Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 11 of 206
Found at i:3273183 original size:15 final size:17
Alignment explanation
Indices: 3273165--3273196 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3273155 CAGAATAGAA
3273165 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
3273180 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
3273197 GGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:3274344 original size:37 final size:39
Alignment explanation
Indices: 3274285--3274380 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
3274275 CGGATAGATT
* * * *
3274285 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
3274322 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
3274361 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
3274381 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:3277959 original size:22 final size:22
Alignment explanation
Indices: 3277931--3277979 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
3277921 GGATTAGAGT
3277931 CAAAACATGAAAGACAAAAACA
1 CAAAACATGAAAGACAAAAACA
3277953 CAAAACATGAAAGACAAAAACA
1 CAAAACATGAAAGACAAAAACA
3277975 CAAAA
1 CAAAA
3277980 ATATATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.69, C:0.18, G:0.08, T:0.04
Consensus pattern (22 bp):
CAAAACATGAAAGACAAAAACA
Found at i:3278173 original size:20 final size:20
Alignment explanation
Indices: 3278148--3278209 Score: 85
Period size: 19 Copynumber: 3.2 Consensus size: 20
3278138 AAACTACAAA
*
3278148 AAATAATTTTCTAAATTTCT
1 AAATAATTTTCTAAAATTCT
3278168 AAATAATTTTC-AAAATTCT
1 AAATAATTTTCTAAAATTCT
3278187 AAAT-ATTTAT-TAAAATTCT
1 AAATAATTT-TCTAAAATTCT
3278206 AAAT
1 AAAT
3278210 TTTATATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 4 0.10
19 24 0.62
20 11 0.28
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATAATTTTCTAAAATTCT
Found at i:3278245 original size:20 final size:20
Alignment explanation
Indices: 3278217--3278257 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3278207 AATTTTATAT
*
3278217 TTTTTAAAAAAT-TATAAAAA
1 TTTTAAAAAAATCT-TAAAAA
3278237 TTTTAAAAAAATCTTAAAAA
1 TTTTAAAAAAATCTTAAAAA
3278257 T
1 T
3278258 ATATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTTAAAAAAATCTTAAAAA
Found at i:3281325 original size:23 final size:23
Alignment explanation
Indices: 3281298--3281342 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
3281288 GAAAAATATT
3281298 AAATATATATA-TTTTTATTTTTA
1 AAATATA-ATAGTTTTTATTTTTA
3281321 AAATATAATAGTTTTTTATTTT
1 AAATATAATAG-TTTTTATTTT
3281343 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 7 0.35
24 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
AAATATAATAGTTTTTATTTTTA
Found at i:3281453 original size:9 final size:9
Alignment explanation
Indices: 3281439--3281466 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3281429 CTTTGTTACA
3281439 ACAATTAAT
1 ACAATTAAT
3281448 ACAATTAAT
1 ACAATTAAT
3281457 ACAATTAAT
1 ACAATTAAT
3281466 A
1 A
3281467 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:3281488 original size:68 final size:68
Alignment explanation
Indices: 3281409--3281618 Score: 370
Period size: 68 Copynumber: 3.1 Consensus size: 68
3281399 TCAAGTTTGT
* *
3281409 TTTACTAATCAAATGTTAGACTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
3281474 AAA
66 AAA
*
3281477 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTACTAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
3281542 AAA
66 AAA
3281545 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
3281608 AAT
66 AAA
3281611 TTTACTAA
1 TTTACTAA
3281619 CAATTAATTT
Statistics
Matches: 137, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
66 26 0.19
67 1 0.01
68 110 0.80
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:3281519 original size:9 final size:9
Alignment explanation
Indices: 3281507--3281531 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3281497 TTTTATTACA
3281507 ACAATTAAT
1 ACAATTAAT
3281516 ACAATTAAT
1 ACAATTAAT
3281525 ACAATTA
1 ACAATTA
3281532 CTAATTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:3281628 original size:16 final size:16
Alignment explanation
Indices: 3281607--3281648 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
3281597 AATAATTTGA
*
3281607 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
3281623 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
3281639 TAGTTTTAAT
1 TAATTTTAAT
3281649 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:3281632 original size:22 final size:22
Alignment explanation
Indices: 3281622--3281676 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3281612 TTACTAACAA
* * *
3281622 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
3281644 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
3281666 TTAATTTTAAT
1 TTAATTTTAAT
3281677 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:3282155 original size:31 final size:29
Alignment explanation
Indices: 3282117--3282193 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
3282107 CTAACGGCTC
* *
3282117 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
3282148 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
3282177 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
3282194 TTGAGCCATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 3 0.08
31 15 0.38
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:3288858 original size:17 final size:15
Alignment explanation
Indices: 3288817--3288878 Score: 56
Period size: 15 Copynumber: 4.0 Consensus size: 15
3288807 GTTATAGATG
3288817 AAATAAATAATAA-TA
1 AAAT-AATAATAATTA
3288832 ATAATAATAATAATTA
1 A-AATAATAATAATTA
* *
3288848 AACATTAATAAAAAATA
1 AA-A-TAATAATAATTA
3288865 AAATAA-AATAATTA
1 AAATAATAATAATTA
3288879 TTTTAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.15
15 13 0.33
16 8 0.21
17 12 0.31
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAATAATAATTA
Found at i:3291129 original size:2 final size:2
Alignment explanation
Indices: 3291122--3291170 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3291112 GGTTTGATTC
3291122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3291164 TA TA TA T
1 TA TA TA T
3291171 TGCTCCTCTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3291943 original size:9 final size:7
Alignment explanation
Indices: 3291908--3291945 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
3291898 CTTTTTAAAA
3291908 TATATTT
1 TATATTT
3291915 TATATTT
1 TATATTT
3291922 TATATTT
1 TATATTT
3291929 TATATTT
1 TATATTT
3291936 AATATATTT
1 --TATATTT
3291945 T
1 T
3291946 TTAGTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 22 0.76
9 7 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TATATTT
Found at i:3292465 original size:18 final size:18
Alignment explanation
Indices: 3292434--3292468 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3292424 TGGTGAGGAA
*
3292434 AAGCAACCTGAAGATGCC
1 AAGCAACCTCAAGATGCC
*
3292452 AAGCAGCCTCAAGATGC
1 AAGCAACCTCAAGATGC
3292469 TACTAAAGTG
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:0.37, C:0.29, G:0.23, T:0.11
Consensus pattern (18 bp):
AAGCAACCTCAAGATGCC
Found at i:3295664 original size:41 final size:41
Alignment explanation
Indices: 3295588--3295778 Score: 202
Period size: 41 Copynumber: 4.6 Consensus size: 41
3295578 ATCTTTTGGG
*
3295588 GCTTTAGCGGCGTTTTTAAAGAAAGCGCCGCTAATGCTCAGA
1 GCTTTAGCGGCGTTTTTGAA-AAAGCGCCGCTAATGCTCAGA
** *
3295630 TTTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
1 GCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
** * * * * ** *
3295671 TTTTTAGTGGTGCTTTTGGAAAAGCGCCGCTAATGCTGGGG
1 GCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
** * * * *
3295712 GCTTTAGCGGCGTTTTCCAAGAAGCGCCGTTAATGCTCGGG
1 GCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
3295753 GCTTTAGCGGCGTTTTTGAAAAAGCG
1 GCTTTAGCGGCGTTTTTGAAAAAGCG
3295779 TCGCAAAAAT
Statistics
Matches: 125, Mismatches: 24, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 109 0.87
42 16 0.13
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (41 bp):
GCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
Found at i:3296197 original size:14 final size:15
Alignment explanation
Indices: 3296169--3296201 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
3296159 AAGGTTTATA
