Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 17 of 163
Found at i:4831975 original size:18 final size:18
Alignment explanation
Indices: 4831954--4832015 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
4831944 TAAATTCTAA
4831954 TATATATTAGAATTTATT
1 TATATATTAGAATTTATT
**
4831972 TATATATT-TTATTTA-T
1 TATATATTAGAATTTATT
*
4831988 AATATATTAGAATATTATAT
1 TATATATTAGAAT-TTAT-T
4832008 TA-ATATTA
1 TATATATTA
4832016 TTTTTATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
16 8 0.24
17 7 0.21
18 11 0.32
19 6 0.18
20 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TATATATTAGAATTTATT
Found at i:4831993 original size:34 final size:35
Alignment explanation
Indices: 4831955--4832023 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
4831945 AAATTCTAAT
4831955 ATATATTAGAAT-TTAT-TTATATATT-TTATTTATA
1 ATATATTAGAATATTATATTA-ATATTATT-TTTATA
4831989 ATATATTAGAATATTATATTAATATTATTTTTATA
1 ATATATTAGAATATTATATTAATATTATTTTTATA
4832024 TTATTGATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
34 12 0.38
35 15 0.47
36 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (35 bp):
ATATATTAGAATATTATATTAATATTATTTTTATA
Found at i:4832017 original size:46 final size:44
Alignment explanation
Indices: 4831902--4832025 Score: 110
Period size: 46 Copynumber: 2.7 Consensus size: 44
4831892 ATATTAGATG
*
4831902 TTAGAATATTA-ATTCTATTATATATTTATATATTCTATTATATAAA
1 TTAGAATATTATA-T-TAATAT-TATTTATATATTCTATTATATAAA
** * *
4831948 TTCTAATA-TATATTAGA-ATTTATTTATATATTTTATTTATAATATA
1 TTAGAATATTATATTA-ATA-TTATTTATATATTCTA-TTAT-ATAAA
*
4831994 TTAGAATATTATATTAATATTATTTTTATATT
1 TTAGAATATTATATTAATATTATTTATATATT
4832026 ATTGATATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
44 17 0.27
45 8 0.13
46 30 0.48
47 8 0.13
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (44 bp):
TTAGAATATTATATTAATATTATTTATATATTCTATTATATAAA
Found at i:4832053 original size:15 final size:15
Alignment explanation
Indices: 4832033--4832096 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
4832023 ATTATTGATA
4832033 TATTTCTATTTTATT
1 TATTTCTATTTTATT
4832048 TATTTCCT-TTTTA--
1 TATTT-CTATTTTATT
*
4832061 TA--T-TA-TTTATC
1 TATTTCTATTTTATT
4832072 TATTTCTATTTTATT
1 TATTTCTATTTTATT
4832087 TATTTC-ATTT
1 TATTTCTATTT
4832097 GCATTTAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 17
0.69 0.02 0.29
Matches are distributed among these distances:
9 5 0.12
11 3 0.08
13 3 0.08
14 6 0.15
15 21 0.52
16 2 0.05
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTCTATTTTATT
Found at i:4832059 original size:39 final size:39
Alignment explanation
Indices: 4832016--4832092 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
4832006 ATTAATATTA
4832016 TTTTTATATTATTGATATATTTCTATTTTATTTATTTCC
1 TTTTTATATTATTGATATATTTCTATTTTATTTATTTCC
* *
4832055 TTTTTATATTATTTATCTATTTCTATTTTATTTATTTC
1 TTTTTATATTATTGATATATTTCTATTTTATTTATTTC
4832093 ATTTGCATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.22, C:0.08, G:0.01, T:0.69
Consensus pattern (39 bp):
TTTTTATATTATTGATATATTTCTATTTTATTTATTTCC
Found at i:4832069 original size:24 final size:23
Alignment explanation
Indices: 4832042--4832096 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
4832032 ATATTTCTAT
4832042 TTTATTTATTTCCT-TTTTATATTA
1 TTTATTTATTT-CTATTTTAT-TTA
*
4832066 TTTATCTATTTCTATTTTATTTA
1 TTTATTTATTTCTATTTTATTTA
4832089 TTTCATTT
1 TTT-ATTT
4832097 GCATTTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTATTTATTTCTATTTTATTTA
Found at i:4832087 original size:19 final size:19
Alignment explanation
Indices: 4831967--4832089 Score: 81
Period size: 19 Copynumber: 6.4 Consensus size: 19
4831957 ATATTAGAAT
4831967 TTATTTATATATTT-TAT-
1 TTATTTATATATTTCTATA
* ***
4831984 TTA-TAATATATTAGAATA
1 TTATTTATATATTTCTATA
*
4832002 TTATATTAATATTATTTTTATA
1 TTAT-TT-ATA-TATTTCTATA
* *
4832024 TTATTGATATATTTCTATT
1 TTATTTATATATTTCTATA
* * *
4832043 TTATTTATTTCCTTTTTATA
1 TTATTTATAT-ATTTCTATA
* *
4832063 TTATTTATCTATTTCTATT
1 TTATTTATATATTTCTATA
4832082 TTATTTAT
1 TTATTTAT
4832090 TTCATTTGCA
Statistics
Matches: 80, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
16 8 0.10
17 5 0.06
18 3 0.04
19 30 0.38
20 19 0.24
21 4 0.05
22 11 0.14
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATTTATATATTTCTATA
Found at i:4833317 original size:28 final size:28
Alignment explanation
Indices: 4833285--4833344 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
4833275 AAAACGGGAC
*
4833285 TTTTGGA-TACCCGAGGGCAAAATGGTAA
1 TTTTGGACTACCAG-GGGCAAAATGGTAA
**
4833313 TTTTGGACTTGCAGGGGCAAAATGGTAA
1 TTTTGGACTACCAGGGGCAAAATGGTAA
4833341 TTTT
1 TTTT
4833345 TGGTGAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (28 bp):
TTTTGGACTACCAGGGGCAAAATGGTAA
Found at i:4833358 original size:29 final size:28
Alignment explanation
Indices: 4833326--4833475 Score: 94
Period size: 29 Copynumber: 5.1 Consensus size: 28
4833316 TGGACTTGCA
4833326 GGGGCAAAATGGTAATTTTTGGTGAAATT
1 GGGGCAAAATGGTAA-TTTTGGTGAAATT
*
4833355 GGGGTCGAAAATGG-AATTTTGG-AAAATTT
1 GGGG-C-AAAATGGTAATTTTGGTGAAA-TT
* *
4833384 GGGGGTAAAATGGTAATTTTGGTAAAATT
1 -GGGGCAAAATGGTAATTTTGGTGAAATT
**
4833413 GAGGTTAAAAATGG-AATTTT-G-GAAAGTTT
1 G-GG-GCAAAATGGTAATTTTGGTGAAA--TT
* *
4833442 GGGGGTAAAATGGTCATTTTTGGTGAAATCT
1 -GGGGCAAAATGGT-AATTTTGGTGAAAT-T
4833473 GGG
1 GGG
4833476 TTAAAAATGG
Statistics
Matches: 97, Mismatches: 8, Indels: 31
0.71 0.06 0.23
Matches are distributed among these distances:
27 3 0.03
28 19 0.20
29 34 0.35
30 28 0.29
31 9 0.09
32 4 0.04
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (28 bp):
GGGGCAAAATGGTAATTTTGGTGAAATT
Found at i:4833375 original size:58 final size:57
Alignment explanation
Indices: 4833303--4833522 Score: 239
Period size: 59 Copynumber: 3.7 Consensus size: 57
4833293 ACCCGAGGGC
* * **
4833303 AAAATGGTAATTTTGG-ACTTGCAGGGGCAAAATGGTAATTTTTGGTGAAATTGGGGTCG
1 AAAATGG-AATTTTGGAATTTG--GGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTA
* *
4833362 AAAATGGAATTTTGGAAAATTTGGGGGTAAAATGGTAA-TTTTGGTAAAATTGAGGTTA
1 AAAATGGAATTTTGG--AATTTGGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTA
*
4833420 AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTCATTTTTGGTGAAATCT-GGGTTA
1 AAAATGGAATTTTGG-AA-TTTGGGGGTAAAATGGTAATTTTTGGTGAAAT-TGGGGTTA
* *
4833479 AAAATGGAAGTTTGGGAAGTCTGGGGGTAAAATAGGTAATTTTT
1 AAAATGGAA-TTTTGGAA-TTTGGGGGTAAAAT-GGTAATTTTT
4833523 AGAAGTTTTA
Statistics
Matches: 141, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
57 3 0.02
58 57 0.40
59 62 0.44
60 15 0.11
61 4 0.03
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (57 bp):
AAAATGGAATTTTGGAATTTGGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTA
Found at i:4833394 original size:59 final size:59
Alignment explanation
Indices: 4833326--4833522 Score: 272
Period size: 59 Copynumber: 3.3 Consensus size: 59
4833316 TGGACTTGCA
* ** *
4833326 GGGGCAAAATGGTAATTTTTGGTGAAATTGGGGTCGAAAATGGAATTTTGGAAAATTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTG
* *
4833385 GGGGTAAAATGGTAA-TTTTGGTAAAATTGAGGTTAAAAATGGAATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTG
* * * *
4833443 GGGGTAAAATGGTCATTTTTGGTGAAATCT-GGGTTAAAAATGGAAGTTTGGGAAGTCTG
1 GGGGTAAAATGGTAATTTTTGGTGAAAT-TGGGGTTAAAAATGGAATTTTGGAAAGTTTG
4833502 GGGGTAAAATAGGTAATTTTT
1 GGGGTAAAAT-GGTAATTTTT
4833523 AGAAGTTTTA
Statistics
Matches: 122, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
58 52 0.43
59 60 0.49
60 10 0.08
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTG
Found at i:4833509 original size:29 final size:29
Alignment explanation
Indices: 4833362--4833510 Score: 108
Period size: 29 Copynumber: 5.1 Consensus size: 29
4833352 ATTGGGGTCG
* * *
4833362 AAAATGGAATTTTGGAAAATTTGGGGGT-
1 AAAATGGAATTTTGGGAAGTCTGGGGGTA
* * * *
4833390 AAAATGGTAATTTTGGTAAAAT-TGAGGTTA
1 AAAATGG-AATTTTGG-GAAGTCTGGGGGTA
* *
4833420 AAAATGGAATTTTGGAAAGTTTGGGGGT-
1 AAAATGGAATTTTGGGAAGTCTGGGGGTA
* * *
4833448 AAAATGGTCATTTTTGGTGAAATCT-GGGTTA
1 AAAATGG--AATTTTGG-GAAGTCTGGGGGTA
*
4833479 AAAATGGAAGTTTGGGAAGTCTGGGGGTA
1 AAAATGGAATTTTGGGAAGTCTGGGGGTA
4833508 AAA
1 AAA
4833511 TAGGTAATTT
Statistics
Matches: 98, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
28 24 0.24
29 40 0.41
30 23 0.23
31 11 0.11
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.32
Consensus pattern (29 bp):
AAAATGGAATTTTGGGAAGTCTGGGGGTA
Found at i:4833542 original size:59 final size:57
Alignment explanation
Indices: 4833326--4833550 Score: 195
Period size: 59 Copynumber: 3.8 Consensus size: 57
4833316 TGGACTTGCA
* * * * *
4833326 GGGGCAAAATGGTAATTTTTGGTGAAA-TTGGGGTCGAAAATGGAATTTTGGAAAATTTG
1 GGGGTAAAATGGTAATTTTT--AGAAATTTAGGGT-AAAAATGGAATTTTGGAAAGTTTG
* *
4833385 GGGGTAAAATGGTAATTTTGGTA-AAATTGAGGTTAAAAATGGAATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTT--TAGAAATTTAGGGTAAAAATGGAATTTTGGAAAGTTTG
* * * * * *
4833443 GGGGTAAAATGGTCATTTTTGGTGAAATCT-GGGTTAAAAATGGAAGTTTGGGAAGTCTG
1 GGGGTAAAATGGTAATTTTT--AGAAATTTAGGG-TAAAAATGGAATTTTGGAAAGTTTG
* * *
4833502 GGGGTAAAATAGGTAATTTTTAGAAGTTTTAGGGTCAAAATGTAATTTT
1 GGGGTAAAAT-GGTAATTTTTAGAA-ATTTAGGGTAAAAATGGAATTTT
