Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 9 of 193
Found at i:3218102 original size:58 final size:59
Alignment explanation
Indices: 3217640--3218109 Score: 301
Period size: 60 Copynumber: 8.1 Consensus size: 59
3217630 GGCCGACACT
* * * * *
3217640 AAAAAATTTGAATTTTTTATCTTACAAAAAAGGGGTGTCGGCCATACAATGACCAAGA-C
1 AAAAAAATT-AATTTTTTATCTGATAAAAAAGGGGTGTCGGCCATGCAATGACCAACATC
* * * * *** *
3217699 AAAAAAATTGATTTTTTACCAGATAAAAAAGGGGTGTCGGCCATACAATGGTTAACATT
1 AAAAAAATTAATTTTTTATCTGATAAAAAAGGGGTGTCGGCCATGCAATGACCAACATC
* * * ** *
3217758 AAAAAAATTGATTTTTTACCGGATAGAAAAAAGGGGTGTCGGCCATGCAATGGGCAATAT-
1 AAAAAAATTAATTTTTTATCTGAT--AAAAAAGGGGTGTCGGCCATGCAATGACCAACATC
* ** * * * *
3217818 AAAAAAATTTCAATTTTTTATCTGACAAAAAA-GAATGTCGGTCATGTAATGACTAACACC
1 AAAAAAA-TT-AATTTTTTATCTGATAAAAAAGGGGTGTCGGCCATGCAATGACCAACATC
* ** * * *
3217878 CAAAAAA--AA--TTTTATCTGATAAAAATACTGGTGTCGGCCAATGC-ATGGCCAACGTT
1 AAAAAAATTAATTTTTTATCTGATAAAAA-AGGGGTGTCGGCC-ATGCAATGACCAACATC
* * *** *
3217934 AGAAAAAA--AA----TTATCTGAT-AAAAAGAGAGTGTCGGTCATGCAATGGTAAACAAC
1 A-AAAAAATTAATTTTTTATCTGATAAAAAAG-GGGTGTCGGCCATGCAATGACCAACATC
* *
3217988 AAAAAAATTAATTTTTTA-CTAGATAAAAAAGGAGGTATCGGCAATGCAAT-AGCCAACATC
1 AAAAAAATTAATTTTTTATCT-GATAAAAAAGG-GGTGTCGGCCATGCAATGA-CCAACATC
* * * * *
3218048 AAAAAATTTAAATTTTTATCTGACAAAAAA-GGGTGTCGGCCGTGCAATGACCAACACC
1 AAAAAAATTAATTTTTTATCTGATAAAAAAGGGGTGTCGGCCATGCAATGACCAACATC
3218106 AAAA
1 AAAA
3218110 TTTTTTTATC
Statistics
Matches: 321, Mismatches: 66, Indels: 49
0.74 0.15 0.11
Matches are distributed among these distances:
53 11 0.03
54 35 0.11
55 12 0.04
56 16 0.05
57 11 0.03
58 66 0.21
59 58 0.18
60 67 0.21
61 34 0.11
62 11 0.03
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (59 bp):
AAAAAAATTAATTTTTTATCTGATAAAAAAGGGGTGTCGGCCATGCAATGACCAACATC
Found at i:3218155 original size:229 final size:228
Alignment explanation
Indices: 3217724--3218172 Score: 528
Period size: 229 Copynumber: 2.0 Consensus size: 228
3217714 TTACCAGATA
* * ** * *
3217724 AAAAAGGGGTGTCGGCCATACAATGGTTAACATTAAAAAAATTGATTTTTTACCGGATAGAAAAA
1 AAAAAGGAGTGTCGGCCATACAATGGTAAACAACAAAAAAATTAATTTTTTACCAGATA-AAAAA
* * * * * *
3217789 AGGGGTGTCGGCCATGCAATGGGCAATATAAAAAAATTTCAATTTTTTATCTGACAAAAAAGAAT
65 AGGGGTATCGGCAATGCAATAGCCAACATAAAAAAATTTCAAATTTTTATCTGACAAAAAAGAAT
* * * ** *
3217854 GTCGGTCATGTAATGACTAACACCCAAAAAAAATTTTATCTGATAAAAATACTGGTGTCGGCCAA
130 GTCGGCCATGCAATGACCAACACCCAAAAAAAATTTTATCTGATAAAAATACTAATGTCGACCAA
**
3217919 TGCATGGCCAACGTTAGAAAAAAAATTATCTGAT
195 TGCATGGCCAACACTAGAAAAAAAATTATCTGAT
* * *
3217953 AAAAAGAGAGTGTCGGTCATGCAATGGTAAACAACAAAAAAATTAATTTTTTACTAGAT-AAAAA
1 AAAAAG-GAGTGTCGGCCATACAATGGTAAACAACAAAAAAATTAATTTTTTACCAGATAAAAAA
* **
3218017 AGGAGGTATCGGCAATGCAATAGCCAACATCAAAAAATTT-AAATTTTTATCTGACAAAAAAGGG
65 AGG-GGTATCGGCAATGCAATAGCCAACATAAAAAAATTTCAAATTTTTATCTGACAAAAAAGAA
* ***
3218081 TGTCGGCCGTGCAATGACCAACA-CC-AAAATTTTTTTATCTGATAAAAAAAATACTAATGTCGA
129 TGTCGGCCATGCAATGACCAACACCCAAAAAAAATTTTATCTGAT---AAAAATACTAATGTCGA
* *
3218144 TCAGTGCATGGCCAACACTAGAAAAAAAA
191 CCAATGCATGGCCAACACTAGAAAAAAAA
3218173 ATCTAACAAA
Statistics
Matches: 183, Mismatches: 32, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
226 15 0.08
227 2 0.01
228 48 0.26
229 75 0.41
230 43 0.23
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (228 bp):
AAAAAGGAGTGTCGGCCATACAATGGTAAACAACAAAAAAATTAATTTTTTACCAGATAAAAAAA
GGGGTATCGGCAATGCAATAGCCAACATAAAAAAATTTCAAATTTTTATCTGACAAAAAAGAATG
TCGGCCATGCAATGACCAACACCCAAAAAAAATTTTATCTGATAAAAATACTAATGTCGACCAAT
GCATGGCCAACACTAGAAAAAAAATTATCTGAT
Found at i:3222975 original size:4 final size:4
Alignment explanation
Indices: 3222966--3223006 Score: 64
Period size: 4 Copynumber: 10.0 Consensus size: 4
3222956 TTTAGGAGTG
*
3222966 AAGA AAGA AAGA AATA AAGA AAGA AAGA AAGA AAGA GAAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA -AAGA
3223007 TGCAGTGGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
4 30 0.88
5 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:3228902 original size:31 final size:30
Alignment explanation
Indices: 3228833--3228902 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
3228823 CAATGGTAAA
*
3228833 AGGGCTAAAGTGAGAATTTCACTATAGTAC
1 AGGGCCAAAGTGAGAATTTCACTATAGTAC
***
3228863 AGGGCCAAAGTGAGAATTTTGTTATAGTAC
1 AGGGCCAAAGTGAGAATTTCACTATAGTAC
3228893 ATGGGCCAAA
1 A-GGGCCAAA
3228903 ACAAGTTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 27 0.77
31 8 0.23
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.26
Consensus pattern (30 bp):
AGGGCCAAAGTGAGAATTTCACTATAGTAC
Found at i:3233857 original size:24 final size:25
Alignment explanation
Indices: 3233821--3233885 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 25
3233811 AATAAAAACA
* * *
3233821 TAAAATTTTAAAATTATAATT-TTT
1 TAAAATATAAAAATTATAATATTTT
* *
3233845 TAAAATATAAAAA-AATCATATTTT
1 TAAAATATAAAAATTATAATATTTT
3233869 T-AAA-ATAAAAATTATAA
1 TAAAATATAAAAATTATAA
3233886 AAAATAAACT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
22 7 0.22
23 10 0.31
24 15 0.47
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
TAAAATATAAAAATTATAATATTTT
Found at i:3233910 original size:7 final size:7
Alignment explanation
Indices: 3233900--3233931 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
3233890 TAAACTCTTT
3233900 AAAATTC
1 AAAATTC
3233907 AAAATTC
1 AAAATTC
3233914 AAAATTC
1 AAAATTC
3233921 AAAATTC
1 AAAATTC
3233928 AAAA
1 AAAA
3233932 ATAATTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAATTC
Found at i:3236801 original size:2 final size:2
Alignment explanation
Indices: 3236794--3236818 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3236784 CCTAAAACCT
3236794 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 T
3236819 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3240911 original size:23 final size:23
Alignment explanation
Indices: 3240881--3240925 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3240871 ATTTAGTTTC
3240881 TATCTAGAATGTCATAAAAATAA
1 TATCTAGAATGTCATAAAAATAA
*
3240904 TATCTAGAATGTCATAGAAATA
1 TATCTAGAATGTCATAAAAATA
3240926 GTGTGGGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (23 bp):
TATCTAGAATGTCATAAAAATAA
Found at i:3246704 original size:18 final size:19
Alignment explanation
Indices: 3246676--3246718 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3246666 GGAAAAAAAT
*
3246676 ATTTTGTAAA-TATTTTGA
1 ATTTTGAAAATTATTTTGA
*
3246694 TTTTTGAAAATTATTTTGA
1 ATTTTGAAAATTATTTTGA
3246713 ATTTTG
1 ATTTTG
3246719 TTATTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (19 bp):
ATTTTGAAAATTATTTTGA
Found at i:3250488 original size:21 final size:22
Alignment explanation
Indices: 3250445--3250489 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
3250435 TAGATCCCAT
3250445 ATTTCAAACCTTAGAACCCTGA
1 ATTTCAAACCTTAGAACCCTGA
* * *
3250467 ATTTTAAACTTTA-AACCTTGA
1 ATTTCAAACCTTAGAACCCTGA
3250488 AT
1 AT
3250490 CTTGAACCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.36
Consensus pattern (22 bp):
ATTTCAAACCTTAGAACCCTGA
Found at i:3268083 original size:4 final size:4
Alignment explanation
Indices: 3268074--3268098 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3268064 ATTGGACAAA
3268074 ACCC ACCC ACCC ACCC ACCC ACCC A
1 ACCC ACCC ACCC ACCC ACCC ACCC A
3268099 TAGCACATGC
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:0.28, C:0.72, G:0.00, T:0.00
Consensus pattern (4 bp):
ACCC
Found at i:3269100 original size:15 final size:15
Alignment explanation
Indices: 3269059--3269105 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3269049 TTTGATAAAA
* *
3269059 AAAAATTAAGTAGT-
1 AAAATTTAAGTATTG
*
3269073 AAAATATTTAGTATTG
1 AAAAT-TTAAGTATTG
3269089 AAAATTTAAGTATTG
1 AAAATTTAAGTATTG
3269104 AA
1 AA
3269106 TTTAAGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.15
15 18 0.67
16 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (15 bp):
AAAATTTAAGTATTG
Found at i:3274633 original size:15 final size:16
Alignment explanation
Indices: 3274607--3274639 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3274597 TAATAAACTG
3274607 AAAAATTAAAGTACTA
1 AAAAATTAAAGTACTA
3274623 AAAAATT-AAGTACTA
1 AAAAATTAAAGTACTA
3274638 AA
1 AA
3274640 CTTTATAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (16 bp):
AAAAATTAAAGTACTA
Found at i:3275450 original size:130 final size:132
Alignment explanation
Indices: 3275204--3275452 Score: 353
Period size: 130 Copynumber: 1.9 Consensus size: 132
3275194 GGTTTAATTC
* * *
3275204 CTCTTCTACTCAATTTTGTATTTTTTATTTCATGTTGCTTTAAGCTTTTTCAATTTTTAATTAAT
1 CTCTCCTACTCAATTTTGTATTTTTTATTTCATGTTGCTTCAA-C-ATTT--ATTTTTAATTAAT
*
3275269 ATTTTTAACATATTAGCTCATTGGTTAGATGGTTAGATAGTTGTGATTACATCCAGCCTCAAGTT
62 ATTTTTAACATATTAGCTCATTGGTTAGATGGTTAGATAGTTGTGAGTACATCCAGCCTCAAGTT
3275334 CGATTT
127 CGATTT
*
3275340 CTCTCCTACTC-ATATTTGTATTTTTTATTTCTTGTTGCTTCAA-ATTT-TTTTTAATTAATATT
1 CTCTCCTACTCAAT-TTTGTATTTTTTATTTCATGTTGCTTCAACATTTATTTTTAATTAATATT
* *
3275402 TTTAACATATTAGCTTC-TTTGTTAGATGGTTAGATAGTTGTGGGTACATCC
65 TTTAACATATTAGC-TCATTGGTTAGATGGTTAGATAGTTGTGAGTACATCC
3275453 TTGAATCTCA
Statistics
Matches: 104, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
130 60 0.58
131 2 0.02
133 3 0.03
135 2 0.02
136 37 0.36
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.51
Consensus pattern (132 bp):
CTCTCCTACTCAATTTTGTATTTTTTATTTCATGTTGCTTCAACATTTATTTTTAATTAATATTT
TTAACATATTAGCTCATTGGTTAGATGGTTAGATAGTTGTGAGTACATCCAGCCTCAAGTTCGAT
TT
Found at i:3275490 original size:130 final size:125
