Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 55
Found at i:3077458 original size:13 final size:13
Alignment explanation
Indices: 3077440--3077465 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3077430 TATTTTTTTC
3077440 TTGTTTAATTGAT
1 TTGTTTAATTGAT
3077453 TTGTTTAATTGAT
1 TTGTTTAATTGAT
3077466 GTGTAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (13 bp):
TTGTTTAATTGAT
Found at i:3077617 original size:14 final size:14
Alignment explanation
Indices: 3077598--3077624 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3077588 GAAAGTTAAA
3077598 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
3077612 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
3077625 AGTCAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.30, T:0.41
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:3078917 original size:18 final size:18
Alignment explanation
Indices: 3078894--3078930 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3078884 ATTTATATAT
3078894 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
3078912 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
3078930 A
1 A
3078931 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:3079342 original size:25 final size:25
Alignment explanation
Indices: 3079313--3079364 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
3079303 GAACATTATT
*
3079313 TTCAAATAATGTACCCATAACAATG
1 TTCAAATAATGTACCCACAACAATG
3079338 TTCAAATAATGTACCCACAACAATG
1 TTCAAATAATGTACCCACAACAATG
3079363 TT
1 TT
3079365 TAATTGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (25 bp):
TTCAAATAATGTACCCACAACAATG
Found at i:3082066 original size:24 final size:24
Alignment explanation
Indices: 3082032--3082079 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3082022 CCGAAACATC
3082032 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3082056 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3082080 CAAATTTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3082228 original size:12 final size:12
Alignment explanation
Indices: 3082207--3082240 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3082197 GGTTGTGGGT
*
3082207 TTTGAGATTGTG
1 TTTGATATTGTG
3082219 TTTGATATTGTG
1 TTTGATATTGTG
*
3082231 TTTGGTATTG
1 TTTGATATTG
3082241 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:3083075 original size:20 final size:20
Alignment explanation
Indices: 3083050--3083123 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
3083040 TTAAATTTGT
*
3083050 GTTGTGAATTCGAAAATCGA
1 GTTGTGAATTTGAAAATCGA
*
3083070 GTTGTGAATTTGAAATTC-A
1 GTTGTGAATTTGAAAATCGA
* *
3083089 GTATTGTGAATTTGGAAATCGC
1 G--TTGTGAATTTGAAAATCGA
*
3083111 GTTGCGAATTTGA
1 GTTGTGAATTTGA
3083124 CTTTTGTGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 2 0.05
20 26 0.59
21 15 0.34
22 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGTGAATTTGAAAATCGA
Found at i:3083175 original size:20 final size:20
Alignment explanation
Indices: 3083131--3083177 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3083121 TGACTTTTGT
3083131 GTTGCGATTTACAAATTCGA
1 GTTGCGATTTACAAATTCGA
* * *
3083151 TTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGA
3083171 GTTGCGA
1 GTTGCGA
3083178 ATTTGGAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGA
Found at i:3093681 original size:38 final size:38
Alignment explanation
Indices: 3093638--3093715 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
3093628 ATATGTAAGG
3093638 ATGTTTGAACAATTCTTGTCAAATGATTGAGTATTTGA
1 ATGTTTGAACAATTCTTGTCAAATGATTGAGTATTTGA
3093676 ATGTTTGAACAATTCTTGTCAAATGATTGAGTATTTGA
1 ATGTTTGAACAATTCTTGTCAAATGATTGAGTATTTGA
3093714 AT
1 AT
3093716 ATATACTACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (38 bp):
ATGTTTGAACAATTCTTGTCAAATGATTGAGTATTTGA
Found at i:3093705 original size:22 final size:22
Alignment explanation
Indices: 3093642--3093705 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
3093632 GTAAGGATGT
3093642 TTGAACAATTCTTGTCAAATGA
1 TTGAACAATTCTTGTCAAATGA
** *
3093664 TTG-AGTA-T-TTG---AATGT
1 TTGAACAATTCTTGTCAAATGA
3093680 TTGAACAATTCTTGTCAAATGA
1 TTGAACAATTCTTGTCAAATGA
3093702 TTGA
1 TTGA
3093706 GTATTTGAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
16 7 0.23
17 2 0.07
18 1 0.03
19 6 0.20
20 1 0.03
21 2 0.07
22 11 0.37
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (22 bp):
TTGAACAATTCTTGTCAAATGA
Found at i:3094422 original size:21 final size:21
Alignment explanation
Indices: 3094391--3094440 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3094381 TCATATGTCC
3094391 TATTTTAAGTTTAGGATT-TA
1 TATTTTAAGTTTAGGATTCTA
* *
3094411 TGATTTTGAGTTTATGATTCTA
1 T-ATTTTAAGTTTAGGATTCTA
3094433 TATTTTAA
1 TATTTTAA
3094441 AATTTAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 21 0.84
22 3 0.12
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (21 bp):
TATTTTAAGTTTAGGATTCTA
Found at i:3095835 original size:15 final size:15
Alignment explanation
Indices: 3095812--3095841 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3095802 ACTCCCATAA
*
3095812 AGTTTTGAAACTGAG
1 AGTTCTGAAACTGAG
3095827 AGTTCTGAAACTGAG
1 AGTTCTGAAACTGAG
3095842 CAGAACAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (15 bp):
AGTTCTGAAACTGAG
Found at i:3099705 original size:20 final size:22
Alignment explanation
Indices: 3099657--3099707 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
3099647 GCTAATTTTG
*
3099657 GTATCGATACCATATTAGGGTA
1 GTATCGATACCATAGTAGGGTA
*
3099679 GTATCGATACCATGGTAGGG-A
1 GTATCGATACCATAGTAGGGTA
3099700 -TATCGATA
1 GTATCGATA
3099708 TTGAAGGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 8 0.30
21 1 0.04
22 18 0.67
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (22 bp):
GTATCGATACCATAGTAGGGTA
Found at i:3100100 original size:59 final size:59
Alignment explanation
Indices: 3100033--3100483 Score: 767
Period size: 59 Copynumber: 7.6 Consensus size: 59
3100023 TACCAAATGC
* *
3100033 TAAGGAATTAATACTAAGTGTATGAATTTCCATATAGGGCACTTCATGTGCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
*
3100092 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGTACTTCGTGTGCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
3100151 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
*
3100210 TAATGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
3100269 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
*
3100328 TAATGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
* * * * * * * *
3100387 TAAGGTATTCTTACTAAGGGTATGAATTTCCATATAGCGCAATTTGTGTGCTAAAATGT
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
* *
3100446 TAAGGAATTCATACTAAGTGTATGAATTTTCGTATAGG
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGG
3100484 AAATGTATAT
Statistics
Matches: 370, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 370 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34
Consensus pattern (59 bp):
TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
Found at i:3102692 original size:23 final size:22
Alignment explanation
Indices: 3102666--3102734 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
3102656 CACCACAACT
3102666 CGTATAAATGCACCGAAGTGCCA
1 CGTA-AAATGCACCGAAGTGCCA
* *
3102689 CGTAAAATTGCATCGAAGTGCCG
1 CGTAAAA-TGCACCGAAGTGCCA
* *
3102712 CGTAGAATTGCACCGTAGTGCCA
1 CGTA-AAATGCACCGAAGTGCCA
3102735 TATAAGCTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 3 0.08
23 33 0.87
24 2 0.05
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (22 bp):
CGTAAAATGCACCGAAGTGCCA
Found at i:3103001 original size:31 final size:30
Alignment explanation
Indices: 3102957--3103016 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
3102947 TATTGTATAG
*
3102957 ACATATAATTTCCATACCTT-TATCACATAA
1 ACATATAATTTCCAT-CATTGTATCACATAA
*
3102987 ACATATCATGTTCCATCATTGTATCACATA
1 ACATATAAT-TTCCATCATTGTATCACATA
3103017 GCTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCATTGTATCACATAA
Found at i:3108872 original size:20 final size:19
Alignment explanation
Indices: 3108849--3108886 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
3108839 CTGAAAATTT
3108849 AGTATCGATACTATGGTAAA
1 AGTATCGATACTA-GGTAAA
3108869 AGTATCGATACTAGGTAA
1 AGTATCGATACTAGGTAA
3108887 CATCGAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (19 bp):
AGTATCGATACTAGGTAAA
Found at i:3109060 original size:94 final size:94
Alignment explanation
Indices: 3108886--3109060 Score: 207
Period size: 94 Copynumber: 1.9 Consensus size: 94
3108876 ATACTAGGTA
**
3108886 ACATCGAACATAATTTTGGTATCAATACCGGAAGGGTTATCGGTACCATAACATAGTAGTATCGA
1 ACATCGAACATAATTTTGGTATCAATACCGGAAGGGTTATCAATACCATAACATAGTAGTATCGA
* * *
3108951 TATCAGGGTGTGGGTATCGATACCAAGCC
66 TACCAGAGTGAGGGTATCGATACCAAGCC
*
3108980 ACATCGAAGC-TAATTTTGGTATCGATACCGGAAAGAGG-TATCAATACCAT-A-ATAGGATAGT
1 ACATCGAA-CATAATTTTGGTATCAATACCGG-AAG-GGTTATCAATACCATAACATA-G-TAGT
*
3109041 ATCGATACCATAGT-AGGGTA
61 ATCGATACCAGAGTGAGGGTA
3109061 GTATCGATAC
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
93 3 0.04
94 35 0.51
95 29 0.42
96 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (94 bp):
ACATCGAACATAATTTTGGTATCAATACCGGAAGGGTTATCAATACCATAACATAGTAGTATCGA
TACCAGAGTGAGGGTATCGATACCAAGCC
Found at i:3109078 original size:22 final size:22
Alignment explanation
Indices: 3109017--3109090 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
3109007 CCGGAAAGAG
* * *
3109017 GTATCAATACCATAATAGGATA
1 GTATCGATACCATAGTAGGGTA
3109039 GTATCGATACCATAGTAGGGTA
1 GTATCGATACCATAGTAGGGTA
*
3109061 GTATCGATACCATGGTAGGG--
1 GTATCGATACCATAGTAGGGTA
3109081 GTATCGATAC
1 GTATCGATAC
3109091 TGAAGGGCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.21
22 38 0.79
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (22 bp):
GTATCGATACCATAGTAGGGTA
Found at i:3109517 original size:59 final size:59