3296169 GATTATGGAATTAGG
1 GATTATGGAATTAGG
3296184 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
3296198 GATT
1 GATT
3296202 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:3296251 original size:14 final size:14
Alignment explanation
Indices: 3296232--3296278 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
3296222 TAAGGTTTAT
3296232 GGGTTAGGGGTTAA
1 GGGTTAGGGGTTAA
*
3296246 GGGTTAGAGGTTAA
1 GGGTTAGGGGTTAA
* * *
3296260 GAGTTAGGGATTTA
1 GGGTTAGGGGTTAA
3296274 GGGTT
1 GGGTT
3296279 TATGGATTCG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.45, T:0.32
Consensus pattern (14 bp):
GGGTTAGGGGTTAA
Found at i:3296365 original size:7 final size:7
Alignment explanation
Indices: 3296353--3296409 Score: 50
Period size: 7 Copynumber: 8.7 Consensus size: 7
3296343 TAAATAATGT
3296353 TTAGGGG
1 TTAGGGG
3296360 TTAGGGG
1 TTAGGGG
*
3296367 TTAGGGA
1 TTAGGGG
*
3296374 TTCGGGG
1 TTAGGGG
*
3296381 -T-CGGG
1 TTAGGGG
3296386 TTA-GGG
1 TTAGGGG
3296392 TTA-GGG
1 TTAGGGG
*
3296398 TTAGGGT
1 TTAGGGG
3296405 TTAGG
1 TTAGG
3296410 ATTTAGATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
5 3 0.07
6 14 0.33
7 25 0.60
ACGTcount: A:0.14, C:0.04, G:0.51, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:3296392 original size:6 final size:6
Alignment explanation
Indices: 3296357--3296405 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
3296347 TAATGTTTAG
* * *
3296357 GGGTTA GGGGTTA GGGATTC GGGGTC GGGTTA GGGTTA GGGTTA GGGTT
1 GGGTTA -GGGTTA GGG-TTA GGGTTA GGGTTA GGGTTA GGGTTA GGGTT
3296406 TAGGATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 26 0.70
7 11 0.30
ACGTcount: A:0.12, C:0.04, G:0.53, T:0.31
Consensus pattern (6 bp):
GGGTTA
Found at i:3296519 original size:101 final size:96
Alignment explanation
Indices: 3296296--3296519 Score: 236
Period size: 101 Copynumber: 2.2 Consensus size: 96
3296286 TCGATGTCAG
* *
3296296 GTTAGGGTTTAGGGTTT--AGATTAATTAGTGTGTTTGAATTTATATATTAAATAATGTTTAGGG
1 GTTA-GGTTTAGGGTTTAGAGATTAATTAGTATGTTTGAATTTATATATTAAATAAGGTTTAGGG
*
3296359 GTTAGGGGTTAGGGATTCGGGGTCGGGTTAGG
65 GTTAGGGGTTAGGGATTCGGGGTCGGGTTAGA
* * *
3296391 GTTAGGGTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAAGGTTT
1 GTTAGGTTTAGGGTTTA-G----AGATTAATTAGTATGTTTGAATTTATATATTAAATAAGGTTT
* * * * *
3296456 AGGGGTTAGTGGTTAGGGGTTTGGTGTTTGTGGTTAAGA
61 AGGGGTTAGGGGTTAGGGATTCGG-GGTCG-GGTT-AGA
3296495 GTTAGTGATTTAGGGTTTAGAGATT
1 GTTAG-G-TTTAGGGTTTAGAGATT
3296520 CAAGGTCAGC
Statistics
Matches: 105, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
94 11 0.10
95 4 0.04
101 64 0.61
102 3 0.03
103 4 0.04
104 7 0.07
105 2 0.02
106 10 0.10
ACGTcount: A:0.24, C:0.01, G:0.32, T:0.43
Consensus pattern (96 bp):
GTTAGGTTTAGGGTTTAGAGATTAATTAGTATGTTTGAATTTATATATTAAATAAGGTTTAGGGG
TTAGGGGTTAGGGATTCGGGGTCGGGTTAGA
Found at i:3297636 original size:115 final size:118
Alignment explanation
Indices: 3297409--3297639 Score: 378
Period size: 115 Copynumber: 2.0 Consensus size: 118
3297399 CGCAAAAGGT
* *
3297409 AAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTACAAAAATAGCTCC
1 AAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAGCGCC
* *
3297474 ATTTTAGCATAGCAAAACAATGTCGTTTTATTCCAAATGAAATAATTTTTTGC
66 ATTTTAGCATAGCAAAACAATATCATTTTATTCCAAATGAAATAATTTTTTGC
3297527 AAGCAATAGCGGCGTTTTTATAAAAAACGCCAC-AAAAATAATTTTACTTTAAAAAAATAGCGCC
1 AAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAGCGCC
* **
3297591 A-TTTA-TATAGCAAAACGGTATCATTTTATTCCAAATGAAATAATTTTTT
66 ATTTTAGCATAGCAAAACAATATCATTTTATTCCAAATGAAATAATTTTTT
3297640 ACGATATTTT
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
115 39 0.37
116 4 0.04
117 30 0.28
118 33 0.31
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (118 bp):
AAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAGCGCC
ATTTTAGCATAGCAAAACAATATCATTTTATTCCAAATGAAATAATTTTTTGC
Found at i:3302387 original size:43 final size:43
Alignment explanation
Indices: 3302353--3302580 Score: 273
Period size: 43 Copynumber: 5.3 Consensus size: 43
3302343 TTTTTGCTAG
* * *
3302353 AAGCGCTGCTAAAGATCATGGTCTATAGCGGCGTTTGTGGGAA
1 AAGCGCTGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGAGAA
* * *
3302396 AAGCG-TCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGT-AAAA
1 AAGCGCT-GCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGAGAA
* *
3302438 AAGCGCTGCTAAAGGTCATGGTCTTTAACGGTGTTTGTG-GAA
1 AAGCGCTGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGAGAA
* * * *
3302480 AAGTGCCGCTAAAGGTCGTGGTCTTTAGTGGCGTTTGTGAGAA
1 AAGCGCTGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGAGAA
* * *
3302523 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAA
1 AAGCGCTGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGAGAA
*
3302566 AAGCGCCGCTGAAAG
1 AAGCGCTGCT-AAAG
3302581 TTAGCGACGC
Statistics
Matches: 161, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
42 70 0.43
43 87 0.54
44 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.27
Consensus pattern (43 bp):
AAGCGCTGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGAGAA
Found at i:3302449 original size:85 final size:86
Alignment explanation
Indices: 3302353--3302580 Score: 334
Period size: 85 Copynumber: 2.7 Consensus size: 86
3302343 TTTTTGCTAG
* * *
3302353 AAGCGCTGCTAAAGATCATGGTCTATAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCGTGGT
1 AAGCGCTGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGT
3302418 CTATAGCGGCGTTTGT-AAAA
66 CTATAGCGGCGTTTGTGAAAA
* * *
3302438 AAGCGCTGCTAAAGGTCATGGTCTTTAACGGTGTTTGT-GGAAAAGTGCCGCTAAAGGTCGTGGT
1 AAGCGCTGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGT
* * *
3302502 CTTTAGTGGCGTTTGTGAGAA
66 CTATAGCGGCGTTTGTGAAAA
* *
3302523 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTGAAAG
1 AAGCGCTGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT-AAAG
3302581 TTAGCGACGC
Statistics
Matches: 126, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
84 38 0.30
85 71 0.56
86 13 0.10
87 4 0.03
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.27
Consensus pattern (86 bp):
AAGCGCTGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGT
CTATAGCGGCGTTTGTGAAAA
Found at i:3305358 original size:17 final size:17
Alignment explanation
Indices: 3305317--3305350 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3305307 TGGTGTTTTG
*
3305317 CTTACTTTATTTATTTA
1 CTTATTTTATTTATTTA
3305334 CTTATTTTATTTTATTT
1 CTTATTTTA-TTTATTT
3305351 TTTATTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (17 bp):
CTTATTTTATTTATTTA
Found at i:3305363 original size:14 final size:14
Alignment explanation
Indices: 3305346--3305387 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
3305336 TATTTTATTT
*
3305346 TATTTTTTATTTTC
1 TATTCTTTATTTTC
*
3305360 TATTCTTCATTTTC
1 TATTCTTTATTTTC
*
3305374 TATTCTTTCTTTTC
1 TATTCTTTATTTTC
3305388 GCATTCAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTCTTTATTTTC
Found at i:3305546 original size:22 final size:22
Alignment explanation
Indices: 3305490--3305540 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
3305480 TAAACTTTGT
*
3305490 TATACACATATATTTCTTTTATA
1 TATATACATATATTT-TTTTATA
*
3305513 TATATACATATATTTTTTTTTA
1 TATATACATATATTTTTTTATA
3305535 TATATA
1 TATATA
3305541 TTTATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATACATATATTTTTTTATA
Found at i:3305551 original size:22 final size:23
Alignment explanation
Indices: 3305490--3305552 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
3305480 TAAACTTTGT
*
3305490 TATACACATAT-ATTTCTTTTATA
1 TATATACATATAATTT-TTTTATA
*
3305513 TATATACATAT-ATTTTTTTTTA
1 TATATACATATAATTTTTTTATA
**
3305535 TATATATTTATAATTTTT
1 TATATACATATAATTTTT
3305553 ATCTATTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (23 bp):
TATATACATATAATTTTTTTATA
Found at i:3305552 original size:24 final size:24
Alignment explanation
Indices: 3305490--3305541 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
3305480 TAAACTTTGT
* *
3305490 TATACACATATA-TTTCTTTTATA
1 TATATACATATATTTTTTTTTATA
3305513 TATATACATATATTTTTTTTTATA
1 TATATACATATATTTTTTTTTATA
3305537 TATAT
1 TATAT
3305542 TTATAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATACATATATTTTTTTTTATA
Found at i:3313073 original size:17 final size:16
Alignment explanation
