Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 10 of 313
Found at i:3238111 original size:24 final size:24
Alignment explanation
Indices: 3238073--3238203 Score: 167
Period size: 23 Copynumber: 5.4 Consensus size: 24
3238063 CTTGAGGCCT
*
3238073 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
*
3238098 AGCCCTTTTTATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
* *
3238122 AACCC-TTTAATAACTGGGGCGTA
1 AGCCCTTTTAATAACTGGGGCATA
*
3238145 ATCCCTTTTTATCATAACTGGGGCATA
1 AGCCC-TTTTA--ATAACTGGGGCATA
3238172 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
3238195 AGCCCTTTT
1 AGCCCTTTT
3238204 TCACTTCCTC
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
23 39 0.42
24 25 0.27
25 12 0.13
27 17 0.18
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:3238183 original size:50 final size:48
Alignment explanation
Indices: 3238080--3238204 Score: 189
Period size: 50 Copynumber: 2.6 Consensus size: 48
3238070 CCTAGCCTCT
*
3238080 TTTAATAACTGGGGCAAAAGCCC-TTTTTATAACTGGGGCATAAACCC
1 TTTAATAACTGGGGCATAAGCCCTTTTTTATAACTGGGGCATAAACCC
* * *
3238127 TTTAATAACTGGGGCGTAATCCCTTTTTATCATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTT-T-ATAACTGGGGCATAAACCC
3238177 TTTAATAACTGGGGCATAAGCCCTTTTT
1 TTTAATAACTGGGGCATAAGCCCTTTTT
3238205 CACTTCCTCC
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
47 20 0.29
48 4 0.06
49 1 0.01
50 44 0.64
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (48 bp):
TTTAATAACTGGGGCATAAGCCCTTTTTTATAACTGGGGCATAAACCC
Found at i:3238281 original size:20 final size:20
Alignment explanation
Indices: 3238253--3238319 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
3238243 TTATGAATAC
*
3238253 ATCAAGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
3238273 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
3238293 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
3238313 ACCATGT
1 ATCATGT
3238320 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:3238388 original size:25 final size:25
Alignment explanation
Indices: 3238356--3238403 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
3238346 ATACATAAAC
* *
3238356 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
3238381 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
3238404 CATGTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:3239190 original size:27 final size:27
Alignment explanation
Indices: 3239157--3239646 Score: 199
Period size: 27 Copynumber: 18.1 Consensus size: 27
3239147 TTGGTAAATC
*
3239157 TACAAACCAAGGGTATTTCAGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
** *
3239184 TGTAAA-CTAGTGGTATTTCTA-TAATTTT
1 TACAAATCAAG-GGTATTTC-AGTAA-TTT
* * *
3239212 TAGAAAGTCAAGGGTATTTCTGTAACTT
1 TACAAA-TCAAGGGTATTTCAGTAATTT
** * **
3239240 TGTAAATCAGGGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* *
3239267 TACAAATTAAGGGTATTTCGGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* * **
3239294 CACAAA-CCAGTGGTATTTTGGTAATTT
1 TACAAATCAAG-GGTATTTCAGTAATTT
* **
3239321 TACAAA-CTAGGGGTATTTTGGTAATTT
1 TACAAATC-AAGGGTATTTCAGTAATTT
** *
3239348 TACAAATTGAGGGTATTTCTGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* * *
3239375 TACAAACCAAGGGTATTTTAGCAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* * *
3239402 TACAGA-CTACGGTA-TTCTAGTAATTT
1 TACAAATCAAGGGTATTTC-AGTAATTT
** * *** *
3239428 TGTAAATCGAGGGTAAAACAGTAATTC
1 TACAAATCAAGGGTATTTCAGTAATTT
** ***
3239455 TGTAAATCAAGGGTAAAGCAGTAATTCT
1 TACAAATCAAGGGTATTTCAGTAATT-T
*** * * *
3239483 ATA-AAATCAAGGGTAAAACGGTACTTC
1 -TACAAATCAAGGGTATTTCAGTAATTT
** * *** * *
3239510 TGTAAATCGAGGGTAAAACGGTAATTA
1 TACAAATCAAGGGTATTTCAGTAATTT
** *** *
3239537 TGTAAATTGGGGGTACTTT-GGTAATTT
1 TACAAATCAAGGGTA-TTTCAGTAATTT
*
3239564 TACAAGTCGAA-GGTATTTCAGTAATTT
1 TACAAATC-AAGGGTATTTCAGTAATTT
* *
3239591 TACAAATCGAGGGTATTTCAGTATTTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* *
3239618 TACAAA-CTAAGCGTATTTCGGTAATTT
1 TACAAATC-AAGGGTATTTCAGTAATTT
3239645 TA
1 TA
3239647 GTAAACTAAA
Statistics
Matches: 361, Mismatches: 82, Indels: 40
0.75 0.17 0.08
Matches are distributed among these distances:
25 2 0.01
26 27 0.07
27 281 0.78
28 36 0.10
29 12 0.03
30 3 0.01
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (27 bp):
TACAAATCAAGGGTATTTCAGTAATTT
Found at i:3239309 original size:54 final size:54
Alignment explanation
Indices: 3239145--3239392 Score: 223
Period size: 54 Copynumber: 4.6 Consensus size: 54
3239135 TACAAGGGTG
* * * ** *
3239145 TTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACTAGTGGTA
1 TTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAATTTTACAAACCAGTGGTA
* * * * * ** * *
3239199 TTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTCTGTAACTTTGTAAATCAGGGGTA
1 TTT-TGGTAA-TTTTACAAA-CCAAGGGTATTTCGGTAATTTTACAAACCAGTGGTA
** *
3239255 TTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAGTGGTA
1 TTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAATTTTACAAACCAGTGGTA
* * * **
3239309 TTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATTGAG-GGTA
1 TTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAATTTTACAAA-CCAGTGGTA
3239363 TTTCT-GTAATTTTACAAACCAAGGGTATTT
1 TTT-TGGTAATTTTACAAACCAAGGGTATTT
3239393 TAGCAATTTT
Statistics
Matches: 160, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
54 105 0.66
55 19 0.12
56 36 0.22
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (54 bp):
TTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAATTTTACAAACCAGTGGTA
Found at i:3239343 original size:81 final size:81
Alignment explanation
Indices: 3239248--3239428 Score: 258
Period size: 81 Copynumber: 2.2 Consensus size: 81
3239238 TTTGTAAATC
3239248 AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACC-AGTGGTATTT
1 AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAAG-GGTATTT
* *
3239312 TGGTAATTTTACAAACT
65 TAGCAATTTTACAAACT
* * *
3239329 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCTGTAATTTTACAAACCAAGGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTT
*
3239394 AGCAATTTTACAGACT
66 AGCAATTTTACAAACT
* * *
3239410 A-CGGTATTCTAGTAATTTT
1 AGGGGTATTTTGGTAATTTT
3239429 GTAAATCGAG
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
80 15 0.17
81 73 0.81
82 2 0.02
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.40
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTT
AGCAATTTTACAAACT
Found at i:3239511 original size:55 final size:55
Alignment explanation
Indices: 3239431--3239535 Score: 156
Period size: 55 Copynumber: 1.9 Consensus size: 55
3239421 GTAATTTTGT
* *
3239431 AAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAGCAGTAATTCTATA
1 AAATCAAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATA
* * * *
3239486 AAATCAAGGGTAAAACGGTACTTCTGTAAATCGAGGGTAAAACGGTAATT
1 AAATCAAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATT
3239536 ATGTAAATTG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (55 bp):
AAATCAAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATA
Found at i:3239660 original size:27 final size:27
Alignment explanation
Indices: 3239557--3239661 Score: 90
Period size: 27 Copynumber: 3.9 Consensus size: 27
3239547 GGGTACTTTG
* *
3239557 GTAATTTTACAAGTCGAAG-GTATTTCA
1 GTAATTTTACAA-ACTAAGAGTATTTCA
* *
3239584 GTAATTTTACAAA-TCGAGGGTATTTCA
1 GTAATTTTACAAACT-AAGAGTATTTCA
* * *
3239611 GTATTTTTACAAACTAAGCGTATTTCG
1 GTAATTTTACAAACTAAGAGTATTTCA
*
3239638 GTAATTTTAGTAAACTAA-AGTATT
1 GTAATTTTA-CAAACTAAGAGTATT
3239662 CTAAACAGGG
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.03
27 54 0.84
28 8 0.12
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGAGTATTTCA
Found at i:3242678 original size:24 final size:24
Alignment explanation
Indices: 3242627--3242721 Score: 140
Period size: 24 Copynumber: 4.0 Consensus size: 24
3242617 GCTTTATCAT
*
3242627 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
3242652 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
3242676 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
3242699 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
3242722 TCACTTCCTC
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.35
24 30 0.46
25 12 0.18
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:3242702 original size:23 final size:23
Alignment explanation
Indices: 3242648--3242720 Score: 128
Period size: 23 Copynumber: 3.1 Consensus size: 23
3242638 CCTAGCCTCT
*
3242648 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
3242671 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
3242695 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
3242718 TTT
1 TTT
3242721 TTCACTTCCT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 26 0.54
24 22 0.46
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:3242799 original size:20 final size:20
Alignment explanation
Indices: 3242771--3242837 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
3242761 TTATGATTAC
*
3242771 ATCACGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
3242791 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
3242811 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
3242831 ACCATGT
1 ATCATGT
3242838 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:3242906 original size:25 final size:25
Alignment explanation
Indices: 3242874--3242921 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3242864 ATACATAAAC
* * *
3242874 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
3242899 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
3242922 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:3244142 original size:27 final size:27
Alignment explanation
Indices: 3244080--3244157 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
3244070 GGGCATATTC
3244080 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
3244107 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
* *
3244134 GTCTTTTTACC-TAATAGGGGTATT
1 GTCATTTTACCAT-ACAGGGGTATT
3244158 TTAGTCATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.05
27 40 0.93
28 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:3244228 original size:27 final size:27
Alignment explanation
Indices: 3244175--3244507 Score: 226
Period size: 27 Copynumber: 12.3 Consensus size: 27
3244165 TTTCATCCTA
* * * *
3244175 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
** *
3244202 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* * * *
3244229 CAATGGTATTTCT-ATAATTTTTAGAAAGT
1 CAAGGGTATTT-TGGTAA-TTTTATAAA-C
* * *
3244258 CAAGGGTATTTCT-GTAACTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTATAAAC
* * *
3244285 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAC
** * * *
3244312 TGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
