGGTTCGAAGGAC
1 TCTGTTAATAGGGCCTGTTATGGATGCGGTTCGAAGGAC
54942524 TCTGTTAATAGGGCCTGTTATGGATGCGGTTCGAAGGAC
1 TCTGTTAATAGGGCCTGTTATGGATGCGGTTCGAAGGAC
54942563 CACTTCATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (39 bp):
TCTGTTAATAGGGCCTGTTATGGATGCGGTTCGAAGGAC
Found at i:54947768 original size:30 final size:30
Alignment explanation
Indices: 54947732--54947832 Score: 136
Period size: 28 Copynumber: 3.5 Consensus size: 30
54947722 GACAAGATTG
* *
54947732 GCACTAAGTGTGCGGGTTTAAAATTATACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
*
54947762 GCACTAAGTGTGCGAGTTT--GATTATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
54947790 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
54947819 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
54947833 GATTCACTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
28 24 0.38
29 20 0.32
30 19 0.30
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:54947844 original size:29 final size:29
Alignment explanation
Indices: 54947732--54947836 Score: 108
Period size: 29 Copynumber: 3.6 Consensus size: 29
54947722 GACAAGATTG
* * *
54947732 GCACTAAGTGTGCGGGTTTAAAATTATACA
1 GCACTAAGTGTGCGGATTGAAAA-TATATA
* *
54947762 GCACTAAGTGTGCGAGTTTG--ATTATATA
1 GCACTAAGTGTGCG-GATTGAAAATATATA
*
54947790 GCACTAAGTGTGC-GAGCTGAAAATATATA
1 GCACTAAGTGTGCGGA-TTGAAAATATATA
54947819 GCACTAAGTGTGCGGATT
1 GCACTAAGTGTGCGGATT
54947837 CACTATATGC
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
26 1 0.02
27 2 0.03
28 18 0.29
29 22 0.35
30 16 0.26
31 3 0.05
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGATTGAAAATATATA
Found at i:54954015 original size:43 final size:42
Alignment explanation
Indices: 54953876--54954042 Score: 142
Period size: 43 Copynumber: 3.9 Consensus size: 42
54953866 ATATAGCTCT
* * * *
54953876 TACAATGCC-ATATCCCAGATATGGTCTTACATGTTAT-CACA
1 TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCCA-A
* * * * *
54953917 TATCGATGCCATTGTCCCAGACA-GCGTCTTACACGAAATCGAT
1 TA-CAATGCCAATGTCCCAGACATG-GTCTTACACGTAATCCAA
* * *
54953960 TAACGATTCCAATGTCCTAGACATGGTCTTACACGTAATCTCAA
1 T-ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATC-CAA
* *
54954004 TACAATGCCAATGTCCTAGACATGGTCTTACATGTAATC
1 TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATC
54954043 ATATCTCTAT
Statistics
Matches: 101, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
41 2 0.02
42 7 0.07
43 87 0.86
44 5 0.05
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (42 bp):
TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCCAA
Found at i:54958007 original size:21 final size:20
Alignment explanation
Indices: 54957983--54958084 Score: 86
Period size: 20 Copynumber: 5.2 Consensus size: 20
54957973 CACTTCAAAT
*
54957983 ATTTTTAACTCAAGTGAAACA
1 ATTTTTAAATCAAGT-AAACA
*
54958004 A-TTTTAAATCGAGTAAA-A
1 ATTTTTAAATCAAGTAAACA
** *
54958022 A-TTTTAAATTGAGTGAAACG
1 ATTTTTAAATCAAGT-AAACA
*
54958042 ATTTTTAAATCAAGTAAAAA
1 ATTTTTAAATCAAGTAAACA
*
54958062 CATTTTTAAA-CAAGTAAAAA
1 -ATTTTTAAATCAAGTAAACA
54958082 ATT
1 ATT
54958085 GCTCAAAACA
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
18 14 0.20
19 9 0.13
20 25 0.36
21 21 0.30
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (20 bp):
ATTTTTAAATCAAGTAAACA
Found at i:54958010 original size:20 final size:20