Indices: 3313048--3313081 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3313038 TTATTTTTTA
3313048 ATTATTTTTTAAATTT
1 ATTATTTTTTAAATTT
*
3313064 ATTATATTTTTTAATTT
1 ATTAT-TTTTTAAATTT
3313081 A
1 A
3313082 ATCTTTAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTATTTTTTAAATTT
Found at i:3325212 original size:21 final size:21
Alignment explanation
Indices: 3325174--3325218 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3325164 TTCTGTTAGA
* * *
3325174 AGATAAGTATATGTTTAAAAT
1 AGATAAGCATAGGGTTAAAAT
*
3325195 AGATAAGCATAGGGTTAAGAT
1 AGATAAGCATAGGGTTAAAAT
3325216 AGA
1 AGA
3325219 GTTTGTCACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (21 bp):
AGATAAGCATAGGGTTAAAAT
Found at i:3326906 original size:28 final size:24
Alignment explanation
Indices: 3326852--3326907 Score: 58
Period size: 28 Copynumber: 2.2 Consensus size: 24
3326842 TTTTATGCGA
*
3326852 TAATAATTTATTTTATGTATATTT
1 TAATAATTTATTTTATGTATATAT
*
3326876 TAATATATTTATATATTCATGTTTATAT
1 TAATA-ATTTAT-T-TT-ATGTATATAT
3326904 TAAT
1 TAAT
3326908 TTTTTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 5 0.19
25 6 0.23
26 1 0.04
27 2 0.08
28 12 0.46
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (24 bp):
TAATAATTTATTTTATGTATATAT
Found at i:3327890 original size:17 final size:17
Alignment explanation
Indices: 3327861--3327914 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
3327851 TGAGAAAAGC
*
3327861 TTTTACTAATTTTTATA
1 TTTTAATAATTTTTATA
* *
3327878 TTTTAATAGTTTTTATT
1 TTTTAATAATTTTTATA
*
3327895 TTTTTATAATTTTT-TA
1 TTTTAATAATTTTTATA
3327911 TTTT
1 TTTT
3327915 TTAAATATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
16 5 0.16
17 26 0.84
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTAATAATTTTTATA
Found at i:3327924 original size:18 final size:17
Alignment explanation
Indices: 3327870--3327924 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
3327860 CTTTTACTAA
* *
3327870 TTTTTATATTTTAATAG
1 TTTTTATTTTTTAATAT
*
3327887 TTTTTATTTTTTTATAAT
1 TTTTTATTTTTTAAT-AT
3327905 TTTTTATTTTTTAAATAT
1 TTTTTATTTTTT-AATAT
3327923 TT
1 TT
3327925 AAGAAGGACC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 13 0.41
18 17 0.53
19 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTTTATTTTTTAATAT
Found at i:3330397 original size:19 final size:18
Alignment explanation
Indices: 3330350--3330397 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
3330340 TTTTTTATAA
*
3330350 TTAAAAATATTTTTTACTT
1 TTAAAAA-ATTTTTTAATT
* *
3330369 TTTAATAATTTTTTAAATT
1 TTAAAAAATTTTTT-AATT
3330388 TTAAAAAATT
1 TTAAAAAATT
3330398 AATTAATTAC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAAAAAATTTTTTAATT
Found at i:3347491 original size:60 final size:60
Alignment explanation
Indices: 3347369--3347497 Score: 177
Period size: 60 Copynumber: 2.1 Consensus size: 60
3347359 CCTTGGGCAA
* ** * * *
3347369 AATAGTGGGCAGTACTTTGTGCCGAATGCAGGTTAGTCTCTTGGGCCAGCTAGTGGATAG
1 AATAGTGGGCAGTACTTTGGGCCGAATGCAGGCCAGTCTCTTGGGCCAGCTACTAGACAG
* *
3347429 AATAGTGGGCAGTATTTTGGGCCGAATGCAGGCCAGTCTCTTGGGCCTGCTACTAGACAG
1 AATAGTGGGCAGTACTTTGGGCCGAATGCAGGCCAGTCTCTTGGGCCAGCTACTAGACAG
*
3347489 AATAATGGG
1 AATAGTGGG
3347498 TCGAATAGTG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (60 bp):
AATAGTGGGCAGTACTTTGGGCCGAATGCAGGCCAGTCTCTTGGGCCAGCTACTAGACAG
Found at i:3347510 original size:60 final size:60
Alignment explanation
Indices: 3347389--3347510 Score: 138
Period size: 60 Copynumber: 2.0 Consensus size: 60
3347379 AGTACTTTGT
** * * * * * **
3347389 GCCGAATGCAGGTTAGTCTCTTGGGCCAGCTAGTGGATAGAATAGTGGGCAGTATTTTGG
1 GCCGAATGCAGGCCAGTCTCTTGGGCCAGCTACTAGACAGAATAATGGGCAGAATAGTGG
*
3347449 GCCGAATGCAGGCCAGTCTCTTGGGCCTGCTACTAGACAGAATAATGGGTC-GAATAGTGG
1 GCCGAATGCAGGCCAGTCTCTTGGGCCAGCTACTAGACAGAATAATGGG-CAGAATAGTGG
3347509 GC
1 GC
3347511 GGGCCAATCC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 50 0.98
61 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.25
Consensus pattern (60 bp):
GCCGAATGCAGGCCAGTCTCTTGGGCCAGCTACTAGACAGAATAATGGGCAGAATAGTGG
Found at i:3353700 original size:30 final size:30
Alignment explanation
Indices: 3353654--3353747 Score: 161
Period size: 30 Copynumber: 3.1 Consensus size: 30
3353644 ATTTATTATG
*
3353654 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
3353685 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
*
3353715 CCATTATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
3353745 CCA
1 CCA
3353748 TAAATATGGA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
30 54 0.89
31 7 0.11
ACGTcount: A:0.26, C:0.27, G:0.06, T:0.41
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:3353709 original size:15 final size:15
Alignment explanation
Indices: 3353664--3353740 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 15
3353654 CCAATATCTC
3353664 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
3353679 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
3353694 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
3353709 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
3353724 GATACCCATATCTTT
1 GATACCCATATCTTT
3353739 GA
1 GA
3353741 CTTTCCATAA
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.20
15 28 0.61
16 9 0.20
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.43
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:3358353 original size:30 final size:30
Alignment explanation
Indices: 3358307--3358400 Score: 118
Period size: 30 Copynumber: 3.1 Consensus size: 30
3358297 ATTTGTTATG
*
3358307 CCAATATCTCGATACCCATATATTTGACTTT
1 CCAATAT-TTGATACCCATATATTTGACTTT
3358338 CCAATATTTGATACCCATA-ACTTTGACTTT
1 CCAATATTTGATACCCATATA-TTTGACTTT
* * * *
3358368 CTATTATTTGGTACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATATTTGACTTT
3358398 CCA
1 CCA
3358401 TAAATATGGA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
29 1 0.02
30 47 0.85
31 7 0.13
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.41
Consensus pattern (30 bp):
CCAATATTTGATACCCATATATTTGACTTT
Found at i:3362289 original size:19 final size:18
Alignment explanation
Indices: 3362247--3362291 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3362237 GTGTGCCCTG
* *
3362247 GCTGTATGGAAGTGCCCC
1 GCTGTGTGGAAGTGCCCA
3362265 GACTGTGTGGAAGTGCCCAA
1 G-CTGTGTGGAAGTGCCC-A
3362285 GCTGTGT
1 GCTGTGT
3362292 AGGGGTCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 21 0.91
20 1 0.04
ACGTcount: A:0.18, C:0.22, G:0.36, T:0.24
Consensus pattern (18 bp):
GCTGTGTGGAAGTGCCCA
Found at i:3362329 original size:21 final size:21
Alignment explanation
Indices: 3362300--3362355 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
3362290 GTAGGGGTCT
*
3362300 ACACACCCGTGTGAAGGCCAC
1 ACACGCCCGTGTGAAGGCCAC
* **
3362321 ACACGCCCGTGTGGAGGGGAC
1 ACACGCCCGTGTGAAGGCCAC
*
3362342 ACACGCCTGTGTGA
1 ACACGCCCGTGTGA
3362356 GAGCCCGTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.32, G:0.32, T:0.12
Consensus pattern (21 bp):
ACACGCCCGTGTGAAGGCCAC
Found at i:3380899 original size:14 final size:15
Alignment explanation
Indices: 3380880--3380908 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3380870 ATCATTTGAG
3380880 TATATTTGT-GTTTT
1 TATATTTGTGGTTTT
3380894 TATATTTGTGGTTTT
1 TATATTTGTGGTTTT
3380909 CACACGCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.69
Consensus pattern (15 bp):
TATATTTGTGGTTTT
Found at i:3382811 original size:24 final size:23
Alignment explanation
Indices: 3382784--3382844 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
3382774 AAGAAGTACC
3382784 TAACAAATTAACATAAATAAAACA
1 TAACAAATTAACATAAATAAAA-A
* *
3382808 TAACAAATTTAAAATAACTAAAAA
1 TAACAAA-TTAACATAAATAAAAA
*
3382832 AAACAAA-TAACAT
1 TAACAAATTAACAT
3382845 GCAAGAAGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 5 0.16
24 14 0.44
25 13 0.41
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.21
Consensus pattern (23 bp):
TAACAAATTAACATAAATAAAAA
Found at i:3383467 original size:23 final size:23
Alignment explanation
Indices: 3383414--3383469 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
3383404 TAGCATAACA
*
3383414 AATAATACATGATGAAATTAAAT
1 AATAATATATGATGAAATTAAAT
*
3383437 AATAATATATGAT-AAATTCAA-
1 AATAATATATGATGAAATTAAAT
*
3383458 ACTAATATATGA
1 AATAATATATGA