Alignment explanation
Indices: 3109401--3110138 Score: 1102
Period size: 59 Copynumber: 12.5 Consensus size: 59
3109391 TACCAAATGC
*
3109401 TAAGGAATTCATACTAAGTGTATGAA-TTCCATATAGGGCACTTCATGTGCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
* * *
3109459 TAAGGAATTCATACTAAGTGTATGAATTTTCATATAGGGCACTTCATGTTCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
*
3109518 TAAGGAATTCATACTAATTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
* * *
3109577 TAAAGAATTCATATTAATTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
*
3109636 TAAGGAATTCATACTAAGTGTATGAATTCCCATATAGGGCACTTCGTGTGCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
* *
3109695 TAAGGAATTCATTCTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCCAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
* * * ** *
3109754 TAAGGAATTCATACTAAGTGTATGAATTTTCATATATGGCACATCAAGTTCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
* * * * **
3109813 TACGGAATTCATATTAAGTGTATAAATTTCCATATAGGGCACTTTGCATGCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
* *
3109872 TAAGGAATTCATACCAAGTGTATGAATTTCTATATAGGGCACTTCGTGTGCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
* * *
3109931 TCAGGAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTCGTTTGCTAACATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
* * * * *
3109990 TAAGGAATTCATGCTAGGGGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATGC
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
* * * *
3110049 TAAGGAATTCATACTAAGTGTATGAATTTCTATATTGGGCACCTT-GTTTGCTAAAATGA
1 TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCA-CTTCGTGTGCTAACATGA
* *
3110108 TTAGAAATTCATACTAAGTGTATGAATTTCC
1 TAAGGAATTCATACTAAGTGTATGAATTTCC
3110139 GTATGGAAAA
Statistics
Matches: 613, Mismatches: 65, Indels: 3
0.90 0.10 0.00
Matches are distributed among these distances:
58 26 0.04
59 584 0.95
60 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (59 bp):
TAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGA
Found at i:3120739 original size:32 final size:33
Alignment explanation
Indices: 3120686--3120754 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 33
3120676 AAATCGGGTT
* * *
3120686 GGGTCGGAGTCGGGTGTAGGATATATATTTTTC
1 GGGTCGGAGTCGGATGTAGGATATAAAATTTTC
3120719 GGGTCGG-GTCGGATAG-AGGATATAAAATTTTC
1 GGGTCGGAGTCGGAT-GTAGGATATAAAATTTTC
3120751 GGGT
1 GGGT
3120755 TTAGGCGGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 24 0.75
33 8 0.25
ACGTcount: A:0.22, C:0.09, G:0.38, T:0.32
Consensus pattern (33 bp):
GGGTCGGAGTCGGATGTAGGATATAAAATTTTC
Found at i:3121163 original size:91 final size:91
Alignment explanation
Indices: 3121008--3121189 Score: 328
Period size: 91 Copynumber: 2.0 Consensus size: 91
3120998 ATCACCCCAA
* *
3121008 AATCTTACTGAAGTTTTGGACTGAAAATAAAGTGCACGAGCAACAACCAACGAATGCTGATGCTT
1 AATCTTACTGAAGTTTTGGACTGAAAATAAAGTGCACGACCAACAACCAACAAATGCTGATGCTT
*
3121073 TCTTTCAGCAATTGTATTTTGCTGAG
66 TCTTGCAGCAATTGTATTTTGCTGAG
3121099 AATCTTACTGAAGTTTTGGACTGAAAATAAAGTGCACGACCAACAACCAACAAATGCTGATGCTT
1 AATCTTACTGAAGTTTTGGACTGAAAATAAAGTGCACGACCAACAACCAACAAATGCTGATGCTT
*
3121164 TCTTGCGGCAATTGTATTTTGCTGAG
66 TCTTGCAGCAATTGTATTTTGCTGAG
3121190 GTGTCCCTAC
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 87 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (91 bp):
AATCTTACTGAAGTTTTGGACTGAAAATAAAGTGCACGACCAACAACCAACAAATGCTGATGCTT
TCTTGCAGCAATTGTATTTTGCTGAG
Found at i:3123057 original size:20 final size:20
Alignment explanation
Indices: 3123015--3123068 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
3123005 TTTCACGTGG
**
3123015 GTATCGATACTCACCTGGGA
1 GTATCGATACTCACCCCGGA
**
3123035 GTATCGATACTCACCCCTTA
1 GTATCGATACTCACCCCGGA
*
3123055 GTAACGATACTCAC
1 GTATCGATACTCAC
3123069 TTGGGTATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
GTATCGATACTCACCCCGGA
Found at i:3132009 original size:6 final size:6
Alignment explanation
Indices: 3131998--3132034 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
3131988 TGATGAAAAA
3131998 GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG G
1 GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG G
3132035 TGTTAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.84, T:0.00
Consensus pattern (6 bp):
GGAGGG
Found at i:3134557 original size:42 final size:40
Alignment explanation
Indices: 3134511--3134622 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 40
3134501 CAAATATAAG
3134511 AAATTGATTTATAAATTT-AAAAATAAAATGATATTATTTTGA
1 AAATTGATTTATAAATTTAAAAAATAAAATGA-A-T-TTTTGA
* * * *
3134553 AAATTAAATTAT-ATTTTAAAAAACAAAATGAATTTTTGA
1 AAATTGATTTATAAATTTAAAAAATAAAATGAATTTTTGA
* * * *
3134592 AAAATGATTTAGAACTTTCAAAAATGAAAAT
1 AAATTGATTTATAAATTTAAAAAAT-AAAAT
3134623 TAAAGAGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
39 14 0.25
40 10 0.18
41 10 0.18
42 22 0.39
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (40 bp):
AAATTGATTTATAAATTTAAAAAATAAAATGAATTTTTGA
Found at i:3135271 original size:18 final size:18
Alignment explanation
Indices: 3135250--3135347 Score: 74
Period size: 18 Copynumber: 5.2 Consensus size: 18
3135240 TTACAAATGA
3135250 TATCTATCTAACAATTGT
1 TATCTATCTAACAATTGT
* * *
3135268 TATCCT-TCACTTACAAATGA
1 TAT-CTAT--CTAACAATTGT
3135288 TATCTATCTAACAATTGT
1 TATCTATCTAACAATTGT
* * *
3135306 TATCCT-TCATTTACAAATGA
1 TAT-CTATC--TAACAATTGT
3135326 TATCTATCTAACAATTGT
1 TATCTATCTAACAATTGT
3135344 TATC
1 TATC
3135348 CATTTCAAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
18 28 0.47
19 8 0.13
20 24 0.40
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (18 bp):
TATCTATCTAACAATTGT
Found at i:3135286 original size:38 final size:38
Alignment explanation
Indices: 3135235--3135348 Score: 219
Period size: 38 Copynumber: 3.0 Consensus size: 38
3135225 TGTATGTGCT
3135235 TTCACTTACAAATGATATCTATCTAACAATTGTTATCC
1 TTCACTTACAAATGATATCTATCTAACAATTGTTATCC
3135273 TTCACTTACAAATGATATCTATCTAACAATTGTTATCC
1 TTCACTTACAAATGATATCTATCTAACAATTGTTATCC
*
3135311 TTCATTTACAAATGATATCTATCTAACAATTGTTATCC
1 TTCACTTACAAATGATATCTATCTAACAATTGTTATCC
3135349 ATTTCAAATG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 75 1.00
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.40
Consensus pattern (38 bp):
TTCACTTACAAATGATATCTATCTAACAATTGTTATCC
Found at i:3142565 original size:39 final size:39
Alignment explanation
Indices: 3142497--3142629 Score: 167
Period size: 39 Copynumber: 3.4 Consensus size: 39
3142487 TCTATGAGTT
* * * *
3142497 GTAAGTCCTTACCGCAAGCTCCTCTACTTTGTGCTCAAG
1 GTAAGTCCTTACCGCAGGCTCTTCGACTTTGTGCTCAGG
* * *
3142536 ATAAGTCCTTACCGCAGGCTCTTCGACTTTATGTTCAGG
1 GTAAGTCCTTACCGCAGGCTCTTCGACTTTGTGCTCAGG
* *
3142575 GTAAGTCCTCACCGCAGGCTCTTCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAGGCTCTTCGACTTTGTGCTCAGG
* *
3142614 GTAAGTTCTTATCGCA
1 GTAAGTCCTTACCGCA
3142630 TGATCCTCTG
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.32
Consensus pattern (39 bp):
GTAAGTCCTTACCGCAGGCTCTTCGACTTTGTGCTCAGG
Found at i:3143076 original size:2 final size:2
Alignment explanation
Indices: 3143069--3143138 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
3143059 CGATTTTCTG
3143069 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
3143111 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
3143139 GTTTATCATA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3150751 original size:21 final size:21
Alignment explanation
Indices: 3150678--3150792 Score: 69
Period size: 20 Copynumber: 5.6 Consensus size: 21
3150668 CAATTTCCAG
3150678 ATTCGCAATGCGATTCTGA-CT-
1 ATTCGCAATGCGATT-T-ACCTA
* * *
3150699 A-TCGCATTGCGATTTCCCAA
1 ATTCGCAATGCGATTTACCTA
* ** *
3150719 ATTTGCGTTGCGATTTTCCTA
1 ATTCGCAATGCGATTTACCTA
* *
3150740 ATTCGCAATGCGA-ATACGTA
1 ATTCGCAATGCGATTTACCTA
* *
3150760 AATCGCAATGCGATTTACGTA
1 ATTCGCAATGCGATTTACCTA
*
3150781 A-TCGCATTGCGA
1 ATTCGCAATGCGA
3150793 ATTAGGAAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
19 2 0.03
20 39 0.53
21 33 0.45
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTCGCAATGCGATTTACCTA
Found at i:3150767 original size:20 final size:20
Alignment explanation
Indices: 3150742--3150808 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
3150732 TTTTCCTAAT
3150742 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
3150762 TCGCAATGCGATTTACGT-AA
1 TCGCAATGCGA-ATACGTAAA
* * *
3150782 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
3150803 TCGCAA
1 TCGCAA
3150809 CGAGATTCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 26 0.68
21 12 0.32
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:3150772 original size:41 final size:41
Alignment explanation
Indices: 3150727--3150808 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
3150717 AAATTTGCGT
* *
3150727 TGCGATTTTCCTAATTCGCAATGCGAA-TACGTAAATCGCAA
1 TGCGATTTACCTAA-TCGCAATGCGAATTACGAAAATCGCAA
* * *
3150768 TGCGATTTACGTAATCGCATTGCGAATTAGGAAAATCGCAA
1 TGCGATTTACCTAATCGCAATGCGAATTACGAAAATCGCAA
3150809 CGAGATTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 11 0.31
41 24 0.69
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (41 bp):
TGCGATTTACCTAATCGCAATGCGAATTACGAAAATCGCAA
Found at i:3154250 original size:20 final size:19
Alignment explanation
Indices: 3154222--3154265 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
3154212 CAATCATCTT
*
3154222 AATGTCTATCACAACGCGGA
1 AATGACTATCACAACGC-GA
* *
3154242 AATGACTATCGCAATGCGA
1 AATGACTATCACAACGCGA
3154261 AATGA
1 AATGA
3154266 AAATCGCAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (19 bp):
AATGACTATCACAACGCGA
Found at i:3154264 original size:19 final size:17
Alignment explanation
Indices: 3154249--3154329 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 17
3154239 GGAAATGACT