*
3244339 C-AGTGGTATTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTTGGTAATTTTATAAAC
* * *
3244366 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* * * * *
3244393 CAGGGGTATTTTAGCAATTTTACAGAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
3244420 C-AGGGTATTTTGGTAATTTTACT-GAT
1 CAAGGGTATTTTGGTAATTTTA-TAAAC
* *
3244446 CGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* * *
3244473 CAAGGGTATTTTAGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAC
*
3244500 CGAGGGTA
1 CAAGGGTA
3244508 AAACAGTAAT
Statistics
Matches: 248, Mismatches: 49, Indels: 18
0.79 0.16 0.06
Matches are distributed among these distances:
26 24 0.10
27 195 0.79
28 14 0.06
29 15 0.06
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTATAAAC
Found at i:3244473 original size:80 final size:81
Alignment explanation
Indices: 3244286--3244493 Score: 258
Period size: 80 Copynumber: 2.6 Consensus size: 81
3244276 TTTGTAAATC
*** ** * *
3244286 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGCAATTTTACAAACCAGTGGTATTTT
*
3244351 GGTAATTTTACAAACT
66 GGTAATTTTACAAACG
* *
3244367 AGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGCAATTTTACAGACCAG-GGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGCAATTTTACAAACCAGTGGTATTTT
* *
3244431 GGTAATTTTACTGATCG
66 GGTAATTTTAC-AAACG
** *
3244448 A-GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTT
1 AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGCAATTTT
3244494 GTAAATCGAG
Statistics
Matches: 110, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
80 60 0.55
81 50 0.45
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.40
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGCAATTTTACAAACCAGTGGTATTTT
GGTAATTTTACAAACG
Found at i:3244515 original size:27 final size:27
Alignment explanation
Indices: 3244485--3244588 Score: 154
Period size: 27 Copynumber: 3.9 Consensus size: 27
3244475 AGGGTATTTT
* *
3244485 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
*
3244512 AGTAATTCTATAAATCAAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
3244539 AGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
* * *
3244566 GGTAATTCTGTAAATCGGGGGTA
1 AGTAATTCTATAAATCGAGGGTA
3244589 CTTTGGTAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (27 bp):
AGTAATTCTATAAATCGAGGGTAAAAC
Found at i:3244534 original size:134 final size:134
Alignment explanation
Indices: 3244288--3244534 Score: 282
Period size: 134 Copynumber: 1.8 Consensus size: 134
3244278 TGTAAATCAG
* *
3244288 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGG
1 GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTAG
* ***** * *
3244353 TAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGCAATTTTACAG
66 TAATTTTACAAACGAGGGGTAAAACAGTAATTCTACAAACCAAGGGTATTTTAGCAATTTTACAG
3244418 ACCA
131 ACCA
** * ***
3244422 GGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAACCAAG-GGTATTTTA
1 GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAACC-AGTGGTATTTTA
** * *
3244486 GTAATTTTGTAAATCGA-GGGTAAAACAGTAATTCTATAAATCAAGGGTA
65 GTAATTTTACAAA-CGAGGGGTAAAACAGTAATTCTACAAACCAAGGGTA
3244535 AAACAGTAAT
Statistics
Matches: 91, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
134 87 0.96
135 4 0.04
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (134 bp):
GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTAG
TAATTTTACAAACGAGGGGTAAAACAGTAATTCTACAAACCAAGGGTATTTTAGCAATTTTACAG
ACCA
Found at i:3244598 original size:54 final size:54
Alignment explanation
Indices: 3244458--3244599 Score: 158
Period size: 54 Copynumber: 2.6 Consensus size: 54
3244448 AGGGTATTTT
* * * * *
3244458 GGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAAC
1 GGTAATTCTGTAAATCAAGGGTAATTTAGTAATTCTATAAATCGAGGGTAAAAC
* * ***
3244512 AGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAAC
1 GGTAATTCTGTAAATCAAGGGTAATTTAGTAATTCTATAAATCGAGGGTAAAAC
** * *
3244566 GGTAATTCTGTAAATCGGGGGTACTTTGGTAATT
1 GGTAATTCTGTAAATCAAGGGTAATTTAGTAATT
3244600 TTACAAGTCG
Statistics
Matches: 69, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (54 bp):
GGTAATTCTGTAAATCAAGGGTAATTTAGTAATTCTATAAATCGAGGGTAAAAC
Found at i:3244615 original size:27 final size:27
Alignment explanation
Indices: 3244594--3244683 Score: 119
Period size: 27 Copynumber: 3.3 Consensus size: 27
3244584 GGGTACTTTG
*
3244594 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
*
3244621 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
* * *
3244648 GTATTTTTACAAA-CTAAGCGTATTTCG
1 GTAATTTTACAAATCGAAG-GTATTTCA
3244675 GTAATTTTA
1 GTAATTTTA
3244684 GTAAACTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 3 0.05
27 52 0.95
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAATCGAAGGTATTTCA
Found at i:3244635 original size:54 final size:54
Alignment explanation
Indices: 3244577--3244683 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
3244567 GTAATTCTGT
* * *
3244577 AAATCGGGGGTACTTT-GGTAATTTTACAAGTCGAAG-GTATTTCAGTAATTTTAC
1 AAATCGAGGGTA-TTTCAGTAATTTTACAA-ACGAAGCGTATTTCAGTAATTTTAC
* * *
3244631 AAATCGAGGGTATTTCAGTATTTTTACAAACTAAGCGTATTTCGGTAATTTTA
1 AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGCGTATTTCAGTAATTTTA
3244684 GTAAACTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 7 0.16
54 38 0.84
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (54 bp):
AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGCGTATTTCAGTAATTTTAC
Found at i:3244697 original size:27 final size:27
Alignment explanation
Indices: 3244594--3244698 Score: 90
Period size: 27 Copynumber: 3.9 Consensus size: 27
3244584 GGGTACTTTG
* *
3244594 GTAATTTTACAAGTCGAAG-GTATTTCA
1 GTAATTTTACAA-ACTAAGAGTATTTCA
* *
3244621 GTAATTTTACAAA-TCGAGGGTATTTCA
1 GTAATTTTACAAACT-AAGAGTATTTCA
* * *
3244648 GTATTTTTACAAACTAAGCGTATTTCG
1 GTAATTTTACAAACTAAGAGTATTTCA
*
3244675 GTAATTTTAGTAAACTAA-AGTATT
1 GTAATTTTA-CAAACTAAGAGTATT
3244699 CTAAACAGGG
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.03
27 54 0.84
28 8 0.12
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGAGTATTTCA
Found at i:3249114 original size:16 final size:16
Alignment explanation
Indices: 3249093--3249125 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3249083 GTAAGCTAAC
3249093 TTAGCTTAGTAAGCCT
1 TTAGCTTAGTAAGCCT
*
3249109 TTAGCTTAGTATGCCT
1 TTAGCTTAGTAAGCCT
3249125 T
1 T
3249126 AAGCAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (16 bp):
TTAGCTTAGTAAGCCT
Found at i:3257116 original size:13 final size:14
Alignment explanation
Indices: 3257087--3257117 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3257077 TTTGGTTTTC
3257087 TTTATTTTACTTAA
1 TTTATTTTACTTAA
3257101 TTTATTTTAC-TAA
1 TTTATTTTACTTAA
3257114 TTTA
1 TTTA
3257118 CAATTTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATTTTACTTAA
Found at i:3259333 original size:19 final size:20
Alignment explanation
Indices: 3259309--3259354 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
3259299 GAAATAAATT
3259309 TCAATT-AATCAACCTAGAG
1 TCAATTCAATCAACCTAGAG
**
3259328 TCAATTGCTTTCAACCTAGAG
1 TCAATT-CAATCAACCTAGAG
3259349 TCAATT
1 TCAATT
3259355 TCTTTTACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
21 17 0.74
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (20 bp):
TCAATTCAATCAACCTAGAG
Found at i:3259343 original size:21 final size:21
Alignment explanation
Indices: 3259317--3259359 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3259307 TTTCAATTAA
3259317 TCAACCTAGAGTCAATTGCTT
1 TCAACCTAGAGTCAATTGCTT
*
3259338 TCAACCTAGAGTCAATTTCTT
1 TCAACCTAGAGTCAATTGCTT
3259359 T
1 T
3259360 TACTTTCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (21 bp):
TCAACCTAGAGTCAATTGCTT
Found at i:3259781 original size:20 final size:20
Alignment explanation
Indices: 3259744--3259788 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
3259734 TTGATTTAGC
*
3259744 TTTTTTATTTTGATTTTAAT
1 TTTTTTATTTTGAATTTAAT
3259764 ATTTTTTATTTT-AATTTAAT
1 -TTTTTTATTTTGAATTTAAT
3259784 TTTTT
1 TTTTT
3259789 ACATTCTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 7 0.30
21 11 0.48
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTTTATTTTGAATTTAAT
Found at i:3276415 original size:13 final size:14
Alignment explanation
Indices: 3276394--3276426 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3276384 TTTATTAATG
3276394 AAATATATTAAA-AT
1 AAAT-TATTAAATAT
3276408 AAATTATTAAATAT
1 AAATTATTAAATAT
3276422 AAATT
1 AAATT
3276427 TATATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATTATTAAATAT
Found at i:3293053 original size:27 final size:27
Alignment explanation
Indices: 3293005--3293220 Score: 202
Period size: 27 Copynumber: 8.0 Consensus size: 27
3292995 AAACATACAT
* * **
3293005 CACATAGGGGCAAAACATTCATCCTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
*
3293032 CACATAAGGGCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
** **
3293059 CTTATAAGGGCAAAATTGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
3293086 CACATAAGGACAAAACCGTCATTTTAA
1 CACATAAGGGCAAAACAGTCATTTTAC
*
3293113 CACATAAGGGCAAAACAGTCATTTTGC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
3293140 CACATAAGGACAAAA-TGTCATTTTAT
1 CACATAAGGGCAAAACAGTCATTTTAC
** ** * *
3293166 TGCATAAGGAAAAAATC-TTCATTTTAA
1 CACATAAGGGCAAAA-CAGTCATTTTAC
*
3293193 CACTTAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
3293220 C
1 C
3293221 TTATAGGGGT
Statistics
Matches: 152, Mismatches: 34, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
26 21 0.14
27 131 0.86
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTTTAC
Found at i:3293202 original size:80 final size:81
Alignment explanation
Indices: 3293032--3293220 Score: 263
Period size: 80 Copynumber: 2.3 Consensus size: 81
3293022 TTCATCCTAC
* ** * *
3293032 CACATAAGGGCAAAATAGTCATTTTACCTTATAAGGGCAAAATTGTCATTTTACCACATAAGGAC
1 CACATAAGGGCAAAACAGTCATTTTACCACATAAGGACAAAATTGTCATTTTACCACATAAGGAA
3293097 AAAACCGTCATTTTAA
66 AAAACCGTCATTTTAA
* ***
3293113 CACATAAGGGCAAAACAGTCATTTTGCCACATAAGGACAAAA-TGTCATTTTATTGCATAAGGAA
1 CACATAAGGGCAAAACAGTCATTTTACCACATAAGGACAAAATTGTCATTTTACCACATAAGGAA
* *
3293177 AAAATCTTCATTTTAA
66 AAAACCGTCATTTTAA
*
3293193 CACTTAAGGGCAAAACAGTCATTTTACC
1 CACATAAGGGCAAAACAGTCATTTTACC
3293221 TTATAGGGGT
Statistics
Matches: 95, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
80 58 0.61
81 37 0.39
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (81 bp):
CACATAAGGGCAAAACAGTCATTTTACCACATAAGGACAAAATTGTCATTTTACCACATAAGGAA
AAAACCGTCATTTTAA
Found at i:3293239 original size:27 final size:26
Alignment explanation
Indices: 3293208--3293515 Score: 334
Period size: 27 Copynumber: 11.5 Consensus size: 26
3293198 AAGGGCAAAA
*