3383470 AGAACCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 11 0.37
22 7 0.23
23 12 0.40
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (23 bp):
AATAATATATGATGAAATTAAAT
Found at i:3383537 original size:23 final size:23
Alignment explanation
Indices: 3383521--3383595 Score: 84
Period size: 24 Copynumber: 3.3 Consensus size: 23
3383511 AATGAAAATT
3383521 TTAAAATAATAACAATGATAAAC
1 TTAAAATAATAACAATGATAAAC
*
3383544 TTACAATAATAATGC-ATGATAAAC
1 TTAAAATAATAA--CAATGATAAAC
*
3383568 TTAAAATAAT-AC-ATGAAAAAC
1 TTAAAATAATAACAATGATAAAC
3383589 TTTAAAA
1 -TTAAAA
3383596 AAACAAATAC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
21 9 0.20
22 6 0.13
23 12 0.26
24 18 0.39
25 1 0.02
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.28
Consensus pattern (23 bp):
TTAAAATAATAACAATGATAAAC
Found at i:3383597 original size:24 final size:23
Alignment explanation
Indices: 3383523--3383651 Score: 79
Period size: 21 Copynumber: 5.5 Consensus size: 23
3383513 TGAAAATTTT
3383523 AAAATAATAACAATGATAAACTTACA
1 AAAATAAT-AC-ATGATAAACTTA-A
* *
3383549 ATAATAATGCATGATAAACTT--
1 AAAATAATACATGATAAACTTAA
*
3383570 AAAATAATACATGAAAAACTTTAAA
1 AAAATAATACATGATAAAC-TT-AA
*
3383595 AAAACAAATACATGATAAA-TTAA
1 AAAA-TAATACATGATAAACTTAA
** * *
3383618 GTAATATTA-ATGA-ATAATTTAA
1 AAAATAATACATGATA-AACTTAA
3383640 AATAATAATACA
1 AA-AATAATACA
3383652 GTAAAATAAT
Statistics
Matches: 80, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
20 1 0.01
21 22 0.28
22 9 0.11
23 10 0.12
24 14 0.17
25 5 0.06
26 19 0.24
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (23 bp):
AAAATAATACATGATAAACTTAA
Found at i:3383694 original size:27 final size:24
Alignment explanation
Indices: 3383654--3383712 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
3383644 ATAATACAGT
3383654 AAAATAATATTGATGATGAGTTTA
1 AAAATAATATTGATGATGAGTTTA
3383678 AAAATAATATTGATGATGAGTTTA
1 AAAATAATATTGATGATGAGTTTA
3383702 AAAATAATATT
1 AAAATAATATT
3383713 AAGCTTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (24 bp):
AAAATAATATTGATGATGAGTTTA
Found at i:3395673 original size:22 final size:23
Alignment explanation
Indices: 3395648--3395703 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
3395638 AAAATAATAA
*
3395648 AATATTTAAAATA-TTTTTAATT
1 AATATTTAAAATACTTTATAATT
*
3395670 AATATTTTATATATACTTTATAATT
1 AATA-TTTA-AAATACTTTATAATT
3395695 AA-ATTTAAA
1 AATATTTAAA
3395704 TTTAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 5 0.18
23 8 0.29
24 5 0.18
25 10 0.36
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTAAAATACTTTATAATT
Found at i:3398289 original size:26 final size:27
Alignment explanation
Indices: 3398235--3398291 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
3398225 AATTTTAAAA
* *
3398235 TATTTTTAAAATACTTTTTTTAATTTT
1 TATTTTTAAAATACATTTTTTAATGTT
**
3398262 TATTTTTAAAATA-ATTTTTTGGTGTT
1 TATTTTTAAAATACATTTTTTAATGTT
3398288 TATT
1 TATT
3398292 AAAAAATGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (27 bp):
TATTTTTAAAATACATTTTTTAATGTT
Found at i:3399628 original size:18 final size:18
Alignment explanation
Indices: 3399593--3399628 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3399583 CAAAAAGATC
*
3399593 CTAAGTCACAACGTATCA
1 CTAAGTCACAACGCATCA
*
3399611 CTAAGTCACAATGCATCA
1 CTAAGTCACAACGCATCA
3399629 GGCTTACACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (18 bp):
CTAAGTCACAACGCATCA
Found at i:3401257 original size:18 final size:18
Alignment explanation
Indices: 3401225--3401259 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3401215 GTTGAACTAT
3401225 ATTTTATAATTTTTAATA
1 ATTTTATAATTTTTAATA
3401243 ATTTT-TAATTATTTAAT
1 ATTTTATAATT-TTTAAT
3401260 TTGAACCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTATAATTTTTAATA
Found at i:3401775 original size:2 final size:2
Alignment explanation
Indices: 3401770--3401794 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3401760 GAAAAAAAAG
3401770 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
3401795 TTTTCGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3405678 original size:9 final size:9
Alignment explanation
Indices: 3405661--3405691 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3405651 TCGAGTTGAT
3405661 TCGAATAAC
1 TCGAATAAC
*
3405670 TCGATTAAC
1 TCGAATAAC
3405679 TCGAATAAC
1 TCGAATAAC
3405688 TCGA
1 TCGA
3405692 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:3405934 original size:34 final size:35
Alignment explanation
Indices: 3405890--3405956 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
3405880 CAGTAAAATG
3405890 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
3405924 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
3405957 TGGGTGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:3406060 original size:26 final size:26
Alignment explanation
Indices: 3406032--3406085 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
3406022 CCGGAAAAGT
*
3406032 TATTTTTATATATATTAATATATTTTTA
1 TATTTTTATATAT-TAAAT-TATTTTTA
*
3406060 TATTTTTATATTTTAAATTATTTTTA
1 TATTTTTATATATTAAATTATTTTTA
3406086 CATATATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.33
27 4 0.17
28 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
TATTTTTATATATTAAATTATTTTTA
Found at i:3411677 original size:2 final size:2
Alignment explanation
Indices: 3411672--3411701 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3411662 TACACACAAG
3411672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3411702 GATTAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3414577 original size:2 final size:2
Alignment explanation
Indices: 3414570--3414600 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3414560 TCTAATTAAT
*
3414570 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3414601 GTAGGTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3415442 original size:2 final size:2
Alignment explanation
Indices: 3415435--3415468 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3415425 TTAACTAATA
3415435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3415469 CATGAAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3416434 original size:2 final size:2
Alignment explanation
Indices: 3416427--3416457 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3416417 CATAAGATAA
3416427 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3416458 TATCTTCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3419697 original size:3 final size:3
Alignment explanation
Indices: 3419689--3419791 Score: 197
Period size: 3 Copynumber: 34.3 Consensus size: 3
3419679 TTTTACTTTT
3419689 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3419737 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3419785 TTA TTA T
1 TTA TTA T
3419792 GATTTCATAC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 98 1.00
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3422101 original size:3 final size:3
Alignment explanation
Indices: 3422016--3422085 Score: 52
Period size: 3 Copynumber: 22.3 Consensus size: 3
3422006 ACAACTTAAA
* * * *
3422016 AAT AAT AAC AAT ACAT -AT AAT AAT AGT AGT AAA AAT AAGT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
*
3422062 AAT ACGAT AAT AAT AAT AGT AAT A
1 AAT A--AT AAT AAT AAT AAT AAT A
3422086 TTTTAAAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
2 2 0.04
3 44 0.81
4 5 0.09
5 3 0.06
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3427656 original size:29 final size:30
Alignment explanation
Indices: 3427621--3427679 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
3427611 TATGGTTTAA
3427621 TATGTAATTGTATACATG-AACTTTGATTT
1 TATGTAATTGTATACATGAAACTTTGATTT
* *
3427650 TATGTAATTTTATACATGAAATTTTGATTT
1 TATGTAATTGTATACATGAAACTTTGATTT
3427680 GATCCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (30 bp):
TATGTAATTGTATACATGAAACTTTGATTT
Found at i:3427689 original size:30 final size:29
Alignment explanation
Indices: 3427626--3427690 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
3427616 TTTAATATGT
* * **
3427626 AATTGTATACATGAACTTTGATTTTATGT
1 AATTTTATACATGAACTTTGATTTGATCC
*
3427655 AATTTTATACATGAAATTTTGATTTGATCC
1 AATTTTATACATG-AACTTTGATTTGATCC
3427685 AATTTT
1 AATTTT
3427691 TTATAAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (29 bp):
AATTTTATACATGAACTTTGATTTGATCC
