Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008025.1 Hibiscus syriacus cultivar Beakdansim tig00110500_pilon, whole genome shotgun sequence
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: 2744542
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 12
Found at i:2058718 original size:24 final size:24
Alignment explanation
Indices: 2058684--2058737 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2058674 CTGAAACATC
2058684 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2058708 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2058732 ATCAAA
1 ATCAAA
2058738 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2058751 original size:24 final size:24
Alignment explanation
Indices: 2058684--2058751 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2058674 CTGAAACATC
* * *
2058684 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2058708 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2058732 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2058752 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2059582 original size:20 final size:20
Alignment explanation
Indices: 2059558--2059726 Score: 110
Period size: 20 Copynumber: 8.3 Consensus size: 20
2059548 AAATTCAGTG
* *
2059558 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
2059578 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
*
2059598 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
* * *
2059618 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
* * *
2059638 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
* * * *
2059658 TTGCAAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
* *
2059678 TTGCGATAGTCGGAAAAATCGAA
1 TTGCGATAGTC---AGAATCGCA
* *
2059701 ATGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
2059721 TTGCGA
1 TTGCGA
2059727 ATCTGGAAAC
Statistics
Matches: 128, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 110 0.86
21 1 0.01
23 16 0.12
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:2059637 original size:40 final size:40
Alignment explanation
Indices: 2059558--2059688 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 40
2059548 AAATTCAGTG
* * * * * *
2059558 TTGCGACAGTCAGAATCGCGTTGCGATAGT-CAGAATCGCA
1 TTGCGATAGTCATAATCGCATTGCGAT-TTACATATTCGCA
2059598 TTGCGATAGTCATAATCGCATTGCGATTTACATATTCGCA
1 TTGCGATAGTCATAATCGCATTGCGATTTACATATTCGCA
* * *
2059638 TTGCGAT-TTACATATTCGCATTGCAATTTACATATTCGCA
1 TTGCGATAGT-CATAATCGCATTGCGATTTACATATTCGCA
2059678 TTGCGATAGTC
1 TTGCGATAGTC
2059689 GGAAAAATCG
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.03
40 75 0.96
41 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (40 bp):
TTGCGATAGTCATAATCGCATTGCGATTTACATATTCGCA
Found at i:2060847 original size:30 final size:27
Alignment explanation
Indices: 2060798--2060853 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
2060788 TAATTCTTTC
*
2060798 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATTTATATATATA-TTATTA
2060826 TTTTCATAATATTTATATATATATTATT
1 TTTTCA-AA-ATTTATATATATATTATT
2060854 TTATTAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 7 0.28
30 12 0.48
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATTTATATATATATTATTA
Found at i:2060861 original size:26 final size:27
Alignment explanation
Indices: 2060798--2060855 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
2060788 TAATTCTTTC
* *
2060798 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCATAATATTTATATATAC-TATTA
2060826 TTTTCATAATATTTATATATA-TATTA
1 TTTTCATAATATTTATATATACTATTA
2060852 TTTT
1 TTTT
2060856 ATTAATGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 9 0.32
28 19 0.68
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTTCATAATATTTATATATACTATTA
Found at i:2073351 original size:124 final size:124
Alignment explanation
Indices: 2073114--2074034 Score: 1512
Period size: 124 Copynumber: 7.5 Consensus size: 124
2073104 CATTCGATGG
* * * *
2073114 ATCAACATTTCC-GGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
2073178 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCATAGAAGGAGATAGATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
2073237 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
2073302 AATAAGAAGAGCTTGTTCAACCTTTTGCATAACTCCATCACAAAAGGAGATAGATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
* * *
2073361 ATCAACTTTTCTAGAAAATGTTTATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
2073426 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
2073485 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
2073550 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTTTATCACAGAAAGAGATAGATCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
2073609 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
2073674 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
2073733 ATCAACTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 ATCAACTTTTCCAG-AAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
*
2073798 TAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
65 TAATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
* * *
2073858 ATCAACTTTTCCAGAGAAAGGTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * * * * *
2073922 AACGAGAAGAACTTGTTCAACCTTTTGTATGA-TCTATCACAGAAGAAGATAGATTAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
** * *
2073980 ATCAACATTTT-CAGAAGTA-TTTATAATGAGAAGAACTCATCTGAAGAA-GAAGAAG
1 ATCAAC-TTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAG
2074035 TAGAACTTGT
Statistics
Matches: 757, Mismatches: 38, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
121 34 0.04
122 34 0.04
123 59 0.08
124 508 0.67
125 122 0.16
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (124 bp):
ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
Found at i:2074284 original size:3 final size:3
Alignment explanation
Indices: 2074264--2074303 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
2074254 TAATTTTAAA
2074264 TAT TAT T-T TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TA
2074304 AAAATTTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 3 0.09
3 30 0.88
4 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2075700 original size:4 final size:4
Alignment explanation
Indices: 2075693--2075726 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2075683 TAATAAATAA
2075693 TATT TATT TATT TATT TATT TATT TATT T-TT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT
2075727 AAATTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:2076602 original size:77 final size:78
Alignment explanation
Indices: 2076516--2076675 Score: 187
Period size: 77 Copynumber: 2.1 Consensus size: 78
2076506 AGAAATACGA
* ** * * * * ** *
2076516 TTGCACCCAATAATGTTGTGGTTCACTAAGAAATATGTTGTGATATGTAATGTTAATA-TTTTTA
1 TTGCACCCAAGAATGTCATGATTCACTAAGAAATAGGTTGCGATATGAAAACTTAAAATTTTTTA
*
2076580 TTAATAAAATAGG
66 ATAATAAAATAGG
* *
2076593 TTGCGCCCAAGAATGTCATGATTCACTAATAAATAGGTTGCGATATGAAAACTTAAAATTTTTTA
1 TTGCACCCAAGAATGTCATGATTCACTAAGAAATAGGTTGCGATATGAAAACTTAAAATTTTTTA
*
2076658 ATAATAAAATGGG
66 ATAATAAAATAGG
2076671 TTGCA
1 TTGCA
2076676 ACTAAAATTT
Statistics
Matches: 67, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
77 46 0.69
78 21 0.31
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (78 bp):
TTGCACCCAAGAATGTCATGATTCACTAAGAAATAGGTTGCGATATGAAAACTTAAAATTTTTTA
ATAATAAAATAGG
Found at i:2078638 original size:2 final size:2
Alignment explanation
Indices: 2078631--2078659 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2078621 AGATTGATTT
2078631 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
2078660 TCTGGTATTT
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:2080875 original size:17 final size:17
Alignment explanation
Indices: 2080834--2080905 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
2080824 ATTCATGCAT
2080834 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
2080851 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
2080869 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
*
2080886 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
2080903 CTA
1 CTA
2080906 ACTCTTAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
17 34 0.72
18 13 0.28
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:2086201 original size:44 final size:44
Alignment explanation
Indices: 2086153--2086281 Score: 183
Period size: 43 Copynumber: 3.0 Consensus size: 44
2086143 GTTTTTTAAC
2086153 AAAAAATGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
1 AAAAAATGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
* *
2086197 -AAAAACGCCGCAATAGGTGTTGATATTTAGTGGCGTTTGTT-AG
1 AAAAAATGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TTCAG
* *
2086240 AAAAAATGCCGTAATAGGT-TATGATGTTTAGCGGCGTTTTTC
1 AAAAAATGCCGCAATAGGTGT-TGATATTTAGCGGCGTTTTTC
2086282 TCTAAAACGT
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
43 41 0.55
44 34 0.45
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (44 bp):
AAAAAATGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
Found at i:2086207 original size:43 final size:43
Alignment explanation
Indices: 2086154--2086317 Score: 170
Period size: 43 Copynumber: 3.8 Consensus size: 43
2086144 TTTTTTAACA
*
2086154 AAAAATGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
*
2086197 AAAAACGCCGCAATAGGTGTTGATATTTAGTGGCGTTTGTT-AG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TTCAG
* * * **
2086240 AAAAAATGCCGTAATAGGT-TATGATGTTTAGCGGCGTTTTTCTC
1 -AAAAACGCCGCAATAGGTGT-TGATATTTAGCGGCGTTTTTCAG
* * * * * *
2086284 TAAAACGTCGCAGTAGTTATTGATGTTTAGCGGC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGC
2086318 CGCAGTAGGT
Statistics
Matches: 102, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
43 67 0.66
44 35 0.34
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
Found at i:2086307 original size:87 final size:87
Alignment explanation
Indices: 2086153--2086313 Score: 216
Period size: 87 Copynumber: 1.9 Consensus size: 87
2086143 GTTTTTTAAC
* *
2086153 AAAAAATGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAGAAAAACGCCGCAATAGGTGTT
1 AAAAAATGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCACAAAAACGCCGCAATAGGTATT
2086218 GATATTTAGTGGCGTTTGTTAG
66 GATATTTAGTGGCGTTTGTTAG
* * * * * * *
2086240 AAAAAATGCCGTAATAGGT-TATGATGTTTAGCGGCGTTTTTCTCTAAAACGTCGCAGTAGTTAT
1 AAAAAATGCCGCAATAGGTGT-TGATATTTAGCGGCGTTTTTCACAAAAACGCCGCAATAGGTAT
*
2086304 TGATGTTTAG
65 TGATATTTAG
2086314 CGGCCGCAGT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
86 1 0.02
87 62 0.98
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (87 bp):
AAAAAATGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCACAAAAACGCCGCAATAGGTATT
GATATTTAGTGGCGTTTGTTAG
Found at i:2086861 original size:21 final size:21
Alignment explanation
Indices: 2086837--2086886 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2086827 GCTTCTTTCT
*
2086837 CTGCTTCCGCTACTGCTCTGG
1 CTGCTTCCGCTACTGCTCTCG
* * *
2086858 CTGCTTCTGCTGCTGCTCTCT
1 CTGCTTCCGCTACTGCTCTCG
2086879 CTGCTTCC
1 CTGCTTCC
2086887 CTTGCTTCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.40, G:0.20, T:0.38
Consensus pattern (21 bp):
CTGCTTCCGCTACTGCTCTCG
Found at i:2086892 original size:21 final size:20
Alignment explanation
Indices: 2086805--2086888 Score: 60
Period size: 21 Copynumber: 4.0 Consensus size: 20
2086795 GTTGATATGA
* * *
2086805 TGCTTCTCTCTGTGCTGCCAC
1 TGCTGCTCTCTCTGCTTCC-C
* *