3293208 CAGTCATTTTACCTTATAGGGGTATTAT
1 CAGTCATTTTACCCTAT-GGGGTATT-T
3293236 -AGTCATTTTACCCTATGGAGGTATTT
1 CAGTCATTTTACCCTATGG-GGTATTT
*
3293262 -TGATCATTTTACCCTATGCGGGTATTT
1 CAG-TCATTTTACCCTATG-GGGTATTT
** *
3293289 TGGTCATTTTACCCTATCGGGTATTT
1 CAGTCATTTTACCCTATGGGGTATTT
* *
3293315 CGGTCATTTTACCCTACGAGGGTATTT
1 CAGTCATTTTACCCTATG-GGGTATTT
*
3293342 CAGTCATTTTACCCTACGGGGGTATTT
1 CAGTCATTTTACCCTA-TGGGGTATTT
** *
3293369 TGGTAATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTAT-GGGGTATTT
*
3293396 CAATCATTTTA-CCTATGGGGGTATTT
1 CAGTCATTTTACCCTAT-GGGGTATTT
3293422 CAGTCATTTTACCCTATGAGGGTATTT
1 CAGTCATTTTACCCTATG-GGGTATTT
* *
3293449 TAGTTATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTAT-GGGGTATTT
*
3293476 CGGTCATTTTACCCTATGAGGGTATTT
1 CAGTCATTTTACCCTATG-GGGTATTT
* *
3293503 CGGTCACTTTACC
1 CAGTCATTTTACC
3293516 TTCCGGCCCA
Statistics
Matches: 245, Mismatches: 24, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
26 54 0.22
27 187 0.76
28 4 0.02
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (26 bp):
CAGTCATTTTACCCTATGGGGTATTT
Found at i:3293328 original size:80 final size:82
Alignment explanation
Indices: 3293210--3293515 Score: 394
Period size: 80 Copynumber: 3.8 Consensus size: 82
3293200 GGGCAAAACA
* * *
3293210 GTCATTTTACCTTATAGGGGTATTAT-AGTCATTTTACCCTATGGA-GGTATTT-TGATCATTTT
1 GTCATTTTACCCTATGGGGGTATT-TCAGTCATTTTACCCTATGGAGGGTATTTCAG-TCATTTT
*
3293272 ACCCTATGCGGGTATTTTG
64 ACCCTATGAGGGTATTTTG
* * *
3293291 GTCATTTTACCCTAT-CGGGTATTTCGGTCATTTTACCCTA-CGAGGGTATTTCAGTCATTTTAC
1 GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATGGAGGGTATTTCAGTCATTTTAC
* *
3293354 CCTACGGGGGTATTTTG
66 CCTATGAGGGTATTTTG
* *
3293371 GTAATTTTACCCTATGGGGGTATTTCAATCATTTTA-CCTATGG-GGGTATTTCAGTCATTTTAC
1 GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATGGAGGGTATTTCAGTCATTTTAC
*
3293434 CCTATGAGGGTATTTTA
66 CCTATGAGGGTATTTTG
* * * *
3293451 GTTATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT-GAGGGTATTTCGGTCACTTTAC
1 GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATGGAGGGTATTTCAGTCATTTTAC
3293515 C
66 C
3293516 TTCCGGCCCA
Statistics
Matches: 198, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
79 3 0.02
80 138 0.70
81 57 0.29
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.42
Consensus pattern (82 bp):
GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATGGAGGGTATTTCAGTCATTTTAC
CCTATGAGGGTATTTTG
Found at i:3293516 original size:107 final size:106
Alignment explanation
Indices: 3293208--3293516 Score: 422
Period size: 107 Copynumber: 2.9 Consensus size: 106
3293198 AAGGGCAAAA
* * * *
3293208 CAGTCATTTTACCTTAT-AGGGGTATTATAGTCATTTTACCCTATGGAGGTATTTTGATCATTTT
1 CAGTCATTTTACCCTATGA-GGGTATTTTAGTCATTTTACCCTATGGGGGTATTTTGGTCATTTT
* *
3293272 ACCCTATGCGGGTATTTTGGTCATTTTACCCTATCGGGTATTT
65 ACCCTATGAGGGTATTTCGGTCATTTTA-CCTATCGGGTATTT
* * * * *
3293315 CGGTCATTTTACCCTACGAGGGTATTTCAGTCATTTTACCCTACGGGGGTATTTTGGTAATTTTA
1 CAGTCATTTTACCCTATGAGGGTATTTTAGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTA
* ** *
3293380 CCCTATGGGGGTATTTCAATCATTTTACCTATGGGGGTATTT
66 CCCTATGAGGGTATTTCGGTCATTTTACCTAT-CGGGTATTT
* *
3293422 CAGTCATTTTACCCTATGAGGGTATTTTAGTTATTTTACCCTATGGGGGTATTTCGGTCATTTTA
1 CAGTCATTTTACCCTATGAGGGTATTTTAGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTA
*
3293487 CCCTATGAGGGTATTTCGGTCACTTTACCT
66 CCCTATGAGGGTATTTCGGTCATTTTACCT
3293517 TCCGGCCCAA
Statistics
Matches: 175, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
106 5 0.03
107 169 0.97
108 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (106 bp):
CAGTCATTTTACCCTATGAGGGTATTTTAGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTA
CCCTATGAGGGTATTTCGGTCATTTTACCTATCGGGTATTT
Found at i:3301095 original size:12 final size:12
Alignment explanation
Indices: 3301078--3301105 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3301068 CTTACGATAT
3301078 CCATAATACCAA
1 CCATAATACCAA
3301090 CCATAATACCAA
1 CCATAATACCAA
3301102 CCAT
1 CCAT
3301106 GTACTCATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (12 bp):
CCATAATACCAA
Found at i:3315580 original size:25 final size:25
Alignment explanation
Indices: 3315546--3315598 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
3315536 CGCTATGGAA
3315546 GTGGGAAAGAGGAACAATAGACTTT
1 GTGGGAAAGAGGAACAATAGACTTT
*
3315571 GTGGGAAAGAGTAACAATAGACTTT
1 GTGGGAAAGAGGAACAATAGACTTT
3315596 GTG
1 GTG
3315599 AGTGGGTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.32, T:0.23
Consensus pattern (25 bp):
GTGGGAAAGAGGAACAATAGACTTT
Found at i:3322569 original size:16 final size:16
Alignment explanation
Indices: 3322550--3322595 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
3322540 ACAAATCCCG
*
3322550 AAAAGTCGAAATGCCA
1 AAAAGCCGAAATGCCA
*
3322566 AAAAGCCGAAATGTCA
1 AAAAGCCGAAATGCCA
*
3322582 AAAAGCCAAAATGC
1 AAAAGCCGAAATGC
3322596 TGAAAAGATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.52, C:0.20, G:0.17, T:0.11
Consensus pattern (16 bp):
AAAAGCCGAAATGCCA
Found at i:3322574 original size:24 final size:24
Alignment explanation
Indices: 3322547--3322602 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
3322537 TCGACAAATC
* *
3322547 CCGAAAAGTCGAAATGCCAAAAAG
1 CCGAAAAGTCAAAAAGCCAAAAAG
* *
3322571 CCGAAATGTCAAAAAGCCAAAATG
1 CCGAAAAGTCAAAAAGCCAAAAAG
*
3322595 CTGAAAAG
1 CCGAAAAG
3322603 ATGAAAGTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.20, G:0.20, T:0.11
Consensus pattern (24 bp):
CCGAAAAGTCAAAAAGCCAAAAAG
Found at i:3322855 original size:28 final size:28
Alignment explanation
Indices: 3322823--3322934 Score: 118
Period size: 28 Copynumber: 4.0 Consensus size: 28
3322813 CATGACTGTA
* *
3322823 AATGTGATTTGGGTCTAGT-GGCCATATG
1 AATGTGA-TTGGGCCTAATGGGCCATATG
* * *
3322851 AATGTGATTTGGGCCTAATGAGCCAGATA
1 AATGTGA-TTGGGCCTAATGGGCCATATG
*
3322880 AATGTGAATGGGCCTAATGGGCCATATG
1 AATGTGATTGGGCCTAATGGGCCATATG
* * *
3322908 AAAGAGATTGGGCCTAGTGGGCCATAT
1 AATGTGATTGGGCCTAATGGGCCATAT
3322935 ACATAGGTAT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
28 57 0.81
29 13 0.19
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (28 bp):
AATGTGATTGGGCCTAATGGGCCATATG
Found at i:3329911 original size:27 final size:27
Alignment explanation
Indices: 3329874--3329938 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
3329864 TCGGTCATTC
3329874 ACCCT-CAAGGGCAAAAT-AGTCATTTT
1 ACCCTACAAGGG-AAAATCAGTCATTTT
* **
3329900 ACCCTACAAGGGTATGTCAGTCATTTT
1 ACCCTACAAGGGAAAATCAGTCATTTT
*
3329927 ACACTACAAGGG
1 ACCCTACAAGGG
3329939 TATTTCGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 7 0.21
27 26 0.79
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (27 bp):
ACCCTACAAGGGAAAATCAGTCATTTT
Found at i:3329939 original size:27 final size:27
Alignment explanation
Indices: 3329891--3329956 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
3329881 AGGGCAAAAT
*
3329891 AGTCATTTTACCCTACAAGGGTATGTC
1 AGTCATTTTACACTACAAGGGTATGTC
*
3329918 AGTCATTTTACACTACAAGGGTATTTC
1 AGTCATTTTACACTACAAGGGTATGTC
* *
3329945 GGTAATTTTACA
1 AGTCATTTTACA
3329957 AATTAAGGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (27 bp):
AGTCATTTTACACTACAAGGGTATGTC
Found at i:3329964 original size:27 final size:27
Alignment explanation
Indices: 3329935--3330352 Score: 432
Period size: 27 Copynumber: 15.7 Consensus size: 27
3329925 TTACACTACA
**
3329935 AGGGTATTTCGGTAATTTTACAAATTA
1 AGGGTATTTCGGTAATTTTACAAATCG
* * * *
3329962 AGGATATTTTGATAATTTTACAAATTG
1 AGGGTATTTCGGTAATTTTACAAATCG
* *
3329989 AGGGTGTTTCGATAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * *
3330016 AGGGTGTTTCGGTAATTTCAAAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
*
3330043 AGGGTA-TTCGGTAATTTTACAAATCA
1 AGGGTATTTCGGTAATTTTACAAATCG
* * *
3330069 AGGGTATTTCAGTAATTTCAC-AATTG
1 AGGGTATTTCGGTAATTTTACAAATCG
*
3330095 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* *
3330122 GGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * * *
3330149 AGGGTGTTTCGATAATTTCACAAATTG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * *
3330176 GGGGTATTTCAGTAATTTTACAAATTG
1 AGGGTATTTCGGTAATTTTACAAATCG
* *
3330203 A-GGTATTTCAGTAATTTCAC-AATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* **
3330228 AGGGTATTTTGGTAATTTTACAAATTA
1 AGGGTATTTCGGTAATTTTACAAATCG
** * *
3330255 AGGGTATTTTAGTAATTTCA-AAATTG
1 AGGGTATTTCGGTAATTTTACAAATCG
* *
3330281 AGGCTATTTTGGTAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * *
3330308 AAGGCATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
**
3330335 AGGGTATTTTAGTAATTT
1 AGGGTATTTCGGTAATTT
3330353 CTCTTTATTA
Statistics
Matches: 328, Mismatches: 58, Indels: 10
0.83 0.15 0.03
Matches are distributed among these distances:
25 5 0.02
26 100 0.30
27 223 0.68
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTACAAATCG
Found at i:3330067 original size:53 final size:54
Alignment explanation
Indices: 3329935--3330352 Score: 445
Period size: 53 Copynumber: 7.8 Consensus size: 54
3329925 TTACACTACA
* ** * * *
3329935 AGGGTATTTCGGTAATTTTACAAATTAAGGATATTTTGATAATTTTACAAATTG
1 AGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTG
* * * * *
3329989 AGGGTGTTTCGATAATTTTACAAATCGAGGGTGTTTCGGTAATTTCAAAAATCG
1 AGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTG
* * * *
3330043 AGGGTA-TTCGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTCAC-AATTG
1 AGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTG
* * *
3330095 AGGGTATTTCGATAATTTTACAAATCGGGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTG
* * * * *
3330149 AGGGTGTTTCGATAATTTCACAAATTGGGGGTATTTCAGTAATTTTACAAATTG
1 AGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTG
* * *
3330203 A-GGTATTTC-AGTAATTTCAC-AATCGAGGGTATTTTGGTAATTTTACAAATTA
1 AGGGTATTTCGA-TAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTG
* * * * * *
3330255 AGGGTATTT-TAGTAATTTCA-AAATTGAGGCTATTTTGGTAATTTTACAAATCG
1 AGGGTATTTCGA-TAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTG
* * **
3330308 AAGGCATTTCGATAATTTTACAAATCGAGGGTATTTTAGTAATTT
1 AGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTT
3330353 CTCTTTATTA
Statistics
Matches: 308, Mismatches: 48, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
52 39 0.13
53 146 0.47
54 123 0.40
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (54 bp):
AGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTG
Found at i:3330165 original size:133 final size:134
Alignment explanation
Indices: 3329933--3330353 Score: 526
Period size: 133 Copynumber: 3.2 Consensus size: 134
3329923 TTTTACACTA
* * * * *
3329933 CAAGGGTATTTCGGTAATTTTACAAATTAAGGATATTTTGATAATTTTACAAATTGAGGGTGTTT
1 CAAGGGTATTTCAGTAATTTCAC-AATTGAGGGTATTTTGATAATTTTACAAATTGAGGGTATTT