Alignment explanation
Indices: 3275257--3275526 Score: 298
Period size: 130 Copynumber: 2.1 Consensus size: 125
3275247 GCTTTTTCAA
*
3275257 TTTTTAATTAATATTTTTAACATATTAGCTCATTGGTTAGATGGTTAGATAGTTGTGATTACATC
1 TTTTTAATTAATATTTTTAACATATTAGCTCATTGGTTAGATGGTTAGATAGTTGTGAGTACATC
* * ** *
3275322 CAGCCTCAAGTTCGATTTCTCTCCTACTCATATTTGTATTTTTTATTTCTTGTTGCTTCAAATTT
66 CAACCTCAAGTT--ATTTCTCTCATAAGCATATTTGTATTTTTTATTT-ATGTTGCTTCAAA--T
* *
3275387 TTTTTAATTAATATTTTTAACATATTAGCTTC-TTTGTTAGATGGTTAGATAGTTGTGGGTACAT
1 TTTTTAATTAATATTTTTAACATATTAGC-TCATTGGTTAGATGGTTAGATAGTTGTGAGTACAT
* * *
3275451 CCTTGAATCTCAGGGTT-TTT-T-T-ATAAGCATATTAATGTATTTTTTATTTATGTTGTTTCAA
65 CC---AACCTCA-AGTTATTTCTCTCATAAGCATATT--TGTATTTTTTATTTATGTTGCTTCAA
3275512 AT
124 AT
3275514 TTTTTAATTAATA
1 TTTTTAATTAATA
3275527 AATATATTGT
Statistics
Matches: 122, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
127 14 0.11
128 8 0.07
129 12 0.10
130 75 0.61
131 5 0.04
133 5 0.04
134 3 0.02
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.51
Consensus pattern (125 bp):
TTTTTAATTAATATTTTTAACATATTAGCTCATTGGTTAGATGGTTAGATAGTTGTGAGTACATC
CAACCTCAAGTTATTTCTCTCATAAGCATATTTGTATTTTTTATTTATGTTGCTTCAAAT
Found at i:3281370 original size:16 final size:16
Alignment explanation
Indices: 3281349--3281382 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3281339 TTCAACAGAG
3281349 AAGCTTTACCATGAAT
1 AAGCTTTACCATGAAT
3281365 AAGCTTTACCATGAAT
1 AAGCTTTACCATGAAT
3281381 AA
1 AA
3281383 CTACTCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (16 bp):
AAGCTTTACCATGAAT
Found at i:3285363 original size:16 final size:16
Alignment explanation
Indices: 3285332--3285361 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3285322 ACATGTGTCT
3285332 TTTTTTTAAATATTTA
1 TTTTTTTAAATATTTA
3285348 TTTTTTT-AATATTT
1 TTTTTTTAAATATTT
3285362 TACTGTATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:3287867 original size:4 final size:4
Alignment explanation
Indices: 3287860--3287884 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3287850 ACACACACAC
3287860 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
3287885 AAATAACATG
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:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:3289089 original size:7 final size:7
Alignment explanation
Indices: 3289079--3289103 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3289069 CTCTAAACCT
3289079 TAAATTC
1 TAAATTC
3289086 TAAATTC
1 TAAATTC
3289093 TAAATTC
1 TAAATTC
3289100 TAAA
1 TAAA
3289104 CCAGAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAATTC
Found at i:3308408 original size:31 final size:32
Alignment explanation
Indices: 3308365--3308425 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
3308355 TGGAATTTAG
* *
3308365 TCTCTATATTTTT-TATTTTCATAAATTTAATC
1 TCTCTATATTTTTAAATTTT-AAAAATTTAATC
3308397 TCTCTAT-TTTTTAAATTTTAAAAATTTAA
1 TCTCTATATTTTTAAATTTTAAAAATTTAA
3308426 GTCCAATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (32 bp):
TCTCTATATTTTTAAATTTTAAAAATTTAATC
Found at i:3308415 original size:32 final size:29
Alignment explanation
Indices: 3308358--3308425 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 29
3308348 ATAAATTTGG
* *
3308358 AATTTAGTCTCTATATTTTTTATTTTCATA
1 AATTTAATCTCTATATTTTTTATTTT-AAA
*
3308388 AATTTAATCTCTCTATTTTTTAAATTTTAAA
1 AATTTAATCTCTATATTTTTT--ATTTTAAA
3308419 AATTTAA
1 AATTTAA
3308426 GTCCAATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 19 0.58
31 9 0.27
32 5 0.15
ACGTcount: A:0.34, C:0.09, G:0.01, T:0.56
Consensus pattern (29 bp):
AATTTAATCTCTATATTTTTTATTTTAAA
Found at i:3310010 original size:42 final size:42
Alignment explanation
Indices: 3309955--3310040 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
3309945 AAGAGTTGAT
*
3309955 TATTCTTTTCAATTTTGAAAAGATGTTTTTTTTTCTCAATTA
1 TATTATTTTCAATTTTGAAAAGATGTTTTTTTTTCTCAATTA
3309997 TATTATTTTCAATTTTGAAAAGATGTTTTTTTTTCTCAATTA
1 TATTATTTTCAATTTTGAAAAGATGTTTTTTTTTCTCAATTA
3310039 TA
1 TA
3310041 CCAATAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.08, G:0.07, T:0.57
Consensus pattern (42 bp):
TATTATTTTCAATTTTGAAAAGATGTTTTTTTTTCTCAATTA
Found at i:3313294 original size:20 final size:21
Alignment explanation
Indices: 3313253--3313301 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
3313243 TATAAATAAT
*
3313253 AAAATTTGTTATCTCGACTCG
1 AAAATTTTTTATCTCGACTCG
*
3313274 AAAATTTTTTA-CTCGATTCG
1 AAAATTTTTTATCTCGACTCG
3313294 AAAATTTT
1 AAAATTTT
3313302 CAAATTGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (21 bp):
AAAATTTTTTATCTCGACTCG
Found at i:3323475 original size:24 final size:24
Alignment explanation
Indices: 3323448--3323495 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3323438 AAATGAAATT
*
3323448 AAAAAACACA-AAAATTGTAAAAAA
1 AAAAAACACATAAAAAT-TAAAAAA
*
3323472 AAAAAATACATAAAAATTAAAAAA
1 AAAAAACACATAAAAATTAAAAAA
3323496 TTAGACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (24 bp):
AAAAAACACATAAAAATTAAAAAA
Found at i:3330860 original size:19 final size:18
Alignment explanation
Indices: 3330836--3330891 Score: 94
Period size: 19 Copynumber: 3.0 Consensus size: 18
3330826 TTCCGTTTTT
3330836 ATCTGTTAACATTTGTTTG
1 ATCTGTTAACA-TTGTTTG
3330855 ATCTGTTAACACTTGTTTG
1 ATCTGTTAACA-TTGTTTG
3330874 ATCTGTTAACATTGTTTG
1 ATCTGTTAACATTGTTTG
3330892 GGATTTGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
18 7 0.19
19 29 0.81
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.50
Consensus pattern (18 bp):
ATCTGTTAACATTGTTTG
Found at i:3330926 original size:29 final size:29
Alignment explanation
Indices: 3330867--3330926 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
3330857 CTGTTAACAC
* * *
3330867 TTGTTTGATCTGTTAACATTGTTTGGGAT
1 TTGTTTGATCTGTTAACACTATTTGAGAT
* *
3330896 TTGTTTGATCTGTTAATACTATTTGATAT
1 TTGTTTGATCTGTTAACACTATTTGAGAT
3330925 TT
1 TT
3330927 AGGGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.20, C:0.07, G:0.18, T:0.55
Consensus pattern (29 bp):
TTGTTTGATCTGTTAACACTATTTGAGAT
Found at i:3333085 original size:24 final size:24
Alignment explanation
Indices: 3333020--3333085 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
3333010 TTATTCTGAC
*
3333020 TTGTATTCTATTTTTTAATATTATT
1 TTGTATACTATTTTTT-ATATTATT
** * * *
3333045 TTGTATGTTGTTCTTTATTTTATT
1 TTGTATACTATTTTTTATATTATT
3333069 TTGTATACTATTTTTTA
1 TTGTATACTATTTTTTA
3333086 ATACCCTAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
24 20 0.62
25 12 0.38
ACGTcount: A:0.20, C:0.05, G:0.08, T:0.68
Consensus pattern (24 bp):
TTGTATACTATTTTTTATATTATT
Found at i:3333163 original size:11 final size:11
Alignment explanation
Indices: 3333122--3333178 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
3333112 TGCTATGTTT
*
3333122 TGTTGGATTTA
1 TGTTGGCTTTA
* *
3333133 TGATGACTTTA
1 TGTTGGCTTTA
3333144 TGTCT-GCTTTA
1 TGT-TGGCTTTA
*
3333155 TTTTGGCTTTAA
1 TGTTGGCTTT-A
3333167 TGTTGGCTTTA
1 TGTTGGCTTTA
3333178 T
1 T
3333179 ATTGAATGAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
10 1 0.03
11 24 0.67
12 11 0.31
ACGTcount: A:0.16, C:0.09, G:0.21, T:0.54
Consensus pattern (11 bp):
TGTTGGCTTTA
Found at i:3335062 original size:3 final size:3
Alignment explanation
Indices: 3335054--3335091 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3335044 AATCTCCATT
3335054 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3335092 ATGCCCTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:3342534 original size:22 final size:22
Alignment explanation
Indices: 3342500--3342542 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3342490 CAATAAATTA
*
3342500 TTTTAAAGTTATAAAAATTATTT
1 TTTTAAAGATAT-AAAATTATTT
3342523 TTTTAAA-ATATAAAATTATT
1 TTTTAAAGATATAAAATTATT
3342543 AAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 3 0.16
23 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTAAAGATATAAAATTATTT
Found at i:3342546 original size:16 final size:16
Alignment explanation
Indices: 3342525--3342575 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
3342515 AATTATTTTT
3342525 TTAAAATATAAAATTA
1 TTAAAATATAAAATTA
*
3342541 TTAAAAT-T---ATTT
1 TTAAAATATAAAATTA
*
3342553 TTTAAATATAAAATTA
1 TTAAAATATAAAATTA
3342569 TTAAAAT
1 TTAAAAT
3342576 CATCATCTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
12 9 0.33
13 1 0.04
15 1 0.04
16 16 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATAAAATTA
Found at i:3342562 original size:28 final size:30
Alignment explanation
Indices: 3342503--3342575 Score: 114
Period size: 28 Copynumber: 2.5 Consensus size: 30
3342493 TAAATTATTT
* *
3342503 TAAAGTTATAAAAATTATTTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTTAAAATA
3342533 TAAAATTATTAAAATTA-TTTTTT-AAATA
1 TAAAATTATTAAAATTATTTTTTTAAAATA
3342561 TAAAATTATTAAAAT
1 TAAAATTATTAAAAT
3342576 CATCATCTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 20 0.49
29 6 0.15
30 15 0.37
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTTAAAATA
Found at i:3343377 original size:21 final size:22
Alignment explanation
Indices: 3343353--3343394 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3343343 AATTAATTTT
*
3343353 AATAA-ATTTATATTTTTAAAA
1 AATAATATTTATAATTTTAAAA
*
3343374 AATAATTTTTATAATTTTAAA
1 AATAATATTTATAATTTTAAA
3343395 TTCATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATAATATTTATAATTTTAAAA
Found at i:3347027 original size:29 final size:30
Alignment explanation
Indices: 3346969--3347046 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
3346959 AAATTGAATC
* *
3346969 AAATCAAAATTTTATATATAAAATTGTACA-