4833551 CTAAAATTTT
Statistics
Matches: 134, Mismatches: 22, Indels: 20
0.76 0.12 0.11
Matches are distributed among these distances:
56 1 0.01
58 48 0.36
59 72 0.54
60 12 0.09
61 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTAGAAATTTAGGGTAAAAATGGAATTTTGGAAAGTTTG
Found at i:4833547 original size:29 final size:29
Alignment explanation
Indices: 4833514--4833578 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
4833504 GGTAAAATAG
* *
4833514 GTAATTTT-TAGAAGTTTTAGGGTCAAAAT
1 GTAATTTTCTA-AAATTTTAAGGTCAAAAT
4833543 GTAATTTTCTAAAATTTTAAGGTCAAAAT
1 GTAATTTTCTAAAATTTTAAGGTCAAAAT
4833572 GTAATTT
1 GTAATTT
4833579 CTGGACTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 31 0.94
30 2 0.06
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (29 bp):
GTAATTTTCTAAAATTTTAAGGTCAAAAT
Found at i:4835538 original size:12 final size:13
Alignment explanation
Indices: 4835515--4835570 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 13
4835505 ACTTTGGACT
4835515 TTTTTAATTTAAA
1 TTTTTAATTTAAA
4835528 TTTTTAA-TTAAA
1 TTTTTAATTTAAA
*
4835540 TTTAAATTTATTTCAAA
1 TTT---TTAATTT-AAA
4835557 TATTTTAATTTAAA
1 T-TTTTAATTTAAA
4835571 ATGAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
12 8 0.23
13 7 0.20
14 3 0.09
15 9 0.26
16 2 0.06
17 4 0.11
18 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAATTTAAA
Found at i:4843840 original size:10 final size:10
Alignment explanation
Indices: 4843810--4843858 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
4843800 ACATTAACAA
4843810 TTAATTAATTT
1 TTAA-TAATTT
*
4843821 TTAAT-TTTT
1 TTAATAATTT
*
4843830 TTTATAA-TT
1 TTAATAATTT
4843839 TTAATAATTT
1 TTAATAATTT
4843849 TTAA-AATTT
1 TTAATAATTT
4843858 T
1 T
4843859 AAAAAATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 21 0.66
10 7 0.22
11 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTAATAATTT
Found at i:4846842 original size:41 final size:41
Alignment explanation
Indices: 4846797--4846874 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
4846787 TTTAAAAAGG
4846797 GGGCAAAGTTCTACCGACATTATT-TTCTCTACATACACAGA
1 GGGCAAAGTTCTACCGACATTATTATT-TCTACATACACAGA
* *
4846838 GGGCAAAGTTCTACCGGCATTATTATTTTTACATACA
1 GGGCAAAGTTCTACCGACATTATTATTTCTACATACA
4846875 AGACTCAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (41 bp):
GGGCAAAGTTCTACCGACATTATTATTTCTACATACACAGA
Found at i:4849291 original size:20 final size:20
Alignment explanation
Indices: 4849261--4849334 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
4849251 AACTATTTTG
* *
4849261 ATAATAGTAATTAATG-TTT
1 ATAATAATAATAAATGCTTT
4849280 AGTAATAATAATAAATGCTTT
1 A-TAATAATAATAAATGCTTT
* *
4849301 AATAATATTAATAAATGTTTT
1 -ATAATAATAATAAATGCTTT
*
4849322 ATAATAATGATAA
1 ATAATAATAATAA
4849335 TCATTAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
19 1 0.02
20 24 0.52
21 20 0.43
22 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.42
Consensus pattern (20 bp):
ATAATAATAATAAATGCTTT
Found at i:4849292 original size:41 final size:41
Alignment explanation
Indices: 4849242--4849346 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 41
4849232 AATAATATTA
* * * * *
4849242 AATATTAATAACTATTTTGATAATAGTAATTAATG-TTTAGT
1 AATAATAATAAATACTTTAATAATAGTAATAAATGTTTTA-T
* *
4849283 AATAATAATAAATGCTTTAATAATATTAATAAATGTTTTAT
1 AATAATAATAAATACTTTAATAATAGTAATAAATGTTTTAT
* *
4849324 AATAATGAT-AAT-CATTAATAATA
1 AATAATAATAAATACTTTAATAATA
4849347 TTTTTAATAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
39 10 0.19
40 3 0.06
41 37 0.69
42 4 0.07
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.43
Consensus pattern (41 bp):
AATAATAATAAATACTTTAATAATAGTAATAAATGTTTTAT
Found at i:4849305 original size:18 final size:17
Alignment explanation
Indices: 4849282--4849329 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 17
4849272 TAATGTTTAG
4849282 TAATAATAATAAATGCTT
1 TAATAATAATAAATG-TT
4849300 TAATAATATTAATAAATGTT
1 TAAT-A-A-TAATAAATGTT
*
4849320 TTATAATAAT
1 TAATAATAAT
4849330 GATAATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 4 0.15
18 5 0.19
19 2 0.08
20 6 0.23
21 9 0.35
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
TAATAATAATAAATGTT
Found at i:4849341 original size:30 final size:30
Alignment explanation
Indices: 4849302--4849359 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
4849292 AAATGCTTTA
4849302 ATAATATTAATAA-ATGTTTT-ATAATAATG
1 ATAATATTAATAATAT-TTTTAATAATAATG
4849331 ATAATCATTAATAATATTTTTAATAATAA
1 ATAAT-ATTAATAATATTTTTAATAATAA
4849360 AAAAAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 5 0.19
30 12 0.46
31 9 0.35
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (30 bp):
ATAATATTAATAATATTTTTAATAATAATG
Found at i:4850437 original size:29 final size:30
Alignment explanation
Indices: 4850395--4850729 Score: 129
Period size: 29 Copynumber: 11.5 Consensus size: 30
4850385 CAAACTTTCT
4850395 AAAATT-CCATTTTAACCCTAATTTTACCC
1 AAAATTACCATTTTAACCCTAATTTTACCC
* *
4850424 AAAATTACCA-TTTAACCCCCGAACTTT--CC
1 AAAATTACCATTTTAA--CCCTAATTTTACCC
* * *
4850453 AAAATT-TCATTTTAAACCTCAATTTCACCC
1 AAAATTACCATTTTAACCCT-AATTTTACCC
* * * *
4850483 AAAATCACCATTTTACCCCTGAACTTT--CT
1 AAAATTACCATTTTAACCCT-AATTTTACCC
* * *
4850512 AAAA-TCCCA-TTTAACCCCAATTTTACCA
1 AAAATTACCATTTTAACCCTAATTTTACCC
* *
4850540 AAAATTACCATTTTACCCCTAAACTTT--CC
1 AAAATTACCATTTTAACCCT-AATTTTACCC
** * *
4850569 AAAA-T-CTCATTTTAACCCCGATTTCACCA
1 AAAATTAC-CATTTTAACCCTAATTTTACCC
* *
4850598 AAAATTACTATTTT-ACCTACTAACTTT--CC
1 AAAATTACCATTTTAACC--CTAATTTTACCC
* * * *
4850627 AAAA--ACCTATTTTTAGCCCCAATTTCACCA
1 AAAATTACC-A-TTTTAACCCTAATTTTACCC
** * * *
4850657 AAAATTACTGTTTTACCCCCGAACTTT--CC
1 AAAATTACCATTTTA-ACCCTAATTTTACCC
* *
4850686 AAAATT-CCATTTTCAACCCTAATTTCACCA
1 AAAATTACCATTTT-AACCCTAATTTTACCC
4850716 AAAATTA-CATTTTA
1 AAAATTACCATTTTA
4850730 CCCCCGAAAG
Statistics
Matches: 216, Mismatches: 58, Indels: 64
0.64 0.17 0.19
Matches are distributed among these distances:
26 5 0.02
27 15 0.07
28 43 0.20
29 64 0.30
30 48 0.22
31 39 0.18
32 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCTAATTTTACCC
Found at i:4850495 original size:59 final size:58
Alignment explanation
Indices: 4850382--4850737 Score: 405
Period size: 59 Copynumber: 6.1 Consensus size: 58
4850372 GCTCTCTAGG
* * * * * *
4850382 CCCCAAACTTTCTAAAATTCCATTTTAACCCTAATTTTACCCAAAATTACCATTTAAC
1 CCCCGAACTTTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
* * * *
4850440 CCCCGAACTTTCCAAAATTTCATTTTAAACCTCAATTTCACCCAAAATCACCATTTTAC
1 CCCCGAACTTTCCAAAATTCCATTTT-AACCCCAATTTCACCAAAAATTACCATTTTAC
* * * *
4850499 CCCTGAACTTTCTAAAATCCCA-TTTAACCCCAATTTTACCAAAAATTACCATTTTAC
1 CCCCGAACTTTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
** * *
4850556 CCCTAAACTTTCCAAAA-TCTCATTTTAACCCCGATTTCACCAAAAATTACTATTTTAC
1 CCCCGAACTTTCCAAAATTC-CATTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
** * * * **
4850614 CTACTAACTTTCCAAAA-ACCTATTTTTAGCCCCAATTTCACCAAAAATTACTGTTTTAC
1 CCCCGAACTTTCCAAAATTCC-A-TTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
*
4850673 CCCCGAACTTTCCAAAATTCCATTTTCAACCCTAATTTCACCAAAAATTA-CATTTTAC
1 CCCCGAACTTTCCAAAATTCCATTTT-AACCCCAATTTCACCAAAAATTACCATTTTAC
4850731 CCCCGAA
1 CCCCGAA
4850738 AGTTAAAAAT
Statistics
Matches: 253, Mismatches: 38, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
56 1 0.00
57 46 0.18
58 90 0.36
59 114 0.45
60 2 0.01
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (58 bp):
CCCCGAACTTTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
Found at i:4850683 original size:174 final size:174
Alignment explanation
Indices: 4850382--4850733 Score: 424
Period size: 174 Copynumber: 2.0 Consensus size: 174
4850372 GCTCTCTAGG
* * * * *
4850382 CCCCAAACTTTCTAAAATTCCATTTTAACCCTAATTTTACCCAAAATTACCATTTAACCCCCGAA
1 CCCCAAACTTTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCATTTAACCCACGAA
** * * * *
4850447 CTTTCCAAAATTTCATTTTAAACCTCAATTTCACCCAAAATCACCATTTTACCCCTGAACTTTCT
66 CTTTCCAAAACCTCATTTTAAACCCCAATTTCACCAAAAATCACCATTTTACCCCCGAACTTTCC
*
4850512 AAAATCCCA-TTT-AACCCCAATTTTACCAAAAATTACCATTTTA
131 AAAATCCCATTTTCAACCCCAATTTCACCAAAAATTA-CATTTTA
* * * * *
4850555 CCCCTAAACTTTCCAAAA-TCTCATTTTAACCCCGATTTCACCAAAAATTACTATTTTACCTACT
1 CCCC-AAACTTTCCAAAATTC-CATTTTAACCCCAATTTCACCAAAAATTACCATTTAACCCACG
* * * **
4850619 AACTTTCCAAAAACCT-ATTTTTAGCCCCAATTTCACCAAAAATTACTGTTTTACCCCCGAACTT
64 AACTTTCC-AAAACCTCATTTTAAACCCCAATTTCACCAAAAATCACCATTTTACCCCCGAACTT
* *
4850683 TCCAAAATTCCATTTTCAACCCTAATTTCACCAAAAATTACATTTTA
128 TCCAAAATCCCATTTTCAACCCCAATTTCACCAAAAATTACATTTTA
4850730 CCCC
1 CCCC
4850734 CGAAAGTTAA
Statistics
Matches: 150, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
173 6 0.04
174 104 0.69
175 19 0.13
176 21 0.14
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (174 bp):
CCCCAAACTTTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCATTTAACCCACGAA
CTTTCCAAAACCTCATTTTAAACCCCAATTTCACCAAAAATCACCATTTTACCCCCGAACTTTCC
AAAATCCCATTTTCAACCCCAATTTCACCAAAAATTACATTTTA
Found at i:4856625 original size:82 final size:82
Alignment explanation