Alignment explanation
Indices: 54957985--54958076 Score: 82
Period size: 21 Copynumber: 4.7 Consensus size: 20
54957975 CTTCAAATAT
*
54957985 TTTTAACTCAAGTGAAACAA
1 TTTTAAATCAAGTGAAACAA
*
54958005 TTTTAAATCGAGT-AAA-AA
1 TTTTAAATCAAGTGAAACAA
** *
54958023 TTTTAAATTGAGTGAAACGAT
1 TTTTAAATCAAGTGAAAC-AA
* *
54958044 TTTTAAATCAAGTAAAAACAT
1 TTTTAAATCAAGT-GAAACAA
54958065 TTTTAAA-CAAGT
1 TTTTAAATCAAGT
54958077 AAAAAATTGC
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
18 14 0.23
19 6 0.10
20 16 0.26
21 21 0.34
22 4 0.07
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (20 bp):
TTTTAAATCAAGTGAAACAA
Found at i:54958026 original size:18 final size:18
Alignment explanation
Indices: 54958003--54958061 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
54957993 CAAGTGAAAC
54958003 AATTTTAAATCGAGTAAA
1 AATTTTAAATCGAGTAAA
*
54958021 AATTTTAAATTGAGTGAAA
1 AATTTTAAATCGAGT-AAA
* *
54958040 CGATTTTTAAATCAAGTAAA
1 --AATTTTAAATCGAGTAAA
54958060 AA
1 AA
54958062 CATTTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
18 15 0.45
19 3 0.09
20 3 0.09
21 12 0.36
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (18 bp):
AATTTTAAATCGAGTAAA
Found at i:54958026 original size:39 final size:42
Alignment explanation
Indices: 54957983--54958076 Score: 108
Period size: 38 Copynumber: 2.4 Consensus size: 42
54957973 CACTTCAAAT
* *
54957983 ATTTTTAACTCAAGTGAAAC-AATTTTAAATCGAGT-AAAA-
1 ATTTTTAAATCAAGTGAAACGAATTTTAAATCAAGTAAAAAC
** *
54958022 A-TTTTAAATTGAGTGAAACGATTTTTAAATCAAGTAAAAAC
1 ATTTTTAAATCAAGTGAAACGAATTTTAAATCAAGTAAAAAC
54958063 ATTTTTAAA-CAAGT
1 ATTTTTAAATCAAGT
54958077 AAAAAATTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
38 15 0.34
39 14 0.32
40 4 0.09
41 4 0.09
42 7 0.16
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (42 bp):
ATTTTTAAATCAAGTGAAACGAATTTTAAATCAAGTAAAAAC
Found at i:54958028 original size:38 final size:39
Alignment explanation
Indices: 54957985--54958061 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
54957975 CTTCAAATAT
* *
54957985 TTTTAACTCAAGTGAAAC-AATTTTAAATCGAGTAAAAA
1 TTTTAAATCAAGTGAAACGAATTTTAAATCAAGTAAAAA
** *
54958023 TTTTAAATTGAGTGAAACGATTTTTAAATCAAGTAAAAA
1 TTTTAAATCAAGTGAAACGAATTTTAAATCAAGTAAAAA
54958062 CATTTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
38 15 0.45
39 18 0.55
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.34
Consensus pattern (39 bp):
TTTTAAATCAAGTGAAACGAATTTTAAATCAAGTAAAAA
Found at i:54958282 original size:103 final size:103
Alignment explanation
Indices: 54958095--54958282 Score: 236
Period size: 103 Copynumber: 1.8 Consensus size: 103
54958085 GCTCAAAACA
* * * * *
54958095 AAAAGTATCGATAGTTTTCAATAAGTATCGATACCTATAAATTTTTGTCGATACCTTTTCTGGTA
1 AAAAGTATCGATACTTATCAATAAGTATCGATACCAATAAATTTTTCTCGATACCTTTTCTAGTA
* *
54958160 TCGATATGAAAATGTCATTCTGGAGTTTTTATCAAAGT
66 TCGATACGAAAATGACATTCTGGAGTTTTTATCAAAGT
* * * *
54958198 AAAATTATCGATACTTATCATTAAGTATCGATA-CAATGATATTTTTCTTGATACCTTTT-TCAG
1 AAAAGTATCGATACTTATCAATAAGTATCGATACCAAT-AAATTTTTCTCGATACCTTTTCT-AG
*
54958261 TATCGATACGAAATTGACATTC
64 TATCGATACGAAAATGACATTC
54958283 CGACTTTGAA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
102 4 0.06
103 67 0.94
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (103 bp):