1 AAATCAAAA-TTTATGTATAAAATTATACAT
* *
3346999 AAATCAAAATTTATGTATGATATTATACATT
1 AAATCAAAATTTATGTATAAAATTATACA-T
* *
3347030 TAATCAAAGTTTATGTA
1 AAATCAAAATTTATGTA
3347047 AAATTTTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.40
30 9 0.22
31 15 0.38
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (30 bp):
AAATCAAAATTTATGTATAAAATTATACAT
Found at i:3350931 original size:424 final size:424
Alignment explanation
Indices: 3350143--3350991 Score: 1698
Period size: 424 Copynumber: 2.0 Consensus size: 424
3350133 TGATGATTGT
3350143 CTTGTCAGAGTGACTTAACTATTAAGAGTGTGTTTTTTAGATCCTAGTGAAATAGTGTTCATGAT
1 CTTGTCAGAGTGACTTAACTATTAAGAGTGTGTTTTTTAGATCCTAGTGAAATAGTGTTCATGAT
3350208 GGAAGAATTATGATTAACGAAGCAAGGCGGGTGAAAACCATATGGGTTTTAGGACACTATGGTGA
66 GGAAGAATTATGATTAACGAAGCAAGGCGGGTGAAAACCATATGGGTTTTAGGACACTATGGTGA
3350273 TATGAAAGTCGTTGGATGACAGATATGTATATAAATATGATAAAATAACTATATTATTAAGTTGA
131 TATGAAAGTCGTTGGATGACAGATATGTATATAAATATGATAAAATAACTATATTATTAAGTTGA
3350338 TACTTTGATATAAGGTTCGAATTGCAAATTATACAAATTATATTGTAGAAATATGTAACAATATA
196 TACTTTGATATAAGGTTCGAATTGCAAATTATACAAATTATATTGTAGAAATATGTAACAATATA
3350403 GCACCTGCCCTATTGTTAGGCTGGTCTTTAATTTCTTCTGTGGTAGCTTTTCAGTAACATGATTA
261 GCACCTGCCCTATTGTTAGGCTGGTCTTTAATTTCTTCTGTGGTAGCTTTTCAGTAACATGATTA
3350468 GATGAATCCCTAGAGAGATATGATTGTGTCCCATGCCATGTCATGATGCTTGGCGTGAAGATGAA
326 GATGAATCCCTAGAGAGATATGATTGTGTCCCATGCCATGTCATGATGCTTGGCGTGAAGATGAA
3350533 CTTAGTGTTGGAAAACAAGTCATAAGGTTTGCGG
391 CTTAGTGTTGGAAAACAAGTCATAAGGTTTGCGG
3350567 CTTGTCAGAGTGACTTAACTATTAAGAGTGTGTTTTTTAGATCCTAGTGAAATAGTGTTCATGAT
1 CTTGTCAGAGTGACTTAACTATTAAGAGTGTGTTTTTTAGATCCTAGTGAAATAGTGTTCATGAT
3350632 GGAAGAATTATGATTAACGAAGCAAGGCGGGTGAAAACCATATGGGTTTTAGGACACTATGGTGA
66 GGAAGAATTATGATTAACGAAGCAAGGCGGGTGAAAACCATATGGGTTTTAGGACACTATGGTGA
3350697 TATGAAAGTCGTTGGATGACAGATATGTATATAAATATGATAAAATAACTATATTATTAAGTTGA
131 TATGAAAGTCGTTGGATGACAGATATGTATATAAATATGATAAAATAACTATATTATTAAGTTGA
3350762 TACTTTGATATAAGGTTCGAATTGCAAATTATACAAATTATATTGTAGAAATATGTAACAATATA
196 TACTTTGATATAAGGTTCGAATTGCAAATTATACAAATTATATTGTAGAAATATGTAACAATATA
3350827 GCACCTGCCCTATTGTTAGGCTGGTCTTTAATTTCTTCTGTGGTAGCTTTTCAGTAACATGATTA
261 GCACCTGCCCTATTGTTAGGCTGGTCTTTAATTTCTTCTGTGGTAGCTTTTCAGTAACATGATTA
3350892 GATGAATCCCTAGAGAGATATGATTGTGTCCCATGCCATGTCATGATGCTTGGCGTGAAGATGAA
326 GATGAATCCCTAGAGAGATATGATTGTGTCCCATGCCATGTCATGATGCTTGGCGTGAAGATGAA
3350957 CTTAGTGTTGGAAAACAAGTCATAAGGTTTGCGG
391 CTTAGTGTTGGAAAACAAGTCATAAGGTTTGCGG
3350991 C
1 C
3350992 CCCCTCTTCC
Statistics
Matches: 425, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
424 425 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (424 bp):
CTTGTCAGAGTGACTTAACTATTAAGAGTGTGTTTTTTAGATCCTAGTGAAATAGTGTTCATGAT
GGAAGAATTATGATTAACGAAGCAAGGCGGGTGAAAACCATATGGGTTTTAGGACACTATGGTGA
TATGAAAGTCGTTGGATGACAGATATGTATATAAATATGATAAAATAACTATATTATTAAGTTGA
TACTTTGATATAAGGTTCGAATTGCAAATTATACAAATTATATTGTAGAAATATGTAACAATATA
GCACCTGCCCTATTGTTAGGCTGGTCTTTAATTTCTTCTGTGGTAGCTTTTCAGTAACATGATTA
GATGAATCCCTAGAGAGATATGATTGTGTCCCATGCCATGTCATGATGCTTGGCGTGAAGATGAA
CTTAGTGTTGGAAAACAAGTCATAAGGTTTGCGG
Found at i:3353470 original size:29 final size:30
Alignment explanation
Indices: 3353410--3353474 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
3353400 TTAATAGTAT
* * *
3353410 TTTTATAATTTTTAAAAGATTAAATTAAAA
1 TTTTATAATTTTTAAAAAATCAAAATAAAA
**
3353440 TTTTATAA-TTTTAAAAAATCAAAATGTAA
1 TTTTATAATTTTTAAAAAATCAAAATAAAA
3353469 TTTTAT
1 TTTTAT
3353475 TTTTATTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTTATAATTTTTAAAAAATCAAAATAAAA
Found at i:3353939 original size:23 final size:23
Alignment explanation
Indices: 3353913--3353968 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
3353903 ATGTAAATAG
*
3353913 AATTTCATTACAAAAAATATGGA
1 AATTTTATTACAAAAAATATGGA
3353936 AATTTTATTACAAAAAATATGGA
1 AATTTTATTACAAAAAATATGGA
3353959 AATTTTATTA
1 AATTTTATTA
3353969 TTGGCACACC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (23 bp):
AATTTTATTACAAAAAATATGGA
Found at i:3360729 original size:12 final size:12
Alignment explanation
Indices: 3360712--3360743 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
3360702 GTTGGCTTTA
3360712 GTTTTCGTATTG
1 GTTTTCGTATTG
3360724 GTTTTCGTATTG
1 GTTTTCGTATTG
3360736 GTTTTCGT
1 GTTTTCGT
3360744 GGTTTACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.09, G:0.25, T:0.59
Consensus pattern (12 bp):
GTTTTCGTATTG
Found at i:3363567 original size:109 final size:109
Alignment explanation
Indices: 3363430--3363659 Score: 383
Period size: 109 Copynumber: 2.1 Consensus size: 109
3363420 TTTACTGAGA
3363430 GTTTCGTGGTAATTATGGAGATGATTTTATATCCCATTTGTAAGTGTCTTATGAGATTTATGGTT
1 GTTTCGTGGTAATTATGGAGATGATTTTATATCCCATTTGTAAGTGTCTTATGAGATTTATGGTT
*
3363495 TTGTTTATTGGTTTGCTCTTCAAGATTTTGAACTTTGTATTTGG
66 TTGTTTATTGGTTTGCTCTTCAAGATTTTAAACTTTGTATTTGG
* * *
3363539 GTTTCGTGGTAATTATGGAGAT-AGTTTTATATTCCTTTTGTGAGTGTCTTATGAGATTTATGGT
1 GTTTCGTGGTAATTATGGAGATGA-TTTTATATCCCATTTGTAAGTGTCTTATGAGATTTATGGT
*
3363603 TTTGTTTATTGGTTTGCTCTTCGAGATTTTAAACTTTGTATTTGG
65 TTTGTTTATTGGTTTGCTCTTCAAGATTTTAAACTTTGTATTTGG
*
3363648 GTTTTG-GGTAAT
1 GTTTCGTGGTAAT
3363660 GTACATTTAG
Statistics
Matches: 114, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
108 7 0.06
109 107 0.94
ACGTcount: A:0.19, C:0.07, G:0.23, T:0.50
Consensus pattern (109 bp):
GTTTCGTGGTAATTATGGAGATGATTTTATATCCCATTTGTAAGTGTCTTATGAGATTTATGGTT
TTGTTTATTGGTTTGCTCTTCAAGATTTTAAACTTTGTATTTGG
Found at i:3364524 original size:21 final size:21
Alignment explanation
Indices: 3364458--3364526 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
3364448 TAGTGCAGAC
3364458 TTCTACCGATACAAGAGATAGT
1 TTCTACCGATACAAGAGAT-GT
*
3364480 TT-TACCTATACAAGAGA-GT
1 TTCTACCGATACAAGAGATGT
**
3364499 CTTCTACCGATACAAGTTATGT
1 -TTCTACCGATACAAGAGATGT
3364521 TTCTAC
1 TTCTAC
3364527 TAATACCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 2 0.05
20 2 0.05
21 32 0.80
22 4 0.10
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.33
Consensus pattern (21 bp):
TTCTACCGATACAAGAGATGT
Found at i:3368620 original size:14 final size:14
Alignment explanation
Indices: 3368598--3368642 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3368588 TAATAACATA
3368598 AATAATTAAAAAAT
1 AATAATTAAAAAAT
*
3368612 AATATTTAAAAAAT
1 AATAATTAAAAAAT
* *
3368626 AAATGATTAAAATAT
1 -AATAATTAAAAAAT
3368641 AA
1 AA
3368643 CATAAGTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
AATAATTAAAAAAT
Found at i:3368635 original size:15 final size:14
Alignment explanation
Indices: 3368595--3368642 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
3368585 AAATAATAAC
3368595 ATAAATAATTAAAAA
1 ATAAAT-ATTAAAAA
3368610 AT-AATATTTAAAAA
1 ATAAATA-TTAAAAA
*
3368624 ATAAATGATTAAAAT
1 ATAAAT-ATTAAAAA
3368639 ATAA
1 ATAA
3368643 CATAAGTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 1 0.03
14 12 0.41
15 15 0.52
16 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
ATAAATATTAAAAA
Found at i:3370843 original size:18 final size:18
Alignment explanation
Indices: 3370820--3370854 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3370810 TTATTGACTG
*
3370820 AATCGATTTAATTCGATT
1 AATCGATCTAATTCGATT
*
3370838 AATCGATCTAGTTCGAT
1 AATCGATCTAATTCGAT
3370855 CGAATGTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (18 bp):
AATCGATCTAATTCGATT
Found at i:3376742 original size:48 final size:48
Alignment explanation
Indices: 3376690--3376790 Score: 202
Period size: 48 Copynumber: 2.1 Consensus size: 48
3376680 ACAATCCACT
3376690 AAAATCAAAATTAAGTTCATAAAAACTTTCATTTCAACTAAAGAGAGG
1 AAAATCAAAATTAAGTTCATAAAAACTTTCATTTCAACTAAAGAGAGG
3376738 AAAATCAAAATTAAGTTCATAAAAACTTTCATTTCAACTAAAGAGAGG
1 AAAATCAAAATTAAGTTCATAAAAACTTTCATTTCAACTAAAGAGAGG
3376786 AAAAT
1 AAAAT
3376791 TAAGATAAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (48 bp):
AAAATCAAAATTAAGTTCATAAAAACTTTCATTTCAACTAAAGAGAGG
Found at i:3387831 original size:31 final size:29
Alignment explanation
Indices: 3387796--3387901 Score: 86
Period size: 31 Copynumber: 3.5 Consensus size: 29
3387786 TTGGAAGTTC
*
3387796 TAATTAAAATTTTTAAAACTTTTAGAAGGCG
1 TAATTAAAATTTTTAAAA-TTTT-GAAGGCA
* * * *
3387827 TAATTAGAATTTCTAATAAATTTGAAGAGCC
1 TAATTAAAATTTTTAA-AATTTTGAAG-GCA
** *
3387858 TAATTAAAAGTTTCAAAAATTTTTAAGGCA
1 TAATTAAAA-TTTTTAAAATTTTGAAGGCA
*
3387888 TAATGAAAATTTTT
1 TAATTAAAATTTTT
3387902 TAGATTTTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
29 3 0.05
30 14 0.23
31 35 0.58
32 8 0.13
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (29 bp):
TAATTAAAATTTTTAAAATTTTGAAGGCA
Found at i:3389200 original size:21 final size:21
Alignment explanation
Indices: 3389166--3389206 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3389156 AGGTAAACTT
*
3389166 TGTTCTTACAATCTCGAGACA
1 TGTTCTTACAATCTCAAGACA
* *
3389187 TGTTCTTTCTATCTCAAGAC
1 TGTTCTTACAATCTCAAGAC
3389207 TTAATGGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTTCTTACAATCTCAAGACA
Found at i:3391505 original size:58 final size:58
Alignment explanation
Indices: 3391420--3391705 Score: 294
Period size: 58 Copynumber: 4.9 Consensus size: 58
3391410 ATAGGTCCTT
* * *
3391420 AAACTATCCAAAAATTTCATTTATAACCCCGATTTTACCAAAATTACCATTTTACCCCC
1 AAACTTTCC-AAAATTCCATTTTTAACCCCGATTTTACCAAAATTACCATTTTACCCCC
* * ** ** *
3391479 GAACCTTCCAAAATTCCATTTTTAACCCTAAAACTT-CCAAAAATTACCATTTTACCCCT
1 AAACTTTCCAAAATTCCATTTTTAACCC-CGATTTTACC-AAAATTACCATTTTACCCCC
* * * *
3391538 AAACTTTCCAAAA-TCCTTTTTTAACCCCGATTTCACTAAAAATTACCATTTTACCCCT
