Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 10 of 153
Found at i:3135879 original size:14 final size:15
Alignment explanation
Indices: 3135860--3135892 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3135850 TTAACTTAAC
*
3135860 TTTTTATTTTC-ATT
1 TTTTTATGTTCAATT
3135874 TTTTTATGTTCAATT
1 TTTTTATGTTCAATT
3135889 TTTT
1 TTTT
3135893 GAATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTATGTTCAATT
Found at i:3137862 original size:11 final size:10
Alignment explanation
Indices: 3137846--3137884 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 10
3137836 AGATGTTTAG
3137846 TTATTTGTTTT
1 TTATTT-TTTT
3137857 TTATTTTATTT
1 TTATTTT-TTT
3137868 TTATTTTTGTT
1 TTATTTTT-TT
3137879 TTATTT
1 TTATTT
3137885 AATTTTTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.08
11 24 0.92
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:3137871 original size:22 final size:22
Alignment explanation
Indices: 3137846--3137891 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3137836 AGATGTTTAG
*
3137846 TTATTTGTT-TTTTATTTTATTT
1 TTATTT-TTGTTTTATTTAATTT
3137868 TTATTTTTGTTTTATTTAATTT
1 TTATTTTTGTTTTATTTAATTT
3137890 TT
1 TT
3137892 CACAATAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.80
Consensus pattern (22 bp):
TTATTTTTGTTTTATTTAATTT
Found at i:3139537 original size:15 final size:16
Alignment explanation
Indices: 3139501--3139535 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3139491 TTAAAAAGTT
3139501 TTTTAAAATCTTAATA
1 TTTTAAAATCTTAATA
3139517 TTTTAAAAT-TTAATTA
1 TTTTAAAATCTTAA-TA
3139533 TTT
1 TTT
3139536 AAGGGAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAAAATCTTAATA
Found at i:3139699 original size:28 final size:27
Alignment explanation
Indices: 3139647--3139702 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
3139637 TGAAGGGTTT
*
3139647 AAAAATAAATATAAATAATTTTTTTAA
1 AAAAATAAATATAAATAATATTTTTAA
* *
3139674 AAAAATAAATATTAATTATCATTTTTAA
1 AAAAATAAATATAAATAAT-ATTTTTAA
3139702 A
1 A
3139703 CATAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAAATAAATATAAATAATATTTTTAA
Found at i:3143354 original size:12 final size:12
Alignment explanation
Indices: 3143324--3143354 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3143314 TTTAATTATC
*
3143324 ATATATATACAT
1 ATATATTTACAT
3143336 ATATATTTACAT
1 ATATATTTACAT
3143348 ATATATT
1 ATATATT
3143355 ATATGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATATTTACAT
Found at i:3144679 original size:19 final size:19
Alignment explanation
Indices: 3144655--3144696 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
3144645 CCTATAATTA
3144655 TATTAATTATATTGTTTTT
1 TATTAATTATATTGTTTTT
3144674 TATTAATTATATTGTTTTT
1 TATTAATTATATTGTTTTT
3144693 TATT
1 TATT
3144697 TTATTTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TATTAATTATATTGTTTTT
Found at i:3147642 original size:22 final size:22
Alignment explanation
Indices: 3147617--3147659 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3147607 TATCGAAATA
3147617 ATAACAATAAAATAATAGCAAT
1 ATAACAATAAAATAATAGCAAT
* * *
3147639 ATAATAGTAAAATGATAGCAA
1 ATAACAATAAAATAATAGCAA
3147660 AACAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.23
Consensus pattern (22 bp):
ATAACAATAAAATAATAGCAAT
Found at i:3151155 original size:33 final size:33
Alignment explanation
Indices: 3151113--3151182 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
3151103 TCAGTAGTTT
3151113 CTTCAACACGATTTTAATGATAATCCAAAGTAA
1 CTTCAACACGATTTTAATGATAATCCAAAGTAA
3151146 CTTCAACACGATTTTAATGATAATCCAAAGTAA
1 CTTCAACACGATTTTAATGATAATCCAAAGTAA
3151179 CTTC
1 CTTC
3151183 TGTTGGTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (33 bp):
CTTCAACACGATTTTAATGATAATCCAAAGTAA
Found at i:3154107 original size:16 final size:16
Alignment explanation
Indices: 3154087--3154139 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
3154077 TTGGTTCGCT
*
3154087 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
* *
3154103 GTAATAGAATAGATGC
1 GTAATGGAATAGAGGC
3154119 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
3154135 GTAAT
1 GTAAT
3154140 AGGTAATTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.40, C:0.04, G:0.32, T:0.25
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:3154203 original size:44 final size:46
Alignment explanation
Indices: 3154121--3154213 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
3154111 ATAGATGCGT
* *
3154121 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
3154167 AATGAAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
3154211 AAT
1 AAT
3154214 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 24 0.53
45 3 0.07
46 18 0.40
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.37
Consensus pattern (46 bp):
AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:3154209 original size:39 final size:44
Alignment explanation
Indices: 3154121--3154226 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 44
3154111 ATAGATGCGT
*
3154121 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATGG
*
3154167 AATGAAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
*
3154206 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
3154227 CATAAGGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 18 0.33
40 2 0.04
43 1 0.02
44 13 0.24
45 3 0.05
46 18 0.33
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
Found at i:3154435 original size:56 final size:57
Alignment explanation
Indices: 3154317--3154437 Score: 131
Period size: 56 Copynumber: 2.1 Consensus size: 57
3154307 TTTTAATATG
* *
3154317 TTAA-TTAATATAAATAATAAATAATTTAATCATATTTTAACACAATTATTATTAAA
1 TTAATTTAATATAAATAATAAATAATTTAATAACATTTTAACACAATTATTATTAAA
* * * * * *
3154373 TATAATTTAATA-AAA-AATATATAATTTAATAACATTCTTAATATAATTTTTCTTATA
1 T-TAATTTAATATAAATAATAAATAATTTAATAACATT-TTAACACAATTATTATTAAA
3154430 TTAATTTA
1 TTAATTTA
3154438 CTTAAATTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
56 26 0.48
57 22 0.41
58 6 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (57 bp):
TTAATTTAATATAAATAATAAATAATTTAATAACATTTTAACACAATTATTATTAAA
Found at i:3156136 original size:68 final size:68
Alignment explanation
Indices: 3156018--3156158 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 68
3156008 AATATTATGT
3156018 ATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTCAATATCATAATTAGATAGCTAC
1 ATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTCAATATCATAATTAGATAGCTAC
3156083 AAA
66 AAA
* *
3156086 ATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAATTCTCGAA-ATCATAATTAGGTAGCTA
1 ATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTC-AATATCATAATTAGATAGCTA
3156150 CAAA
65 CAAA
3156154 ATCAT
1 ATCAT
3156159 ACATAAATTA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
68 68 0.97
69 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (68 bp):
ATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTCAATATCATAATTAGATAGCTAC
AAA
Found at i:3165709 original size:37 final size:35
Alignment explanation
Indices: 3165616--3165712 Score: 115
Period size: 36 Copynumber: 2.7 Consensus size: 35
3165606 TAAAATAACC
* *
3165616 AGTATTCTAATATAACAATCGAATTAAAAGAAAAAT
1 AGTATTCTAAGATAACAATCG-ATTAAAAAAAAAAT
*
3165652 AATATTCT-AGCATAACAATCGATTCAAAAAAAAAAGT
1 AGTATTCTAAG-ATAACAATCGATT-AAAAAAAAAA-T
*
3165689 AGTATTCTAAGATAATAATCGATT
1 AGTATTCTAAGATAACAATCGATT
3165713 TAAACATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
35 4 0.08
36 26 0.50
37 20 0.38
38 2 0.04
ACGTcount: A:0.52, C:0.10, G:0.09, T:0.29
Consensus pattern (35 bp):
AGTATTCTAAGATAACAATCGATTAAAAAAAAAAT
Found at i:3165737 original size:58 final size:58
Alignment explanation
Indices: 3165665--3165811 Score: 174
Period size: 55 Copynumber: 2.5 Consensus size: 58
3165655 ATTCTAGCAT
* * *
3165665 AACAATCGATTCAAAAAAAAAAGTAGTATTCTAAGATAATAATCGATTTAAACATATA