AAAAGTATCGATACTTATCAATAAGTATCGATACCAATAAATTTTTCTCGATACCTTTTCTAGTA
TCGATACGAAAATGACATTCTGGAGTTTTTATCAAAGT
Found at i:54971445 original size:29 final size:29
Alignment explanation
Indices: 54971412--54971542 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
54971402 GTGACGAGAT
54971412 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
54971441 TGGCACTAAGTGTGCATGCTGG-AATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ***
54971469 TGGCACTAAGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
54971498 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
54971527 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
54971543 AAATCGAGTA
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
28 27 0.31
29 59 0.69
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:54971475 original size:28 final size:29
Alignment explanation
Indices: 54971412--54971483 Score: 128
Period size: 28 Copynumber: 2.5 Consensus size: 29
54971402 GTGACGAGAT
*
54971412 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
54971441 TGGCACTAAGTGTGCATGCTGG-AATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
54971469 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
54971484 GAGCTCGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 21 0.50
29 21 0.50
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:54977493 original size:20 final size:19
Alignment explanation
Indices: 54977453--54977495 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
54977443 GGTGACTAAA
*
54977453 TTAACAAAAAATAATATCT
1 TTAACAAAAAAGAATATCT
54977472 TTAACAAAAATAGAGATA-CT
1 TTAACAAAAA-AGA-ATATCT
54977492 TTAA
1 TTAA
54977496 AATTTAGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 8 0.38
21 3 0.14
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (19 bp):
TTAACAAAAAAGAATATCT
Found at i:54979613 original size:17 final size:18
Alignment explanation
Indices: 54979593--54979626 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54979583 TGTTTGTTTA
54979593 TTTTTCTTATTT-ATTTG
1 TTTTTCTTATTTGATTTG
*
54979610 TTTTTGTTATTTGATTT
1 TTTTTCTTATTTGATTT
54979627 ATCTCCTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (18 bp):
TTTTTCTTATTTGATTTG
Found at i:54979994 original size:8 final size:8
Alignment explanation
Indices: 54979981--54980021 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
54979971 TAGATACATT
54979981 TTTTAATA
1 TTTTAATA
54979989 TTTTAATA
1 TTTTAATA
54979997 TTTTAAT-
1 TTTTAATA
*
54980004 TTTTAGT-
1 TTTTAATA
54980011 TTTTAATA
1 TTTTAATA
54980019 TTT
1 TTT
54980022 ATTTTTATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 12 0.40
8 18 0.60
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (8 bp):
TTTTAATA
Found at i:54980013 original size:7 final size:7
Alignment explanation
Indices: 54979980--54980028 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
54979970 ATAGATACAT
54979980 TTTTTAA
1 TTTTTAA
54979987 TATTTTAA
1 T-TTTTAA
54979995 TATTTTAA
1 T-TTTTAA
*
54980003 TTTTTAG
1 TTTTTAA
54980010 TTTTTAA
1 TTTTTAA
*
54980017 TATTT-A
1 TTTTTAA
54980023 TTTTTA
1 TTTTTA
54980029 TTCTCCTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 5 0.14
7 16 0.44
8 15 0.42
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (7 bp):
TTTTTAA
Found at i:54980705 original size:18 final size:17