1 AAACTTTCCAAAATTCCATTTTTAACCCCGATTTTAC-CAAAATTACCATTTTACCCCC
* * *
3391596 AAACTTTCCAAAA-TCTCA-TTTAAACCCCGATTTCACCAAAAATTACCATTTTACCCTC
1 AAACTTTCCAAAATTC-CATTTTTAACCCCGATTTTACC-AAAATTACCATTTTACCCCC
* * *
3391654 AAACTTTCCAAAATTCCATTTTTAACCCCAAATTTTCCCGAAATTA-CATTTT
1 AAACTTTCCAAAATTCCATTTTTAACCCC-GATTTTACCAAAATTACCATTTT
3391706 TGCCATCGAG
Statistics
Matches: 189, Mismatches: 29, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
57 2 0.01
58 124 0.66
59 57 0.30
60 6 0.03
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (58 bp):
AAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCAAAATTACCATTTTACCCCC
Found at i:3391676 original size:29 final size:28
Alignment explanation
Indices: 3391457--3391706 Score: 135
Period size: 29 Copynumber: 8.6 Consensus size: 28
3391447 CCCGATTTTA
* *
3391457 CCAAAATTACCA-TTTTACCCCCGAACCTT
1 CCAAAATT-CCATTTTTA-CCCCAAACTTT
*
3391486 CCAAAATTCCATTTTTAACCCTAAAAC-TT
1 CCAAAATTCCATTTTT-ACCC-CAAACTTT
3391515 CCAAAAATTACCA-TTTTACCCCTAAACTTT
1 CC-AAAATT-CCATTTTTACCCC-AAACTTT
* *
3391545 CCAAAA-TCCTTTTTTAACCCC-GA-TTT
1 CCAAAATTCCATTTTT-ACCCCAAACTTT
3391571 CACTAAAAATTACCA-TTTTACCCCTAAACTTT
1 C-C--AAAATT-CCATTTTTACCCC-AAACTTT
** *
3391603 CCAAAA-TCTCATTTAAACCCC-GA-TTT
1 CCAAAATTC-CATTTTTACCCCAAACTTT
3391629 CACCAAAAATTACCA-TTTTACCCTCAAACTTT
1 --CC-AAAATT-CCATTTTTACCC-CAAACTTT
*
3391661 CCAAAATTCCATTTTTAACCCCAAATTTT
1 CCAAAATTCCATTTTT-ACCCCAAACTTT
* *
3391690 CCCGAAATTACATTTTT
1 -CCAAAATTCCATTTTT
3391707 GCCATCGAGA
Statistics
Matches: 175, Mismatches: 16, Indels: 59
0.70 0.06 0.24
Matches are distributed among these distances:
26 7 0.04
27 6 0.03
28 16 0.09
29 83 0.47
30 47 0.27
31 9 0.05
32 7 0.04
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (28 bp):
CCAAAATTCCATTTTTACCCCAAACTTT
Found at i:3414878 original size:181 final size:181
Alignment explanation
Indices: 3414570--3414912 Score: 542
Period size: 181 Copynumber: 1.9 Consensus size: 181
3414560 ATCCAAATAC
* * * * * *
3414570 AAATCATCCAATTGAGTCTTATATCGTTAGAATTTTCATTAATTAAATTCTTTGGCAATTAATTT
1 AAATCATCCAATTGAGCCTTAAATCATTAGAATTCTCATTAATTAAATTCTTTGACAATTAACTT
* * * * *
3414635 AATGGTTGACTGTTAAAGAGCATTTAGCATAATGAAAAGTTATCAATTTCATGGACTTTAATTAG
66 AATGGTTGACCGTCAAAGAGCATTTAGCATAATGAAAAGTTACCAATTTCATGAAATTTAATTAG
*
3414700 TTAAAATGTGATTTCAATGTTTGATACGTAAAAATTAATTTACTTTTTTCG
131 TTAAAATGTGATGTCAATGTTTGATACGTAAAAATTAATTTACTTTTTTCG
3414751 AAATCATCCAATTGAGCCTTAAATCATTAGAATTCTCATTAATTAAATTCTTTGACAATTAACTT
1 AAATCATCCAATTGAGCCTTAAATCATTAGAATTCTCATTAATTAAATTCTTTGACAATTAACTT
* * * *
3414816 AGTGGTTGACCGTCAAAGGGCATTTAGGATAATGAGAAGTTACCAATTTCATGAAATTTAATTAG
66 AATGGTTGACCGTCAAAGAGCATTTAGCATAATGAAAAGTTACCAATTTCATGAAATTTAATTAG
3414881 TTAAAATGTGATGTCAATGTTTGATACGTAAA
131 TTAAAATGTGATGTCAATGTTTGATACGTAAA
3414913 TAAAATTTTA
Statistics
Matches: 146, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
181 146 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (181 bp):
AAATCATCCAATTGAGCCTTAAATCATTAGAATTCTCATTAATTAAATTCTTTGACAATTAACTT
AATGGTTGACCGTCAAAGAGCATTTAGCATAATGAAAAGTTACCAATTTCATGAAATTTAATTAG
TTAAAATGTGATGTCAATGTTTGATACGTAAAAATTAATTTACTTTTTTCG
Found at i:3422667 original size:14 final size:14
Alignment explanation
Indices: 3422648--3422681 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3422638 TTTTTGGAAG
*
3422648 AGGAAAAGAGAGAA
1 AGGAAAAGAAAGAA
*
3422662 AGGAAAAGAAAGCA
1 AGGAAAAGAAAGAA
3422676 AGGAAA
1 AGGAAA
3422682 GGGTTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (14 bp):
AGGAAAAGAAAGAA
Found at i:3425497 original size:16 final size:17
Alignment explanation
Indices: 3425476--3425507 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3425466 TTACCCTTAT
3425476 AATTAT-AAATACATAA
1 AATTATAAAATACATAA
3425492 AATTATAAAATACATA
1 AATTATAAAATACATA
3425508 TGTGAGTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTATAAAATACATAA
Found at i:3427598 original size:20 final size:20
Alignment explanation
Indices: 3427575--3427614 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3427565 AAAAATTAAT
3427575 ACTTTCAAAATTTAACTTAC
1 ACTTTCAAAATTTAACTTAC
* *
3427595 ACTTTCAAGATTTATCTTAC
1 ACTTTCAAAATTTAACTTAC
3427615 CTCATGTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (20 bp):
ACTTTCAAAATTTAACTTAC
Found at i:3436144 original size:120 final size:120
Alignment explanation
Indices: 3435931--3436179 Score: 489
Period size: 120 Copynumber: 2.1 Consensus size: 120
3435921 AATTTAGTGA
*
3435931 CCTTGAATGTAATTTACCCATAAATTAAAAGATAGTGAGGTTGGGGGGGCGTGGGTTGCTGGGAA
1 CCTTGTATGTAATTTACCCATAAATTAAAAGATAGTGAGGTTGGGGGGGCGTGGGTTGCTGGGAA
3435996 ATTGGTTGATGAGATTTGTTTTGTAGCTAGTATGATAAAAAGAGCCATAGCCACC
66 ATTGGTTGATGAGATTTGTTTTGTAGCTAGTATGATAAAAAGAGCCATAGCCACC
3436051 CCTTGTATGTAATTTACCCATAAATTAAAAGATAGTGAGGTTGGGGGGGCGTGGGTTGCTGGGAA
1 CCTTGTATGTAATTTACCCATAAATTAAAAGATAGTGAGGTTGGGGGGGCGTGGGTTGCTGGGAA
3436116 ATTGGTTGATGAGATTTGTTTTGTAGCTAGTATGATAAAAAGAGCCATAGCCACC
66 ATTGGTTGATGAGATTTGTTTTGTAGCTAGTATGATAAAAAGAGCCATAGCCACC
3436171 CCTTGTATG
1 CCTTGTATG
3436180 GGGCCAATTC
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 128 1.00
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.31
Consensus pattern (120 bp):
CCTTGTATGTAATTTACCCATAAATTAAAAGATAGTGAGGTTGGGGGGGCGTGGGTTGCTGGGAA
ATTGGTTGATGAGATTTGTTTTGTAGCTAGTATGATAAAAAGAGCCATAGCCACC
Found at i:3438956 original size:40 final size:40
Alignment explanation
Indices: 3438898--3438973 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
3438888 AGCAACGAGC
*
3438898 GTTTCAGGCACTTTGTAACCTCACCTGGTAAGTAGCCATA
1 GTTTCAGGCACTTGGTAACCTCACCTGGTAAGTAGCCATA
3438938 GTTTCAGGCACTTGGTAACCTCACCTGGTAAGTAGC
1 GTTTCAGGCACTTGGTAACCTCACCTGGTAAGTAGC
3438974 TCATTGGTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (40 bp):
GTTTCAGGCACTTGGTAACCTCACCTGGTAAGTAGCCATA
Found at i:3445276 original size:2 final size:2
Alignment explanation
Indices: 3445269--3445295 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3445259 TAGTCATCAT
3445269 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
3445296 TAGTGGGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3445969 original size:22 final size:23
Alignment explanation
Indices: 3445942--3445997 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
3445932 ATTTTATTGT
3445942 TATTATTTTAATATT-ATATAAC
1 TATTATTTTAATATTAATATAAC
* * * *
3445964 TCTTATTTTATTATTAATTTTAC
1 TATTATTTTAATATTAATATAAC
3445987 TATTATTTTAA
1 TATTATTTTAA
3445998 AGGAATTTGC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTATTTTAATATTAATATAAC
Found at i:3445985 original size:12 final size:11
Alignment explanation
Indices: 3445942--3445996 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
3445932 ATTTTATTGT
*
3445942 TATTATTTTAA
1 TATTATTTTAC
* *
3445953 TATTATATAAC
1 TATTATTTTAC
* *
3445964 TCTTATTTTAT
1 TATTATTTTAC
3445975 TATTAATTTTAC
1 TATT-ATTTTAC
3445987 TATTATTTTA
1 TATTATTTTA
3445997 AAGGAATTTG
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 24 0.71
12 10 0.29
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTATTTTAC
Found at i:3446104 original size:32 final size:32
Alignment explanation
Indices: 3446044--3446105 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
3446034 ATCTAATTAT
*
3446044 AAATATTTTTTTAATTTATTTTTAATTTTTGGA
1 AAATATTTTTTTAA-TTAATTTTAATTTTTGGA
3446077 AAATATTTATTTTAA-TAATTTTAATTTTT
1 AAATATTT-TTTTAATTAATTTTAATTTTT
3446106 CATATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 13 0.48
33 8 0.30
34 6 0.22
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (32 bp):
AAATATTTTTTTAATTAATTTTAATTTTTGGA
Found at i:3452570 original size:25 final size:24
Alignment explanation
Indices: 3452513--3452571 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
3452503 AAAAATAAGT
* *
3452513 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATCA
3452536 TATATTATAATTTTTACTAAT-TCA
1 TATATTATAATTTTT-CTAATATCA
*
3452560 TATTTTAATAAT
1 TATATT-ATAAT
3452572 AATTATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 16 0.53
25 10 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATCA
Found at i:3452632 original size:58 final size:57
Alignment explanation
Indices: 3452532--3452690 Score: 196
Period size: 58 Copynumber: 2.7 Consensus size: 57
3452522 TTTTTCTAAT
*
3452532 ATTATATATTATAATTT-TTACTAATTCATATTTTAATAATAATTATATTAAAAATATTATTAA
1 ATTATATATTAT--TTTATTA--AATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAA
*
3452595 ATTATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATAATTAA
1 ATTATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAA
*
3452652 ATTA-ATTAATATTTTTATTAAATTATATTTAATAATAAT
1 ATTATA-TATTA-TTTTATTAAATTATATTTAATAATAAT
3452691 CATTAAAATT
Statistics
Matches: 90, Mismatches: 3, Indels: 11
0.87 0.03 0.11
Matches are distributed among these distances:
56 1 0.01
57 20 0.22
58 44 0.49
59 3 0.03
60 4 0.04
61 3 0.03
62 3 0.03
63 12 0.13
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.52
Consensus pattern (57 bp):
ATTATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAA
Found at i:3452641 original size:26 final size:26
Alignment explanation
Indices: 3452609--3452690 Score: 74
Period size: 32 Copynumber: 2.9 Consensus size: 26
3452599 TATATTATTT
3452609 TATTAAATTATATTTAATAATAATTA
1 TATTAAATTATATTTAATAATAATTA
* * * *
3452635 TGTTAAAATATAATTAAATTAATTAATATTTT
1 TATT-AAAT-T-A-T-ATTTAA-TAATAATTA
3452667 TATTAAATTATATTTAATAATAAT
1 TATTAAATTATATTTAATAATAAT
3452691 CATTAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
26 9 0.21
27 9 0.21
28 2 0.05
29 2 0.05