3154249 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
3154268 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
3154282 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
3154301 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
3154315 ATCGCAATGCGAAAT
1 ATCGCAATGCGAAAT
3154330 AAAAATCGCA
Statistics
Matches: 50, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
14 16 0.32
16 10 0.20
17 9 0.18
19 15 0.30
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:3154291 original size:33 final size:33
Alignment explanation
Indices: 3154249--3154360 Score: 206
Period size: 33 Copynumber: 3.4 Consensus size: 33
3154239 GGAAATGACT
3154249 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3154282 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
3154315 ATCGCAATGCGAAATAAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3154348 ATCGCAATGCGAA
1 ATCGCAATGCGAA
3154361 TTTAGTTTCG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3154338 original size:19 final size:19
Alignment explanation
Indices: 3154249--3154340 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
3154239 GGAAATGACT
3154249 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3154268 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3154282 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3154301 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
3154315 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
3154334 ATCGCAA
1 ATCGCAA
3154341 CGAGGGAATC
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 20 0.34
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 26 0.45
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3154377 original size:19 final size:19
Alignment explanation
Indices: 3154355--3154416 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
3154345 GGAATCGCAA
3154355 TGCGAATTT-AGTTTCGCGT
1 TGCGAATTTCA-TTTCGCGT
*
3154374 TGCGATTTTCATTTCGCGT
1 TGCGAATTTCATTTCGCGT
* * *
3154393 TGCGATTTTCATTTTGCAT
1 TGCGAATTTCATTTCGCGT
3154412 TGCGA
1 TGCGA
3154417 TAGTCATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
19 38 0.97
20 1 0.03
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.45
Consensus pattern (19 bp):
TGCGAATTTCATTTCGCGT
Found at i:3154417 original size:19 final size:19
Alignment explanation
Indices: 3154366--3154417 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
3154356 GCGAATTTAG
*
3154366 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
3154385 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
3154404 TTTTGCATTGCGAT
1 TTTCGCATTGCGAT
3154418 AGTCATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:3154423 original size:19 final size:19
Alignment explanation
Indices: 3154382--3154426 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3154372 GTTGCGATTT
* * **
3154382 TCATTTCGCGTTGCGATTT
1 TCATTTTGCATTGCGATAG
3154401 TCATTTTGCATTGCGATAG
1 TCATTTTGCATTGCGATAG
3154420 TCATTTT
1 TCATTTT
3154427 TGCCTTCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.49
Consensus pattern (19 bp):
TCATTTTGCATTGCGATAG
Found at i:3154543 original size:14 final size:14
Alignment explanation
Indices: 3154524--3154560 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3154514 CATCAATTAA
3154524 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3154538 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3154552 ACAAATCAA
1 ACAAATCAA
3154561 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3155979 original size:42 final size:42
Alignment explanation
Indices: 3155924--3156016 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
3155914 CCTCTTCAAC
* * * * *
3155924 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCG-AG
1 GATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAAG
* *
3155965 GAATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAAG
1 G-ATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAAG
3156008 GATGATAGG
1 GATGATAGG
3156017 CGAGTCGGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.02
42 39 0.91
43 3 0.07
ACGTcount: A:0.25, C:0.16, G:0.38, T:0.22
Consensus pattern (42 bp):
GATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAAG
Found at i:3156447 original size:33 final size:33
Alignment explanation
Indices: 3156410--3156487 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
3156400 TCTGGAACTT
3156410 AAAATCGCAACGAGAGAATCACAACGCGAAATA
1 AAAATCGCAACGAGAGAATCACAACGCGAAATA
* * *
3156443 AAAATCGCAACGAGAGAATCGCAATGCGAAATT
1 AAAATCGCAACGAGAGAATCACAACGCGAAATA
3156476 AAAATCGCAACG
1 AAAATCGCAACG
3156488 CGATTATAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCACAACGCGAAATA
Found at i:3156453 original size:19 final size:19
Alignment explanation
Indices: 3156426--3156490 Score: 50
Period size: 19 Copynumber: 3.7 Consensus size: 19
3156416 GCAACGAGAG
*
3156426 AATCACAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
* *
3156445 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATAAA
* *
3156459 AATCGCAATGCGAAATTAA
1 AATCGCAACGCGAAATAAA
3156478 AATCGCAACGCGA
1 AATCGCAACGCGA
3156491 TTATAGTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 20 0.57
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:3156521 original size:20 final size:19
Alignment explanation
Indices: 3156496--3156591 Score: 95
Period size: 19 Copynumber: 4.9 Consensus size: 19
3156486 CGCGATTATA
*
3156496 GTTTCGCGTTGCAATTTTT
1 GTTTCGCGTTGCGATTTTT
3156515 GGTTTCGCGTTGCGATTTTCT
1 -GTTTCGCGTTGCGATTTT-T
* * *
3156536 -TCTCTCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTT
3156554 GTTTCGCGTTGCGATTTTT
1 GTTTCGCGTTGCGATTTTT
* * *
3156573 ATTCTCTCGTTGTGATTTT
1 GTT-TCGCGTTGCGATTTT
3156592 CATTTCAACC
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
19 32 0.51
20 30 0.48
21 1 0.02
ACGTcount: A:0.07, C:0.19, G:0.22, T:0.52
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTT
Found at i:3156578 original size:39 final size:38
Alignment explanation
Indices: 3156502--3156597 Score: 129
Period size: 39 Copynumber: 2.5 Consensus size: 38
3156492 TATAGTTTCG
* * *
3156502 CGTTGCAATTTTTGGTTTCGCGTTGCGATTTTCTTCTCT
1 CGTTGCGA-TTTTCGTTTCGCGTTGCGATTTTATTCTCT
3156541 CGTTGCGATTTTCGTTTCGCGTTGCGATTTTTATTCTCT
1 CGTTGCGATTTTCGTTTCGCGTTGCGA-TTTTATTCTCT
* *
3156580 CGTTGTGATTTTCATTTC
1 CGTTGCGATTTTCGTTTC
3156598 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 18 0.35
39 33 0.65
ACGTcount: A:0.08, C:0.20, G:0.20, T:0.52
Consensus pattern (38 bp):
CGTTGCGATTTTCGTTTCGCGTTGCGATTTTATTCTCT
Found at i:3156846 original size:94 final size:94
Alignment explanation
Indices: 3156688--3157059 Score: 582
Period size: 94 Copynumber: 4.1 Consensus size: 94
3156678 ATGGATTGCA
* *
3156688 TTAC-TTCAACCAAAAGACAAAACAAAGAC-AATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
3156751 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAAACGAACAAAT
*
3156780 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
3156845 TTAGCAGAATTAGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAAACGAACAAAT
3156874 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
3156939 TTAGCAG-ATTGGCAGCAAACGAATAAAT
66 TTAGCAGAATTGGCAGCAAACGAACAAAT
* *
3156967 TTAC-TTCAACCAAAAGACAAAACAAAAACAAATACTAACTTCACAGTGTT----AATAAACAG-
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
3157026 TTAGCAGTATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAAACGAACAAAT
3157055 TTACT
1 TTACT
3157060 AAGCAATCTA
Statistics
Matches: 264, Mismatches: 12, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
87 7 0.03
88 32 0.12
92 49 0.19
93 46 0.17
94 130 0.49
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAAACGAACAAAT
Found at i:3156955 original size:187 final size:181
Alignment explanation
Indices: 3156688--3157059 Score: 586
Period size: 187 Copynumber: 2.0 Consensus size: 181
3156678 ATGGATTGCA
*
3156688 TTAC-TTCAACCAAAAGACAAAACAAAGACAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAATACTAACTTCACAGTATTAAAGAATACACAGTT
* *
3156752 TAGCAGAATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGATAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAAACGAACAAATTTAC-TTCAACCAAAAGACAAAACAAAAACAAATACT
*
3156817 AACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTAGCAGCAACCGAACAAAT
130 AACTTCACAGTGTT----AATAAACAG-TTAGCAGAATTAGCAGCAACCGAACAAAT
*
3156874 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTAACTTCACAGTATTAAAGAATACACAGT
*
3156939 TTAGCAG-ATTGGCAGCAAACGAATAAATTTACTTCAACCAAAAGACAAAACAAAAACAAATACT
65 TTAGCAGAATTGGCAGCAAACGAACAAATTTACTTCAACCAAAAGACAAAACAAAAACAAATACT
* * *
3157003 AACTTCACAGTGTTAATAAACAGTTAGCAGTATTGGCAGCAACCGAATAAAT
130 AACTTCACAGTGTTAATAAACAGTTAGCAGAATTAGCAGCAACCGAACAAAT
3157055 TTACT
1 TTACT
3157060 AAGCAATCTA
Statistics
Matches: 175, Mismatches: 9, Indels: 9
0.91 0.05 0.05
Matches are distributed among these distances:
181 31 0.18
182 8 0.05
186 48 0.27
187 49 0.28
188 39 0.22
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (181 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAATACTAACTTCACAGTATTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAAACGAACAAATTTACTTCAACCAAAAGACAAAACAAAAACAAATACTA
ACTTCACAGTGTTAATAAACAGTTAGCAGAATTAGCAGCAACCGAACAAAT
Found at i:3158788 original size:20 final size:19
Alignment explanation
Indices: 3158743--3158864 Score: 59
Period size: 20 Copynumber: 6.8 Consensus size: 19
3158733 TCTTTTGGTT
*
3158743 GAAATGAAAATCGTAACGA
1 GAAATGAAAATCGCAACGA
* *
3158762 GAGAATGAAATTCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
3158783 GAAATGACTATCG-ATACGA
1 GAAATGAAAATCGCA-ACGA
*
3158802 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
3158816 GAAATAAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
3158835 G--A-G--AATCGCAATGT
1 GAAATGAAAATCGCAACGA
3158849 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3158865 TGCGATTTTG
