Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 12 of 132
Found at i:3382102 original size:15 final size:15
Alignment explanation
Indices: 3382055--3382113 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
3382045 TAAAAAATAC
3382055 TTATATA-TTTTTAT
1 TTATATATTTTTTAT
** *
3382069 TT-TAATATTTAATAA
1 TTAT-ATATTTTTTAT
3382084 TTATATATTTTTTAT
1 TTATATATTTTTTAT
3382099 TTAT-TGATTTTTTAT
1 TTATAT-ATTTTTTAT
3382114 ATAGTTATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
13 1 0.03
14 6 0.17
15 27 0.77
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
TTATATATTTTTTAT
Found at i:3385487 original size:15 final size:15
Alignment explanation
Indices: 3385463--3385496 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3385453 ATAAATTGTT
3385463 AAAA-ATATAATAAC
1 AAAATATATAATAAC
3385477 AAAATATATAATAAC
1 AAAATATATAATAAC
3385492 AAAAT
1 AAAAT
3385497 TTAAGAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATATATAATAAC
Found at i:3398584 original size:25 final size:25
Alignment explanation
Indices: 3398556--3398611 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
3398546 ATCAATATAC
3398556 TATTATCTATCTATACAATTAGTGG
1 TATTATCTATCTATACAATTAGTGG
*
3398581 TATTATCTATCTATACTATTAGTGG
1 TATTATCTATCTATACAATTAGTGG
*
3398606 CATTAT
1 TATTAT
3398612 AAATAAGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.46
Consensus pattern (25 bp):
TATTATCTATCTATACAATTAGTGG
Found at i:3407630 original size:3 final size:3
Alignment explanation
Indices: 3407622--3407652 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3407612 GACATTTTGA
3407622 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3407653 AACTTACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3410769 original size:30 final size:30
Alignment explanation
Indices: 3410716--3410916 Score: 197
Period size: 30 Copynumber: 6.9 Consensus size: 30
3410706 TTTTCTTTCC
* * *
3410716 CATTTTAACCTC-AAACTTTTCTAAAATTT
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
* * *
3410745 TATTTTAACCCCTAAACTTCTCTAAAATTA
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
* *
3410775 CATTTTGA-CCCTAAACTTTTCCAAAAATA
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
3410804 CATTTTAACCCCTAAACTTTTCCAAAATTA
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
*
3410834 CATTTTAA-CCCTAAA--TTTCCAAAAGTCA
1 CATTTTAACCCCTAAACTTTTCCAAAA-TTA
*
3410862 CATTTTCAACCTC-AAA-TTTTCCAAAAGTT-
1 CATTTT-AACCCCTAAACTTTTCCAAAA-TTA
*
3410891 CAATTTTAATCCC-AAA-TTTTCCAAAA
1 C-ATTTTAACCCCTAAACTTTTCCAAAA
3410917 GTTTTAATTT
Statistics
Matches: 149, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
27 9 0.06
28 8 0.05
29 65 0.44
30 67 0.45
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.37
Consensus pattern (30 bp):
CATTTTAACCCCTAAACTTTTCCAAAATTA
Found at i:3410793 original size:59 final size:59
Alignment explanation
Indices: 3410716--3410916 Score: 202
Period size: 59 Copynumber: 3.4 Consensus size: 59
3410706 TTTTCTTTCC
* * ** *
3410716 CATTTTAA-CCTCAAACTTTTCTAAAATTTTATTTTAACCCCTAAACTTCTCTAAAATTA
1 CATTTTAACCCT-AAACTTTTCCAAAAATACATTTTAACCCCTAAACTTCTCCAAAATTA
* *
3410775 CATTTTGACCCTAAACTTTTCCAAAAATACATTTTAACCCCTAAACTTTTCCAAAATTA
1 CATTTTAACCCTAAACTTTTCCAAAAATACATTTTAACCCCTAAACTTCTCCAAAATTA
* * *
3410834 CATTTTAACCCTAAA--TTTCCAAAAGTCACATTTTCAACCTC-AAA-TTTTCCAAAAGTT-
1 CATTTTAACCCTAAACTTTTCCAAAAAT-ACATTTT-AACCCCTAAACTTCTCCAAAA-TTA
3410891 CAATTTTAATCCC-AAA-TTTTCCAAAA
1 C-ATTTTAA-CCCTAAACTTTTCCAAAA
3410917 GTTTTAATTT
Statistics
Matches: 125, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
57 21 0.17
58 22 0.18
59 79 0.63
60 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.37
Consensus pattern (59 bp):
CATTTTAACCCTAAACTTTTCCAAAAATACATTTTAACCCCTAAACTTCTCCAAAATTA
Found at i:3410908 original size:58 final size:58
Alignment explanation
Indices: 3410746--3410918 Score: 212
Period size: 59 Copynumber: 3.0 Consensus size: 58
3410736 CTAAAATTTT
* * * *
3410746 ATTTTAACCCCTAAACTTCTCTAAAATTACATTTTGACCCTAAACTTTTCCAAAAATAC
1 ATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTAAA-TTTTCCAAAAGTAC
3410805 ATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTAAA-TTTCCAAAAGTCAC
1 ATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTAAATTTTCCAAAAGT-AC
*
3410863 ATTTTCAACCTC-AAA-TTTTCCAAAAGTT-CAATTTTAATCCC-AAATTTTCCAAAAGT
1 ATTTT-AACCCCTAAACTTTTCCAAAA-TTAC-ATTTTAA-CCCTAAATTTTCCAAAAGT
3410919 TTTAATTTTG
Statistics
Matches: 103, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
57 21 0.20
58 22 0.21
59 60 0.58
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (58 bp):
ATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTAAATTTTCCAAAAGTAC
Found at i:3410917 original size:29 final size:30
Alignment explanation
Indices: 3410746--3410919 Score: 163
Period size: 29 Copynumber: 5.9 Consensus size: 30
3410736 CTAAAATTTT
* *
3410746 ATTTTAACCCCTAAACTTCTCTAAAA-TT-AC
1 ATTTTAA-CCCTAAA-TTTTCCAAAAGTTCAC
* *
3410776 ATTTTGACCCTAAACTTTTCCAAAA-AT-AC
1 ATTTTAACCCTAAA-TTTTCCAAAAGTTCAC
3410805 ATTTTAACCCCTAAACTTTTCCAAAA-TT-AC
1 ATTTTAA-CCCTAAA-TTTTCCAAAAGTTCAC
3410835 ATTTTAACCCTAAA-TTTCCAAAAG-TCAC
1 ATTTTAACCCTAAATTTTCCAAAAGTTCAC
3410863 ATTTTCAA-CCTCAAATTTTCCAAAAGTTCA-
1 ATTTT-AACCCT-AAATTTTCCAAAAGTTCAC
3410893 ATTTTAATCCC-AAATTTTCCAAAAGTT
1 ATTTTAA-CCCTAAATTTTCCAAAAGTT
3410920 TTAATTTTGA
Statistics
Matches: 129, Mismatches: 6, Indels: 19
0.84 0.04 0.12
Matches are distributed among these distances:
27 10 0.08
28 10 0.08
29 55 0.43
30 49 0.38
31 5 0.04
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.36
Consensus pattern (30 bp):
ATTTTAACCCTAAATTTTCCAAAAGTTCAC
Found at i:3413241 original size:21 final size:21
Alignment explanation
Indices: 3413196--3413239 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3413186 AATTTTAAAA
*
3413196 TTTAGTAATTATACTTTTATT
1 TTTAGAAATTATACTTTTATT
*
3413217 TTTAGAAATTTTA-TTTTATT
1 TTTAGAAATTATACTTTTATT
3413237 TTT
1 TTT
3413240 TAAATTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTAGAAATTATACTTTTATT
Found at i:3415481 original size:19 final size:19
Alignment explanation
Indices: 3415454--3415494 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3415444 CTACATCAGC
*
3415454 AAATGAATTTAAACTTAAA
1 AAATGAATTAAAACTTAAA
* *
3415473 AAATTAATTAAAATTTAAA
1 AAATGAATTAAAACTTAAA
3415492 AAA
1 AAA
3415495 ACATTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
AAATGAATTAAAACTTAAA
Found at i:3417534 original size:23 final size:23
Alignment explanation
Indices: 3417490--3417534 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3417480 TTTTAATTTA
3417490 TTAAAATTTTTTATATAGTTATC
1 TTAAAATTTTTTATATAGTTATC
* *
3417513 TTAACATTATTTTA-ATATTTAT
1 TTAAAATT-TTTTATATAGTTAT
3417535 ATTAGAGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (23 bp):
TTAAAATTTTTTATATAGTTATC
Found at i:3423464 original size:14 final size:14
Alignment explanation
Indices: 3423447--3423491 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
3423437 TTTAAATATA
3423447 ATTTTTTATACAAT
1 ATTTTTTATACAAT
*
3423461 ATTTTTTTTATCAA-
1 ATTTTTTATA-CAAT
3423475 ATTTTTTATACAAT
1 ATTTTTTATACAAT
3423489 ATT
1 ATT
3423492 AAGACTAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.11
14 21 0.78
15 3 0.11
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTTTTATACAAT
Found at i:3423795 original size:16 final size:16
Alignment explanation
Indices: 3423774--3423804 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3423764 TATATACTTA
3423774 ATATTATTAAATAATG
1 ATATTATTAAATAATG
*
3423790 ATATTATTATATAAT
1 ATATTATTAAATAAT
3423805 CACTTTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
ATATTATTAAATAATG
Found at i:3425495 original size:26 final size:25
Alignment explanation
Indices: 3425450--3425547 Score: 117
Period size: 25 Copynumber: 3.9 Consensus size: 25
3425440 TTTCTCATCT
*
3425450 CAATTTTATCCC-ACTAAAATTTTGA
1 CAATTTTA-CCCAAGTAAAATTTTGA
*
3425475 CAATTTTATCCCCAGTAAAATTTTGA
1 CAATTTTA-CCCAAGTAAAATTTTGA
* *
3425501 CGATTTTACCTAAGTAAAATTTTGA
1 CAATTTTACCCAAGTAAAATTTTGA
* *
3425526 CGATTTTACCTAAGTAAAATTT
1 CAATTTTACCCAAGTAAAATTT
3425548 CAAGAAAATT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
25 49 0.72
26 19 0.28
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (25 bp):
CAATTTTACCCAAGTAAAATTTTGA
Found at i:3428073 original size:31 final size:28
Alignment explanation
Indices: 3428046--3428098 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
3428036 TCTTTTTATA
3428046 TTAGT-AATAATGTAGATATTAATTTTT
1 TTAGTGAATAATGTAGATATTAATTTTT
*
3428073 TTGGTGAATAATGTAGATATTAATTT
1 TTAGTGAATAATGTAGATATTAATTT
3428099 AAGACTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (28 bp):
TTAGTGAATAATGTAGATATTAATTTTT
Found at i:3429212 original size:3 final size:3
Alignment explanation
Indices: 3429204--3429234 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3429194 GTGATTTTAT
3429204 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3429235 AAAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3429454 original size:20 final size:20
Alignment explanation
Indices: 3429381--3429455 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 20
3429371 TCTATATTTA
*
3429381 TTTTTAATAATATTA-TTATAT
1 TTTTTAAT-ATAATATTTAT-T
* *
3429402 TTTTTAATA-AATTTTTA-C
1 TTTTTAATATAATATTTATT
*
3429420 TTTTTGAT-T-ATATTTATT
1 TTTTTAATATAATATTTATT
3429438 TTTTTAATATAATATTTA
1 TTTTTAATATAATATTTA
3429456 AAATTATTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