30 2 0.05
31 9 0.21
32 10 0.23
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (26 bp):
TATTAAATTATATTTAATAATAATTA
Found at i:3452877 original size:46 final size:44
Alignment explanation
Indices: 3452785--3452878 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
3452775 ATTACAACAT
* *
3452785 CATTCCATTCAACCAAACACAAGAATATTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
*
3452829 CATTCCAATCAACCAAACA-ATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACA-AGAA-TA-TGATTACAGCTCTATTC
3452875 CATT
1 CATT
3452879 ACAGCGAACC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 2 0.05
46 20 0.45
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
Found at i:3455823 original size:3 final size:3
Alignment explanation
Indices: 3455815--3455855 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3455805 TATATAACTT
3455815 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3455856 TATTAATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3463980 original size:17 final size:18
Alignment explanation
Indices: 3463955--3464003 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
3463945 CAAAATCTAA
*
3463955 TTTAATAAAAATATT-AT
1 TTTATTAAAAATATTAAT
3463972 TTTATT-AAAATATTAAT
1 TTTATTAAAAATATTAAT
3463989 TTT-TTAAATAATATT
1 TTTATTAAA-AATATT
3464004 TTATCTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 10 0.36
17 12 0.43
18 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTATTAAAAATATTAAT
Found at i:3463995 original size:16 final size:16
Alignment explanation
Indices: 3463962--3464007 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
3463952 TAATTTAATA
3463962 AAAATATTATTTTATT
1 AAAATATTATTTTATT
3463978 AAAATATTAATTTT-TT
1 AAAATATT-ATTTTATT
*
3463994 -AAATAATATTTTAT
1 AAAATATTATTTTAT
3464008 CTATTACTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.19
15 7 0.26
16 10 0.37
17 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAAATATTATTTTATT
Found at i:3465071 original size:22 final size:23
Alignment explanation
Indices: 3465029--3465078 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
3465019 TATTTAAACC
*
3465029 TAAACCCAAACTCAATACCAA-T
1 TAAACCCAAACTCAAGACCAATT
*
3465051 TAAACCCAAAC-CTAAGCCCAATT
1 TAAACCCAAACTC-AAGACCAATT
3465074 TAAAC
1 TAAAC
3465079 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 17 0.71
23 6 0.25
ACGTcount: A:0.48, C:0.32, G:0.02, T:0.18
Consensus pattern (23 bp):
TAAACCCAAACTCAAGACCAATT
Found at i:3465312 original size:16 final size:16
Alignment explanation
Indices: 3465291--3465326 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3465281 ATATTTATTG
3465291 ATTTTAATAAATATAA
1 ATTTTAATAAATATAA
* *
3465307 ATTTTAATAATTATTA
1 ATTTTAATAAATATAA
3465323 ATTT
1 ATTT
3465327 CATATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTAATAAATATAA
Found at i:3477276 original size:15 final size:15
Alignment explanation
Indices: 3477256--3477286 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3477246 TTTAAGAATG
3477256 TCTAAAATAATTAAC
1 TCTAAAATAATTAAC
*
3477271 TCTAAAATATTTAAC
1 TCTAAAATAATTAAC
3477286 T
1 T
3477287 AAAAGATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (15 bp):
TCTAAAATAATTAAC
Found at i:3485485 original size:18 final size:20
Alignment explanation
Indices: 3485462--3485511 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3485452 TGAATGATAA
*
3485462 TAATAATAATAAA-G-GTTT
1 TAATAATAATAAATGTATTT
3485480 TAATAATAATAAATGTATTT
1 TAATAATAATAAATGTATTT
*
3485500 TAATAATGATAA
1 TAATAATAATAA
3485512 TAATAACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 13 0.46
19 1 0.04
20 14 0.50
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (20 bp):
TAATAATAATAAATGTATTT
Found at i:3486570 original size:30 final size:30
Alignment explanation
Indices: 3486534--3486858 Score: 358
Period size: 30 Copynumber: 10.9 Consensus size: 30
3486524 CTCTGTAAGT
*
3486534 CCCAAAACTTTT-TAAAGATTACATTTTAAC
1 CCCAAAACTTTTCCAAA-ATTACATTTTAAC
* * *
3486564 CTCAAAACTTTTCCAAAAATATATTTTAAC
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
3486594 CCCAAAACTTTTCCAAAATTACATTTTAAC
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
** *
3486624 CTTAAAGA-TTTTCCAAAAATTACATTTTGAC
1 CCCAAA-ACTTTTCC-AAAATTACATTTTAAC
* *
3486655 CCTAAAACTTTTCCAAAATTACA-TTTGAC
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
* * *
3486684 CCCAAAAC-TTTCAAAAATTACA-CTTGAC
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
* *
3486712 CCCAAAACTTTTTCAAAATTACATTTTGAC
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
3486742 CCCAAAACTTTTCCAAAATTACATTTTGAA-
1 CCCAAAACTTTTCCAAAATTACATTTT-AAC
* * *
3486772 CCTAAAGCTTTTTCCAAAATCACATTTTAAC
1 CCCAAAAC-TTTTCCAAAATTACATTTTAAC
* * * *
3486803 CCAAAAACTTTTCTAATATTACATTTTGA-
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
*
3486832 CCCAAAACTTTTCCAATATTACATTTT
1 CCCAAAACTTTTCCAAAATTACATTTT
3486859 TGACCCCGAT
Statistics
Matches: 256, Mismatches: 30, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
28 26 0.10
29 50 0.20
30 125 0.49
31 55 0.21
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
CCCAAAACTTTTCCAAAATTACATTTTAAC
Found at i:3486636 original size:60 final size:60
Alignment explanation
Indices: 3486534--3486858 Score: 367
Period size: 61 Copynumber: 5.5 Consensus size: 60
3486524 CTCTGTAAGT
* * * *
3486534 CCCAAAACTTTT-TAAAGATTACATTTTAACCTCAAAACTTTTCCAAAAATATATTTTAAC
1 CCCAAAACTTTTCCAAA-ATTACATTTTAACCCCAAAACTTTTCCAAAAATACATTTTGAC
**
3486594 CCCAAAACTTTTCCAAAATTACATTTTAACCTTAAAGA-TTTTCCAAAAATTACATTTTGAC
1 CCCAAAACTTTTCCAAAATTACATTTTAACCCCAAA-ACTTTTCCAAAAA-TACATTTTGAC
* * *
3486655 CCTAAAACTTTTCCAAAATTACA-TTTGACCCCAAAAC-TTT-CAAAAATTACA-CTTGAC
1 CCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAAA-TACATTTTGAC
* * * *
3486712 CCCAAAACTTTTTCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGAA
1 CCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAAATACATTTTGAC
* * * * * * *
3486772 CCTAAAGCTTTTTCCAAAATCACATTTTAACCCAAAAACTTTTCTAATATTACATTTTGA-
1 CCCAAAAC-TTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAAATACATTTTGAC
*
3486832 CCCAAAACTTTTCCAATATTACATTTT
1 CCCAAAACTTTTCCAAAATTACATTTT
3486859 TGACCCCGAT
Statistics
Matches: 230, Mismatches: 26, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
57 26 0.11
58 25 0.11
59 28 0.12
60 71 0.31
61 80 0.35
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.36
Consensus pattern (60 bp):
CCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAAATACATTTTGAC
Found at i:3486824 original size:148 final size:149
Alignment explanation
Indices: 3486534--3486842 Score: 419
Period size: 148 Copynumber: 2.1 Consensus size: 149
3486524 CTCTGTAAGT
* * * * *
3486534 CCCAAAACTTTTTAAAGATTACATTTTAACCTCAAAACTTTTCCAAAAATATATTTTAACCCCAA
1 CCCAAAAC-TTTCAAAAATTACATCTTAACCCCAAAACTTTTCCAAAAATACATTTTAACCCCAA
* * *
3486599 AACTTTTCCAAAATTACATTTTAACCTTAAAGATTTTCCAAAAATTACATTTTGACCCTAAAACT
65 AACTTTTCCAAAATTACATTTTAACCTTAAAGATTTTCCAAAAATCACATTTTAACCCAAAAACT
3486664 TTTCCAAAATTACA-TTTGA
130 TTTCCAAAATTACATTTTGA
* * * *
3486683 CCCCAAAACTTTCAAAAATTACA-CTTGACCCCAAAACTTTTTCAAAATTACATTTTGACCCCAA
1 -CCCAAAACTTTCAAAAATTACATCTTAACCCCAAAACTTTTCCAAAAATACATTTTAACCCCAA
*
3486747 AACTTTTCCAAAATTACATTTTGAACC-TAAAGCTTTTTCC-AAAATCACATTTTAACCCAAAAA
65 AACTTTTCCAAAATTACATTTT-AACCTTAAAG-ATTTTCCAAAAATCACATTTTAACCCAAAAA
* *
3486810 CTTTTCTAATATTACATTTTGA
128 CTTTTCCAAAATTACATTTTGA
3486832 CCCAAAACTTT
1 CCCAAAACTTT
3486843 TCCAATATTA
Statistics
Matches: 141, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
148 106 0.75
149 27 0.19
150 8 0.06
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (149 bp):
CCCAAAACTTTCAAAAATTACATCTTAACCCCAAAACTTTTCCAAAAATACATTTTAACCCCAAA
ACTTTTCCAAAATTACATTTTAACCTTAAAGATTTTCCAAAAATCACATTTTAACCCAAAAACTT
TTCCAAAATTACATTTTGA
Found at i:3497445 original size:32 final size:32
Alignment explanation
Indices: 3497401--3497462 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
3497391 CATCTATTTT
*
3497401 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTAAACTCTTTGACAACACGAAAAATC
*
3497433 CATTGTTAAACTCTTTGACAACATGAAAAA
1 CATTGTTAAACTCTTTGACAACACGAAAAA
3497463 ACCAAAAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTAAACTCTTTGACAACACGAAAAATC
Found at i:3499143 original size:13 final size:13
Alignment explanation
Indices: 3499112--3499149 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
3499102 TGGTCGGATA
*
3499112 AAATATTTAATTT
1 AAATATTCAATTT
*
3499125 -AATATTGAATTT
1 AAATATTCAATTT
3499137 AAATATTCAATTT
1 AAATATTCAATTT
3499150 TATTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (13 bp):
AAATATTCAATTT
Found at i:3499315 original size:21 final size:21
Alignment explanation
Indices: 3499291--3499332 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3499281 AGTAAATTAC
3499291 TAAA-AAAATTAATACATAAAA
1 TAAATAAAA-TAATACATAAAA
* *
3499312 TAAATACAATAATAGATAAAA
1 TAAATAAAATAATACATAAAA
3499333 CGAGATGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAATAAAATAATACATAAAA
Found at i:3509616 original size:23 final size:23
Alignment explanation
Indices: 3509542--3509782 Score: 160
Period size: 23 Copynumber: 10.6 Consensus size: 23
3509532 TAAACGGAAC
* * *
3509542 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
3509564 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
3509586 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
3509612 AAACAGAGAGTATACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
3509632 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