Statistics
Matches: 75, Mismatches: 14, Indels: 28
0.64 0.12 0.24
Matches are distributed among these distances:
14 18 0.24
15 1 0.01
16 3 0.04
17 3 0.04
19 23 0.31
20 25 0.33
21 2 0.03
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.15
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:3158835 original size:33 final size:33
Alignment explanation
Indices: 3158798--3158864 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
3158788 GACTATCGAT
3158798 ACGAGAGAATCGCAACGCGAAATAAAAATCGCA
1 ACGAGAGAATCGCAACGCGAAATAAAAATCGCA
* * *
3158831 ACGAGAGAATCGCAATGTGAAATGAAAATCGCA
1 ACGAGAGAATCGCAACGCGAAATAAAAATCGCA
3158864 A
1 A
3158865 TGCGATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (33 bp):
ACGAGAGAATCGCAACGCGAAATAAAAATCGCA
Found at i:3158934 original size:20 final size:19
Alignment explanation
Indices: 3158865--3158935 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
3158855 AAAATCGCAA
**
3158865 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
3158884 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
**
3158903 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
3158923 TGCGATTTTCATT
1 TGCGATTTTCATT
3158936 CTCGAAACTA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
19 29 0.64
20 16 0.36
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:3159500 original size:20 final size:20
Alignment explanation
Indices: 3159477--3159567 Score: 119
Period size: 20 Copynumber: 4.5 Consensus size: 20
3159467 CGATAGTCAG
*
3159477 ATTCGAATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
3159497 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
3159517 AATTTGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* *
3159538 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3159558 ATTCGCATTG
1 ATTCGCATTG
3159568 TGAATTAGGA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 42 0.71
21 17 0.29
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:3164310 original size:2 final size:2
Alignment explanation
Indices: 3164303--3164333 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3164293 TCAATCTACA
3164303 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3164334 ATTTACGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3164423 original size:13 final size:13
Alignment explanation
Indices: 3164405--3164446 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3164395 AATGACACGC
*
3164405 AATGTAAGTCGTA
1 AATGTAAGTCATA
3164418 AATGTAAGTCATA
1 AATGTAAGTCATA
**
3164431 AATGTGTGTCATA
1 AATGTAAGTCATA
3164444 AAT
1 AAT
3164447 TTATGACACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (13 bp):
AATGTAAGTCATA
Found at i:3177913 original size:24 final size:24
Alignment explanation
Indices: 3177886--3177985 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
3177876 GATATCAAAA
*
3177886 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
3177910 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
3177934 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
3177958 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
3177982 ATCA
1 ATCA
3177986 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:3177985 original size:48 final size:48
Alignment explanation
Indices: 3177879--3177987 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
3177869 AAACGGAGAT
* * * * *
3177879 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
3177927 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
3177975 ATCAGAAATCAGA
1 ATCAGAAATCAGA
3177988 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:3180488 original size:13 final size:13
Alignment explanation
Indices: 3180470--3180501 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
3180460 CAACGGTCAA
3180470 CGGGTCAACGGGT
1 CGGGTCAACGGGT
3180483 CGGGTCAACGGGT
1 CGGGTCAACGGGT
3180496 CGGGTC
1 CGGGTC
3180502 GGGTAAACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:3180501 original size:18 final size:18
Alignment explanation
Indices: 3180464--3180541 Score: 111
Period size: 18 Copynumber: 4.2 Consensus size: 18
3180454 TCCATTCAAC
3180464 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
3180485 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
3180503 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
3180521 GGTTAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
3180539 GGT
1 GGT
3180542 TGTGACCGGT
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
18 44 0.80
21 11 0.20
ACGTcount: A:0.14, C:0.19, G:0.49, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:3180542 original size:18 final size:18
Alignment explanation
Indices: 3180478--3180542 Score: 112
Period size: 18 Copynumber: 3.6 Consensus size: 18
3180468 AACGGGTCAA
*
3180478 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTTAACGGGT
*
3180496 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTTAACGGGT
3180514 CGGGTCGGGTTAACGGGT
1 CGGGTCGGGTTAACGGGT
3180532 CGGGTCGGGTT
1 CGGGTCGGGTT
3180543 GTGACCGGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.11, C:0.18, G:0.51, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTTAACGGGT
Found at i:3182693 original size:24 final size:24
Alignment explanation
Indices: 3182666--3182765 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
3182656 GATATCAAAA
*
3182666 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
3182690 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
3182714 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
3182738 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
3182762 ATCA
1 ATCA
3182766 GATAAAATTC
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:3182765 original size:48 final size:48
Alignment explanation
Indices: 3182659--3182767 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
3182649 AAACGGAGAT
* * * * *
3182659 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
3182707 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
3182755 ATCAGAAATCAGA
1 ATCAGAAATCAGA
3182768 TAAAATTCAT
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:3185250 original size:13 final size:13
Alignment explanation
Indices: 3185228--3185260 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3185218 CTCCGGTCAA
3185228 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
3185241 CGGGTTAACGGGT
1 CGGGTCAACGGGT
3185254 CGGGTCA
1 CGGGTCA
3185261 GGTAAACGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:3185259 original size:18 final size:18
Alignment explanation
Indices: 3185236--3185313 Score: 76
Period size: 18 Copynumber: 4.6 Consensus size: 18
3185226 AACGGGTCAA
3185236 CGGGTCGGGTTAACGGGT
1 CGGGTCGGGTTAACGGGT
* *
3185254 CGGGTCAGG-TAA----A
1 CGGGTCGGGTTAACGGGT
*
3185267 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTTAACGGGT
* *
3185285 TGGGTCGGGTAAACGGGT
1 CGGGTCGGGTTAACGGGT
3185303 CGGGTCGGGTT
1 CGGGTCGGGTT
3185314 GTGACCGGTC
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
13 8 0.17
14 2 0.04
17 3 0.06
18 34 0.72
ACGTcount: A:0.15, C:0.15, G:0.49, T:0.21
Consensus pattern (18 bp):
CGGGTCGGGTTAACGGGT
Found at i:3185269 original size:31 final size:31
Alignment explanation
Indices: 3185234--3185307 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
3185224 TCAACGGGTC
*
3185234 AACGGGTCGGGTTAACGGGTCGGGTCAGGTA
1 AACGGGTCGGGTAAACGGGTCGGGTCAGGTA
* *
3185265 AACGGGTCGGGTAAACGGGTTGGGTCGGGTA
1 AACGGGTCGGGTAAACGGGTCGGGTCAGGTA
3185296 AACGGGTCGGGT
1 AACGGGTCGGGT
3185308 CGGGTTGTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.19, C:0.15, G:0.47, T:0.19
Consensus pattern (31 bp):
AACGGGTCGGGTAAACGGGTCGGGTCAGGTA
Found at i:3185307 original size:13 final size:13
Alignment explanation
Indices: 3185254--3185289 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3185244 GTTAACGGGT
*
3185254 CGGGTCAGGTAAA
1 CGGGTCGGGTAAA
3185267 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
*
3185280 CGGGTTGGGT
1 CGGGTCGGGT
3185290 CGGGTAAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:3192414 original size:24 final size:24
Alignment explanation
Indices: 3192369--3192416 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3192359 AGGTAAAGAA
* *
3192369 TTACCTAAAACAATATTTTTTTTT
1 TTACCTAAAACAATAATGTTTTTT
*
3192393 TTACCTAAAACATTAATGTTTTTT
1 TTACCTAAAACAATAATGTTTTTT
3192417 AACATTTCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.52
Consensus pattern (24 bp):
TTACCTAAAACAATAATGTTTTTT
Found at i:3194347 original size:37 final size:37
Alignment explanation
Indices: 3194297--3194368 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
3194287 CCTTAGTTGC
3194297 CTCTGATGGTCTTCTAATTGAGGAAGAGATTACCCGT
1 CTCTGATGGTCTTCTAATTGAGGAAGAGATTACCCGT
3194334 CTCTGATGGTCTTCTAATTGAGGAAGAGATTACCC
1 CTCTGATGGTCTTCTAATTGAGGAAGAGATTACCC
3194369 TTTCTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (37 bp):
CTCTGATGGTCTTCTAATTGAGGAAGAGATTACCCGT
Found at i:3213228 original size:35 final size:35
Alignment explanation
Indices: 3213180--3213247 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
3213170 AAGTCTCTAC
* *
3213180 AGGTTCAGCTCGATCAAATTGGTAATTCCTTATAT
1 AGGTTCAGATCGATCAAACTGGTAATTCCTTATAT
* *
3213215 AGGTTCAGATCGATCGAGCTGGTAATTCCTTAT
1 AGGTTCAGATCGATCAAACTGGTAATTCCTTAT
3213248 GGACCTAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (35 bp):
AGGTTCAGATCGATCAAACTGGTAATTCCTTATAT
Found at i:3214726 original size:28 final size:29
Alignment explanation
Indices: 3214693--3214754 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
3214683 TTTGCTGACG
*
3214693 TGACAGTTAAC-CCGTTAGCTCTCTAACA
1 TGACAGTTAACTCCGTTAACTCTCTAACA
3214721 TGACAGTTAACTCCGTTAACTCTCTAACA
1 TGACAGTTAACTCCGTTAACTCTCTAACA
3214750 TGACA
1 TGACA
3214755 ACTTCTTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (29 bp):