1 AACAATCGATTCAAAAAAAAAAGTAGTATTCTAACATAACAATCAATTTAAACATATA
* * *
3165723 AATAATCGATTC--AAAAGAAA-CAGTATTCTAACATAACAATCAATTTAAACATATA
1 AACAATCGATTCAAAAAAAAAAGTAGTATTCTAACATAACAATCAATTTAAACATATA
* *
3165778 AACAATTGATTCAAAAGAAGAAGAAGTTGTATTC
1 AACAATCGATTCAAAA-AA-AA-AAGTAGTATTC
3165812 CACCTTAACA
Statistics
Matches: 72, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
55 41 0.57
56 7 0.10
57 2 0.03
58 13 0.18
59 1 0.01
60 2 0.03
61 6 0.08
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.27
Consensus pattern (58 bp):
AACAATCGATTCAAAAAAAAAAGTAGTATTCTAACATAACAATCAATTTAAACATATA
Found at i:3165858 original size:18 final size:18
Alignment explanation
Indices: 3165835--3165869 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3165825 GATTCAAAAG
3165835 ATGTAGTATTTCAACATT
1 ATGTAGTATTTCAACATT
3165853 ATGTAGTATTTCAACAT
1 ATGTAGTATTTCAACAT
3165870 GATCTATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (18 bp):
ATGTAGTATTTCAACATT
Found at i:3170241 original size:5 final size:5
Alignment explanation
Indices: 3170231--3170256 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3170221 AAAGAGAGTT
3170231 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
3170257 AAGAGAGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:3174084 original size:20 final size:20
Alignment explanation
Indices: 3174059--3174098 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3174049 TGTTTATACA
3174059 TCATCTAACTTATATTTCAT
1 TCATCTAACTTATATTTCAT
*
3174079 TCATCTAATTTATATTTCAT
1 TCATCTAACTTATATTTCAT
3174099 GTAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (20 bp):
TCATCTAACTTATATTTCAT
Found at i:3175444 original size:16 final size:16
Alignment explanation
Indices: 3175411--3175444 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3175401 GTCTCGTGTT
* *
3175411 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
3175427 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
3175443 AA
1 AA
3175445 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:3178270 original size:21 final size:21
Alignment explanation
Indices: 3178244--3178284 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3178234 AGACGAGCAA
* *
3178244 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3178265 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3178285 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3180223 original size:16 final size:16
Alignment explanation
Indices: 3180190--3180223 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3180180 GGAGATTGTT
* *
3180190 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
3180206 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
3180222 AA
1 AA
3180224 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:3190344 original size:9 final size:9
Alignment explanation
Indices: 3190330--3190354 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3190320 GATAATATTG
3190330 AAATAAAAT
1 AAATAAAAT
3190339 AAATAAAAT
1 AAATAAAAT
3190348 AAATAAA
1 AAATAAA
3190355 TATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:3196728 original size:22 final size:23
Alignment explanation
Indices: 3196697--3196739 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3196687 TATTATTAGA
*
3196697 TATTTATAAATTATT-ATATATT
1 TATTTATAAAATATTAATATATT
*
3196719 TATTTTTAAAATATTAATATA
1 TATTTATAAAATATTAATATA
3196740 AACATTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTTATAAAATATTAATATATT
Found at i:3197531 original size:20 final size:20
Alignment explanation
Indices: 3197503--3197544 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3197493 ATTTTGCCCC
*
3197503 ATATCTTATAATAAATATAA
1 ATATATTATAATAAATATAA
* *
3197523 ATATATTATTATATATATAA
1 ATATATTATAATAAATATAA
3197543 AT
1 AT
3197545 TTCCCAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATTATAATAAATATAA
Found at i:3209216 original size:12 final size:12
Alignment explanation
Indices: 3209201--3209237 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
3209191 GATTAATTCT
3209201 AAAATTATATAA
1 AAAATTATATAA
*
3209213 AAAATAATAT-A
1 AAAATTATATAA
3209224 AAAATTAT-TAA
1 AAAATTATATAA
3209235 AAA
1 AAA
3209238 TTAATTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 1 0.05
11 12 0.55
12 9 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATTATATAA
Found at i:3209220 original size:23 final size:21
Alignment explanation
Indices: 3209201--3209243 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3209191 GATTAATTCT
3209201 AAAATTATATAAAAAATAATATA
1 AAAATTAT-TAAAAAATAAT-TA
*
3209224 AAAATTATTAAAAATTAATT
1 AAAATTATTAAAAAATAATT
3209244 TGTTTATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 10 0.53
23 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATTATTAAAAAATAATTA
Found at i:3209235 original size:10 final size:11
Alignment explanation
Indices: 3209201--3209240 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
3209191 GATTAATTCT
3209201 AAAATTATATAA
1 AAAATTATAT-A
*
3209213 AAAATAATATA
1 AAAATTATATA
3209224 AAAATTAT-TA
1 AAAATTATATA
3209234 AAAATTA
1 AAAATTA
3209241 ATTTGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 8 0.31
12 9 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATTATATA
Found at i:3214611 original size:24 final size:24
Alignment explanation
Indices: 3214583--3214634 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3214573 TTAGTAAGTC
** *
3214583 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTACACTAACAAATGCT
* *
3214607 AAATATATTACACTAACAAATGCT
1 AAATAAACTACACTAACAAATGCT
3214631 AAAT
1 AAAT
3214635 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAACTACACTAACAAATGCT
Found at i:3214748 original size:54 final size:54
Alignment explanation
Indices: 3214678--3214837 Score: 320
Period size: 54 Copynumber: 3.0 Consensus size: 54
3214668 ACTTGCAAAA
3214678 AATCTCTTAGAATTTGGGTCACACAACTCTAACAATCTCCACCTTGACACGAGC
1 AATCTCTTAGAATTTGGGTCACACAACTCTAACAATCTCCACCTTGACACGAGC
3214732 AATCTCTTAGAATTTGGGTCACACAACTCTAACAATCTCCACCTTGACACGAGC
1 AATCTCTTAGAATTTGGGTCACACAACTCTAACAATCTCCACCTTGACACGAGC
3214786 AATCTCTTAGAATTTGGGTCACACAACTCTAACAATCTCCACCTTGACACGA
1 AATCTCTTAGAATTTGGGTCACACAACTCTAACAATCTCCACCTTGACACGA
3214838 ATTCTTACAA
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.26
Consensus pattern (54 bp):
AATCTCTTAGAATTTGGGTCACACAACTCTAACAATCTCCACCTTGACACGAGC
Found at i:3217034 original size:278 final size:278
Alignment explanation
Indices: 3216537--3217094 Score: 1116
Period size: 278 Copynumber: 2.0 Consensus size: 278
3216527 GATCCGATCC
3216537 TCCGTATATTTTCACGTCAATCTACAAGAGACATTGAATACACTCAAGTAAGCTTATAGAAACTT
1 TCCGTATATTTTCACGTCAATCTACAAGAGACATTGAATACACTCAAGTAAGCTTATAGAAACTT
3216602 AGTAAGTTCATAGGCACAAAACATAAATCTTACCAAACATTTATACACTTATACATTATACACCG
66 AGTAAGTTCATAGGCACAAAACATAAATCTTACCAAACATTTATACACTTATACATTATACACCG
3216667 TTACTAAGTTTACCTGTCAACCACAATCACTGATGAGTCCCTTGGTATAAACTCACTACTACTTA
131 TTACTAAGTTTACCTGTCAACCACAATCACTGATGAGTCCCTTGGTATAAACTCACTACTACTTA
3216732 TCCTTTTACTATAATTCTTTTGGGCCCATTTGTCACTTACCATCCTTAATCAAAATTAGGGAACG
196 TCCTTTTACTATAATTCTTTTGGGCCCATTTGTCACTTACCATCCTTAATCAAAATTAGGGAACG
3216797 GTTACGGAAAATTGAGTA
261 GTTACGGAAAATTGAGTA
3216815 TCCGTATATTTTCACGTCAATCTACAAGAGACATTGAATACACTCAAGTAAGCTTATAGAAACTT
1 TCCGTATATTTTCACGTCAATCTACAAGAGACATTGAATACACTCAAGTAAGCTTATAGAAACTT
3216880 AGTAAGTTCATAGGCACAAAACATAAATCTTACCAAACATTTATACACTTATACATTATACACCG
66 AGTAAGTTCATAGGCACAAAACATAAATCTTACCAAACATTTATACACTTATACATTATACACCG
3216945 TTACTAAGTTTACCTGTCAACCACAATCACTGATGAGTCCCTTGGTATAAACTCACTACTACTTA
131 TTACTAAGTTTACCTGTCAACCACAATCACTGATGAGTCCCTTGGTATAAACTCACTACTACTTA
3217010 TCCTTTTACTATAATTCTTTTGGGCCCATTTGTCACTTACCATCCTTAATCAAAATTAGGGAACG
196 TCCTTTTACTATAATTCTTTTGGGCCCATTTGTCACTTACCATCCTTAATCAAAATTAGGGAACG
3217075 GTTACGGAAAATTGAGTA
261 GTTACGGAAAATTGAGTA
3217093 TC
1 TC
3217095 TCACTTCCAC
Statistics