Found at i:3434118 original size:15 final size:15
Alignment explanation
Indices: 3434098--3434128 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3434088 ACCTTCCATC
*
3434098 ATAATAATATTTATT
1 ATAATAATAATTATT
3434113 ATAATAATAATTATT
1 ATAATAATAATTATT
3434128 A
1 A
3434129 GAAGAAGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATAATAATTATT
Found at i:3435589 original size:63 final size:63
Alignment explanation
Indices: 3435487--3435610 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
3435477 GCACACATTC
* * *
3435487 CACATAACCGTGCTGGGCTTGTTTTATCTGTAAGTAAATTTTGAACAACGCTAGTAAGCTTAT
1 CACATAACCGTGCTGGGCTTGTTTTAACTATAAGCAAATTTTGAACAACGCTAGTAAGCTTAT
* *
3435550 CACATAACCGTGCTGGGCTTGTTTTAACTATAAGCAAATTTTGAGCAACGTTAGTAAGCTT
1 CACATAACCGTGCTGGGCTTGTTTTAACTATAAGCAAATTTTGAACAACGCTAGTAAGCTT
3435611 TTCAATTTTG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (63 bp):
CACATAACCGTGCTGGGCTTGTTTTAACTATAAGCAAATTTTGAACAACGCTAGTAAGCTTAT
Found at i:3436816 original size:17 final size:17
Alignment explanation
Indices: 3436787--3436834 Score: 80
Period size: 17 Copynumber: 2.8 Consensus size: 17
3436777 ATAAATAAAC
3436787 AATTAAA-TAAATTAGA
1 AATTAAATTAAATTAGA
3436803 AATTAAATTAAATTAGA
1 AATTAAATTAAATTAGA
3436820 AATTAAATTCAAATT
1 AATTAAATT-AAATT
3436835 TTGTAAACAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.23
17 18 0.60
18 5 0.17
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
AATTAAATTAAATTAGA
Found at i:3449312 original size:18 final size:19
Alignment explanation
Indices: 3449289--3449329 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3449279 ATATGTATAT
3449289 AAAATA-ATAAAA-AATAAA
1 AAAATATATAAAACAA-AAA
3449307 AAAATATATAAAACAAAAA
1 AAAATATATAAAACAAAAA
3449326 AAAA
1 AAAA
3449330 CTTATTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
19 13 0.62
20 2 0.10
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAATATATAAAACAAAAA
Found at i:3449319 original size:17 final size:18
Alignment explanation
Indices: 3449289--3449327 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3449279 ATATGTATAT
*
3449289 AAAATAATAAAAAATAAA
1 AAAATAATAAAAAACAAA
*
3449307 AAAAT-ATATAAAACAAA
1 AAAATAATAAAAAACAAA
3449324 AAAA
1 AAAA
3449328 AACTTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAATAATAAAAAACAAA
Found at i:3449464 original size:13 final size:14
Alignment explanation
Indices: 3449439--3449469 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
3449429 AAAGAAAAAC
3449439 AATATATATATATA
1 AATATATATATATA
3449453 AATATA-ATATATA
1 AATATATATATATA
3449466 AATA
1 AATA
3449470 AACTAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATATATATATATA
Found at i:3449540 original size:18 final size:19
Alignment explanation
Indices: 3449517--3449562 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
3449507 TATATAAATG
*
3449517 TATATATAAAAAATG-AAA
1 TATATATAAAAAACGTAAA
*
3449535 TATATA-ACAAAAACGTAAG
1 TATATATA-AAAAACGTAAA
3449554 TATATATAA
1 TATATATAA
3449563 CCTATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 1 0.04
18 12 0.52
19 9 0.39
20 1 0.04
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (19 bp):
TATATATAAAAAACGTAAA
Found at i:3449789 original size:3 final size:3
Alignment explanation
Indices: 3449781--3449820 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3449771 GTATATATGT
3449781 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3449821 CAGCTTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3449856 original size:26 final size:26
Alignment explanation
Indices: 3449783--3449849 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 26
3449773 ATATATGTAT
* * *
3449783 AATAATAATAATAATAA--TAATAAT
1 AATAACAATAATAACAACTTAATAAC
* *
3449807 AATAATAATAATAACAGCTTAATAAC
1 AATAACAATAATAACAACTTAATAAC
*
3449833 AATAACAATATTAACAA
1 AATAACAATAATAACAA
3449850 ACTAATATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 15 0.43
26 20 0.57
ACGTcount: A:0.63, C:0.07, G:0.01, T:0.28
Consensus pattern (26 bp):
AATAACAATAATAACAACTTAATAAC
Found at i:3455607 original size:15 final size:15
Alignment explanation
Indices: 3455589--3455620 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3455579 CAATAGTGCA
3455589 AGCTTGATTGAAATC
1 AGCTTGATTGAAATC
3455604 AGCTTGATTGAAATC
1 AGCTTGATTGAAATC
3455619 AG
1 AG
3455621 ATGGACGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (15 bp):
AGCTTGATTGAAATC
Found at i:3457393 original size:29 final size:30
Alignment explanation
Indices: 3457339--3457397 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
3457329 ATTTCAAAAT
*
3457339 TATATATGAACTTTAATTTAATGTGCAATTG
1 TATATATGAACTTTAATTT-AGGTGCAATTG
*
3457370 TATATATGAATTTTAATTT-GGTGCAATT
1 TATATATGAACTTTAATTTAGGTGCAATT
3457398 ATACACGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (30 bp):
TATATATGAACTTTAATTTAGGTGCAATTG
Found at i:3461738 original size:15 final size:15
Alignment explanation
Indices: 3461718--3461749 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3461708 ACCTTCCATC
*
3461718 ATAATAATATTTATT
1 ATAATAATAATTATT
3461733 ATAATAATAATTATT
1 ATAATAATAATTATT
3461748 AT
1 AT
3461750 TATTAGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAATAATAATTATT
Found at i:3461741 original size:18 final size:18
Alignment explanation
Indices: 3461718--3461752 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3461708 ACCTTCCATC
3461718 ATAATAA-TATTTATTATA
1 ATAATAATTA-TTATTATA
3461736 ATAATAATTATTATTAT
1 ATAATAATTATTATTAT
3461753 TAGAAGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATAATAATTATTATTATA
Found at i:3462897 original size:37 final size:36
Alignment explanation
Indices: 3462856--3462960 Score: 94
Period size: 32 Copynumber: 3.0 Consensus size: 36
3462846 TTTTTTTACT
3462856 AAATTAATATTTAGATGCTACTTTGTATTAGTTTATC
1 AAATTAATATTTAGATGCTACTTT-TATTAGTTTATC
* * * * *
3462893 AAATTAA-ACTAAGAATGTTA-ATTT-TT--TTTACC
1 AAATTAATATTTAG-ATGCTACTTTTATTAGTTTATC
*
3462925 AAATTAATATTTAGATACTACTTTCTATTAGTTTAT
1 AAATTAATATTTAGATGCTACTTT-TATTAGTTTAT
3462961 TAAAGGGTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 14
0.67 0.15 0.19
Matches are distributed among these distances:
32 16 0.32
33 6 0.12
34 3 0.06
35 3 0.06
36 6 0.12
37 16 0.32
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.48
Consensus pattern (36 bp):
AAATTAATATTTAGATGCTACTTTTATTAGTTTATC
Found at i:3463121 original size:62 final size:61
Alignment explanation
Indices: 3462979--3463119 Score: 185
Period size: 62 Copynumber: 2.3 Consensus size: 61
3462969 AAAATATAAA
* * *
3462979 ATTGATACCCGAACTTGTCCACTTCTCCTAGATTAATACTTATGGTTTTTTTTTTGTCCCAG
1 ATTGGTACCCGAACTTTTCCACTTATCCTAGATTAATACTTATGG-TTTTTTTTTGTCCCAG
* * *
3463041 ATTGGTACCCGAACTTTTCCACTTATCTTAGATTAATACTTATGAG-TTTTTTTTGTCTCAT
1 ATTGGTACCCGAACTTTTCCACTTATCCTAGATTAATACTTATG-GTTTTTTTTTGTCCCAG
* *
3463102 ATTGGTGCCTGAACTTTT
1 ATTGGTACCCGAACTTTT
3463120 TCTCCGTCTA
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
61 29 0.41
62 40 0.57
63 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.45
Consensus pattern (61 bp):
ATTGGTACCCGAACTTTTCCACTTATCCTAGATTAATACTTATGGTTTTTTTTTGTCCCAG
Found at i:3469064 original size:18 final size:18
Alignment explanation
Indices: 3469032--3469070 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3469022 TTATAATTCT
*
3469032 TATACGTACACACATATA
1 TATACGTACACACATACA
* *
3469050 TATACGTATAGACATACA
1 TATACGTACACACATACA
3469068 TAT
1 TAT
3469071 TTTCATTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (18 bp):
TATACGTACACACATACA
Found at i:3473544 original size:9 final size:10
Alignment explanation
Indices: 3473528--3473583 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
3473518 TTCACTTGAG
3473528 AAAAAAAAGA
1 AAAAAAAAGA
*
3473538 AACAAAAAGA
1 AAAAAAAAGA
*
3473548 AAAAAGAA-A
1 AAAAAAAAGA
* *
3473557 AGAAAAACGA
1 AAAAAAAAGA
3473567 AAAAGAAAAGA
1 AAAA-AAAAGA
3473578 GAAAAA
1 -AAAAA
3473584 GGATAGGCCA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
9 6 0.17
10 19 0.54
11 6 0.17
12 4 0.11
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:3473548 original size:19 final size:18
Alignment explanation
Indices: 3473526--3473575 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
3473516 ACTTCACTTG
3473526 AGAAAAAAAAGAAACAAAA