TGACAGTTAACTCCGTTAACTCTCTAACA
Found at i:3215567 original size:3 final size:3
Alignment explanation
Indices: 3215559--3216380 Score: 1131
Period size: 3 Copynumber: 283.7 Consensus size: 3
3215549 TTCCTAAACA
* *
3215559 AAG AAG AAG AAG AAG AAG AAG AAG AGG AAG AAG AGG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * * * *
3215607 AGG AAG AAG AGG AAG AGG AAG AGG AAG AGG AAG AAG AAG AAG AGG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
3215655 AAG AGG AAG AAG -AG AAG AAG AAG AAG -AG AAG -AG AAG AAG AAAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG
3215698 AAG AAG AGAG AAG AAAG AAG AAG AAG AAG -AG AAG AAG AAG AAG AAG
1 AAG AAG A-AG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
3215744 AAG AA- AAG AAG AGG AAG AAG AAG AAG AGG AAG AAG AGG AAG AAG -AG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3215790 AAG AAG AAG AAG -AG AAG -AG AAG AAG AAG AA- AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
3215835 AAG AAG AAG AAG AAG -AG AAG AAAG AAG AAA AAG -AG AAG AA- AAG
1 AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG
3215878 AAG AAG AAG AAG AAG AA- AAG AAG AAG AAG AAG AAG AAG -AG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3215924 AAG AAG AAG AA- AAG AAG AAG AAG AAG AAG AAG -AG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3215970 AAG -AG AAG AAG AAG AAG AAAG AAG AAG -AG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
3216014 AAG AAG AAG AAG AAG AAG AAG -AG AAG -AG AGG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3216060 AAG -AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3216106 AAG AAGG AA- AAG -AG AAG AAG AAG AAG -AG AA- AAG -AG AAG -AG
1 AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
3216146 AAG AAG AAG AAG -AG GAG AAG AAG -AG AAG AAG AAG AAG AAG AAG AA-
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
3216191 AAG AAG AAG AAG -AG AAG AA- AAG AAG -AG AAG AAG AAG AGG AAG AGAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG
* * * *
3216237 AAG AAG AGG AAG AGG AAG AGG AAG AAG AAG AGG AAG -AG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
3216284 AGG AAG AAG -AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
3216331 AAG AAG AAG AAG AAG AAG TAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3216379 AA
1 AA
3216381 AAGTTGTTGT
Statistics
Matches: 733, Mismatches: 43, Indels: 86
0.85 0.05 0.10
Matches are distributed among these distances:
2 72 0.10
3 640 0.87
4 21 0.03
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3217660 original size:36 final size:36
Alignment explanation
Indices: 3217591--3217660 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
3217581 TTTTTTTATC
* *
3217591 ATTAAAGAAAACATACATGGTGTATTTAAGGATTAA
1 ATTAAAGAAAACATACATGATATATTTAAGGATTAA
3217627 ATTAAAGAAAACATACATGATATA-TTAATGGATT
1 ATTAAAGAAAACATACATGATATATTTAA-GGATT
3217661 TGTGCAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 4 0.13
36 27 0.87
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (36 bp):
ATTAAAGAAAACATACATGATATATTTAAGGATTAA
Found at i:3219185 original size:21 final size:21
Alignment explanation
Indices: 3219160--3219201 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3219150 CATATAAAAC
*
3219160 TGTCCCGAAGGACCTCGTATA
1 TGTCCCGAAGGACCACGTATA
3219181 TGTCCCGAAGGACCACGTATA
1 TGTCCCGAAGGACCACGTATA
3219202 ACATATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (21 bp):
TGTCCCGAAGGACCACGTATA
Found at i:3226028 original size:21 final size:21
Alignment explanation
Indices: 3225978--3226028 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3225968 TGCCATCTCT
*
3225978 GCAGGGTTACATTCCTAGCCC
1 GCAGGGTTTCATTCCTAGCCC
*
3225999 TCAGGGTTTCATTCCTAGCCC
1 GCAGGGTTTCATTCCTAGCCC
3226020 GCAGGGTTT
1 GCAGGGTTT
3226029 TATGACACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.29
Consensus pattern (21 bp):
GCAGGGTTTCATTCCTAGCCC
Found at i:3226583 original size:34 final size:34
Alignment explanation
Indices: 3226545--3226609 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
3226535 TTTTAATATG
3226545 CAAATTATAGTATTCGAAATTTAAAATTAAAATA
1 CAAATTATAGTATTCGAAATTTAAAATTAAAATA
* *
3226579 CAAATTATGGTATTCGAAATTTAACATTAAA
1 CAAATTATAGTATTCGAAATTTAAAATTAAA
3226610 TTCAACTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (34 bp):
CAAATTATAGTATTCGAAATTTAAAATTAAAATA
Found at i:3226903 original size:63 final size:63
Alignment explanation
Indices: 3226802--3226926 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 63
3226792 CAATGTCACG
* *
3226802 ACCAACTTATCACTTCACATTTATTCAATTTATCCATAACATTTTATGCAATATACTCAAACA
1 ACCAACTTATCACTTAACATTTATTCAATTTATCCATAACATTTTATCCAATATACTCAAACA
* * * * *
3226865 ACCAA-TTAATCACTTAACATTTTTTTAATTTATTCATAACATTTTATCCAATTTATTCAAAC
1 ACCAACTT-ATCACTTAACATTTATTCAATTTATCCATAACATTTTATCCAATATACTCAAAC
3226927 TTCACATAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 2 0.04
63 52 0.96
ACGTcount: A:0.38, C:0.21, G:0.01, T:0.41
Consensus pattern (63 bp):
ACCAACTTATCACTTAACATTTATTCAATTTATCCATAACATTTTATCCAATATACTCAAACA
Found at i:3227391 original size:117 final size:117
Alignment explanation
Indices: 3227184--3227534 Score: 578
Period size: 117 Copynumber: 3.0 Consensus size: 117
3227174 AGAAATAATA
3227184 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
3227249 TCTAACAAAATAATCGAAGGCGCGCCCCCGAGAACGCGCCTTCACCACTTTG
66 TCTGACAAAATAATCGAAGGCGCGCCCCCGAGAACGCGCCTTCACCACTTTG
***
3227301 GGTACTGACATGAATAGTGCTATCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * *
3227366 TCTGACAAAATAATCGAAGGTGCGCCCCCGGGAATGCGCCTTCACCACTTTG
66 TCTGACAAAATAATCGAAGGCGCGCCCCCGAGAACGCGCCTTCACCACTTTG
* * *
3227418 GGCACTGACATGAATATTACCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* *
3227483 TCTGACAAAATAATTGAAGGCGCGCCCCC-AGGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATCGAAGGCGCGCCCCCGA-GAACGCGCCTTCACCACTTTG
3227535 CCAAGTCCCC
Statistics
Matches: 215, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
117 215 1.00
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.21
Consensus pattern (117 bp):
GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
TCTGACAAAATAATCGAAGGCGCGCCCCCGAGAACGCGCCTTCACCACTTTG
Found at i:3230744 original size:21 final size:21
Alignment explanation
Indices: 3230718--3230759 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3230708 AATAATTAAT
*
3230718 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
3230739 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
3230760 TAATAACTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:3231429 original size:60 final size:61
Alignment explanation
Indices: 3231361--3231476 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
3231351 AAAATACCAA
* *
3231361 CGTGGCATCCAACTCAGCAT-AACCCATATAAAGAGCATCCCCGGGGATGCGCCTTACACG
1 CGTGGCATCCAACTCAGCATAAACCCAGATAAAGAGCATCCCCGAGGATGCGCCTTACACG
* * * * * *
3231421 CGTGGCATCCCAGTCAGTATAAACTCAGGTAAAGCGCATCCCCGAGGATGCGCCTT
1 CGTGGCATCCAACTCAGCATAAACCCAGATAAAGAGCATCCCCGAGGATGCGCCTT
3231477 TGTGTCACCT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
60 17 0.36
61 30 0.64
ACGTcount: A:0.27, C:0.32, G:0.23, T:0.18
Consensus pattern (61 bp):
CGTGGCATCCAACTCAGCATAAACCCAGATAAAGAGCATCCCCGAGGATGCGCCTTACACG
Found at i:3231689 original size:2 final size:2
Alignment explanation
Indices: 3231682--3231720 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
3231672 TCTCTTGTTC
3231682 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3231721 ATTAAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3231721 original size:10 final size:10
Alignment explanation
Indices: 3231682--3231733 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
3231672 TCTCTTGTTC
3231682 ATATAT-ATAT
1 ATATATAAT-T
3231692 ATATATATATAT
1 ATATATA-AT-T
3231704 ATATATAATT
1 ATATATAATT
3231714 ATATATAATT
1 ATATATAATT
*
3231724 A-AAATAATT
1 ATATATAATT
3231733 A
1 A
3231734 GATAAATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
9 8 0.21
10 18 0.46
11 2 0.05
12 11 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
ATATATAATT
Found at i:3231743 original size:17 final size:19
Alignment explanation
Indices: 3231708--3231748 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
3231698 ATATATATAT
*
3231708 ATAATTATATATAATTAAA
1 ATAATTAGATATAATTAAA
*
3231727 ATAATTAGATA-AATAAAA
1 ATAATTAGATATAATTAAA
3231745 ATAA
1 ATAA
3231749 ATAATTAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAATTAGATATAATTAAA
Found at i:3231749 original size:23 final size:24
Alignment explanation
Indices: 3231723--3231775 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
3231713 TATATATAAT
3231723 TAAAATAATT-AGATAAATAAAAA
1 TAAAATAATTAAGATAAATAAAAA
* *
3231746 T-AAATAATTAAGATTAATAATAA
1 TAAAATAATTAAGATAAATAAAAA
3231769 -AAAATAA
1 TAAAATAA
3231776 AAAAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (24 bp):
TAAAATAATTAAGATAAATAAAAA
Found at i:3231803 original size:26 final size:26
Alignment explanation
Indices: 3231768--3231829 Score: 117
Period size: 25 Copynumber: 2.4 Consensus size: 26
3231758 ATTAATAATA
3231768 AAAAATAAAAAAATATTTGTTAAAAG
1 AAAAATAAAAAAATATTTGTTAAAAG
3231794 AAAAAT-AAAAAATATTTGTTAAAAG
1 AAAAATAAAAAAATATTTGTTAAAAG
3231819 AAAAATAAAAA
1 AAAAATAAAAA
3231830 GTTAATAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 25 0.71
26 10 0.29
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (26 bp):
AAAAATAAAAAAATATTTGTTAAAAG
Found at i:3242219 original size:14 final size:14
Alignment explanation
Indices: 3242187--3242237 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3242177 AATAAGAGGA
* *
3242187 TAAAGAAAAT-AAG
1 TAAATAAAATAAAC
3242200 TAAATAAAATAAAC
1 TAAATAAAATAAAC
*
3242214 TAAATATAATAAAC
1 TAAATAAAATAAAC
*
3242228 AAAATGAAAA
1 TAAAT-AAAA
3242238 GAGTAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 9 0.29