*
3329998 CGATAATTTTACAAATCGAGGGTGTTTCGGTAATTTCAAAAATCGAGGGTA-TTCGGTAATTTTA
65 CGATAATTTTACAAATCGAGGGTGTTTCGGTAATTTCACAAATCGAGGGTATTTCGGTAATTTTA
3330062 CAAAT
130 CAAAT
* * *
3330067 CAAGGGTATTTCAGTAATTTCACAATTGAGGGTATTTCGATAATTTTACAAATCGGGGGTATTTC
1 CAAGGGTATTTCAGTAATTTCACAATTGAGGGTATTTTGATAATTTTACAAATTGAGGGTATTTC
* * * *
3330132 GATAATTTTACAAATCGAGGGTGTTTCGATAATTTCACAAATTGGGGGTATTTCAGTAATTTTAC
66 GATAATTTTACAAATCGAGGGTGTTTCGGTAATTTCACAAATCGAGGGTATTTCGGTAATTTTAC
3330197 AAAT
131 AAAT
** * * *
3330201 TGA-GGTATTTCAGTAATTTCACAATCGAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTT-
1 CAAGGGTATTTCAGTAATTTCACAATTGAGGGTATTTTGATAATTTTACAAATTGAGGGTATTTC
* * * * * * * * * *
3330264 TAGTAATTTCA-AAATTGAGGCTATTTTGGTAATTTTACAAATCGAAGGCATTTCGATAATTTTA
66 GA-TAATTTTACAAATCGAGGGTGTTTCGGTAATTTCACAAATCGAGGGTATTTCGGTAATTTTA
3330328 CAAAT
130 CAAAT
* *
3330333 CGAGGGTATTTTAGTAATTTC
1 CAAGGGTATTTCAGTAATTTC
3330354 TCTTTATTAT
Statistics
Matches: 247, Mismatches: 37, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
132 49 0.20
133 159 0.64
134 39 0.16
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (134 bp):
CAAGGGTATTTCAGTAATTTCACAATTGAGGGTATTTTGATAATTTTACAAATTGAGGGTATTTC
GATAATTTTACAAATCGAGGGTGTTTCGGTAATTTCACAAATCGAGGGTATTTCGGTAATTTTAC
AAAT
Found at i:3330711 original size:28 final size:28
Alignment explanation
Indices: 3330674--3330731 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
3330664 CTTTAGGCCA
*
3330674 AATCTCATTCACATGGCCCATCAAACCC
1 AATCACATTCACATGGCCCATCAAACCC
* * *
3330702 AATCACATTCATATGGCTCATCAAGCCC
1 AATCACATTCACATGGCCCATCAAACCC
3330730 AA
1 AA
3330732 CTATTTCCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.09, T:0.22
Consensus pattern (28 bp):
AATCACATTCACATGGCCCATCAAACCC
Found at i:3333123 original size:46 final size:46
Alignment explanation
Indices: 3333073--3333196 Score: 194
Period size: 46 Copynumber: 2.7 Consensus size: 46
3333063 GTTGAGCATC
* * *
3333073 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATCCGAACGCT
* *
3333119 CGAACTCGTTGACTTGAGTCCGAGTTCACTTATGGATCCGAACGCT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATCCGAACGCT
*
3333165 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
3333197 GGGGCGGCTT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.30
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATCCGAACGCT
Found at i:3340268 original size:93 final size:93
Alignment explanation
Indices: 3340109--3340279 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
3340099 GGATGGTTGA
* * * **
3340109 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTAGTTGAGCTGAGTCCAAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGT
3340174 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
3340202 GCATCCGTACTAGTTGAGCTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTAGTTGAGCTGAGTCCAAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGT
3340267 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
3340280 ACTTAGGGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTAGTTGAGCTGAGTCCAAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:3340273 original size:46 final size:45
Alignment explanation
Indices: 3340113--3340286 Score: 165
Period size: 46 Copynumber: 3.8 Consensus size: 45
3340103 GGTTGAGCAT
* * *
3340113 CCGAACTCGTTGAGTTGAGTCCAAGTTCACTTACGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAACGC
* * * *
3340159 TCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAAC---GC
* * *
3340204 ATCCGTACTAGTTGAGCTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAACGC
*
3340252 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGG
3340287 GGCGGGTTAC
Statistics
Matches: 101, Mismatches: 18, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 5 0.05
46 55 0.54
47 24 0.24
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAACGC
Found at i:3348753 original size:30 final size:29
Alignment explanation
Indices: 3348692--3348753 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
3348682 ATAAAATAGG
* **
3348692 CTAAATTGTGAAATTTATAAATTGATGGA
1 CTAAAATGTGAAATAAATAAATTGATGGA
3348721 CTAAAATGTGAAATAAATGAAATGTG-TGGA
1 CTAAAATGTGAAATAAAT-AAAT-TGATGGA
3348751 CTA
1 CTA
3348754 GCATGAATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 15 0.54
30 11 0.39
31 2 0.07
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (29 bp):
CTAAAATGTGAAATAAATAAATTGATGGA
Found at i:3352159 original size:13 final size:13
Alignment explanation
Indices: 3352141--3352166 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3352131 GAGTAATCGA
3352141 ACACGGGCGTGTC
1 ACACGGGCGTGTC
3352154 ACACGGGCGTGTC
1 ACACGGGCGTGTC
3352167 CCTACCGAGC
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:0.15, C:0.31, G:0.38, T:0.15
Consensus pattern (13 bp):
ACACGGGCGTGTC
Found at i:3359308 original size:29 final size:28
Alignment explanation
Indices: 3359266--3359356 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 28
3359256 ACATGGCTTG
* *
3359266 GAAT-TGATTCGGGCTGGATGAGCCATAT
1 GAATGTGATTTGGGCT-AATGAGCCATAT
*
3359294 GAATGTGATTTGGGCCTAATGGGCCATAT
1 GAATGTGATTTGGG-CTAATGAGCCATAT
* * *
3359323 GAATGAGA-TTGGGCCTAGTGGGCCATAT
1 GAATGTGATTTGGG-CTAATGAGCCATAT
*
3359351 GCATGT
1 GAATGT
3359357 ATGTAGACTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 27 0.50
29 25 0.46
30 2 0.04
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (28 bp):
GAATGTGATTTGGGCTAATGAGCCATAT
Found at i:3359344 original size:28 final size:29
Alignment explanation
Indices: 3359287--3359351 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 29
3359277 GGCTGGATGA
*
3359287 GCCATATGAATGTGATTTGGGCCTAATGG
1 GCCATATGAATGAGATTTGGGCCTAATGG
*
3359316 GCCATATGAATGAGA-TTGGGCCTAGTGG
1 GCCATATGAATGAGATTTGGGCCTAATGG
3359344 GCCATATG
1 GCCATATG
3359352 CATGTATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 20 0.59
29 14 0.41
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.28
Consensus pattern (29 bp):
GCCATATGAATGAGATTTGGGCCTAATGG
Found at i:3369750 original size:55 final size:55
Alignment explanation
Indices: 3369648--3369773 Score: 137
Period size: 55 Copynumber: 2.3 Consensus size: 55
3369638 AAGCCTTGCA
* * * * *
3369648 AAAC-AACACAGGCGTGCCACACGCCAGTGTGCAAGACCCATTATTGAAACTGAG
1 AAACTAACACGGGCGTGCCACACGCCAGTGTCCAACACCCATGATTGAAACTGAC
* * * * * *
3369702 AAACTAGCACGGGCGTGCGACACGCCCGTGTCCAACACCCATGGTTGAACCTGTC
1 AAACTAACACGGGCGTGCCACACGCCAGTGTCCAACACCCATGATTGAAACTGAC
*
3369757 AAATTAACACGGGCGTG
1 AAACTAACACGGGCGTG
3369774 AGGCTTACAC
Statistics
Matches: 58, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
54 4 0.07
55 54 0.93
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.16
Consensus pattern (55 bp):
AAACTAACACGGGCGTGCCACACGCCAGTGTCCAACACCCATGATTGAAACTGAC
Found at i:3372496 original size:26 final size:26
Alignment explanation
Indices: 3372433--3372537 Score: 142
Period size: 26 Copynumber: 4.1 Consensus size: 26
3372423 GCCTAGCCTC
*
3372433 TTTCAAT-AACTGGGGCAAAAGCCC-
1 TTTCAATAAACTGGGGCATAAGCCCT
** **
3372457 TTTCGGTACTCTGGGGCATAAGCCCT
1 TTTCAATAAACTGGGGCATAAGCCCT
3372483 TTTCAATAAACTGGGGCATAAGCCCT
1 TTTCAATAAACTGGGGCATAAGCCCT
*
3372509 TTTCAATAAACTCGGGCATAAGCCCT
1 TTTCAATAAACTGGGGCATAAGCCCT
3372535 TTT
1 TTT
3372538 GCACTTCCTC
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
24 5 0.07
25 14 0.20
26 50 0.72
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (26 bp):
TTTCAATAAACTGGGGCATAAGCCCT
Found at i:3372612 original size:20 final size:20
Alignment explanation
Indices: 3372587--3372633 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3372577 TTATGAATAC
3372587 ATCATGTGCATATCATA-CA
1 ATCATGTGCATATCATATCA
3372606 TATCATGTGCATATCATATCA
1 -ATCATGTGCATATCATATCA
3372627 ATCATGT
1 ATCATGT
3372634 ATATAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATATCA
Found at i:3372697 original size:25 final size:25
Alignment explanation
Indices: 3372669--3372716 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3372659 ATAAGTAAAC
* * *
3372669 CCTAGGGGTATAACGGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
3372694 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGGGGCAAAACAGTCATTTT
3372717 CATAATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:3380061 original size:18 final size:18
Alignment explanation
Indices: 3380035--3380069 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3380025 TCGTAACGTT
*
3380035 GTGTTGTTTGGAAAACAA
1 GTGTCGTTTGGAAAACAA
*
3380053 GTGTCGTTTTGAAAACA
1 GTGTCGTTTGGAAAACA
3380070 CGTCCTAAGT
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:0.09, G:0.26, T:0.34
Consensus pattern (18 bp):
GTGTCGTTTGGAAAACAA
Found at i:3380705 original size:25 final size:24
Alignment explanation
Indices: 3380663--3380735 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 24
3380653 GCTTTATCAT
*
3380663 ATAACTGGAGGCCT-AGCCTCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTCA
3380688 ATAACTGGGGCATAAGCCCTTTTCA
1 ATAACTGGGGCATAAGCCC-TTTCA
3380713 ATAAACTGGGGCATAAGCCCTTT
1 AT-AACTGGGGCATAAGCCCTTT
3380736 TGCACTTCCT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
24 5 0.11
25 22 0.50
26 17 0.39
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTCA
Found at i:3380726 original size:26 final size:25
Alignment explanation
Indices: 3380683--3380736 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 25
3380673 GCCTAGCCTC
3380683 TTTCAATAACTGGGGCATAAGCCCT
1 TTTCAATAACTGGGGCATAAGCCCT
3380708 TTTCAATAAACTGGGGCATAAGCCCT
1 TTTCAAT-AACTGGGGCATAAGCCCT
3380734 TTT
1 TTT
3380737 GCACTTCCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (25 bp):
TTTCAATAACTGGGGCATAAGCCCT
Found at i:3380811 original size:20 final size:20
Alignment explanation
Indices: 3380786--3380832 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3380776 TTATGAATAC
3380786 ATCATGTGCATATCATA-CA
1 ATCATGTGCATATCATATCA
3380805 TATCATGTGCATATCATATCA
1 -ATCATGTGCATATCATATCA
3380826 ATCATGT
1 ATCATGT
3380833 ATATAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATATCA
Found at i:3380896 original size:25 final size:25
Alignment explanation
Indices: 3380868--3380915 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3380858 ATAAGTAAAC
* * *
3380868 CCTAGGGGTATAACGGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
3380893 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGGGGCAAAACAGTCATTTT
3380916 CATAATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:3383325 original size:40 final size:40
Alignment explanation
Indices: 3383227--3383609 Score: 486
Period size: 40 Copynumber: 9.6 Consensus size: 40
3383217 TCCTCGTTCA
* * * * *
3383227 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