Indices: 4856488--4856653 Score: 296
Period size: 82 Copynumber: 2.0 Consensus size: 82
4856478 AGAAAAGTGA
*
4856488 AAGACATTAGGTCTCCGCTACGATGGGTATGACAGTAAATGGTCAAAATCGGGATGATTTCGAGG
1 AAGACATTAGGTCTCCGCTACGATGGGTATGACAGTAAATGGTCAAAATCGGGATGATTACGAGG
* *
4856553 GATAATGAGTGTATGAT
66 GATAAGGAGTGTATCAT
*
4856570 AAGACATTAGGTCTCCGCTACGATGGGTATGGCAGTAAATGGTCAAAATCGGGATGATTACGAGG
1 AAGACATTAGGTCTCCGCTACGATGGGTATGACAGTAAATGGTCAAAATCGGGATGATTACGAGG
4856635 GATAAGGAGTGTATCAT
66 GATAAGGAGTGTATCAT
4856652 AA
1 AA
4856654 TGGAGACTGA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.25
Consensus pattern (82 bp):
AAGACATTAGGTCTCCGCTACGATGGGTATGACAGTAAATGGTCAAAATCGGGATGATTACGAGG
GATAAGGAGTGTATCAT
Found at i:4863335 original size:200 final size:199
Alignment explanation
Indices: 4862986--4863622 Score: 1096
Period size: 200 Copynumber: 3.2 Consensus size: 199
4862976 ACAAAACATT
* *
4862986 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAGCGCTCAACACGAGCCAAT
1 GAGGCAGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
*
4863051 CTTCGAACCCAGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
66 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
*
4863116 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
131 TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
4863181 TAAGC
196 -AAGC
*
4863186 GAGGCAGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACACTCAACACGAGCCAAT
1 GAGGCAGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
4863251 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
66 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* *
4863316 TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTAAGAAGATCCAGAGAAGCGAATCAAAA
131 TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
4863381 CAAGC
196 -AAGC
4863386 GAGGCAGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
1 GAGGCAGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
4863451 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
66 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* * *
4863516 TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCTTGAGGAGATCTAGAGAAGCGAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
* *
4863581 CAGAT
196 AAG-C
* *
4863586 GA-TCACGATCATCTTCCTGATGAGACACAGAGAAGAA
1 GAGGCA-G-TCATCTTCCTGATGAGATACAGAGAAGAA
4863623 GACTAGGTCA
Statistics
Matches: 416, Mismatches: 18, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
199 4 0.01
200 384 0.92
201 28 0.07
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.19
Consensus pattern (199 bp):
GAGGCAGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
AAGC
Found at i:4864030 original size:17 final size:17
Alignment explanation
Indices: 4863991--4864031 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4863981 TAGATTTATT
**
4863991 TTAAATTTAAATTTGCA
1 TTAAATTTAAATTTAAA
*
4864008 TAAAATTTAAATTTAAA
1 TTAAATTTAAATTTAAA
4864025 TTAAATT
1 TTAAATT
4864032 AGATAAACTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:4864782 original size:21 final size:20
Alignment explanation
Indices: 4864749--4864804 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
4864739 AATAGTAATT
*
4864749 AATGTTTAGTAATAACAATA
1 AATGTTTAATAATAACAATA
**
4864769 AATGCTTTAATAATATTAATA
1 AATG-TTTAATAATAACAATA
*
4864790 AATGTTTTATAATAA
1 AATGTTTAATAATAA
4864805 TGATAATCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (20 bp):
AATGTTTAATAATAACAATA
Found at i:4864803 original size:20 final size:20
Alignment explanation
Indices: 4864718--4864803 Score: 75
Period size: 20 Copynumber: 4.2 Consensus size: 20
4864708 AATAATATTA
* *
4864718 AATATTAATAACTATTTTGAT
1 AATATTAATAAATGTTTT-AT
* *
4864739 AATAGTAATTAATG-TTTAGT
1 AATATTAATAAATGTTTTA-T
** *
4864759 AATAACAATAAATGCTTTAAT
1 AATATTAATAAATG-TTTTAT
4864780 AATATTAATAAATGTTTTAT
1 AATATTAATAAATGTTTTAT
4864800 AATA
1 AATA
4864804 ATGATAATCA
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
19 1 0.02
20 24 0.47
21 23 0.45
22 3 0.06
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (20 bp):
AATATTAATAAATGTTTTAT
Found at i:4864810 original size:20 final size:21
Alignment explanation
Indices: 4864737--4864822 Score: 72
Period size: 20 Copynumber: 4.3 Consensus size: 21
4864727 AACTATTTTG
* *
4864737 ATAATAGTAATTAATG-TTTA
1 ATAATAATAATAAATGCTTTA
* *
4864757 GTAATAACAATAAATGCTTTA
1 ATAATAATAATAAATGCTTTA
* *
4864778 ATAATATTAATAAATG-TTTT
1 ATAATAATAATAAATGCTTTA
* *
4864798 ATAATAATGAT-AAT-CATTA
1 ATAATAATAATAAATGCTTTA
4864817 ATAATA
1 ATAATA
4864823 TTTTTAATAA
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
19 11 0.21
20 24 0.46
21 17 0.33
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (21 bp):
ATAATAATAATAAATGCTTTA
Found at i:4864817 original size:30 final size:30
Alignment explanation
Indices: 4864778--4864835 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
4864768 AAATGCTTTA
4864778 ATAATATTAATAA-ATGTTTT-ATAATAATG
1 ATAATATTAATAATAT-TTTTAATAATAATG
4864807 ATAATCATTAATAATATTTTTAATAATAA
1 ATAAT-ATTAATAATATTTTTAATAATAA
4864836 AAAAAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 5 0.19
30 12 0.46
31 9 0.35
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (30 bp):
ATAATATTAATAATATTTTTAATAATAATG
Found at i:4865913 original size:29 final size:29
Alignment explanation
Indices: 4865881--4865972 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
4865871 TCCATTTTTA
4865881 ACCCCAATTTTACCCAAAATTACCATTTG
1 ACCCCAATTTTACCCAAAATTACCATTTG
*
4865910 ACCCCCAAACTTT--CCAAAATT-CCATTTTG
1 A-CCCC-AATTTTACCCAAAATTACCA-TTTG
** * * *
4865939 ACCCTGATTTCACCAAAAATTACCATTTT
1 ACCCCAATTTTACCCAAAATTACCATTTG
4865968 ACCCC
1 ACCCC
4865973 CAAACTTTCC
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
27 3 0.06
28 6 0.12
29 28 0.57
30 7 0.14
31 5 0.10
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.30
Consensus pattern (29 bp):
ACCCCAATTTTACCCAAAATTACCATTTG
Found at i:4865978 original size:58 final size:58
Alignment explanation
Indices: 4865853--4866324 Score: 501
Period size: 58 Copynumber: 8.1 Consensus size: 58
4865843 GCTCTCTAGT
** * * * *
4865853 CCCCAAACTTTTTAAAATTCCATTTTTAACCCCAATTTTACCCAAAATTACCATTTGAC
1 CCCCAAACTTTCCAAAATTCCA-TTTTAACCCTAATTTCACCAAAAATTACCATTTTAC
* *
4865912 CCCCAAACTTTCCAAAATTCCATTTTGACCCTGATTTCACCAAAAATTACCATTTTAC
1 CCCCAAACTTTCCAAAATTCCATTTTAACCCTAATTTCACCAAAAATTACCATTTTAC
** * *
4865970 CCCCAAACTTTCCAAAATTTAATTTTTGACCCTAATTTCACCAAAAATTACCA-CTTAC
1 CCCCAAACTTTCCAAAATTCCA-TTTTAACCCTAATTTCACCAAAAATTACCATTTTAC
* *
4866028 CCCCAAACTTTCTAAAATTCCATTTTTAACCCCAATTTCA-CATAAAATTACCATTTTAC
1 CCCCAAACTTTCCAAAATTCCA-TTTTAACCCTAATTTCACCA-AAAATTACCATTTTAC
* * *
4866087 CCCCAAACTTTCCAAAATCCCATTTTAACCTTGATTTCACCAAAAATTACCATTTTAC
1 CCCCAAACTTTCCAAAATTCCATTTTAACCCTAATTTCACCAAAAATTACCATTTTAC
* * *
4866145 CCCTAAACTTTCCAAAA-TCTCATTTTAA-CCTCGATTTCACCAAAAAATT-CTATTTTAC
1 CCCCAAACTTTCCAAAATTC-CATTTTAACCCT-AATTTCACC-AAAAATTACCATTTTAC
* * * * * * *
4866203 CCACTAACTTTCTAAAA-CCCTATTTTTAA-CCTCAATTTTACTAAAAATTACCGTTTTAC
1 CCCCAAACTTTCCAAAATTCC-A-TTTTAACCCT-AATTTCACCAAAAATTACCATTTTAC
** * *
4866262 CCTGAAACTTTTCAAAATTCCATTTTCGACCCTAATTTCACCAAAAATTA-CATTTTTAC
1 CCCCAAACTTTCCAAAATTCCATTTT-AACCCTAATTTCACCAAAAATTACCA-TTTTAC
4866321 CCCC
1 CCCC
4866325 GAAAGTCAAA
Statistics
Matches: 350, Mismatches: 49, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
57 6 0.02
58 197 0.56
59 142 0.41
60 5 0.01
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (58 bp):
CCCCAAACTTTCCAAAATTCCATTTTAACCCTAATTTCACCAAAAATTACCATTTTAC
Found at i:4866066 original size:117 final size:116
Alignment explanation
Indices: 4865853--4866324 Score: 508
Period size: 117 Copynumber: 4.0 Consensus size: 116
4865843 GCTCTCTAGT
** * * * *
4865853 CCCCAAACTTTTTAAAATTCCATTTTTAACCCCAATTTTACCCAAAATTACCATTTGACCCCCAA
1 CCCCAAACTTTCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCATTT-ACCCCCAA
* **
4865918 ACTTTCCAAAATTCCATTTTGACCCTGATTTCACCAAAAATTACCATTTTAC
65 ACTTTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
*** * *
4865970 CCCCAAACTTTCCAAAATTTAATTTTTGACCCTAATTTCACCAAAAATTACCACTTACCCCCAAA
1 CCCCAAACTTTCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCATTTACCCCCAAA
*
4866035 CTTTCTAAAATTCCATTTTTAACCCCAATTTCA-CATAAAATTACCATTTTAC
66 CTTTCCAAAATTCCA-TTTTAACCCCAATTTCACCA-AAAATTACCATTTTAC
* * *
4866087 CCCCAAACTTTCCAAAATCCCA-TTTTAACCTTGATTTCACCAAAAATTACCATTTTACCCCTAA
1 CCCCAAACTTTCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCA-TTTACCCCCAA
* * *
4866151 ACTTTCCAAAA-TCTCATTTTAACCTCGATTTCACCAAAAAATT-CTATTTTAC
65 ACTTTCCAAAATTC-CATTTTAACCCCAATTTCACC-AAAAATTACCATTTTAC
* * * * * * **
4866203 CCACTAACTTTCTAAAA-CCCTATTTTTAA-CCTCAATTTTACTAAAAATTACCGTTTTACCCTG
1 CCCCAAACTTTCCAAAATCCC-ATTTTTAACCCT-AATTTCACCAAAAATTACC-ATTTACCCCC
* * *
4866266 AAACTTTTCAAAATTCCATTTTCGACCCTAATTTCACCAAAAATTA-CATTTTTAC
63 AAACTTTCCAAAATTCCATTTT-AACCCCAATTTCACCAAAAATTACCA-TTTTAC
4866321 CCCC
1 CCCC
4866325 GAAAGTCAAA
Statistics
Matches: 299, Mismatches: 42, Indels: 27
0.81 0.11 0.07
Matches are distributed among these distances:
115 3 0.01
116 94 0.31
117 179 0.60