Matches: 280, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
278 280 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (278 bp):
TCCGTATATTTTCACGTCAATCTACAAGAGACATTGAATACACTCAAGTAAGCTTATAGAAACTT
AGTAAGTTCATAGGCACAAAACATAAATCTTACCAAACATTTATACACTTATACATTATACACCG
TTACTAAGTTTACCTGTCAACCACAATCACTGATGAGTCCCTTGGTATAAACTCACTACTACTTA
TCCTTTTACTATAATTCTTTTGGGCCCATTTGTCACTTACCATCCTTAATCAAAATTAGGGAACG
GTTACGGAAAATTGAGTA
Found at i:3217212 original size:50 final size:51
Alignment explanation
Indices: 3217137--3217250 Score: 185
Period size: 50 Copynumber: 2.3 Consensus size: 51
3217127 CTTACGTATG
* *
3217137 ATCACTTATCACTTGTCTCTGATCAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* *
3217187 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
3217238 ATCACTTGTCACT
1 ATCACTTGTCACT
3217251 GATCAGAAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
50 35 0.60
51 23 0.40
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
Found at i:3232715 original size:26 final size:27
Alignment explanation
Indices: 3232686--3232749 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
3232676 AATTGATGTA
3232686 TAATTTAATATTAA-TTAAATAATAAT
1 TAATTTAATATTAAGTTAAATAATAAT
*
3232712 TAATTTAA-A-TAATGTTTAATAATAAT
1 TAATTTAATATTAA-GTTAAATAATAAT
3232738 TAA-TTAATATTA
1 TAATTTAATATTA
3232750 CTTATTCTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
24 3 0.09
25 5 0.15
26 23 0.70
27 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TAATTTAATATTAAGTTAAATAATAAT
Found at i:3232731 original size:16 final size:16
Alignment explanation
Indices: 3232691--3232724 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3232681 ATGTATAATT
3232691 TAAT-ATTAA-TTAAA
1 TAATAATTAATTTAAA
3232705 TAATAATTAATTTAAA
1 TAATAATTAATTTAAA
3232721 TAAT
1 TAAT
3232725 GTTTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 5 0.28
16 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAATTAATTTAAA
Found at i:3232749 original size:10 final size:10
Alignment explanation
Indices: 3232690--3232749 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
3232680 GATGTATAAT
3232690 TTAATATTAA
1 TTAATATTAA
*
3232700 TTAAATAATAA
1 TT-AATATTAA
3232711 TTAAT-TTAA
1 TTAATATTAA
* *
3232720 ATAATGTTTAA
1 TTAAT-ATTAA
3232731 -TAATAATTAA
1 TTAAT-ATTAA
3232741 TTAATATTA
1 TTAATATTA
3232750 CTTATTCTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 7 0.17
10 17 0.41
11 17 0.41
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (10 bp):
TTAATATTAA
Found at i:3241581 original size:8 final size:8
Alignment explanation
Indices: 3241568--3241605 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
3241558 AATTAAAGTG
3241568 AATTATTA
1 AATTATTA
3241576 AATTATTA
1 AATTATTA
*
3241584 AATTAATAA
1 AATT-ATTA
3241593 AATTATTA
1 AATTATTA
3241601 AATTA
1 AATTA
3241606 AGGATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
AATTATTA
Found at i:3243824 original size:11 final size:10
Alignment explanation
Indices: 3243806--3243831 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3243796 ATCAACACCC
3243806 TCTTTTTTTT
1 TCTTTTTTTT
3243816 TCTTTTTTTT
1 TCTTTTTTTT
3243826 TCTTTT
1 TCTTTT
3243832 CCTTTGTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:3244823 original size:28 final size:28
Alignment explanation
Indices: 3244779--3244838 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
3244769 TATATTATAC
* *
3244779 TATATTATTTTAATATTTAATAGTTTTA
1 TATATTATTTTAATATTGAAAAGTTTTA
* *
3244807 TATATT-TTTTATTTATTGAAAATTTTTA
1 TATATTATTTTA-ATATTGAAAAGTTTTA
3244835 TATA
1 TATA
3244839 GTCATCGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (28 bp):
TATATTATTTTAATATTGAAAAGTTTTA
Found at i:3248013 original size:4 final size:4
Alignment explanation
Indices: 3248004--3248028 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3247994 CACCATTTAA
3248004 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
3248029 TTACATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:3249781 original size:3 final size:3
Alignment explanation
Indices: 3249773--3249805 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3249763 CTCAGCACCC
3249773 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3249806 ATTTCTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3259643 original size:21 final size:21
Alignment explanation
Indices: 3259617--3259657 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3259607 ATCTGCTCAA
* *
3259617 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3259638 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3259658 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3264424 original size:21 final size:21
Alignment explanation
Indices: 3264398--3264438 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3264388 ATCTGCTCAA
* *
3264398 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3264419 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3264439 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3269912 original size:20 final size:21
Alignment explanation
Indices: 3269889--3269934 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
3269879 AAAAAAATTT
* *
3269889 AAAATAAAT-ATAATTTATTA
1 AAAATAAATAAAAATATATTA
*
3269909 AAAA-GAATAAAAATATATTA
1 AAAATAAATAAAAATATATTA
3269929 AAAATA
1 AAAATA
3269935 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATAAATAAAAATATATTA
Found at i:3270176 original size:38 final size:38
Alignment explanation
Indices: 3270132--3270207 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3270122 TAAAATAAGA
3270132 AAAAAAATACACTGCTTTAAGCCACTTGCAAAAGAACT
1 AAAAAAATACACTGCTTTAAGCCACTTGCAAAAGAACT
3270170 AAAAAAATACACTGCTTTAAGCCACTTGCAAAAGAACT
1 AAAAAAATACACTGCTTTAAGCCACTTGCAAAAGAACT
3270208 TTCAAAAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (38 bp):
AAAAAAATACACTGCTTTAAGCCACTTGCAAAAGAACT
Found at i:3274917 original size:17 final size:18
Alignment explanation
Indices: 3274897--3274940 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
3274887 TATAATCTTA
3274897 TTTTA-ATATTAATAATTT
1 TTTTATATATTAA-AATTT
*
3274915 TTTTATTTATTAAAA-TT
1 TTTTATATATTAAAATTT
3274932 TTTTATATA
1 TTTTATATA
3274941 ATCATCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 10 0.43
18 7 0.30
19 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATATATTAAAATTT
Found at i:3288026 original size:14 final size:14
Alignment explanation
Indices: 3288001--3288033 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3287991 ACACTTATCT
3288001 AAATATTCAAATAA
1 AAATATTCAAATAA
3288015 GAAATA-TCAAATAA
1 -AAATATTCAAATAA
3288029 AAATA
1 AAATA
3288034 ATTAGGGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 8 0.44
15 5 0.28
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATATTCAAATAA
Found at i:3297477 original size:24 final size:24
Alignment explanation
Indices: 3297450--3297495 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3297440 AAGCTCATGC
*
3297450 GAGCCAATATC-GGATAGCTCCGAA
1 GAGCCAATAACGGGA-AGCTCCGAA
3297474 GAGCCAATAACGGGAAGCTCCG
1 GAGCCAATAACGGGAAGCTCCG
3297496 GATAGCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.33, C:0.26, G:0.28, T:0.13
Consensus pattern (24 bp):
GAGCCAATAACGGGAAGCTCCGAA
Found at i:3300111 original size:15 final size:17
Alignment explanation
Indices: 3300082--3300113 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3300072 TAGTTGAGAA
3300082 TTTTATGTAACAATTTT
1 TTTTATGTAACAATTTT
3300099 TTTTAT-TAA-AATTTT
1 TTTTATGTAACAATTTT
3300114 ACATAGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTATGTAACAATTTT
Found at i:3307628 original size:31 final size:30
Alignment explanation
Indices: 3307569--3307628 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
3307559 TAATTGAGTT
* *
3307569 TAAATTTTAAAATATGAAAAGTGGAATGAC
1 TAAATTTTAAAATATGAAAAATGAAATGAC
* *
3307599 TAAATTCTTAAAATTTGAAAAATTAAATGA
1 TAAATT-TTAAAATATGAAAAATGAAATGA