3383266 AATGCCTTCGGGACATAACCCGGATTTAATAGCTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
3383306 AATGCCTTCGGGACCTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
3383346 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
3383386 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
3383426 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
3383466 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
3383506 AAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATTTAATAACTCGCACG
** * * * *
3383546 AATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
3383586 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
3383610 CAGCATTCAA
Statistics
Matches: 312, Mismatches: 26, Indels: 11
0.89 0.07 0.03
Matches are distributed among these distances:
39 39 0.12
40 261 0.84
41 12 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:3383618 original size:41 final size:41
Alignment explanation
Indices: 3383541--3383618 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
3383531 TTTGTATCTC
* * *
3383541 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
3383582 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
3383619 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:3383913 original size:143 final size:143
Alignment explanation
Indices: 3383655--3383939 Score: 534
Period size: 143 Copynumber: 2.0 Consensus size: 143
3383645 TTTCATTTGC
*
3383655 GAAACTCAAACACAAGGCACATATCGTCCTTGCACATTCGGCTCAATAGCCTCACATAGAGCATG
1 GAAACTCAAACACAAGGCACATATCATCCTTGCACATTCGGCTCAATAGCCTCACATAGAGCATG
* *
3383720 ATTTAATCTCATTGTAATTTAAGCTCTCTTACTCAAGAACTTACCTCGGGTGTTGTCGAACGATT
66 ATTTAATCACATCGTAATTTAAGCTCTCTTACTCAAGAACTTACCTCGGGTGTTGTCGAACGATT
3383785 CCGCTAGCTATTT
131 CCGCTAGCTATTT
*
3383798 GAAACTCAAACACAAGGCACATGTCATCCTTGCACATTCGGCTCAATAGCCTCACATAGAGCATG
1 GAAACTCAAACACAAGGCACATATCATCCTTGCACATTCGGCTCAATAGCCTCACATAGAGCATG
3383863 ATTTAATCACATCGTAATTTAAGCTCTCTTACTCAAGAACTTACCTCGGGTGTTGTCGAACGATT
66 ATTTAATCACATCGTAATTTAAGCTCTCTTACTCAAGAACTTACCTCGGGTGTTGTCGAACGATT
3383928 CCGCTAGCTATT
131 CCGCTAGCTATT
3383940 CGACCACTTT
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
143 138 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (143 bp):
GAAACTCAAACACAAGGCACATATCATCCTTGCACATTCGGCTCAATAGCCTCACATAGAGCATG
ATTTAATCACATCGTAATTTAAGCTCTCTTACTCAAGAACTTACCTCGGGTGTTGTCGAACGATT
CCGCTAGCTATTT
Found at i:3391510 original size:40 final size:40
Alignment explanation
Indices: 3391412--3391674 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
3391402 TCCTCGTTCA
* * * * *
3391412 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
3391451 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
3391491 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
3391531 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
3391571 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
3391611 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
3391651 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
3391675 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:3395256 original size:24 final size:26
Alignment explanation
Indices: 3395205--3395256 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
3395195 ATCGATAGAA
**
3395205 ATTATAAGTTGAGAATAATTTATTTTG
1 ATTATAAGTTGAGAAT-ATTTAGCTTG
3395232 ATTATAAGTTGAGAAT-TTT-GCTTG
1 ATTATAAGTTGAGAATATTTAGCTTG
3395256 A
1 A
3395257 GGACAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 4 0.17
25 3 0.13
27 16 0.70
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (26 bp):
ATTATAAGTTGAGAATATTTAGCTTG
Found at i:3398127 original size:16 final size:16
Alignment explanation
Indices: 3398090--3398121 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3398080 TCGGCAAATC
3398090 CCGAAATGCCAAAAAG
1 CCGAAATGCCAAAAAG
*
3398106 CCGAAATGCCGAAAAG
1 CCGAAATGCCAAAAAG
3398122 TTGAAAGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.25, G:0.22, T:0.06
Consensus pattern (16 bp):
CCGAAATGCCAAAAAG
Found at i:3398391 original size:29 final size:29
Alignment explanation
Indices: 3398342--3398427 Score: 108
Period size: 28 Copynumber: 3.0 Consensus size: 29
3398332 ACATGGCTTG
*
3398342 GAATTT-ATTCGGGCC-ATATGGGCCATAT
1 GAATTTGATTTGGGCCTA-ATGGGCCATAT
3398370 GAATTTGATTTGGGCCTAATGGGCCATAT
1 GAATTTGATTTGGGCCTAATGGGCCATAT
*
3398399 GAA--TGACATTGGGCCTAATGGGCCATAT
1 GAATTTGA-TTTGGGCCTAATGGGCCATAT
3398427 G
1 G
3398428 CATGTATGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
27 3 0.06
28 27 0.51
29 22 0.42
30 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (29 bp):
GAATTTGATTTGGGCCTAATGGGCCATAT
Found at i:3400350 original size:46 final size:46
Alignment explanation
Indices: 3400283--3400405 Score: 183
Period size: 46 Copynumber: 2.7 Consensus size: 46
3400273 GATATTTGGG
* *
3400283 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGAATGCAAA
* * *
3400329 CATCCGAACTCGTTAAGTTGAGTCCGATTTCACTTATGAATGCAAA
1 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGAATGCAAA
* *
3400375 CGTCTGAACTCGTTGAGTTGAGTCTGAGTTC
1 CATCCGAACTCGTTGAGTTGAGTCTGAGTTC
3400406 GTGAAATGTT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGAATGCAAA
Found at i:3400792 original size:38 final size:38
Alignment explanation
Indices: 3400741--3400819 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
3400731 AAGATGATGA
3400741 ATGATGAATAGAAATGTGATACATGTTTTGGTGATATT
1 ATGATGAATAGAAATGTGATACATGTTTTGGTGATATT
3400779 ATGATGAATAGAAATGTGATACATGTTTTGGTGATATT
1 ATGATGAATAGAAATGTGATACATGTTTTGGTGATATT
3400817 ATG
1 ATG
3400820 CTAATGTTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (38 bp):
ATGATGAATAGAAATGTGATACATGTTTTGGTGATATT
Found at i:3403787 original size:17 final size:18
Alignment explanation
Indices: 3403765--3403798 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3403755 CACATTGAAG
3403765 TGTTTT-AATGAAAACCT
1 TGTTTTCAATGAAAACCT
*
3403782 TGTTTTCATTGAAAACC
1 TGTTTTCAATGAAAACC
3403799 CTTCTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (18 bp):
TGTTTTCAATGAAAACCT
Found at i:3404985 original size:29 final size:29
Alignment explanation
Indices: 3404914--3405038 Score: 153
Period size: 29 Copynumber: 4.3 Consensus size: 29
3404904 AAGTCTACAT
* * *
3404914 ACATGCATATGGCCCACTAGGCCC-AATG
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
3404942 TCATTCTTATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* * *
3404971 ATATTCATATGGCCCATTAGCCCCAAATT
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
3405000 ACATTCATACGGCCCATTAGGCCAAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
3405029 ACATTCATAT
1 ACATTCATAT
3405039 ACATGCTTTC
Statistics
Matches: 80, Mismatches: 16, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
28 20 0.25
29 60 0.75
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:3423120 original size:64 final size:64
Alignment explanation
Indices: 3423019--3423147 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
3423009 AGCAGTAGCG
*
3423019 TTTTGGAAAAATTACCATAAATTGTGGGAGTTGAGTTAAAGGCTGAATAAAATATGTAATTAAA
1 TTTTGGAAAAATTACCATAAATTGTGGGAGTTGAGTTAAAAGCTGAATAAAATATGTAATTAAA
* * *
3423083 TTTTGGAAAACTTACCATAAATTGTGGGAGTTGAGTTAAAAGCTGGATAAATTATGTAATTAAA
1 TTTTGGAAAAATTACCATAAATTGTGGGAGTTGAGTTAAAAGCTGAATAAAATATGTAATTAAA
3423147 T
1 T
3423148 CTTAATGAGT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.34
Consensus pattern (64 bp):
TTTTGGAAAAATTACCATAAATTGTGGGAGTTGAGTTAAAAGCTGAATAAAATATGTAATTAAA
Found at i:3423808 original size:47 final size:47
Alignment explanation
Indices: 3423742--3424121 Score: 688
Period size: 47 Copynumber: 8.1 Consensus size: 47
3423732 GAAATGATAG
3423742 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3423789 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3423836 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3423883 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3423930 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3423977 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3424024 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
3424071 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3424118 TAAG
1 TAAG
3424122 TCCCGAAGGG
Statistics
Matches: 323, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 323 1.00
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:3425556 original size:40 final size:40
Alignment explanation
Indices: 3425498--3425862 Score: 568
Period size: 40 Copynumber: 9.1 Consensus size: 40
3425488 GAGAATTGAG
3425498 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
* *
3425538 AGTGATATATCCGAGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
* *
3425578 AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
* * *
3425618 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
* *
3425658 AGTGATATATCCGGGCTAAGTCCAGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
*
3425698 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
* *
3425738 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
* * *
3425778 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
* *
3425818 AGTGATATATCCGGGCTAGGTCCCGAAGAGCAATCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
*
3425858 GGTGA
1 AGTGA
3425863 CGTGTATTCG
Statistics
Matches: 302, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 302 1.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
Found at i:3426053 original size:25 final size:25
Alignment explanation
Indices: 3426029--3426075 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
3426019 AATAACGAAT
3426029 TAATAAGA-GCACTATGTGTGTGAA
1 TAATAAGAGGCACTATGTGTGTGAA
* * *
3426053 TGATTAGAGGCACTGTGTGTGTG
1 TAATAAGAGGCACTATGTGTGTG
3426076 CGAATTCCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.28, C:0.09, G:0.32, T:0.32
Consensus pattern (25 bp):
TAATAAGAGGCACTATGTGTGTGAA
Found at i:3433198 original size:78 final size:78
Alignment explanation
Indices: 3433069--3433223 Score: 274
Period size: 78 Copynumber: 2.0 Consensus size: 78
3433059 TGAAATAAAA
*
3433069 ATACGAACAACTATGTTATAATTTGACTGTTATCTGTTGACACTGCTTAAAACTGACTAAGCATT
1 ATACGAACAACTATGTTATAATTAGACTGTTATCTGTTGACACTGCTTAAAACTGACTAAGCATT
3433134 GTAATGCTTACTT
66 GTAATGCTTACTT
* * *
3433147 ATACGACCAACTATGTTATAATTAGATTGTTATCTGTTGACACTGCTTAAAACTTACTAAGCATT
1 ATACGAACAACTATGTTATAATTAGACTGTTATCTGTTGACACTGCTTAAAACTGACTAAGCATT
3433212 GTAATGCTTACT
66 GTAATGCTTACT
3433224 CTGTTTACTC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (78 bp):
ATACGAACAACTATGTTATAATTAGACTGTTATCTGTTGACACTGCTTAAAACTGACTAAGCATT
GTAATGCTTACTT
Found at i:3441503 original size:17 final size:18
Alignment explanation
Indices: 3441481--3441514 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3441471 CACATTGAAG