Alignment explanation
Indices: 54980683--54980725 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
54980673 CGAAATTGGG
54980683 TAATTAATCGAA-TTAA
1 TAATTAATCGAACTTAA
*
54980699 CTAAATTAACCGAACTTAA
1 -T-AATTAATCGAACTTAA
54980718 TAATTAAT
1 TAATTAAT
54980726 AATACAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.32
18 11 0.50
19 4 0.18
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.35
Consensus pattern (17 bp):
TAATTAATCGAACTTAA
Found at i:54985281 original size:33 final size:33
Alignment explanation
Indices: 54985235--54985382 Score: 93
Period size: 33 Copynumber: 4.4 Consensus size: 33
54985225 ATTGCCATGG
*
54985235 CCAACCATGGTCTTACATTCGTAGTGCCATAAC
1 CCAACTATGGTCTTACATTCGTAGTGCCATAAC
** *
54985268 CCAGTTATGGTCTTATCA-TCAG-AATGCCATAAC
1 CCAACTATGGTCTTA-CATTC-GTAGTGCCATAAC
* * * * * **
54985301 CCAACTATGATCTTACTTATAGATATTGCCACAGT
1 CCAACTATGGTCTTACAT-TCG-TAGTGCCATAAC
* * **
54985336 CCAACCATGGTCTTACGTTCAAAGTGCCATAAC
1 CCAACTATGGTCTTACATTCGTAGTGCCATAAC
**
54985369 CCAGTTATGGTCTT
1 CCAACTATGGTCTT
54985383 TTCATTAAAA
Statistics
Matches: 83, Mismatches: 26, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
32 1 0.01
33 55 0.66
34 5 0.06
35 22 0.27
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (33 bp):
CCAACTATGGTCTTACATTCGTAGTGCCATAAC
Found at i:54985342 original size:101 final size:101
Alignment explanation
Indices: 54985235--54985451 Score: 299
Period size: 101 Copynumber: 2.1 Consensus size: 101
54985225 ATTGCCATGG
** *
54985235 CCAACCATGGTCTTACATTCGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAA
1 CCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAA
* * * *
54985300 CCCAACTATGATCTTACTTATAGATATTGCCACAGT
66 CCCAACTATGATATTACATATAAACATTGCCACAGT
* * * *
54985336 CCAACCATGGTCTTACGTTCAAAGTGCCATAACCCAGTTATGGTCTTTTCATTAAAATGCCATAG
1 CCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAA
* * **
54985401 CCCAGCTATGGTATTACATATAAACATTGCCATGGT
66 CCCAACTATGATATTACATATAAACATTGCCACAGT
54985437 CCAACCATGGTCTTA
1 CCAACCATGGTCTTA
54985452 TCCGTCAATT
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (101 bp):
CCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAA
CCCAACTATGATATTACATATAAACATTGCCACAGT
Found at i:54993534 original size:28 final size:29
Alignment explanation
Indices: 54993467--54993567 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
54993457 ATAGTGAATC
*
54993467 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
54993496 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
54993524 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
54993554 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54993568 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:55001444 original size:28 final size:29
Alignment explanation
Indices: 55001377--55001477 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
55001367 ATAGTGAATC
*
55001377 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
55001406 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
55001434 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
55001464 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55001478 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:55008331 original size:12 final size:12
Alignment explanation