3509651 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
3509674 AATCAAAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
3509697 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
* *
3509722 AAACAGAGAGCATACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
3509745 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
3509768 AATAACAGAGAGCAC
1 -A-AACAGAGAGCAC
3509783 GAGACGTGCT
Statistics
Matches: 171, Mismatches: 30, Indels: 33
0.73 0.13 0.14
Matches are distributed among these distances:
16 9 0.05
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 18 0.11
23 87 0.51
24 3 0.02
25 39 0.23
26 8 0.05
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:3509709 original size:48 final size:46
Alignment explanation
Indices: 3509635--3509803 Score: 200
Period size: 48 Copynumber: 3.6 Consensus size: 46
3509625 ACAAAGTACT
* *
3509635 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCAAA
1 GAGCACACACAGTGCTAATCAGAGAGCACACGAAGTGCTAATCAGA
* *
3509681 GAGCACACACAGTGCTAATAACAGAGAGCACGA-GACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCAC-ACGAAGTGCTAATCAGA
*
3509729 GAGCATACACAGTGCTAATCAGAGAGCACAC-ACAGTGCTAATAACAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACACGA-AGTGCTAAT--CAGA
*
3509777 GAGCACGAGAC-GTGCTAATCAGAGAGC
1 GAGCAC-ACACAGTGCTAATCAGAGAGC
3509804 GCGCTAGTGT
Statistics
Matches: 106, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
45 2 0.02
46 35 0.33
48 65 0.61
49 4 0.04
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACACGAAGTGCTAATCAGA
Found at i:3509755 original size:71 final size:71
Alignment explanation
Indices: 3509646--3509803 Score: 273
Period size: 71 Copynumber: 2.2 Consensus size: 71
3509636 AGCACACAAA
3509646 GTGCTAATCAGAGAGCACACGAAGTGCTAATCAAAGAGCACACACAGTGCTAATAACAGAGAGCA
1 GTGCTAATCAGAGAGCACACGAAGTGCTAATCAAAGAGCACACACAGTGCTAATAACAGAGAGCA
3509711 CGAGAC
66 CGAGAC
* * *
3509717 GTGCTAAACAGAGAGCATAC-ACAGTGCTAATCAGAGAGCACACACAGTGCTAATAACAGAGAGC
1 GTGCTAATCAGAGAGCACACGA-AGTGCTAATCAAAGAGCACACACAGTGCTAATAACAGAGAGC
3509781 ACGAGAC
65 ACGAGAC
3509788 GTGCTAATCAGAGAGC
1 GTGCTAATCAGAGAGC
3509804 GCGCTAGTGT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
70 1 0.01
71 81 0.99
ACGTcount: A:0.40, C:0.22, G:0.25, T:0.13
Consensus pattern (71 bp):
GTGCTAATCAGAGAGCACACGAAGTGCTAATCAAAGAGCACACACAGTGCTAATAACAGAGAGCA
CGAGAC
Found at i:3509799 original size:23 final size:23
Alignment explanation
Indices: 3509635--3509803 Score: 200
Period size: 23 Copynumber: 7.2 Consensus size: 23
3509625 ACAAAGTACT
*
3509635 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
*
3509658 GAGCACACGA-AGTGCTAATCAAA
1 GAGCACAC-ACAGTGCTAATCAGA
3509681 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACACAGTGCTAAT--CAGA
* *
3509706 GAGCACGAGAC-GTGCTAAACAGA
1 GAGCAC-ACACAGTGCTAATCAGA
*
3509729 GAGCATACACAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
3509752 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACACAGTGCTAAT--CAGA
*
3509777 GAGCACGAGAC-GTGCTAATCAGA
1 GAGCAC-ACACAGTGCTAATCAGA
3509800 GAGC
1 GAGC
3509804 GCGCTAGTGT
Statistics
Matches: 128, Mismatches: 9, Indels: 18
0.83 0.06 0.12
Matches are distributed among these distances:
22 4 0.03
23 83 0.65
24 1 0.01
25 34 0.27
26 6 0.05
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
GAGCACACACAGTGCTAATCAGA
Found at i:3513113 original size:17 final size:17
Alignment explanation
Indices: 3513091--3513129 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
3513081 CTCCACCTTG
* *
3513091 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
3513108 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
3513125 ACAAG
1 ACAAG
3513130 TTCTTCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:3517376 original size:528 final size:527
Alignment explanation
Indices: 3516380--3517435 Score: 1740
Period size: 528 Copynumber: 2.0 Consensus size: 527
3516370 ACTAATTACA
3516380 ATAAGTGTAATTGGGTCAACATAAATAGCTTAACAGTTTAATATACTTAACTAATCTGTTTAGAG
1 ATAAGTGTAATTGGGTCAACATAAATAGCTTAACAGTTTAATATACTTAACTAATCTGTTTAGAG
* *
3516445 AAGTTCAAACGGTCGATTCTGGTTAATAATCGAACCATACTAGAACTAACCACTAAACGAGCTCG
66 AAGTTCAAACGGTCGATTCCGATTAATAATCGAACCATACTAGAACTAACCACTAAACGAGCTCG
3516510 AAACCGAAAAACATTAAACAAGTGCATAAACCATCTCTAGAACCTTAATTCCATAGTCACCATTT
131 AAACCGAAAAACATTAAACAAGTGCATAAACCATCTCTAGAACCTTAATTCCATAGTCACCATTT
*
3516575 TTATATATCTATATAGCAATGAACTCAATCTTTAACATTGGAAGCATGCTTTCATACTAAGCAAA
196 TTATATATCTATATAGCAATGAACTCAATCTTTAACATTGGAAGCATGCATTCATACTAAGCAAA
* * *
3516640 CTAGTGGGACAGCCGATGGCGTAAACTGAAGGTTAAAGGCTCGAGGTAAAAAATTAACGGAAAAA
261 CTAGTGGGACAGCCGATGACGTAAACTGAAGGTTAAAGGCTCGAGCTAAAAAACTAACGGAAAAA
* * * *
3516705 GCGAGAGACGGATAAACAACGGCACTAGAAGTCACTTAACGGGGGGTGGGGTGTCGTCTATGTGC
326 GCGAGAGACGAAAAAACAACGGCACTAGAAGTCACTTAACGGGGGGTGAGGTGTCGTCTATGTGA
* * * *
3516770 ATAAGTCACAAAAAGGCTCCCTGTTCATGGAACAGATTAAGAATAGTGCCCATAGGAAGATTCAA
391 ATAAGTCACAAAAAGGCTCCCCGTTCAGGGAACAGATTAAGAATAGCGACCATAGGAAGATTCAA
* * **
3516835 CAATCACAAGCTCCTAGATGTAGGGCAGGCCATCCTCCACCCAGAAAACATCGCTTTTCTGTCGT
456 CAATCACAAGCTCCTAGATGTA-GGCAGGCCATCCTCCACCCAGAAAACATCCCTCTTCTACCGT
3516900 AATCCTTC
520 AATCCTTC
* *
3516908 ATAAGTGTAATTGGGTCAACCTAACTAGCTTAACAGTTTAATATACTTAACTAATCTGTTTAGAG
1 ATAAGTGTAATTGGGTCAACATAAATAGCTTAACAGTTTAATATACTTAACTAATCTGTTTAGAG
*
3516973 ATGATT-AAACGGTCGATTCCGATTAATAATCGAACCATACTAGAACTAACCACTAAACGAGCTC
66 AAG-TTCAAACGGTCGATTCCGATTAATAATCGAACCATACTAGAACTAACCACTAAACGAGCTC
* * *
3517037 GAAGCTGAAAAACATTAAACAAGTGCATAAACCATCTCTAGAACCTTGATTCCATAGTCACCATT
130 GAAACCGAAAAACATTAAACAAGTGCATAAACCATCTCTAGAACCTTAATTCCATAGTCACCATT
*
3517102 TTTATATATCTATATGGCAATGAACTCAATCTTTAACATTGGAAGCATGCATTCATACTAAGCAA
195 TTTATATATCTATATAGCAATGAACTCAATCTTTAACATTGGAAGCATGCATTCATACTAAGCAA
* * * * *
3517167 ACTAGTTGGACAGCCGATGACGCT-AGCTGAAGTTTAAAGGCTGGAGCTAAAAAACTGACGGAAA
260 ACTAGTGGGACAGCCGATGACG-TAAACTGAAGGTTAAAGGCTCGAGCTAAAAAACTAACGGAAA
3517231 AAGCGAGAGACGAAAAAACAACGGCACTAGAAGTCACTTAACGGGGGGTGAGGTGTCGTCTATGT
324 AAGCGAGAGACGAAAAAACAACGGCACTAGAAGTCACTTAACGGGGGGTGAGGTGTCGTCTATGT
* * *
3517296 GAATAAGTCACATAAAGGCTCCCCG-TCCGGAGAACAGATTAAGAATAGCGATCATAGGAAGATT
389 GAATAAGTCACAAAAAGGCTCCCCGTTCAGG-GAACAGATTAAGAATAGCGACCATAGGAAGATT
* *
3517360 CAACAATCACAAGCTCCTAGATGTAGGCAGGGCTTCCTCCACCCAGAAAACATCCCTCTTCTACC
453 CAACAATCACAAGCTCCTAGATGTAGGCAGGCCATCCTCCACCCAGAAAACATCCCTCTTCTACC
3517425 GTAATCCTTC
518 GTAATCCTTC
3517435 A
1 A
3517436 CGAGCGAGAA
Statistics
Matches: 490, Mismatches: 35, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
527 48 0.10
528 439 0.90
529 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (527 bp):
ATAAGTGTAATTGGGTCAACATAAATAGCTTAACAGTTTAATATACTTAACTAATCTGTTTAGAG
AAGTTCAAACGGTCGATTCCGATTAATAATCGAACCATACTAGAACTAACCACTAAACGAGCTCG
AAACCGAAAAACATTAAACAAGTGCATAAACCATCTCTAGAACCTTAATTCCATAGTCACCATTT
TTATATATCTATATAGCAATGAACTCAATCTTTAACATTGGAAGCATGCATTCATACTAAGCAAA
CTAGTGGGACAGCCGATGACGTAAACTGAAGGTTAAAGGCTCGAGCTAAAAAACTAACGGAAAAA
GCGAGAGACGAAAAAACAACGGCACTAGAAGTCACTTAACGGGGGGTGAGGTGTCGTCTATGTGA
ATAAGTCACAAAAAGGCTCCCCGTTCAGGGAACAGATTAAGAATAGCGACCATAGGAAGATTCAA
CAATCACAAGCTCCTAGATGTAGGCAGGCCATCCTCCACCCAGAAAACATCCCTCTTCTACCGTA
ATCCTTC
Found at i:3523104 original size:17 final size:17
Alignment explanation
Indices: 3523089--3523163 Score: 80
Period size: 17 Copynumber: 4.2 Consensus size: 17
3523079 TTTGGGTTTG
*
3523089 AATTTAGTTTAAGTTTA
1 AATTTAGTTTAAATTTA
3523106 AACTTTTAAGTTTAAATTTA
1 AA--TTT-AGTTTAAATTTA
*
3523126 AATTAAGTTTAAATTT-
1 AATTTAGTTTAAATTTA
*
3523142 AATTTGAATTTAAATTTA
1 AATTT-AGTTTAAATTTA
3523160 AATT
1 AATT
3523164 AATTAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.08
17 23 0.47
18 6 0.12
19 3 0.06
20 13 0.27
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (17 bp):
AATTTAGTTTAAATTTA
Found at i:3523136 original size:11 final size:11
Alignment explanation
Indices: 3523117--3523165 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
3523107 ACTTTTAAGT
3523117 TTAAATTTAAA
1 TTAAATTTAAA
*
3523128 TTAAGTTTAAA
1 TTAAATTTAAA
* *
3523139 TTTAATTTGAAT
1 TTAAATTT-AAA
3523151 TTAAATTTAAA
1 TTAAATTTAAA
3523162 TTAA
1 TTAA
3523166 TTAAAAAAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
11 22 0.71
12 9 0.29
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:3523142 original size:23 final size:23
Alignment explanation
Indices: 3523110--3523167 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
3523100 AGTTTAAACT
* *
3523110 TTTAAGTTTAAATTT-AAATTAAG
1 TTTAAATTT-AATTTGAAATTAAA
*
3523133 TTTAAATTTAATTTGAATTTAAA
1 TTTAAATTTAATTTGAAATTAAA
3523156 TTTAAA-TTAATT
1 TTTAAATTTAATT
3523168 AAAAAAGTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.35
23 20 0.65
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (23 bp):
TTTAAATTTAATTTGAAATTAAA
Found at i:3523161 original size:6 final size:6
Alignment explanation
Indices: 3523096--3523163 Score: 68
Period size: 6 Copynumber: 11.3 Consensus size: 6
3523086 TTGAATTTAG
* * *
3523096 TTTAAG TTTAAA CTTTTAAG TTTAAA TTTAAA -TTAAG TTTAAA TTT-AA
1 TTTAAA TTTAAA --TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
3523144 TTTGAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
3523164 AATTAAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
5 9 0.17
6 38 0.73
8 5 0.10
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:3523975 original size:24 final size:24
Alignment explanation
Indices: 3523948--3523998 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
3523938 TGGTACCGCT
3523948 GTCGCCGGAGCTCCCGTTGGGATC