1 AGAAAAAAAA-AAACAAAA
* *
3473545 AGAAAAAAGAAAAGAAAA
1 AGAAAAAAAAAAACAAAA
3473563 ACGAAAAAGAAAA
1 A-GAAAAA-AAAA
3473576 GAGAAAAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 15 0.58
20 3 0.12
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAAAAACAAAA
Found at i:3473557 original size:12 final size:12
Alignment explanation
Indices: 3473542--3473582 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
3473532 AAAAGAAACA
3473542 AAAAGAAAAAAG
1 AAAAGAAAAAAG
*
3473554 AAAAGAAAAACG
1 AAAAGAAAAAAG
*
3473566 AAAAAGAAAAGAG
1 -AAAAGAAAAAAG
3473579 AAAA
1 AAAA
3473583 AGGATAGGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:3473557 original size:13 final size:13
Alignment explanation
Indices: 3473526--3473584 Score: 68
Period size: 13 Copynumber: 4.6 Consensus size: 13
3473516 ACTTCACTTG
3473526 AGAAAAA-AAAGAA
1 AGAAAAAGAAA-AA
*
3473539 ACAAAAAGAAAAA
1 AGAAAAAGAAAAA
3473552 AG-AAAAGAAAAA
1 AGAAAAAGAAAAA
* *
3473564 CGAAAAAGAAAAG
1 AGAAAAAGAAAAA
3473577 AGAAAAAG
1 AGAAAAAG
3473585 GATAGGCCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
12 11 0.28
13 25 0.64
14 3 0.08
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAAAAA
Found at i:3473571 original size:18 final size:18
Alignment explanation
Indices: 3473530--3473582 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
3473520 CACTTGAGAA
*
3473530 AAAAAAG-AAACAAAAAG
1 AAAAAAGAAAAGAAAAAG
3473547 AAAAAAGAAAAGAAAAACG
1 AAAAAAGAAAAGAAAAA-G
3473566 -AAAAAGAAAAGAGAAAA
1 AAAAAAGAAAAGA-AAAA
3473583 AGGATAGGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 7 0.22
18 20 0.62
19 5 0.16
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAGAAAAAG
Found at i:3474702 original size:88 final size:88
Alignment explanation
Indices: 3474556--3474939 Score: 562
Period size: 86 Copynumber: 4.4 Consensus size: 88
3474546 ATGAAGTTAC
* *
3474556 CAGATCTTGCCTTCCTGCATTGACGGCGAAGCAGATCAAAGACACAAACCTTGTCTCTCTCGGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGGTT
*
3474621 GTAGCAGAGCTGGTTGAATACAA
66 GTAGCAGAGCTGGTTGAAGACAA
* *
3474644 CAGATCTTGCCTTCCTGCGTTGACAGCGAAGCAGATCAAAGACACAAACCTTG-C-CTCTCGATT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGGTT
*
3474707 GTAGCAGAGCTGGTTGAATACAA
66 GTAGCAGAGCTGGTTGAAGACAA
* *
3474730 CAGATCTTGCCTTCCTGCGTTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCAGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGGTT
*
3474795 GTAGCAGAGTTGGTTGAAGACAA
66 GTAGCAGAGCTGGTTGAAGACAA
* * *
3474818 CAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-GA-ACACAAACCTTGCCTCTCTCGGTC
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGGTT
* ***
3474881 GTAGTAGAGCTGGTTGAAGATTG
66 GTAGCAGAGCTGGTTGAAGACAA
* *
3474904 CAGATCTTGCCTTCCTGTATTTGGCAGC-AAGCAGAT
1 CAGATCTTGCCTTCCTGCA-TTGACAGCGAAGCAGAT
3474940 TGAAGATGGT
Statistics
Matches: 273, Mismatches: 20, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
86 150 0.55
87 9 0.03
88 114 0.42
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGGTT
GTAGCAGAGCTGGTTGAAGACAA
Found at i:3474741 original size:42 final size:41
Alignment explanation
Indices: 3474612--3474829 Score: 111
Period size: 44 Copynumber: 5.0 Consensus size: 41
3474602 AACCTTGTCT
3474612 CTCTCGGTTGTAGCAGAGCTGGTTGAATACAACAGATCTTGC
1 CTCTC-GTTGTAGCAGAGCTGGTTGAATACAACAGATCTTGC
* * * ** * * *
3474654 CTTCCTGCGTTGACAGC-GAAGCAGATCAAAGAC-ACAAACCTTGC
1 C-T-CT-CGTTG-TAGCAG-AGCTGGTTGAATACAACAGATCTTGC
3474698 CTCTCGATTGTAGCAGAGCTGGTTGAATACAACAGATCTTGC
1 CTCTCG-TTGTAGCAGAGCTGGTTGAATACAACAGATCTTGC
* * * ** * * *
3474740 CTTCCTGCGTTGACAGC-GAAGCAGATCAAAGAC-ACAAACCTTGCC
1 C-T-CT-CGTTG-TAGCAG-AGCTGGTTGAATACAACAGATCTTG-C
* *
3474785 TCTCTCAGTTGTAGCAGAGTTGGTTGAAGACAACAGATCTTGC
1 -CTCTC-GTTGTAGCAGAGCTGGTTGAATACAACAGATCTTGC
3474828 CT
1 CT
3474830 TCCTGCATTA
Statistics
Matches: 126, Mismatches: 32, Indels: 36
0.65 0.16 0.19
Matches are distributed among these distances:
41 14 0.11
42 19 0.15
43 17 0.13
44 46 0.37
45 29 0.23
46 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (41 bp):
CTCTCGTTGTAGCAGAGCTGGTTGAATACAACAGATCTTGC
Found at i:3474846 original size:174 final size:174
Alignment explanation
Indices: 3474556--3474939 Score: 558
Period size: 174 Copynumber: 2.2 Consensus size: 174
3474546 ATGAAGTTAC
* * *
3474556 CAGATCTTGCCTTCCTGCATTGACGGCGAAGCAGATCAAAGACACAAACCTTGTCTCTCTCGGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCAGTT
* * *
3474621 GTAGCAGAGCTGGTTGAATACAACAGATCTTGCCTTCCTGCGTTGACAGCGAAGCAGATCAAAGA
66 GTAGCAGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AA-A
* *
3474686 CACAAACCTTG-C-CTCTCGATTGTAGCAGAGCTGGTTGAATACAA
129 CACAAACCTTGCCTCTCTCGATCGTAGCAGAGCTGGTTGAAGACAA
*
3474730 CAGATCTTGCCTTCCTGCGTTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCAGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCAGTT
* *
3474795 GTAGCAGAGTTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAACA
66 GTAGCAGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAACA
* * ***
3474860 CAAACCTTGCCTCTCTCGGTCGTAGTAGAGCTGGTTGAAGATTG
131 CAAACCTTGCCTCTCTCGATCGTAGCAGAGCTGGTTGAAGACAA
* *
3474904 CAGATCTTGCCTTCCTGTATTTGGCAGC-AAGCAGAT
1 CAGATCTTGCCTTCCTGCA-TTGACAGCGAAGCAGAT
3474940 TGAAGATGGT
Statistics
Matches: 188, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
172 12 0.06
173 2 0.01
174 167 0.89
175 7 0.04
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (174 bp):
CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCAGTT
GTAGCAGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAACA
CAAACCTTGCCTCTCTCGATCGTAGCAGAGCTGGTTGAAGACAA
Found at i:3475018 original size:43 final size:43
Alignment explanation
Indices: 3474970--3475216 Score: 138
Period size: 43 Copynumber: 5.4 Consensus size: 43
3474960 TCCCTGACTA
*
3474970 CAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGGTTAG
1 CAGTGGAATACATTGAAGCCGATAATTCTATCTCCCTGGTTAG
* * * * * * **
3475013 TAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCACTGACTA-
1 CAGTGGAATACATTGAAG--C--CGAT---A-ATTCTATCTCCCTGGTTAG
* *
3475063 CAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTAGTTAG
1 CAGTGGAATACATTGAAGCCGATAATTCTATCTCCCTGGTTAG
* * * * **
3475106 CAGTGGAATAGATTGAAGATCGAAGATGGCAGATTTTACCTCCCTGACTA-
1 CAGTGGAATACATTGAAG--C--CGAT---A-ATTCTATCTCCCTGGTTAG
* * *
3475156 CAGTGGAGTACATTGAAGTCGATAATTCTATCTCCCTGGTTGG
1 CAGTGGAATACATTGAAGCCGATAATTCTATCTCCCTGGTTAG
* *
3475199 TAGTGGAATAGATTGAAG
1 CAGTGGAATACATTGAAG
3475217 ATTACAGATC
Statistics
Matches: 147, Mismatches: 39, Indels: 36
0.66 0.18 0.16
Matches are distributed among these distances:
42 25 0.17
43 48 0.33
45 2 0.01
46 6 0.04
47 6 0.04
48 1 0.01
50 33 0.22
51 26 0.18
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (43 bp):
CAGTGGAATACATTGAAGCCGATAATTCTATCTCCCTGGTTAG
Found at i:3475053 original size:93 final size:93
Alignment explanation
Indices: 3474942--3475218 Score: 491
Period size: 93 Copynumber: 3.0 Consensus size: 93
3474932 AAGCAGATTG
*
3474942 AAGATGGTAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCT
1 AAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCT
3475007 GGTTAGTAGTGGAATAGATTGAAGATCA
66 GGTTAGTAGTGGAATAGATTGAAGATCA
*
3475035 AAGATGGCAGATTTTACCTCACTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCT
1 AAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCT
* * *
3475100 AGTTAGCAGTGGAATAGATTGAAGATCG
66 GGTTAGTAGTGGAATAGATTGAAGATCA
*
3475128 AAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGTCGATAATTCTATCTCCCT
1 AAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCT
*
3475193 GGTTGGTAGTGGAATAGATTGAAGAT
66 GGTTAGTAGTGGAATAGATTGAAGAT
3475219 TACAGATCTT
Statistics
Matches: 174, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 174 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (93 bp):
AAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCT
GGTTAGTAGTGGAATAGATTGAAGATCA
Found at i:3475280 original size:40 final size:40
Alignment explanation
Indices: 3475225--3475596 Score: 383
Period size: 40 Copynumber: 8.9 Consensus size: 40
3475215 AGATTACAGA
*
3475225 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAAAATCAAG
* *
3475265 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGAC--AA-AATCAAG
* *
3475308 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAAACCAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGAC----AAAATCAAG