Indices: 55008309--55008335 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55008299 TTAGACACAA
55008309 GCGAAGACACGG
1 GCGAAGACACGG
55008321 GCGAAGACACGG
1 GCGAAGACACGG
55008333 GCG
1 GCG
55008336 TGTCTAGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.26, G:0.44, T:0.00
Consensus pattern (12 bp):
GCGAAGACACGG
Found at i:55008365 original size:28 final size:29
Alignment explanation
Indices: 55008325--55008380 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
55008315 ACACGGGCGA
*
55008325 AGACACGGGCGTGT-CTAGGCAGTGTGAG
1 AGACACGAGCGTGTGCTAGGCAGTGTGAG
* *
55008353 AGACACGAGCGTGTGCTTGGCCGTGTGA
1 AGACACGAGCGTGTGCTAGGCAGTGTGA
55008381 AAACCCCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.20, C:0.20, G:0.41, T:0.20
Consensus pattern (29 bp):
AGACACGAGCGTGTGCTAGGCAGTGTGAG
Found at i:55017632 original size:14 final size:14
Alignment explanation
Indices: 55017601--55017641 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
55017591 TAAGTTCTTC
55017601 AAATT-ATTAA-TT
1 AAATTAATTAATTT
55017613 -AATTAATTAATTT
1 AAATTAATTAATTT
*
55017626 AAATTAAATAATTT
1 AAATTAATTAATTT
55017640 AA
1 AA
55017642 GTTTAAAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 4 0.16
12 5 0.20
13 2 0.08
14 14 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AAATTAATTAATTT
Found at i:55017780 original size:9 final size:9
Alignment explanation
Indices: 55017765--55017816 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
55017755 TTGGGTTAAG
55017765 AAATTAATT
1 AAATTAATT
* *
55017774 TAATTAA-G
1 AAATTAATT
55017782 AAATTAATT
1 AAATTAATT
* *
55017791 TAGTTAATT
1 AAATTAATT
*
55017800 AAATTGATT
1 AAATTAATT
55017809 AAATTAAT
1 AAATTAAT
55017817 ATTTTGGGAA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (9 bp):
AAATTAATT
Found at i:55017780 original size:17 final size:17
Alignment explanation
Indices: 55017760--55017797 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
55017750 TAGAATTGGG
55017760 TTAAGAAATTAATTTAA
1 TTAAGAAATTAATTTAA
*
55017777 TTAAGAAATTAATTTAG
1 TTAAGAAATTAATTTAA
55017794 TTAA
1 TTAA
55017798 TTAAATTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (17 bp):
TTAAGAAATTAATTTAA
Found at i:55019207 original size:26 final size:27
Alignment explanation
Indices: 55019156--55019209 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
55019146 ATCATTTAGA
55019156 AGACTTAGAAATTTTTTTCAAGGAAAC
1 AGACTTAGAAATTTTTTTCAAGGAAAC
* *
55019183 AGACTTCGAAATTTTTTTCAAGAAAAC
1 AGACTTAGAAATTTTTTTCAAGGAAAC
55019210 CCTGTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (27 bp):
AGACTTAGAAATTTTTTTCAAGGAAAC
Found at i:55021140 original size:24 final size:24
Alignment explanation
Indices: 55021113--55021185 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
55021103 ATTCAAGCCG
*
55021113 GCACACATAGTGCCATTCGACTTC
1 GCACACATAGTGCCATTCGACTCC
* *
55021137 GCACACATAGTGCCATTCAAATCC
1 GCACACATAGTGCCATTCGACTCC
*
55021161 GCACACTTAGTGCCAATATCGACTC
1 GCACACATAGTGCC-AT-TCGACTC
55021186 ATATGATAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 34 0.83
25 2 0.05
26 5 0.12
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.23
Consensus pattern (24 bp):
GCACACATAGTGCCATTCGACTCC
Found at i:55028889 original size:24 final size:24
Alignment explanation
Indices: 55028862--55028934 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