2086826 TGCTTCTTTCTCTGCTTCCGC
1 TGCTGCTCTCTCTGCTTCC-C
* ** *
2086847 TACTGCTCTGGCTGCTTCTGC
1 TGCTGCTCTCTCTGCTTC-CC
2086868 TGCTGCTCTCTCTGCTTCCC
1 TGCTGCTCTCTCTGCTTCCC
2086888 T
1 T
2086889 TGCTTCATTT
Statistics
Matches: 48, Mismatches: 14, Indels: 3
0.74 0.22 0.05
Matches are distributed among these distances:
20 2 0.04
21 46 0.96
ACGTcount: A:0.02, C:0.38, G:0.18, T:0.42
Consensus pattern (20 bp):
TGCTGCTCTCTCTGCTTCCC
Found at i:2094786 original size:18 final size:18
Alignment explanation
Indices: 2094735--2094787 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
2094725 TGCTGGTGGT
2094735 GGTTGCGCTGGTGGA-AA
1 GGTTGCGCTGGTGGAGAA
* * *
2094752 GCTTGCACTGCTGGAGAA
1 GGTTGCGCTGGTGGAGAA
*
2094770 GGTTGCGCTGGTAGAGAA
1 GGTTGCGCTGGTGGAGAA
2094788 TGTTAGGAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.23
Consensus pattern (18 bp):
GGTTGCGCTGGTGGAGAA
Found at i:2095884 original size:41 final size:41
Alignment explanation
Indices: 2095827--2096020 Score: 225
Period size: 41 Copynumber: 4.8 Consensus size: 41
2095817 AAAAAAAATA
2095827 CCACTATTGATT-ACACTATT-CTGGCGTTTGT-TAAAAAACG
1 CCACTATTGATTAACACTATTGC-GGCGTTTGTCT-AAAAACG
* * *
2095867 CCATTATTAATTAACACTATTGCGGCGTTTGTCTAAAAACA
1 CCACTATTGATTAACACTATTGCGGCGTTTGTCTAAAAACG
* ** * *
2095908 CCACTATTGATTAAAAGGATTGCGGCGTTTTTCTAAAAACT
1 CCACTATTGATTAACACTATTGCGGCGTTTGTCTAAAAACG
* *
2095949 CCATTATTGATTAACACTATTGCGGTGTTTGTCTAAAAACG
1 CCACTATTGATTAACACTATTGCGGCGTTTGTCTAAAAACG
* *
2095990 CCACTATAT-ATTATCACTATTGCGGCTTTTG
1 CCACTAT-TGATTAACACTATTGCGGCGTTTG
2096021 AGGAATAAAC
Statistics
Matches: 129, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
40 10 0.08
41 116 0.90
42 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (41 bp):
CCACTATTGATTAACACTATTGCGGCGTTTGTCTAAAAACG
Found at i:2096162 original size:83 final size:83
Alignment explanation
Indices: 2096049--2096270 Score: 309
Period size: 83 Copynumber: 2.7 Consensus size: 83
2096039 ATGTGTAATA
* * * * *
2096049 TATTACGGTGTTTATGGTATAAACGCCGCTAATTTACCACTCTATTGCGGCATTTTGGCTCAATC
1 TATTATGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTCTATTGCGGCATTTTAGCTAAATC
* *
2096114 GCTGCAAAATTTATACTC
66 CCCGCAAAATTTATACTC
* * * *
2096132 TATTATGGCGTTTGTGGTATAAACGTCGCTAATTTACTATTCTATTGCGGCGTTTTAGCTAAATC
1 TATTATGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTCTATTGCGGCATTTTAGCTAAATC
*
2096197 CCCGTAAAATTTATACTC
66 CCCGCAAAATTTATACTC
* * *
2096215 TATTGTGGCTTTTGTGGTATAAACGCCGCTAATTTACCACCCTATTGCGGCATTTT
1 TATTATGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTCTATTGCGGCATTTT
2096271 TTATAAAAAC
Statistics
Matches: 120, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 120 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (83 bp):
TATTATGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTCTATTGCGGCATTTTAGCTAAATC
CCCGCAAAATTTATACTC
Found at i:2096261 original size:42 final size:43
Alignment explanation
Indices: 2096063--2096270 Score: 155
Period size: 41 Copynumber: 5.0 Consensus size: 43
2096053 ACGGTGTTTA
*
2096063 TGGTATAAACGCCGCTAATTTACCACTCTATTGCGGCATTTTG
1 TGGTATAAACGCCGCTAATTTACTACTCTATTGCGGCATTTTG
* * * * * ** *
2096106 -GCT-CAATCGCTGCAAAATTTA-TACTCTATTATGGC-GTTTG
1 TGGTATAAACGCCGC-TAATTTACTACTCTATTGCGGCATTTTG
* * *
2096146 TGGTATAAACGTCGCTAATTTACTATTCTATTGCGGCGTTTT-
1 TGGTATAAACGCCGCTAATTTACTACTCTATTGCGGCATTTTG
* * * * *
2096188 AGCTA-AATCCCCG-TAAAATTTA-TACTCTATTGTGGC-TTTTG
1 TGGTATAAACGCCGCT--AATTTACTACTCTATTGCGGCATTTTG
* *
2096229 TGGTATAAACGCCGCTAATTTACCACCCTATTGCGGCATTTT
1 TGGTATAAACGCCGCTAATTTACTACTCTATTGCGGCATTTT
2096271 TTATAAAAAC
Statistics
Matches: 120, Mismatches: 33, Indels: 24
0.68 0.19 0.14
Matches are distributed among these distances:
40 9 0.08
41 52 0.43
42 51 0.43
43 8 0.07
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (43 bp):
TGGTATAAACGCCGCTAATTTACTACTCTATTGCGGCATTTTG
Found at i:2103113 original size:3 final size:3
Alignment explanation
Indices: 2103105--2103168 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
2103095 CTTTTAATAC
2103105 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2103153 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
2103169 ATGTTACATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2116326 original size:7 final size:6
Alignment explanation
Indices: 2116306--2116388 Score: 52
Period size: 6 Copynumber: 14.7 Consensus size: 6
2116296 ATTTTGCCTG
* * *
2116306 AAAAAT GAAAA- AAAATT AAAAAT -AAAAT GAAAAAT -AAAAG AAAAA-
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT AAAAAT
* * * *
2116351 AATAAG AAAAAT AAGAA- AAAAAG AAAAAT -AAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
2116389 TGAGGGTTCA
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
5 25 0.42
6 29 0.49
7 5 0.08
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:2116338 original size:12 final size:12
Alignment explanation
Indices: 2116307--2116364 Score: 63
Period size: 11 Copynumber: 5.2 Consensus size: 12
2116297 TTTTGCCTGA
2116307 AAAATG-AAAA-
1 AAAATGAAAAAT
*
2116317 AAAATTAAAAAT
1 AAAATGAAAAAT
2116329 AAAATGAAAAAT
1 AAAATGAAAAAT
2116341 AAAA-GAAAAA-
1 AAAATGAAAAAT
2116351 AATAA-GAAAAAT
1 AA-AATGAAAAAT
2116363 AA
1 AA
2116365 GAAAAAAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
10 7 0.17
11 18 0.43
12 17 0.40
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAATGAAAAAT
Found at i:2116344 original size:17 final size:18
Alignment explanation
Indices: 2116316--2116391 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 18
2116306 AAAAATGAAA
*
2116316 AAAAATTAAAAATAAAATG
1 AAAAA-TAAGAATAAAATG
*
2116335 AAAAATAAAAGAAAAAAATAAG
1 AAAAAT--AAGAATAAAAT--G
*
2116357 AAAAATAAGAA-AAAAAG
1 AAAAATAAGAATAAAATG
2116374 AAAAATAA-AATAAAATG
1 AAAAATAAGAATAAAATG
2116391 A
1 A
2116392 GGGTTCAAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
16 2 0.04
17 15 0.31
18 1 0.02
19 9 0.19
20 14 0.29
22 7 0.15
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAAATAAGAATAAAATG
Found at i:2116348 original size:11 final size:11
Alignment explanation
Indices: 2116323--2116388 Score: 66
Period size: 11 Copynumber: 5.9 Consensus size: 11
2116313 AAAAAAAATT
2116323 AAAAATAAAATG
1 AAAAATAAAA-G
2116335 AAAAATAAAAG
1 AAAAATAAAAG
2116346 AAAAA-AATAAG
1 AAAAATAA-AAG
2116357 AAAAATAAGAA-
1 AAAAATAA-AAG
*
2116368 AAAAAGAAAA-
1 AAAAATAAAAG
2116378 ATAAAATAAAA
1 A-AAAATAAAA
2116389 TGAGGGTTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
10 5 0.10
11 29 0.60
12 14 0.29
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.11
Consensus pattern (11 bp):
AAAAATAAAAG
Found at i:2116349 original size:22 final size:21
Alignment explanation
Indices: 2116306--2116388 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 21
2116296 ATTTTGCCTG
2116306 AAAAATGAAAAA-AAATTA-AAA
1 AAAAATGAAAAATAAA--AGAAA
2116327 ATAAAATGAAAAATAAAAGAAA
1 A-AAAATGAAAAATAAAAGAAA
*
2116349 AAAATAAGAAAAAT--AAG-AA
1 AAAA-ATGAAAAATAAAAGAAA
*
2116368 AAAAA-GAAAAATAAAATAAA
1 AAAAATGAAAAATAAAAGAAA
2116388 A
1 A
2116389 TGAGGGTTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
17 7 0.13
18 1 0.02
19 8 0.15
20 6 0.11
21 5 0.09
22 23 0.43
23 3 0.06
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (21 bp):
AAAAATGAAAAATAAAAGAAA
Found at i:2116362 original size:9 final size:9
Alignment explanation
Indices: 2116348--2116381 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
2116338 AATAAAAGAA
2116348 AAAAATAAG
1 AAAAATAAG
2116357 AAAAATAAG
1 AAAAATAAG
2116366 AAAAA-AAG
1 AAAAATAAG
2116374 AAAAATAA
1 AAAAATAA
2116382 AATAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (9 bp):
AAAAATAAG
Found at i:2117770 original size:110 final size:110
Alignment explanation
Indices: 2117548--2118000 Score: 710
Period size: 110 Copynumber: 4.1 Consensus size: 110
2117538 CAGGTTCGAT
* *
2117548 CCTGATTCAATGGATCAACTTTCCCAGATCTGATATTCCCCCAGAAA-AAGCAGAACAGATCCCT
1 CCTGATTCAATGGATCAACTTTCCCAGATCTGATATTCCCTCA-AAAGAAGCGGAACAGAT-CCT
*
2117612 CTCTTTTAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTAC
64 CTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTAC
*
2117659 CCTGATTCAATGGATCAACTTTCCCAGATCTGATATTCCCTCAAAAGAAGTGGAACAGATCCTCT
1 CCTGATTCAATGGATCAACTTTCCCAGATCTGATATTCCCTCAAAAGAAGCGGAACAGATCCTCT
*
2117724 CTTTCAAGATTTGATATTCACTGAGTGACAGCGGAACAAGTCTAC
66 CTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTAC
* *
2117769 CCTGATTCAATGGATCAATTTTCCCAGATCTGATATTCCCTCAGAAGAAGCGGAACAGATCCTCT
1 CCTGATTCAATGGATCAACTTTCCCAGATCTGATATTCCCTCAAAAGAAGCGGAACAGATCCTCT
* * * * *
2117834 CTTTGAAGATTTGATATTCCCTGAATGACATCAGAACAAGCCTAC
66 CTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTAC
* *
2117879 CCTGATTAAATGGATCAACTTTCCCAGATCTGATATTCCCTCAGAAGAAGCGGAACAGATCCATC
1 CCTGATTCAATGGATCAACTTTCCCAGATCTGATATTCCCTCAAAAGAAGCGGAACAGATCC-TC
* * **
2117944 TCTTTCAAGATTTGATATTCCATGAGTGATAATGGAACAAGTCTAC
65 TCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTAC
2117990 CCTGATTCAAT
1 CCTGATTCAAT
2118001 CTTCCCTGAA
Statistics
Matches: 315, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
110 212 0.67
111 103 0.33
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (110 bp):
CCTGATTCAATGGATCAACTTTCCCAGATCTGATATTCCCTCAAAAGAAGCGGAACAGATCCTCT
CTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTAC
Found at i:2117958 original size:221 final size:221
Alignment explanation
Indices: 2117548--2118000 Score: 739
Period size: 221 Copynumber: 2.0 Consensus size: 221
2117538 CAGGTTCGAT
2117548 CCTGATTCAATGGATCAACTTTCCCAGATCTGATATTCCCCCAGAAAAAGCAGAACAGATCCCTC
1 CCTGATTCAATGGATCAACTTTCCCAGATCTGATATTCCCCCAGAAAAAGCAGAACAGATCCCTC
* * * * *
2117613 TCTTTTAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAAC
66 TCTTTGAAGATTTGATATTCCCTGAATGACAGCAGAACAAGCCTACCCTGATTAAATGGATCAAC
*
2117678 TTTCCCAGATCTGATATTCCCTCAAAAGAAGTGGAACAGATCCTCTCTTTCAAGATTTGATATT-
131 TTTCCCAGATCTGATATTCCCTCAAAAGAAGCGGAACAGATCCTCTCTTTCAAGATTTGATATTC
*
2117742 CACTGAGTGACAGCGGAACAAGTCTAC
196 CA-TGAGTGACAACGGAACAAGTCTAC
* * * *
2117769 CCTGATTCAATGGATCAATTTTCCCAGATCTGATATTCCCTCAGAAGAAGCGGAACAGAT-CCTC
1 CCTGATTCAATGGATCAACTTTCCCAGATCTGATATTCCCCCAGAAAAAGCAGAACAGATCCCTC
*
2117833 TCTTTGAAGATTTGATATTCCCTGAATGACATCAGAACAAGCCTACCCTGATTAAATGGATCAAC
66 TCTTTGAAGATTTGATATTCCCTGAATGACAGCAGAACAAGCCTACCCTGATTAAATGGATCAAC
*
2117898 TTTCCCAGATCTGATATTCCCTCAGAAGAAGCGGAACAGATCCATCTCTTTCAAGATTTGATATT
131 TTTCCCAGATCTGATATTCCCTCAAAAGAAGCGGAACAGATCC-TCTCTTTCAAGATTTGATATT
* *
2117963 CCATGAGTGATAATGGAACAAGTCTAC
195 CCATGAGTGACAACGGAACAAGTCTAC
2117990 CCTGATTCAAT
1 CCTGATTCAAT
2118001 CTTCCCTGAA
Statistics
Matches: 215, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
220 104 0.48
221 109 0.51
222 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (221 bp):
CCTGATTCAATGGATCAACTTTCCCAGATCTGATATTCCCCCAGAAAAAGCAGAACAGATCCCTC
TCTTTGAAGATTTGATATTCCCTGAATGACAGCAGAACAAGCCTACCCTGATTAAATGGATCAAC
TTTCCCAGATCTGATATTCCCTCAAAAGAAGCGGAACAGATCCTCTCTTTCAAGATTTGATATTC
CATGAGTGACAACGGAACAAGTCTAC
Found at i:2118219 original size:3 final size:3
Alignment explanation
Indices: 2118211--2118238 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2118201 CTTTTAATAC
2118211 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2118239 ATGTTACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2119319 original size:2 final size:2
Alignment explanation
Indices: 2119312--2119390 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