*
3475352 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAAAATCAAG
* * * *
3475393 TCTTCTCTCACTAAGCAGTAGTGGAGCAGACGGAAGAAACCACATA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGAC---A-AAATCA-A-G
* **
3475439 TCTTATCTCCCTAAGCAATAGTGGAGCAGATC-GCATCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAAAATCAAG
*
3475479 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAACCACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAATCA-AG
**
3475520 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-GCATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAAAATCAAG
3475561 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGAC-AAAA
3475597 AAAACCAATC
Statistics
Matches: 282, Mismatches: 28, Indels: 43
0.80 0.08 0.12
Matches are distributed among these distances:
39 4 0.01
40 120 0.43
41 11 0.04
42 37 0.13
43 36 0.13
44 11 0.04
45 34 0.12
46 28 0.10
47 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAATCAAG
Found at i:3475384 original size:128 final size:127
Alignment explanation
Indices: 3475221--3475607 Score: 499
Period size: 128 Copynumber: 3.1 Consensus size: 127
3475211 TTGAAGATTA
3475221 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
3475286 TGGAGCAGACGAAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAAAC
66 TGGAGCAGACG-AAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAAAC
* *
3475349 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTCTCTCACTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
* * *
3475414 TGGAGCAGACGGAAGAAACCACATATCTTATCTCCCTAAGCAATAGTGGAGCAGATCG-----CA
66 TGGAGCAGAC-GAAGAAA-C-CA-GTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAAAAA
*
3475474 TC
126 AC
* * *
3475476 AAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAAAACCACAGATCTTATCTCCCTAAGCAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCA-AG-TCTTATCTCCCTAAGCAG
* * *
3475539 TAGTGGAGCAGATC---GCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAAA
63 TAGTGGAGCAGA-CGAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAAA
3475601 C
127 C
3475602 CA-ATCT
1 CAGATCT
3475608 CATCCCCATG
Statistics
Matches: 225, Mismatches: 19, Indels: 32
0.82 0.07 0.12
Matches are distributed among these distances:
121 2 0.01
122 29 0.13
123 1 0.00
124 1 0.00
125 3 0.01
126 40 0.18
127 6 0.03
128 107 0.48
129 3 0.01
130 2 0.01
131 29 0.13
132 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (127 bp):
CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
TGGAGCAGACGAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAAAC
Found at i:3475419 original size:168 final size:164
Alignment explanation
Indices: 3475225--3475595 Score: 498
Period size: 168 Copynumber: 2.2 Consensus size: 164
3475215 AGATTACAGA
* * * *
3475225 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCA-A-GTCTTATCTCCCTAAGCAGTAGT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAACCACATATCTTATCTCCCTAAGCAATAGT
*
3475287 GGAGCAGA-CGAAAGAAACCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAAACCA
65 GGAGCAGATC----GAAACAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGAC--AAAAAAA-CA
3475351 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
123 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
* *
3475393 TCTTCTCTCACTAAGCAGTAGTGGAGCAGACGGAAGAAACCACATATCTTATCTCCCTAAGCAAT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGAC----GAAACCACATATCTTATCTCCCTAAGCAAT
* * **
3475458 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAACCACAGATC
62 AGTGGAGCAGATCGAAACAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAAAACAGATC
*
3475523 TTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
127 TTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
3475561 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAA
3475596 AAAAACCAAT
Statistics
Matches: 181, Mismatches: 14, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
164 4 0.02
167 1 0.01
168 100 0.55
169 5 0.03
171 36 0.20
172 4 0.02
173 1 0.01
174 29 0.16
175 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (164 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAACCACATATCTTATCTCCCTAAGCAATAGTG
GAGCAGATCGAAACAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAAAACAGATCTTAT
CTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
Found at i:3475743 original size:17 final size:18
Alignment explanation
Indices: 3475711--3475744 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3475701 GGACTGGAAT
*
3475711 GAAGCTACTTGAAGAAGA
1 GAAGCTACTAGAAGAAGA
3475729 GAAGC-ACTAGAAGAAG
1 GAAGCTACTAGAAGAAG
3475745 TCAAAACTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.12, G:0.29, T:0.12
Consensus pattern (18 bp):
GAAGCTACTAGAAGAAGA
Found at i:3477439 original size:18 final size:18
Alignment explanation
Indices: 3477407--3477445 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3477397 TTATAATTCT
*
3477407 TATACGTACACACATATA
1 TATACGTACACACATACA
* *
3477425 TATACGTATAGACATACA
1 TATACGTACACACATACA
3477443 TAT
1 TAT
3477446 TTTCATTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (18 bp):
TATACGTACACACATACA
Found at i:3479619 original size:17 final size:17
Alignment explanation
Indices: 3479579--3479620 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3479569 ATAAATAAAC
*
3479579 AATTAAA-TAAATCAGG
1 AATTAAATTAAATCAGA
* *
3479595 AATAAAATTAAATTAGA
1 AATTAAATTAAATCAGA
3479612 AATTAAATT
1 AATTAAATT
3479621 CGAATTTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (17 bp):
AATTAAATTAAATCAGA
Found at i:3481532 original size:14 final size:14
Alignment explanation
Indices: 3481513--3481544 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3481503 TTTTTAAATG
3481513 TTATTTTAAAATAA
1 TTATTTTAAAATAA
3481527 TTATTTTAAAATAA
1 TTATTTTAAAATAA
3481541 TTAT
1 TTAT
3481545 ATATGTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATTTTAAAATAA
Found at i:3485592 original size:22 final size:23
Alignment explanation
Indices: 3485567--3485622 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
3485557 AAAATAATAA
*
3485567 AATATTTAAAATA-TTTTTAATT
1 AATATTTAAAATACTTTATAATT
*
3485589 AATATTTTATATATACTTTATAATT
1 AATA-TTTA-AAATACTTTATAATT
3485614 AA-ATTTAAA
1 AATATTTAAA
3485623 TTTAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 5 0.18
23 8 0.29
24 5 0.18
25 10 0.36
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTAAAATACTTTATAATT
Found at i:3491556 original size:18 final size:18
Alignment explanation
Indices: 3491521--3491556 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3491511 CAAAAAGATC
*
3491521 CTAAGTCACAACGTATCA
1 CTAAGTCACAACGCATCA
*
3491539 CTAAGTCACAATGCATCA
1 CTAAGTCACAACGCATCA
3491557 GGCTTACACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (18 bp):
CTAAGTCACAACGCATCA
Found at i:3494455 original size:16 final size:17
Alignment explanation
Indices: 3494417--3494455 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3494407 ATAACTAATG
* *
3494417 TAAAGTAATATATAAGG
1 TAAAATAATATATAAGC
3494434 TAAAATAATATA-AAGC
1 TAAAATAATATATAAGC
3494450 TAAAAT
1 TAAAAT
3494456 GAAGTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (17 bp):
TAAAATAATATATAAGC
Found at i:3504388 original size:21 final size:22
Alignment explanation
Indices: 3504344--3504390 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3504334 TAATAATGAT
*
3504344 TTTTTAAAATATATACATTTAA
1 TTTTTAAAATATATACATTAAA
3504366 TTTTTAAATATATATA-A-TAAA
1 TTTTTAAA-ATATATACATTAAA
3504387 TTTT
1 TTTT
3504391 CTAACTGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 9 0.39
23 7 0.30
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTTAAAATATATACATTAAA
Found at i:3506630 original size:18 final size:18
Alignment explanation
Indices: 3506604--3506664 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 18
3506594 TAAATTTGTA
3506604 TCAGATTTAGACCTATCT
1 TCAGATTTAGACCTATCT
*
3506622 TCAGGTTTAGTAGACCTATCT
1 TCA-GATT--TAGACCTATCT
*
3506643 TCATATTTAGACCTATCT
1 TCAGATTTAGACCTATCT
3506661 TCAG
1 TCAG
3506665 GATTAGGACC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 17 0.47
19 3 0.08
20 2 0.06
21 14 0.39
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (18 bp):
TCAGATTTAGACCTATCT
Found at i:3506670 original size:18 final size:18