3307629 GTATAGAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (30 bp):
TAAATTTTAAAATATGAAAAATGAAATGAC
Found at i:3312671 original size:42 final size:42
Alignment explanation
Indices: 3312612--3312698 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
3312602 TAGCAGATAA
3312612 TGTAAGACCAGGATAAAGCCCATTGTAACTTTTCAGCAAAAC
1 TGTAAGACCAGGATAAAGCCCATTGTAACTTTTCAGCAAAAC
3312654 TGTAAGACCAGGATAAAGCCCATTGTAACTTTTCAGCAAAAC
1 TGTAAGACCAGGATAAAGCCCATTGTAACTTTTCAGCAAAAC
3312696 TGT
1 TGT
3312699 TTGGTATTCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (42 bp):
TGTAAGACCAGGATAAAGCCCATTGTAACTTTTCAGCAAAAC
Found at i:3338411 original size:3 final size:3
Alignment explanation
Indices: 3338403--3338457 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
3338393 ATTGGAGGAA
* * * * *
3338403 CTG CTG CTG CTG CTG CTG CTG TTG CTG TTG TTG TTG CTG TTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
3338451 CTG CTG C
1 CTG CTG C
3338458 AAAAGCATTG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.25, G:0.33, T:0.42
Consensus pattern (3 bp):
CTG
Found at i:3341133 original size:13 final size:13
Alignment explanation
Indices: 3341115--3341141 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3341105 GAGCCATGCA
3341115 GAACAAACGAAAT
1 GAACAAACGAAAT
3341128 GAACAAACGAAAT
1 GAACAAACGAAAT
3341141 G
1 G
3341142 GACTCAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.15, G:0.19, T:0.07
Consensus pattern (13 bp):
GAACAAACGAAAT
Found at i:3345309 original size:17 final size:17
Alignment explanation
Indices: 3345287--3345320 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3345277 ATCCACTAAT
*
3345287 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
3345304 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
3345321 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:3348341 original size:17 final size:17
Alignment explanation
Indices: 3348319--3348352 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3348309 ATCCACTAAT
*
3348319 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
3348336 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
3348353 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:3350923 original size:30 final size:30
Alignment explanation
Indices: 3350889--3350950 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
3350879 CTTAACAAGT
3350889 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
* *
3350919 AAATGTCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
3350949 AA
1 AA
3350951 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:3351835 original size:17 final size:17
Alignment explanation
Indices: 3351803--3351849 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
3351793 AAACTAATGG
*
3351803 TAATTTTTTTAA-GAGA
1 TAATTTTTTAAATGAGA
3351819 GT-ATTTTTTAAATGAGA
1 -TAATTTTTTAAATGAGA
3351836 TAATTTTTTTAAAT
1 TAA-TTTTTTAAAT
3351850 ATTAGTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 10 0.38
17 6 0.23
18 10 0.38
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (17 bp):
TAATTTTTTAAATGAGA
Found at i:3353021 original size:18 final size:19
Alignment explanation
Indices: 3352991--3353027 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3352981 TTTGCAAATC
3352991 AAATATTTATTATAAATTT
1 AAATATTTATTATAAATTT
*
3353010 AAATATTT-TTATTAATTT
1 AAATATTTATTATAAATTT
3353028 TAAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATATTTATTATAAATTT
Found at i:3353029 original size:19 final size:18
Alignment explanation
Indices: 3352991--3353063 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 18
3352981 TTTGCAAATC
*
3352991 AAATATTTATTATAAATTT
1 AAATATTT-TTATAATTTT
3353010 AAATATTTTTATTAATTTT
1 AAATATTTTTA-TAATTTT
*
3353029 AAAATAATTTTAATAATTTT
1 -AAAT-ATTTTTATAATTTT
* *
3353049 ATA-ATTATTATAATT
1 AAATATTTTTATAATT
3353064 ATTTGAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
17 10 0.22
18 3 0.07
19 16 0.35
20 11 0.24
21 6 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AAATATTTTTATAATTTT
Found at i:3353039 original size:20 final size:20
Alignment explanation
Indices: 3353010--3353072 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
3353000 TTATAAATTT
* *
3353010 AAATATTTTTATTAATTTTA
1 AAATAATTTTAATAATTTTA
3353030 AAATAATTTTAATAATTTTA
1 AAATAATTTTAATAATTTTA
* * * * *
3353050 TAATTATTATAATTATTTGA
1 AAATAATTTTAATAATTTTA
3353070 AAA
1 AAA
3353073 ACTACATTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
AAATAATTTTAATAATTTTA
Found at i:3353043 original size:9 final size:9
Alignment explanation
Indices: 3353005--3353063 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
3352995 ATTTATTATA
*
3353005 AATTTAAAT
1 AATTTTAAT
* *
3353014 ATTTTTATT
1 AATTTTAAT
3353023 AATTTTAAAAT
1 AATTTT--AAT
3353034 AATTTTAAT
1 AATTTTAAT
3353043 AATTTT-AT
1 AATTTTAAT
3353051 AATTATT-AT
1 AATT-TTAAT
3353060 AATT
1 AATT
3353064 ATTTGAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
8 6 0.14
9 28 0.67
11 8 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTTAAT
Found at i:3353067 original size:29 final size:29
Alignment explanation
Indices: 3352997--3353067 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
3352987 AATCAAATAT
*
3352997 TTATTATAA-ATTTAAATATTTTTATTAA
1 TTATTATAATATTTAAATAATTTTATTAA
* *
3353025 TT-TTAAAATAATTTTAATAATTTTA-TAA
1 TTATTATAAT-ATTTAAATAATTTTATTAA
3353053 TTATTATAATTATTT
1 TTATTATAA-TATTT
3353068 GAAAAACTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
27 5 0.14
28 7 0.20
29 22 0.63
30 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTATTATAATATTTAAATAATTTTATTAA
Found at i:3354482 original size:50 final size:49
Alignment explanation
Indices: 3354376--3354480 Score: 113
Period size: 50 Copynumber: 2.1 Consensus size: 49
3354366 TTTTTGAATT
* * * * *
3354376 TTTTAAGAATTAAGACTAAATTGATAGAATGTGTAAAGTTAAGGGTTAAA
1 TTTTAA-AATTAAGACCAAATTGATAGAATGTATAAAATTAAGAGCTAAA
3354426 TTTTTAAAATTAAGACCAAATTGATAGAAT-TAATAAACATTAGAGAGCTAAA
1 -TTTTAAAATTAAGACCAAATTGATAGAATGT-ATAAA-ATTA-AGAGCTAAA
3354478 TTT
1 TTT
3354481 AATATTATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
49 1 0.02
50 26 0.57
51 12 0.26
52 7 0.15
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (49 bp):
TTTTAAAATTAAGACCAAATTGATAGAATGTATAAAATTAAGAGCTAAA
Found at i:3355122 original size:21 final size:22
Alignment explanation
Indices: 3355098--3355148 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
3355088 ATCTTTCCAT
*
3355098 TTTTGTTTTC-AGGTATATTTC
1 TTTTGTTTTCGAGGTAGATTTC
* *
3355119 TTTTGTTTCCGAGTTAGATTTC
1 TTTTGTTTTCGAGGTAGATTTC
3355141 -TTTGTTTT
1 TTTTGTTTT
3355149 GTTGTTGATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.16, T:0.63
Consensus pattern (22 bp):
TTTTGTTTTCGAGGTAGATTTC
Found at i:3356513 original size:159 final size:159
Alignment explanation
Indices: 3356217--3356775 Score: 935
Period size: 159 Copynumber: 3.5 Consensus size: 159
3356207 CAGGACTTAC
* * * * * *
3356217 GGGGATAAGGTTGATAAAAATGATGACAA--GGTGTCGGATAAACGCTCAGCT-GATCAGGTGAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGT-TC-GATAAAAGCTCTGATAG-TCAAGTG--
* *
3356279 AAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGTTGATC
61 AAA-AAGAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATC
* *
3356344 AGGTGGAAAAGAGCTCAAATGAAGTTTTCCCTAAA
125 AGGTGAAAAAGAGATCAAATGAAGTTTTCCCTAAA
3356379 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
3356444 GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
66 GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
3356509 AAAAGAGATCAAATGAAGTTTTCCCTAAA
131 AAAAGAGATCAAATGAAGTTTTCCCTAAA
3356538 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
3356603 GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
66 GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
3356668 AAAAGAGATCAAATGAAGTTTTCCCTAAA
131 AAAAGAGATCAAATGAAGTTTTCCCTAAA
*