2119302 TTTGTAATAG
2119312 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2119354 TA TA 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 TA TA T
2119391 CAAAATTATG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2119889 original size:2 final size:2
Alignment explanation
Indices: 2119882--2119956 Score: 70
Period size: 2 Copynumber: 39.5 Consensus size: 2
2119872 TTTAAGTGTT
* *
2119882 TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA T- TA T- TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2119922 CA TA T- TA TG TA -A TA TA TA TA TA T- TA TA GTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
2119957 GCATAACATG
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
1 5 0.08
2 52 0.88
3 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2120272 original size:2 final size:2
Alignment explanation
Indices: 2120265--2120314 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2120255 TGCATGGCTA
2120265 AT AT AT AT AT AT 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
2120307 AT AT AT AT
1 AT AT AT AT
2120315 GTTAATATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2122153 original size:16 final size:16
Alignment explanation
Indices: 2122132--2122170 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
2122122 TCGGCTGGTT
2122132 GATGTTTCTGTGTGTA
1 GATGTTTCTGTGTGTA
2122148 GATGTTTCTGTGTGTA
1 GATGTTTCTGTGTGTA
*
2122164 GCTGTTT
1 GATGTTT
2122171 TCATAACAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.10, C:0.08, G:0.31, T:0.51
Consensus pattern (16 bp):
GATGTTTCTGTGTGTA
Found at i:2124506 original size:60 final size:63
Alignment explanation
Indices: 2124362--2124506 Score: 183
Period size: 62 Copynumber: 2.4 Consensus size: 63
2124352 TAGTTTGAAA
* * * *
2124362 CATTTTATAACTTTTAATAGT-AAGGGGACTCAACAAAGCAACACATATGATAGTTGAGTGAC
1 CATTTTGTAACTTTTAATAGTCGAGGGGACTCAACAAAACAACACATATGATAGTTGAGGGAC
* *
2124424 CATTTTGTAACTTTTAATAGTCGA-GGGATTCAACAAAACAACACACTAT-A-A-TTGTGGGAC
1 CATTTTGTAACTTTTAATAGTCGAGGGGACTCAACAAAACAACACA-TATGATAGTTGAGGGAC
*
2124484 TATTTTGTAACTTTTAATAGTCG
1 CATTTTGTAACTTTTAATAGTCG
2124507 GATGACTCAA
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
60 29 0.39
61 1 0.01
62 40 0.54
63 4 0.05
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (63 bp):
CATTTTGTAACTTTTAATAGTCGAGGGGACTCAACAAAACAACACATATGATAGTTGAGGGAC
Found at i:2126753 original size:2 final size:2
Alignment explanation
Indices: 2126712--2126740 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2126702 AATTAACTTT
2126712 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
2126741 GCGTATGATA
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:2127282 original size:2 final size:2
Alignment explanation
Indices: 2127270--2127298 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2127260 TTATCTAACC
2127270 AT AT A- 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
2127299 TATTCTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2127675 original size:13 final size:13
Alignment explanation
Indices: 2127657--2127686 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2127647 GAGATTATGA
*
2127657 AAAATTGAAAGAT
1 AAAATTGAAAAAT
2127670 AAAATTGAAAAAT
1 AAAATTGAAAAAT
2127683 AAAA
1 AAAA
2127687 AATTGTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (13 bp):
AAAATTGAAAAAT
Found at i:2128166 original size:22 final size:22
Alignment explanation
Indices: 2128141--2128184 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2128131 TGGACATGGA
2128141 CTCCACATGTATGAGGTTTTTT
1 CTCCACATGTATGAGGTTTTTT
2128163 CTCCACATGTATGAGGTTTTTT
1 CTCCACATGTATGAGGTTTTTT
2128185 TTTGTCACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (22 bp):
CTCCACATGTATGAGGTTTTTT
Found at i:2129864 original size:28 final size:27
Alignment explanation
Indices: 2129828--2129882 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
2129818 TCAATTTAGT
2129828 CATACTTTT-AATAAATTAAAATAAATTA
1 CATACTTTTAAATAAA--AAAATAAATTA
* *
2129856 CATATTTTTAAATGAAAAAATAAATTA
1 CATACTTTTAAATAAAAAAATAAATTA
2129883 TTTTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.46
28 8 0.33
29 5 0.21
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (27 bp):
CATACTTTTAAATAAAAAAATAAATTA
Found at i:2129916 original size:22 final size:21
Alignment explanation
Indices: 2129891--2129950 Score: 57
Period size: 25 Copynumber: 2.6 Consensus size: 21
2129881 TATTTTTAAA
2129891 TTAAGTTAATACTAAAATATATT
1 TTAAGTTAATA-TAAAATATA-T
*
2129914 TAATAAGTTAATATAAAAATATTT
1 T--TAAGTTAATAT-AAAATATAT
*
2129938 TTAAATTAATATA
1 TTAAGTTAATATA
2129951 TAAAATTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 1 0.03
22 10 0.31
23 1 0.03
24 3 0.09
25 17 0.53
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (21 bp):
TTAAGTTAATATAAAATATAT
Found at i:2129925 original size:25 final size:23
Alignment explanation
Indices: 2129892--2129956 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 23
2129882 ATTTTTAAAT
2129892 TAAGTTAATACTAAAATATATTTAA
1 TAAGTTAATA-TAAAA-ATATTTAA
*
2129917 TAAGTTAATATAAAAATATTT-T
1 TAAGTTAATATAAAAATATTTAA
*
2129939 TAAATTAATATATAAAAT
1 TAAGTTAATATA-AAAAT
2129957 TATATTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.30
23 11 0.30
24 5 0.14
25 10 0.27
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.42
Consensus pattern (23 bp):
TAAGTTAATATAAAAATATTTAA
Found at i:2130342 original size:30 final size:29
Alignment explanation
Indices: 2130306--2130367 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
2130296 CTCGAAAAAT
2130306 CACCGGTAACCGA-TATATTTACCGATCTAA
1 CACCGGTAA--GATTATATTTACCGATCTAA
* *
2130336 CACCGGTTAGATTATATTTCCCGATCTAA
1 CACCGGTAAGATTATATTTACCGATCTAA
2130365 CAC
1 CAC
2130368 TCGTAGAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 19 0.66
30 8 0.28
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (29 bp):
CACCGGTAAGATTATATTTACCGATCTAA
Found at i:2130452 original size:49 final size:50
Alignment explanation
Indices: 2130395--2130504 Score: 136
Period size: 49 Copynumber: 2.2 Consensus size: 50
2130385 GCTCCTTGCC
**
2130395 CCGCGCTATATACTGATTTGGCGT-CACGTGGGGTATA-GCGCCCCCTG-T
1 CCGCGCTATATACTGACATGGCGTACACGT-GGGTATACGCGCCCCCTGAT
* *
2130443 ACCGCGCTATATGCTGACATGGCTTACACGTGGGTATAGCGCGCCCCCTGAT
1 -CCGCGCTATATACTGACATGGCGTACACGTGGGTATA-CGCGCCCCCTGAT
2130495 CCGCGCTATA
1 CCGCGCTATA
2130505 GTTGTTTATC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
49 27 0.51
50 5 0.09
51 20 0.38
52 1 0.02
ACGTcount: A:0.17, C:0.31, G:0.27, T:0.25
Consensus pattern (50 bp):
CCGCGCTATATACTGACATGGCGTACACGTGGGTATACGCGCCCCCTGAT
Found at i:2130636 original size:10 final size:10
Alignment explanation
Indices: 2130621--2130645 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2130611 ACACCATATT
2130621 CTCTCAAATA
1 CTCTCAAATA
2130631 CTCTCAAATA
1 CTCTCAAATA
2130641 CTCTC
1 CTCTC
2130646 TCTGTTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (10 bp):
CTCTCAAATA
Found at i:2130723 original size:17 final size:18
Alignment explanation
Indices: 2130687--2130727 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2130677 ATATTATGTA
*
2130687 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
2130705 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
2130722 TTTACT
1 TTTACT
2130728 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:2138303 original size:322 final size:322
Alignment explanation
Indices: 2137718--2138361 Score: 1216
Period size: 322 Copynumber: 2.0 Consensus size: 322
2137708 ACTCTGCAGG
2137718 CAATGTCAAAGGAACTCCCAATACTGATGTCGATAACTGCATAGGATCGATTCTTTAACCTGAAA
1 CAATGTCAAAGGAACTCCCAATACTGATGTCGATAACTGCATAGGATCGATTCTTTAACCTGAAA
* **
2137783 TGGTGAGTAACAGTGTAAACTTTGGGAAAGCTCAGTAATAAAGAACTACAAGATGACACTGCAGG
66 TGGTGAGCAACAGTGTAAACTTTGGGAAAGCTCAGTAATAAAGAACTACAAGATGACACTAAAGG
2137848 ACATGTAGACAAATGACAAAAGCATAAAACTTTTTTATTGATCCAGGCATATACAGGTTCTAGTG
131 ACATGTAGACAAATGACAAAAGCATAAAACTTTTTTATTGATCCAGGCATATACAGGTTCTAGTG
2137913 ATGAGTTGAGGTTCCACAAATATTTTTAAGGTAATGATACATGCATGATCATGACCAACTTTCTC
196 ATGAGTTGAGGTTCCACAAATATTTTTAAGGTAATGATACATGCATGATCATGACCAACTTTCTC
*
2137978 CATAACTTGATTATTCCATGGACGTTCTTCATTGCTACTTCTAAGGGAGTTGTTCCTTACTC
261 CATAACTTGATTATTCCATGGACGTTCTTCATTGCTACTTCTAAGGGAGTTCTTCCTTACTC
*
2138040 CAATGTCAAAGGAACTCCCAATACTGATGTTGATAACTGCATAGGATCGATTCTTTAACCTGAAA
1 CAATGTCAAAGGAACTCCCAATACTGATGTCGATAACTGCATAGGATCGATTCTTTAACCTGAAA
2138105 TGGTGAGCAACAGTGTAAACTTTGGGAAAGCTCAGTAATAAAGAACTACAAGATGACACTAAAGG
66 TGGTGAGCAACAGTGTAAACTTTGGGAAAGCTCAGTAATAAAGAACTACAAGATGACACTAAAGG
* *
2138170 ACATGTAGATAAATGACAAAAGGATAAAACTTTTTTATTGATCCAGGCATATACAGGTTCTAGTG
131 ACATGTAGACAAATGACAAAAGCATAAAACTTTTTTATTGATCCAGGCATATACAGGTTCTAGTG
2138235 ATGAGTTGAGGTTCCACAAATATTTTTAAGGTAATGATACATGCATGATCATGACCAACTTTCTC
196 ATGAGTTGAGGTTCCACAAATATTTTTAAGGTAATGATACATGCATGATCATGACCAACTTTCTC
*
2138300 CATAACTTGATTATTCCATGGTCGTTCTTCATTGCTACTTCTAAGGGAGTTCTTCCTTACTC
261 CATAACTTGATTATTCCATGGACGTTCTTCATTGCTACTTCTAAGGGAGTTCTTCCTTACTC
2138362 TATCTTATAT
Statistics
Matches: 314, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
322 314 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (322 bp):
CAATGTCAAAGGAACTCCCAATACTGATGTCGATAACTGCATAGGATCGATTCTTTAACCTGAAA
TGGTGAGCAACAGTGTAAACTTTGGGAAAGCTCAGTAATAAAGAACTACAAGATGACACTAAAGG
ACATGTAGACAAATGACAAAAGCATAAAACTTTTTTATTGATCCAGGCATATACAGGTTCTAGTG
ATGAGTTGAGGTTCCACAAATATTTTTAAGGTAATGATACATGCATGATCATGACCAACTTTCTC
CATAACTTGATTATTCCATGGACGTTCTTCATTGCTACTTCTAAGGGAGTTCTTCCTTACTC
Found at i:2139522 original size:19 final size:20
Alignment explanation
Indices: 2139498--2139548 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2139488 CGGCCAAGAG
*
2139498 CATGTATTTTCATT-AAAGT
1 CATGTATTTTCATTAAAAAT
2139517 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
*
2139537 CATGCATTTTCA
1 CATGTATTTTCA
2139549 AAGGGATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:2143475 original size:19 final size:20
Alignment explanation
Indices: 2143448--2143498 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2143438 CGGCTAAGAG
*
2143448 CATGTATTTTCATT-AAAGT
1 CATGTATTTTCATTAAAAAT
*
2143467 CATGCATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
2143487 CATGTATTTTCA
1 CATGTATTTTCA
2143499 AAGGGATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:2164982 original size:45 final size:46
Alignment explanation
Indices: 2164918--2165010 Score: 170
Period size: 45 Copynumber: 2.0 Consensus size: 46
2164908 TTGTTTAACA
2164918 AAAATTATCGTTAAAATAACATTGGTTACTA-TTTTTTTTCAGAAT
1 AAAATTATCGTTAAAATAACATTGGTTACTATTTTTTTTTCAGAAT
2164963 AAAATTATCGTTAAAATAACATTGGTTACTATTTTTTTTTTCAGAAT
1 AAAATTATCGTTAAAATAACATTGGTTACTA-TTTTTTTTTCAGAAT
2165010 A
1 A
2165011 TTGATTATGT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 31 0.67
47 15 0.33
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (46 bp):
AAAATTATCGTTAAAATAACATTGGTTACTATTTTTTTTTCAGAAT
Found at i:2171261 original size:13 final size:13
Alignment explanation
Indices: 2171228--2171262 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2171218 TGCTCGATCG
2171228 AAATAAAAAATAA
1 AAATAAAAAATAA
2171241 AACA-AAAAAATAA
1 AA-ATAAAAAATAA
2171254 AAATAAAAA
1 AAATAAAAA
2171263 TGTAATGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.05
13 18 0.90
14 1 0.05
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:2179412 original size:15 final size:14
Alignment explanation