118 23 0.08
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (116 bp):
CCCCAAACTTTCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCATTTACCCCCAAA
CTTTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
Found at i:4866129 original size:28 final size:28
Alignment explanation
Indices: 4866098--4866189 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
4866088 CCCAAACTTT
*
4866098 CCAAAATCCCATTTTAACCTTGATTTCA
1 CCAAAATCCCATTTTAACCTAGATTTCA
* * *
4866126 CCAAAAATTACCATTTTACCCCTAAACTTT--
1 CC-AAAA-TCCCATTTTA-ACCTAGA-TTTCA
* *
4866156 CCAAAATCTCATTTTAACCTCGATTTCA
1 CCAAAATCCCATTTTAACCTAGATTTCA
4866184 CCAAAA
1 CCAAAA
4866190 AATTCTATTT
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
26 3 0.06
27 4 0.08
28 16 0.33
29 8 0.16
30 11 0.22
31 4 0.08
32 3 0.06
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (28 bp):
CCAAAATCCCATTTTAACCTAGATTTCA
Found at i:4866144 original size:175 final size:174
Alignment explanation
Indices: 4865853--4866324 Score: 621
Period size: 175 Copynumber: 2.7 Consensus size: 174
4865843 GCTCTCTAGT
* * *
4865853 CCCCAAACTTTTTAAAATTCCATTTTTAACCCCAATTTTACCCAAAATTACCATTTGACCCCCAA
1 CCCCAAACTTTCTAAAATTCCATTTTTAACCCCAATTTTA-CTAAAATTACCATTTTACCCCCAA
4865918 ACTTTCCAAAATTCCATTTTGACCCTGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
65 ACTTTCCAAAATTCCATTTTGACCCTGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
* *
4865983 AAAATTTAATTTTTGACC-CTAATTTCACC-AAAAATTACCA-CTTAC
130 AAAATCTAA-TTTTAACCTC-AATTTCACCAAAAAATT-CCATCTTAC
*
4866028 CCCCAAACTTTCTAAAATTCCATTTTTAACCCCAATTTCACATAAAATTACCATTTTACCCCCAA
1 CCCCAAACTTTCTAAAATTCCATTTTTAACCCCAATTTTAC-TAAAATTACCATTTTACCCCCAA
* * * *
4866093 ACTTTCCAAAATCCCATTTTAACCTTGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCC
65 ACTTTCCAAAATTCCATTTTGACCCTGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
* * * *
4866158 AAAATCTCATTTTAACCTCGATTTCACCAAAAAATTCTATTTTAC
130 AAAATCTAATTTTAACCTCAATTTCACCAAAAAATTCCATCTTAC
* * * * * **
4866203 CCACTAACTTTCTAAAA-CCCTATTTTTAACCTCAATTTTACTAAAAATTACCGTTTTACCCTGA
1 CCCCAAACTTTCTAAAATTCC-ATTTTTAACCCCAATTTTACT-AAAATTACCATTTTACCCCCA
* *
4866267 AACTTTTCAAAATTCCATTTTCGACCCTAATTTCACCAAAAATTA-CATTTTTACCCCC
64 AACTTTCCAAAATTCCATTTT-GACCCTGATTTCACCAAAAATTACCA-TTTTACCCCC
4866325 GAAAGTCAAA
Statistics
Matches: 261, Mismatches: 28, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
174 21 0.08
175 211 0.81
176 29 0.11
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (174 bp):
CCCCAAACTTTCTAAAATTCCATTTTTAACCCCAATTTTACTAAAATTACCATTTTACCCCCAAA
CTTTCCAAAATTCCATTTTGACCCTGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCA
AAATCTAATTTTAACCTCAATTTCACCAAAAAATTCCATCTTAC
Found at i:4866190 original size:29 final size:29
Alignment explanation
Indices: 4866100--4866190 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 29
4866090 CAAACTTTCC
* *
4866100 AAAATCCCATTTTAACCTTGATTTCACCA
1 AAAATCTCATTTTAACCTAGATTTCACCA
* *
4866129 AAAAT-TACCATTTTACCCCTAAACTTT--CC-
1 AAAATCT--CATTTTA-ACCTAGA-TTTCACCA
*
4866158 AAAATCTCATTTTAACCTCGATTTCACCA
1 AAAATCTCATTTTAACCTAGATTTCACCA
4866187 AAAA
1 AAAA
4866191 ATTCTATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
26 3 0.06
27 4 0.09
28 9 0.19
29 14 0.30
30 10 0.21
31 4 0.09
32 3 0.06
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAATCTCATTTTAACCTAGATTTCACCA
Found at i:4888357 original size:61 final size:61
Alignment explanation
Indices: 4888272--4888400 Score: 154
Period size: 61 Copynumber: 2.1 Consensus size: 61
4888262 ATTTATGCAT
* ** * * *
4888272 TCTATCAATTT-GATTCTAAATATAAAAATTTTAATAAATTTAGCTC-TCAATATTTACAAAA
1 TCTATCATTTTAG-TTCTAAATATAAAAAACTTAACAAATTTAGC-CGCCAACATTTACAAAA
* *
4888333 TTTATCATTTTAGTTCTAATTATAAAAAACTTAACAAATTTAGCCGCCAACATTTACAAAA
1 TCTATCATTTTAGTTCTAAATATAAAAAACTTAACAAATTTAGCCGCCAACATTTACAAAA
4888394 TCTATCA
1 TCTATCA
4888401 ATTAGTCCTA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 1 0.02
61 55 0.96
62 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.39
Consensus pattern (61 bp):
TCTATCATTTTAGTTCTAAATATAAAAAACTTAACAAATTTAGCCGCCAACATTTACAAAA
Found at i:4901065 original size:2 final size:2
Alignment explanation
Indices: 4901058--4901101 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
4901048 AATTTATCTG
* * * *
4901058 CA CA CA CA CA CA CA CA CA CA CA AA CA TA CA TA CA CA CA TA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
4901100 CA
1 CA
4901102 TCCACATACA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.52, C:0.41, G:0.00, T:0.07
Consensus pattern (2 bp):
CA
Found at i:4904431 original size:13 final size:13
Alignment explanation
Indices: 4904413--4904437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4904403 TTGGGTCACA
4904413 AATAAGAAAATAT
1 AATAAGAAAATAT
4904426 AATAAGAAAATA
1 AATAAGAAAATA
4904438 ATTAAAATAT
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:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (13 bp):
AATAAGAAAATAT
Found at i:4904947 original size:33 final size:33
Alignment explanation
Indices: 4904905--4904972 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
4904895 TAAAAAAATA
*
4904905 ATAATACGAAAACATTGTATATAAGCTGTAATT
1 ATAATACGAAAACAATGTATATAAGCTGTAATT
* *
4904938 ATAATACGAAAACAATGTATCTTAGCTGTAATT
1 ATAATACGAAAACAATGTATATAAGCTGTAATT
4904971 AT
1 AT
4904973 CTGTCCAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (33 bp):
ATAATACGAAAACAATGTATATAAGCTGTAATT
Found at i:4905179 original size:29 final size:28
Alignment explanation
Indices: 4905116--4905170 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
4905106 ATATAAACAA
*
4905116 TATA-AAAATAATTAATTATGAAAATAG
1 TATAGAAAATAATTAAATATGAAAATAG
4905143 TATAGAAAATAGATTAAATATGAAAATA
1 TATAGAAAATA-ATTAAATATGAAAATA
4905171 TTAACGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.16
28 6 0.24
29 15 0.60
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (28 bp):
TATAGAAAATAATTAAATATGAAAATAG
Found at i:4906092 original size:18 final size:17
Alignment explanation
Indices: 4906059--4906099 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
4906049 TAATATATTT
4906059 AATTAAATAACTTAAAC
1 AATTAAATAACTTAAAC
4906076 AACTTAAAGTAAC-TAAAC
1 AA-TTAAA-TAACTTAAAC
4906094 AATTAA
1 AATTAA
4906100 TAAATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (17 bp):
AATTAAATAACTTAAAC
Found at i:4909287 original size:17 final size:17
Alignment explanation
Indices: 4909265--4909299 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4909255 CACCACCACG
4909265 ACCATGCGTCTGACACC
1 ACCATGCGTCTGACACC
* *
4909282 ACCATGCTTCTGCCACC
1 ACCATGCGTCTGACACC
4909299 A
1 A
4909300 TCGCATACGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.43, G:0.14, T:0.20
Consensus pattern (17 bp):
ACCATGCGTCTGACACC
Found at i:4910174 original size:26 final size:23
Alignment explanation
Indices: 4910145--4910202 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 23
4910135 GTCATTCGAA
*
4910145 CTTTATTTTTATTTTAATTCAATCC
1 CTTT-TTTTTATTTTAAAT-AATCC
*
4910170 TCTTTTTATTTCTTTTAAATAATCC
1 -CTTTTT-TTTATTTTAAATAATCC
4910195 CTTTTTTT
1 CTTTTTTT
4910203 ATGTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 2 0.07
24 6 0.21
25 7 0.24
26 14 0.48
ACGTcount: A:0.21, C:0.16, G:0.00, T:0.64
Consensus pattern (23 bp):
CTTTTTTTTATTTTAAATAATCC
Found at i:4910420 original size:16 final size:17
Alignment explanation
Indices: 4910399--4910430 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4910389 ATCTAGCTTT
4910399 ATATATTT-ATTTGTTA
1 ATATATTTCATTTGTTA
4910415 ATATATTTCATTTGTT
1 ATATATTTCATTTGTT
4910431 TTGAGTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.62
Consensus pattern (17 bp):
ATATATTTCATTTGTTA
Found at i:4914532 original size:9 final size:9
Alignment explanation
Indices: 4914518--4914543 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
4914508 CACACACTCT
4914518 TAAAAGAAG
1 TAAAAGAAG
4914527 TAAAAGAAG
1 TAAAAGAAG
4914536 TAAAAGAA
1 TAAAAGAA
4914544 CAACAAAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (9 bp):
TAAAAGAAG
Found at i:4920747 original size:2 final size:2
Alignment explanation
Indices: 4920734--4920770 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4920724 TTGTCATCAA
*
4920734 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4920771 GTGCCTACTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4928346 original size:9 final size:9
Alignment explanation
Indices: 4928322--4928352 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
4928312 TTCAATTATT
4928322 TTTAATTTA
1 TTTAATTTA
4928331 GTTTAATTTA
1 -TTTAATTTA
4928341 TTTAATTTA
1 TTTAATTTA
4928350 TTT
1 TTT
4928353 TAAATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (9 bp):
TTTAATTTA
Found at i:4928354 original size:10 final size:10
Alignment explanation
Indices: 4928321--4928355 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
4928311 ATTCAATTAT
4928321 TTTTAATTTA
1 TTTTAATTTA
*
4928331 GTTTAATTTA
1 TTTTAATTTA
4928341 -TTTAATTTA
1 TTTTAATTTA
4928350 TTTTAA
1 TTTTAA
4928356 ATTTTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:4931526 original size:2 final size:2