17 6 0.14
18 14 0.33
19 3 0.07
20 11 0.26
21 8 0.19
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (20 bp):
TTTTTAATATAATATTTATT
Found at i:3429858 original size:23 final size:22
Alignment explanation
Indices: 3429831--3429897 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
3429821 GAGGATTGAA
3429831 ATTAAATTATATATTTTTATTAT
1 ATTAAATTATATA-TTTTATTAT
*
3429854 ATTAAA-AATATAATTTTATTAT
1 ATTAAATTATAT-ATTTTATTAT
*
3429876 TTTAATAATT-TATATTTTATTA
1 ATT-A-AATTATATATTTTATTA
3429898 ATTTTAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 15 0.41
23 17 0.46
24 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTAAATTATATATTTTATTAT
Found at i:3429893 original size:15 final size:16
Alignment explanation
Indices: 3429863--3429901 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
3429853 TATTAAAAAT
3429863 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
3429880 ATAATTTA-TATTTTA
1 ATAATTTATTATTTTA
*
3429895 TTAATTT
1 ATAATTT
3429902 TAAAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:3429901 original size:24 final size:23
Alignment explanation
Indices: 3429834--3429906 Score: 85
Period size: 22 Copynumber: 3.1 Consensus size: 23
3429824 GATTGAAATT
*
3429834 AAATTATATATTTTTATTATATTAA
1 AAATT-TATA-TTTTATTATTTTAA
*
3429859 AAATATA-ATTTTATTATTTTAA
1 AAATTTATATTTTATTATTTTAA
*
3429881 TAATTTATATTTTATTAATTTTAA
1 AAATTTATATTTTATT-ATTTTAA
3429905 AA
1 AA
3429907 TATTAAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 18 0.44
23 9 0.22
24 10 0.24
25 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATTTATATTTTATTATTTTAA
Found at i:3429950 original size:29 final size:27
Alignment explanation
Indices: 3429856--3429963 Score: 98
Period size: 29 Copynumber: 3.9 Consensus size: 27
3429846 TTTATTATAT
3429856 TAAAAATATAATTTTATTATTTT--AA
1 TAAAAATATAATTTTATTATTTTAAAA
**
3429881 T-AATTTAT-ATTTTATTAATTTTAAAA
1 TAAAAATATAATTTTATT-ATTTTAAAA
* *
3429907 TATTAAATTAAAATTTTATTATTTTAGAAA
1 TA--AAAATATAATTTTATTATTTTA-AAA
3429937 GTAAAAATATAATTTTATTATTATTAA
1 -TAAAAATATAATTTTATTATT-TTAA
3429964 TTTAAAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
23 8 0.12
24 10 0.15
25 1 0.01
26 3 0.04
29 29 0.43
30 14 0.21
31 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TAAAAATATAATTTTATTATTTTAAAA
Found at i:3429995 original size:82 final size:82
Alignment explanation
Indices: 3429856--3430020 Score: 226
Period size: 82 Copynumber: 2.0 Consensus size: 82
3429846 TTTATTATAT
* * * * * *
3429856 TAAAAATATAATTTTATTATTTTAATAATTTATATTTTATTAATTTTAAAATATTAAATTAAAAT
1 TAAAAATATAATTTTATTATTTTAAT-ATTAAAATTTTATAAATTATAAAAAATTAAATAAAAAT
3429921 TTTATTATTTT-AGAAAG
65 TTTATTATTTTAAGAAAG
3429938 TAAAAATATAATTTTATTATTATTAAT-TTAAAATTTTATAAATTATAAAAAATTTAAATAAAAA
1 TAAAAATATAATTTTATTATT-TTAATATTAAAATTTTATAAATTATAAAAAA-TTAAATAAAAA
*
3430002 TTTTTTTATTTTAAGAAAG
64 TTTTATTATTTTAAGAAAG
3430021 ATCGTGGCTT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
81 20 0.27
82 42 0.58
83 11 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (82 bp):
TAAAAATATAATTTTATTATTTTAATATTAAAATTTTATAAATTATAAAAAATTAAATAAAAATT
TTATTATTTTAAGAAAG
Found at i:3436748 original size:99 final size:99
Alignment explanation
Indices: 3436570--3436755 Score: 243
Period size: 99 Copynumber: 1.9 Consensus size: 99
3436560 GAAGATGTTA
** *
3436570 GATTATCTCGATTTAAAGAAAGGTTGCACCTAGTAAGTTAAGGTGCAAAAATTTCAAAATCGAAG
1 GATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAAAATTTCAAAATCGAAG
*
3436635 ATAATGAAACATTGCCTCGATTAAAAGGGTATTC
66 ATAAAGAAACATTGCCTCGATTAAAAGGGTATTC
* * * *
3436669 GATTATTTTGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCGC-AAAGTTTCGAATACTCGA
1 GATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAAAATTTC-AA-AATCGA
*
3436733 A-ATAAA-AGAATATTGCCTCGATT
64 AGATAAAGA-AACATTGCCTCGATT
3436756 TTAAAGTTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
98 8 0.11
99 61 0.81
100 6 0.08
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (99 bp):
GATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAAAATTTCAAAATCGAAG
ATAAAGAAACATTGCCTCGATTAAAAGGGTATTC
Found at i:3437162 original size:29 final size:30
Alignment explanation
Indices: 3437126--3437423 Score: 177
Period size: 29 Copynumber: 10.1 Consensus size: 30
3437116 GGACATCCGG
3437126 GGGT-AAAATGGTAA-TTTTGGAAGTTTCA
1 GGGTCAAAATGGTAATTTTTGGAAGTTTCA
3437154 GGGTCAAAAATGG-AATTTTTGGAAGTTT-A
1 GGGTC-AAAATGGTAATTTTTGGAAGTTTCA
*
3437183 GGGTCAAAAATGG-AATTTTTGGAAGTTTTA
1 GGGTC-AAAATGGTAATTTTTGGAAGTTTCA
*
3437213 GGG-CAAAAAT-GTAATTTTTGGAAGTTTAA
1 GGGTC-AAAATGGTAATTTTTGGAAGTTTCA
*
3437242 GGGTCAAAATGG-AATTTTTGAAAG-TTCA
1 GGGTCAAAATGGTAATTTTTGGAAGTTTCA
*** * * **
3437270 CGGGT-AAAAACATGATTTTAGGAAGTTTTG
1 -GGGTCAAAATGGTAATTTTTGGAAGTTTCA
*
3437300 GGGTTAAAAAT-GTAA-TTTTGAAGAAGTTTC-
1 GGG-TCAAAATGGTAATTTTTG--GAAGTTTCA
* *
3437330 GAGGTTAAAAT-GTAA-TTTTGGAAAAGTTAC-
1 G-GGTCAAAATGGTAATTTTTGG--AAGTTTCA
* *
3437360 GAGGTTAAAAT-GTAAATTTTTGAGAA-ATTCGA
1 G-GGTCAAAATGGT-AATTTTTG-GAAGTTTC-A
*
3437392 GGGTCAAAAT-ATAATTTTTGGACAGTTT-A
1 GGGTCAAAATGGTAATTTTTGGA-AGTTTCA
3437421 GGG
1 GGG
3437424 ACCTCTAGAG
Statistics
Matches: 223, Mismatches: 23, Indels: 47
0.76 0.08 0.16
Matches are distributed among these distances:
28 13 0.06
29 99 0.44
30 76 0.34
31 28 0.13
32 6 0.03
33 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (30 bp):
GGGTCAAAATGGTAATTTTTGGAAGTTTCA
Found at i:3437166 original size:30 final size:29
Alignment explanation
Indices: 3437140--3437318 Score: 188
Period size: 29 Copynumber: 6.1 Consensus size: 29
3437130 AAAATGGTAA
3437140 TTTTGGAAGTTTCAGGGTCAAAAATGGAAT
1 TTTTGGAAGTTTCAGGGTCAAAAAT-GAAT
3437170 TTTTGGAAGTTT-AGGGTCAAAAATGGAAT
1 TTTTGGAAGTTTCAGGGTCAAAAAT-GAAT
*
3437199 TTTTGGAAGTTTTAGGG-CAAAAATGTAAT
1 TTTTGGAAGTTTCAGGGTCAAAAATG-AAT
*
3437228 TTTTGGAAGTTTAAGGGTC-AAAATGGAAT
1 TTTTGGAAGTTTCAGGGTCAAAAAT-GAAT
* *
3437257 TTTTGAAAG-TTCACGGGTAAAAACATG-AT
1 TTTTGGAAGTTTCA-GGGTCAAAA-ATGAAT
* ** *
3437286 TTTAGGAAGTTTTGGGGTTAAAAATGTAAT
1 TTTTGGAAGTTTCAGGGTCAAAAATG-AAT
3437316 TTT
1 TTT
3437319 GAAGAAGTTT
Statistics
Matches: 130, Mismatches: 9, Indels: 20
0.82 0.06 0.13
Matches are distributed among these distances:
28 7 0.05
29 92 0.71
30 29 0.22
31 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
TTTTGGAAGTTTCAGGGTCAAAAATGAAT
Found at i:3437172 original size:58 final size:58
Alignment explanation
Indices: 3437099--3437279 Score: 169
Period size: 58 Copynumber: 3.1 Consensus size: 58
3437089 AAAATCGGGA
*
3437099 TCAAAAATAGG-ATTTTTGGACA-TCCGGGGGT-AAAATGGTAA-TTTTGGAAGTTTCAGGG
1 TCAAAAAT-GGAATTTTTGGA-AGT-CGAGGGTAAAAATGG-AATTTTTGGAAGTTTCAGGG
** *
3437157 TCAAAAATGGAATTTTTGGAAGTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTTAGGG
1 TCAAAAATGGAATTTTTGGAAGTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTCAGGG
* ** * *
3437216 -CAAAAATGTAATTTTTGGAAGTTTAAGGGTCAAAATGGAATTTTTGAAAG-TTCACGGG
1 TCAAAAATGGAATTTTTGGAAG-TCGAGGGTAAAAATGGAATTTTTGGAAGTTTCA-GGG
3437274 T-AAAAA
1 TCAAAAA
3437280 CATGATTTTA
Statistics
Matches: 106, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
57 10 0.09
58 66 0.62
59 30 0.28
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (58 bp):
TCAAAAATGGAATTTTTGGAAGTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAGGG
Found at i:3437201 original size:87 final size:86
Alignment explanation
Indices: 3437099--3437295 Score: 213
Period size: 87 Copynumber: 2.3 Consensus size: 86
3437089 AAAATCGGGA
* ** *
3437099 TCAAAAATAGGATTTTTGGACA-TCCGGGGGTAAAATGGTAA-TTTTGGAAGTTTCAGGGTCAAA
1 TCAAAAATAGGATTTTTGGA-AGTCCAGGGCAAAAAT-GTAATTTTTGGAAGTTTAAGGGTC-AA
*
3437162 AATGGAATTTTTGGAAGTTTAGGG
63 AATGGAATTTTTGAAAGTTTAGGG
**
3437186 TCAAAAAT-GGAATTTTTGGAAGTTTTAGGGCAAAAATGTAATTTTTGGAAGTTTAAGGGTCAAA
1 TCAAAAATAGG-ATTTTTGGAAG-TCCAGGGCAAAAATGTAATTTTTGGAAGTTTAAGGGTCAAA
*
3437250 ATGGAATTTTTGAAAGTTCACGGG
64 ATGGAATTTTTGAAAGTTTA-GGG
* * *
3437274 T-AAAAACATGATTTTAGGAAGT
1 TCAAAAATAGGATTTTTGGAAGT
3437296 TTTGGGGTTA
Statistics
Matches: 93, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
86 4 0.04
87 57 0.61
88 32 0.34
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (86 bp):
TCAAAAATAGGATTTTTGGAAGTCCAGGGCAAAAATGTAATTTTTGGAAGTTTAAGGGTCAAAAT
GGAATTTTTGAAAGTTTAGGG
Found at i:3437410 original size:30 final size:29
Alignment explanation
Indices: 3437301--3437411 Score: 118
Period size: 30 Copynumber: 3.7 Consensus size: 29
3437291 GAAGTTTTGG
3437301 GGTTAAAAATGTAA-TTTTGAAGAAGTTTCGA
1 GGTT-AAAATGTAATTTTTGAA-AAG-TTCGA
*
3437332 GGTTAAAATGTAATTTTGGAAAAGTTACGA
1 GGTTAAAATGTAATTTTTGAAAAGTT-CGA
3437362 GGTTAAAATGTAAATTTTTGAGAAA-TTCGA
1 GGTTAAAATGT-AATTTTTGA-AAAGTTCGA
* *
3437392 GGGTCAAAATATAATTTTTG
1 -GGTTAAAATGTAATTTTTG
3437412 GACAGTTTAG
Statistics
Matches: 71, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
29 2 0.03
30 37 0.52
31 29 0.41
32 3 0.04
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.36
Consensus pattern (29 bp):
GGTTAAAATGTAATTTTTGAAAAGTTCGA
Found at i:3441354 original size:17 final size:17
Alignment explanation
Indices: 3441334--3441372 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3441324 TAGTTGAACC
*
3441334 AATTTAATAAAATTTTT
1 AATTTAATAAAAATTTT
**
3441351 AATTTTTTAAAAATTTT
1 AATTTAATAAAAATTTT
3441368 AATTT
1 AATTT
3441373 TTTAATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTAATAAAAATTTT
Found at i:3441383 original size:17 final size:17
Alignment explanation