Indices: 2179392--2179421 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2179382 GATCGAAATG
2179392 AAAAATAAAACAAAA
1 AAAAATAAAA-AAAA
2179407 AAAAATAAAAAAAA
1 AAAAATAAAAAAAA
2179421 A
1 A
2179422 TGTAATGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAAATAAAAAAAA
Found at i:2203579 original size:15 final size:15
Alignment explanation
Indices: 2203559--2203590 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2203549 AAATTCATTT
2203559 TTCTTTTAATTTTAA
1 TTCTTTTAATTTTAA
*
2203574 TTCTTTTATTTTTAA
1 TTCTTTTAATTTTAA
2203589 TT
1 TT
2203591 TTACCTTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (15 bp):
TTCTTTTAATTTTAA
Found at i:2205890 original size:4 final size:4
Alignment explanation
Indices: 2205881--2205988 Score: 51
Period size: 4 Copynumber: 28.8 Consensus size: 4
2205871 TTTTTCTTCT
* * *
2205881 TTTA TTTA TTTAA TATA TTCT- TTTA -TTA -TTA CTTA TTTT TTTA TTTCA
1 TTTA TTTA TTT-A TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A
*
2205929 TTTA -TTA -TTA -TTA TTT- TATT- TTTA TGTT- TTTG TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA T-TTA TTTA TTTA TTTA TTTA
2205973 -TT- TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTT
2205989 TTATCTAACA
Statistics
Matches: 85, Mismatches: 6, Indels: 26
0.73 0.05 0.22
Matches are distributed among these distances:
3 28 0.33
4 47 0.55
5 10 0.12
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:2205959 original size:14 final size:13
Alignment explanation
Indices: 2205896--2205992 Score: 72
Period size: 14 Copynumber: 7.2 Consensus size: 13
2205886 TTATTTAATA
*
2205896 TATTCTTTTATTAT
1 TATT-TTTTATTTT
* *
2205910 TACTTATT-TTTT
1 TATTTTTTATTTT
*
2205922 TATTTCATTTATTAT
1 TATTT--TTTATTTT
2205937 TATTATTTTATTTT
1 TATT-TTTTATTTT
* *
2205951 TATGTTTT-TGTT
1 TATTTTTTATTTT
2205963 TATTTATTTATTTT
1 TATTT-TTTATTTT
*
2205977 TATTTATTATTTT
1 TATTTTTTATTTT
2205990 TAT
1 TAT
2205993 CTAACATTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 13
0.72 0.13 0.14
Matches are distributed among these distances:
12 14 0.22
13 20 0.31
14 23 0.35
15 7 0.11
16 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:2205976 original size:18 final size:17
Alignment explanation
Indices: 2205918--2205988 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 17
2205908 ATTACTTATT
2205918 TTTTTATTTCATT-TATTA
1 TTTTTATTT-ATTAT-TTA
*
2205936 TTATTATTTTATT-TTTA
1 TTTTTA-TTTATTATTTA
*
2205953 TGTTTTTGTTTATTTATTTA
1 --TTTTTATTTA-TTATTTA
2205973 TTTTTATTTATTATTT
1 TTTTTATTTATTATTT
2205989 TTATCTAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
17 9 0.20
18 22 0.50
19 9 0.20
20 4 0.09
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTATTTATTATTTA
Found at i:2206757 original size:21 final size:21
Alignment explanation
Indices: 2206711--2206758 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2206701 GATTGGACGA
*
2206711 AGAGGAAAAAACAAAGAAGAT
1 AGAGGAAAAAACAAACAAGAT
* *
2206732 GGAGGAAAAAATCAAACAA-TT
1 AGAGGAAAAAA-CAAACAAGAT
2206753 AGAGGA
1 AGAGGA
2206759 CCAAATGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.60, C:0.06, G:0.25, T:0.08
Consensus pattern (21 bp):
AGAGGAAAAAACAAACAAGAT
Found at i:2209872 original size:85 final size:85
Alignment explanation
Indices: 2209721--2210469 Score: 851
Period size: 85 Copynumber: 8.8 Consensus size: 85
2209711 GAAATACTGG
* * * * *
2209721 CAGCGTAGCTCAAGGCGAGAAGAGATATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
*
2209786 TCAAAGGCATATCCAATTTA
66 TCAAAGGCATATCAAATTTA
* ** *
2209806 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAGTAAAGACCTTTGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
* * *
2209871 TCAAAGACACATCCAATTTA
66 TCAAAGGCATATCAAATTTA
* * * * * * * *
2209891 CAACATAGCTCAAGGTGAAAAGGGCTATCTATCAGCAATGACCTTCGAGTTCGATTACACTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
* * *
2209956 TCAAAGACACATGAAATTTA
66 TCAAAGGCATATCAAATTTA
*
2209976 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTGT-GAGTTTGATTACATTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCT-TCGAGTTCGATTACATTCAG
2210040 CTCAAAGGCATATCAAATTTA
65 CTCAAAGGCATATCAAATTTA
* * *
2210061 CAACATAACTCAAGGCGAGAAGGGTTATATGTCAACAAAAGACCTTCGAGTTCGATTACATTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACATTCAG
* * *
2210126 CTCAAAGGTATATCCAGTTTA
65 CTCAAAGGCATATCAAATTTA
* * * * *
2210147 CAGCATAGCTCAAGGCGAGAAGGGCTAGT-TGTCATCAAAGACCTTCAAGTTTGATTACACTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGTTA-TCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAG
2210211 CTCAAAGGCATATCAAATTTA
65 CTCAAAGGCATATCAAATTTA
* * * * *
2210232 CAGTATAACTCAAGGTGAGAAGTGTTATCTGTCACCAAAAGACCTTCGAGTTCGATTACATTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACATTCAG
*
2210297 CTCAAAGGAATATCAAATTTA
65 CTCAAAGGCATATCAAATTTA
* * * ** * * *
2210318 CTGCATAGCTCAAGGTGAGAATGACTATCTATCAACCAAGACCTACGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
* * *
2210383 TGAAGGGCATATCAAATTCA
66 TCAAAGGCATATCAAATTTA
* * ** ** * *
2210403 TAGCATAGCTTAAGTTGAGAA-AATCTATTTGTCAACAAA-AACTGTCGAGTTCGATT-CGATTC
1 CAGCATAGCTCAAGGCGAGAAGGGT-TATCTGTCAACAAAGACCT-TCGAGTTCGATTAC-ATTC
2210465 AGCTC
63 AGCTC
2210470 GACGACACAT
Statistics
Matches: 566, Mismatches: 89, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
84 6 0.01
85 413 0.73
86 146 0.26
87 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (85 bp):
CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
TCAAAGGCATATCAAATTTA
Found at i:2210188 original size:171 final size:169
Alignment explanation
Indices: 2209729--2210400 Score: 842
Period size: 171 Copynumber: 3.9 Consensus size: 169
2209719 GGCAGCGTAG
* * *
2209729 CTCAAGGCGAGAAGAGATATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGC
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGC
* * * **
2209794 ATATCCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAGTAAAGACCTTTGAGTTCG
66 ATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACC-TTGAGTTCG
* * * *
2209859 ATTACATTCAGCTCAAAGACACATCCAATTTACAACATAG
130 ATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAA
* * * * * * *
2209899 CTCAAGGTGAAAAGGGCTATCTATCAGCAATGACCTTCGAGTTCGATTACACTCAGCTCAAAGAC
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGC
* * * *
2209964 ACATGAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTGTGAGTTTG
66 ATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCT-TGAGTTCG
2210029 ATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAA
130 ATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAA
* *
2210069 CTCAAGGCGAGAAGGGTTATATGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGG
1 CTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG
* * * * *
2210134 TATATCCAGTTTACAGCATAGCTCAAGGCGAGAAGGGCTAGT-TGTCATCAAAGACCTTCAAGTT
65 CATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTA-TCTGTCAACAAAGACCTT-GAGTT
* * **
2210198 TGATTACACTCAGCTCAAAGGCATATCAAATTTACAGTATAA
128 CGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAA
* * * *
2210240 CTCAAGGTGAGAAGTGTTATCTGTCACCAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGG
1 CTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG
* * * * * * * *
2210305 AATATCAAATTTACTGCATAGCTCAAGGTGAGAATGACTATCTATCAACCAAGACCTACGAGTTC
65 CATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCT-TGAGTTC
* *
2210370 GATTACATTCAGCTGAAGGGCATATCAAATT
129 GATTACATTCAGCTCAAAGGCATATCAAATT
2210401 CATAGCATAG
Statistics
Matches: 436, Mismatches: 60, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
169 1 0.00
170 172 0.39
171 262 0.60
172 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (169 bp):
CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGC
ATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTGAGTTCGA
TTACATTCAGCTCAAAGGCATATCAAATTTACAACATAA
Found at i:2210410 original size:256 final size:255
Alignment explanation
Indices: 2209729--2210412 Score: 897
Period size: 256 Copynumber: 2.7 Consensus size: 255
2209719 GGCAGCGTAG
* *
2209729 CTCAAGGCGAGAAGAGATATCTGTCAACC-AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG
1 CTCAAGGCGAGAAGAGTTATCTGTC-ACCAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGG
* ** *
2209793 CATATCCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAGTAAAGACCTTTGAGTTC
65 CATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTC
* * * *
2209858 GATTACATTCAGCTCAAAGACACATCCAATTTACAACATAGCTCAAGGTGAAAAGGGCTATCTAT
130 GATTACATTCAGCTCAAAGGCATATCCAATTTACAGCATAGCTCAAGGCGAAAAGGGCTATCTAT
* * * *
2209923 CAGCAATGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACATGAAATTTACAGCATAG
195 CAGCAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGACACATCAAATTTACAGCATAA
* * *
2209984 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTGT-GAGTTTGATTACATTCAGCTCAAAGG
1 CTCAAGGCGAGAAGAGTTATCTGTCACCAAAGACCT-TCGAGTTCGATTACATTCAGCTCAAAGG
* *
2210048 CATATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATATGTCAACAAAAGACCTTCGAGTT
65 CATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTT
* * *
2210113 CGATTACATTCAGCTCAAAGGTATATCCAGTTTACAGCATAGCTCAAGGCGAGAAGGGCTAGT-T
129 CGATTACATTCAGCTCAAAGGCATATCCAATTTACAGCATAGCTCAAGGCGAAAAGGGCTA-TCT
* * * * * *
2210177 GTCATCAAAGACCTTCAAGTTTGATTACACTCAGCTCAAAGGCATATCAAATTTACAGTATAA
193 ATCAGCAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGACACATCAAATTTACAGCATAA
* *
2210240 CTCAAGGTGAGAAGTGTTATCTGTCACCAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGG
1 CTCAAGGCGAGAAGAGTTATCTGTCACC-AAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGG
* * * * * ** * * *
2210305 AATATCAAATTTACTGCATAGCTCAAGGTGAGAATGACTATCTATCAACCAAGACCTACGAGTTC
65 CATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTC
* * * * *
2210370 GATTACATTCAGCTGAAGGGCATATCAAATTCATAGCATAGCT
130 GATTACATTCAGCTCAAAGGCATATCCAATTTACAGCATAGCT
2210413 TAAGTTGAGA
Statistics
Matches: 372, Mismatches: 51, Indels: 11
0.86 0.12 0.03
Matches are distributed among these distances:
254 2 0.01
255 98 0.26
256 199 0.53
257 73 0.20
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (255 bp):
CTCAAGGCGAGAAGAGTTATCTGTCACCAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGC
ATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCG
ATTACATTCAGCTCAAAGGCATATCCAATTTACAGCATAGCTCAAGGCGAAAAGGGCTATCTATC
AGCAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGACACATCAAATTTACAGCATAA
Found at i:2210828 original size:3 final size:3
Alignment explanation
Indices: 2210816--2210892 Score: 70
Period size: 3 Copynumber: 26.3 Consensus size: 3
2210806 TTAAATTAAA
* * *
2210816 ATT A-T ATT ATT A-T ATT ATT ATT ATT ATT ATA ACT ATT A-T ATT ATA
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
2210861 ATAC ATT ATT ATT ATT AAT ATT ACT ATT ATT A
1 AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2210893 ATGTTACATA
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
2 6 0.10
3 51 0.86
4 2 0.03
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:2210869 original size:36 final size:34
Alignment explanation
Indices: 2210816--2210890 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 34
2210806 TTAAATTAAA
* *
2210816 ATTATATTATTATATTATTATTATTATTATAACT
1 ATTATATTATTACATTATTATTATTAATATAACT
*
2210850 ATTATATTATAATACATTATTATTATTAATATTACT
1 ATTATATTAT--TACATTATTATTATTAATATAACT
2210886 ATTAT
1 ATTAT
2210891 TAATGTTACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 10 0.28
36 26 0.72
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (34 bp):