55028852 ATTCAAGCCG
*
55028862 GCACACATAGTGCCATTCGACTTC
1 GCACACATAGTGCCATTCGACTCC
* *
55028886 GCACACATAGTGCCATTCAAATCC
1 GCACACATAGTGCCATTCGACTCC
*
55028910 GCACACTTAGTGCCAATATCGACTC
1 GCACACATAGTGCC-AT-TCGACTC
55028935 ATATGATAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 34 0.83
25 2 0.05
26 5 0.12
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.23
Consensus pattern (24 bp):
GCACACATAGTGCCATTCGACTCC
Found at i:55039476 original size:33 final size:33
Alignment explanation
Indices: 55039405--55039664 Score: 114
Period size: 33 Copynumber: 7.8 Consensus size: 33
55039395 CATTTTCCTT
* ** *
55039405 GTGCCATAGTCCAAATATGGTCTTATACATGCAT-
1 GTGCCATAGCCCAACCATGGTC-T-TACATTCATA
* *
55039439 -TGCCATGGCCCAACCATGGTCTTACATTCGTA
1 GTGCCATAGCCCAACCATGGTCTTACATTCATA
* ***
55039471 GTGCCATAACCCAGTTATGGTCTTATCA-TCATA
1 GTGCCATAGCCCAACCATGGTCTTA-CATTCATA
* * * **
55039504 ATGCCATAGCCCAACTATGATCTTACTTATAGATA
1 GTGCCATAGCCCAACCATGGTCTTAC--ATTCATA
* * * *
55039539 TTGCCATAGTCCAACCATGGTCTTACGTTCAAA
1 GTGCCATAGCCCAACCATGGTCTTACATTCATA
* *** * *
55039572 GTGCCATAACCCAGTTATGGTCTTTTCATT-AAA
1 GTGCCATAGCCCAACCATGGTC-TTACATTCATA
* * * * * *
55039605 ATGCCATAGCCCAGCTATGGTATTACATATAAACA
1 GTGCCATAGCCCAACCATGGTCTTACAT-T-CATA
* * *
55039640 TTGCCATGGTCCAACCATGGTCTTA
1 GTGCCATAGCCCAACCATGGTCTTA
55039665 TTCGTCAATT
Statistics
Matches: 169, Mismatches: 47, Indels: 19
0.72 0.20 0.08
Matches are distributed among these distances:
31 7 0.04
32 7 0.04
33 101 0.60
34 8 0.05
35 46 0.27
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (33 bp):
GTGCCATAGCCCAACCATGGTCTTACATTCATA
Found at i:55039553 original size:101 final size:101
Alignment explanation
Indices: 55039436--55039664 Score: 332
Period size: 101 Copynumber: 2.3 Consensus size: 101
55039426 CTTATACATG
* **
55039436 CATTGCCATGGCCCAACCATGGTCTTACATTCGTAGTGCCATAACCCAGTTATGGTCTTATCATC
1 CATTGCCATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATC
* * * *
55039501 ATAATGCCATAGCCCAACTATGATCTTACTTATAGA
66 AAAATGCCATAGCCCAACTATGATATTACATATAAA
* * * * *
55039537 TATTGCCATAGTCCAACCATGGTCTTACGTTCAAAGTGCCATAACCCAGTTATGGTCTTTTCATT
1 CATTGCCATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATC
* *
55039602 AAAATGCCATAGCCCAGCTATGGTATTACATATAAA
66 AAAATGCCATAGCCCAACTATGATATTACATATAAA
55039638 CATTGCCATGGTCCAACCATGGTCTTA
1 CATTGCCATGGTCCAACCATGGTCTTA
55039665 TTCGTCAATT
Statistics
Matches: 112, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 112 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (101 bp):
CATTGCCATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATC
AAAATGCCATAGCCCAACTATGATATTACATATAAA
Found at i:55051484 original size:12 final size:12
Alignment explanation
Indices: 55051467--55051501 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
55051457 CTGGGTTTTT
55051467 AGACACGGGCGA
1 AGACACGGGCGA
*
55051479 AGACACGGGCAA
1 AGACACGGGCGA
55051491 AGACACGGGCG
1 AGACACGGGCG
55051502 TGTCTAGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.34, C:0.26, G:0.40, T:0.00
Consensus pattern (12 bp):
AGACACGGGCGA
Found at i:55059049 original size:29 final size:29
Alignment explanation
Indices: 55058990--55059088 Score: 159
Period size: 28 Copynumber: 3.5 Consensus size: 29
55058980 ACAGTAAGTC