3356697 GGGGATAAGGTTGACAAAAATAATGACAATGTGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
*
3356762 GAGCTCAAATGAAG
66 GAGTTCAAATGAAG
3356776 TTTTCCCATC
Statistics
Matches: 382, Mismatches: 12, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
159 328 0.86
160 3 0.01
162 45 0.12
163 3 0.01
164 3 0.01
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (159 bp):
GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
AAAAGAGATCAAATGAAGTTTTCCCTAAA
Found at i:3361728 original size:16 final size:15
Alignment explanation
Indices: 3361696--3361771 Score: 50
Period size: 15 Copynumber: 5.0 Consensus size: 15
3361686 CTTTTATTGT
3361696 TTTTTTTATAATAAA
1 TTTTTTTATAATAAA
**
3361711 TTTTTTTATTGTATAA
1 TTTTTTTATAATA-AA
* *
3361727 TTGTTTT-TCATAAA
1 TTTTTTTATAATAAA
3361741 TTTGTTTGT-TAATATAA
1 TTT-TTT-TATAATA-AA
*
3361758 -ATTTTTATAATAAA
1 TTTTTTTATAATAAA
3361772 AATATTACCA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
14 7 0.15
15 25 0.52
16 14 0.29
17 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.59
Consensus pattern (15 bp):
TTTTTTTATAATAAA
Found at i:3366906 original size:51 final size:51
Alignment explanation
Indices: 3366851--3367402 Score: 519
Period size: 51 Copynumber: 10.9 Consensus size: 51
3366841 GTGAAAGTGT
*
3366851 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* * * * * * * * *
3366902 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAA-ATAA
*
3366953 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* * * * * * * * *
3367004 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAA-ATAA
*
3367055 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* * * * ** * * * * *
3367106 TGGTCACATGTGTAATACTAAGTGAAGGCTACAATATGTACCGAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAA-ATAA
* * *
3367157 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* * * * * *
3367208 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAA--TAA
* * * *
3367259 TAGTCACATATGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAA-ACT
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-A
* * * *
3367309 TGATCACGTGTATAGTACTATGTGAAGGCTATTACGTGAACCG-TAAA-AA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* *
3367358 TTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 -TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
3367403 ATGATAATAG
Statistics
Matches: 397, Mismatches: 91, Indels: 26
0.77 0.18 0.05
Matches are distributed among these distances:
50 87 0.22
51 306 0.77
52 4 0.01
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (51 bp):
TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
Found at i:3367026 original size:102 final size:102
Alignment explanation
Indices: 3366850--3367402 Score: 844
Period size: 102 Copynumber: 5.4 Consensus size: 102
3366840 AGTGAAAGTG
3366850 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
3366915 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
3366952 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
3367017 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
3367054 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* *
3367119 AATACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
* *
3367156 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* *
3367221 AGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCT
66 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
* * * * * * * *
3367258 TTAGTCACATATGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAA-ACTTGATCACGTGTA
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTG
* ** * * **
3367321 TAGTACTATGTGAAGGCTATTACGTGAACCGTA-AA-AA
65 TAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCT
* * *
3367358 TTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGA
3367403 ATGATAATAG
Statistics
Matches: 419, Mismatches: 29, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
100 39 0.09
101 42 0.10
102 338 0.81
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (102 bp):
TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
Found at i:3369440 original size:19 final size:18
Alignment explanation
Indices: 3369399--3369443 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
3369389 TTGAAATTTT
* *
3369399 TAAAAATATAAAAATATA
1 TAAAAATTTAAAAAAATA
3369417 T-AAAATTTAAAAAAATAA
1 TAAAAATTTAAAAAAAT-A
3369435 TAAAAATTT
1 TAAAAATTT
3369444 TTTTTATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 13 0.57
18 3 0.13
19 7 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAATTTAAAAAAATA
Found at i:3372476 original size:35 final size:35
Alignment explanation
Indices: 3372430--3372501 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
3372420 GTTATCTATA
3372430 TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
1 TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
3372465 TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
1 TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
3372500 TG
1 TG
3372502 ACATAATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (35 bp):
TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
Found at i:3380501 original size:43 final size:43
Alignment explanation
Indices: 3380465--3380611 Score: 240
Period size: 43 Copynumber: 3.4 Consensus size: 43
3380455 TCCCGGACAG
3380465 GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
1 GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
* * *
3380508 GATCTTACACGAAAACACAGGTTGATGCCAACGTCCCAGACGT
1 GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
* * *
3380551 GGTCTTACACGAAAACCCAAGTCGATGCCAACATCCTAGACGT
1 GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
3380594 GGTCTTACACGAAAACAC
1 GGTCTTACACGAAAACAC
3380612 TTATCAGAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 94 1.00
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (43 bp):
GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
Found at i:3387132 original size:2 final size:2
Alignment explanation
Indices: 3387127--3387247 Score: 242
Period size: 2 Copynumber: 60.5 Consensus size: 2
3387117 TATATAATAA
3387127 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3387169 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3387211 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3387248 AACCCTAAGG
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 119 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3407885 original size:27 final size:27
Alignment explanation
Indices: 3407855--3407909 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
3407845 ATGATGAAAT
3407855 TGATACATGGAACAAAACATTACTTGA
1 TGATACATGGAACAAAACATTACTTGA
* *
3407882 TGATACATGGAACACAACATTAGTTGA
1 TGATACATGGAACAAAACATTACTTGA
3407909 T
1 T
3407910 CCATGATGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (27 bp):
TGATACATGGAACAAAACATTACTTGA
Found at i:3409223 original size:35 final size:35
Alignment explanation
Indices: 3409177--3409252 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
3409167 TATTTTATAC
* * *
3409177 TTAATTTTTATGGTT-CTTTATGATTATCCTGCCCA
1 TTAATTCTTAT-GTTGCATTATGATTACCCTGCCCA
3409212 TTAATTCTTATGTTGCATTATGATTACCCTGCCCA
1 TTAATTCTTATGTTGCATTATGATTACCCTGCCCA
*
3409247 TCAATT
1 TTAATT
3409253 TTTTTCATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
34 3 0.08
35 33 0.92
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (35 bp):
TTAATTCTTATGTTGCATTATGATTACCCTGCCCA
Found at i:3419712 original size:10 final size:10
Alignment explanation
Indices: 3419697--3419729 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
3419687 TGAGCACTAA
3419697 ACATACACAC
1 ACATACACAC
3419707 ACATACACAC
1 ACATACACAC
3419717 ACATACACAC
1 ACATACACAC
3419727 ACA
1 ACA
3419730 CACATATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.52, C:0.39, G:0.00, T:0.09
Consensus pattern (10 bp):
ACATACACAC
Found at i:3425762 original size:27 final size:23