ATTATATTATTACATTATTATTATTAATATAACT
Found at i:2214847 original size:178 final size:178
Alignment explanation
Indices: 2214547--2214910 Score: 552
Period size: 178 Copynumber: 2.0 Consensus size: 178
2214537 ATCCATGGAG
* *
2214547 AAGGACATCCGATGAATGAAGAAATCTGAAGCTATGGAAGAATTCTGTCAAATGTGTAAAGGCCA
1 AAGGACATCCGATGAATGAAGAAATCTGAAGCTATGGAAGAATTCTGTCAAAGGTGCAAAGGCCA
* *
2214612 AGATGTTGACTCAAGAGATAGATACGGTCATACCAAGGACGAAAAAACCTTTCATAGAGACATGA
66 AGATGTTGACTCAAGAGATAGATACAGTCATACCAAGGACGAAAAAACCCTTCATAGAGACATGA
* * *
2214677 AGACCGCTTCACATTGGAGGTAAGAATGGAGATC-TCAAGATACAATCT
131 AGACCACTTCACATTAGAGGTAAGAATAGAGATCGT-AAGATACAATCT
* *
2214725 GAGGACATCCGATGAATGAAGAAATCTGAAGCTATTGAAGAATTCCT-TCAAAGGTGCAAAGGCC
1 AAGGACATCCGATGAATGAAGAAATCTGAAGCTATGGAAGAATT-CTGTCAAAGGTGCAAAGGCC
* ** * * *
2214789 AAGATGTTGACTCAAGAGATAGATATAGTCATATTAAGGACGAGAAGACCCTTCATAGAGATATG
65 AAGATGTTGACTCAAGAGATAGATACAGTCATACCAAGGACGAAAAAACCCTTCATAGAGACATG
*
2214854 AAGACCACTTCACATTAGAGGTAAGAATAGAGATCGTAAGATTCAATCT
130 AAGACCACTTCACATTAGAGGTAAGAATAGAGATCGTAAGATACAATCT
2214903 AAGGACAT
1 AAGGACAT
2214911 TTATCGTCAT
Statistics
Matches: 167, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
178 164 0.98
179 3 0.02
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.22
Consensus pattern (178 bp):
AAGGACATCCGATGAATGAAGAAATCTGAAGCTATGGAAGAATTCTGTCAAAGGTGCAAAGGCCA
AGATGTTGACTCAAGAGATAGATACAGTCATACCAAGGACGAAAAAACCCTTCATAGAGACATGA
AGACCACTTCACATTAGAGGTAAGAATAGAGATCGTAAGATACAATCT
Found at i:2219409 original size:10 final size:10
Alignment explanation
Indices: 2219394--2219444 Score: 58
Period size: 9 Copynumber: 5.5 Consensus size: 10
2219384 AGATGAAAAG
2219394 GAAAAAATGA
1 GAAAAAATGA
2219404 GAAAAAAATGA
1 G-AAAAAATGA
2219415 GAAAAAAT--
1 GAAAAAATGA
2219423 G-AAAAATGA
1 GAAAAAATGA
2219432 -AAAAAATGA
1 GAAAAAATGA
2219441 -AAAA
1 GAAAA
2219445 TGAAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
7 6 0.16
8 1 0.03
9 12 0.32
10 8 0.22
11 10 0.27
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.10
Consensus pattern (10 bp):
GAAAAAATGA
Found at i:2219427 original size:17 final size:16
Alignment explanation
Indices: 2219407--2219453 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
2219397 AAAATGAGAA
2219407 AAAAATGAGAAAAAATG
1 AAAAATGA-AAAAAATG
2219424 AAAAATGAAAAAAATG
1 AAAAATGAAAAAAATG
2219440 AAAAATGAAAAAAA
1 AAAAATGAAAAAAA
2219454 AATGAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 22 0.73
17 8 0.27
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.11
Consensus pattern (16 bp):
AAAAATGAAAAAAATG
Found at i:2219454 original size:17 final size:17
Alignment explanation
Indices: 2219407--2219459 Score: 81
Period size: 16 Copynumber: 3.1 Consensus size: 17
2219397 AAAATGAGAA
*
2219407 AAAAATGAGAAAAAATG
1 AAAAATGAAAAAAAATG
2219424 AAAAATG-AAAAAAATG
1 AAAAATGAAAAAAAATG
2219440 AAAAATGAAAAAAAAATG
1 AAAAATG-AAAAAAAATG
2219458 AA
1 AA
2219460 TAAAAGGGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 15 0.45
17 7 0.21
18 11 0.33
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.11
Consensus pattern (17 bp):
AAAAATGAAAAAAAATG
Found at i:2219456 original size:11 final size:11
Alignment explanation
Indices: 2219395--2219464 Score: 56
Period size: 11 Copynumber: 6.3 Consensus size: 11
2219385 GATGAAAAGG
*
2219395 AAAAAATGAGA
1 AAAAAATGAAA
*
2219406 AAAAAATG-AG
1 AAAAAATGAAA
2219416 AAAAAATGAAA
1 AAAAAATGAAA
2219427 AATGAAAA--AAA
1 AA--AAAATGAAA
*
2219438 TGAAAAATGAAA
1 -AAAAAATGAAA
2219450 AAAAAATGAATA
1 AAAAAATGAA-A
2219462 AAA
1 AAA
2219465 GGGGGTTCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
10 12 0.26
11 23 0.49
12 8 0.17
13 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:2219464 original size:9 final size:9
Alignment explanation
Indices: 2219404--2219453 Score: 63
Period size: 7 Copynumber: 5.9 Consensus size: 9
2219394 GAAAAAATGA
2219404 GAAAAAAAT
1 GAAAAAAAT
2219413 GAGAAAAAAT
1 GA-AAAAAAT
2219423 G--AAAAAT
1 GAAAAAAAT
2219430 GAAAAAAAT
1 GAAAAAAAT
2219439 G--AAAAAT
1 GAAAAAAAT
2219446 GAAAAAAA
1 GAAAAAAA
2219454 AATGAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
7 14 0.39
9 14 0.39
10 8 0.22
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (9 bp):
GAAAAAAAT
Found at i:2220581 original size:55 final size:55
Alignment explanation
Indices: 2220505--2221082 Score: 642
Period size: 55 Copynumber: 10.7 Consensus size: 55
2220495 TTGAAGCATC
* * * *
2220505 AAGATTGTTCGAGTCTTATACTTTCTCAAGGAATAGGAAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* * *
2220560 ACGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCATACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* *
2220615 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATATGGAGCATACACGTTTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* * * *
2220670 AAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGATACGTTTGTTA
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* *
2220721 AAGATTGTTCGAGTGTTATACTCTCTGAAGAAATAGGGAGCAGACACGTTTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* * ** * *
2220776 AAGA---TT-GAGTCCTATACTCTTTGAAGGAATAGGGAGTGGATACTTTTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
** *
2220827 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATATAGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* *
2220882 AAGATTGTTCGAGTCTTATAATCTCTGAAGGAATAGGGAGCATACACGTTTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* ** * * *
2220937 --TA-TAAT-GAGTCATATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTCG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* * * * * * * *
2220988 AAGGTTGTTCAAGTCCTATACTCTCTGAAGGAATAGAGAACATACTCGATTT-ATG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG-TTTGTTG
* * * * * *
2221043 AAGATTGTTTGAGTTTTACACTCCCTGAAGCAAGAGGGAG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAG
2221083 AGAACCCGCT
Statistics
Matches: 436, Mismatches: 74, Indels: 26
0.81 0.14 0.05
Matches are distributed among these distances:
51 124 0.28
52 6 0.01
53 1 0.00
54 6 0.01
55 296 0.68
56 3 0.01
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (55 bp):
AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
Found at i:2220730 original size:161 final size:158
Alignment explanation
Indices: 2220515--2221082 Score: 638
Period size: 161 Copynumber: 3.5 Consensus size: 158
2220505 AAGATTGTTC
* * * * *
2220515 GAGTCTTATACTTTCTCAAGGAATAGGAAGCAGACACGATTGTTGACGATTGTTCGAGTCTTATA
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATA
* *
2220580 CTCTCTGAAGGAATAGGGAGCATACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
66 CTCTCTGAAGGAATAGGGAGCATACACGTTTGTTGAAGA-T-TT-GAGTCATATACTCTCTGAAG
* **
2220645 GAATATGGAGCATACACGTTTGTTGAAGATT
128 GAATAGGGAGCGGACACGTTTGTTGAAGATT
* * * * *
2220676 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGATACGTTTGTTAAAGATTGTTCGAGTGTTATA
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATA
* * * *
2220741 CTCTCTGAAGAAATAGGGAGCAGACACGTTTGTTGAAGA-TTGAGTCCTATACTCTTTGAAGGAA
66 CTCTCTGAAGGAATAGGGAGCATACACGTTTGTTGAAGATTTGAGTCATATACTCTCTGAAGGAA
* * *
2220805 TAGGGAGTGGATACTTTTGTTGAAGATTGTT
131 TAGGGAGCGGACACGTTTGTTGAAGA---TT
* **
2220836 CGAGTCTTATACTCTCTGAAGGAATATAGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTAT
1 -GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTAT
* * * *
2220901 AATCTCTGAAGGAATAGGGAGCATACACGTTTGTTGTATA-ATGAGTCATATACTCTCTGAAGGA
65 ACTCTCTGAAGGAATAGGGAGCATACACGTTTGTTGAAGATTTGAGTCATATACTCTCTGAAGGA
* *
2220965 ATAGGGAGCGGACACGTTTGTCGAAGGTT
130 ATAGGGAGCGGACACGTTTGTTGAAGATT
* * * * * *
2220994 GTTCAAGTCCTATACTCTCTGAAGGAATAGAGAACATACTCGATT-TATGAAGATTGTTTGAGTT
1 G----AGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT-TGAAGATTGTTCGAGTC
* * * *
2221058 TTACACTCCCTGAAGCAAGAGGGAG
61 TTATACTCTCTGAAGGAATAGGGAG
2221083 AGAACCCGCT
Statistics
Matches: 344, Mismatches: 54, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
157 42 0.12
158 4 0.01
160 3 0.01
161 295 0.86
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (158 bp):
GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATA
CTCTCTGAAGGAATAGGGAGCATACACGTTTGTTGAAGATTTGAGTCATATACTCTCTGAAGGAA
TAGGGAGCGGACACGTTTGTTGAAGATT
Found at i:2220732 original size:106 final size:106
Alignment explanation
Indices: 2220505--2221082 Score: 608
Period size: 106 Copynumber: 5.4 Consensus size: 106
2220495 TTGAAGCATC
* * * * *
2220505 AAGATTGTTCGAGTCTTATACTTTCTCAAGGAATAGGAAGCAGACACGATTGTTGACGATTGTTC
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGA---TT-
* * *
2220570 GAGTCTTATACTCTCTGAAGGAATAGGGAGCATACACGATTGTTG
62 GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* *
2220615 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATATGGAGCATACACGTTTGTTGAAGATTGAGT
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGAGT
* * *
2220680 CCTATACTCTCTGAAGGAATAGGGAGCGGATACGTTTGTTA
66 CCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* *
2220721 AAGATTGTTCGAGTGTTATACTCTCTGAAGAAATAGGGAGCAGACACGTTTGTTGAAGATTGAGT
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGAGT
* ** * *
2220786 CCTATACTCTTTGAAGGAATAGGGAGTGGATACTTTTGTTG
66 CCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
** *
2220827 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATATAGAGCAGACACGATTGTTGAAGATTGTTC
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGA---TT-
* * *
2220892 GAGTCTTATAATCTCTGAAGGAATAGGGAGCATACACGTTTGTTG
62 GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* ** * * * *
2220937 --TA-TAAT-GAGTCATATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTCGAAGGTTGTTC
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTG---
* * * * *
2220998 AAGTCCTATACTCTCTGAAGGAATAGAGAACATACTCGATTT-ATG
63 -AGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACG-TTTGTTG
* * * * * *
2221043 AAGATTGTTTGAGTTTTACACTCCCTGAAGCAAGAGGGAG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAG
2221083 AGAACCCGCT
Statistics
Matches: 396, Mismatches: 59, Indels: 26
0.82 0.12 0.05
Matches are distributed among these distances:
102 1 0.00
103 2 0.01
106 267 0.67
107 7 0.02
108 2 0.01
109 4 0.01
110 113 0.29
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (106 bp):
AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGAGT
CCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
Found at i:2225511 original size:18 final size:18
Alignment explanation
Indices: 2225479--2225522 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
2225469 TTCTTTAATA
2225479 TTTTCTTTTTATTTT-GT
1 TTTTCTTTTTATTTTAGT
2225496 TTTTCTTTTCTATTTTAGT
1 TTTTCTTTT-TATTTTAGT
2225515 TTTTCTTT
1 TTTTCTTT
2225523 CCAAATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 9 0.36
18 6 0.24
19 10 0.40
ACGTcount: A:0.07, C:0.09, G:0.05, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTATTTTAGT
Found at i:2225523 original size:18 final size:17
Alignment explanation
Indices: 2225479--2225523 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
2225469 TTCTTTAATA
*
2225479 TTTTCTTTTTATTTTGT
1 TTTTCTTTCTATTTTGT
2225496 TTTTCTTTTCTATTTTAGT
1 TTTTC-TTTCTATTTT-GT
2225515 TTTTCTTTC
1 TTTTCTTTC
2225524 CAAATGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 13 0.52
19 7 0.28
ACGTcount: A:0.07, C:0.11, G:0.04, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTATTTTGT
Found at i:2225791 original size:28 final size:29
Alignment explanation
Indices: 2225759--2225825 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