1 GTCGCCGGAGCTCCCGTTGGGATC
3523972 GTCGCCGGAGCTCCCGTTGGGATC
1 GTCGCCGGAGCTCCCGTTGGGATC
3523996 GTC
1 GTC
3523999 TCCGAAACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.08, C:0.33, G:0.37, T:0.22
Consensus pattern (24 bp):
GTCGCCGGAGCTCCCGTTGGGATC
Found at i:3524009 original size:24 final size:24
Alignment explanation
Indices: 3523948--3524013 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
3523938 TGGTACCGCT
* *
3523948 GTCGCCGGAGCTCCCGTTGGGATC
1 GTCGCCGAAACTCCCGTTGGGATC
* *
3523972 GTCGCCGGAGCTCCCGTTGGGATC
1 GTCGCCGAAACTCCCGTTGGGATC
*
3523996 GTCTCCGAAACT-CCGTTG
1 GTCGCCGAAACTCCCGTTG
3524014 TTGTTGTGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 6 0.15
24 33 0.85
ACGTcount: A:0.11, C:0.33, G:0.33, T:0.23
Consensus pattern (24 bp):
GTCGCCGAAACTCCCGTTGGGATC
Found at i:3524995 original size:30 final size:29
Alignment explanation
Indices: 3524972--3525138 Score: 162
Period size: 30 Copynumber: 5.7 Consensus size: 29
3524962 AAACTTTTTG
3524972 AAAATTACATTTTTACCCCCAAACTTTCC-
1 AAAATTACATTTTTACCCCCAAAC-TTCCA
* * * *
3525001 AAAATT-CTATTCTTGA-TCCTAAACTTTCTA
1 AAAATTAC-ATT-TTTACCCCCAAAC-TTCCA
*
3525031 AAAATTACATTTTTACCCCTTAAACTTCCA
1 AAAATTACATTTTTACCCC-CAAACTTCCA
*
3525061 AAAATTACATTTTTACCCCTTAAACTTCCA
1 AAAATTACATTTTTACCCC-CAAACTTCCA
**
3525091 AAAATTACA-TTTTACCCCCAAACTTCTT
1 AAAATTACATTTTTACCCCCAAACTTCCA
*
3525119 AAAATTCCATTTTTGACCCC
1 AAAATTACATTTTT-ACCCC
3525139 GATTTTTTAA
Statistics
Matches: 119, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
28 16 0.13
29 35 0.29
30 62 0.52
31 6 0.05
ACGTcount: A:0.35, C:0.27, G:0.01, T:0.37
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCCAAACTTCCA
Found at i:3525114 original size:89 final size:89
Alignment explanation
Indices: 3524972--3525138 Score: 209
Period size: 89 Copynumber: 1.9 Consensus size: 89
3524962 AAACTTTTTG
* *
3524972 AAAATTACATTTTTACCCCCAAACTTTCCAAAATTCTATTCTTGATCCTAAACTTTCTAAAAATT
1 AAAATTACATTTTTACCCCCAAACTTTCCAAAATTCTATTCTTGACCCCAAAC-TTCTAAAAATT
3525037 ACATTTTT-ACCCCTTAAACTTCCA
65 ACATTTTTGACCCCTTAAACTTCCA
* *
3525061 AAAATTACATTTTTACCCCTTAAAC-TTCCAAAAATTAC-ATT-TT-ACCCCCAAACTTCTTAAA
1 AAAATTACATTTTTACCCC-CAAACTTTCC-AAAATT-CTATTCTTGA-CCCCAAACTTCTAAAA
*
3525122 ATTCCATTTTTGACCCC
62 ATTACATTTTTGACCCC
3525139 GATTTTTTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
88 18 0.26
89 36 0.53
90 13 0.19
91 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.01, T:0.37
Consensus pattern (89 bp):
AAAATTACATTTTTACCCCCAAACTTTCCAAAATTCTATTCTTGACCCCAAACTTCTAAAAATTA
CATTTTTGACCCCTTAAACTTCCA
Found at i:3525269 original size:29 final size:29
Alignment explanation
Indices: 3525205--3525267 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
3525195 CTAAACTTTC
*
3525205 CCAAAATTACCATTTTGCCCCTCGAGTGT
1 CCAAAATTACCATTTTGCCCCTCGAGTAT
* *
3525234 CCAAAATTACCATTTTGCCTCT-GGGTAT
1 CCAAAATTACCATTTTGCCCCTCGAGTAT
3525262 CCAAAA
1 CCAAAA
3525268 ATCACATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.30
Consensus pattern (29 bp):
CCAAAATTACCATTTTGCCCCTCGAGTAT
Found at i:3530071 original size:17 final size:17
Alignment explanation
Indices: 3530049--3530088 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3530039 TCTCCACCTT
* *
3530049 AACAAGAATTCTCTACG
1 AACAAGAACTCTCAACG
3530066 AACAAGAACTCTCAACG
1 AACAAGAACTCTCAACG
3530083 AACAAG
1 AACAAG
3530089 TTCTCCACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.25, G:0.12, T:0.15
Consensus pattern (17 bp):
AACAAGAACTCTCAACG
Found at i:3533075 original size:4 final size:4
Alignment explanation
Indices: 3533066--3533092 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3533056 CCCGAGTATT
3533066 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
3533093 TACTTTCATT
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3533125 original size:14 final size:13
Alignment explanation
Indices: 3533108--3533138 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3533098 TCATTTTTTT
*
3533108 AAAAAAATTTTAA
1 AAAAAAAATTTAA
3533121 AAAAAAAATTTAA
1 AAAAAAAATTTAA
3533134 AAAAA
1 AAAAA
3533139 GTTTGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAAAATTTAA
Found at i:3533198 original size:6 final size:6
Alignment explanation
Indices: 3533187--3533227 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 6
3533177 TATTTATTTC
3533187 ATTTTT ATTTTT ATTTTT A-TTTT A-TTTT ATTTTT AATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT -ATTTTT
3533228 TTAATTATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 10 0.30
6 17 0.52
7 6 0.18
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:3533204 original size:12 final size:12
Alignment explanation
Indices: 3533187--3533227 Score: 59
Period size: 11 Copynumber: 3.5 Consensus size: 12
3533177 TATTTATTTC
3533187 ATTTTTATTTTT
1 ATTTTTATTTTT
3533199 ATTTTTA-TTTT
1 ATTTTTATTTTT
3533210 A-TTTTATTTTT
1 ATTTTTATTTTT
3533221 AATTTTT
1 -ATTTTT
3533228 TTAATTATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.19
11 9 0.35
12 8 0.31
13 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:3533221 original size:11 final size:11
Alignment explanation
Indices: 3533179--3533219 Score: 57
Period size: 12 Copynumber: 3.7 Consensus size: 11
3533169 AATTAGTTTA
*
3533179 TTTATTTCATT
1 TTTATTTTATT
3533190 TTTATTTTTATT
1 TTTA-TTTTATT
3533202 TTTATTTTA-T
1 TTTATTTTATT
3533212 TTTATTTT
1 TTTATTTT
3533220 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 9 0.32
11 9 0.32
12 10 0.36
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:3541423 original size:21 final size:20
Alignment explanation
Indices: 3541394--3541432 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3541384 TGATTTTCTA
3541394 TGAACTTTTATAACTGTTTAT
1 TGAACTTTTATAA-TGTTTAT
* *
3541415 TGAATTTTTTTAATGTTT
1 TGAACTTTTATAATGTTT
3541433 TATACATTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (20 bp):
TGAACTTTTATAATGTTTAT
Found at i:3550459 original size:28 final size:28
Alignment explanation
Indices: 3550427--3550481 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
3550417 TACTCACGTT
* *
3550427 TGTATTCAATTAGGATATTTGTTTAAAA
1 TGTATTCAACTAGAATATTTGTTTAAAA
3550455 TGTATTCAACTAGAATATTTGTTTAAA
1 TGTATTCAACTAGAATATTTGTTTAAA
3550482 GGGATTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.45
Consensus pattern (28 bp):
TGTATTCAACTAGAATATTTGTTTAAAA
Found at i:3556159 original size:58 final size:56
Alignment explanation
Indices: 3555998--3556166 Score: 180
Period size: 58 Copynumber: 3.0 Consensus size: 56
3555988 AAGTAGTAAT
* * * *
3555998 ATTATTATAATTTTTACTAATTCATATTTTAATAATAATTATATTAAAA-AGTTATTA
1 ATTATTATTATTTTTATTAATTTATA-TTTAATAATAATTATATTAAAATA-TAATTA
* * * *
3556055 ATTACATATTA-TTTTATTAAATTACATTTAATAATAATTATGTTAAAATATAATTAA
1 ATTA-TTATTATTTTTATTAATTTATATTTAATAATAATTATATTAAAATATAATT-A
* * *
3556112 ATTATTTATTATTTTTATTAATTTATATTTAATAAGAATTTTATTAAAATTTAAT
1 ATTA-TTATTATTTTTATTAATTTATATTTAATAATAATTATATTAAAATATAAT
3556167 AACAATAATC
Statistics
Matches: 92, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
56 25 0.27
57 26 0.28
58 41 0.45
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (56 bp):
ATTATTATTATTTTTATTAATTTATATTTAATAATAATTATATTAAAATATAATTA
Found at i:3556330 original size:48 final size:43
Alignment explanation
Indices: 3556247--3556341 Score: 118
Period size: 43 Copynumber: 2.1 Consensus size: 43
3556237 ATTACAACAC
* *
3556247 CATTCCATTCAACCAAATACAAAATACTATTACAACTCTATTA
1 CATTCCATTCAACCAAAAACAAAATACTATTACAACCCTATTA
*
3556290 CATTCCATTCAACCAAACAACTAAGAATTACTGATTACAACCCTATTC
1 CATTCCATTCAACCAAA-AAC-AA-AA-TACT-ATTACAACCCTATTA
3556338 CATT
1 CATT
3556342 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
43 17 0.39
44 2 0.05
45 2 0.05
46 2 0.05
47 4 0.09
48 17 0.39
ACGTcount: A:0.41, C:0.27, G:0.02, T:0.29
Consensus pattern (43 bp):
CATTCCATTCAACCAAAAACAAAATACTATTACAACCCTATTA
Found at i:3556421 original size:19 final size:20
Alignment explanation
Indices: 3556385--3556426 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
3556375 GTATAATTGT
**
3556385 ATTTTTACAATTTTAATTAA
1 ATTTTTACAATTGAAATTAA
*
3556405 ATTTTT-CAATTGAAATTTA
1 ATTTTTACAATTGAAATTAA
3556424 ATT
1 ATT
3556427 AAAAATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (20 bp):
ATTTTTACAATTGAAATTAA
Found at i:3562210 original size:21 final size:21
Alignment explanation
Indices: 3562179--3562230 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
3562169 AGAGAGGTAT
*
3562179 GAAGTAGAAGGAGAAGGAGAA
1 GAAGAAGAAGGAGAAGGAGAA
* * *
3562200 TAAGAAGAAGGGGAAGGGGAA
1 GAAGAAGAAGGAGAAGGAGAA
*
3562221 GAAGAGGAAG
1 GAAGAAGAAG
3562231 AGGAAGAAGC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.46, T:0.04
Consensus pattern (21 bp):
GAAGAAGAAGGAGAAGGAGAA
Found at i:3562221 original size:15 final size:15
Alignment explanation
Indices: 3562203--3562239 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3562193 AGGAGAATAA
* *
3562203 GAAGAAGGGGAAGGG
1 GAAGAAGAGGAAGAG
3562218 GAAGAAGAGGAAGAG
1 GAAGAAGAGGAAGAG
3562233 GAAGAAG
1 GAAGAAG
3562240 CACTTTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (15 bp):
GAAGAAGAGGAAGAG
Found at i:3562235 original size:21 final size:21
Alignment explanation
Indices: 3562191--3562236 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3562181 AGTAGAAGGA
* *
3562191 GAAGGAGAATAAGAAGAAGGG
1 GAAGGAGAAGAAGAAGAAGAG
* *
3562212 GAAGGGGAAGAAGAGGAAGAG
1 GAAGGAGAAGAAGAAGAAGAG
3562233 GAAG
1 GAAG
3562237 AAGCACTTTT
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:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (21 bp):