Indices: 3441341--3441377 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3441331 ACCAATTTAA
*
3441341 TAAAATTTTTAATTTTT
1 TAAAAATTTTAATTTTT
3441358 TAAAAATTTTAATTTTT
1 TAAAAATTTTAATTTTT
3441375 TAA
1 TAA
3441378 TTATTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAAAAATTTTAATTTTT
Found at i:3448427 original size:12 final size:12
Alignment explanation
Indices: 3448410--3448434 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3448400 ATAACATCCA
3448410 AACAACCAAAAT
1 AACAACCAAAAT
3448422 AACAACCAAAAT
1 AACAACCAAAAT
3448434 A
1 A
3448435 GCAGTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (12 bp):
AACAACCAAAAT
Found at i:3456169 original size:21 final size:21
Alignment explanation
Indices: 3456145--3456191 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3456135 ACTCATCTAT
3456145 TAAATGTAAA-AATAATAAATA
1 TAAAT-TAAATAATAATAAATA
*
3456166 TAAATTAAATATTAATAAATA
1 TAAATTAAATAATAATAAATA
*
3456187 AAAAT
1 TAAAT
3456192 ACCTAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TAAATTAAATAATAATAAATA
Found at i:3458263 original size:24 final size:24
Alignment explanation
Indices: 3458235--3458286 Score: 81
Period size: 22 Copynumber: 2.2 Consensus size: 24
3458225 CAGTATTGGT
3458235 ATTTTTTAATAAAAT-T-TTTATA
1 ATTTTTTAATAAAATCTATTTATA
*
3458257 ATTTTTTAATAAATTCTATTTATA
1 ATTTTTTAATAAAATCTATTTATA
3458281 ATTTTT
1 ATTTTT
3458287 GAAGTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 14 0.52
23 1 0.04
24 12 0.44
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTTTAATAAAATCTATTTATA
Found at i:3466561 original size:2 final size:2
Alignment explanation
Indices: 3466554--3466594 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3466544 ACACTTTGCA
3466554 AT AT 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 AT AT A
3466595 AAGTATGACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3468031 original size:31 final size:31
Alignment explanation
Indices: 3467996--3468055 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
3467986 TAGGCCCGCA
* * *
3467996 TATATTGTTTTTATTTTTAA-AATATTTATAT
1 TATATTATTTTAATATTTAATAAT-TTTATAT
3468027 TATATTATTTTAATATTTAATAATTTTAT
1 TATATTATTTTAATATTTAATAATTTTAT
3468056 TCATTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (31 bp):
TATATTATTTTAATATTTAATAATTTTATAT
Found at i:3479796 original size:56 final size:56
Alignment explanation
Indices: 3479736--3479848 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
3479726 AAAAGAAGAG
3479736 AAAGAAGAGCTTTGGTTAGTGTGAATGAAAAAGGCTATATAACAACCATTTTAATA
1 AAAGAAGAGCTTTGGTTAGTGTGAATGAAAAAGGCTATATAACAACCATTTTAATA
*
3479792 AAAGAAGAGCTTTGGTTGGTGTGAATGAAAAAGGCTATATAACAACCATTTTAATA
1 AAAGAAGAGCTTTGGTTAGTGTGAATGAAAAAGGCTATATAACAACCATTTTAATA
3479848 A
1 A
3479849 TTCAATGACT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.28
Consensus pattern (56 bp):
AAAGAAGAGCTTTGGTTAGTGTGAATGAAAAAGGCTATATAACAACCATTTTAATA
Found at i:3485909 original size:11 final size:11
Alignment explanation
Indices: 3485879--3485920 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
3485869 ATTGTGTTTG
3485879 ATTACGA-TTA
1 ATTACGATTTA
*
3485889 ATTACAATTTA
1 ATTACGATTTA
* *
3485900 ATTATGATTTG
1 ATTACGATTTA
3485911 ATTACGATTT
1 ATTACGATTT
3485921 TGTTATAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (11 bp):
ATTACGATTTA
Found at i:3501494 original size:11 final size:11
Alignment explanation
Indices: 3501480--3501523 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
3501470 TTTATAAAAG
*
3501480 TTTTATTGTAT
1 TTTTATTTTAT
3501491 TTTTAATTTTAT
1 TTTT-ATTTTAT
*
3501503 TTTAATTTTAGT
1 TTTTATTTTA-T
3501515 TTTTATTTT
1 TTTTATTTT
3501524 TAAAAGTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:3501505 original size:12 final size:12
Alignment explanation
Indices: 3501488--3501525 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
3501478 AGTTTTATTG
3501488 TATTTTTAATTT
1 TATTTTTAATTT
3501500 TA-TTTTAATTT
1 TATTTTTAATTT
*
3501511 TAGTTTTTATTTT
1 TA-TTTTTAATTT
3501524 TA
1 TA
3501526 AAAGTCATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 11 0.48
12 2 0.09
13 10 0.43
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (12 bp):
TATTTTTAATTT
Found at i:3508541 original size:28 final size:25
Alignment explanation
Indices: 3508510--3508565 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 25
3508500 AACATCACTC
*
3508510 AAATTAACTAATAAGATGAACAAAAATT
1 AAATT-ACTAA-AAAATG-ACAAAAATT
*
3508538 AAATTACTAAAAAATGCCAAAAATT
1 AAATTACTAAAAAATGACAAAAATT
3508563 AAA
1 AAA
3508566 AAAAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 11 0.42
26 5 0.19
27 5 0.19
28 5 0.19
ACGTcount: A:0.62, C:0.09, G:0.05, T:0.23
Consensus pattern (25 bp):
AAATTACTAAAAAATGACAAAAATT
Found at i:3511858 original size:21 final size:21
Alignment explanation
Indices: 3511819--3511859 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3511809 ATATGAGAAG
* * *
3511819 ATTGCTATAAGTTTTAAAAAT
1 ATTGCTAAAAATTTGAAAAAT
3511840 ATTGCTAAAAATTTGAAAAA
1 ATTGCTAAAAATTTGAAAAA
3511860 AAGGGAAAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (21 bp):
ATTGCTAAAAATTTGAAAAAT
Found at i:3515294 original size:15 final size:15
Alignment explanation
Indices: 3515274--3515323 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 15
3515264 TTAAGATTAG
3515274 TTAAAAATATATTTT
1 TTAAAAATATATTTT
*
3515289 TTAAAATTATTTATTTT
1 TTAAAA--ATATATTTT
3515306 TTAAAAATA-ATTTCT
1 TTAAAAATATATTT-T
3515321 TTA
1 TTA
3515324 CATTTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 4 0.13
15 12 0.40
17 14 0.47
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAAAAATATATTTT
Found at i:3515312 original size:18 final size:17
Alignment explanation
Indices: 3515283--3515318 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3515273 GTTAAAAATA
*
3515283 TATTTTTTAAAATTATT
1 TATTTTTTAAAATAATT
3515300 TATTTTTTAAAAATAATT
1 TATTTTTT-AAAATAATT
3515318 T
1 T
3515319 CTTTACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTTTTAAAATAATT
Found at i:3523069 original size:24 final size:24
Alignment explanation
Indices: 3523023--3523070 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3523013 TAAATCTTGA
*
3523023 AAAAAAAAACCTATTTGACCAATT
1 AAAAAAAAACCTATTTCACCAATT
3523047 AAAAAAAAACCTATATTCA-CAATT
1 AAAAAAAAACCTAT-TTCACCAATT
3523071 TAGCCCTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.25
Consensus pattern (24 bp):
AAAAAAAAACCTATTTCACCAATT
Found at i:3532653 original size:11 final size:11
Alignment explanation
Indices: 3532624--3532673 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
3532614 ATATTTAAAT
*
3532624 AATAATAATAA
1 AATAATAGTAA
3532635 AATAATAGTAA
1 AATAATAGTAA
* **
3532646 TATAATAGCGA
1 AATAATAGTAA
*
3532657 AATAATTGTAA
1 AATAATAGTAA
3532668 AATAAT
1 AATAAT
3532674 GGCAAAACAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (11 bp):
AATAATAGTAA
Found at i:3532680 original size:11 final size:11
Alignment explanation
Indices: 3532633--3532693 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
3532623 TAATAATAAT
*
3532633 AAAATAATAGT
1 AAAATAATAGC
*
3532644 AATATAATAGC
1 AAAATAATAGC
* * *
3532655 GAAATAATTGT
1 AAAATAATAGC
*
3532666 AAAATAATGGC
1 AAAATAATAGC
* *
3532677 AAAACAATATC
1 AAAATAATAGC
3532688 AAAATA
1 AAAATA
3532694 GTGGAAATAG
Statistics
Matches: 37, Mismatches: 13, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.59, C:0.07, G:0.10, T:0.25
Consensus pattern (11 bp):
AAAATAATAGC
Found at i:3541320 original size:22 final size:18
Alignment explanation
Indices: 3541273--3541320 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
3541263 TTATATTCTC
3541273 GGAGTTTCAAAATTTGAA
1 GGAGTTTCAAAATTTGAA
3541291 GGACGTTTCGAGAAATTTTGAA
1 GGA-GTTTC-A-AAA-TTTGAA
3541313 GAGAGTTT
1 G-GAGTTT
3541321 TTATCGCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 5 0.20
20 1 0.04
21 3 0.12
22 11 0.44
23 2 0.08
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (18 bp):
GGAGTTTCAAAATTTGAA
Found at i:3542153 original size:29 final size:30
Alignment explanation
Indices: 3542121--3542243 Score: 89
Period size: 29 Copynumber: 4.2 Consensus size: 30
3542111 TCAATAATGA
3542121 AATTTTGGAAAGTTTAGGTGT-AAAATGGT
1 AATTTTGGAAAGTTTAGGTGTAAAAATGGT
***
3542150 AATTTTTGGTGAAA-TCGGGGT-TAAAAATGG-
1 AA-TTTT-G-GAAAGTTTAGGTGTAAAAATGGT
* *
3542180 AATTTTGGAAAGTTTAGG-GTTAAAATAGT
1 AATTTTGGAAAGTTTAGGTGTAAAAATGGT
* * *
3542209 AATTTTTGG-AAGTTTTGGGGTCAAAAT-GT
1 AA-TTTTGGAAAGTTTAGGTGTAAAAATGGT
3542238 AATTTT
1 AATTTT
3542244 TTGAAGTTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
27 4 0.05
28 15 0.20
29 20 0.27
30 20 0.27
31 12 0.16
32 4 0.05
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (30 bp):
AATTTTGGAAAGTTTAGGTGTAAAAATGGT
Found at i:3542184 original size:59 final size:59
Alignment explanation
Indices: 3542083--3542217 Score: 191
Period size: 59 Copynumber: 2.3 Consensus size: 59
3542073 ACCCGAGGGC
* *
3542083 AAAATGGTAATTTTTGGTAAAATTGAGGTCAATAATGAAATTTTGGAAAGTTTA-GGTGT
1 AAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTTAGGGT-T
* * * *
3542142 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGTT
1 AAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTTAGGGTT
*
3542201 AAAATAGTAATTTTTGG
1 AAAATGGTAATTTTTGG
3542218 AAGTTTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 65 0.96
60 3 0.04
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.37
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTTAGGGTT
Found at i:3542218 original size:30 final size:30
Alignment explanation
Indices: 3542123--3542287 Score: 105
Period size: 30 Copynumber: 5.6 Consensus size: 30
3542113 AATAATGAAA
*
3542123 TTTTGGAAAGTTTA-GGTGTAAAATGGTAAT
1 TTTTGGAAAGTTTAGGGT-TAAAATAGTAAT
** *
3542153 TTTTGGTGAAA--TCGGGGTTAAAA-ATGGAA-
1 TTTT-G-GAAAGTTTAGGGTTAAAATA-GTAAT
3542182 TTTTGGAAAGTTTAGGGTTAAAATAGTAAT
1 TTTTGGAAAGTTTAGGGTTAAAATAGTAAT
* *
3542212 TTTTGG-AAGTTTTGGGGTCAAAAT-GTAAT
1 TTTTGGAAAG-TTTAGGGTTAAAATAGTAAT
* * *
3542241 TTTTTG-AAGTTTTAGGGTCAAAAATA-TAGT
1 TTTTGGAAAG-TTTAGGGT-TAAAATAGTAAT
* *
3542271 TTTTGGACAGTTCAGGG
1 TTTTGGAAAGTTTAGGG
3542288 ACCTACAAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
27 4 0.04
28 1 0.01
29 41 0.38
30 51 0.48
31 6 0.06
32 4 0.04
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.39
Consensus pattern (30 bp):
TTTTGGAAAGTTTAGGGTTAAAATAGTAAT
Found at i:3542229 original size:59 final size:59
Alignment explanation
Indices: 3542116--3542282 Score: 148
Period size: 59 Copynumber: 2.8 Consensus size: 59
3542106 TGAGGTCAAT
* * *
3542116 AATGAAATTTTGGAAAGTTTA-GGTGTAAAATGGTAATTTTTGGTGAA--ATCGGGGTTAAA
1 AATGAAATTTTGGAAAGTTTAGGGTCTAAAATAGTAATTTTT-G-GAAGTTTCGGGG-TAAA
* * *
3542175 AATGGAATTTTGGAAAGTTTAGGGT-TAAAATAGTAATTTTTGGAAGTTTTGGGGTCAA
1 AATGAAATTTTGGAAAGTTTAGGGTCTAAAATAGTAATTTTTGGAAGTTTCGGGGTAAA
* * * *
3542233 AATGTAATTTTTTG-AAGTTTTAGGGTCAAAAATA-TAGTTTTTGGACAGTT
1 AATG-AAATTTTGGAAAG-TTTAGGGTCTAAAATAGTAATTTTTGGA-AGTT
3542283 CAGGGACCTA
Statistics
Matches: 91, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
57 3 0.03
58 11 0.12
59 64 0.70
60 13 0.14
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (59 bp):
AATGAAATTTTGGAAAGTTTAGGGTCTAAAATAGTAATTTTTGGAAGTTTCGGGGTAAA
Found at i:3542244 original size:29 final size:29
Alignment explanation
Indices: 3542173--3542282 Score: 116
Period size: 30 Copynumber: 3.7 Consensus size: 29
3542163 ATCGGGGTTA
* *
3542173 AAAATGGAA-TTTTGGAAAG-TTTAGGGTT
1 AAAATGTAATTTTTGG-AAGTTTTAGGGTC
*
3542201 AAAATAGTAATTTTTGGAAGTTTTGGGGTC
1 AAAAT-GTAATTTTTGGAAGTTTTAGGGTC
*
3542231 AAAATGTAATTTTTTGAAGTTTTAGGGTC
1 AAAATGTAATTTTTGGAAGTTTTAGGGTC
* *
3542260 AAAAATATAGTTTTTGGACAGTT
1 -AAAATGTAATTTTTGGA-AGTT
3542283 CAGGGACCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.07
29 28 0.41
30 32 0.46
31 4 0.06
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.40
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTTTAGGGTC
Found at i:3542618 original size:32 final size:32
Alignment explanation
Indices: 3542560--3542620 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
3542550 GCCAAATTTA
*
3542560 AAAATAATTAAAAGTACAAAAGGGACCAAATC
1 AAAATAATTAAAAATACAAAAGGGACCAAATC
*
3542592 AAAATAATTAAAAAATACAGAA-GGACCAA
1 AAAATAATT-AAAAATACAAAAGGGACCAA
3542621 GTGCACAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 16 0.62
33 10 0.38
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.15
Consensus pattern (32 bp):
AAAATAATTAAAAATACAAAAGGGACCAAATC
Found at i:3544247 original size:13 final size:13
Alignment explanation
Indices: 3544231--3544255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3544221 AAATAAATTT
3544231 AATCTTTAAAATA
1 AATCTTTAAAATA
3544244 AATCTTTAAAAT
1 AATCTTTAAAAT
3544256 GAATTTAAAT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
AATCTTTAAAATA
Found at i:3545210 original size:7 final size:7
Alignment explanation
Indices: 3545198--3545222 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3545188 AATCTTCAAA
3545198 CTATTGT
1 CTATTGT
3545205 CTATTGT
1 CTATTGT
3545212 CTATTGT
1 CTATTGT
3545219 CTAT
1 CTAT
3545223 GGCGGTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.12, T:0.56
Consensus pattern (7 bp):
CTATTGT
Found at i:3547422 original size:20 final size:21
Alignment explanation
Indices: 3547399--3547439 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3547389 AACTTAAACA
*
3547399 TTAACGTAAGT-AATTAAAAT
1 TTAACATAAGTAAATTAAAAT
*
3547419 TTAACATAATTAAATTAAAAT
1 TTAACATAAGTAAATTAAAAT
3547440 GACTATTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (21 bp):
TTAACATAAGTAAATTAAAAT
Found at i:3553771 original size:2 final size:2
Alignment explanation
Indices: 3553766--3553805 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3553756 TGCAGCGACA
3553766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3553806 TAATTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3554795 original size:81 final size:79
Alignment explanation
Indices: 3554632--3554804 Score: 197
Period size: 81 Copynumber: 2.1 Consensus size: 79
3554622 AACATTTGAA
* * * *
3554632 TAGGAGATTTAGAACCTGACAAATATTTTAATTATTATTTAAAAATTAAAAAAAATAAGATTAAG
1 TAGGA-ATTTAAAACCTGACAAATATTCTAATTAATATTTAAAAATTAAAAAAAATAAGATTAAA
*
3554697 ACACATCTCATTTTTTT
65 ACACATCTC--TCTTTT
3554714 TAGGAATTTAAAACCTGACAAATATTCTAATTAATATTTAAAAATTAAAAAATTAAATCAA-ATT
1 TAGGAATTTAAAACCTGACAAATATTCTAATTAATATTTAAAAATT-AAAAA--AAAT-AAGATT
*
3554778 AAAACACGTCTC-CTTTT
62 AAAACACATCTCTCTTTT
3554795 TGGAGGAATT
1 T--AGGAATT
3554805 AAGAAAAGAT
Statistics
Matches: 79, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
81 43 0.54
82 10 0.13
83 7 0.09
84 17 0.22
85 2 0.03
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.36
Consensus pattern (79 bp):
TAGGAATTTAAAACCTGACAAATATTCTAATTAATATTTAAAAATTAAAAAAAATAAGATTAAAA
CACATCTCTCTTTT
Found at i:3577643 original size:15 final size:15
Alignment explanation
Indices: 3577623--3577653 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3577613 AATCAAAAAC
*
3577623 TGAATCGAATCAAAT
1 TGAATCAAATCAAAT
3577638 TGAATCAAATCAAAT
1 TGAATCAAATCAAAT
3577653 T
1 T
3577654 ATAATAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (15 bp):
TGAATCAAATCAAAT
Found at i:3577810 original size:23 final size:23
Alignment explanation
Indices: 3577768--3577811 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3577758 ACATTGTTTG
*
3577768 TAAATTTAATTCTTATTTTTATA
1 TAAATTTAATTCTTAATTTTATA
* *
3577791 TAAATTTGATTTTTAATTTTA
1 TAAATTTAATTCTTAATTTTA
3577812 AAAAAAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TAAATTTAATTCTTAATTTTATA
Found at i:3583556 original size:20 final size:20
Alignment explanation
Indices: 3583511--3583557 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
3583501 TTTCAAATAT
*
3583511 ATTAAAAAATTGCATAACAA
1 ATTAAAAAATTACATAACAA
*
3583531 ATTTAAAAAATTAATATAAC-A
1 A-TTAAAAAATT-ACATAACAA
3583552 ATTAAA
1 ATTAAA
3583558 TATGATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.26
21 12 0.52
22 5 0.22
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (20 bp):
ATTAAAAAATTACATAACAA
Found at i:3599647 original size:18 final size:17
Alignment explanation
Indices: 3599624--3599669 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
3599614 AAGGTCTAGC
*
3599624 TTATTTTTTAAACATAT
1 TTATTTTTTAAACAAAT
**
3599641 ATTATTTTTTATCCAAAT
1 -TTATTTTTTAAACAAAT
3599659 TTATTTTTTAA
1 TTATTTTTTAA
3599670 TTTATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTTTTTAAACAAAT
Found at i:3599838 original size:206 final size:206
Alignment explanation
Indices: 3599479--3599889 Score: 759
Period size: 206 Copynumber: 2.0 Consensus size: 206
3599469 TAACTGATAT
* *
3599479 AAAGTCTATAATATCTATACAATAGAGAATGTATTGATATTTGCTACGAGATATTGGTACCTTTG
1 AAAGCCTATAATATCTATACAATAGAGAATGTATTGATATTTGCTACCAGATATTGGTACCTTTG
3599544 GGAGGGCATCAATATTTTTTACGAGGTATTGGTACCTTAAACATATAACCAAGTAAAAAAAACTT
66 GGAGGGCATCAATATTTTTTACGAGGTATTGGTACCTTAAACATATAACCAAGTAAAAAAAACTT
**
3599609 TACTCAAGGTCTAGCTTATTTTTTAAACATATATTATTTTTTATCCAAATTTATTTTTTAATTTA
131 TACTCAAAATCTAGCTTATTTTTTAAACATATATTATTTTTTATCCAAATTTATTTTTTAATTTA
3599674 TATTTTTGTTC
196 TATTTTTGTTC
3599685 AAAGCCTATAATATCTATACAATAGAGAATGTATTGATATTTGCTACCAGATATTGGTACCTTTG
1 AAAGCCTATAATATCTATACAATAGAGAATGTATTGATATTTGCTACCAGATATTGGTACCTTTG
* *
3599750 GGAGGGCATCAATATTTTTTACGAGGTATTGGTACCTTAAACATATATCCAAGTAAAAAAAATTT
66 GGAGGGCATCAATATTTTTTACGAGGTATTGGTACCTTAAACATATAACCAAGTAAAAAAAACTT
*
3599815 TACTCAAAATCTAGGTTATTTTTTAAACATATATTATTTTTTATCCAAATTTATTTTTTAATTTA
131 TACTCAAAATCTAGCTTATTTTTTAAACATATATTATTTTTTATCCAAATTTATTTTTTAATTTA
3599880 TATTTTTGTT
196 TATTTTTGTT
3599890 TAAACTTTCT
Statistics
Matches: 198, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
206 198 1.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (206 bp):
AAAGCCTATAATATCTATACAATAGAGAATGTATTGATATTTGCTACCAGATATTGGTACCTTTG
GGAGGGCATCAATATTTTTTACGAGGTATTGGTACCTTAAACATATAACCAAGTAAAAAAAACTT
TACTCAAAATCTAGCTTATTTTTTAAACATATATTATTTTTTATCCAAATTTATTTTTTAATTTA
TATTTTTGTTC
Found at i:3599853 original size:18 final size:17
Alignment explanation
Indices: 3599830--3599875 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
3599820 AAAATCTAGG
*
3599830 TTATTTTTTAAACATAT
1 TTATTTTTTAAACAAAT
**
3599847 ATTATTTTTTATCCAAAT
1 -TTATTTTTTAAACAAAT
3599865 TTATTTTTTAA
1 TTATTTTTTAA
3599876 TTTATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTTTTTAAACAAAT
Found at i:3603131 original size:3 final size:3
Alignment explanation
Indices: 3603123--3603149 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3603113 TCTGAATTTG
3603123 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
3603150 AATGGTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:3608592 original size:23 final size:23
Alignment explanation
Indices: 3608561--3608611 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
3608551 GACAAAAATA
* *
3608561 TTAAGTTCGAAAAATGGGTTTGG
1 TTAAATTCGAAAAATGAGTTTGG