Alignment explanation
Indices: 3425709--3425756 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3425699 AACATAGCAC
3425709 TAAATAAAAGCAAGAAGGCATCT
1 TAAATAAAAGCAAGAAGGCATCT
3425732 TAAATAAAAGCAAGAAGGCATCT
1 TAAATAAAAGCAAGAAGGCATCT
3425755 TA
1 TA
3425757 GGTAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (23 bp):
TAAATAAAAGCAAGAAGGCATCT
Found at i:3428393 original size:23 final size:23
Alignment explanation
Indices: 3428367--3428417 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3428357 TTAACTAATT
*
3428367 TTATAAATATATATTAAAATATA
1 TTATAAATATATATTAAAAAATA
** * *
3428390 TTATACTTATTTCTTAAAAAATA
1 TTATAAATATATATTAAAAAATA
3428413 TTATA
1 TTATA
3428418 GAATTCGTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATAAATATATATTAAAAAATA
Found at i:3432104 original size:19 final size:20
Alignment explanation
Indices: 3432068--3432105 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3432058 TTTAAAACTT
* *
3432068 AAAATAAAAAACAGTTTAAG
1 AAAAGAAAAAACACTTTAAG
3432088 AAAAGAAAAAA-ACTTTAA
1 AAAAGAAAAAACACTTTAA
3432106 AATATGAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.18
Consensus pattern (20 bp):
AAAAGAAAAAACACTTTAAG
Found at i:3437641 original size:9 final size:9
Alignment explanation
Indices: 3437627--3437718 Score: 157
Period size: 9 Copynumber: 10.2 Consensus size: 9
3437617 TCGGGTATTT
*
3437627 TTCGGTTAA
1 TTCGGGTAA
*
3437636 TTCGGTTAA
1 TTCGGGTAA
*
3437645 TTCGGTTAA
1 TTCGGGTAA
3437654 TTCGGGTAA
1 TTCGGGTAA
3437663 TTCGGGTAA
1 TTCGGGTAA
3437672 TTCGGGTAA
1 TTCGGGTAA
3437681 TTCGGGTAA
1 TTCGGGTAA
3437690 TTCGGGTAA
1 TTCGGGTAA
3437699 TTCGGGTAA
1 TTCGGGTAA
3437708 TTCGGGTAA
1 TTCGGGTAA
3437717 TT
1 TT
3437719 TTTAACCAAA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
9 82 1.00
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:3437896 original size:12 final size:12
Alignment explanation
Indices: 3437879--3437903 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3437869 AGTAATTTCG
3437879 GGTCGGTTAACC
1 GGTCGGTTAACC
3437891 GGTCGGTTAACC
1 GGTCGGTTAACC
3437903 G
1 G
3437904 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:3438895 original size:3 final size:3
Alignment explanation
Indices: 3438887--3438913 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3438877 TTTTCTCCAT
3438887 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
3438914 CTTTTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:3440477 original size:63 final size:65
Alignment explanation
Indices: 3440404--3440537 Score: 227
Period size: 63 Copynumber: 2.1 Consensus size: 65
3440394 AATTAAGAGT
* *
3440404 TAATTTTTCTTAGATAATTACGTTTATTTTCTTTAAATTAAGAG-T-TTTTTTTAATTTAATGTA
1 TAATTTTTCTTAGATAAGTACATTTATTTTCTTTAAATTAAGAGTTGTTTTTTTAATTTAATGTA
3440467 TAATTTTTCTTAGATAAGTACATTTATTTTCTTTAAATTAAGAGTTGTTTTTTTAATTTAATGTA
1 TAATTTTTCTTAGATAAGTACATTTATTTTCTTTAAATTAAGAGTTGTTTTTTTAATTTAATGTA
*
3440532 TTATTT
1 TAATTT
3440538 ATTTTATTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
63 42 0.64
64 1 0.02
65 23 0.35
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.57
Consensus pattern (65 bp):
TAATTTTTCTTAGATAAGTACATTTATTTTCTTTAAATTAAGAGTTGTTTTTTTAATTTAATGTA
Found at i:3443246 original size:30 final size:30
Alignment explanation
Indices: 3443175--3443246 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
3443165 CCACCCCAAG
* * *
3443175 TTTTTGAAAATTTTAGTTATACCCTTAAAA
1 TTTTTGAAAATTTTAATTAGACCCCTAAAA
* *
3443205 TTTTCTG-AAATTTTAATTAGGCCCCTCAAA
1 TTTT-TGAAAATTTTAATTAGACCCCTAAAA
3443235 TTTTTGAAAATT
1 TTTTTGAAAATT
3443247 ATTATTAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 2 0.06
30 31 0.89
31 2 0.06
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (30 bp):
TTTTTGAAAATTTTAATTAGACCCCTAAAA
Found at i:3451077 original size:185 final size:185
Alignment explanation
Indices: 3450765--3451125 Score: 551
Period size: 185 Copynumber: 2.0 Consensus size: 185
3450755 ACTAATGATC
* *
3450765 ATAACATTCTAATGATTCAAGGCCACTGCATGCATATATGTGATAAGCTCTCGTTGTTGCCTTTG
1 ATAACATTCTAATGATTCAAGGCCACTGCATGCATATATGTGATAAGCTCTCGTTGTTACCTCTG
* * *
3450830 TTGTTCCAACAATATTCACCAATATAGACACTTACTGGCTCTTCTTCATAGCTGTAAATGCATGC
66 TCGTTCCAACAATATTCACCAAAATAGACACTTACTGGCTCATCTTCATAGCTGTAAATGCATGC
* * *
3450895 AAACATGATCATTCATTCATTATTATTATCATCATTAATTTTTTTAATGGCATTT
131 AAACATGATCATTCATTCATTAGTATCATCATCATCAATTTTTTTAATGGCATTT
* *
3450950 ATAACATTCTAATGATTCAAGGCCATTGCATGCATATATTTGATAAGCTCTCGTTGTTACCTCTG
1 ATAACATTCTAATGATTCAAGGCCACTGCATGCATATATGTGATAAGCTCTCGTTGTTACCTCTG
* * * * ** *
3451015 TCGTTTCAACGATATTCACCAAAATAGACACTTGCTGTCTCATCTTTGTTGCTGTAAATGCATGC
66 TCGTTCCAACAATATTCACCAAAATAGACACTTACTGGCTCATCTTCATAGCTGTAAATGCATGC
* *
3451080 AAACATGATCATTTATTCTTTAGTATCATCATCATCAATTTTTTTA
131 AAACATGATCATTCATTCATTAGTATCATCATCATCAATTTTTTTA
3451126 CTGATGTATG
Statistics
Matches: 157, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
185 157 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (185 bp):
ATAACATTCTAATGATTCAAGGCCACTGCATGCATATATGTGATAAGCTCTCGTTGTTACCTCTG
TCGTTCCAACAATATTCACCAAAATAGACACTTACTGGCTCATCTTCATAGCTGTAAATGCATGC
AAACATGATCATTCATTCATTAGTATCATCATCATCAATTTTTTTAATGGCATTT
Found at i:3454424 original size:43 final size:43
Alignment explanation
Indices: 3454376--3454461 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
3454366 GACACACAGA
3454376 GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
1 GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
3454419 GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
1 GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
3454462 CAACCAACCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (43 bp):
GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
Found at i:3476624 original size:19 final size:20
Alignment explanation
Indices: 3476601--3476652 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
3476591 TTTATAACGT
3476601 CGTAAAAAAATTATAAAAAG
1 CGTAAAAAAATTATAAAAAG
* *
3476621 -GTAAAGAAA-TATAAAATG
1 CGTAAAAAAATTATAAAAAG
3476639 CGTAAAAAAATTAT
1 CGTAAAAAAATTAT
3476653 CGTACTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 8 0.30
19 16 0.59
20 3 0.11
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.23
Consensus pattern (20 bp):
CGTAAAAAAATTATAAAAAG
Found at i:3476887 original size:20 final size:21
Alignment explanation
Indices: 3476864--3476903 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3476854 TATAAAAAAA
*
3476864 TTAC-AGTTTTTTATATTTTT
1 TTACGAGTTTTTTAAATTTTT
*
3476884 TTACGATTTTTTTAAATTTT
1 TTACGAGTTTTTTAAATTTT
3476904 AATAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (21 bp):
TTACGAGTTTTTTAAATTTTT
Found at i:3503043 original size:13 final size:13
Alignment explanation
Indices: 3503025--3503089 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
3503015 AGTTTAGTAT
*
3503025 TGTTTTTGAGAAG
1 TGTTTTTGAAAAG
*
3503038 TGTTTTTAAAAAG
1 TGTTTTTGAAAAG
** *
3503051 TGTCGTGGAAAAG
1 TGTTTTTGAAAAG
* *
3503064 TGATTTTGAGAAG
1 TGTTTTTGAAAAG
*
3503077 TATTTTTGAAAAG
1 TGTTTTTGAAAAG
3503090 ATTGGTTTAA
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.32, C:0.02, G:0.26, T:0.40
Consensus pattern (13 bp):
TGTTTTTGAAAAG
Found at i:3503768 original size:79 final size:79
Alignment explanation
Indices: 3503669--3503825 Score: 278
Period size: 79 Copynumber: 2.0 Consensus size: 79
3503659 CAAACTAAGT
*
3503669 AACCACCCTTCAATTCTTTCTATATAAACAAGACAAATTTCATGACCTTAAGCAGACTGCAATAG
1 AACCACCCTTCAATTCTTTCTATATAAACAAGACAAATTTCATGACCTTAAGCAGACAGCAATAG
3503734 AGGTTCCAATAGAC
66 AGGTTCCAATAGAC
* * *
3503748 AACCACCCTTCAATTCTTTCTATATAAACAAGACAAATTTCATGAGCTTAAGCGGACAGCAATGG
1 AACCACCCTTCAATTCTTTCTATATAAACAAGACAAATTTCATGACCTTAAGCAGACAGCAATAG
3503813 AGGTTCCAATAGA
66 AGGTTCCAATAGA
3503826 GGCAGAAAGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (79 bp):