14 19 0.61
15 3 0.10
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.20
Consensus pattern (14 bp):
TAAATAAAATAAAC
Found at i:3242502 original size:52 final size:51
Alignment explanation
Indices: 3242408--3242516 Score: 130
Period size: 52 Copynumber: 2.1 Consensus size: 51
3242398 TTATAGTAAA
* * *
3242408 TAAATATATATATAAAAAGAAAGGGGGAAAATAATAATAATAAAGAAATAAT
1 TAAATATATATATAAAAACAAAGGGAGAAAAAAATAATAATAAA-AAATAAT
* * * *
3242460 TAAATATATATATAAATACTAATGGAGAAACAAAATAA-AATAAAAAATATT
1 TAAATATATATATAAAAACAAAGGGAGAAA-AAAATAATAATAAAAAATAAT
3242511 TAAATA
1 TAAATA
3242517 GGCCAAAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
51 12 0.24
52 31 0.63
53 6 0.12
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (51 bp):
TAAATATATATATAAAAACAAAGGGAGAAAAAAATAATAATAAAAAATAAT
Found at i:3244650 original size:79 final size:78
Alignment explanation
Indices: 3244512--3244663 Score: 178
Period size: 79 Copynumber: 1.9 Consensus size: 78
3244502 CTGGAACTGG
* * * * *
3244512 GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAACTTATGCTGTCTTGAGTCC
1 GAAATTGTTTGTTGACAATCAACCGCCCCTTCGCCGTGAAGTTGAACTTATACTATCTTGAGACC
3244577 AATATCCTGAGTT
66 AATATCCTGAGTT
** * * * * * *
3244590 GAAAGTTGTTTGTTGTTAATCAACCGCCCCTTCGTCGTGAAGTTTAGCTTGTATTATCTTGGGAC
1 GAAA-TTGTTTGTTGACAATCAACCGCCCCTTCGCCGTGAAGTTGAACTTATACTATCTTGAGAC
3244655 CAATATCCT
65 CAATATCCT
3244664 TCGTTGTGGA
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
78 4 0.07
79 56 0.93
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (78 bp):
GAAATTGTTTGTTGACAATCAACCGCCCCTTCGCCGTGAAGTTGAACTTATACTATCTTGAGACC
AATATCCTGAGTT
Found at i:3245274 original size:78 final size:78
Alignment explanation
Indices: 3245158--3245308 Score: 196
Period size: 78 Copynumber: 1.9 Consensus size: 78
3245148 TTGGAACTGG
* * * *
3245158 GAAATTGTTTGTTGACAGTCAGCCGCCCTTTCGCCGTGAAGTTGAGCTTATGCTGTCTTGAGTCC
1 GAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTATGCTATCTTGAGACC
3245223 AATATCCTGAGTT
66 AATATCCTGAGTT
* * * * * *
3245236 GAAAGTTG-TTGTTGATAATCAGTCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTATCTTGGGAC
1 GAAA-TTGTTTGTTGACAATCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTATGCTATCTTGAGAC
3245300 CAATATCCT
65 CAATATCCT
3245309 TCGTTGTGAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
78 59 0.95
79 3 0.05
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.35
Consensus pattern (78 bp):
GAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTATGCTATCTTGAGACC
AATATCCTGAGTT
Found at i:3245429 original size:106 final size:106
Alignment explanation
Indices: 3245244--3245450 Score: 308
Period size: 106 Copynumber: 2.0 Consensus size: 106
3245234 TTGAAAGTTG
* * * *
3245244 TTGTTGATAATCAGTCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTATCTTGGGACCAATATCCT
1 TTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGCTATCTTGAGACCAATATCCT
* *
3245309 TCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTAT
66 TCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTAT
* * * *
3245350 TTGTTGACAGTCAGCCGCCCCTTCG-CTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAGTATCC
1 TTGTTGACAATCAGCCGCCCCTTCGTC-GTGAAGTTGAGCTTGTGCTATCTTGAGACCAATATCC
3245414 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
65 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
3245451 GCCCCTTCGT
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
105 1 0.01
106 89 0.99
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (106 bp):
TTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGCTATCTTGAGACCAATATCCT
TCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTAT
Found at i:3246576 original size:11 final size:11
Alignment explanation
Indices: 3246560--3246619 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
3246550 ACCCACCTTA
3246560 TTTTTCTTTTC
1 TTTTTCTTTTC
*
3246571 TTTTTCTTTTG
1 TTTTTCTTTTC
*
3246582 TTCTT-TTTTC
1 TTTTTCTTTTC
*
3246592 TCTTT-TTTTC
1 TTTTTCTTTTC
3246602 TCTTTTCTTTTTC
1 T-TTTTC-TTTTC
3246615 TTTTT
1 TTTTT
3246620 TCAATTTAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 13 0.32
11 17 0.43
12 4 0.10
13 6 0.15
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.82
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:3246587 original size:8 final size:8
Alignment explanation
Indices: 3246571--3246613 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
3246561 TTTTCTTTTC
3246571 TTTTTCTT
1 TTTTTCTT
*
3246579 TTGTTCTT
1 TTTTTCTT
3246587 TTTTCTCTT
1 TTTT-TCTT
3246596 TTTTTC-T
1 TTTTTCTT
*
3246603 CTTTTCTT
1 TTTTTCTT
3246611 TTT
1 TTT
3246614 CTTTTTTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 6 0.21
8 15 0.52
9 8 0.28
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:3246590 original size:10 final size:9
Alignment explanation
Indices: 3246560--3246620 Score: 52
Period size: 9 Copynumber: 6.3 Consensus size: 9
3246550 ACCCACCTTA
3246560 TTTTTCTTT
1 TTTTTCTTT
3246569 TCTTTT-TCTT
1 T-TTTTCT-TT
*
3246579 TTGTTCTTT
1 TTTTTCTTT
*
3246588 TTTCTCTTT
1 TTTTTCTTT
3246597 TTTTCTCTTTT
1 TTTT-TC-TTT
3246608 CTTTTTCTTT
1 -TTTTTCTTT
3246618 TTT
1 TTT
3246621 CAATTTAGGG
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
9 20 0.48
10 13 0.31
11 5 0.12
12 4 0.10
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:3246592 original size:21 final size:21
Alignment explanation
Indices: 3246564--3246618 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 21
3246554 ACCTTATTTT
3246564 TCTTTTCTTTTTCTTTTG-T-
1 TCTTTTCTTTTTCTTTTGTTC
* *
3246583 TC-TTT-TTTCTCTTTTTTTC
1 TCTTTTCTTTTTCTTTTGTTC
3246602 TCTTTTCTTTTTCTTTT
1 TCTTTTCTTTTTCTTTT
3246619 TTCAATTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 9 0.31
18 4 0.14
19 4 0.14
20 3 0.10
21 9 0.31
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (21 bp):
TCTTTTCTTTTTCTTTTGTTC
Found at i:3246619 original size:21 final size:20
Alignment explanation
Indices: 3246560--3246620 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
3246550 ACCCACCTTA
3246560 TTTTTCTTTTCTTTTTC-TT
1 TTTTTCTTTTCTTTTTCTTT
* *
3246579 TTGTTC-TTT-TTTCTCTTT
1 TTTTTCTTTTCTTTTTCTTT
3246597 TTTTCTCTTTTCTTTTTCTTT
1 TTTT-TCTTTTCTTTTTCTTT
3246618 TTT
1 TTT
3246621 CAATTTAGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 5 0.15
18 8 0.24
19 7 0.21
20 3 0.09
21 11 0.32
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTTCTTTTCTTTTTCTTT
Found at i:3246663 original size:62 final size:63
Alignment explanation
Indices: 3246596--3246717 Score: 192
Period size: 63 Copynumber: 2.0 Consensus size: 63
3246586 TTTTTCTCTT
* * *
3246596 TTTTTCTCTTTTCTTTTTC-TTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTCTCTTTTATTTTTCTTTTTTTCAACTTAGGACGCCCTTTCGGGTTTTCACCCTAAACG
* *
3246658 TTTTTCTTTTTTATTTTTCTTTTTTTCAACTTAGGACGCCCTTTCGGGTTTTCATCCTAA
1 TTTTTCTCTTTTATTTTTCTTTTTTTCAACTTAGGACGCCCTTTCGGGTTTTCACCCTAA
3246718 GCGAAGTACT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
62 17 0.31
63 37 0.69
ACGTcount: A:0.12, C:0.22, G:0.11, T:0.54
Consensus pattern (63 bp):
TTTTTCTCTTTTATTTTTCTTTTTTTCAACTTAGGACGCCCTTTCGGGTTTTCACCCTAAACG
Found at i:3246676 original size:13 final size:13
Alignment explanation
Indices: 3246658--3246682 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3246648 ACCCTAAACG
3246658 TTTTTCTTTTTTA
1 TTTTTCTTTTTTA
3246671 TTTTTCTTTTTT
1 TTTTTCTTTTTT
3246683 TCAACTTAGG
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:0.04, C:0.08, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTA
Found at i:3246730 original size:63 final size:62
Alignment explanation
Indices: 3246604--3246731 Score: 166
Period size: 63 Copynumber: 2.0 Consensus size: 62
3246594 TTTTTTTCTC
* * * *** *
3246604 TTTTCTTTTTCTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACGTTTTTCTT
1 TTTTATTTTTCTTTTTTCAACTTAGGACGCCCTTTCGGGTTTTCACCCTAAACGAAGTACTT
* *
3246666 TTTTATTTTTCTTTTTTTCAACTTAGGACGCCCTTTCGGGTTTTCATCCTAAGCGAAGTACTT
1 TTTTATTTTTC-TTTTTTCAACTTAGGACGCCCTTTCGGGTTTTCACCCTAAACGAAGTACTT
3246729 TTT
1 TTT
3246732 GACTGCATCT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
62 10 0.18
63 46 0.82
ACGTcount: A:0.14, C:0.21, G:0.13, T:0.52
Consensus pattern (62 bp):
TTTTATTTTTCTTTTTTCAACTTAGGACGCCCTTTCGGGTTTTCACCCTAAACGAAGTACTT
Found at i:3253637 original size:17 final size:20
Alignment explanation
Indices: 3253592--3253637 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 20
3253582 TTCGGAAGGG
3253592 ACAGTCCTGAGATGTTCTTCC
1 ACAGT-CTGAGATGTTCTTCC
*
3253613 ATAGTCTGAG-TG-TCTT-C
1 ACAGTCTGAGATGTTCTTCC
3253630 ACAGTCTG
1 ACAGTCTG
3253638 GAACCGAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 8 0.35
18 4 0.17
19 2 0.09
20 5 0.22
21 4 0.17
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (20 bp):
ACAGTCTGAGATGTTCTTCC
Found at i:3256163 original size:14 final size:13
Alignment explanation
Indices: 3256088--3256132 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
3256078 GAATAAGAGG
*
3256088 ATAAAGAAAATAA
1 ATAAATAAAATAA
*
3256101 GTAAATAAAATAA
1 ATAAATAAAATAA
*
3256114 ACTAAATATAATAA
1 A-TAAATAAAATAA
3256128 ATAAA
1 ATAAA
3256133 ATGAAAAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (13 bp):
ATAAATAAAATAA
Found at i:3257642 original size:2 final size:2
Alignment explanation
Indices: 3257635--3257663 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3257625 TGTTATATGT
3257635 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
3257664 GTAACACATG
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:3271251 original size:12 final size:12
Alignment explanation
Indices: 3271234--3271350 Score: 60
Period size: 12 Copynumber: 9.1 Consensus size: 12
3271224 ATAGCATAAG
3271234 AAAAAAAGCA-AA
1 AAAAAAAG-AGAA
3271246 AAAAAAAGAGAA
1 AAAAAAAGAGAA
*