2225749 TTTTTACCTT
2225759 TTTTTCATTTTCTTATT-ATATA-TATTAA
1 TTTTTCATTTTCTTATTCATATATTATT-A
* *
2225787 TTTTTC-TTTTTTTATTCATCTATTATTA
1 TTTTTCATTTTCTTATTCATATATTATTA
*
2225815 TTTTTTATTTT
1 TTTTTCATTTT
2225826 ATTTTATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 9 0.27
28 16 0.48
29 8 0.24
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (29 bp):
TTTTTCATTTTCTTATTCATATATTATTA
Found at i:2226093 original size:13 final size:12
Alignment explanation
Indices: 2226067--2226136 Score: 61
Period size: 13 Copynumber: 5.4 Consensus size: 12
2226057 ATTTAATAAA
2226067 TTTTTATATTATT
1 TTTTTAT-TTATT
*
2226080 TATTTTGTTTATT
1 T-TTTTATTTATT
*
2226093 TCATTTATTT-TT
1 T-TTTTATTTATT
2226105 ATTTTTATTTTATT
1 -TTTTTA-TTTATT
2226119 TTTTTATTTATT
1 TTTTTATTTATT
2226131 ATTTTT
1 -TTTTT
2226137 TATCTAACAT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
12 12 0.26
13 28 0.60
14 7 0.15
ACGTcount: A:0.19, C:0.01, G:0.01, T:0.79
Consensus pattern (12 bp):
TTTTTATTTATT
Found at i:2226107 original size:6 final size:6
Alignment explanation
Indices: 2226096--2226136 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
2226086 GTTTATTTCA
*
2226096 TTTATT TTTATT TTTATT TTATTTT TTTATT TATTATT TTT
1 TTTATT TTTATT TTTATT TT-TATT TTTATT T-TTATT TTT
2226137 TATCTAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:2226110 original size:25 final size:25
Alignment explanation
Indices: 2226073--2226136 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
2226063 TAAATTTTTA
2226073 TATTATTTA-TTTT-GTTTATTTCATT
1 TATT-TTTATTTTTAGTTTATTT-ATT
* *
2226098 TATTTTTATTTTTATTTTATTTTTT
1 TATTTTTATTTTTAGTTTATTTATT
2226123 TATTTATTATTTTT
1 TATTT-TTATTTTT
2226137 TATCTAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 4 0.12
25 15 0.44
26 15 0.44
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (25 bp):
TATTTTTATTTTTAGTTTATTTATT
Found at i:2226118 original size:17 final size:18
Alignment explanation
Indices: 2226066--2226139 Score: 65
Period size: 17 Copynumber: 4.4 Consensus size: 18
2226056 TATTTAATAA
2226066 ATTTTTA-TA-TTA-TTT
1 ATTTTTATTATTTATTTT
2226081 ATTTTGT-TTATTTCA-TTT
1 ATTTT-TATTATTT-ATTTT
2226099 ATTTTTATT-TTTATTTT
1 ATTTTTATTATTTATTTT
*
2226116 ATTTTT-TTATTTATTAT
1 ATTTTTATTATTTATTTT
2226133 -TTTTTAT
1 ATTTTTAT
2226140 CTAACATTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
15 5 0.10
16 11 0.22
17 23 0.46
18 11 0.22
ACGTcount: A:0.20, C:0.01, G:0.01, T:0.77
Consensus pattern (18 bp):
ATTTTTATTATTTATTTT
Found at i:2227459 original size:19 final size:17
Alignment explanation
Indices: 2227425--2227473 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 17
2227415 TTAATAATGC
*
2227425 TATTACTTTATGTCATTA
1 TATTATTTTAT-TCATTA
2227443 TTATTATTTCTATTCATTA
1 -TATTATTT-TATTCATTA
2227462 TATTATTTTATT
1 TATTATTTTATT
2227474 TTAAACACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
18 8 0.29
19 13 0.46
20 3 0.11
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (17 bp):
TATTATTTTATTCATTA
Found at i:2227640 original size:16 final size:18
Alignment explanation
Indices: 2227611--2227644 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2227601 CCAAAATAAT
2227611 AATATATGATTAAATTAA
1 AATATATGATTAAATTAA
2227629 AATATAT-A-TAAATTAA
1 AATATATGATTAAATTAA
2227645 TTGTCAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AATATATGATTAAATTAA
Found at i:2228939 original size:137 final size:137
Alignment explanation
Indices: 2228747--2229399 Score: 881
Period size: 137 Copynumber: 4.8 Consensus size: 137
2228737 AGATCCAACT
* * *
2228747 GGTGTATGACATTGTTCCTTCATGATGAGGACGTCTGGCCATCTTTGAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* * * *
2228812 TGGTTCCTTCGTGATGAAGACATCTGCCTATCTAAGAATGACT-TGGCTCCTACGTGATGAGGAG
66 TGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGA-TGTTGCTCCTTCGTGATGAGGAG
*
2228876 ATCTGATC
130 TTCTGATC
* * * * * *
2228884 GATAGATGACAATGTTCTTTCGTGATGAGGACGTCTGGACAACTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
2228949 TGGTTCCTTCGTGATGAGGACA------TATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
66 TGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
2229008 TCTGATC
131 TCTGATC
* * * *
2229015 GGTGTATGACATTGCTCCTTTGTGATGAGGACGTCTGGACATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* * * *
2229080 AGATTCATTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCATTCGTGATGAGGAGT
66 TGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
*
2229145 TTTGATC
131 TCTGATC
* * *
2229152 GGTGGATGACATTGTTCCTTCGTGATGATGACATATGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAAC-
* *
2229217 AT-GTTCCTTCATGATGAGGACATCTGGCTATCTAAGAATGATGTTTCTCCTTCGTGATGAGGAG
65 ATGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAG
*
2229281 TTCTGATA
130 TTCTGATC
* * *
2229289 GGTGGATGACATTGTTCATTCATGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* ** * * * *
2229354 CGGTTTATTCGTGATGAGGAAATTTGGCCATCTAAGGATGATGTTG
66 TGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTG
2229400 ATCGACATGA
Statistics
Matches: 453, Mismatches: 54, Indels: 18
0.86 0.10 0.03
Matches are distributed among these distances:
130 1 0.00
131 115 0.25
136 1 0.00
137 335 0.74
138 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (137 bp):
GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
TGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
TCTGATC
Found at i:2229225 original size:268 final size:269
Alignment explanation
Indices: 2228747--2229399 Score: 898
Period size: 268 Copynumber: 2.4 Consensus size: 269
2228737 AGATCCAACT
*
2228747 GGTGTATGACATTGTTCCTTCATGATGAGGACGTCTGGCCATCTTTGAAGATATTTGAGATAACA
1 GGTGTATGACATTGTTCCTTCATGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* * * * * *
2228812 TGGTTCCTTCGTGATGAAGACATCTGCCTATCTAAGAATGACT-TGGCTCCTACGTGATGAGGAG
66 AGGTTCATTCGTGATGAGGACATCTGGCTATCTAAGAATGA-TGTTGCTCATACGTGATGAGGAG
* * *
2228876 ATCTGATCGATAGATGACAATGTTCTTTCGTGATGAGGACGTCTGGACAACTTTAAAGATATTTG
130 ATCTGATCGATAGATGACAATGTTCCTTCGTGATGAGGACATATGGACAACTTTAAAGATATTTG
*
2228941 AGATAACATGGTTCCTTCGTGATGAGGACA-TATCTAAGAATGATGTTGCTCCTTCGTGATGAGG
195 AGATAACATGGTTCCTTCATGATGAGGACACTATCTAAGAATGATGTTGCTCCTTCGTGATGAGG
*
2229005 AGTTCTGATC
260 AGTTCTGATA
* ** *
2229015 GGTGTATGACATTGCTCCTTTGTGATGAGGACGTCTGGACATCTTTAAAGATATTTGAGATAACA
1 GGTGTATGACATTGTTCCTTCATGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* * *
2229080 AGATTCATTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCATTCGTGATGAGGAGT
66 AGGTTCATTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCATACGTGATGAGGAGA
* * * * * * *
2229145 TTTGATCGGTGGATGACATTGTTCCTTCGTGATGATGACATATGGCCATCTTTAAAGATATTTGA
131 TCTGATCGATAGATGACAATGTTCCTTCGTGATGAGGACATATGGACAACTTTAAAGATATTTGA
*
2229210 GATAACAAT-GTTCCTTCATGATGAGGACATCTGGCTATCTAAGAATGATGTTTCTCCTTCGTGA
196 GATAAC-ATGGTTCCTTCATGATGAGGACA-----CTATCTAAGAATGATGTTGCTCCTTCGTGA
2229274 TGAGGAGTTCTGATA
255 TGAGGAGTTCTGATA
* * *
2229289 GGTGGATGACATTGTTCATTCATGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGTATGACATTGTTCCTTCATGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* * * * * *
2229354 CGGTTTATTCGTGATGAGGAAATTTGGCCATCTAAGGATGATGTTG
66 AGGTTCATTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTG
2229400 ATCGACATGA
Statistics
Matches: 336, Mismatches: 41, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
267 1 0.00
268 194 0.58
269 2 0.01
274 139 0.41
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (269 bp):
GGTGTATGACATTGTTCCTTCATGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
AGGTTCATTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCATACGTGATGAGGAGA
TCTGATCGATAGATGACAATGTTCCTTCGTGATGAGGACATATGGACAACTTTAAAGATATTTGA
GATAACATGGTTCCTTCATGATGAGGACACTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGA
GTTCTGATA
Found at i:2229600 original size:124 final size:124
Alignment explanation
Indices: 2229445--2229681 Score: 384
Period size: 124 Copynumber: 1.9 Consensus size: 124
2229435 ATGGATGCAT
* * *
2229445 TGTTGCTGGTGGACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCATCGTGA
1 TGTTGCTGGTGGAAACGATATCCTTCGTCGTGAAGTTGAAATCGTAGATGGCCCCTTCATCATGA
*
2229510 AGTTAAGCCTCGAATTGGATATCATTCACTGTGAAGTTGCAATCCAATCTAAAGATGAA
66 AGTTAAGCCTCGAATTGGATATCATTCACTGTGAAGTTGAAATCCAATCTAAAGATGAA
* * *
2229569 TGTTGCTGGTGGAAACGATATCCTTCGTCGTGAAGTTGAAATCGTAGATGGCTCTTTCGTCATGA
1 TGTTGCTGGTGGAAACGATATCCTTCGTCGTGAAGTTGAAATCGTAGATGGCCCCTTCATCATGA
* **
2229634 AGTTAAGCCTCGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAAT
66 AGTTAAGCCTCGAATTGGATATCATTCACTGTGAAGTTGAAATCCAAT
2229682 GTTGCTGACA
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
124 103 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (124 bp):
TGTTGCTGGTGGAAACGATATCCTTCGTCGTGAAGTTGAAATCGTAGATGGCCCCTTCATCATGA
AGTTAAGCCTCGAATTGGATATCATTCACTGTGAAGTTGAAATCCAATCTAAAGATGAA
Found at i:2229772 original size:108 final size:108
Alignment explanation
Indices: 2229583--2230050 Score: 780
Period size: 108 Copynumber: 4.3 Consensus size: 108
2229573 GCTGGTGGAA
* * *
2229583 ACGATATCCTTCGTCGTGAAGTTGAAATCGTAGATGGCT-CTTTCGTCATGAAGTTAAGCCTCGA
1 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTT-GTCATGAAGTTGAGCCTTGA
2229647 ATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATGTTGCTGAC
65 ATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATGTTGCTGAC
* * *
2229691 ACGATATCCTTCATCGTGAAGTTGAAATTGTGGATGGCTCCTTTGTCGTGAAGTTGAGCCTTGAA
1 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTTGTCATGAAGTTGAGCCTTGAA
2229756 TTGGATATCCTTCGTTGTGAAGTTGAAATCCAATGTTGCTGAC
66 TTGGATATCCTTCGTTGTGAAGTTGAAATCCAATGTTGCTGAC
* * *
2229799 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGAC-CCGTCT-TCGTTAAGTTGAGCCTTG
1 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGG-CTCC-TTTGTCATGAAGTTGAGCCTTG
*
2229862 AATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATGTTGCTGAC
64 AATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATGTTGCTGAC
* *
2229907 ACGATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCTCCTTCGTCATGAAGTTGAGCCTTGAA
1 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTTGTCATGAAGTTGAGCCTTGAA
2229972 TTGGATATCCTTCGTTGTGAAGTTGAAATCCAATGTTGCTGAC
66 TTGGATATCCTTCGTTGTGAAGTTGAAATCCAATGTTGCTGAC
2230015 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
1 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
2230051 TGTGGGCACG
Statistics
Matches: 337, Mismatches: 18, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
107 2 0.01
108 328 0.97
109 7 0.02
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (108 bp):
ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTTGTCATGAAGTTGAGCCTTGAA
TTGGATATCCTTCGTTGTGAAGTTGAAATCCAATGTTGCTGAC
Found at i:2230245 original size:48 final size:48
Alignment explanation
Indices: 2230172--2230322 Score: 149
Period size: 55 Copynumber: 3.0 Consensus size: 48
2230162 ATTGTGTTGT
* *
2230172 TTTGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGA
1 TTTGAATTCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGA
** * * * * *
2230220 TTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAGTCTTTGGTTGTATTGC
1 TTTGAATTCAATATCCTTCGTTGTGAAGTTGAAAT--TGAC--T--CTG-AATGA
*
2230275 TTTGAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGA
1 TTTGAATTCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGA
2230323 AACTAAAAAG
Statistics
Matches: 79, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