Alignment explanation
Indices: 4931519--4931575 Score: 50
Period size: 2 Copynumber: 30.0 Consensus size: 2
4931509 TTTATTCCAA
* *
4931519 AT AT AT AT AT AT AT AT AT AT AT A- AC AT -T AT AT AT TT GA- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
4931559 TT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
4931576 TCAAATTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
1 4 0.09
2 41 0.91
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4936625 original size:22 final size:22
Alignment explanation
Indices: 4936600--4936641 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4936590 ATTTTAGCAA
*
4936600 AATTAACATTTACTGTTTAACC
1 AATTAACATCTACTGTTTAACC
*
4936622 AATTATCATCTACTGTTTAA
1 AATTAACATCTACTGTTTAA
4936642 TAAAGTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (22 bp):
AATTAACATCTACTGTTTAACC
Found at i:4939699 original size:16 final size:17
Alignment explanation
Indices: 4939680--4939713 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4939670 TATATATATA
4939680 TATATATTGC-AATTTT
1 TATATATTGCTAATTTT
*
4939696 TATATATTTCTAATTTT
1 TATATATTGCTAATTTT
4939713 T
1 T
4939714 GCACTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (17 bp):
TATATATTGCTAATTTT
Found at i:4939737 original size:26 final size:26
Alignment explanation
Indices: 4939668--4939738 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 26
4939658 TTTGCAAATA
* *
4939668 TATATATATATATATATATTGCAATTTT
1 TATATATTTATA-AT-TTTTGCAATTTT
* *
4939696 TATATATTTCTAATTTTTGCACTTTT
1 TATATATTTATAATTTTTGCAATTTT
*
4939722 TATACT-TTTATCATTTT
1 TATA-TATTTATAATTTT
4939739 AATATTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 23 0.64
27 3 0.08
28 10 0.28
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (26 bp):
TATATATTTATAATTTTTGCAATTTT
Found at i:4939761 original size:18 final size:17
Alignment explanation
Indices: 4939691--4939765 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
4939681 ATATATTGCA
*
4939691 ATTTTTATATATTTCTA-
1 ATTTTTATA-ATTTTTAT
** *
4939708 ATTTTTGCACTTTTTAT
1 ATTTTTATAATTTTTAT
* * *
4939725 ACTTTTATCATTTTAAT
1 ATTTTTATAATTTTTAT
4939742 ATTTTTATGAATTTTTAT
1 ATTTTTAT-AATTTTTAT
4939760 ATTTTT
1 ATTTTT
4939766 TTATGATTTT
Statistics
Matches: 43, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
16 5 0.12
17 25 0.58
18 13 0.30
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (17 bp):
ATTTTTATAATTTTTAT
Found at i:4939763 original size:8 final size:8
Alignment explanation
Indices: 4939691--4939765 Score: 53
Period size: 8 Copynumber: 8.8 Consensus size: 8
4939681 ATATATTGCA
4939691 ATTTTTAT
1 ATTTTTAT
4939699 ATATTTCTA-
1 AT-TTT-TAT
**
4939708 ATTTTTGC
1 ATTTTTAT
4939716 ACTTTTTAT
1 A-TTTTTAT
*
4939725 ACTTTTAT
1 ATTTTTAT
*
4939733 CATTTTAAT
1 -ATTTTTAT
4939742 ATTTTTAT
1 ATTTTTAT
4939750 GAATTTTTAT
1 --ATTTTTAT
4939760 ATTTTT
1 ATTTTT
4939766 TTATGATTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
7 1 0.02
8 25 0.47
9 17 0.32
10 10 0.19
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (8 bp):
ATTTTTAT
Found at i:4939768 original size:20 final size:18
Alignment explanation
Indices: 4939735--4939786 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
4939725 ACTTTTATCA
*
4939735 TTTTAATATTTTTATGAAT
1 TTTTAATTTTTTTATG-AT
4939754 TTTTATATTTTTTTATGAT
1 TTTTA-ATTTTTTTATGAT
*
4939773 TTTTAATTATTTTA
1 TTTTAATTTTTTTA
4939787 ACAAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 8 0.27
19 12 0.40
20 10 0.33
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (18 bp):
TTTTAATTTTTTTATGAT
Found at i:4939775 original size:18 final size:17
Alignment explanation
Indices: 4939727--4939785 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 17
4939717 CTTTTTATAC
*
4939727 TTTTATCATTTTAATAT
1 TTTTATGATTTTAATAT
*
4939744 TTTTATGAATTTTTATATTT
1 TTTTATG-A-TTTTA-ATAT
4939764 TTTTATGATTTTTAATTAT
1 TTTTATGA-TTTTAA-TAT
4939783 TTT
1 TTT
4939786 AACAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 6 0.17
18 2 0.06
19 17 0.49
20 10 0.29
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTATGATTTTAATAT
Found at i:4942905 original size:26 final size:28
Alignment explanation
Indices: 4942857--4942914 Score: 84
Period size: 26 Copynumber: 2.1 Consensus size: 28
4942847 ATACTTCATG
*
4942857 TTAATTTTTCTGAATATTTTTATTATTT
1 TTAATTTTTCTGAATATTTTTATAATTT
*
4942885 TTAA-TTTT-TGACTATTTTTATAATTT
1 TTAATTTTTCTGAATATTTTTATAATTT
4942911 TTAA
1 TTAA
4942915 ATCATTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 20 0.71
27 4 0.14
28 4 0.14
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (28 bp):
TTAATTTTTCTGAATATTTTTATAATTT
Found at i:4944589 original size:24 final size:24
Alignment explanation
Indices: 4944561--4944619 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
4944551 TAGAGTAATA
*
4944561 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
4944585 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
4944609 AGAGTTTAACT
1 AGAGTTTAACT
4944620 AAAAGATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:4946613 original size:24 final size:24
Alignment explanation
Indices: 4946552--4946614 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
4946542 TAGAGTAATA
* *
4946552 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
4946576 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
4946600 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
4946615 GATTATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:4947218 original size:31 final size:30
Alignment explanation
Indices: 4947167--4947260 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 30
4947157 AAATTAAAAC
* *
4947167 TTTT-AAAATGGTTAAATAACGGTCAAATT
1 TTTTCAAAATGATCAAATAACGGTCAAATT
* * *
4947196 TTTTCAAATATGCTCAAATAAC-GCCTAAACT
1 TTTTCAAA-ATGATCAAATAACGGTC-AAATT
* * *
4947227 TTTTGAAAATGATTAAATAAAGGTCAAATT
1 TTTTCAAAATGATCAAATAACGGTCAAATT
4947257 TTTT
1 TTTT
4947261 TCGAGTACAC
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
29 4 0.08
30 23 0.45
31 24 0.47
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (30 bp):
TTTTCAAAATGATCAAATAACGGTCAAATT
Found at i:4951739 original size:26 final size:26
Alignment explanation
Indices: 4951710--4951766 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
4951700 AAATTTGAAG
4951710 ATTAATCTT-TTAAAAAGAATTAAATT
1 ATTAATCTTATTAAAAA-AATTAAATT
*
4951736 ATT-ATGTTGATTAAAAAAATTAAATT
1 ATTAATCTT-ATTAAAAAAATTAAATT
*
4951762 TTTAA
1 ATTAA
4951767 CGATGTTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 4 0.15
26 14 0.54
27 8 0.31
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (26 bp):
ATTAATCTTATTAAAAAAATTAAATT
Found at i:4971570 original size:19 final size:19
Alignment explanation
Indices: 4971546--4971589 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4971536 TCTGTTAGGT
* *
4971546 AGTTAGCATTGGTTAAGGC
1 AGTTAGCATTAGTTAAGAC
* *
4971565 AGTTAGTATTAGTTGAGAC
1 AGTTAGCATTAGTTAAGAC
4971584 AGTTAG
1 AGTTAG
4971590 TAAGTTTCTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.34
Consensus pattern (19 bp):
AGTTAGCATTAGTTAAGAC
Found at i:4972967 original size:21 final size:21
Alignment explanation
Indices: 4972928--4972967 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4972918 CTCTTGAAGC
*
4972928 ACCTCTTGCTCCCCTAAAATA
1 ACCTCTTGCTCCCCGAAAATA
* *
4972949 ACCTCTTGTTCCTCGAAAA
1 ACCTCTTGCTCCCCGAAAA
4972968 CCACCTCTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.35, G:0.07, T:0.30
Consensus pattern (21 bp):
ACCTCTTGCTCCCCGAAAATA
Found at i:4974666 original size:22 final size:21
Alignment explanation
Indices: 4974627--4974671 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4974617 AAAAACAAAT
*
4974627 AAAAAAATTATGATAAAAGGA
1 AAAAAAATTATGATAAAAAGA
* *
4974648 AAAAAAATTTTGTTCAAAAAGA
1 AAAAAAATTATGAT-AAAAAGA
4974670 AA
1 AA
4974672 CACACATACG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.22
Consensus pattern (21 bp):
AAAAAAATTATGATAAAAAGA
Found at i:4975518 original size:24 final size:25
Alignment explanation
Indices: 4975467--4975518 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
4975457 TCTGGTTTTG
* *
4975467 ACAAAAATGCATGAAATTATATACC
1 ACAAAAATGCATGAAATTATAAAAC
* *
4975492 ACAAATATGCATTAAA-TATAAAAC
1 ACAAAAATGCATGAAATTATAAAAC
4975516 ACA
1 ACA
4975519 TTTTAACTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.23
Consensus pattern (25 bp):
ACAAAAATGCATGAAATTATAAAAC
Found at i:4985709 original size:18 final size:17
Alignment explanation
Indices: 4985686--4985720 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
4985676 AAAAAGGAAA
4985686 AAAAGAAGAGAAGAAAAT
1 AAAAGAAGAGAA-AAAAT
4985704 AAAAGAAGAGAAAAAAT
1 AAAAGAAGAGAAAAAAT
4985721 GGAGATGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (17 bp):
AAAAGAAGAGAAAAAAT
Found at i:4988353 original size:12 final size:13
Alignment explanation
Indices: 4988325--4988357 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
4988315 ATTACCAACT
4988325 ATAATTTATTGATC
1 ATAA-TTATTGATC
4988339 ATAATTATT-ATC
1 ATAATTATTGATC
4988351 ATAATTA
1 ATAATTA