3271258 AAAAAGAAAAGAGA
1 AAAAA-AAGAGA-A
* *
3271272 AAAGAATGA-AA
1 AAAAAAAGAGAA
*
3271283 GAAGAAAAAGAATAA
1 -AA-AAAAAG-AGAA
*
3271298 AAAACAAAAAGAA
1 AAAA-AAAGAGAA
*
3271311 AGAAAAAGAAGAA
1 AAAAAAAG-AGAA
3271324 AAATAAAAGA-AA
1 AAA-AAAAGAGAA
3271336 AAAGAAAAGAAGAA
1 AAA-AAAAG-AGAA
3271350 A
1 A
3271351 GGAAGAAGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 22
0.70 0.10 0.19
Matches are distributed among these distances:
11 2 0.02
12 31 0.38
13 27 0.33
14 19 0.23
15 2 0.02
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (12 bp):
AAAAAAAGAGAA
Found at i:3271257 original size:22 final size:22
Alignment explanation
Indices: 3271232--3271340 Score: 79
Period size: 22 Copynumber: 5.0 Consensus size: 22
3271222 ATATAGCATA
3271232 AGAAAAAAAGCAAAA-AAAAAAG
1 AGAAAAAAAG-AAAAGAAAAAAG
*
3271254 AGAAAAAAAGAAAAGAGAAAAG
1 AGAAAAAAAGAAAAGAAAAAAG
*
3271276 A-ATGAAAGAAGAAAAAGAATAAAA-
1 AGA--AAAAAAG-AAAAGAA-AAAAG
*
3271300 A-ACAAAAAG-AAAG-AAAAAG
1 AGAAAAAAAGAAAAGAAAAAAG
* *
3271319 A-AGAAAAATAAAAGAAAAAAG
1 AGAAAAAAAGAAAAGAAAAAAG
3271340 A
1 A
3271341 AAAGAAGAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
18 4 0.06
19 8 0.11
20 8 0.11
21 12 0.17
22 22 0.31
23 6 0.08
24 8 0.11
25 4 0.06
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.03
Consensus pattern (22 bp):
AGAAAAAAAGAAAAGAAAAAAG
Found at i:3271313 original size:26 final size:26
Alignment explanation
Indices: 3271231--3271350 Score: 90
Period size: 26 Copynumber: 4.6 Consensus size: 26
3271221 GATATAGCAT
3271231 AAGAAAAA-AAGCAAAAA-AAAAAGAGA
1 AAGAAAAAGAAG-AAAAATAAAAA-AGA
* * *
3271257 AA-AAAAGAAAAGAGAAAAGAATGAAAG-
1 AAGAAAA-AGAAGA-AAAATAA-AAAAGA
*
3271284 AAGAAAAAGAATAAAAA-ACAAAAAGA
1 AAGAAAAAGAAGAAAAATA-AAAAAGA
*
3271310 AAGAAAAAGAAGAAAAATAAAAGAAAA
1 AAGAAAAAGAAGAAAAATAAAA-AAGA
3271337 AAG-AAAAGAAGAAA
1 AAGAAAAAGAAGAAA
3271351 GGAAGAAGAA
Statistics
Matches: 78, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
25 9 0.12
26 39 0.50
27 20 0.26
28 8 0.10
29 2 0.03
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.03
Consensus pattern (26 bp):
AAGAAAAAGAAGAAAAATAAAAAAGA
Found at i:3271336 original size:69 final size:68
Alignment explanation
Indices: 3271236--3271364 Score: 183
Period size: 69 Copynumber: 1.9 Consensus size: 68
3271226 AGCATAAGAA
* *
3271236 AAAAAGCAAAAAAAAAAGAGAAAAAAAGAAAAGAGAAAAGAATGAAA-GAAGAA-AAAGAATAAA
1 AAAAAGCAAAAAAAAAAGAAAAAAAAAGAAAAAAGAAAAGAA-GAAAGGAAGAAGAAAGAATAAA
3271299 AAAC
65 AAAC
3271303 AAAAAG-AAAGAAAAAGAAGAAAAATAAAAGAAAAAAGAAAAGAAGAAAGGAAGAAGAAAGAA
1 AAAAAGCAAA-AAAAA-AAGAAAAA-AAAAGAAAAAAGAAAAGAAGAAAGGAAGAAGAAAGAA
3271365 AACCGATCAA
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
66 3 0.05
67 11 0.20
68 11 0.20
69 24 0.44
70 6 0.11
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (68 bp):
AAAAAGCAAAAAAAAAAGAAAAAAAAAGAAAAAAGAAAAGAAGAAAGGAAGAAGAAAGAATAAAA
AAC
Found at i:3272801 original size:76 final size:75
Alignment explanation
Indices: 3272722--3273058 Score: 376
Period size: 76 Copynumber: 4.4 Consensus size: 75
3272712 TGAGATTGTT
* * *
3272722 TTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAATTTTACTCGAAAGAAGATATTTCATTTAA
1 TTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTACTCGAAACAAGACATTTCATTTAA
3272787 CTCAAGATTG
66 CTCAAGATTG
* * * * * * *
3272797 TTTTTCTTAAAACACGGTTTGTTTCGCTTGAGACAATGTTTACTCTAAAGAATACATTTCATTTC
1 TTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAAT-TTTACTCGAAACAAGACATTTCATTTA
3272862 ACTCAAGATTG
65 ACTCAAGATTG
* * *
3272873 TTTTTCTTAAAACATA-CTTTGTCAT-GCTTGAGACAATTTTTATTCAAAACAAGACATTTCATT
1 TTTTTCTTAAAACA-AGATTTGTC-TCGCTTGAGACAA-TTTTACTCGAAACAAGACATTTCATT
*
3272936 TCACT-ATAGATTG
63 TAACTCA-AGATTG
** * * *
3272949 TTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTTTACCCGAAACAAGA-ATATTCATTT
1 TTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACA-ATTTTACTCGAAACAAGACAT-TTCATTT
3273013 AACTCAAGATTG
64 AACTCAAGATTG
* * *
3273025 TTTTTCTTAAAACCAGATTTTATCTAGCTTGAGA
1 TTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGA
3273059 TTGTTTCCCT
Statistics
Matches: 224, Mismatches: 27, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
75 38 0.17
76 169 0.75
77 17 0.08
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (75 bp):
TTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTACTCGAAACAAGACATTTCATTTAA
CTCAAGATTG
Found at i:3273061 original size:37 final size:37
Alignment explanation
Indices: 3272943--3273098 Score: 116
Period size: 37 Copynumber: 4.1 Consensus size: 37
3272933 ATTTCACTAT
* *
3272943 AGATTGTTTTTCTTAAAACAAGA-TTCATCTCGCTTG
1 AGATTGTTTTTCTCAAAACAAGATTTCATCTAGCTTG
* * * * * **
3272979 AGATAGTTTTTACCCGAAACAAGAATATTCATTTAACTCA
1 AGATTGTTTTT-CTCAAAACAAG-AT-TTCATCTAGCTTG
* * *
3273019 AGATTGTTTTTCTTAAAACCAGATTTTATCTAGCTTG
1 AGATTGTTTTTCTCAAAACAAGATTTCATCTAGCTTG
** * *
3273056 AGATTGTTTCCCTCAAAACAGAAGATTTTATCTCGCTTG
1 AGATTGTTTTTCTCAAAAC--AAGATTTCATCTAGCTTG
3273095 AGAT
1 AGAT
3273099 AATTTCCCTC
Statistics
Matches: 90, Mismatches: 24, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
36 10 0.11
37 32 0.36
38 3 0.03
39 27 0.30
40 18 0.20
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (37 bp):
AGATTGTTTTTCTCAAAACAAGATTTCATCTAGCTTG
Found at i:3273094 original size:39 final size:39
Alignment explanation
Indices: 3273039--3273526 Score: 656
Period size: 39 Copynumber: 12.5 Consensus size: 39
3273029 TCTTAAAACC
* * *
3273039 AGATTTTATCTAGCTTGAGATTGTTTCCCTCAAAACAGA
1 AGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGA
* *
3273078 AGATTTTATCTCGCTTGAGATAATTTCCCTCAAAACAGA
1 AGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGA
* *
3273117 AGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACATA
1 AGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGA
* *
3273156 AGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAA
1 AGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGA
*
3273195 AGATTTTATCTCG-TTGGAGATAGTTTCCCTCGAAATAGA
1 AGATTTTATCTCGCTT-GAGATAGTTTCCCTCGAAACAGA
* * * *
3273234 AGATTTTATCTTGCTTGATATAGTTTCCCTTGAAACATA
1 AGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGA
* * *
3273273 AGATTTTATCTCGCATGAGATAGTTTGCCTCGAAACATA
1 AGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGA
* * *
3273312 AGATCTTGTCTCGCTTGAGATAGTTTCCTTCGAAACAGA
1 AGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGA
* * *
3273351 AGATTTTGTCTCGTTTGAGATAGTTTCACTCGAAACAGA
1 AGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGA
* * *
3273390 AGATTTTGTCTCGTTTGAGATCGTTTCCCTCGAAACAGA
1 AGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGA
* * * *
3273429 AGATTTTGTCTCACTTAAGATAGTTTTCCTCGAAACAGA
1 AGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGA
* *
3273468 AGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAA
1 AGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGA
*
3273507 AGA-TTTATCTCACTTGAGAT
1 AGATTTTATCTCGCTTGAGAT
3273527 TATTTTTTCT
Statistics
Matches: 402, Mismatches: 45, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
38 18 0.04
39 382 0.95
40 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (39 bp):
AGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGA
Found at i:3273748 original size:59 final size:59
Alignment explanation
Indices: 3273567--3273751 Score: 180
Period size: 59 Copynumber: 3.2 Consensus size: 59
3273557 CAGAGGGGTT
* * * *
3273567 AACATTTCTTTTG-TTCGATTCACAACACTTCGAATCAGCGATGCCTCACTTGAAGGACC
1 AACATTTCCTTTGCTT-GATTCACAACACTTCGAATCAACGACGCCTCACTTGAGGGACC
* * * * * ** **
3273626 AACATTT-CTTTTCTCGATTTGA-AACACTTCGAATCAACAACGCCCCACCAGAGGGGTTC
1 AACATTTCCTTTGCTTGA-TTCACAACACTTCGAATCAACGACGCCTCACTTGA-GGGACC
* *
3273685 -ACATTTCCTTTGCTTGATTCACAACATTTTGAATCAACGACGCCTCACTTGAGGGACC
1 AACATTTCCTTTGCTTGATTCACAACACTTCGAATCAACGACGCCTCACTTGAGGGACC
3273743 AACATTTCC
1 AACATTTCC
3273752 AGTAAGGAAT
Statistics
Matches: 96, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
58 42 0.44
59 54 0.56
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (59 bp):
AACATTTCCTTTGCTTGATTCACAACACTTCGAATCAACGACGCCTCACTTGAGGGACC
Found at i:3277463 original size:21 final size:21
Alignment explanation
Indices: 3277439--3277484 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3277429 TTGTTGGTGT
*
3277439 TGATGATAAAGTTATTTTGAA
1 TGATGATAAAGTTAATTTGAA
***
3277460 TGATGATTGTGTTAATTTGAA
1 TGATGATAAAGTTAATTTGAA
3277481 TGAT
1 TGAT
3277485 AATGATGATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.46
Consensus pattern (21 bp):
TGATGATAAAGTTAATTTGAA
Found at i:3277496 original size:21 final size:21
Alignment explanation
Indices: 3277454--3277497 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3277444 ATAAAGTTAT
* *
3277454 TTTGAATGATGATTGTGTTAA
1 TTTGAATGATGAATGTGATAA
3277475 TTTGAATGAT-AATGATGATAA
1 TTTGAATGATGAATG-TGATAA
3277496 TT
1 TT
3277498 ATGTTGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.45
Consensus pattern (21 bp):
TTTGAATGATGAATGTGATAA
Found at i:3279488 original size:76 final size:76
Alignment explanation
Indices: 3279305--3279513 Score: 341
Period size: 76 Copynumber: 2.8 Consensus size: 76
3279295 ATTTTAAATA
*
3279305 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGAATTTTAATT-AGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
*
3279369 GGATATTATTT
66 GAATATTATTT
3279380 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
3279445 GAATATTATTT
66 GAATATTATTT
* * * *
3279456 TTATATTTTATCGTTGTTTTATGCATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTA
3279514 GGATTTAAGA
Statistics
Matches: 126, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
75 61 0.48
76 65 0.52
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
GAATATTATTT
Found at i:3287709 original size:76 final size:76
Alignment explanation