AACCACCCTTCAATTCTTTCTATATAAACAAGACAAATTTCATGACCTTAAGCAGACAGCAATAG
AGGTTCCAATAGAC
Found at i:3507976 original size:12 final size:13
Alignment explanation
Indices: 3507953--3507981 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3507943 ATAAATAAAA
3507953 ATAAATAAAACAT
1 ATAAATAAAACAT
3507966 ATAAA-AAAACAT
1 ATAAATAAAACAT
3507978 ATAA
1 ATAA
3507982 TTTTCGGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (13 bp):
ATAAATAAAACAT
Found at i:3512110 original size:25 final size:25
Alignment explanation
Indices: 3512082--3512130 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
3512072 AATATGTAAA
3512082 GTTAATTTAAAATTTTCATCGACCG
1 GTTAATTTAAAATTTTCATCGACCG
*
3512107 GTTAATTTAAAATTTTCATTGACC
1 GTTAATTTAAAATTTTCATCGACC
3512131 CAGTTGGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (25 bp):
GTTAATTTAAAATTTTCATCGACCG
Found at i:3516120 original size:21 final size:22
Alignment explanation
Indices: 3516091--3516137 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3516081 CAGAAGGAGT
*
3516091 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3516113 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3516134 GAGT
1 GAGT
3516138 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:3517501 original size:24 final size:23
Alignment explanation
Indices: 3517421--3517501 Score: 58
Period size: 25 Copynumber: 3.3 Consensus size: 23
3517411 TTATCTTAAA
3517421 AATTAATATTTTAGTATTAAAAA-AT
1 AATTAA-A-TTTAGT-TTAAAAATAT
* **
3517446 AATTTAATTTTTTTTAAAAAT-T
1 AATTAAATTTAGTTTAAAAATAT
3517468 AATAGCTAAATTTAGTTTAAAAATGAT
1 AAT---TAAATTTAGTTTAAAAAT-AT
3517495 AATTAAA
1 AATTAAA
3517502 ATGACAAATG
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
22 11 0.25
23 4 0.09
24 5 0.11
25 20 0.45
27 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.44
Consensus pattern (23 bp):
AATTAAATTTAGTTTAAAAATAT
Found at i:3533465 original size:3 final size:3
Alignment explanation
Indices: 3533457--3533497 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
3533447 AATGGAAATA
*
3533457 ATC ATC ATC AGC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
3533498 ATATATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:3534692 original size:16 final size:17
Alignment explanation
Indices: 3534657--3534690 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3534647 AGGGTATTTT
3534657 ATAAAAATATTATAAAA
1 ATAAAAATATTATAAAA
3534674 ATAAAAAT-TTACTAAAA
1 ATAAAAATATTA-TAAAA
3534691 TATTATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAATATTATAAAA
Found at i:3534737 original size:26 final size:27
Alignment explanation
Indices: 3534680--3534803 Score: 191
Period size: 27 Copynumber: 4.6 Consensus size: 27
3534670 AAAAATAAAA
*
3534680 ATTTACTAAAATAT-TATAACTTTTTTTT
1 ATTTACCAAAATATATA-AAC-TTTTTTT
3534708 ATTTACCAAAATAT-TACAA-TTTTTTT
1 ATTTACCAAAATATATA-AACTTTTTTT
3534734 ATTTACCAAAATATATAAACTTTTTTT
1 ATTTACCAAAATATATAAACTTTTTTT
3534761 ATTTACCAAAATATATAAACTTTTTTT
1 ATTTACCAAAATATATAAACTTTTTTT
3534788 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
3534804 CAAAAAAAAA
Statistics
Matches: 92, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
26 23 0.25
27 52 0.57
28 17 0.18
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTACCAAAATATATAAACTTTTTTT
Found at i:3534899 original size:27 final size:26
Alignment explanation
Indices: 3534845--3534929 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 26
3534835 TTGACACCAA
*
3534845 CCAATTAAATTGGCGGCACCAAAT-GTG
1 CCAAATAAATTGGCGGCACC--ATGGTG
*
3534872 CCAAATAAATTGGTGGCACCATTGGTG
1 CCAAATAAATTGGCGGCACCA-TGGTG
* *
3534899 CCAAAGT-CATTAGCGGCACCATGGTG
1 CCAAA-TAAATTGGCGGCACCATGGTG
3534925 CCAAA
1 CCAAA
3534930 AGAAAAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
25 1 0.02
26 11 0.22
27 37 0.74
28 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (26 bp):
CCAAATAAATTGGCGGCACCATGGTG
Found at i:3535031 original size:19 final size:19
Alignment explanation
Indices: 3535004--3535073 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
3534994 TCAACTCATT
*
3535004 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
3535023 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
3535041 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
3535060 TTTTAATTTAATAA
1 TTTTAATTTAATAA
3535074 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:3535054 original size:37 final size:37
Alignment explanation
Indices: 3535009--3535079 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
3534999 TCATTTTTTT
3535009 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
3535046 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
3535080 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:3535519 original size:27 final size:28
Alignment explanation
Indices: 3535446--3535542 Score: 178
Period size: 28 Copynumber: 3.5 Consensus size: 28
3535436 TTTTTTTTAT
3535446 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
3535474 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
*
3535502 ATATTTTGGTAAAT-AAAAAAACTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
3535529 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
3535543 TTTTATTTTT
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
27 26 0.38
28 42 0.62
ACGTcount: A:0.47, C:0.01, G:0.13, T:0.38
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:3546339 original size:23 final size:23
Alignment explanation
Indices: 3546312--3546357 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3546302 TTTTTGTTAA
3546312 GCCTGTATGTTCATTCATTTTGC
1 GCCTGTATGTTCATTCATTTTGC
3546335 GCCTGTATGTTCATTCATTTTGC
1 GCCTGTATGTTCATTCATTTTGC
3546358 AATTTTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (23 bp):
GCCTGTATGTTCATTCATTTTGC
Found at i:3550650 original size:22 final size:24
Alignment explanation
Indices: 3550625--3550669 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3550615 TCATACATTA
3550625 TAAAAG-AAAATA-CAAAAAAAAG
1 TAAAAGAAAAATATCAAAAAAAAG
*
3550647 TAAAGGAAAAATATCAAAAAAAA
1 TAAAAGAAAAATATCAAAAAAAA
3550670 AATGAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 9 0.45
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (24 bp):
TAAAAGAAAAATATCAAAAAAAAG
Found at i:3564055 original size:10 final size:10
Alignment explanation
Indices: 3564040--3564068 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3564030 TCATCTTTCC
3564040 TATTATATCA
1 TATTATATCA
3564050 TATTATATCA
1 TATTATATCA
3564060 TATTATATC
1 TATTATATC
3564069 TATGTGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (10 bp):
TATTATATCA
Found at i:3564727 original size:11 final size:12
Alignment explanation
Indices: 3564699--3564729 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3564689 AAATTACTTT
3564699 TAAAAAATATTG
1 TAAAAAATATTG
3564711 TAAAAAATATTG
1 TAAAAAATATTG
3564723 TAAAAAA
1 TAAAAAA
3564730 GTAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (12 bp):
TAAAAAATATTG
Found at i:3567061 original size:13 final size:13
Alignment explanation
Indices: 3567043--3567067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3567033 TTTAATAAAA
3567043 TTTTATATTTAAT
1 TTTTATATTTAAT
3567056 TTTTATATTTAA
1 TTTTATATTTAA
3567068 AAATTCTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTATATTTAAT
Found at i:3582783 original size:46 final size:46
Alignment explanation
Indices: 3582711--3582866 Score: 255
Period size: 46 Copynumber: 3.5 Consensus size: 46
3582701 TAATCAGTGA
*
3582711 CAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
3582757 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
3582803 CAAGTGACAAAGTGATAAGTGGTAGC-GTGGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
3582848 C-AGAGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
3582867 ATCATACGTA
Statistics
Matches: 106, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
43 12 0.11
44 5 0.05
45 18 0.17