4988358 ACATACCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 5 0.26
14 4 0.21
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (13 bp):
ATAATTATTGATC
Found at i:4989550 original size:19 final size:19
Alignment explanation
Indices: 4989528--4989572 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4989518 TTATATTAGG
4989528 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
4989547 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
4989566 ATTTAAT
1 ATTTAAT
4989573 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:4993025 original size:19 final size:19
Alignment explanation
Indices: 4992982--4993065 Score: 80
Period size: 19 Copynumber: 4.1 Consensus size: 19
4992972 AAAGAAAAAC
*
4992982 AATTCAAAATAATTTTTCAAA
1 AATTTAAAATAATTTTT--AA
4993003 AATTTAAAATAATTTTTAA
1 AATTTAAAATAATTTTTAA
*
4993022 AATTTAAAAT-ATTTATAAA
1 AATTTAAAATAATTT-TTAA
4993041 AATTCTAAAATTTATATTTTTAA
1 AATT-TAAAA--TA-ATTTTTAA
4993064 AA
1 AA
4993066 AATTATAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.07
19 19 0.35
20 5 0.09
21 16 0.30
22 1 0.02
23 5 0.09
24 4 0.07
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTTAAAATAATTTTTAA
Found at i:4993040 original size:18 final size:20
Alignment explanation
Indices: 4992982--4993051 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 20
4992972 AAAGAAAAAC
* *
4992982 AATTCAAAATAATTTTTCAAA
1 AATTTAAAATAATTTAT-AAA
*
4993003 AATTTAAAATAATTT-TTAA
1 AATTTAAAATAATTTATAAA
4993022 AATTTAAAAT-ATTTATAAA
1 AATTTAAAATAATTTATAAA
4993041 AATTCTAAAAT
1 AATT-TAAAAT
4993052 TTATATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
18 4 0.09
19 19 0.43
20 7 0.16
21 14 0.32
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTAAAATAATTTATAAA
Found at i:4993064 original size:24 final size:25
Alignment explanation
Indices: 4993030--4993078 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4993020 AAAATTTAAA
*
4993030 ATATTTAT-AAAAATTCTAAAATTT
1 ATATTTATAAAAAATTATAAAATTT
*
4993054 ATATTTTTAAAAAATTATAAAATTT
1 ATATTTATAAAAAATTATAAAATTT
4993079 TAAAAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATTTATAAAAAATTATAAAATTT
Found at i:4993092 original size:18 final size:18
Alignment explanation
Indices: 4993058--4993093 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4993048 AAATTTATAT
*
4993058 TTTTAAAAAATTATAAAA
1 TTTTAAAAAAATATAAAA
*
4993076 TTTTAAAAAAATCTAAAA
1 TTTTAAAAAAATATAAAA
4993094 GTATATATAA
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:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTTAAAAAAATATAAAA
Found at i:4996651 original size:18 final size:17
Alignment explanation
Indices: 4996624--4996658 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4996614 AATATGAAAA
4996624 ATATAATATTTATATATT
1 ATATAATATTTAT-TATT
*
4996642 ATATACTATTTATTATT
1 ATATAATATTTATTATT
4996659 CCTAACACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATAATATTTATTATT
Found at i:4998265 original size:22 final size:23
Alignment explanation
Indices: 4998240--4998286 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
4998230 ATATTATGAG
*
4998240 TTTA-AATATTATTAAAATAATA
1 TTTACAATATTATAAAAATAATA
* *
4998262 TTTACTATTTTATAAAAATAATA
1 TTTACAATATTATAAAAATAATA
4998285 TT
1 TT
4998287 GAGATTTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTACAATATTATAAAAATAATA
Found at i:4998293 original size:22 final size:23
Alignment explanation
Indices: 4998248--4998293 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4998238 AGTTTAAATA
* * *
4998248 TTATTAAAATAATATTTACTATT
1 TTATAAAAATAATATTGACGATT
4998271 TTATAAAAATAATATTGA-GATT
1 TTATAAAAATAATATTGACGATT
4998293 T
1 T
4998294 GGGTGATAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
TTATAAAAATAATATTGACGATT
Found at i:4999481 original size:2 final size:2
Alignment explanation
Indices: 4999474--4999502 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4999464 ACTTTTCACG
4999474 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4999503 AATTCACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5000064 original size:16 final size:16
Alignment explanation
Indices: 5000041--5000112 Score: 101
Period size: 16 Copynumber: 4.5 Consensus size: 16
5000031 CGTTTGGTTC
5000041 GCTGTAATAGG-ATAGA
1 GCTGTAAT-GGAATAGA
*
5000057 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
5000073 ACTGTAATGGAATATA
1 GCTGTAATGGAATAGA
5000089 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
5000105 GCTGTAAT
1 GCTGTAAT
5000113 CAGTAATTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
15 2 0.04
16 47 0.96
ACGTcount: A:0.38, C:0.06, G:0.29, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:5000151 original size:46 final size:44
Alignment explanation
Indices: 5000094--5000187 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
5000084 ATATAGCTGT
* *
5000094 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAAT-AAT-ATTC-ATGTGTTTGGTTGAATGG
*
5000140 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
5000184 AATG
1 AATG
5000188 ATGCTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:5000349 original size:58 final size:55
Alignment explanation
Indices: 5000282--5000427 Score: 177
Period size: 58 Copynumber: 2.5 Consensus size: 55
5000272 AATTTTAATG
*
5000282 ATTATTATTAAATATAATTGAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATT-AATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
*
5000340 ATTATTATTAAATATAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAA-TTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
5000398 ATTATTATTAAAATATGAATTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTAATAAAAAT
5000428 GATAATATAT
Statistics
Matches: 79, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
57 3 0.04
58 41 0.52
59 18 0.23
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.47
Consensus pattern (55 bp):
ATTATTATTAAATATAATTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:5007025 original size:40 final size:40
Alignment explanation
Indices: 5006970--5007057 Score: 176
Period size: 40 Copynumber: 2.2 Consensus size: 40
5006960 TAAACTCCCA
5006970 AAAAAAATCTTGAATAACCCATTCTCATCGCCCTTATATT
1 AAAAAAATCTTGAATAACCCATTCTCATCGCCCTTATATT
5007010 AAAAAAATCTTGAATAACCCATTCTCATCGCCCTTATATT
1 AAAAAAATCTTGAATAACCCATTCTCATCGCCCTTATATT
5007050 AAAAAAAT
1 AAAAAAAT
5007058 TTGTTTAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.31
Consensus pattern (40 bp):
AAAAAAATCTTGAATAACCCATTCTCATCGCCCTTATATT
Found at i:5007673 original size:16 final size:17
Alignment explanation
Indices: 5007648--5007680 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5007638 CCCTATAATT
5007648 ATATAATTATT-TATAA
1 ATATAATTATTATATAA
*
5007664 ATATATTTATTATATAA
1 ATATAATTATTATATAA
5007681 TTTTATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATAATTATTATATAA
Found at i:5013147 original size:32 final size:32
Alignment explanation
Indices: 5013111--5013216 Score: 203
Period size: 32 Copynumber: 3.3 Consensus size: 32
5013101 GAAGGGCTTT
5013111 AAAGGAGTTGGAGCGTGTGCAAATGGCTCTAG
1 AAAGGAGTTGGAGCGTGTGCAAATGGCTCTAG
5013143 AAAGGAGTTGGAGCGTGTGCAAATGGCTCTAG
1 AAAGGAGTTGGAGCGTGTGCAAATGGCTCTAG
5013175 AAAGGAGTTGGAGCGTGTGCAAATGGCTCTAG
1 AAAGGAGTTGGAGCGTGTGCAAATGGCTCTAG
*
5013207 AAAGGCGTTG
1 AAAGGAGTTG
5013217 TAGCAAAAAA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 73 1.00
ACGTcount: A:0.28, C:0.12, G:0.38, T:0.22
Consensus pattern (32 bp):
AAAGGAGTTGGAGCGTGTGCAAATGGCTCTAG
Found at i:5021180 original size:11 final size:11
Alignment explanation
Indices: 5021164--5021193 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5021154 TAAAAAAAAT
5021164 ATTTTTTAATA
1 ATTTTTTAATA
5021175 ATTTTTTAATA
1 ATTTTTTAATA
*
5021186 TTTTTTTA
1 ATTTTTTA
5021194 GATTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTTTTTAATA
Found at i:5021191 original size:10 final size:10
Alignment explanation
Indices: 5021161--5021191 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
5021151 CATTAAAAAA
5021161 AATATTTTTT
1 AATATTTTTT
5021171 AATAATTTTTT
1 AAT-ATTTTTT
5021182 AATATTTTTT
1 AATATTTTTT
5021192 TAGATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
AATATTTTTT
Found at i:5021882 original size:14 final size:14
Alignment explanation
Indices: 5021860--5021891 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5021850 TCCCTTTGTT
*
5021860 TTAGGTATATTTTG
1 TTAGCTATATTTTG
5021874 TTAGCTATATTTTG
1 TTAGCTATATTTTG
5021888 TTAG
1 TTAG
5021892 GTATCTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.19, T:0.56
Consensus pattern (14 bp):
TTAGCTATATTTTG
Found at i:5023544 original size:14 final size:14
Alignment explanation
Indices: 5023504--5023538 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5023494 ATCATATTTT
5023504 AAATATTTCTATTA
1 AAATATTTCTATTA
5023518 AAATATTTCTATTA
1 AAATATTTCTATTA
*
5023532 AATTATT
1 AAATATT
5023539 ATTATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (14 bp):
AAATATTTCTATTA
Found at i:5029290 original size:2 final size:2
Alignment explanation
Indices: 5029283--5029319 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5029273 TGAAATTAAA