3441481 TGTTTT-ATCGAAAACCT
1 TGTTTTCATCGAAAACCT
*
3441498 TGTTTTCATTGAAAACC
1 TGTTTTCATCGAAAACC
3441515 CTTCAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (18 bp):
TGTTTTCATCGAAAACCT
Found at i:3443887 original size:27 final size:27
Alignment explanation
Indices: 3443845--3443917 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
3443835 CGCCCCTTTA
*
3443845 AGCCCAATCTCATTCATATGGCCCATC
1 AGCCCAATCACATTCATATGGCCCATC
3443872 -GCCCTAATCACATTCATATGGCCCATC
1 AGCCC-AATCACATTCATATGGCCCATC
3443899 AGGCCCAATCACATTCATA
1 A-GCCCAATCACATTCATA
3443918 GTCATGCAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 4 0.10
27 21 0.50
28 13 0.31
29 4 0.10
ACGTcount: A:0.29, C:0.36, G:0.11, T:0.25
Consensus pattern (27 bp):
AGCCCAATCACATTCATATGGCCCATC
Found at i:3447400 original size:49 final size:50
Alignment explanation
Indices: 3447333--3447579 Score: 300
Period size: 49 Copynumber: 5.0 Consensus size: 50
3447323 AGCTATTGTG
* *
3447333 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
* * * * *
3447383 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-AGTT
* * * * * *
3447433 CGATCACGTGTGTAGTACTAAGTACAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
* * *
3447483 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
* * *
3447533 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAG
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
3447580 CTTCGGCTAC
Statistics
Matches: 165, Mismatches: 30, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
49 81 0.49
50 47 0.28
51 37 0.22
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
Found at i:3447470 original size:28 final size:27
Alignment explanation
Indices: 3447438--3447521 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 27
3447428 AACTTCGATC
3447438 ACGTGTGTAGTACTAAGTACAGGCTACT
1 ACGTGTGTAGTACTAAGT-CAGGCTACT
* * *
3447466 ACGTGTATCAG-A-T-GGTTAGG-T-C-
1 ACGTGTGT-AGTACTAAGTCAGGCTACT
3447488 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGT-CAGGCTACT
3447516 ACGTGT
1 ACGTGT
3447522 ACCGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (27 bp):
ACGTGTGTAGTACTAAGTCAGGCTACT
Found at i:3459452 original size:23 final size:23
Alignment explanation
Indices: 3459426--3459472 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3459416 CATTCTATTA
*
3459426 TCATACCCATGCCATTACTATGC
1 TCATACCCATGCCATTACCATGC
* * *
3459449 TCATTCTCATGCTATTACCATGC
1 TCATACCCATGCCATTACCATGC
3459472 T
1 T
3459473 AATGTCACGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (23 bp):
TCATACCCATGCCATTACCATGC
Found at i:3464672 original size:46 final size:46
Alignment explanation
Indices: 3463788--3464650 Score: 1663
Period size: 46 Copynumber: 18.7 Consensus size: 46
3463778 TGTAACCCGC
* * * * * *
3463788 CCATAAGCGAACTCGGAATCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3463834 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3463880 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3463926 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3463972 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3464018 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3464064 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3464110 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3464156 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3464202 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAG-ACATTCGCAT
3464249 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3464295 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3464341 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3464387 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3464433 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3464479 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3464525 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3464571 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
3464617 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
3464651 GGATGCTCAA
Statistics
Matches: 810, Mismatches: 6, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
46 764 0.94
47 46 0.06
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
Found at i:3473478 original size:46 final size:46
Alignment explanation
Indices: 3473425--3473600 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
3473415 TATTTGGGCA
* * *
3473425 TCCGAACTCGTTCAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACG
* * * * *
3473471 TCCGAACTTGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAA--A--CG
3473518 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACG
*
3473564 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTCATGG
3473601 GCAGGTTACA
Statistics
Matches: 109, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 6 0.06
45 5 0.05
46 61 0.56
47 28 0.26
48 3 0.03
50 6 0.06
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACG
Found at i:3473580 original size:93 final size:93
Alignment explanation
Indices: 3473421--3473592 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
3473411 GGGATATTTG
* * *
3473421 GGCATCCGAACTCGTTCAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTTGTTGAG
1 GGCATCCGAACTCGTTCAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCGAACTCGTTGAG
3473486 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
3473514 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACG-CCTGAGCTCGTTGA
1 GGCATCCGAACTCGTTCAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCC-GAACTCGTTGA
3473578 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
3473593 ACTCATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTCAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:3475491 original size:6 final size:6
Alignment explanation
Indices: 3475471--3475515 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
3475461 TTTAAAAAAA
* * *
3475471 TTTTAT TTATTAT TTTTAT TTTTAT TTTCAC TTTTAT CTTTAT TT
1 TTTTAT TT-TTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
3475516 ATCTTATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:3479027 original size:45 final size:45
Alignment explanation
Indices: 3478978--3479101 Score: 187
Period size: 45 Copynumber: 2.8 Consensus size: 45
3478968 CATTTCATCA
* *
3478978 GCATTATAGCCTGCTAGGCTCGAAA-GCCTGAATAGTATCTCACCT
1 GCATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAGTATCTCACCG
* *
3479023 GCATTATAGCCTGCTAGGCCCAAAGGCCCGAATAGTGTCTCACCG
1 GCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCG
*
3479068 GCATAATAGCCTGCTAGGCTCAAAGGCCCGAATA
1 GCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA
3479102 TAATACTAGC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
44 3 0.04
45 69 0.96
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (45 bp):
GCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCG
Found at i:3479142 original size:38 final size:38
Alignment explanation
Indices: 3479094--3479481 Score: 524
Period size: 38 Copynumber: 10.2 Consensus size: 38
3479084 GGCTCAAAGG
* * * *
3479094 CCCGAATATAATACTAGCACTAGGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
3479132 CCCGGATATAATACCAGCATGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* * **
3479170 CCCGGATATATTGCCAGCACGAAGCCTGCGGCCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
3479208 CCCGGATATAATACCAGCACGAAACCTGCGGGAATTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
3479246 CTCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* * * * *
3479284 CTCGGATATATTACCAGCATGAAGCATGCAGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
3479322 CCCGGATATAATACCAGCATGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* * **
3479360 CCCGGATATATTGCCAGCACGAAGCCTGCGGCCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
3479398 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* * **
3479436 CCAGGATATATTACCAGCACGAAGCCTGCGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
3479474 GCCGGATA
1 CCCGGATA
3479482 CAAATATCAT
Statistics
Matches: 308, Mismatches: 42, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 308 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:3479859 original size:43 final size:46
Alignment explanation
Indices: 3479751--3479949 Score: 234
Period size: 45 Copynumber: 4.5 Consensus size: 46
3479741 ATATAACATT
** * *
3479751 TCATTTCACCGGCATTATAGCCCGCTAGGCTCAAAGGCTCGAATAA
1 TCATTTCACCGGCATTATAGCCTACTAAGCTCAAAGGCCCGAATAA
* *
3479797 T-ATTTCACCGGCATCATAGCCTACTAAGCTTAAA-GCCCG-AT-A
1 TCATTTCACCGGCATTATAGCCTACTAAGCTCAAAGGCCCGAATAA
** * *
3479839 TCATTTCACCGGCATTATAGCCCGCTAGGCTCAAAGGCTCGAATAA
1 TCATTTCACCGGCATTATAGCCTACTAAGCTCAAAGGCCCGAATAA
* *
3479885 T-ATTTCACCGGCATCATAGCCTACTAAGCTTAAA-GCCCG-AT-A
1 TCATTTCACCGGCATTATAGCCTACTAAGCTCAAAGGCCCGAATAA
3479927 TCATTTCACCGGCATTATAGCCT
1 TCATTTCACCGGCATTATAGCCT
3479950 GCTAGGCCCG
Statistics
Matches: 129, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
42 4 0.03
43 52 0.40
44 12 0.09
45 58 0.45
46 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (46 bp):
TCATTTCACCGGCATTATAGCCTACTAAGCTCAAAGGCCCGAATAA
Found at i:3479900 original size:88 final size:88
Alignment explanation
Indices: 3479751--3479956 Score: 403
Period size: 88 Copynumber: 2.3 Consensus size: 88
3479741 ATATAACATT
3479751 TCATTTCACCGGCATTATAGCCCGCTAGGCTCAAAGGCTCGAATAATATTTCACCGGCATCATAG
1 TCATTTCACCGGCATTATAGCCCGCTAGGCTCAAAGGCTCGAATAATATTTCACCGGCATCATAG
3479816 CCTACTAAGCTTAAAGCCCGATA
66 CCTACTAAGCTTAAAGCCCGATA
3479839 TCATTTCACCGGCATTATAGCCCGCTAGGCTCAAAGGCTCGAATAATATTTCACCGGCATCATAG
1 TCATTTCACCGGCATTATAGCCCGCTAGGCTCAAAGGCTCGAATAATATTTCACCGGCATCATAG
3479904 CCTACTAAGCTTAAAGCCCGATA
66 CCTACTAAGCTTAAAGCCCGATA
*
3479927 TCATTTCACCGGCATTATAGCCTGCTAGGC
1 TCATTTCACCGGCATTATAGCCCGCTAGGC
3479957 CCGAAGCCCG
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 117 1.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (88 bp):
TCATTTCACCGGCATTATAGCCCGCTAGGCTCAAAGGCTCGAATAATATTTCACCGGCATCATAG
CCTACTAAGCTTAAAGCCCGATA
Found at i:3479964 original size:43 final size:44
Alignment explanation
Indices: 3479751--3479973 Score: 256
Period size: 43 Copynumber: 5.1 Consensus size: 44
3479741 ATATAACATT
* *
3479751 TCATTTCACCGGCATTATAGCCCGCTAGGCTCAAAGGCTCGAATAA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAA-GCCCGAAT-A
* * * *
3479797 T-ATTTCACCGGCATCATAGCCTACTAAGCTTAAAGCCCG-ATA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGAATA
* *
3479839 TCATTTCACCGGCATTATAGCCCGCTAGGCTCAAAGGCTCGAATAA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAA-GCCCGAAT-A
* * * *
3479885 T-ATTTCACCGGCATCATAGCCTACTAAGCTTAAAGCCCG-ATA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGAATA
* *