48 34 0.43
49 2 0.03
50 2 0.03
51 1 0.01
52 1 0.01
53 2 0.03
54 2 0.03
55 35 0.44
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (48 bp):
TTTGAATTCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGA
Found at i:2230252 original size:103 final size:103
Alignment explanation
Indices: 2230117--2230322 Score: 331
Period size: 103 Copynumber: 2.0 Consensus size: 103
2230107 GAAGTTGAGC
* * *
2230117 TTTGAATTAGATATCCTTGGTCATGAAGTTGAAATCCAATCTTTGATTGTGTTGTTTTGAGTTCA
1 TTTGAATTAGATATCCTTCGTCATGAAGTTGAAATCCAATCTTTGATTGTATTGCTTTGAGTTCA
2230182 ATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGA
66 ATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGA
* ** * *
2230220 TTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAGTCTTTGGTTGTATTGCTTTGAGTTCA
1 TTTGAATTAGATATCCTTCGTCATGAAGTTGAAATCCAATCTTTGATTGTATTGCTTTGAGTTCA
*
2230285 ATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGA
66 ATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGA
2230323 AACTAAAAAG
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 94 1.00
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (103 bp):
TTTGAATTAGATATCCTTCGTCATGAAGTTGAAATCCAATCTTTGATTGTATTGCTTTGAGTTCA
ATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGA
Found at i:2230388 original size:64 final size:57
Alignment explanation
Indices: 2230276--2230435 Score: 162
Period size: 58 Copynumber: 2.7 Consensus size: 57
2230266 TTGTATTGCT
* *
2230276 TTGAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTTATTTG
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGA--C---ATG-AA-TGAAAAGTTATTTG
* * *
2230340 TTGAGTCCAATATCCTTCGCTGTGAAGTTG-ACTCTGA-ATGAAACTGAAAAGTTGTTTG
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT-TGACATG-AA-TGAAAAGTTATTTG
*
2230398 TTGAGTCCAATATCCTTCGTTGTGAAGTTTAAATTGAC
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAC
2230436 TCTAAAAGTC
Statistics
Matches: 85, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
58 50 0.59
59 2 0.02
63 2 0.02
64 31 0.36
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (57 bp):
TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACATGAATGAAAAGTTATTTG
Found at i:2230399 original size:58 final size:58
Alignment explanation
Indices: 2230304--2230426 Score: 210
Period size: 58 Copynumber: 2.1 Consensus size: 58
2230294 GTTGTGAAGT
*
2230304 TGAAATTGACTCTGAATGAAACTAAAAAGTTATTTGTTGAGTCCAATATCCTTCGCTG
1 TGAAGTTGACTCTGAATGAAACTAAAAAGTTATTTGTTGAGTCCAATATCCTTCGCTG
* * *
2230362 TGAAGTTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAGTCCAATATCCTTCGTTG
1 TGAAGTTGACTCTGAATGAAACTAAAAAGTTATTTGTTGAGTCCAATATCCTTCGCTG
2230420 TGAAGTT
1 TGAAGTT
2230427 TAAATTGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (58 bp):
TGAAGTTGACTCTGAATGAAACTAAAAAGTTATTTGTTGAGTCCAATATCCTTCGCTG
Found at i:2230884 original size:18 final size:17
Alignment explanation
Indices: 2230838--2230876 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
2230828 AGTCTCAGAA
2230838 AAACTGTTTCATTTATG
1 AAACTGTTTCATTTATG
2230855 AAACTGTTTCATTTATG
1 AAACTGTTTCATTTATG
*
2230872 GAACT
1 AAACT
2230877 CTTTTCATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (17 bp):
AAACTGTTTCATTTATG
Found at i:2231910 original size:52 final size:50
Alignment explanation
Indices: 2231830--2231977 Score: 181
Period size: 52 Copynumber: 2.9 Consensus size: 50
2231820 ATATCCCAAG
* * * *
2231830 CTTTTTATGTTGGTGTGAGCCTTCAAGATGCCTCACATGGATTACTT-CTGT
1 CTTTTTATGCTGATGTGAGCCTTTAAGATGCC-CACATGGATAACTTGC-GT
*
2231881 CTTTTTCATGCTGATGTGAGCCTTTAAGATACCCACATGGATAACTTGCGT
1 CTTTTT-ATGCTGATGTGAGCCTTTAAGATGCCCACATGGATAACTTGCGT
*
2231932 CTTTTTTTATGCTGATGTGAGCCTTTAAGATGCTCCAGATGGATAA
1 C--TTTTTATGCTGATGTGAGCCTTTAAGATGC-CCACATGGATAA
2231978 TATGGACCTT
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
51 22 0.26
52 47 0.55
53 16 0.19
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39
Consensus pattern (50 bp):
CTTTTTATGCTGATGTGAGCCTTTAAGATGCCCACATGGATAACTTGCGT
Found at i:2233380 original size:10 final size:10
Alignment explanation
Indices: 2233367--2233468 Score: 56
Period size: 10 Copynumber: 10.6 Consensus size: 10
2233357 TTTTTTTTTC
2233367 TTTTCTCTTT
1 TTTTCTCTTT
2233377 TTTT-TC---
1 TTTTCTCTTT
2233383 TTTTCTCTTT
1 TTTTCTCTTT
2233393 TTTTCT-TTT
1 TTTTCTCTTT
*
2233402 TCTTTTTCTTT
1 T-TTTCTCTTT
* *
2233413 TTTTTTATTT
1 TTTTCTCTTT
*
2233423 TTTTAT-TTAT
1 TTTTCTCTT-T
* *
2233433 TTTTTTATTT
1 TTTTCTCTTT
* *
2233443 TTTTTTATTT
1 TTTTCTCTTT
2233453 TTTT-TCATTT
1 TTTTCTC-TTT
2233463 TTTTCT
1 TTTTCT
2233469 GATGGATGAG
Statistics
Matches: 77, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
6 4 0.05
7 2 0.03
9 9 0.12
10 55 0.71
11 7 0.09
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:2233397 original size:31 final size:30
Alignment explanation
Indices: 2233359--2233456 Score: 110
Period size: 30 Copynumber: 3.2 Consensus size: 30
2233349 TGATTCAATT
*
2233359 TTTTTTTCTTTTCTCTTTTT-TTTCTTTTCTC
1 TTTTTTTCTTTT-TCTTTTTCTTT-TTTTCTA
*
2233390 TTTTTTTCTTTTTCTTTTTCTTTTTTTTTA
1 TTTTTTTCTTTTTCTTTTTCTTTTTTTCTA
* * *
2233420 TTTTTTTATTTATT-TTTTTATTTTTTTTTA
1 TTTTTTTCTTT-TTCTTTTTCTTTTTTTCTA
2233450 TTTTTTT
1 TTTTTTT
2233457 TCATTTTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
30 44 0.72
31 17 0.28
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (30 bp):
TTTTTTTCTTTTTCTTTTTCTTTTTTTCTA
Found at i:2233463 original size:16 final size:14
Alignment explanation
Indices: 2233357--2233466 Score: 98
Period size: 16 Copynumber: 7.5 Consensus size: 14
2233347 CCTGATTCAA
2233357 TTTTTTTTTCTTTTC
1 TTTTTTTTT-TTTTC
2233372 TCTTTTTTTTCTTTTC
1 T-TTTTTTTT-TTTTC
2233388 TCTTTTTTTCTTTTTC
1 T-TTTTTTT-TTTTTC
2233404 TTTTTCTTTTTTTT-
1 TTTTT-TTTTTTTTC
* * *
2233418 TATTTTTTTATTTA
1 TTTTTTTTTTTTTC
*
2233432 TTTTTTTATTTTT-
1 TTTTTTTTTTTTTC
*
2233445 TTTTATTTTTTTTC
1 TTTTTTTTTTTTTC
2233459 ATTTTTTT
1 -TTTTTTT
2233467 CTGATGGATG
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
13 18 0.22
14 14 0.17
15 16 0.20
16 32 0.40
17 1 0.01
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTTTTTC
Found at i:2233466 original size:1 final size:1
Alignment explanation
Indices: 2233357--2233457 Score: 76
Period size: 1 Copynumber: 101.0 Consensus size: 1
2233347 CCTGATTCAA
* * * * * * * * * *
2233357 TTTTTTTTTCTTTTCTCTTTTTTTTCTTTTCTCTTTTTTTCTTTTTCTTTTTCTTTTTTTTTATT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
2233422 TTTTTATTTATTTTTTTATTTTTTTTTATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2233458 CATTTTTTTC
Statistics
Matches: 72, Mismatches: 28, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:2235946 original size:20 final size:20
Alignment explanation
Indices: 2235884--2235971 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
2235874 AATATAAATA
*
2235884 CAAACATGAAGATGTGAATG
1 CAAACATGAAAATGTGAATG
* * *
2235904 TAAA-ATGAAAATGTAAATA
1 CAAACATGAAAATGTGAATG
*
2235923 CAAACATAAAAATGTGAATG
1 CAAACATGAAAATGTGAATG
2235943 C-AA-ATGCAAAGATGTGAATG
1 CAAACATG-AAA-ATGTGAATG
*
2235963 TAAA-ATGAA
1 CAAACATGAA
2235972 TATAAAAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
18 2 0.04
19 20 0.37
20 27 0.50
21 5 0.09
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (20 bp):
CAAACATGAAAATGTGAATG
Found at i:2237820 original size:22 final size:21
Alignment explanation
Indices: 2237792--2237838 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
2237782 TTAATAATGC
2237792 TATTATTT-TATGTCATTATTAT
1 TATTATTTCTAT-TCATTA-TAT
2237814 TATTATTTCTATTCATTATAT
1 TATTATTTCTATTCATTATAT
2237835 TATT
1 TATT
2237839 TTATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.29
22 14 0.58
23 3 0.12
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTATTTCTATTCATTATAT
Found at i:2239423 original size:18 final size:18
Alignment explanation
Indices: 2239400--2239435 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2239390 TTAGTATATA
*
2239400 TGTTAAATAGCACTGATT
1 TGTTAAATAGCACCGATT
2239418 TGTTAAATAGCACCGATT
1 TGTTAAATAGCACCGATT
2239436 AAGTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (18 bp):
TGTTAAATAGCACCGATT
Found at i:2241842 original size:203 final size:203
Alignment explanation
Indices: 2241493--2241898 Score: 794
Period size: 203 Copynumber: 2.0 Consensus size: 203
2241483 GGGCATTCAG
*
2241493 ATATGATTTGTACTTCCATCCTGAATGTGTACCGAGTTTGATTTGTTGTTTCCCTGGAAATAAAA
1 ATATGATTCGTACTTCCATCCTGAATGTGTACCGAGTTTGATTTGTTGTTTCCCTGGAAATAAAA
2241558 TATCGGCAAATAAGTTCGAATATCGGAGCTTGAATTCTTCGATAAATTTGGAGATATCCCCTAAT
66 TATCGGCAAATAAGTTCGAATATCGGAGCTTGAATTCTTCGATAAATTTGGAGATATCCCCTAAT
*
2241623 GGGAGTAGTAGGAGCAGAATTTTGAGCTTTGCTGTCTGTCTTGTGGCCGGTCTCACTCCCTGCCA
131 GGGAGTAGTAGGAGCAGAATTTTGAGCTTTGCTGTCTGCCTTGTGGCCGGTCTCACTCCCTGCCA
2241688 CGTCTTCT
196 CGTCTTCT
2241696 ATATGATTCGTACTTCCATCCTGAATGTGTACCGAGTTTGATTTGTTGTTTCCCTGGAAATAAAA
1 ATATGATTCGTACTTCCATCCTGAATGTGTACCGAGTTTGATTTGTTGTTTCCCTGGAAATAAAA
2241761 TATCGGCAAATAAGTTCGAATATCGGAGCTTGAATTCTTCGATAAATTTGGAGATATCCCCTAAT
66 TATCGGCAAATAAGTTCGAATATCGGAGCTTGAATTCTTCGATAAATTTGGAGATATCCCCTAAT
2241826 GGGAGTAGTAGGAGCAGAATTTTGAGCTTTGCTGTCTGCCTTGTGGCCGGTCTCACTCCCTGCCA
131 GGGAGTAGTAGGAGCAGAATTTTGAGCTTTGCTGTCTGCCTTGTGGCCGGTCTCACTCCCTGCCA
2241891 CGTCTTCT
196 CGTCTTCT
2241899 TTACTCTTAA
Statistics
Matches: 201, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
203 201 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (203 bp):
ATATGATTCGTACTTCCATCCTGAATGTGTACCGAGTTTGATTTGTTGTTTCCCTGGAAATAAAA
TATCGGCAAATAAGTTCGAATATCGGAGCTTGAATTCTTCGATAAATTTGGAGATATCCCCTAAT
GGGAGTAGTAGGAGCAGAATTTTGAGCTTTGCTGTCTGCCTTGTGGCCGGTCTCACTCCCTGCCA
CGTCTTCT
Found at i:2244689 original size:16 final size:16
Alignment explanation
Indices: 2244668--2244702 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2244658 TGTTGCTCGA
*
2244668 CTCGTTGTTCATTAAG
1 CTCGTTGCTCATTAAG
2244684 CTCGTTGCTCATTAAG
1 CTCGTTGCTCATTAAG
2244700 CTC
1 CTC
2244703 ACTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (16 bp):
CTCGTTGCTCATTAAG
Found at i:2246311 original size:25 final size:25
Alignment explanation
Indices: 2246280--2246332 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
2246270 ATACATATAC
2246280 ATATATATATTAACAAATAAATCTTAA
1 ATATATATA-TAACAAATAAAT-TTAA
* *
2246307 ATATATATATAATACATAAATTTAA
1 ATATATATATAACAAATAAATTTAA
2246332 A
1 A
2246333 AAAAACATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 10 0.42
27 9 0.38
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (25 bp):
ATATATATATAACAAATAAATTTAA
Found at i:2256656 original size:24 final size:24
Alignment explanation
Indices: 2256623--2256677 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2256613 CCTTTTTAAT
*
2256623 TTTTTAAAAAATAAA-ATTTATAAA
1 TTTTTAAAAAA-AAATATATATAAA
* *
2256647 TTTTTGAAAAAAAATATATATTAA
1 TTTTTAAAAAAAAATATATATAAA
2256671 TTTTTAA
1 TTTTTAA
2256678 TACTTTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TTTTTAAAAAAAAATATATATAAA
Found at i:2260779 original size:125 final size:126
Alignment explanation
Indices: 2260588--2260821 Score: 308
Period size: 125 Copynumber: 1.8 Consensus size: 126
2260578 CTAAAAATGA
* * *
2260588 AGGCTCTAATATTAACCCTAATAAATTATTGAATCGAGTAATCGAAATGGACCATCGACCAATAA
1 AGGCTCTAATAATAACCC--ATAAATTATTGAATCGAATAATCAAAATGGACCATCGACCAATAA
** *
2260653 GGTTAGGGCGAAATTGAATTATCCCCTAATTAAAGGAATAAAGTGAAATTAAGGCTAAAGTGG
64 GGCGAGGGCGAAATCGAATTATCCCCTAATTAAAGGAATAAAGTGAAATTAAGGCTAAAGTGG