Indices: 3287602--3287887 Score: 520
Period size: 76 Copynumber: 3.8 Consensus size: 76
3287592 ATTTTAAATA
3287602 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
*
3287667 GGTTATTATTT
66 GGATATTATTT
*
3287678 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAATATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
3287743 GGATATTATTT
66 GGATATTATTT
*
3287754 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
3287819 GGATATTATTT
66 GGATATTATTT
*
3287830 TTATATTTTATCTTTATTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTATTTTAATTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTA
3287888 GGATTTAAGA
Statistics
Matches: 203, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
75 5 0.02
76 198 0.98
ACGTcount: A:0.27, C:0.01, G:0.12, T:0.60
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
GGATATTATTT
Found at i:3287761 original size:32 final size:31
Alignment explanation
Indices: 3287719--3287780 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
3287709 TTTAAATAGG
3287719 TTTTAATATTTTA-ATTAAGTTTTAGGATATTA
1 TTTTAATATTTTATATT-AGTTTTAGG-TATTA
* *
3287751 TTTTTATATTTTATATTTGTTTTAGGTATT
1 TTTTAATATTTTATATTAGTTTTAGGTATT
3287781 TTAGTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 4 0.15
32 20 0.74
33 3 0.11
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (31 bp):
TTTTAATATTTTATATTAGTTTTAGGTATTA
Found at i:3300863 original size:22 final size:22
Alignment explanation
Indices: 3300835--3300916 Score: 119
Period size: 22 Copynumber: 3.7 Consensus size: 22
3300825 CAATAAACGG
3300835 AAGTGCCTTAGCACTGATACTA
1 AAGTGCCTTAGCACTGATACTA
* * *
3300857 AAGTGCCTCAGCACTGTTACAA
1 AAGTGCCTTAGCACTGATACTA
* *
3300879 AAGTGCATTCGCACTGATACTA
1 AAGTGCCTTAGCACTGATACTA
3300901 AAGTGCCTTAGCACTG
1 AAGTGCCTTAGCACTG
3300917 CTAGCATATA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (22 bp):
AAGTGCCTTAGCACTGATACTA
Found at i:3306784 original size:37 final size:37
Alignment explanation
Indices: 3306644--3306979 Score: 246
Period size: 37 Copynumber: 9.2 Consensus size: 37
3306634 CTTAACATCA
* * * * * *
3306644 TTTCACTTTAAACATAAATTTTGTCTCACATGAGACAAT
1 TTTCTCTTGAAACA-AAATTTTATCTCACTTGAGA-TAG
* * *
3306683 TTTCCCTTGAAATACAAATCTTATCTCACTTGAGATAG
1 TTTCTCTTGAAACA-AAATTTTATCTCACTTGAGATAG
* * * *
3306721 TTTCTCTTAAAAC-AAATTTCATCTCACTCGATATAG
1 TTTCTCTTGAAACAAAATTTTATCTCACTTGAGATAG
*
3306757 TTTCTCTTGAAACAAAATTTTATCTCACTTGAGATAT
1 TTTCTCTTGAAACAAAATTTTATCTCACTTGAGATAG
* * * * *
3306794 TTTCCCTT-AAA-AAATTTTTGTCTCACTTGAGACAT
1 TTTCTCTTGAAACAAAATTTTATCTCACTTGAGATAG
* *
3306829 TTTCTCTTGAAACAAAAGTTTATCTCACTTGAGATAT
1 TTTCTCTTGAAACAAAATTTTATCTCACTTGAGATAG
* * *
3306866 TTTC-CTATG----AAAGTTCTAGTCTCACTCGAGATAG
1 TTTCTCT-TGAAACAAAATTTTA-TCTCACTTGAGATAG
* * *
3306900 TTTCTCTCGAAACAAAAAATTTATCTCGCTTGAGATAG
1 TTTCTCTTGAAAC-AAAATTTTATCTCACTTGAGATAG
* * *
3306938 TTTTTGCTTG----AAAATTTTCGTCTCACTTGAGACAG
1 TTTCT-CTTGAAACAAAATTTT-ATCTCACTTGAGATAG
3306973 TTTCTCT
1 TTTCTCT
3306980 AGAGACAGAA
Statistics
Matches: 236, Mismatches: 48, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
33 6 0.03
34 27 0.11
35 47 0.20
36 39 0.17
37 52 0.22
38 28 0.12
39 37 0.16
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAATTTTATCTCACTTGAGATAG
Found at i:3306840 original size:72 final size:72
Alignment explanation
Indices: 3306659--3306979 Score: 317
Period size: 72 Copynumber: 4.4 Consensus size: 72
3306649 CTTTAAACAT
* * * * * *
3306659 AAATTTT-GTCTCACATGAGACAATTTTCCCTTGAAATACAAATCTTATCTCACTTGAGATAGTT
1 AAATTTTCGTCTCACTTGAGAC-AGTTTCTCTTGAAACA-AAATTTTATCTCACTTGAGATATTT
*
3306723 TCTCTTAAA
64 TCCCTTAAA
* * * * *
3306732 ACAAATTTCATCTCACTCGATATAGTTTCTCTTGAAACAAAATTTTATCTCACTTGAGATATTTT
1 A-AATTTTCGTCTCACTTGAGACAGTTTCTCTTGAAACAAAATTTTATCTCACTTGAGATATTTT
3306797 CCCTTAAA
65 CCCTTAAA
* * *
3306805 AAATTTTTGTCTCACTTGAGACATTTTCTCTTGAAACAAAAGTTTATCTCACTTGAGATATTTT-
1 AAATTTTCGTCTCACTTGAGACAGTTTCTCTTGAAACAAAATTTTATCTCACTTGAGATATTTTC
*
3306869 CC-TATGA
66 CCTTA-AA
* * * * * * * *
3306876 AAGTTCTAGTCTCACTCGAGATAGTTTCTCTCGAAACAAAAAATTTATCTCGCTTGAGATAGTTT
1 AAATTTTCGTCTCACTTGAGACAGTTTCTCTTGAAAC-AAAATTTTATCTCACTTGAGATA-TTT
** *
3306941 TTGCTT-GA
64 TCCCTTAAA
3306949 AAATTTTCGTCTCACTTGAGACAGTTTCTCT
1 AAATTTTCGTCTCACTTGAGACAGTTTCTCT
3306980 AGAGACAGAA
Statistics
Matches: 205, Mismatches: 36, Indels: 14
0.80 0.14 0.05
Matches are distributed among these distances:
70 2 0.01
71 33 0.16
72 76 0.37
73 65 0.32
74 19 0.09
75 10 0.05
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (72 bp):
AAATTTTCGTCTCACTTGAGACAGTTTCTCTTGAAACAAAATTTTATCTCACTTGAGATATTTTC
CCTTAAA
Found at i:3306955 original size:144 final size:146
Alignment explanation
Indices: 3306662--3306979 Score: 389
Period size: 144 Copynumber: 2.2 Consensus size: 146
3306652 TAAACATAAA
* * *
3306662 TTTTGTCTCACATGAGACAATTTTCCCTTGAAATACAAATCTTATCTCACTTGAGATAGTTTCTC
1 TTTTGTCTCACTTGAGAC-ATTTTCTCTTGAAACACAAATCTTATCTCACTTGAGATAGTTTCTC
* * * *
3306727 TTAAAACAAATTTCATCTCACTCGATATAGTTTCTCTTGAAACAAAATTTTATCTCACTTGAGAT
65 CTAAAACAAATTTCATCTCACTCGAGATAGTTTCTCTCGAAACAAAAATTTATCTCACTTGAGAT
3306792 ATTTTCCCTTAAAAAAT
130 ATTTTCCCTTAAAAAAT
3306809 TTTTGTCTCACTTGAGACATTTTCTCTTGAAACA-AAAGT-TTATCTCACTTGAGATA-TTT-TC
1 TTTTGTCTCACTTGAGACATTTTCTCTTGAAACACAAA-TCTTATCTCACTTGAGATAGTTTCTC
** * *
3306870 CT--ATGAAAGTTCTAGTCTCACTCGAGATAGTTTCTCTCGAAACAAAAAATTTATCTCGCTTGA
65 CTAAAACAAATTTC-A-TCTCACTCGAGATAGTTTCTCTCGAAAC-AAAAATTTATCTCACTTGA
** *
3306933 GATAGTTTTTGCTT-GAAAAT
127 GATA-TTTTCCCTTAAAAAAT
* *
3306953 TTTCGTCTCACTTGAGACAGTTTCTCT
1 TTTTGTCTCACTTGAGACATTTTCTCT
3306980 AGAGACAGAA
Statistics
Matches: 150, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
141 7 0.05
142 1 0.01
143 29 0.19
144 54 0.36
145 27 0.18
146 15 0.10
147 17 0.11
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (146 bp):
TTTTGTCTCACTTGAGACATTTTCTCTTGAAACACAAATCTTATCTCACTTGAGATAGTTTCTCC
TAAAACAAATTTCATCTCACTCGAGATAGTTTCTCTCGAAACAAAAATTTATCTCACTTGAGATA
TTTTCCCTTAAAAAAT
Found at i:3307207 original size:20 final size:20
Alignment explanation
Indices: 3307182--3307229 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
3307172 GATTACATTC
3307182 ATGACTTTACACACATGTGT
1 ATGACTTTACACACATGTGT
3307202 ATGACTTTACACACATGTGT
1 ATGACTTTACACACATGTGT
3307222 ATGACTTT
1 ATGACTTT
3307230 GTATATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (20 bp):
ATGACTTTACACACATGTGT
Found at i:3308190 original size:21 final size:21
Alignment explanation
Indices: 3308144--3308189 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 21
3308134 AATCCCTTTT
*
3308144 TTATTATATTTATATACATTA
1 TTATTATATTTATACACATTA
3308165 TTATTATA-TTAT-CACA-TA
1 TTATTATATTTATACACATTA
3308183 TTATTAT
1 TTATTAT
3308190 TTGTACATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 9 0.38
19 3 0.12
20 4 0.17
21 8 0.33
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTATATTTATACACATTA
Found at i:3319765 original size:22 final size:21
Alignment explanation
Indices: 3319732--3319782 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
3319722 ACCAAAATCA
3319732 AACAAAACCGAAATTAACCTG
1 AACAAAACCGAAATTAACCTG
*
3319753 AACATAAATCGAAATTAACCTG
1 AACA-AAACCGAAATTAACCTG
3319775 AACCAAAA
1 AA-CAAAA
3319783 GTAACACGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 4 0.15
22 21 0.78
23 2 0.07
ACGTcount: A:0.55, C:0.22, G:0.08, T:0.16
Consensus pattern (21 bp):
AACAAAACCGAAATTAACCTG
Found at i:3320018 original size:70 final size:68
Alignment explanation
Indices: 3319938--3320068 Score: 217
Period size: 70 Copynumber: 1.9 Consensus size: 68
3319928 AAATAGTAAT
* * *
3319938 AAATAAAGTTTACTTATCTTACTTGTTATAAAAATATTAGATTTATAATAAAAATAATAGAAAAC
1 AAATAAAGTTTACTTATCTTAATTGATAT-AAAATAATAGATTTATAAT-AAAATAATAGAAAAC
3320003 AACTA
64 AACTA
3320008 AAATAAAGTTTACTTATCTTAATTGATATAAAATAATAGATTTATAATAAAATAATAGAAA
1 AAATAAAGTTTACTTATCTTAATTGATATAAAATAATAGATTTATAATAAAATAATAGAAA
3320069 GTTTAATATT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
68 13 0.22
69 18 0.31
70 27 0.47
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (68 bp):
AAATAAAGTTTACTTATCTTAATTGATATAAAATAATAGATTTATAATAAAATAATAGAAAACAA
CTA
Found at i:3320321 original size:231 final size:230
Alignment explanation
Indices: 3319871--3320284 Score: 566
Period size: 231 Copynumber: 1.8 Consensus size: 230
3319861 AACTAATTTT
* * *
3319871 TAAAAAAATAGAAAGTTTAAGAGGAATATAAAAGTAAGAAACTAATTATAAGATTGAAAATAGTA
1 TAAAAAAATAGAAAATTTAAGAGGAATATAAAAGTAAGAAACTAATTATAAGATTGAAAACAATA
*
3319936 ATAAATAAAGTTTACTTATCTTACTTGTTATAAAAATATTAGATTTATAATAAAAATAATAGAAA
66 ATAAATAAAGTTTACTTATCTTACTTGTTATAAAAATATTAGATTTATAATAAAAATAAAAGAAA
** * * * * * *
3320001 ACAACTAAAATAAAGTTTACTTATCTTAATTGATATAAAATAATAGATTTATAATAAAATAATAG
131 ACAACTAAAATAAAGTAAAATAATATTAATT-ATATAAAAAAATAGATATAAAATAAAATAATAG
* * * ***
3320066 AAAGTTTAATATTTCTCTTAAATATTAGATTTATAA
195 AAAGATTAAAATTACAAATAAATATTAGATTTATAA
* * *
3320102 TAAAATAATAGAAAATTTAAGAGGAATATAAAAGTAAGAATCTAATTGTAAGATTGAAAACAATA
1 TAAAAAAATAGAAAATTTAAGAGGAATATAAAAGTAAGAAACTAATTATAAGATTGAAAACAATA
*
3320167 ATAAATAAAGTTTACTTATCTTACTTGTTATAAAAATATTATATTTATAATAAAAA-AAAAGAAA
66 ATAAATAAAGTTTACTTATCTTACTTGTTATAAAAATATTAGATTTATAATAAAAATAAAAGAAA
3320231 ACAACTAAAAATAAAG-AAAATAATATTAGATT-TATAATAAAAATA-ATATAAAAT
131 ACAACT-AAAATAAAGTAAAATAATATTA-ATTATATAA-AAAAATAGATATAAAAT
3320285 TTCCTTATGT
Statistics
Matches: 164, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
229 12 0.07
230 26 0.16
231 126 0.77
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (230 bp):
TAAAAAAATAGAAAATTTAAGAGGAATATAAAAGTAAGAAACTAATTATAAGATTGAAAACAATA
ATAAATAAAGTTTACTTATCTTACTTGTTATAAAAATATTAGATTTATAATAAAAATAAAAGAAA
ACAACTAAAATAAAGTAAAATAATATTAATTATATAAAAAAATAGATATAAAATAAAATAATAGA
AAGATTAAAATTACAAATAAATATTAGATTTATAA
Done.