3479927 TCATTTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGAATA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGAATA
3479971 TCA
1 TCA
3479974 CATTTCGATA
Statistics
Matches: 147, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
42 4 0.03
43 64 0.44
44 18 0.12
45 58 0.39
46 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (44 bp):
TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGAATA
Found at i:3485250 original size:45 final size:45
Alignment explanation
Indices: 3485160--3485319 Score: 184
Period size: 45 Copynumber: 3.6 Consensus size: 45
3485150 CTGACATTTC
* * * * *
3485160 GCCTGCTAGGATC-AAGGCCAGATTA-TCATTTCATCGGCATTATA
1 GCCTGCTAGGCTCAAAGGCCCGAATAGT-ATCTCACCGGCATTATA
*
3485204 GCCTGCTAGGCTCGAAA-GCCCGAATAGTATCTCACCTGCATTATA
1 GCCTGCTAGGCTC-AAAGGCCCGAATAGTATCTCACCGGCATTATA
* *
3485249 GCCTGCTAGGC-CTAAAGGCCCGAATAGTGTCTCACCGGCATAATA
1 GCCTGCTAGGCTC-AAAGGCCCGAATAGTATCTCACCGGCATTATA
*
3485294 GCCTGCTAGGCTCAAAGGCCCAAATA
1 GCCTGCTAGGCTCAAAGGCCCGAATA
3485320 TAATACTAGC
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
44 16 0.16
45 80 0.80
46 4 0.04
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (45 bp):
GCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGCATTATA
Found at i:3485360 original size:38 final size:38
Alignment explanation
Indices: 3485317--3485509 Score: 269
Period size: 38 Copynumber: 5.1 Consensus size: 38
3485307 AAAGGCCCAA
* * *
3485317 ATATAATACTAGCACTAGGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* * *
3485355 ATATAATACCAGCACGAAGCCTGTGGGAATTAACCCAG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
3485393 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* *
3485431 ATATAATACCAGCATGAAGCCTGTGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* ** *
3485469 ATATATTACCAGCACGAAGCCTGCGGTCTTTAAGCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
3485507 ATA
1 ATA
3485510 CAAATATCAT
Statistics
Matches: 136, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 136 1.00
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:3485443 original size:76 final size:76
Alignment explanation
Indices: 3485312--3485509 Score: 297
Period size: 76 Copynumber: 2.6 Consensus size: 76
3485302 GGCTCAAAGG
* * * * *
3485312 CCCAAATATAATACTAGCACTAGGCCTGCGGGATTTAACCCGGATATAATACCAGCACGAAGCCT
1 CCCAGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACGAAGCCT
3485377 GTGGGAATTAA
66 GTGGGAATTAA
*
3485388 CCCAGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCATGAAGCCT
1 CCCAGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACGAAGCCT
*
3485453 GTGGGATTTAA
66 GTGGGAATTAA
* ** *
3485464 CCCGGATATATTACCAGCACGAAGCCTGCGGTCTTTAAGCCGGATA
1 CCCAGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATA
3485510 CAAATATCAT
Statistics
Matches: 111, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 111 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (76 bp):
CCCAGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACGAAGCCT
GTGGGAATTAA
Found at i:3485887 original size:43 final size:43
Alignment explanation
Indices: 3485779--3485913 Score: 164
Period size: 43 Copynumber: 3.1 Consensus size: 43
3485769 ATATAACATT
* *
3485779 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCTCGAATAA
1 TCATTTCACCGGCATTATAGCCTACTAGGCTCAAA-GC-CCAAT-A
* *
3485825 T-ATTTCACCGGCATCATAGCCTACTATGCTCAAAGCCCAATA
1 TCATTTCACCGGCATTATAGCCTACTAGGCTCAAAGCCCAATA
* * *
3485867 TCATTTCACCGGCATTATAGCCTTCTAGGCCCGAAGCCCGAATA
1 TCATTTCACCGGCATTATAGCCTACTAGGCTCAAAGCCC-AATA
3485911 TCA
1 TCA
3485914 CATTTCGATA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
42 2 0.03
43 36 0.46
44 9 0.12
45 30 0.38
46 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (43 bp):
TCATTTCACCGGCATTATAGCCTACTAGGCTCAAAGCCCAATA
Found at i:3486922 original size:310 final size:310
Alignment explanation
Indices: 3486360--3486978 Score: 1220
Period size: 310 Copynumber: 2.0 Consensus size: 310
3486350 TTCCAATCGG
*
3486360 TTTAACAAGCATAAGTATATATCGTATACCTGACCAACTTAATGTATTGAACGAAATCGATTGTC
1 TTTAACAAGCATAAGTATATATCGCATACCTGACCAACTTAATGTATTGAACGAAATCGATTGTC
3486425 GATTTAACACAAGGTCTCATAGTTGAACATAAACATGAAACCATTTCTTATATGTTCGATTCACA
66 GATTTAACACAAGGTCTCATAGTTGAACATAAACATGAAACCATTTCTTATATGTTCGATTCACA
3486490 TCAATCATCAAATTCATTTAATTCACATGTACTTAATTAGGTTGTTCGTACCTGAATAGTTTACT
131 TCAATCATCAAATTCATTTAATTCACATGTACTTAATTAGGTTGTTCGTACCTGAATAGTTTACT
3486555 TTACGCAACGAATCCACATATCGTATTAGCCCATAGTCTTATAGCACCACACTTTTAATAGTTTA
196 TTACGCAACGAATCCACATATCGTATTAGCCCATAGTCTTATAGCACCACACTTTTAATAGTTTA
3486620 CCGGCAATTTGCCTGCTAGGTAATAACCTGATTTCATCACCGGCCATAAA
261 CCGGCAATTTGCCTGCTAGGTAATAACCTGATTTCATCACCGGCCATAAA
*
3486670 TTTAACATGCATAAGTATATATCGCATACCTGACCAACTTAATGTATTGAACGAAATCGATTGTC
1 TTTAACAAGCATAAGTATATATCGCATACCTGACCAACTTAATGTATTGAACGAAATCGATTGTC
3486735 GATTTAACACAAGGTCTCATAGTTGAACATAAACATGAAACCATTTCTTATATGTTCGATTCACA
66 GATTTAACACAAGGTCTCATAGTTGAACATAAACATGAAACCATTTCTTATATGTTCGATTCACA
3486800 TCAATCATCAAATTCATTTAATTCACATGTACTTAATTAGGTTGTTCGTACCTGAATAGTTTACT
131 TCAATCATCAAATTCATTTAATTCACATGTACTTAATTAGGTTGTTCGTACCTGAATAGTTTACT
3486865 TTACGCAACGAATCCACATATCGTATTAGCCCATAGTCTTATAGCACCACACTTTTAATAGTTTA
196 TTACGCAACGAATCCACATATCGTATTAGCCCATAGTCTTATAGCACCACACTTTTAATAGTTTA
3486930 CCGGCAATTTGCCTGCTAGGTAATAACCTGATTTCATCACCGGCCATAA
261 CCGGCAATTTGCCTGCTAGGTAATAACCTGATTTCATCACCGGCCATAA
3486979 GCCTGCTAGA
Statistics
Matches: 307, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
310 307 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (310 bp):
TTTAACAAGCATAAGTATATATCGCATACCTGACCAACTTAATGTATTGAACGAAATCGATTGTC
GATTTAACACAAGGTCTCATAGTTGAACATAAACATGAAACCATTTCTTATATGTTCGATTCACA
TCAATCATCAAATTCATTTAATTCACATGTACTTAATTAGGTTGTTCGTACCTGAATAGTTTACT
TTACGCAACGAATCCACATATCGTATTAGCCCATAGTCTTATAGCACCACACTTTTAATAGTTTA
CCGGCAATTTGCCTGCTAGGTAATAACCTGATTTCATCACCGGCCATAAA
Found at i:3490873 original size:27 final size:28
Alignment explanation
Indices: 3490843--3490901 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
3490833 CAATCTTATG
*
3490843 CATATGGCCCAT-TGCCCCAATCACATT
1 CATATGGCCCATCAGCCCCAATCACATT
*
3490870 CATATGGCCCATCAGGCCCAATCACATT
1 CATATGGCCCATCAGCCCCAATCACATT
3490898 CATA
1 CATA
3490902 GTCATGCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 12 0.41
28 17 0.59
ACGTcount: A:0.29, C:0.36, G:0.12, T:0.24
Consensus pattern (28 bp):
CATATGGCCCATCAGCCCCAATCACATT
Found at i:3490897 original size:28 final size:27
Alignment explanation
Indices: 3490827--3490901 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
3490817 TTGGCCCCTT
** *
3490827 TAGGCCCAATCTTATGCATATGGCCCA
1 TAGGCCCAATCACATTCATATGGCCCA
* *
3490854 TTGCCCCAATCACATTCATATGGCCCA
1 TAGGCCCAATCACATTCATATGGCCCA
3490881 TCAGGCCCAATCACATTCATA
1 T-AGGCCCAATCACATTCATA
3490902 GTCATGCAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.28, C:0.33, G:0.13, T:0.25
Consensus pattern (27 bp):
TAGGCCCAATCACATTCATATGGCCCA
Found at i:3491141 original size:16 final size:17
Alignment explanation
Indices: 3491115--3491166 Score: 72
Period size: 16 Copynumber: 3.2 Consensus size: 17
3491105 GCAGCCAAAC
* *
3491115 TTCTGGCTTTTCAGCAT
1 TTCTAGCTTTTCGGCAT
3491132 TT-TAGCTTTTCGGCAT
1 TTCTAGCTTTTCGGCAT
3491148 TTCTA-CTTTTCGGCAT
1 TTCTAGCTTTTCGGCAT
3491164 TTC
1 TTC
3491167 GGGATTTGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
16 28 0.88
17 4 0.12
ACGTcount: A:0.12, C:0.23, G:0.15, T:0.50
Consensus pattern (17 bp):
TTCTAGCTTTTCGGCAT
Found at i:3495486 original size:81 final size:81
Alignment explanation
Indices: 3495376--3495634 Score: 254
Period size: 81 Copynumber: 3.2 Consensus size: 81
3495366 TATAGGGTAG
* * *
3495376 AATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTTGATTAGTAAAATTACCAAAA
1 AATTACCAAAATACCCCTGGTTTGCAAAATTACCAAAATACCCTTGATTAGTAAAATTACCAAAA
* **
3495441 TGCCC-CTGGTTTGTAA
66 TACCCTC-AATTTGTAA
* * * * *
3495457 AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGATTAGTGAAATTATCGAAA
1 AATTACCAAAATACCCCTGGTTTGCAAAATTACCAAAATACCCTTGATTAGTAAAATTACCAAAA
*
3495522 TACCCTCAATTTTTAA
66 TACCCTCAATTTGTAA
** * * * * * * **
3495538 AATTACCAAAATACCCCTAATTTGGAAATTTATCGAAATACCCTTGATTTGGAAAATTATAAAAA
1 AATTACCAAAATACCCCTGGTTTGCAAAATTACCAAAATACCCTTGATTAGTAAAATTACCAAAA
**
3495603 TACACCT-AATTTACAA
66 TAC-CCTCAATTTGTAA
3495619 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
3495635 TTGGGAAATA
Statistics
Matches: 149, Mismatches: 26, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
80 2 0.01
81 143 0.96
82 4 0.03
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (81 bp):
AATTACCAAAATACCCCTGGTTTGCAAAATTACCAAAATACCCTTGATTAGTAAAATTACCAAAA
TACCCTCAATTTGTAA
Found at i:3495559 original size:27 final size:27
Alignment explanation
Indices: 3495376--3495634 Score: 225
Period size: 27 Copynumber: 9.6 Consensus size: 27
3495366 TATAGGGTAG
* * * **
3495376 AATTACTAAAATACCCTTGGTTTACAA
1 AATTACCAAAATACCCCTGATTTGTAA
* *
3495403 AATTACCAAAATACCCTTGATTAGTAA
1 AATTACCAAAATACCCCTGATTTGTAA
* *
3495430 AATTACCAAAATGCCCCTGGTTTGTAA
1 AATTACCAAAATACCCCTGATTTGTAA
*
3495457 AATTACCAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCCTGATTTGTAA
* *
3495484 AATTACCAAAATACCCCTGATTAGTGA
1 AATTACCAAAATACCCCTGATTTGTAA
* * * *
3495511 AATTATCGAAATA-CCCTCAATTTTTAA
1 AATTACCAAAATACCCCT-GATTTGTAA
* *
3495538 AATTACCAAAATACCCCTAATTTGGAA
1 AATTACCAAAATACCCCTGATTTGTAA
* * * * *
3495565 ATTTATCGAAATACCCTTGATTTGGAA
1 AATTACCAAAATACCCCTGATTTGTAA
** * * **
3495592 AATTATAAAAATACACCTAATTTACAA
1 AATTACCAAAATACCCCTGATTTGTAA
3495619 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
3495635 TTGGGAAATA
Statistics
Matches: 191, Mismatches: 38, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
26 5 0.03
27 182 0.95
28 4 0.02
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGATTTGTAA
Found at i:3496000 original size:41 final size:41
Alignment explanation
Indices: 3495939--3496059 Score: 197
Period size: 41 Copynumber: 3.0 Consensus size: 41
3495929 GGAGGAAGAA
* * *
3495939 ATTGAGGATCGCATGATTGCTTGGCGACTGTGGATCCACTG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACTG
*
3495980 ATTGAGGATCGTATGGTTGCTTGACGACCGTGGATCCACTG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACTG
*
3496021 ATTAAGGATCGCATGGTTGCTTGACGACCGTGGATCCAC
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCAC
3496060 CAGTGGCTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.28
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACTG
Found at i:3500634 original size:40 final size:39
Alignment explanation
Indices: 3500573--3500665 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 39
3500563 TCTTGGTATT
* *
3500573 GCACACTTAGTCCCTCATATAGCCGAAGCTATTCCAATTC