3608584 TTAAATTCGAAAAATGAGTTTGG
1 TTAAATTCGAAAAATGAGTTTGG
3608607 TTAAA
1 TTAAA
3608612 AAAATTAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (23 bp):
TTAAATTCGAAAAATGAGTTTGG
Found at i:3623145 original size:28 final size:27
Alignment explanation
Indices: 3623106--3623169 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 27
3623096 TCAAATCCAA
* *
3623106 ATTGCAAAATTTATGAAAGCTTTTGTG
1 ATTGCAAAATTTATAAAAGCTTTTGAG
3623133 ATTGTCAAAATTTATAAAAGCTTTTGAG
1 ATTG-CAAAATTTATAAAAGCTTTTGAG
3623161 ATTGACAAA
1 ATTG-CAAA
3623170 CTAATATGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 4 0.12
28 29 0.88
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.38
Consensus pattern (27 bp):
ATTGCAAAATTTATAAAAGCTTTTGAG
Found at i:3626345 original size:31 final size:31
Alignment explanation
Indices: 3626310--3626375 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
3626300 TTAATAGCCT
*
3626310 AGTGATTTAAACAAAAAATTTCAAATAGTTC
1 AGTGACTTAAACAAAAAATTTCAAATAGTTC
* * * * *
3626341 AGTGACTTAGATAAAAACTTTTAAATGGTTC
1 AGTGACTTAAACAAAAAATTTCAAATAGTTC
3626372 AGTG
1 AGTG
3626376 TTGTAATAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (31 bp):
AGTGACTTAAACAAAAAATTTCAAATAGTTC
Found at i:3627957 original size:33 final size:34
Alignment explanation
Indices: 3627893--3627956 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
3627883 AAACCGAAGT
3627893 TAAAACGATTTTAGTTGAAAATAGAGAAAAAAGG
1 TAAAACGATTTTAGTTGAAAATAGAGAAAAAAGG
3627927 TAAAACGATTTTAGTTG-AAATA-AGAAAAAA
1 TAAAACGATTTTAGTTGAAAATAGAGAAAAAA
3627957 ATAAAAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 8 0.27
33 5 0.17
34 17 0.57
ACGTcount: A:0.55, C:0.03, G:0.17, T:0.25
Consensus pattern (34 bp):
TAAAACGATTTTAGTTGAAAATAGAGAAAAAAGG
Found at i:3648785 original size:24 final size:24
Alignment explanation
Indices: 3648753--3648803 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3648743 CAAGAATATG
*
3648753 AAAGGTTAAAAAAAATGAAAGGTT
1 AAAGATTAAAAAAAATGAAAGGTT
** *
3648777 AAAGATTAAAGGAGATGAAAGGTT
1 AAAGATTAAAAAAAATGAAAGGTT
3648801 AAA
1 AAA
3648804 CATCCATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.20
Consensus pattern (24 bp):
AAAGATTAAAAAAAATGAAAGGTT
Found at i:3654795 original size:29 final size:29
Alignment explanation
Indices: 3654763--3654904 Score: 87
Period size: 30 Copynumber: 4.9 Consensus size: 29
3654753 TGTACATTCG
3654763 GGGGTAAAATGGTAATTTTTGGAAAAATA
1 GGGGTAAAATGGTAATTTTTGGAAAAATA
* * ** *
3654792 GGGGTCAAAAAT-GAAATTTTTAG-AAGTTC
1 GGGGT--AAAATGGTAATTTTTGGAAAAATA
* *
3654821 GAGGGTAAAATGGTAATTTTGGGAAAAATC
1 G-GGGTAAAATGGTAATTTTTGGAAAAATA
* * **
3654851 GAGGTCAAAAATGG-ATTTTTTGG-AAGTTCA
1 GGGGT--AAAATGGTAATTTTTGGAAAAAT-A
*
3654881 CGGGTAAAATGGTAA-TTTTGGAAA
1 GGGGTAAAATGGTAATTTTTGGAAA
3654905 GTTTAGGGTT
Statistics
Matches: 84, Mismatches: 19, Indels: 20
0.68 0.15 0.16
Matches are distributed among these distances:
28 18 0.21
29 26 0.31
30 28 0.33
31 12 0.14
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.30
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGAAAAATA
Found at i:3654800 original size:59 final size:58
Alignment explanation
Indices: 3654759--3655016 Score: 233
Period size: 59 Copynumber: 4.4 Consensus size: 58
3654749 TTTTTGTACA
* *
3654759 TTCGGGGGTAAAATGGTAATTTTTGGAAAAATAGGGGTCAAAAATGAAATTTTTAGAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAAAATAGAGGTCAAAAATGAAATTTTT-GAAG
* * * *
3654818 TTCGAGGGTAAAATGGTAATTTTGGGAAAAATCGAGGTCAAAAATGGATTTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAAAATAGAGGTCAAAAATGAAATTTTT-GAAG
** * *
3654877 TTC-ACGGGTAAAATGGTAA-TTTTGGAAAGTTTAG-GGTTAAAAATGAAATTTTGGAAAG
1 TTCGA-GGGTAAAATGGTAATTTTTGGAAA-AATAGAGGTCAAAAATGAAATTTTTG-AAG
* ** * *
3654935 TTCGAGGGTAAAAAT-ATAA-TTTTCAAAAACATCAG-GGTCAAAAATGGAATTTTGGAAAG
1 TTCGAGGGT-AAAATGGTAATTTTTGGAAAA-AT-AGAGGTCAAAAATGAAATTTTTG-AAG
*
3654994 TTTGAGGGTAAAAAT-GTAATTTT
1 TTCGAGGGT-AAAATGGTAATTTT
3655017 AAGACAGTTT
Statistics
Matches: 167, Mismatches: 24, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
57 1 0.01
58 45 0.27
59 118 0.71
60 3 0.02
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (58 bp):
TTCGAGGGTAAAATGGTAATTTTTGGAAAAATAGAGGTCAAAAATGAAATTTTTGAAG
Found at i:3654955 original size:117 final size:117
Alignment explanation
Indices: 3654764--3655016 Score: 288
Period size: 117 Copynumber: 2.2 Consensus size: 117
3654754 GTACATTCGG
*
3654764 GGGTAAAATGGTAATTTTTGGAAAAATAGGGGTCAAAAATGAAATTTTTAGAAGTTCGAGGGTAA
1 GGGTAAAATGGTAA-TTTTGGAAAAATAGGGGTCAAAAATGAAATTTTGAGAAGTTCGAGGGTAA
* ** *
3654829 AATGGTAATTTTGGGAAAA-ATC-GAGGTCAAAAATGGATTTTTTGG-AAG-TTCA
65 AATGATAATTTT-CAAAAACATCAG-GGTCAAAAATGGA-ATTTTGGAAAGTTTCA
** *
3654881 CGGGTAAAATGGTAATTTTGGAAAGTTTA-GGGTTAAAAATGAAATTTTG-GAAAGTTCGAGGGT
1 -GGGTAAAATGGTAATTTTGGAAA-AATAGGGGTCAAAAATGAAATTTTGAG-AAGTTCGAGGGT
*
3654944 AAAAAT-ATAATTTTCAAAAACATCAGGGTCAAAAATGGAATTTTGGAAAGTTTGA
63 -AAAATGATAATTTTCAAAAACATCAGGGTCAAAAATGGAATTTTGGAAAGTTTCA
3654999 GGGTAAAAAT-GTAATTTT
1 GGGT-AAAATGGTAATTTT
3655017 AAGACAGTTT
Statistics
Matches: 118, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
116 11 0.09
117 77 0.65
118 30 0.25
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (117 bp):
GGGTAAAATGGTAATTTTGGAAAAATAGGGGTCAAAAATGAAATTTTGAGAAGTTCGAGGGTAAA
ATGATAATTTTCAAAAACATCAGGGTCAAAAATGGAATTTTGGAAAGTTTCA
Found at i:3655026 original size:30 final size:29
Alignment explanation
Indices: 3654882--3655016 Score: 139
Period size: 29 Copynumber: 4.6 Consensus size: 29
3654872 GGAAGTTCAC
3654882 GGGT-AAAATGGTAATTTTGGAAAGTTT-A
1 GGGTAAAAAT-GTAATTTTGGAAAGTTTGA
* *
3654910 GGGTTAAAAATGAAATTTTGGAAAGTTCGA
1 GGG-TAAAAATGTAATTTTGGAAAGTTTGA
* ** *** *
3654940 GGGTAAAAATATAATTTTCAAAAACATCA
1 GGGTAAAAATGTAATTTTGGAAAGTTTGA
*
3654969 GGGTCAAAAATGGAATTTTGGAAAGTTTGA
1 GGGT-AAAAATGTAATTTTGGAAAGTTTGA
3654999 GGGTAAAAATGTAATTTT
1 GGGTAAAAATGTAATTTT
3655017 AAGACAGTTT
Statistics
Matches: 83, Mismatches: 20, Indels: 7
0.75 0.18 0.06
Matches are distributed among these distances:
28 3 0.04
29 50 0.60
30 30 0.36
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.32
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTGGAAAGTTTGA
Found at i:3655995 original size:18 final size:17
Alignment explanation
Indices: 3655974--3656016 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
3655964 TATTAAATAT
3655974 TATTAATTATTTAATAAA
1 TATT-ATTATTTAATAAA
3655992 TATTATTA-TTAATAAA
1 TATTATTATTTAATAAA
3656008 -ATTATTATT
1 TATTATTATT
3656017 ATTATCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.29
16 9 0.38
17 4 0.17
18 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTATTATTTAATAAA
Found at i:3656013 original size:15 final size:16
Alignment explanation
Indices: 3655974--3656017 Score: 63
Period size: 15 Copynumber: 2.7 Consensus size: 16
3655964 TATTAAATAT
3655974 TATTAATTATTTAATAAA
1 TATT-ATTA-TTAATAAA
3655992 TATTATTATTAATAAA
1 TATTATTATTAATAAA
3656008 -ATTATTATTA
1 TATTATTATTA
3656018 TTATCATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.38
16 8 0.31
17 4 0.15
18 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTATTATTAATAAA
Found at i:3656017 original size:18 final size:18
Alignment explanation
Indices: 3655967--3656020 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
3655957 CTTTTTTTAT
3655967 TAAATATTATTAATTATTTAA
1 TAAA-ATTATT-ATTA-TTAA
3655988 T-AAA-TATTATTATTAA
1 TAAAATTATTATTATTAA
3656004 TAAAATTATTATTATTA
1 TAAAATTATTATTATTA
3656021 TCATTAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.16
17 7 0.23
18 15 0.48
19 1 0.03
20 2 0.06
21 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAAAATTATTATTATTAA
Found at i:3656019 original size:24 final size:24
Alignment explanation
Indices: 3655992--3656037 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3655982 ATTTAATAAA
*
3655992 TATTATTATTAATAAAATTATTAT
1 TATTATCATTAATAAAATTATTAT
*
3656016 TATTATCATTAATGAAATTATT
1 TATTATCATTAATAAAATTATT
3656038 TAATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TATTATCATTAATAAAATTATTAT
Found at i:3656882 original size:18 final size:17
Alignment explanation
Indices: 3656849--3656935 Score: 84
Period size: 17 Copynumber: 5.1 Consensus size: 17
3656839 AATATATAAA
**
3656849 TAAATTTAATTTAAATT
1 TAAATTTAAAATAAATT
*
3656866 TAAATTTTAAAACAAATT
1 TAAA-TTTAAAATAAATT
*
3656884 TCAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
* *
3656901 TATATTCAAAATAAATT
1 TAAATTTAAAATAAATT
** *
3656918 TAACCTTAAAGTAAATT
1 TAAATTTAAAATAAATT
3656935 T
1 T
3656936 TAAAATGAGT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
17 43 0.77
18 13 0.23
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.43
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:3657588 original size:194 final size:199
Alignment explanation
Indices: 3657262--3657689 Score: 589
Period size: 194 Copynumber: 2.2 Consensus size: 199
3657252 TACTTCTTAT
* * * ** * *
3657262 TATCTCATCAGGAAGATAACCGCCCCGTTTGTTTCAATCCGCTTCTTTGTATCTCATCAAGAAGA
1 TATCTCATTAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTCATCAAGAAGA
* * * *
3657327 CGAATTTGGTCCACTTCTTAGTGTCTCATCAAGAAGCTAACCTTTTTATTGCTTCGCCCTACTTC
66 CGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTACTTC
3657392 TCAGTATCTCACCAGGAAGCTGGGGTTCGAAGA-TT-T-GT-TTG-CATTAAGTTGGTATACTTC
131 TCAGTATCTCACCAGGAAGCTGGGGTTCGAAGATTTCTCGTATTGACATTAAGTTGGTATACTTC
3657452 TCTG
196 TCTG
* * *
3657456 TATCTCATTAGGAAGATGACCGCCTCACTTGTTTCAATTCTCTTCTCTGTACCTCATCAGGAAGA