Alignment explanation
Indices: 3506610--3506675 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 18
3506600 TGTATCAGAT
3506610 TTAGACCTATCTTCAGGTTTA
1 TTAGACCTATCTTCAGG---A
* *
3506631 GTAGACCTATCTTCA-TA
1 TTAGACCTATCTTCAGGA
3506648 TTTAGACCTATCTTCAGGA
1 -TTAGACCTATCTTCAGGA
3506667 TTAGGACCT
1 TTA-GACCT
3506676 TGGTTGACTC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 1 0.03
18 17 0.45
19 6 0.16
21 14 0.37
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (18 bp):
TTAGACCTATCTTCAGGA
Found at i:3507256 original size:3 final size:3
Alignment explanation
Indices: 3507248--3507295 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
3507238 TTTTACAGTC
3507248 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3507296 GTTATTAGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:3507966 original size:24 final size:24
Alignment explanation
Indices: 3507939--3508014 Score: 125
Period size: 24 Copynumber: 3.2 Consensus size: 24
3507929 AATCAAAGTC
3507939 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
3507963 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
3507987 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
3508011 AAAT
1 AAAT
3508015 TTTCTAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:3511886 original size:41 final size:41
Alignment explanation
Indices: 3511829--3511930 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
3511819 GCATAGCGCT
*
3511829 TAGCAGGCTTATTGCCGGTGAAACACTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
* *
3511870 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
*
3511911 TAGCGGGC-TAAGTGCCGGTG
1 TAGCAGGCTTAA-TGCCGGTG
3511931 TACTGAATCA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
40 3 0.05
41 53 0.95
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.28
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
Found at i:3515342 original size:24 final size:24
Alignment explanation
Indices: 3515292--3515343 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3515282 AATCAAAGTC
* *
3515292 AAATATATTATGCTAATAAATGGT
1 AAATATATTATACTAATAAATAGT
* *
3515316 AAATATATTATACTCATAAATATT
1 AAATATATTATACTAATAAATAGT
3515340 AAAT
1 AAAT
3515344 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATAGT
Found at i:3519647 original size:18 final size:20
Alignment explanation
Indices: 3519626--3519665 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
3519616 AGAGAGTTTG
3519626 AAGGAAGAAA-AGA-GAGAA
1 AAGGAAGAAAGAGAGGAGAA
3519644 AAGGAAGAAAGAGAGGAGAA
1 AAGGAAGAAAGAGAGGAGAA
3519664 AA
1 AA
3519666 CAGATAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.50
19 3 0.15
20 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
AAGGAAGAAAGAGAGGAGAA
Found at i:3519820 original size:25 final size:25
Alignment explanation
Indices: 3519764--3519830 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
3519754 ACTAATACTC
* * *
3519764 ACCAAAACGCACCGTCTAATTAACA
1 ACCAAAACTCACCGTTTAACTAACA
* *
3519789 ACTAAAACTCACCGTTTAACTAATA
1 ACCAAAACTCACCGTTTAACTAACA
* *
3519814 CCCAAAACTCCCCGTTT
1 ACCAAAACTCACCGTTT
3519831 TCAGTAACTA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.39, C:0.33, G:0.06, T:0.22
Consensus pattern (25 bp):
ACCAAAACTCACCGTTTAACTAACA
Found at i:3526473 original size:15 final size:16
Alignment explanation
Indices: 3526453--3526482 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3526443 TAACAAAAAG
3526453 AACCCAA-AACCCACA
1 AACCCAATAACCCACA
3526468 AACCCAATAACCCAC
1 AACCCAATAACCCAC
3526483 CTAAACACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (16 bp):
AACCCAATAACCCACA
Found at i:3527651 original size:8 final size:8
Alignment explanation
Indices: 3527638--3527671 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
3527628 CTCATAATAT
3527638 ATATTTTC
1 ATATTTTC
3527646 ATATTTTC
1 ATATTTTC
3527654 ATATTTT-
1 ATATTTTC
3527661 ATGATTTTC
1 AT-ATTTTC
3527670 AT
1 AT
3527672 CTATTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 2 0.08
8 20 0.83
9 2 0.08
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62
Consensus pattern (8 bp):
ATATTTTC
Found at i:3528085 original size:108 final size:109
Alignment explanation
Indices: 3527889--3528201 Score: 538
Period size: 109 Copynumber: 2.9 Consensus size: 109
3527879 AAATATTTCT
* * *
3527889 AAATGAGGCAATGTTTTGCGTTTGGAAGTTCGAGAAAACATGTCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
3527954 TTTCTCGTTCAACCAAATAGCTTAATATCCTTTT-AAATTTTTA
66 TTTCTCGTTCAACCAAATAGCTTAATATCCTTTTAAAATTTTTA
*
3527997 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTTGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
*
3528062 TTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAATTTTTA
66 TTTCTCGTTCAACCAAATAGCTTAATATCCTTTTAAAATTTTTA
* *
3528106 AAATAAGGCAATGTTTTACGTTTGGAAATTCGAAAAAACATGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
* *
3528171 TTTCTCGTTCAACCAAATAGCTAAACATCCT
66 TTTCTCGTTCAACCAAATAGCTTAATATCCT
3528202 CTTGAATTTA
Statistics
Matches: 193, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
108 94 0.49
109 99 0.51
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (109 bp):
AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
TTTCTCGTTCAACCAAATAGCTTAATATCCTTTTAAAATTTTTA
Found at i:3531749 original size:12 final size:12
Alignment explanation
Indices: 3531732--3531758 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3531722 GAGATATTTC
3531732 ACTAGTCTATGG
1 ACTAGTCTATGG
3531744 ACTAGTCTATGG
1 ACTAGTCTATGG
3531756 ACT
1 ACT
3531759 TAACCGAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (12 bp):
ACTAGTCTATGG
Found at i:3538975 original size:32 final size:31
Alignment explanation
Indices: 3538930--3539025 Score: 167
Period size: 31 Copynumber: 3.1 Consensus size: 31
3538920 CTTAGATAAT
3538930 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
3538961 TTTAAAGAGTTTTTATTAGGATTCAATTACT-
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
3538992 TTTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTT-AAAGAGTTTTATTAGGATTCAATTACTC
3539024 TT
1 TT
3539026 GTAATTTGCC
Statistics
Matches: 62, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:3547289 original size:54 final size:54
Alignment explanation
Indices: 3547230--3547333 Score: 199
Period size: 54 Copynumber: 1.9 Consensus size: 54
3547220 GACACAACAG
*
3547230 CATAGATGACGAAGATGTGAACAATCCCATTAAGCTCGGTAATGGAACGAGCAA
1 CATAGATGACGAAGATGTGAACAATCCCATTAAGCTCAGTAATGGAACGAGCAA
3547284 CATAGATGACGAAGATGTGAACAATCCCATTAAGCTCAGTAATGGAACGA
1 CATAGATGACGAAGATGTGAACAATCCCATTAAGCTCAGTAATGGAACGA
3547334 ATGAACCACC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.19
Consensus pattern (54 bp):
CATAGATGACGAAGATGTGAACAATCCCATTAAGCTCAGTAATGGAACGAGCAA
Found at i:3558023 original size:17 final size:17
Alignment explanation
Indices: 3558001--3558034 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3557991 AGTTTTTAAG
3558001 ATAATTTTCTCTAATGC
1 ATAATTTTCTCTAATGC
3558018 ATAATTTTCTCTAATGC
1 ATAATTTTCTCTAATGC
3558035 TCCCACATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (17 bp):
ATAATTTTCTCTAATGC
Found at i:3559947 original size:6 final size:6
Alignment explanation
Indices: 3559938--3559967 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3559928 ACCCGCATCC
*
3559938 GCACCA GCACCA GCACCA GCAACA GCACCA
1 GCACCA GCACCA GCACCA GCACCA GCACCA
3559968 TGGGCCAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.37, C:0.47, G:0.17, T:0.00
Consensus pattern (6 bp):
GCACCA
Found at i:3566947 original size:24 final size:21
Alignment explanation
Indices: 3566904--3566950 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
3566894 ACAAATCTTG
*
3566904 AAATATAAAAAATATTTTTTT
1 AAATATAAAAAAAATTTTTTT
*
3566925 AAATATAATAAAAAATTAATTTT
1 AAATATAA-AAAAAATT-TTTTT
3566948 AAA
1 AAA
3566951 CCTGAGCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 7 0.32
23 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATATAAAAAAAATTTTTTT
Found at i:3567498 original size:4 final size:4
Alignment explanation
Indices: 3567489--3567513 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3567479 GTTTCACTAT
3567489 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
3567514 CATTGCTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Done.