55058990 CGCACACTTAGTGCT-TA-ATATTCAAACT
1 CGCACACTTAGTGCTATACA-ATTCAAACT
*
55059018 CGCACACTTAGTACTATACAATTCAAACT
1 CGCACACTTAGTGCTATACAATTCAAACT
55059047 CGCACACTTAGTGCTATACAATT-AAACT
1 CGCACACTTAGTGCTATACAATTCAAACT
55059075 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55059089 CAATCTCATT
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
28 33 0.49
29 33 0.49
30 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCTATACAATTCAAACT
Found at i:55060209 original size:17 final size:18
Alignment explanation
Indices: 55060172--55060209 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
55060162 AACTTTTTTT
55060172 TTCCTTTGTTTTCATCATA
1 TTCCTTTGTTTTCAT-ATA
*
55060191 TTCCTTTTTTTTCAT-TA
1 TTCCTTTGTTTTCATATA
55060208 TT
1 TT
55060210 TTATTCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.13, C:0.18, G:0.03, T:0.66
Consensus pattern (18 bp):
TTCCTTTGTTTTCATATA
Found at i:55066825 original size:29 final size:29
Alignment explanation
Indices: 55066764--55066862 Score: 168
Period size: 28 Copynumber: 3.5 Consensus size: 29
55066754 ACAGTAAGTC
55066764 CGCACACTTAGTGCT-TA-ATATTCAAACT
1 CGCACACTTAGTGCTATACA-ATTCAAACT
55066792 CGCACACTTAGTGCTATACAATTCAAACT
1 CGCACACTTAGTGCTATACAATTCAAACT
55066821 CGCACACTTAGTGCTATACAATT-AAACT
1 CGCACACTTAGTGCTATACAATTCAAACT
55066849 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55066863 CAATCTCATT
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
28 34 0.49
29 34 0.49
30 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCTATACAATTCAAACT
Found at i:55069662 original size:9 final size:9
Alignment explanation
Indices: 55069647--55069698 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
55069637 TTGGGTTAAG
55069647 AAATTAATT
1 AAATTAATT
* *
55069656 TAATTAA-G
1 AAATTAATT
55069664 AAATTAATT
1 AAATTAATT
* *
55069673 TAGTTAATT
1 AAATTAATT
*
55069682 AAATTGATT
1 AAATTAATT
55069691 AAATTAAT
1 AAATTAAT
55069699 ATTTTGGGAA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (9 bp):
AAATTAATT
Found at i:55069662 original size:17 final size:17
Alignment explanation
Indices: 55069642--55069679 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
55069632 TAGAATTGGG
55069642 TTAAGAAATTAATTTAA
1 TTAAGAAATTAATTTAA
*
55069659 TTAAGAAATTAATTTAG
1 TTAAGAAATTAATTTAA
55069676 TTAA
1 TTAA
55069680 TTAAATTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (17 bp):
TTAAGAAATTAATTTAA
Found at i:55071079 original size:27 final size:27
Alignment explanation
Indices: 55071039--55071090 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
55071029 CATTTAAAAA
*
55071039 ACTTAGAAAATTTTTTCAAGGAAACAG
1 ACTTAGAAAATTTTTTCAAGAAAACAG
*
55071066 ACTTAGAAATTTTTTTCAAGAAAAC
1 ACTTAGAAAATTTTTTCAAGAAAAC
55071091 CCTGTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (27 bp):
ACTTAGAAAATTTTTTCAAGAAAACAG
Found at i:55074369 original size:29 final size:29
Alignment explanation
Indices: 55074329--55074388 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
55074319 CCTCCTCGGT
*
55074329 TTTTTTTTTTAATTTTGAT-AGGGTTAGGG
1 TTTTTTTTTTAATTTTG-TGAGGGTTAAGG
55074358 TTTTTTTTTTAATTTTGTGAGGGTTAAGG
1 TTTTTTTTTTAATTTTGTGAGGGTTAAGG
55074387 TT
1 TT
55074389 AAGGCTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (29 bp):
TTTTTTTTTTAATTTTGTGAGGGTTAAGG
Done.