1 TATCTCATTAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTCATCAAGAAGA
* *
3657521 CGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTC
66 CGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTACTTC
* * * * *
3657586 TCAGTTTCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCGTATTGAACCTTGAGTTGGTATACT
131 TCAGTATCTCACCAGGAAGCTGGGGTTCGAAGATTT-CTCGTATTG-ACATTAAGTTGGTATACT
3657651 TCTCTG
194 TCTCTG
* *
3657657 TATCTCATTAGGAAGACGATCGCCTCAC-TGTTT
1 TATCTCATTAGGAAGATGACCGCCTCACTTGTTT
3657690 GTGGATAATC
Statistics
Matches: 204, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
194 144 0.71
195 2 0.01
197 1 0.00
198 2 0.01
199 3 0.01
200 5 0.02
201 47 0.23
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (199 bp):
TATCTCATTAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTCATCAAGAAGA
CGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTACTTC
TCAGTATCTCACCAGGAAGCTGGGGTTCGAAGATTTCTCGTATTGACATTAAGTTGGTATACTTC
TCTG
Found at i:3669750 original size:30 final size:31
Alignment explanation
Indices: 3669706--3669813 Score: 118
Period size: 30 Copynumber: 3.6 Consensus size: 31
3669696 ACTCGAGGGG
3669706 AAAATGGTAATTTTTGGAAAAATTGGGGTTA
1 AAAATGGTAATTTTTGGAAAAATTGGGGTTA
**
3669737 AAAATGG-AATTTTTGG-AAGTTTAGGGG-T-
1 AAAATGGTAATTTTTGGAAAAATT-GGGGTTA
* * * *
3669765 AAAATGGTAATTTTGGGAAAAATCGAGGTCA
1 AAAATGGTAATTTTTGGAAAAATTGGGGTTA
3669796 AAAATGG-AATTTTTGGAA
1 AAAATGGTAATTTTTGGAA
3669814 GTTCAAGAGT
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
28 7 0.11
29 16 0.25
30 26 0.41
31 14 0.22
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.32
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGAAAAATTGGGGTTA
Found at i:3669770 original size:59 final size:59
Alignment explanation
Indices: 3669678--3670013 Score: 312
Period size: 59 Copynumber: 5.7 Consensus size: 59
3669668 CTCGGGGGGT
* * ** *
3669678 AAAATGGTAATTTTGGACACTCGAGGGG-AAAATGGTAATTTTTGGAAAAATTGGGGTTA
1 AAAATGG-AATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAGAAAAATTGGGGTTA
** * * *
3669737 AAAATGGAATTTTTGG-AAGTTTAGGGGTAAAATGGTAATTTTGGGAAAAATCGAGGTCA
1 AAAATGGAA-TTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAGAAAAATTGGGGTTA
* * * ** *
3669796 AAAATGGAATTTTTGG-AAGTTCAAGAGTAAAATGGTAATTTTTAGAAAGTTTGAGGTTA
1 AAAATGGAA-TTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAGAAAAATTGGGGTTA
* * *
3669855 AAAATGAAATTTTGGAAAGTTT-GGAGGTAAAATTGTAATTTTTA-AAAAGTTTGGGGTTA
1 AAAATGGAATTTTGGAAAGTTTAGG-GGTAAAATGGTAATTTTTAGAAAA-ATTGGGGTTA
** * * * *
3669914 TTAATGGAATTTTGGAAAGTTTAGGGGTAAAA-GTGT-ATTTTTCAAAAAAACTAGGGTCA
1 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATG-GTAATTTTT-AGAAAAATTGGGGTTA
3669973 AAAATGGAATTTTGGAAAGTTTTA-GGGTAAAAT-GTAATTTT
1 AAAATGGAATTTTGGAAAG-TTTAGGGGTAAAATGGTAATTTT
3670014 AGGATAGTTT
Statistics
Matches: 231, Mismatches: 34, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
58 27 0.12
59 194 0.84
60 10 0.04
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (59 bp):
AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAGAAAAATTGGGGTTA
Found at i:3669857 original size:30 final size:29
Alignment explanation
Indices: 3669706--3669935 Score: 150
Period size: 29 Copynumber: 7.8 Consensus size: 29
3669696 ACTCGAGGGG
** *
3669706 AAAATGGTAATTTTTGGAAAAATTGGGGTT
1 AAAATGG-AATTTTTGGAAAGTTTGAGGTT
*
3669736 AAAAATGGAATTTTTGG-AAGTTT-AGGGGT
1 -AAAATGGAATTTTTGGAAAGTTTGA-GGTT
* ** * *
3669765 AAAATGGTAATTTTGGGAAAAATCGAGGTCA
1 AAAATGG-AATTTTTGGAAAGTTTGAGGT-T
**
3669796 AAAATGGAATTTTTGG-AAGTTCAAGAG-T
1 AAAATGGAATTTTTGGAAAGTTTGAG-GTT
*
3669824 AAAATGGTAATTTTTAGAAAGTTTGAGGTT
1 AAAATGG-AATTTTTGGAAAGTTTGAGGTT
*
3669854 AAAAAT-GAAATTTTGGAAAGTTTGGAGG-T
1 -AAAATGGAATTTTTGGAAAGTTT-GAGGTT
* ** *
3669883 AAAATTGTAATTTTTAAAAAGTTTGGGGTT
1 AAAA-TGGAATTTTTGGAAAGTTTGAGGTT
*
3669913 ATTAATGGAA-TTTTGGAAAGTTT
1 A-AAATGGAATTTTTGGAAAGTTT
3669936 AGGGGTAAAA
Statistics
Matches: 155, Mismatches: 29, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
28 18 0.12
29 60 0.39
30 55 0.35
31 22 0.14
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAAGTTTGAGGTT
Found at i:3670023 original size:29 final size:27
Alignment explanation
Indices: 3669674--3670027 Score: 138
Period size: 29 Copynumber: 12.1 Consensus size: 27
3669664 GATACTCGGG
* * **
3669674 GGGTAAAATGGTAATTTTGGACACTCGA
1 GGGTAAAATGG-AATTTTGGAAAGTTTA
* ** *
3669702 GGGGAAAATGGTAATTTTTGGAAAAATTG
1 GGGTAAAATGG-AA-TTTTGGAAAGTTTA
3669731 GGGTTAAAAATGGAATTTTTGG-AAGTTTA
1 GGG-T-AAAATGGAA-TTTTGGAAAGTTTA
** *
3669760 GGGGTAAAATGGTAATTTTGGGAAA-AATC
1 -GGGTAAAATGG-AATTTT-GGAAAGTTTA
*
3669789 GAGGTCAAAAATGGAATTTTTGG-AAGTTCAA
1 G-GGT--AAAATGGAA-TTTTGGAAAGTT-TA
* *
3669820 GAGTAAAATGGTAATTTTTAGAAAGTTTGA
1 GGGTAAAATGG-AA-TTTTGGAAAGTTT-A
* * *
3669850 GGTTAAAAATGAAATTTTGGAAAGTTTG
1 GGGT-AAAATGGAATTTTGGAAAGTTTA
* ** *
3669878 GAGGTAAAATTGTAATTTTTAAAAAGTTTG
1 G-GGTAAAA-TGGAA-TTTTGGAAAGTTTA
*
3669908 GGGTTATTAATGGAATTTTGGAAAGTTTA
1 GGG-TA-AAATGGAATTTTGGAAAGTTTA
* * ** ***
3669937 GGGGTAAAAGTGTATTTTTCAAAAAAACTA
1 -GGGTAAAA-TGGAATTTT-GGAAAGTTTA
3669967 GGGTCAAAAATGGAATTTTGGAAAGTTTTA
1 GGGT--AAAATGGAATTTTGGAAAG-TTTA
* *
3669997 GGGTAAAATGTAATTTTAGGATAGTTTA
1 GGGTAAAATGGAATTTT-GGAAAGTTTA
3670025 GGG
1 GGG
3670028 ACTTCAGGGC
Statistics
Matches: 245, Mismatches: 52, Indels: 58
0.69 0.15 0.16
Matches are distributed among these distances:
28 58 0.24
29 86 0.35
30 70 0.29
31 31 0.13
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.34
Consensus pattern (27 bp):
GGGTAAAATGGAATTTTGGAAAGTTTA
Found at i:3671013 original size:18 final size:17
Alignment explanation
Indices: 3670992--3671034 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
3670982 TATTAAATAT
3670992 TATTAATTATTTAATAAA
1 TATT-ATTATTTAATAAA
3671010 TATTATTA-TTAATAAA
1 TATTATTATTTAATAAA
3671026 -ATTATTATT
1 TATTATTATT
3671035 ATTATCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.29
16 9 0.38
17 4 0.17
18 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTATTATTTAATAAA
Found at i:3671031 original size:15 final size:16
Alignment explanation
Indices: 3670992--3671035 Score: 63
Period size: 15 Copynumber: 2.7 Consensus size: 16
3670982 TATTAAATAT
3670992 TATTAATTATTTAATAAA
1 TATT-ATTA-TTAATAAA
3671010 TATTATTATTAATAAA
1 TATTATTATTAATAAA
3671026 -ATTATTATTA
1 TATTATTATTA
3671036 TTATCATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.38
16 8 0.31
17 4 0.15
18 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTATTATTAATAAA
Found at i:3671035 original size:18 final size:18
Alignment explanation
Indices: 3670985--3671038 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
3670975 CTTTTTTTAT
3670985 TAAATATTATTAATTATTTAA
1 TAAA-ATTATT-ATTA-TTAA
3671006 T-AAA-TATTATTATTAA
1 TAAAATTATTATTATTAA
3671022 TAAAATTATTATTATTA
1 TAAAATTATTATTATTA
3671039 TCATTAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.16
17 7 0.23
18 15 0.48
19 1 0.03
20 2 0.06
21 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAAAATTATTATTATTAA
Found at i:3671037 original size:24 final size:24
Alignment explanation
Indices: 3671010--3671055 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3671000 ATTTAATAAA
*
3671010 TATTATTATTAATAAAATTATTAT
1 TATTATCATTAATAAAATTATTAT
*
3671034 TATTATCATTAATGAAATTATT
1 TATTATCATTAATAAAATTATT
3671056 TAATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TATTATCATTAATAAAATTATTAT
Found at i:3671890 original size:35 final size:34
Alignment explanation
Indices: 3671849--3671955 Score: 115
Period size: 35 Copynumber: 3.1 Consensus size: 34
3671839 TATAATAAGT
* *
3671849 TTTAAATTTAAATATAAATCTAAATTTATATTAAA
1 TTTAAATTTAAA-ATAAATCTAAATTTAAAATAAA
* *
3671884 TTTAAATTTTAAAACAAATTTAAATTTAAAATAAA
1 TTTAAA-TTTAAAATAAATCTAAATTTAAAATAAA
* * * **
3671919 TTTATATTCAAAATAAATTTAACCTTAAAATAAA
1 TTTAAATTTAAAATAAATCTAAATTTAAAATAAA
3671953 TTT
1 TTT
3671956 TAAAATGAGT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
34 27 0.44
35 29 0.47
36 6 0.10
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATCTAAATTTAAAATAAA
Found at i:3671896 original size:7 final size:6
Alignment explanation
Indices: 3671849--3671940 Score: 66
Period size: 6 Copynumber: 15.8 Consensus size: 6
3671839 TATAATAAGT
* * *
3671849 TTTAAA TTTAAA TATAAA TCTAAA TTTATA -TTAAA TTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
** * * * *
3671897 -ACAAA TTTAAA TTTAAA -ATAAA TTTATA TTCAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
3671941 CCTTAAAATA
Statistics
Matches: 64, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
5 14 0.22
6 44 0.69
7 6 0.09
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:3671902 original size:29 final size:29
Alignment explanation
Indices: 3671850--3671905 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
3671840 ATAATAAGTT
*
3671850 TTAAATTTAAATATAAATCTAAATTTATA
1 TTAAATTTAAATATAAAACTAAATTTATA
*
3671879 TTAAATTTAAATTTTAAAAC-AAATTTA
1 TTAAATTTAAA-TATAAAACTAAATTTA
3671906 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (29 bp):
TTAAATTTAAATATAAAACTAAATTTATA
Found at i:3671931 original size:17 final size:17
Alignment explanation
Indices: 3671849--3671955 Score: 124
Period size: 17 Copynumber: 6.2 Consensus size: 17
3671839 TATAATAAGT
3671849 TTTAAATTTAAATATAAA
1 TTTAAATTTAAA-ATAAA
* * *
3671867 TCTAAATTTATATTAAA
1 TTTAAATTTAAAATAAA
*
3671884 TTTAAATTTTAAAACAAA
1 TTTAAA-TTTAAAATAAA
3671902 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