5029283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5029320 GGAGTATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5037059 original size:56 final size:56
Alignment explanation
Indices: 5036989--5037116 Score: 238
Period size: 56 Copynumber: 2.3 Consensus size: 56
5036979 TTATTATAAT
5036989 AAATGTTTTTGTCTTCCATTTTAGAATATAATAAATTGAGTGAGTTTTATGACGTA
1 AAATGTTTTTGTCTTCCATTTTAGAATATAATAAATTGAGTGAGTTTTATGACGTA
5037045 AAATGTTTTTGTCTTCCATTTTAGAATATAATAAATTGAGTGAGTTTTATGACGTA
1 AAATGTTTTTGTCTTCCATTTTAGAATATAATAAATTGAGTGAGTTTTATGACGTA
* *
5037101 AAATGCTTTTGACTTC
1 AAATGTTTTTGTCTTC
5037117 GTTGATATTA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 70 1.00
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.45
Consensus pattern (56 bp):
AAATGTTTTTGTCTTCCATTTTAGAATATAATAAATTGAGTGAGTTTTATGACGTA
Found at i:5042902 original size:42 final size:42
Alignment explanation
Indices: 5042855--5042938 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
5042845 AAAAGGAGTT
*
5042855 GTTTATGAGTGTTATTT-AGGAATAAAATTATATTTAGGTTTA
1 GTTTATGAGTGTT-TTTGAAGAATAAAATTATATTTAGGTTTA
* *
5042897 GTTTATGAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTA
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTAGGTTTA
5042939 AAAATATTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.08
42 35 0.92
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (42 bp):
GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTAGGTTTA
Found at i:5043168 original size:7 final size:7
Alignment explanation
Indices: 5043123--5043177 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
5043113 TTATTCGAAT
5043123 AATTCG-
1 AATTCGA
5043129 AATTCGAA
1 AATTCG-A
5043137 AATT--A
1 AATTCGA
5043142 AATTC--
1 AATTCGA
5043147 AATTCG-
1 AATTCGA
*
5043153 AACTCGA
1 AATTCGA
5043160 AATTCGA
1 AATTCGA
5043167 AATTCGA
1 AATTCGA
5043174 AATT
1 AATT
5043178 TTTTTCGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
5 10 0.24
6 11 0.26
7 17 0.40
8 4 0.10
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (7 bp):
AATTCGA
Found at i:5050553 original size:126 final size:125
Alignment explanation
Indices: 5050149--5050674 Score: 566
Period size: 126 Copynumber: 4.2 Consensus size: 125
5050139 TAAAAAGCGA
* * * * * *
5050149 ATCTCTCAAGTCGATTGAGTTTAGTCATTTAG-TTGGATTAGTATGAGTGTT-TTTTCAATGTAT
1 ATCTCTCAAGTCGATTGAGTTTAGTCAATCAGCTT-GATTGGCATGAGTATTGTTTTCAATGTAA
* * * * *
5050212 GAAGAAGT-AGGTTTGAGTACGTTGAAGC-CTGTTATTTATGGGTTGGGGAGATC--AAAGTAG
65 GAAGATGTGA-G-TTGAGTGCGTTGAAACTC-ATTATTTATGGGTTGGGGAGGTCAAAAAGTAG
* * ** * *
5050272 ATCTCTCAAGTCGATTGAGTTTAGTCAATTAGCTCGATTGATATGAGTATTGTCCTT-AGTGTAA
1 ATCTCTCAAGTCGATTGAGTTTAGTCAATCAGCTTGATTGGCATGAGTATTGT-TTTCAATGTAA
* * * * * *
5050336 GAGGACGTGAGTTCAAGTGCGTTGAAATTTATTATTTATGGGTT-GAGAGGTCAAAAAGTAG
65 GAAGATGTGAGTT-GAGTGCGTTGAAACTCATTATTTATGGGTTGGGGAGGTCAAAAAGTAG
* *
5050397 ATCTCTCAAGTCGATTGAGTTTAG-CGAATCAGTTTGATTGGCATGAGTATTGTTTTCACTGTAA
1 ATCTCTCAAGTCGATTGAGTTTAGTC-AATCAGCTTGATTGGCATGAGTATTGTTTTCAATGTAA
* * * * * **
5050461 GAGGATGTGAGCTTGAGTGTGCTGAAGCGCATTATTTATAAGTTGGGGAGGTCAAAAAGTAG
65 GAAGATGTGAG-TTGAGTGCGTTGAAACTCATTATTTATGGGTTGGGGAGGTCAAAAAGTAG
* * *
5050523 ATCTTTCAAGTCGATTGAGTTTAGTCAATCAGCTTGATTGGCATGTGTATTATTTTCAATGTAAG
1 ATCTCTCAAGTCGATTGAGTTTAGTCAATCAGCTTGATTGGCATGAGTATTGTTTTCAATGTAAG
*
5050588 AAGATGTGAGTTGAAGTGCGTTGAAATTCATTATTTATGGGTTGGGGAGGTCAAAAAGTAG
66 AAGATGTGAGTTG-AGTGCGTTGAAACTCATTATTTATGGGTTGGGGAGGTCAAAAAGTAG
* *
5050649 ATTTTTCAAGTCGATTGAGTTTAGTC
1 ATCTCTCAAGTCGATTGAGTTTAGTC
5050675 GAGTGCATTG
Statistics
Matches: 339, Mismatches: 50, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
123 52 0.15
124 40 0.12
125 96 0.28
126 150 0.44
127 1 0.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.36
Consensus pattern (125 bp):
ATCTCTCAAGTCGATTGAGTTTAGTCAATCAGCTTGATTGGCATGAGTATTGTTTTCAATGTAAG
AAGATGTGAGTTGAGTGCGTTGAAACTCATTATTTATGGGTTGGGGAGGTCAAAAAGTAG
Found at i:5052340 original size:3 final size:3
Alignment explanation
Indices: 5052332--5052366 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5052322 CTTCACCTTT
5052332 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
5052367 GCAGCGACCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:5052758 original size:23 final size:23
Alignment explanation
Indices: 5052714--5052758 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5052704 GTAAGCATTA
* **
5052714 AAATAATAATAAAAATTTTTAAT
1 AAATAAAAATAAAAATAATTAAT
*
5052737 AAATAAAAATATAAATAATTAA
1 AAATAAAAATAAAAATAATTAA
5052759 ATATTAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATAAAAATAAAAATAATTAAT
Found at i:5055555 original size:2 final size:2
Alignment explanation
Indices: 5055548--5055579 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5055538 TTGTCATTCT
5055548 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
5055580 TGCATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5055588 original size:2 final size:2
Alignment explanation
Indices: 5055583--5055615 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5055573 ACACACATGC
5055583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5055616 ATAACTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5057076 original size:40 final size:40
Alignment explanation
Indices: 5057005--5057081 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
5056995 CGCACAATGG
* ** *
5057005 GTTGGAAGAGTTAAAGAAGTGGCTGCTTCATCAGGAGACT
1 GTTGGAAGAGTCAAAGAAGTCACTGCATCATCAGGAGACT
* *
5057045 GTTGGAAGAGTCATAGAAGTCACTGCATCATCGGGAG
1 GTTGGAAGAGTCAAAGAAGTCACTGCATCATCAGGAG
5057082 CATCTGCATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.23
Consensus pattern (40 bp):
GTTGGAAGAGTCAAAGAAGTCACTGCATCATCAGGAGACT
Found at i:5058076 original size:12 final size:12
Alignment explanation
Indices: 5058059--5058185 Score: 76
Period size: 12 Copynumber: 10.1 Consensus size: 12
5058049 ATAACATTCA
5058059 AACAACAAAAAT
1 AACAACAAAAAT
* *
5058071 AACAACCAAAAC
1 AACAACAAAAAT
*
5058083 AGCAACAAAAAT
1 AACAACAAAAAT
*
5058095 AACAGCAAGCAACATTAAA
1 -A-A-CAA-CAA-A--AAT
5058114 AACAACAAAAAT
1 AACAACAAAAAT
** *
5058126 AGTAACAAAAAC
1 AACAACAAAAAT
*
5058138 ACCAACAAAAAT
1 AACAACAAAAAT
* *
5058150 AACAGCAAAAAC
1 AACAACAAAAAT
*
5058162 AAC-ACGAAAAT
1 AACAACAAAAAT
*
5058173 AACAACCAAAAT
1 AACAACAAAAAT
5058185 A
1 A
5058186 GTAAAAAAAG
Statistics
Matches: 86, Mismatches: 21, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
11 8 0.09
12 59 0.69
13 1 0.01
14 1 0.01
15 6 0.07
16 6 0.07
17 2 0.02
18 1 0.01
19 2 0.02
ACGTcount: A:0.67, C:0.21, G:0.05, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:5058098 original size:15 final size:15
Alignment explanation
Indices: 5058080--5058157 Score: 51
Period size: 15 Copynumber: 5.5 Consensus size: 15
5058070 TAACAACCAA
5058080 AACAGCAACAAAAAT
1 AACAGCAACAAAAAT
* *
5058095 AACAGCAAGCAACATT
1 AACAGCAA-CAAAAAT
* *
5058111 AAAAACAACAAAAAT
1 AACAGCAACAAAAAT
*
5058126 ---AGTAAC--AAA-
1 AACAGCAACAAAAAT
*
5058135 AACACCAACAAAAAT
1 AACAGCAACAAAAAT
5058150 AACAGCAA
1 AACAGCAA
5058158 AAACAACACG
Statistics
Matches: 45, Mismatches: 11, Indels: 14
0.64 0.16 0.20
Matches are distributed among these distances:
10 3 0.07
12 8 0.18
14 3 0.07
15 20 0.44
16 11 0.24
ACGTcount: A:0.65, C:0.21, G:0.06, T:0.08
Consensus pattern (15 bp):
AACAGCAACAAAAAT
Found at i:5058182 original size:24 final size:22
Alignment explanation
Indices: 5058111--5058183 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
5058101 AAGCAACATT
**
5058111 AAAAACAACA-AAAATAGTAAC
1 AAAAACAACACAAAATAACAAC
* *
5058132 AAAAACACCAACAAAAATAACAGC
1 AAAAACAAC-AC-AAAATAACAAC
5058156 AAAAACAACACGAAAATAACAAC
1 AAAAACAACAC-AAAATAACAAC
*
5058179 CAAAA
1 AAAAA
5058184 TAGTAAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 8 0.20
22 1 0.02
23 16 0.39
24 16 0.39
ACGTcount: A:0.70, C:0.21, G:0.04, T:0.05
Consensus pattern (22 bp):
AAAAACAACACAAAATAACAAC
Found at i:5058200 original size:20 final size:20
Alignment explanation
Indices: 5058177--5058214 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5058167 GAAAATAACA
* *
5058177 ACCAAAATAGTAAAAAAAGC
1 ACCAAAACAATAAAAAAAGC
5058197 ACCAAAACAATAAAAAAA
1 ACCAAAACAATAAAAAAA
5058215 ATACAAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.16, G:0.05, T:0.08
Consensus pattern (20 bp):
ACCAAAACAATAAAAAAAGC
Found at i:5058233 original size:32 final size:33
Alignment explanation
Indices: 5058197--5058258 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
5058187 TAAAAAAAGC
5058197 ACCAAAACAATAAAAAA-AATACAAAAACAGTA
1 ACCAAAACAATAAAAAACAATACAAAAACAGTA
** *
5058229 ACCAAAACGGTAAAAAACAATACCAAAACA
1 ACCAAAACAATAAAAAACAATACAAAAACA
5058259 ACAATATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.68, C:0.19, G:0.05, T:0.08
Consensus pattern (33 bp):
ACCAAAACAATAAAAAACAATACAAAAACAGTA
Found at i:5058528 original size:14 final size:14
Alignment explanation
Indices: 5058509--5058536 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5058499 TTTTTTTATT
5058509 TTTTTAAATATTTA
1 TTTTTAAATATTTA
5058523 TTTTTAAATATTTA
1 TTTTTAAATATTTA