* * * * ** *
2260716 AGGCTCTAATAATAACCC-TAAATTATTGAGTGGAATAATCAAAATGGATCATTGGGCATTAAGG
1 AGGCTCTAATAATAACCCATAAATTATTGAATCGAATAATCAAAATGGACCATCGACCAATAAGG
* *
2260780 CGAGGGCTAAATCGAATTATCCCCTAATTAAAGGACTAAAGT
66 CGAGGGCGAAATCGAATTATCCCCTAATTAAAGGAATAAAGT
2260822 TGATTATTAT
Statistics
Matches: 91, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
125 74 0.81
128 17 0.19
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (126 bp):
AGGCTCTAATAATAACCCATAAATTATTGAATCGAATAATCAAAATGGACCATCGACCAATAAGG
CGAGGGCGAAATCGAATTATCCCCTAATTAAAGGAATAAAGTGAAATTAAGGCTAAAGTGG
Found at i:2262757 original size:17 final size:17
Alignment explanation
Indices: 2262723--2262774 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2262713 ACCGGACAAA
* *
2262723 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
2262740 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
2262757 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
2262772 TTT
1 TTT
2262775 CTACTGTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:2262997 original size:31 final size:31
Alignment explanation
Indices: 2262955--2263043 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 31
2262945 TAAAAATTTA
* * *
2262955 GGTACTGAAATGAAACAAAAAGTTAACGATG
1 GGTACTAAAATGAAACAAAAAGTAAACGACG
* * *
2262986 GGTACTAAAATGAAATAAAAAGTAAATGCCG
1 GGTACTAAAATGAAACAAAAAGTAAACGACG
*
2263017 GGTACTAAAATGAAACAATAAGTAAAC
1 GGTACTAAAATGAAACAAAAAGTAAAC
2263044 TTTAGGCATG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (31 bp):
GGTACTAAAATGAAACAAAAAGTAAACGACG
Found at i:2263179 original size:27 final size:29
Alignment explanation
Indices: 2263148--2263208 Score: 92
Period size: 27 Copynumber: 2.2 Consensus size: 29
2263138 TTTAGTCATG
2263148 CAATATAGTTACAA-CTACCACAT-G-AAA
1 CAATATAGTTACAAGC-ACCACATGGAAAA
2263175 CAATATAGTTACAAGCACCACATGGAAAA
1 CAATATAGTTACAAGCACCACATGGAAAA
2263204 CAATA
1 CAATA
2263209 AAAAAACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 21 0.68
28 2 0.06
29 8 0.26
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.20
Consensus pattern (29 bp):
CAATATAGTTACAAGCACCACATGGAAAA
Found at i:2264149 original size:52 final size:52
Alignment explanation
Indices: 2264012--2264158 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 52
2264002 CCTGATAGTC
* * * *
2264012 GTTATTATTAGCGAATTTTGCTAGTGACAAATAATATTCTCAAATAATAATT
1 GTTATTATAAGCGAATTTAGCTAGTGACAAATAATGTTCCCAAATAATAATT
* * * **
2264064 GTTATTATAAGCAAATTTAGCTAGTAACGAATAATGTTCCCACCTAATAATT
1 GTTATTATAAGCGAATTTAGCTAGTGACAAATAATGTTCCCAAATAATAATT
* * * *
2264116 GTTATTATAAGCGAATTTAACTAATGGCAAATAATGTTACCAA
1 GTTATTATAAGCGAATTTAGCTAGTGACAAATAATGTTCCCAA
2264159 CTGCTTTGGA
Statistics
Matches: 78, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 78 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (52 bp):
GTTATTATAAGCGAATTTAGCTAGTGACAAATAATGTTCCCAAATAATAATT
Found at i:2264538 original size:43 final size:43
Alignment explanation
Indices: 2264490--2264591 Score: 158
Period size: 39 Copynumber: 2.5 Consensus size: 43
2264480 CATTATATGC
2264490 CCTAGCCAAATCTACAATATATATGACATTAATATCTACATGA
1 CCTAGCCAAATCTACAATATATATGACATTAATATCTACATGA
*
2264533 CCTAGCCAAATATAC---A-ATATGACATTAATATCTACATGA
1 CCTAGCCAAATCTACAATATATATGACATTAATATCTACATGA
*
2264572 CCTAGCCAAATCTGCAATAT
1 CCTAGCCAAATCTACAATAT
2264592 GACCTTGCCA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
39 36 0.69
40 1 0.02
42 1 0.02
43 14 0.27
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (43 bp):
CCTAGCCAAATCTACAATATATATGACATTAATATCTACATGA
Found at i:2264555 original size:22 final size:21
Alignment explanation
Indices: 2264520--2264604 Score: 52
Period size: 22 Copynumber: 4.1 Consensus size: 21
2264510 ATATGACATT
* *
2264520 AATATCTACATGACCTAGCCA
1 AATATCAATATGACCTAGCCA
**
2264541 AATATACAATATGA-C-A--TT
1 AATAT-CAATATGACCTAGCCA
* *
2264559 AATATCTACATGACCTAGCCA
1 AATATCAATATGACCTAGCCA
* *
2264580 AATCTGCAATATGACCTTGCCA
1 AATAT-CAATATGACCTAGCCA
2264602 AAT
1 AAT
2264605 TTACTTGTCC
Statistics
Matches: 46, Mismatches: 12, Indels: 11
0.67 0.17 0.16
Matches are distributed among these distances:
17 6 0.13
18 6 0.13
19 1 0.02
20 1 0.02
21 10 0.22
22 22 0.48
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (21 bp):
AATATCAATATGACCTAGCCA
Found at i:2271374 original size:60 final size:60
Alignment explanation
Indices: 2271263--2271473 Score: 189
Period size: 60 Copynumber: 3.5 Consensus size: 60
2271253 GCTCATTCAC
* * ** * * *
2271263 TTTGTGCATAGGGTAAGTCCTTATGGACCCGGGGGAACTC-CCATAAGGTGGCTCCTTTGT
1 TTTGTGCATTGGGTATGTCCTTATGGACATGAGAGAACTCACC-TCAGGTGGCTCCTTTGT
** *
2271323 TTTGTGCATTGGGTATGTCCTTATGGAGC-T-AGAGACACTCACCTCTTGTGGCTCCTTTGC
1 TTTGTGCATTGGGTATGTCCTTATGGA-CATGAGAGA-ACTCACCTCAGGTGGCTCCTTTGT
* * * ** *
2271383 TTTGTGTATTGGGT-TAGTCCTTATGGACATGAGGGAACTCCCCTCAGGTGATTGCTTT-T
1 TTTGTGCATTGGGTAT-GTCCTTATGGACATGAGAGAACTCACCTCAGGTGGCTCCTTTGT
*
2271442 CTTTGTGCATTGGGTAAGTCCTTATGGACATG
1 -TTTGTGCATTGGGTATGTCCTTATGGACATG
2271474 GGGGTACTTC
Statistics
Matches: 123, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
59 5 0.04
60 111 0.90
61 7 0.06
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (60 bp):
TTTGTGCATTGGGTATGTCCTTATGGACATGAGAGAACTCACCTCAGGTGGCTCCTTTGT
Found at i:2271997 original size:16 final size:16
Alignment explanation
Indices: 2271976--2272015 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
2271966 AAGAATCAAT
2271976 CATCAGCAGATATCGA
1 CATCAGCAGATATCGA
2271992 CATCAGCAGATATCGA
1 CATCAGCAGATATCGA
2272008 CATCAGCA
1 CATCAGCA
2272016 ATGGGAGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (16 bp):
CATCAGCAGATATCGA
Found at i:2272613 original size:43 final size:44
Alignment explanation
Indices: 2272564--2272647 Score: 134
Period size: 43 Copynumber: 1.9 Consensus size: 44
2272554 CTTGATTTCA
2272564 AATTTAAATAAATTAATAAAATTATATCTCAAT-TTTTATTTTT
1 AATTTAAATAAATTAATAAAATTATATCTCAATATTTTATTTTT
* * *
2272607 AATTTAAATAAATTAATAAATTTATTTTTCAATATTTTATT
1 AATTTAAATAAATTAATAAAATTATATCTCAATATTTTATT
2272648 AATTTTTACG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 30 0.81
44 7 0.19
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (44 bp):
AATTTAAATAAATTAATAAAATTATATCTCAATATTTTATTTTT
Found at i:2303363 original size:77 final size:77
Alignment explanation
Indices: 2303236--2303468 Score: 378
Period size: 77 Copynumber: 3.0 Consensus size: 77
2303226 ACACTCATTA
* * * * *
2303236 GAGAGATTTTGAACTCCAAATTAAGTTGGATGGCTTAAGGGATAATTGTCCTAAATATGGTATTA
1 GAGAGATTTTGAACTCCAAATTAAGTTGGATGACTAAAGGGATAATTGTCCCAGATAGGGTATTA
2303301 TGGTAGATTTTT
66 TGGTAGATTTTT
2303313 GAGAGATTTTGAACTCCAAATTAAGTTGGATGACTAAAGGGATAATTGTCCCAGATAGGGTATTA
1 GAGAGATTTTGAACTCCAAATTAAGTTGGATGACTAAAGGGATAATTGTCCCAGATAGGGTATTA
2303378 TGGTAGATTTTTT
66 TGGTAGA-TTTTT
* *
2303391 TAGAGATTTTGAACTCCAAATTAAGTTGGATGACTAAAGGGATAATTATCCCAGATAGGGT-TTA
1 GAGAGATTTTGAACTCCAAATTAAGTTGGATGACTAAAGGGATAATTGTCCCAGATAGGGTATT-
2303455 ATGGTAGATTTTT
65 ATGGTAGATTTTT
2303468 G
1 G
2303469 GCAAAAAGGC
Statistics
Matches: 146, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
77 74 0.51
78 72 0.49
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.36
Consensus pattern (77 bp):
GAGAGATTTTGAACTCCAAATTAAGTTGGATGACTAAAGGGATAATTGTCCCAGATAGGGTATTA
TGGTAGATTTTT
Found at i:2303421 original size:78 final size:78
Alignment explanation
Indices: 2303236--2303467 Score: 378
Period size: 78 Copynumber: 3.0 Consensus size: 78
2303226 ACACTCATTA
* * * * *
2303236 GAGAGATTTTGAACTCCAAATTAAGTTGGATGGCTTAAGGGATAATTGTCCTAAATATGGTATTA
1 GAGAGATTTTGAACTCCAAATTAAGTTGGATGACTAAAGGGATAATTGTCCCAGATAGGGTATTA
2303301 TGGTAGA-TTTTT
66 TGGTAGATTTTTT
2303313 GAGAGATTTTGAACTCCAAATTAAGTTGGATGACTAAAGGGATAATTGTCCCAGATAGGGTATTA
1 GAGAGATTTTGAACTCCAAATTAAGTTGGATGACTAAAGGGATAATTGTCCCAGATAGGGTATTA
2303378 TGGTAGATTTTTT
66 TGGTAGATTTTTT
* *
2303391 TAGAGATTTTGAACTCCAAATTAAGTTGGATGACTAAAGGGATAATTATCCCAGATAGGGT-TTA
1 GAGAGATTTTGAACTCCAAATTAAGTTGGATGACTAAAGGGATAATTGTCCCAGATAGGGTATT-
2303455 ATGGTAGATTTTT
65 ATGGTAGATTTTT
2303468 GGCAAAAAGG
Statistics
Matches: 146, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
77 69 0.47
78 77 0.53
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (78 bp):
GAGAGATTTTGAACTCCAAATTAAGTTGGATGACTAAAGGGATAATTGTCCCAGATAGGGTATTA
TGGTAGATTTTTT
Found at i:2303775 original size:35 final size:35
Alignment explanation
Indices: 2303735--2303805 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
2303725 TGTCTCGTTT
*
2303735 AAAGGGGTTTTAGTGTTTGATCTAGGGGTTAGATG
1 AAAGGGGTTTTAGTGTTCGATCTAGGGGTTAGATG
2303770 AAAGGGGTTTTAGTGTTCGATCTAGGGGTTAGATG
1 AAAGGGGTTTTAGTGTTCGATCTAGGGGTTAGATG
2303805 A
1 A
2303806 GGAGACGAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.24, C:0.04, G:0.37, T:0.35
Consensus pattern (35 bp):
AAAGGGGTTTTAGTGTTCGATCTAGGGGTTAGATG
Found at i:2305404 original size:3 final size:3
Alignment explanation
Indices: 2305390--2305516 Score: 206
Period size: 3 Copynumber: 43.0 Consensus size: 3
2305380 CATCTTACTT
2305390 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2305437 -GA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA T-A TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
2305481 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2305517 GAGTAGTTAG
Statistics
Matches: 116, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
2 5 0.04
3 108 0.93
4 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2309123 original size:16 final size:17
Alignment explanation
Indices: 2309100--2309134 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2309090 AGTCGAAAAA
*
2309100 TAAAAAATATGACTTTT
1 TAAAAATTATGACTTTT
*
2309117 TAAAAATTTTGACTTTT
1 TAAAAATTATGACTTTT
2309134 T
1 T
2309135 GGTCAAAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (17 bp):
TAAAAATTATGACTTTT
Found at i:2309300 original size:22 final size:22
Alignment explanation
Indices: 2309275--2309326 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
2309265 AGTCAACTCT
2309275 CGGTCAACGCCGATCAAAGGTC
1 CGGTCAACGCCGATCAAAGGTC
2309297 CGGTCAACGCCGATCAAAGGTC
1 CGGTCAACGCCGATCAAAGGTC
*
2309319 CGATCAAC
1 CGGTCAAC
2309327 AGTGGTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.29, C:0.33, G:0.25, T:0.13
Consensus pattern (22 bp):
CGGTCAACGCCGATCAAAGGTC
Found at i:2309321 original size:12 final size:12
Alignment explanation
Indices: 2309284--2309325 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
2309274 TCGGTCAACG
2309284 CCGATCAAAGGT
1 CCGATCAAAGGT
* *
2309296 CCGGTC-AACG-
1 CCGATCAAAGGT
2309306 CCGATCAAAGGT
1 CCGATCAAAGGT
2309318 CCGATCAA
1 CCGATCAA
2309326 CAGTGGTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
10 5 0.21
11 6 0.25
12 13 0.54
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.14
Consensus pattern (12 bp):
CCGATCAAAGGT
Found at i:2317850 original size:32 final size:31
Alignment explanation
Indices: 2317806--2317880 Score: 88
Period size: 26 Copynumber: 2.5 Consensus size: 31
2317796 TAAACCGAAA
*
2317806 ATATGATACCCGAACCCAAACTGCATCCGACTG
1 ATATGA-ACCCGAACCC-AACTACATCCGACTG
2317839 ATATGAACCCG-----AACTACATCCGACTG
1 ATATGAACCCGAACCCAACTACATCCGACTG
2317865 ATATGAACCCGAACCC
1 ATATGAACCCGAACCC
2317881 GAAATTAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
26 25 0.69
32 5 0.14
33 6 0.17
ACGTcount: A:0.35, C:0.33, G:0.15, T:0.17
Consensus pattern (31 bp):
ATATGAACCCGAACCCAACTACATCCGACTG
Done.