1 GCACACTTAGT-GCTCATATAGCCGAAGCTATTCCAAATC
* * *
3500613 GCACACTTAGTGCTACTTATAGCTGAAGCTATTTCAAATC
1 GCACACTTAGTGCT-CATATAGCCGAAGCTATTCCAAATC
3500653 GCACACTTAGTGC
1 GCACACTTAGTGC
3500666 CGAACATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 2 0.04
40 45 0.96
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (39 bp):
GCACACTTAGTGCTCATATAGCCGAAGCTATTCCAAATC
Found at i:3503583 original size:19 final size:20
Alignment explanation
Indices: 3503546--3503583 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3503536 ATAAGGTGGT
3503546 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
3503566 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
3503584 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:3505689 original size:13 final size:13
Alignment explanation
Indices: 3505671--3505695 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3505661 GGTTTGTTTA
3505671 TTAAACTAATTAT
1 TTAAACTAATTAT
3505684 TTAAACTAATTA
1 TTAAACTAATTA
3505696 ACTGACTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTAATTAT
Found at i:3508167 original size:20 final size:20
Alignment explanation
Indices: 3508142--3508189 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3508132 ATCGATCCAA
* *
3508142 TATCGATACTTTTCTTAAGG
1 TATCGATACATTTCCTAAGG
3508162 TATCGATACATTTCCTAAGG
1 TATCGATACATTTCCTAAGG
3508182 TATCGATA
1 TATCGATA
3508190 TTCCTACTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTCCTAAGG
Found at i:3511011 original size:47 final size:46
Alignment explanation
Indices: 3510936--3511051 Score: 171
Period size: 47 Copynumber: 2.5 Consensus size: 46
3510926 TCGGCCAAGA
3510936 GAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGT
1 GAAAGTGTATG-ATGTGATAAGGCCGAATGGCCAATGTGATGAATGT
*
3510983 GAACATGTGTATG-TGTGATAAGGCCGAATGGCCAATGTGATGGATGT
1 GAA-A-GTGTATGATGTGATAAGGCCGAATGGCCAATGTGATGAATGT
*
3511030 GAAAGTGTATAAATGTGATAAG
1 GAAAGTGTAT-GATGTGATAAG
3511052 TCCCGAAGGG
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
45 6 0.10
46 1 0.02
47 48 0.76
48 1 0.02
49 7 0.11
ACGTcount: A:0.33, C:0.08, G:0.32, T:0.28
Consensus pattern (46 bp):
GAAAGTGTATGATGTGATAAGGCCGAATGGCCAATGTGATGAATGT
Found at i:3512165 original size:53 final size:53
Alignment explanation
Indices: 3512085--3512189 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
3512075 GAAACGAAAC
*
3512085 GGTCATATGAGTGGTATGTTAAGAGATAATTAGGTTTTCGTGAGACAGGGCCT
1 GGTCATATGAGTGGTACGTTAAGAGATAATTAGGTTTTCGTGAGACAGGGCCT
3512138 GGTCATATGAGTGGTACGTTAAGAGATAATTAGGTTTTCGTGAGACAGGGCC
1 GGTCATATGAGTGGTACGTTAAGAGATAATTAGGTTTTCGTGAGACAGGGCC
3512190 AGAACGGTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.27, C:0.10, G:0.32, T:0.30
Consensus pattern (53 bp):
GGTCATATGAGTGGTACGTTAAGAGATAATTAGGTTTTCGTGAGACAGGGCCT
Found at i:3513689 original size:40 final size:40
Alignment explanation
Indices: 3513330--3513677 Score: 502
Period size: 40 Copynumber: 8.7 Consensus size: 40
3513320 AGGTCTCGAC
*
3513330 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
3513369 GATGTATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
3513409 GATGTACCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
3513449 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * *
3513489 GATGTACCCGGGCTAAGTCCCGAAGAACATTTGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
3513529 GATGTATCCGGACTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
3513569 GATGTATCCGGGCTAAGTTCCGAAGAGCACTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * * * *
3513609 AATATATCCGTGCTAA-ACCTCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCC-CGAAGAGCATTCGTGCTAGT
* * *
3513649 GTTATATCCGGGCTAGGTCCCGAAGAGCA
1 GATGTATCCGGGCTAAGTCCCGAAGAGCA
3513678 ATCATGCTGG
Statistics
Matches: 275, Mismatches: 31, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
39 5 0.02
40 268 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:3513883 original size:25 final size:25
Alignment explanation
Indices: 3513854--3513904 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
3513844 GTGTAATAAC
3513854 GAATGAATAAGA-GCACTGTGTGTGT
1 GAATG-ATAAGAGGCACTGTGTGTGT
*
3513879 GAATGATTAGAGGCACTGTGTGTGT
1 GAATGATAAGAGGCACTGTGTGTGT
3513904 G
1 G
3513905 CGAATTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.27, C:0.08, G:0.35, T:0.29
Consensus pattern (25 bp):
GAATGATAAGAGGCACTGTGTGTGT
Found at i:3516222 original size:47 final size:47
Alignment explanation
Indices: 3516165--3516515 Score: 567
Period size: 47 Copynumber: 7.4 Consensus size: 47
3516155 ATTGATGTAC
* * * * *
3516165 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
3516212 AAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
3516261 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
3516308 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
3516355 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
3516402 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
* * * * * * *
3516449 AAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
*
3516496 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
3516516 TCCCGAAGGG
Statistics
Matches: 287, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 244 0.85
49 43 0.15
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
Found at i:3520999 original size:12 final size:11
Alignment explanation
Indices: 3520966--3521052 Score: 59
Period size: 12 Copynumber: 7.6 Consensus size: 11
3520956 TATGTCTTTC
*
3520966 AAAAAAAAAAT
1 AAAATAAAAAT
**
3520977 AAAATTGAAAT
1 AAAATAAAAAT
3520988 GAAAATAAAAAT
1 -AAAATAAAAAT
*
3521000 CAAAAGAAAAAT
1 -AAAATAAAAAT
*
3521012 AAAAAATAAAAT
1 AAAATA-AAAAT
* *
3521024 AAAGTTAAGAAT
1 AAA-ATAAAAAT
*
3521036 -AAATAATAAT
1 AAAATAAAAAT
3521046 AAAATAA
1 AAAATAA
3521053 GAGGAGTCAA
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
10 6 0.10
11 21 0.36
12 31 0.53
13 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:3521010 original size:18 final size:18
Alignment explanation
Indices: 3520964--3521016 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 18
3520954 GATATGTCTT
* *
3520964 TCAAAAAAAAAATAAAAT
1 TCAAAAGAAAAATAAAAA
* *
3520982 TGAAATG-AAAATAAAAA
1 TCAAAAGAAAAATAAAAA
3520999 TCAAAAGAAAAATAAAAA
1 TCAAAAGAAAAATAAAAA
3521017 ATAAAATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (18 bp):
TCAAAAGAAAAATAAAAA
Found at i:3521053 original size:21 final size:21
Alignment explanation
Indices: 3521015--3521054 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3521005 GAAAAATAAA
*
3521015 AAATAAAATAAAGTTAAGAAT
1 AAATAAAATAAAGATAAGAAT
3521036 AAATAATAATAAA-ATAAGA
1 AAATAA-AATAAAGATAAGA
3521055 GGAGTCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (21 bp):
AAATAAAATAAAGATAAGAAT
Found at i:3526493 original size:27 final size:27
Alignment explanation
Indices: 3526462--3526639 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
3526452 TAAATTGTAC
3526462 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
3526489 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3526515 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
3526543 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
3526571 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3526598 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
3526625 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
3526640 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:3526576 original size:82 final size:81
Alignment explanation
Indices: 3526463--3526618 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
3526453 AAATTGTACA
* *
3526463 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
3526527 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
3526544 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
3526609 TGCGAGTTGA
65 TGCGAATTGA
3526619 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:3526630 original size:82 final size:81
Alignment explanation
Indices: 3526459--3526639 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
3526449 GATTAAATTG
* *
3526459 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
3526524 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
3526540 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
3526604 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
3526622 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
3526640 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:3529782 original size:13 final size:13
Alignment explanation
Indices: 3529764--3529788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3529754 GTTCTGTTTA
3529764 TTAAACTAATTAT
1 TTAAACTAATTAT
3529777 TTAAACTAATTA
1 TTAAACTAATTA
3529789 AAGCAAAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTAATTAT
Found at i:3543663 original size:36 final size:36
Alignment explanation
Indices: 3543623--3543699 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
3543613 CTTCAACAAG
3543623 AGGTAAGTAGGAAAGTGAATAAGTACGGGAAGATCC
1 AGGTAAGTAGGAAAGTGAATAAGTACGGGAAGATCC
* * * * *
3543659 AGGTATGTATGATAGTGAATAAGTATGGGACGATCC
1 AGGTAAGTAGGAAAGTGAATAAGTACGGGAAGATCC
3543695 AGGTA
1 AGGTA
3543700 TGAATGATAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.38, C:0.08, G:0.32, T:0.22
Consensus pattern (36 bp):
AGGTAAGTAGGAAAGTGAATAAGTACGGGAAGATCC
Found at i:3543700 original size:36 final size:36
Alignment explanation
Indices: 3543636--3543708 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
3543626 TAAGTAGGAA
*
3543636 AGTGAATAAGTACGGGAAGATCCAGGTATGTATGAT
1 AGTGAATAAGTACGGGAAGATCCAGGTATGAATGAT
* *
3543672 AGTGAATAAGTATGGGACGATCCAGGTATGAATGAT
1 AGTGAATAAGTACGGGAAGATCCAGGTATGAATGAT
3543708 A
1 A
3543709 CCTAAGTGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.37, C:0.08, G:0.30, T:0.25
Consensus pattern (36 bp):
AGTGAATAAGTACGGGAAGATCCAGGTATGAATGAT
Found at i:3559823 original size:68 final size:64
Alignment explanation
Indices: 3559706--3559856 Score: 162
Period size: 68 Copynumber: 2.3 Consensus size: 64
3559696 ATACAGATGG
* * * * *
3559706 TATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGTGTACAAGAGAGCTATGAGACAT
1 TATGTAGCTAGGTCGCATGGATGATGCTGAGTGCACACCATGTGTACAAGAGAGCTACG-G-CA-
3559771 TA
63 TA
* * *
3559773 TAATGTAGCTAGGTCGCATGGGTGATGCT-ATGTGTACACCATGTAG-ACAAGAGAGCTACGGGA
1 T-ATGTAGCTAGGTCGCATGGATGATGCTGA-GTGCACACCATGT-GTACAAGAGAGCTACGGCA
3559836 TA
63 TA
3559838 TATGTAGCTAGGTCGCATG
1 TATGTAGCTAGGTCGCATG
3559857 CGTGGTTCCA
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
64 18 0.25
65 3 0.04
66 1 0.01
67 3 0.04
68 47 0.64
69 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.27
Consensus pattern (64 bp):
TATGTAGCTAGGTCGCATGGATGATGCTGAGTGCACACCATGTGTACAAGAGAGCTACGGCATA
Done.