46 71 0.67
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:3583466 original size:36 final size:36
Alignment explanation
Indices: 3583419--3583491 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
3583409 TGGTAATGCC
3583419 TCGTACCCTATTCCGGTGTTGGATACGAGTAAGGGG
1 TCGTACCCTATTCCGGTGTTGGATACGAGTAAGGGG
*
3583455 TCGTACCCTATTCCGGTGTTGGATACGGGTAAGGGG
1 TCGTACCCTATTCCGGTGTTGGATACGAGTAAGGGG
3583491 T
1 T
3583492 GTTACACATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.29
Consensus pattern (36 bp):
TCGTACCCTATTCCGGTGTTGGATACGAGTAAGGGG
Found at i:3583599 original size:33 final size:33
Alignment explanation
Indices: 3583537--3583599 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
3583527 ATAATAATTA
* *
3583537 TATTAAAATATGATTAAATTATTTATTATTTTT
1 TATTAAAATATGATTAAAATAATTATTATTTTT
3583570 TATTAAAATAT-ATTCAACAATAATT-TTATT
1 TATTAAAATATGATT-AA-AATAATTATTATT
3583600 AAAATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 3 0.12
33 18 0.69
34 5 0.19
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (33 bp):
TATTAAAATATGATTAAAATAATTATTATTTTT
Found at i:3583792 original size:16 final size:16
Alignment explanation
Indices: 3583768--3583821 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
3583758 TGAATTACTG
*
3583768 ATTATAACTCTATTCC
1 ATTACAACTCTATTCC
*
3583784 ATTACAACTCTATTCA
1 ATTACAACTCTATTCC
*
3583800 ATTACAGC-CTTATTCC
1 ATTACAACTC-TATTCC
3583816 ATTACA
1 ATTACA
3583822 GTAACCAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 1 0.03
16 32 0.97
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:3583822 original size:16 final size:17
Alignment explanation
Indices: 3583774--3583822 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
3583764 ACTGATTATA
3583774 ACTCTATTCCATTACA-
1 ACTCTATTCCATTACAG
*
3583790 ACTCTATTCAATTACAG
1 ACTCTATTCCATTACAG
*
3583807 CCT-TATTCCATTACAG
1 ACTCTATTCCATTACAG
3583823 TAACCAAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 27 0.93
17 2 0.07
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.37
Consensus pattern (17 bp):
ACTCTATTCCATTACAG
Found at i:3585801 original size:4 final size:4
Alignment explanation
Indices: 3585792--3585818 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3585782 CGACCACCCT
3585792 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA
3585819 TGCTTTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:3586121 original size:14 final size:13
Alignment explanation
Indices: 3586104--3586149 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
3586094 TTTAAAGTTA
3586104 TAAAAATAAATTTT
1 TAAAAATAAA-TTT
3586118 TAAAAAT--A-TT
1 TAAAAATAAATTT
3586128 TAAAAATAAATATT
1 TAAAAATAAAT-TT
3586142 TAAAAATA
1 TAAAAATA
3586150 TAAAAAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.32
12 2 0.07
14 17 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAAAATAAATTT
Found at i:3586131 original size:24 final size:23
Alignment explanation
Indices: 3586104--3586165 Score: 88
Period size: 24 Copynumber: 2.7 Consensus size: 23
3586094 TTTAAAGTTA
3586104 TAAAAATAAATTTTTAAAAATATT
1 TAAAAATAAATTTTTAAAAATA-T
*
3586128 TAAAAATAAATATTTAAAAATAT
1 TAAAAATAAATTTTTAAAAATAT
* *
3586151 AAAAAATAGATTTTT
1 TAAAAATAAATTTTT
3586166 TTTTAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 13 0.38
24 21 0.62
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAAAATAAATTTTTAAAAATAT
Found at i:3588255 original size:20 final size:21
Alignment explanation
Indices: 3588210--3588259 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
3588200 ATTTTAAATT
*
3588210 TAAAAAA-TATGTAAAAATTA
1 TAAAAAATTATGTAAAAAGTA
*
3588230 T-TAAAATTAT-TAAAAAGTA
1 TAAAAAATTATGTAAAAAGTA
3588249 TAAAAAATTAT
1 TAAAAAATTAT
3588260 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
TAAAAAATTATGTAAAAAGTA
Found at i:3589158 original size:18 final size:18
Alignment explanation
Indices: 3589112--3589160 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
3589102 GACTTTGTAC
3589112 TTTTTCTTTTTAATCATT
1 TTTTTCTTTTTAATCATT
*
3589130 TTTATT-ATTTTATAT-ATT
1 TTT-TTCTTTTTA-ATCATT
3589148 TTTTTCTTTTTAA
1 TTTTTCTTTTTAA
3589161 CTTTCCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTCTTTTTAATCATT
Found at i:3591659 original size:33 final size:33
Alignment explanation
Indices: 3591617--3591681 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
3591607 CTAAAAAAAC
*
3591617 CAATTGCAAACAATCTTTCAATAATGCTTTTAA
1 CAATTGCAAACAATCTTTCAACAATGCTTTTAA
*
3591650 CAATTGCAAACAATCTTTTAACAATGCTTTTA
1 CAATTGCAAACAATCTTTCAACAATGCTTTTA
3591682 TCATTTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.37
Consensus pattern (33 bp):
CAATTGCAAACAATCTTTCAACAATGCTTTTAA
Found at i:3603854 original size:124 final size:124
Alignment explanation
Indices: 3603634--3603884 Score: 502
Period size: 124 Copynumber: 2.0 Consensus size: 124
3603624 TAGAATGAGA
3603634 AAGGAGATGGTAGAGAGTAACTTTGATAAAGAAACAGTCGGATGCACCGGGACAACTGATACTCA
1 AAGGAGATGGTAGAGAGTAACTTTGATAAAGAAACAGTCGGATGCACCGGGACAACTGATACTCA
3603699 TAGTAGAAATCAAGGTTCAGGTCTTCGCAGGGAGCCCTCCTTCTCTCGCTGGGTCGATG
66 TAGTAGAAATCAAGGTTCAGGTCTTCGCAGGGAGCCCTCCTTCTCTCGCTGGGTCGATG
3603758 AAGGAGATGGTAGAGAGTAACTTTGATAAAGAAACAGTCGGATGCACCGGGACAACTGATACTCA
1 AAGGAGATGGTAGAGAGTAACTTTGATAAAGAAACAGTCGGATGCACCGGGACAACTGATACTCA
3603823 TAGTAGAAATCAAGGTTCAGGTCTTCGCAGGGAGCCCTCCTTCTCTCGCTGGGTCGATG
66 TAGTAGAAATCAAGGTTCAGGTCTTCGCAGGGAGCCCTCCTTCTCTCGCTGGGTCGATG
3603882 AAG
1 AAG
3603885 ATGGGATAAT
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 127 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.22
Consensus pattern (124 bp):
AAGGAGATGGTAGAGAGTAACTTTGATAAAGAAACAGTCGGATGCACCGGGACAACTGATACTCA
TAGTAGAAATCAAGGTTCAGGTCTTCGCAGGGAGCCCTCCTTCTCTCGCTGGGTCGATG
Found at i:3610123 original size:13 final size:14
Alignment explanation
Indices: 3610097--3610136 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
3610087 CGCTTAAGGG
3610097 ATTTACATCATTATT
1 ATTTACA-CATTATT
3610112 A-TTACACATTA-T
1 ATTTACACATTATT
3610124 ATTTACAC-TTATT
1 ATTTACACATTATT
3610137 TGGAAGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.22
13 12 0.52
14 5 0.22
15 1 0.04
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTACACATTATT
Found at i:3610570 original size:21 final size:22
Alignment explanation
Indices: 3610536--3610589 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
3610526 CACACTAAAT
*
3610536 ATAAAAAAATAATAACATTTTA
1 ATAAAAAAATAATAAAATTTTA
*
3610558 ATAAAAAGA-AATAAAATTTT-
1 ATAAAAAAATAATAAAATTTTA
*
3610578 -TTAAAAAATAAT
1 ATAAAAAAATAAT
3610590 TTAATGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 6 0.22
20 3 0.11
21 10 0.37
22 8 0.30
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAAAAAAATAATAAAATTTTA
Found at i:3613984 original size:3 final size:3
Alignment explanation
Indices: 3613976--3614011 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3613966 CAAGACATTA
3613976 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3614012 TTGCTTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:3619683 original size:87 final size:87
Alignment explanation
Indices: 3619547--3619724 Score: 338
Period size: 87 Copynumber: 2.0 Consensus size: 87
3619537 CCAGCAGCAG
3619547 CAGCAGCATAACTCCGTCGTCCTTTCTCTTTATCACTCTCGTGTTCGGCCTTAGACGCCACTGAA
1 CAGCAGCATAACTCCGTCGTCCTTTCTCTTTATCACTCTCGTGTTCGGCCTTAGACGCCACTGAA
*
3619612 GTACCTCTCTCCTGTCCAGTTC
66 GTACCTCTCTCCTGTCCAGCTC
*
3619634 CAGCAGCATAACTCCGTCGTCCTTTCTCTTTATCACTCTCGTGTTCGGCCTTAGACGCCATTGAA
1 CAGCAGCATAACTCCGTCGTCCTTTCTCTTTATCACTCTCGTGTTCGGCCTTAGACGCCACTGAA
3619699 GTACCTCTCTCCTGTCCAGCTC
66 GTACCTCTCTCCTGTCCAGCTC
3619721 CAGC
1 CAGC
3619725 TCCAGCCCCA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.16, C:0.36, G:0.16, T:0.31
Consensus pattern (87 bp):
CAGCAGCATAACTCCGTCGTCCTTTCTCTTTATCACTCTCGTGTTCGGCCTTAGACGCCACTGAA
GTACCTCTCTCCTGTCCAGCTC
Done.