3671919 TTTATATTCAAAATAAA
1 TTTAAATTTAAAATAAA
**
3671936 TTTAACCTTAAAATAAA
1 TTTAAATTTAAAATAAA
3671953 TTT
1 TTT
3671956 TAAAATGAGT
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
17 50 0.68
18 24 0.32
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:3672559 original size:24 final size:24
Alignment explanation
Indices: 3672514--3672559 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
3672504 AATGTTAAAA
* **
3672514 AAGATGGAAGGTTAAAGGTCAAGG
1 AAGATGAAAGGTTAAACATCAAGG
*
3672538 AAGATGAAATGTTAAACATCAA
1 AAGATGAAAGGTTAAACATCAA
3672560 TTTAACAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.26, T:0.20
Consensus pattern (24 bp):
AAGATGAAAGGTTAAACATCAAGG
Found at i:3679024 original size:18 final size:18
Alignment explanation
Indices: 3678999--3679037 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3678989 TAAAAAATCC
*
3678999 AAAATAT-ATATTTTTAA
1 AAAATATAAAATTTTTAA
3679016 AAAATTATAAAATTTTTAA
1 AAAA-TATAAAATTTTTAA
3679035 AAA
1 AAA
3679038 GAATTCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 3 0.16
19 12 0.63
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATATAAAATTTTTAA
Found at i:3679037 original size:20 final size:19
Alignment explanation
Indices: 3679008--3679077 Score: 54
Period size: 21 Copynumber: 3.6 Consensus size: 19
3678998 CAAAATATAT
3679008 ATTTTT-AAAAAATTATAAA
1 ATTTTTAAAAAAATT-TAAA
3679027 ATTTTTAAAAAGAATTCTAAA
1 ATTTTTAAAAA-AATT-TAAA
* * * *
3679048 GATGTATAAAGAAAGTTAAA
1 -ATTTTTAAAAAAATTTAAA
3679068 A-TTTTAAAAA
1 ATTTTTAAAAA
3679078 TTTTCTAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
18 6 0.15
19 7 0.17
20 8 0.20
21 11 0.28
22 8 0.20
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (19 bp):
ATTTTTAAAAAAATTTAAA
Found at i:3679104 original size:19 final size:19
Alignment explanation
Indices: 3679064--3679106 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3679054 TAAAGAAAGT
* **
3679064 TAAAATTTTAAAAATTTTC
1 TAAAAATTTAAAAATTGCC
3679083 TAAAAATTTAAAAATTGCC
1 TAAAAATTTAAAAATTGCC
3679102 TAAAA
1 TAAAA
3679107 TAATAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAAAATTTAAAAATTGCC
Found at i:3680765 original size:31 final size:31
Alignment explanation
Indices: 3680727--3680832 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 31
3680717 CTACAACATA
*
3680727 GGTCACCCAACTATTGTCCGTTTTCATTTTT
1 GGTCACCCAACTATTGTCCCTTTTCATTTTT
** ** * *
3680758 GGTCACCCAACTACAAGT-TTTTTTTA-ATTT
1 GGTCACCCAACTA-TTGTCCCTTTTCATTTTT
*
3680788 GGTCACCCAACTATTGTCCCTTTTCTTTTTT
1 GGTCACCCAACTATTGTCCCTTTTCATTTTT
*
3680819 GGTCACCTAACTAT
1 GGTCACCCAACTAT
3680833 CAATTTGTTA
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
29 2 0.03
30 20 0.34
31 34 0.59
32 2 0.03
ACGTcount: A:0.20, C:0.25, G:0.11, T:0.43
Consensus pattern (31 bp):
GGTCACCCAACTATTGTCCCTTTTCATTTTT
Found at i:3681329 original size:29 final size:31
Alignment explanation
Indices: 3681282--3681345 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 31
3681272 AAAGGGAGCA
*
3681282 AAAAAAATCTCGATCAGTT-AGATTACCAAATT
1 AAAAAAATCTCGATCAGTTGAG-TGACCAAA-T
3681314 AAAAAAAT-T-GAT-AGTTGAGTGACCAAAT
1 AAAAAAATCTCGATCAGTTGAGTGACCAAAT
3681342 AAAA
1 AAAA
3681346 GAGCAATAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
28 5 0.17
29 11 0.37
30 5 0.17
31 1 0.03
32 8 0.27
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.25
Consensus pattern (31 bp):
AAAAAAATCTCGATCAGTTGAGTGACCAAAT
Found at i:3681813 original size:19 final size:21
Alignment explanation
Indices: 3681770--3681815 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3681760 TTCATTTTTA
*
3681770 ATAAAATACATAAAATATTTT
1 ATAAAATACATAAAATATGTT
*
3681791 ATAAAATACATATAA-A-GTT
1 ATAAAATACATAAAATATGTT
3681810 ATAAAA
1 ATAAAA
3681816 ATATTTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
20 1 0.04
21 14 0.61
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAAATACATAAAATATGTT
Found at i:3686282 original size:18 final size:18
Alignment explanation
Indices: 3686251--3686291 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3686241 TGGCTCCACC
*
3686251 AAAAATAAAATATATATT
1 AAAATTAAAATATATATT
* *
3686269 TAAATTAAACTATATATT
1 AAAATTAAAATATATATT
3686287 AAAAT
1 AAAAT
3686292 ATTATATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTAAAATATATATT
Found at i:3686414 original size:11 final size:11
Alignment explanation
Indices: 3686378--3686414 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3686368 AATTTTTAAA
3686378 AAATAAATAAT
1 AAATAAATAAT
*
3686389 AAACAAATAAT
1 AAATAAATAAT
*
3686400 AAATAAATAAG
1 AAATAAATAAT
3686411 AAAT
1 AAAT
3686415 TTATAGGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:3686569 original size:96 final size:97
Alignment explanation
Indices: 3686355--3686577 Score: 260
Period size: 95 Copynumber: 2.3 Consensus size: 97
3686345 ATAACTCCAA
*
3686355 AAAAATAAATTTAAATTTTTAAAAAATAAATAATAAACAAATAATAAATAAATAAGAAATTTATA
1 AAAAA-AAATTTAAATTTTTAAAAAATAAATAAGAAACAAATAATAAATAAATAAGAAATTTATA
* *
3686420 GGAAAGTGGTGACGCCATTTAATATGGCACCAC
65 GGAAAGTGGTGACACCATTTAATATGACACCAC
** ** * *
3686453 CCAAAAAATTTAAATTTTTAAAAAATAAATAAGAAA-TTATTATAAA-AAAT-TGAAATATGTA-
1 AAAAAAAATTTAAATTTTTAAAAAATAAATAAGAAACAAATAATAAATAAATAAGAAAT-T-TAT
*
3686514 ACGG-AAGTGGTGGCACCACTTT-ATATGACACCAC
64 A-GGAAAGTGGTGACACCA-TTTAATATGACACCAC
3686548 AAAAAAAATTTTAAATTTTTAAAAAATAAA
1 AAAAAAAA-TTTAAATTTTTAAAAAATAAA
3686578 AAAATAATAA
Statistics
Matches: 108, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
94 5 0.05
95 35 0.32
96 35 0.32
97 30 0.28
98 3 0.03
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (97 bp):
AAAAAAAATTTAAATTTTTAAAAAATAAATAAGAAACAAATAATAAATAAATAAGAAATTTATAG
GAAAGTGGTGACACCATTTAATATGACACCAC
Found at i:3690678 original size:60 final size:59
Alignment explanation
Indices: 3690613--3690768 Score: 226
Period size: 60 Copynumber: 2.6 Consensus size: 59
3690603 GAATAATCAT
* *
3690613 TTTGTAACTTTTAATAGTTG-GATGACCAAAAAAGAAAAGAAAACATAATTGGACGATTAA
1 TTTGTAACTTTTTATAATTGAG-TGA-CAAAAAAGAAAAGAAAACATAATTGGACGATTAA
** *
3690673 TTTGTAACTTTTTATAATTGAGTGATCAAAAAAGAAAAGAAAACATAATTGGGTGATTAT
1 TTTGTAACTTTTTATAATTGAGTGA-CAAAAAAGAAAAGAAAACATAATTGGACGATTAA
3690733 TTTGTAACTTTTTATAATTGAGTGACAAAAAA-AAAA
1 TTTGTAACTTTTTATAATTGAGTGACAAAAAAGAAAA
3690769 CCTATAACTA
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
58 4 0.04
59 7 0.08
60 77 0.87
61 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (59 bp):
TTTGTAACTTTTTATAATTGAGTGACAAAAAAGAAAAGAAAACATAATTGGACGATTAA
Found at i:3691156 original size:51 final size:51
Alignment explanation
Indices: 3691095--3691222 Score: 247
Period size: 51 Copynumber: 2.5 Consensus size: 51
3691085 ATATAACTCT
3691095 AGTCTGAACGATTGGTCTAGACCGATACGTCAATTAATTCTTAATCTAATC
1 AGTCTGAACGATTGGTCTAGACCGATACGTCAATTAATTCTTAATCTAATC
*
3691146 AGTCTAAACGATTGGTCTAGACCGATACGTCAATTAATTCTTAATCTAATC
1 AGTCTGAACGATTGGTCTAGACCGATACGTCAATTAATTCTTAATCTAATC
3691197 AGTCTGAACGATTGGTCTAGACCGAT
1 AGTCTGAACGATTGGTCTAGACCGAT
3691223 CTTGATAACG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 75 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (51 bp):
AGTCTGAACGATTGGTCTAGACCGATACGTCAATTAATTCTTAATCTAATC
Found at i:3692086 original size:17 final size:17
Alignment explanation
Indices: 3692064--3692183 Score: 127
Period size: 17 Copynumber: 7.1 Consensus size: 17
3692054 AATCATTTTA
*
3692064 AAATTTATTTTAAAATT
1 AAATTTATTTTAAATTT
* *
3692081 AAATTTATGTTAAAGTT
1 AAATTTATTTTAAATTT
3692098 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
*
3692115 AGATTTA--TTAAATTT
1 AAATTTATTTTAAATTT
*
3692130 AAATTTAATTTAAATTT
1 AAATTTATTTTAAATTT
* * *
3692147 AGAATTAATGTAAAATTT
1 A-AATTTATTTTAAATTT
* *
3692165 AAAATTATTATAAATTT
1 AAATTTATTTTAAATTT
3692182 AA
1 AA
3692184 TAGAGTGTCC
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
15 14 0.16
17 58 0.68
18 13 0.15
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:3692110 original size:11 final size:11
Alignment explanation
Indices: 3692064--3692147 Score: 64
Period size: 11 Copynumber: 7.6 Consensus size: 11
3692054 AATCATTTTA
*
3692064 AAATTTATTTT
1 AAATTTAATTT
*
3692075 AAAATTAAATTT
1 -AAATTTAATTT
** * *
3692087 ATGTTAAAGTT
1 AAATTTAATTT
*
3692098 AAATTTATTTT
1 AAATTTAATTT
3692109 AAATTTAGATTT
1 AAATTTA-ATTT
*
3692121 --ATTAAATTT
1 AAATTTAATTT
3692130 AAATTTAATTT
1 AAATTTAATTT
3692141 AAATTTA
1 AAATTTA
3692148 GAATTAATGT
Statistics
Matches: 56, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 36 0.64
12 12 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:3692115 original size:6 final size:6
Alignment explanation
Indices: 3692072--3692152 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
3692062 TAAAATTTAT
* * * *
3692072 TTTAAA ATTAAA TTT--A TGTTAAA GTTAAA TTT-AT TTTAAA TTTAGA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA
3692118 TTT--A -TTAAA TTTAAA TTT-AA TTTAAA TTTAGAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TT
3692153 AATGTAAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
3 2 0.03
4 3 0.05
5 12 0.20
6 37 0.63
7 5 0.08
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:3692834 original size:9 final size:9
Alignment explanation
Indices: 3692820--3692855 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
3692810 AGAGTATTTA
3692820 AATATTAAT
1 AATATTAAT
**
3692829 AATATTGTT
1 AATATTAAT
3692838 AATATTAAT
1 AATATTAAT
3692847 AATATTAAT
1 AATATTAAT