5058537 ATAATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTAAATATTTA
Found at i:5058686 original size:16 final size:16
Alignment explanation
Indices: 5058665--5058708 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
5058655 ATTACATCAT
5058665 ATATAAAAATTACAAA
1 ATATAAAAATTACAAA
*
5058681 ATATAAAATATTATAAA
1 ATATAAAA-ATTACAAA
*
5058698 CT-TAAAAATTA
1 ATATAAAAATTA
5058709 GTCGGTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.16
16 13 0.52
17 8 0.32
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (16 bp):
ATATAAAAATTACAAA
Found at i:5062789 original size:25 final size:24
Alignment explanation
Indices: 5062740--5062790 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5062730 GTTATGTATT
*
5062740 ATTTTTCTAATATTATATATTATA
1 ATTTTTCTAATATCATATATTATA
*
5062764 ATTTTTACTAAT-TCATATTTTAATA
1 ATTTTT-CTAATATCATATATT-ATA
5062789 AT
1 AT
5062791 AATTATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTTCTAATATCATATATTATA
Found at i:5062920 original size:58 final size:58
Alignment explanation
Indices: 5062759--5062925 Score: 214
Period size: 58 Copynumber: 2.9 Consensus size: 58
5062749 ATATTATATA
* * *
5062759 TTATAATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAT
* * *
5062819 ATATTA-TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
*
5062876 TTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAATTTAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAATATAAT
5062926 AACAATAATC
Statistics
Matches: 94, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
57 22 0.23
58 55 0.59
59 9 0.10
60 8 0.09
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (58 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
Found at i:5063120 original size:16 final size:16
Alignment explanation
Indices: 5063081--5063136 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
5063071 TGAATTATTG
* *
5063081 ATTACAGCCCTATTCT
1 ATTACAGCTCTATTCC
5063097 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
* * *
5063113 ATTGCAGCTTTATTTC
1 ATTACAGCTCTATTCC
5063129 ATTACAGC
1 ATTACAGC
5063137 GAACCAAACG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.25, C:0.27, G:0.09, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:5063909 original size:46 final size:46
Alignment explanation
Indices: 5063827--5063919 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
5063817 AATGACGGTC
* ***
5063827 AGATGATCAACTAGTTCAGGGTCTAGAACTTTCATACAGGGTTTAT
1 AGATAATCAACTAGTTCAGGGTCTAGAACCCGCATACAGGGTTTAT
*
5063873 AGATAATCAACTAGTTCAGGGTCTAGGACCCGCATACAGGGTTTAT
1 AGATAATCAACTAGTTCAGGGTCTAGAACCCGCATACAGGGTTTAT
5063919 A
1 A
5063920 TATAGGAAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (46 bp):
AGATAATCAACTAGTTCAGGGTCTAGAACCCGCATACAGGGTTTAT
Found at i:5068471 original size:131 final size:130
Alignment explanation
Indices: 5068204--5068573 Score: 492
Period size: 131 Copynumber: 2.8 Consensus size: 130
5068194 GTTAGCCTCC
* * * * * *
5068204 CTTGGTTCCGTCATTACAATCAAGAGATGATGTGAGTATCTCGCTTTTGTTGGGATTTGAA-CCC
1 CTTGGCTCCGCCATTACAACCAAGAGATGACGTGAGTGTCTCGCTTTTGGTGGGATTTGAACCCC
* * * **
5068268 TCGACCTATATTATATAGATCAATTGTTGAGGCATATGAGAACAGGGGTAAGGTCTTTGCTAACC
66 T-GACCTATACTATATAGATCAATTGTTGAGGCATATGGGAACAAGGGTAAGGTCCCTGCTAACC
5068333 T
130 T
* * *
5068334 CTTTGGCTCCGCCATTACAACCAAGAGATGACATGAGTGTTTCGCTTTTGGTGGGATTTAAACCC
1 C-TTGGCTCCGCCATTACAACCAAGAGATGACGTGAGTGTCTCGCTTTTGGTGGGATTTGAACCC
* *
5068399 CTGACCTATACTATATAGATCAATTGTTGAGGCATATGGGAACAAGGGT-GGGTCCCTGCTAGCC
65 CTGACCTATACTATATAGATCAATTGTTGAGGCATATGGGAACAAGGGTAAGGTCCCTGCTA-AC
5068463 CTT
129 C-T
* * * * * *
5068466 CTTGGCTCCGCCATTACAACTAAGAGATGACGTGAATGTCTCGCCTTTGGTGGGATTCGAACTCT
1 CTTGGCTCCGCCATTACAACCAAGAGATGACGTGAGTGTCTCGCTTTTGGTGGGATTTGAACCCC
5068531 TGACCTATACTATATAGATCAATTGTTGAGGCATATGGGAACA
66 TGACCTATACTATATAGATCAATTGTTGAGGCATATGGGAACA
5068574 GGGGCTAATA
Statistics
Matches: 211, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
130 10 0.05
131 195 0.92
132 6 0.03
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (130 bp):
CTTGGCTCCGCCATTACAACCAAGAGATGACGTGAGTGTCTCGCTTTTGGTGGGATTTGAACCCC
TGACCTATACTATATAGATCAATTGTTGAGGCATATGGGAACAAGGGTAAGGTCCCTGCTAACCT
Found at i:5079252 original size:6 final size:6
Alignment explanation
Indices: 5079243--5079272 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5079233 ATAATAATTA
*
5079243 TATATC TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT
5079273 AGATCACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (6 bp):
TATATT
Found at i:5082543 original size:64 final size:63
Alignment explanation
Indices: 5082460--5082588 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 63
5082450 ATGTGAGCCT
*
5082460 TCCATGGTTGCGATGCCAACTCGATCAACTTTGAAAACTTTCCATTTTGATTCTCAAATGGTCC
1 TCCATGGTCGCGATGCCAACTCGATCAACTTTGAAAACTTTCCATTTTGATTCTCAAATGG-CC
* *
5082524 TCCATGGTCGTGATGCCAACTCGATCAACTTTGAAAACTTTCTATTTTGATTCTCAAATGGCC
1 TCCATGGTCGCGATGCCAACTCGATCAACTTTGAAAACTTTCCATTTTGATTCTCAAATGGCC
5082587 TC
1 TC
5082589 AGGCTAACGA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
63 4 0.06
64 58 0.94
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (63 bp):
TCCATGGTCGCGATGCCAACTCGATCAACTTTGAAAACTTTCCATTTTGATTCTCAAATGGCC
Found at i:5083093 original size:22 final size:24
Alignment explanation
Indices: 5083037--5083093 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
5083027 TGTTTAGAAG
*
5083037 ATAA-TAATTTAAATTTTATATTT
1 ATAATTAATTTAAATTATATATTT
5083060 ATCAAATT-ATTT-AATTATAT-TTT
1 AT--AATTAATTTAAATTATATATTT
5083083 ATAATTAATTT
1 ATAATTAATTT
5083094 TAAGTAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
21 4 0.14
22 4 0.14
23 7 0.24
24 7 0.24
25 6 0.21
26 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
ATAATTAATTTAAATTATATATTT
Found at i:5086843 original size:64 final size:65
Alignment explanation
Indices: 5086737--5086868 Score: 196
Period size: 64 Copynumber: 2.0 Consensus size: 65
5086727 ATGTCGCAAC
*
5086737 ATGAGCCCTCCATGGTCGTGATGTCAACTCCATAAACTTTGAAAACTTTCCATTTTGGTTCTCAA
1 ATGAGCCCTCCATGGTCGCGATGTCAACTCCATAAACTTTGAAAACTTTCCATTTTGGTTCTCAA
** * *
5086802 ATGA-CCCTCCATGGTCGCGATG-CTAACTCGGTCAACTTTGAAACCTTTCCATTTTGGTTCTCA
1 ATGAGCCCTCCATGGTCGCGATGTC-AACTCCATAAACTTTGAAAACTTTCCATTTTGGTTCTCA
5086865 A
65 A
5086866 ATG
1 ATG
5086869 GCCTTGGGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
63 1 0.02
64 56 0.92
65 4 0.07
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (65 bp):
ATGAGCCCTCCATGGTCGCGATGTCAACTCCATAAACTTTGAAAACTTTCCATTTTGGTTCTCAA
Found at i:5090041 original size:14 final size:15
Alignment explanation
Indices: 5090018--5090055 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
5090008 ATAAAATACA
5090018 TTTTGT-AAAAA-GT
1 TTTTGTGAAAAACGT
5090031 TTTTGTGAAAAAGCGT
1 TTTTGTGAAAAA-CGT
5090047 TTTTGTGAA
1 TTTTGTGAA
5090056 TGTATACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 5 0.23
16 11 0.50
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (15 bp):
TTTTGTGAAAAACGT
Found at i:5097782 original size:24 final size:24
Alignment explanation
Indices: 5097731--5097782 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5097721 TTAATTGAGG
5097731 ATTT-AATATATTCATTCTTAATT
1 ATTTAAATATATTCATTCTTAATT
* * **
5097754 GTTTAAATATATTCGTTCTTCCTT
1 ATTTAAATATATTCATTCTTAATT
5097778 ATTTA
1 ATTTA
5097783 TTTTTTTGCC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTTAAATATATTCATTCTTAATT
Found at i:5098101 original size:19 final size:19
Alignment explanation
Indices: 5098060--5098101 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5098050 TCATGCTATT
* *
5098060 TTTTTTGGATATTTATATT
1 TTTTTTGAATATTTATATA
5098079 TTTTTTGAATATTTGA-ATA
1 TTTTTTGAATATTT-ATATA
5098098 TTTT
1 TTTT
5098102 ATAATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.67
Consensus pattern (19 bp):
TTTTTTGAATATTTATATA
Found at i:5098101 original size:21 final size:19
Alignment explanation
Indices: 5098056--5098092 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5098046 TATTTCATGC
*
5098056 TATTTTTTTTGGATATTTA
1 TATTTTTTTTGAATATTTA
5098075 TATTTTTTTTGAATATTT
1 TATTTTTTTTGAATATTT
5098093 GAATATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (19 bp):
TATTTTTTTTGAATATTTA
Found at i:5098485 original size:30 final size:32
Alignment explanation
Indices: 5098435--5098498 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
5098425 TATAATTTGA
5098435 TATTGAACAATTCGAAAA-TTTTTATTTAAGT
1 TATTGAACAATTCGAAAATTTTTTATTTAAGT
*
5098466 TATTGAACTATTC-AAAATTTTTTATTTAAGT
1 TATTGAACAATTCGAAAATTTTTTATTTAAGT
5098497 TA
1 TA
5098499 CTAGATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (32 bp):
TATTGAACAATTCGAAAATTTTTTATTTAAGT
Found at i:5116598 original size:21 final size:22
Alignment explanation
Indices: 5116572--5116613 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5116562 AATAAAATCA
*
5116572 ACAT-AATCAAAATATATCTAG
1 ACATAAATCAAAACATATCTAG
*
5116593 ACATAAATCGAAACATATCTA
1 ACATAAATCAAAACATATCTA
5116614 AATAGAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.26
Consensus pattern (22 bp):
ACATAAATCAAAACATATCTAG
Done.