GAAGGAGAAGAAGAAGAAGAG
Found at i:3563116 original size:7 final size:8
Alignment explanation
Indices: 3563103--3563131 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3563093 GGTTTTAATG
3563103 AAAAAAAT
1 AAAAAAAT
3563111 AAAAAAAT
1 AAAAAAAT
3563119 AAAAAAAT
1 AAAAAAAT
3563127 AAAAA
1 AAAAA
3563132 GCGGGAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:3566839 original size:9 final size:9
Alignment explanation
Indices: 3566825--3566851 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3566815 CTCATTAGAG
3566825 TAATAAAAA
1 TAATAAAAA
3566834 TAATAAAAA
1 TAATAAAAA
3566843 TAATAAAAA
1 TAATAAAAA
3566852 ACAACAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
TAATAAAAA
Found at i:3571227 original size:26 final size:26
Alignment explanation
Indices: 3571148--3571241 Score: 80
Period size: 26 Copynumber: 3.5 Consensus size: 26
3571138 CTTTAAGTAT
* ** * *
3571148 CAAATTAGAAAAAAAAGTTTAAGTGC
1 CAAATTAAAAAAAAAAACTTAAATAC
** *
3571174 CAAATTAAAAAATATCAACTTTAGATAC
1 CAAATTAAAAAA-AAAAAC-TTAAATAC
3571202 CAAATTAAAAAAAAAAACTTAAATAC
1 CAAATTAAAAAAAAAAACTTAAATAC
* *
3571228 TAAATTTAAAAAAA
1 CAAATTAAAAAAAA
3571242 TCAAATTAAG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
26 30 0.57
27 6 0.11
28 17 0.32
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (26 bp):
CAAATTAAAAAAAAAAACTTAAATAC
Found at i:3571233 original size:54 final size:53
Alignment explanation
Indices: 3571082--3571245 Score: 141
Period size: 54 Copynumber: 2.9 Consensus size: 53
3571072 TTGACAAATA
* * * *
3571082 TAATACCAAATTAGACCAAAATAAAACTTGAGTATTAAATTAGGAAAAAGTGTCAACTT
1 TAATACCAAATTA-A--AAAAAAAAACTTAAGTACTAAATTA--AAAAA-TATCAACTT
* * ** * *
3571141 TAAGTATCAAATTAGAAAAAAAAGTTTAAGTGCCAAATTAAAAAATATCAACTT
1 TAA-TACCAAATTAAAAAAAAAAACTTAAGTACTAAATTAAAAAATATCAACTT
*
3571195 TAGATACCAAATTAAAAAAAAAAACTTAAATACTAAATTTAAAAAA-ATCAA
1 TA-ATACCAAATTAAAAAAAAAAACTTAAGTACTAAA-TTAAAAAATATCAA
3571246 ATTAAGGTAA
Statistics
Matches: 85, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
54 41 0.48
55 14 0.16
57 18 0.21
59 3 0.04
60 9 0.11
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (53 bp):
TAATACCAAATTAAAAAAAAAAACTTAAGTACTAAATTAAAAAATATCAACTT
Found at i:3571250 original size:27 final size:26
Alignment explanation
Indices: 3571173--3571250 Score: 77
Period size: 28 Copynumber: 2.9 Consensus size: 26
3571163 AGTTTAAGTG
* *
3571173 CCAAATTAAAAAATATCAACTTTAGATA
1 CCAAATTAAAAAA-ATCAA-ATTAAATA
*
3571201 CCAAATTAAAAAAA-AAAACTTAAATA
1 CCAAATTAAAAAAATCAAA-TTAAATA
*
3571227 CTAAATTTAAAAAAATCAAATTAA
1 CCAAA-TTAAAAAAATCAAATTAA
3571251 GGTAACAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
26 12 0.29
27 14 0.33
28 16 0.38
ACGTcount: A:0.62, C:0.12, G:0.01, T:0.26
Consensus pattern (26 bp):
CCAAATTAAAAAAATCAAATTAAATA
Found at i:3573593 original size:16 final size:16
Alignment explanation
Indices: 3573554--3573602 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
3573544 TGGATTCTTC
3573554 TACTTCATTTTTA--TT
1 TACTT-ATTTTTATTTT
3573569 TACTTATTTATTATTTT
1 TACTTATTT-TTATTTT
*
3573586 TA-TTATTTTTCTTTT
1 TACTTATTTTTATTTT
3573601 TA
1 TA
3573603 ATTTATTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.13
15 16 0.53
16 6 0.20
17 4 0.13
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (16 bp):
TACTTATTTTTATTTT
Found at i:3574410 original size:29 final size:30
Alignment explanation
Indices: 3574356--3574412 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
3574346 TAAAAATGTA
* *
3574356 ATTTTTAAAGGATTAAATTAAAATTTTATC
1 ATTTTTAAAGGATCAAAATAAAATTTTATC
*
3574386 ATTTTTAAA-GATCAAAATATAATTTTA
1 ATTTTTAAAGGATCAAAATAAAATTTTA
3574413 CCTTCACTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (30 bp):
ATTTTTAAAGGATCAAAATAAAATTTTATC
Found at i:3574684 original size:3 final size:3
Alignment explanation
Indices: 3574678--3574707 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3574668 TTATTATTAC
*
3574678 CAT CAT CAT CAT CAT CAT CAC CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
3574708 TATTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
CAT
Found at i:3583723 original size:17 final size:16
Alignment explanation
Indices: 3583685--3583727 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
3583675 TTGAAAGAAA
3583685 AAAAAAT-TGTATGAAT
1 AAAAAATAT-TATGAAT
*
3583701 AAAAAATATTATGGAT
1 AAAAAATATTATGAAT
3583717 AATAAAATATT
1 AA-AAAATATT
3583728 GTTTTATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (16 bp):
AAAAAATATTATGAAT
Found at i:3584240 original size:30 final size:30
Alignment explanation
Indices: 3584205--3584266 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
3584195 TTTCTCCTTC
*
3584205 TCTTCTTAATATTTTACTAAAAATCATTTA
1 TCTTCTTAATATTTTACTAAAAATCAGTTA
*
3584235 TCTTCTTAATATTTTACTAAAAGTCAGTTA
1 TCTTCTTAATATTTTACTAAAAATCAGTTA
3584265 TC
1 TC
3584267 ATGTCCTTCA
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:0.34, C:0.15, G:0.03, T:0.48
Consensus pattern (30 bp):
TCTTCTTAATATTTTACTAAAAATCAGTTA
Found at i:3587782 original size:115 final size:116
Alignment explanation
Indices: 3587573--3587813 Score: 412
Period size: 115 Copynumber: 2.1 Consensus size: 116
3587563 ATGCCTAGGG
*
3587573 ATTACCACAGAGATGCTGACCTAGCAAGAGGCCACTCTTTGTAAACACAACATAACCTAGCAGCT
1 ATTA-CACAGAGATGCTGACCTAGCAAGAGGCCACTCTTTGTAAACACAACATAACCTAGAAGCT
* *
3587638 ACTCAAGAACCTAAAAGAGGTTATGTAAATCCACCTACAGCTCCATATCTCT
65 ACTCAAGAACCTAAAAGAGGTTATATAAATCCACCTACAGCTCCAGATCTCT
*
3587690 ATTACACAGAGATGCTGACCTAGCAAG-GGCCACTCTTTGTAAACACAACATAACCTAGAATCTA
1 ATTACACAGAGATGCTGACCTAGCAAGAGGCCACTCTTTGTAAACACAACATAACCTAGAAGCTA
*
3587754 CTCAAGAACCTAAAAGAGGTTATATAAATGCACCTACAGCTCCAGATCTCT
66 CTCAAGAACCTAAAAGAGGTTATATAAATCCACCTACAGCTCCAGATCTCT
*
3587805 TTTACACAG
1 ATTACACAG
3587814 TAAAGAAGAT
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
115 91 0.77
116 23 0.19
117 4 0.03
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.23
Consensus pattern (116 bp):
ATTACACAGAGATGCTGACCTAGCAAGAGGCCACTCTTTGTAAACACAACATAACCTAGAAGCTA
CTCAAGAACCTAAAAGAGGTTATATAAATCCACCTACAGCTCCAGATCTCT
Found at i:3592355 original size:16 final size:16
Alignment explanation
Indices: 3592336--3592384 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 16
3592326 TTTTATTAAA
3592336 ATTATGTTTTTAATAT
1 ATTATGTTTTTAATAT
* *
3592352 ATTATG-TTATATTAT
1 ATTATGTTTTTAATAT
3592367 ATTA--TTTTT-ATAT
1 ATTATGTTTTTAATAT
3592380 ATTAT
1 ATTAT
3592385 ACAATTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 7 0.26
14 3 0.11
15 11 0.41
16 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (16 bp):
ATTATGTTTTTAATAT
Found at i:3596881 original size:32 final size:32
Alignment explanation
Indices: 3596845--3596906 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
3596835 AGCTTTTGGT
*
3596845 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTAAACAATGGA
3596877 TTTTTCATGTTGTCAAAGAGTTAAACAATG
1 TTTTTCATGTTGTCAAAGAGTTAAACAATG
3596907 AAAATAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTAAACAATGGA
Found at i:3614441 original size:17 final size:17
Alignment explanation
Indices: 3614419--3614452 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3614409 CAATTGGTTT
3614419 GCTCATTTCCGATTAAA
1 GCTCATTTCCGATTAAA
3614436 GCTCATTTCCGATTAAA
1 GCTCATTTCCGATTAAA
3614453 CTAAGAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (17 bp):
GCTCATTTCCGATTAAA
Found at i:3622340 original size:156 final size:158
Alignment explanation
Indices: 3622003--3622484 Score: 709
Period size: 156 Copynumber: 3.0 Consensus size: 158
3621993 TGACCCGAGA
* * *
3622003 TCGTACTGAAGTACAACAATTAATTCCATGACAATAACTAACACAATCGACCGCAACAACAGACT
1 TCGTACCGAAGTACAACAATTGATTCCGTGACAATAACTAACACAATCGACCGCAACAACAGACT
* * *
3622068 TCAATTAAACGAAAAATAAAGTTCCCGAAAAATGCAAAAAAAAAAAAATAGAGAGAACAAGAATG
66 TCAATTAAACGAAAAATAAAGTTCTCGAAGAAT---AAAAAAAAAAAACAGAGAGAACAAGAATG
3622133 GAGTTCTTTCTTTCTGGTAGTTTTCACGTTC
128 GAGTTCTTTCTTTCTGGTAGTTTTCACGTTC
* * *
3622164 TCGTACCGAAGTACAGCAATTGATTCTGTGACAATAACTAACACAATCGACCGCAACAACAGACA
1 TCGTACCGAAGTACAACAATTGATTCCGTGACAATAACTAACACAATCGACCGCAACAACAGACT
*
3622229 TCAATTAAACGAAAAATAAAGTTCTCGAAGAAT-ACAAAAAAAAA-AGAGAGAACAAGAATGGAG
66 TCAATTAAACGAAAAATAAAGTTCTCGAAGAATAAAAAAAAAAAACAGAGAGAACAAGAATGGAG
3622292 TTCTTTCTTTCTGGTAGTTTTCACGTTC
131 TTCTTTCTTTCTGGTAGTTTTCACGTTC
* *
3622320 TCGTATCGAAGTACAACAATTGATTCCGTGACAATAACTAACACAATCGACTGCAACAACAGACT
1 TCGTACCGAAGTACAACAATTGATTCCGTGACAATAACTAACACAATCGACCGCAACAACAGAC-
*
3622385 TTC-ATTAAATGAAAAATAAAGTTCTCGAAGAATGCAAAAAAAAAAAAAGAAAACAGAGAGAACA
65 TTCAATTAAACGAAAAATAAAGTTCTCGAAGAAT-------AAAAAAAA-AAAACAGAGAGAACA
*
3622449 AGAATGGAGTTCTTTCATTCTGGTAGTTTTCACGTT
122 AGAATGGAGTTCTTTCTTTCTGGTAGTTTTCACGTT
3622485 AAACCAGTTT
Statistics
Matches: 293, Mismatches: 17, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
156 136 0.46
157 12 0.04
161 90 0.31
164 6 0.02
165 4 0.01
166 45 0.15
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (158 bp):
TCGTACCGAAGTACAACAATTGATTCCGTGACAATAACTAACACAATCGACCGCAACAACAGACT
TCAATTAAACGAAAAATAAAGTTCTCGAAGAATAAAAAAAAAAAACAGAGAGAACAAGAATGGAG
TTCTTTCTTTCTGGTAGTTTTCACGTTC
Found at i:3627455 original size:18 final size:19
Alignment explanation
Indices: 3627432--3627467 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3627422 TAAAATATAA
*
3627432 TTTTATTTTTAT-ATTAAT
1 TTTTATATTTATGATTAAT
3627450 TTTTATATTTATGATTAA
1 TTTTATATTTATGATTAA
3627468 ATCAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTATATTTATGATTAAT
Done.