3692856 GGCAGTAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (9 bp):
AATATTAAT
Found at i:3693997 original size:30 final size:30
Alignment explanation
Indices: 3693963--3694244 Score: 300
Period size: 30 Copynumber: 9.4 Consensus size: 30
3693953 CAGAAACTAT
* * *
3693963 ATTTTGACCCCCAAACTTTTTAAAAATTAC
1 ATTTTAACCCCAAAACTTTTCAAAAATTAC
* *
3693993 ATTTTAACCCTAAAAATTTTCAAAAATTAC
1 ATTTTAACCCCAAAACTTTTCAAAAATTAC
* *
3694023 ATTTTGACCCTAAAACTTTTCAAAAATTAC
1 ATTTTAACCCCAAAACTTTTCAAAAATTAC
** *
3694053 ATTTTAACCTAAAAACTTTTCTAAAATTAC
1 ATTTTAACCCCAAAACTTTTCAAAAATTAC
* * *
3694083 ATTTTAACCCTAAAACTTTTCCAAAATTAT
1 ATTTTAACCCCAAAACTTTTCAAAAATTAC
3694113 ATTTTAACCCCCAAAACTTTTCCAAAAA-TAC
1 ATTTTAA-CCCCAAAACTTTT-CAAAAATTAC
* * * *
3694144 ATTTTGACCTCAAAGCTTTTCCAAAATTAC
1 ATTTTAACCCCAAAACTTTTCAAAAATTAC
* * * *
3694174 ATTTTGACCTCAAAATTTTTTC-AAAATTAT
1 ATTTTAACCCCAAAA-CTTTTCAAAAATTAC
*
3694204 ATTTTAACCCCGAAAC-TTTCAAAAATTACC
1 ATTTTAACCCCAAAACTTTTCAAAAATTA-C
*
3694234 ATTTTACCCCC
1 ATTTTAACCCC
3694245 GAATCTTCCA
Statistics
Matches: 215, Mismatches: 31, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
28 4 0.02
29 12 0.06
30 169 0.79
31 25 0.12
32 5 0.02
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (30 bp):
ATTTTAACCCCAAAACTTTTCAAAAATTAC
Found at i:3694164 original size:91 final size:89
Alignment explanation
Indices: 3693963--3694238 Score: 335
Period size: 90 Copynumber: 3.1 Consensus size: 89
3693953 CAGAAACTAT
* * *
3693963 ATTTTGACCCCCAAACTTTT-TAAAAATTACATTTTAACCCTAAAAATTTTCAAAAATTACATTT
1 ATTTTGA-CCTCAAACTTTTCT-AAAATTACATTTTAACCCTAAAAATTTTCCAAAATTATATTT
* *
3694027 TGACCCTAAAACTTTTCAAAAATTAC
64 TAACCCCAAAACTTTTCAAAAATTAC
* * *
3694053 ATTTTAACCTAAAAACTTTTCTAAAATTACATTTTAACCCTAAAACTTTTCCAAAATTATATTTT
1 ATTTTGACCT-CAAACTTTTCTAAAATTACATTTTAACCCTAAAAATTTTCCAAAATTATATTTT
3694118 AACCCCCAAAACTTTTCCAAAAA-TAC
65 AA-CCCCAAAACTTTT-CAAAAATTAC
* * * *
3694144 ATTTTGACCTCAAAGCTTTTCCAAAATTACATTTTGA-CCTCAAAATTTTTTCAAAATTATATTT
1 ATTTTGACCTCAAA-CTTTTCTAAAATTACATTTTAACCCT-AAAAATTTTCCAAAATTATATTT
*
3694208 TAACCCCGAAAC-TTTCAAAAATTACC
64 TAACCCCAAAACTTTTCAAAAATTA-C
3694234 ATTTT
1 ATTTT
3694239 ACCCCCGAAT
Statistics
Matches: 163, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
88 6 0.04
89 7 0.04
90 75 0.46
91 69 0.42
92 6 0.04
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.38
Consensus pattern (89 bp):
ATTTTGACCTCAAACTTTTCTAAAATTACATTTTAACCCTAAAAATTTTCCAAAATTATATTTTA
ACCCCAAAACTTTTCAAAAATTAC
Found at i:3694242 original size:29 final size:29
Alignment explanation
Indices: 3693963--3694329 Score: 246
Period size: 30 Copynumber: 12.4 Consensus size: 29
3693953 CAGAAACTAT
* * *
3693963 ATTTTGACCCCCAAACTTTTTAAAAATTAC
1 ATTTTAACCCCAAAAC-TTTCAAAAATTAC
* *
3693993 ATTTTAACCCTAAAAATTTTCAAAAATTAC
1 ATTTTAACCC-CAAAACTTTCAAAAATTAC
* *
3694023 ATTTTGACCCTAAAACTTTTCAAAAATTAC
1 ATTTTAACCCCAAAAC-TTTCAAAAATTAC
** *
3694053 ATTTTAACCTAAAAACTTTTCTAAAATTAC
1 ATTTTAACCCCAAAAC-TTTCAAAAATTAC
* * *
3694083 ATTTTAACCCTAAAACTTTTCCAAAATTAT
1 ATTTTAACCCCAAAAC-TTTCAAAAATTAC
3694113 ATTTTAACCCCCAAAACTTTTCCAAAAA-TAC
1 ATTTTAA-CCCCAAAAC-TTT-CAAAAATTAC
* * * *
3694144 ATTTTGACCTCAAAGCTTTTCCAAAATTAC
1 ATTTTAACCCCAAAAC-TTTCAAAAATTAC
* * * *
3694174 ATTTTGACCTCAAAATTTTTTC-AAAATTAT
1 ATTTTAACCCCAAAA--CTTTCAAAAATTAC
*
3694204 ATTTTAACCCCGAAACTTTCAAAAATTACC
1 ATTTTAACCCCAAAACTTTCAAAAATTA-C
* * * * *
3694234 ATTTTACCCCCGAATC-TTCCAAAATTCC
1 ATTTTAACCCCAAAACTTTCAAAAATTAC
* *
3694262 ATTTTTACCCC--GA-TTTCACCAAAATTACC
1 ATTTTAACCCCAAAACTTTCA--AAAATTA-C
* * *
3694291 ATTTT-ACCCTTAAAACTTTC-CAAATTCC
1 ATTTTAACCC-CAAAACTTTCAAAAATTAC
3694319 ATTTTAACCCC
1 ATTTTAACCCC
3694330 GATTTCACAA
Statistics
Matches: 273, Mismatches: 46, Indels: 38
0.76 0.13 0.11
Matches are distributed among these distances:
26 3 0.01
28 30 0.11
29 40 0.15
30 163 0.60
31 28 0.10
32 9 0.03
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (29 bp):
ATTTTAACCCCAAAACTTTCAAAAATTAC
Found at i:3694272 original size:28 final size:28
Alignment explanation
Indices: 3694195--3694385 Score: 119
Period size: 28 Copynumber: 6.7 Consensus size: 28
3694185 AAAATTTTTT
* *
3694195 CAAAATTA-TATTTTAACCCCGAAACTTTC
1 CAAAATTACCATTTT-ACCCCGAATC-TTC
*
3694224 AAAAATTACCATTTTACCCCCGAATCTTC
1 CAAAATTACCATTTTA-CCCCGAATCTTC
3694253 CAAAATT-CCATTTTTACCCCG-AT-TTCAC
1 CAAAATTACCA-TTTTACCCCGAATCTT--C
** *
3694281 CAAAATTACCATTTTACCCTTAAAACTTTC
1 CAAAATTACCATTTTACCC-CGAATC-TTC
3694311 C-AAATT-CCATTTTAACCCCG-AT-TTC
1 CAAAATTACCATTTT-ACCCCGAATCTTC
* ****
3694336 ACAAAAATTACCATTTTGCCCCGAAAAGCC
1 -C-AAAATTACCATTTTACCCCGAATCTTC
*
3694366 CAAAATTACCATTTTGCCCC
1 CAAAATTACCATTTTACCCC
3694386 TGGGTATCCA
Statistics
Matches: 131, Mismatches: 14, Indels: 35
0.73 0.08 0.19
Matches are distributed among these distances:
25 3 0.02
26 3 0.02
27 3 0.02
28 60 0.46
29 43 0.33
30 17 0.13
32 2 0.02
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (28 bp):
CAAAATTACCATTTTACCCCGAATCTTC
Found at i:3694316 original size:57 final size:57
Alignment explanation
Indices: 3694223--3694380 Score: 196
Period size: 57 Copynumber: 2.8 Consensus size: 57
3694213 CCGAAACTTT
* * *
3694223 CAAAAATTACCATTTTACCCCCGAATCTTCCAAAATTCCATTTTTACCCCGATTTCA
1 CAAAAATTACCATTTTACCCCCAAAACTTCCAAAATTCCATTTTAACCCCGATTTCA
* **
3694280 CCAAAATTACCATTTTACCCTTAAAACTTTCC-AAATTCCATTTTAACCCCGATTTCA
1 CAAAAATTACCATTTTACCCCCAAAAC-TTCCAAAATTCCATTTTAACCCCGATTTCA
* *
3694337 CAAAAATTACCATTTTGCCCCGAAAAGC--CCAAAATTACCATTTT
1 CAAAAATTACCATTTTACCCCCAAAA-CTTCCAAAATT-CCATTTT
3694381 GCCCCTGGGT
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
55 2 0.02
56 5 0.06
57 75 0.86
58 5 0.06
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (57 bp):
CAAAAATTACCATTTTACCCCCAAAACTTCCAAAATTCCATTTTAACCCCGATTTCA
Found at i:3694350 original size:29 final size:27
Alignment explanation
Indices: 3694195--3694352 Score: 110
Period size: 29 Copynumber: 5.6 Consensus size: 27
3694185 AAAATTTTTT
*
3694195 CAAAATTA-TATTTTAACCCCGAAACTTTC
1 CAAAATTACCATTTTAACCCCG--A-TTTC
* *
3694224 AAAAATTACCATTTTACCCCCGAATCTTC
1 CAAAATTACCATTTTAACCCCG-AT-TTC
*
3694253 CAAAATT-CCATTTTTACCCCGATTTCAC
1 CAAAATTACCATTTTAACCCCGATTT--C
**
3694281 CAAAATTACCATTTT-ACCCTTAAAACTTTC
1 CAAAATTACCATTTTAACCC---CGA-TTTC
3694311 C-AAATT-CCATTTTAACCCCGATTTC
1 CAAAATTACCATTTTAACCCCGATTTC
3694336 ACAAAAATTACCATTTT
1 -C-AAAATTACCATTTT
3694353 GCCCCGAAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
25 4 0.04
26 4 0.04
27 2 0.02
28 37 0.35
29 41 0.39
30 13 0.12
31 1 0.01
32 3 0.03
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.35
Consensus pattern (27 bp):
CAAAATTACCATTTTAACCCCGATTTC
Found at i:3697045 original size:11 final size:11
Alignment explanation
Indices: 3697022--3697084 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
3697012 TCAAATTTAT
3697022 TTTAATCTTAAA
1 TTTAAT-TTAAA
*
3697034 TTTATTTTAAA
1 TTTAATTTAAA
*
3697045 TTCAATTTAAA
1 TTTAATTTAAA
*
3697056 TTTAAATTTGAA
1 TTT-AATTTAAA
3697068 TTTAATTTAAA
1 TTTAATTTAAA
3697079 TTTAAT
1 TTTAAT
3697085 GTTATTATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
11 29 0.66
12 15 0.34
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:3697081 original size:17 final size:16
Alignment explanation
Indices: 3697032--3697100 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 16
3697022 TTTAATCTTA
* *
3697032 AATTTATTTTAAATTC
1 AATTTAATTTAAATTT
3697048 AATTTAAATTTAAATTT
1 AATTT-AATTTAAATTT
3697065 GAATTTAATTTAAATTT
1 -AATTTAATTTAAATTT
3697082 AATGTT-ATTATAAATTT
1 AAT-TTAATT-TAAATTT
3697099 AA
1 AA
3697101 AAAGAAAGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
16 11 0.23
17 31 0.66
18 5 0.11
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (16 bp):
AATTTAATTTAAATTT
Found at i:3697101 original size:6 final size:6
Alignment explanation
Indices: 3697029--3697083 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
3697019 TATTTTAATC
* * *
3697029 TTAAAT TT-ATT TTAAA- TTCAAT TTAAAT TTAAAT TTGAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
3697074 TTAAAT TTAA
1 TTAAAT TTAA
3697084 TGTTATTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
5 13 0.32
6 28 0.68
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:3697303 original size:20 final size:21
Alignment explanation
Indices: 3697278--3697317 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3697268 GTGCCTACTG
*
3697278 CTGCTGGCCACC-AGCTCCAT
1 CTGCTGACCACCAAGCTCCAT
3697298 CTGCTGACCACCAAGCTCCA
1 CTGCTGACCACCAAGCTCCA
3697318 CCATGCCCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.20, C:0.45, G:0.17, T:0.17
Consensus pattern (21 bp):
CTGCTGACCACCAAGCTCCAT
Found at i:3697869 original size:19 final size:20
Alignment explanation
Indices: 3697843--3697889 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
3697833 TAATAACTAT
3697843 TAAT-ATAATAAAT-ATTAA
1 TAATAATAATAAATAATTAA
* *
3697861 TAATAATAA-CAATAATTAG
1 TAATAATAATAAATAATTAA
3697880 TAATAATAAT
1 TAATAATAAT
3697890 GCTAGTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
TAATAATAATAAATAATTAA
Found at i:3697875 original size:25 final size:25
Alignment explanation
Indices: 3697827--3697876 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3697817 ATAGTAGCTA
* *
3697827 AAATATTAATAACTATTAATATAAT
1 AAATATTAATAACTAATAAAATAAT
3697852 AAATATTAATAA-TAATAACAATAAT
1 AAATATTAATAACTAATAA-AATAAT
3697877 TAGTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (25 bp):
AAATATTAATAACTAATAAAATAAT
Done.